RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15187
(298 letters)
>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 = 91.2 bits (227), Expect = 1e-23
Identities = 37/113 (32%), Positives = 59/113 (52%), Gaps = 25/113 (22%)
Query: 139 NEKPKGGNTIFVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
P+ GNT++V G ++ LR FS FG I +SM+ + FV
Sbjct: 9 RRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFV-------------- 54
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASST 251
T++ ES+D+A+ E+NGT V+ V+LKV++AR+Q P+ D+ S+
Sbjct: 55 -------TYEKMESADQAVAELNGTQVESVQLKVNIARKQ----PMLDSGPSS 96
>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 = 87.5 bits (217), Expect = 9e-22
Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 21/110 (19%)
Query: 139 NEKPKGGNTIFVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
P+ GNT++V G ++ LR FS FG I +SM+ + FV
Sbjct: 33 RRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFV-------------- 78
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAA 248
T++ ES+D+A+ E+NGT V+ V+LKV++AR+Q + +
Sbjct: 79 -------TYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAATGKS 121
>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 = 68.1 bits (167), Expect = 1e-14
Identities = 26/103 (25%), Positives = 45/103 (43%), Gaps = 23/103 (22%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
N+ T++ G +G++++ +RQ FS FG+I + V +G+
Sbjct: 18 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIR--VFPEKGY------------ 63
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV F + ES+ AI VNGT ++G +K +
Sbjct: 64 -------SFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99
>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 = 68.0 bits (167), Expect = 1e-14
Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 23/100 (23%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSDKAIT 197
P G IF++ I + L FS FG I C V + +G+
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY-------------- 47
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV F++ E++++AI ++NG + K+ V +
Sbjct: 48 -----GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 82
>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 = 67.6 bits (166), Expect = 1e-14
Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 24/102 (23%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG--RGFVTFDSPESSDKA 195
+ + N ++V+ GI +E LR+ FS FG I S + +E G +GF
Sbjct: 11 TRYQVVN-LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGF------------ 57
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV F SPE + KA+TE+NG V L V+LA+R
Sbjct: 58 -------GFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQR 92
>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 = 1e-14
Identities = 27/106 (25%), Positives = 43/106 (40%), Gaps = 26/106 (24%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR--GFVTFDSPES 191
E P+G N +F+ ++ L Q F FG + V ++ + F
Sbjct: 19 QKEGPEGAN-LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCF-------- 69
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV++D+P S+ AI +NG + +LKV L R
Sbjct: 70 -----------GFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 66.8 bits (164), Expect = 2e-14
Identities = 22/103 (21%), Positives = 42/103 (40%), Gaps = 23/103 (22%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGR--GFVTFDSPESSDK 194
+ G IFV+ + + L+ F+ G + +++E G+ G
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGC----------- 50
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
G V F+SPE +++A +NG + G ++ V + R
Sbjct: 51 --------GVVKFESPEVAERACRMMNGMKLSGREIDVRIDRN 85
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 67.4 bits (165), Expect = 2e-14
Identities = 27/103 (26%), Positives = 43/103 (41%), Gaps = 26/103 (25%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR--GFVTFDSPESSD 193
E P+G N +F+ ++ L F FG + V ++ + F
Sbjct: 36 EGPEGCN-LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCF---------- 84
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV+FD+P+S+ AI +NG V +LKV L +
Sbjct: 85 ---------GFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 66.2 bits (162), Expect = 4e-14
Identities = 16/103 (15%), Positives = 28/103 (27%), Gaps = 23/103 (22%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
P T ++ +E L F FG I +G
Sbjct: 20 IRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH--YPEKGC------------ 65
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
F+ +D+ E + I + QG L+ + +
Sbjct: 66 -------CFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 65.0 bits (159), Expect = 1e-13
Identities = 27/106 (25%), Positives = 43/106 (40%), Gaps = 23/106 (21%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVS--MEVEKGRGFVTFDSPESSD 193
E + V + LRQ F FGKI V +GF
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF---------- 71
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQL 239
GFVTF++ +D+A +++GT V+G K++V+ A ++
Sbjct: 72 ---------GFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108
>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 = 63.4 bits (155), Expect = 3e-13
Identities = 20/103 (19%), Positives = 39/103 (37%), Gaps = 23/103 (22%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
+ ++V+ SEE + + F+ V+K R +
Sbjct: 10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE--RVKKIRDY-------------- 53
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
FV F + E + +A+ +NG + G ++V+LA+ K
Sbjct: 54 -----AFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 91
>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 = 63.4 bits (155), Expect = 6e-13
Identities = 17/108 (15%), Positives = 34/108 (31%), Gaps = 25/108 (23%)
Query: 135 RLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSP 189
++A ++ N +++ + E+ L FG++ S + G RG
Sbjct: 16 QMAKQQEQDPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV------ 68
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GF +S E + I NG ++ +
Sbjct: 69 -------------GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 103
>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 = 62.7 bits (153), Expect = 7e-13
Identities = 20/102 (19%), Positives = 40/102 (39%), Gaps = 23/102 (22%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
+ + +FV I+EE +R+ F +GK V + +KG GF+
Sbjct: 8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFI----------- 56
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
++ ++ A E++ ++G +L+V A
Sbjct: 57 ----------RLETRTLAEIAKVELDNMPLRGKQLRVRFACH 88
>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 = 62.3 bits (152), Expect = 8e-13
Identities = 30/111 (27%), Positives = 47/111 (42%), Gaps = 28/111 (25%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKG-----RGFVTFDSPESS 192
G + +F++ +EE L+ FS G I C++S + K GF
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGF--------- 52
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAP 243
GFV + PE + KA+ ++ G V G KL+V ++ R K A
Sbjct: 53 ----------GFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPAS 93
>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 = 62.7 bits (153), Expect = 1e-12
Identities = 21/106 (19%), Positives = 41/106 (38%), Gaps = 24/106 (22%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGR--GFVTFDSPES 191
+ + G+T+FV + + L++ FS+ G + +E + G+ G
Sbjct: 7 GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGI-------- 58
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
G VTF+ + +AI+ NG + + V + R
Sbjct: 59 -----------GTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER 93
>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 = 62.3 bits (152), Expect = 1e-12
Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 23/103 (22%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS--MEVEKGRGFVTFDSPESSD 193
+E + V + LRQ F FGKI V +GF
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF---------- 57
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFVTF++ +D+A +++GT V+G K++V+ A
Sbjct: 58 ---------GFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 91
>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 = 64.7 bits (158), Expect = 1e-12
Identities = 21/133 (15%), Positives = 48/133 (36%), Gaps = 27/133 (20%)
Query: 109 LKVSKRETNDDRTPVDKKVYGESLLTRLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSI 166
LK+ R +D + + + P + +F+ G ++++ +++ +
Sbjct: 80 LKI--RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTS 137
Query: 167 FGKI--CSVSMEVEKG--RGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNG 222
FG + ++ + G +G+ F + +D+AI +NG
Sbjct: 138 FGPLKAFNLVKDSATGLSKGY-------------------AFCEYVDINVTDQAIAGLNG 178
Query: 223 THVQGVKLKVSLA 235
+ KL V A
Sbjct: 179 MQLGDKKLLVQRA 191
Score = 49.3 bits (118), Expect = 2e-07
Identities = 17/134 (12%), Positives = 41/134 (30%), Gaps = 35/134 (26%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSMEV-----------EKGRGFVTFDSPESS 192
++V GI+EE + F+ ++ ++ +K F+ F S + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASSTT 252
+A+ +G QG LK+ + +++ S
Sbjct: 65 TQAM----------------------AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYV 102
Query: 253 WSAIACHQSLKGNH 266
++ +
Sbjct: 103 PGVVSTVVPDSAHK 116
>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 = 63.7 bits (156), Expect = 1e-12
Identities = 21/106 (19%), Positives = 38/106 (35%), Gaps = 25/106 (23%)
Query: 138 PNEKPKGGNTIFVQ--GAGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPES 191
+FV + +E LR F F V +++ G RG+
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY-------- 131
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV+F S + + A+ + G + G L+++ A +
Sbjct: 132 -----------GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 48.3 bits (116), Expect = 3e-07
Identities = 15/86 (17%), Positives = 37/86 (43%), Gaps = 22/86 (25%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEK---GRGFVTFDSPESSDKAITDDCARGFVTFDSPE 211
I+E+ L+Q+F + G I ++ + ++K + FV +
Sbjct: 12 ITEDILKQYFQVGGPIANIKIMIDKNNKNVNY-------------------AFVEYHQSH 52
Query: 212 SSDKAITEVNGTHVQGVKLKVSLARR 237
++ A+ +NG ++ +K++ A +
Sbjct: 53 DANIALQTLNGKQIENNIVKINWAFQ 78
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 64.3 bits (157), Expect = 2e-12
Identities = 27/151 (17%), Positives = 59/151 (39%), Gaps = 38/151 (25%)
Query: 93 AIQPEDSEPVDSKPKFLKVSKRETNDDRTPVDKKVYGESLLTRLAPNEKPKGGNTIFVQG 152
A++ +S + + +KV + P+ + E+ + N I+V
Sbjct: 86 ALEQMNSVMLGGRN--IKVGRPSNIGQAQPIIDQ-----------LAEEARAFNRIYVAS 132
Query: 153 --AGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPESSDKAITDDCARGFVT 206
+S++ ++ F FGKI +++ + G +G+ GF+
Sbjct: 133 VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGY-------------------GFIE 173
Query: 207 FDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
++ +SS A++ +N + G L+V A
Sbjct: 174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204
Score = 57.7 bits (140), Expect = 4e-10
Identities = 23/128 (17%), Positives = 47/128 (36%), Gaps = 29/128 (22%)
Query: 135 RLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDS 188
+ ++V + E+ +RQ F+ FG I S+ M + +GF
Sbjct: 18 AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGF----- 72
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA----RRQLKVAPI 244
FV ++ PE++ A+ ++N + G +KV + Q + +
Sbjct: 73 --------------AFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL 118
Query: 245 NDAASSTT 252
+ A +
Sbjct: 119 AEEARAFN 126
>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 = 63.0 bits (154), Expect = 3e-12
Identities = 16/102 (15%), Positives = 36/102 (35%), Gaps = 22/102 (21%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
++K + T+ + I+E+ L++ F +I V + K +G
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGI------------ 138
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
++ F S ++K + E G + G + +
Sbjct: 139 -------AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 54.5 bits (132), Expect = 3e-09
Identities = 18/109 (16%), Positives = 36/109 (33%), Gaps = 29/109 (26%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGR----GFVTFDSP 189
+ +F+ S L+ S ++ ++V G G+V F+S
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 64
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
E +KA+ E+ G V G ++K+ + +
Sbjct: 65 EDLEKAL----------------------ELTGLKVFGNEIKLEKPKGR 91
>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 = 63.5 bits (155), Expect = 4e-12
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 23/104 (22%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSD 193
P+ + G IF++ I + L FS FG I C V + +G+
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY---------- 145
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV F++ E++++AI ++NG + K+ V +
Sbjct: 146 ---------GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180
Score = 47.3 bits (113), Expect = 1e-06
Identities = 15/88 (17%), Positives = 35/88 (39%), Gaps = 23/88 (26%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEK----GRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
++E L + FS G I S+ + + G+ +V F P
Sbjct: 27 VTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY-------------------AYVNFQQP 67
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARRQ 238
+++A+ +N ++G +++ ++R
Sbjct: 68 ADAERALDTMNFDVIKGKPVRIMWSQRD 95
>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 = 59.8 bits (146), Expect = 4e-12
Identities = 24/101 (23%), Positives = 43/101 (42%), Gaps = 25/101 (24%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDSPESSDKA 195
G + ++++G G +++ L + +GKI S ++K +G+
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY------------ 49
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV FDSP ++ KA+T + + VQ K S
Sbjct: 50 -------GFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS 83
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 60.8 bits (148), Expect = 5e-12
Identities = 24/103 (23%), Positives = 36/103 (34%), Gaps = 25/103 (24%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
E +FV+ + E L + F FG + V + GF
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----NGF------------ 67
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV F+ ES+ KAI EV+G L+V ++
Sbjct: 68 -------AFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103
>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 = 60.0 bits (146), Expect = 5e-12
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 22/92 (23%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGF 204
T++V G I+E LR HF FG+I ++++ + F+ F + ++++ A
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEK------ 67
Query: 205 VTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
N V G +L V R
Sbjct: 68 --------------SFNKLIVNGRRLNVKWGR 85
>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 = 61.5 bits (150), Expect = 8e-12
Identities = 18/107 (16%), Positives = 41/107 (38%), Gaps = 25/107 (23%)
Query: 135 RLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDS 188
R + G + +F+ G ++++ +++ + FG + ++ + G +G+
Sbjct: 84 RPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGY----- 138
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
F + +D+AI +NG + KL V A
Sbjct: 139 --------------AFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 48.4 bits (116), Expect = 3e-07
Identities = 16/105 (15%), Positives = 33/105 (31%), Gaps = 35/105 (33%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEV-----------EKGRGFVTFDSPESSD 193
++V GI+EE + F+ ++ ++ +K F+ F S + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
+A+ +G QG LK+
Sbjct: 66 QAM----------------------AFDGIIFQGQSLKIRRPHDY 88
>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 = 60.9 bits (148), Expect = 8e-12
Identities = 29/105 (27%), Positives = 43/105 (40%), Gaps = 25/105 (23%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS--MEVEKGR--GFVTFDSPES 191
N +P + V + E LRQ F +G I SV + E + G+
Sbjct: 35 MNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY-------- 86
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV F S S+ +AI +NG ++ +LKV+LA
Sbjct: 87 -----------GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120
>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 = 59.6 bits (145), Expect = 8e-12
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 25/95 (26%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
+FV+ ++EE L + FS FGK+ V + +
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL----KDY-------------------A 48
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
F+ FD + + KA+ E+NG ++G +++ A+
Sbjct: 49 FIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP 83
>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 = 59.5 bits (145), Expect = 9e-12
Identities = 25/101 (24%), Positives = 41/101 (40%), Gaps = 26/101 (25%)
Query: 144 GGNTIFVQG--AGISEEFLRQHFSIFGKICS---VSMEVEKG--RGFVTFDSPESSDKAI 196
G + IF+ I E+ L FS FG I + + + G +G+
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGY------------- 50
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
F+ F S ++SD AI +NG ++ + VS A +
Sbjct: 51 ------AFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK 85
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 26/104 (25%), Positives = 38/104 (36%), Gaps = 24/104 (23%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM---EVEKGRGFVTFDSPES 191
+ + T+FV A + EE L + F G + V++ K + F
Sbjct: 8 MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSF-------- 59
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
GFV F PES AI +NG + G + VS
Sbjct: 60 -----------GFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92
>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 = 62.7 bits (153), Expect = 1e-11
Identities = 13/110 (11%), Positives = 33/110 (30%), Gaps = 25/110 (22%)
Query: 134 TRLAPNEKPKGGNTIFVQG--AGISE-EFLRQHFSIFGKICSVSM---EVEKGRGFVTFD 187
+ V G ++ + L + S + + + +GF
Sbjct: 173 DAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGF---- 228
Query: 188 SPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
+ +++ E +++A + +G + G L+VS
Sbjct: 229 ---------------AVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
Score = 57.7 bits (140), Expect = 8e-10
Identities = 15/106 (14%), Positives = 35/106 (33%), Gaps = 24/106 (22%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
+ + I ++G ++ + + S + V+K +G
Sbjct: 15 TERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE---LKYCFVDKYKGT------------ 59
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKV 241
FVT + E ++ AI + + ++ +L V L +
Sbjct: 60 -------AFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALL 98
Score = 53.8 bits (130), Expect = 2e-08
Identities = 11/88 (12%), Positives = 28/88 (31%), Gaps = 23/88 (26%)
Query: 155 ISEEFLRQHFSIFGKICSV----SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
++++ + FG + S + +G+ GF +
Sbjct: 107 LTQQQFEELVRPFGSLERCFLVYSERTGQSKGY-------------------GFAEYMKK 147
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARRQ 238
+S+ +A +++ G + L V
Sbjct: 148 DSAARAKSDLLGKPLGPRTLYVHWTDAG 175
>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 = 60.7 bits (148), Expect = 2e-11
Identities = 23/106 (21%), Positives = 39/106 (36%), Gaps = 28/106 (26%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPES 191
E K N ++V I+++ L F +G I ++ + G RG
Sbjct: 83 GGESIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV-------- 133
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGV--KLKVSLA 235
FV ++ E + +AI+ +N +G L V LA
Sbjct: 134 -----------AFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 56.8 bits (138), Expect = 4e-10
Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 23/90 (25%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+++ L F G I + + + G+ FV F S
Sbjct: 15 MTDRELYALFRAIGPINTCRIMRDYKTGYSYGY-------------------AFVDFTSE 55
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
S +AI +NG V+ +LKVS AR +
Sbjct: 56 MDSQRAIKVLNGITVRNKRLKVSYARPGGE 85
>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 = 60.3 bits (147), Expect = 2e-11
Identities = 23/107 (21%), Positives = 42/107 (39%), Gaps = 28/107 (26%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPE 190
+ + N ++V G ++++ L Q FS +G+I + ++ G RG
Sbjct: 81 PSSASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGV------- 132
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGV--KLKVSLA 235
GF+ FD +++AI +NG G + V A
Sbjct: 133 ------------GFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 53.3 bits (129), Expect = 6e-09
Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 23/90 (25%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEK----GRGFVTFDSPESSDKAITDDCARGFVTFDSP 210
+++E R F G+I S + +K G+ GFV + P
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGY-------------------GFVNYIDP 54
Query: 211 ESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
+ ++KAI +NG +Q +KVS AR
Sbjct: 55 KDAEKAINTLNGLRLQTKTIKVSYARPSSA 84
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 58.6 bits (142), Expect = 3e-11
Identities = 14/102 (13%), Positives = 28/102 (27%), Gaps = 25/102 (24%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKA 195
+ + E FL+ +G++ V + K G
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGL------------ 50
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
V F S + + + ++ T V G + L +
Sbjct: 51 -------ARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK 85
>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 = 57.6 bits (140), Expect = 4e-11
Identities = 21/108 (19%), Positives = 38/108 (35%), Gaps = 28/108 (25%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQH----FSIFGKICSVS-MEVEKGRGFVTFDSPE 190
P +P +TI++ I ++ L++ FS FG+I + K RG
Sbjct: 3 PETRPN--HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ------- 53
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV F S+ A+ + G +++ A+
Sbjct: 54 ------------AFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89
>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 = 57.6 bits (140), Expect = 5e-11
Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 25/102 (24%)
Query: 141 KPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
K ++V G S L + F FG I ++ + KG F
Sbjct: 13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTI--DHVKGDSF--------------- 55
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQG--VKLKVSLARRQ 238
++ ++S +++ A ++ G + G +L+V A+
Sbjct: 56 ----AYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93
>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 = 57.2 bits (139), Expect = 5e-11
Identities = 18/104 (17%), Positives = 37/104 (35%), Gaps = 25/104 (24%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
+T++V ++ L + FS +GK+ V++ + K +G
Sbjct: 9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV-------- 60
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
F+ F +S+ +N + G +K S+A
Sbjct: 61 -----------AFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>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 = 57.2 bits (139), Expect = 6e-11
Identities = 24/106 (22%), Positives = 40/106 (37%), Gaps = 25/106 (23%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
P + V G +E LR+ FS +G I VS+ + + RGF
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF-------- 59
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
FV F++ + + +A NG + G +++VS
Sbjct: 60 -----------AFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>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 = 56.4 bits (137), Expect = 8e-11
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 25/97 (25%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDD 199
++V G + ++ L F FG I + + E EK RGF
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGF---------------- 51
Query: 200 CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F+ E + AI +N + + G ++V+LA+
Sbjct: 52 ---AFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>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 = 61.8 bits (149), Expect = 9e-11
Identities = 38/260 (14%), Positives = 85/260 (32%), Gaps = 53/260 (20%)
Query: 30 LKRPIEAKDAREVARKLLKSGAINPIVRPPKRCEQEGF-------KRPRGLERKLTETDR 82
+ KD +++ + +L I+ I+ K+ +++ + E R
Sbjct: 29 FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLR 88
Query: 83 STVSAYQPF--SAIQPEDSEPVDSKPKFLKVSKRETNDDRTPVDKKVYGESLLTRL---A 137
Y F S I+ E +P +++ R ND++ V +L
Sbjct: 89 IN---Y-KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144
Query: 138 PNEKPKGGNTIFVQG-AGISEEFLRQHFSIFGKICSV-------SMEVEKGRGF----VT 185
+P + + G G GK + S +V+ F +
Sbjct: 145 LELRPAKN--VLIDGVLG------------SGK--TWVALDVCLSYKVQCKMDFKIFWLN 188
Query: 186 F---DSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVA 242
+SPE+ + + + + + SD + H +L+ L + +
Sbjct: 189 LKNCNSPETVLEMLQKLLYQ--IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 243 PI--NDAASSTTWSA--IAC 258
+ + ++ W+A ++C
Sbjct: 247 LLVLLNVQNAKAWNAFNLSC 266
>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 = 60.0 bits (146), Expect = 1e-10
Identities = 26/132 (19%), Positives = 55/132 (41%), Gaps = 40/132 (30%)
Query: 124 DKKVYGESLLTRLA-PNEKPKGGNTIFVQGAGI----------SEEFLRQHFSIFGKICS 172
K+ G +L+T+++ P EK K ++ ++G I E LR+ F FG I
Sbjct: 181 GLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEK 240
Query: 173 VSM-------EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHV 225
+++ F+ F++ +S+++A+ ++N + +
Sbjct: 241 INIPAGQKEHSFNNCCAFMVFENKDSAERAL----------------------QMNRSLL 278
Query: 226 QGVKLKVSLARR 237
++ VSLA +
Sbjct: 279 GNREISVSLADK 290
Score = 53.1 bits (128), Expect = 3e-08
Identities = 15/100 (15%), Positives = 34/100 (34%), Gaps = 24/100 (24%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGRGFVTFDSPESSD 193
+ + T+ V+ ++ + ++F G I V+ ++K F
Sbjct: 34 ALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRF---------- 83
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVS 233
+ F + + AIT+ + V ++ VS
Sbjct: 84 ---------ARIEFARYDGALAAITKTHKV-VGQNEIIVS 113
Score = 51.1 bits (123), Expect = 1e-07
Identities = 12/101 (11%), Positives = 30/101 (29%), Gaps = 25/101 (24%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICS----VSMEVEKGRGFVTFDSPESSDKAITDD 199
T+++ ++ +R + S+ R F
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF---------------- 161
Query: 200 CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
++ S E + + ++NG ++G L ++ K
Sbjct: 162 ---AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK 199
>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 = 57.0 bits (138), Expect = 1e-10
Identities = 24/117 (20%), Positives = 45/117 (38%), Gaps = 33/117 (28%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI----------CSVSMEVEKGR--GF 183
++ + I+VQG ++ + L F G + + ++ E G+ G
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 184 VTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
V+++ P ++ A+ +G QG KLKVSLAR++
Sbjct: 68 -------------------ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
>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 = 56.6 bits (137), Expect = 1e-10
Identities = 23/98 (23%), Positives = 40/98 (40%), Gaps = 24/98 (24%)
Query: 145 GNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVE---KGRGFVTFDSPESSDKAITDD 199
+F+ G +E+ L+ F G I V + + K RGF
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGF---------------- 50
Query: 200 CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
F+TF++P + A ++NG + G +KV A++
Sbjct: 51 ---AFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK 85
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 24/106 (22%), Positives = 41/106 (38%), Gaps = 25/106 (23%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPE 190
+ ++V G + ++ L F FG I + + E EK RGF
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGF------- 56
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F+ E + AI +N + + G ++V+LA+
Sbjct: 57 ------------AFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>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 = 55.7 bits (135), Expect = 2e-10
Identities = 19/105 (18%), Positives = 38/105 (36%), Gaps = 25/105 (23%)
Query: 141 KPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
K + V + + LR F +G + +E + + +
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPV----IECDIVKDY--------------- 46
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAP 243
FV + E + +AI ++ T QG ++ V L+ +L+ A
Sbjct: 47 ----AFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAS 87
>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 = 55.2 bits (134), Expect = 2e-10
Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 25/98 (25%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVS----MEVEKGRGFVTFDSPESSDKAITDD 199
+FV + +E LR F F S M+ RG+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY---------------- 45
Query: 200 CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV+F S + + A+ + G + G L+++ A +
Sbjct: 46 ---GFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80
>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 = 55.3 bits (134), Expect = 3e-10
Identities = 28/104 (26%), Positives = 40/104 (38%), Gaps = 25/104 (24%)
Query: 139 NEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESS 192
+ G +FV+ SEE L + FS +G + + +K +GF
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGF--------- 52
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FVTF PE + KA EV+G QG L V +
Sbjct: 53 ----------AFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86
>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 = 55.8 bits (135), Expect = 4e-10
Identities = 17/107 (15%), Positives = 38/107 (35%), Gaps = 24/107 (22%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG---RGFVTFDSPES 191
E + G + V G+S+ +++ F+ FG + +++ ++ G
Sbjct: 27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGT-------- 78
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
V F+ + KA+ + G + G + + L Q
Sbjct: 79 -----------ADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 55.5 bits (134), Expect = 4e-10
Identities = 28/118 (23%), Positives = 42/118 (35%), Gaps = 33/118 (27%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI----------CSVSMEVEKGR--GFVT 185
+ NTIFVQG ++ E + +F G I ++ + E G+ G
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE-- 59
Query: 186 FDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAP 243
V+FD P S+ AI +G G +KVS A R+
Sbjct: 60 -----------------ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100
>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 = 57.2 bits (138), Expect = 4e-10
Identities = 28/161 (17%), Positives = 53/161 (32%), Gaps = 33/161 (20%)
Query: 93 AIQPEDSEPVDSKPKFLKVSKRET-----NDDRTPVDKKVYGESLLTRLAPNEKPKGGN- 146
A+ + + KP + +SK + K YG S L R N
Sbjct: 57 AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116
Query: 147 -----TIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDD 199
T+ + +SEE L+ FS G + +K R
Sbjct: 117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM---------------- 160
Query: 200 CARGFVTFDSPESSDKAITEVNGTHV-QGVKLKVSLARRQL 239
+ S E + +A+ +++ + + L+VS ++ +
Sbjct: 161 ---ALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198
Score = 49.5 bits (118), Expect = 2e-07
Identities = 15/103 (14%), Positives = 36/103 (34%), Gaps = 23/103 (22%)
Query: 144 GGNTIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC 200
G + + V ++ + L F ++G + V K + +
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV--------------------KILFNKK 41
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAP 243
V + A++ +NG + G ++++L++ Q P
Sbjct: 42 ENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLP 84
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 54.5 bits (132), Expect = 5e-10
Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 26/108 (24%)
Query: 136 LAPNEKPKGGNTIFV---QGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESS 192
+ + +F+ +S+E L + FS +G I ++++ F
Sbjct: 1 MTEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAF--------- 47
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
GF+ FD+P+S AI + G KL + ++ +
Sbjct: 48 ----------GFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNAR 85
>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 = 54.1 bits (131), Expect = 6e-10
Identities = 19/102 (18%), Positives = 37/102 (36%), Gaps = 25/102 (24%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+ IFV A + + LR F G++ +E + + +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRV----IECDVVKDY------------- 45
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV + + AI ++NG V+G ++ V L+ +
Sbjct: 46 ------AFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81
>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 = 58.0 bits (139), Expect = 6e-10
Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 28/109 (25%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQH----FSIFGKICSVS-MEVEKGRGFVTFDSP 189
P +P +TI++ I ++ L++ FS FG+I + K RG
Sbjct: 3 VPETRPN--HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ------ 54
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV F S+ A+ + G +++ A+
Sbjct: 55 -------------AFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 90
Score = 47.9 bits (113), Expect = 1e-06
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 21/85 (24%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
+E L F+ F V + V FV FD+ +
Sbjct: 218 ETNELMLSMLFNQFPGFKEVRL-VPGRHDI-------------------AFVEFDNEVQA 257
Query: 214 DKAITEVNGTHV-QGVKLKVSLARR 237
A + G + Q +K+S A++
Sbjct: 258 GAARDALQGFKITQNNAMKISFAKK 282
>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 = 54.1 bits (131), Expect = 7e-10
Identities = 14/98 (14%), Positives = 39/98 (39%), Gaps = 26/98 (26%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSM-----EVEKGRGFVTFDSPESSDKAITD 198
+ + ++++ + + FS +GKI + M +G+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGY--------------- 49
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+V F++P+ ++KA+ ++G + G ++ +
Sbjct: 50 ----AYVEFENPDEAEKALKHMDGGQIDGQEITATAVL 83
>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 = 54.6 bits (132), Expect = 7e-10
Identities = 18/99 (18%), Positives = 35/99 (35%), Gaps = 24/99 (24%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGR--GFVTFDSPESSDKAI 196
+ G + V G+S+ +++ F+ FG + + GR G
Sbjct: 26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGT------------- 72
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
V F+ + KA+ + NG + G + + L
Sbjct: 73 ------ADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 105
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 53.9 bits (130), Expect = 8e-10
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGR-GFVTFDSPESSDKAI 196
++FV G G+ L ++F FG + SV M+ +KG V + + +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL 62
>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 = 54.6 bits (132), Expect = 9e-10
Identities = 17/100 (17%), Positives = 35/100 (35%), Gaps = 25/100 (25%)
Query: 145 GNTIFVQG--AGISEEFLRQHFSIFGKICSVS----MEVEKGRGFVTFDSPESSDKAITD 198
++++ ++E L F+ F + M + RG
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQ--------------- 69
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
F+TF + E + +A+ VNG + G L + + +
Sbjct: 70 ----AFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105
>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 = 54.2 bits (131), Expect = 9e-10
Identities = 21/107 (19%), Positives = 34/107 (31%), Gaps = 23/107 (21%)
Query: 134 TRLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM--EVEKGRGFVTFDSP 189
E T++V ++E + Q FS G S M E +
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPY------ 57
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F + A+ +NG + G ++KV+ A
Sbjct: 58 -------------CFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT 91
>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 = 55.6 bits (135), Expect = 9e-10
Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 26/107 (24%)
Query: 135 RLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDS 188
R P ++ IFV G + + + FS +G I + ++K RGF
Sbjct: 77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGF----- 131
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
GFVT+DS ++ D+ + + K+++ A
Sbjct: 132 --------------GFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRA 163
Score = 44.1 bits (105), Expect = 1e-05
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 147 TIFVQGAG--ISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITD 198
+F+ G +E+ LR++F +G + + + GR GF++F+ P S D+ +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
>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 = 57.0 bits (138), Expect = 1e-09
Identities = 20/121 (16%), Positives = 44/121 (36%), Gaps = 25/121 (20%)
Query: 123 VDKKVYGESLLTRLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG 180
+ + +S L + +FV I+EE ++ F +G+ V + ++G
Sbjct: 2 MGFTIDIKSFLKP--GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG 59
Query: 181 RGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
GF+ +S ++ A E++GT ++ L++ A
Sbjct: 60 FGFI---------------------RLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA 98
Query: 241 V 241
+
Sbjct: 99 L 99
Score = 52.4 bits (126), Expect = 4e-08
Identities = 19/94 (20%), Positives = 29/94 (30%), Gaps = 25/94 (26%)
Query: 135 RLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSP 189
L G + V+ +S E L Q FS FG + + ++G G
Sbjct: 87 PLRIRFATHGAA-LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGK------ 139
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGT 223
GFV F + + KA+
Sbjct: 140 -------------GFVEFAAKPPARKALERCGDG 160
>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 = 53.5 bits (129), Expect = 1e-09
Identities = 27/112 (24%), Positives = 40/112 (35%), Gaps = 33/112 (29%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI----------CSVSMEVEKGR--GF 183
+ NTIFVQG ++ E + +F G I ++ + E G+ G
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
Query: 184 VTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
V+FD P S+ AI +G G +KVS A
Sbjct: 66 -------------------ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 53.4 bits (129), Expect = 1e-09
Identities = 17/102 (16%), Positives = 37/102 (36%), Gaps = 22/102 (21%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDK 194
++K + T+ + I+E+ L++ F +I VS + K +G
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKSKGI----------- 55
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
++ F S ++K + E G + G + +
Sbjct: 56 --------AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 89
>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 = 53.4 bits (129), Expect = 2e-09
Identities = 23/103 (22%), Positives = 39/103 (37%), Gaps = 26/103 (25%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVE---KGRGFVTFDSPESSDK 194
E NT+FV G + E +R F+ +G + V + + +G+
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGY----------- 52
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV+F + K + + + G KLK+ A R
Sbjct: 53 --------GFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIR 85
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 53.2 bits (128), Expect = 2e-09
Identities = 15/100 (15%), Positives = 33/100 (33%), Gaps = 20/100 (20%)
Query: 141 KPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITD 198
K + + ++ + E L +G + S
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---------------- 54
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
A VT+ S + + +A+ ++NG ++ LKV+ +
Sbjct: 55 --AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 54.4 bits (131), Expect = 2e-09
Identities = 24/104 (23%), Positives = 39/104 (37%), Gaps = 25/104 (24%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
++V G + ++ L F FG I + + E EK RGF
Sbjct: 56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGF-------- 107
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
FV F+ E + AI +N + + G ++V+LA
Sbjct: 108 -----------AFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 52.9 bits (128), Expect = 2e-09
Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 25/99 (25%)
Query: 144 GGNTIFVQGA--GISEEFLRQHFSIFGKICSVS--MEVEKGR--GFVTFDSPESSDKAIT 197
G + ++V I+E+ LR F FGKI ++ + + GR G+
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGY-------------- 49
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GF+TF E + +A+ ++NG + G ++V
Sbjct: 50 -----GFITFSDSECARRALEQLNGFELAGRPMRVGHVT 83
>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 = 53.0 bits (128), Expect = 2e-09
Identities = 22/106 (20%), Positives = 37/106 (34%), Gaps = 25/106 (23%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
G T+ V S + LR+ F +G++ V + + RGF
Sbjct: 6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGF-------- 57
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
FV F + A ++G + G +L+V +AR
Sbjct: 58 -----------AFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARY 92
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 53.1 bits (128), Expect = 2e-09
Identities = 11/97 (11%), Positives = 38/97 (39%), Gaps = 24/97 (24%)
Query: 145 GNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKG---RGFVTFDSPESSDKAITDD 199
+ +F+ G ++E L + G + + + + +G
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL---------------- 60
Query: 200 CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+V +++ + +A+ +++G ++ +KV+++
Sbjct: 61 ---AYVEYENESQASQAVMKMDGMTIKENIIKVAISN 94
>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 = 53.0 bits (128), Expect = 2e-09
Identities = 23/107 (21%), Positives = 37/107 (34%), Gaps = 25/107 (23%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
PN + TI V E L++ F FG I + + + +GF
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGF-------- 59
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
F++F E + +AI V+G + L V A+
Sbjct: 60 -----------AFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95
>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 = 53.0 bits (128), Expect = 2e-09
Identities = 27/97 (27%), Positives = 44/97 (45%), Gaps = 25/97 (25%)
Query: 146 NTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDD 199
+FV G +E+ L Q FS +G+I V + E ++ RGF
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGF---------------- 56
Query: 200 CARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFVTF++ + + A+ +NG V G +++V A
Sbjct: 57 ---GFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG 90
>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 = 52.8 bits (127), Expect = 3e-09
Identities = 15/97 (15%), Positives = 35/97 (36%), Gaps = 26/97 (26%)
Query: 145 GNTIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCA 201
+ +F+ A + + + FS +G++ S+ +G+
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH----KGY------------------ 64
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV + + + A+ NG + G L +++A
Sbjct: 65 -AFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100
>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 = 54.2 bits (131), Expect = 4e-09
Identities = 15/98 (15%), Positives = 33/98 (33%), Gaps = 27/98 (27%)
Query: 147 TIFVQG--AGISEEFLRQHFSIFGKICSVSM------EVEKGRGFVTFDSPESSDKAITD 198
+FV SE+ LR+ F +G + +++ + +G
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC--------------- 49
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FVTF + +++ +A ++ V +
Sbjct: 50 ----CFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMK 83
Score = 53.4 bits (129), Expect = 7e-09
Identities = 20/105 (19%), Positives = 32/105 (30%), Gaps = 28/105 (26%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSPESSD 193
N + +F+ +E +R FS FG+I + G RG
Sbjct: 90 NNAVEDRK-LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGC---------- 138
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHV---QGVKLKVSLA 235
FVTF + + AI ++ + V A
Sbjct: 139 ---------AFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>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 = 53.2 bits (128), Expect = 4e-09
Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 25/107 (23%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
P + V G +E LR+ FS +G I VS+ + + RGF
Sbjct: 39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF-------- 90
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
FV F++ + + +A NG + G +++V + +
Sbjct: 91 -----------AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
>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 = 52.3 bits (126), Expect = 4e-09
Identities = 25/105 (23%), Positives = 43/105 (40%), Gaps = 25/105 (23%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPES 191
+ G ++V I+E+ LR F FG+I S+ + E + +G+
Sbjct: 19 LQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY-------- 70
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GF+TF E + KA+ ++NG + G +KV
Sbjct: 71 -----------GFITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104
>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 = 51.0 bits (123), Expect = 6e-09
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITD 198
IFV G EE +R++F FG++ + M+ + + F+TF E K +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 51.5 bits (124), Expect = 6e-09
Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 21/101 (20%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
+ T+ + +EE L++ F I + K +G+
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGY------------ 55
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
F+ F S E + +A+ N ++G +++ L
Sbjct: 56 -------AFIEFASFEDAKEALNSCNKREIEGRAIRLELQG 89
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 53.3 bits (128), Expect = 8e-09
Identities = 19/133 (14%), Positives = 45/133 (33%), Gaps = 24/133 (18%)
Query: 111 VSKRETNDDRTPVDKKVYGESLLTRLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFG 168
++ P+ K + + E + G + V G+S+ +++ F+ FG
Sbjct: 54 RNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 113
Query: 169 KICSVSMEVEKG---RGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHV 225
+ +++ ++ G V F+ + KA+ + G +
Sbjct: 114 TLKKAAVDYDRSGRSLGT-------------------ADVHFERRADALKAMKQYKGVPL 154
Query: 226 QGVKLKVSLARRQ 238
G + + L Q
Sbjct: 155 DGRPMDIQLVASQ 167
>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 = 51.6 bits (124), Expect = 8e-09
Identities = 18/95 (18%), Positives = 31/95 (32%), Gaps = 22/95 (23%)
Query: 145 GNTIFVQG--AGISEEFLRQHFSIFGKICSVSM-EVEKGRGFVTFDSPESSDKAITDDCA 201
I+V I + + F +G I + + G F
Sbjct: 22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPF------------------ 63
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
FV F+ P ++ A+ +G G +L+V R
Sbjct: 64 -AFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 23/83 (27%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESS 213
+E+ +R F +GK+ + + + GFV + ++
Sbjct: 19 EATEQEIRSLFEQYGKVLECDII----KNY-------------------GFVHIEDKTAA 55
Query: 214 DKAITEVNGTHVQGVKLKVSLAR 236
+ AI ++ + GV + V ++
Sbjct: 56 EDAIRNLHHYKLHGVNINVEASK 78
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 50.8 bits (122), Expect = 1e-08
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 20/82 (24%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ L + FS +G + +V + GF FV F+ P ++
Sbjct: 12 AGKGELERAFSYYGPLRTVWI-ARNPPGF-------------------AFVEFEDPRDAE 51
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
A+ ++G + G +++V L+
Sbjct: 52 DAVRGLDGKVICGSRVRVELST 73
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 16/96 (16%), Positives = 33/96 (34%), Gaps = 25/96 (26%)
Query: 147 TIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDC 200
+++ +EE + S G + ++ M + + +G+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGY----------------- 46
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
F+ F ESS A+ +NG + LK +
Sbjct: 47 --AFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS 80
>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 = 50.7 bits (122), Expect = 1e-08
Identities = 23/108 (21%), Positives = 40/108 (37%), Gaps = 25/108 (23%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPE 190
P + T++V G +SE L + F G + + M + +G+
Sbjct: 7 GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY------- 59
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
GFV F S E +D AI ++ + G ++V+ A
Sbjct: 60 ------------GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH 95
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 51.7 bits (124), Expect = 1e-08
Identities = 23/128 (17%), Positives = 48/128 (37%), Gaps = 25/128 (19%)
Query: 117 NDDRTPVDKKVYGESLLTRLAPNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVS 174
+ + + G ++ P +G ++ V S + LR+ F +G++ V
Sbjct: 19 SHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY 78
Query: 175 M----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKL 230
+ ++ RGF FV F ++ A+ ++G + G +L
Sbjct: 79 IPRDRYTKESRGF-------------------AFVRFHDKRDAEDAMDAMDGAVLDGREL 119
Query: 231 KVSLARRQ 238
+V +AR
Sbjct: 120 RVQMARYG 127
>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 = 53.1 bits (127), Expect = 2e-08
Identities = 16/106 (15%), Positives = 35/106 (33%), Gaps = 22/106 (20%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDK 194
T+ + +SEE L+ FS G + +K R
Sbjct: 143 NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKM----------- 191
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHV-QGVKLKVSLARRQL 239
+ S E + +A+ +++ + + L+VS ++ +
Sbjct: 192 --------ALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 229
Score = 48.1 bits (114), Expect = 8e-07
Identities = 15/110 (13%), Positives = 37/110 (33%), Gaps = 23/110 (20%)
Query: 137 APNEKPKGGNTIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSD 193
P G + + V ++ + L F ++G + V + + +
Sbjct: 26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI-LFNKKEN---------- 74
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAP 243
V + A++ +NG + G ++++L++ Q P
Sbjct: 75 ---------ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLP 115
>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 = 50.3 bits (121), Expect = 2e-08
Identities = 20/115 (17%), Positives = 38/115 (33%), Gaps = 29/115 (25%)
Query: 129 GESLLTRLAPNEKPKGGNTIFVQ--GAGISEEFLRQHFSIFGKICSVS-MEVEKGR---- 181
G +L + +F+ S L+ S ++ ++V G
Sbjct: 1 GSHMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKF 60
Query: 182 GFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G+V F+S E +KA+ E+ G V G ++K+ +
Sbjct: 61 GYVDFESAEDLEKAL----------------------ELTGLKVFGNEIKLEKPK 93
>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 = 50.0 bits (120), Expect = 2e-08
Identities = 22/110 (20%), Positives = 42/110 (38%), Gaps = 27/110 (24%)
Query: 134 TRLAPNEKPKGGNTIFV---QGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPE 190
+ L P + +F+ +S+E L + FS +G I ++++ F
Sbjct: 12 SGLVPRGSH-MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----NAF------- 59
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLK 240
GF+ FD+P+S AI + G KL + ++ +
Sbjct: 60 ------------GFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97
>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 = 50.4 bits (121), Expect = 2e-08
Identities = 23/108 (21%), Positives = 38/108 (35%), Gaps = 23/108 (21%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDS 188
G T+F++ EE L + FG + V + + KG F F +
Sbjct: 7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 66
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
E++ K + ++ E G + G +LKV LA
Sbjct: 67 QEAAQKCL---------------AAASLEAEGGGLKLDGRQLKVDLAV 99
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 49.0 bits (118), Expect = 3e-08
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAI 196
IFV G + E ++ +F FGK+ + + R GFVTF+S + +K
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58
>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 = 49.9 bits (119), Expect = 3e-08
Identities = 10/44 (22%), Positives = 17/44 (38%)
Query: 154 GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
G+S L G + ++ M K F + + E S +A
Sbjct: 38 GVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 81
>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 = 51.0 bits (122), Expect = 3e-08
Identities = 25/151 (16%), Positives = 53/151 (35%), Gaps = 28/151 (18%)
Query: 96 PEDSEPVDSKPKFLKVSKRETNDDRTPVDKKVYGESLLTR---LAPNEKPKGGNTIFVQG 152
E + ++ F + + D D ++ + +G ++ V
Sbjct: 18 TEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDN 77
Query: 153 A--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVT 206
S + LR+ F +G++ V + ++ RGF FV
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF-------------------AFVR 118
Query: 207 FDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
F ++ A+ ++G + G +L+V +AR
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARY 149
>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 = 48.7 bits (117), Expect = 4e-08
Identities = 20/96 (20%), Positives = 38/96 (39%), Gaps = 25/96 (26%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVS----MEVEKGRGFVTFDSPESSDKAITDDCA 201
+FV I+ + F+ FG+I M K +G+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGY------------------ 50
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
GFV+F + ++ AI ++ G + G +++ + A R
Sbjct: 51 -GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85
>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 = 49.7 bits (119), Expect = 5e-08
Identities = 14/98 (14%), Positives = 32/98 (32%), Gaps = 22/98 (22%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGRGFVTFDSPESSDKAITD 198
P+ ++++ I+ E + F +G I + + RG
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGT--------------- 49
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+V ++ + A+ ++G +V L V
Sbjct: 50 ----AYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN 83
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 49.1 bits (117), Expect = 5e-08
Identities = 15/103 (14%), Positives = 35/103 (33%), Gaps = 22/103 (21%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKA 195
P E ++V L++ G + + + + R
Sbjct: 12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQGPRRR------------ 58
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
F+ + ++ +A++ + G + L+V+LAR+Q
Sbjct: 59 -------AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94
>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 = 49.3 bits (118), Expect = 6e-08
Identities = 26/124 (20%), Positives = 49/124 (39%), Gaps = 26/124 (20%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS----MEVEKGRGFVTFDSPES 191
+ +FV I+ E ++ F+ FG+I M K +G+
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY-------- 59
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASST 251
GFV+F + ++ AI ++ G + G +++ + A R+ AP + S+T
Sbjct: 60 -----------GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK-PPAPKSTYESNT 107
Query: 252 TWSA 255
S
Sbjct: 108 KQSG 111
>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 = 48.6 bits (116), Expect = 6e-08
Identities = 14/102 (13%), Positives = 28/102 (27%), Gaps = 24/102 (23%)
Query: 144 GGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCA 201
G + I V+ + + + + V++ +
Sbjct: 4 GSSGILVKNLPQDSNCQEVHDLLKDYDL---KYCYVDRNKRT------------------ 42
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAP 243
FVT + E + AI + +G L V L +
Sbjct: 43 -AFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCS 83
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 47.9 bits (115), Expect = 8e-08
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITDD 199
+F+ G ++E LR++F FG++ C V + R GFVTF DK +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
>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 = 48.3 bits (116), Expect = 8e-08
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAI 196
IFV G E LR++F FG + + + EK R GF+TF+ +S D+A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 49.8 bits (119), Expect = 8e-08
Identities = 19/110 (17%), Positives = 35/110 (31%), Gaps = 25/110 (22%)
Query: 134 TRLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFD 187
+ K T++V +EE + + FS G I + M + GF
Sbjct: 28 DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGF---- 83
Query: 188 SPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
FV + S ++ A+ +NGT + ++
Sbjct: 84 ---------------CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 118
>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 = 50.9 bits (121), Expect = 8e-08
Identities = 20/160 (12%), Positives = 47/160 (29%), Gaps = 30/160 (18%)
Query: 93 AIQPEDSEPVDSKPKFLKVSKRETNDDR----TPVDKKVYGESLLTRLAPNEKPKG---- 144
AI ++ + + + VSK+ Y + +R P+
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117
Query: 145 -----GNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
N + A ++EE + G S++V G+
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKS--------------- 162
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARR 237
+ + G + +DS + + + +N ++ +
Sbjct: 163 ERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202
Score = 43.9 bits (103), Expect = 1e-05
Identities = 16/98 (16%), Positives = 34/98 (34%), Gaps = 23/98 (23%)
Query: 144 GGNTIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC 200
+ V G + ++ + + F ++G + V K G
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-PGA----------------- 44
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
V + D+AIT +N + G K+ V ++++
Sbjct: 45 --AMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQP 80
>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 = 48.6 bits (116), Expect = 8e-08
Identities = 20/107 (18%), Positives = 37/107 (34%), Gaps = 21/107 (19%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
+ V+G + E L + FG IC V M K + V F++ +S+ + +T
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTF----- 70
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASS 250
++ G + + + + P N SS
Sbjct: 71 --------------AADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 22/115 (19%), Positives = 36/115 (31%), Gaps = 28/115 (24%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKG--RGFVTFDSPES 191
+ + + +FV SEE + + F FG I + + G +G
Sbjct: 8 SESRGGRDRK-LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGC-------- 58
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHV---QGVKLKVSLARRQLKVAP 243
FV F S + AI ++G+ L V A + P
Sbjct: 59 -----------AFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGP 102
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 14/98 (14%), Positives = 33/98 (33%), Gaps = 24/98 (24%)
Query: 142 PKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDD 199
G N +++ ++ + LRQ F + + ++ G FV
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFV--------------- 49
Query: 200 CARGFVTFDSPESSDKAITEVNG-THVQGVKLKVSLAR 236
+ + +AI ++G + G ++V +
Sbjct: 50 ------DYPDQNWAIRAIETLSGKVELHGKIMEVDYSV 81
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDS 188
+ + + V G +E+ L+++FS FG++ V +++ G GFV F
Sbjct: 7 GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
Query: 189 PESSDKAITD 198
E+ K ++
Sbjct: 67 YETQVKVMSQ 76
>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 = 48.3 bits (115), Expect = 1e-07
Identities = 26/95 (27%), Positives = 38/95 (40%), Gaps = 17/95 (17%)
Query: 146 NTIFVQG--AGISEEFL---RQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC 200
N +FV G +++ + ++F FGKI V + S S
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS----YAGSQGPS-------- 63
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
A +VT+ E + +AI VN V G LK SL
Sbjct: 64 ASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 48.3 bits (115), Expect = 1e-07
Identities = 10/95 (10%), Positives = 32/95 (33%), Gaps = 21/95 (22%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
I ++ ++E + FGK+ ++ M K + F+ ++ E+++ +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYT--- 73
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
++G + + + +
Sbjct: 74 ----------------SVTPVLRGQPIYIQFSNHK 92
>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 = 48.3 bits (115), Expect = 1e-07
Identities = 11/109 (10%), Positives = 35/109 (32%), Gaps = 23/109 (21%)
Query: 134 TRLAPNEKPKG--GNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSP 189
+ + +K G + ++ ++E + FGK+ ++ M K + F+ +
Sbjct: 2 SSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATE 61
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
E++ + H++ + + + +
Sbjct: 62 EAAITMVNY-------------------YSAVTPHLRNQPIYIQYSNHK 91
>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 = 48.0 bits (115), Expect = 1e-07
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 25/103 (24%)
Query: 140 EKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSD 193
+ ++FV +EE L+ FS G + S + E K +G+
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGY---------- 52
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GF + E++ A+ +NG G L+V A
Sbjct: 53 ---------GFCEYQDQETALSAMRNLNGREFSGRALRVDNAA 86
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 48.0 bits (115), Expect = 1e-07
Identities = 16/103 (15%), Positives = 38/103 (36%), Gaps = 25/103 (24%)
Query: 140 EKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSD 193
++ G +FV G +EE + F+ +G+I ++ + +G+
Sbjct: 18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY---------- 67
Query: 194 KAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
V +++ + + A+ +NG + G + V
Sbjct: 68 ---------TLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101
>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 = 48.4 bits (115), Expect = 1e-07
Identities = 10/95 (10%), Positives = 32/95 (33%), Gaps = 21/95 (22%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARG 203
I ++ ++E + FGK+ ++ M K + F+ ++ E+++ +
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNY----- 86
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
++G + + + +
Sbjct: 87 --------------YTSVTPVLRGQPIYIQFSNHK 107
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 14/64 (21%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGRGFVTFDSPESSDKA 195
+ G+ +FV ++ E L+Q F +G++ V + + FVTF + +
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSL 64
Query: 196 ITDD 199
+D
Sbjct: 65 CGED 68
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 47.3 bits (113), Expect = 2e-07
Identities = 14/105 (13%), Positives = 31/105 (29%), Gaps = 31/105 (29%)
Query: 145 GNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEK------GRGFVTFDSPESSDKAI 196
+TI ++ + + S + + ++ + K RGF
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGF------------- 55
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGTH----VQGVKLKVSLARR 237
FV S + + + + H + G + V A+
Sbjct: 56 ------AFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGRGFVTFDSPESSDKAITDD 199
+FV ++E+ LR+ FS +G + V + + FVTF + + +D
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGED 62
>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 = 49.2 bits (118), Expect = 2e-07
Identities = 27/104 (25%), Positives = 37/104 (35%), Gaps = 26/104 (25%)
Query: 138 PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKG----RGFVTFDSPES 191
IFV G E LR +F +GKI + + ++G RGF
Sbjct: 97 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGF-------- 148
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
FVTFD +S DK + + V G +V A
Sbjct: 149 -----------AFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA 180
Score = 46.1 bits (110), Expect = 3e-06
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 8/74 (10%)
Query: 134 TRLAPNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVT 185
++ ++P+ +F+ G ++E LR HF +G + C V + R GFVT
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 186 FDSPESSDKAITDD 199
+ + E D A+
Sbjct: 62 YATVEEVDAAMNAR 75
>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 = 46.7 bits (112), Expect = 2e-07
Identities = 18/98 (18%), Positives = 35/98 (35%), Gaps = 30/98 (30%)
Query: 147 TIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSPESSDKAITD 198
+I+V G + E L HF G + V++ + KG ++ F ES ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-- 65
Query: 199 DCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
++ + +G ++KV R
Sbjct: 66 --------------------ALDESLFRGRQIKVIPKR 83
>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 = 46.8 bits (112), Expect = 3e-07
Identities = 13/91 (14%), Positives = 23/91 (25%), Gaps = 25/91 (27%)
Query: 154 GISEEFLRQHFSIFGKI----CSVSMEVEKGR--GFVTFDSPESSDKAITDDCARGFVTF 207
++E L + G G+ GF V
Sbjct: 12 WTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGF-------------------ALVGV 52
Query: 208 DSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
S SS K + + + G V+ + +
Sbjct: 53 GSEASSKKLMDLLPKRELHGQNPVVTPSNKL 83
>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 = 46.4 bits (111), Expect = 3e-07
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 8/59 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITD 198
+FV G S++ L+ +F+ FG++ C++ M+ GR GF+ F S +K +
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72
>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 = 46.9 bits (112), Expect = 3e-07
Identities = 21/108 (19%), Positives = 35/108 (32%), Gaps = 30/108 (27%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDS 188
+ + + T+F A I L FS GK+ V + + KG +V F
Sbjct: 17 NLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+S AI + G + GV + V ++
Sbjct: 77 IQSVPLAI----------------------GLTGQRLLGVPIIVQASQ 102
>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 = 46.5 bits (111), Expect = 5e-07
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITDD 199
+F+ G ++E LR++F FG++ C V + R GFVTF DK +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
>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 = 46.0 bits (110), Expect = 5e-07
Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 26/96 (27%)
Query: 147 TIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDKAITDDC 200
I+V + E +++ FS FGK+ +V + E +K +GF
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGF----------------- 45
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV ES +AI +++ T G ++V+ A
Sbjct: 46 --GFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEAN 78
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 46.8 bits (111), Expect = 5e-07
Identities = 16/126 (12%), Positives = 36/126 (28%), Gaps = 28/126 (22%)
Query: 120 RTPVDKKVYGESLLTRLAPNEKPKGGNTIFVQG--AGISEEFLRQH----FSIFGKICSV 173
+++ L P+ +P + + + +E L+ S G I +
Sbjct: 6 AAKFERQHMDSPDLGSTPPHTEPS--QVVLITNINPEVPKEKLQALLYALASSQGDILDI 63
Query: 174 -SMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
+ G ++ F + ES+ + G QG L +
Sbjct: 64 VVDLSDDNSGK-------------------AYIVFATQESAQAFVEAFQGYPFQGNPLVI 104
Query: 233 SLARRQ 238
+ +
Sbjct: 105 TFSETP 110
>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 = 46.5 bits (111), Expect = 6e-07
Identities = 14/102 (13%), Positives = 36/102 (35%), Gaps = 25/102 (24%)
Query: 141 KPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDK 194
+ G +FV E+ +++ F +G+I ++ + +G+
Sbjct: 22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGY----------- 70
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
V +++ + + A +NG + G ++V
Sbjct: 71 --------ALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 104
>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 = 46.3 bits (110), Expect = 6e-07
Identities = 20/119 (16%), Positives = 33/119 (27%), Gaps = 23/119 (19%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
+ I + AG +++ FS FG + V + +G
Sbjct: 4 GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL--PEGGIT------------- 48
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSA 255
V F P + KA + + V L + A + A S A
Sbjct: 49 ------AIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPA 101
>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 = 47.5 bits (113), Expect = 6e-07
Identities = 17/131 (12%), Positives = 43/131 (32%), Gaps = 26/131 (19%)
Query: 113 KRETNDDRTPVDKKVYGESLLTRLAPN-EKPKGGNTIFVQGA--GISEEFLRQHFSIFGK 169
++N + L P ++ G +FV E+ +++ F +G+
Sbjct: 39 GSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGE 98
Query: 170 ICSVSM----EVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHV 225
I ++ + +G+ V +++ + + A +NG +
Sbjct: 99 IKNIHLNLDRRTGFSKGY-------------------ALVEYETHKQALAAKEALNGAEI 139
Query: 226 QGVKLKVSLAR 236
G ++V
Sbjct: 140 MGQTIQVDWCF 150
>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 = 46.1 bits (110), Expect = 7e-07
Identities = 24/104 (23%), Positives = 41/104 (39%), Gaps = 24/104 (23%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGR--GFVTFDSPESS 192
PN + + T+FV+G +EE L++ F + + + E G GF
Sbjct: 7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA-RIVTDRETGSSKGF--------- 56
Query: 193 DKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
GFV F+S E + A + + G K+ + A+
Sbjct: 57 ----------GFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>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 = 46.1 bits (110), Expect = 7e-07
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITD 198
+FV G ++E LR +FS +G++ C + + + GFV F P +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 47.2 bits (112), Expect = 7e-07
Identities = 17/108 (15%), Positives = 30/108 (27%), Gaps = 27/108 (25%)
Query: 139 NEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI----CSVSMEVEKGR--GFVTFDSPE 190
+ ++V +++ L Q G + G+ G+
Sbjct: 49 SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGY------- 101
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
V S S K + + G + G K+ V A RQ
Sbjct: 102 ------------AEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
>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 = 46.7 bits (111), Expect = 7e-07
Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 10/84 (11%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
+ E+ L+ F + S + + + F+ + +++
Sbjct: 57 VQEKDLKYIFGRYVDFSSETQRIM--FDIRLMKEGRMKGQ--------AFIGLPNEKAAA 106
Query: 215 KAITEVNGTHVQGVKLKVSLARRQ 238
KA+ E NG + G + V AR
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSA 130
>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 = 46.8 bits (111), Expect = 8e-07
Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 20/82 (24%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++ L + F +G + SV + GF FV F+ P +
Sbjct: 85 GNKTELERAFGYYGPLRSVWV-ARNPPGF-------------------AFVEFEDPRDAA 124
Query: 215 KAITEVNGTHVQGVKLKVSLAR 236
A+ E++G + G +++V L+
Sbjct: 125 DAVRELDGRTLCGCRVRVELSN 146
>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 = 46.1 bits (110), Expect = 9e-07
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITDD 199
IFV G ++ LR++F FG I V + + G+ GFVT ++++A D
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
>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 = 46.2 bits (110), Expect = 9e-07
Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 25/102 (24%)
Query: 141 KPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDSPESSDK 194
+ G +FV G +EE + F+ +G+I ++ + +G+
Sbjct: 18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY----------- 66
Query: 195 AITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
V +++ + + A+ +NG + G + V
Sbjct: 67 --------TLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100
>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 = 45.4 bits (108), Expect = 1e-06
Identities = 20/117 (17%), Positives = 39/117 (33%), Gaps = 28/117 (23%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKG--RGFVTFDSPE 190
+ K +F+ + E+ L+ F FGKI +V + G +G
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGC------- 57
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHV---QGVKLKVSLARRQLKVAPI 244
F+T+ ES+ KA + ++ ++V A + +
Sbjct: 58 ------------AFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSG 102
>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 = 47.0 bits (111), Expect = 2e-06
Identities = 14/110 (12%), Positives = 26/110 (23%), Gaps = 27/110 (24%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI----CSVSMEVEKG--RGFVTFDS 188
+++ ++E L + G G +GF
Sbjct: 60 VVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGF----- 114
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
V S SS K + + + G V+ +Q
Sbjct: 115 --------------ALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 44.3 bits (105), Expect = 2e-06
Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 12/63 (19%)
Query: 146 NTIFVQGA--------GISEEFLRQHFSIFGKICSVSMEVE----KGRGFVTFDSPESSD 193
+ I V + + + FS FGKI + E KG F+ + SP +
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 194 KAI 196
A+
Sbjct: 62 DAV 64
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 44.4 bits (105), Expect = 2e-06
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 140 EKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
K + ++G G+ E L + FG I V + +K + V F+ + A+
Sbjct: 16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAV 74
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 44.3 bits (105), Expect = 3e-06
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 12/71 (16%)
Query: 138 PNEKPKGGNTIFVQGA--------GISEEFLRQHFSIFGKICSVSMEVE----KGRGFVT 185
P E + I V + + + FS FGKI + E KG F+
Sbjct: 8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLE 67
Query: 186 FDSPESSDKAI 196
+ SP + A+
Sbjct: 68 YASPAHAVDAV 78
>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 = 44.6 bits (106), Expect = 3e-06
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 148 IFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGR----GFVTFDSPESSDKAITD 198
+F+ G +EE LR ++ +GK+ C V + R GFVTF S D A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
>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 = 44.7 bits (106), Expect = 3e-06
Identities = 21/108 (19%), Positives = 38/108 (35%), Gaps = 30/108 (27%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDS 188
A +K +++V G + + L HFS G I +++ + KG ++ F
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
S D A+ ++ T +G +KV R
Sbjct: 88 RNSVDAAV----------------------AMDETVFRGRTIKVLPKR 113
>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 = 43.8 bits (104), Expect = 3e-06
Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 28/98 (28%)
Query: 145 GNTIFVQG--AGISEEFLRQHFSIFG------KICSVSMEVEKGRGFVTFDSPESSDKAI 196
++++ + E F+ + F+ G KI + G+
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIR-NRLTGIPAGY------------- 54
Query: 197 TDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
FV F +++K + ++NG + G
Sbjct: 55 ------CFVEFADLATAEKCLHKINGKPLPGATPAKRF 86
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 43.0 bits (102), Expect = 7e-06
Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 27/112 (24%)
Query: 147 TIFVQ--GAGISEEFLRQHFS-IFGKICSVSM---EVEKGRGFVTFDSPESSDKAITDDC 200
++FV + + L + F ++ + + +G+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGY----------------- 53
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVK-LKVSLA-RRQLKVAPINDAASS 250
GFV F +A+TE G G K +++S+A + +V P+ SS
Sbjct: 54 --GFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 45.2 bits (106), Expect = 1e-05
Identities = 12/50 (24%), Positives = 17/50 (34%)
Query: 147 TIFVQGAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAI 196
E +R FS G I + K GFV F +++ A
Sbjct: 147 NSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAK 196
>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 = 42.9 bits (101), Expect = 1e-05
Identities = 16/96 (16%), Positives = 29/96 (30%), Gaps = 24/96 (25%)
Query: 143 KGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC 200
+ N + V G S + L+ H G +C D
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYA--------------------DVYRDGT 52
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G V F E A+ +++ T + + + + R
Sbjct: 53 --GVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR 86
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 42.4 bits (100), Expect = 1e-05
Identities = 22/118 (18%), Positives = 36/118 (30%), Gaps = 40/118 (33%)
Query: 142 PKG-GNTIFVQGA--------GISEEFLRQHFSIFGKICSVSM----EVEKGRGFVTFDS 188
P G I V GA + ++ L FS GK+ ++ K +GF
Sbjct: 2 PLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGF----- 56
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPIND 246
FV S + K I +G + + +L + + D
Sbjct: 57 --------------LFVECGSMNDAKKIIKSFHGKRLDL--------KHRLFLYTMKD 92
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 21/106 (19%), Positives = 37/106 (34%), Gaps = 25/106 (23%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI-CSVSMEV-EKGR--GFVTFDSPE 190
+ G I VQ +S + + F + I SV ++ EKG G
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE------- 59
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
V F+S + + A+ ++N + K+K+ L
Sbjct: 60 ------------AMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGS 93
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 21/106 (19%), Positives = 41/106 (38%), Gaps = 29/106 (27%)
Query: 140 EKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-------KGRGFVTFDSPE 190
K + + I V+ ++ +R+ FS FG++ +V + + +G GFV F + +
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+ KA + TH+ G +L + A
Sbjct: 70 DAKKAFN--------------------ALCHSTHLYGRRLVLEWAD 95
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 25/105 (23%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI-CSVSMEV-EKGR--GFVTFDSPE 190
+ G I VQ +S + + F + I SV ++ EKG G
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE------- 59
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLA 235
V F+S + + A+ ++N + K+K+S
Sbjct: 60 ------------AMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 41.6 bits (98), Expect = 2e-05
Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 146 NTIFVQGAG--ISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAITD 198
+++++G + + +++ G++ ++ M KG FV FDS ES+ K +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 71
Query: 199 D 199
Sbjct: 72 P 72
>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 = 38.8 bits (90), Expect = 3e-04
Identities = 11/63 (17%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 138 PNEKPKGGNTIFVQG---AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDK 194
++K + G I + +G S+ + + +GKI + + K + F+ ++ E +
Sbjct: 18 FDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMA 77
Query: 195 AIT 197
+
Sbjct: 78 MVD 80
>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 = 39.0 bits (91), Expect = 3e-04
Identities = 16/96 (16%), Positives = 29/96 (30%), Gaps = 24/96 (25%)
Query: 143 KGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDC 200
+ N + V G S + L+ H G +C D
Sbjct: 14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYA--------------------DVYRDGT 53
Query: 201 ARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G V F E A+ +++ T + + + + R
Sbjct: 54 --GVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR 87
>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 = 37.4 bits (87), Expect = 6e-04
Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 33/90 (36%)
Query: 154 GISEEFLRQHFSIFGK-----------ICSVSMEVEKGRGFVTFDSPESSDKAITDDCAR 202
GI+EE + F+ + + +V + +K F+ F S + + +A+
Sbjct: 17 GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM------ 70
Query: 203 GFVTFDSPESSDKAITEVNGTHVQGVKLKV 232
+G QG LK+
Sbjct: 71 ----------------AFDGIIFQGQSLKI 84
>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 = 39.0 bits (90), Expect = 6e-04
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 156 SEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSPESSDKAI 196
+ + +++ G++ ++ M KG FV FDS ES+ K +
Sbjct: 122 TLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 167
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 37.5 bits (87), Expect = 7e-04
Identities = 15/101 (14%), Positives = 29/101 (28%), Gaps = 22/101 (21%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVS-MEVEKGRGFVTFDSPESSDKA 195
++ P I ++ G S + L+ + S + G
Sbjct: 22 SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGT------------ 69
Query: 196 ITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
G + F S E +A+ +N +G + V
Sbjct: 70 -------GALEFPSEEILVEALERLNNIEFRGSVITVERDD 103
>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 = 39.6 bits (92), Expect = 0.001
Identities = 53/306 (17%), Positives = 89/306 (29%), Gaps = 108/306 (35%)
Query: 2 AKYTLTKKSLQAQK-APRPEPERTQASSTLKRPIEAKDAREVARKLLKSGAI-----NPI 55
L K + A+ A RP ++ ++S L R + +A+ V AI N
Sbjct: 118 KTKELIKNYITARIMAKRPFDKK--SNSALFRAVGEGNAQLV--------AIFGGQGNT- 166
Query: 56 VRPPKRCEQEGFKRPRGLE-RKLTETDRSTVSAYQPFSA--IQPEDSEPVDSKPKF---L 109
+ F+ E R L +T V FSA + +D++ F L
Sbjct: 167 --------DDYFE-----ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL 213
Query: 110 KVSKRETNDDRTP------------------------VDKKVYGESLLTRLAPNE--KPK 143
+ + N TP V K+ G P E
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLG------FTPGELRSYL 267
Query: 144 GGNTIFVQG----AGIS-----EEF-------LRQHFSIFGKICSVSMEVEKG-RGFVTF 186
G T QG I+ E F + F I G R + +
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFI-------------GVRCYEAY 314
Query: 187 DSPESSDKAITDDCARGF--------VTFDSPESSDKAITEVNGTHVQGVKLKVSL--AR 236
+ + D ++ + E + + N G ++++SL
Sbjct: 315 PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGA 374
Query: 237 RQLKVA 242
+ L V+
Sbjct: 375 KNLVVS 380
>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 = 36.9 bits (86), Expect = 0.001
Identities = 19/108 (17%), Positives = 37/108 (34%), Gaps = 35/108 (32%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-------KGRGFVTFDS 188
P P T F+ ++EE +++ F I +V + E KG G+ F+
Sbjct: 11 PKSPPY---TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 66
Query: 189 PESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+S A+ +N + +++V +A
Sbjct: 67 LDSLLSAL----------------------SLNEESLGNKRIRVDVAD 92
>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 = 36.4 bits (85), Expect = 0.001
Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 41/111 (36%)
Query: 138 PNEKPKGGNTIFVQGAG-----ISEEFLRQHFSIFGKICSVSMEVE-------KGRGFVT 185
P P T F+ G ++EE +++ F I +V + E KG G+
Sbjct: 15 PKSPPY---TAFL---GNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAE 67
Query: 186 FDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
F+ +S A+ +N + +++V +A
Sbjct: 68 FEDLDSLLSAL----------------------SLNEESLGNRRIRVDVAD 96
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 36.9 bits (85), Expect = 0.002
Identities = 18/92 (19%), Positives = 29/92 (31%), Gaps = 13/92 (14%)
Query: 139 NEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI--CSVSMEVEKGRG------FVTFDS 188
+ G +FV G I E+ + F FG + K F+ F
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
Query: 189 PESSDKAITD---DCARGFVTFDSPESSDKAI 217
S I + + ++ SP DK +
Sbjct: 62 ESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 36.5 bits (84), Expect = 0.002
Identities = 12/60 (20%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 143 KGGNTIFVQG--AGISEEFLRQHFSIFGKICS---VSMEVEKGRGFVTFDSPESSDKAIT 197
GG + V+G + +E L +F + +S + G +TF P +++ +
Sbjct: 6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLA 65
>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 = 38.2 bits (88), Expect = 0.002
Identities = 11/46 (23%), Positives = 18/46 (39%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAIT 197
G G+S L G + ++ M K F + + E S +A
Sbjct: 29 GNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYV 74
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 35.9 bits (82), Expect = 0.002
Identities = 8/50 (16%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 152 GAGISEEFLRQHFSIFGKICSVSM-EVEKGRGFVTFDSPESSDKAITDDC 200
G S++ L + +G++ ++ + + G V F + ++++ A+ ++
Sbjct: 26 KGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV 75
>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 = 36.6 bits (84), Expect = 0.004
Identities = 17/95 (17%), Positives = 34/95 (35%), Gaps = 22/95 (23%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++ + L Q FS FG + + K F + + + P S+
Sbjct: 58 VTLDVLHQIFSKFGTVLK-IITFTKNNQF------------------QALLQYADPVSAQ 98
Query: 215 KAITEVNGTHV--QGVKLKVSLAR-RQLKVAPIND 246
A ++G ++ L++ ++ L V ND
Sbjct: 99 HAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNND 133
>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 = 35.2 bits (81), Expect = 0.006
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 129 GESLLTRLAPNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI-CSVSMEVE-----KG 180
G + R + + + ++G G ++E + Q FS + +++ V+ G
Sbjct: 26 GGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITG 85
Query: 181 RGFVTFDSPESSDKAI 196
FV F S E ++KA+
Sbjct: 86 EAFVQFASQELAEKAL 101
>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 = 34.3 bits (79), Expect = 0.011
Identities = 11/108 (10%), Positives = 30/108 (27%), Gaps = 26/108 (24%)
Query: 137 APNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKI-CSVSMEVE---KGRGFVTFDSPE 190
+ + I++ + Q +V + V+ +G G
Sbjct: 7 GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ------- 59
Query: 191 SSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQ 238
V F + + + K+ ++ + G + V + +
Sbjct: 60 ------------ALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLE 94
>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 = 33.9 bits (78), Expect = 0.013
Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 8/67 (11%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSP 189
+ + G+ + ++G +E + FS V +E+ G V F +
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATH 65
Query: 190 ESSDKAI 196
E + A+
Sbjct: 66 EDAVAAM 72
>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 = 36.0 bits (82), Expect = 0.014
Identities = 33/219 (15%), Positives = 64/219 (29%), Gaps = 24/219 (10%)
Query: 81 DRSTVSAYQPFSAIQPEDSEPVDSKPKFLKVSKRETNDDRTPVDKKVYGESLLTRLA--- 137
++ Y + E +P D+ P ++ E + + + + + T L
Sbjct: 31 EKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWD 90
Query: 138 ----PNEKPKGGNTIFVQG--AGISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPES 191
PN + T+FV +E LR+ F ++G I + M
Sbjct: 91 PHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHM---------------V 135
Query: 192 SDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAASST 251
K F+ ++ A +G + G ++ V + R +
Sbjct: 136 YSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGG 195
Query: 252 TWSAIACHQSLKGNHKDKRHQVIYDDDIFGEEPPLEDPD 290
+ H + YD+ P D D
Sbjct: 196 LGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRD 234
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 34.2 bits (78), Expect = 0.015
Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 22/95 (23%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
++ + L Q FS FG + + + K F + + + P S+
Sbjct: 40 VTLDVLHQIFSKFGTVLKI-ITFTKNNQF------------------QALLQYADPVSAQ 80
Query: 215 KAITEVNGTHV--QGVKLKVSLAR-RQLKVAPIND 246
A ++G ++ L++ ++ L V ND
Sbjct: 81 HAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNND 115
>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 = 33.6 bits (77), Expect = 0.018
Identities = 14/103 (13%), Positives = 34/103 (33%), Gaps = 29/103 (28%)
Query: 146 NTIFVQG--AGISEEFLRQHFSIFGK------ICSVSMEVEKGRGFVTFDSPESSDKAIT 197
+F+ G E + + + + + + + + K RGF
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGF-------------- 54
Query: 198 DDCARGFVTFDSPESSDKAITEVN--GTHVQGVKLKVSLARRQ 238
FV ++S ++ A ++ + G ++ V A +
Sbjct: 55 -----AFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE 92
>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 = 33.2 bits (76), Expect = 0.020
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 8/68 (11%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSP 189
P + V G E +R F ++ +V + + G G V F SP
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSP 66
Query: 190 ESSDKAIT 197
+ + +A+
Sbjct: 67 QDTFEALK 74
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 32.6 bits (75), Expect = 0.032
Identities = 20/107 (18%), Positives = 33/107 (30%), Gaps = 34/107 (31%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE------KGRGFVTFDSP 189
P E P T +V + + F I SV + + KG +V FD
Sbjct: 11 PTEPP---YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEV 66
Query: 190 ESSDKAITDDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLAR 236
+S +A+ +G + L+V +A
Sbjct: 67 DSLKEAL----------------------TYDGALLGDRSLRVDIAE 91
>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 = 32.1 bits (73), Expect = 0.056
Identities = 13/50 (26%), Positives = 18/50 (36%)
Query: 173 VSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNG 222
V E K + + P D C + FV F S KA+ + G
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
>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 = 32.0 bits (73), Expect = 0.056
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 8/67 (11%)
Query: 139 NEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKIC-SVSMEVE-----KGRGFVTFDSPE 190
+ + ++G G S+E + Q FS + +++ V+ G FV F S E
Sbjct: 9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQE 68
Query: 191 SSDKAIT 197
++KA+
Sbjct: 69 IAEKALK 75
>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 = 32.1 bits (73), Expect = 0.071
Identities = 10/67 (14%), Positives = 22/67 (32%), Gaps = 8/67 (11%)
Query: 138 PNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKI-CSVSMEVE-----KGRGFVTFDSP 189
+ G ++++G + + F + S+ + G GFV F +
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
Query: 190 ESSDKAI 196
A+
Sbjct: 78 ADYKAAL 84
>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 = 32.1 bits (73), Expect = 0.098
Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 8/67 (11%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSP 189
+ G+ + ++G +E + FS V +E+ G V F +
Sbjct: 38 EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATH 96
Query: 190 ESSDKAI 196
E + A+
Sbjct: 97 EEAVAAM 103
>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 = 30.7 bits (70), Expect = 0.13
Identities = 11/70 (15%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 137 APNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEVE-----KGRGFVTFDSP 189
+ +T+ ++GA ++E+ + + + K ++ + G FV F +
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNE 60
Query: 190 ESSDKAITDD 199
E +A+ +
Sbjct: 61 EEVKQALKCN 70
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 30.8 bits (69), Expect = 0.20
Identities = 18/97 (18%), Positives = 31/97 (31%), Gaps = 22/97 (22%)
Query: 155 ISEEFLRQHFSIFGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSD 214
I+ + L + GK+ + ++ + V F+S +
Sbjct: 37 ITVDVLYTVCNPVGKV-QRIVIFKRNGI-------------------QAMVEFESVLCAQ 76
Query: 215 KAITEVNGTHVQG--VKLKVSLARRQLKVAPINDAAS 249
KA +NG + LK+ AR ND S
Sbjct: 77 KAKAALNGADIYAGCCTLKIEYARPTRLNVIRNDNDS 113
>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 = 30.5 bits (69), Expect = 0.22
Identities = 9/39 (23%), Positives = 16/39 (41%)
Query: 184 VTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNG 222
V + ++ + + FV F + KAI +NG
Sbjct: 55 VIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 93
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 30.2 bits (68), Expect = 0.27
Identities = 11/74 (14%), Positives = 21/74 (28%), Gaps = 11/74 (14%)
Query: 134 TRLAPNEKPKGGNTIFVQGA--GISEEFLRQHFSIFGKICSVSMEV---------EKGRG 182
+A + + ++G + E + F I + G
Sbjct: 12 NEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDA 71
Query: 183 FVTFDSPESSDKAI 196
FV F E + A+
Sbjct: 72 FVLFACEEYAQNAL 85
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 30.1 bits (67), Expect = 0.28
Identities = 8/48 (16%), Positives = 22/48 (45%)
Query: 202 RGFVTFDSPESSDKAITEVNGTHVQGVKLKVSLARRQLKVAPINDAAS 249
+ F + +S+++A + V G ++ VS + ++ + +S
Sbjct: 48 SAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCETSGPSS 95
>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 = 29.9 bits (66), Expect = 0.54
Identities = 7/39 (17%), Positives = 14/39 (35%), Gaps = 18/39 (46%)
Query: 63 EQEGFKRPRGLERKLTETDRSTVSAYQPFSAIQPEDSEP 101
E++ K+ L+ +++ Y DS P
Sbjct: 18 EKQALKK---LQ--------ASLKLYAD-------DSAP 38
Score = 27.6 bits (60), Expect = 3.5
Identities = 5/18 (27%), Positives = 9/18 (50%), Gaps = 2/18 (11%)
Query: 125 KKVYGESLLTRLAPNEKP 142
KK+ ++ L A + P
Sbjct: 23 KKL--QASLKLYADDSAP 38
>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 = 28.7 bits (64), Expect = 0.94
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 10/81 (12%)
Query: 129 GESLLTRLAPNEKPKGGNTIFVQGA--GISEEFLRQHFS---IFGKICSVSMEVE----- 178
G S + + + G + ++G S E ++ S I + V
Sbjct: 1 GSSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60
Query: 179 KGRGFVTFDSPESSDKAITDD 199
G FV +S + A+ D
Sbjct: 61 SGEAFVELESEDDVKLALKKD 81
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 28.5 bits (64), Expect = 1.2
Identities = 7/56 (12%), Positives = 18/56 (32%), Gaps = 19/56 (33%)
Query: 167 FGKICSVSMEVEKGRGFVTFDSPESSDKAITDDCARGFVTFDSPESSDKAITEVNG 222
G + + ++ +G V +V S ++ A+ ++G
Sbjct: 41 HGGVIHIYVDKNSAQGNV-------------------YVKCPSIAAAIAAVNALHG 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 = 27.5 bits (61), Expect = 2.3
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 155 ISEEFLRQHFSIFGKICSV-----SMEVEKGRGFVTFDSPESSDKAI 196
EE + +G++ + + G +V F E ++KA+
Sbjct: 39 FFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAV 85
Score = 26.4 bits (58), Expect = 4.7
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 204 FVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
+V F E ++KA+ ++N G + L
Sbjct: 72 YVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
>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 = 27.1 bits (60), Expect = 3.2
Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 10/70 (14%)
Query: 140 EKPKGGNTIFVQGA--GISEEFLRQHFS---IFGKICSVSMEVE-----KGRGFVTFDSP 189
E+ I QG + E + FS I + + +G + +S
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 190 ESSDKAITDD 199
+ KA+
Sbjct: 66 QDVQKALEKH 75
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 27.1 bits (60), Expect = 3.4
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 157 EEFLRQHFSIFGKICSVSM-------EVEKGRGFVTFDSPESSDKAITDDCARGF 204
E ++ +GK+ + + E R F+ F+ ES+ KA+ D R F
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYF 81
Score = 26.3 bits (58), Expect = 5.2
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 198 DDCARGFVTFDSPESSDKAITEVNGTHVQGVKLKVSL 234
D+ R F+ F+ ES+ KA+ ++NG + G +K
Sbjct: 54 DEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 27.0 bits (60), Expect = 4.0
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 204 FVTFDSPESSDKAITEVNG 222
V+F PE +D I ++G
Sbjct: 68 SVSFRDPEEADYCIQTLDG 86
Score = 26.2 bits (58), Expect = 7.3
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 157 EEFLRQHFSIFGKICSVSM--EVEKGRGFVTFDSPESSDKAI 196
E LR S FG+I + + G V+F PE +D I
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCI 81
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.4 bits (60), Expect = 4.1
Identities = 14/90 (15%), Positives = 29/90 (32%), Gaps = 16/90 (17%)
Query: 13 AQKAPRPEPE--RTQASSTLKRPIEAKDAREVARKL-LKSGAINPIVRPPKRCEQEGFKR 69
EPE R KR ++ DA + + A + + E + +
Sbjct: 76 QADRLTQEPESIRKWREEQRKR-LQELDAASKVMEQEWREKA---------KKDLEEWNQ 125
Query: 70 PRGLERKLTETDRSTVSAYQPFSAIQPEDS 99
+ ++ + + A + F QP+
Sbjct: 126 RQ--SEQVEKNKINNRIADKAFYQ-QPDAD 152
>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 = 26.5 bits (58), Expect = 7.3
Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 10/71 (14%)
Query: 139 NEKPKGGNTIFVQGA--GISEEFLRQHFS---IFGKICSVSMEVE-----KGRGFVTFDS 188
+ G + ++G S E ++ S I V G FV S
Sbjct: 38 GPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGS 97
Query: 189 PESSDKAITDD 199
+ A+ D
Sbjct: 98 EDDVKMALKKD 108
>3jtz_A Integrase; four stranded beta-sheet, DNA binding protein; 1.30A
{Yersinia pestis} PDB: 3rmp_A
Length = 88
Score = 25.5 bits (57), Expect = 9.3
Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 35 EAKDAREVARKLLKSGAINP 54
+A+ RE RK+L IN
Sbjct: 63 DARQQREGIRKMLALN-INL 81
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 0.129 0.366
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,287,998
Number of extensions: 247326
Number of successful extensions: 1002
Number of sequences better than 10.0: 1
Number of HSP's gapped: 701
Number of HSP's successfully gapped: 222
Length of query: 298
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 205
Effective length of database: 4,105,140
Effective search space: 841553700
Effective search space used: 841553700
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: 57 (25.7 bits)