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:                 /db/iprscan/data/Pfam.bin
Sequence file:            /db/iprscan/tmp/20080811/iprscan-20080811-21481051/chunk_1/iprscan-20080811-21481051.nocrc
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Query sequence: ha03446
Accession:      [none]
Description:    [none]

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
PF06209.4.ls Cofactor of BRCA1 (COBRA1)                    1347.1          0   1
PF06209.4.fs Cofactor of BRCA1 (COBRA1)                    1345.1          0   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
PF06209.4.fs   1/1     183   657 .]     1   479 []  1345.1        0
PF06209.4.ls   1/1     183   657 .]     1   479 []  1347.1        0

Alignments of top-scoring domains:
PF06209.4.fs: domain 1 of 1, from 183 to 657: score 1345.1, E = 0
                   *->mpslqPVVMcvLkhlPkvpeKkLklvmaDkELYkdcavEVKRQIWqD
                      mpslqPVVMcv+khlPkvpeKkLklvmaDkELY++cavEVKRQIWqD
     ha03446   183    MPSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQD 229  

                   NQaLFGDEVSPLLkQYIlEKEaaLFSdeLsllhnFFsPsPKtRRQGEVVq
                   NQaLFGDEVSPLLkQYIlEKE+aLFS+eLs+lhnFFsPsPKtRRQGEVVq
     ha03446   230 NQALFGDEVSPLLKQYILEKESALFSTELSVLHNFFSPSPKTRRQGEVVQ 279  

                   KLtqMiGknVKLYDMVLQFLRTLFLRTRNVHYcTLRAELLMsLHDLdvsd
                   +Lt+M+GknVKLYDMVLQFLRTLFLRTRNVHYcTLRAELLMsLHDLdv +
     ha03446   280 RLTRMVGKNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGE 329  

                   IisVDPCHKFtWCLDACIREkfVDaKRaRELQGFLDgvKkGQEQVLGDLS
                   I++VDPCHKFtWCLDACIRE+fVD+KRaRELQGFLDgvKkGQEQVLGDLS
     ha03446   330 ICTVDPCHKFTWCLDACIRERFVDSKRARELQGFLDGVKKGQEQVLGDLS 379  

                   MiLCDPfAiNtLalStiriLQeLisqeglPRdspdLlLLLRmLaLGqgAW
                   MiLCDPfAiNtLalSt+r+LQeL+ qe+lPRdspdLlLLLR+LaLGqgAW
     ha03446   380 MILCDPFAINTLALSTVRHLQELVGQETLPRDSPDLLLLLRLLALGQGAW 429  

                   dmIDSQvFKEPkldsevvTkFLPaLMSlvVDDytfhveqKLPaeEkesai
                   dmIDSQvFKEPk++ e++T+FLP+LMS +VDDytf+v+qKLPaeEk    
     ha03446   430 DMIDSQVFKEPKMEVELITRFLPMLMSFLVDDYTFNVDQKLPAEEK---- 475  

                   tsieypgtlPeafekYiqenrvAcelglYYtLHiakqrnknallRllpiL
                   + + yp+tlPe+f+k++qe+r+Ace+glYY+LHi+kqrnknallRllp+L
     ha03446   476 APVSYPNTLPESFTKFLQEQRMACEVGLYYVLHITKQRNKNALLRLLPGL 525  

                   vetkdDlAfeDiFLHlLtgllillsDEFanEdFCtglFDeFLltgltrKe
                   vet++DlAf+DiFLHlLtg l ll+DEFa+EdFC++lFD+F+lt+++rKe
     ha03446   526 VETFGDLAFGDIFLHLLTGNLALLADEFALEDFCSSLFDGFFLTASPRKE 575  

                   NVhRHvLrLLlhlHqkvaparLetLmKaLePtaQssEsVkeLYenLkekl
                   NVhRH LrLL hlH +vap++Le+L+KaLePt+Qs+E+VkeLY++L+ekl
     ha03446   576 NVHRHALRLLIHLHPRVAPSKLEALQKALEPTGQSGEAVKELYSQLGEKL 625  

                   etldltkesPaqpeEtPdlDlpLksVptPgtl<-*
                   e+ld++k+sPaq++EtP+l lpL+sVp+P++l   
     ha03446   626 EQLDHRKPSPAQAAETPALELPLPSVPAPAPL    657  

PF06209.4.ls: domain 1 of 1, from 183 to 657: score 1347.1, E = 0
                   *->mpslqPVVMcvLkhlPkvpeKkLklvmaDkELYkdcavEVKRQIWqD
                      mpslqPVVMcv+khlPkvpeKkLklvmaDkELY++cavEVKRQIWqD
     ha03446   183    MPSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQD 229  

                   NQaLFGDEVSPLLkQYIlEKEaaLFSdeLsllhnFFsPsPKtRRQGEVVq
                   NQaLFGDEVSPLLkQYIlEKE+aLFS+eLs+lhnFFsPsPKtRRQGEVVq
     ha03446   230 NQALFGDEVSPLLKQYILEKESALFSTELSVLHNFFSPSPKTRRQGEVVQ 279  

                   KLtqMiGknVKLYDMVLQFLRTLFLRTRNVHYcTLRAELLMsLHDLdvsd
                   +Lt+M+GknVKLYDMVLQFLRTLFLRTRNVHYcTLRAELLMsLHDLdv +
     ha03446   280 RLTRMVGKNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGE 329  

                   IisVDPCHKFtWCLDACIREkfVDaKRaRELQGFLDgvKkGQEQVLGDLS
                   I++VDPCHKFtWCLDACIRE+fVD+KRaRELQGFLDgvKkGQEQVLGDLS
     ha03446   330 ICTVDPCHKFTWCLDACIRERFVDSKRARELQGFLDGVKKGQEQVLGDLS 379  

                   MiLCDPfAiNtLalStiriLQeLisqeglPRdspdLlLLLRmLaLGqgAW
                   MiLCDPfAiNtLalSt+r+LQeL+ qe+lPRdspdLlLLLR+LaLGqgAW
     ha03446   380 MILCDPFAINTLALSTVRHLQELVGQETLPRDSPDLLLLLRLLALGQGAW 429  

                   dmIDSQvFKEPkldsevvTkFLPaLMSlvVDDytfhveqKLPaeEkesai
                   dmIDSQvFKEPk++ e++T+FLP+LMS +VDDytf+v+qKLPaeEk    
     ha03446   430 DMIDSQVFKEPKMEVELITRFLPMLMSFLVDDYTFNVDQKLPAEEK---- 475  

                   tsieypgtlPeafekYiqenrvAcelglYYtLHiakqrnknallRllpiL
                   + + yp+tlPe+f+k++qe+r+Ace+glYY+LHi+kqrnknallRllp+L
     ha03446   476 APVSYPNTLPESFTKFLQEQRMACEVGLYYVLHITKQRNKNALLRLLPGL 525  

                   vetkdDlAfeDiFLHlLtgllillsDEFanEdFCtglFDeFLltgltrKe
                   vet++DlAf+DiFLHlLtg l ll+DEFa+EdFC++lFD+F+lt+++rKe
     ha03446   526 VETFGDLAFGDIFLHLLTGNLALLADEFALEDFCSSLFDGFFLTASPRKE 575  

                   NVhRHvLrLLlhlHqkvaparLetLmKaLePtaQssEsVkeLYenLkekl
                   NVhRH LrLL hlH +vap++Le+L+KaLePt+Qs+E+VkeLY++L+ekl
     ha03446   576 NVHRHALRLLIHLHPRVAPSKLEALQKALEPTGQSGEAVKELYSQLGEKL 625  

                   etldltkesPaqpeEtPdlDlpLksVptPgtl<-*
                   e+ld++k+sPaq++EtP+l lpL+sVp+P++l   
     ha03446   626 EQLDHRKPSPAQAAETPALELPLPSVPAPAPL    657  

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