RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17497
(806 letters)
>1ug0_A Splicing factor 4; SURP domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Mus musculus} SCOP: a.217.1.1
Length = 88
Score = 102 bits (255), Expect = 2e-26
Identities = 20/70 (28%), Positives = 30/70 (42%)
Query: 343 VKVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWK 402
+KV P +I ++ FV GP E + M NP + FL + S +YYR K
Sbjct: 17 IKVSPPEGAETRRVIEKLARFVAEGGPELEKVAMEDYKDNPAFTFLHDKNSREFLYYRRK 76
Query: 403 MYSILQGDQP 412
+ I +
Sbjct: 77 VAEIRKSGPS 86
>2km4_A Regulator of TY1 transposition protein 103; CTD-interacting domain,
RNA polymerase II binding protein, phosphoprotein; NMR
{Saccharomyces cerevisiae} PDB: 2l0i_A*
Length = 142
Score = 103 bits (258), Expect = 4e-26
Identities = 17/137 (12%), Positives = 46/137 (33%), Gaps = 10/137 (7%)
Query: 463 RHRLEDFLRNLTPERVKVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGRLYLV 522
+ L L + ++ A + + A ++ E E + S +K+ LYL+
Sbjct: 5 SEQFTTKLNTLEDSQESISSASKWLLLQYRDAPKVAEMWKEYMLRPSVNTRRKLLGLYLM 64
Query: 523 SDILHNCGIKISNASFYRRGFESRLFQIFTEMHITYVNLESRLKAEGLRTRVMQVFRAWE 582
+ ++ K ++ F ++ LK ++ +V +
Sbjct: 65 NHVVQQA--KGQKIIQFQDSFGKVAAEVL---GRINQEFPRDLKK-----KLSRVVNILK 114
Query: 583 DWAVYPKDYLIKLQNVF 599
+ ++ K + ++
Sbjct: 115 ERNIFSKQVVNDIERSL 131
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 101 bits (254), Expect = 6e-26
Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 9/90 (10%)
Query: 188 FDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAF 247
S P T Y+GN+ TE L+ +F +G + K + C F+ +
Sbjct: 20 IRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY---------PEKGCCFIKY 70
Query: 248 MNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
+ + L Q ++ GWGK
Sbjct: 71 DTHEQAAVCIVALANFPFQGRNLRTGWGKE 100
>4flb_A Regulation of nuclear PRE-mRNA domain-containing; structural
genomics consortium, SGC, protein binding; 1.80A {Homo
sapiens}
Length = 132
Score = 99.3 bits (247), Expect = 1e-24
Identities = 28/143 (19%), Positives = 58/143 (40%), Gaps = 15/143 (10%)
Query: 459 SNSQRHRLEDFLRNLTPERVKVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGR 518
+ + L+ +++T + +C+E+ I M+ L + ++
Sbjct: 3 AGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAY--PHRLNL 60
Query: 519 LYLVSDILHNCGIKISNASFYRRGFESRLFQIFTEMHITYVNLESRLKAEGLRTRVMQVF 578
YL +D++ NC K NA +R F L + + +K + V ++F
Sbjct: 61 FYLANDVIQNCKRK--NAIIFRESFADVLPEAA-----------ALVKDPSVSKSVERIF 107
Query: 579 RAWEDWAVYPKDYLIKLQNVFLG 601
+ WED VYP++ ++ L+
Sbjct: 108 KIWEDRNVYPEEMIVALREALST 130
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 95.1 bits (237), Expect = 1e-23
Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 9/99 (9%)
Query: 181 QEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
Q + + P +Y G + +T+Q + + F +G + I++ +
Sbjct: 11 QLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF---------PEK 61
Query: 241 NCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKSVP 279
FV F + A+ +NG ++ + +K WGK P
Sbjct: 62 GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 100
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 92.0 bits (229), Expect = 8e-23
Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 12/94 (12%)
Query: 186 GSFDSG--DPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCG 243
GS S D T LY+G L ITE L F ++G + +I ++ + + C
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV---------QRQQCA 51
Query: 244 FVAFMNRKDGERALKY-LNGKDVQSYEMKLGWGK 276
F+ F R+ E A + N V + + WG+
Sbjct: 52 FIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 92.7 bits (231), Expect = 9e-23
Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 192 DPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRK 251
D LY+GNL+ +TE ++++F + GP S K++ E FV F +
Sbjct: 12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT-----EHTSNDPYCFVEFYEHR 66
Query: 252 DGERALKYLNGKDVQSYEMKLGWGKS 277
D AL +NG+ + E+K+ W +
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWATT 92
>1x4o_A Splicing factor 4; structural genomics, NPPSFA, national project on
protein structural and functional analyses; NMR {Mus
musculus} SCOP: a.217.1.1
Length = 78
Score = 91.4 bits (227), Expect = 1e-22
Identities = 17/68 (25%), Positives = 28/68 (41%)
Query: 344 KVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWKM 403
KV P D L ++ F+ GP E + + N + FL++ S + YYR K+
Sbjct: 8 KVSPPEDEEAKNLAEKLARFIADGGPEVETIALQNNRENQAFSFLYDPNSQGYRYYRQKL 67
Query: 404 YSILQGDQ 411
+
Sbjct: 68 DEFRKSGP 75
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 92.4 bits (230), Expect = 2e-22
Identities = 28/107 (26%), Positives = 51/107 (47%), Gaps = 4/107 (3%)
Query: 171 AEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWP 230
+ S I + S++ G+P LYL NL+P++TE+ L+ +F R+ I +
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEP-NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQF- 59
Query: 231 RSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
R R F+ F N++ +AL +NG + + + +GK+
Sbjct: 60 --RMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104
>4fld_A Regulation of nuclear PRE-mRNA domain-containing 1B; structural
genomics consortium, SGC, protein binding; 2.00A {Homo
sapiens}
Length = 135
Score = 91.2 bits (226), Expect = 7e-22
Identities = 27/139 (19%), Positives = 53/139 (38%), Gaps = 13/139 (9%)
Query: 463 RHRLEDFLRNLTPERVKVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGRLYLV 522
LE L L+ + V ++ + H A I L ++K+ LYL
Sbjct: 6 ESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHREL--RKAKSNRKLTFLYLA 63
Query: 523 SDILHNCGIKISNASFYRRGFESRLFQIFTEMHITYVNLESRLKAEGLRTRVMQVFRAWE 582
+D++ N + R FES L F+ + EG + + ++ W+
Sbjct: 64 NDVIQNS---KRKGPEFTREFESVLVDAFSHVARE--------ADEGCKKPLERLLNIWQ 112
Query: 583 DWAVYPKDYLIKLQNVFLG 601
+ +VY +++ +L+
Sbjct: 113 ERSVYGGEFIQQLKLSMED 131
>2e60_A SFRS8 protein, splicing factor, arginine/serine-rich 8; SURP
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 101
Score = 83.1 bits (205), Expect = 2e-19
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 345 VVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWKMY 404
V +P + +I R FV R+G FE M+ K+ N + FL + + YY++
Sbjct: 19 VELPPTAKMHAIIERTASFVCRQGAQFEIMLKAKQARNSQFDFLRFD-HYLNPYYKFIQK 77
Query: 405 SILQGDQPKEWRT 417
++ +G
Sbjct: 78 AMKEGRYTVLAEN 90
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 84.5 bits (210), Expect = 4e-19
Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 7/103 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
TNL + L +T+++L +F GP+ + +IM D + FV F + D +R
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIM---RDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 256 ALKYLNGKDVQSYEMKLGW--GKSVPIPSYPIYIPPKMLELTV 296
A+K LNG V++ +K+ + I +Y+ L T+
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPGGESIKDTNLYV--TNLPRTI 101
Score = 76.8 bits (190), Expect = 1e-16
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
TNLY+ NL IT+ QL IFG+YG + I+ D+ R R FV + R++ +
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR---DKLTGRPRGVAFVRYNKREEAQ 145
Query: 255 RALKYLNGKDVQ 266
A+ LN +
Sbjct: 146 EAISALNNVIPE 157
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 81.9 bits (203), Expect = 5e-19
Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 11/87 (12%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
TT L++G L P + L F R+G + +I + +G + ++ + + +
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV---------KGDSFAYIQYESLDAAQ 67
Query: 255 RALKYLNGKDVQSYEMKL--GWGKSVP 279
A + G + + +L + KS P
Sbjct: 68 AACAKMRGFPLGGPDRRLRVDFAKSGP 94
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 83.8 bits (208), Expect = 6e-19
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 3/79 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
TNL + L +T+++ +FG G + S K++ D+ + GFV +++ KD E+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLV---RDKITGQSLGYGFVNYIDPKDAEK 59
Query: 256 ALKYLNGKDVQSYEMKLGW 274
A+ LNG +Q+ +K+ +
Sbjct: 60 AINTLNGLRLQTKTIKVSY 78
Score = 74.1 bits (183), Expect = 2e-15
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
NLY+ L +T+++L ++F +YG + + +I+ D+ R GF+ F R + E
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV---DQVTGVSRGVGFIRFDKRIEAE 144
Query: 255 RALKYLNGKDVQ 266
A+K LNG+
Sbjct: 145 EAIKGLNGQKPS 156
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 81.2 bits (201), Expect = 1e-18
Identities = 21/103 (20%), Positives = 44/103 (42%), Gaps = 11/103 (10%)
Query: 175 SAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDE 234
S+ + + G+ T L++ + E +L EIFG +GP+ +KI+
Sbjct: 11 SSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------ 64
Query: 235 EKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
FV F + +A++ ++GK + +++ + K
Sbjct: 65 -----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL 102
>2dt6_A Splicing factor 3 subunit 1; structure genomics, SF3A120, SURP
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: a.217.1.1
Length = 64
Score = 79.0 bits (195), Expect = 2e-18
Identities = 23/57 (40%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 356 LIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWKMYSILQGDQP 412
++ + FV R GP FEA I EI+NP + FL N P H YYR K+ +G
Sbjct: 6 IVDKTASFVARNGPEFEARIRQNEINNPKFNFLNPN-DPYHAYYRHKVSEFKEGKAQ 61
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 78.6 bits (194), Expect = 1e-17
Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 11/92 (11%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
LY+ + +T L F +G + + + RNC FV +
Sbjct: 35 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD---------PPRNCAFVTYEKM 83
Query: 251 KDGERALKYLNGKDVQSYEMKLGWGKSVPIPS 282
+ ++A+ LNG V+S ++K+ + P+
Sbjct: 84 ESADQAVAELNGTQVESVQLKVNIARKQPMLD 115
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 77.3 bits (191), Expect = 2e-17
Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
+ L++GNL P ITE+++ ++F +YG + I + + GF+ R E
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---------KDKGFGFIRLETRTLAEI 66
Query: 256 ALKYLNGKDVQSYEMKLGWGKSVPIPS 282
A L+ ++ ++++ + +
Sbjct: 67 AKVELDNMPLRGKQLRVRFACHSASLT 93
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 77.3 bits (191), Expect = 2e-17
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
LY+ NL +E+ + + F P A ++ + R+ FV F NR+D
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK---------KIRDYAFVHFSNREDAV 65
Query: 255 RALKYLNGKDVQSYEMKLGWGKSVP 279
A+K LNGK + +++ K V
Sbjct: 66 EAMKALNGKVLDGSPIEVTLAKPVD 90
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 76.1 bits (188), Expect = 4e-17
Identities = 18/78 (23%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
++++G+L+P+IT + F +G ++ +++ D + + GFV+F N+ D E A
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVK---DMATGKSKGYGFVSFFNKWDAENA 64
Query: 257 LKYLNGKDVQSYEMKLGW 274
++ + G+ + +++ W
Sbjct: 65 IQQMGGQWLGGRQIRTNW 82
>2e5z_A SFRS8 protein, splicing factor, arginine/serine-rich 8; SURP
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 90
Score = 76.1 bits (187), Expect = 4e-17
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 343 VKVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWK 402
V ++P + +I ++ E+V R G FE + K + + FL + YY +K
Sbjct: 14 VAAIIPPPPDVQPVIDKLAEYVARNGLKFETSVRAKN--DQRFEFLQPW-HQYNAYYEFK 70
Query: 403 MYSILQGDQPKE 414
LQ +
Sbjct: 71 KQFFLQKEGGDS 82
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 80.0 bits (198), Expect = 4e-17
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
+LY+G+L+P +TE L E F GP+ SI++ D R +V F D ER
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR---DMITRRSLGYAYVNFQQPADAER 72
Query: 256 ALKYLNGKDVQSYEMKLGW 274
AL +N ++ +++ W
Sbjct: 73 ALDTMNFDVIKGKPVRIMW 91
Score = 75.0 bits (185), Expect = 2e-15
Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 5/83 (6%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
N+++ NL+ I + L + F +G + S K++ DE ++G GFV F ++ E
Sbjct: 103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC---DENGSKG--YGFVHFETQEAAE 157
Query: 255 RALKYLNGKDVQSYEMKLGWGKS 277
RA++ +NG + ++ +G KS
Sbjct: 158 RAIEKMNGMLLNDRKVFVGRFKS 180
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 76.2 bits (188), Expect = 5e-17
Identities = 22/93 (23%), Positives = 44/93 (47%), Gaps = 11/93 (11%)
Query: 187 SFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVA 246
S SG L++ NL +TE+ L + F ++G L +K + ++ F+
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-----------KDYAFIH 51
Query: 247 FMNRKDGERALKYLNGKDVQSYEMKLGWGKSVP 279
F R +A++ +NGKD++ +++ + K
Sbjct: 52 FDERDGAVKAMEEMNGKDLEGENIEIVFAKPPD 84
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 75.4 bits (186), Expect = 8e-17
Identities = 19/89 (21%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
LY+ + +T L F +G + + + RNC FV +
Sbjct: 11 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD---------PPRNCAFVTYEKM 59
Query: 251 KDGERALKYLNGKDVQSYEMKLGWGKSVP 279
+ ++A+ LNG V+S ++K+ + P
Sbjct: 60 ESADQAVAELNGTQVESVQLKVNIARKQP 88
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 78.5 bits (194), Expect = 4e-16
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L + NL P +T+QQ E+ +G L +++ E + + GF +M + R
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY---SERTGQSKGYGFAEYMKKDSAAR 152
Query: 256 ALKYLNGKDVQSYEMKLGW 274
A L GK + + + W
Sbjct: 153 AKSDLLGKPLGPRTLYVHW 171
Score = 64.6 bits (158), Expect = 2e-11
Identities = 7/82 (8%), Positives = 24/82 (29%), Gaps = 5/82 (6%)
Query: 196 TNLYLGNLNPKITE-QQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
L + L P + L ++ + + + + + + E
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC----GQDGQLKGFAVLEYETAEMAE 240
Query: 255 RALKYLNGKDVQSYEMKLGWGK 276
A + +G + +++ +
Sbjct: 241 EAQQQADGLSLGGSHLRVSFCA 262
Score = 60.4 bits (147), Expect = 5e-10
Identities = 15/102 (14%), Positives = 35/102 (34%), Gaps = 14/102 (13%)
Query: 173 PPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRS 232
P I E T+ F + + + L +T Q++ ++ Y +
Sbjct: 4 DPEEIRKRLEHTERQFRNR----RKILIRGLPGDVTNQEVHDLLSDYELK-YCFVD---- 54
Query: 233 DEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGW 274
+ + FV +N + E A+ + ++ E+ +
Sbjct: 55 -----KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL 91
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 72.9 bits (180), Expect = 5e-16
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
T NL++G+LN + ++ L F + S +MW D + R GFV+F ++ D +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW---DMQTGSSRGYGFVSFTSQDDAQ 57
Query: 255 RALKYLNGKDVQSYEMKLGW 274
A+ + G+D+ +++ W
Sbjct: 58 NAMDSMQGQDLNGRPLRINW 77
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 72.7 bits (179), Expect = 7e-16
Identities = 21/83 (25%), Positives = 40/83 (48%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
G ++ L++ NLN TE+ L +F + G + S I ++ GFV +
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 251 KDGERALKYLNGKDVQSYEMKLG 273
+ ++ALK L G V +++++
Sbjct: 61 EQAQKALKQLQGHTVDGHKLEVR 83
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 76.2 bits (188), Expect = 8e-16
Identities = 13/90 (14%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
+Y+ +++ +++ + +F +G + S + D + + GF+ + + +
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR---DPTTGKHKGYGFIEYEKAQSSQ 181
Query: 255 RALKYLNGKDVQSYEMKLGWGKSVPIPSYP 284
A+ +N D+ +++G + P+P
Sbjct: 182 DAVSSMNLFDLGGQYLRVGKAVTPPMPLLT 211
Score = 72.7 bits (179), Expect = 1e-14
Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
+ +Y+G++ ++ E + + F +GP+ SI + W D + + FV +
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW---DSVTMKHKGFAFVEYEVP 80
Query: 251 KDGERALKYLNGKDVQSYEMKLGW 274
+ + AL+ +N + +K+G
Sbjct: 81 EAAQLALEQMNSVMLGGRNIKVGR 104
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 74.5 bits (184), Expect = 1e-15
Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 4/77 (5%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
LY+GNL+ ITE L + F GP+A+IKIM +++ + N FV + D AL
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN----KNVNYAFVEYHQSHDANIAL 58
Query: 258 KYLNGKDVQSYEMKLGW 274
+ LNGK +++ +K+ W
Sbjct: 59 QTLNGKQIENNIVKINW 75
Score = 70.6 bits (174), Expect = 3e-14
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
NL++G+LN + ++ L F + S +MW D + R GFV+F ++ D + A
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW---DMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 257 LKYLNGKDVQSYEMKLGW 274
+ + G+D+ +++ W
Sbjct: 146 MDSMQGQDLNGRPLRINW 163
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 72.8 bits (179), Expect = 1e-15
Identities = 18/79 (22%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
++++G+L+P+IT + + F +G ++ +++ D + + GFV+F N+ D E
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVK---DMATGKSKGYGFVSFFNKWDAEN 72
Query: 256 ALKYLNGKDVQSYEMKLGW 274
A++ + G+ + +++ W
Sbjct: 73 AIQQMGGQWLGGRQIRTNW 91
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 76.3 bits (188), Expect = 2e-15
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 9/79 (11%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L++GNL ITE+ +F RYG + + I R R GF+ +R E
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN---------RDRGFGFIRLESRTLAEI 73
Query: 256 ALKYLNGKDVQSYEMKLGW 274
A L+G ++S +++ +
Sbjct: 74 AKAELDGTILKSRPLRIRF 92
Score = 64.7 bits (158), Expect = 1e-11
Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
L + NL+P ++ + L + F ++GP+ ++ +++ R GFV F +
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV----DDRGRATGKGFVEFAAKPPAR 151
Query: 255 RALKYLNGKDV 265
+AL+
Sbjct: 152 KALERCGDGAF 162
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 70.6 bits (174), Expect = 3e-15
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 193 PCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKD 252
T +++G L +T+ +MEIF YG + I + R ++G +V F N +
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG--YAYVEFENPDE 59
Query: 253 GERALKYLNGKDV 265
E+ALK+++G +
Sbjct: 60 AEKALKHMDGGQI 72
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 70.2 bits (173), Expect = 3e-15
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
G ++ LY+ L P T+Q L+++ YG + S K + D+ + + GFV F +
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI---LDKTTNKCKGYGFVDFDSP 57
Query: 251 KDGERALKYLNGKDVQ 266
++A+ L VQ
Sbjct: 58 SAAQKAVTALKASGVQ 73
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 70.5 bits (173), Expect = 7e-15
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
LY+ NL KIT +++ +IFG+YGP+ I++ R +V + + D +
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG------NTPETRGTAYVVYEDIFDAK 61
Query: 255 RALKYLNGKDVQSYEMKLGW 274
A+ +L+G +V + + + +
Sbjct: 62 NAVDHLSGFNVSNRYLVVLY 81
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 70.1 bits (172), Expect = 8e-15
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 3/76 (3%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
G + LN + E L ++ +YG + ++I+ + V F +
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILL---HPRTRKHLGLARVLFTST 58
Query: 251 KDGERALKYLNGKDVQ 266
+ + +K L+ V
Sbjct: 59 RGAKETVKNLHLTSVM 74
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 69.6 bits (171), Expect = 8e-15
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 4/92 (4%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
G F + + +++GNL ++ E+ L E+F + GPL + I D E + ++ GFV
Sbjct: 7 GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTIC---KDRE-GKPKSFGFV 62
Query: 246 AFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
F + + A+ LNG + + + S
Sbjct: 63 CFKHPESVSYAIALLNGIRLYGRPINVSGPSS 94
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 70.0 bits (172), Expect = 8e-15
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
+S L++G LN + +E+ ++ +F +G + ++ R + ++G C FV F
Sbjct: 9 ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVL--RGPDGSSKG--CAFVKFS 64
Query: 249 NRKDGERALKYLNGKDV 265
+ + + A+ L+G
Sbjct: 65 SHTEAQAAIHALHGSQT 81
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 70.5 bits (173), Expect = 8e-15
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
NL++ +L + T+ L F +G + S K+ D++ + + GFV+F N +
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI---DKQTSLSKCFGFVSFDNPDSAQV 97
Query: 256 ALKYLNGKDVQS 267
A+K +NG V +
Sbjct: 98 AIKAMNGFQVGT 109
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 72.8 bits (179), Expect = 8e-15
Identities = 16/108 (14%), Positives = 40/108 (37%), Gaps = 5/108 (4%)
Query: 167 YSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIK 226
Y ++Y + L++G L + + Q+ E+ +GPL +
Sbjct: 88 YQPLPGMSENPSVYVPGVVSTVVPDSA--HKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 145
Query: 227 IMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGW 274
++ D + F +++ ++A+ LNG + ++ +
Sbjct: 146 LVK---DSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Score = 60.4 bits (147), Expect = 1e-10
Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 3/111 (2%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMW--PRSDEEKARGRNCGFVAFMNRKDGER 255
LY+GN+ ITE+ +M+ F L + P + + +N F+ F + + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 256 ALKYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFN 306
A+ +G Q +K+ P + V
Sbjct: 67 AMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 71.9 bits (177), Expect = 9e-15
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 3/82 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMW-PRSDEEKARGRNCGFVAFMNRKDGE 254
+++G + +E+ L E+F +YG + I ++ + +++G C FV F RK
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG--CCFVTFYTRKAAL 61
Query: 255 RALKYLNGKDVQSYEMKLGWGK 276
A L+ V K
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMK 83
Score = 71.5 bits (176), Expect = 1e-14
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
L++G ++ K TE + +F +G + +I+ R + +RG C FV F R +
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL--RGPDGLSRG--CAFVTFTTRAMAQ 150
Query: 255 RALKYLNGKDV 265
A+K ++
Sbjct: 151 TAIKAMHQAQT 161
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 68.8 bits (169), Expect = 1e-14
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 11/94 (11%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
GS S +T L++GN++P T Q+L F YGP+ I+ ++ FV
Sbjct: 1 GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-----------KDYAFV 49
Query: 246 AFMNRKDGERALKYLNGKDVQSYEMKLGWGKSVP 279
+D A++ L+ + Q M + S
Sbjct: 50 HMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL 83
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 71.0 bits (174), Expect = 1e-14
Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 10/110 (9%)
Query: 160 KGVLKGVYSEEAEPPSAIAIYQEE----TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEI 215
G+LK + S+ S Y+++ + + LY+GNL+ TE+Q+ E+
Sbjct: 3 GGLLKALRSDSYVELSQ---YRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYEL 59
Query: 216 FGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDV 265
F + G + I + D+ K FV + +R D E A++Y+NG +
Sbjct: 60 FSKSGDIKKIIMGL---DKMKKTACGFCFVEYYSRADAENAMRYINGTRL 106
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 69.2 bits (170), Expect = 2e-14
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
TNLY+ NL + EQ+L + +G + S +I+ R +RG GF + + E
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRIL--RDSSGTSRG--VGFARMESTEKCEA 81
Query: 256 ALKYLNGKDVQS 267
+ + NGK +++
Sbjct: 82 VIGHFNGKFIKT 93
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 68.4 bits (168), Expect = 2e-14
Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 11/92 (11%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLME----IFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
P T +Y+ NLN KI + +L + IF R+G + I + K RG FV
Sbjct: 4 ETRPNHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS----RSLKMRG--QAFV 56
Query: 246 AFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
F AL+ + G M++ + K+
Sbjct: 57 IFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 88
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 69.9 bits (171), Expect = 2e-14
Identities = 27/101 (26%), Positives = 47/101 (46%), Gaps = 3/101 (2%)
Query: 179 IYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLAS--IKIMWPRSDEEK 236
+ S++ G+P +Y+ NL + E+ L IFGRY +S +IM+ ++
Sbjct: 30 METLSVFRSYEPGEP-NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE 88
Query: 237 ARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
R + F+ N K +ALK NG + M + + +S
Sbjct: 89 GRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 68.9 bits (169), Expect = 2e-14
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L++ N+ + + L ++FG++G + ++I+ +E ++G GFV F N D +R
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII---FNERGSKG--FGFVTFENSADADR 84
Query: 256 ALKYLNGKDV 265
A + L+G V
Sbjct: 85 AREKLHGTVV 94
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 70.7 bits (174), Expect = 3e-14
Identities = 14/80 (17%), Positives = 35/80 (43%), Gaps = 3/80 (3%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
L++G L + + Q+ E+ +GPL + ++ D + F +++ +
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK---DSATGLSKGYAFCEYVDINVTD 150
Query: 255 RALKYLNGKDVQSYEMKLGW 274
+A+ LNG + ++ +
Sbjct: 151 QAIAGLNGMQLGDKKLLVQR 170
Score = 61.9 bits (151), Expect = 3e-11
Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 5/94 (5%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMW--PRSDEEKARGRNCGFVAFMNRKDGER 255
LY+GN+ ITE+ +M+ F L + P + + +N F+ F + + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 256 ALKYLNGKDVQSYEMKLGWGKSVPIPSYP--IYI 287
A+ +G Q +K+ ++I
Sbjct: 67 AMA-FDGIIFQGQSLKIRRPHDYQPLPGAHKLFI 99
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 68.0 bits (167), Expect = 3e-14
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 11/76 (14%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
SG L++GNL + TEQ++ +F +YG + I+ +N GFV +
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-----------KNYGFVHIED 51
Query: 250 RKDGERALKYLNGKDV 265
+ E A++ L+ +
Sbjct: 52 KTAAEDAIRNLHHYKL 67
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 68.4 bits (168), Expect = 3e-14
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
NLY+ NL+ I +++L + F +G + S K+M E R + GFV F + ++ +
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-----EGGRSKGFGFVCFSSPEEATK 70
Query: 256 ALKYLNGKDVQS 267
A+ +NG+ V +
Sbjct: 71 AVTEMNGRIVAT 82
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 68.5 bits (168), Expect = 3e-14
Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
+ C +Y+GNL P I + + ++F +YG + I + R G FV F
Sbjct: 18 AGNNDCR--IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR------GGPPFAFVEFE 69
Query: 249 NRKDGERALKYLNGKDVQSYEMKLGWGKS 277
+ +D E A+ +G D Y +++ + +S
Sbjct: 70 DPRDAEDAVYGRDGYDYDGYRLRVEFPRS 98
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 68.5 bits (168), Expect = 3e-14
Identities = 20/82 (24%), Positives = 45/82 (54%), Gaps = 5/82 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L++ N+ + + L ++FG++G + ++I+ +E ++G GFV F N D +R
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII---FNERGSKGF--GFVTFENSADADR 70
Query: 256 ALKYLNGKDVQSYEMKLGWGKS 277
A + L+G V+ ++++ +
Sbjct: 71 AREKLHGTVVEGRKIEVNNATA 92
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 68.5 bits (168), Expect = 3e-14
Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 4/105 (3%)
Query: 168 SEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKI 227
S + P ++ +G L + NL+ +++ + E+F +G L +
Sbjct: 2 SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61
Query: 228 MWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKL 272
+ RS R V F + D +A+K NG + M +
Sbjct: 62 HYDRSG----RSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 102
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 68.1 bits (167), Expect = 4e-14
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 9/94 (9%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYG-PLASIKIMWPRSDEEKARGRNCGF 244
GS S +L++G+L P + E + F G + S+KI+ + F
Sbjct: 1 GSSGSSGM-AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIR---NRLTGIPAGYCF 56
Query: 245 VAFMNRKDGERALKYLNGKDV----QSYEMKLGW 274
V F + E+ L +NGK + + KL +
Sbjct: 57 VEFADLATAEKCLHKINGKPLPGATPAKRFKLNY 90
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 67.6 bits (166), Expect = 4e-14
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 4/82 (4%)
Query: 184 TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCG 243
+ G+ + DP L + L+ TE+ L E+F +YGP+A + I++ D++ R R
Sbjct: 5 SSGNRANPDP-NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY---DQQSRRSRGFA 60
Query: 244 FVAFMNRKDGERALKYLNGKDV 265
FV F N D + A + NG ++
Sbjct: 61 FVYFENVDDAKEAKERANGMEL 82
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 68.1 bits (167), Expect = 4e-14
Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
NL++ +L + +Q L+++F +G + S K+ D++ + GFV++ N +
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI---DKQTNLSKCFGFVSYDNPVSAQA 82
Query: 256 ALKYLNGKDVQS 267
A++ +NG +
Sbjct: 83 AIQSMNGFQIGM 94
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 68.1 bits (167), Expect = 5e-14
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 4/79 (5%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L++G LN + E+ L +FG++GP++ + ++ R+ ++ R F+ F N D +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT----SKSRGFAFITFENPADAKN 63
Query: 256 ALKYLNGKDVQSYEMKLGW 274
A K +NGK + +K+
Sbjct: 64 AAKDMNGKSLHGKAIKVEQ 82
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 67.2 bits (165), Expect = 5e-14
Identities = 19/85 (22%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLAS-IKIMWPRSDEEKARGRNCGFVAFMN 249
G ++ +++GNL+P+I E+ L + F +G + KIM D + + F+ F +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR---DPDTGNSKGYAFINFAS 57
Query: 250 RKDGERALKYLNGKDVQSYEMKLGW 274
+ A++ +NG+ + + + + +
Sbjct: 58 FDASDAAIEAMNGQYLCNRPITVSY 82
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 67.4 bits (165), Expect = 8e-14
Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 3/80 (3%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
GS D L++G + + E+ L +F +G + + ++ D + C F+
Sbjct: 4 GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVL---KDRFTGMHKGCAFL 60
Query: 246 AFMNRKDGERALKYLNGKDV 265
+ R+ +A L+ +
Sbjct: 61 TYCERESALKAQSALHEQKT 80
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 67.4 bits (165), Expect = 8e-14
Identities = 18/98 (18%), Positives = 38/98 (38%), Gaps = 14/98 (14%)
Query: 183 ETKGSFDSGDPCTTN--LYLGNLNP-KITEQQLMEIFGRYGPLASIKIMWPRSDEEKARG 239
+ + DP + N +++GNLN + + + IF +YG +A +
Sbjct: 13 QASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH----------- 61
Query: 240 RNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
+ FV + N + A+ NG+ + + +
Sbjct: 62 KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 66.5 bits (163), Expect = 9e-14
Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 11/90 (12%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
T +++GN++ T Q+L +F R G + ++ ++ FV D +
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-----------KDYAFVHMEKEADAK 57
Query: 255 RALKYLNGKDVQSYEMKLGWGKSVPIPSYP 284
A+ LNGK+V+ + + S P
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKKSGP 87
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 67.4 bits (165), Expect = 1e-13
Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 4/91 (4%)
Query: 183 ETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNC 242
++ G L + NL+ +++ + E+F +G L + + RS R
Sbjct: 23 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG----RSLGT 78
Query: 243 GFVAFMNRKDGERALKYLNGKDVQSYEMKLG 273
V F R D +A+K G + M +
Sbjct: 79 ADVHFERRADALKAMKQYKGVPLDGRPMDIQ 109
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 69.7 bits (170), Expect = 1e-13
Identities = 22/124 (17%), Positives = 41/124 (33%), Gaps = 9/124 (7%)
Query: 195 TTNLYLGNLNP-KITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDG 253
+ L + L+ K+ ++ +F YG + +K M + V +
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK--------PGAAMVEMADGYAV 55
Query: 254 ERALKYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFNAQPASKD 313
+RA+ +LN + +M + K I Y S + P
Sbjct: 56 DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115
Query: 314 KHRI 317
K+RI
Sbjct: 116 KNRI 119
Score = 62.8 bits (152), Expect = 3e-11
Identities = 24/148 (16%), Positives = 54/148 (36%), Gaps = 11/148 (7%)
Query: 133 IKKKSNLEMFKEELK--MIQEEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDS 190
I +N MF +++ + ++ + G+ G S + S + + + +
Sbjct: 59 ITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
+ L+ N ++TE+ EI G + + K+ + G + + ++
Sbjct: 119 IQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV---KVFSGKSERSSSGLLEWDSK 175
Query: 251 KDGERALKYLNGKDV------QSYEMKL 272
D L +LN + Y +KL
Sbjct: 176 SDALETLGFLNHYQMKNPNGPYPYTLKL 203
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 66.5 bits (163), Expect = 1e-13
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
SG + L++ NL+ +E+ L ++F YGPL+ + D + + FV FM
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYP---IDSLTKKPKGFAFVTFM 58
Query: 249 NRKDGERALKYLNGKDVQ 266
+ +A ++G+ Q
Sbjct: 59 FPEHAVKAYAEVDGQVFQ 76
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 66.8 bits (163), Expect = 1e-13
Identities = 18/91 (19%), Positives = 30/91 (32%), Gaps = 9/91 (9%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
GS S T + NL ++ E F R+G L + + G V
Sbjct: 1 GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL---------PEGGITAIV 51
Query: 246 AFMNRKDGERALKYLNGKDVQSYEMKLGWGK 276
F+ + +A ++L + L W
Sbjct: 52 EFLEPLEARKAFRHLAYSKFHHVPLYLEWAP 82
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 69.5 bits (170), Expect = 1e-13
Identities = 23/125 (18%), Positives = 44/125 (35%), Gaps = 9/125 (7%)
Query: 195 TTNLYLGNLNPK-ITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDG 253
+ L + NLNP+ +T Q L +FG YG + +KI++ + V +
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF--------NKKENALVQMADGNQA 54
Query: 254 ERALKYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFNAQPASKD 313
+ A+ +LNG + +++ K + + L P +
Sbjct: 55 QLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQ 114
Query: 314 KHRIP 318
P
Sbjct: 115 NIFPP 119
Score = 63.8 bits (155), Expect = 1e-11
Identities = 17/99 (17%), Positives = 46/99 (46%), Gaps = 8/99 (8%)
Query: 180 YQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARG 239
+++ +F + P + L+L N+ P ++E+ L +F G + + +
Sbjct: 105 FKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-------KD 157
Query: 240 RNCGFVAFMNRKDGERALKYLNGKDV-QSYEMKLGWGKS 277
R + + ++ +AL L+ D+ +++ +++ + KS
Sbjct: 158 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 66.5 bits (163), Expect = 1e-13
Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
+ + NL+ E L E+F +G ++ I + D+ + + F++F R+D
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLA---KDKTTGQSKGFAFISFHRREDAA 71
Query: 255 RALKYLNGKDVQSYEMKLGWGK 276
RA+ ++G + + W K
Sbjct: 72 RAIAGVSGFGYDHLILNVEWAK 93
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 68.0 bits (167), Expect = 2e-13
Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 179 IYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKAR 238
I E+ KG L NL+ ITE +L E+F +I + K++
Sbjct: 83 IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVS-QDGKSK 136
Query: 239 GRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGW 274
G ++ F + D E+ L+ G ++ + L +
Sbjct: 137 G--IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170
Score = 64.5 bits (158), Expect = 3e-12
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 5/82 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
NL++GNLNP + +L + ++ D R G+V F + +D E+
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV----DVRTGTNRKFGYVDFESAEDLEK 69
Query: 256 ALKYLNGKDVQSYEMKLGWGKS 277
AL+ L G V E+KL K
Sbjct: 70 ALE-LTGLKVFGNEIKLEKPKG 90
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 66.7 bits (163), Expect = 2e-13
Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 4/110 (3%)
Query: 156 RHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEI 215
H G++ + G+ + DP L + L+ TE+ L E+
Sbjct: 8 HHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDP-NCCLGVFGLSLYTTERDLREV 66
Query: 216 FGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDV 265
F +YGP+A + I++ D++ R R FV F N D + A + NG ++
Sbjct: 67 FSKYGPIADVSIVY---DQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 113
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 65.4 bits (160), Expect = 3e-13
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 8/99 (8%)
Query: 179 IYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKAR 238
+ ++ +GS + NL++GNLNP + +L + ++ D
Sbjct: 4 MLEDPVEGSESTTP---FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV----DVRTGT 56
Query: 239 GRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
R G+V F + +D E+AL+ L G V E+KL K
Sbjct: 57 NRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG 94
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 66.3 bits (162), Expect = 3e-13
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 3/91 (3%)
Query: 181 QEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
Q + NL + + + E QL ++F RYGP+ S+KI+ D E + R
Sbjct: 28 QHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIV---CDRETRQSR 84
Query: 241 NCGFVAFMNRKDGERALKYLNGKDVQSYEMK 271
GFV F + ++A+ LNG ++ + +K
Sbjct: 85 GYGFVKFQSGSSAQQAIAGLNGFNILNKRLK 115
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 64.9 bits (159), Expect = 4e-13
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 184 TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCG 243
+ G P + +Y+ NL +T L IF +YG + + IM D++ + +
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIM---KDKDTRKSKGVA 61
Query: 244 FVAFMNRKDGERALKYLNGKDV 265
F+ F+++ + + +N K +
Sbjct: 62 FILFLDKDSAQNCTRAINNKQL 83
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 72.6 bits (177), Expect = 4e-13
Identities = 80/597 (13%), Positives = 159/597 (26%), Gaps = 176/597 (29%)
Query: 99 EDKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKKKSNLEMFKEELKMIQEEREERHK 158
+D S EE ++ K S L+ + K++ ++ F EE+ R
Sbjct: 39 QDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV--------LRIN 90
Query: 159 YKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGR 218
YK ++ + +E+ +P +Y E LY N N + + R
Sbjct: 91 YKFLMSPIKTEQRQPSMMTRMYIE-----------QRDRLY--NDNQVFAKYNVS----R 133
Query: 219 YGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLN-GKDVQSYEMKLGWGKS 277
P ++ +AL L K+V + G GK+
Sbjct: 134 LQPYLKLR----------------------------QALLELRPAKNVLIDGVL-GSGKT 164
Query: 278 V------------PIPSYPIY--------IPPKMLEL-------------TVPPPPSGLP 304
+ I+ P +LE+ + S +
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIK 224
Query: 305 FNAQPASKDKHRIPKLRPGEP-L-------TREDLDRLD---QIL----NQAYVKVVVPT 349
+ R+ K +P E L + + + +IL + +
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAA 284
Query: 350 DRTLLMLIHRMVEFVVREGPMFEAMIMNKEIS---------NPLY-----RFLFENQSPA 395
T + L H + E ++ NP + + A
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDG--LA 342
Query: 396 HI-YYR----WKMYSILQGD----QPKEWRTN--EFRMFDGGSVWRPPP-MNLFTQGMPD 443
++ K+ +I++ +P E+R +F S P ++L +
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP-SAHIPTILLSLIWFDVIK 401
Query: 444 ELVEEEVESKTKGSL----SNSQRHRLEDFLRNLTPERVKVAEAMVFCMEHSDAAEEICE 499
V V K SL + L +
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL---------------------- 439
Query: 500 CIMESLSNESTALHKKIGRLYLVSDILHNCGIKISNASFYRRGF------ESRLFQIFTE 553
ALH+ I Y + + + Y + T
Sbjct: 440 -------ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 554 MHITYVN---LESRLKAEGL-RTRVMQVFRAWEDWAVYPKDYLIKLQNVFLGLSDAV 606
+ +++ LE +++ + + + Y K Y+ + L +A+
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFY-KPYICDNDPKYERLVNAI 548
Score = 66.4 bits (161), Expect = 3e-11
Identities = 73/540 (13%), Positives = 165/540 (30%), Gaps = 122/540 (22%)
Query: 148 MIQEEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKI 207
M E E +++YK +L ++++ +FD D +
Sbjct: 7 MDFETGEHQYQYKDILS--------------VFEDAFVDNFDCKD------VQDMPKSIL 46
Query: 208 TEQQLMEIFGRYGPL-ASIKIMWPRSDE---------EKARGRNCGFVAFMNRKDGERAL 257
+++++ I + ++++ W + E+ N F+ M+ E+
Sbjct: 47 SKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL--MSPIKTEQRQ 104
Query: 258 KYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFNAQPASKDKHRI 317
+ + +L + + Y + L+L + +
Sbjct: 105 PSMMTRMYIEQRDRL-YNDNQVFAKYNVSRLQPYLKL-------------------RQAL 144
Query: 318 PKLRPGEP-------------LTRE---DLDRLDQILNQAY-VKV-VVPTDRTLLM---- 355
+LRP + + + ++ + + + + + T+L
Sbjct: 145 LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204
Query: 356 LIHRMV-EFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWKMYSILQGDQPKE 414
L++++ + R + I L R L +L
Sbjct: 205 LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE-------NCLLVL--LNV-- 253
Query: 415 WRTNEFRMFDGGS-VWRPPPMNLFTQGMPDELVEEEVESKTKGSLSNSQRHRLEDFLRNL 473
+ F+ + L T + V + + + T +S L+ L
Sbjct: 254 QNAKAWNAFNLSCKI-------LLTTR--FKQVTDFLSAATTTHIS------LDHHSMTL 298
Query: 474 TPERVKVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGR----LYLVSDILHNC 529
TP+ VK D E+ LS + ++ + ++ D L
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 530 GIKIS----NASFYRRGFESRLFQIFTE-MHITYVNLESRLKAEGLRTRVMQVFRAWEDW 584
I+ S + YR+ F+ +F HI + L + + +++ VM V +
Sbjct: 359 -IESSLNVLEPAEYRKMFDR--LSVFPPSAHIPTILLS-LIWFDVIKSDVMVVVNKLHKY 414
Query: 585 AV---YPKDYLIKLQNVFLGLSDAVPLDANNGNEEDEDLDG-APLSDVDGEDLDGVPLDG 640
++ PK+ I + +++L + N +D D +DL LD
Sbjct: 415 SLVEKQPKESTISIPSIYL---ELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Score = 61.4 bits (148), Expect = 1e-09
Identities = 74/616 (12%), Positives = 168/616 (27%), Gaps = 229/616 (37%)
Query: 2 DRATMKKQIAEQKLKAFSIGSMGAKRTLSKKEQEEQ-KKKEQE----------------- 43
+ M + EQ+ + ++ + AK +S+ + + ++ E
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK 163
Query: 44 ---AAAAQAFEEFVATFQENPAAKTNKV-WVKAGTYDAGRRREDTSEKGKLYKPQSRLQE 99
A + K+ W+ + + + +L
Sbjct: 164 TWVALDVCLSYKVQCKMD-------FKIFWLNLKNCN---------SPETVLEMLQKL-- 205
Query: 100 DKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKKKSNLEMFKEELKMIQEEREERHKY 159
++ + K + + EL+ + + + Y
Sbjct: 206 -----------LYQI-------DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK----PY 243
Query: 160 KG---VLKGVYSEEAEPPSAIAIYQEETKGSFDSGDPC----TT---------------N 197
+ VL V + + + +F+ C TT +
Sbjct: 244 ENCLLVLLNVQNAK--------AWN-----AFNLS--CKILLTTRFKQVTDFLSAATTTH 288
Query: 198 LYLGNLNPKITEQQLMEIFGRY---------------GPLASIKIMWPRSDEEKARGRNC 242
+ L + + +T ++ + +Y P + I+ + A N
Sbjct: 289 ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR-LSIIAESIRDGLATWDNW 347
Query: 243 GFVAFMNRKDG-ERALKYLNGKDVQSYEMKLG-WGKSVPIPSYPIYIPPKMLELTVPPPP 300
V E +L L + + +L + S IP +L L
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH-------IPTILLSL------ 394
Query: 301 SGLPFNAQPASKDKHRIPKLRPGEPLTREDLDRLDQILNQAYVKVVV---PTDRTL-LML 356
+ F+ + + D + ++N+ + +V P + T+ +
Sbjct: 395 --IWFD-------------------VIKSD---VMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 357 IHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHI--Y-YRWKMYSILQGDQPK 413
I+ ++ + I++ N F ++ P ++ Y Y + + + P+
Sbjct: 431 IYLELKVKLENEYALHRSIVDH--YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE 488
Query: 414 EWRTNEFRM--FD----------GGSVWRPPP--MNLFTQ------------GMPDELVE 447
FRM D + W +N Q + LV
Sbjct: 489 RM--TLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVN 546
Query: 448 EEVESKTKGSLSNSQRHRLEDFLRNLTPERVKVAEAMVFCMEHSDAAEEICECIME-SLS 506
+ DFL E + C +++D ++ +L
Sbjct: 547 A-----------------ILDFLPK--------IEENLICSKYTD--------LLRIALM 573
Query: 507 NESTAL----HKKIGR 518
E A+ HK++ R
Sbjct: 574 AEDEAIFEEAHKQVQR 589
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 64.6 bits (158), Expect = 5e-13
Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 3/88 (3%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
+ +YLG++ TE+Q++++ GP+ ++K+M+ D + R + F+ F + +
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF---DPQTGRSKGYAFIEFRDLESSA 58
Query: 255 RALKYLNGKDVQSYEMKLGWGKSVPIPS 282
A++ LNG + S +K G+ + I
Sbjct: 59 SAVRNLNGYQLGSRFLKCGYSSNSDISG 86
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 64.6 bits (158), Expect = 6e-13
Identities = 18/87 (20%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 192 DPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRK 251
T+ + + N+ + ++++ E+F +G L ++++ + RG GFV F+ ++
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG--FGFVDFITKQ 69
Query: 252 DGERALKYL-NGKDVQSYEMKLGWGKS 277
D ++A L + + + L W S
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWADS 96
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 65.0 bits (159), Expect = 7e-13
Identities = 23/84 (27%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
G + N+++ NL+ I + L + F +G + S K++ DE ++G GFV F +
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC---DENGSKGY--GFVHFETQ 55
Query: 251 KDGERALKYLNGKDVQSYEMKLGW 274
+ ERA++ +NG + ++ +G
Sbjct: 56 EAAERAIEKMNGMLLNDRKVFVGR 79
Score = 32.6 bits (75), Expect = 0.12
Identities = 7/34 (20%), Positives = 13/34 (38%)
Query: 178 AIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQ 211
++E + + TN+Y+ N P T
Sbjct: 80 FKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA 113
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 66.1 bits (161), Expect = 7e-13
Identities = 26/146 (17%), Positives = 52/146 (35%), Gaps = 11/146 (7%)
Query: 134 KKKSNLEMFKEELKM-IQEEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGD 192
K E E + E+ +++ + G ++ + + D
Sbjct: 9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRD 68
Query: 193 --PCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
P +Y+GNL + +L FG YGPL S+ + FV F +
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR--------NPPGFAFVEFEDP 120
Query: 251 KDGERALKYLNGKDVQSYEMKLGWGK 276
+D A++ L+G+ + +++
Sbjct: 121 RDAADAVRELDGRTLCGCRVRVELSN 146
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 64.2 bits (157), Expect = 7e-13
Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
L + NL + + L +F +YG + + I + R FV F +R+D +
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIP---REPHTKAPRGFAFVRFHDRRDAQ 69
Query: 255 RALKYLNGKDVQSYEMK 271
A ++G ++ E++
Sbjct: 70 DAEAAMDGAELDGRELR 86
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 64.2 bits (157), Expect = 8e-13
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+Y+G L+ K++E L E+F + GP+ + + D + + GFV F++ +D + A+
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMP---KDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 258 KYLNGKDVQSYEMKLGWGK 276
K ++ + +++
Sbjct: 75 KIMDMIKLYGKPIRVNKAS 93
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 64.6 bits (158), Expect = 8e-13
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 3/93 (3%)
Query: 184 TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCG 243
+ G LY+G+L+ ITE L IF +G + SI++M D E R + G
Sbjct: 15 MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM---DSETGRSKGYG 71
Query: 244 FVAFMNRKDGERALKYLNGKDVQSYEMKLGWGK 276
F+ F + + ++AL+ LNG ++ MK+G
Sbjct: 72 FITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 71.2 bits (174), Expect = 9e-13
Identities = 115/671 (17%), Positives = 186/671 (27%), Gaps = 239/671 (35%)
Query: 184 TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMW---PRSDEEKARGR 240
+ GS + T + QL E F + P + P + E G+
Sbjct: 12 SHGSLEHVLLVPTASF-------FIASQLQEQFNKILPEPTEGFAADDEPTTPAELV-GK 63
Query: 241 NCGFVAFMNRKDG----ERALK---------YLNGKDVQSY--------EMKLGWGKSVP 279
G+V+ + ++ L YL G D+ + + L K +
Sbjct: 64 FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL- 122
Query: 280 IPSYPIYIPPKMLELTVP-PPPSGLPFNAQPASKDKHRIPKLRPGEPLTREDLDRLDQIL 338
I +Y M + S L F A + ++ + G+ T + + L + L
Sbjct: 123 IKNY--ITARIMAKRPFDKKSNSAL-FRA--VGEGNAQLVAIFGGQGNTDDYFEEL-RDL 176
Query: 339 NQAYVKVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIY 398
Q Y +V LI + L + ++
Sbjct: 177 YQTYHVLVGD-------LIKFS--------------------AETLSELIRTTLDAEKVF 209
Query: 399 YRWKMYSILQGDQPKEWRTNEFRMFDGGSVWRPP-----------PMNLFTQGMPDELVE 447
QG EW N P P+ Q L
Sbjct: 210 T--------QGLNILEWLENPSN--------TPDKDYLLSIPISCPLIGVIQ-----LAH 248
Query: 448 EEVESKTKGSLSNSQRHRLEDFLRNLTPERVKVAEAMV--FCMEHSDAAEEICECIMESL 505
V +K G + + L +L+ T ++ +V + +D+ E + +++
Sbjct: 249 YVVTAKLLG-FTPGE---LRSYLKGAT----GHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 506 SNESTAL-------HKKIGRLYLVSDIL-----HNCGIK-----ISNASFYRRGFESRLF 548
T L ++ L IL +N G+ ISN +
Sbjct: 301 ----TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT----------- 345
Query: 549 QIFTEMHITYVNLESRLKAEGLRTRVMQVFRAWEDWAVYPKDYLIKLQNVFLGLSDAV-- 606
Q + ++ N S L A QV I L N G + V
Sbjct: 346 QEQVQDYVNKTN--SHLPAGK------QVE--------------ISLVN---GAKNLVVS 380
Query: 607 --PLDANNGNEEDEDLDG---------APLSDVDGEDLDGVPLDGAALMKSLQRLP---- 651
P + L G AP G D +P L S + LP
Sbjct: 381 GPP----------QSLYGLNLTLRKAKAP----SGLDQSRIPFSERKLKFSNRFLPVASP 426
Query: 652 -HSS---SAPD--EDDIDGVPCTYNITS------ATMDGEDLDGVPMDKVKP-ARAATFI 698
HS A D D+ ++N T DG DL + + +
Sbjct: 427 FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRL 486
Query: 699 PSKWETVEENEDSAVTSSKWDDVEQSESKDDSNSKGTGLTSSRRGDLSSERIQG------ 752
P KWET + + + + D G G +S G L+ G
Sbjct: 487 PVKWETTTQFKATHIL-----DF------------GPG-GASGLGVLTHRNKDGTGVRVI 528
Query: 753 -----DSGEDD 758
D DD
Sbjct: 529 VAGTLDINPDD 539
Score = 68.5 bits (167), Expect = 7e-12
Identities = 108/656 (16%), Positives = 181/656 (27%), Gaps = 224/656 (34%)
Query: 70 VKAGTYDAGRRREDTSEKGKLYKPQSRLQEDKDSSASKAEEYARLLG--DKKTESQRLKK 127
V ++ + ++ K L +P D D + AE + LG E ++ +
Sbjct: 22 VPTASFFIASQLQEQFNK-ILPEPTEGFAAD-DEPTTPAELVGKFLGYVSSLVEPSKVGQ 79
Query: 128 NNKIDIKKKSNLEMFKEE-----------LKMIQEEREERHKYKGVLKGVY--------S 168
+++ L F+ K++QE K K ++K
Sbjct: 80 FDQV---LNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRP 136
Query: 169 EEAEPPSAIAIYQEETKGSFDSGDPCTTNLYL-----GNLNPKITEQQLMEIFGRYGPLA 223
+ + SA+ F + L GN + E L +++ Y L
Sbjct: 137 FDKKSNSAL----------FRAVGEGNAQLVAIFGGQGNTDDYFEE--LRDLYQTYHVLV 184
Query: 224 SIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGK---SVPI 280
I + + + D E+ + G ++ W + + P
Sbjct: 185 GDLI-------KFSAETLSELIR--TTLDAEKV--FTQGLNILE------WLENPSNTPD 227
Query: 281 PSYPIYIPPKMLELTVPPPPSGLPFNAQPASKDKH-----RIPKLRPGEPLTREDLDRLD 335
Y + IP + P G+ Q A H ++ PGE L
Sbjct: 228 KDYLLSIP-------ISCPLIGV---IQLA----HYVVTAKLLGFTPGE---------LR 264
Query: 336 QILNQA--YVKVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQS 393
L A + + +V + E +E+ LF
Sbjct: 265 SYLKGATGHSQGLV-------------TAVAIAETDSWESFF---VSVRKAITVLF---- 304
Query: 394 PAHIYYR-WKMY-------SILQGDQPKEWRTNEFRMFDGGSVWRPPPMNLFTQGMPDEL 445
I R ++ Y SIL+ NE G P PM L + E
Sbjct: 305 --FIGVRCYEAYPNTSLPPSILE----DSLENNE------GV---PSPM-LSISNLTQEQ 348
Query: 446 VEEEVESKTKG----------SLSNSQRH-----------RLEDFLRNL----------T 474
V++ V KT SL N ++ L LR
Sbjct: 349 VQDYVN-KTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI 407
Query: 475 P--ERVKVAEAMVF----CMEHSDAAEEICECIMESLSNESTALHKKIGRLYLVSDILHN 528
P ER K+ + F HS + I + L + + + D
Sbjct: 408 PFSER-KLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFN--------AKD---- 454
Query: 529 CGIKISNASFYRRGFESRLFQIFTEMHITYVNLESRLKAEGLRTRVMQVFRA---WEDWA 585
I+I ++ F +L L V + R WE
Sbjct: 455 --IQIP------------VYDTFDG-----SDLRV-LSGSISERIVDCIIRLPVKWETTT 494
Query: 586 VYPKDYLIKLQNVF--LGLSDAVPLDANNGNEEDEDLDGAPLSDVDGEDLDGVPLD 639
+ +++ F G S L N DG + + LD P D
Sbjct: 495 QFKATHIL----DFGPGGASGLGVLTHRN-------KDGTGVRVIVAGTLDINPDD 539
Score = 58.5 bits (141), Expect = 8e-09
Identities = 81/502 (16%), Positives = 144/502 (28%), Gaps = 190/502 (37%)
Query: 394 PAHIYYRWKMYSILQGDQPKEWRTNEFRMFDGGSVWRPPPMNLFTQG----MPDEL---- 445
P ++ S LQ +F P P F P EL
Sbjct: 23 PTASFFI---ASQLQ---------EQFNK------ILPEPTEGFAADDEPTTPAELVGKF 64
Query: 446 ---VEEEVESKTKGSLSNSQRHRLEDFLRN-LTPERVKVAEAMVFCMEHSDAAEEICECI 501
V VE G L +F L + H+ AA+
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI-----------HALAAK------ 107
Query: 502 MESLSNESTALHKKIGRLYLVSDILHNCGI-KISNASFYR---RGFESRLFQIF-----T 552
+ ++ + K++ + Y+ + I+ K SN++ +R G ++L IF T
Sbjct: 108 LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG-NAQLVAIFGGQGNT 166
Query: 553 EMHITYVNLESRLKAEGLRTRVMQVFRAWEDWAVYP---KDYLIKLQNVFLGLSDAVPLD 609
+ Y E LR + Y D + L
Sbjct: 167 D---DYFE-------E-LRDL----------YQTYHVLVGDLIKFSAETLSELIR----- 200
Query: 610 ANNGNEEDEDLDGAPLSDVDGEDLDGVPLDGAALMKSLQRLPHSSSAPDEDDIDGVP--- 666
+ +D E + L+ +++ L+ + S+ PD+D + +P
Sbjct: 201 ----------------TTLDAEKVFTQGLN---ILEWLE---NPSNTPDKDYLLSIPISC 238
Query: 667 --------CTYNITSATMD---GEDLD------GVPMDKVKPARAATFI-PSK-WETVEE 707
Y +T+ + GE G V A I + WE+
Sbjct: 239 PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV----TAVAIAETDSWESFFV 294
Query: 708 NEDSAVTSSKW-----------DDVEQSESKDDSNSKGTGLTS---SRRGDLSSERIQGD 753
+ A+T + + S + DS G+ S S L+ E++Q
Sbjct: 295 SVRKAITVLFFIGVRCYEAYPNTSLPPSILE-DSLENNEGVPSPMLSISN-LTQEQVQ-- 350
Query: 754 SGEDDSAAREEKKEANKSERSDRKKSPS-------------PAA--------REEKKEA- 791
+ + N + ++ S P + R+ K +
Sbjct: 351 ---------DYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG 401
Query: 792 ---NKSERSDRKKSPS----PV 806
++ S+RK S PV
Sbjct: 402 LDQSRIPFSERKLKFSNRFLPV 423
Score = 51.2 bits (122), Expect = 2e-06
Identities = 103/561 (18%), Positives = 167/561 (29%), Gaps = 205/561 (36%)
Query: 32 KEQEEQKKKEQEAAAAQAFEEFVATF----------------QENPAAKTNKVWVKAGTY 75
E K + + EF + + KT K +K Y
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT-KELIKN--Y 126
Query: 76 DAGRRREDTSEKGKLYKPQSRLQEDKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKK 135
R K S L A+ A + G Q
Sbjct: 127 ITARIMAKRPFDK---KSNSALFR--AVGEGNAQLVA-IFG-----GQ------------ 163
Query: 136 KSNLEMFKEELKMIQEEREERHKYKGVLKGVYSEEAE--------PPSAIAIYQEETKGS 187
N + + EEL+ + + Y ++ + AE A ++ T+G
Sbjct: 164 -GNTDDYFEELRDLYQT------YHVLVGDLIKFSAETLSELIRTTLDAEKVF---TQG- 212
Query: 188 FDSG----DPCTT--NLYLGNLN---PKITEQQLMEIFGRYGPLASIKIMWPRSDEEKAR 238
+ +P T YL ++ P I QL Y + + K++ E ++
Sbjct: 213 LNILEWLENPSNTPDKDYLLSIPISCPLIGVIQL----AHY--VVTAKLLGFTPGELRSY 266
Query: 239 -----GRNCGFVA------------FMNRKDGERALKYL--NGKDVQSYEMKLGWGKSVP 279
G + G V F +A+ L G V+ YE
Sbjct: 267 LKGATGHSQGLVTAVAIAETDSWESF--FVSVRKAITVLFFIG--VRCYE---------- 312
Query: 280 IPSYP-IYIPPKMLELTV-----PPPP----SGLP----------FNAQ-PASKDKHRIP 318
+YP +PP +LE ++ P P S L N+ PA K I
Sbjct: 313 --AYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVE-IS 369
Query: 319 KLR--P------GEPLTREDLDRLDQILNQAYVKVVVPT--DRTLLMLIHRMVEFVVREG 368
L G P + L L+ L K P+ D++ R + F R+
Sbjct: 370 -LVNGAKNLVVSGPP---QSLYGLNLTLR----KAKAPSGLDQS------R-IPFSERK- 413
Query: 369 PMFEAMIMNKEISNPLYRFL--FENQSPAHIYYRWKMYSILQGDQPK---EWRTNEFRM- 422
F RFL SP H + ++ D K + + ++
Sbjct: 414 LKFS------------NRFLPVA---SPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIP 458
Query: 423 -FD--GGSVWRPPPMNLFTQGMPDELVEEEV--ESKTKGSLSNSQRHRLEDF-------L 470
+D GS R ++ ++ + D ++ V E+ T+ + H L DF L
Sbjct: 459 VYDTFDGSDLRVLSGSI-SERIVDCIIRLPVKWETTTQFKAT----HIL-DFGPGGASGL 512
Query: 471 RNLTPE-------RVKVAEAM 484
LT RV VA +
Sbjct: 513 GVLTHRNKDGTGVRVIVAGTL 533
Score = 39.6 bits (92), Expect = 0.004
Identities = 42/313 (13%), Positives = 81/313 (25%), Gaps = 135/313 (43%)
Query: 320 LRPGEPLTREDLDRLDQILNQAYVKVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKE 379
L ++ +R D Y ++ +V P
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYG----------FSILD-----IVINNP--------VN 1671
Query: 380 ISNPLYRFLFENQSPAHIYYRWKMYSILQGDQPKEWRTNEFRMFDGGS------VWRPPP 433
++ F + I + YS + + + + ++F + +R
Sbjct: 1672 LT-----IHFGGEKGKRIR---ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK 1723
Query: 434 --MNL--FTQGMP---DELVE----EEVESKTK----------------------GSLSN 460
++ FTQ P L+E E+++SK +S
Sbjct: 1724 GLLSATQFTQ--PALT--LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMS- 1778
Query: 461 SQRHRLED-----FLR-----NLTP--ERVKVAEAMV----------FCMEHSDAAEEIC 498
+E F R P E + M+ F E A + +
Sbjct: 1779 -----IESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE---ALQYVV 1830
Query: 499 ECIMES------------------LSNESTALHKKIGRLYLVSDILHNCGI-KISNA--- 536
E + + + + AL V+++L+ + KI
Sbjct: 1831 ERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDT-------VTNVLNFIKLQKIDIIELQ 1883
Query: 537 -SFYRRGFESRLF 548
S E LF
Sbjct: 1884 KSLSLEEVEGHLF 1896
Score = 37.3 bits (86), Expect = 0.022
Identities = 38/218 (17%), Positives = 63/218 (28%), Gaps = 77/218 (35%)
Query: 213 MEIFGRYGPLASIKIMWPRSDEEKARGRNCGF----VAFMNRK------DGER------- 255
M+++ A + +W R+D GF + N GE+
Sbjct: 1633 MDLYKTS-KAA--QDVWNRAD--NHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIREN 1687
Query: 256 --ALKYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFNAQPAS-- 311
A+ + D + K+ + SY +L T QPA
Sbjct: 1688 YSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQ---------FTQPALTL 1738
Query: 312 ---------KDKHRIPK--------LRPGE-----------PLTREDLDRLDQILNQ--A 341
K K IP L GE + E L + +
Sbjct: 1739 MEKAAFEDLKSKGLIPADATFAGHSL--GEYAALASLADVMSI--ESLVEV---VFYRGM 1791
Query: 342 YVKVVVPTDRTLLMLIHRMVEFVVREGPMFEAMIMNKE 379
++V VP D L + M+ + G + A ++E
Sbjct: 1792 TMQVAVPRD-ELGRSNYGMIA--INPGRV--AASFSQE 1824
Score = 33.9 bits (77), Expect = 0.30
Identities = 27/155 (17%), Positives = 47/155 (30%), Gaps = 57/155 (36%)
Query: 484 MVFCME---HSDAAEEI----CECIMESLSNESTALHKKIGRLYLVSDILHNCGIK---I 533
M M+ S AA+++ ++ S I V+ +H G K I
Sbjct: 1631 M--GMDLYKTSKAAQDVWNRADNHFKDTYG-FSIL---DIVINNPVNLTIHFGGEKGKRI 1684
Query: 534 SNASFYRRGFESRLFQ-----------IFTEMH-----ITYVNLESRLKAEGLRTRVMQ- 576
R + + +F+ IF E++ T+ + + L T+ Q
Sbjct: 1685 ------RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS----ATQFTQP 1734
Query: 577 --------VFRAWEDWAVYPKDYLIKLQNVFLGLS 603
F + + P D F G S
Sbjct: 1735 ALTLMEKAAFEDLKSKGLIPAD------ATFAGHS 1763
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 64.3 bits (157), Expect = 1e-12
Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
+ +++ NL+ K+ ++L E+F G + I+ + K+RG G V F
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADIL--EDKDGKSRG--IGTVTFEQ 65
Query: 250 RKDGERALKYLNGKDVQSYEMK 271
+ +A+ NG+ + M
Sbjct: 66 SIEAVQAISMFNGQLLFDRPMH 87
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 64.5 bits (157), Expect = 1e-12
Identities = 11/113 (9%), Positives = 36/113 (31%), Gaps = 11/113 (9%)
Query: 169 EEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITE----QQLMEIFGRYGPLAS 224
A + + + +P + + N+NP++ + L + G +
Sbjct: 4 TAAAKFERQHMDSPDLGSTPPHTEPSQV-VLITNINPEVPKEKLQALLYALASSQGDILD 62
Query: 225 IKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
I + ++ F ++ + ++ G Q + + + ++
Sbjct: 63 IVVD------LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSET 109
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 64.8 bits (158), Expect = 1e-12
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
LY+G L ++ ++ L F +G + I+I D E + R FV F +D
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL---DYETEKHRGFAFVEFELAEDAAA 120
Query: 256 ALKYLNGKDV 265
A+ +N ++
Sbjct: 121 AIDNMNESEL 130
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 62.9 bits (154), Expect = 1e-12
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
LY+G L ++ ++ L F +G + I+I E + R FV F +D
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAA 64
Query: 256 ALKYLNGKDV 265
A+ +N ++
Sbjct: 65 AIDNMNESEL 74
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 68.1 bits (167), Expect = 2e-12
Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 3/81 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L++ N P T++ + ++ +A + P +R ++ +++D
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL-PSLRFNTSRR--FAYIDVTSKEDARY 174
Query: 256 ALKYLNGKDVQSYEMKLGWGK 276
++ LNG ++ Y +
Sbjct: 175 CVEKLNGLKIEGYTLVTKVSN 195
Score = 64.2 bits (157), Expect = 3e-11
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 4/85 (4%)
Query: 196 TNLYLGNLNPKIT-EQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
+ + NL+ ++ E L E F +G + I I + + C F+ F N+ E
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC--CAFMVFENKDSAE 268
Query: 255 RALKYLNGKDVQSYEMKLGWGKSVP 279
RAL+ +N + + E+ + P
Sbjct: 269 RALQ-MNRSLLGNREISVSLADKKP 292
Score = 58.5 bits (142), Expect = 2e-09
Identities = 11/94 (11%), Positives = 32/94 (34%), Gaps = 6/94 (6%)
Query: 170 EAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMW 229
+ P+A + ++ + + + T + + NL + ++ + F GP+ + +
Sbjct: 17 DEGSPAAAGLTSKKANEAL-TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA- 74
Query: 230 PRSDEEKARGRNCGFVAFMNRKDGERALKYLNGK 263
+K + F A+ +
Sbjct: 75 --DSLKKNFR--FARIEFARYDGALAAITKTHKV 104
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 63.2 bits (154), Expect = 2e-12
Identities = 20/93 (21%), Positives = 42/93 (45%), Gaps = 8/93 (8%)
Query: 184 TKGSFDSGDPC--TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRN 241
+ GS S L + N+ P + + L + +YG + S + + +D E A
Sbjct: 2 SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV--NTDSETA---- 55
Query: 242 CGFVAFMNRKDGERALKYLNGKDVQSYEMKLGW 274
V + ++ +AL LNG ++++ +K+ +
Sbjct: 56 VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY 88
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 63.0 bits (154), Expect = 2e-12
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
L++G L+ EQ L ++F +YG ++ + ++ D E R R GFV F N D + A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK---DRETQRSRGFGFVTFENIDDAKDA 70
Query: 257 LKYLNGKDV 265
+ +NGK V
Sbjct: 71 MMAMNGKSV 79
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 66.6 bits (162), Expect = 2e-12
Identities = 28/126 (22%), Positives = 51/126 (40%), Gaps = 11/126 (8%)
Query: 193 PCTTNLYLGNLNPK-ITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRK 251
+ L + NLNP+ +T Q L +FG YG + +KI++ + + V +
Sbjct: 32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADGN 83
Query: 252 DGERALKYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFNAQPAS 311
+ A+ +LNG + +++ K + + LT S L +P S
Sbjct: 84 QAQLAMSHLNGHKLHGKPIRITLSKHQNVQ--LPREGQEDQGLTKDYGNSPLHRFKKPGS 141
Query: 312 KDKHRI 317
K+ I
Sbjct: 142 KNFQNI 147
Score = 65.8 bits (160), Expect = 3e-12
Identities = 18/146 (12%), Positives = 61/146 (41%), Gaps = 8/146 (5%)
Query: 133 IKKKSNLEMFKEELKMIQEEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGD 192
+ + ++ + +++ + + + + + S + +++ +F +
Sbjct: 89 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 148
Query: 193 PCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKD 252
P + L+L N+ P ++E+ L +F G + + + R + + ++
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-------KDRKMALIQMGSVEE 201
Query: 253 GERALKYLNGKDV-QSYEMKLGWGKS 277
+AL L+ D+ +++ +++ + KS
Sbjct: 202 AVQALIDLHNHDLGENHHLRVSFSKS 227
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 62.7 bits (153), Expect = 2e-12
Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 10/90 (11%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
SG LY+GNL+P +T L ++FG + +++ FV +
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---------LKSGYAFVDYP 52
Query: 249 NRKDGERALKYLNGK-DVQSYEMKLGWGKS 277
++ RA++ L+GK ++ M++ + S
Sbjct: 53 DQNWAIRAIETLSGKVELHGKIMEVDYSVS 82
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 62.7 bits (153), Expect = 2e-12
Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 12/90 (13%)
Query: 184 TKGSFDSGDPCTTNLYLGNLN-PKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNC 242
+ G G + L++GNL ++++ L IF YG + I I
Sbjct: 11 SSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------NAF 59
Query: 243 GFVAFMNRKDGERALKYLNGKDVQSYEMKL 272
GF+ F N + A++ + + ++ L
Sbjct: 60 GFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 62.9 bits (153), Expect = 3e-12
Identities = 14/83 (16%), Positives = 34/83 (40%), Gaps = 3/83 (3%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
S C L++G + ++++E + I++ S +K + R FV + +
Sbjct: 5 SSGNCR--LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYA-SAADKMKNRGFAFVEYES 61
Query: 250 RKDGERALKYLNGKDVQSYEMKL 272
+ A + L +Q + ++
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQI 84
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 62.7 bits (153), Expect = 3e-12
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
+Y+GNL + +L F YGPL ++ I FV F + +D E A
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI--------ARNPPGFAFVEFEDPRDAEDA 53
Query: 257 LKYLNGKDVQSYEMKLGWGKSVP 279
++ L+GK + +++ +P
Sbjct: 54 VRGLDGKVICGSRVRVELSTGMP 76
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 64.5 bits (157), Expect = 4e-12
Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 4/106 (3%)
Query: 167 YSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIK 226
YS P ++ G L + NL+ +++ + E+F +G L
Sbjct: 60 YSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 119
Query: 227 IMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKL 272
+ + RS R V F R D +A+K G + M +
Sbjct: 120 VDYDRSG----RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 61.8 bits (151), Expect = 4e-12
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 12/81 (14%)
Query: 193 PCTTNLYLGNLNPK-ITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRK 251
P + L++GNL K ++++ L IF YG + I I GF+ F N +
Sbjct: 8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-----------NAFGFIQFDNPQ 56
Query: 252 DGERALKYLNGKDVQSYEMKL 272
A++ + + ++ L
Sbjct: 57 SVRDAIECESQEMNFGKKLIL 77
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 61.8 bits (151), Expect = 4e-12
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
SG +++ NL T + L + F G + I + K++G CG V F +
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIK---MENGKSKG--CGVVKFES 57
Query: 250 RKDGERALKYLNGKDVQ 266
+ ERA + +NG +
Sbjct: 58 PEVAERACRMMNGMKLS 74
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 61.9 bits (151), Expect = 6e-12
Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
S L++ L T+++L EI +G + ++++ R+ + + +V +
Sbjct: 11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAG----KPKGLAYVEYE 66
Query: 249 NRKDGERALKYLNGKDVQ 266
N +A+ ++G ++
Sbjct: 67 NESQASQAVMKMDGMTIK 84
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 61.4 bits (150), Expect = 7e-12
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 3/75 (4%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
G ++ LY+G+L+ ITE L IF +G + +I +M D + R + GF+ F +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK---DSDTGRSKGYGFITFSDS 57
Query: 251 KDGERALKYLNGKDV 265
+ RAL+ LNG ++
Sbjct: 58 ECARRALEQLNGFEL 72
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 62.9 bits (153), Expect = 9e-12
Identities = 20/116 (17%), Positives = 45/116 (38%), Gaps = 4/116 (3%)
Query: 151 EEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQ 210
E+ +++ + G ++ + + + T+L + NL + +
Sbjct: 27 EKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEG-MTSLKVDNLTYRTSPD 85
Query: 211 QLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQ 266
L +F +YG + + I D R FV F +++D E A+ ++G +
Sbjct: 86 TLRRVFEKYGRVGDVYIPR---DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 138
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 65.7 bits (159), Expect = 9e-12
Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 11/92 (11%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLME----IFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
P T +Y+ NLN KI + +L + IF ++G + I + K RG FV
Sbjct: 5 ETRPNHT-IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS----RSLKMRG--QAFV 57
Query: 246 AFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
F AL+ + G M++ + K+
Sbjct: 58 IFKEVSSATNALRSMQGFPFYDKPMRIQYAKT 89
Score = 52.2 bits (124), Expect = 3e-07
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 9/81 (11%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
L+L NL + E L +F ++ ++++ + FV F N A
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLV--------PGRHDIAFVEFDNEVQAGAA 260
Query: 257 LKYLNGKDV-QSYEMKLGWGK 276
L G + Q+ MK+ + K
Sbjct: 261 RDALQGFKITQNNAMKISFAK 281
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 62.1 bits (151), Expect = 1e-11
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
T+L + NL + + L +F +YG + + I D R FV F +++D E
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIP---RDRYTKESRGFAFVRFHDKRDAE 103
Query: 255 RALKYLNGKDV 265
A+ ++G +
Sbjct: 104 DAMDAMDGAVL 114
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 61.1 bits (148), Expect = 1e-11
Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 16/92 (17%)
Query: 195 TTNLYLGN--LNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKD 252
T +L + N L ++ QL+ + + G + ++ + + F + ++
Sbjct: 25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP---------PNKPYSFARYRTTEE 75
Query: 253 GERALKYLNGKDV-----QSYEMKLGWGKSVP 279
+RA LNGK+V Q + L + + V
Sbjct: 76 SKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQ 107
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 62.9 bits (153), Expect = 1e-11
Identities = 27/147 (18%), Positives = 56/147 (38%), Gaps = 6/147 (4%)
Query: 131 IDIKKKSNLEMFKEELKMIQEEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDS 190
+DI E+ ++ + I +E+ KG G S E + + E +
Sbjct: 5 LDIDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEP 64
Query: 191 GD---PCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAF 247
G L++ +++ + E ++ E F YG + +I + D + V +
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL---DRRTGFSKGYALVEY 121
Query: 248 MNRKDGERALKYLNGKDVQSYEMKLGW 274
K A + LNG ++ +++ W
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTIQVDW 148
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 60.0 bits (146), Expect = 2e-11
Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 2/75 (2%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
T + L N+ P +M Y LA I + D++ + R FV +
Sbjct: 5 HHHHMDT-IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIK-DKQTQQNRGFAFVQLSS 62
Query: 250 RKDGERALKYLNGKD 264
D + L+ L
Sbjct: 63 AMDASQLLQILQSLH 77
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 60.2 bits (146), Expect = 2e-11
Identities = 14/89 (15%), Positives = 33/89 (37%), Gaps = 8/89 (8%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
G P ++Y+GNL L G + +++ W R F+ +
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQGP-------RRRAFLHYP 64
Query: 249 NRKDGERALKYLNGKDVQSYEMKLGWGKS 277
+ ++A+ L G + + +++ +
Sbjct: 65 DSAAAQQAVSCLQGLRLGTDTLRVALARQ 93
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 60.3 bits (147), Expect = 2e-11
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 3/70 (4%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
LY+G L ++ ++ L F +G + I+I E + R FV F +D
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---ETEKHRGFAFVEFELAEDAAA 69
Query: 256 ALKYLNGKDV 265
A+ +N ++
Sbjct: 70 AIDNMNESEL 79
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 59.5 bits (144), Expect = 4e-11
Identities = 15/81 (18%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 198 LYLGNLNPKITEQQLM---EIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
+++ L+ ++ + +++ E FG++G + + I S +V ++ +D
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 255 RALKYLNGKDVQSYEMKLGWG 275
RA++ +N V +K G
Sbjct: 78 RAIQCVNNVVVDGRTLKASLG 98
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 59.4 bits (144), Expect = 4e-11
Identities = 12/86 (13%), Positives = 28/86 (32%), Gaps = 10/86 (11%)
Query: 181 QEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
+ GS + +++ L + E L+E ++G + + +M +
Sbjct: 2 SSGSSGSHHKVSV-SPVVHVRGLCESVVEADLVEALEKFGTICYVMMM---------PFK 51
Query: 241 NCGFVAFMNRKDGERALKYLNGKDVQ 266
V F N + + + V
Sbjct: 52 RQALVEFENIDSAKECVTFAADVPVY 77
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 59.2 bits (144), Expect = 5e-11
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 197 NLYLGNLNPKITEQQLMEIFG-RYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
+L++G+L P + + L E F Y K++ ++ + GFV F + + +R
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVL----DQTGVSKGYGFVKFTDELEQKR 66
Query: 256 ALKYLNGK-DVQSYEMKLGW 274
AL G + S ++L
Sbjct: 67 ALTECQGAVGLGSKPVRLSV 86
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 58.1 bits (141), Expect = 8e-11
Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
SG P T + + N+ ++ ++++ F Y + + +++ G V
Sbjct: 6 SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPG-SVCLKYNEKGMPTG--EAMV 62
Query: 246 AFMNRKDGERALKYLNGKDVQSYEMKL 272
AF +R + A+ LN + + S ++KL
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKL 89
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 58.5 bits (142), Expect = 8e-11
Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 3/82 (3%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
SG P T + + N+ ++ ++++ F Y + + +++ G V
Sbjct: 6 SGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPG-SVCLKYNEKGMPTG--EAMV 62
Query: 246 AFMNRKDGERALKYLNGKDVQS 267
AF +R + A+ LN + + S
Sbjct: 63 AFESRDEATAAVIDLNDRPIGS 84
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 58.0 bits (141), Expect = 1e-10
Identities = 20/77 (25%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
+ D ++++GN+ + TE+QL +IF GP+ S +++ D E + + GF + +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLV---YDRETGKPKGYGFCEYQD 59
Query: 250 RKDGERALKYLNGKDVQ 266
++ A++ LNG++
Sbjct: 60 QETALSAMRNLNGREFS 76
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 57.3 bits (139), Expect = 2e-10
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 8/81 (9%)
Query: 185 KGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGF 244
G+ T L L NL+ TE+ L E+F + IK+ + + + F
Sbjct: 6 SGNSTWSGESKT-LVLSNLSYSATEETLQEVFEKATF---IKVP----QNQNGKSKGYAF 57
Query: 245 VAFMNRKDGERALKYLNGKDV 265
+ F + +D + AL N +++
Sbjct: 58 IEFASFEDAKEALNSCNKREI 78
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 57.1 bits (138), Expect = 2e-10
Identities = 11/69 (15%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++ L + E L+E +GP++ + +M + V F + A+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM---------PKKRQALVEFEDVLGACNAV 74
Query: 258 KYLNGKDVQ 266
Y +
Sbjct: 75 NYAADNQIY 83
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 57.3 bits (139), Expect = 2e-10
Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLAS-IKIMWPR----SDEEKARGRNCGFVAFMNR 250
+++ L +T + + + F + G + + K P +D E + + V+F +
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 251 KDGERALKYLNGKDVQSYEMK 271
+ A+ + +GK+ +K
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIK 94
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 56.5 bits (137), Expect = 4e-10
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 7/82 (8%)
Query: 187 SFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVA 246
S G +++G ++ ++ E ++ F RYG + +KI+ R+ ++G GFV+
Sbjct: 1 SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG--VSKG--YGFVS 56
Query: 247 FMNRKDGERAL---KYLNGKDV 265
F N D ++ + +GK +
Sbjct: 57 FYNDVDVQKIVESQINFHGKKL 78
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 59.8 bits (144), Expect = 5e-10
Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 19/107 (17%)
Query: 180 YQEETKGSFDSGDPCTTNLYLGNLNPKIT---------EQQLMEIFGRYGPLASIKIMWP 230
Y+E+ G T LY+G ++ + E ++ +F R G + I+ +
Sbjct: 120 YREDMGGIGSFRKKNKT-LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-- 176
Query: 231 RSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
+NCGFV F + + E A + ++ + + K +
Sbjct: 177 -------ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRR 216
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 56.6 bits (137), Expect = 6e-10
Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLAS-IKIMWPR----SDEEKARGRNCGFVAFMNR 250
+++ L +T + + + F + G + + K P +D E + + V+F +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 251 KDGERALKYLNGKDVQSYEMK 271
+ A+ + +GK+ +K
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIK 88
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 56.2 bits (136), Expect = 7e-10
Identities = 12/69 (17%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
+++ NL+ E+ L E+ ++G L ++++ + + C F FM ++ ++
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV---LHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 256 ALKYLNGKD 264
L + +
Sbjct: 73 CLAAASLEA 81
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 55.2 bits (134), Expect = 8e-10
Identities = 12/72 (16%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
++Y+GN++ T ++L F G + + I+ D+ + ++ F +++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTIL---CDKFSGHPKGFAYIEFSDKESVR 62
Query: 255 RALKYLNGKDVQ 266
+L L+ +
Sbjct: 63 TSLA-LDESLFR 73
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 55.9 bits (135), Expect = 9e-10
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLAS-IKIMWPR----SDEEKARGRNCGFVAFMNR 250
+ +Y+ LN +T L + F + G + + P D+E + + V++ +
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 251 KDGERALKYLNGKDVQSYEMK 271
+ A+++ +GKD Q ++K
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLK 96
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 55.3 bits (134), Expect = 1e-09
Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 3/86 (3%)
Query: 196 TNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
L++ ++ + TE+ + + F YG + +I + D + V + K+ +
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLN---LDRRTGYLKGYTLVEYETYKEAQA 80
Query: 256 ALKYLNGKDVQSYEMKLGWGKSVPIP 281
A++ LNG+D+ + + W P
Sbjct: 81 AMEGLNGQDLMGQPISVDWCFVRGPP 106
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 57.4 bits (138), Expect = 3e-09
Identities = 15/144 (10%), Positives = 38/144 (26%), Gaps = 5/144 (3%)
Query: 168 SEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGP--LASI 225
+ P + + + LY+GNL T++ L E G + I
Sbjct: 41 MDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEI 100
Query: 226 KIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQSYEMKLGWGKSVPIPSYPI 285
K + + + V + ++ + L +++ + + + +
Sbjct: 101 KFFE---NRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEM 157
Query: 286 YIPPKMLELTVPPPPSGLPFNAQP 309
+ P
Sbjct: 158 QSRKTTQSGQMSGEGKAGPPGGSS 181
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 54.7 bits (132), Expect = 3e-09
Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 181 QEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
+++ L++ ++ + TE+ + + F YG + +I + D +
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL---DRRTGYLK 64
Query: 241 NCGFVAFMNRKDGERALKYLNGKDV 265
V + K+ + A++ LNG+D+
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDL 89
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 53.7 bits (129), Expect = 3e-09
Identities = 10/69 (14%), Positives = 29/69 (42%), Gaps = 9/69 (13%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
L++ L ++TE +++ + +G + +I ++ +G+N F+ + +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILML---------KGKNQAFLELATEEAAITMV 68
Query: 258 KYLNGKDVQ 266
Y +
Sbjct: 69 NYYSAVTPH 77
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 54.2 bits (130), Expect = 4e-09
Identities = 10/86 (11%), Positives = 31/86 (36%), Gaps = 9/86 (10%)
Query: 181 QEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
+ G S + +++ L +TE +++ + +G + ++ ++ +G+
Sbjct: 17 RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML---------KGK 67
Query: 241 NCGFVAFMNRKDGERALKYLNGKDVQ 266
N F+ + + Y
Sbjct: 68 NQAFIEMNTEEAANTMVNYYTSVTPV 93
>1sz9_A PCF11 protein; RNA polymerase II CTD interacting domain, arm
repeats, transcription; 2.10A {Saccharomyces cerevisiae}
SCOP: a.118.9.4 PDB: 1sza_A* 2bf0_X
Length = 144
Score = 54.7 bits (131), Expect = 4e-09
Identities = 30/152 (19%), Positives = 54/152 (35%), Gaps = 26/152 (17%)
Query: 466 LEDF---LRNLT-PERVKVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGRLYL 521
++DF L LT R + E+ A+ + I + +K+ Y
Sbjct: 9 VKDFNSILEELTFNSRPIITTLTKLAEENISCAQYFVDAIESRIEK--CMPKQKLYAFYA 66
Query: 522 VSDILHNCGIKISNASFYRRGFESRLFQIFTEMHITYVNLESRLKAEGLRTRVMQVFRAW 581
+ I N G S Y F LF ++ + L RT+++ +F+ W
Sbjct: 67 LDSICKNVG------SPYTIYFSRNLFNLYKRTY--------LLVDNTTRTKLINMFKLW 112
Query: 582 EDW-----AVYPKDYLIKLQNVFLGLSDAVPL 608
+ ++ L K++ FL + A L
Sbjct: 113 LNPNDTGLPLFEGSALEKIEQ-FLIKASAAAL 143
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 54.3 bits (131), Expect = 5e-09
Identities = 18/99 (18%), Positives = 35/99 (35%), Gaps = 9/99 (9%)
Query: 168 SEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKI 227
+ A E K D ++Y+GN++ T Q L F G + I I
Sbjct: 14 TAGAYTEGPPQPLSAEEKKEIDKR-----SVYVGNVDYGSTAQDLEAHFSSCGSINRITI 68
Query: 228 MWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQ 266
+ D+ + ++ F R + A+ ++ +
Sbjct: 69 L---CDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVFR 103
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 54.2 bits (130), Expect = 9e-09
Identities = 15/101 (14%), Positives = 34/101 (33%), Gaps = 5/101 (4%)
Query: 168 SEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGP--LASI 225
EP ++ +Y+G+ + T+QQL+++ G + +
Sbjct: 28 PVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87
Query: 226 KIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQ 266
K + + + V + + L+ L GK +
Sbjct: 88 KFA---ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN 125
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 53.1 bits (128), Expect = 9e-09
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
L++ +++ + E ++ E F YG + +I + D + V + K A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLN---LDRRTGFSKGYALVEYETHKQALAAK 85
Query: 258 KYLNGKDV 265
+ LNG ++
Sbjct: 86 EALNGAEI 93
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 52.9 bits (127), Expect = 9e-09
Identities = 8/69 (11%), Positives = 27/69 (39%), Gaps = 9/69 (13%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++ L +TE +++ + +G + ++ ++ +G+N F+ + +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML---------KGKNQAFIEMNTEEAANTMV 69
Query: 258 KYLNGKDVQ 266
Y
Sbjct: 70 NYYTSVTPV 78
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 52.2 bits (126), Expect = 9e-09
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
N+Y+GNL T +Q+ E+F ++G + ++K++ D E + + GFV M + A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLI---YDRETKKPKGFGFVE-MQEESVSEA 58
Query: 257 LKYLNGKDVQ 266
+ L+ D
Sbjct: 59 IAKLDNTDFM 68
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 52.2 bits (126), Expect = 1e-08
Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 5/72 (6%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGP--LASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
LY+GNL T++ L E G + IK + + + V + +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFF---ENRANGQSKGFALVGVGSEASSK 59
Query: 255 RALKYLNGKDVQ 266
+ + L +++
Sbjct: 60 KLMDLLPKRELH 71
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 52.6 bits (127), Expect = 1e-08
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 185 KGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGF 244
G P + L++ L+ TE+ L E F +I+ D E + GF
Sbjct: 6 SGPNARSQP-SKTLFVKGLSEDTTEETLKESFDGSV---RARIVT---DRETGSSKGFGF 58
Query: 245 VAFMNRKDGERALKYLNGKDV 265
V F + +D + A + + ++
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEI 79
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 51.3 bits (123), Expect = 2e-08
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMW--PRSDEEKARGRNCGFVAFMNRKDGER 255
LY+GN+ ITE+ +M+ F L + P + + +N F+ F + + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 256 ALKYLNGKDVQSYEMKLG 273
A+ +G Q +K+
Sbjct: 69 AMA-FDGIIFQGQSLKIR 85
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 51.1 bits (123), Expect = 3e-08
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 8/78 (10%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
L NL+ ITE +L E+F + R + + + ++ F
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEI--------RLVSQDGKSKGIAYIEFK 61
Query: 249 NRKDGERALKYLNGKDVQ 266
+ D E+ L+ G ++
Sbjct: 62 SEADAEKNLEEKQGAEID 79
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 50.5 bits (121), Expect = 4e-08
Identities = 9/83 (10%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
++ + + NL Q++ ++ Y R + FV +N + +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDL----------KYCYVDRNKRTAFVTLLNGEQAQ 54
Query: 255 RALKYLNGKDVQSYEMKLGWGKS 277
A++ + + ++ + +
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPT 77
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 50.7 bits (122), Expect = 4e-08
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 7/84 (8%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
GS S + +++G + E +L E F ++G + + ++ D EK R R GF+
Sbjct: 1 GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMI---YDAEKQRPRGFGFI 57
Query: 246 AFMNRKDGERALK----YLNGKDV 265
F + + ++A+ + GK V
Sbjct: 58 TFEDEQSVDQAVNMHFHDIMGKKV 81
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 50.1 bits (120), Expect = 7e-08
Identities = 11/67 (16%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 199 YLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALK 258
+ + + ++ L +F + G + +++ DE + + FV + D ++ +K
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPI---DEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 259 YLNGKDV 265
+GK +
Sbjct: 73 SFHGKRL 79
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 51.4 bits (124), Expect = 1e-07
Identities = 13/75 (17%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
T +++G + P + ++ E F ++G + ++M D++ + R GFV + + +
Sbjct: 87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM---LDKDTGQSRGFGFVTYDSADAVD 143
Query: 255 RALK----YLNGKDV 265
R + + +
Sbjct: 144 RVCQNKFIDFKDRKI 158
Score = 50.6 bits (122), Expect = 2e-07
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
+ +++G LN TE L E FG+YG + +KIM D R R GF++F +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIM---KDPATGRSRGFGFLSFEKPSSVD 59
Query: 255 RALK---YLNGKDV 265
+K L+GK +
Sbjct: 60 EVVKTQHILDGKVI 73
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 49.2 bits (118), Expect = 1e-07
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+LGNL +TE+ + E F +++++ S+ E+ +G G+ F + AL
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKG--FGYAEFEDLDSLLSAL 78
Query: 258 KYLNGKDVQ 266
LN + +
Sbjct: 79 S-LNEESLG 86
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 49.6 bits (119), Expect = 1e-07
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 4/69 (5%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
++ L +I + L + F G + ++I+ SD R + +V F + A+
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRII---SDRNSRRSKGIAYVEFCEIQSVPLAI 84
Query: 258 KYLNGKDVQ 266
L G+ +
Sbjct: 85 G-LTGQRLL 92
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 49.2 bits (118), Expect = 2e-07
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 7/81 (8%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
D T +++G L T+ L + F +G + ++ +D + + R GFV
Sbjct: 11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVI---TDRQTGKSRGYGFVTMA 67
Query: 249 NRKDGERALK----YLNGKDV 265
+R ERA K ++G+
Sbjct: 68 DRAAAERACKDPNPIIDGRKA 88
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 48.8 bits (117), Expect = 2e-07
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+LGNL +TE+ + E F +++++ S+ E+ +G G+ F + AL
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKG--FGYAEFEDLDSLLSAL 74
Query: 258 KYLNGKDVQ 266
LN + +
Sbjct: 75 S-LNEESLG 82
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 48.0 bits (115), Expect = 2e-07
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 11/78 (14%)
Query: 191 GDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
G ++ +++G +TE +L E F +YG + + I P R FV F +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF--------RAFAFVTFADD 52
Query: 251 KDGERALK---YLNGKDV 265
+ + + G V
Sbjct: 53 QIAQSLCGEDLIIKGISV 70
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 48.6 bits (116), Expect = 3e-07
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 10/75 (13%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+ + L P + Q L + G + + G V F+ ++D A+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVY----------RDGTGVVEFVRKEDMTYAV 67
Query: 258 KYLNGKDVQSYEMKL 272
+ L+ +S+E +
Sbjct: 68 RKLDNTKFRSHEGET 82
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 47.5 bits (114), Expect = 3e-07
Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 7/72 (9%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++G L+P E+++ E FG +G + SI++ D + + R F+ F + ++ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELP---MDNKTNKRRGFCFITFKEEEPVKKIM 58
Query: 258 K----YLNGKDV 265
+ +
Sbjct: 59 EKKYHNVGLSKC 70
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 47.7 bits (113), Expect = 6e-07
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARG--RNCGFVAF 247
SG + +++G L P I E ++ F R+GP + + WP E K+ + F+ F
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGP---LVVDWPHKAESKSYFPPKGYAFLLF 59
Query: 248 MNRKDGERALK 258
+ +
Sbjct: 60 QEESSVQALID 70
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 47.1 bits (112), Expect = 9e-07
Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 186 GSFDSGDPCTTN-LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGF 244
GS S P + + NL + Q L ++ + S G
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETT------FSSVNTRDFDGTGA 71
Query: 245 VAFMNRKDGERALKYLNGKDVQSYEMKL 272
+ F + + AL+ LN + + + +
Sbjct: 72 LEFPSEEILVEALERLNNIEFRGSVITV 99
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 46.8 bits (112), Expect = 1e-06
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 184 TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCG 243
+ G +SG L++G L+ T++ L F +YG + IM D+ + R G
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIM---KDKTTNQSRGFG 61
Query: 244 FVAFMNRKDGERALK----YLNGKDV 265
FV F + L L+G+++
Sbjct: 62 FVKFKDPNCVGTVLASRPHTLDGRNI 87
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 45.5 bits (109), Expect = 1e-06
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++G L+ T + + F ++G + +M D+ R R GFV F + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLM---FDKTTNRHRGFGFVTFESEDIVEKVC 58
Query: 258 K----YLNGKDV 265
+ +N K V
Sbjct: 59 EIHFHEINNKMV 70
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 45.6 bits (109), Expect = 1e-06
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++G L+ + T++ L E FG++G + +M D R R GFV FM++ ++ L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVM---RDPLTKRSRGFGFVTFMDQAGVDKVL 59
Query: 258 K----YLNGKDV 265
L+ K +
Sbjct: 60 AQSRHELDSKTI 71
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 46.3 bits (110), Expect = 2e-06
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 7/88 (7%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLA-SIKIMWPRSDEEKARGRNCGF 244
G D ++ N+ IT+ +++ ++ ++ + +G
Sbjct: 7 GEGDVNSAKVC-AHITNIPFSITKMDVLQFLEGIPVDENAVHVL----VDNNGQGLGQAL 61
Query: 245 VAFMNRKDGERALKYLNGKDVQSYEMKL 272
V F N D ++ + L+ K + E +
Sbjct: 62 VQFKNEDDARKSER-LHRKKLNGREAFV 88
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 48.1 bits (115), Expect = 2e-06
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 7/81 (8%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
+++G + E L + F +YG + I+IM +D + R FV F
Sbjct: 98 PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM---TDRGSGKKRGFAFVTFD 154
Query: 249 NRKDGERALK----YLNGKDV 265
+ ++ + +NG +
Sbjct: 155 DHDSVDKIVIQKYHTVNGHNC 175
Score = 47.7 bits (114), Expect = 3e-06
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 195 TTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGE 254
L++G L+ + T++ L F ++G L +M D R R GFV + ++ +
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVM---RDPNTKRSRGFGFVTYATVEEVD 69
Query: 255 RALK----YLNGKDV 265
A+ ++G+ V
Sbjct: 70 AAMNARPHKVDGRVV 84
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 45.4 bits (108), Expect = 3e-06
Identities = 20/88 (22%), Positives = 32/88 (36%), Gaps = 14/88 (15%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
SG ++++ + QL E F +GP+AS+ + K +G V +
Sbjct: 3 SGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMD-------KDKGV-FAIVEMGD 54
Query: 250 RKDGERALK----YLNGK--DVQSYEMK 271
E L L G V+ E K
Sbjct: 55 VGAREAVLSQSQHSLGGHRLRVRPREQK 82
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 44.9 bits (107), Expect = 3e-06
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 7/72 (9%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++G L+ +++ L + F ++G + I D R R GF+ F + E+ L
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIK---MDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 258 K----YLNGKDV 265
L+G+ +
Sbjct: 71 DQKEHRLDGRVI 82
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 46.6 bits (110), Expect = 4e-06
Identities = 14/93 (15%), Positives = 35/93 (37%), Gaps = 9/93 (9%)
Query: 186 GSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFV 245
G +G + + NL +T L +IF ++G + I + +
Sbjct: 37 GMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF-------TKNNQFQALL 89
Query: 246 AFMNRKDGERALKYLNGKDV--QSYEMKLGWGK 276
+ + + A L+G+++ +++ + K
Sbjct: 90 QYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.7 bits (106), Expect = 5e-06
Identities = 11/67 (16%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 197 NLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
++Y+ T + E G + +I++ R+ + +G FV F + + ++
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR--RTLHKAFKG--SIFVVFDSIESAKKF 68
Query: 257 LKYLNGK 263
++ K
Sbjct: 69 VETPGQK 75
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 45.4 bits (107), Expect = 7e-06
Identities = 19/107 (17%), Positives = 41/107 (38%), Gaps = 11/107 (10%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+ + NL +T L +IF ++G + I + + + + + A
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF-------TKNNQFQALLQYADPVSAQHAK 83
Query: 258 KYLNGKDV--QSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSG 302
L+G+++ +++ + K + Y K + T P PSG
Sbjct: 84 LSLDGQNIYNACCTLRIDFSKLTSLNVK--YNNDKSRDYTRPDLPSG 128
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.1 bits (105), Expect = 8e-06
Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 6/84 (7%)
Query: 185 KGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGF 244
T++L + L K TEQ L E F +G + +++ D + + GF
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVK---KDLKTGHSKGFGF 61
Query: 245 VAFMNRKDGERALK---YLNGKDV 265
V F + + + ++G+
Sbjct: 62 VRFTEYETQVKVMSQRHMIDGRWC 85
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 44.2 bits (105), Expect = 8e-06
Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 5/69 (7%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
Y+GNL + + IF + S++++ D++ + + +V F + AL
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLV---RDKDTDKFKGFCYVEFDEVDSLKEAL 73
Query: 258 KYLNGKDVQ 266
+G +
Sbjct: 74 T-YDGALLG 81
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 44.5 bits (105), Expect = 1e-05
Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 4/83 (4%)
Query: 181 QEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
Q+ +GS + + L L T++++++ F + + + P E K G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL-PVDPEGKITG- 85
Query: 241 NCGFVAFMNRKDGERALKYLNGK 263
FV F +++ E+AL + +
Sbjct: 86 -EAFVQFASQELAEKALG-KHKE 106
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 44.2 bits (105), Expect = 1e-05
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+++G L+ + T++ L E FG++G + +M D R R GFV FM++ ++ L
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVM---RDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 258 K----YLNGKDV 265
L+ K +
Sbjct: 85 AQSRHELDSKTI 96
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 44.0 bits (104), Expect = 1e-05
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 10/75 (13%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+ + L P + Q L + G + + G V F+ ++D A+
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVY----------RDGTGVVEFVRKEDMTYAV 68
Query: 258 KYLNGKDVQSYEMKL 272
+ L+ +S+E +
Sbjct: 69 RKLDNTKFRSHEGET 83
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 43.4 bits (103), Expect = 1e-05
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
SG C T + L +TE+ +ME P +I+I R+ G FV F N
Sbjct: 6 SGTTCHT-VKLRGAPFNVTEKNVMEFLAPLKP-VAIRI--VRNAHGNKTG--YIFVDFSN 59
Query: 250 RKDGERALKYLNGKDVQSYEMKLGWGKSVP 279
++ ++ALK N + + +++ KS P
Sbjct: 60 EEEVKQALK-CNREYMGGRYIEVFREKSGP 88
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 47.5 bits (112), Expect = 1e-05
Identities = 26/144 (18%), Positives = 51/144 (35%), Gaps = 4/144 (2%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
GD T L++ +N TE +L F YGP+ I ++ + + R F+ + +
Sbjct: 98 QGDAFKT-LFVARVNYDTTESKLRREFEVYGPIKRIHMV---YSKRSGKPRGYAFIEYEH 153
Query: 250 RKDGERALKYLNGKDVQSYEMKLGWGKSVPIPSYPIYIPPKMLELTVPPPPSGLPFNAQP 309
+D A K+ +GK + + + + + + L T ++
Sbjct: 154 ERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGR 213
Query: 310 ASKDKHRIPKLRPGEPLTREDLDR 333
++ P D DR
Sbjct: 214 DDTSRYDERPGPSPLPHRDRDRDR 237
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 42.8 bits (101), Expect = 1e-05
Identities = 11/73 (15%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 198 LYLGNLNPKITEQQ-------LMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNR 250
+ + N+ P++ + + +IF ++G + + ++ K +G F+ + +
Sbjct: 4 IVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE---EDGKTKG--YIFLEYASP 57
Query: 251 KDGERALKYLNGK 263
A+K +G
Sbjct: 58 AHAVDAVKNADGY 70
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 44.4 bits (105), Expect = 2e-05
Identities = 15/101 (14%), Positives = 31/101 (30%), Gaps = 6/101 (5%)
Query: 167 YSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIK 226
S A + + F +++ L K TE + F P+ +
Sbjct: 18 GSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVH 76
Query: 227 IMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGKDVQS 267
I + + G V F ++ A+ + ++Q
Sbjct: 77 I--EIGPDGRVTG--EADVEFATHEEAVAAMS-KDRANMQH 112
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 43.0 bits (102), Expect = 2e-05
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 12/84 (14%)
Query: 185 KGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGF 244
+GS + +++G +T ++L + F +YG + + I P R F
Sbjct: 2 RGS-HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF--------RAFAF 52
Query: 245 VAFMNRKDGERALK---YLNGKDV 265
V F + K + + G V
Sbjct: 53 VTFADDKVAQSLCGEDLIIKGISV 76
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 42.3 bits (100), Expect = 5e-05
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
L++G L+ + TE+ L + ++G L +M D R R GFV F + + + A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVM---RDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 258 K----YLNGKDV 265
++G+ V
Sbjct: 87 AARPHSIDGRVV 98
>3d9j_A RNA-binding protein 16; SCAF8, RNA polymerase II CTD interacting
domain, arm repeats phospho-CTD, phosphoprotein,
transcription; 1.60A {Homo sapiens} PDB: 3d9k_A* 3d9l_A*
3d9m_A* 3d9n_A* 3d9p_A* 3d9i_A 3d9o_A* 2diw_A
Length = 145
Score = 43.2 bits (101), Expect = 6e-05
Identities = 11/120 (9%), Positives = 41/120 (34%), Gaps = 12/120 (10%)
Query: 487 CMEHSDAAEEICECIMESLSNESTALHKKIGRLYLVSDILHNCGIKIS-NASFYRRGFES 545
++ + + + + + + K+ LY++ I+ + + F +
Sbjct: 33 AIKAIKFYKHVVQSVEKFIQKCKPE--YKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSN 90
Query: 546 RLFQIFTEMHITYVNLESRLKAEGLRTRVMQVFRAWEDWAVYPKDYLIKLQNVFLGLSDA 605
+ F ++ ++++++V W+ V+ + + L ++ L
Sbjct: 91 NIISTFQNLYRC---------PGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAALEHH 141
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 41.6 bits (98), Expect = 6e-05
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 8/86 (9%)
Query: 184 TKGSFDSGDPCTTN--LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRN 241
+ GS S TT +++ L + TE + F P + I + + G
Sbjct: 2 SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHI--EIGPDGRVTG-- 56
Query: 242 CGFVAFMNRKDGERALKYLNGKDVQS 267
V F +D A+ + ++Q
Sbjct: 57 EADVEFATHEDAVAAMA-KDKANMQH 81
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 42.1 bits (99), Expect = 7e-05
Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 5/86 (5%)
Query: 182 EETKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRN 241
++ S + +YL L + + +++ F + + I KA G
Sbjct: 13 QKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVED-SIYIAYGPNGKATG-- 68
Query: 242 CGFVAFMNRKDGERALKYLNGKDVQS 267
GFV F N D + AL + + + +
Sbjct: 69 EGFVEFRNEADYKAALC-RHKQYMGN 93
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 41.6 bits (98), Expect = 7e-05
Identities = 11/76 (14%), Positives = 32/76 (42%), Gaps = 13/76 (17%)
Query: 196 TNLYLGNLNPKITEQQ-------LMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFM 248
+ + + N+ P++ + + +IF ++G + + ++ K +G F+ +
Sbjct: 16 SVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE---EDGKTKG--YIFLEYA 69
Query: 249 NRKDGERALKYLNGKD 264
+ A+K +G
Sbjct: 70 SPAHAVDAVKNADGYK 85
>2dt7_B Splicing factor 3 subunit 1; structure genomics, SF3A120, SF3A60,
SURP domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.217.1.1
Length = 85
Score = 40.6 bits (95), Expect = 1e-04
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 354 LMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRW 401
L ++ +FV R G F +M KE N + FL P H + +
Sbjct: 32 LDVVKLTAQFVARNGRQFLTQLMQKEQRNYQFDFL----RPQHSLFNY 75
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 42.5 bits (99), Expect = 2e-04
Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 192 DPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRK 251
D ++Y+ T + E G + +I++ R+ + +G FV F + +
Sbjct: 106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM--RRTLHKAFKG--SIFVVFDSIE 161
Query: 252 DGERALKYLNGK 263
++ ++ K
Sbjct: 162 SAKKFVETPGQK 173
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 39.7 bits (93), Expect = 4e-04
Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 6/84 (7%)
Query: 184 TKGSFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCG 243
+ G +P + + + E + + F ++ + + + G G
Sbjct: 5 SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRV-DAVHL--LKDHVGRNNG--NG 59
Query: 244 FVAFMNRKDGERALKYLNGKDVQS 267
V F++ +D ALK N +
Sbjct: 60 LVKFLSPQDTFEALK-RNRMLMIQ 82
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 39.9 bits (93), Expect = 4e-04
Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 4/64 (6%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLAS--IKIMWPRSDEEKARGRNCGFVAFMNRKDGER 255
+ + L T ++++ FG++ P+ I++ + + G FV F + +
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTG--DAFVLFACEEYAQN 83
Query: 256 ALKY 259
AL+
Sbjct: 84 ALRK 87
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 39.0 bits (91), Expect = 5e-04
Identities = 11/61 (18%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 198 LYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERAL 257
+ L L +++++++ F + + + + + R FV F +++ E+AL
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTL---PVDFQGRSTGEAFVQFASQEIAEKAL 74
Query: 258 K 258
K
Sbjct: 75 K 75
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 38.0 bits (88), Expect = 0.002
Identities = 11/70 (15%), Positives = 30/70 (42%), Gaps = 10/70 (14%)
Query: 198 LYLGNL-NPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
++L NL + ++ ++++ YG + + +M R ++ F+ R+D
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM---------RMKSQAFIEMETREDAMAM 78
Query: 257 LKYLNGKDVQ 266
+ + K +
Sbjct: 79 VDHCLKKALW 88
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 39.0 bits (90), Expect = 0.002
Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 79 RRREDTSEKGKLYKPQ--SRLQEDKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKKK 136
R ++ E + ++ + RLQE D+++ E+ R K E +++ +++ K
Sbjct: 79 RLTQE-PESIRKWREEQRKRLQE-LDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKI 136
Query: 137 SNLEMFKEELKMIQEEREE 155
+N + Q+ +
Sbjct: 137 NNRI---ADKAFYQQPDAD 152
Score = 33.2 bits (75), Expect = 0.21
Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 13/70 (18%)
Query: 5 TMKKQIAEQKLKAFSIGSMGAKRTLSKKEQEEQKKKEQEAAAAQAFEEFVATFQENPAA- 63
+++K EQ+ KR + ++E A + EE+ E
Sbjct: 86 SIRKWREEQR-----------KRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKN 134
Query: 64 -KTNKVWVKA 72
N++ KA
Sbjct: 135 KINNRIADKA 144
Score = 31.3 bits (70), Expect = 0.82
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 748 ERIQGDSGEDDSAAREEKKEANKSERSDRKKSPSPAAREEKKEANKSERSDRKK 801
+R+Q + +E +E K + + + + E+ E NK K
Sbjct: 96 KRLQ-ELDAASKVMEQEWREKAKKDLEEWNQR-----QSEQVEKNKINNRIADK 143
Score = 30.1 bits (67), Expect = 2.0
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 95 SRLQEDKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKKKSNLEMFKEELKMIQEERE 154
RL ++ +S EE + L + S+ + K K +LE + + Q E+
Sbjct: 78 DRLTQEPESIRKWREEQRKRLQELDAASK--VMEQEWREKAKKDLEEWNQR----QSEQV 131
Query: 155 ERHK 158
E++K
Sbjct: 132 EKNK 135
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 37.2 bits (85), Expect = 0.007
Identities = 9/28 (32%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 152 EREERHKYKGVLKGVYSEEAEPPSAIAI 179
E++ K + LK +Y++++ P A+AI
Sbjct: 18 EKQALKKLQASLK-LYADDSAP--ALAI 42
Score = 30.7 bits (68), Expect = 1.1
Identities = 6/22 (27%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 764 EKKEANKSERSDRKKSP--SPA 783
EK+ K + S + + +PA
Sbjct: 18 EKQALKKLQASLKLYADDSAPA 39
Score = 27.6 bits (60), Expect = 9.7
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 86 EKGKLYKPQSRLQEDKDSSA 105
EK L K Q+ L+ D SA
Sbjct: 18 EKQALKKLQASLKLYADDSA 37
>1ux6_A Thrombospondin-1; extracellular matrix, calcium binding, L-type
lectin, glycoprotein, cell adhesion, calcium-binding,
heparin- binding; 1.9A {Homo sapiens} SCOP: b.29.1.16
g.75.1.1
Length = 350
Score = 38.5 bits (89), Expect = 0.008
Identities = 19/85 (22%), Positives = 31/85 (36%), Gaps = 24/85 (28%)
Query: 601 GLSDAVPLDANNGNEEDEDLDGAPLSDVDGEDLDGVPLDGAALMKSLQRLPHSSSAPDED 660
L+D PL+ N ++ D D D + + +D+D DG ++
Sbjct: 11 ALADNCPLEHN-PDQLDSDSDRIGDTCDNNQDIDE---DG-----------------HQN 49
Query: 661 DIDGVPCTYNITSATMDGEDLDGVP 685
++D P N A D DG
Sbjct: 50 NLDNCPYVPNANQADHDK---DGKG 71
Score = 31.9 bits (72), Expect = 0.90
Identities = 31/144 (21%), Positives = 47/144 (32%), Gaps = 16/144 (11%)
Query: 604 DAVPLDANNGNEEDEDLDGAP-LSDVDGEDLDGVPLDGAALMKSLQRLPHSS-------- 654
D P N N+ D D DG D D +D DG+P D L P
Sbjct: 52 DNCPYVPN-ANQADHDKDGKGDACDHD-DDNDGIPDDKDNCR--LVPNPDQKDSDGDGRG 107
Query: 655 -SAPDEDDIDGVPCTYNI--TSATMDGEDLDGVPMDKVKPARAATFIPSKWETVEENEDS 711
+ D+ D D VP +I + + D M + P + P+ + E
Sbjct: 108 DACKDDFDHDSVPDIDDICPENVDISETDFRRFQMIPLDPKGTSQNDPNWVVRHQGKELV 167
Query: 712 AVTSSKWDDVEQSESKDDSNSKGT 735
+S + + + GT
Sbjct: 168 QTVNSDPGLAVGYDEFNAVDFSGT 191
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 36.2 bits (83), Expect = 0.009
Identities = 20/92 (21%), Positives = 28/92 (30%), Gaps = 10/92 (10%)
Query: 183 ETKGSFDSGDPCTTNLYLGNLNP--KITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGR 240
G+ D L L NP IT L + G + I I
Sbjct: 11 TRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN--------G 62
Query: 241 NCGFVAFMNRKDGERALKYLNGKDVQSYEMKL 272
V F + ++A LNG D+ + L
Sbjct: 63 IQAMVEFESVLCAQKAKAALNGADIYAGCCTL 94
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 35.7 bits (82), Expect = 0.014
Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 9/76 (11%)
Query: 187 SFDSGDPCTTNLYLGNLNPKITEQQLMEIFGRY---GPLASIKIMWPRSDEEKARGRNCG 243
+ G+ + L L + + + +A + + E + G
Sbjct: 11 GPEGGEGYV--VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHF--IYTREGRQSG--EA 64
Query: 244 FVAFMNRKDGERALKY 259
FV + D + ALK
Sbjct: 65 FVELESEDDVKLALKK 80
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 34.7 bits (79), Expect = 0.014
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 9/76 (11%)
Query: 190 SGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMN 249
+ ++ L L NL +I L + ++GPL S + +
Sbjct: 2 AMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHP---------YLNQGIALCKYTT 52
Query: 250 RKDGERALKYLNGKDV 265
R++ +A LN +
Sbjct: 53 REEANKAQMALNNCVL 68
>1yo8_A Thrombospondin-2; EGF, Ca(2+)-binding domains, lectin domain,
disulfide, cell; HET: NAG MAN; 2.60A {Homo sapiens} PDB:
2rhp_A*
Length = 634
Score = 36.9 bits (85), Expect = 0.030
Identities = 31/138 (22%), Positives = 40/138 (28%), Gaps = 25/138 (18%)
Query: 604 DAVPLDANNGNEEDEDLDGAPLSDVDGEDLDGVPLDGAALMKSLQRLPHSSSAPDED-DI 662
D P +N N+ D D DG + +D DGVP D + ED D
Sbjct: 327 DNCPYISN-ANQADHDRDGQGDACDPDDDNDGVPDDRDN-------CRLVFNPDQEDLDG 378
Query: 663 DGVPCTYNITSATMDGEDLDGVP--MDKVKPARAATFIPSKWETVEENEDSAVTSSKWDD 720
DG D D D +P D + ET N K
Sbjct: 379 DGRGD------ICKDDFDNDNIPDIDD------VCPENNAISETDFRNFQMVPLDPKGTT 426
Query: 721 VEQSESKDDSNSKGTGLT 738
Q + +G L
Sbjct: 427 --QIDPNWVIRHQGKELV 442
Score = 30.0 bits (67), Expect = 3.6
Identities = 18/85 (21%), Positives = 27/85 (31%), Gaps = 4/85 (4%)
Query: 601 GLSDAVPLDANNGNEEDEDLDGAPLSDV--DGEDLDGVP--LDGAALMKSLQRLPHSSSA 656
G+ D N + EDLDG D+ D D D +P D ++ +
Sbjct: 357 GVPDDRDNCRLVFNPDQEDLDGDGRGDICKDDFDNDNIPDIDDVCPENNAISETDFRNFQ 416
Query: 657 PDEDDIDGVPCTYNITSATMDGEDL 681
D G G++L
Sbjct: 417 MVPLDPKGTTQIDPNWVIRHQGKEL 441
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 34.1 bits (78), Expect = 0.030
Identities = 10/70 (14%), Positives = 26/70 (37%), Gaps = 10/70 (14%)
Query: 198 LYLGNL-NPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERA 256
+++ + K QL+++ +G +++ I+ N F+ +D + A
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL---------NKINEAFIEMATTEDAQAA 68
Query: 257 LKYLNGKDVQ 266
+ Y
Sbjct: 69 VDYYTTTPAL 78
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 34.2 bits (78), Expect = 0.044
Identities = 12/106 (11%), Positives = 23/106 (21%), Gaps = 3/106 (2%)
Query: 155 ERHKYKGVLKGVYSEEAEPPSAIAIYQEETKGSFDSGDPCTTNLYLGNLNPKITEQQLME 214
H + V + L L + + +
Sbjct: 4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQN 63
Query: 215 IFGRYGPLASIK-IMWPRSDEEKARGRNCGFVAFMNRKDGERALKY 259
+ + + E + G FV + D + ALK
Sbjct: 64 FLSDCTIHDGAAGVHFIYTREGRQSG--EAFVELGSEDDVKMALKK 107
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 33.7 bits (77), Expect = 0.047
Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 4/71 (5%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRYGPLASIK-IMWPRSDEEKARGRNCGFVAF 247
+ D + L T + ++ F I + + + K RG +
Sbjct: 6 EEVDDVFL-IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRG--DALIEM 62
Query: 248 MNRKDGERALK 258
+ +D ++AL+
Sbjct: 63 ESEQDVQKALE 73
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 35.1 bits (80), Expect = 0.078
Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 19/112 (16%)
Query: 195 TTNLYLGNLNPK--ITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKD 252
T +L + N ++ QL+ + + G + ++ + F + ++
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL---------LMPPNKPYSFARYRTTEE 68
Query: 253 GERALKYLNGKDVQSYEMKLGWGKSVPI-PSYPIYIPPKMLELTVPPPPSGL 303
+RA LNGK+V G+ + + ++ + K EL P GL
Sbjct: 69 SKRAYVTLNGKEVVDDL-----GQKITLYLNFVEKVQWK--ELRPQALPPGL 113
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 32.8 bits (74), Expect = 0.088
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 16/91 (17%)
Query: 191 GDPCTTNLYLGNL----NPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVA 246
C T LY+ NL + K +L + G K++ +
Sbjct: 5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGG----KVLSITG--------CSAILR 52
Query: 247 FMNRKDGERALKYLNGKDVQSYEMKLGWGKS 277
F+N+ ERA K + +DV + + +
Sbjct: 53 FINQDSAERAQKRMENEDVFGNRIIVSFTPK 83
>1x4p_A Putative splicing factor, arginine/serine-rich 14; SURP domain,
SFRS14 protein, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.217.1.1
Length = 66
Score = 31.3 bits (70), Expect = 0.14
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 2/62 (3%)
Query: 350 DRTLLMLIHRMVEFVVREGPMFEAMIMNKEISNPLYRFLFENQSPAHIYYRWKMYSILQG 409
+ + I ++V+ V+ + + KE +P Y FL + S + YY+ K+ + +
Sbjct: 4 GSSGVGTIDQLVKRVIEGSLSPKERTLLKE--DPAYWFLSDENSLEYKYYKLKLAEMQRS 61
Query: 410 DQ 411
Sbjct: 62 GP 63
>3fby_A COMP, cartilage oligomeric matrix protein; signature domain, cell
adhesion, disease mutation, dwarfism, EGF-like domain,
glycoprotein, secreted; HET: NAG MAN; 3.15A {Homo
sapiens}
Length = 551
Score = 34.5 bits (79), Expect = 0.16
Identities = 17/85 (20%), Positives = 25/85 (29%), Gaps = 23/85 (27%)
Query: 601 GLSDAVPLDANNGNEEDEDLDGAPLSDVDGEDLDGVPLDGAALMKSLQRLPHSSSAPDED 660
DA + N++ +D D D +D+DG D +
Sbjct: 135 KWGDACDNCRSQKNDDQKDTDQDGRGDACDDDIDG---DR-----------------IRN 174
Query: 661 DIDGVPCTYNITSATMDGEDLDGVP 685
D P N DG DG+
Sbjct: 175 QADNCPRVPNSDQKDSDG---DGIG 196
Score = 33.8 bits (77), Expect = 0.23
Identities = 17/85 (20%), Positives = 22/85 (25%), Gaps = 26/85 (30%)
Query: 601 GLSDAVPLDANNGNEEDEDLDGAPLSDVDGEDLDGVPLDGAALMKSLQRLPHSSSAPDED 660
D N+G E D+D + D D DG DG +
Sbjct: 79 CRKDNCVTVPNSGQE---DVDRDGIGDACDPDADG---DG-----------------VPN 115
Query: 661 DIDGVPCTYNITSATMDGEDLDGVP 685
+ D P N D D
Sbjct: 116 EKDNCPLVRNPDQRNTDE---DKWG 137
Score = 32.6 bits (74), Expect = 0.60
Identities = 21/83 (25%), Positives = 24/83 (28%), Gaps = 26/83 (31%)
Query: 603 SDAVPLDANNGNEEDEDLDGAPLSDVDGEDLDGVPLDGAALMKSLQRLPHSSSAPDEDDI 662
D P N+ E D D DG + D +D DGVP D
Sbjct: 237 RDNCPTVPNSAQE-DSDHDGQGDACDDDDDNDGVP----------------------DSR 273
Query: 663 DGVPCTYNITSATMDGEDLDGVP 685
D N D DGV
Sbjct: 274 DNCRLVPNPGQEDADR---DGVG 293
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 32.1 bits (72), Expect = 0.17
Identities = 9/60 (15%), Positives = 22/60 (36%), Gaps = 8/60 (13%)
Query: 204 NPKITEQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNGK 263
++ L+ + +YG + ++ + ++ V F K E A++ G
Sbjct: 26 KGGYSKDVLLRLLQKYGEVLNLVL--------SSKKPGTAVVEFATVKAAELAVQNEVGL 77
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 31.4 bits (71), Expect = 0.31
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 209 EQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNG 262
E+ E+ +YG + + + + + G +V F +D E+A+ LN
Sbjct: 41 EEVFTEMEEKYGEVEEMNV--CDNLGDHLVGN--VYVKFRREEDAEKAVIDLNN 90
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 33.3 bits (75), Expect = 0.42
Identities = 13/125 (10%), Positives = 41/125 (32%), Gaps = 8/125 (6%)
Query: 673 SATMDGEDL----DGVPMDKVKPARAATFIPSKWETVEENEDSAVTSSKWDDVEQSESKD 728
+ MD DL + P++ + + ++ + + E E+
Sbjct: 33 TEFMDSTDLFDVFEETPVELPTDSNGEKNADTNVGDTPDHTQDKKHGLEEEKEEHEENNS 92
Query: 729 DSNSKGTGLTSSRRGDLSSERIQGDSGEDDSAAREEKKEANKSERSDRKKSPSPAAREEK 788
++ + S++ + DS +E +E + S+ ++ +
Sbjct: 93 ENKK----IKSNKSKTEDKNKKVVVPVLADSFEQEASREVDASKGLTNSETLQVEQDGKV 148
Query: 789 KEANK 793
+ +++
Sbjct: 149 RLSHQ 153
>3clj_A Protein NRD1; CTD-interacting domain, nucleus, phosphoprotein, RNA
polymer binding protein, RNA binding protein; 2.10A
{Saccharomyces cerevisiae}
Length = 157
Score = 31.7 bits (71), Expect = 0.45
Identities = 18/124 (14%), Positives = 48/124 (38%), Gaps = 5/124 (4%)
Query: 479 KVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGRLYLVSDIL---HNCGIKISN 535
++ + + ++H D +I I++ K+G LY++ I + SN
Sbjct: 24 RIKKLTTYALDHIDIESKIISLIIDYS--RLCPDSHKLGSLYIIDSIGRAYLDETRSNSN 81
Query: 536 ASFYRRGFESRLFQIFTEMHITYVNLESRLKAEGLRTRVMQVFRAWEDWAVYPKDYLIKL 595
+S + G + E+ ++ + + ++ + W+ ++ K YL +
Sbjct: 82 SSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAI 141
Query: 596 QNVF 599
++
Sbjct: 142 RSKC 145
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 32.5 bits (74), Expect = 0.75
Identities = 22/135 (16%), Positives = 50/135 (37%), Gaps = 11/135 (8%)
Query: 25 AKRTLSKKEQEEQKKKEQEAAAAQAFEEFVATFQENPAAKTNKVWVKAGTYDAGRRREDT 84
K+ L + E + + E+E +Q + Q+ ++ + R++
Sbjct: 921 KKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAA-----RQKLQ 975
Query: 85 SEKGKLYKPQSRLQEDKDSSASKAEEYARLLGDKK---TESQRLKKNNKIDIKKKSNLEM 141
EK ++++ +D ++ +L ++K L N + +K NL
Sbjct: 976 LEKVTA---DGKIKKMEDDILIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTK 1032
Query: 142 FKEELKMIQEEREER 156
K + + + E E R
Sbjct: 1033 LKNKHESMISELEVR 1047
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 30.1 bits (68), Expect = 0.80
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 209 EQQLMEIFGRYGPLASIKIMWPRSDEEKARGRNCGFVAFMNRKDGERALKYLNG 262
+ + + +YG + SI+I P E FV F + D ++A++ L G
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKI-FVEFTSVFDCQKAMQGLTG 81
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 29.7 bits (67), Expect = 1.5
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 209 EQQLMEIFGRYGPLASIKIMWPRSDEEK-ARGRNCGFVAFMNRKDGERALKYLNG 262
E ++ E G++G + + I + EE+ A FV F + +A++ LNG
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 93
>2y3a_B Phosphatidylinositol 3-kinase regulatory subunit; transferase,
phosphoinositide 3-kinase, RTK; HET: GD9; 3.30A {Mus
musculus}
Length = 302
Score = 30.8 bits (69), Expect = 1.6
Identities = 17/106 (16%), Positives = 41/106 (38%), Gaps = 7/106 (6%)
Query: 80 RREDTSEKGKLYKPQSRLQEDKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKKKSNL 139
+++ ++ + ++L+ K+ EY +L + SQ L+ K++ +
Sbjct: 3 QQDQVVKEDSVEAVGAQLKVYHQQYQDKSREYDQLYEEYTRTSQELQM-------KRTAI 55
Query: 140 EMFKEELKMIQEEREERHKYKGVLKGVYSEEAEPPSAIAIYQEETK 185
E F E +K+ +E+ + + K + E I +
Sbjct: 56 EAFNETIKIFEEQGQTQEKCSKEYLERFRREGNEKEMQRILLNSER 101
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 28.8 bits (64), Expect = 2.0
Identities = 18/87 (20%), Positives = 28/87 (32%), Gaps = 20/87 (22%)
Query: 189 DSGDPCTTNLYLGNLNPKITEQQLMEIFGRY-----GPLASIKIMWPRSDEEKARGRNCG 243
SG + + L P + ++ L F GP+ S + R G
Sbjct: 2 SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-----------RLGCGG 50
Query: 244 FVAFMNRKDGERALK----YLNGKDVQ 266
+ F D ER L L+G +
Sbjct: 51 VLTFREPADAERVLAQADHELHGAQLS 77
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 30.5 bits (69), Expect = 3.0
Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 13/86 (15%)
Query: 89 KLYKPQSRLQEDKDSSASKAEEYARLLGDKKTESQRLKK----------NNKIDIKKKSN 138
K+ + Q ++ E S E+ L TE+++L+ K + +
Sbjct: 929 KIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLS 988
Query: 139 LEMFKEELKMIQEEREERHKYKGVLK 164
L+ EE+ +++E + K ++
Sbjct: 989 LQ---EEIAKLRKELHQTQTEKKTIE 1011
>3sb1_A Hydrogenase expression protein; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, HUPH, unkno
function; HET: PGE; 1.67A {Thiobacillus denitrificans}
Length = 160
Score = 29.1 bits (65), Expect = 3.4
Identities = 14/63 (22%), Positives = 19/63 (30%), Gaps = 12/63 (19%)
Query: 296 VPPPPSGLPFNAQP-ASKDKHRIPKLRPGE----------PLTREDLDRLDQILNQAYVK 344
P + NA P + + L PLT DL+ L L V
Sbjct: 36 APVETARS-GNALPLLREIAEHLHHLLETGEASTIDLSALPLTPGDLEWLRAELGGGEVS 94
Query: 345 VVV 347
V +
Sbjct: 95 VTL 97
>4ets_A Ferric uptake regulation protein; metal binding protein,
transcription factor; 2.10A {Campylobacter jejuni subsp}
Length = 162
Score = 28.9 bits (65), Expect = 4.1
Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 13/73 (17%)
Query: 465 RLEDFLRN----LTPERVKVAEAMVFCMEHSDAAEEICECIMESLSNESTALHKKIGR-- 518
R + LR T +R + + + H E + I ++ + +G
Sbjct: 19 RFKKILRQGGLKYTKQREVLLKTLYHSDTHYT-PESLYMEIKQAEPD------LNVGIAT 71
Query: 519 LYLVSDILHNCGI 531
+Y ++L +
Sbjct: 72 VYRTLNLLEEAEM 84
>2j63_A AP-endonuclease; base excision repair, lyase; 2.48A {Leishmania
major}
Length = 467
Score = 29.6 bits (66), Expect = 4.7
Identities = 17/134 (12%), Positives = 28/134 (20%), Gaps = 6/134 (4%)
Query: 22 SMGAKRTLSKKEQEEQKKKEQEAAAAQAFEEFVATFQENPAAKTNKVWVKAGTYDAGRRR 81
M +KR + + + A Q A T
Sbjct: 20 HMASKRCRQCSGDSASSSTSSLSPSELPPSKKAAGGQRVTAEVEVAPITTDATSATVTAA 79
Query: 82 EDTSEKGKLYKPQSR------LQEDKDSSASKAEEYARLLGDKKTESQRLKKNNKIDIKK 135
+K P R + + E L KK+E + +
Sbjct: 80 GGAKKKATTGSPARRTSSAAKITNGDAGELIRTAEALAALNAKKSEKEIWSDVVPFVRRT 139
Query: 136 KSNLEMFKEELKMI 149
+ K I
Sbjct: 140 TDSDFDPSRMYKFI 153
>3u61_A DNA polymerase accessory protein 62; AAA+, ATP hydrolase, clamp
loader, sliding clamp, primer-TEM DNA, DNA binding
protein-DNA complex; HET: DNA ADP 08T; 3.20A
{Enterobacteria phage T4} PDB: 3u5z_A* 3u60_A*
Length = 199
Score = 28.7 bits (64), Expect = 6.1
Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 22/91 (24%)
Query: 87 KGKLYKPQSRLQEDKDS-------------SASKAEEYARLLGDKKTESQRLKKNNKIDI 133
+GK Y ++L ED + + A Y +L K +
Sbjct: 103 RGKRYGKWAKLVEDSTEVLIIKLLAKRYQVNTNDAINYKSILT---------KNGKLPLV 153
Query: 134 KKKSNLEMFKEELKMIQEEREERHKYKGVLK 164
K+ + + LK + + +E+ + K +
Sbjct: 154 LKELKGLVTDDFLKEVTKNVKEQKQLKKLAL 184
>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F
1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H*
2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...
Length = 149
Score = 27.6 bits (62), Expect = 8.9
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 12/64 (18%)
Query: 28 TLSKKEQEEQKKKEQEAAAAQAFEEFVATFQENPAAKTNKVWVKAGTYDAGRRREDTSEK 87
T E E ++ E EA A+ A ++ A +T + KAG ++
Sbjct: 40 TKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAG------------DE 87
Query: 88 GKLY 91
GKL+
Sbjct: 88 GKLF 91
>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules,
epigenetic regulation, trimethylaion of lysine residue,
ligase-DNA binding protein; HET: M3L; 2.90A {Homo
sapiens}
Length = 226
Score = 28.2 bits (62), Expect = 9.3
Identities = 34/182 (18%), Positives = 60/182 (32%), Gaps = 26/182 (14%)
Query: 628 VDGEDLDGVPLDGA---ALMKSLQRLPHSSSAPDEDDIDGVPCTYNITSATMDGEDLDGV 684
VD D + GA A + + R S A +ED Y++ D +GV
Sbjct: 9 VDARDTN----MGAWFEAQVVRVTRKAPSRPALEED------VIYHVK---YDDYPENGV 55
Query: 685 PMDKVKPARAATFIPSKWETVEE--------NEDSAVTSSKWDDVEQSESKDDSNSKGTG 736
+ RA KW+ +E N D+ W D E S ++ ++
Sbjct: 56 VQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELY 115
Query: 737 LTSSRRGDLSSERIQGDSGEDDSAAREEKKEANKSERSDRKKSPSPAAREEKKEANKSER 796
D ++ D+ E E + + ++ P+ + K + N+ R
Sbjct: 116 ANVVLGDDSLNDCRIIFV--DEVFKIERPGEGSPMVDNPMRRKSGPSCKHCKDDVNRLCR 173
Query: 797 SD 798
Sbjct: 174 VC 175
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.312 0.130 0.372
Gapped
Lambda K H
0.267 0.0570 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 12,163,202
Number of extensions: 757818
Number of successful extensions: 1982
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1729
Number of HSP's successfully gapped: 291
Length of query: 806
Length of database: 6,701,793
Length adjustment: 101
Effective length of query: 705
Effective length of database: 3,881,772
Effective search space: 2736649260
Effective search space used: 2736649260
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 61 (27.6 bits)