forester/archive/RIO/others/hmmer/tutorial/rrm.slx

   1 #=ID rrm
   2 #=AC PF00076
   3 #=DE RNA recognition motif. (aka RRM, RBD, or RNP domain)
   4 # AU   Sean Eddy
   5 # GA   HMM_iterative_training
   6 # GA   Bic_raw 25 hmmls 10
   7 # CC   There is no separation between signal and noise.
   8 # AL   HMM_simulated_annealing
   9 # AM   hmma -qR
  10 # SE   Published_alignment
  11 # RN   [1]
  12 # RM   94119674
  13 # RA   Birney E., Kumar S., Krainer A.R.
  14 # RL   NAR 21:5803-5816(1993).
  15 # DR   PROSITE; PDOC00030;
  16 # DR   SCOP; 1SXL; sf;
  17 # CC   -!- The RRM motif is probably diagnostic of an RNA binding protein.
  18 # CC   -!- RRMs are found in a variety of RNA binding proteins, including
  19 # CC       various hnRNP proteins, proteins implicated in regulation
  20 # CC       of alternative splicing, and protein components
  21 # CC       of snRNPs. The motif also appears in a few single stranded
  22 # CC       DNA binding proteins.
  23 # CC   -!- The RRM structure consists of four strands
  24 # CC        and two helices arranged in an alpha/beta sandwich.
  25 # SQ   70
  26 CABA_MOUSE/77-148  MFVGGL.SWDTSKKDLKD....YFTKFGEVVDCTIKMD.........PNT
  27 CABA_MOUSE/161-232 IFVGGL.NPEATEEKIRE....YFGQFGEIEAIELPID.........PKL
  28 CST2_HUMAN/18-89   VFVGNI.PYEATEEQLKD....IFSEVGPVVSFRLVYD.........RET
  29 ELAV_DROME/250-322 LYVSGL.PKTMTQQELEA....IFAPFGAIITSRILQNa........GND
  30 ELAV_DROME/404-475 IFIYNL.APETEEAALWQ....LFGPFGAVQSVKIVKD.........PTT
  31 EWS_HUMAN/363-442  IYVQGL.NDSVTLDDLAD....FFKQCGVVKMNKRTGQpmih.iyldKET
  32 GBP2_YEAST/124-193 IFVRNL.TFDCTPEDLKE....LFGTVGEVVEADIIT...........SK
  33 GBP2_YEAST/221-291 VFIINL.PYSMNWQSLKD....MFKECGHVLRADVELD..........FN
  34 GBP2_YEAST/351-421 IYCSNL.PFSTARSDLFD....LFGPIGKINNAELKPQ..........EN
  35 GR10_BRANA/8-79    CFVGGL.AWATGDAELER....TFSQFGEVIDSKIIND.........RET
  36 HUD_HUMAN/48-119   LIVNYL.PQNMTQEEFRS....LFGSIGEIESCKLVRD.........KIT
  37 IF4B_HUMAN/98-169  AFLGNL.PYDVTEESIKE....FFRGLNISAVRLPREP.........SNP
  38 MSSP_HUMAN/31-102  LYIRGL.PPHTTDQDLVK....LCQPYGKIVSTKAILD.........KTT
  39 NAM8_YEAST/165-237 IFVGDL.APNVTESQLFE....LFiNRYASTSHAKIVHD........QVT
  40 NOP3_YEAST/127-190 LFVRPF.PLDVQESELNE....IFGPFGPMKEVKILN.............
  41 NOP3_YEAST/202-270 ITMKNL.PEGCSWQDLKD....LARENSLETTFSSVN............T
  42 NOP4_YEAST/28-98   LFVRSI.PQDVTDEQLAD....FFSNFAPIKHAVVVKD..........TN
  43 NOP4_YEAST/292-367 VFVRNV.PYDATEESLAP....HFSKFGSVKYALPVID.........KST
  44 NSR1_YEAST/170-241 IFVGRL.SWSIDDEWLKK....EFEHIGGVIGARVIYE.........RGT
  45 NSR1_YEAST/269-340 LFLGNL.SFNADRDAIFE....LFAKHGEVVSVRIPTH.........PET
  46 NUCL_CHICK/283-353 LFVKNL.TPTKDYEELRT....AIKEFFGKKNLQVSEV..........RI
  47 NUCL_CHICK/373-440 LFVKNL.PYRVTEDEMKN....VFENALEVRLVLNKE.............
  48 PABP_DROME/4-75    LYVGDL.PQDVNESGLFD....KFSSAGPVLSIRVCRD.........VIT
  49 PABP_DROME/92-162  VFIKNL.DRAIDNKAIYD....TFSAFGNILSCKVATD..........EK
  50 PABP_DROME/183-254 VYVKNF.TEDFDDEKLKE....FFEPYGKITSYKVMSK..........ED
  51 PABP_SCHPO/249-319 VYIKNL.DTEITEQEFSD....LFGQFGEITSLSLVKD..........QN
  52 PES4_YEAST/93-164  LFIGDL.HETVTEETLKG....IFKKYPSFVSAKVCLD.........SVT
  53 PES4_YEAST/305-374 IFIKNL.PTITTRDDILN....FFSEVGPIKSIYLSN...........AT
  54 PSF_HUMAN/373-443  LSVRNL.SPYVSNELLEE....AFSQFGPIERAVVIVD..........DR
  55 PUB1_YEAST/76-146  LYVGNL.DKAITEDILKQ....YFQVGGPIANIKIMID..........KN
  56 PUB1_YEAST/163-234 LFVGDL.NVNVDDETLRN....AFKDFPSYLSGHVMWD.........MQT
  57 PUB1_YEAST/342-407 AYIGNI.PHFATEADLIP....LFQNFGFILDFKHYPE............
  58 RB97_DROME/34-105  LFIGGL.APYTTEENLKL....FYGQWGKVVDVVVMRD.........AAT
  59 RN15_YEAST/20-91   VYLGSI.PYDQTEEQILD....LCSNVGPVINLKMMFD.........PQT
  60 RNP1_YEAST/37-109  LYVGNL.PKNCRKQDLRD....LFEPNYGKITINMLKKk........PLK
  61 RO28_NICSY/99-170  LFVGNL.PYDIDSEGLAQ....LFQQAGVVEIAEVIYN.........RET
  62 RO33_NICSY/116-187 LYVGNL.PFSMTSSQLSE....IFAEAGTVANVEIVYD.........RVT
  63 RO33_NICSY/219-290 LYVANL.SWALTSQGLRD....AFADQPGFMSAKVIYD.........RSS
  64 ROA1_BOVIN/106-177 IFVGGI.KEDTEEHHLRD....YFEQYGKIEVIEIMTD.........RGS
  65 ROC_HUMAN/18-82    VFIGNLnTLVVKKSDVEA....IFSKYGKIVGCSVHK.............
  66 ROG_HUMAN/10-81    LFIGGL.NTETNEKALEA....VFGKYGRIVEVLLMKD.........RET
  67 RT19_ARATH/33-104  LYIGGL.SPGTDEHSLKD....AFSSFNGVTEARVMTN.........KVT
  68 RU17_DROME/104-175 LFIARI.NYDTSESKLRR....EFEFYGPIKKIVLIHD.........QES
  69 RU1A_HUMAN/12-84   IYINNL.NEKIKKDELKkslyAIFSQFGQILDILVSRS............
  70 RU1A_HUMAN/210-276 LFLTNL.PEETNELMLSM....LFNQFPGFKEVRLVPG............
  71 RU1A_YEAST/229-293 LLIQNL.PSGTTEQLLSQ....ILGNEALVEIRLVSV.............
  72 RU2B_HUMAN/9-81    IYINNM.NDKIKKEELKRslyaLFSQFGHVVDIVALK............T
  73 RU2B_HUMAN/153-220 LFLNNL.PEETNEMMLSM....LFNQFPGFKEVRLVPG............
  74 SC35_CHICK/16-87   LKVDNL.TYRTSPDTLRR....VFEKYGRVGDVYIPRD.........RYT
  75 SP33_HUMAN/17-85   IYVGNL.PPDIRTKDIED....VFYKYGAIRDIDLKNR............
  76 SP33_HUMAN/122-186 VVVSGL.PPSGSWQDLKD....HMREAGDVCYADVYRD............
  77 SQD_DROME/58-128   LFVGGL.SWETTEKELRD....HFGKYGEIESINVKTD.........PQT
  78 SQD_DROME/138-208  IFVGGL.TTEISDEEIKT....YFGQFGNIVEVEMPLD.........KQK
  79 SR55_DROME/5-68    VYVGGL.PYGVRERDLER....FFKGYGRTRDILIKN.............
  80 SSB1_YEAST/39-114  IFIGNV.AHECTEDDLKQ....LFvEEFGDEVSVEIPIKeh.....tDGH
  81 SSB1_YEAST/188-268 LYINNV.PFKATKEEVAE....FFGTDADSISLPMRKMrdqhtgrifTSD
  82 SXLF_DROME/127-198 LIVNYL.PQDMTDRELYA....LFRAIGPINTCRIMRD.........YKT
  83 SXLF_DROME/213-285 LYVTNL.PRTITDDQLDT....IFGKYGSIVQKNILRD.........KLT
  84 TIA1_HUMAN/9-78    LYVGNL.SRDVTEALILQ....LFSQIGPCKNCKMIMD...........T
  85 TIA1_HUMAN/97-168  VFVGDL.SPQITTEDIKA....AFAPFGRISDARVVKD.........MAT
  86 TIA1_HUMAN/205-270 VYCGGV.TSGLTEQLMRQ....TFSPFGQIMEIRVFPD............
  87 TRA2_DROME/99-170  IGVFGL.NTNTSQHKVRE....LFNKYGPIERIQMVID.........AQT
  88 U2AF_HUMAN/261-332 LFIGGL.PNYLNDDQVKE....LLTSFGPLKAFNLVKD.........SAT
  89 U2AF_SCHPO/312-383 IYISNL.PLNLGEDQVVE....LLKPFGDLLSFQLIKN.........IAD
  90 WHI3_YEAST/540-615 LYVGNL.PSDATEQELRQ....LFSGQEGFRRLSFRNKnt......tSNG
  91 X16_HUMAN/12-78    VYVGNL.GNNGNKTELER....AFGYYGPLRSVWVARN............
  92 YHC4_YEAST/348-415 IFVGQL.DKETTREELNR....RFSTHGKIQDINLIFK............
  93 YHH5_YEAST/315-384 ILVKNL.PSDTTQEEVLD....YFSTIGPIKSVFISE...........KQ
  94 YIS1_YEAST/66-136  IFVGNI.TPDVTPEQIED....HFKDCGQIKRITLLYD.........RNT
  95 YIS5_YEAST/33-104  IYIGNL.NRELTEGDILT....VFSEYGVPVDVILSRD.........ENT
  96
  97 CABA_MOUSE/77-148  GRSRGFGFILFKDS....SSVEKVLDQKEH.RLDGRVIDP.K
  98 CABA_MOUSE/161-232 NKRRGFVFITFKEE....DPVKKVLEKKFH.TVSGSKCEI.K
  99 CST2_HUMAN/18-89   GKPKGYGFCEYQDQ....ETALSAMRNLNG.REFSGRALR.V
 100 ELAV_DROME/250-322 TQTKGVGFIRFDKR....EEATRAIIALNG.TTPSSCTDP.I
 101 ELAV_DROME/404-475 NQCKGYGFVSMTNY....DEAAMAIRALNG.YTMGNRVLQ.V
 102 EWS_HUMAN/363-442  GKPKGDATVSYEDP....PTAKAAVEWFDG.KDFQGSKLK.V
 103 GBP2_YEAST/124-193 GHHRGMGTVEFTKN....ESVQDAISKFDG.ALFMDRKLM.V
 104 GBP2_YEAST/221-291 GFSRGFGSVIYPTE....DEMIRAIDTFNG.MEVEGRVLE.V
 105 GBP2_YEAST/351-421 GQPTGVAVVEYENL....VDADFCIQKLNN.YNYGGCSLQ.I
 106 GR10_BRANA/8-79    GRSRGFGFVTFKDE....KSMKDAIDEMNG.KELDGRTIT.V
 107 HUD_HUMAN/48-119   GQSLGYGFVNYIDP....KDAEKAINTLNG.LRLQTKTIK.V
 108 IF4B_HUMAN/98-169  ERLKGFGYAEFEDL....DSLLSALSLNEE.SLGNRRIRV.D
 109 MSSP_HUMAN/31-102  NKCKGYGFVDFDSP....AAAQKAVSALKA.SGVQAQKAK.Q
 110 NAM8_YEAST/165-237 GMSKGYGFVKFTNS....DEQQLALSEMQG.VFLNGRAIK.V
 111 NOP3_YEAST/127-190 ....GFAFVEFEEA....ESAAKAIEEVHG.KSFANQPLE.V
 112 NOP3_YEAST/202-270 RDFDGTGALEFPSE....EILVEALERLNN.IEFRGSVIT.V
 113 NOP4_YEAST/28-98   KRSRGFGFVSFAVE....DDTKEALAKARK.TKFNGHILR.V
 114 NOP4_YEAST/292-367 GLAKGTAFVAFKDQytynECIKNAPAAGST.SLLIGDDVM.P
 115 NSR1_YEAST/170-241 DRSRGYGYVDFENK....SYAEKAIQEMQG.KEIDGRPIN.C
 116 NSR1_YEAST/269-340 EQPKGFGYVQFSNM....EDAKKALDALQG.EYIDNRPVR.L
 117 NUCL_CHICK/283-353 GSSKRFGYVDFLSA....EDMDKALQ.LNG.KKLMGLEIKlE
 118 NUCL_CHICK/373-440 GSSKGMAYIEFKTE....AEAEKALEEKQG.TEVDGRAMV.I
 119 PABP_DROME/4-75    RRSLGYAYVNFQQP....ADAERALDTMNF.DLVRNKPIR.I
 120 PABP_DROME/92-162  GNSKGYGFVHFETE....EAANTSIDKVNG.MLLNGKKVY.V
 121 PABP_DROME/183-254 GKSKGFGFVAFETT....EAAEAAVQALNGkDMGEGKSLY.V
 122 PABP_SCHPO/249-319 DKPRGFGFVNYANH....ECAQKAVDELND.KEYKGKKLY.V
 123 PES4_YEAST/93-164  KKSLGHGYLNFEDK....EEAEKAMEELNY.TKVNGKEIR.I
 124 PES4_YEAST/305-374 KVKYLWAFVTYKNS....SDSEKAIKRYNN.FYFRGKKLL.V
 125 PSF_HUMAN/373-443  GRSTGKGIVEFASK....PAARKAFERCSE.GVFLLTTTP.R
 126 PUB1_YEAST/76-146  NKNVNYAFVEYHQS....HDANIALQTLNG.KQIENNIVK.I
 127 PUB1_YEAST/163-234 GSSRGYGFVSFTSQ....DDAQNAMDSMQG.QDLNGRPLR.I
 128 PUB1_YEAST/342-407 ...KGCCFIKYDTH....EQAAVCIVALAN.FPFQGRNLR.T
 129 RB97_DROME/34-105  KRSRGFGFITYTKS....LMVDRAQENRPH.IIDGKTVEA.K
 130 RN15_YEAST/20-91   GRSKGYAFIEFRDL....ESSASAVRNLNG.YQLGSRFLK.C
 131 RNP1_YEAST/37-109  KPLKRFAFIEFQEG....VNLKKVKEKMNG.KIFMNEKIV.I
 132 RO28_NICSY/99-170  DRSRGFGFVTMSTV....EEADKAVELYSQ.YDLNGRLLT.V
 133 RO33_NICSY/116-187 DRSRGFAFVTMGSV....EEAKEAIRLFDG.SQVGGRTVK.V
 134 RO33_NICSY/219-290 GRSRGFGFITFSSA....EAMNSALDTMNE.VELEGRPLR.L
 135 ROA1_BOVIN/106-177 GKKRGFAFVTFDDH....DSVDKIVIQKYH.TVNGHNCEV.R
 136 ROC_HUMAN/18-82    ....GFAFVQYVNE....RNARAAVAGEDG.RMIAGQVLD.I
 137 ROG_HUMAN/10-81    NKSRGFAFVTFESP....ADAKDAARDMNG.KSLDGKAIK.V
 138 RT19_ARATH/33-104  GRSRGYGFVNFISE....DSANSAISAMNG.QELNGFNIS.V
 139 RU17_DROME/104-175 GKPKGYAFIEYEHE....RDMHAAYKHADG.KKIDSKRVL.V
 140 RU1A_HUMAN/12-84   LKMRGQAFVIFKEV....SSATNALRSMQG.FPFYDKPMR.I
 141 RU1A_HUMAN/210-276 ..RHDIAFVEFDNE....VQAGAARDALQG.FKITQNNAM.K
 142 RU1A_YEAST/229-293 ...RNLAFVEYETV....ADATKIKNQLGS.TYKLQNNDV.T
 143 RU2B_HUMAN/9-81    MKMRGQAFVIFKEL....GSSTNALRQLQG.FPFYGKPMR.I
 144 RU2B_HUMAN/153-220 ..RHDIAFVEFEND....GQAGAARDALQGfKITPSHAMK.I
 145 SC35_CHICK/16-87   KESRGFAFVRFHDK....RDAEDAMDAMDG.AVLDGRELR.V
 146 SP33_HUMAN/17-85   RGGPPFAFVEFEDP....RDAEDAVYGRDG.YDYDGYRLR.V
 147 SP33_HUMAN/122-186 ....GTGVVEFVRK....EDMTYAVRKLDN.TKFRSHEGE.T
 148 SQD_DROME/58-128   GRSRGFAFIVFTNT....EAIDKVSA.ADE.HIINSKKVD.P
 149 SQD_DROME/138-208  SQRKGFCFITFDSE....QVVTDLLK.TPK.QKIAGKEVD.V
 150 SR55_DROME/5-68    ....GYGFVEFEDY....RDADDAVYELNG.KELLGERVV.V
 151 SSB1_YEAST/39-114  IPASKHALVKFPTK....IDFDNIKENYDT.KVVKDREIH.I
 152 SSB1_YEAST/188-268 SANRGMAFVTFSGE....NVDIEAKAEEFK.GKVFGDREL.T
 153 SXLF_DROME/127-198 GYSFGYAFVDFTSE....MDSQRAIKVLNG.ITVRNKRLK.V
 154 SXLF_DROME/213-285 GRPRGVAFVRYNKR....EEAQEAISALNNvIPEGGSQPL.S
 155 TIA1_HUMAN/9-78    AGNDPYCFVEFHEH....RHAAAALAAMNG.RKIMGKEVK.V
 156 TIA1_HUMAN/97-168  GKSKGYGFVSFFNK....WDAENAIQQMGG.QWLGGRQIR.T
 157 TIA1_HUMAN/205-270 ...KGYSFVRFNSH....ESAAHAIVSVNG.TTIEGHVVK.C
 158 TRA2_DROME/99-170  QRSRGFCFIYFEKL....SDARAAKDSCSG.IEVDGRRIR.V
 159 U2AF_HUMAN/261-332 GLSKGYAFCEYVDI....NVTDQAIAGLNG.MQLGDKKLL.V
 160 U2AF_SCHPO/312-383 GSSKGFCFCEFKNP....SDAEVAISGLDG.KDTYGNKLH.A
 161 WHI3_YEAST/540-615 HSHGPMCFVEFDDV....SFATRALAELYGrQLPRSTVSS.K
 162 X16_HUMAN/12-78    ..PPGFAFVEFEDP....RDAADAVRELDG.RTLCGCRVR.V
 163 YHC4_YEAST/348-415 .PTNIFAFIKYETE....EAAAAALESENH.AIFLNKTMH.V
 164 YHH5_YEAST/315-384 ANTPHKAFVTYKNE....EESKKAQKCLNK.TIFKNHTIW.V
 165 YIS1_YEAST/66-136  GTPKGYGYIEFESP....AYREKALQ.LNG.GELKGKKIA.V
 166 YIS5_YEAST/33-104  GESQGFAYLKYEDQ....RSTILAVDNLNG.FKIGGRALK.I
 167