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). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: /data11/genetics/InterProScan/iprscan/data/Pfam Sequence file: /cdna4/shimazu/full/sj/sj04110/interpro/cnk_1/seq.in - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: sj04110 705 Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- C1q C1q domain 265.4 7.4e-76 1 Collagen Collagen triple helix repeat (20 copies) 175.5 8.6e-49 7 Extensin_2 Extensin-like region -131.9 0.25 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Collagen 1/7 111 169 .. 1 60 [] 18.5 0.00017 Collagen 2/7 175 233 .. 1 60 [] 31.0 2.8e-05 Collagen 3/7 239 297 .. 1 60 [] 23.4 9.5e-05 Collagen 4/7 298 356 .. 1 60 [] 21.8 0.00012 Extensin_2 1/1 13 392 .. 1 385 [] -131.9 0.25 Collagen 5/7 360 419 .. 1 60 [] 50.3 4.4e-11 Collagen 6/7 420 479 .. 1 60 [] 49.2 8.8e-11 Collagen 7/7 480 538 .. 1 60 [] 29.2 4.6e-05 C1q 1/1 578 702 .. 1 137 [] 265.4 7.4e-76 Alignments of top-scoring domains: Collagen: domain 1 of 7, from 111 to 169: score 18.5, E = 0.00017 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pGp+GppG G++GppG +G+ GppG pG +G+PG +G G sj04110 111 GQPGPAGPPGFS-RMGKAGPPGLPGKVGPPGQPGLRGEPGIRGDQGL 156 pGppGapGapGpp<-* +GppG+pG pGp sj04110 157 RGPPGPPGLPGPS 169 Collagen: domain 2 of 7, from 175 to 233: score 31.0, E = 2.8e-05 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG +G pGppG G+pGp+G++G+pG++G +G++G G+pG pG+ sj04110 175 GKPGAQGVPGPPGFQGEPGPQGEPGPPGDRGLKGDNG-VGQPGLPGA 220 pGppGapGapGpp<-* pG+ GapG+pG p sj04110 221 PGQGGAPGPPGLP 233 Collagen: domain 3 of 7, from 239 to 297: score 23.4, E = 9.5e-05 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G+pG+ G pG+pG +G++GppG +G++G+pG+ G++GpPG +G+ G sj04110 239 GKPGLDGLPGAPGDKGESGPPGVPGPRGEPGAVGPKGPPGVDGV-GV 284 pGppGapGapGpp<-* pG +G pG+ Gp sj04110 285 PGAAGLPGPQGPS 297 Collagen: domain 4 of 7, from 298 to 356: score 21.8, E = 0.00012 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G++G+pG +GppG Gp G G +G pGp+G++G++G PG G G sj04110 298 GAKGEPGTRGPPGLIGPTGY-GMPGLPGPKGDRGPAGVPGLLGDRGE 343 pGppGapGapGpp<-* pG++G+pG+ Gp sj04110 344 PGEDGEPGEQGPQ 356 Extensin_2: domain 1 of 1, from 13 to 392: score -131.9, E = 0.25 *->lltlvvalvslslpseasakYsYsSPPPpekpYvYkSPPpPspkyvy ll l+++lv + p +s + +Y+ P+ sj04110 13 LLLLLLVLVLGCGPRASSGGGAGGAAGYAPVKYIQ-----PM----Q 50 kSPPPpkkpY......vYsSPPP..PsyvykSPPPPkpyvYkSPPpPkyv k P p p+++++++ + P P P + P PP ++ + PP P+ sj04110 51 KGPVGP--PFregkgqYLEMPLPllPMDLKGEPGPPGKPGPRGPPGPPGF 98 YkSPPpPvykYkSPPPPthsppPpyvykSPPPPpkkyvykSpPpptPvYk P ++ P P PP + k Pp P sj04110 99 PGKPGMGKPGLHGQPGPA------------GPPGFSRMGKAGPPGLP--- 133 YkSPPPPpyvYkspPpPvkkripyvYkSPPPPpPYvYkSpPppvkkyiyk k PP ++ + P r + PP Pp P p+ sj04110 134 GKVGPPGQPGLRGEP---GIRGDQGLRGPPGPPG-----LPGPS------ 169 sppppephkYvYkSPPPPpPYvyesvpeqkikYvYkSPPPPkksYk.sps + p ++ P PP + e+ p + PP + k+ sj04110 170 GITIPGKP-GAQGVPGPPG-FQGEPGP------QGEPGPPGDRGLKgDNG 211 ppkyVYkSpPpPvipykYkSPPPPkkkyspaPrkpyvYkSPPPPtyvYkS ++ +P P PP + ++ kp P P + S sj04110 212 VGQPGLPGAPG-----QGGAPGPPGLPGPAGLGKPGLDGLPGAPGDKGES 256 pPpPyk..pptppkiyksPPPPtP...vyvYkspPpippiksssppPvyv Pp +++ +p+ + PP + +v+ P p +s + + sj04110 257 GPPGVPgpRGEPGAVGPKGPPGVDgvgVPGAAGLPG--PQGPSGAKGEPG 304 YkSpPppvysPPPPyvYssPPPPvy......................... + pP P Y P P ++++++ + ++ ++++++++++++ sj04110 305 TRGPPGLI----GPTGYGMPGLPGPkgdrgpagvpgllgdrgepgedgep 350 .............vynsaPvykksPPkhhYiYsSP..PPphh<-* +++++++ ++++++ sa + + P+ + + P++PP + sj04110 351 geqgpqglggppgLPGSAGLPGRRGPPGPKGEAGPggPPGVP 392 Collagen: domain 5 of 7, from 360 to 419: score 50.3, E = 4.4e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppG+pG++G+pG +GppGp+G+aG+ GppG pG +G +Gp G +G sj04110 360 GPPGLPGSAGLPGRRGPPGPKGEAGPGGPPGVPGIRGDQGPSGLAGK 406 pGppGapGapGpp<-* pG pG+ G pG+ sj04110 407 PGVPGERGLPGAH 419 Collagen: domain 6 of 7, from 420 to 479: score 49.2, E = 8.8e-11 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp GppGp Gp+G+pG +G+pG pG aGa G +G+ G pG+PG +Gp G sj04110 420 GPPGPTGPKGEPGFTGRPGGPGVAGALGQKGDLGLPGQPGLRGPSGI 466 pGppGapGapGpp<-* pG +G++G+ Gp sj04110 467 PGLQGPAGPIGPQ 479 Collagen: domain 7 of 7, from 480 to 538: score 29.2, E = 4.6e-05 *->GppGppGppGppGppGppGppGpaGapGppGppGepGpPGppGppGp G pG+ G+pG+pGppG+ G +G++G +Gp GppG pG+PG GppGp sj04110 480 GLPGLKGEPGLPGPPGE-GRAGEPGTAGPTGPPGVPGSPGITGPPGP 525 pGppGapGapGpp<-* pGppG+pGapG+ sj04110 526 PGPPGPPGAPGAF 538 C1q: domain 1 of 1, from 578 to 702: score 265.4, E = 7.4e-76 *->AFtvirstnrpPaEmsnpgqpViFdeVLyNqqghYdpsTGkFtCkvP AFt+++++ ++Pa g+pV+Fd++LyN+++ Y+p+TG+FtC+v sj04110 578 AFTAVLTS-PFPA----SGMPVKFDRTLYNGHSGYNPATGIFTCPVG 619 GlYyFsFhvsskgtRqnvcVsLmrSSrngvrqkVmefcdeyakgtyqvaS G+YyF++hv++kgt nv+V+L++ n+v+ +++++dey+kg++++aS sj04110 620 GVYYFAYHVHVKGT--NVWVALYK---NNVP--ATYTYDEYKKGYLDQAS 662 GGavLqLrqGDrVWLelddkqtngllggegvhSvFSGFLl<-* GGavLqLr++D+VW++++++q+ngl+++e++hS+FSGFLl sj04110 663 GGAVLQLRPNDQVWVQMPSDQANGLYSTEYIHSSFSGFLL 702 //