Mercurial > repos > guerler > springsuite
changeset 10:860bd6f8f480 draft
"planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"
| author | guerler |
|---|---|
| date | Sat, 01 Aug 2020 04:16:19 -0400 |
| parents | 4ac5d5a9b21c |
| children | 21a7dd67b483 |
| files | spring_minz.xml test-data/6W37_A.hhr test-data/6W4H_A.hhr test-data/6W4H_B.hhr test-data/6W9C_A.hhr test-data/6W9Q_A.hhr test-data/6WEY_A.hhr test-data/6WJI_A.hhr test-data/6WLC_A.hhr test-data/7BQY_A.hhr test-data/dbCAN_random.txt test-data/dbCAN_result.txt test-data/index.txt test-data/pdb70_random.txt test-data/pdb70_result.txt test-data/result.txt |
| diffstat | 16 files changed, 1349 insertions(+), 21 deletions(-) [+] |
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--- a/spring_minz.xml Sat Aug 01 02:13:31 2020 -0400 +++ b/spring_minz.xml Sat Aug 01 04:16:19 2020 -0400 @@ -14,13 +14,31 @@ <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/> - <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="10" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/> + <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/> </inputs> <outputs> <data format="txt" name="output" /> </outputs> <tests> <test> + <param name="target" value="7BQY_A.hhr"/> + <param name="idx" value="10"/> + <param name="inputs"> + <collection type="list"> + <element name="6W37_A.hhr" value="6W37_A.hhr" /> + <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> + <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> + <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> + <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> + <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> + <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> + <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> + </collection> + </param> + <param name="crossreference" value="dbCAN_random.txt"/> + <output name="output" file="dbCAN_result.txt"/> + </test> + <test> <param name="target" value="NP_000282.1.hhr"/> <param name="inputs"> <collection type="list"> @@ -30,8 +48,8 @@ <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" /> </collection> </param> - <param name="crossreference" value="index.txt"/> - <output name="output" file="result.txt"/> + <param name="crossreference" value="pdb70_random.txt"/> + <output name="output" file="pdb70_result.txt"/> </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6W37_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6W37_A +Match_columns 66 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:11 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_684.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_833.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 CAG81347.1|CBM19|426-466|7e-13 38.5 0.21 0.00033 21.3 0.0 25 32-56 16-40 (44) + 2 BAE59978.1|GT59|35-538|9.4e-14 5.4 4.6 0.0072 21.6 0.0 12 27-38 308-321 (418) + 3 ADI26643.1|GH52|20-439|6.2e-21 3.7 7.4 0.012 21.0 0.0 30 25-54 141-176 (418) + 4 AWM09982.1|GH5_39.hmm|1.8e-97| 2.6 11 0.018 18.6 0.0 26 15-40 153-178 (305) + 5 ACY95489.1|CBM14|33-88|9.4e-16 2.4 12 0.019 14.0 0.0 18 5-24 29-46 (81) + 6 ABO94043.1|GH5_32.hmm|1.7e-156 2.4 13 0.02 19.2 0.0 17 45-61 238-254 (341) + 7 ABQ06203.1|PL36.hmm|2.8e-93|60 2.0 15 0.024 17.3 0.0 15 43-57 75-89 (197) + 8 AXR41035.1|GH43_27.hmm|1.6e-11 2.0 16 0.025 18.3 0.0 18 48-65 2-19 (323) + 9 CCA69005.1|AA7||49-484 1.9 16 0.025 18.9 0.0 10 57-66 34-43 (456) + 10 CAA54566.1|PL22|32-145|1.6e-32 1.9 17 0.026 15.9 0.0 22 41-62 21-42 (177) + +No 1 +>CAG81347.1|CBM19|426-466|7e-13 +Probab=38.48 E-value=0.21 Score=21.26 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=20.7 Template_Neff=3.400 + +Q 6W37_A 32 HPLADNKFALTCFSTQFAFACPDGV 56 (66) +Q Consensus 32 hpladnkfaltcfstqfafacpdgv 56 (66) + .=-+|.||++.-+..-.-+.||.|. +T Consensus 16 sCt~~g~f~iC~~G~WV~~~Cp~gt 40 (44) +T CAG81347.1|CBM 16 ACTADGKFAVCDHGKWVTTECPSGT 40 (44) +Confidence 3346889999999988899999886 + + +No 2 +>BAE59978.1|GT59|35-538|9.4e-149 +Probab=5.38 E-value=4.6 Score=21.57 Aligned_cols=12 Identities=50% Similarity=0.609 Sum_probs=8.3 Template_Neff=4.400 + +Q 6W37_A 27 GNSPFHP--LADNK 38 (66) +Q Consensus 27 gnspfhp--ladnk 38 (66) + -++..|| ||||+ +T Consensus 308 ~fTivHPflLADNR 321 (418) +T BAE59978.1|GT5 308 FFTIVHPFLLADNR 321 (418) +Confidence 3566677 78885 + + +No 3 +>ADI26643.1|GH52|20-439|6.2e-219 +Probab=3.69 E-value=7.4 Score=20.97 Aligned_cols=30 Identities=17% Similarity=0.271 Sum_probs=17.5 Template_Neff=2.800 + +Q 6W37_A 25 YEGNSPFHPLA------DNKFALTCFSTQFAFACPD 54 (66) +Q Consensus 25 yegnspfhpla------dnkfaltcfstqfafacpd 54 (66) + |||+.|+.|+. +.+..=.....+.+||+++ +T Consensus 141 ~eg~~~~s~mr~l~d~~~~~~~G~~~gr~~g~at~~ 176 (418) +T ADI26643.1|GH5 141 LEGTDPYSSMRRISDDTDGQLIGVGQGRITGIATNS 176 (418) +Confidence 67887776654 2344434445566777765 + + +No 4 +>AWM09982.1|GH5_39.hmm|1.8e-97|57-349 +Probab=2.60 E-value=11 Score=18.56 Aligned_cols=26 Identities=23% Similarity=0.267 Sum_probs=19.6 Template_Neff=4.500 + +Q 6W37_A 15 LLKEPCSSGTYEGNSPFHPLADNKFA 40 (66) +Q Consensus 15 llkepcssgtyegnspfhpladnkfa 40 (66) + |+-.|+.-+.+|+---++||+|.+.. +T Consensus 153 lIv~g~~w~~~e~L~~l~PlaD~Nvv 178 (305) +T AWM09982.1|GH5 153 LIVSGANWQRIESLVALRPLADPNVI 178 (305) +Confidence 44456666678889999999998754 + + +No 5 +>ACY95489.1|CBM14|33-88|9.4e-16 +Probab=2.45 E-value=12 Score=14.02 Aligned_cols=18 Identities=39% Similarity=0.743 Sum_probs=10.1 Template_Neff=6.300 + +Q 6W37_A 5 YQECVRGTTVLLKEPCSSGT 24 (66) +Q Consensus 5 yqecvrgttvllkepcssgt 24 (66) + |-.|+.|..++ ..|..|. +T Consensus 29 Yy~C~~g~~~~--~~Cp~g~ 46 (81) +T ACY95489.1|CBM 29 YYICVNGKPVE--FSCPPGL 46 (81) +Confidence 55676665433 3666554 + + +No 6 +>ABO94043.1|GH5_32.hmm|1.7e-156|162-501 +Probab=2.36 E-value=13 Score=19.21 Aligned_cols=17 Identities=35% Similarity=0.595 Sum_probs=10.6 Template_Neff=2.300 + +Q 6W37_A 45 STQFAFACPDGVKHVYQ 61 (66) +Q Consensus 45 stqfafacpdgvkhvyq 61 (66) + ++.-||+|.|-+.+|-| +T Consensus 238 ~~Gca~sCsD~~e~va~ 254 (341) +T ABO94043.1|GH5 238 PRGCAFSCSDSEEQVAQ 254 (341) +Confidence 34457777777776543 + + +No 7 +>ABQ06203.1|PL36.hmm|2.8e-93|60-255 +Probab=2.05 E-value=15 Score=17.27 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.5 Template_Neff=1.000 + +Q 6W37_A 43 CFSTQFAFACPDGVK 57 (66) +Q Consensus 43 cfstqfafacpdgvk 57 (66) + --|..|.+-||.|.. +T Consensus 75 ggsarfmwycpngsn 89 (197) +T ABQ06203.1|PL3 75 GGSARFMWYCPNGSN 89 (197) +Confidence 347788899998864 + + +No 8 +>AXR41035.1|GH43_27.hmm|1.6e-119|344-677 +Probab=1.96 E-value=16 Score=18.30 Aligned_cols=18 Identities=56% Similarity=0.637 Sum_probs=14.2 Template_Neff=3.500 + +Q 6W37_A 48 FAFACPDGVKHVYQLRAR 65 (66) +Q Consensus 48 fafacpdgvkhvyqlrar 65 (66) + ||-|-|-||-.|.|-|.| +T Consensus 2 ~~~~~~~~~~~~~~~~~R 19 (323) +T AXR41035.1|GH4 2 FADAQPTGVLDVVQTRGR 19 (323) +Confidence 566788999888887765 + + +No 9 +>CCA69005.1|AA7||49-484 +Probab=1.92 E-value=16 Score=18.89 Aligned_cols=10 Identities=50% Similarity=0.408 Sum_probs=6.3 Template_Neff=4.100 + +Q 6W37_A 57 KHVYQLRARS 66 (66) +Q Consensus 57 khvyqlrars 66 (66) + ++=.|+|+|| +T Consensus 34 ~~gv~vr~RS 43 (456) +T CCA69005.1|AA7 34 KLGVQVRIRS 43 (456) +Confidence 3336778776 + + +No 10 +>CAA54566.1|PL22|32-145|1.6e-32 +Probab=1.89 E-value=17 Score=15.88 Aligned_cols=22 Identities=23% Similarity=0.264 Sum_probs=14.4 Template_Neff=5.400 + +Q 6W37_A 41 LTCFSTQFAFACPDGVKHVYQL 62 (66) +Q Consensus 41 ltcfstqfafacpdgvkhvyql 62 (66) + .+--|..+-|..|||.+-.|+. +T Consensus 21 ~~~dg~~~~f~~~d~~~~~~~~ 42 (177) +T CAA54566.1|PL2 21 FEGDGCTHEFWVPDGSAFDYVS 42 (177) +Confidence 3344667788888887665543 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6W4H_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6W4H_A +Match_columns 333 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:03 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_688.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_829.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 CAA16605.1|GT77|149-346|1.8e-5 6.5 3.6 0.0056 24.7 0.0 27 230-256 189-217 (227) + 2 EOY02636.1|GT96||31-333 6.2 3.9 0.006 26.8 0.0 29 226-254 124-158 (304) + 3 AAF14068.1|GT11|63-333|1e-95 4.2 6.3 0.0098 22.9 0.0 12 206-217 227-238 (272) + 4 AAC45780.1|CBM26|490-567|2.8e- 2.9 10 0.016 19.0 0.0 6 9-14 30-35 (77) + 5 CAG86794.1|GT91|125-678|5e-175 2.0 15 0.024 23.6 0.0 31 281-315 282-312 (458) + 6 CAA70732.1|GT16|90-439|6e-176 1.5 22 0.034 22.3 0.0 13 68-80 276-288 (350) + 7 BAE58124.1|GH93|42-352|1.5e-12 1.4 24 0.037 21.2 0.0 42 76-118 222-274 (311) + 8 BAI50574.1|PL18|188-375|3.3e-1 1.4 24 0.037 20.3 0.0 26 93-126 61-86 (188) + 9 AEO58137.1|AA3_1|AA8|CBM1|1.1. 1.3 25 0.039 24.1 0.0 64 53-119 690-759 (815) + 10 ABQ42392.1|CE8|283-579|4.2e-11 1.3 25 0.039 20.3 0.0 26 86-111 208-233 (290) + +No 1 +>CAA16605.1|GT77|149-346|1.8e-54 +Probab=6.55 E-value=3.6 Score=24.70 Aligned_cols=27 Identities=33% Similarity=0.541 Sum_probs=17.0 Template_Neff=6.000 + +Q 6W4H_A 230 IGCNYLGKPR--REQQIDGYYVMHANYII 256 (333) +Q Consensus 230 igcnylgkpr--reqqidgyyvmhanyii 256 (333) + -||.|.-.-+ .++....-|.|||||++ +T Consensus 189 ng~~~F~~~~~~~~~~~~~p~~vHan~~~ 217 (227) +T CAA16605.1|GT7 189 NGCTYFVQRRKDYSRDKLKPYTVHANYCP 217 (227) +Confidence 3565544333 33345567999999986 + + +No 2 +>EOY02636.1|GT96||31-333 +Probab=6.19 E-value=3.9 Score=26.80 Aligned_cols=29 Identities=31% Similarity=0.574 Sum_probs=22.1 Template_Neff=3.200 + +Q 6W4H_A 226 AFLLIGCNY------LGKPRREQQIDGYYVMHANY 254 (333) +Q Consensus 226 aflligcny------lgkprreqqidgyyvmhany 254 (333) + -.-||||.- ...|+|-+|..|..+||..= +T Consensus 124 Y~YL~G~dN~lAk~h~~~~~~~dkVGG~~imh~dD 158 (304) +T EOY02636.1|GT9 124 YGYLIGCDNELAKLHTRHPERCDKVGGVIIMHIDD 158 (304) +Confidence 345788853 34578999999999999764 + + +No 3 +>AAF14068.1|GT11|63-333|1e-95 +Probab=4.20 E-value=6.3 Score=22.91 Aligned_cols=12 Identities=33% Similarity=1.326 Sum_probs=9.7 Template_Neff=7.300 + +Q 6W4H_A 206 GHFAWWTAFVTN 217 (333) +Q Consensus 206 ghfawwtafvtn 217 (333) + +-|+||.|+... +T Consensus 227 STFSWW~A~L~~ 238 (272) +T AAF14068.1|GT1 227 STFSWWAAYLNK 238 (272) +Confidence 469999998764 + + +No 4 +>AAC45780.1|CBM26|490-567|2.8e-23 +Probab=2.89 E-value=10 Score=18.95 Aligned_cols=6 Identities=83% Similarity=1.353 Sum_probs=3.3 Template_Neff=5.200 + +Q 6W4H_A 9 PGVAMP 14 (333) +Q Consensus 9 pgvamp 14 (333) + ||++|- +T Consensus 30 PG~~Mt 35 (77) +T AAC45780.1|CBM 30 PGVAMT 35 (77) +Confidence 555554 + + +No 5 +>CAG86794.1|GT91|125-678|5e-175 +Probab=2.02 E-value=15 Score=23.58 Aligned_cols=31 Identities=32% Similarity=0.502 Sum_probs=21.4 Template_Neff=4.600 + +Q 6W4H_A 281 LKLRRGTAVMSLKEGQIINDMILSSLLSKGRRLII 315 (333) +Q Consensus 281 lklrrgtavmslkegqiindmilssllskgrrlii 315 (333) + -.||.||..+.+. |.|.. +...+.++|.+-| +T Consensus 282 g~LRGGT~lv~ip--~~ip~--~~~~l~~~ReiWv 312 (458) +T CAG86794.1|GT9 282 GPLRGGTNLVNIP--QLIPS--LKKHLPKNREIWV 312 (458) +Confidence 3589999998877 44443 6667777777654 + + +No 6 +>CAA70732.1|GT16|90-439|6e-176 +Probab=1.51 E-value=22 Score=22.30 Aligned_cols=13 Identities=54% Similarity=0.861 Sum_probs=10.4 Template_Neff=2.900 + +Q 6W4H_A 68 VPYNMRVIHFGAG 80 (333) +Q Consensus 68 vpynmrvihfgag 80 (333) + +|-..||+|||-- +T Consensus 276 ~~~~PRv~H~G~C 288 (350) +T CAA70732.1|GT1 276 VPRGPRVFHFGDC 288 (350) +Confidence 7788899999743 + + +No 7 +>BAE58124.1|GH93|42-352|1.5e-123 +Probab=1.39 E-value=24 Score=21.15 Aligned_cols=42 Identities=29% Similarity=0.470 Sum_probs=24.0 Template_Neff=4.700 + +Q 6W4H_A 76 HFGAGSDKGVAPGTAVLRR-------QWL----PTGTLLLVDSDLNDDFVVSDA 118 (333) +Q Consensus 76 hfgagsdkgvapgtavlrr-------qwl----ptgtlllvdsdlnddfvvsda 118 (333) + +||...+ |...-|+.-+. -|+ |.|+|+++.....+-|..... +T Consensus 222 ~Wg~~~~-g~~v~t~~g~~~~gaPyV~w~p~gg~nG~lvvs~~t~~~~~~n~~~ 274 (311) +T BAE58124.1|GH9 222 NWGDPTD-GTRVRTADGGQPAGAPYVTWLPDGGPNGTLVVSGQTDESSFGNQAG 274 (311) +Confidence 4555555 44444443221 378 788888887766665554433 + + +No 8 +>BAI50574.1|PL18|188-375|3.3e-111 +Probab=1.38 E-value=24 Score=20.30 Aligned_cols=26 Identities=38% Similarity=0.423 Sum_probs=18.7 Template_Neff=1.800 + +Q 6W4H_A 93 RRQWLPTGTLLLVDSDLNDDFVVSDADSSTLIGD 126 (333) +Q Consensus 93 rrqwlptgtlllvdsdlnddfvvsdadsstligd 126 (333) + ...--.|||+++| .|||.++|-++.. +T Consensus 61 QhHa~DTgTi~kv--------YvsDt~esgf~ds 86 (188) +T BAI50574.1|PL1 61 QHHASDTGTISKV--------YVSDTDESGFIDS 86 (188) +Confidence 3344568888876 5889999888743 + + +No 9 +>AEO58137.1|AA3_1|AA8|CBM1|1.1.99.18|7-827 +Probab=1.33 E-value=25 Score=24.07 Aligned_cols=64 Identities=27% Similarity=0.385 Sum_probs=42.3 Template_Neff=3.200 + +Q 6W4H_A 53 KYTQLCQYLNTLTLAVPYNMRVIHFG----AGSDKGVAPGTAVLRR--QWLPTGTLLLVDSDLNDDFVVSDAD 119 (333) +Q Consensus 53 kytqlcqylntltlavpynmrvihfg----agsdkgvapgtavlrr--qwlptgtlllvdsdlnddfvvsdad 119 (333) + .-+-+.+|++.+ -|-+||-=|+= -|.|.|-..||+|..- +-.-|.-|.+||-.+-.+.+..... +T Consensus 690 ~~~T~~~yV~~~---~~~~~~sNHWvGTakmGtddGr~~GtaVVD~NTKVyGTdNLFVVDASI~P~mptgNp~ 759 (815) +T AEO58137.1|AA3 690 STTTAEDYVDSY---DPSNRRSNHWMGTAKMGTDDGRSGGTAVVDLNTKVYGTDNLFVVDASIFPGMPTGNPS 759 (815) +Confidence 334456777777 57788888874 3777788999999754 3344555777776666655554443 + + +No 10 +>ABQ42392.1|CE8|283-579|4.2e-119 +Probab=1.32 E-value=25 Score=20.29 Aligned_cols=26 Identities=27% Similarity=0.608 Sum_probs=20.8 Template_Neff=5.700 + +Q 6W4H_A 86 APGTAVLRRQWLPTGTLLLVDSDLND 111 (333) +Q Consensus 86 apgtavlrrqwlptgtlllvdsdlnd 111 (333) + +++...|-|-|-|.+..++.++.+.+ +T Consensus 208 ~~~~~yLGRpW~~~~~vvf~~t~~~~ 233 (290) +T ABQ42392.1|CE8 208 PDGKVYLGRPWRPYSRVVFMNSYMGD 233 (290) +Confidence 35678899999999888888887743 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6W4H_B.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6W4H_B +Match_columns 121 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:04 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_687.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_830.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 CAR47543.1|CBM41|103-205|3.4e- 8.7 2.5 0.0038 19.7 0.0 27 76-102 41-67 (106) + 2 ACD98010.1|GH129||3-627 3.5 7.8 0.012 24.0 0.0 15 4-18 235-249 (657) + 3 ACI15933.1|GH162|22-524 3.3 8.6 0.013 23.0 0.0 59 5-72 186-244 (498) + 4 ACY95489.1|CBM14|33-88|9.4e-16 3.0 9.7 0.015 16.0 0.0 25 93-120 43-68 (81) + 5 ABN52033.1|CE3|36-223|2.1e-57 2.4 13 0.02 18.3 0.0 12 68-79 177-188 (195) + 6 AAI70505.1|CBM47|47-174|1.7e-4 2.2 13 0.021 16.9 0.0 12 77-88 106-117 (128) + 7 BAE59978.1|GT59|35-538|9.4e-14 2.2 14 0.021 20.8 0.0 28 45-73 3-30 (418) + 8 AJQ99710.1|GH13_18.hmm|7.1e-11 1.9 16 0.026 19.9 0.0 32 6-37 229-261 (343) + 9 AIQ50255.1|CBM77|PL1||627-727 1.7 19 0.03 16.8 0.0 14 17-30 30-43 (103) + 10 CAA44713.1|GT15|70-340|4.1e-13 1.7 19 0.03 18.9 0.0 16 5-20 228-243 (279) + +No 1 +>CAR47543.1|CBM41|103-205|3.4e-19 +Probab=8.71 E-value=2.5 Score=19.70 Aligned_cols=27 Identities=22% Similarity=0.425 Sum_probs=22.3 Template_Neff=6.300 + +Q 6W4H_B 76 CDLKGKYVQIPTTCANDPVGFTLLKNT 102 (121) +Q Consensus 76 cdlkgkyvqipttcandpvgftllknt 102 (121) + -|--|+|+.||..-....+||.+.++. +T Consensus 41 ~D~yGay~~v~l~~~~~~vgfIv~~~~ 67 (106) +T CAR47543.1|CBM 41 KDDYGAYADVPLKEGASKIGFIVRNGD 67 (106) +Confidence 345799999999888888999998854 + + +No 2 +>ACD98010.1|GH129||3-627 +Probab=3.53 E-value=7.8 Score=23.98 Aligned_cols=15 Identities=47% Similarity=0.831 Sum_probs=12.4 Template_Neff=2.800 + +Q 6W4H_B 4 VDAAKAYKDYLASSG 18 (121) +Q Consensus 4 vdaakaykdylassg 18 (121) + ||.||+|+.|...+| +T Consensus 235 vdmaK~YR~ya~e~G 249 (657) +T ACD98010.1|GH1 235 VDMCKAYRSYANERG 249 (657) +Confidence 788999999977665 + + +No 3 +>ACI15933.1|GH162|22-524 +Probab=3.28 E-value=8.6 Score=22.96 Aligned_cols=59 Identities=20% Similarity=0.374 Sum_probs=38.9 Template_Neff=3.000 + +Q 6W4H_B 5 DAAKAYKDYLASSGGQPITNCVKMLCTHTGTGQAITVVTTPEANMDQESFGGASCCLYCRCHIDHPNP 72 (121) +Q Consensus 5 daakaykdylassggqpitncvkmlcthtgtgqaitvvttpeanmdqesfggascclycrchidhpnp 72 (121) + +.||.|..|+.- -+.|.+++.-.-.|-=.|+|.+..-.+.+....+... |.|++|.|-. +T Consensus 186 ~La~rw~~~~~~----m~~na~~iFY~g~G~I~aVt~I~d~~~~~~~~~Y~~~-----~~~~LdDPYE 244 (498) +T ACI15933.1|GH1 186 DLAKRWQAWLDY----MANNAATIFYNGNGKIRAVTQIKDISAPVTPNNYQNE-----GTCYLDDPYE 244 (498) +Confidence 456666666543 3456777776666666677777666666666666655 7889998864 + + +No 4 +>ACY95489.1|CBM14|33-88|9.4e-16 +Probab=2.96 E-value=9.7 Score=15.97 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=12.9 Template_Neff=6.300 + +Q 6W4H_B 93 PVGFTLLKNTTVCTVCGMWKGY-GCSCDQ 120 (121) +Q Consensus 93 pvgftllknttvctvcgmwkgy-gcscdq 120 (121) + |.|+..-..+..|.. ..-. .||||. +T Consensus 43 p~g~~FD~~~~~C~~---~~~v~~C~~~~ 68 (81) +T ACY95489.1|CBM 43 PPGLVFDPETQTCDW---PENVDDCSNCS 68 (81) +Confidence 345555555555533 2223 588875 + + +No 5 +>ABN52033.1|CE3|36-223|2.1e-57 +Probab=2.35 E-value=13 Score=18.27 Aligned_cols=12 Identities=33% Similarity=0.700 Sum_probs=8.1 Template_Neff=5.600 + +Q 6W4H_B 68 DHPNPKGFCDLK 79 (121) +Q Consensus 68 dhpnpkgfcdlk 79 (121) + -|||..|+-.+. +T Consensus 177 vHPn~~Gy~kmA 188 (195) +T ABN52033.1|CE3 177 VHPNDAGYKKMA 188 (195) +Confidence 489988865443 + + +No 6 +>AAI70505.1|CBM47|47-174|1.7e-41 +Probab=2.25 E-value=13 Score=16.85 Aligned_cols=12 Identities=25% Similarity=0.728 Sum_probs=9.4 Template_Neff=5.800 + +Q 6W4H_B 77 DLKGKYVQIPTT 88 (121) +Q Consensus 77 dlkgkyvqiptt 88 (121) + .++|+||.|--. +T Consensus 106 ~~~GRYV~V~l~ 117 (128) +T AAI70505.1|CBM 106 GMEGRYVRVVLP 117 (128) +Confidence 589999987654 + + +No 7 +>BAE59978.1|GT59|35-538|9.4e-149 +Probab=2.21 E-value=14 Score=20.79 Aligned_cols=28 Identities=39% Similarity=0.606 Sum_probs=22.2 Template_Neff=4.400 + +Q 6W4H_B 45 PEANMDQESFGGASCCLYCRCHIDHPNPK 73 (121) +Q Consensus 45 peanmdqesfggascclycrchidhpnpk 73 (121) + ||.-|| |.|-=..+=-||+-+-++=+|| +T Consensus 3 pePYmD-EiFHIpQaQ~YC~G~f~~WDpK 30 (418) +T BAE59978.1|GT5 3 PEPYMD-EIFHIPQAQRYCRGRFRQWDPK 30 (418) +Confidence 667777 6677777888999998887776 + + +No 8 +>AJQ99710.1|GH13_18.hmm|7.1e-110|80-422 +Probab=1.91 E-value=16 Score=19.88 Aligned_cols=32 Identities=28% Similarity=0.365 Sum_probs=23.3 Template_Neff=4.200 + +Q 6W4H_B 6 AAKAYKDYLASSGG-QPITNCVKMLCTHTGTGQ 37 (121) +Q Consensus 6 aakaykdylassgg-qpitncvkmlcthtgtgq 37 (121) + -+++.++++++... +.-++++.+|-+|-|-|- +T Consensus 229 ~~~~L~~W~~~~p~~~~~~~~fnflasHDGIGl 261 (343) +T AJQ99710.1|GH1 229 NARALAKWLKSLPPPSDGTTYFNFLASHDGIGL 261 (343) +Confidence 35667777776544 445789999999999874 + + +No 9 +>AIQ50255.1|CBM77|PL1||627-727 +Probab=1.67 E-value=19 Score=16.83 Aligned_cols=14 Identities=29% Similarity=0.617 Sum_probs=10.7 Template_Neff=2.600 + +Q 6W4H_B 17 SGGQPITNCVKMLC 30 (121) +Q Consensus 17 sggqpitncvkmlc 30 (121) + ..|...|.|.||-- +T Consensus 30 YnGltLTqcLKiEs 43 (103) +T AIQ50255.1|CBM 30 YNGLTLTQCLKIES 43 (103) +Confidence 35778899999853 + + +No 10 +>CAA44713.1|GT15|70-340|4.1e-134 +Probab=1.67 E-value=19 Score=18.92 Aligned_cols=16 Identities=44% Similarity=0.769 Sum_probs=11.2 Template_Neff=4.200 + +Q 6W4H_B 5 DAAKAYKDYLASSGGQ 20 (121) +Q Consensus 5 daakaykdylassggq 20 (121) + ++-.+|-+||.++||. +T Consensus 228 ~~Y~~yF~~LD~~GGF 243 (279) +T CAA44713.1|GT1 228 EAYRDYFEYLDKSGGF 243 (279) +Confidence 3445667788888884 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6W9C_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,156 @@ +Query 6W9C_A +Match_columns 313 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:06 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_686.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_831.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 ACY47587.1|GH78|346-867|5.6e-2 14.0 1.3 0.002 29.4 0.0 93 67-162 209-319 (496) + 2 AAO76127.1|GH143 5.8 4.2 0.0066 28.3 0.0 34 63-96 261-299 (574) + 3 AUO30192.1|GH149|2.4.1.-|0|1-1 5.1 5 0.0077 29.9 0.0 53 96-162 947-1007(1153) + 4 AHA42547.2|GH5_2 4.1 6.5 0.01 21.7 0.0 27 5-31 66-96 (97) + 5 AAW84061.1|PL10.hmm|1e-110|56- 3.6 7.5 0.012 24.2 0.0 86 57-144 37-135 (288) + 6 ADJ39760.1|GT63|1-340|1.6e-218 3.6 7.6 0.012 24.8 0.0 29 44-72 289-329 (340) + 7 ANS64378.1|GH43_22.hmm|8.3e-76 3.0 9.5 0.015 22.6 0.0 16 47-62 17-32 (244) + 8 ACY49347.1|GH105|46-385|1.1e-1 2.1 14 0.022 21.8 0.0 28 90-119 169-196 (329) + 9 ABG84856.1|PL8|420-695|7e-98 1.8 17 0.027 20.6 0.0 14 4-17 152-165 (263) + 10 AHG92795.1|GH43_29.hmm|2.4e-57 1.5 22 0.034 21.2 0.0 24 89-112 52-76 (279) + +No 1 +>ACY47587.1|GH78|346-867|5.6e-200 +Probab=14.01 E-value=1.3 Score=29.37 Aligned_cols=93 Identities=17% Similarity=0.196 Sum_probs=55.5 Template_Neff=7.200 + +Q 6W9C_A 67 FEYYHTTDPSFLGRYMSALNHTKKWKYPQVNG--LT------SIKWAD-----N-----NCYLATALLTLQQIELKFNPP 128 (313) +Q Consensus 67 feyyhttdpsflgrymsalnhtkkwkypqvng--lt------sikwad-----n-----ncylatalltlqqielkfnpp 128 (313) + --|.++-|.++|.++..++..--.|-..+++. -. -..|.+ + |++++-+|..+.+|.-....+ +T Consensus 209 ~~Y~~~GD~~~l~~~y~~~~~~l~~~~~~~~~~g~~~l~~~~~gDW~~~~~~~~~~~~~~a~~~~~l~~~a~lA~~LG~~ 288 (496) +T ACY47587.1|GH7 209 DYYRYYGDKEFLEEQYPSMKRWLDYLESRADDDGNWGLWDTGFGDWLDDPPAGGTDLVATAYYYYSLRLMAELAEALGKT 288 (496) +Confidence 34567889999988877776555555555533 11 255555 2 778888888888887777766 + + +Q 6W9C_A 129 ALQDAYYRARAGEAANFCALILAYCNKTVGELGD 162 (313) +Q Consensus 129 alqdayyrarageaanfcalilaycnktvgelgd 162 (313) + +.. +.|+.+|.+... |+.-.+-|..-|...| +T Consensus 289 ~~a-~~y~~~a~~lk~--a~~~~~~~~~~G~y~~ 319 (496) +T ACY47587.1|GH7 289 EDA-ARYRALAERLKA--AFNKEFWDPDTGRYAD 319 (496) +Confidence 553 345666555432 2222333444454544 + + +No 2 +>AAO76127.1|GH143 +Probab=5.76 E-value=4.2 Score=28.33 Aligned_cols=34 Identities=35% Similarity=0.699 Sum_probs=26.2 Template_Neff=2.500 + +Q 6W9C_A 63 RVEAFEYYHTTDPSFLGRYMSALN-----HTKKWKYPQV 96 (313) +Q Consensus 63 rveafeyyhttdpsflgrymsaln-----htkkwkypqv 96 (313) + ..+||.|||-.|-...|-+-.||- .-|.|.|+.+ +T Consensus 261 ~ykAFsyYhlpDGrvVgLWK~altsiS~D~GktW~y~p~ 299 (574) +T AAO76127.1|GH1 261 GYKAFSYYHLPDGRVVGLWKHALTSISEDGGKTWSYNPL 299 (574) +Confidence 358999999999988887776664 3467887654 + + +No 3 +>AUO30192.1|GH149|2.4.1.-|0|1-1154 +Probab=5.08 E-value=5 Score=29.90 Aligned_cols=53 Identities=36% Similarity=0.506 Sum_probs=33.5 Template_Neff=3.200 + +Q 6W9C_A 96 VNGLTSIKWADNNCYLATALLTLQQIELKF-----NP---PALQDAYYRARAGEAANFCALILAYCNKTVGELGD 162 (313) +Q Consensus 96 vngltsikwadnncylatalltlqqielkf-----np---palqdayyrarageaanfcalilaycnktvgelgd 162 (313) + -.||-||-|-- .+-.||..|..-++. ++ .+|.+.||+.|+|-. .||+-.+-|- +T Consensus 947 YEGLGsIYWHM----VSKLLLAvqE~~~~Ai~~~~~~~~~~~L~~~YyeIr~GIG----------~~KsPe~YGA 1007 (1153) +T AUO30192.1|GH1 947 YEGLGSIYWHM----VSKLLLAVQENCLDAIEQGADSEVIGKLADHYYEIRAGIG----------FNKSPELYGA 1007 (1153) +Confidence 46999999952 333444444433322 32 468999999999954 3566665554 + + +No 4 +>AHA42547.2|GH5_2 +Probab=4.12 E-value=6.5 Score=21.71 Aligned_cols=27 Identities=33% Similarity=0.395 Sum_probs=19.9 Template_Neff=1.800 + +Q 6W9C_A 5 VFTTVDN----INLHTQVVDMSMTYGQQFGP 31 (313) +Q Consensus 5 vfttvdn----inlhtqvvdmsmtygqqfgp 31 (313) + =||||++ -+|...|+..+-.|.-|||. +T Consensus 66 gfttVatat~nc~lYiyvkqAp~Sf~lqFgs 96 (97) +T AHA42547.2|GH5 66 GFTTVATATMNCALYIYVKQAPSSFTLQFGS 96 (97) +Confidence 3777775 45667788888888888873 + + +No 5 +>AAW84061.1|PL10.hmm|1e-110|56-346 +Probab=3.63 E-value=7.5 Score=24.18 Aligned_cols=86 Identities=29% Similarity=0.338 Sum_probs=59.3 Template_Neff=4.300 + +Q 6W9C_A 57 PNDDT---LRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYP-----QVNGL-----TSIKWADNNCYLATALLTLQQIEL 123 (313) +Q Consensus 57 pnddt---lrveafeyyhttdpsflgrymsalnhtkkwkyp-----qvngl-----tsikwadnncylatalltlqqiel 123 (313) + .|+-| ||.-|--|-.|.|+.+..-....|+..-+-.|| |+--+ ..|...||- +.-.|..|+.|.- +T Consensus 37 DN~AT~tei~~LA~~y~~t~~~~Yr~A~~kGl~yLL~aQY~nGGWPQ~yP~~~~Y~~~ITfNDdA--M~~vl~lL~di~~ 114 (288) +T AAW84061.1|PL1 37 DNGATTTEIRFLARAYKATGDERYRDAALKGLDYLLAAQYPNGGWPQFYPLRGGYHDHITFNDDA--MVNVLELLRDIAE 114 (288) +Confidence 45544 566677788888888887777777766555543 33322 246666664 4556777788887 + + +Q 6W9C_A 124 KFNPPALQDAYYRARAGEAAN 144 (313) +Q Consensus 124 kfnppalqdayyrarageaan 144 (313) + +-+|-++-|+-+|+||.+|.+ +T Consensus 115 ~~~~f~fvd~~~r~ra~~A~~ 135 (288) +T AAW84061.1|PL1 115 GKPPFDFVDAARRARARQAVD 135 (288) +Confidence 777778888889999988765 + + +No 6 +>ADJ39760.1|GT63|1-340|1.6e-218 +Probab=3.62 E-value=7.6 Score=24.76 Aligned_cols=29 Identities=34% Similarity=0.527 Sum_probs=23.1 Template_Neff=1.400 + +Q 6W9C_A 44 PHNSHEGKTFYV------------LPNDDTLRVEAFEYYHT 72 (313) +Q Consensus 44 phnshegktfyv------------lpnddtlrveafeyyht 72 (313) + .||--+...||| +.|||.||.|..+|-|. +T Consensus 289 ~~~i~~~~~fyv~nr~elid~in~~k~~~~~r~e~l~~qh~ 329 (340) +T ADJ39760.1|GT6 289 KHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHD 329 (340) +Confidence 366667778887 56889999999999885 + + +No 7 +>ANS64378.1|GH43_22.hmm|8.3e-76|54-270 +Probab=3.00 E-value=9.5 Score=22.64 Aligned_cols=16 Identities=31% Similarity=0.746 Sum_probs=13.6 Template_Neff=5.100 + +Q 6W9C_A 47 SHEGKTFYVLPNDDTL 62 (313) +Q Consensus 47 shegktfyvlpnddtl 62 (313) + |++|.+||+++-|+.+ +T Consensus 17 s~dgdkfyiiATDL~i 32 (244) +T ANS64378.1|GH4 17 SPDGDKFYIIATDLRI 32 (244) +Confidence 7899999999988654 + + +No 8 +>ACY49347.1|GH105|46-385|1.1e-131 +Probab=2.15 E-value=14 Score=21.82 Aligned_cols=28 Identities=29% Similarity=0.627 Sum_probs=22.0 Template_Neff=6.200 + +Q 6W9C_A 90 KWKYPQVNGLTSIKWADNNCYLATALLTLQ 119 (313) +Q Consensus 90 kwkypqvngltsikwadnncylatalltlq 119 (313) + .|--| .|...+-|+-.|...+.||..+- +T Consensus 169 ~wa~~--t~~s~~fW~RgnGW~~~aL~~~L 196 (329) +T ACY49347.1|GH1 169 NWADP--TGGSPAFWGRGNGWVAMALVDVL 196 (329) +Confidence 34444 78899999999999999887653 + + +No 9 +>ABG84856.1|PL8|420-695|7e-98 +Probab=1.83 E-value=17 Score=20.63 Aligned_cols=14 Identities=29% Similarity=0.344 Sum_probs=10.3 Template_Neff=6.200 + +Q 6W9C_A 4 KVFTTVDNINLHTQ 17 (313) +Q Consensus 4 kvfttvdninlhtq 17 (313) + .|.|||||-.+... +T Consensus 152 ~v~TTi~qr~~~~~ 165 (263) +T ABG84856.1|PL8 152 PVETTIEQRKLNGK 165 (263) +Confidence 46788888877665 + + +No 10 +>AHG92795.1|GH43_29.hmm|2.4e-57|84-380 +Probab=1.51 E-value=22 Score=21.20 Aligned_cols=24 Identities=17% Similarity=0.476 Sum_probs=16.6 Template_Neff=4.100 + +Q 6W9C_A 89 KKWK-YPQVNGLTSIKWADNNCYLA 112 (313) +Q Consensus 89 kkwk-ypqvngltsikwadnncyla 112 (313) + +.|+ ++.+-.++.++||+++.+-+ +T Consensus 52 ~nWtdhg~~l~~~~F~WA~~~AwA~ 76 (279) +T AHG92795.1|GH4 52 VNWTDHGSVLSPKDFSWAKGDAWAS 76 (279) +Confidence 4554 45677788999998665543 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6W9Q_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6W9Q_A +Match_columns 123 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:07 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_685.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_832.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 AJP22991.1|PL8_1.hmm|1.4e-102| 4.4 6 0.0093 22.3 0.0 21 37-57 7-27 (271) + 2 ACE81431.1|GH5_15.hmm|2.3e-124 4.2 6.2 0.0097 22.5 0.0 31 29-61 223-253 (300) + 3 CAG81347.1|CBM19|426-466|7e-13 3.5 8 0.012 16.1 0.0 9 21-29 33-41 (44) + 4 ATY34423.1|PL10_2.hmm|5.1e-141 2.8 10 0.016 21.0 0.0 58 13-70 168-226 (275) + 5 AAK94929.1|CBM55|16-61|2.6e-25 2.3 13 0.02 15.5 0.0 11 19-29 25-35 (46) + 6 ABS47913.1|PL8_2.hmm|2.6e-99|6 2.0 15 0.024 19.3 0.0 17 59-78 57-73 (248) + 7 SCV09658.1|GH137 2.0 15 0.024 20.7 0.0 31 37-69 210-248 (367) + 8 EEO46747.1|CBM58|202-318|3.8e- 2.0 16 0.025 17.7 0.0 12 93-104 37-48 (116) + 9 QDM21448.1|AA3||6-537 1.7 19 0.029 21.2 0.0 33 50-83 80-112 (644) + 10 CBJ37966.1|GH28|235-654|7.7e-4 1.7 19 0.029 18.3 0.0 17 18-34 3-19 (345) + +No 1 +>AJP22991.1|PL8_1.hmm|1.4e-102|443-692 +Probab=4.39 E-value=6 Score=22.31 Aligned_cols=21 Identities=43% Similarity=0.604 Sum_probs=16.8 Template_Neff=2.700 + +Q 6W9Q_A 37 NALAYYNTTKGGRFVLALLSD 57 (123) +Q Consensus 37 nalayynttkggrfvlallsd 57 (123) + .-++|||..++=-|.|.+-|+ +T Consensus 7 Dkl~y~Na~~dF~FaLSm~S~ 27 (271) +T AJP22991.1|PL8 7 DKLAYYNAEKDFAFGLSMHSK 27 (271) +Confidence 357899998888888888765 + + +No 2 +>ACE81431.1|GH5_15.hmm|2.3e-124|99-401 +Probab=4.23 E-value=6.2 Score=22.52 Aligned_cols=31 Identities=32% Similarity=0.473 Sum_probs=17.3 Template_Neff=2.300 + +Q 6W9Q_A 29 TQTACTDDNALAYYNTTKGGRFVLALLSDLQDL 61 (123) +Q Consensus 29 tqtactddnalayynttkggrfvlallsdlqdl 61 (123) + -+++|+||- .---.+--|.+-|..=+++|+- +T Consensus 223 i~tsCtd~~--~~~~p~ivGEWSLsvpdn~q~t 253 (300) +T ACE81431.1|GH5 223 IETSCTDDV--NTHGPTIVGEWSLSVPDNVQDT 253 (300) +Confidence 467888882 1111233466667666666653 + + +No 3 +>CAG81347.1|CBM19|426-466|7e-13 +Probab=3.47 E-value=8 Score=16.11 Aligned_cols=9 Identities=44% Similarity=0.892 Sum_probs=6.1 Template_Neff=3.400 + +Q 6W9Q_A 21 QMSCAAGTT 29 (123) +Q Consensus 21 qmscaagtt 29 (123) + .+.|++|++ +T Consensus 33 ~~~Cp~gt~ 41 (44) +T CAG81347.1|CBM 33 TTECPSGTT 41 (44) +Confidence 467777765 + + +No 4 +>ATY34423.1|PL10_2.hmm|5.1e-141|81-355 +Probab=2.82 E-value=10 Score=21.01 Aligned_cols=58 Identities=19% Similarity=0.363 Sum_probs=37.2 Template_Neff=2.400 + +Q 6W9Q_A 13 ELSPVALRQMSCAAGTTQTACTD-DNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSD 70 (123) +Q Consensus 13 elspvalrqmscaagttqtactd-dnalayynttkggrfvlallsdlqdlkwarfpksd 70 (123) + ++.|+--|-.--+|=+++|.|+. .+-+-||.-|..-+|.-.+=..+.=|.-.++|... +T Consensus 168 dl~Pa~ARtyEP~a~~~htTa~~i~~l~~fY~lTgD~kyLaripeAi~wLesvk~p~~~ 226 (275) +T ATY34423.1|PL1 168 DLKPAGARTYEPAALATHTTAANIRQLMDFYELTGDKKYLARIPEAIDWLESVKLPPDQ 226 (275) +Confidence 56777777666565555555554 34567888888877765555545555556677766 + + +No 5 +>AAK94929.1|CBM55|16-61|2.6e-25 +Probab=2.30 E-value=13 Score=15.48 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=7.6 Template_Neff=2.700 + +Q 6W9Q_A 19 LRQMSCAAGTT 29 (123) +Q Consensus 19 lrqmscaagtt 29 (123) + -.+|+|.+|+. +T Consensus 25 ~~~~~C~~gtv 35 (46) +T AAK94929.1|CBM 25 GKPMKCPGGTV 35 (46) +Confidence 35678888863 + + +No 6 +>ABS47913.1|PL8_2.hmm|2.6e-99|635-880 +Probab=2.03 E-value=15 Score=19.29 Aligned_cols=17 Identities=41% Similarity=0.851 Sum_probs=11.8 Template_Neff=4.100 + +Q 6W9Q_A 59 QDLKWARFPKSDGTGTIYTE 78 (123) +Q Consensus 59 qdlkwarfpksdgtgtiyte 78 (123) + .-..|.|+| ||-||... +T Consensus 57 ~GWDWNR~P---GtTtihLP 73 (248) +T ABS47913.1|PL8 57 EGWDWNRYP---GTTTIHLP 73 (248) +Confidence 457899998 56666543 + + +No 7 +>SCV09658.1|GH137 +Probab=2.03 E-value=15 Score=20.73 Aligned_cols=31 Identities=35% Similarity=0.761 Sum_probs=22.2 Template_Neff=2.600 + +Q 6W9Q_A 37 NALAYYNTT--------KGGRFVLALLSDLQDLKWARFPKS 69 (123) +Q Consensus 37 nalayyntt--------kggrfvlallsdlqdlkwarfpks 69 (123) + .-.-|||.. ++-|.-+|.-.|+ +.|.||++. +T Consensus 210 ~FvmyYNA~g~s~~~~~k~EriGmAvS~Dm--~~W~Ry~~n 248 (367) +T SCV09658.1|GH1 210 PFVMYYNAKGDSLKNNKKGERIGMAVSDDM--VHWKRYGKN 248 (367) +Confidence 345677754 5578888887777 469999875 + + +No 8 +>EEO46747.1|CBM58|202-318|3.8e-68 +Probab=1.97 E-value=16 Score=17.68 Aligned_cols=12 Identities=50% Similarity=0.949 Sum_probs=8.9 Template_Neff=1.700 + +Q 6W9Q_A 93 PKVKYLYFIKGL 104 (123) +Q Consensus 93 pkvkylyfikgl 104 (123) + ...|||||-.|+ +T Consensus 37 ~~akYLY~Gegi 48 (116) +T EEO46747.1|CBM 37 DGAKYLYFGEGI 48 (116) +Confidence 345999997765 + + +No 9 +>QDM21448.1|AA3||6-537 +Probab=1.71 E-value=19 Score=21.21 Aligned_cols=33 Identities=24% Similarity=0.487 Sum_probs=15.6 Template_Neff=4.300 + +Q 6W9Q_A 50 FVLALLSDLQDLKWARFPKSDGTGTIYTELEPPC 83 (123) +Q Consensus 50 fvlallsdlqdlkwarfpksdgtgtiyteleppc 83 (123) + ||--...|-++.+-...--.-..|++|+ +.||- +T Consensus 80 fv~hy~d~~~~~r~~~~t~~~~~G~~yv-~~pP~ 112 (644) +T QDM21448.1|AA3 80 FVRHYADDTRQARDPKYTYRTPDGGYYV-LDPPA 112 (644) +Confidence 4444444333333222222345677887 66653 + + +No 10 +>CBJ37966.1|GH28|235-654|7.7e-46 +Probab=1.70 E-value=19 Score=18.26 Aligned_cols=17 Identities=35% Similarity=0.651 Sum_probs=7.9 Template_Neff=6.800 + +Q 6W9Q_A 18 ALRQMSCAAGTTQTACT 34 (123) +Q Consensus 18 alrqmscaagttqtact 34 (123) + .|.|-.|.|..-..+|. +T Consensus 3 ~~~~~~~~~~~~~~~~~ 19 (345) +T CBJ37966.1|GH2 3 NLAQTACTASWAAAACA 19 (345) +Confidence 34444554444444443 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6WEY_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6WEY_A +Match_columns 193 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:15 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_683.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_834.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 O29635_ARCFU/4-168 7.5 3 0.0047 19.8 0.0 18 44-61 61-78 (170) + 2 AAO69110.1|GH13_26.hmm|1.3e-96 7.0 3.3 0.0051 25.1 0.0 51 69-119 6-56 (300) + 3 ADI28148.1|GH4|6-186|8.8e-81 3.1 9.2 0.014 20.2 0.0 21 22-42 124-144 (179) + 4 ADH08008.1|GH5_48.hmm|7.7e-154 2.6 11 0.018 22.3 0.0 31 107-137 46-77 (316) + 5 AAZ26198.1|GH13_27.hmm|4.2e-15 2.2 14 0.021 21.9 0.0 30 125-154 222-251 (319) + 6 AAM37385.1|GH121|19-1450|0 2.2 14 0.022 25.7 0.0 64 11-76 188-256 (1400) + 7 CAA37453.1|CBM25|698-758|0.095 2.1 14 0.022 16.9 0.0 38 38-76 13-50 (78) + 8 BAF60961.1|GT26|55-224|9.8e-76 1.9 16 0.026 18.1 0.0 19 20-38 89-107 (171) + 9 ACS87816.1|GT40|137-346|7.4e-9 1.9 17 0.026 20.2 0.0 23 44-66 37-59 (212) + 10 ADV06884.1|GH35|10-328|8.8e-12 1.6 20 0.031 19.6 0.0 31 38-71 251-281 (301) + +No 1 +>O29635_ARCFU/4-168 +Probab=7.50 E-value=3 Score=19.76 Aligned_cols=18 Identities=33% Similarity=0.303 Sum_probs=13.2 Template_Neff=9.500 + +Q 6WEY_A 44 LKHGGGVAGALNKATNNA 61 (193) +Q Consensus 44 lkhgggvagalnkatnna 61 (193) + ...+.|.++|+|++...| +T Consensus 61 ~~~n~G~~~A~n~g~~~a 78 (170) +T O29635_ARCFU/4 61 RPRNRGKAGARNAGLRAA 78 (170) +Confidence 344558999999887665 + + +No 2 +>AAO69110.1|GH13_26.hmm|1.3e-96|23-309 +Probab=6.97 E-value=3.3 Score=25.12 Aligned_cols=51 Identities=31% Similarity=0.444 Sum_probs=36.3 Template_Neff=4.200 + +Q 6WEY_A 69 YIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVVNNKKGGEEDIQLLKSAY 119 (193) +Q Consensus 69 yiatngplkvggscvlsghnlakhclhvvgpnvvnnkkggeediqllksay 119 (193) + |++.-|--.+=-|-++...-=..|...|+-|+-+|..-|||+..+.|..+. +T Consensus 6 Yl~~LGishlY~SPil~A~pGStHGYDvvDp~~inpelGge~gl~~L~~~l 56 (300) +T AAO69110.1|GH1 6 YLADLGISHLYASPILTARPGSTHGYDVVDPTRINPELGGEEGLRRLAAAL 56 (300) +Confidence 444333333334555555555679999999999999999999988876654 + + +No 3 +>ADI28148.1|GH4|6-186|8.8e-81 +Probab=3.07 E-value=9.2 Score=20.22 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=16.8 Template_Neff=5.400 + +Q 6WEY_A 22 DIVEEAKKVKPTTVVVNAANV 42 (193) +Q Consensus 22 diveeakkvkpttvvvnaanv 42 (193) + ||.+..++.-|...++|.+|- +T Consensus 124 ~ia~~ie~~~P~AwliNytNP 144 (179) +T ADI28148.1|GH4 124 DIAKDMEEYCPDAWLLNYTNP 144 (179) +Confidence 567777778899999998874 + + +No 4 +>ADH08008.1|GH5_48.hmm|7.7e-154|75-403 +Probab=2.59 E-value=11 Score=22.34 Aligned_cols=31 Identities=26% Similarity=0.317 Sum_probs=23.7 Template_Neff=2.900 + +Q 6WEY_A 107 GGEEDIQLLKSAYENFNQ-HEEVLLAPLLSAG 137 (193) +Q Consensus 107 ggeediqllksayenfnq-heevllapllsag 137 (193) + --++|+++||.....+.+ ...|.|+||-.-| +T Consensus 46 Lv~~Dl~~Lk~~LD~A~~aglKVVltpLSLPg 77 (316) +T ADH08008.1|GH5 46 LVKADLAKLKAVLDAAHAAGLKVVLTPLSLPG 77 (316) +Confidence 357899999999988765 4678888875444 + + +No 5 +>AAZ26198.1|GH13_27.hmm|4.2e-155|41-357 +Probab=2.23 E-value=14 Score=21.92 Aligned_cols=30 Identities=30% Similarity=0.497 Sum_probs=23.7 Template_Neff=2.600 + +Q 6WEY_A 125 HEEVLLAPLLSAGIFGADDPPIIHSLRVCV 154 (193) +Q Consensus 125 heevllapllsagifgaddppiihslrvcv 154 (193) + .++..|.|.|..--.||-|-|...++|-.. +T Consensus 222 ~y~~FL~PyL~~T~~~AYDFPLf~tir~Af 251 (319) +T AAZ26198.1|GH1 222 DYELFLQPYLQETRHGAYDFPLFNTIRKAF 251 (319) +Confidence 456778999999999999999887766543 + + +No 6 +>AAM37385.1|GH121|19-1450|0 +Probab=2.18 E-value=14 Score=25.65 Aligned_cols=64 Identities=31% Similarity=0.440 Sum_probs=43.2 Template_Neff=2.400 + +Q 6WEY_A 11 LTDNNVYIKNADIVEEAKKVKPTTVVVNAANVYLKHGGGV-----AGALNKATNNAMQVESDDYIATNGPL 76 (193) +Q Consensus 11 ltdnnvyiknadiveeakkvkpttvvvnaanvylkhgggv-----agalnkatnnamqvesddyiatngpl 76 (193) + +|+|||-+.|-.|- ...-.++|+.+-|+.-|-.|+.|- -.+.|+.|.-.-....|.+.+..|.| +T Consensus 188 IT~nNv~Vtnl~v~--~~~~a~~t~~l~a~SP~a~~~~g~eLtG~~~~~N~lTti~pRlsGdgf~~~g~~L 256 (1400) +T AAM37385.1|GH1 188 ITYNNVAVANLTVS--STGGAPHTVTLQAASPYAQHGDGNELTGRVDAKNNLTTIFPRLSGDGFTVSGGRL 256 (1400) +Confidence 58999988876553 344567889999999999998752 34555555555555555555555544 + + +No 7 +>CAA37453.1|CBM25|698-758|0.095 +Probab=2.14 E-value=14 Score=16.91 Aligned_cols=38 Identities=26% Similarity=0.306 Sum_probs=26.5 Template_Neff=5.000 + +Q 6WEY_A 38 NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPL 76 (193) +Q Consensus 38 naanvylkhgggvagalnkatnnamqvesddyiatngpl 76 (193) + ++.++||-.|-|-. +-..+..-+|+-+.+.+....=+| +T Consensus 13 g~~~vylHyg~~~~-~Wt~vp~~~M~~~~~g~~~~TI~~ 50 (78) +T CAA37453.1|CBM 13 GWSNVYLHYGYGGG-SWTNVPGVAMEKACDGWWKKTIDL 50 (78) +Confidence 56778887754433 777788889998888865554444 + + +No 8 +>BAF60961.1|GT26|55-224|9.8e-76 +Probab=1.90 E-value=16 Score=18.13 Aligned_cols=19 Identities=21% Similarity=0.386 Sum_probs=14.3 Template_Neff=6.300 + +Q 6WEY_A 20 NADIVEEAKKVKPTTVVVN 38 (193) +Q Consensus 20 nadiveeakkvkpttvvvn 38 (193) + +.+++++.++.+|+-|+|- +T Consensus 89 ~~~i~~~I~~~~~d~l~vg 107 (171) +T BAF60961.1|GT2 89 EEAIIERINASGPDILFVG 107 (171) +Confidence 5677788888888877764 + + +No 9 +>ACS87816.1|GT40|137-346|7.4e-95 +Probab=1.85 E-value=17 Score=20.18 Aligned_cols=23 Identities=26% Similarity=0.353 Sum_probs=18.6 Template_Neff=2.900 + +Q 6WEY_A 44 LKHGGGVAGALNKATNNAMQVES 66 (193) +Q Consensus 44 lkhgggvagalnkatnnamqves 66 (193) + -.+.-|-|||+|.....|+|-.- +T Consensus 37 ~p~N~GYA~AvN~GlR~AL~~p~ 59 (212) +T ACS87816.1|GT4 37 FPENIGYAGAVNEGLRHALSFPF 59 (212) +Confidence 34567999999999999998654 + + +No 10 +>ADV06884.1|GH35|10-328|8.8e-129 +Probab=1.61 E-value=20 Score=19.64 Aligned_cols=31 Identities=42% Similarity=0.473 Sum_probs=22.2 Template_Neff=5.600 + +Q 6WEY_A 38 NAANVYLKHGGGVAGALNKATNNAMQVESDDYIA 71 (193) +Q Consensus 38 naanvylkhgggvagalnkatnnamqvesddyia 71 (193) + +..|.|+-|||-=-|.+|-+.. .+.|-||-| +T Consensus 251 ~~~n~YM~hGGTNfg~~~g~~~---~~tsYDy~A 281 (301) +T ADV06884.1|GH3 251 TSVNYYMFHGGTNFGFTNGANF---QTTSYDYDA 281 (301) +Confidence 5678999999987777665544 556777744 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6WJI_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6WJI_A +Match_columns 108 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:16 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_682.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_835.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 ADJ39760.1|GT63|1-340|1.6e-218 12.6 1.5 0.0023 26.0 0.0 24 81-104 49-72 (340) + 2 ABV04693.1|GH104|4-149|1.2e-65 6.8 3.4 0.0053 20.8 0.0 26 71-96 65-90 (144) + 3 ADF51355.1|GH89|74-731|1.3e-27 4.6 5.6 0.0088 23.9 0.0 43 51-93 168-217 (663) + 4 AOH85032.1|PL22_2.hmm|9.2e-63| 3.3 8.3 0.013 20.7 0.0 23 58-80 200-228 (238) + 5 AFR03652.1|PL2_1.hmm|0|24-554 3.1 9.1 0.014 22.4 0.0 22 2-23 232-253 (529) + 6 AAM43285.1|GH43_9.hmm|1.1e-139 3.1 9.1 0.014 21.0 0.0 16 27-42 7-22 (292) + 7 ADB10624.1|GH53|89-472|9e-82 2.9 9.8 0.015 20.6 0.0 46 53-106 127-173 (341) + 8 ABS49747.1|PL2|17-549|2.7e-271 2.9 10 0.016 22.4 0.0 33 2-34 234-270 (530) + 9 ADL41529.1|CBM27|38-215|8.3e-5 2.8 10 0.016 18.6 0.0 21 65-85 143-163 (166) + 10 CCH00347.1|GH43_15.hmm|2e-122| 2.7 11 0.017 20.5 0.0 24 36-59 37-60 (276) + +No 1 +>ADJ39760.1|GT63|1-340|1.6e-218 +Probab=12.60 E-value=1.5 Score=25.95 Aligned_cols=24 Identities=29% Similarity=0.474 Sum_probs=21.0 Template_Neff=1.400 + +Q 6WJI_A 81 IKLDDKDPNFKDQVILLNKHIDAY 104 (108) +Q Consensus 81 iklddkdpnfkdqvillnkhiday 104 (108) + +..||-|||--|.||..|..|.-| +T Consensus 49 ~~fd~vd~n~ydr~~vvn~s~nf~ 72 (340) +T ADJ39760.1|GT6 49 KSFDEVDVNDYDRLIVVNSSINFF 72 (340) +Confidence 568999999999999999888755 + + +No 2 +>ABV04693.1|GH104|4-149|1.2e-65 +Probab=6.81 E-value=3.4 Score=20.75 Aligned_cols=26 Identities=38% Similarity=0.603 Sum_probs=22.8 Template_Neff=4.400 + +Q 6WJI_A 71 SGTWLTYTGAIKLDDKDPNFKDQVIL 96 (108) +Q Consensus 71 sgtwltytgaiklddkdpnfkdqvil 96 (108) + +.||-.|...++|.|-.|...|++.+ +T Consensus 65 ~~tW~~~~~~l~l~dFsP~~QD~~A~ 90 (144) +T ABV04693.1|GH1 65 SRTWDEYRKQLGLPDFSPESQDRVAL 90 (144) +Confidence 45899999999999999999999764 + + +No 3 +>ADF51355.1|GH89|74-731|1.3e-276 +Probab=4.59 E-value=5.6 Score=23.93 Aligned_cols=43 Identities=28% Similarity=0.493 Sum_probs=33.7 Template_Neff=4.700 + +Q 6WJI_A 51 FAPSASAFFGMSRIG-------MEVTPSGTWLTYTGAIKLDDKDPNFKDQ 93 (108) +Q Consensus 51 fapsasaffgmsrig-------mevtpsgtwltytgaiklddkdpnfkdq 93 (108) + ..|-..+|.|+---+ ..|++-|.|-.+...--||..||-|..- +T Consensus 168 MtPVLPaF~G~VP~~f~~~~P~a~i~~~g~W~gF~~~~~LdP~dplF~~I 217 (663) +T ADF51355.1|GH8 168 MTPVLPAFAGHVPAAFKEKNPDAKITRQGNWGGFDRPYFLDPEDPLFAKI 217 (663) +Confidence 356677787775443 4788999999999988999999998753 + + +No 4 +>AOH85032.1|PL22_2.hmm|9.2e-63|205-432 +Probab=3.34 E-value=8.3 Score=20.73 Aligned_cols=23 Identities=30% Similarity=0.764 Sum_probs=15.6 Template_Neff=2.600 + +Q 6WJI_A 58 FFGMSRIG------MEVTPSGTWLTYTGA 80 (108) +Q Consensus 58 ffgmsrig------mevtpsgtwltytga 80 (108) + ...|++-. ...||.|.|+.++.- +T Consensus 200 LVnm~~H~Y~lEPN~~FtPDgkw~iFrsN 228 (238) +T AOH85032.1|PL2 200 LVNMSRHNYRLEPNVHFTPDGKWIIFRSN 228 (238) +Confidence 34566543 346899999998764 + + +No 5 +>AFR03652.1|PL2_1.hmm|0|24-554 +Probab=3.10 E-value=9.1 Score=22.39 Aligned_cols=22 Identities=41% Similarity=0.611 Sum_probs=18.3 Template_Neff=1.400 + +Q 6WJI_A 2 PRQKRTATKAYNVTQAFGRRGP 23 (108) +Q Consensus 2 prqkrtatkaynvtqafgrrgp 23 (108) + ||.|.|.--.|..||+..|..+ +T Consensus 232 prdkktglgvyqftqalkr~et 253 (529) +T AFR03652.1|PL2 232 PRDKKTGLGVYQFTQALKRAET 253 (529) +Confidence 7889999999999999877543 + + +No 6 +>AAM43285.1|GH43_9.hmm|1.1e-139|60-332 +Probab=3.10 E-value=9.1 Score=21.01 Aligned_cols=16 Identities=38% Similarity=0.981 Sum_probs=14.0 Template_Neff=2.900 + +Q 6WJI_A 27 QGNFGDQELIRQGTDY 42 (108) +Q Consensus 27 qgnfgdqelirqgtdy 42 (108) + .|+..|..++|.|.|| +T Consensus 7 ~Gd~pDPsilRdG~dY 22 (292) +T AAM43285.1|GH4 7 AGDYPDPSILRDGDDY 22 (292) +Confidence 4778899999999988 + + +No 7 +>ADB10624.1|GH53|89-472|9e-82 +Probab=2.93 E-value=9.8 Score=20.62 Aligned_cols=46 Identities=28% Similarity=0.414 Sum_probs=32.8 Template_Neff=4.700 + +Q 6WJI_A 53 PSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDP-NFKDQVILLNKHIDAYKT 106 (108) +Q Consensus 53 psasaffgmsrigmevtpsgtwltytgaiklddkdp-nfkdqvillnkhidaykt 106 (108) + -.+...-.|-.||-|+++.=-| -+.+.+ +|..-.-|||.-|+|-|. +T Consensus 127 ~~~Gv~pdmVQVGNEin~GmlW--------p~G~~~~~~~~~a~LlnaG~~AVr~ 173 (341) +T ADB10624.1|GH5 127 KDAGVTPDMVQVGNEINNGMLW--------PDGKSSGNWDNLAQLLNAGIKAVRE 173 (341) +Confidence 4455566788899998876555 233444 788888899998888764 + + +No 8 +>ABS49747.1|PL2|17-549|2.7e-271 +Probab=2.85 E-value=10 Score=22.35 Aligned_cols=33 Identities=30% Similarity=0.546 Sum_probs=26.2 Template_Neff=2.800 + +Q 6WJI_A 2 PRQKRTATKAYNVTQAFGRRG-P---EQTQGNFGDQE 34 (108) +Q Consensus 2 prqkrtatkaynvtqafgrrg-p---eqtqgnfgdqe 34 (108) + +|++.|.--.|..+|...|.. | .+|+.-|||.. +T Consensus 234 aR~peTGl~vYQFs~p~~r~~~P~dd~~T~S~~GDRA 270 (530) +T ABS49747.1|PL2 234 ARNPETGLPVYQFSSPLKRQPIPTDDNDTQSWFGDRA 270 (530) +Confidence 577888888999999987665 4 47889999864 + + +No 9 +>ADL41529.1|CBM27|38-215|8.3e-50 +Probab=2.85 E-value=10 Score=18.61 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=15.0 Template_Neff=4.500 + +Q 6WJI_A 65 GMEVTPSGTWLTYTGAIKLDD 85 (108) +Q Consensus 65 gmevtpsgtwltytgaikldd 85 (108) + +|.+---|.-+.|+|.|-||. +T Consensus 143 ~l~i~I~G~~~~y~GpIYiDN 163 (166) +T ADL41529.1|CBM 143 QLVIGIAGQNTNYKGPIYIDN 163 (166) +Confidence 344445677888999998875 + + +No 10 +>CCH00347.1|GH43_15.hmm|2e-122|40-315 +Probab=2.66 E-value=11 Score=20.47 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=17.4 Template_Neff=2.300 + +Q 6WJI_A 36 IRQGTDYKHWPQIAQFAPSASAFF 59 (108) +Q Consensus 36 irqgtdykhwpqiaqfapsasaff 59 (108) + |-..+|.-||..|....|+++.+. +T Consensus 37 I~~S~DlvhWE~V~R~v~pt~s~~ 60 (276) +T CCH00347.1|GH4 37 ILHSTDLVHWERVSRVVPPTWSFL 60 (276) +Confidence 445678889999988777665543 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6WLC_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,140 @@ +Query 6WLC_A +Match_columns 361 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:18 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_681.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_836.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 AAQ38148.1|GH12|99-246|3.8e-53 10.0 2 0.0032 24.8 0.0 20 54-73 20-39 (152) + 2 BAO41893.1|AA1_2.hmm|8.3e-157| 4.3 6.1 0.0095 25.9 0.0 44 12-62 171-214 (339) + 3 ALJ42190.1|194-452 2.4 13 0.02 22.3 0.0 14 86-99 160-173 (257) + 4 SCG78792.1|GH43_30.hmm|3.7e-96 2.4 13 0.02 22.8 0.0 33 156-188 134-166 (269) + 5 CAL37005.1|GH150|3.2.1.-|0|1-9 2.3 13 0.021 26.7 0.0 45 49-105 73-131 (942) + 6 AAF53285.2|GT92|406-770|5.4e-1 2.1 15 0.023 22.5 0.0 23 230-252 20-42 (321) + 7 ABQ89210.1|CE7|3-319|2e-146 1.9 17 0.026 22.0 0.0 22 252-273 182-203 (316) + 8 APU50764.1|CBM63||136-214 1.8 18 0.028 18.0 0.0 23 279-301 32-54 (78) + 9 APK54672.1|GT103 1.7 18 0.028 21.9 0.0 33 207-239 2-34 (232) + 10 AAO00509.1|GH107|87-420|2.9e-1 1.6 19 0.03 22.6 0.0 26 226-251 183-210 (329) + +No 1 +>AAQ38148.1|GH12|99-246|3.8e-53 +Probab=9.99 E-value=2 Score=24.85 Aligned_cols=20 Identities=30% Similarity=0.680 Sum_probs=17.2 Template_Neff=6.200 + +Q 6WLC_A 54 KTTLPVNVAFELWAKRNIKP 73 (361) +Q Consensus 54 kttlpvnvafelwakrnikp 73 (361) + .+.++.|+|+++|..|+.++ +T Consensus 20 ~~~~~~n~AyDiw~~~~~~~ 39 (152) +T AAQ38148.1|GH1 20 PSNGPYNVAYDIWLSRDPNH 39 (152) +Confidence 57889999999999998663 + + +No 2 +>BAO41893.1|AA1_2.hmm|8.3e-157|51-392 +Probab=4.30 E-value=6.1 Score=25.90 Aligned_cols=44 Identities=32% Similarity=0.485 Sum_probs=28.2 Template_Neff=3.800 + +Q 6WLC_A 12 FNVVNKGHFDGQQGEVPVSIIINNNNTVYTKVDGVDVELFENKTTLPVNVA 62 (361) +Q Consensus 12 fnvvnkghfdgqqgevpvsiiinnnntvytkvdgvdvelfenkttlpvnva 62 (361) + +.++|-|-|-+|. +.|..-+---..|||++||-.+ -..|.+.+| +T Consensus 171 lRiIN~gaf~~~y------~~iegH~m~IIEvDGv~v~p~~-~~~l~i~va 214 (339) +T BAO41893.1|AA1 171 LRIINMGAFVSQY------FWIEGHEMTIVEVDGVYVEPYT-TDMLYISVA 214 (339) +Confidence 4467777776653 3444555555789999999877 344555555 + + +No 3 +>ALJ42190.1|194-452 +Probab=2.39 E-value=13 Score=22.33 Aligned_cols=14 Identities=43% Similarity=0.859 Sum_probs=10.5 Template_Neff=5.300 + +Q 6WLC_A 86 DIAANTVIWDYKRD 99 (361) +Q Consensus 86 diaantviwdykrd 99 (361) + .|+.|..||||-.. +T Consensus 160 ~~t~nI~iWDY~~n 173 (257) +T ALJ42190.1|194 160 KITNNIYIWDYVVN 173 (257) +Confidence 35678899999654 + + +No 4 +>SCG78792.1|GH43_30.hmm|3.7e-96|10-279 +Probab=2.39 E-value=13 Score=22.76 Aligned_cols=33 Identities=27% Similarity=0.352 Sum_probs=24.4 Template_Neff=4.700 + +Q 6WLC_A 156 TEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQF 188 (361) +Q Consensus 156 tegsvkglqpsvgpkqaslngvtligeavktqf 188 (361) + ++|...|..+..--.+.+-+|++++|++++-.- +T Consensus 134 ~DGn~~g~~t~i~lq~l~~DG~~l~G~~~~Ll~ 166 (269) +T SCG78792.1|GH4 134 NDGNACGQPTWIWLQRLSADGLTLTGEPVELLR 166 (269) +Confidence 455556666666667788999999999986543 + + +No 5 +>CAL37005.1|GH150|3.2.1.-|0|1-942 +Probab=2.29 E-value=13 Score=26.68 Aligned_cols=45 Identities=33% Similarity=0.674 Sum_probs=30.7 Template_Neff=3.000 + +Q 6WLC_A 49 ELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVD--IAA------------NTVIWDYKRDDAPAHI 105 (361) +Q Consensus 49 elfenkttlpvnvafelwakrnikpvpevkilnnlgvd--iaa------------ntviwdykrddapahi 105 (361) + .|++|+. +--+-|++|+.. +||=|.| +|| +-.+|.||.+++|-.- +T Consensus 73 ~LW~n~l--Sgfmnhdiw~~D----------InnDG~DEIlaAnAdG~iYClns~GkLLW~Fk~n~~pm~s 131 (942) +T CAL37005.1|GH1 73 ILWENKL--SGFMNHDIWCED----------INNDGNDEILAANADGTIYCLNSKGKLLWKFKPNEAPMYS 131 (942) +Confidence 4788876 556779999864 3444444 233 3468999999999653 + + +No 6 +>AAF53285.2|GT92|406-770|5.4e-118 +Probab=2.07 E-value=15 Score=22.47 Aligned_cols=23 Identities=39% Similarity=0.566 Sum_probs=16.1 Template_Neff=5.400 + +Q 6WLC_A 230 MDEFIERYKLEGYAFEHIVYGDF 252 (361) +Q Consensus 230 mdefieryklegyafehivygdf 252 (361) + +-||||-|+|.|-.+=++-.+.. +T Consensus 20 ivEfIEyykL~GathF~fY~~~i 42 (321) +T AAF53285.2|GT9 20 IVEFIEYYKLQGATHFYFYAGNI 42 (321) +Confidence 56899999999985544444444 + + +No 7 +>ABQ89210.1|CE7|3-319|2e-146 +Probab=1.87 E-value=17 Score=22.01 Aligned_cols=22 Identities=41% Similarity=0.410 Sum_probs=18.4 Template_Neff=5.500 + +Q 6WLC_A 252 FSHSQLGGLHLLLIGLAKRFKE 273 (361) +Q Consensus 252 fshsqlgglhllliglakrfke 273 (361) + ...||=|||-|...+|..|.+. +T Consensus 182 ~G~SQGGglala~aaL~~~i~~ 203 (316) +T ABQ89210.1|CE7 182 TGGSQGGGLALAAAALDPRIKA 203 (316) +Confidence 3479999999999999887664 + + +No 8 +>APU50764.1|CBM63||136-214 +Probab=1.76 E-value=18 Score=17.99 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=18.5 Template_Neff=4.800 + +Q 6WLC_A 279 EEDFIPMDSTVKNYFITDAQTGS 301 (361) +Q Consensus 279 eedfipmdstvknyfitdaqtgs 301 (361) + ..+++++..+--|||+.+...|. +T Consensus 32 gg~W~~~~R~~YNyf~~~~g~G~ 54 (78) +T APU50764.1|CBM 32 GGTWVSLPRTDYNYFVIPSGLGP 54 (78) +Confidence 55788888888999999776664 + + +No 9 +>APK54672.1|GT103 +Probab=1.75 E-value=18 Score=21.89 Aligned_cols=33 Identities=27% Similarity=0.346 Sum_probs=24.5 Template_Neff=2.800 + +Q 6WLC_A 207 TQSRNLQEFKPRSQMEIDFLELAMDEFIERYKL 239 (361) +Q Consensus 207 tqsrnlqefkprsqmeidflelamdefierykl 239 (361) + .|-...-.+-.++.|..++|-|.+-|-++|-+. +T Consensus 2 ~~~~~~~s~~~~~~~d~~~i~LsLPET~~RR~~ 34 (232) +T APK54672.1|GT1 2 SQYKSIFSQCEISPQDVDFICLSLPETIERRRD 34 (232) +Confidence 344455556677888899999999998888653 + + +No 10 +>AAO00509.1|GH107|87-420|2.9e-175 +Probab=1.65 E-value=19 Score=22.59 Aligned_cols=26 Identities=35% Similarity=0.760 Sum_probs=19.6 Template_Neff=2.000 + +Q 6WLC_A 226 LELAMDEFIERYK--LEGYAFEHIVYGD 251 (361) +Q Consensus 226 lelamdefieryk--legyafehivygd 251 (361) + +|..+.|+-.||. ..|+-|+|-.+|| +T Consensus 183 ~~~Iv~~~a~RYGslIDgWwFDhs~~gd 210 (329) +T AAO00509.1|GH1 183 AENIVEEYAQRYGSLIDGWWFDHSECGD 210 (329) +Confidence 4555666777776 5799999998888 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/7BQY_A.hhr Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,156 @@ +Query 7BQY_A +Match_columns 301 +No_of_seqs 1 out of 1 +Neff 1 +Searched_HMMs 641 +Date Sat Aug 1 03:09:19 2020 +Command hhsearch -e 0.001 -i /Users/guerler/galaxy/database/files/000/dataset_680.dat -d hhdb -o /Users/guerler/galaxy/database/files/000/dataset_837.dat + + No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM + 1 QCE11709.1|AA1||29-571 71.4 0.023 3.6E-05 43.5 0.0 77 64-142 282-369 (613) + 2 CAY81704.1|GT62|170-480|2.4e-1 12.6 1.5 0.0023 28.7 0.0 16 28-43 143-159 (267) + 3 ABO94043.1|GH5_32.hmm|1.7e-156 12.2 1.5 0.0024 29.5 0.0 62 157-224 78-141 (341) + 4 CAK38741.1|GT69|68-319|4.4e-96 11.9 1.6 0.0025 27.7 0.0 15 29-43 113-127 (236) + 5 F4RB90_MELLP/225-387 11.9 1.6 0.0025 26.5 0.0 21 209-229 119-139 (163) + 6 CAC34265.1|CBM50|45-95|0.0083 6.6 3.6 0.0056 18.3 0.0 14 104-117 5-18 (46) + 7 ALJ49469.1|GH147|3.2.1.23|0|1- 5.6 4.4 0.0068 29.2 0.0 68 117-190 205-282 (849) + 8 EEU61164.1|CBM62|446-579|2.3e- 5.4 4.6 0.0071 23.3 0.0 25 13-41 38-62 (131) + 9 AAQ83841.1|GH13_28.hmm|8.2e-50 4.7 5.5 0.0086 25.6 0.0 39 139-186 147-187 (317) + 10 CAH09708.1|GH123|60-598|1.6e-2 4.0 6.7 0.01 26.5 0.0 24 231-254 183-206 (535) + +No 1 +>QCE11709.1|AA1||29-571 +Probab=71.37 E-value=0.023 Score=43.54 Aligned_cols=77 Identities=31% Similarity=0.490 Sum_probs=55.1 Template_Neff=4.600 + +Q 7BQY_A 64 HNFLVQAGN-VQLRVIGHSMQNCVLKLKVD----------TANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRP 132 (301) +Q Consensus 64 hnflvqagn-vqlrvighsmqncvlklkvd----------tanpktpkykfvriqpgqtfsvlacyngspsgvyqcamrp 132 (301) + ..|-|+.|. ..||+|.-.+ ||-|.++++ -.--|.-++..+.|-|||+++||.-.|.+| +-|.-+.++ +T Consensus 282 ~~~~V~~GKtYrLRiINA~l-n~~l~f~IanH~lTVVe~DGsYtkP~~td~i~I~pGQt~dVLltAdQ~~-g~Yym~a~~ 359 (613) +T QCE11709.1|AA1 282 FKFTVEPGKTYRLRIINAGL-NTELFFSIANHNLTVVEVDGSYTKPFTTDSLDIHPGQTYDVLLTADQPP-GDYYMAASP 359 (613) +Confidence 345555553 4678887777 777666654 444555678889999999999999998865 679999999 + + +Q 7BQY_A 133 NFTIKGSFLN 142 (301) +Q Consensus 133 nftikgsfln 142 (301) + .++-...|-| +T Consensus 360 ~~~~~~~fdn 369 (613) +T QCE11709.1|AA1 360 YFSCQVPFDN 369 (613) +Confidence 8865533433 + + +No 2 +>CAY81704.1|GT62|170-480|2.4e-129 +Probab=12.64 E-value=1.5 Score=28.69 Aligned_cols=16 Identities=44% Similarity=0.736 Sum_probs=13.3 Template_Neff=3.500 + +Q 7BQY_A 28 NGLWLD-DVVYCPRHVI 43 (301) +Q Consensus 28 nglwld-dvvycprhvi 43 (301) + --+|+| ||+-||..+| +T Consensus 143 WVlW~DaDI~~~P~tlI 159 (267) +T CAY81704.1|GT6 143 WVLWRDADIVETPPTII 159 (267) +Confidence 358998 8999998887 + + +No 3 +>ABO94043.1|GH5_32.hmm|1.7e-156|162-501 +Probab=12.23 E-value=1.5 Score=29.53 Aligned_cols=62 Identities=32% Similarity=0.530 Sum_probs=39.9 Template_Neff=2.300 + +Q 7BQY_A 157 VSFCYMHHMELPTGVHAGTDLEGNF--YGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFT 224 (301) +Q Consensus 157 vsfcymhhmelptgvhagtdlegnf--ygpfvdrqtaqaagtdttitvnvlawlyaavingdrwflnrft 224 (301) + -..|+||.| |-|..+||- .|-+ |..|.++.+-| .+..||+-|.|.|+- ..-..|+-+..-|+ +T Consensus 78 rv~~~lh~m--PGGas~gt~-~Gv~Ph~~~f~~~~~v~--~~G~~~~~n~l~W~~-~L~~d~k~~v~G~t 141 (341) +T ABO94043.1|GH5 78 RVVCDLHNM--PGGASNGTY-NGVWPHPPMFWRHKDVQ--DTGRTIIHNFLNWLN-SLSEDDKMAVHGFT 141 (341) +Confidence 457999987 666666652 3332 34477777766 455789999999974 44555665554443 + + +No 4 +>CAK38741.1|GT69|68-319|4.4e-96 +Probab=11.92 E-value=1.6 Score=27.69 Aligned_cols=15 Identities=53% Similarity=1.165 Sum_probs=12.7 Template_Neff=4.300 + +Q 7BQY_A 29 GLWLDDVVYCPRHVI 43 (301) +Q Consensus 29 glwlddvvycprhvi 43 (301) + =+||.||+.||..++ +T Consensus 113 vlFlNDV~f~p~DvL 127 (236) +T CAK38741.1|GT6 113 VLFLNDVVFCPDDVL 127 (236) +Confidence 479999999998764 + + +No 5 +>F4RB90_MELLP/225-387 +Probab=11.89 E-value=1.6 Score=26.48 Aligned_cols=21 Identities=43% Similarity=0.771 Sum_probs=17.4 Template_Neff=4.000 + +Q 7BQY_A 209 YAAVINGDRWFLNRFTTTLND 229 (301) +Q Consensus 209 yaavingdrwflnrftttlnd 229 (301) + -+--||..|||+|-|..-|+. +T Consensus 119 N~kKiNSHrW~Fnaf~~~L~P 139 (163) +T F4RB90_MELLP/2 119 NAKKINSHRWFFNAFGPQLQP 139 (163) +Confidence 466799999999999887764 + + +No 6 +>CAC34265.1|CBM50|45-95|0.0083 +Probab=6.57 E-value=3.6 Score=18.31 Aligned_cols=14 Identities=21% Similarity=0.330 Sum_probs=11.3 Template_Neff=6.600 + +Q 7BQY_A 104 VRIQPGQTFSVLAC 117 (301) +Q Consensus 104 vriqpgqtfsvlac 117 (301) + .++++|+|+.-+|- +T Consensus 5 y~V~~GDtl~~IA~ 18 (46) +T CAC34265.1|CBM 5 YTVKSGDTLWSIAK 18 (46) +Confidence 36889999988884 + + +No 7 +>ALJ49469.1|GH147|3.2.1.23|0|1-869 +Probab=5.63 E-value=4.4 Score=29.22 Aligned_cols=68 Identities=37% Similarity=0.423 Sum_probs=41.2 Template_Neff=3.700 + +Q 7BQY_A 117 CYNGSPSGVYQ------CAMRPNFTIKGSFLNGSCGS----VGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFV 186 (301) +Q Consensus 117 cyngspsgvyq------camrpnftikgsflngscgs----vgfnidydcvsfcymhhmelptgvhagtdlegnfygpfv 186 (301) + |+.|.+.+|-. -|||..-.-|--|-|=|-.. .-++-+-|-.+|- --|||.-+|..|+|||. |.| +T Consensus 205 ~H~g~~~~vt~YInrMv~a~r~tG~~KPiFYNISes~~~a~A~~~s~idG~TFQ-----WYPtGLv~~~tl~GN~L-P~V 278 (849) +T ALJ49469.1|GH1 205 HHSGPPEEVTAYINRMVKAIRKTGWKKPIFYNISESPHFADAVCNSNIDGITFQ-----WYPTGLVSGHTLNGNFL-PNV 278 (849) +Confidence 55566665533 35665555566666655411 1122233455553 35999999999999975 777 + + +Q 7BQY_A 187 DRQT 190 (301) +Q Consensus 187 drqt 190 (301) + |+-. +T Consensus 279 d~Y~ 282 (849) +T ALJ49469.1|GH1 279 DRYT 282 (849) +Confidence 7643 + + +No 8 +>EEU61164.1|CBM62|446-579|2.3e-53 +Probab=5.42 E-value=4.6 Score=23.35 Aligned_cols=25 Identities=28% Similarity=0.634 Sum_probs=18.8 Template_Neff=3.000 + +Q 7BQY_A 13 VEGCMVQVTCGTTTLNGLWLDDVVYCPRH 41 (301) +Q Consensus 13 vegcmvqvtcgtttlnglwlddvvycprh 41 (301) + ..||-+++--|...- +..+.||||+ +T Consensus 38 ~~~~w~g~Dlg~~~~----i~~i~Y~PR~ 62 (131) +T EEU61164.1|CBM 38 ANGGWVGLDLGAGVE----ISAIRYCPRN 62 (131) +Confidence 356777777776544 7789999998 + + +No 9 +>AAQ83841.1|GH13_28.hmm|8.2e-50|58-317 +Probab=4.66 E-value=5.5 Score=25.60 Aligned_cols=39 Identities=31% Similarity=0.603 Sum_probs=26.1 Template_Neff=3.200 + +Q 7BQY_A 139 SFLNG--SCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFV 186 (301) +Q Consensus 139 sflng--scgsvgfnidydcvsfcymhhmelptgvhagtdlegnfygpfv 186 (301) + .||+- .||.-||..|- .-|.|||.....+ ..++|+.-.. +T Consensus 147 ~fL~~~vd~GaDGFRfDa-------AKHIELp~d~~~~--~~sdfW~~il 187 (317) +T AAQ83841.1|GH1 147 DFLNDCVDDGADGFRFDA-------AKHIELPDDPDDN--YGSDFWPNIL 187 (317) +Confidence 35553 57888998775 6899999987644 4455554443 + + +No 10 +>CAH09708.1|GH123|60-598|1.6e-247 +Probab=3.98 E-value=6.7 Score=26.51 Aligned_cols=24 Identities=38% Similarity=0.583 Sum_probs=20.9 Template_Neff=3.700 + +Q 7BQY_A 231 NLVAMKYNYEPLTQDHVDILGPLS 254 (301) +Q Consensus 231 nlvamkynyepltqdhvdilgpls 254 (301) + --||--|+-+|-+|.|.+++.|.. +T Consensus 183 ~avARy~~V~~WS~eHf~~mrp~m 206 (535) +T CAH09708.1|GH1 183 YAVARYYGVEPWSQEHFDAMRPYM 206 (535) +Confidence 347888999999999999999964 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbCAN_random.txt Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,15 @@ +CAA16605.1 0_0_0 CAA16605.1 +EOY02636.1 0_0_0 CAA16605.1 +AAF14068.1 0_0_0 EOY02636.1 +AAC45780.1 0_0_0 AAF14068.1 +AAC45780.1 0_0_0 AAC45780.1 +CAY81704.1 0_0_0 CAR47543.1 +CAK38741.1 0_0_0 ACD98010.1 +AJP22991.1 0_0_0 ACI15933.1 +ABO94043.1 0_0_0 ACY95489.1 +ACE81431.1 0_0_0 ABN52033.1 +AAK94929.1 0_0_0 ACY47587.1 +CAG81347.1 0_0_0 AAO76127.1 +CAG81347.1 0_0_0 AUO30192.1 +ATY34423.1 0_0_0 AHA42547.2 +QCE11709.1 0_0_0 AAW84061.1 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbCAN_result.txt Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,3 @@ +6W9C_A.hhr 24.2 +6W4H_B.hhr 24.0 +6W37_A.hhr 14.0
--- a/test-data/index.txt Sat Aug 01 02:13:31 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -6W4H_B 0_0_0 1XM9_A -6YZ1_B 0_0_0 3L6X_A -6SPB_2 0_0_0 5D5K_C -3UWD_A 0_0_0 3NMZ_A -5FFO_H 0_0_0 6N4X_A -3RJR_C 0_0_0 6N52_B -5VQF_C 0_0_0 6N51_B -5NTU_A 0_0_0 6W2Y_A -2WZB_A 0_0_0 2WZB_A -1HDI_A 0_0_0 1HDI_A -6Y3A_A 0_0_0 6Y3A_A -3UWD_A 0_0_0 3UWD_A -5FFO_H 0_0_0 5FFO_H -3RJR_C 0_0_0 3RJR_C -5VQF_C 0_0_0 5VQF_C -5NTU_A 0_0_0 5NTU_A \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pdb70_random.txt Sat Aug 01 04:16:19 2020 -0400 @@ -0,0 +1,16 @@ +6W4H_B 0_0_0 1XM9_A +6YZ1_B 0_0_0 3L6X_A +6SPB_2 0_0_0 5D5K_C +3UWD_A 0_0_0 3NMZ_A +5FFO_H 0_0_0 6N4X_A +3RJR_C 0_0_0 6N52_B +5VQF_C 0_0_0 6N51_B +5NTU_A 0_0_0 6W2Y_A +2WZB_A 0_0_0 2WZB_A +1HDI_A 0_0_0 1HDI_A +6Y3A_A 0_0_0 6Y3A_A +3UWD_A 0_0_0 3UWD_A +5FFO_H 0_0_0 5FFO_H +3RJR_C 0_0_0 3RJR_C +5VQF_C 0_0_0 5VQF_C +5NTU_A 0_0_0 5NTU_A \ No newline at end of file