text: user235: I am trying to identify proteins that carry a consensus target sequence for a kinase. Usually if I am working with, for e.g. transcription factors binding to DNA I would use position weight matrices (PWMs) from one of a number of databases of PWMs to search the sequences with something like FIMO.
  However, I don't know of any databases that contain protein motif PWMs. Specially I am looking for one for yeast Cdc28, but it seems like it would be a generally useful resource that I can't believe doesn't exist. For example, while the MEME suite was originally developed to identify protein motifs, and ouputs PWMs, all of its databases refer to DNA or RNA. 
  
  user298: PFam has HMM models for protein domains, this is almost certainly what you're after. You can download all PFam-A models from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz.
  Then, you're looking for the "Pkinase", PF00069 family (I found this simply by searching the PFam website for "kinase"), so extract it from the file:
  zcat Pfam-A.hmm.gz | awk -vRS='//' -vORS='//' '/PF00069/' > PF00069.pfam
  
  Then, format it for HMMER format (you will need to install HMMER)
  hmmpress PF00069.hmm
  
  And now you can use it to search your sequences (fasta or flat file, probably others; see the documentation for details):
  hmmscan PF00069.hmm prots.pep 
  
  I tried this on a fasta file with the sequences of CBK1_YEAST, CSK21_YEAST (kinases) and FLNA_HUMAN (non-kinase control) and got:
  # hmmscan :: search sequence(s) against a profile database
  # HMMER 3.1b2 (February 2015); http://hmmer.org/
  # Copyright (C) 2015 Howard Hughes Medical Institute.
  # Freely distributed under the GNU General Public License (GPLv3).
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # query sequence file:             prots.pep
  # target HMM database:             PF00069.hmm
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  
  Query:       sp|P53894|CBK1_YEAST  [L=756]
  Description: Serine/threonine-protein kinase CBK1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CBK1 PE=1 SV=1
  Scores for complete sequence (score includes all domains):
     --- full sequence ---   --- best 1 domain ---    -#dom-
      E-value  score  bias    E-value  score  bias    exp  N  Model    Description
      ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2.7e-64  203.2   9.0    3.5e-46  143.8   0.2    3.1  3  Pkinase   Protein kinase domain
  
  
  Domain annotation for each model (and alignments):
  >> Pkinase  Protein kinase domain
     #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
   ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
     1 ?   -2.9   3.2      0.19      0.19     198     226 ..     222     243 ..     191     277 .. 0.57
     2 !  143.8   0.2   3.5e-46   3.5e-46       1     153 [.     352     505 ..     352     522 .. 0.95
     3 !   63.6   0.0   9.8e-22   9.8e-22     154     264 .]     568     672 ..     551     672 .. 0.83
  
    Alignments for each domain:
    == domain 1  score: -2.9 bits;  conditional E-value: 0.19
                             TTSSCHHHHHHHHHTHHHHHHHCTSHH.. CS
                 Pkinase 198 sgekgkekvekeldqlekilkilgetkek 226
                             + +++++++++      + ++i ++++++
    sp|P53894|CBK1_YEAST 222 Q-QQQQQQQQQ------QHMQIQQQQQQQ 243
                             1.111111111......122222221222 PP
  
    == domain 2  score: 143.8 bits;  conditional E-value: 3.5e-46
                             EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEEHHCCCHHHH.HHHHHHHHHHHHHSSTTB--EEEEEEESSEEEEEEE--TTEBHHHH CS
                 Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladl 88 
                             +++++ +G+G+fG+V  + +k+tgki+A+K++ k+++ kk++  +v +E  +l+ +++p +v ly++f++ ++lyl++e+++gg+l+++
    sp|P53894|CBK1_YEAST 352 FHTVKVIGKGAFGEVRLVQKKDTGKIYAMKTLLKSEMYKKDQlAHVKAERDVLAGSDSPWVVSLYYSFQDAQYLYLIMEFLPGGDLMTM 440
                             67899********************************999999********************************************** PP
  
                             HHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEECCSSCS CS
                 Pkinase  89 lsrkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                             l r + ++e+ +++++++ + ++e +H+ g+iHrD+Kp+NiLid +g++K++DFGl++ ++++++
    sp|P53894|CBK1_YEAST 441 LIRWQLFTEDVTRFYMAECILAIETIHKLGFIHRDIKPDNILIDIRGHIKLSDFGLSTGFHKTHD 505
                             **999*****************************************************9999876 PP
  
    == domain 3  score: 63.6 bits;  conditional E-value: 9.8e-22
                             BCTCCSCGGGS-HHHHTTSTCSHHHHHHHHHHHHHHHHHSS-STTTSSCHHHHHHHHHTHHHHHHHCTSHH......TTS-HHHHHHHH CS
                 Pkinase 154 ltsfvgtreYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaselseeakdllk 242
                             + s vgt++Y+APE+  +++y++++D+WslG i+ye l g ppf +e+ +e+++k+++          e+++++p + ++s ea dl++
    sp|P53894|CBK1_YEAST 568 AYSTVGTPDYIAPEIFLYQGYGQECDWWSLGAIMYECLIGWPPFCSETPQETYRKIMNF---------EQTLQFPDDIHISYEAEDLIR 647
                             6789*****************************************66665533333333.........557799*************** PP
  
                             HHT-SSGCCSTT....HHHHHTSGGG CS
                 Pkinase 243 kllkkdpkkRlt....aeellqhpyl 264
                             +ll+    +Rl+    a+e+++hp++
    sp|P53894|CBK1_YEAST 648 RLLTHA-DQRLGrhggADEIKSHPFF 672
                             ***875.678877779********98 PP
  
  
  
  Internal pipeline statistics summary:
  -------------------------------------
  Query sequence(s):                         1  (756 residues searched)
  Target model(s):                           1  (264 nodes)
  Passed MSV filter:                         1  (1); expected 0.0 (0.02)
  Passed bias filter:                        1  (1); expected 0.0 (0.02)
  Passed Vit filter:                         1  (1); expected 0.0 (0.001)
  Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
  Initial search space (Z):                  1  [actual number of targets]
  Domain search space  (domZ):               1  [number of targets reported over threshold]
  # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
  # Mc/sec: inf
  //
  Query:       sp|P15790|CSK21_YEAST  [L=372]
  Description: Casein kinase II subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CKA1 PE=1 SV=1
  Scores for complete sequence (score includes all domains):
     --- full sequence ---   --- best 1 domain ---    -#dom-
      E-value  score  bias    E-value  score  bias    exp  N  Model    Description
      ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7.5e-62  195.1   7.2    3.2e-55  173.4   0.7    2.1  2  Pkinase   Protein kinase domain
  
  
  Domain annotation for each model (and alignments):
  >> Pkinase  Protein kinase domain
     #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
   ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
     1 !   25.5   1.1   4.3e-10   4.3e-10       1      60 [.      40      94 ..      40     115 .. 0.87
     2 !  173.4   0.7   3.2e-55   3.2e-55      56     264 .]     128     363 ..     101     363 .. 0.92
  
    Alignments for each domain:
    == domain 1  score: 25.5 bits;  conditional E-value: 4.3e-10
                             EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEEHHCCCHHHHHHHHHHHHHHHHHSSTTB CS
                  Pkinase  1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpni 60
                             ye ++k+G+G++++V+++v+ +++ ++++K++k  k+kk k     rEikil  l+ +++
    sp|P15790|CSK21_YEAST 40 YEIENKVGRGKYSEVFQGVKLDSKVKIVIKMLKPVKKKKIK-----REIKILTDLSNEKV 94
                             78999****************************99888855.....7******9998877 PP
  
    == domain 2  score: 173.4 bits;  conditional E-value: 3.2e-55
                              S.STTB--EEEEEEE..SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE CS
                  Pkinase  56 k.hpnivrlyevfee..kdelylvleyveggeladllsrkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKi 139
                              + h ni++l++++++  +++  lv+eyv++ ++  l+    +l++ e+++++ ++l++l+y+Hs+gi+HrD+Kp+N++id ++++l++
    sp|P15790|CSK21_YEAST 128 NgHANIIHLFDIIKDpiSKTPALVFEYVDNVDFRILYP---KLTDLEIRFYMFELLKALDYCHSMGIMHRDVKPHNVMIDhKNKKLRL 212
                              35*************8878888*********9988887...5**************************************66677*** PP
  
                              -SGTTSEECCSSCSBCTCCSCGGGS-HHHH.TTSTCSHHHHHHHHHHHHHHHHHSS-STTTSSCHHHHHHHHHTHHHHHHHCTSHH.. CS
                  Pkinase 140 tDFGlakelessskltsfvgtreYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkek 226
                              +D+Gla+ ++ + +++ +v++r +  PE+l ++++y+ + D+Ws G +l++++++++pf   +g++    ++dql+ki+k+lg+++++
    sp|P15790|CSK21_YEAST 213 IDWGLAEFYHVNMEYNVRVASRFFKGPELLvDYRMYDYSLDLWSFGTMLASMIFKREPFF--HGTS----NTDQLVKIVKVLGTSDFE 294
                              ******************************999***************************..3443....789**********77766 PP
  
                              ....TTS...............................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                  Pkinase 227 lpeasel...............................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                  +                                 ++e++dl+++ll++d+++Rlta+e++ hp++
    sp|P15790|CSK21_YEAST 295 KYLLKYEitlprefydmdqyirkpwhrfindgnkhlsgNDEIIDLIDNLLRYDHQERLTAKEAMGHPWF 363
                              5554444588999999****************************************************9 PP
  
  
  
  Internal pipeline statistics summary:
  -------------------------------------
  Query sequence(s):                         1  (372 residues searched)
  Target model(s):                           1  (264 nodes)
  Passed MSV filter:                         1  (1); expected 0.0 (0.02)
  Passed bias filter:                        1  (1); expected 0.0 (0.02)
  Passed Vit filter:                         1  (1); expected 0.0 (0.001)
  Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
  Initial search space (Z):                  1  [actual number of targets]
  Domain search space  (domZ):               1  [number of targets reported over threshold]
  # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
  # Mc/sec: 4.91
  //
  Query:       sp|P21333|FLNA_HUMAN  [L=2647]
  Description: Filamin-A OS=Homo sapiens GN=FLNA PE=1 SV=4
  Scores for complete sequence (score includes all domains):
     --- full sequence ---   --- best 1 domain ---    -#dom-
      E-value  score  bias    E-value  score  bias    exp  N  Model    Description
      ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  
     [No hits detected that satisfy reporting thresholds]
  
  
  Domain annotation for each model (and alignments):
  
     [No targets detected that satisfy reporting thresholds]
  
  
  Internal pipeline statistics summary:
  -------------------------------------
  Query sequence(s):                         1  (2647 residues searched)
  Target model(s):                           1  (264 nodes)
  Passed MSV filter:                         0  (0); expected 0.0 (0.02)
  Passed bias filter:                        0  (0); expected 0.0 (0.02)
  Passed Vit filter:                         0  (0); expected 0.0 (0.001)
  Passed Fwd filter:                         0  (0); expected 0.0 (1e-05)
  Initial search space (Z):                  1  [actual number of targets]
  Domain search space  (domZ):               0  [number of targets reported over threshold]
  # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
  # Mc/sec: inf
  //
  
  
  HMMER is a great tool and can also analyse multiple sequence alignments to build the hmms if that's what you need. I strongly urge you to reads its documentation which is both informative and a surpisingly fun read (it includes such phrases as "Their format is “proprietary”, which is an open source term of art that means both “I haven’t found time
  to document them yet” and “I still might decide to change them arbitrarily without telling you”").
  
original_text: 235: <p>I am trying to identify proteins that carry a consensus target sequence for a kinase. Usually if I am working with, for e.g. transcription factors binding to DNA I would use position weight matrices (PWMs) from one of a number of databases of PWMs to search the sequences with something like FIMO.</p>
  
  <p>However, I don't know of any databases that contain protein motif PWMs. Specially I am looking for one for yeast Cdc28, but it seems like it would be a generally useful resource that I can't believe doesn't exist. For example, while the MEME suite was originally developed to identify protein motifs, and ouputs PWMs, all of its databases refer to DNA or RNA. </p>
   298: <p><a href="http://pfam.xfam.org/f" rel="nofollow noreferrer">PFam</a> has HMM models for protein domains, this is almost certainly what you're after. You can download all PFam-A models from <a href="ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz" rel="nofollow noreferrer">ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz</a>.</p>
  
  <p>Then, you're looking for the "Pkinase", PF00069 family (I found this simply by searching the PFam website for "kinase"), so extract it from the file:</p>
  
  <pre><code>zcat Pfam-A.hmm.gz | awk -vRS='//' -vORS='//' '/PF00069/' &gt; PF00069.pfam
  </code></pre>
  
  <p>Then, format it for HMMER format (you will need to install <a href="http://hmmer.org/" rel="nofollow noreferrer">HMMER</a>)</p>
  
  <pre><code>hmmpress PF00069.hmm
  </code></pre>
  
  <p>And now you can use it to search your sequences (fasta or flat file, probably others; see the <a href="http://www.csb.yale.edu/userguides/seq/hmmer/docs/" rel="nofollow noreferrer">documentation</a> for details):</p>
  
  <pre><code>hmmscan PF00069.hmm prots.pep 
  </code></pre>
  
  <p>I tried this on a fasta file with the sequences of <a href="http://www.uniprot.org/uniprot/P53894.fasta" rel="nofollow noreferrer">CBK1_YEAST</a>, <a href="http://www.uniprot.org/uniprot/P15790.fasta" rel="nofollow noreferrer">CSK21_YEAST</a> (kinases) and <a href="http://www.uniprot.org/uniprot/P21333.fasta" rel="nofollow noreferrer">FLNA_HUMAN</a> (non-kinase control) and got:</p>
  
  <pre><code># hmmscan :: search sequence(s) against a profile database
  # HMMER 3.1b2 (February 2015); http://hmmer.org/
  # Copyright (C) 2015 Howard Hughes Medical Institute.
  # Freely distributed under the GNU General Public License (GPLv3).
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # query sequence file:             prots.pep
  # target HMM database:             PF00069.hmm
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  
  Query:       sp|P53894|CBK1_YEAST  [L=756]
  Description: Serine/threonine-protein kinase CBK1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CBK1 PE=1 SV=1
  Scores for complete sequence (score includes all domains):
     --- full sequence ---   --- best 1 domain ---    -#dom-
      E-value  score  bias    E-value  score  bias    exp  N  Model    Description
      ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2.7e-64  203.2   9.0    3.5e-46  143.8   0.2    3.1  3  Pkinase   Protein kinase domain
  
  
  Domain annotation for each model (and alignments):
  &gt;&gt; Pkinase  Protein kinase domain
     #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
   ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
     1 ?   -2.9   3.2      0.19      0.19     198     226 ..     222     243 ..     191     277 .. 0.57
     2 !  143.8   0.2   3.5e-46   3.5e-46       1     153 [.     352     505 ..     352     522 .. 0.95
     3 !   63.6   0.0   9.8e-22   9.8e-22     154     264 .]     568     672 ..     551     672 .. 0.83
  
    Alignments for each domain:
    == domain 1  score: -2.9 bits;  conditional E-value: 0.19
                             TTSSCHHHHHHHHHTHHHHHHHCTSHH.. CS
                 Pkinase 198 sgekgkekvekeldqlekilkilgetkek 226
                             + +++++++++      + ++i ++++++
    sp|P53894|CBK1_YEAST 222 Q-QQQQQQQQQ------QHMQIQQQQQQQ 243
                             1.111111111......122222221222 PP
  
    == domain 2  score: 143.8 bits;  conditional E-value: 3.5e-46
                             EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEEHHCCCHHHH.HHHHHHHHHHHHHSSTTB--EEEEEEESSEEEEEEE--TTEBHHHH CS
                 Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladl 88 
                             +++++ +G+G+fG+V  + +k+tgki+A+K++ k+++ kk++  +v +E  +l+ +++p +v ly++f++ ++lyl++e+++gg+l+++
    sp|P53894|CBK1_YEAST 352 FHTVKVIGKGAFGEVRLVQKKDTGKIYAMKTLLKSEMYKKDQlAHVKAERDVLAGSDSPWVVSLYYSFQDAQYLYLIMEFLPGGDLMTM 440
                             67899********************************999999********************************************** PP
  
                             HHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEECCSSCS CS
                 Pkinase  89 lsrkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                             l r + ++e+ +++++++ + ++e +H+ g+iHrD+Kp+NiLid +g++K++DFGl++ ++++++
    sp|P53894|CBK1_YEAST 441 LIRWQLFTEDVTRFYMAECILAIETIHKLGFIHRDIKPDNILIDIRGHIKLSDFGLSTGFHKTHD 505
                             **999*****************************************************9999876 PP
  
    == domain 3  score: 63.6 bits;  conditional E-value: 9.8e-22
                             BCTCCSCGGGS-HHHHTTSTCSHHHHHHHHHHHHHHHHHSS-STTTSSCHHHHHHHHHTHHHHHHHCTSHH......TTS-HHHHHHHH CS
                 Pkinase 154 ltsfvgtreYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaselseeakdllk 242
                             + s vgt++Y+APE+  +++y++++D+WslG i+ye l g ppf +e+ +e+++k+++          e+++++p + ++s ea dl++
    sp|P53894|CBK1_YEAST 568 AYSTVGTPDYIAPEIFLYQGYGQECDWWSLGAIMYECLIGWPPFCSETPQETYRKIMNF---------EQTLQFPDDIHISYEAEDLIR 647
                             6789*****************************************66665533333333.........557799*************** PP
  
                             HHT-SSGCCSTT....HHHHHTSGGG CS
                 Pkinase 243 kllkkdpkkRlt....aeellqhpyl 264
                             +ll+    +Rl+    a+e+++hp++
    sp|P53894|CBK1_YEAST 648 RLLTHA-DQRLGrhggADEIKSHPFF 672
                             ***875.678877779********98 PP
  
  
  
  Internal pipeline statistics summary:
  -------------------------------------
  Query sequence(s):                         1  (756 residues searched)
  Target model(s):                           1  (264 nodes)
  Passed MSV filter:                         1  (1); expected 0.0 (0.02)
  Passed bias filter:                        1  (1); expected 0.0 (0.02)
  Passed Vit filter:                         1  (1); expected 0.0 (0.001)
  Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
  Initial search space (Z):                  1  [actual number of targets]
  Domain search space  (domZ):               1  [number of targets reported over threshold]
  # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
  # Mc/sec: inf
  //
  Query:       sp|P15790|CSK21_YEAST  [L=372]
  Description: Casein kinase II subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CKA1 PE=1 SV=1
  Scores for complete sequence (score includes all domains):
     --- full sequence ---   --- best 1 domain ---    -#dom-
      E-value  score  bias    E-value  score  bias    exp  N  Model    Description
      ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7.5e-62  195.1   7.2    3.2e-55  173.4   0.7    2.1  2  Pkinase   Protein kinase domain
  
  
  Domain annotation for each model (and alignments):
  &gt;&gt; Pkinase  Protein kinase domain
     #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
   ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
     1 !   25.5   1.1   4.3e-10   4.3e-10       1      60 [.      40      94 ..      40     115 .. 0.87
     2 !  173.4   0.7   3.2e-55   3.2e-55      56     264 .]     128     363 ..     101     363 .. 0.92
  
    Alignments for each domain:
    == domain 1  score: 25.5 bits;  conditional E-value: 4.3e-10
                             EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEEHHCCCHHHHHHHHHHHHHHHHHSSTTB CS
                  Pkinase  1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpni 60
                             ye ++k+G+G++++V+++v+ +++ ++++K++k  k+kk k     rEikil  l+ +++
    sp|P15790|CSK21_YEAST 40 YEIENKVGRGKYSEVFQGVKLDSKVKIVIKMLKPVKKKKIK-----REIKILTDLSNEKV 94
                             78999****************************99888855.....7******9998877 PP
  
    == domain 2  score: 173.4 bits;  conditional E-value: 3.2e-55
                              S.STTB--EEEEEEE..SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE CS
                  Pkinase  56 k.hpnivrlyevfee..kdelylvleyveggeladllsrkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKi 139
                              + h ni++l++++++  +++  lv+eyv++ ++  l+    +l++ e+++++ ++l++l+y+Hs+gi+HrD+Kp+N++id ++++l++
    sp|P15790|CSK21_YEAST 128 NgHANIIHLFDIIKDpiSKTPALVFEYVDNVDFRILYP---KLTDLEIRFYMFELLKALDYCHSMGIMHRDVKPHNVMIDhKNKKLRL 212
                              35*************8878888*********9988887...5**************************************66677*** PP
  
                              -SGTTSEECCSSCSBCTCCSCGGGS-HHHH.TTSTCSHHHHHHHHHHHHHHHHHSS-STTTSSCHHHHHHHHHTHHHHHHHCTSHH.. CS
                  Pkinase 140 tDFGlakelessskltsfvgtreYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkek 226
                              +D+Gla+ ++ + +++ +v++r +  PE+l ++++y+ + D+Ws G +l++++++++pf   +g++    ++dql+ki+k+lg+++++
    sp|P15790|CSK21_YEAST 213 IDWGLAEFYHVNMEYNVRVASRFFKGPELLvDYRMYDYSLDLWSFGTMLASMIFKREPFF--HGTS----NTDQLVKIVKVLGTSDFE 294
                              ******************************999***************************..3443....789**********77766 PP
  
                              ....TTS...............................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                  Pkinase 227 lpeasel...............................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                  +                                 ++e++dl+++ll++d+++Rlta+e++ hp++
    sp|P15790|CSK21_YEAST 295 KYLLKYEitlprefydmdqyirkpwhrfindgnkhlsgNDEIIDLIDNLLRYDHQERLTAKEAMGHPWF 363
                              5554444588999999****************************************************9 PP
  
  
  
  Internal pipeline statistics summary:
  -------------------------------------
  Query sequence(s):                         1  (372 residues searched)
  Target model(s):                           1  (264 nodes)
  Passed MSV filter:                         1  (1); expected 0.0 (0.02)
  Passed bias filter:                        1  (1); expected 0.0 (0.02)
  Passed Vit filter:                         1  (1); expected 0.0 (0.001)
  Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
  Initial search space (Z):                  1  [actual number of targets]
  Domain search space  (domZ):               1  [number of targets reported over threshold]
  # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
  # Mc/sec: 4.91
  //
  Query:       sp|P21333|FLNA_HUMAN  [L=2647]
  Description: Filamin-A OS=Homo sapiens GN=FLNA PE=1 SV=4
  Scores for complete sequence (score includes all domains):
     --- full sequence ---   --- best 1 domain ---    -#dom-
      E-value  score  bias    E-value  score  bias    exp  N  Model    Description
      ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  
     [No hits detected that satisfy reporting thresholds]
  
  
  Domain annotation for each model (and alignments):
  
     [No targets detected that satisfy reporting thresholds]
  
  
  Internal pipeline statistics summary:
  -------------------------------------
  Query sequence(s):                         1  (2647 residues searched)
  Target model(s):                           1  (264 nodes)
  Passed MSV filter:                         0  (0); expected 0.0 (0.02)
  Passed bias filter:                        0  (0); expected 0.0 (0.02)
  Passed Vit filter:                         0  (0); expected 0.0 (0.001)
  Passed Fwd filter:                         0  (0); expected 0.0 (1e-05)
  Initial search space (Z):                  1  [actual number of targets]
  Domain search space  (domZ):               0  [number of targets reported over threshold]
  # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
  # Mc/sec: inf
  //
  </code></pre>
  
  <hr>
  
  <p>HMMER is a great tool and can also analyse multiple sequence alignments to build the hmms if that's what you need. I strongly urge you to reads <a href="http://www.csb.yale.edu/userguides/seq/hmmer/docs/" rel="nofollow noreferrer">its documentation</a> which is both informative and a surpisingly fun read (it includes such phrases as "<em>Their format is “proprietary”, which is an open source term of art that means both “I haven’t found time
  to document them yet” and “I still might decide to change them arbitrarily without telling you”</em>").</p>
  