pkinase.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    pkinase
#=GF AC    PF00069
#=GF DE    Protein kinase domain
#=GF AU    Sonnhammer ELL
#=GF GA    -57.9 -57.9
#=GF TC    -58.0 -58.0
#=GF TC    -57.7 -57.7
#=GF AL    Clustalw
#=GF SE    Unknown
#=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    byscore
#=GF RN    [1]
#=GF RM    92065863
#=GF RT    Protein kinase catalytic domain sequence database:
#=GF RT    identification of conserved features of primary structure
#=GF RT    and classification of family members. 
#=GF RA    Hanks SK, Quinn AM; 
#=GF RL    Methods Enzymol 1991;200:38-62.
#=GF RN    [2]
#=GF RM    95285959
#=GF RT    Protein kinases 6. The eukaryotic protein kinase
#=GF RT    superfamily: kinase (catalytic) domain structure and
#=GF RT    classification. 
#=GF RA    Hanks SK, Hunter T; 
#=GF RL    FASEB J 1995;9:576-596.
#=GF RN    [3]
#=GF RM    97172697
#=GF RT    The protein kinases of budding yeast: six score and more. 
#=GF RA    Hunter T, Plowman GD; 
#=GF RL    Trends Biochem Sci 1997;22:18-22.
#=GF DR    PROSITE; PDOC00100;
#=GF DR    PROSITE; PDOC00212;
#=GF DR    PROSITE; PDOC00213;
#=GF DR    PROSITE; PDOC00629;
#=GF DR    PROSITE_PROFILE; PS50011;
#=GF DR    PRINTS; PR00109;
#=GF DC    Protein kinase; unclassified specificity.
#=GF DR    SMART; STYKc;
#=GF DC    Serine/Threonine protein kinases, catalytic domain
#=GF DR    SMART; S_TKc;
#=GF DC    Tyrosine kinase, catalytic domain
#=GF DR    SMART; TyrKc;
#=GF DR    SCOP; 1apm; sf;
#=GF DR    URL; http://www.sdsc.edu/Kinases/pk_home.html;
#=GF DR    HOMSTRAD; kinase;
#=GF DR    HOMSTRAD; TyrKc;
#=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; PB000086;
#=GF DR    PFAMB; PB000335;
#=GF DR    PFAMB; PB000344;
#=GF DR    PFAMB; PB000408;
#=GF DR    PFAMB; PB000443;
#=GF DR    PFAMB; PB000580;
#=GF DR    PFAMB; PB000648;
#=GF DR    PFAMB; PB001166;
#=GF DR    PFAMB; PB001282;
#=GF DR    PFAMB; PB001675;
#=GF DR    PFAMB; PB002083;
#=GF DR    PFAMB; PB003052;
#=GF DR    PFAMB; PB003187;
#=GF DR    PFAMB; PB004571;
#=GF DR    PFAMB; PB006268;
#=GF DR    PFAMB; PB006391;
#=GF DR    PFAMB; PB008253;
#=GF DR    PFAMB; PB010424;
#=GF DR    PFAMB; PB012301;
#=GF DR    PFAMB; PB012575;
#=GF DR    PFAMB; PB020547;
#=GF DR    PFAMB; PB021560;
#=GF DR    PFAMB; PB023760;
#=GF DR    PFAMB; PB024533;
#=GF DR    PFAMB; PB027255;
#=GF DR    PFAMB; PB031172;
#=GF DR    PFAMB; PB031216;
#=GF DR    PFAMB; PB033452;
#=GF DR    PFAMB; PB036938;
#=GF DR    PFAMB; PB037024;
#=GF DR    PFAMB; PB038323;
#=GF DR    PFAMB; PB038346;
#=GF DR    PFAMB; PB039314;
#=GF DR    PFAMB; PB041100;
#=GF DR    PFAMB; PB046211;
#=GF DR    PFAMB; PB048611;
#=GF DR    PFAMB; PB049203;
#=GF DR    PFAMB; PB054829;
#=GF DR    PFAMB; PB058545;
#=GF DR    PFAMB; PB058834;
#=GF DR    PFAMB; PB060285;
#=GF DR    PFAMB; PB062899;
#=GF DR    PFAMB; PB064409;
#=GF DR    PFAMB; PB066246;
#=GF DR    PFAMB; PB069361;
#=GF DR    PFAMB; PB070955;
#=GF DR    PFAMB; PB071888;
#=GF DR    PFAMB; PB073183;
#=GF DR    PFAMB; PB073185;
#=GF DR    PFAMB; PB073255;
#=GF DR    PFAMB; PB073537;
#=GF DR    PFAMB; PB073697;
#=GF DR    PFAMB; PB073751;
#=GF DR    PFAMB; PB073810;
#=GF DR    PFAMB; PB073837;
#=GF DR    PFAMB; PB074054;
#=GF DR    PFAMB; PB074563;
#=GF DR    PFAMB; PB074567;
#=GF DR    PFAMB; PB074578;
#=GF DR    PFAMB; PB074582;
#=GF DR    PFAMB; PB074695;
#=GF DR    PFAMB; PB074703;
#=GF DR    PFAMB; PB074794;
#=GF DR    PFAMB; PB074799;
#=GF DR    PFAMB; PB074881;
#=GF DR    PFAMB; PB074921;
#=GF DR    PFAMB; PB075005;
#=GF DR    PFAMB; PB075039;
#=GF DR    PFAMB; PB075148;
#=GF DR    PFAMB; PB075235;
#=GF DR    PFAMB; PB075282;
#=GF DR    PFAMB; PB075298;
#=GF DR    PFAMB; PB075333;
#=GF DR    PFAMB; PB075789;
#=GF DR    PFAMB; PB075804;
#=GF DR    PFAMB; PB075824;
#=GF DR    PFAMB; PB075828;
#=GF DR    PFAMB; PB076125;
#=GF DR    PFAMB; PB076133;
#=GF DR    PFAMB; PB076265;
#=GF DR    PFAMB; PB076308;
#=GF DR    INTERPRO; IPR000719;
#=GF SQ    67

#=GS WEE1_HUMAN/299-569   AC    P30291
#=GS TTK_HUMAN/509-775    AC    P33981
#=GS STE7_YEAST/191-466   AC    P06784
#=GS MKK1_YEAST/221-488   AC    P32490
#=GS BYR1_SCHPO/66-320    AC    P10506
#=GS ST20_YEAST/620-871   AC    Q03497
#=GS CC15_YEAST/25-272    AC    P27636
#=GS BYR2_SCHPO/394-658   AC    P28829
#=GS NINC_DROME/16-282    AC    P10676
#=GS SPK1_YEAST/198-466   AC    P22216
#=GS KIN1_SCHPO/125-395   AC    P22987
#=GS CDR1_SCHPO/12-258    AC    P07334
#=GS K6A1_MOUSE/407-664   AC    P18653
#=GS KPBH_RAT/24-291      AC    P31325
#=GS KCC4_MOUSE/42-296    AC    P08414
#=GS CDPK_SOYBN/34-292    AC    P28583
#=GS KPK2_PLAFK/111-364   AC    Q02595
#=GS KMLS_CHICK/1453-1708 AC    P11799
#=GS MEK1_YEAST/162-444   AC    P24719
#=GS CHK1_SCHPO/10-272    AC    P34208
#=GS CC5_YEAST/82-337     AC    P32562
#=GS PKD1_DICDI/36-291    AC    P34100
#=GS KI82_YEAST/324-602   AC    P25341
#=GS KAKT_MLVAT/171-429   AC    P31748
#=GS KGP1_DROME/457-717   AC    Q03042
#=GS ARK1_BOVIN/191-453   AC    P21146
#=GS FUSE_DROME/4-254     AC    P23647
#=GS PIM1_HUMAN/38-290    AC    P11309
#=GS KAB7_YEAST/1096-1354 AC    P31374
#=GS SGV1_YEAST/60-366    AC    P23293
#=GS CC21_MEDSA/1-284     AC    P24923
#=GS KI28_YEAST/7-290     AC    P06242
#=GS MAK_RAT/4-284        AC    P20793
#=GS KKIA_HUMAN/5-288     AC    Q00532
#=GS CTK1_YEAST/183-469   AC    Q03957
#=GS KG3A_RAT/119-403     AC    P18265
#=GS MK04_HUMAN/20-312    AC    P31152
#=GS ERK1_CANAL/68-371    AC    P28869
#=GS KC21_CHICK/39-324    AC    P21868
#=GS CLK1_MOUSE/160-476   AC    P22518
#=GS NPR1_YEAST/438-742   AC    P22211
#=GS SAT4_YEAST/316-590   AC    P25333
#=GS KKL6_YEAST/192-508   AC    P28708
#=GS RAN1_SCHPO/18-295    AC    P08092
#=GS TRKA_HUMAN/510-781   AC    P04629
#=GS KSYK_PIG/364-619     AC    Q00655
#=GS BFR2_HUMAN/367-643   AC    Q01742
#=GS ABL1_CAEEL/311-562   AC    P03949