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:            31620976.fa
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Query sequence: gi|31620976|emb|CAD58978.1|
Accession:      [none]
Description:    Jacob [Rattus norvegicus]

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
TP1             Nuclear transition protein 1              3.4          2   1
PRD             PRD domain                                3.7        2.6   1
TIR             TIR domain                                0.9        5.4   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
IFRD            Interferon-related developmental regu    -0.2        6.5   1

Parsed for domains:
Model           Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------        ------- ----- -----    ----- -----      -----  -------
TP1               1/1      10    30 ..    38    54 .]     3.4        2
IQ                1/1      16    30 ..     1    15 [.     7.8      0.4
NUP               1/1      78    86 ..     1     9 [.    -0.2      6.3
c-SKI_SMAD_bind   1/1     114   130 ..    82    98 .]     1.6      6.1
IFRD              1/1     115   126 ..   354   365 .]    -0.2      6.5
PRD               1/1     119   131 ..     1    13 [.     3.7      2.6
TIR               1/1     166   181 ..   131   150 .]     0.9      5.4

Alignments of top-scoring domains:
TP1: domain 1 of 1, from 10 to 30: score 3.4, E = 2
                   *->KsRKRgDDAn....RnyRsHL<-*
                      K RKR  D  +  +Rn+R HL
  gi|3162097    10    KRRKRENDSAsviqRNFRKHL    30

IQ: domain 1 of 1, from 16 to 30: score 7.8, E = 0.4
                CS    HHHCHHHHHHHHHHH
                   *->rraaikIQaawRGyl<-*
                       ++a +IQ+ +R +l
  gi|3162097    16    NDSASVIQRNFRKHL    30

NUP: domain 1 of 1, from 78 to 86: score -0.2, E = 6.3
                   *->iqpKVmvIt<-*
                       +pKVm+I+
  gi|3162097    78    LPPKVMLIS    86

c-SKI_SMAD_bind: domain 1 of 1, from 114 to 130: score 1.6, E = 6.1
                CS    CHHHHHHHHHHHHCC--
                   *->eeakLeqvLeevkekFd<-*
                      e+a+ e +Lee++ k +
  gi|3162097   114    EHATFEDILEEIEKKLN    130

IFRD: domain 1 of 1, from 115 to 126: score -0.2, E = 6.5
                   *->RstFRDVlrfvE<-*
                      ++tF D+l+ +E
  gi|3162097   115    HATFEDILEEIE    126

PRD: domain 1 of 1, from 119 to 131: score 3.7, E = 2.6
                CS    HHHHHHHHHHHTS
                   *->eelleeiekklqi<-*
                      e++leeiekkl+i
  gi|3162097   119    EDILEEIEKKLNI    131

TIR: domain 1 of 1, from 166 to 181: score 0.9, E = 5.4
                CS    SG.....GGCCHHHHHHHHH
                   *->dktersqsdrikfWkkalya<-*
                      +k+e    d+i+fWk++
  gi|3162097   166    EKEE----DMIHFWKRLSRL    181

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