RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14139
(327 letters)
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 153 bits (386), Expect = 4e-45
Identities = 40/198 (20%), Positives = 66/198 (33%), Gaps = 28/198 (14%)
Query: 117 GALGKASGSSEMLMKLARTTPYYK---RNRPHICSFWVKGECRRGEECPYRHEKPTDPDD 173
G G S ++ + + + C F+ KG C G +C Y H P + D
Sbjct: 40 GFAGNTRFVSPFALQPQLHSGKTRGDNDGQLFFCLFFAKGMCCLGPKCEYLHHIPDEEDI 99
Query: 174 PLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLT------- 226
++ D + A K TLYVG + L
Sbjct: 100 G--KLALRTEVL---DCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPA 154
Query: 227 --EQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILG-------- 276
E +R F + G+I + + + C F+++ + AE A E N+ +L
Sbjct: 155 QIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDD 214
Query: 277 ---GRRLNIKWGRAQANR 291
G L +KW +
Sbjct: 215 RREGTGLLVKWANEDPDP 232
>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 = 130 bits (328), Expect = 2e-38
Identities = 56/80 (70%), Positives = 68/80 (85%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
EDKTITTLYVG LGD +TE DLR+HFYQFGEIR++T++ +QQCAFIQ+ +R AAE A
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAA 65
Query: 267 EHSFNKVILGGRRLNIKWGR 286
E SFNK+I+ GRRLN+KWGR
Sbjct: 66 EKSFNKLIVNGRRLNVKWGR 85
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 108 bits (271), Expect = 1e-29
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 1/89 (1%)
Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR 259
+ + +TT Y+GN+ TE DL F FG I ++ C FI+Y +
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTH 73
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
A + + GR L WG+ +
Sbjct: 74 EQAAVCIV-ALANFPFQGRNLRTGWGKER 101
>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 = 103 bits (258), Expect = 1e-27
Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
T+Y G + LT+Q +R F FG+I + + ++ +F+++++ +A A+
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAI 78
Query: 267 EHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
S N + G + WG+ + +
Sbjct: 79 V-SVNGTTIEGHVVKCYWGKESPDMTSGPS 107
>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 = 101 bits (253), Expect = 7e-27
Identities = 24/108 (22%), Positives = 40/108 (37%), Gaps = 3/108 (2%)
Query: 190 PVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ 249
P + + + + TLYV +T LR F FG I +++ +
Sbjct: 16 PRGSHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR 73
Query: 250 QCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAE 297
CAF+ Y +A+ AV N + +L + R Q T +
Sbjct: 74 NCAFVTYEKMESADQAVA-ELNGTQVESVQLKVNIARKQPMLDAATGK 120
>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 = 92.4 bits (230), Expect = 1e-23
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 3/93 (3%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
S+ + + TLYV +T LR F FG I +++ + CAF+ Y
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58
Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
+A+ AV N + +L + R Q
Sbjct: 59 MESADQAVA-ELNGTQVESVQLKVNIARKQPML 90
>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 = 90.8 bits (226), Expect = 4e-23
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
T L+VG LG + L F +FG IR++ + A+IQY S AA+AA
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77
Query: 274 ILGG-RRLNIKWGRAQANRG 292
+ G RRL + + ++ + G
Sbjct: 78 LGGPDRRLRVDFAKSGPSSG 97
>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 = 85.8 bits (213), Expect = 3e-21
Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 1/93 (1%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTS 258
S+ + L+VGNL +TE+++R F ++G+ V I + FI+ +
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLET 60
Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
R AE A + + L G++L +++ A+
Sbjct: 61 RTLAEIAKV-ELDNMPLRGKQLRVRFACHSASL 92
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 83.9 bits (208), Expect = 2e-20
Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 4/99 (4%)
Query: 193 EKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCA 252
L+ R S M E T L+V + E +L + F FG ++ V I A
Sbjct: 12 SGLVPRGSHMHHRQEGELSN-TRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFA 68
Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
F+++ +A A+E + + L + + + A R
Sbjct: 69 FVEFEEAESAAKAIEE-VHGKSFANQPLEVVYSKLPAKR 106
>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 = 81.2 bits (201), Expect = 1e-19
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 1/92 (1%)
Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR 259
S+ D ++ LYV NL +E+ + F + + AF+ +++R
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
A A++ + N +L G + + +
Sbjct: 62 EDAVEAMK-ALNGKVLDGSPIEVTLAKPVDKD 92
>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 = 79.3 bits (196), Expect = 8e-19
Identities = 21/100 (21%), Positives = 47/100 (47%), Gaps = 7/100 (7%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------C 251
S+ P+ +T + + V N+ + ++++R+ F FGE+++V + K
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
F+ + ++ A+ A + L GRRL ++W ++
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100
>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 = 78.6 bits (194), Expect = 2e-18
Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 5/107 (4%)
Query: 186 GVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVT 244
G + L +AS + + P+ + +++GNL + + D+ F ++G + +
Sbjct: 1 GSSGSSGMSLKLQASNVTNKNDPKSIN-SRVFIGNLNTALVKKSDVETIFSKYGRVAGCS 59
Query: 245 ILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
+ + AF+QY++ A AAV N +L G+ L+I
Sbjct: 60 V--HKGYAFVQYSNERHARAAVL-GENGRVLAGQTLDINMAGEPKPD 103
>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 = 78.1 bits (193), Expect = 2e-18
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 5/92 (5%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQCAFIQYTSRPAAEA 264
+D TLYVGNL +TE + F Q G +S + S F+++ A A
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 70
Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
A+ + N + G+ + + W +++ +
Sbjct: 71 ALA-AMNGRKILGKEVKVNWATTPSSQKSGPS 101
>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 = 77.1 bits (190), Expect = 5e-18
Identities = 14/75 (18%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
++V L + + E DL + +FG I V ++ ++ A +++ + +A+ V + V
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPV 76
Query: 274 ILGGRRLNIKWGRAQ 288
+ G++ + ++
Sbjct: 77 YIAGQQAFFNYSTSK 91
>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 = 76.5 bits (189), Expect = 6e-18
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFN-K 272
LY+GNL +T DLR F + +L K AF+ Y + A A+E + + K
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIE-TLSGK 67
Query: 273 VILGGRRLNIKWGRAQANRG 292
V L G+ + + + ++ R
Sbjct: 68 VELHGKIMEVDYSVSKKLRS 87
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 76.6 bits (189), Expect = 9e-18
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSF 270
+ L+V NL + +TE+ L F QFG++ V L + AFI + R A A+E
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAME-EM 65
Query: 271 NKVILGGRRLNIKWGRAQANRGED 294
N L G + I + + + ++
Sbjct: 66 NGKDLEGENIEIVFAKPPDQKRKE 89
>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 = 76.2 bits (188), Expect = 1e-17
Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 4/96 (4%)
Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQY 256
S + P +YVGNL + +D+ D FY++G IR + + +++ AF+++
Sbjct: 9 SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEF 68
Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
AE AV + + G RL +++ R+ G
Sbjct: 69 EDPRDAEDAV-YGRDGYDYDGYRLRVEFPRSGRGTG 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 = 76.2 bits (188), Expect = 1e-17
Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 7/101 (6%)
Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFI 254
S+ L+VG L + +E+D+ F FG I T+L CAF+
Sbjct: 2 SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFV 61
Query: 255 QYTSRPAAEAAVEHSFNKVIL--GGRRLNIKWGRAQANRGE 293
+++S A+AA+ + L +K+ G
Sbjct: 62 KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGP 102
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 73.3 bits (180), Expect = 1e-16
Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
+++ L D + E DL + +FG I V ++ K++ A +++ A AV + + N++
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQI 82
Query: 274 ILGGRRLNIKWGRAQ 288
+ G + + +Q
Sbjct: 83 YIAGHPAFVNYSTSQ 97
>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 = 72.6 bits (179), Expect = 2e-16
Identities = 18/100 (18%), Positives = 45/100 (45%), Gaps = 11/100 (11%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTILSKQQ---CAFIQYTSR 259
PE + T+Y+ NL +K+ + +L+ + +FG+I + + + AF+ +
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEV 61
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELK 299
+A A+ + + I++ + ++ A++K
Sbjct: 62 SSATNALRS-MQGFPFYDKPMRIQYAKTDSDI---IAKMK 97
>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 = 73.1 bits (180), Expect = 2e-16
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVE 267
+T++V NL K+ + L++ F G + IL S+ + + A A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSR-GIGTVTFEQSIEAVQAIS 74
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
FN +L R +++K +G+
Sbjct: 75 -MFNGQLLFDRPMHVKMDERALPKGD 99
>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 = 72.3 bits (178), Expect = 2e-16
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 5/87 (5%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE 267
K T L+VGN+ T Q+LR F ++G + I + AF+ A A+
Sbjct: 5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI--VKDYAFVHMERAEDAVEAIR 62
Query: 268 HSFNKVILGGRRLNIKW--GRAQANRG 292
+ G+R++++ R + G
Sbjct: 63 -GLDNTEFQGKRMHVQLSTSRLRTASG 88
>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 = 72.3 bits (178), Expect = 4e-16
Identities = 27/101 (26%), Positives = 44/101 (43%), Gaps = 8/101 (7%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------ 250
R M P + LY+ NL ++TE+DL F +F E + I +
Sbjct: 10 IRKIPMFSSYNPGEPN-KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG 68
Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
AFI + ++ A A+ N L G+ L I++G+ + R
Sbjct: 69 QAFITFPNKEIAWQALH-LVNGYKLYGKILVIEFGKNKKQR 108
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 71.9 bits (177), Expect = 4e-16
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 214 TTLYVGNL-GDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
+ L++GNL ++++DL F +G I + I K FIQ+ + + A+E ++
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE-CESQ 67
Query: 273 VILGGRRLNIKWGRAQANRGED 294
+ G++L ++ + A D
Sbjct: 68 EMNFGKKLILEVSSSNARPQFD 89
>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 = 72.0 bits (177), Expect = 5e-16
Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 8/100 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAE 263
PPE LY+ NL K+T +++ D F ++G IR + + + + A++ Y A+
Sbjct: 4 PPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLE 303
AV+H + + R L + ANR + K + E
Sbjct: 62 NAVDH-LSGFNVSNRYLVV--LYYNANRAFQKMDTKKKEE 98
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 71.7 bits (176), Expect = 6e-16
Identities = 19/106 (17%), Positives = 41/106 (38%), Gaps = 11/106 (10%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
+ L D + E L+D ++GE+ V IL + A + +TS A+ V+
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALP 313
+ + + G ++ + +G+ + + P +P
Sbjct: 67 N-LHLTSVMGNIIHAQL----DIKGQQRMKYYELIVNGSYTPQTVP 107
>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 = 70.7 bits (174), Expect = 7e-16
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
L++GNL + TEQ++R F Q+G++ I + F+ + AAE A+ + +
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDI--IKNYGFVHIEDKTAAEDAIRN-LHHY 65
Query: 274 ILGGRRLNIKWGRAQANRG 292
L G +N++ + ++
Sbjct: 66 KLHGVNINVEASKNKSKAS 84
>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 = 71.2 bits (175), Expect = 8e-16
Identities = 22/98 (22%), Positives = 43/98 (43%), Gaps = 5/98 (5%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFI 254
S+ + T L+V N+ + + DLR F QFG+I V I+ ++ F+
Sbjct: 1 GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 60
Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
+ + A+ A E + ++ GR++ + A+
Sbjct: 61 TFENSADADRARE-KLHGTVVEGRKIEVNNATARVMTN 97
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 71.0 bits (174), Expect = 8e-16
Identities = 15/75 (20%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
+++ L +TE ++ FG++ ++ +L + AFI+ + AA V + +
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTP 77
Query: 274 ILGGRRLNIKWGRAQ 288
+L G+ + I++ +
Sbjct: 78 VLRGQPIYIQFSNHK 92
>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 = 70.7 bits (174), Expect = 9e-16
Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 6/91 (6%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILS----KQQC-AF 253
+S + P +++ T++VGNL ++ E+ L + F Q G + VTI K + F
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGF 61
Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
+ + + A+ N + L GR +N+
Sbjct: 62 VCFKHPESVSYAIA-LLNGIRLYGRPINVSG 91
>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 = 70.3 bits (173), Expect = 1e-15
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
++VGN+ T Q+LR F + G + + + AF+ A+AA+ N
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDV--VKDYAFVHMEKEADAKAAIA-QLNGK 66
Query: 274 ILGGRRLNIKWGRAQANR 291
+ G+R+N++ +
Sbjct: 67 EVKGKRINVELSTKGQKK 84
>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 = 72.6 bits (179), Expect = 1e-15
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 7/88 (7%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
T L V L +T+++L F G I + I+ + AF+ +TS ++ A++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDT 295
N + + +RL + + R +DT
Sbjct: 64 -VLNGITVRNKRLKVSYARPGGESIKDT 90
Score = 67.2 bits (165), Expect = 9e-14
Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAA 262
E T LYV NL +T+ L F ++G I IL + AF++Y R A
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 263 EAAVEHSFNKVILGG--RRLNIKW 284
+ A+ N VI G + L+++
Sbjct: 145 QEAISA-LNNVIPEGGSQPLSVRL 167
>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 = 70.0 bits (172), Expect = 2e-15
Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 214 TTLYVGNL-GDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
+ L++GNL ++++DL F +G I + I K FIQ+ + + A+ ++
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAI-EXESQ 79
Query: 273 VILGGRRLNIKWGRAQA 289
+ G++L ++ + A
Sbjct: 80 EMNFGKKLILEVSSSNA 96
>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 = 72.3 bits (178), Expect = 2e-15
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEHSF 270
L++G + K TE D+R F FG+I IL CAF+ +T+R A+ A++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Query: 271 NKVIL--GGRRLNIKW 284
+ + +K+
Sbjct: 158 QAQTMEGCSSPMVVKF 173
Score = 68.8 bits (169), Expect = 3e-14
Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---------SKQQCAFIQYTSRPAAEA 264
++VG + +E+DLR+ F Q+G + + +L SK C F+ + +R AA
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSK-GCCFVTFYTRKAALE 62
Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
A N +L G I+ A + + + K+
Sbjct: 63 AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKL 98
>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 = 70.7 bits (173), Expect = 2e-15
Identities = 19/95 (20%), Positives = 43/95 (45%), Gaps = 2/95 (2%)
Query: 195 LMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFI 254
L+ R S M + +++ L +TE ++ FG++ ++ +L + AFI
Sbjct: 14 LVPRGSHMGDSRSAGVPS-RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFI 72
Query: 255 QYTSRPAAEAAVEH-SFNKVILGGRRLNIKWGRAQ 288
+ + AA V + + +L G+ + I++ +
Sbjct: 73 EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 69.8 bits (171), Expect = 2e-15
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 4/80 (5%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL---SKQQCAFIQYTSRPAAEA 264
P+ + I L + N+ L + L Q+G + S + S+ + Y+S+ A
Sbjct: 10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQ 69
Query: 265 AVEHSFNKVILGGRRLNIKW 284
A++ N L L + +
Sbjct: 70 ALDK-LNGFQLENFTLKVAY 88
>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 = 72.2 bits (177), Expect = 2e-15
Identities = 30/117 (25%), Positives = 50/117 (42%), Gaps = 6/117 (5%)
Query: 214 TTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFN 271
+ L V NL +++T Q L F +G+++ V IL ++ A +Q A+ A+ H N
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH-LN 62
Query: 272 KVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPG---LPGALPPPPKDFFNLSNP 325
L G+ + I + Q + + L G L P K+F N+ P
Sbjct: 63 GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119
Score = 60.3 bits (146), Expect = 5e-11
Identities = 24/125 (19%), Positives = 46/125 (36%), Gaps = 8/125 (6%)
Query: 164 RHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGD 223
+H+ P + DQ + Y +K + + PP TL++ N+
Sbjct: 77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKK--PGSKNFQNIFPPS----ATLHLSNIPP 130
Query: 224 KLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFNKVILGGRRLN 281
++E+DL+ F G + ++ A IQ S A A+ N + L
Sbjct: 131 SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR 190
Query: 282 IKWGR 286
+ + +
Sbjct: 191 VSFSK 195
>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 = 69.2 bits (170), Expect = 4e-15
Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 14/92 (15%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---------CAFIQYTSRPAAEA 264
+ L++ NL TE+ L+ F + G I+S TI K+ F++Y A+
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 265 AVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
A++ + G +L ++ + R A
Sbjct: 66 ALK-QLQGHTVDGHKLEVR----ISERATKPA 92
>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 = 73.2 bits (180), Expect = 4e-15
Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 202 MPKLDPPEDKT--ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSR 259
L P E L+VGNL +TE+D + F ++GE V I + FI+ SR
Sbjct: 9 KSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESR 68
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQAN 290
AE A + IL R L I++ A
Sbjct: 69 TLAEIAKA-ELDGTILKSRPLRIRFATHGAA 98
Score = 65.9 bits (161), Expect = 1e-12
Identities = 17/108 (15%), Positives = 36/108 (33%), Gaps = 5/108 (4%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAAVEH 268
L V NL ++ + L F QFG + ++ + F+++ ++P A A+E
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPP 316
+ L ++ + ++ PP
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPP 204
>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 = 69.1 bits (169), Expect = 4e-15
Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNKV 273
L++ L ++TE ++ FG++ ++ +L + AF++ + AA V + S
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTP 76
Query: 274 ILGGRRLNIKW 284
L + + I++
Sbjct: 77 HLRNQPIYIQY 87
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 69.5 bits (170), Expect = 6e-15
Identities = 19/115 (16%), Positives = 43/115 (37%), Gaps = 8/115 (6%)
Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTIL- 246
+ S PP + + + N+ ++ ++ L+ Y G+I + +
Sbjct: 8 KFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL 67
Query: 247 --SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELK 299
A+I + ++ +A+A VE F G L I + ++ + L+
Sbjct: 68 SDDNSGKAYIVFATQESAQAFVEA-FQGYPFQGNPLVITFSETPQSQVAEDGSLE 121
>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 = 68.7 bits (168), Expect = 7e-15
Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTIL-------SKQQCAFIQYTSRPAAEAA 265
L++G + +++ + + E + V + + AF++Y S AA A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 266 VEH-SFNKVILGGRRLNIKWGRAQANRGEDTAE 297
++ L G ++ + W + + ED E
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVME 101
>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 = 72.3 bits (178), Expect = 8e-15
Identities = 16/95 (16%), Positives = 26/95 (27%), Gaps = 7/95 (7%)
Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQD-LRDHFYQFGEIRSVTILSKQQ-----CAFIQY 256
P L V L + D L + Q A ++Y
Sbjct: 174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEY 233
Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
+ AE A + + + LGG L + +
Sbjct: 234 ETAEMAEEAQQ-QADGLSLGGSHLRVSFCAPGPPG 267
Score = 69.2 bits (170), Expect = 1e-13
Identities = 21/94 (22%), Positives = 32/94 (34%), Gaps = 10/94 (10%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
L V NL LT+Q + FG + ++ ++ F +Y + +A A
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAELKVR 301
LG R L + W A L R
Sbjct: 156 D-LLGKPLGPRTLYVHW--TD-AGQLTPALLHSR 185
Score = 62.3 bits (152), Expect = 3e-11
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
+ + L +T Q++ D + ++ + + AF+ + AEAA+ F++
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINA-FHQS 80
Query: 274 ILGGRRLNIKWGRAQAN 290
L R L+++ A
Sbjct: 81 RLRERELSVQLQPTDAL 97
>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 = 68.9 bits (169), Expect = 8e-15
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 8/92 (8%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSR 259
+T L V NL +++ D+++ F +FG ++ + S A + + R
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL-GTADVHFERR 86
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
A A++ + V L GR ++I+ +Q +
Sbjct: 87 ADALKAMK-QYKGVPLDGRPMDIQLVASQIDL 117
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 68.0 bits (167), Expect = 9e-15
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 7/84 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEH 268
++V NL T + L+D F + G + I SK C +++ S AE A
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSK-GCGVVKFESPEVAERACRM 67
Query: 269 SFNKVILGGRRLNIKWGRAQANRG 292
N + L GR ++++ R +
Sbjct: 68 -MNGMKLSGREIDVRIDRNASGPS 90
>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 = 68.3 bits (167), Expect = 9e-15
Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 1/79 (1%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
++ T + NL ++++ F +FG + V + A +++ A A
Sbjct: 4 GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAF 63
Query: 267 EHSFNKVILGGRRLNIKWG 285
H L ++W
Sbjct: 64 RH-LAYSKFHHVPLYLEWA 81
>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 = 68.4 bits (168), Expect = 1e-14
Identities = 21/97 (21%), Positives = 38/97 (39%), Gaps = 8/97 (8%)
Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----- 246
+ + ++ +++ T LY+ NL + EQ+L + FG++ S IL
Sbjct: 4 GSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG 63
Query: 247 -SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
S+ F + S EA + H FN +
Sbjct: 64 TSR-GVGFARMESTEKCEAVIGH-FNGKFIKTPPGVS 98
>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 = 68.0 bits (167), Expect = 1e-14
Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 7/100 (7%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------A 252
S+ T+ V NL + E DL++ F FG I + + + A
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
FI + R A A+ + LN++W + N G
Sbjct: 61 FISFHRREDAARAIA-GVSGFGYDHLILNVEWAKPSTNSG 99
>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 = 68.1 bits (167), Expect = 1e-14
Identities = 24/107 (22%), Positives = 45/107 (42%), Gaps = 13/107 (12%)
Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAF 253
S+ P + T+++ NL E+ L + QFG+++ V ++ CAF
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 254 IQYTSRPAAEAAVE-----HSFNKVILGGRRLNIKW--GRAQANRGE 293
Q+ ++ AA+ + + L GR+L + R +A G
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 67.5 bits (165), Expect = 1e-14
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 2/84 (2%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILSKQQCAFIQYTSRPAAEAAVE 267
+YVGNL DL+ + G + +T ++ AF+ Y AA+ AV
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVS 74
Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
+ LG L + R Q ++
Sbjct: 75 -CLQGLRLGTDTLRVALARQQRDK 97
>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 = 67.7 bits (166), Expect = 1e-14
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQY 256
+T L V NL +++ D+++ F +FG ++ + S A + +
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL-GTADVHF 77
Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNI 282
+ A A++ +N V L GR +NI
Sbjct: 78 ERKADALKAMK-QYNGVPLDGRPMNI 102
>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 = 70.1 bits (172), Expect = 2e-14
Identities = 23/130 (17%), Positives = 48/130 (36%), Gaps = 14/130 (10%)
Query: 175 LADQNIK-DRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDH 233
Q++K R + + + L++G L + L + +++
Sbjct: 75 FQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL 134
Query: 234 FYQFGEIRSVTI-------LSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
FG +++ + LSK AF +Y + A+ N + LG ++L ++
Sbjct: 135 LTSFGPLKAFNLVKDSATGLSK-GYAFCEYVDINVTDQAIA-GLNGMQLGDKKLLVQR-- 190
Query: 287 AQANRGEDTA 296
A+ G A
Sbjct: 191 --ASVGAKNA 198
Score = 68.1 bits (167), Expect = 8e-14
Identities = 25/122 (20%), Positives = 40/122 (32%), Gaps = 15/122 (12%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAE 263
LYVGN+ +TE+ + D F + +T AF+++ S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLPGALPPPPKDFF-NL 322
A+ F+ +I G+ L I+ +E P K F L
Sbjct: 66 QAMA--FDGIIFQGQSLKIRRPHDYQPL-PGMSENPSVYVPGVVSTVVPDSAHKLFIGGL 122
Query: 323 SN 324
N
Sbjct: 123 PN 124
>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 = 69.2 bits (170), Expect = 2e-14
Identities = 13/93 (13%), Positives = 36/93 (38%), Gaps = 7/93 (7%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAE 263
E T L++GNL + +L+ + + ++ + ++ + S E
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 68
Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
A+E + + G + ++ + + ++ A
Sbjct: 69 KALE--LTGLKVFGNEIKLEKPKGRDSKKVRAA 99
Score = 66.5 bits (163), Expect = 2e-13
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEA 264
D + + TL NL +TE +L++ F EIR V+ K + A+I++ S AE
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEK 151
Query: 265 AVEHSFNKVILGGRRLNIKW 284
+E + GR +++ +
Sbjct: 152 NLE-EKQGAEIDGRSVSLYY 170
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 67.3 bits (165), Expect = 2e-14
Identities = 21/78 (26%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKVI 274
+YVGNLG + +L F +G +R+V I AF+++ AE AV + +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAV-RGLDGKV 61
Query: 275 LGGRRLNIKWGRAQANRG 292
+ G R+ ++ R
Sbjct: 62 ICGSRVRVELSTGMPRRS 79
>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 = 68.8 bits (169), Expect = 2e-14
Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 7/88 (7%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
T L V L +T+++ R F GEI S ++ + F+ Y AE A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDT 295
+ N + L + + + + R + D
Sbjct: 63 -TLNGLRLQTKTIKVSYARPSSASIRDA 89
Score = 64.1 bits (157), Expect = 1e-12
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 206 DPPEDKTITT-LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTS 258
P LYV L +T+++L F Q+G I + IL Q FI++
Sbjct: 80 RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139
Query: 259 RPAAEAAVEHSFNKVILGGRR-LNIKW 284
R AE A++ + G + +K+
Sbjct: 140 RIEAEEAIKGLNGQKPSGATEPITVKF 166
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 67.4 bits (165), Expect = 2e-14
Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 8/95 (8%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
+D L++G + L E+DL+ F +FG+I +T+L + CAF+ Y R
Sbjct: 6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65
Query: 260 PAAEAAVEHSFNKVIL--GGRRLNIKWGRAQANRG 292
+A A + L R + +K +++ G
Sbjct: 66 ESALKAQSALHEQKTLPGMNRPIQVKPADSESRGG 100
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 69.6 bits (171), Expect = 3e-14
Identities = 28/117 (23%), Positives = 48/117 (41%), Gaps = 9/117 (7%)
Query: 194 KLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-- 251
+ M R S + ++ +YVG++ +L E +R F FG I+S+ +
Sbjct: 11 QQMGRGSAAQR--QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK 68
Query: 252 ----AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEP 304
AF++Y AA+ A+E N V+LGGR + + +L
Sbjct: 69 HKGFAFVEYEVPEAAQLALEQ-MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124
Score = 66.2 bits (162), Expect = 5e-13
Identities = 28/130 (21%), Positives = 46/130 (35%), Gaps = 21/130 (16%)
Query: 187 VNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL 246
V P + +L +YV ++ L++ D++ F FG+I+S T+
Sbjct: 102 VGRPSNIG--QAQPIIDQLAEEARAF-NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLA 158
Query: 247 SKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
FI+Y +++ AV S N LGG+ L + A
Sbjct: 159 RDPTTGKHKGYGFIEYEKAQSSQDAVS-SMNLFDLGGQYLRVGK-----------AVTPP 206
Query: 301 RLEPVPGLPG 310
P PG
Sbjct: 207 MPLLTPATPG 216
>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 = 66.3 bits (162), Expect = 3e-14
Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
+ + V NL Q++ D + ++ + ++ AF+ + A+ A++ F++
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQ-MFHQY 63
Query: 274 ILGGRRLNIKWGRAQA 289
G+ L ++ A
Sbjct: 64 SFRGKDLIVQLQPTDA 79
>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 = 66.9 bits (164), Expect = 3e-14
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 7/92 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRP 260
P+ + TL V NL + + LR F ++G + V I + AF+++ R
Sbjct: 7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRR 66
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
A+ A + L GR L ++ R
Sbjct: 67 DAQDAEAA-MDGAELDGRELRVQVARYGRRDL 97
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 68.3 bits (167), Expect = 4e-14
Identities = 22/112 (19%), Positives = 46/112 (41%), Gaps = 6/112 (5%)
Query: 185 YGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVT 244
Y P+ +K +T L V NL +++ D+++ F +FG ++
Sbjct: 60 YSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 119
Query: 245 ILSKQQ-----CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
+ + A + + R A A++ + V L GR ++I+ +Q +
Sbjct: 120 VDYDRSGRSLGTADVHFERRADALKAMK-QYKGVPLDGRPMDIQLVASQIDL 170
>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 = 66.7 bits (163), Expect = 5e-14
Identities = 28/110 (25%), Positives = 41/110 (37%), Gaps = 15/110 (13%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------- 251
S+ DP ED + +YV L D +T DL D F Q G ++ +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 252 -------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
A + Y P A+AAVE F+ G +L + R +
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVE-WFDGKDFQGSKLKVSLARKKPPMNSG 109
>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 = 66.2 bits (162), Expect = 7e-14
Identities = 20/96 (20%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRP 260
PE++ T++ L ++ +DL D F G++R V I+S + A++++
Sbjct: 19 SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
+ A+ L G + ++ +A+ NR +
Sbjct: 79 SVPLAIG--LTGQRLLGVPIIVQASQAEKNRLSGPS 112
>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 = 68.5 bits (167), Expect = 9e-14
Identities = 32/147 (21%), Positives = 59/147 (40%), Gaps = 9/147 (6%)
Query: 184 YYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG-DKLTEQDLRDHFYQFGEIRS 242
++ + V +P L + + L V NL +++T Q L F +G+++
Sbjct: 8 HHHSSGLVPRGSHMGRIAIPGLAGAGN---SVLLVSNLNPERVTPQSLFILFGVYGDVQR 64
Query: 243 VTIL-SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAEL--- 298
V IL +K++ A +Q A+ A+ H N L G+ + I + Q + +
Sbjct: 65 VKILFNKKENALVQMADGNQAQLAMSH-LNGHKLHGKPIRITLSKHQNVQLPREGQEDQG 123
Query: 299 KVRLEPVPGLPGALPPPPKDFFNLSNP 325
+ L P K+F N+ P
Sbjct: 124 LTKDYGNSPLHRFKKPGSKNFQNIFPP 150
Score = 63.1 bits (153), Expect = 7e-12
Identities = 22/129 (17%), Positives = 43/129 (33%), Gaps = 7/129 (5%)
Query: 160 ECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVG 219
+ + + YG N P+ + + PP TL++
Sbjct: 103 RITLSKHQNVQLPREGQEDQGLTKDYG-NSPLHRFKKPGSKNFQNIFPPS----ATLHLS 157
Query: 220 NLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFNKVILGG 277
N+ ++E+DL+ F G + ++ A IQ S A A+ N +
Sbjct: 158 NIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGEN 217
Query: 278 RRLNIKWGR 286
L + + +
Sbjct: 218 HHLRVSFSK 226
>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 = 69.6 bits (171), Expect = 1e-13
Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 7/90 (7%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
TL++ N T++++RD + L + A+I TS+ A VE
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGEDTAE 297
N + + G L K +
Sbjct: 178 -KLNGLKIEGYTLVTKVSNPLEKSKRTDSA 206
Score = 67.7 bits (166), Expect = 4e-13
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLT-EQDLRDHFYQFGEIRSVTILSKQQ----- 250
+ K + + NL +L E LR+ F FG I + I + Q+
Sbjct: 194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFN 253
Query: 251 --CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
CAF+ + ++ +AE A++ N+ +LG R +++
Sbjct: 254 NCCAFMVFENKDSAERALQ--MNRSLLGNREISVSL 287
Score = 61.5 bits (150), Expect = 5e-11
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 6/86 (6%)
Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ----CAFIQYTS 258
++ +TT+ V NL + + +F G I V + + A I++
Sbjct: 31 ANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR 90
Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKW 284
A AA+ +K ++G + +
Sbjct: 91 YDGALAAITK-THK-VVGQNEIIVSH 114
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 65.4 bits (160), Expect = 1e-13
Identities = 11/101 (10%), Positives = 37/101 (36%), Gaps = 6/101 (5%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----C 251
+ + L++ L T+++L + G ++ + +++ +
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL 60
Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
A+++Y + A AV + + + + + + + G
Sbjct: 61 AYVEYENESQASQAVM-KMDGMTIKENIIKVAISNSGPSSG 100
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 65.0 bits (159), Expect = 1e-13
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKV 273
+++V + L ++F FG + SV + + A ++ A EA + S +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHS- 68
Query: 274 ILGGRRLNIK 283
LGG RL ++
Sbjct: 69 -LGGHRLRVR 77
>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 = 66.9 bits (164), Expect = 1e-13
Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 7/85 (8%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
D L++G L + L + +++ FG +++ ++ AF +Y
Sbjct: 87 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKW 284
+ A+ N + LG ++L ++
Sbjct: 147 NVTDQAIA-GLNGMQLGDKKLLVQR 170
Score = 65.3 bits (160), Expect = 4e-13
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 13/81 (16%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAE 263
LYVGN+ +TE+ + D F + +T AF+++ S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 264 AAVEHSFNKVILGGRRLNIKW 284
A+ F+ +I G+ L I+
Sbjct: 66 QAMA--FDGIIFQGQSLKIRR 84
>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 = 65.3 bits (159), Expect = 1e-13
Identities = 10/72 (13%), Positives = 27/72 (37%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNK 272
+ G LG+ ++ L + G + ++ + + +F +Y + ++ A K
Sbjct: 27 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGK 86
Query: 273 VILGGRRLNIKW 284
++ I
Sbjct: 87 EVVDDLGQKITL 98
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 65.1 bits (159), Expect = 2e-13
Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 7/102 (6%)
Query: 196 MARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC---- 251
M R S PP+ + +T+L V NL + + LR F ++G + V I +
Sbjct: 30 MGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR 89
Query: 252 --AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
AF+++ + AE A++ + +L GR L ++ R
Sbjct: 90 GFAFVRFHDKRDAEDAMDA-MDGAVLDGRELRVQMARYGRPP 130
>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 = 64.7 bits (158), Expect = 2e-13
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQC-AFIQYTSRPAAEAAVEH 268
L++G L + E+ L+ F + G I V ++ SK + AFI + + A+ A +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK- 66
Query: 269 SFNKVILGGRRLNIKWGRAQANRG 292
N L G+ + ++ + + +
Sbjct: 67 DMNGKSLHGKAIKVEQAKKPSFQS 90
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 64.1 bits (157), Expect = 3e-13
Identities = 26/94 (27%), Positives = 42/94 (44%), Gaps = 7/94 (7%)
Query: 200 STMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AF 253
S+ + L V L TE+DLR+ F ++G I V+I+ QQ AF
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA 287
+ + + A+ A E N + L GRR+ + +
Sbjct: 62 VYFENVDDAKEAKE-RANGMELDGRRIRVSGPSS 94
>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 = 63.7 bits (156), Expect = 3e-13
Identities = 15/85 (17%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-------AFIQYTSRPAAEAAV 266
T +++G L +T+ + + F +G+I+ + + ++ A++++ + AE A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 267 EHSFNKVILGGRRLNIKWGRAQANR 291
+H + + G+ + A R
Sbjct: 65 KH-MDGGQIDGQEITATAVLAPWPR 88
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 64.3 bits (157), Expect = 3e-13
Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 10/99 (10%)
Query: 195 LMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---- 250
L+ R S M + + K L+V N+ + + DLR F QFG+I V I+ ++
Sbjct: 14 LVPRGSHMNTENKSQPKR---LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70
Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
F+ + + A+ A E + ++ GR++ + A A
Sbjct: 71 FGFVTFENSADADRARE-KLHGTVVEGRKIEV--NNATA 106
>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 = 64.2 bits (157), Expect = 3e-13
Identities = 23/95 (24%), Positives = 48/95 (50%), Gaps = 7/95 (7%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
DP D+++ +++VGN+ + TE+ L+D F + G + S ++ ++ F +Y +
Sbjct: 1 DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
A +A+ + N GR L + ++ N+ E
Sbjct: 61 ETALSAMR-NLNGREFSGRALRVDNAASEKNKEEL 94
>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 = 63.8 bits (156), Expect = 3e-13
Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 5/91 (5%)
Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSV--TILSKQQCAFIQYTSRP 260
P TL NL +TE +L++ F EIR V SK A+I++ S
Sbjct: 7 PCTSKKVRAA-RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGI-AYIEFKSEA 64
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
AE +E + GR +++ + +
Sbjct: 65 DAEKNLEE-KQGAEIDGRSVSLYYTGEKGGT 94
>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 = 63.8 bits (156), Expect = 4e-13
Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 7/87 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
L+V NL +E+DL F +G + + AF+ + A A
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGED 294
+ + GR L++ + +
Sbjct: 69 -EVDGQVFQGRMLHVLPSTIKKEASQS 94
>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 = 63.4 bits (155), Expect = 4e-13
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
LYVG L +++ ++ L F FG+I + I + AF+++ A AA++
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
+ N+ L GR + + + +
Sbjct: 73 -NMNESELFGRTIRVNLAKPMRIKES 97
>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 = 64.8 bits (158), Expect = 4e-13
Identities = 25/126 (19%), Positives = 45/126 (35%), Gaps = 11/126 (8%)
Query: 182 DRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR 241
D Y + + P PE + L V + + E LR F ++G I
Sbjct: 11 DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIE 70
Query: 242 SVTIL-------SKQQC-AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
SV I+ S+ F+++ S +A+ A+ N + +RL + + R
Sbjct: 71 SVKIVCDRETRQSR--GYGFVKFQSGSSAQQAIA-GLNGFNILNKRLKVALAASGHQRPG 127
Query: 294 DTAELK 299
+
Sbjct: 128 IAGAVG 133
>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 = 63.4 bits (155), Expect = 5e-13
Identities = 17/87 (19%), Positives = 42/87 (48%), Gaps = 11/87 (12%)
Query: 208 PEDKTITT-LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----AFIQYTSRPA 261
PE K + ++VG + ++ E ++R F ++G ++ V I++ + F+ + +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD 62
Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQ 288
+ VE +++ G++L + A
Sbjct: 63 VQKIVE---SQINFHGKKLKLG--PAI 84
>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 = 65.2 bits (159), Expect = 5e-13
Identities = 23/143 (16%), Positives = 58/143 (40%), Gaps = 13/143 (9%)
Query: 171 PDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTI------TTLYVGNLGDK 224
++ K R +G + E + + + D + L+V ++ ++
Sbjct: 24 VRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEE 83
Query: 225 LTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGR 278
E ++++ F +GEI+++ + ++ A ++Y + A AA E N + G+
Sbjct: 84 AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNGAEIMGQ 142
Query: 279 RLNIKWGRAQANRGEDTAELKVR 301
+ + W + + +E + R
Sbjct: 143 TIQVDWCFVKGPKRVKKSEKRRR 165
>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 = 63.4 bits (155), Expect = 5e-13
Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 10/103 (9%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQ 250
+ S+ P + +D T+ YVG L +K++E L + F Q G + + + Q
Sbjct: 2 SSGSSGPISERNQDATV---YVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG 58
Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
F+++ S A+ A++ + + L G+ + + A
Sbjct: 59 YGFVEFLSEEDADYAIK-IMDMIKLYGKPIRVNKASAHNKNLS 100
>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 = 64.5 bits (157), Expect = 7e-13
Identities = 25/137 (18%), Positives = 50/137 (36%), Gaps = 12/137 (8%)
Query: 167 KPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKL-----DPPEDKTITTLYVGNL 221
+ D GV+ + T+ + + + +T+L V NL
Sbjct: 19 EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNL 78
Query: 222 GDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVIL 275
+ + LR F ++G + V I + AF+++ + AE A++ + +L
Sbjct: 79 TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA-MDGAVL 137
Query: 276 GGRRLNIKWGRAQANRG 292
GR L ++ R
Sbjct: 138 DGRELRVQMARYGRPPD 154
>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 = 63.1 bits (154), Expect = 8e-13
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 7/99 (7%)
Query: 198 RASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------ 251
A+ M LYVG+L +TE LR F FG I S+ ++ +
Sbjct: 11 MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70
Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQAN 290
FI ++ A+ A+E N L GR + + + +
Sbjct: 71 GFITFSDSECAKKALE-QLNGFELAGRPMKVGHVTERTD 108
>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 = 64.1 bits (156), Expect = 9e-13
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 2/85 (2%)
Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPA 261
+ +YVGNLG+ + +L F +G +RSV + AF+++
Sbjct: 63 HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRD 122
Query: 262 AEAAVEHSFNKVILGGRRLNIKWGR 286
A AV + L G R+ ++
Sbjct: 123 AADAVRE-LDGRTLCGCRVRVELSN 146
>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 = 63.2 bits (154), Expect = 9e-13
Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 8/110 (7%)
Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ- 250
A + ++ ++YVGN+ T QDL HF G I +TIL +
Sbjct: 15 AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74
Query: 251 -----CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDT 295
A+I++ R + +AAV ++ + GR + + R T
Sbjct: 75 GHPKGYAYIEFAERNSVDAAVA--MDETVFRGRTIKVLPKRTNMPGISST 122
>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 = 64.1 bits (156), Expect = 9e-13
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI----LSKQQC--AFIQYTSRPAAEAAVE 267
TLYVGNL TE+ + + F + G+I+ + + + K C F++Y SR AE A+
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 268 HSFNKVILGGRRLNIKW 284
N L R + W
Sbjct: 100 -YINGTRLDDRIIRTDW 115
>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 = 65.4 bits (160), Expect = 9e-13
Identities = 27/117 (23%), Positives = 50/117 (42%), Gaps = 10/117 (8%)
Query: 206 DPPEDKTI-TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSR 259
DP K+ +++ NL + + L D F FG I S ++ SK F+ + ++
Sbjct: 95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK-GYGFVHFETQ 153
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRL--EPVPGLPGALPP 314
AAE A+E N ++L R++ + +++ R + VP G+
Sbjct: 154 EAAERAIE-KMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGR 209
Score = 63.8 bits (156), Expect = 3e-12
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 206 DPPEDK-TITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQC-AFIQYTS 258
+P + +LYVG+L +TE L + F G I S+ + + A++ +
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGED 294
AE A++ + N ++ G+ + I W +Q +
Sbjct: 67 PADAERALD-TMNFDVIKGKPVRIMW--SQRDPSLR 99
>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 = 62.8 bits (153), Expect = 1e-12
Identities = 23/106 (21%), Positives = 45/106 (42%), Gaps = 9/106 (8%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-------SKQQC 251
S+ + ++VG+L ++T +D++ F FG I ++ SK
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY- 59
Query: 252 AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAE 297
F+ + ++ AE A++ LGGR++ W + + T E
Sbjct: 60 GFVSFFNKWDAENAIQ-QMGGQWLGGRQIRTNWATRKPPAPKSTYE 104
>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 = 62.2 bits (152), Expect = 1e-12
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
+ LYVG+L +TE LR F FG+I ++ ++ FI ++ A A+E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGE 293
N L GR + + + + G
Sbjct: 66 -QLNGFELAGRPMRVGHVTERLDGGS 90
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 62.8 bits (153), Expect = 1e-12
Identities = 21/103 (20%), Positives = 46/103 (44%), Gaps = 7/103 (6%)
Query: 190 PVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQ 249
P+A ++ A+ E L++ +L + T+ DL F FG + S + +
Sbjct: 17 PLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK 76
Query: 250 QC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
Q F+ + + +A+ A++ + N +G +RL ++ +
Sbjct: 77 QTSLSKCFGFVSFDNPDSAQVAIK-AMNGFQVGTKRLKVQLKK 118
>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 = 66.4 bits (161), Expect = 1e-12
Identities = 19/92 (20%), Positives = 42/92 (45%), Gaps = 8/92 (8%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFY----QFGEIRSVTILSKQQ---CAFIQYTSR 259
PE + T+Y+ NL +K+ + +L+ Y QFG+I + + + AF+ +
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEV 62
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
+A A+ S + + I++ + ++
Sbjct: 63 SSATNALR-SMQGFPFYDKPMRIQYAKTDSDI 93
Score = 56.4 bits (135), Expect = 3e-09
Identities = 30/210 (14%), Positives = 64/210 (30%), Gaps = 10/210 (4%)
Query: 80 DTALKIKDDIPKSDVNKEYYIQNMDHEIGKID--STTPAGALGKASGSSEMLMKLARTTP 137
D ++I+ SD+ + ++ + + + K + +
Sbjct: 79 DKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQ 138
Query: 138 YYKRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMA 197
P + + + + PY P LA I +
Sbjct: 139 GPVPGMPPM-TQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQ------LM 191
Query: 198 RASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQY 256
P E+ L++ NL ++ E L F QF + V ++ + AF+++
Sbjct: 192 PGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEF 251
Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKWGR 286
+ A AA + I + I + +
Sbjct: 252 DNEVQAGAARDALQGFKITQNNAMKISFAK 281
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 24/112 (21%), Positives = 50/112 (44%), Gaps = 10/112 (8%)
Query: 186 GVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI 245
G + + + + + PE L++ +L + +QDL F FG + S +
Sbjct: 1 GSSGSSGLTQQSIGAAGSQKEGPEG---ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKV 57
Query: 246 LSKQQC------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
+Q F+ Y + +A+AA++ S N +G +RL ++ R++ +
Sbjct: 58 FIDKQTNLSKCFGFVSYDNPVSAQAAIQ-SMNGFQIGMKRLKVQLKRSKNDS 108
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 62.1 bits (151), Expect = 2e-12
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 7/81 (8%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAE 263
D ++Y+ T D+++ G++ ++ + F+ + S +A+
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66
Query: 264 AAVEHSFNKVILGGRRLNIKW 284
VE L I +
Sbjct: 67 KFVET--PGQKYKETDLLILF 85
>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 = 61.4 bits (150), Expect = 2e-12
Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 210 DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAE 263
+ ++YVGN+ T ++L HF+ G + VTIL + A+I+++ + +
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 264 AAVEHSFNKVILGGRRLNIKWGR 286
++ ++ + GR++ + R
Sbjct: 63 TSLA--LDESLFRGRQIKVIPKR 83
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 62.9 bits (153), Expect = 2e-12
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 7/92 (7%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------A 252
S T LYVG L +++ ++ L F FG+I + I + A
Sbjct: 49 GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108
Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
F+++ A AA++ + N+ L GR + +
Sbjct: 109 FVEFELAEDAAAAID-NMNESELFGRTIRVNL 139
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPA 261
+ +T+YV NL LT DL F ++G++ VTI+ + AFI + + +
Sbjct: 11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
Query: 262 AEAAVEHSFNKVILGGRRL 280
A+ + N L GR +
Sbjct: 71 AQNCTR-AINNKQLFGRVI 88
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----AFIQYTSRPAAEAAVEHS 269
+++ NL + + L D F FG I S ++ + F+ + ++ AAE A+E
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE-K 64
Query: 270 FNKVILGGRRLNIKWGRAQANRGEDTAE 297
N ++L R++ + +++ R +
Sbjct: 65 MNGMLLNDRKVFVGRFKSRKEREAELGA 92
>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 = 61.5 bits (150), Expect = 3e-12
Identities = 17/92 (18%), Positives = 37/92 (40%), Gaps = 7/92 (7%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
L+VG L EQ L F ++G+I V ++ ++ F+ + +
Sbjct: 5 SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENI 64
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
A+ A+ + N + GR++ + ++
Sbjct: 65 DDAKDAMM-AMNGKSVDGRQIRVDQAGKSSDN 95
>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 = 64.4 bits (156), Expect = 3e-12
Identities = 27/159 (16%), Positives = 49/159 (30%), Gaps = 12/159 (7%)
Query: 177 DQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQ 236
+DR Y P P + LY+GNL T++DL + +
Sbjct: 32 GDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS 91
Query: 237 FG--EIRSVTIL-------SKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRA 287
G +I + SK + S +++ ++ K L G+ +
Sbjct: 92 LGVNDILEIKFFENRANGQSKGFA-LVGVGSEASSKKLMD-LLPKRELHGQNPVVTPVNK 149
Query: 288 QA-NRGEDTAELKVRLEPVPGLPGALPPPPKDFFNLSNP 325
Q ++ E + + + G A PP
Sbjct: 150 QFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQG 188
>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 = 60.6 bits (148), Expect = 3e-12
Identities = 17/76 (22%), Positives = 27/76 (35%), Gaps = 11/76 (14%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTI-------LSKQQC-AFIQYTSRPAAEAA 265
+ LY+ L T+QDL +G+I S K F+ + S AA+ A
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCK--GYGFVDFDSPSAAQKA 63
Query: 266 VEHSFNKVILGGRRLN 281
V + +
Sbjct: 64 VTA-LKASGVQAQMAK 78
>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 = 62.2 bits (151), Expect = 3e-12
Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 14/90 (15%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSV------------TILSKQQCAFIQYTSRPA 261
+YV NL + E+DL+ F ++ + S K Q AFI + A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQ-AFIGLPNEKA 104
Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
A A++ N +L G+ + +++ R+ +
Sbjct: 105 AAKALK-EANGYVLFGKPMVVQFARSARPK 133
>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 = 61.1 bits (149), Expect = 3e-12
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-----SKQQCAFIQYTSRPAAEAAVEHSF 270
LYV NL D + ++ LR F FG I S ++ SK F+ ++S A AV
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK-GFGFVCFSSPEEATKAVT-EM 75
Query: 271 NKVILGGRRLNIKWGRAQANR 291
N I+ + L + + + R
Sbjct: 76 NGRIVATKPLYVALAQRKEER 96
>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 = 60.7 bits (148), Expect = 4e-12
Identities = 18/87 (20%), Positives = 36/87 (41%), Gaps = 7/87 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
+Y+G++ TE+ + D G + ++ ++ Q AFI++ ++ +AV
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGED 294
+ N LG R L + G
Sbjct: 63 -NLNGYQLGSRFLKCGYSSNSDISGVS 88
>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 = 60.4 bits (147), Expect = 6e-12
Identities = 23/98 (23%), Positives = 43/98 (43%), Gaps = 6/98 (6%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--CAFI 254
+ S+ E KT L + NL TE+ L++ F + I+ + + AFI
Sbjct: 2 SSGSSGNSTWSGESKT---LVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFI 58
Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
++ S A+ A+ S NK + GR + ++ + +
Sbjct: 59 EFASFEDAKEALN-SCNKREIEGRAIRLELQGPRGSPN 95
>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 = 60.3 bits (147), Expect = 6e-12
Identities = 12/90 (13%), Positives = 33/90 (36%), Gaps = 7/90 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----AFIQYTSRPA 261
E T L++GNL + +L+ + + ++ + ++ + S
Sbjct: 11 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 70
Query: 262 AEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
E A+E + + G + ++ + +
Sbjct: 71 LEKALE--LTGLKVFGNEIKLEKPKGRDGT 98
>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 = 62.8 bits (152), Expect = 6e-12
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 214 TTLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTIL-SKQQCAFIQYTSRPAAEAAVEHSFN 271
L V L K+ + + F +G + V + SK A ++ A + A+ H N
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH-LN 63
Query: 272 KVILGGRRLNIKWGRAQ 288
+ G+++N+ +
Sbjct: 64 NNFMFGQKMNVCVSKQP 80
Score = 52.4 bits (125), Expect = 3e-08
Identities = 12/119 (10%), Positives = 33/119 (27%), Gaps = 7/119 (5%)
Query: 170 DPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQD 229
P ++D D + ++ L+ N ++TE++
Sbjct: 80 PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEEN 139
Query: 230 LRDHFYQFGEIRSVTILS------KQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
+ + G R ++ + +++ S+ A + N +
Sbjct: 140 FFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLG-FLNHYQMKNPNGPY 197
>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 = 59.9 bits (146), Expect = 7e-12
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
LYVG L +++ ++ L F FG+I + I + AF+++ A AA++
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 268 HSFNKVILGGRRLNIKWGR 286
+ N+ L GR + + +
Sbjct: 68 -NMNESELFGRTIRVNLAK 85
>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 = 61.8 bits (151), Expect = 7e-12
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL----SKQQC-AFIQYTSRPAAEAAVEHS 269
LYVGNL +TE L+ +F G I ++ I+ +K AF++Y A A++ +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ-T 60
Query: 270 FNKVILGGRRLNIKWGRAQANRGEDT 295
N + + I W A ++ +
Sbjct: 61 LNGKQIENNIVKINW--AFQSQQSSS 84
Score = 59.1 bits (144), Expect = 7e-11
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 206 DPPEDKTIT-TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTS 258
T L+VG+L + ++ LR+ F F S ++ Q F+ +TS
Sbjct: 79 SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138
Query: 259 RPAAEAAVEHSFNKVILGGRRLNIKW 284
+ A+ A++ S L GR L I W
Sbjct: 139 QDDAQNAMD-SMQGQDLNGRPLRINW 163
>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 = 60.5 bits (147), Expect = 1e-11
Identities = 33/136 (24%), Positives = 52/136 (38%), Gaps = 18/136 (13%)
Query: 162 PYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNL 221
+ H + P R + + M R S D L V L
Sbjct: 4 SHHHHHHSSGLVP--------RGSHMASMTGGQQMGRGSRHVGNRANPDPN-CCLGVFGL 54
Query: 222 GDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHSFNKVIL 275
TE+DLR+ F ++G I V+I+ QQ AF+ + + A+ A E N + L
Sbjct: 55 SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE-RANGMEL 113
Query: 276 GGRRLNIKWGRAQANR 291
GRR+ + + + R
Sbjct: 114 DGRRIRVDF--SITKR 127
>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 = 60.0 bits (146), Expect = 1e-11
Identities = 27/119 (22%), Positives = 46/119 (38%), Gaps = 11/119 (9%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----- 251
+ + +D T T ++VG L T+ LR +F FG+I +++ +Q
Sbjct: 1 GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
Query: 252 -AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVPGLP 309
F+ R AAE A + I+ GR+ N+ A + + V G
Sbjct: 61 YGFVTMADRAAAERACKDPNP--IIDGRKANVN--LAYL-GAKPRSLQTGFAIGVSGPS 114
>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 = 59.0 bits (143), Expect = 1e-11
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 13/79 (16%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-----------AFIQYTSRPAAEA 264
LYVGN+ +TE+ + D F + +T AF+++ S
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 265 AVEHSFNKVILGGRRLNIK 283
A+ F+ +I G+ L I+
Sbjct: 69 AMA--FDGIIFQGQSLKIR 85
>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 = 60.6 bits (148), Expect = 2e-11
Identities = 18/93 (19%), Positives = 40/93 (43%), Gaps = 13/93 (13%)
Query: 202 MPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQ 255
+P+ + + I +VG +G + ++ + F Q+G I ++ + F+
Sbjct: 79 IPRDEQDKTGKI---FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT 135
Query: 256 YTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
Y S A + ++ + R++ IK RA+
Sbjct: 136 YDSADAVDRVCQN--KFIDFKDRKIEIK--RAE 164
Score = 51.8 bits (125), Expect = 2e-08
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 12/92 (13%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
+++G L TE +LR++F ++G + + I+ F+ + + + V+
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63
Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDTAELKV 300
+ IL G+ ++ K RA R E K+
Sbjct: 64 --TQHILDGKVIDPK--RAIP-RDEQDKTGKI 90
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 18/106 (16%), Positives = 47/106 (44%), Gaps = 7/106 (6%)
Query: 192 AEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC 251
E++ + P L+V ++ ++ E ++++ F +GEI+++ + ++
Sbjct: 5 YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64
Query: 252 ------AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
A ++Y + A AA E + N + G+ + + W + +
Sbjct: 65 GFSKGYALVEYETHKQALAAKE-ALNGAEIMGQTIQVDWCFVKGPK 109
>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 = 58.3 bits (141), Expect = 4e-11
Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 2/80 (2%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
PP ++ + V L + QDL+DH + G++ + +++ + AV
Sbjct: 9 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAV 67
Query: 267 EHSFNKVILGGRRLNIKWGR 286
+ + R
Sbjct: 68 R-KLDNTKFRSHEGETAYIR 86
>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 = 60.4 bits (147), Expect = 4e-11
Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 11/98 (11%)
Query: 198 RASTMPKLDPPE-DKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----- 251
RA + P T+ ++VG + + E LRD+F Q+G+I + I++ +
Sbjct: 88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG 147
Query: 252 -AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQ 288
AF+ + + + V + + G ++ +A
Sbjct: 148 FAFVTFDDHDSVDKIVIQKY--HTVNGHNCEVR--KAL 181
Score = 56.1 bits (136), Expect = 1e-09
Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 9/107 (8%)
Query: 202 MPKLDPP-EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFI 254
M K + P E + + L++G L + T++ LR HF Q+G + ++ F+
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 255 QYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVR 301
Y + +AA+ + GR + K ++ + A L V+
Sbjct: 61 TYATVEEVDAAMNA--RPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 105
>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 = 58.5 bits (142), Expect = 4e-11
Identities = 20/93 (21%), Positives = 44/93 (47%), Gaps = 7/93 (7%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRP 260
P L+V + ++ TE+D+ D F ++GEI+++ + ++ ++Y +
Sbjct: 16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQANRGE 293
A+AA+E N L G+ +++ W +
Sbjct: 76 EAQAAME-GLNGQDLMGQPISVDWCFVRGPPKG 107
>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 = 58.0 bits (141), Expect = 4e-11
Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 10/89 (11%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRP 260
++VG + E +LR++F +FG + V ++ + FI +
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
+ + AV + + G+++ +K RA+
Sbjct: 64 SVDQAVNM--HFHDIMGKKVEVK--RAEP 88
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 57.3 bits (139), Expect = 6e-11
Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 15/92 (16%)
Query: 203 PKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----------- 251
T++V LG+ +T + + D+F Q G I++ +
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 252 ---AFIQYTSRPAAEAAVEHSFNKVILGGRRL 280
A + + P+A+AA++ F+ G +
Sbjct: 63 KGEATVSFDDPPSAKAAID-WFDGKEFSGNPI 93
>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 = 56.7 bits (138), Expect = 7e-11
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
L+VG+L + ++ LR+ F F S ++ Q F+ +TS+ A+ A++ S
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD-S 62
Query: 270 FNKVILGGRRLNIKW 284
L GR L I W
Sbjct: 63 MQGQDLNGRPLRINW 77
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 57.3 bits (139), Expect = 9e-11
Identities = 19/79 (24%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
L+V + ++ TE+D+ D F ++GEI+++ + ++ ++Y + A+AA+E
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 268 HSFNKVILGGRRLNIKWGR 286
N L G+ +++ W
Sbjct: 84 -GLNGQDLMGQPISVDWCF 101
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 58.0 bits (140), Expect = 1e-10
Identities = 16/118 (13%), Positives = 35/118 (29%), Gaps = 9/118 (7%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSKQQC--- 251
+ + +YVG+ T+Q L G ++ + +
Sbjct: 39 NKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQS 98
Query: 252 ---AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELKVRLEPVP 306
A + S + +E +L G +++++ Q + K VP
Sbjct: 99 KGYAEVVVASENSVHKLLE-LLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRVP 155
>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 = 56.4 bits (136), Expect = 2e-10
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 13/83 (15%)
Query: 215 TLYVGNLGDKLTEQDL---RDHFYQFGEIRSVTILSKQQ---------CAFIQYTSRPAA 262
++V L +L + ++ ++F +FG+I V I + A++ Y A
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 263 EAAVEHSFNKVILGGRRLNIKWG 285
A++ N V++ GR L G
Sbjct: 77 LRAIQ-CVNNVVVDGRTLKASLG 98
>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 = 55.7 bits (135), Expect = 2e-10
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAAEAAVEHSFNKVI 274
++VG +TE +LR+ F Q+G++ V I + AF+ + A++ +I
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG---EDLI 64
Query: 275 LGGRRLNIKWGRAQ 288
+ G ++I A+
Sbjct: 65 IKGISVHIS--NAE 76
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 56.3 bits (136), Expect = 3e-10
Identities = 18/92 (19%), Positives = 40/92 (43%), Gaps = 15/92 (16%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC--------------AFIQYTSR 259
T++V LG+ +T + + D+F Q G I++ + A + +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANR 291
P+A+AA++ F+ G + + + +A+
Sbjct: 68 PSAKAAID-WFDGKEFSGNPIKVSFATRRADF 98
>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 = 55.3 bits (134), Expect = 3e-10
Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 204 KLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-AFIQYTSRPAA 262
+ + ++VG + +T ++L+ F Q+GE+ V I + AF+ + A
Sbjct: 2 RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61
Query: 263 EAAVEHSFNKVILGGRRLNIKWGRAQ 288
++ +I+ G ++I A+
Sbjct: 62 QSLCG---EDLIIKGISVHIS--NAE 82
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 54.1 bits (131), Expect = 7e-10
Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 10/87 (11%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRP 260
++ ++VG L +++DL+D+F +FGE+ TI FI +
Sbjct: 5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64
Query: 261 AAEAAVEHSFNKVILGGRRLNIKWGRA 287
+ E ++ ++ L GR ++ K +A
Sbjct: 65 SVEKVLDQKEHR--LDGRVIDPK--KA 87
>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 = 54.6 bits (132), Expect = 7e-10
Identities = 21/102 (20%), Positives = 42/102 (41%), Gaps = 13/102 (12%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC----- 251
+ S+ P KT L+V L + TE+ L++ F I++ ++
Sbjct: 2 SSGSSGPNARSQPSKT---LFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKG 55
Query: 252 -AFIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQANRG 292
F+ + S A+AA E + + G ++ + W + + G
Sbjct: 56 FGFVDFNSEEDAKAAKE-AMEDGEIDGNKVTLDWAKPKGEGG 96
>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 = 54.2 bits (131), Expect = 9e-10
Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 11/97 (11%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSR 259
+ + L V L K TEQDL+++F FGE+ V + + F+++T
Sbjct: 8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTA 296
+ + ++ GR + K + + +D+
Sbjct: 68 ETQVKVMS---QRHMIDGRWCDCK--LPNSKQSQDSG 99
>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 = 53.8 bits (130), Expect = 1e-09
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 7/75 (9%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
T + V N+ ++ ++ D FY + I L + A + + SR A AAV
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 268 HSFNKVILGGRRLNI 282
N +G R++ +
Sbjct: 76 -DLNDRPIGSRKVKL 89
>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 = 53.7 bits (130), Expect = 1e-09
Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 9/84 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSKQQC------AFIQYTSRPAAEAAVE 267
LY+GNL T++DL + + G +I + + A + S +++ ++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 268 HSFNKVILGGRRLNIKWGRAQANR 291
K L G+ + +
Sbjct: 64 -LLPKRELHGQNPVVTPSNKLEHH 86
>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 = 54.4 bits (131), Expect = 1e-09
Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 2/80 (2%)
Query: 207 PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAV 266
PP ++ + V L + QDL+DH + G++ + +++ + AV
Sbjct: 10 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAV 68
Query: 267 EHSFNKVILGGRRLNIKWGR 286
+ + R
Sbjct: 69 R-KLDNTKFRSHEGETAYIR 87
>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 = 52.5 bits (127), Expect = 2e-09
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
++VG L E+ +R++F FGE+ S+ + + FI + + +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 270 FNKVILGGRRLNIK 283
++ +G + IK
Sbjct: 62 YH--NVGLSKCEIK 73
>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 = 53.0 bits (128), Expect = 2e-09
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC-------AFIQYTSRPAAEAAVE 267
+++GNL ++ E+ L D F FG I + + AFI + S A++AA+E
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 268 HSFNKVILGGRRLNIKWGRAQANRG 292
+ N L R + + + + ++G
Sbjct: 67 -AMNGQYLCNRPITVSYAFKKDSKG 90
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 52.9 bits (128), Expect = 2e-09
Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTIL-------SKQQCAFIQYTSRPAAEAAVEH 268
++VG+L ++T + F FG I ++ SK F+ + ++ AE A++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGY-GFVSFFNKWDAENAIQ- 66
Query: 269 SFNKVILGGRRLNIKW 284
LGGR++ W
Sbjct: 67 QMGGQWLGGRQIRTNW 82
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 53.1 bits (128), Expect = 2e-09
Identities = 9/93 (9%), Positives = 32/93 (34%), Gaps = 12/93 (12%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFG--EIRSVTILSKQQC------AFIQYT 257
T+ + N+ + + + ++ ++ +Q AF+Q +
Sbjct: 3 HHHHHHM-DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61
Query: 258 SRPAAEAAVEH---SFNKVILGGRRLNIKWGRA 287
S A ++ + + G+ + + + ++
Sbjct: 62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>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 = 53.4 bits (129), Expect = 3e-09
Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 11/96 (11%)
Query: 201 TMPKLD-PPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAF 253
T+P E + L++G L + TE+ LR+++ Q+G++ ++ F
Sbjct: 14 TVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73
Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
+ ++S +AA+ + + GR + K RA A
Sbjct: 74 VTFSSMAEVDAAMAARPHS--IDGRVVEPK--RAVA 105
>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 = 52.6 bits (126), Expect = 4e-09
Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 3/88 (3%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNL-GDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQ 255
K D ++ +++ NL ++ + +G+I++ ++ + AFI+
Sbjct: 10 PEGKPDQKFDQKQELG-RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIE 68
Query: 256 YTSRPAAEAAVEH-SFNKVILGGRRLNI 282
+R A A V+H + GR + +
Sbjct: 69 METREDAMAMVDHCLKKALWFQGRCVKV 96
>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 = 54.0 bits (129), Expect = 5e-09
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--QQCAFI 254
+ A+ + + + V NL +T L F +FG + + +K Q A +
Sbjct: 30 SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALL 89
Query: 255 QYTSRPAAEAAVEHSFNKVIL-GGRRLNIKWGRAQ 288
QY +A+ A + I L I + +
Sbjct: 90 QYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 124
>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 = 51.9 bits (125), Expect = 5e-09
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVE 267
T + V N+ ++ ++ D FY + I L + A + + SR A AAV
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 268 HSFNKVILGGRRLNIK 283
N +G R++ +
Sbjct: 76 -DLNDRPIGSRKVKLV 90
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 51.3 bits (124), Expect = 6e-09
Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 10/78 (12%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEHS 269
++VG L T +D++ +F QFG++ ++ + F+ + S E E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60
Query: 270 FNKVILGGRRLNIKWGRA 287
+ + + + K +A
Sbjct: 61 -HFHEINNKMVECK--KA 75
>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 = 51.4 bits (124), Expect = 6e-09
Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 8/85 (9%)
Query: 213 ITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAV 266
+ +YVGNL T + +++ F QFG++ +V ++ ++ F++ + A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 267 EHSFNKVILGGRRLNIKWGRAQANR 291
+ GR + + + +
Sbjct: 60 A-KLDNTDFMGRTIRVTEANPKKSL 83
>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 = 51.9 bits (125), Expect = 7e-09
Identities = 14/87 (16%), Positives = 36/87 (41%), Gaps = 10/87 (11%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRPAAEAAVE 267
T ++GNL +TE+ +++ F I +V + + + ++ + +A+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 268 HSFNKVILGGRRLNIKWGRAQANRGED 294
N+ LG +R+ + ++
Sbjct: 76 --LNEESLGNKRIRVDVADQAQDKDSG 100
>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 = 51.9 bits (125), Expect = 7e-09
Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 10/97 (10%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CA 252
+S ++ I L+VG L T++ LR +F Q+GE+ I+ +
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 253 FIQYTSRPAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
F+++ + + L GR ++ K
Sbjct: 62 FVKFKDPNCVGTVLASRPHT--LDGRNIDPK--PCTP 94
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 52.3 bits (125), Expect = 1e-08
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSK--QQCAFI 254
+ A+ + + + V NL +T L F +FG + + +K Q A +
Sbjct: 12 SAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALL 71
Query: 255 QYTSRPAAEAAVEHSFNKVIL-GGRRLNIKWGRAQ 288
QY +A+ A + I L I + +
Sbjct: 72 QYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 51.2 bits (122), Expect = 2e-08
Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 2/85 (2%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-CAFIQYTSRPAAEA 264
DP + L + N +T L G+++ + I + A +++ S A+
Sbjct: 18 DPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQK 77
Query: 265 AVEHSFNKVILGGR-RLNIKWGRAQ 288
A I G L I++ R
Sbjct: 78 AKAALNGADIYAGCCTLKIEYARPT 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 = 50.3 bits (121), Expect = 2e-08
Identities = 14/90 (15%), Positives = 37/90 (41%), Gaps = 10/90 (11%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
+ +++G L + T++ LR++F QFGE++ ++ F+ + +
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQA 289
+ + ++ L + ++ K A
Sbjct: 78 AGVDKVLAQ--SRHELDSKTIDPK--VAFP 103
>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 = 50.6 bits (121), Expect = 3e-08
Identities = 15/109 (13%), Positives = 38/109 (34%), Gaps = 9/109 (8%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR-SVTILSKQQ-----CAFIQYTSR 259
+ +Y+ L + + + D F + + S+ I F+++ +
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWG-RAQANRGEDTAELKVRLEPVPG 307
+AA+ +K +G R + + + D +++ P G
Sbjct: 78 ADYKAALC--RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 50.2 bits (120), Expect = 3e-08
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 215 TLYVGNLG-DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEH-SFNK 272
+++ + K L FG I + IL+K AFI+ + A+AAV++ +
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTP 76
Query: 273 VILGGRRLNI 282
++ G+ + +
Sbjct: 77 ALVFGKPVRV 86
>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 = 49.6 bits (119), Expect = 4e-08
Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 18/95 (18%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGE-IRSVTI-------LSKQQCAFIQYTSRPAAEAA 265
+L++G+L + E + F GE + SV I + C F+++ AE
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYC-FVEFADLATAEKC 68
Query: 266 VEHSFNKVILGG----RRLNIKWGRAQANRGEDTA 296
+ N L G +R + + A ++
Sbjct: 69 LH-KINGKPLPGATPAKRFKLNY----ATYSGPSS 98
>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 = 49.4 bits (118), Expect = 6e-08
Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 8/76 (10%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEI-RSVTILSKQQ-----CAFIQYTSRPAAEAAVE 267
++ N+ +T+ D+ +V +L A +Q+ + A +
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75
Query: 268 HSFNKVILGGRRLNIK 283
++ L GR +
Sbjct: 76 --LHRKKLNGREAFVH 89
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 48.8 bits (116), Expect = 7e-08
Identities = 15/86 (17%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 214 TTLYVGNLGDKLTEQDLR----DHFYQFGEIRSVTIL---SKQQCAFIQYTSRPAAEAAV 266
+ V N+ +L+ ++L+ + F + G+++SV + Q A +Q + A AV
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAV 69
Query: 267 EHSFNKVILGGRRLNIKWGRAQANRG 292
++ +G +++ + +
Sbjct: 70 NS-LHRYKIGSKKILVSLATGASGPS 94
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 48.8 bits (117), Expect = 8e-08
Identities = 16/87 (18%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQ-FGEIRSVTILSKQQC-----AFIQYTSRPAAEAAVEH 268
+L+VG+L + + L + F + + R ++ Q F+++T + A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 269 SFNKVILGGRRLNIKWGRAQANRGEDT 295
V LG + + + +A+R +
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPV 97
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-------CAFIQYTSRPAAEAAVE 267
T ++GNL +TE+ +++ F I +V + + + ++ + +A+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 268 HSFNKVILGGRRLNI 282
N+ LG RR+ +
Sbjct: 80 --LNEESLGNRRIRV 92
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 47.5 bits (114), Expect = 1e-07
Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSRPAAEAAVEHS 269
+++G L + T++ LR++F QFGE++ ++ F+ + + + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61
Query: 270 FNKVILGGRRLNIKWGRA 287
++ L + ++ K A
Sbjct: 62 -SRHELDSKTIDPK--VA 76
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 47.3 bits (113), Expect = 2e-07
Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 9/86 (10%)
Query: 215 TLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQC------AFIQYTSRPAAEAAVEH 268
T YVGNL + D+ F IRSV ++ + ++++ + + A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74
Query: 269 SFNKVILGGRRLNIKWGRAQANRGED 294
++ +LG R L + +
Sbjct: 75 -YDGALLGDRSLRVDIAEGRKQDKSG 99
>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 = 47.6 bits (113), Expect = 3e-07
Identities = 14/105 (13%), Positives = 33/105 (31%), Gaps = 8/105 (7%)
Query: 185 YGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVT 244
+ + + + + L T++++ F + +
Sbjct: 14 LVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGI 73
Query: 245 ILSKQQ------CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNIK 283
L AF+Q+ S+ AE A+ +K +G R + +
Sbjct: 74 TLPVDPEGKITGEAFVQFASQELAEKALG--KHKERIGHRYIEVF 116
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 47.1 bits (112), Expect = 4e-07
Identities = 11/71 (15%), Positives = 30/71 (42%), Gaps = 4/71 (5%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ---CAFIQYTSRPAAEAAVEHSFNK 272
+ + NL + + QDL+D + + + ++ + +++ S A+E N
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALER-LNN 89
Query: 273 VILGGRRLNIK 283
+ G + ++
Sbjct: 90 IEFRGSVITVE 100
>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 = 46.3 bits (110), Expect = 8e-07
Identities = 14/90 (15%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 199 ASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAF 253
+S P + + V + E D+RD F+ + +V +L
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGL 60
Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIK 283
+++ S A++ N++++ R + +
Sbjct: 61 VKFLSPQDTFEALK--RNRMLMIQRYVEVS 88
>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 = 45.6 bits (108), Expect = 2e-06
Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 9/105 (8%)
Query: 183 RYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRS 242
R + + M R S + + T +++ L K TE D+ + F +R
Sbjct: 17 RGSHMASMTGGQQMGRGSGDSE-FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR- 74
Query: 243 VTILSKQQ-----CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
V I A +++ + A AA+ ++ + R + +
Sbjct: 75 VHIEIGPDGRVTGEADVEFATHEEAVAAMSK--DRANMQHRYIEL 117
>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 = 44.7 bits (106), Expect = 2e-06
Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 8/84 (9%)
Query: 206 DPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ------CAFIQYTSR 259
+ P+ + + L +++++ F + + L AF+Q+ S+
Sbjct: 8 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67
Query: 260 PAAEAAVEHSFNKVILGGRRLNIK 283
AE A++ +K +G R + I
Sbjct: 68 EIAEKALK--KHKERIGHRYIEIF 89
>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 = 45.6 bits (107), Expect = 5e-06
Identities = 12/88 (13%), Positives = 29/88 (32%), Gaps = 7/88 (7%)
Query: 202 MPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQY 256
+ D ++Y+ T D+++ G++ ++ + F+ +
Sbjct: 98 EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 157
Query: 257 TSRPAAEAAVEHSFNKVILGGRRLNIKW 284
S +A+ VE L I +
Sbjct: 158 DSIESAKKFVET--PGQKYKETDLLILF 183
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 42.8 bits (101), Expect = 1e-05
Identities = 9/69 (13%), Positives = 27/69 (39%), Gaps = 9/69 (13%)
Query: 217 YVGNLGDKLTEQDLRDHFYQFGEIRSVTI-------LSKQQCAFIQYTSRPAAEAAVEHS 269
+ + + ++ L F + G++ ++ +K F++ S A+ ++
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTK-GFLFVECGSMNDAKKIIKS- 73
Query: 270 FNKVILGGR 278
F+ L +
Sbjct: 74 FHGKRLDLK 82
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 12/89 (13%), Positives = 36/89 (40%), Gaps = 8/89 (8%)
Query: 209 EDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAE 263
T T+ + +TE+++ + ++ I+ F+ +++ +
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVK 64
Query: 264 AAVEHSFNKVILGGRRLNIKWGRAQANRG 292
A++ N+ +GGR + + ++ + G
Sbjct: 65 QALK--CNREYMGGRYIEVFREKSGPSSG 91
>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 = 45.2 bits (106), Expect = 1e-05
Identities = 32/142 (22%), Positives = 55/142 (38%), Gaps = 13/142 (9%)
Query: 164 RHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKL-DPPEDKTIT-----TLY 217
E P D P + ++R E+ T K+ DP D TL+
Sbjct: 47 EFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLF 106
Query: 218 VGNLGDKLTEQDLRDHFYQFGEIRSVTIL------SKQQCAFIQYTSRPAAEAAVEHSFN 271
V + TE LR F +G I+ + ++ + AFI+Y +A +H+ +
Sbjct: 107 VARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA-D 165
Query: 272 KVILGGRRLNIKWGRAQANRGE 293
+ GRR+ + R + +G
Sbjct: 166 GKKIDGRRVLVDVERGRTVKGW 187
>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 = 42.6 bits (100), Expect = 2e-05
Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 10/83 (12%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQ-----CAFIQYTSR 259
PE + + L + +D+++ + V + ++ AF++ S
Sbjct: 12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE 71
Query: 260 PAAEAAVEHSFNKVILGGRRLNI 282
+ A++ ++ +G R + +
Sbjct: 72 DDVKLALKK--DRESMGHRYIEV 92
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 42.7 bits (100), Expect = 2e-05
Identities = 11/81 (13%), Positives = 28/81 (34%), Gaps = 13/81 (16%)
Query: 216 LYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ--------CAFIQYTSRPAAEAAVE 267
++VG L + E ++ F +FG + + AF+ + + +A ++
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 268 HSF-----NKVILGGRRLNIK 283
+ + + K
Sbjct: 71 ACLEEDGKLYLCVSSPTIKDK 91
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 42.0 bits (99), Expect = 2e-05
Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 18/89 (20%)
Query: 203 PKLDPPEDKTITTLYVGNL-------GDKLTEQDLRDHFYQFGEIRSVTI-----LSKQQ 250
P+ D I V N+ +KL + + F +FG+I + +K
Sbjct: 8 PQEADGIDSVI---VVDNVPQVGPDRLEKL-KNVIHKIFSKFGKITNDFYPEEDGKTKG- 62
Query: 251 CAFIQYTSRPAAEAAVEHSFNKVILGGRR 279
F++Y S A AV++ + L +
Sbjct: 63 YIFLEYASPAHAVDAVKN-ADGYKLDKQH 90
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 42.2 bits (99), Expect = 3e-05
Identities = 13/95 (13%), Positives = 32/95 (33%), Gaps = 11/95 (11%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQFGEIR----SVTILSKQQ-- 250
++ + + + L T +++ F Q I + ++
Sbjct: 7 GGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR 66
Query: 251 ---CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
AF+ + A+ A+ +K +LG R + +
Sbjct: 67 PTGDAFVLFACEEYAQNALRK--HKDLLGKRYIEL 99
>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 = 40.5 bits (95), Expect = 7e-05
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 211 KTITTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQ-----CAFIQYTSRPAAEAA 265
T +++ L + TE D+ + F V I A +++ + A AA
Sbjct: 13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71
Query: 266 VEHSFNKVILGGRR 279
+ +K + R
Sbjct: 72 MA--KDKANMQHRY 83
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 39.3 bits (92), Expect = 9e-05
Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 15/78 (19%)
Query: 214 TTLYVGNL-------GDKLTEQDLRDHFYQFGEIRSVTI-----LSKQQCAFIQYTSRPA 261
+ + V N+ +KL + + F +FG+I + +K F++Y S
Sbjct: 2 SVIVVDNVPQVGPDRLEKL-KNVIHKIFSKFGKITNDFYPEEDGKTK-GYIFLEYASPAH 59
Query: 262 AEAAVEHSFNKVILGGRR 279
A AV++ + L +
Sbjct: 60 AVDAVKN-ADGYKLDKQH 76
>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 = 39.8 bits (93), Expect = 1e-04
Identities = 16/100 (16%), Positives = 35/100 (35%), Gaps = 14/100 (14%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQ-----CAFIQYTSR 259
E + + L T +D+ + F + L + A I+ S
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 260 PAAEAAVEHSFNKVILGGRRLNIKWGRAQANRGEDTAELK 299
+ A+E +++ +G R + + + N + A +K
Sbjct: 66 QDVQKALEK--HRMYMGQRYVEVY----EINNEDVDALMK 99
>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1
Length = 98
Score = 39.3 bits (91), Expect = 1e-04
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 144 PHIC-SFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKD 182
C + G C G++C + H+ T+ L D+ + D
Sbjct: 36 DFPCKLYHTTGNCINGDDCMFSHDPLTEETRELLDKMLAD 75
Score = 38.9 bits (90), Expect = 2e-04
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 133 ARTTPYYKRNRPHICSFWVKGECRRGEECPYRHEK 167
+ + + +C F++ G C R E CPY H
Sbjct: 2 SSGSSGELPKKRELCKFYITGFCARAENCPYMHGD 36
>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit;
CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 77
Score = 38.7 bits (90), Expect = 2e-04
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 140 KRNRPHICSFWVKGECRRGEECPYRHE 166
+ +C W++G C++G++C + HE
Sbjct: 6 SGEKTVVCKHWLRGLCKKGDQCEFLHE 32
Score = 37.2 bits (86), Expect = 6e-04
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 139 YKRNRPHICSFWVKGECRRGEECPYRHEKPTD 170
Y + C F+ K +ECP+ H P
Sbjct: 33 YDMTKMPECYFYSKFGECSNKECPFLHIDPES 64
>2rhk_C Cleavage and polyadenylation specificity factor subunit 4;
influenza A, nonstructural protein, viral protein: HOST
complex, Zn finger; 1.95A {Homo sapiens}
Length = 72
Score = 37.9 bits (88), Expect = 3e-04
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 140 KRNRPHICSFWVKGECRRGEECPYRHE 166
+ +C W++G C++G++C + HE
Sbjct: 12 SGEKTVVCKHWLRGLCKKGDQCEFLHE 38
Score = 34.1 bits (78), Expect = 0.006
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 139 YKRNRPHICSFWVKGECRRGEECPYRHEKP 168
Y + C F+ K +ECP+ H P
Sbjct: 39 YDMTKMSECYFYSKFGECSNKECPFLHIDP 68
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 37.7 bits (87), Expect = 4e-04
Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 214 TTLYVGNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKV 273
+ L + NL ++ LR Q G + S Q A +YT+R A A + N
Sbjct: 8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQM-ALNNC 66
Query: 274 ILGGRRLNI 282
+L +
Sbjct: 67 VLANTTIFA 75
>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 = 41.0 bits (95), Expect = 5e-04
Identities = 50/426 (11%), Positives = 104/426 (24%), Gaps = 131/426 (30%)
Query: 4 SKTSSTYNRQSWEDATKEKYG-------KECKICARPFTVFRWCPGARMR-------FKK 49
SK + E+ + Y E + + ++ R R F K
Sbjct: 73 SKQEEMVQK-FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ---RDRLYNDNQVFAK 128
Query: 50 TEVCQTCARLKNVCQ--TCLLDLE-------YG--------LPIQV-RDTALKIK----- 86
V RL+ + LL+L G + + V ++ K
Sbjct: 129 YNVS----RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184
Query: 87 -------DDIPKSDVNKEYYIQNMDHEIGKIDSTTPAGALGKASGSSEMLMKLAR--TTP 137
+ P++ + +Q + ++I ++ + + +L R +
Sbjct: 185 FWLNLKNCNSPETVLEM---LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 138 YYKR---------NRPHICSFWVKGECR-----RGEECPYRHEKPTDPDDPLADQNI--K 181
Y+ N +F C+ R ++ TD +I
Sbjct: 242 PYENCLLVLLNVQNAKAWNAF--NLSCKILLTTRFKQV-------TDFLSAATTTHISLD 292
Query: 182 DRYYGVNDPVAEKLMARASTMPKLD-PPEDKTITTLYVGNLG------------------ 222
+ + L+ + D P E T + +
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNC 352
Query: 223 -----------DKLTEQDLRDHFYQFGEIR-SVTILSKQQCAFIQYTSRPAAEAAVEHSF 270
+ L + R F + S I + + V
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLH 412
Query: 271 NKVILGGRRLNIKWG--------RAQANRGEDTAELKVRL-----EPVPGLPGALPPPPK 317
++ + + + E+ L + P L PP
Sbjct: 413 KYSLVEKQPKESTISIPSIYLELKVKL---ENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469
Query: 318 D--FFN 321
D F++
Sbjct: 470 DQYFYS 475
Score = 34.8 bits (79), Expect = 0.036
Identities = 45/338 (13%), Positives = 82/338 (24%), Gaps = 97/338 (28%)
Query: 15 WEDATKEKYGKECKICA--RPFTVFRWCPGARMRFKKTEVCQ---TCARLKNVCQTCLLD 69
+ CKI R V + A + T +K++ L
Sbjct: 254 QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313
Query: 70 LEYGLPIQVRDT--------ALKIKDDIPKSDVNKEYYIQNMDHEIGK-IDSTTPAGALG 120
LP +V T A I+D + D K + I ++ PA
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA---- 369
Query: 121 KASGSSEMLMKLARTTPYYKR--------NRPH--ICSFWVKGECRRGEECPYR-----H 165
E R + R + P + W + H
Sbjct: 370 ------EY-----R--KMFDRLSVFPPSAHIPTILLSLIWFDVI----KSDVMVVVNKLH 412
Query: 166 EKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLDPPEDKTITTLYVGNLG--- 222
+ L ++ K+ + + +L + L ++I Y
Sbjct: 413 KYS------LVEKQPKESTISIPS-IYLELKVKLENEYAL----HRSIVDHYNIPKTFDS 461
Query: 223 DKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
D L L +FY I + + F V L+
Sbjct: 462 DDLIPPYLDQYFYS----------------HIGHHLKNIEHPERMTLFRMVF-----LDF 500
Query: 283 KWGRAQANRGEDTAELKVRLEPVP-GLPGALPPPPKDF 319
++ K+R + G++ +
Sbjct: 501 RFLEQ-----------KIRHDSTAWNASGSILNTLQQL 527
>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 = 38.4 bits (89), Expect = 6e-04
Identities = 11/94 (11%), Positives = 33/94 (35%), Gaps = 10/94 (10%)
Query: 197 ARASTMPKLDPPEDKTITTLYVGNLGDKLTEQDLRDHFYQF---GEIRSVTILSKQQ--- 250
+ + PE + + L + +D+++ V + ++
Sbjct: 28 QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQ 87
Query: 251 --CAFIQYTSRPAAEAAVEHSFNKVILGGRRLNI 282
AF++ S + A++ ++ +G R + +
Sbjct: 88 SGEAFVELGSEDDVKMALKK--DRESMGHRYIEV 119
>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 = 37.7 bits (87), Expect = 0.006
Identities = 47/280 (16%), Positives = 90/280 (32%), Gaps = 89/280 (31%)
Query: 125 SSEMLMKLARTTPYYKRNRPHICSF--WVKGECRRGEE---------CP---------Y- 163
S+E L +L RTT ++ + W++ ++ CP Y
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV 250
Query: 164 --RHEKPTDPDDPLADQNIKDRYYGV----NDPVAEKLMARASTMPKLDPPEDKTITTL- 216
P ++ G V +A + K IT L
Sbjct: 251 VTAKLLGFTPG------ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF 304
Query: 217 YVG----------NLGDKLTEQDLRDHFYQFGEIR-----SVTILSKQQC-AFIQYTSR- 259
++G +L + +D ++ E S++ L+++Q ++ T+
Sbjct: 305 FIGVRCYEAYPNTSLPPSIL-EDSLEN----NEGVPSPMLSISNLTQEQVQDYVNKTNSH 359
Query: 260 -PAAEA---AVEHSFNKVILGG-----RRLNIKWGRAQANRGEDTAEL-----KVRLE-- 303
PA + ++ + +++ G LN+ +A+A G D + + K++
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR 419
Query: 304 --PV------PGLPGALPPPPKDF------FN---LSNPV 326
PV L A KD FN + PV
Sbjct: 420 FLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV 459
>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 = 36.3 bits (83), Expect = 0.012
Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 216 LYVGN--LGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVE--HSFN 271
L V N LG+ ++ L + G + ++ + + +F +Y + ++ A +
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKE 80
Query: 272 KVILGGRRL 280
V G+++
Sbjct: 81 VVDDLGQKI 89
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 33.4 bits (76), Expect = 0.021
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 9/81 (11%)
Query: 208 PEDKTITTLYVGNLGDKLTEQDLRDHF-----YQFGEIRSVTILSKQQCAFIQYTSRPAA 262
+ V L + ++ L +F G + S L + + A
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG--GVLTFREPADA 60
Query: 263 EAAVEHSFNKVILGGRRLNIK 283
E + + ++ L G +L+++
Sbjct: 61 ERVLAQADHE--LHGAQLSLR 79
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 33.8 bits (77), Expect = 0.023
Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 3/91 (3%)
Query: 196 MARASTMPKLDPPEDKTITTLYV-GNLGDKLTEQDLRDHFYQFGEIRSVTILSKQQCAFI 254
M + E+K L G+L D+ +DL F GEI+ + + + I
Sbjct: 1 MRGSHHHHHHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGII 60
Query: 255 QYTS--RPAAEAAVEHSFNKVILGGRRLNIK 283
+ + A A + + + L + + +
Sbjct: 61 LFKEKAKEALGKAKDANNGNLQLRNKEVTWE 91
>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein;
NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A
Length = 77
Score = 32.6 bits (74), Expect = 0.027
Identities = 8/38 (21%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 134 RTTPYYKRNRPHICSFWVK-GECRRGEECPYRHEKPTD 170
R + + + +C + G C G C + H D
Sbjct: 40 RQANRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPTED 77
Score = 28.4 bits (63), Expect = 0.72
Identities = 7/21 (33%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 146 IC-SFWVKGECRRGEECPYRH 165
+C ++ G CR G +C + H
Sbjct: 14 LCRTYSESGRCRYGAKCQFAH 34
>3u9g_A Zinc finger CCCH-type antiviral protein 1; zinc finger protein;
1.80A {Rattus norvegicus}
Length = 229
Score = 34.0 bits (77), Expect = 0.043
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 142 NRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQNIKDRYYGVNDPVAEKL 195
R HIC + +G C C H + D +++ G++ V + +
Sbjct: 173 ERLHICEHFTRGNCSYL-NCLRSH----NLMDRKVLTIMREH--GLSPDVVQNI 219
Score = 28.6 bits (63), Expect = 2.2
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 143 RPHICSFWVKGECR----RGEECPYRHEKPTD 170
H+C + G C + C Y H+ ++
Sbjct: 88 SLHLCKLNLLGRCHYAQSQRNLCKYSHDVLSE 119
>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative
splicing, metal- binding, nucleus, RNA-binding, zinc,
zinc-finger, metal binding; 1.50A {Homo sapiens} PDB:
3d2s_A
Length = 70
Score = 31.2 bits (70), Expect = 0.065
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 142 NRPHICSFWVKGECRRGE-ECPYRHEKPTDPDDP 174
+R +C + +G C RGE +C + H + D
Sbjct: 4 DRLEVCREYQRGNCNRGENDCRFAHPADSTMIDT 37
Score = 25.8 bits (56), Expect = 5.7
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 140 KRNRPHICSFWVKGECRRGEECPYRH 165
N +C ++KG C R E+C Y H
Sbjct: 38 NDNTVTVCMDYIKGRCSR-EKCKYFH 62
>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 = 32.0 bits (73), Expect = 0.073
Identities = 12/56 (21%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 227 EQDLRDHFYQFGEIRSVTILSKQQ--CAFIQYTSRPAAEAAVEHSFNKVILGGRRL 280
+DLR +FG+IR + + + A + + A+ ++ + + GGR++
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQ-TLDGRWFGGRQI 94
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI, protein
transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 32.0 bits (72), Expect = 0.086
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 232 DHFYQFGEIRSVTILSKQQCAFIQYTSRPAAEAAVEHSFNKVILGGR 278
F Q+G I + + I+Y S+ A A+ S + I G
Sbjct: 42 LQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL--SKDGRIFGES 86
>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding,
HOST-virus interaction, metal-binding, nucleus,
receptor, transcription, transcription regulation,
zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo
sapiens} PDB: 3dzu_D* 3e00_D* 2env_A
Length = 419
Score = 32.3 bits (73), Expect = 0.19
Identities = 26/232 (11%), Positives = 71/232 (30%), Gaps = 23/232 (9%)
Query: 3 TSKTSSTYNRQSWEDATKEKYGKECKICARPFTVFRW----CPGARMRFKKT-------- 50
+ + E+ + EC++C + F + C G + F++T
Sbjct: 29 YYSEKTQLYNKPHEEPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYD 88
Query: 51 ---EVCQTCARLKNVCQTCLLD--LEYGLPIQ--VRDTALKIKDDIPKSDVNKEYYIQNM 103
C+ + +N CQ C L G+ + + + ++++ + N
Sbjct: 89 RCDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEISSDIDQLNP 148
Query: 104 DHEIGKIDSTTPAGALGKASGSSEMLMKLARTTPYYKRNRPHICSFWVKGECRRGEECPY 163
+ + + + K+ ++ + T ++ I + ++ +
Sbjct: 149 ESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYD--MNSLMMGEDKIKF 206
Query: 164 RHEKPTDPDDPLADQNIKDRYYGVNDPVAEKLMARASTMPKLD--PPEDKTI 213
+H P I + +++ A ++P D+
Sbjct: 207 KHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVT 258
>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform
1, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 98
Score = 30.2 bits (67), Expect = 0.22
Identities = 9/36 (25%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 140 KRNRPHICSFWVKGECRRGE-ECPYRHEKPTDPDDP 174
+ ++ +C + +G C RGE +C + H + D
Sbjct: 16 RTDKLEVCREFQRGNCARGETDCRFAHPADSTMIDT 51
Score = 27.9 bits (61), Expect = 1.5
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 140 KRNRPHICSFWVKGECRRGEECPYRHEKPTDPDDPLADQN 179
N +C ++KG C R E+C Y H A Q+
Sbjct: 52 SDNTVTVCMDYIKGRCMR-EKCKYFHPPAHLQAKIKAAQH 90
>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative
splicing, cytoplasm, metal-binding, nucleus,
RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}
Length = 89
Score = 30.2 bits (67), Expect = 0.23
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 146 ICSFWVKGECRRGE-ECPYRHEKPTDPDDP 174
+C + +G C R + EC + H + +
Sbjct: 19 VCRQFQRGTCSRSDEECKFAHPPKSCQVEN 48
>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 = 28.8 bits (65), Expect = 0.80
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 227 EQDLRDHFYQFGEIRSVTI--LSKQQCAFIQYTSRPAAEAAVE 267
+ D+ + + G + + + S Q +++ S AA AAV
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVN 73
>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module,
phosphoinositide binding, caspase regulation, metal
binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1
g.50.1.1
Length = 120
Score = 29.0 bits (64), Expect = 0.90
Identities = 10/64 (15%), Positives = 16/64 (25%), Gaps = 16/64 (25%)
Query: 4 SKTSSTYNRQSWEDATKEKYGKECKICARPFTVFRWCPGARMRFKKTEVCQTCARLKNVC 63
+ ++ Y+ CK C F + C C + C
Sbjct: 3 AYSNPGYSSFPSPTGL----EPSCKSCGAHFANTARK----------QTCLDCKKN--FC 46
Query: 64 QTCL 67
TC
Sbjct: 47 MTCS 50
>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative
splicing, metal- binding, nucleus, RNA-binding, zinc,
zinc-finger, metal binding; 2.70A {Homo sapiens}
Length = 83
Score = 27.8 bits (61), Expect = 1.2
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 146 ICSFWVKGECRRGE-ECPYRHEKPT 169
+C + +G C R + EC + H +
Sbjct: 11 VCREFQRGTCSRPDTECKFAHPSKS 35
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.5 bits (66), Expect = 1.7
Identities = 26/160 (16%), Positives = 50/160 (31%), Gaps = 55/160 (34%)
Query: 106 EIGKIDSTTPAG---------ALGKAS--GSSEM--LMKLARTTPYYKRNRPHICSFWVK 152
E+G P G A G+ S G EM +M +
Sbjct: 827 EVG------PWGSARTRWEMEAFGEFSLEGCVEMAWIMGFIS---------------YHN 865
Query: 153 GECRRGEECPYRHEKPTDPDDPLADQNIKDRY-----------------YGVNDPVAEKL 195
G + PY + +P+ D+++K +Y + +P +++
Sbjct: 866 GNLKGR---PYTGWVDSKTKEPVDDKDVKAKYETSILEHSGIRLIEPELFNGYNPEKKEM 922
Query: 196 MARASTMPKLDPPE-DKTITTLYVGNLGDKLTEQDLRDHF 234
+ L+P E K + GDK+ ++ +
Sbjct: 923 IQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIPETG 962
>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 = 27.8 bits (62), Expect = 2.1
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 9/62 (14%)
Query: 227 EQDLRDHFYQFGEIRSVTILSKQQ--------CAFIQYTSRPAAEAAVEHSFNKVILGGR 278
+D+RD ++G ++S+ I F+++TS + A+ R
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAM-QGLTGRKFANR 87
Query: 279 RL 280
+
Sbjct: 88 VV 89
>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH
zinc-finger, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 69
Score = 26.8 bits (59), Expect = 2.4
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 146 ICSFWVKGECRRGEECPYRH 165
IC ++ G C G C + H
Sbjct: 22 ICDRYMNGTCPEGNSCKFAH 41
>3rfr_A PMOB; membrane, oxidoreductase; 2.68A {Methylocystis SP} PDB:
3chx_A
Length = 419
Score = 28.2 bits (62), Expect = 3.9
Identities = 18/69 (26%), Positives = 24/69 (34%), Gaps = 5/69 (7%)
Query: 260 PAAEAAVEHSFNKVILGGRRLNI---KWGRAQANRGEDTAELKVRLEPVPGLPGALPPPP 316
A A E S + L R LN +W + N E L ++ P A+ P
Sbjct: 24 APASAHGEKS-QQAFLRMRTLNWYDVQWSKTTVNVNE-EMILSGKVHVFSAWPQAVANPR 81
Query: 317 KDFFNLSNP 325
F N P
Sbjct: 82 VSFLNAGEP 90
>1vlb_A Aldehyde oxidoreductase; iron-sulphur cluster; HET: PCD; 1.28A
{Desulfovibrio gigas} SCOP: a.56.1.1 d.15.4.2 d.41.1.1
d.133.1.1 PDB: 1sij_A* 1zcs_A* 3fah_A* 3fc4_A* 3l4p_A*
Length = 907
Score = 28.0 bits (63), Expect = 4.6
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 5/43 (11%)
Query: 151 VKGECRRGEECPYRHEKPTDPDDP-LADQNIKDRYYGVNDPVA 192
VKG+ R + K D P L D+ + YG D +A
Sbjct: 245 VKGKNRITGLITFPTNKGDGWDRPILCDEKV--FQYG--DCIA 283
>2azw_A MUTT/nudix family protein; MUTT/nudix ,enterococcus faecalis,
structural genomics, PSI, structure initiative; HET:
1PE; 1.90A {Enterococcus faecalis} SCOP: d.113.1.1
Length = 148
Score = 26.7 bits (59), Expect = 7.0
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 254 IQYTSRPAAEAAVEHSFNKVILGGRRLNIKW 284
+ Y +R AA V N ++ + N +
Sbjct: 13 LTYQTRYAAYIIVSKPENNTMVLVQAPNGAY 43
>1fsu_A N-acetylgalactosamine-4-sulfatase; glycosaminoglycan degradation,
hydrolase, glycopr lysosome; HET: ALS NAG; 2.50A {Homo
sapiens} SCOP: c.76.1.2
Length = 492
Score = 27.4 bits (61), Expect = 7.1
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 75 PIQVRDTALKIKDDIPKSDVNKEYY--IQNMDHEIGKI 110
P+QV + LK D I + Y + MD +G +
Sbjct: 203 PLQVPEEYLKPYDFIQDKN-RHHYAGMVSLMDEAVGNV 239
>1wfk_A Zinc finger, FYVE domain containing 19; riken structural
genomics/proteomics initiative, RSGI, structural
genomics, unknown function; NMR {Mus musculus} SCOP:
g.50.1.1
Length = 88
Score = 25.5 bits (56), Expect = 9.4
Identities = 15/66 (22%), Positives = 18/66 (27%), Gaps = 25/66 (37%)
Query: 25 KECKICARPFTVF------RWCPGARMRFKKTEVCQTCARLK-----------NVCQTCL 67
C CA FT+F + C A C C VC+ C
Sbjct: 10 SRCYGCAVKFTLFKKEYGCKNCGRA--------FCNGCLSFSALVPRAGNTQQKVCKQCH 61
Query: 68 LDLEYG 73
L G
Sbjct: 62 TILTRG 67
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
0.318 0.135 0.416
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: 5,123,231
Number of extensions: 304018
Number of successful extensions: 985
Number of sequences better than 10.0: 1
Number of HSP's gapped: 809
Number of HSP's successfully gapped: 241
Length of query: 327
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 233
Effective length of database: 4,077,219
Effective search space: 949992027
Effective search space used: 949992027
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.7 bits)