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]