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hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 myhmms
Sequence file:            test.fa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: pkinase_full
Accession:      [none]
Description:    Dario rerio

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
pkinase  Protein kinase domain                          266.6    3.3e-80   1
pkinase  Protein kinase domain                          265.4    7.6e-80   1
rrm                                                     -42.5        2.5   1
rrm                                                      -8.7        3.7   1
fn3      Fibronectin type III domain                    -45.8        3.7   1
fn3      Fibronectin type III domain                     -9.0        3.8   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
rrm        1/1     169   180 ..    66    77 .]    -8.7      3.7
fn3        1/1     197   200 ..    81    84 .]    -9.0      3.8
rrm        1/1     256   319 ..     1    77 []   -42.5      2.5
pkinase    1/1     258   540 ..     1   294 []   266.6  3.3e-80
pkinase    1/1     258   537 ..     1   289 [.   265.4  7.6e-80
fn3        1/1     434   506 ..     1    84 []   -45.8      3.7

Alignments of top-scoring domains:
rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
                   *->nGkelggrklrv<-*
                      n++    ++l v   
  pkinase_fu   169    NKQDPHQHRLSV    180  

fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
                CS    CCCC   
                   *->GpeS<-*
                      G eS   
  pkinase_fu   197    GGES    200  

rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
                   *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
                         +N++  +d+ e    + F+ +        +++           +
  pkinase_fu   256    ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285  

                   kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
                     +  V++ +ee+ ++  ++++ +  l++   +    
  pkinase_fu   286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP    319  

pkinase: domain 1 of 1, from 258 to 540: score 266.6, E = 3.3e-80
                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
  pkinase_fu   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  

                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
  pkinase_fu   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  

                   ng........................gplsekeakkialQilrGleYLHs
                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL +
  pkinase_fu   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402  

                   ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
                   +++vHRDL+++N+L+ en  +vKiaDFGL+r ++  +++k++ +   p +
  pkinase_fu   403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451  

                   mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
                   +m+PE  ++++ y+s++DvW++Gv+L+E++++g                 
  pkinase_fu   452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483  

                   dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
                           ++P+++       +  ee+ + +++ g  l +p+nc+ el+ 
  pkinase_fu   484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517  

                   LlkkcLnkDPskRpGsatakeilnhpwf<-*
                   L++ c+   P++Rp   ++  i  h  +   
  pkinase_fu   518 LMRLCWSGHPTDRP---SFASI--HRIL    540  

pkinase: domain 1 of 1, from 258 to 537: score 265.4, E = 7.6e-80
                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
  pkinase_fu   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  

                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
  pkinase_fu   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  

                   ng........................gplsekeakkialQilrGleYLHs
                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL +
  pkinase_fu   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYLSE 402  

                   ngivHRDLKpeNILldendgtvKiaDFGLArlle..sssklttfvGTpwY
                   +++vHRDL+++N+L+ en  +vKiaDFGL+r ++  +++k++ +   p +
  pkinase_fu   403 RKFVHRDLATRNCLVAEN-LVVKIADFGLSRNIYaaDYYKASENDAIPIR 451  

                   mmAPEvilegrgysskvDvWSlGviLyElltggplfpgadlpaftggdev
                   +m+PE  ++++ y+s++DvW++Gv+L+E++++g                 
  pkinase_fu   452 WMPPES-IFYNRYTSESDVWAYGVVLWEIFSYG----------------- 483  

                   dqliifvlklPfsdelpktridpleelfriikrpglrlplpsncSeelkd
                           ++P+++       +  ee+ + +++ g  l +p+nc+ el+ 
  pkinase_fu   484 --------MQPYYG-------MAHEEVIYYVRD-GNVLSCPENCPQELYN 517  

                   LlkkcLnkDPskRpGsatakeil<-*
                   L++ c+   P++Rp   ++  i+   
  pkinase_fu   518 LMRLCWSGHPTDRP---SFASIH    537  

fn3: domain 1 of 1, from 434 to 506: score -45.8, E = 3.7
                CS    CCCCCEEEEEECCTTCCEEEEECCC        CCCCCCCEEEEE.E
                   *->PsaPtnltvtdvtstsltlsWsppt........gngpitgYevtyRq
                        a    ++++   + + ++W pp++   ++ +  +++  Y v + +
  pkinase_fu   434    IYAADYYKASE--NDAIPIRWMPPEsifynrytSESDVWAYGVVL-W 477  

                CS CCCCCC  CCCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC   
                   pkngge..wneltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
                   +  + + ++   +                    ++V+  +g+    S   
  pkinase_fu   478 EIFSYGmqPYYGMAHEEV--------------IYYVR--DGN--VLS    506  

//

Query sequence: pkinase_part
Accession:      [none]
Description:    Dario rerio

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
pkinase  Protein kinase domain                          101.5    1.7e-30   1
pkinase  Protein kinase domain                          -94.7    1.5e-05   1
rrm                                                     -42.5        2.5   1
rrm                                                      -8.7        3.7   1
fn3      Fibronectin type III domain                     -9.0        3.8   1
fn3      Fibronectin type III domain                    -52.2        5.9   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
rrm        1/1     169   180 ..    66    77 .]    -8.7      3.7
fn3        1/1     197   200 ..    81    84 .]    -9.0      3.8
fn3        1/1     233   299 ..     1    84 []   -52.2      5.9
rrm        1/1     256   319 ..     1    77 []   -42.5      2.5
pkinase    1/1     258   400 .]     1   116 [.   101.5  1.7e-30
pkinase    1/1     258   400 .]     1   294 []   -94.7  1.5e-05

Alignments of top-scoring domains:
rrm: domain 1 of 1, from 169 to 180: score -8.7, E = 3.7
                   *->nGkelggrklrv<-*
                      n++    ++l v   
  pkinase_pa   169    NKQDPHQHRLSV    180  

fn3: domain 1 of 1, from 197 to 200: score -9.0, E = 3.8
                CS    CCCC   
                   *->GpeS<-*
                      G eS   
  pkinase_pa   197    GGES    200  

fn3: domain 1 of 1, from 233 to 299: score -52.2, E = 5.9
                CS    CCCC CEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
                   *->PsaP.tnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
                      P +  ++l   ++  +s  ls + p  +  i++    +R + ++g  
  pkinase_pa   233    PNPMyQRL---PLLLNSKLLSLEYP--RNNIEY----VR-DIGEG-- 267  

                CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCCCCCC   
                   neltvpgtttsytltgLkPgteYevrVqAvnggGGpeS<-*
                         g   ++   gL P  + ++  +    +  ++S   
  pkinase_pa   268 ----AFGRVFQARAPGLLPTEPFTMVAVKMLKE--EAS    299  

rrm: domain 1 of 1, from 256 to 319: score -42.5, E = 2.5
                   *->lfVgNL..ppdvteedLkdlFsk.fGpivsikivkDhkektketgks
                         +N++  +d+ e    + F+ +        +++           +
  pkinase_pa   256    ---NNIeyVRDIGEGAFGRVFQArAPGL----LPTE----------P 285  

                   kGfaFVeFeseedAekAlealnG.kelggrklrv<-*
                     +  V++ +ee+ ++  ++++ +  l++   +    
  pkinase_pa   286 FTMVAVKMLKEEASTDMQNDFQReAALMSEFDHP    319  

pkinase: domain 1 of 1, from 258 to 400: score 101.5, E = 1.7e-30
                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
  pkinase_pa   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  

                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
  pkinase_pa   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  

                   ng........................gplsekeakkialQilrGleYL<-
                   +  +++++ ++++ ++++  +++++  pls +e ++i +Q++ G++YL  
  pkinase_pa   353 RCatqqpslsrdtltssslvseperyPPLSCQEQLSISKQVAAGMAYL   400  

                   *
                    
  pkinase_pa     -   -    

pkinase: domain 1 of 1, from 258 to 400: score -94.7, E = 1.5e-05
                   *->yelleklGeGsfGkVykakhkd....ktgkiVAvKilkkekesikek
                      +e ++ +GeG+fG+V++a+     +++    VAvK+lk e+ s++  
  pkinase_pa   258    IEYVRDIGEGAFGRVFQARAPGllptEPFTMVAVKMLK-EEASTDMQ 303  

                   .rflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrr
                   ++f+rE++++ +++HpNIvrl+gv+   +++++l +Eym  GdL+++lrr
  pkinase_pa   304 nDFQREAALMSEFDHPNIVRLLGVCA-VGKPMCLMFEYMAYGDLNEFLRR 352  

                   nggplsekeakkialQilrGleYLHsngivHRDLKpeNILldendgtvKi
                   +                                                 
  pkinase_pa   353 RC------------------------------------------------ 354  

                   aDFGLArllesssklttfvGTpwYmmAPEvilegrgysskvDvWSlGviL
                        A++   s + +t++ ++     PE                     
  pkinase_pa   355 -----ATQQP-SLSRDTLTSSSLVS-EPER-------------------- 377  

                   yElltggplfpgadlpaftggdevdqliifvlklPfsdelpktridplee
                                                    +P s             
  pkinase_pa   378 --------------------------------YPPLS------------- 382  

                   lfriikrpglrlplpsncSeelkdLlkkcLnkDPskRpGsatakeilnhp
                         +       + ++S+ +   +                        
  pkinase_pa   383 -----CQ------EQLSISKQVAAGM-----------A------------ 398  

                   wf<-*
                   ++   
  pkinase_pa   399 YL    400  

//

Query sequence: S13421
Accession:      [none]
Description:    S13421 GLOBIN - BRINE SHRIMP, 1405 bases, EDBC29AF checksum.

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
pkinase  Protein kinase domain                         -171.6       0.19   1
rrm                                                     -32.5       0.26   1
rrm                                                      -6.1       0.92   1
fn3      Fibronectin type III domain                    -39.7        1.2   1
pkinase  Protein kinase domain                           -9.2        1.8   1
fn3      Fibronectin type III domain                     -7.5        1.9   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
fn3        1/1     143   224 ..     1    84 []   -39.7      1.2
pkinase    1/1     233   241 ..     1     9 [.    -9.2      1.8
rrm        1/1     440   456 ..     1    17 [.    -6.1     0.92
rrm        1/1     669   731 ..     1    77 []   -32.5     0.26
pkinase    1/1     906  1127 ..     1   294 []  -171.6     0.19
fn3        1/1     923   934 ..     1    12 [.    -7.5      1.9

Alignments of top-scoring domains:
fn3: domain 1 of 1, from 143 to 224: score -39.7, E = 1.2
                CS    C CCCCEEEEEECCTTCCEEEEECCCCCCCCCCEEEEE.ECCCCCCC
                   *->P.saPtnltvtdvtstsltlsWspptgngpitgYevtyRqpknggew
                       + ++t+l++ dv    ++ sWs+ +g+ + tg  v  R + ng  +
      S13421   143    IdLEVTGLSCVDVAN--IQESWSKVSGDLKTTGSVVFQR-MINGH-P 185  

                CS CCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC   
                   neltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                     +++ ++ + + l  L +    +  V  v ++ +G      
      S13421   186 EYQQLFRQFRDVDLDKLGESNSFVAHVFRVVAAFdGIIH    224  

pkinase: domain 1 of 1, from 233 to 241: score -9.2, E = 1.8
                   *->yelleklGe<-*
                        +l+klGe   
      S13421   233    VSTLKKLGE    241  

rrm: domain 1 of 1, from 440 to 456: score -6.1, E = 0.92
                   *->lfVgNLppdvteedLkd<-*
                      + ++ L++   + d+ d   
      S13421   440    VIISFLNEGLRQADIVD    456  

rrm: domain 1 of 1, from 669 to 731: score -32.5, E = 0.26
                   *->lfVgNL.ppdvteedLkdlFskfGpivsikivkDhkektketgkskG
                        V  L+++d+    +   +  f  i   k++ D            +
      S13421   669    --VEELpSTDAFHYHISLVMNRFSSI--GKVIDD------------N 699  

                   faFVeFeseedAekAlealnGkelggr.klrv<-*
                   + FV   ++ + e+ ++ l  k+++   +l++   
      S13421   700 VSFVYLLKKLGREHIKRGLSRKQFDQFvELYI    731  

pkinase: domain 1 of 1, from 906 to 1127: score -171.6, E = 0.19
                   *->yelleklGeGsfGkVykakhkd........ktgkiVAvKilkkekes
                      ++l         G++ ++ +  ++ ++ ++ + ++VAv +     ++
      S13421   906    FKLMH-------GVIEEGLLQLerinpitgLSAREVAVVKQ---TWN 942  

                   ikekrflrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdy
                   + +            L+      ++  fe   + +  v++       +d 
      S13421   943 LVK----------PDLMGVGMRIFKSLFE-AFPAYQAVFPKFSD-VPLDK 980  

                   lrrng....gplsekeakkialQilrGleYLHsngivHRDLKpeNILlde
                   l +    +++ +s    ++   Q+                       lde
      S13421   981 LEDTPavgkHSISVTTKLDELIQT-----------------------LDE 1007 

                   ndgtvKiaDFGLArlle........sssklttfvGTpwYmmAPEvi...l
                   +  ++ +    LAr+l +++   + + +++++f+  +++      ++++l
      S13421  1008 P-ANLAL----LARQLGedhivlrvNKPMFKSFGKVLVRL-----LendL 1047 

                   egrgysskvDvW..SlGviLyElltggplfpgadlpaftggdevdqliif
                    +r  s ++  W++++ vi+ ++  g                        
      S13421  1048 GQRFSSFASRSWhkAYDVIVEYIEEG------------------------ 1073 

                   vlklPfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcL
                    l++ +++       dp   + +  k   l  + ++++ ++l+ L +k++
      S13421  1074 -LQQSYKQ-------DPVTGITDAEKA--LVQESWDLLKPDLLGLGRKIF 1113 

                   nkDPskRpGsatakeilnhpwf<-*
                   +k  +k p      +i     f   
      S13421  1114 TKVFTKHP----DYQI----LF    1127 

fn3: domain 1 of 1, from 923 to 934: score -7.5, E = 1.9
                CS    CCCCCEEEEEEC   
                   *->PsaPtnltvtdv<-*
                        + t+l++++v   
      S13421   923    INPITGLSAREV    934  

//