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:            hmm2/seq/F29D11.1
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Query:  F29D11.1  CE05765  locus:lrp-1 low density lipid receptor-rlated protein status:Partially_confirmed SW:Q04833 protein_id:CAA98124.1

Scores for sequence family classification (score includes all domains):
Model        Description                                Score    E-value  N
--------     -----------                                -----    ------- ---
ldl_recept_a Low-density lipoprotein receptor domain   1298.4          0  35
ldl_recept_b Low-density lipoprotein receptor repeat    570.6     1e-167  30
NHL          NHL repeat                                  10.4       0.41   5
SMP-30       Senescence marker protein-30 (SMP-30)        7.5        0.4   1
sigma54_AID  Sigma-54 factor, Activator interacting d     4.9        7.3   1
AFOR_N       Aldehyde ferredoxin oxidoreductase, N-te     3.1        4.2   1
Pox_I3       Poxvirus I3 ssDNA-binding protein            3.0        5.3   1
tRNA-synt_1e tRNA synthetases class I (C)                 2.2        5.9   1
DUF19        Domain of unknown function DUF19             1.7        6.5   1

Parsed for domains:
Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------     ------- ----- -----    ----- -----      -----  -------
ldl_recept_a   1/35     51    89 ..     1    43 []    46.1  1.9e-12
ldl_recept_a   2/35     90   133 ..     1    43 []    51.2    5e-14
ldl_recept_a   3/35    136   177 ..     1    43 []    34.5  6.6e-09
ldl_recept_a   4/35    180   220 ..     1    43 []    49.0  2.4e-13
ldl_recept_a   5/35    221   259 ..     1    43 []    46.0  1.9e-12
ldl_recept_a   6/35    260   299 ..     1    43 []    40.2  1.2e-10
ldl_recept_b   1/30    436   481 ..     1    47 []    18.2   0.0017
NHL            1/5     470   495 ..     1    26 [.     4.0       28
ldl_recept_b   2/30    483   524 ..     1    47 []    17.5   0.0028
NHL            2/5     513   527 ..     1    15 [.     0.1  3.5e+02
ldl_recept_b   3/30    526   565 ..     1    47 []     9.6     0.46
ldl_recept_b   4/30    567   608 ..     1    45 [.    20.2  0.00047
ldl_recept_b   5/30    610   617 ..     1     8 [.     5.1      8.9
tRNA-synt_1e   1/1     744   756 ..     1    13 [.     2.2      5.9
NHL            3/5     846   862 ..     1    17 [.     2.4       76
ldl_recept_b   6/30    903   933 ..     1    39 [.     4.4       14
Pox_I3         1/1     960   982 ..   270   292 .]     3.0      5.3
ldl_recept_a   7/35   1052  1087 ..     1    36 [.    44.3  6.4e-12
ldl_recept_a   8/35   1099  1140 ..     1    43 []    48.3  3.9e-13
ldl_recept_a   9/35   1144  1184 ..     1    43 []    66.1  1.4e-18
ldl_recept_a  10/35   1185  1225 ..     1    43 []    71.9  2.5e-20
ldl_recept_a  11/35   1226  1265 ..     1    43 []    59.8  1.2e-16
ldl_recept_a  12/35   1268  1309 ..     1    43 []    51.7  3.6e-14
ldl_recept_a  13/35   1311  1352 ..     1    43 []    61.4  3.9e-17
ldl_recept_a  14/35   1366  1398 ..    11    43 .]    13.0    0.023
ldl_recept_b   7/30   1492  1502 ..     1    11 [.     2.5       47
ldl_recept_b   8/30   1524  1565 ..     1    47 []    32.8  1.4e-07
ldl_recept_b   9/30   1567  1609 ..     1    47 []    43.9    1e-10
NHL            4/5    1598  1611 ..     1    14 [.     3.4       40
sigma54_AID    1/1    1620  1628 ..    43    51 .]     4.9      7.3
ldl_recept_b  10/30   1611  1653 ..     1    47 []    50.1  1.9e-12
ldl_recept_b  11/30   1655  1698 ..     1    47 []    24.7  2.6e-05
ldl_recept_b  12/30   1905  1941 ..    15    47 .]     5.9      5.2
ldl_recept_b  13/30   1943  1988 ..     1    47 []    21.9  0.00016
ldl_recept_b  14/30   1990  2027 ..     1    43 [.    19.0    0.001
ldl_recept_b  15/30   2031  2050 ..     1    23 [.     8.8     0.79
ldl_recept_b  16/30   2215  2258 ..     1    47 []    19.1    0.001
ldl_recept_b  17/30   2260  2302 ..     1    47 []    37.1  8.4e-09
ldl_recept_b  18/30   2304  2342 ..     1    45 [.     8.6     0.91
ldl_recept_b  19/30   2344  2360 ..     1    20 [.     9.4     0.52
ldl_recept_b  20/30   2541  2580 ..     1    47 []    12.7    0.061
ldl_recept_b  21/30   2582  2631 ..     1    47 []    32.1  2.1e-07
ldl_recept_b  22/30   2633  2661 ..     1    32 [.    17.2   0.0034
ldl_recept_a  15/35   2790  2831 ..     1    43 []    36.4  1.6e-09
ldl_recept_a  16/35   2841  2870 ..    11    43 .]    34.5  6.2e-09
ldl_recept_a  17/35   2872  2914 ..     1    43 []    56.2  1.5e-15
ldl_recept_a  18/35   2925  2958 ..    10    43 .]    18.9  0.00036
ldl_recept_a  19/35   2959  2999 ..     1    43 []    37.7  6.8e-10
ldl_recept_a  20/35   3012  3046 ..     9    43 .]    35.3  3.6e-09
ldl_recept_a  21/35   3047  3095 ..     1    43 []    35.4  3.4e-09
ldl_recept_a  22/35   3098  3137 ..     1    43 []    53.2  1.2e-14
ldl_recept_a  23/35   3138  3176 ..     1    43 []    64.6  4.1e-18
ldl_recept_a  24/35   3185  3224 ..     1    43 []    40.8  7.8e-11
DUF19          1/1    3262  3274 ..    39    51 ..     1.7      6.5
ldl_recept_b  23/30   3379  3400 ..    24    47 .]     9.2     0.59
ldl_recept_b  24/30   3402  3443 ..     1    47 []    17.1   0.0036
AFOR_N         1/1    3436  3444 ..   228   236 .]     3.1      4.2
ldl_recept_b  25/30   3445  3492 ..     1    47 []    47.1  1.3e-11
ldl_recept_b  26/30   3494  3517 ..     1    27 [.     0.8  1.4e+02
ldl_recept_b  27/30   3535  3577 ..     1    47 []    18.0    0.002
ldl_recept_a  25/35   3625  3668 ..     1    43 []    44.1  7.3e-12
ldl_recept_a  26/35   3669  3705 ..     1    41 [.    24.4  7.6e-06
ldl_recept_a  27/35   3707  3748 ..     1    43 []    43.7    1e-11
ldl_recept_a  28/35   3751  3790 ..     1    43 []    54.7  4.4e-15
ldl_recept_a  29/35   3799  3830 ..    10    41 ..    21.0  8.6e-05
ldl_recept_a  30/35   3831  3873 ..     1    43 []    51.6  3.8e-14
ldl_recept_a  31/35   3876  3914 ..     1    43 []    41.4  5.1e-11
ldl_recept_a  32/35   3915  3953 ..     1    43 []    27.5    9e-07
ldl_recept_a  33/35   3957  3997 ..     1    43 []    62.7  1.6e-17
ldl_recept_a  34/35   3998  4042 ..     1    43 []    53.5    1e-14
ldl_recept_a  35/35   4047  4085 ..     1    43 []    44.0    8e-12
SMP-30         1/1    4219  4241 ..   168   190 ..     7.5      0.4
ldl_recept_b  28/30   4227  4275 ..     1    47 []    53.0  2.9e-13
ldl_recept_b  29/30   4343  4385 ..     1    47 []    30.8    5e-07
ldl_recept_b  30/30   4388  4428 ..     1    47 []    15.2    0.013
NHL            5/5    4439  4454 ..    15    29 .]     0.4  2.9e+02

Alignments of top-scoring domains:
ldl_recept_a: domain 1 of 35, from 51 to 89: score 46.1, E = 1.9e-12
                   *->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
                      s C   ++F+C++g+ CI   w+CDG+ DC DG+DE  ++C+
    F29D11.1    51    SVCN-ENDFRCNDGK-CIRTEWKCDGSGDCSDGEDE--KDCPH    89

ldl_recept_a: domain 2 of 35, from 90 to 133: score 51.2, E = 5e-14
                   *->stCggpdeFqCgsgr....rCIprswvCDGdpDCeDGSDEslenCaa
                      + C+ +d++qC +   ++ +CI+  ++CD   DC+DGSDE  ++C+a
    F29D11.1    90    PGCK-SDQWQCDTYTwhsvSCIAEYQRCDNITDCADGSDE--KDCPA 133

                   <-*

    F29D11.1     -     -

ldl_recept_a: domain 3 of 35, from 136 to 177: score 34.5, E = 6.6e-09
                   *->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
                      ++C+  + F C++gr+C   s++CDG +DC+D SDE  ++C++
    F29D11.1   136    VDCSSQNVFMCADGRQCFDVSKKCDGKYDCRDLSDE-KDSCSR    177

ldl_recept_a: domain 4 of 35, from 180 to 220: score 49.0, E = 2.4e-13
                   *->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
                      + C    +F+C++  +CI +swvCDG+ DC+DGSDE +++C
    F29D11.1   180    TACF-QYQFRCADKTQCIQKSWVCDGSKDCADGSDE-PDTCEF    220

ldl_recept_a: domain 5 of 35, from 221 to 259: score 46.0, E = 1.9e-12
                   *->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
                      ++C  ++eFqC++ r C pr+++CD  +DC+D SDE  + C+
    F29D11.1   221    KKCT-ANEFQCKNKR-CQPRKFRCDYYDDCGDNSDE--DECGE    259

ldl_recept_a: domain 6 of 35, from 260 to 299: score 40.2, E = 1.2e-10
                   *->stCggpdeFqCgsgrrCIprswvCDGdpDCeDGSDEslenCaa<-*
                       +C  p+++ C +   CI ++++CDG+ DC+DG DE  ++C++
    F29D11.1   260    YRCP-PGKWNCPGTGHCIDQLKLCDGSKDCADGADE--QQCSQ    299

ldl_recept_b: domain 1 of 30, from 436 to 481: score 18.2, E = 0.0017
                   *->grlYWtDsslrkIasisvadlnGsdrrtlfsede..dlqhPngIavD
                      ++++WtD   +   s+++ad+++  +   ++    + l  P+ +avD
    F29D11.1   436    RKIFWTDRLAH---SAFSADVDDEGEISQIKKLSlkSLVYPRCLAVD 479

                   pi<-*
                   +i
    F29D11.1   480 WI    481

NHL: domain 1 of 5, from 470 to 495: score 4.0, E = 28
                   *->lnrPhGvavdpsdGrvyVaDsenhrv<-*
                      l +P  +avd  ++++y+ +s++ r+
    F29D11.1   470    LVYPRCLAVDWITNTLYIIESGSRRI    495

ldl_recept_b: domain 2 of 30, from 483 to 524: score 17.5, E = 0.0028
                   *->grlYWtDsslrkIasisvadlnGsdrrtlfsededlqhPngIavDpi
                      + lY ++s+ r   +i v   +G +r +l+++   l  P +Ia+Dp
    F29D11.1   483    NTLYIIESGSR---RIDVSSYDGERRTVLLADG--LTLPLDIALDPL 524

                   <-*

    F29D11.1     -     -

NHL: domain 2 of 5, from 513 to 527: score 0.1, E = 3.5e+02
                   *->lnrPhGvavdpsdGr<-*
                      l+ P ++a+dp  G+
    F29D11.1   513    LTLPLDIALDPLRGE    527

	[output cut off at A = 10 top alignments]


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