Motif confirmation by HMMer


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:                 /home/niguts/usr02/tshini/ykclst/db/Pfam_fs
Sequence file:            hmm5/seq/Y41D4A.2
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Query:  Y41D4A.2  CE27619    status:Partially_confirmed TR:Q95Y22 protein_id:AAK68452.1

Scores for sequence family classification (score includes all domains):
Model         Description                               Score    E-value  N
--------      -----------                               -----    ------- ---
Collagen      Collagen triple helix repeat (20 copies    98.2    1.6e-25   3
Col_cuticle_N Nematode cuticle collagen N-terminal do    44.9      6e-12   1
Peptidase_M50 Peptidase family M50                        6.6       0.88   1

Parsed for domains:
Model         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------      ------- ----- -----    ----- -----      -----  -------
Col_cuticle_N   1/1      21    81 ..     1    66 []    44.9    6e-12
Collagen        1/3     106   137 ..     5    36 ..    15.9    0.007
Collagen        2/3     156   215 ..     1    60 []    47.7  1.3e-11
Collagen        3/3     221   280 ..     1    60 []    50.3  2.4e-12
Peptidase_M50   1/1      17   320 ..   101   132 ..     6.6     0.88

Alignments of top-scoring domains:
Col_cuticle_N: domain 1 of 1, from 21 to 81: score 44.9, E = 6e-12
                   *->SgvAvlacLftvpsiyndInsfqdevmdemdeFKvyaddaWneMvdv
                      S vAv+++ +t+p++yn++ +    ++ e++++K+ a d+W+e+  +
    Y41D4A.2    21    SVVAVISVSVTLPMVYNYVHHVKRSMQTEINFCKGSAKDIWTEVNHL 67

                   qrnvrppskpasarfgrpf<-*
                    + + +     ++r++r+
    Y41D4A.2    68 KSIPAS-----RNRTARQA    81

Collagen: domain 1 of 3, from 106 to 137: score 15.9, E = 0.007
                   *->ppGppGppGppGppGppGpaGapGppGppGep<-*
                      +pG++Gp+G pG+pG pG aGapG pG+pG p
    Y41D4A.2   106    LPGAAGPAGTPGKPGRPGKAGAPGLPGNPGRP    137

Collagen: domain 2 of 3, from 156 to 215: score 47.7, E = 1.3e-11
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      Gp+GppGppGp+G +G  G pG++G+ G pG++G++Gp Gp G pG+
    Y41D4A.2   156    GPAGPPGPPGPAGDAGSDGSPGAPGSDGQPGAAGDKGPAGPNGNPGA 202

                   pGppGapGapGpp<-*
                   pG pG+pG+ G+
    Y41D4A.2   203 PGSPGKPGEDGKS    215

Collagen: domain 3 of 3, from 221 to 280: score 50.3, E = 2.4e-12
                   *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp
                      G+pGp+GppGp+GppG+pG+pG++G pG pGp+G++G PG+pG++G
    Y41D4A.2   221    GAPGPAGPPGPQGPPGAPGQPGHDGQPGTPGPKGPNGNPGAPGADGN 267

                   pGppGapGapGpp<-*
                   pG pG +G +G
    Y41D4A.2   268 PGTPGVAGVAGSG    280

Peptidase_M50: domain 1 of 1, from 17 to 320: score 6.6, E = 0.88
                RF    xxxxxxxxxxxxxxxxxx
                   *->iLAvvllalllllpgvvv.............................
                      ++A+ + a+++++   ++  +  ++ +++ ++  + ++++ ++ ++
    Y41D4A.2    17    AVAFSVVAVISVSVTLPMvynyvhhvkrsmqteinfckgsakdiwte 63

                RF
                   ..................................................
                    ++ ++ + +++++ ++ + + + +++++  ++ ++++  ++ ++  ++
    Y41D4A.2    64 vnhlksipasrnrtarqagydagvngggseasgapgnceacclpgaagpa 113

                RF
                   ..................................................
                   +++++++++++ + ++ ++++++++++++ + ++++++++++++ +++++
    Y41D4A.2   114 gtpgkpgrpgkagapglpgnpgrppqqpcepitpppckpcpqgpagppgp 163

                RF
                   ..................................................
                   +++ ++ +++++++ ++++++++  +++++ +++++++ ++++++++ ++
    Y41D4A.2   164 pgpagdagsdgspgapgsdgqpgaagdkgpagpngnpgapgspgkpgedg 213

                RF
                   ..................................................
                   ++ + +++ +++ ++++++++++ +++++++++++++++++++++++ ++
    Y41D4A.2   214 ksepitpgapgpagppgpqgppgapgqpghdgqpgtpgpkgpngnpgapg 263

                RF                                            xxxxxxx
                   ...........................................assglia
                    ++++++++  +  ++++ ++ +++ +  +++    ++++++ ++++l++
    Y41D4A.2   264 adgnpgtpgvagvagsggekgvcpkycaidggvffedgsrqsfFQTLLQS 313

                RF xxxxxxx
                   llaflal<-*
                    la+ a+
    Y41D4A.2   314 ALAYTAF    320



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