stockholm.2

hmmer源程序

# STOCKHOLM 1.0
#=GF ID   14-3-3
#=GF AC   PF00244
#=GF DE   14-3-3 proteins
#=GF AU   Finn RD
#=GF AL   Clustalw
#=GF SE   Prosite
#=GF GA   25 25
#=GF TC   35.40 35.40
#=GF NC   8.80 8.80
#=GF BM   hmmbuild -f HMM SEED
#=GF BM   hmmcalibrate --seed 0 HMM
#=GF RN   [1]
#=GF RM   95327195
#=GF RT   Structure of a 14-3-3 protein and implications for
#=GF RT   coordination of multiple signalling pathways. 
#=GF RA   Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken A,
#=GF RA   Gamblin SJ; 
#=GF RL   Nature 1995;376:188-191.
#=GF RN   [2]
#=GF RM   95327196
#=GF RT   Crystal structure of the zeta isoform of the 14-3-3 protein. 
#=GF RA   Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington
#=GF RA   R; 
#=GF RL   Nature 1995;376:191-194.
#=GF RN   [3]
#=GF RM   96182649
#=GF RT   Interaction of 14-3-3 with signaling proteins is mediated by
#=GF RT   the recognition of phosphoserine. 
#=GF RA   Muslin AJ, Tanner JW, Allen PM, Shaw AS; 
#=GF RL   Cell 1996;84:889-897.
#=GF RN   [4]
#=GF RM   97424374
#=GF RT   The 14-3-3 protein binds its target proteins with a common
#=GF RT   site located towards the C-terminus. 
#=GF RA   Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, Omata
#=GF RA   S, Ohno S, Isobe T 
#=GF RL   FEBS Lett 1997;413:273-276.
#=GF RN   [5]
#=GF RM   96394689
#=GF RT   Molecular evolution of the 14-3-3 protein family. 
#=GF RA   Wang W, Shakes DC 
#=GF RL   J Mol Evol 1996;43:384-398.
#=GF RN   [6]
#=GF RM   96300316
#=GF RT   Function of 14-3-3 proteins. 
#=GF RA   Jin DY, Lyu MS, Kozak CA, Jeang KT 
#=GF RL   Nature 1996;382:308-308.
#=GF DR   PROSITE; PDOC00633;
#=GF DR   SMART; 14_3_3;
#=GF DR   PRINTS; PR00305;
#=GF SQ   16
1431_ENTHI/4-239    REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDDVLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQAFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
#=GS 1431_ENTHI/4-239   AC P42648
1432_ENTHI/4-238    REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDDVLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADKSLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKEAFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
#=GS 1432_ENTHI/4-238   AC P42649
1433_CAEEL/5-237    VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQDVLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
#=GS 1433_CAEEL/5-237   AC P41932
1433_LYCES/9-246    REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDGILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
#=GS 1433_LYCES/9-246   AC P93209
1433_XENLA/1-227    .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKDVLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKSAFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
#=GS 1433_XENLA/1-227   AC P29309
1434_LYCES/6-243    REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDGILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQAFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
#=GS 1434_LYCES/6-243   AC P42652
143B_VICFA/7-242    RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICIDVMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQAFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
#=GS 143B_VICFA/7-242   AC P42654
143E_HUMAN/4-239    REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCDILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
#=GS 143E_HUMAN/4-239   AC P42655
143F_MOUSE/3-240    REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCNDVLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
#=GS 143F_MOUSE/3-240   AC P11576
143R_ARATH/7-245    RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSGILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQAFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD
#=GS 143R_ARATH/7-245   AC P42647
143S_HUMAN/3-238    RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDTVLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKTTFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE
#=GS 143S_HUMAN/3-238   AC P31947
143T_HUMAN/3-236    KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
#=GS 143T_HUMAN/3-236   AC P27348
143Z_DROME/6-239    KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
#=GS 143Z_DROME/6-239   AC P29310
BMH1_YEAST/4-240    REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDDILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
#=GS BMH1_YEAST/4-240   AC P29311
RA24_SCHPO/6-241    REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQDILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQAFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
#=GS RA24_SCHPO/6-241   AC P42656
RA25_SCHPO/5-240    RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHDVLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQVFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
#=GS RA25_SCHPO/5-240   AC P42657
//
# STOCKHOLM 1.0
#=GF ID    rrm
#=GF AC    PF00076
#=GF DE    RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
#=GF GA    14.6 0.0
#=GF TC    14.5 14.5
#=GF TC    14.6 0.1

ARP2_PLAFA/364-438  VEVTYLF....STYLVNGQTL..IYS.....N.ISVV....LVILY....
CABA_MOUSE/77-147   MFVGGL......SWDTSKKDLKDYFT.....K.FGEV..VDCTIKMD...
GR10_BRANA/8-79     CFVGGL......AWATGDAELERTFS.....Q.FGEV..IDSKIIND...
NSR1_YEAST/170-241  IFVGRL......SWSIDDEWLKKEFE.....H.IGGV..IGARVIYE...
RT19_ARATH/33-104   LYIGGL......SPGTDEHSLKDAFS.....S.FNGV..TEARVMTN...
RO28_NICSY/99-170   LFVGNL......PYDIDSEGLAQLFQ.....Q.AGVV..EIAEVIYN...
RO33_NICSY/116-187  LYVGNL......PFSMTSSQLSEIFA.....E.AGTV..ANVEIVYD...
RO33_NICSY/219-290  LYVANL......SWALTSQGLRDAFA.....D.QPGF..MSAKVIYD...
GBP2_YEAST/221-291  VFIINL......PYSMNWQSLKDMFK.....E.CGHV..LRADVELD...
HUD_HUMAN/48-119    LIVNYL......PQNMTQEEFRSLFG.....S.IGEI..ESCKLVRD...
SXLF_DROME/127-198  LIVNYL......PQDMTDRELYALFR.....A.IGPI..NTCRIMRD...
PABP_DROME/4-75     LYVGDL......PQDVNESGLFDKFS.....S.AGPV..LSIRVCRD...
NAM8_YEAST/165-237  IFVGDL......APNVTESQLFELFI.....NRYAST..SHAKIVHD...
PUB1_YEAST/163-234  LFVGDL......NVNVDDETLRNAFK.....D.FPSY..LSGHVMWD...
TIA1_HUMAN/108-179  VFVGDL......SPQITTEDIKAAFA.....P.FGRI..SDARVVKD...
PES4_YEAST/93-164   LFIGDL......HETVTEETLKGIFK.....K.YPSF..VSAKVCLD...
NOP4_YEAST/28-98    LFVRSI......PQDVTDEQLADFFS.....N.FAPI..KHAVVVKD...
CST2_HUMAN/18-89    VFVGNI......PYEATEEQLKDIFS.....E.VGPV..VSFRLVYD...
RN15_YEAST/20-91    VYLGSI......PYDQTEEQILDLCS.....N.VGPV..INLKMMFD...
YIS1_YEAST/66-136   IFVGNI......TPDVTPEQIEDHFK.....D.CGQI..KRITLLYD...
IF4B_HUMAN/98-168   AFLGNL......PYDVTEESIKEFFR.....G.LNIS...AVRLPR....
NSR1_YEAST/269-340  LFLGNL......SFNADRDAIFELFA.....K.HGEV..VSVRIPTH...
GBP2_YEAST/124-193  IFVRNL......TFDCTPEDLKELFG.....T.VGEV..VEADIIT....
NOP3_YEAST/127-190  LFVRPF......PLDVQESELNEIFG.....P.FGPM..KEVKILN....
U2AF_HUMAN/261-332  LFIGGL......PNYLNDDQVKELLT.....S.FGPL..KAFNLVKD...
U2AF_SCHPO/312-383  IYISNL......PLNLGEDQVVELLK.....P.FGDL..LSFQLIKN...
ELAV_DROME/250-322  LYVSGL......PKTMTQQELEAIFA.....P.FGAI..ITSRILQN...
SXLF_DROME/213-285  LYVTNL......PRTITDDQLDTIFG.....K.YGSI..VQKNILRD...
ELAV_DROME/404-475  IFIYNL......APETEEAALWQLFG.....P.FGAV..QSVKIVKD...
MSSP_HUMAN/31-102   LYIRGL......PPHTTDQDLVKLCQ.....P.YGKI..VSTKAILD...
NONA_DROME/304-369  LYVGNL......TNDITDDELREMFK.....P.YGEI..SEIFSNLD...
PABP_DROME/92-162   VFIKNL......DRAIDNKAIYDTFS.....A.FGNI..LSCKVATD...
PABP_DROME/183-254  VYVKNF......TEDFDDEKLKEFFE.....P.YGKI..TSYKVMS....
PABP_SCHPO/263-333  VYIKNL......DTEITEQEFSDLFG.....Q.FGEI..TSLSLVKD...
PUB1_YEAST/342-407  AYIGNI......PHFATEADLIPLFQ.....N.FGFI..LDFKHYPE...
PUB1_YEAST/76-146   LYVGNL......DKAITEDILKQYFQ.....V.GGPI..ANIKIMID...
TIA1_HUMAN/9-78     LYVGNL......SRDVTEALILQLFS.....Q.IGPC..KNCKMIMD...
TIA1_HUMAN/216-281  VYCGGV......TSGLTEQLMRQTFS.....P.FGQI..MEIRVFPD...
EWS_HUMAN/363-442   IYVQGL......NDSVTLDDLADFFK.....Q.CGVV..K.MNKRTG...
PTB_HUMAN/186-253   IIVENL......FYPVTLDVLHQIFS.....K.FGTV....LKIIT....
ROC_HUMAN/18-82     VFIGNL.....NTLVVKKSDVEAIFS.....K.YGKI..VGCSVHK....
YIS5_YEAST/33-104   IYIGNL......NRELTEGDILTVFS.....E.YGVP..VDVILSRD...
RU1A_HUMAN/12-84    IYINNLNE..KIKKDELKKSLYAIFS.....Q.FGQI..LDILVSR....
RU2B_HUMAN/9-81     IYINNMND..KIKKEELKRSLYALFS.....Q.FGHV..VDIVALK....
CABA_MOUSE/161-231  IFVGGL......NPEATEEKIREYFG.....Q.FGEI..EAIELPID...
ROA1_BOVIN/106-176  IFVGGI......KEDTEEHHLRDYFE.....Q.YGKI..EVIEIMTD...
SQD_DROME/138-208   IFVGGL......TTEISDEEIKTYFG.....Q.FGNI..VEVEMPLD...
RB97_DROME/34-104   LFIGGL......APYTTEENLKLFYG.....Q.WGKV..VDVVVMRD...
SQD_DROME/58-128    LFVGGL......SWETTEKELRDHFG.....K.YGEI..ESINVKTD...
ROG_HUMAN/10-81     LFIGGL......NTETNEKALEAVFG.....K.YGRI..VEVLLMKD...
SFR2_CHICK/16-87    LKVDNL......TYRTSPDTLRRVFE.....K.YGRV..GDVYIPRD...
SFR1_HUMAN/17-85    IYVGNL......PPDIRTKDIEDVFY.....K.YGAI..RDIDLKNR...
SR55_DROME/5-68     VYVGGL......PYGVRERDLERFFK.....G.YGRT..RDILIKN....
SFR3_HUMAN/12-78    VYVGNL......GNNGNKTELERAFG.....Y.YGPL..RSVWVARN...
TRA2_DROME/99-170   IGVFGL......NTNTSQHKVRELFN.....K.YGPI..ERIQMVID...
RU17_DROME/104-175  LFIARI......NYDTSESKLRREFE.....F.YGPI..KKIVLIHD...
GBP2_YEAST/351-421  IYCSNL......PFSTARSDLFDLFG.....P.IGKI..NNAELKP....
RNP1_YEAST/37-109   LYVGNL......PKNCRKQDLRDLFE.....PNYGKI..TINMLKKK...
PES4_YEAST/305-374  IFIKNL......PTITTRDDILNFFS.....E.VGPI..KSIYLSN....
YHH5_YEAST/315-384  ILVKNL......PSDTTQEEVLDYFS.....T.IGPI..KSVFISEK...
YHC4_YEAST/348-415  IFVGQL......DKETTREELNRRFS.....T.HGKI..QDINLIFK...
IF39_YEAST/79-157   IVVNGAPVIPSAKVPVLKKALTSLFS.....K.AGKV..VNMEFPID...
MEI2_SCHPO/197-265  LFVTNL......PRIVPYATLLELFS.....K.LGDV..KGIDTSSL...
NOP4_YEAST/292-363  VFVRNV......PYDATEESLAPHFS.....K.FGSV..KYALPVID...
MODU_DROME/260-326  VVVGLI......GPNITKDDLKTFFE.....K.VAPV..EAVTISSN...
ROF_HUMAN/113-183   VRLRGL......PFGCTKEEIVQFFS.....G.LEIV.PNGITLPVD...
MODU_DROME/342-410  LVVENVG....KHESYSSDALEKIFK.....K.FGDV..EEIDVVC....
NUCL_CHICK/283-352  LFVKNL......TPTKDYEELRTAIK.....EFFGKK...NLQVSEV...
NONA_DROME/378-448  LRVSNL......TPFVSNELLYKSFE.....I.FGPI..ERASITVD...
PSF_HUMAN/373-443   LSVRNL......SPYVSNELLEEAFS.....Q.FGPI..ERAVVIVD...
NOP3_YEAST/202-270  ITMKNL......PEGCSWQDLKDLAR.....E.NSLE..TTFSSVN....
SFR1_HUMAN/122-186  VVVSGL......PPSGSWQDLKDHMR.....E.AGDV..CYADVYRD...
CPO_DROME/453-526   LFVSGL......PMDAKPRELYLLFR.....A.YEGY..EGSLLKV....
WHI3_YEAST/540-614  LYVGNL......PSDATEQELRQLFS.....G.QEGF..RRLSFRNK...
RU1A_HUMAN/210-276  LFLTNL......PEETNELMLSMLFN.....Q.FPGF..KEVRLVPG...
RU2B_HUMAN/153-220  LFLNNL......PEETNEMMLSMLFN.....Q.FPGF..KEVRLVPG...
RU1A_YEAST/229-293  LLIQNL......PSGTTEQLLSQILG.....N.EALV...EIRLVSV...
MODU_DROME/177-246  VFVTNL......PNEYLHKDLVALFA.....K.FGRL..SALQRFTN...
PR24_YEAST/43-111   VLVKNL......PKSYNQNKVYKYFK.....H.CGPI..IHVDVAD....
MODU_DROME/422-484  ILVTNL......TSDATEADLRKVFN.....D.SGEI..ESIIMLG....
PR24_YEAST/212-284  IMIRNL.....STELLDENLLRESFE.....G.FGSI..EKINIPAG...
SSB1_YEAST/39-114   IFIGNV......AHECTEDDLKQLFV.....EEFGDE..VSVEIPIK...
PTB_HUMAN/61-128    IHIRKL......PIDVTEGEVISLGL.....P.FGKV..TNLLMLKG...
RN12_YEAST/200-267  IVIKFQ......GPALTEEEIYSLFR.....R.YGTI....IDIFP....
D111_ARATH/281-360  LLLRNMVG.PGQVDDELEDEVGGECA.....K.YGTV..TRVLIFE....
U2AG_HUMAN/67-142   CAVSDVEM..QEHYDEFFEEVFTEME.....EKYGEV..EEMNVCDN...
IF39_SCHPO/41-124   VVIEGAP....VVEEAKQQDFFRFLSSKVLAK.IGKVKENGFYMPFE...
LA_DROME/151-225    AYAKGF......PLDSQISELLDFTA.....N.YDKV..VNLTMRNS...
LA_HUMAN/113-182    VYIKGF......PTDATLDDIKEWLE.....D.KGQV..LNIQMRR....
PR24_YEAST/119-190  LWMTNF......PPSYTQRNIRDLLQ.....D.INVV.ALSIRLPSL...