hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: /usr1/pfam-23.0/Pfam_fs
Sequence file: 123227893.fa
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Query sequence: gi|123227893|emb|CAM17996.1|
Accession: [none]
Description: nasal embryonic LHRH factor [Mus musculus]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
IQ IQ calmodulin-binding motif 7.8 0.4 1
Ribosomal_L20 Ribosomal protein L20 4.2 0.64 1
TIR TIR domain 3.7 0.78 2
TP1 Nuclear transition protein 1 3.4 2 1
PRD PRD domain 3.7 2.6 1
DUF1813 HSP20-like domain of unknown function 2.4 5.6 1
IMPDH IMP dehydrogenase / GMP reductase dom 0.6 6 1
c-SKI_SMAD_bind c-SKI Smad4 binding domain 1.6 6.1 1
NUP Purine nucleoside permease (NUP) -0.2 6.3 1
Orthopox_N1 Orthopoxvirus N1 protein 0.7 6.4 1
IFRD Interferon-related developmental regu -0.2 6.5 1
Nif11 Nitrogen fixation protein of unknown 2.3 9.6 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Nif11 1/1 8 18 .. 1 11 [. 2.3 9.6
DUF1813 1/1 14 42 .. 1 46 [. 2.4 5.6
TIR 1/2 15 50 .. 117 150 .] 2.8 1.5
Ribosomal_L20 1/1 17 31 .. 1 15 [. 4.2 0.64
TP1 1/1 27 47 .. 38 54 .] 3.4 2
IQ 1/1 33 47 .. 1 15 [. 7.8 0.4
NUP 1/1 95 103 .. 1 9 [. -0.2 6.3
c-SKI_SMAD_bind 1/1 131 147 .. 82 98 .] 1.6 6.1
IFRD 1/1 132 143 .. 354 365 .] -0.2 6.5
PRD 1/1 136 148 .. 1 13 [. 3.7 2.6
TIR 2/2 183 198 .. 131 150 .] 0.9 5.4
Orthopox_N1 1/1 252 265 .. 100 113 .] 0.7 6.4
IMPDH 1/1 273 281 .] 1 9 [. 0.6 6
Alignments of top-scoring domains:
Nif11: domain 1 of 1, from 8 to 18: score 2.3, E = 9.6
*->MseeqLkaFLa<-*
M++++L++FL+
gi|1232278 8 MQAADLRRFLR 18
DUF1813: domain 1 of 1, from 14 to 42: score 2.4, E = 5.6
*->pRqytVfkInlYRNGLilTLlaediiGYvpyrgkdn.tggaryyqrv
R+++Vf+ GY+ ++ + ++ + a +qr+
gi|1232278 14 RRFLRVFR------------------GYAERKRRKReNDSASVIQRN 42
<-*
gi|1232278 - -
TIR: domain 1 of 2, from 15 to 50: score 2.8, E = 1.5
CS HHHHHCT-SEE--SSG... ..GGCCHHHHHHHHH
*->kFgkaflktlkwsgdkter...sqsdrikfWkkalya<-*
+F+ +f+++++++++k e+++ s+++r f+k+++
gi|1232278 15 RFLRVFRGYAERKRRKRENdsaSVIQR-NFRKHLRMV 50
Ribosomal_L20: domain 1 of 1, from 17 to 31: score 4.2, E = 0.64
*->tRVKrGyiaRkRRKK<-*
RV rGy RkRRK+
gi|1232278 17 LRVFRGYAERKRRKR 31
TP1: domain 1 of 1, from 27 to 47: score 3.4, E = 2
*->KsRKRgDDAn....RnyRsHL<-*
K RKR D + +Rn+R HL
gi|1232278 27 KRRKRENDSAsviqRNFRKHL 47
IQ: domain 1 of 1, from 33 to 47: score 7.8, E = 0.4
CS HHHCHHHHHHHHHHH
*->rraaikIQaawRGyl<-*
++a +IQ+ +R +l
gi|1232278 33 NDSASVIQRNFRKHL 47
NUP: domain 1 of 1, from 95 to 103: score -0.2, E = 6.3
*->iqpKVmvIt<-*
+pKVm+I+
gi|1232278 95 LPPKVMLIS 103
c-SKI_SMAD_bind: domain 1 of 1, from 131 to 147: score 1.6, E = 6.1
CS CHHHHHHHHHHHHCC--
*->eeakLeqvLeevkekFd<-*
e+a+ e +Lee++ k +
gi|1232278 131 EHATFEDILEEIEKKLN 147
IFRD: domain 1 of 1, from 132 to 143: score -0.2, E = 6.5
*->RstFRDVlrfvE<-*
++tF D+l+ +E
gi|1232278 132 HATFEDILEEIE 143
PRD: domain 1 of 1, from 136 to 148: score 3.7, E = 2.6
CS HHHHHHHHHHHTS
*->eelleeiekklqi<-*
e++leeiekkl+i
gi|1232278 136 EDILEEIEKKLNI 148
TIR: domain 2 of 2, from 183 to 198: score 0.9, E = 5.4
CS SG.....GGCCHHHHHHHHH
*->dktersqsdrikfWkkalya<-*
+k+e d+i+fWk++
gi|1232278 183 EKEE----DMIHFWKRLSRL 198
Orthopox_N1: domain 1 of 1, from 252 to 265: score 0.7, E = 6.4
*->rmiekyfddlmidl<-*
+mie+yfd + l
gi|1232278 252 QMIETYFDFRLYRL 265
IMPDH: domain 1 of 1, from 273 to 281: score 0.6, E = 6
CS EB-GGGGEE
RF xxxxxxxxx
*->egLTFDDVL<-*
+ L+FDDVL
gi|1232278 273 KLLDFDDVL 281
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