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:            hmm3/seq/F40F4.6
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Query:  F40F4.6  CE04536   EGF-like repeats status:Partially_confirmed TR:Q20219 protein_id:AAA81430.1

Scores for sequence family classification (score includes all domains):
Model           Description                             Score    E-value  N
--------        -----------                             -----    ------- ---
vwa             von Willebrand factor type A domain      87.6    1.5e-26   1
lectin_c        Lectin C-type domain                     29.5    3.2e-06   1
EGF             EGF-like domain                          17.4     0.0032   5
DUF291          Domain of unknown function                8.2          1   1
DUF31           Domain of unknown function DUF31          6.6        1.3   1
HRM             Hormone receptor domain                   5.8        5.6   2
Bowman-Birk_leg Bowman-Birk serine protease inhibitor     5.5        7.3   1
Complex1_17_2kD NADH:ubiquinone oxidoreductase 17.2 k     5.0        4.5   1
PTS-HPr         PTS HPr component phosphorylation sit     4.6        6.6   1
TSNR_N          Thiostrepton-resistance methylase, N      3.8        7.4   1
Prog_receptor   Progesterone receptor                     2.7        1.1   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
EGF               1/5      84    92 ..    32    45 .]     4.1       19
HRM               1/2     391   400 ..    26    35 ..     1.1  1.1e+02
EGF               2/5     371   401 ..     1    45 []     7.5      2.1
DUF291            1/1     412   425 ..    81    96 .]     8.2        1
PTS-HPr           1/1     436   452 ..    71    87 .]     4.6      6.6
TSNR_N            1/1     769   782 ..    44    58 ..     3.8      7.4
EGF               3/5     856   892 ..     1    45 []    18.2   0.0019
lectin_c          1/1    1204  1311 ..     7   125 .]    29.5  3.2e-06
HRM               2/2    1328  1354 ..    53    79 .]     4.8       11
Complex1_17_2kD   1/1    1453  1461 ..     1    11 [.     5.0      4.5
EGF               4/5    1477  1500 ..    12    45 .]     5.5      7.5
Bowman-Birk_leg   1/1    1486  1505 ..    50    67 .]     5.5      7.3
EGF               5/5    1504  1529 ..    12    45 .]    11.9     0.12
DUF31             1/1    1716  1731 ..   114   129 .]     6.6      1.3
Prog_receptor     1/1    2021  2033 ..   557   569 .]     2.7      1.1
vwa               1/1    2013  2200 ..     1   189 []    87.6  1.5e-26

Alignments of top-scoring domains:
EGF: domain 1 of 5, from 84 to 92: score 4.1, E = 19
                   *->ppGdyylsytGkrC<-*
                      +pG     ytG++C
     F40F4.6    84    KPG-----YTGETC    92

HRM: domain 1 of 2, from 391 to 400: score 1.1, E = 1.1e+02
                   *->pCPdyfsGfn<-*
                      +CP++fsGf+
     F40F4.6   391    QCPEGFSGFH    400

EGF: domain 2 of 5, from 371 to 401: score 7.5, E = 2.1
                   *->CapnnpCsngGtCvntpggssdnfggytCeCppGdyylsytGkrC<-
                      C++   C ngG+ ++tp  +       +C+Cp+G     ++G +C
     F40F4.6   371    CSQM-LCANGGF-LPTPTSD-------RCQCPEG-----FSGFHC   401

                   *

     F40F4.6     -   -

DUF291: domain 1 of 1, from 412 to 425: score 8.2, E = 1
                   *->FdFsaGtkdpKLtitI<-*
                      FdF+a   +p+Lt++I
     F40F4.6   412    FDFNA-E-NPTLTLVI    425

PTS-HPr: domain 1 of 1, from 436 to 452: score 4.6, E = 6.6
                   *->eDeeeAiaAlvdlmake<-*
                      e++ e ++++vdl+a+e
     F40F4.6   436    EQATESVQSIVDLLASE    452

TSNR_N: domain 1 of 1, from 769 to 782: score 3.8, E = 7.4
                   *->IRAGVeFiEVYGldt<-*
                      IR GV+ +EVYG+++
     F40F4.6   769    IRDGVQ-TEVYGSSG    782

EGF: domain 3 of 5, from 856 to 892: score 18.2, E = 0.0019
                   *->Capnn...pCsngGtCvntpggssdnfggytCeCppGdyylsytGkr
                      C+p++++++C+n  +C n++       +g +C+CppG     y+G+
     F40F4.6   856    CTPEFtgtYCQNI-ICYNGGT-----ASGDHCVCPPG-----YAGES 891

                   C<-*
                   C
     F40F4.6   892 C    892

lectin_c: domain 1 of 1, from 1204 to 1311: score 29.5, E = 3.2e-06
                   *->eAelaCqkegghAHLvsIqsaeEqsfvvafltsltkksntyaWIGLt
                      +A+++C ++gg   Lv     + +     fl+s++   nt +W+GL+
     F40F4.6  1204    QAKAFCASAGGF--LVDDLTDDKN----GFLKSVAA--NTQFWTGLF 1242

                   dintegtwvwegwetdgspvnyt......enWapgePnnrgnhGgnEdCv
                     n +g+++w      g++ n +  +++ ++Wa+geP++      + +Cv
     F40F4.6  1243 -KNNDGQFYW----DRGTGINPDllnqpiTYWADGEPSDDPT---R-QCV 1283

                   eiytdtdflaGkWnDepCdsklpyvCef<-*
                    +++ ++ +   W  + C +++++ C++
     F40F4.6  1284 YFNGRSGDANKVWTTDTCAEPRAFACQK    1311

HRM: domain 2 of 2, from 1328 to 1354: score 4.8, E = 11
                   *->tenGwwerhpnsnwpwpdytnCtspey<-*
                      ++ Gww+ ++ sn+p  ++ +Ct  +
     F40F4.6  1328    LPAGWWYAKVKSNPPSGYPNMCTMSVR    1354

Complex1_17_2kD: domain 1 of 1, from 1453 to 1461: score 5.0, E = 4.5
                   *->gtlVGeDkfGN<-*
                        +VGeD+fGN
     F40F4.6  1453    --HVGEDEFGN    1461

	[output cut off at A = 10 top alignments]


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