hmmpfam - search a single seq against HMM database
HMMER 2.1.1 (Dec 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
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HMM file:                 /data11/genetics/InterProScan/iprscan/data/Pfam
Sequence file:            /cdna4/rodent/full/goal/mpm/mpm06260/w3open/interpro/cnk_1/seq.in
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Query:  mFLJ00201  ( 640 res)   mpm06260

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
C1q      C1q domain                                     221.8    9.9e-63   1
Collagen Collagen triple helix repeat (20 copies)       179.0    7.6e-50   7
TNF      TNF(Tumour Necrosis Factor) family              -6.6        0.2   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
Collagen   1/7      20    77 ..     1    60 []     4.4    0.001
Collagen   2/7      78   136 ..     1    60 []    31.8  1.6e-05
Collagen   3/7     154   212 ..     1    60 []    29.2  4.6e-05
Collagen   4/7     230   288 ..     1    60 []    26.8  6.2e-05
Collagen   5/7     295   354 ..     1    60 []    56.7  5.2e-13
Collagen   6/7     355   414 ..     1    60 []    49.2  8.8e-11
Collagen   7/7     415   473 ..     1    60 []    28.8  4.9e-05
C1q        1/1     513   637 ..     1   137 []   221.8  9.9e-63
TNF        1/1     535   637 ..     1   142 []    -6.6      0.2

Alignments of top-scoring domains:
Collagen: domain 1 of 7, from 20 to 77: score 4.4, E = 0.001
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pGp+GppGppG pG+pG +G +G  G pGp+G+pG+    G++Gp
   mFLJ00201    20    GKPGPRGPPGPPGFPGKPG-TGKPGVHGQPGPAGPPGFS-RMGKAGP 64   

                   pGppGapGapGpp<-*
                   pG pG+ G+pG+p   
   mFLJ00201    65 PGLPGKVGPPGQP    77   

Collagen: domain 2 of 7, from 78 to 136: score 31.8, E = 1.6e-05
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G +G+pG +G++G +GppGppG +G+ G    pG pG++G+pGppG+
   mFLJ00201    78    GLRGEPGIRGDQGLRGPPGPPGLPGPSGIT-VPGKPGAQGAPGPPGF 123  

                   pGppGapGapGpp<-*
                   +G+pG+ G+pGp+   
   mFLJ00201   124 RGEPGPQGEPGPR    136  

Collagen: domain 3 of 7, from 154 to 212: score 29.2, E = 4.6e-05
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pG++G+pGppG pGp+G  G +G  G pG+pG++G  GppG+pG+
   mFLJ00201   154    GAPGQAGAPGPPGLPGPAGL-GKPGLDGIPGAPGDKGDSGPPGVPGS 199  

                   pGppGapGapGpp<-*
                   +G+pGa G++Gpp   
   mFLJ00201   200 RGEPGAVGPKGPP    212  

Collagen: domain 4 of 7, from 230 to 288: score 26.8, E = 6.2e-05
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp G  G+pG++GppG  Gp G  G pG pGp+G++Gp G+pG  G 
   mFLJ00201   230    GPVGAKGEPGLRGPPGLIGPVG-YGMPGKPGPKGDRGPVGAPGLLGD 275  

                   pGppGapGapGpp<-*
                   +G+pG++G pG+    
   mFLJ00201   276 RGEPGEDGKPGEQ    288  

Collagen: domain 5 of 7, from 295 to 354: score 56.7, E = 5.2e-13
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      GppG+pG++G+pG +GppG +G+ G+ GppG pG +G +Gp G +G 
   mFLJ00201   295    GPPGLPGSAGLPGRRGPPGSKGEVGPGGPPGVPGIRGDQGPNGLAGK 341  

                   pGppGapGapGpp<-*
                   pG pG+ G pG+    
   mFLJ00201   342 PGLPGERGLPGAH    354  

Collagen: domain 6 of 7, from 355 to 414: score 49.2, E = 8.8e-11
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      GppGp Gp+G+pG +G+pG pG aGa G +G+ G pG+PG +Gp G 
   mFLJ00201   355    GPPGPTGPKGEPGFTGRPGGPGVAGALGQKGDLGLPGQPGLRGPSGI 401  

                   pGppGapGapGpp<-*
                   pG +G++G+ Gp    
   mFLJ00201   402 PGLQGPAGPIGPQ    414  

Collagen: domain 7 of 7, from 415 to 473: score 28.8, E = 4.9e-05
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G pG+ G+pG+pGppG+ G  G++G++Gp GppG pG+PG  GppGp
   mFLJ00201   415    GLPGLKGEPGLPGPPGE-GKVGEPGSAGPTGPPGVPGSPGLTGPPGP 460  

                   pGppGapGapGpp<-*
                   pGppG+pGapG+    
   mFLJ00201   461 PGPPGPPGAPGAL    473  

C1q: domain 1 of 1, from 513 to 637: score 221.8, E = 9.9e-63
                   *->AFSAglttnlpppnasgpisetpvvFdkvltNigghYdpaTGkFtCp
                      AF+A+lt   p+p asg+    pv+Fd+ l+N++++Y+paTG+FtCp
   mFLJ00201   513    AFTAVLT--SPFP-ASGM----PVRFDRTLYNGHSGYNPATGIFTCP 552  

                   vpGvYyFsfhvtskgvkrknlkvsLmkNgqpvvsvydqaqdgskldvaSg
                   v GvYyF++hv+   vk++n++v+L+kN++p  ++yd++++g+ ld+aSg
   mFLJ00201   553 VGGVYYFAYHVH---VKGTNVWVALYKNNVPATYTYDEYKKGY-LDQASG 598  

                   svvLqLekGDeVWLrldggernglysdggdtdStFSGFLL<-*
                   ++vLqL++ D+VW+++ ++++nglys ++  +S+FSGFLL   
   mFLJ00201   599 GAVLQLRPNDQVWVQMPSDQANGLYSTEY-IHSSFSGFLL    637  

TNF: domain 1 of 1, from 535 to 637: score -6.6, E = 0.2
                   *->LsWekdrggafllgGlklsngegLvvpqdGlYyvYsQvsFrvyRvag
                      L    ++      +G++   g  +++p+ G+Yy   +v+        
   mFLJ00201   535    LY---NGH-----SGYNPATGI-FTCPVGGVYYFAYHVHVK------ 566  

                   vscsseeedsessspvplthsvyrksdsypspvpLLkavrspctsatsey
                      +           + + +++y++++              p t +  ey
   mFLJ00201   567 ---G-----------TNVWVALYKNNV--------------PATYTYDEY 588  

                   ...wyqsiylggvfqLraGDrlsvnvs.enlslvdlsepgkTfFGaFll<
                   ++++++    g+v qLr +D+++v +++ + + +  +e   + F  Fll 
   mFLJ00201   589 kkgYLDQASGGAVLQLRPNDQVWVQMPsDQANGLYSTEYIHSSFSGFLL  637  

                   -*
                     
   mFLJ00201     -    -    

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