fn3.sto

这是一个基于HMM 模型的生物多序列比对算法的linux实现版本。hmmer

# STOCKHOLM 1.0
#=GF ID    fn3
#=GF AC    PF00041
#=GF DE    Fibronectin type III domain
#=GF AU    Sonnhammer ELL
#=GF GA    7.8 -1.0
#=GF TC    7.7 7.7
#=GF TC    7.9 0.1
#=GF AL    HMM_simulated_annealing
#=GF SE    Swissprot_feature_table
#=GF TP    Domain
#=GF BM    hmmbuild -F HMM_ls SEED
#=GF BM    hmmcalibrate --seed 0 HMM_ls
#=GF BM    hmmbuild -f -F HMM_fs SEED
#=GF BM    hmmcalibrate --seed 0 HMM_fs
#=GF AM    globalfirst
#=GF RN    [1]
#=GF RM    90384924
#=GF RT    Structural design and molecular evolution of a cytokine
#=GF RT    receptor superfamily. 
#=GF RA    Bazan JF; 
#=GF RL    PNAS USA 1990;87:6934-6938.
#=GF RN    [2]
#=GF RM    95106303
#=GF RT    Tracing the spread of fibronectin type III domains in
#=GF RT    bacterial glycohydrolases. 
#=GF RA    Little E, Bork P, Doolittle R; 
#=GF RL    J Mol Evol 1994;39:631-643.
#=GF RC    Definition of fibronectin domains
#=GF RN    [3]
#=GF RM    85284965
#=GF RT    Primary structure of human fibronectin: differential
#=GF RT    splicing may generate at least 10 polypeptides from a
#=GF RT    single gene. 
#=GF RA    Kornblihtt AR, Umezawa K, Vibe-Pedersen K, Baralle FE; 
#=GF RL    EMBO J. 1985;4:1755-1759.
#=GF DR    PROSITE; PDOC00214;
#=GF DR    PRINTS; PR00014;
#=GF DR    SCOP; 1ttf; sf;
#=GF DR    SMART; FN3;
#=GF DR    HOMSTRAD; fn3;
#=GF DC    The following Pfam-B families contain sequences that according to Prodom
#=GF DC    are members of this Pfam-A family.
#=GF DR    PFAMB; PB001437;
#=GF DR    PFAMB; PB004758;
#=GF DR    PFAMB; PB007041;
#=GF DR    PFAMB; PB007646;
#=GF DR    PFAMB; PB012739;
#=GF DR    PFAMB; PB016725;
#=GF DR    PFAMB; PB016744;
#=GF DR    PFAMB; PB018458;
#=GF DR    PFAMB; PB019013;
#=GF DR    PFAMB; PB019702;
#=GF DR    PFAMB; PB020271;
#=GF DR    PFAMB; PB021019;
#=GF DR    PFAMB; PB026405;
#=GF DR    PFAMB; PB029923;
#=GF DR    PFAMB; PB033713;
#=GF DR    PFAMB; PB034308;
#=GF DR    PFAMB; PB047628;
#=GF DR    PFAMB; PB049097;
#=GF DR    PFAMB; PB052872;
#=GF DR    PFAMB; PB063723;
#=GF DR    PFAMB; PB073211;
#=GF DR    PFAMB; PB073567;
#=GF DR    PFAMB; PB073869;
#=GF DR    PFAMB; PB073994;
#=GF DR    PFAMB; PB074195;
#=GF DR    PFAMB; PB074218;
#=GF DR    PFAMB; PB074322;
#=GF DR    PFAMB; PB074352;
#=GF DR    PFAMB; PB074375;
#=GF DR    PFAMB; PB074967;
#=GF DR    PFAMB; PB075286;
#=GF DR    PFAMB; PB075336;
#=GF DR    PFAMB; PB075604;
#=GF DR    PFAMB; PB075661;
#=GF DR    PFAMB; PB075739;
#=GF DR    PFAMB; PB075827;
#=GF DR    PFAMB; PB076019;
#=GF DR    PFAMB; PB076058;
#=GF DR    PFAMB; PB076103;
#=GF DR    PFAMB; PB076165;
#=GF DR    PFAMB; PB076280;
#=GF DR    PFAMB; PB076339;
#=GF DR    INTERPRO; IPR003961;
#=GF DR    PDB; 1qg3 A; 1220; 1310;
#=GF DR    PDB; 1qg3 B; 1220; 1310;
#=GF DR    PDB; 1qg3 A; 1127; 1208;
#=GF DR    PDB; 1qg3 B; 1127; 1208;
#=GF DR    PDB; 1cfb ; 717; 799;
#=GF SQ    108

#=GS EPA1_HUMAN/333-435   AC    P21709
#=GS EPA2_HUMAN/329-420   AC    P29317
#=GS EPA3_CHICK/325-421   AC    P29318
#=GS EPB2_CHICK/326-422   AC    P28693
#=GS NRCA_CHICK/623-709   AC    P35331
#=GS MYPF_CHICK/630-716   AC    P16419
#=GS MPSF_CHICK/801-887   AC    Q02173
#=GS MPSF_CHICK/699-785   AC    Q02173
#=GS MPSF_CHICK/499-585   AC    Q02173
#=GS MPSF_CHICK/371-457   AC    Q02173
#=GS KMLS_CHICK/1318-1403 AC    P11799
#=GS AXO1_CHICK/602-692   AC    P28685
#=GS MPSF_CHICK/600-684   AC    Q02173
#=GS LAR_DROME/322-404    AC    P16621
#=GS MYPF_CHICK/923-1008  AC    P16419
#=GS TIE1_HUMAN/644-729   AC    P35590
#=GS NCA1_BOVIN/509-597   AC    P31836
#=GS EPA4_MOUSE/441-525   AC    Q03137
#=GS EPB2_CHICK/437-521   AC    P28693
#=GS NRCA_CHICK/928-1014  AC    P35331
#=GS LAR_DROME/909-995    AC    P16621
#=GS ITB4_HUMAN/1641-1728 AC    P16144
#=GS ITB4_HUMAN/1528-1612 AC    P16144
#=GS ITB4_HUMAN/1220-1310 AC    P16144
#=GS PTP9_DROME/171-259   AC    P35832
#=GS LAR_DROME/709-800    AC    P16621
#=GS LAR_DROME/417-503    AC    P16621
#=GS EPA2_HUMAN/436-519   AC    P29317
#=GS ITB4_HUMAN/1127-1208 AC    P16144
#=GS CONT_CHICK/799-884   AC    P14781
#=GS AXO1_CHICK/807-896   AC    P28685
#=GS CAML_HUMAN/812-907   AC    P32004
#=GS PTP1_DROME/958-1044  AC    P35992
#=GS NRG_DROME/917-1007   AC    P20241
#=GS TENA_CHICK/1494-1571 AC    P10039
#=GS TENA_CHICK/956-1033  AC    P10039
#=GS TENA_CHICK/1406-1483 AC    P10039
#=GS TENA_CHICK/774-853   AC    P10039
#=GS TENA_CHICK/1317-1395 AC    P10039
#=GS FINC_BOVIN/1327-1406 AC    P07589
#=GS FINC_RAT/1266-1346   AC    P04937
#=GS TENA_CHICK/864-945   AC    P10039
#=GS FINC_BOVIN/780-858   AC    P07589
#=GS FINC_BOVIN/1782-1861 AC    P07589
#=GS FINC_BOVIN/1417-1499 AC    P07589
#=GS FINC_BOVIN/1601-1680 AC    P07589
#=GS FINC_BOVIN/1511-1590 AC    P07589
#=GS FINC_BOVIN/875-955   AC    P07589
#=GS TENA_CHICK/593-671   AC    P10039
#=GS FINC_BOVIN/1693-1771 AC    P07589
#=GS FINC_BOVIN/1142-1225 AC    P07589
#=GS PTP1_DROME/405-485   AC    P35992
#=GS FINC_BOVIN/1236-1316 AC    P07589
#=GS PHB_ALCFA/344-418    AC    P12625
#=GS CHIX_STROI/169-240   AC    Q05638
#=GS CHIT_STRLI/142-219   AC    P36909
#=GS GUNB_CELFI/651-733   AC    P26225
#=GS CHI1_BACCI/465-542   AC    P20533
#=GS APU_THETY/1165-1248  AC    P16950
#=GS APU_THETY/928-1009   AC    P16950
#=GS FINC_BOVIN/577-660   AC    P07589
#=GS NRG_DROME/815-905    AC    P20241
#=GS PTP6_DROME/332-425   AC    P16620
#=GS FAS2_SCHAM/530-616   AC    P22648
#=GS PTPZ_HUMAN/312-401   AC    P23471
#=GS NCA1_BOVIN/610-691   AC    P31836
#=GS FAS2_SCHAM/642-735   AC    P22648
#=GS TIE2_HUMAN/543-626   AC    Q02763
#=GS TENA_CHICK/682-767   AC    P10039
#=GS UFO_HUMAN/327-411    AC    P30530
#=GS TIE1_HUMAN/545-632   AC    P35590
#=GS 7LES_DROME/1799-1891 AC    P13368
#=GS NRG_DROME/717-799    AC    P20241
#=GS NRCA_CHICK/726-810   AC    P35331
#=GS NGCA_CHICK/700-794   AC    Q03696
#=GS TIE2_HUMAN/639-724   AC    Q02763
#=GS LAR_DROME/515-598    AC    P16621
#=GS PTP6_DROME/236-321   AC    P16620
#=GS TIE2_HUMAN/444-529   AC    Q02763
#=GS TIE1_HUMAN/446-533   AC    P35590
#=GS PTPK_MOUSE/290-376   AC    P35822
#=GS PTPB_HUMAN/1355-1434 AC    P23467
#=GS PTP1_DROME/583-661   AC    P35992
#=GS PTP1_DROME/312-394   AC    P35992
#=GS PTP1_DROME/217-301   AC    P35992
#=GS PTP1_DROME/123-205   AC    P35992
#=GS PTPB_HUMAN/1261-1344 AC    P23467
#=GS PTP1_DROME/864-944   AC    P35992
#=GS PTPB_HUMAN/1173-1250 AC    P23467
#=GS PTPB_HUMAN/1085-1162 AC    P23467
#=GS PTPB_HUMAN/467-543   AC    P23467
#=GS PTPB_HUMAN/995-1074  AC    P23467
#=GS PTPB_HUMAN/731-808   AC    P23467
#=GS PTPB_HUMAN/643-725   AC    P23467
#=GS PTPB_HUMAN/554-632   AC    P23467