RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16419
(346 letters)
>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 = 95.0 bits (237), Expect = 1e-24
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCI 94
S +TK+ VGN+S E+R F YG V+ECDIV++Y FVH++ D + I
Sbjct: 2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAI 61
Query: 95 KELNGMMVDGKPMKVVVA 112
+ L+ GK M V ++
Sbjct: 62 RGLDNTEFQGKRMHVQLS 79
Score = 60.3 bits (147), Expect = 6e-12
Identities = 20/46 (43%), Positives = 32/46 (69%)
Query: 301 GFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
G S + K+ +GN++P + + +R FE+YG V+ECD+VK+Y FV
Sbjct: 4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFV 49
Score = 38.4 bits (90), Expect = 3e-04
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP 40
HME E+ AI+ L+ K + ++ +TSR
Sbjct: 50 HMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRT 85
>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 = 92.4 bits (230), Expect = 2e-23
Identities = 23/96 (23%), Positives = 45/96 (46%), Gaps = 2/96 (2%)
Query: 20 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVR 78
+G L+ T++ P + ++VF+GNL+ + +V +F YG V C + +
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK 62
Query: 79 NYGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVAG 113
Y FV + + NG ++ G+ + + +AG
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAG 98
Score = 52.8 bits (127), Expect = 5e-09
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 309 KIFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++FIGN+N + +F KYG+V C V K Y FV
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFV 67
Score = 35.4 bits (82), Expect = 0.005
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 42
N+ R A+ NG+++ + L I A K +
Sbjct: 68 QYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRS 105
>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 = 91.5 bits (228), Expect = 2e-23
Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKE 96
G + T K+FVGN+S + E+R LF G V+ECD+V++Y FVH++ D I +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQ 62
Query: 97 LNGMMVDGKPMKVVVA 112
LNG V GK + V ++
Sbjct: 63 LNGKEVKGKRINVELS 78
Score = 62.6 bits (153), Expect = 7e-13
Identities = 24/44 (54%), Positives = 34/44 (77%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
SS T+KIF+GNV+ + + +R LFE+ G+V+ECDVVK+Y FV
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFV 48
Score = 42.2 bits (100), Expect = 1e-05
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 44
HME + + + AI +LNG+ V K + +E +T + + P+
Sbjct: 49 HMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPS 88
>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 = 91.9 bits (229), Expect = 1e-22
Identities = 31/119 (26%), Positives = 57/119 (47%), Gaps = 12/119 (10%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
++ + + AIK LNG V K LK+ A G + T ++V NL ++ +
Sbjct: 51 DFTSEMDSQRAIKVLNGITVRNKRLKVSYA-RPGGESIKDTNLYVTNLPRTITDDQLDTI 109
Query: 65 FVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDG--KPMKVVVA 112
F YG++V+ +I+R+ FV + + + I LN ++ +G +P+ V +A
Sbjct: 110 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 69.1 bits (170), Expect = 2e-14
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 95
T + V L + E+ LF G + C I+R+ Y FV S D + IK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 96 ELNGMMVDGKPMKV 109
LNG+ V K +KV
Sbjct: 64 VLNGITVRNKRLKV 77
Score = 42.2 bits (100), Expect = 5e-05
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
PG S+ +++ N+ + + + +F KYG +V+ +++ + FV
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136
Score = 41.4 bits (98), Expect = 8e-05
Identities = 7/46 (15%), Positives = 15/46 (32%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ + + + + LF G + C ++ Y FV
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFV 50
>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 = 89.9 bits (224), Expect = 6e-22
Identities = 26/117 (22%), Positives = 53/117 (45%), Gaps = 10/117 (8%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIE-AATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
+ A++ LNG+ + +KI A S++ + T +FVG+L+ N +R
Sbjct: 48 YHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNA 107
Query: 65 FVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
F + + + ++ + YGFV S D + + G ++G+P+++ A
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 60.2 bits (147), Expect = 3e-11
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 47 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP-DINKCIKELN 98
++VGNL +++ F G + I+ + Y FV D N ++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 99 GMMVDGKPMKV 109
G ++ +K+
Sbjct: 63 GKQIENNIVKI 73
Score = 41.0 bits (97), Expect = 1e-04
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
TF +F+G++N E +R F+ + + V+ + YGFV
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134
Score = 34.8 bits (81), Expect = 0.015
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAAT 35
+ ++ + A+ + GQ +N +PL+I A
Sbjct: 135 SFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 32.5 bits (75), Expect = 0.083
Identities = 7/44 (15%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
+++GN++ + ++++ F+ G + ++ + Y FV
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFV 46
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 90.5 bits (225), Expect = 1e-21
Identities = 15/127 (11%), Positives = 49/127 (38%), Gaps = 19/127 (14%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK----------GPNTPTTKVFVGNLSD 54
E E + A++++N ++ + +K+ ++ +++V ++
Sbjct: 76 EYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQ 135
Query: 55 NTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKELNGMMVDGK 105
+ +++ +F +G + + + YGF+ + + +N + G+
Sbjct: 136 DLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 195
Query: 106 PMKVVVA 112
++V A
Sbjct: 196 YLRVGKA 202
Score = 81.2 bits (201), Expect = 3e-18
Identities = 19/98 (19%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 21 GQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--- 77
+ + + +A R+G ++V+VG++ +R+ F P+G + D+
Sbjct: 5 ASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS 64
Query: 78 -----RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
+ + FV + P ++++N +M+ G+ +KV
Sbjct: 65 VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
Score = 45.8 bits (109), Expect = 5e-06
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ +I++ +V+ S + I+ +FE +GK+ + K YGF+
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172
Score = 42.3 bits (100), Expect = 8e-05
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
++++G++ + IR F +G + D+ K + FV
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Score = 33.8 bits (78), Expect = 0.048
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP-NTPTT 45
E + + A+ +N + + L++ A + P TP T
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 214
>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 = 85.7 bits (213), Expect = 3e-21
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELN 98
++ K+F+GNL E+R LF YG V+ECDI++NYGFVHI+ I+ L+
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLH 63
Query: 99 GMMVDGKPMKV 109
+ G + V
Sbjct: 64 HYKLHGVNINV 74
Score = 59.9 bits (146), Expect = 6e-12
Identities = 25/44 (56%), Positives = 33/44 (75%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
S G K+FIGN+ + + IR LFE+YGKV+ECD++KNYGFV
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFV 47
Score = 36.8 bits (86), Expect = 0.001
Identities = 9/42 (21%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTPTT 45
H+E+ AI+ L+ ++ + +EA+ ++ K + P++
Sbjct: 48 HIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSS 89
>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 = 87.7 bits (218), Expect = 5e-21
Identities = 27/117 (23%), Positives = 49/117 (41%), Gaps = 11/117 (9%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
+ +E A+ +G I + LKI P K+F+G L + +V+EL
Sbjct: 57 EFRSVDETTQAMA-FDGIIFQGQSLKIRRP-HDYQPLPGAHKLFIGGLPNYLNDDQVKEL 114
Query: 65 FVPYGTVVECDIVRN--------YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVVVA 112
+G + ++V++ Y F ++ ++ I LNGM + K + V A
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 56.1 bits (136), Expect = 8e-10
Identities = 10/78 (12%), Positives = 29/78 (37%), Gaps = 15/78 (19%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------------RNYGFVHIDSP-DIN 91
+++VGN+ + + F + +N+ F+ S +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 92 KCIKELNGMMVDGKPMKV 109
+ + +G++ G+ +K+
Sbjct: 66 QAMA-FDGIIFQGQSLKI 82
Score = 45.7 bits (109), Expect = 3e-06
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
G K+FIG + + + ++ L +G + ++VK+ Y F
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 141
Score = 38.0 bits (89), Expect = 0.001
Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 13/51 (25%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------------KNYGFV 346
++++GN+ G + E + F ++ KN+ F+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56
Score = 28.0 bits (63), Expect = 2.9
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAAT 35
+ AI LNG + +K L ++ A+
Sbjct: 142 EYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
>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 = 86.9 bits (216), Expect = 1e-20
Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 6/113 (5%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKG-PNTPTTKVFVGNLSDNTRAPEVRE 63
E+ E+ A+ EL G V +K+E R + NLS N E++E
Sbjct: 60 DFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKE 118
Query: 64 LFVPYGTVVECD---IVRNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+F + + ++ S D K ++E G +DG+ + +
Sbjct: 119 VFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171
Score = 68.8 bits (169), Expect = 4e-14
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-D 89
+T +F+GNL+ N E++ + +V R +G+V +S D
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66
Query: 90 INKCIKELNGMMVDGKPMKV 109
+ K + EL G+ V G +K+
Sbjct: 67 LEKAL-ELTGLKVFGNEIKL 85
Score = 43.4 bits (103), Expect = 3e-05
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
G S F +FIGN+NP SV ++ + + VV + +G+V
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 59
Score = 37.2 bits (87), Expect = 0.003
Identities = 4/60 (6%), Positives = 20/60 (33%), Gaps = 3/60 (5%)
Query: 290 TVVVIEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECD---VVKNYGFV 346
+ + + + + N++ + + ++ +FE ++ K ++
Sbjct: 82 EIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYI 141
Score = 31.0 bits (71), Expect = 0.34
Identities = 2/33 (6%), Positives = 14/33 (42%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+++ + ++E G ++ + + + +
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 86.1 bits (214), Expect = 2e-20
Identities = 28/118 (23%), Positives = 48/118 (40%), Gaps = 12/118 (10%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELF 65
+ ++ AI LNG + K +K+ A + ++V L E+ +LF
Sbjct: 51 YIDPKDAEKAINTLNGLRLQTKTIKVSYARPSS-ASIRDANLYVSGLPKTMTQKELEQLF 109
Query: 66 VPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDG--KPMKVVVA 112
YG ++ I+ + GF+ D + + IK LNG G +P+ V A
Sbjct: 110 SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 68.0 bits (167), Expect = 5e-14
Identities = 26/74 (35%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 95
T + V L N E R LF G + C +VR+ YGFV+ P D K I
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 96 ELNGMMVDGKPMKV 109
LNG+ + K +KV
Sbjct: 63 TLNGLRLQTKTIKV 76
Score = 43.3 bits (103), Expect = 2e-05
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ + + + E R LF G++ C +V++ YGFV
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFV 49
Score = 42.9 bits (102), Expect = 3e-05
Identities = 8/55 (14%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
P +S+ +++ + + + + LF +YG+++ ++ + GF+
Sbjct: 81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135
Score = 29.8 bits (68), Expect = 0.67
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 5 HMENDEEGRTAIKELNGQIVN--EKPLKIEAA 34
+ E AIK LNGQ + +P+ ++ A
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 88.9 bits (221), Expect = 2e-20
Identities = 21/114 (18%), Positives = 42/114 (36%), Gaps = 16/114 (14%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
+ N E+ AI + + E+ L ++ + + V NL + + EL
Sbjct: 63 TLLNGEQAEAAINAFHQSRLRERELSVQLQPTD-------ALLCVANLPPSLTQQQFEEL 115
Query: 65 FVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
P+G++ C +V + YGF + +L G + + + V
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 88.5 bits (220), Expect = 3e-20
Identities = 10/119 (8%), Positives = 38/119 (31%), Gaps = 11/119 (9%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK--GPNTPTTKVFVGNLSDNTRAPE-V 61
+ A +L G+ + + L + + + + + V L + +
Sbjct: 143 EYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDAL 202
Query: 62 RELFVPYGTVVECDIVRN-------YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVVVA 112
+ C + + + ++ ++ + ++ +G+ + G ++V
Sbjct: 203 CRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Score = 73.5 bits (181), Expect = 4e-15
Identities = 11/89 (12%), Positives = 31/89 (34%), Gaps = 5/89 (5%)
Query: 24 VNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--YG 81
++ + ++ + + K+ + L + EV +L Y + C + +
Sbjct: 3 LDPEEIRKRLEHTERQF-RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTA 60
Query: 82 FVHIDSP-DINKCIKELNGMMVDGKPMKV 109
FV + + I + + + + V
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSV 89
Score = 43.0 bits (102), Expect = 6e-05
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ + N+ P + + L +G + C +V + YGF
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFA 142
Score = 41.1 bits (97), Expect = 3e-04
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
KI I + + + + L Y + C V K FV
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFV 62
Score = 41.1 bits (97), Expect = 3e-04
Identities = 5/46 (10%), Positives = 13/46 (28%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPG-TSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+ + + PG V+ + C + K + +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 231
Score = 33.8 bits (78), Expect = 0.067
Identities = 5/33 (15%), Positives = 11/33 (33%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
E E A ++ +G + L++
Sbjct: 232 EYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 83.1 bits (206), Expect = 4e-20
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 1/89 (1%)
Query: 25 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVH 84
+ + R+ T++FV + + E+ E+F P+G + E I+ + FV
Sbjct: 12 SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVE 71
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+ K I+E++G +P++VV +
Sbjct: 72 FEEAESAAKAIEEVHGKSFANQPLEVVYS 100
Score = 50.4 bits (121), Expect = 3e-08
Identities = 6/38 (15%), Positives = 16/38 (42%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++F+ + +F +G + E ++ + FV
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFV 70
Score = 34.2 bits (79), Expect = 0.013
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E E AI+E++G+ +PL++ +
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA 104
>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 = 83.1 bits (206), Expect = 5e-20
Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 34 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINK 92
+S +FV NL++ + + F +G + +++Y F+H D K
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVK 60
Query: 93 CIKELNGMMVDGKPMKVVVA 112
++E+NG ++G+ +++V A
Sbjct: 61 AMEEMNGKDLEGENIEIVFA 80
Score = 50.7 bits (122), Expect = 2e-08
Identities = 9/38 (23%), Positives = 21/38 (55%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFV 346
+F+ N+ + E++ F ++GK+ +K+Y F+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFI 50
Score = 36.5 bits (85), Expect = 0.002
Identities = 7/33 (21%), Positives = 17/33 (51%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
H + + A++E+NG+ + + ++I A
Sbjct: 51 HFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP 83
>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 = 85.0 bits (211), Expect = 5e-20
Identities = 26/122 (21%), Positives = 44/122 (36%), Gaps = 14/122 (11%)
Query: 5 HMENDEEGRTAIKELNGQIVNEK---PLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEV 61
+ A L+ V P++++ A S K K+F+G +S ++
Sbjct: 53 TFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDI 112
Query: 62 RELFVPYGTVVECDIVRN-------YGFVHIDSPD-INKCIKELNGMMV---DGKPMKVV 110
R +F +G + EC I+R FV + IK ++ PM V
Sbjct: 113 RVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172
Query: 111 VA 112
A
Sbjct: 173 FA 174
Score = 68.8 bits (169), Expect = 4e-14
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 11/79 (13%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN----------YGFVHIDSP-DINKC 93
K+FVG + ++RELF YG V E +++R+ FV + +
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 94 IKELNGMMVDGKPMKVVVA 112
L+ M V +
Sbjct: 64 QNALHNMKVLPGMHHPIQM 82
Score = 48.0 bits (115), Expect = 6e-07
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 10/48 (20%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN----------YGFV 346
K+F+G V S + +R LFE+YG V E +V+++ FV
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFV 52
Score = 44.9 bits (107), Expect = 7e-06
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
K+FIG ++ + IR +F +G++ EC +++ FV
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFV 141
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 82.3 bits (204), Expect = 6e-20
Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 43 PTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGM 100
P +++F+GNL N ++ +F PYG +++ +I +GF+ D+P + I+ +
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQE 68
Query: 101 MVDGKPMKVVVA 112
M GK + + V+
Sbjct: 69 MNFGKKLILEVS 80
Score = 52.2 bits (126), Expect = 4e-09
Identities = 11/39 (28%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 309 KIFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKNYGFV 346
++FIGN+ S E + +F YG +++ ++ +GF+
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFI 50
Score = 34.9 bits (81), Expect = 0.005
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP 40
+N + R AI+ + ++ K L +E ++S P
Sbjct: 51 QFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARP 86
>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 = 81.6 bits (202), Expect = 1e-19
Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 33 AATSRKGPNTPTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DI 90
++ + +++F+GNL N ++ +F PYG +++ +I +GF+ D+P +
Sbjct: 11 SSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSV 70
Query: 91 NKCIKELNGMMVDGKPMKVVVA 112
I+ + M GK + + V+
Sbjct: 71 RDAIEXESQEMNFGKKLILEVS 92
Score = 53.1 bits (128), Expect = 2e-09
Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGT-SVELIRPLFEKYGKVVECDVVKNYGFV 346
+ +P S + + ++FIGN+ S E + +F YG +++ ++ +GF+
Sbjct: 12 SGLVPRGSHMKS-RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFI 62
Score = 32.3 bits (74), Expect = 0.042
Identities = 8/34 (23%), Positives = 17/34 (50%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+N + R AI+ + ++ K L +E ++S
Sbjct: 63 QFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96
>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 = 82.8 bits (205), Expect = 5e-19
Identities = 26/136 (19%), Positives = 50/136 (36%), Gaps = 29/136 (21%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT-------------------T 45
+ +E A+ +G I + LKI + +
Sbjct: 57 EFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDI-NKCIKE 96
K+F+G L + +V+EL +G + ++V++ Y F ++ ++ I
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 97 LNGMMVDGKPMKVVVA 112
LNGM + K + V A
Sbjct: 176 LNGMQLGDKKLLVQRA 191
Score = 57.3 bits (139), Expect = 5e-10
Identities = 10/78 (12%), Positives = 29/78 (37%), Gaps = 15/78 (19%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------------RNYGFVHIDSP-DIN 91
+++VGN+ + + F + +N+ F+ S +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 92 KCIKELNGMMVDGKPMKV 109
+ + +G++ G+ +K+
Sbjct: 66 QAM-AFDGIIFQGQSLKI 82
Score = 44.3 bits (105), Expect = 2e-05
Identities = 10/60 (16%), Positives = 22/60 (36%), Gaps = 8/60 (13%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ K+FIG + + + ++ L +G + ++VK+ Y F
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161
Score = 35.8 bits (83), Expect = 0.011
Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 13/51 (25%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------------KNYGFV 346
++++GN+ G + E + F ++ KN+ F+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 56
Score = 29.2 bits (66), Expect = 1.6
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+ AI LNG + +K L ++ A+
Sbjct: 163 YVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 194
>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 = 82.7 bits (205), Expect = 7e-19
Identities = 22/112 (19%), Positives = 53/112 (47%), Gaps = 8/112 (7%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN-TPTTKVFVGNLSDNTRAPEVREL 64
+ + A+ +N ++ KP++I + + +F+ NL + + +
Sbjct: 64 FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDT 123
Query: 65 FVPYGTVVECDIV------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
F +G ++ C +V + YGFVH ++ + I+++NGM+++ + + V
Sbjct: 124 FSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
Score = 63.8 bits (156), Expect = 4e-12
Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-D 89
P+ P ++VG+L + + E F P G ++ + R+ Y +V+ P D
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 90 INKCIKELNGMMVDGKPMKV 109
+ + +N ++ GKP+++
Sbjct: 70 AERALDTMNFDVIKGKPVRI 89
Score = 49.2 bits (118), Expect = 3e-07
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFV 346
++ P G IFI N++ + + F +G ++ C VV K YGFV
Sbjct: 92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFV 148
Score = 38.0 bits (89), Expect = 0.002
Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
H E E AI+++NG ++N++ + + SRK + +G + +V +
Sbjct: 149 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK-----EREAELGARAKEFYPYDVPDY 203
Query: 65 FVPYGTVV 72
G +V
Sbjct: 204 AGSSGRIV 211
Score = 33.0 bits (76), Expect = 0.076
Identities = 9/55 (16%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
P S +++G+++P + ++ F G ++ V ++ Y +V
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
>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 = 84.0 bits (208), Expect = 8e-19
Identities = 25/118 (21%), Positives = 43/118 (36%), Gaps = 16/118 (13%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELF 65
+E+ A EL+G I+ +PL+I AT + V NLS + + F
Sbjct: 65 LESRTLAEIAKAELDGTILKSRPLRIRFAT-------HGAALTVKNLSPVVSNELLEQAF 117
Query: 66 VPYGTVVECDIV-------RNYGFVHIDSPD-INKCIKELN-GMMVDGKPMKVVVAGF 114
+G V + +V GFV + K ++ G + + V+
Sbjct: 118 SQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP 175
Score = 77.0 bits (190), Expect = 2e-16
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 27 KPLKIEAATSRKGPN-TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR--NYGFV 83
+ I++ T ++FVGNL + + + LF YG E I R +GF+
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFI 63
Query: 84 HIDSP-DINKCIKELNGMMVDGKPMKV 109
++S EL+G ++ +P+++
Sbjct: 64 RLESRTLAEIAKAELDGTILKSRPLRI 90
Score = 48.9 bits (117), Expect = 7e-07
Identities = 12/40 (30%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++F+GN+ + E + LFE+YG+ E + + +GF+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFI 63
Score = 44.7 bits (106), Expect = 1e-05
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 7/47 (14%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+ + N++P S EL+ F ++G V + VV GFV
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFV 142
>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 = 77.3 bits (191), Expect = 5e-18
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 30 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGF 82
++ K+ V NL +++ELF +GT+ + +
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD 74
Query: 83 VHIDSP-DINKCIKELNGMMVDGKPMKVVVAG 113
VH + D K +K+ NG+ +DG+PM + +
Sbjct: 75 VHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106
Score = 40.3 bits (95), Expect = 7e-05
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
++ G K+ + N++ G S I+ LF ++G + + V V
Sbjct: 17 DSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADV 75
Score = 40.3 bits (95), Expect = 8e-05
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATS 36
H E + A+K+ NG ++ +P+ I+ TS
Sbjct: 76 HFERKADALKAMKQYNGVPLDGRPMNIQLVTS 107
>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 = 77.8 bits (192), Expect = 6e-18
Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 8/90 (8%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVH 84
++ K+ V NL +++ELF +GT+ + + VH
Sbjct: 23 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVH 82
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVVAG 113
+ D K +K+ G+ +DG+PM + +
Sbjct: 83 FERRADALKAMKQYKGVPLDGRPMDIQLVA 112
Score = 40.0 bits (94), Expect = 1e-04
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 7/59 (11%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
++ G K+ + N++ G S I+ LF ++G + + V V
Sbjct: 23 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 81
Score = 40.0 bits (94), Expect = 2e-04
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
H E + A+K+ G ++ +P+ I+ S+
Sbjct: 82 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>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 = 76.5 bits (189), Expect = 8e-18
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 5/85 (5%)
Query: 33 AATSRKGPNTPT--TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP 88
++ S G T T +++FVGNL + E+R+LF YG E I + +GF+ +++
Sbjct: 2 SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETR 61
Query: 89 -DINKCIKELNGMMVDGKPMKVVVA 112
EL+ M + GK ++V A
Sbjct: 62 TLAEIAKVELDNMPLRGKQLRVRFA 86
Score = 50.7 bits (122), Expect = 1e-08
Identities = 17/40 (42%), Positives = 26/40 (65%), Gaps = 2/40 (5%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++F+GN+ P + E +R LFEKYGK E + K +GF+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFI 56
Score = 34.5 bits (80), Expect = 0.007
Identities = 7/38 (18%), Positives = 13/38 (34%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 42
+E A EL+ + K L++ A +
Sbjct: 57 RLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTS 94
>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 = 78.0 bits (192), Expect = 1e-17
Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 4/112 (3%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
+N +G + + + KV+VGNL +N E+
Sbjct: 34 ANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERA 93
Query: 65 FVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
F YG + + RN + FV + P D ++EL+G + G ++V ++
Sbjct: 94 FGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
Score = 47.2 bits (112), Expect = 8e-07
Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 3/66 (4%)
Query: 284 RYQSFGTVVVIEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN- 342
+ + +M S K+++GN+ + + F YG + V +N
Sbjct: 50 KTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP 109
Query: 343 --YGFV 346
+ FV
Sbjct: 110 PGFAFV 115
Score = 28.3 bits (63), Expect = 2.1
Identities = 7/34 (20%), Positives = 18/34 (52%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E+ + A++EL+G+ + +++E + K
Sbjct: 116 EFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK 149
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 76.6 bits (189), Expect = 1e-17
Identities = 19/94 (20%), Positives = 48/94 (51%), Gaps = 7/94 (7%)
Query: 26 EKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RN 79
L + + ++ V N+ R P++R++F +G +++ +I+ +
Sbjct: 11 SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70
Query: 80 YGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+GFV ++ D ++ ++L+G +V+G+ ++V A
Sbjct: 71 FGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
Score = 41.5 bits (98), Expect = 3e-05
Identities = 10/56 (17%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 297 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFV 346
+M + ++ + N+ +R +F ++GK+++ +++ K +GFV
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 74
Score = 38.5 bits (90), Expect = 4e-04
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
EN + A ++L+G +V + +++ AT+R
Sbjct: 76 FENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 76.2 bits (188), Expect = 1e-17
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 42 TPTTKVFVGNLSDNTRAPEVRELFVPYG--TVVECDIVRNYGFVHIDSP-DINKCIKELN 98
+ ++V NL +T + + F V +R+Y FVH + D + +K LN
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALN 72
Query: 99 GMMVDGKPMKVVVA 112
G ++DG P++V +A
Sbjct: 73 GKVLDGSPIEVTLA 86
Score = 41.1 bits (97), Expect = 3e-05
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKNYGFV 346
+++ N+ TS E+I F V +++Y FV
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFV 56
Score = 36.1 bits (84), Expect = 0.003
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTPT 44
H N E+ A+K LNG++++ P+++ A K + P+
Sbjct: 57 HFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPS 97
>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 = 75.4 bits (186), Expect = 2e-17
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----------YGFVHIDSP- 88
++ ++ +F+ NL+ +T ++ +F G + C I + +GFV P
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 89 DINKCIKELNGMMVDGKPMKVVVA 112
K +K+L G VDG ++V ++
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRIS 85
Score = 44.2 bits (105), Expect = 3e-06
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-----------YGFV 346
S G+ +FI N+N T+ E ++ +F K G + C + K +GFV
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFV 55
Score = 38.0 bits (89), Expect = 4e-04
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTK 46
+ E+ + A+K+L G V+ L++ + P + +
Sbjct: 57 YKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97
>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 = 79.3 bits (196), Expect = 5e-17
Identities = 19/125 (15%), Positives = 49/125 (39%), Gaps = 18/125 (14%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR------KGPNTPTTKVFVGNLSDN-TR 57
+ + E+ R +++LNG + L + + ++ + NLS
Sbjct: 165 DVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLD 224
Query: 58 APEVRELFVPYGTVVECDIVRN---------YGFVHIDSPD-INKCIKELNGMMVDGKPM 107
+RE F +G++ + +I F+ ++ D + + ++N ++ + +
Sbjct: 225 ENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREI 283
Query: 108 KVVVA 112
V +A
Sbjct: 284 SVSLA 288
Score = 75.8 bits (187), Expect = 8e-16
Identities = 17/117 (14%), Positives = 43/117 (36%), Gaps = 18/117 (15%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVREL 64
+ AI + + +V + + + T +++ N + +R+L
Sbjct: 87 EFARYDGALAAITKTHK-VVGQNEIIVSHLTE--------CTLWMTNFPPSYTQRNIRDL 137
Query: 65 FVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
V + R + ++ + S D C+++LNG+ ++G + V+
Sbjct: 138 LQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 194
Score = 63.1 bits (154), Expect = 2e-11
Identities = 16/109 (14%), Positives = 34/109 (31%), Gaps = 11/109 (10%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVP 67
+ + + E + K A +R T V V NL + +V + F
Sbjct: 8 ARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELT---TVLVKNLPKSYNQNKVYKYFKH 64
Query: 68 YGTVVECDIVRN------YGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
G ++ D+ + + + I + + +V + V
Sbjct: 65 CGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK-VVGQNEIIV 112
Score = 46.1 bits (110), Expect = 6e-06
Identities = 5/47 (10%), Positives = 16/47 (34%), Gaps = 6/47 (12%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN------YGFV 346
+ + N+ + + F+ G ++ DV + + +
Sbjct: 40 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARI 86
Score = 38.8 bits (91), Expect = 0.002
Identities = 6/46 (13%), Positives = 16/46 (34%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+++ N P + IR L + V + + + ++
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYI 164
Score = 37.3 bits (87), Expect = 0.005
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 10/48 (20%)
Query: 309 KIFIGNVNPGTSVE-LIRPLFEKYGKVVECDVVKN---------YGFV 346
+I I N++ E L+R FE +G + + ++ F+
Sbjct: 212 EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFM 259
Score = 30.7 bits (70), Expect = 0.59
Identities = 5/33 (15%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
EN + A+ ++N ++ + + + A +
Sbjct: 260 VFENKDSAERAL-QMNRSLLGNREISVSLADKK 291
>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 = 74.2 bits (183), Expect = 6e-17
Identities = 18/88 (20%), Positives = 48/88 (54%), Gaps = 7/88 (7%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHI 85
++ + ++ V N+ R P++R++F +G +++ +I+ + +GFV
Sbjct: 3 SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62
Query: 86 DSP-DINKCIKELNGMMVDGKPMKVVVA 112
++ D ++ ++L+G +V+G+ ++V A
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNA 90
Score = 42.3 bits (100), Expect = 2e-05
Identities = 9/44 (20%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN------YGFV 346
++ + N+ +R +F ++GK+++ +++ N +GFV
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 60
Score = 37.6 bits (88), Expect = 7e-04
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
EN + A ++L+G +V + +++ AT+R N
Sbjct: 61 TFENSADADRAREKLHGTVVEGRKIEVNNATARVMTN 97
>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 = 74.2 bits (183), Expect = 8e-17
Identities = 18/91 (19%), Positives = 32/91 (35%), Gaps = 8/91 (8%)
Query: 30 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGF 82
A K T +++ NL + E+ + P+G V+ I+R+ GF
Sbjct: 11 SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 70
Query: 83 VHIDSPDI-NKCIKELNGMMVDGKPMKVVVA 112
++S + I NG + P
Sbjct: 71 ARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101
Score = 37.6 bits (88), Expect = 8e-04
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAA 34
ME+ E+ I NG+ + P
Sbjct: 72 RMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101
Score = 35.7 bits (83), Expect = 0.004
Identities = 6/45 (13%), Positives = 20/45 (44%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
++I N+ + + + + +G+V+ ++++ GF
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFA 71
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 76.0 bits (187), Expect = 9e-17
Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 30 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGF 82
++ K+ V NL +++ELF +GT+ + + +
Sbjct: 74 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD 133
Query: 83 VHIDSP-DINKCIKELNGMMVDGKPMKVVVAG 113
VH + D K +K+ G+ +DG+PM + +
Sbjct: 134 VHFERRADALKAMKQYKGVPLDGRPMDIQLVA 165
Score = 38.7 bits (90), Expect = 9e-04
Identities = 11/59 (18%), Positives = 23/59 (38%), Gaps = 7/59 (11%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
++ G K+ + N++ G S I+ LF ++G + + V + V
Sbjct: 76 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 134
Score = 37.9 bits (88), Expect = 0.002
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP 40
H E + A+K+ G ++ +P+ I+ S+
Sbjct: 135 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170
>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 = 74.3 bits (183), Expect = 1e-16
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 8/89 (8%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVH 84
++ + VFV NL +++E+F G VV DI+ + G V
Sbjct: 3 SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVT 62
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+ + + I NG ++ +PM V +
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVKMD 91
Score = 40.8 bits (96), Expect = 8e-05
Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+ +G+ +F+ N++ + ++ +F G VV D++ + G V
Sbjct: 5 SSGALQAGRLGS-TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61
Score = 36.9 bits (86), Expect = 0.002
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E E AI NGQ++ ++P+ ++
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVKMDERAL 95
>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 = 73.0 bits (180), Expect = 2e-16
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHI 85
++ VFVGNL R + ELF+ G + + I +++GFV
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF 64
Query: 86 DSP-DINKCIKELNGMMVDGKPMKVVVA 112
P ++ I LNG+ + G+P+ V
Sbjct: 65 KHPESVSYAIALLNGIRLYGRPINVSGP 92
Score = 40.3 bits (95), Expect = 6e-05
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+F+GN+ E++ LF + G + + + K++GFV
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFV 62
Score = 36.8 bits (86), Expect = 0.001
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATS 36
++ E AI LNG + +P+ + +S
Sbjct: 64 FKHPESVSYAIALLNGIRLYGRPINVSGPSS 94
>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 = 72.6 bits (179), Expect = 2e-16
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 84
++ + P + V LS T ++RE+F YG + + IV R + FV+
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKV 109
++ D + + NGM +DG+ ++V
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRV 89
Score = 42.2 bits (100), Expect = 1e-05
Identities = 9/59 (15%), Positives = 23/59 (38%), Gaps = 8/59 (13%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ + + + ++ T+ +R +F KYG + + +V + + FV
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Score = 32.6 bits (75), Expect = 0.031
Identities = 6/31 (19%), Positives = 17/31 (54%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATS 36
EN ++ + A + NG ++ + +++ +S
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>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 = 72.7 bits (179), Expect = 3e-16
Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 10/97 (10%)
Query: 25 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 77
E+ KI +S P P +++ NLS ++ LF + I
Sbjct: 7 GEEIRKIPMFSSYN-PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR 65
Query: 78 -RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVVVA 112
R F+ + +I + + +NG + GK + +
Sbjct: 66 MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG 102
Score = 40.7 bits (96), Expect = 8e-05
Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 12/64 (18%)
Query: 295 EARNMPGFSSVG----TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KN 342
E R +P FSS +++ N++P + + LF ++ + + +
Sbjct: 9 EIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG 68
Query: 343 YGFV 346
F+
Sbjct: 69 QAFI 72
Score = 39.6 bits (93), Expect = 2e-04
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 44
N E A+ +NG + K L IE ++K +
Sbjct: 74 FPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK-QRSSG 111
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 72.8 bits (179), Expect = 4e-16
Identities = 21/102 (20%), Positives = 39/102 (38%), Gaps = 9/102 (8%)
Query: 20 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 79
+ AA ++ +F+ +L ++ F+P+G V+ + +
Sbjct: 16 SPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFID 75
Query: 80 --------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+GFV D+P IK +NG V K +KV +
Sbjct: 76 KQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
Score = 37.3 bits (87), Expect = 0.001
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAA 34
+N + + AIK +NG V K LK++
Sbjct: 89 FDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
Score = 35.4 bits (82), Expect = 0.005
Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+FI ++ + + F +G V+ V K +GFV
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFV 87
>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 = 71.9 bits (177), Expect = 4e-16
Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCIK 95
G PTT+++VG L NT + F +G++ D V ++ ++ +S
Sbjct: 12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA 71
Query: 96 ELNGMMVDGKPMKVVV 111
++ G + G ++ V
Sbjct: 72 KMRGFPLGGPDRRLRV 87
Score = 48.0 bits (115), Expect = 1e-07
Identities = 8/40 (20%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++++G + P TS+ + F+++G + D V ++ ++
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYI 58
>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 = 72.9 bits (179), Expect = 5e-16
Identities = 24/122 (19%), Positives = 47/122 (38%), Gaps = 24/122 (19%)
Query: 15 AIKELNGQIVNEKPL-------KIEAATSRK---GPNTPTTKVFVGNLSDNTRAPEVREL 64
E+ + ++ + L + S P P +++V NL+ + + +++ +
Sbjct: 6 DSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYI 65
Query: 65 FVPYGTVVEC------DIV-------RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVV 110
F Y DI + F+ + + K +KE NG ++ GKPM V
Sbjct: 66 FGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQ 125
Query: 111 VA 112
A
Sbjct: 126 FA 127
Score = 37.9 bits (88), Expect = 0.001
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ N++ A+KE NG ++ KP+ ++ A S +
Sbjct: 99 LPNEKAAAKALKEANGYVLFGKPMVVQFARSAR 131
Score = 30.6 bits (69), Expect = 0.41
Identities = 10/69 (14%), Positives = 22/69 (31%), Gaps = 17/69 (24%)
Query: 295 EARNMPGFSSVG----TFKIFIGNVNPGTSVELIRPLFEKYGKVVEC------DVV---- 340
E + F S +I++ N+ + ++ +F +Y D+
Sbjct: 29 EMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE 88
Query: 341 ---KNYGFV 346
K F+
Sbjct: 89 GRMKGQAFI 97
>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 = 71.5 bits (176), Expect = 6e-16
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 7/87 (8%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHID 86
++ + ++V NL D +R+ F P+GT+ ++ +GFV
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFS 63
Query: 87 SP-DINKCIKELNGMMVDGKPMKVVVA 112
SP + K + E+NG +V KP+ V +A
Sbjct: 64 SPEEATKAVTEMNGRIVATKPLYVALA 90
Score = 41.4 bits (98), Expect = 4e-05
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFV 346
+++ N++ G E +R F +G + V+ K +GFV
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFV 60
Score = 38.3 bits (90), Expect = 4e-04
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+ EE A+ E+NG+IV KPL + A +
Sbjct: 62 FSSPEEATKAVTEMNGRIVATKPLYVALAQRK 93
>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 = 72.0 bits (177), Expect = 6e-16
Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 9/90 (10%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV 83
A + +F+ +L ++ ++F+P+G VV + + +GFV
Sbjct: 13 IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 72
Query: 84 HIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
D+P I+ +NG + K +KV +
Sbjct: 73 SYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102
Score = 39.6 bits (93), Expect = 2e-04
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+N + AI+ +NG + K LK++ S+
Sbjct: 74 YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK 105
Score = 36.1 bits (84), Expect = 0.003
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+FI ++ + + +F +G VV V K +GFV
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 72
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 72.0 bits (177), Expect = 6e-16
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 10/85 (11%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-D 89
G P +V L+DN R ++++ YG V E +I+ + V S
Sbjct: 2 GQ-IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60
Query: 90 INKCIKELNGMMVDGKPMKVVVAGF 114
+ +K L+ V G + +
Sbjct: 61 AKETVKNLHLTSVMGNIIHAQLDIK 85
Score = 40.1 bits (94), Expect = 1e-04
Identities = 7/46 (15%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
++ +N ++ + KYG+V E +++ + V
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARV 53
Score = 30.1 bits (68), Expect = 0.38
Identities = 3/33 (9%), Positives = 10/33 (30%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ + +K L+ V + + +
Sbjct: 55 FTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQ 87
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 72.5 bits (178), Expect = 9e-16
Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 9/86 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 84
+ G T ++VG L++ + F+P+G + + I R + FV
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKV 109
+ D I +N + G+ ++V
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRV 137
Score = 43.2 bits (102), Expect = 2e-05
Identities = 7/59 (11%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
G S+ +++G + +++ F +G + + + + + FV
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 110
Score = 30.5 bits (69), Expect = 0.33
Identities = 6/29 (20%), Positives = 13/29 (44%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAA 34
E E+ AI +N + + +++ A
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 71.2 bits (175), Expect = 1e-15
Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 5/93 (5%)
Query: 20 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-- 77
+G N K L+ E ++ P V+ G ++ +R+ F P+G ++E +
Sbjct: 3 SGSSGNTKQLRFEDVVNQSSPKN--CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
Query: 78 RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKV 109
+ Y FV + I +NG ++G +K
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC 93
Score = 43.9 bits (104), Expect = 5e-06
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++ G + G + +L+R F +G+++E V K Y FV
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFV 66
Score = 32.3 bits (74), Expect = 0.050
Identities = 6/37 (16%), Positives = 10/37 (27%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 42
E AI +NG + +K +
Sbjct: 68 FSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 70.7 bits (174), Expect = 1e-15
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHIDSP-DIN 91
++ ++FV NL + +++ F G V+ DI G V +SP
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAE 62
Query: 92 KCIKELNGMMVDGKPMKV 109
+ + +NGM + G+ + V
Sbjct: 63 RACRMMNGMKLSGREIDV 80
Score = 39.9 bits (94), Expect = 9e-05
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFV 346
S G +IF+ N+ + ++++ F + G V+ D+ K G V
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVV 53
Score = 37.2 bits (87), Expect = 8e-04
Identities = 7/38 (18%), Positives = 18/38 (47%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 42
E+ E A + +NG ++ + + + + GP++
Sbjct: 54 KFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSS 91
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 70.6 bits (173), Expect = 1e-15
Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 10/86 (11%)
Query: 34 ATSRKGPNTP----TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----YGFVH 84
+S + P K+ + N+ + + + L V YG V C+ V V
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKV 109
S + + +LNG ++ +KV
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLKV 86
Score = 40.1 bits (94), Expect = 8e-05
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+ I N+ P E++ L +YG V C+ V
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT 50
Score = 34.7 bits (80), Expect = 0.007
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ ++ R A+ +LNG + LK+
Sbjct: 60 TYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM 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 = 69.8 bits (172), Expect = 2e-15
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 9/78 (11%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCI 94
T +FVG+L+ N +R F + + + ++ R YGFV S D +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 95 KELNGMMVDGKPMKVVVA 112
+ G ++G+P+++ A
Sbjct: 61 DSMQGQDLNGRPLRINWA 78
Score = 46.7 bits (112), Expect = 3e-07
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
TF +F+G++N E +R F+ + + V+ + YGFV
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 48
Score = 35.9 bits (84), Expect = 0.002
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+ ++ + A+ + GQ +N +PL+I A
Sbjct: 50 FTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL 81
>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 = 69.7 bits (171), Expect = 2e-15
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYG-TVVECDIVRNYGFVHIDSPDI-NKCIKELNGMM 101
++ + V NL ++ EV +L Y D + FV + + + I+ +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64
Query: 102 VDGKPMKV 109
GK + V
Sbjct: 65 FRGKDLIV 72
Score = 48.9 bits (117), Expect = 5e-08
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYG-KVVECDVVKNYGFV 346
S G+ I + N+ ++ + + L + Y K D K FV
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFV 45
Score = 36.2 bits (84), Expect = 0.002
Identities = 8/42 (19%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK----GPNT 42
+ N E+ + AI+ + K L ++ + GP++
Sbjct: 46 TLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPSS 87
>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 = 70.8 bits (174), Expect = 2e-15
Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 9/89 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 84
++ +K + VFVG+LS +++ F P+G + + +V + YGFV
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+ D I+++ G + G+ ++ A
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWA 92
Score = 45.0 bits (107), Expect = 2e-06
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 8/52 (15%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ F +F+G+++P + E I+ F +G++ + VV K YGFV
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Score = 36.2 bits (84), Expect = 0.003
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTK 46
N + AI+++ GQ + + ++ AT + T +
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYE 104
>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 = 70.9 bits (174), Expect = 2e-15
Identities = 24/120 (20%), Positives = 47/120 (39%), Gaps = 9/120 (7%)
Query: 2 SSGHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEV 61
S H + + ++ + + P + V LS T ++
Sbjct: 4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDL 63
Query: 62 RELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
RE+F YG + + IV R + FV+ ++ D + + NGM +DG+ ++V +
Sbjct: 64 REVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123
Score = 41.3 bits (97), Expect = 6e-05
Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 8/58 (13%)
Query: 297 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ + + ++ T+ +R +F KYG + + +V + + FV
Sbjct: 36 HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93
Score = 33.5 bits (77), Expect = 0.028
Identities = 5/33 (15%), Positives = 20/33 (60%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
EN ++ + A + NG ++ + ++++ + +++
Sbjct: 95 FENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 69.5 bits (171), Expect = 3e-15
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-D 89
GP VFVG+LS + F P+G + + +V + YGFV + D
Sbjct: 1 GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 90 INKCIKELNGMMVDGKPMKVVVA 112
I+++ G + G+ ++ A
Sbjct: 61 AENAIQQMGGQWLGGRQIRTNWA 83
Score = 43.3 bits (103), Expect = 5e-06
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
F +F+G+++P + I F +G++ + VV K YGFV
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFV 53
Score = 34.1 bits (79), Expect = 0.010
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
N + AI+++ GQ + + ++ AT +
Sbjct: 55 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 70.0 bits (172), Expect = 3e-15
Identities = 17/76 (22%), Positives = 40/76 (52%), Gaps = 7/76 (9%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHIDSPDI-NKCIKE 96
+ +F+ NL + + + F +G ++ C +V + YGFVH ++ + + I++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 64
Query: 97 LNGMMVDGKPMKVVVA 112
+NGM+++ + + V
Sbjct: 65 MNGMLLNDRKVFVGRF 80
Score = 54.2 bits (131), Expect = 2e-09
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK-------GPNTPTTKVFVGNLSDNT 56
H E E AI+++NG ++N++ + + SRK T V++ N +
Sbjct: 51 HFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGS 109
Score = 43.4 bits (103), Expect = 8e-06
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFV 346
+G+ IFI N++ + + F +G ++ C VV K YGFV
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFV 50
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCI 94
G + K+++GNLS A ++R+LF + ++ Y FV + I
Sbjct: 3 SGSSGMN-KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAI 61
Query: 95 KELNGMM-VDGKPMKVVVA 112
+ L+G + + GK M+V +
Sbjct: 62 ETLSGKVELHGKIMEVDYS 80
Score = 50.3 bits (121), Expect = 2e-08
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
S G K++IGN++P + + +R LF + V+ Y FV
Sbjct: 4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFV 49
Score = 33.8 bits (78), Expect = 0.013
Identities = 7/35 (20%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 5 HMENDEEGRTAIKELNGQI-VNEKPLKIEAATSRK 38
+ AI+ L+G++ ++ K ++++ + S+K
Sbjct: 50 DYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK 84
>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 = 69.6 bits (171), Expect = 3e-15
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 10/88 (11%)
Query: 35 TSRKGPNT-PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI 85
+ GP+ + V NL+ T +R +F YG V + I R + FV
Sbjct: 3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Query: 86 DSP-DINKCIKELNGMMVDGKPMKVVVA 112
D ++G +DG+ ++V VA
Sbjct: 63 HDRRDAQDAEAAMDGAELDGRELRVQVA 90
Score = 43.0 bits (102), Expect = 8e-06
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 8/49 (16%)
Query: 306 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
G + + N+ TS + +R +FEKYG+V + + + + FV
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60
Score = 34.5 bits (80), Expect = 0.009
Identities = 6/39 (15%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKI-EAATSRKGPNTP 43
+ + + A ++G ++ + L++ A R+ + P
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGP 100
>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 = 69.6 bits (171), Expect = 4e-15
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 9/89 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 84
++ G T ++VG L++ + F+P+G + + I R + FV
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+ D I +N + G+ ++V +A
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLA 89
Score = 40.3 bits (95), Expect = 9e-05
Identities = 5/46 (10%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+++G + +++ F +G + + + + + FV
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 59
Score = 35.7 bits (83), Expect = 0.004
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
E E+ AI +N + + +++ A +
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKE 96
>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 = 71.0 bits (174), Expect = 4e-15
Identities = 24/121 (19%), Positives = 45/121 (37%), Gaps = 15/121 (12%)
Query: 7 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT------PTTKVFVGNLSDNTRAPE 60
E + ++G+ + K T + T + V NL+ T
Sbjct: 27 EKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDT 86
Query: 61 VRELFVPYGTVVECDIVRNY--------GFVHIDSP-DINKCIKELNGMMVDGKPMKVVV 111
+R +F YG V + I R+ FV D + ++G ++DG+ ++V +
Sbjct: 87 LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
Query: 112 A 112
A
Sbjct: 147 A 147
Score = 44.1 bits (104), Expect = 1e-05
Identities = 13/60 (21%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNY--------GFV 346
+ G + + N+ TS + +R +FEKYG+V + + ++ FV
Sbjct: 58 SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117
Score = 34.0 bits (78), Expect = 0.031
Identities = 5/36 (13%), Positives = 19/36 (52%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
+ + A+ ++G +++ + L+++ A + P+
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 154
>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 = 69.2 bits (170), Expect = 4e-15
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 7/84 (8%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHID 86
++ + ++VGNLS + + +LF G C ++ Y FV
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFY 63
Query: 87 SP-DINKCIKELNGMMVDGKPMKV 109
D + +NG + GK +KV
Sbjct: 64 EHRDAAAALAAMNGRKILGKEVKV 87
Score = 39.2 bits (92), Expect = 2e-04
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFV 346
+ +++GN++ + LI LF + G C ++ Y FV
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
Score = 31.8 bits (73), Expect = 0.080
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ A+ +NG+ + K +K+ AT+
Sbjct: 61 EFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS 94
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 68.3 bits (168), Expect = 5e-15
Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIK 95
++VG L++ + F+P+G + + I R + FV + D I
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 96 ELNGMMVDGKPMKVVVA 112
+N + G+ ++V +A
Sbjct: 68 NMNESELFGRTIRVNLA 84
Score = 42.1 bits (100), Expect = 1e-05
Identities = 5/46 (10%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+++G + +++ F +G + + + + + FV
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 54
Score = 31.0 bits (71), Expect = 0.11
Identities = 6/29 (20%), Positives = 13/29 (44%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAA 34
E E+ AI +N + + +++ A
Sbjct: 56 FELAEDAAAAIDNMNESELFGRTIRVNLA 84
>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 = 68.3 bits (168), Expect = 6e-15
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 10/80 (12%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---------RNYGFVHIDSP-DINK 92
TKV +G L+ N + E+F YG + D+ + Y +V ++P + K
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 93 CIKELNGMMVDGKPMKVVVA 112
+K ++G +DG+ +
Sbjct: 63 ALKHMDGGQIDGQEITATAV 82
Score = 40.6 bits (96), Expect = 5e-05
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 9/52 (17%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFV 346
S+ K+ IG + + + I +F YGK+ D+ Y +V
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYV 52
Score = 34.4 bits (80), Expect = 0.006
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
EN +E A+K ++G ++ + + A +
Sbjct: 54 FENPDEAEKALKHMDGGQIDGQEITATAVLAPW 86
>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 = 68.8 bits (169), Expect = 6e-15
Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 12/89 (13%)
Query: 33 AATSRKGPNT---PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YG 81
++ GPN + V NLS++TR +++ELF P+G++ + ++ +
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 82 FVHIDSP-DINKCIKELNGMMVDGKPMKV 109
F+ D + I ++G D + V
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNV 89
Score = 44.5 bits (106), Expect = 3e-06
Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ P + I + N++ T ++ LF +G + + K+ + F+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Score = 35.3 bits (82), Expect = 0.004
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 44
E+ AI ++G + L +E A + P+
Sbjct: 63 SFHRREDAARAIAGVSGFGYDHLILNVEWAKPST-NSGPS 101
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 68.1 bits (167), Expect = 1e-14
Identities = 15/95 (15%), Positives = 34/95 (35%), Gaps = 5/95 (5%)
Query: 18 ELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV 77
+ G P ++ P T ++GN+ ++ LF +G +++
Sbjct: 3 QTIGLPPQVNPQAVDHIIRSAPPRV--TTAYIGNIPHFATEADLIPLFQNFGFILDFKHY 60
Query: 78 --RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKV 109
+ F+ D+ + CI L G+ ++
Sbjct: 61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95
Score = 46.5 bits (111), Expect = 4e-07
Identities = 9/51 (17%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 298 NMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
++ + +IGN+ + + PLF+ +G +++ K F+
Sbjct: 18 HIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFI 68
Score = 28.4 bits (64), Expect = 0.98
Identities = 5/32 (15%), Positives = 9/32 (28%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+ E+ I L + L+ R
Sbjct: 70 YDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101
>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 = 67.2 bits (165), Expect = 1e-14
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 9/78 (11%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DIN 91
++ ++ +++ L T ++ +L PYG +V + + YGFV DSP
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 92 KCIKELNGMMVDGKPMKV 109
K + L V + K
Sbjct: 62 KAVTALKASGVQAQMAKQ 79
Score = 41.7 bits (99), Expect = 2e-05
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 8/51 (15%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
S G+ ++I + PGT+ + + L + YGK+V + K YGFV
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFV 52
Score = 32.9 bits (76), Expect = 0.021
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATS 36
++ + A+ L V + K +S
Sbjct: 54 FDSPSAAQKAVTALKASGVQAQMAKQSGPSS 84
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 68.1 bits (167), Expect = 2e-14
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCI 94
K+F+G L+ T ++ +F +G + E ++ R + F+ ++P D
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 95 KELNGMMVDGKPMKVVVA 112
K++NG + GK +KV A
Sbjct: 66 KDMNGKSLHGKAIKVEQA 83
Score = 46.2 bits (110), Expect = 1e-06
Identities = 12/46 (26%), Positives = 27/46 (58%), Gaps = 7/46 (15%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
K+FIG +N T+ ++++ +F K+G + E ++K+ + F+
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFI 53
Score = 33.5 bits (77), Expect = 0.023
Identities = 10/36 (27%), Positives = 20/36 (55%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
EN + + A K++NG+ ++ K +K+E A +
Sbjct: 55 FENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 67.7 bits (166), Expect = 2e-14
Identities = 16/88 (18%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHI 85
+ R + K+F+ L + E+ E+ +GTV + +V N +V
Sbjct: 6 SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEY 65
Query: 86 DSP-DINKCIKELNGMMVDGKPMKVVVA 112
++ ++ + +++GM + +KV ++
Sbjct: 66 ENESQASQAVMKMDGMTIKENIIKVAIS 93
Score = 40.7 bits (96), Expect = 6e-05
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 7/51 (13%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
+S+ K+FI + + E + + + +G V + +V N +V
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYV 63
Score = 36.5 bits (85), Expect = 0.002
Identities = 7/33 (21%), Positives = 17/33 (51%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
EN+ + A+ +++G + E +K+ + S
Sbjct: 65 YENESQASQAVMKMDGMTIKENIIKVAISNSGP 97
>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 = 67.7 bits (166), Expect = 2e-14
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 36 SRKGPNTPT-TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGFVHIDSP- 88
+GP +++VGNL + R ++ ++F YG + + D+ + FV + P
Sbjct: 13 VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPR 72
Query: 89 DINKCIKELNGMMVDGKPMKVVVA 112
D + +G DG ++V
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFP 96
Score = 41.9 bits (99), Expect = 3e-05
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----KNYGFV 346
+I++GN+ P + I +F KYG + + D+ + FV
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFV 66
Score = 29.2 bits (66), Expect = 0.64
Identities = 7/37 (18%), Positives = 15/37 (40%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
E+ + A+ +G + L++E S +G
Sbjct: 67 EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTG 103
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 84
++ G + K+FVG LS +T + ++F YG + E +V R +GFV
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVVA 112
++ D + +NG VDG+ ++V A
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
Score = 43.0 bits (102), Expect = 1e-05
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+F+G ++ T+ + + +F KYG++ E VVK+ +GFV
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFV 59
Score = 33.4 bits (77), Expect = 0.019
Identities = 8/39 (20%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTP 43
EN ++ + A+ +NG+ V+ + ++++ A + P
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGP 99
>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 = 66.9 bits (164), Expect = 4e-14
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 34 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI 85
A + + + +++VG+L N +R +F P+G + ++ + YGF+
Sbjct: 16 ANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 86 DSPDI-NKCIKELNGMMVDGKPMKVVVA 112
+ K +++LNG + G+PMKV
Sbjct: 76 SDSECAKKALEQLNGFELAGRPMKVGHV 103
Score = 42.3 bits (100), Expect = 2e-05
Identities = 12/57 (21%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 298 NMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
N S G ++++G+++ + +++R +FE +G++ ++ K YGF+
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73
Score = 36.1 bits (84), Expect = 0.003
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ E + A+++LNG + +P+K+ T R
Sbjct: 75 FSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107
>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 = 67.5 bits (165), Expect = 5e-14
Identities = 22/79 (27%), Positives = 32/79 (40%), Gaps = 9/79 (11%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKC 93
+ V + ++R+LF YG + IV R YGFV S +
Sbjct: 41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100
Query: 94 IKELNGMMVDGKPMKVVVA 112
I LNG + K +KV +A
Sbjct: 101 IAGLNGFNILNKRLKVALA 119
Score = 39.0 bits (91), Expect = 5e-04
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ + + +R LFE+YG + +V + YGFV
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89
Score = 36.6 bits (85), Expect = 0.003
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGN 51
++ + AI LNG + K LK+ A S P VG+
Sbjct: 91 FQSGSSAQQAIAGLNGFNILNKRLKVALAASG--HQRPGIAGAVGD 134
>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 = 66.1 bits (162), Expect = 6e-14
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 9/88 (10%)
Query: 34 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI 85
+ G + V+V NL + ++ +F YG VV+ I+ + F+
Sbjct: 6 SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
Query: 86 DSP-DINKCIKELNGMMVDGKPMKVVVA 112
C + +N + G+ +K +A
Sbjct: 66 LDKDSAQNCTRAINNKQLFGRVIKASIA 93
Score = 41.1 bits (97), Expect = 3e-05
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 299 MPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
M G + +++ N+ + + +F KYGKVV+ ++K+ F+
Sbjct: 8 MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63
Score = 31.8 bits (73), Expect = 0.074
Identities = 3/29 (10%), Positives = 12/29 (41%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAA 34
+ + + + +N + + + +K A
Sbjct: 65 FLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 67.1 bits (164), Expect = 6e-14
Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 9/90 (10%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY--------GFV 83
+ T + V NL+ T +R +F YG V + I R+ FV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 84 HIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
D + ++G ++DG+ ++V +A
Sbjct: 95 RFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
Score = 42.8 bits (101), Expect = 2e-05
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 8/60 (13%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNY--------GFV 346
+ P G + + N+ TS + +R +FEKYG+V + + ++ FV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Score = 32.0 bits (73), Expect = 0.12
Identities = 4/33 (12%), Positives = 17/33 (51%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ + A+ ++G +++ + L+++ A +
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128
>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 = 65.7 bits (161), Expect = 6e-14
Identities = 14/79 (17%), Positives = 36/79 (45%), Gaps = 10/79 (12%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---------RNYGFVHIDSP-DI 90
++ ++ +F+GNL + + F +G +++ + + Y F++ S
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 91 NKCIKELNGMMVDGKPMKV 109
+ I+ +NG + +P+ V
Sbjct: 62 DAAIEAMNGQYLCNRPITV 80
Score = 43.0 bits (102), Expect = 8e-06
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 9/52 (17%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV---------KNYGFV 346
S G+ IFIGN++P +L+ F +G +++ + K Y F+
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFI 53
Score = 38.3 bits (90), Expect = 3e-04
Identities = 7/38 (18%), Positives = 18/38 (47%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 42
+ + + AI+ +NGQ + +P+ + A + +
Sbjct: 54 NFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGS 91
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 66.8 bits (163), Expect = 7e-14
Identities = 11/106 (10%), Positives = 34/106 (32%), Gaps = 10/106 (9%)
Query: 17 KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRE----LFVPYGTVV 72
KE + + S P+ V + N++ +++ L G ++
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61
Query: 73 ECDIVRN-----YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVVVA 112
+ + + ++ + + ++ G G P+ + +
Sbjct: 62 DIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 107
Score = 33.3 bits (76), Expect = 0.029
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 9/47 (19%)
Query: 309 KIFIGNVNPGTSVE----LIRPLFEKYGKVVECDVVKN-----YGFV 346
+ I N+NP E L+ L G +++ V + ++
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYI 77
Score = 32.6 bits (74), Expect = 0.070
Identities = 5/33 (15%), Positives = 11/33 (33%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E + ++ G PL I + + +
Sbjct: 79 FATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111
>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 = 65.7 bits (161), Expect = 7e-14
Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DI 90
++ + ++FV NLS + ++ +LF YG + E + + FV P
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 91 NKCIKELNGMMVDGKPMKVVVA 112
K E++G + G+ + V+ +
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPS 85
Score = 41.4 bits (98), Expect = 3e-05
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 8/52 (15%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
S G+ ++F+ N++ +S E + LF YG + E + + FV
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFV 55
Score = 36.4 bits (85), Expect = 0.002
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E A E++GQ+ + L + +T +K
Sbjct: 57 FMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK 89
>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 = 65.7 bits (161), Expect = 7e-14
Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 97
++VGNL + + +V+ELF +G V ++ + +GFV + +++ I +L
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62
Query: 98 NGMMVDGKPMKVVVA 112
+ G+ ++V A
Sbjct: 63 DNTDFMGRTIRVTEA 77
Score = 37.1 bits (87), Expect = 7e-04
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
I++GN+ + E ++ LF ++GKV ++ K +GFV
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV 48
Score = 31.8 bits (73), Expect = 0.059
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
+E AI +L+ + +++ A +K
Sbjct: 51 QEESVSEAIAKLDNTDFMGRTIRVTEANPKKSLE 84
>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 = 65.4 bits (160), Expect = 1e-13
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 84
++ V+VG L + P + ELF+ G VV + + YGFV
Sbjct: 4 GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKV 109
S D + IK ++ + + GKP++V
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRV 89
Score = 37.2 bits (87), Expect = 0.001
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+++G ++ S L+ LF + G VV + K+ YGFV
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV 62
Score = 34.5 bits (80), Expect = 0.008
Identities = 7/33 (21%), Positives = 18/33 (54%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
++E+ AIK ++ + KP+++ A++
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN 96
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 65.4 bits (160), Expect = 1e-13
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 101
KV+VGNL E+ F YG + I RN + FV + P D ++ L+G +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 102 VDGKPMKVVVA 112
+ G ++V ++
Sbjct: 62 ICGSRVRVELS 72
Score = 44.2 bits (105), Expect = 4e-06
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFV 346
K+++GN+ G + F YG + + +N + FV
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFV 42
Score = 28.0 bits (63), Expect = 1.7
Identities = 6/32 (18%), Positives = 18/32 (56%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
E+ + A++ L+G+++ +++E +T
Sbjct: 44 FEDPRDAEDAVRGLDGKVICGSRVRVELSTGM 75
>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 = 65.5 bits (160), Expect = 1e-13
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 6/81 (7%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----YGFVHIDSP-DIN 91
+ P +++ NL A E+ ++F YG + + + +V + D
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 92 KCIKELNGMMVDGKPMKVVVA 112
+ L+G V + + V+
Sbjct: 62 NAVDHLSGFNVSNRYLVVLYY 82
Score = 40.0 bits (94), Expect = 1e-04
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 5/42 (11%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-----YGFV 346
++I N+ + E + +F KYG + + V +V
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYV 52
Score = 32.3 bits (74), Expect = 0.071
Identities = 6/34 (17%), Positives = 16/34 (47%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKG 39
E+ + + A+ L+G V+ + L + + +
Sbjct: 54 YEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRA 87
>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 = 64.5 bits (158), Expect = 2e-13
Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI-N 91
++ ++ ++VG+L N +R +F P+G + ++ + YGF+ +
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 92 KCIKELNGMMVDGKPMKVVVA 112
+ +++LNG + G+PM+V
Sbjct: 62 RALEQLNGFELAGRPMRVGHV 82
Score = 41.0 bits (97), Expect = 3e-05
Identities = 12/51 (23%), Positives = 29/51 (56%), Gaps = 8/51 (15%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
S G+ +++G+++ + +++R +FE +GK+ ++ K YGF+
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFI 52
Score = 34.5 bits (80), Expect = 0.008
Identities = 11/41 (26%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK-GPNTPTT 45
+ E R A+++LNG + +P+++ T R G + P++
Sbjct: 54 FSDSECARRALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 64.6 bits (158), Expect = 2e-13
Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 11/91 (12%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHI 85
++ + K+FVG L+ +V LF P+G + EC ++R FV
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKF 63
Query: 86 DSPDI-NKCIKELNGMMV---DGKPMKVVVA 112
S I L+G + V A
Sbjct: 64 SSHTEAQAAIHALHGSQTMPGASSSLVVKFA 94
Score = 44.6 bits (106), Expect = 3e-06
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
K+F+G +N S E + LF+ +G + EC V++ FV
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFV 61
Score = 28.0 bits (63), Expect = 1.6
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 3/36 (8%)
Query: 6 MENDEEGRTAIKELNGQIVNE---KPLKIEAATSRK 38
+ E + AI L+G L ++ A + K
Sbjct: 63 FSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK 98
>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 = 65.6 bits (161), Expect = 4e-13
Identities = 25/115 (21%), Positives = 48/115 (41%), Gaps = 11/115 (9%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELF 65
E +K I++ K + + A R + T K+FVG + + R E E F
Sbjct: 52 FEKPSSVDEVVK--TQHILDGKVIDPKRAIPRDEQD-KTGKIFVGGIGPDVRPKEFEEFF 108
Query: 66 VPYGTVVECDIV--------RNYGFVHIDSPDINKCIKELNGMMVDGKPMKVVVA 112
+GT+++ ++ R +GFV DS D + + + + +++ A
Sbjct: 109 SQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRA 163
Score = 54.8 bits (133), Expect = 2e-09
Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 11/75 (14%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCI 94
+ K+F+G L+ +T +RE F YGTV + I+++ +GF+ + P +++ +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 95 KELNGMMVDGKPMKV 109
K + ++DGK +
Sbjct: 63 KTQH--ILDGKVIDP 75
Score = 47.5 bits (114), Expect = 8e-07
Identities = 15/46 (32%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG +N T+ + +R F KYG V + ++K+ +GF+
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFL 50
Score = 47.1 bits (113), Expect = 9e-07
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 297 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
R +P T KIF+G + P + F ++G +++ ++ + +GFV
Sbjct: 77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV 134
>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 = 63.5 bits (155), Expect = 4e-13
Identities = 11/86 (12%), Positives = 33/86 (38%), Gaps = 5/86 (5%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHIDS 87
++ + + + + NLS + ++E+F + + Y F+ S
Sbjct: 3 SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFAS 62
Query: 88 P-DINKCIKELNGMMVDGKPMKVVVA 112
D + + N ++G+ +++ +
Sbjct: 63 FEDAKEALNSCNKREIEGRAIRLELQ 88
Score = 36.5 bits (85), Expect = 0.002
Identities = 8/42 (19%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----KNYGFV 346
+ + N++ + E ++ +FEK + K Y F+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFI 58
Score = 34.2 bits (79), Expect = 0.012
Identities = 7/36 (19%), Positives = 17/36 (47%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
+ E+ + A+ N + + + +++E R PN
Sbjct: 60 FASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95
>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 = 66.1 bits (161), Expect = 5e-13
Identities = 19/145 (13%), Positives = 49/145 (33%), Gaps = 40/145 (27%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP------------------------ 40
M + + + A+ LNG ++ KP++I + +
Sbjct: 47 QMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 106
Query: 41 ----------NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHID 86
P+ + + N+ + +++ LF G VV+ R + +
Sbjct: 107 KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMG 166
Query: 87 SPDI-NKCIKELNG-MMVDGKPMKV 109
S + + + +L+ + + ++V
Sbjct: 167 SVEEAVQALIDLHNHDLGENHHLRV 191
Score = 55.7 bits (134), Expect = 2e-09
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 44 TTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELN 98
+ + V NL+ + + LF YG V I+ N V + + LN
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 99 GMMVDGKPMKVVVA 112
G + GKP+++ ++
Sbjct: 63 GHKLHGKPIRITLS 76
Score = 38.3 bits (89), Expect = 0.002
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----KNYGFV 346
+ + + N+ P S E ++ LF G VV+ + +
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALI 163
Score = 37.2 bits (86), Expect = 0.003
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 305 VGTFKIFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKN---YGFV 346
+G + + N+NP + + + LF YG V ++ N V
Sbjct: 1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALV 46
Score = 29.1 bits (65), Expect = 1.7
Identities = 7/34 (20%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 5 HMENDEEGRTAIKELNG-QIVNEKPLKIEAATSR 37
M + EE A+ +L+ + L++ + S
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197
>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 = 63.0 bits (154), Expect = 8e-13
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 10/74 (13%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSPD-INKCIK 95
VFVG + E+R F YG+V E I+ + YGFV + + K ++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 96 ELNGMMVDGKPMKV 109
+ + GK +K+
Sbjct: 69 --SQINFHGKKLKL 80
Score = 46.5 bits (111), Expect = 5e-07
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
+F+G ++ IR F +YG V E ++ + YGFV
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFV 55
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 9/76 (11%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDI-NKC 93
P+ V++G++ + ++ +L G V+ ++ + Y F+ +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 94 IKELNGMMVDGKPMKV 109
++ LNG + + +K
Sbjct: 61 VRNLNGYQLGSRFLKC 76
Score = 38.8 bits (91), Expect = 3e-04
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+++G++ + E I L G V+ ++ K Y F+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFI 49
Score = 34.9 bits (81), Expect = 0.006
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTP 43
+ E +A++ LNG + + LK +++
Sbjct: 51 FRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGVS 88
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 64.2 bits (157), Expect = 2e-12
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 8/104 (7%)
Query: 17 KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDI 76
+++G++V K + R G + K+FVG + ++T +R+ F YG + +I
Sbjct: 77 HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEI 136
Query: 77 V--------RNYGFVHIDSPDINKCIKELNGMMVDGKPMKVVVA 112
+ R + FV D D I V+G +V A
Sbjct: 137 MTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA 180
Score = 51.1 bits (123), Expect = 8e-08
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCI 94
K+F+G LS T +R F +GT+ +C ++R+ +GFV + + ++ +
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Query: 95 KELNGMMVDGKPMKV 109
VDG+ ++
Sbjct: 73 NA-RPHKVDGRVVEP 86
Score = 47.7 bits (114), Expect = 1e-06
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ + KIF+G + T +R FE+YGK+ +++ + + FV
Sbjct: 97 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151
Score = 47.3 bits (113), Expect = 1e-06
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 16/84 (19%), Positives = 37/84 (44%), Gaps = 11/84 (13%)
Query: 40 PNT-PTTKVFVGNLSDNTRAPEVRE----LFVPYGTVVECDIVRN-----YGFVHIDSPD 89
P T P +++ NL++ + E+++ +F +G +++ + R+ FV
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 90 I-NKCIKELNGMMVDGKPMKVVVA 112
++ + G KPM++ A
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYA 86
Score = 34.1 bits (79), Expect = 0.010
Identities = 6/32 (18%), Positives = 15/32 (46%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+ A++ + G +KP++I+ A +
Sbjct: 58 FKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89
Score = 32.2 bits (74), Expect = 0.044
Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 310 IFIGNVNPGTSVELIR----PLFEKYGKVVECDVVKN-----YGFV 346
I+I N+N + ++ +F ++G++++ V ++ FV
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFV 56
>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 = 14/82 (17%), Positives = 31/82 (37%), Gaps = 8/82 (9%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI 90
G ++VGN+ A E+ F G+V I+ + + ++ +
Sbjct: 1 GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
Query: 91 NKCIKELNGMMVDGKPMKVVVA 112
+ L+ + G+ +KV+
Sbjct: 61 VRTSLALDESLFRGRQIKVIPK 82
Score = 39.8 bits (94), Expect = 1e-04
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 8/48 (16%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
I++GNV+ G + E + F G V ++ K + ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI 53
Score = 26.7 bits (60), Expect = 3.2
Identities = 4/30 (13%), Positives = 12/30 (40%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
D+E L+ + + +K+ + +
Sbjct: 57 DKESVRTSLALDESLFRGRQIKVIPKRTNR 86
>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 = 60.8 bits (148), Expect = 5e-12
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-D 89
++ R+ P T ++V + +R F P+G +++ + RN FV +
Sbjct: 5 SSGERRAPRKGNT-LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES 61
Query: 90 INKCIKELNGMMVDGKPMKVVVA 112
++ + ELNG V+ +KV +A
Sbjct: 62 ADQAVAELNGTQVESVQLKVNIA 84
Score = 35.0 bits (81), Expect = 0.006
Identities = 7/39 (17%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+++ + + L+R F +G +++ + +N FV
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFV 54
Score = 30.7 bits (70), Expect = 0.15
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
E E A+ ELNG V LK+ A + +
Sbjct: 56 YEKMESADQAVAELNGTQVESVQLKVNIARKQPMLD 91
>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 = 62.1 bits (151), Expect = 6e-12
Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS 87
++ + ++VGNLS T ++ ELF G + + + + + FV S
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 88 P-DINKCIKELNGMMVDGKPMKV 109
D ++ +NG +D + ++
Sbjct: 91 RADAENAMRYINGTRLDDRIIRT 113
Score = 38.2 bits (89), Expect = 0.001
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+++GN++ T+ E I LF K G + + + + + FV
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86
Score = 32.1 bits (73), Expect = 0.14
Identities = 4/33 (12%), Positives = 16/33 (48%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ + A++ +NG ++++ ++ + K
Sbjct: 88 YYSRADAENAMRYINGTRLDDRIIRTDWDAGFK 120
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 60.0 bits (146), Expect = 6e-12
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 39 GPNTPT-TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCI 94
T T ++VG L D ++R F +G + +V + F+ +
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAA 65
Query: 95 KE-LNGMMVDGKPMKV 109
++ N ++V+G+ + V
Sbjct: 66 EKSFNKLIVNGRRLNV 81
Score = 43.8 bits (104), Expect = 3e-06
Identities = 7/40 (17%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+++G + + +R F ++G++ VV + F+
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFI 53
>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 = 60.9 bits (148), Expect = 7e-12
Identities = 24/115 (20%), Positives = 46/115 (40%), Gaps = 10/115 (8%)
Query: 1 MSSGHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPE 60
M S H + G + + ++ R+ P T ++V +
Sbjct: 1 MGSSHHHHHHSSGLV---PRGSHMGPFR-RSDSFPERRAPRKGNT-LYVYGE--DMTPTL 53
Query: 61 VRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
+R F P+G +++ + RN FV + ++ + ELNG V+ +KV +A
Sbjct: 54 LRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
Score = 37.0 bits (86), Expect = 0.002
Identities = 7/39 (17%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+++ + + L+R F +G +++ + +N FV
Sbjct: 42 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFV 78
Score = 32.8 bits (75), Expect = 0.052
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 44
E E A+ ELNG V LK+ A + + T
Sbjct: 80 YEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDAAT 118
>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 = 60.4 bits (147), Expect = 7e-12
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 11/88 (12%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---------YGFV 83
++ + T+K+ V N+ E+RELF +G + + + +GFV
Sbjct: 4 GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 84 HIDSP-DINKCIKEL-NGMMVDGKPMKV 109
+ D K L + + G+ + +
Sbjct: 64 DFITKQDAKKAFNALCHSTHLYGRRLVL 91
Score = 41.9 bits (99), Expect = 3e-05
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFV 346
T KI + N+ + IR LF +G++ + K +GFV
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
>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 = 8e-12
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 7/84 (8%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP 88
+T +F+GNL+ N E++ + +V R +G+V +S
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68
Query: 89 DINKCIKELNGMMVDGKPMKVVVA 112
+ + EL G+ V G +K+
Sbjct: 69 EDLEKALELTGLKVFGNEIKLEKP 92
Score = 42.2 bits (100), Expect = 2e-05
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
G S F +FIGN+NP SV ++ + + VV + +G+V
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63
Score = 31.5 bits (72), Expect = 0.087
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKG 39
E+ E+ A+ EL G V +K+E R G
Sbjct: 65 FESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDG 97
>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 = 60.9 bits (148), Expect = 8e-12
Identities = 12/89 (13%), Positives = 34/89 (38%), Gaps = 8/89 (8%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFV 83
+ ++ + V+VGN+ + A ++ F G++ I+ + Y ++
Sbjct: 24 QPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83
Query: 84 HIDSPDINKCIKELNGMMVDGKPMKVVVA 112
+ ++ + G+ +KV+
Sbjct: 84 EFAERNSVDAAVAMDETVFRGRTIKVLPK 112
Score = 39.7 bits (93), Expect = 2e-04
Identities = 8/46 (17%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+++GNV+ G++ + + F G + ++ K Y ++
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83
Score = 29.7 bits (67), Expect = 0.52
Identities = 2/33 (6%), Positives = 10/33 (30%), Gaps = 1/33 (3%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
A+ ++ + + +K+ +
Sbjct: 85 FAERNSVDAAV-AMDETVFRGRTIKVLPKRTNM 116
>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 = 59.6 bits (145), Expect = 9e-12
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 10/81 (12%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHIDSP-DINK 92
+ NLS N E++E+F + +V ++ S D K
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIR---LVSQDGKSKGIAYIEFKSEADAEK 68
Query: 93 CIKELNGMMVDGKPMKVVVAG 113
++E G +DG+ + + G
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTG 89
Score = 33.4 bits (77), Expect = 0.020
Identities = 3/36 (8%), Positives = 15/36 (41%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
+++ + ++E G ++ + + + + G
Sbjct: 60 FKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95
Score = 32.6 bits (75), Expect = 0.032
Identities = 4/41 (9%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV---KNYGFV 346
+ N++ + + ++ +FE ++ K ++
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYI 58
>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 = 60.2 bits (146), Expect = 1e-11
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 3/68 (4%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDI--VRNYGFVHIDSP-DINKCIKELNGMM 101
T + NL T A E++E F +G++ + V P + K + L
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSK 70
Query: 102 VDGKPMKV 109
P+ +
Sbjct: 71 FHHVPLYL 78
Score = 39.4 bits (92), Expect = 2e-04
Identities = 8/39 (20%), Positives = 14/39 (35%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDV--VKNYGFV 346
I N+ GT I+ F ++G + + V
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIV 51
Score = 29.0 bits (65), Expect = 0.72
Identities = 10/42 (23%), Positives = 13/42 (30%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTK 46
E R A + L + PL +E A P K
Sbjct: 52 EFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKK 93
>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 = 61.4 bits (149), Expect = 1e-11
Identities = 21/134 (15%), Positives = 45/134 (33%), Gaps = 30/134 (22%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT---------------------PT 44
E DE+G I L + + K + ++ +
Sbjct: 13 FEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEG 72
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 95
+FV ++ + + E++E F YG + + + Y V ++ +
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 96 ELNGMMVDGKPMKV 109
LNG + G+ ++V
Sbjct: 133 ALNGAEIMGQTIQV 146
Score = 42.1 bits (99), Expect = 5e-05
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
SV + +F+ +++ + I+ F YG++ + K Y V
Sbjct: 69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119
Score = 37.1 bits (86), Expect = 0.002
Identities = 5/36 (13%), Positives = 15/36 (41%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
E ++ A + LNG + + ++++ +
Sbjct: 121 YETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 156
>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 = 59.6 bits (145), Expect = 1e-11
Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 12/92 (13%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH 84
++ S + K+F+G + N +++ LF +G + E ++++ F+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 85 IDSP-DINKCIKELNGMMV---DGKPMKVVVA 112
K L+ +P++V A
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPA 93
Score = 45.8 bits (109), Expect = 9e-07
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG + + ++PLFE++GK+ E V+K+ F+
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Score = 28.8 bits (65), Expect = 0.82
Identities = 7/36 (19%), Positives = 13/36 (36%), Gaps = 3/36 (8%)
Query: 6 MENDEEGRTAIKELNGQIVNE---KPLKIEAATSRK 38
E A L+ Q +P++++ A S
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPADSES 97
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 58.9 bits (143), Expect = 2e-11
Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 3/67 (4%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSPDINKCIKELNGMMV 102
VFV + ++ E F+ +G V + ++ + V + + + + +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSL 69
Query: 103 DGKPMKV 109
G ++V
Sbjct: 70 GGHRLRV 76
Score = 45.4 bits (108), Expect = 9e-07
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 3/46 (6%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFV 346
S G +F+ G + F +G V + K+ + V
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIV 50
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 58.5 bits (142), Expect = 3e-11
Identities = 15/88 (17%), Positives = 36/88 (40%), Gaps = 15/88 (17%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGT--VVECDIVRN--------YGFVHIDSP- 88
+ + + N++ +T + PY + V ++++ + FV + S
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 89 DINKCIKELNGM----MVDGKPMKVVVA 112
D ++ ++ L + +DGK + V A
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFA 92
Score = 40.4 bits (95), Expect = 6e-05
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGK--VVECDVVKN--------YGFV 346
I + N+ P T V+ I Y V ++K+ + FV
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFV 58
>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 = 59.3 bits (144), Expect = 3e-11
Identities = 13/94 (13%), Positives = 34/94 (36%), Gaps = 9/94 (9%)
Query: 25 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 77
+ ++ + + +FV + + ++ + F YG + +
Sbjct: 3 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
Query: 78 -RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKV 109
+ Y V ++ ++ LNG + G+P+ V
Sbjct: 63 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
Score = 42.4 bits (100), Expect = 2e-05
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
SV + +F+ V+ + E I F +YG++ + K Y V
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69
Score = 36.6 bits (85), Expect = 0.003
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
E +E + A++ LNGQ + +P+ ++ R P
Sbjct: 71 YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK 106
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 61.3 bits (148), Expect = 3e-11
Identities = 18/116 (15%), Positives = 33/116 (28%), Gaps = 11/116 (9%)
Query: 8 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVP 67
D + V + K A +++GNL+ T ++ E
Sbjct: 32 GDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS 91
Query: 68 YGT--VVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
G ++E N + V + S K + L + G+ V
Sbjct: 92 LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPV 147
Score = 37.4 bits (86), Expect = 0.003
Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 10/62 (16%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKN--------YG 344
A N+ + ++IGN+ T+ E + G ++E +N +
Sbjct: 56 AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115
Query: 345 FV 346
V
Sbjct: 116 LV 117
Score = 31.6 bits (71), Expect = 0.32
Identities = 1/39 (2%), Positives = 12/39 (30%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 44
+ ++ + + L + ++ + + +
Sbjct: 119 VGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEM 157
Score = 26.6 bits (58), Expect = 9.9
Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 1/47 (2%)
Query: 205 SRRFGAVGGPGPLDRFGYPREAYPRDPYPP-PPPPSFLRDRMMGGYP 250
G G PG R +P+ R +P P G P
Sbjct: 168 MSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGP 214
>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 = 58.9 bits (143), Expect = 3e-11
Identities = 15/89 (16%), Positives = 27/89 (30%), Gaps = 8/89 (8%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFV 83
E + VF L+ R ++ + F G V + I+ + +V
Sbjct: 13 EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72
Query: 84 HIDSPDINKCIKELNGMMVDGKPMKVVVA 112
L G + G P+ V +
Sbjct: 73 EFCEIQSVPLAIGLTGQRLLGVPIIVQAS 101
Score = 38.5 bits (90), Expect = 4e-04
Identities = 7/46 (15%), Positives = 14/46 (30%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+F + + F GKV + ++ K +V
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72
Score = 28.8 bits (65), Expect = 0.90
Identities = 8/33 (24%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
+ AI L GQ + P+ ++A+ + K
Sbjct: 74 FCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEK 105
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 58.4 bits (142), Expect = 4e-11
Identities = 13/94 (13%), Positives = 34/94 (36%), Gaps = 9/94 (9%)
Query: 25 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 77
+ ++ + + +FV + + ++ + F YG + +
Sbjct: 4 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63
Query: 78 -RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKV 109
+ Y V ++ ++ LNG + G+P+ V
Sbjct: 64 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
Score = 39.9 bits (94), Expect = 1e-04
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
SV + +F+ V+ + E I F +YG++ + K Y V
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70
Score = 36.1 bits (84), Expect = 0.002
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP 40
E +E + A++ LNGQ + +P+ ++ R P
Sbjct: 72 YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP 106
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 59.5 bits (144), Expect = 4e-11
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 11/91 (12%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGT--VVECDIVRN--------YGF 82
+ G V+VG+ S T ++ ++ G VVE N Y
Sbjct: 44 ILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAE 103
Query: 83 VHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
V + S ++K ++ L G +++G+ + V A
Sbjct: 104 VVVASENSVHKLLELLPGKVLNGEKVDVRPA 134
Score = 34.5 bits (79), Expect = 0.022
Identities = 9/54 (16%), Positives = 19/54 (35%), Gaps = 10/54 (18%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKN--------YGFV 346
+++G+ + T+ + + + G VVE +N Y V
Sbjct: 51 LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEV 104
Score = 32.2 bits (73), Expect = 0.11
Identities = 5/35 (14%), Positives = 17/35 (48%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP 40
+ ++ ++ L G+++N + + + AT +
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 58.3 bits (141), Expect = 4e-11
Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 5/78 (6%)
Query: 37 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK- 95
G P+ + + L + EV L +P+G V +++ I+
Sbjct: 9 HHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTM 68
Query: 96 ----ELNGMMVDGKPMKV 109
++ G+P+ +
Sbjct: 69 VNYYTSVTPVLRGQPIYI 86
Score = 39.8 bits (93), Expect = 1e-04
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
I I + + + L +GKV ++ KN F+
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFI 57
>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 = 58.8 bits (142), Expect = 4e-11
Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 5/79 (6%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK 95
+ P+ + + L + EV L +P+G V +++ I+
Sbjct: 23 DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANT 82
Query: 96 -----ELNGMMVDGKPMKV 109
++ G+P+ +
Sbjct: 83 MVNYYTSVTPVLRGQPIYI 101
Score = 38.4 bits (89), Expect = 6e-04
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
I I + + + L +GKV ++ KN F+
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFI 72
>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 = 58.1 bits (141), Expect = 4e-11
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 15/86 (17%)
Query: 42 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINK 92
T VF+ NLS ++ + E+ +G + +V + F + K
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 93 CIKELN------GMMVDGKPMKVVVA 112
C+ + G+ +DG+ +KV +A
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLA 98
Score = 41.9 bits (99), Expect = 3e-05
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+FI N++ + E + + +++G + VV + F
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 57.5 bits (139), Expect = 5e-11
Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 13/92 (14%)
Query: 33 AATSRKGPNTP-------TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYG 81
++ GP +P V+VGNL + R +++ G V + R
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQGPRRRA 59
Query: 82 FVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
F+H + + L G+ + ++V +A
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
Score = 31.7 bits (72), Expect = 0.080
Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 3/50 (6%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKV---VECDVVKNYGFV 346
PG + +++GN+ V ++ + G V + + F+
Sbjct: 12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61
Score = 30.2 bits (68), Expect = 0.27
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
H + + A+ L G + L++ A ++
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR 95
>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 = 61.4 bits (148), Expect = 5e-11
Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRE----LFVPYGTVVECDIVRN-----YGFVHIDSPDI- 90
P +++ NL++ + E+++ +F +G +++ + R+ FV
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 91 NKCIKELNGMMVDGKPMKVVVA 112
++ + G KPM++ A
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA 87
Score = 51.8 bits (123), Expect = 1e-07
Identities = 18/78 (23%), Positives = 27/78 (34%), Gaps = 5/78 (6%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSPDI-NKCIK 95
N P +F+ NL + T + LF + E +V FV D+
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 96 ELNGM-MVDGKPMKVVVA 112
L G + MK+ A
Sbjct: 263 ALQGFKITQNNAMKISFA 280
Score = 35.2 bits (80), Expect = 0.022
Identities = 9/46 (19%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 310 IFIGNVNPGTSVE----LIRPLFEKYGKVVECDVVKN-----YGFV 346
I+I N+N + + +F ++G++++ V ++ FV
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFV 57
Score = 35.2 bits (80), Expect = 0.022
Identities = 12/111 (10%), Positives = 29/111 (26%), Gaps = 7/111 (6%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK-------GPNTPTTKVFVGNLSDNTR 57
+ A++ + G +KP++I+ A + G + +
Sbjct: 58 IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQE 117
Query: 58 APEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMK 108
P ++ G V+ + + + G P
Sbjct: 118 TPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPG 168
Score = 34.1 bits (77), Expect = 0.058
Identities = 22/140 (15%), Positives = 37/140 (26%), Gaps = 17/140 (12%)
Query: 210 AVGGPGPLDRFGYPREAYPRDPYPPPPPPSFLRDRMMGGYPMKFGLILIPRSQIESLDLC 269
AV G G G + P P P Y G+I P
Sbjct: 124 AVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLA------- 176
Query: 270 GHFKQTKTTIVWSPRYQSFGTVVVIEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFE 329
+ + P + +F+ N+ T+ ++ LF
Sbjct: 177 -------PGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFN 229
Query: 330 KYGKVVECDVV---KNYGFV 346
++ E +V + FV
Sbjct: 230 QFPGFKEVRLVPGRHDIAFV 249
>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 = 57.7 bits (140), Expect = 6e-11
Identities = 22/92 (23%), Positives = 38/92 (41%), Gaps = 15/92 (16%)
Query: 33 AATSRKGPNT---PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYG 81
++ GPN P+ +FV LS++T ++E F V IV + +G
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFG 57
Query: 82 FVHIDSP-DINKCIKELNGMMVDGKPMKVVVA 112
FV +S D + + +DG + + A
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89
Score = 34.9 bits (81), Expect = 0.006
Identities = 5/41 (12%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTPTT 45
++E+ + A + + ++ + ++ A + +G + P++
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
Score = 30.7 bits (70), Expect = 0.17
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 11/59 (18%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ P S + +F+ ++ T+ E ++ F V +V K +GFV
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFV 59
>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 = 57.7 bits (140), Expect = 6e-11
Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 11/95 (11%)
Query: 26 EKPLKIEAATSRKGPNT--PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------ 77
E+ + GP +FV ++ + + E++E F YG + +
Sbjct: 6 ERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTG 65
Query: 78 --RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKV 109
+ Y V ++ + LNG + G+ ++V
Sbjct: 66 FSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
Score = 40.7 bits (96), Expect = 7e-05
Identities = 10/51 (19%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
SV + +F+ +++ + I+ F YG++ + K Y V
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 73
Score = 35.3 bits (82), Expect = 0.005
Identities = 5/33 (15%), Positives = 15/33 (45%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E ++ A + LNG + + ++++ +
Sbjct: 75 YETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 9/76 (11%)
Query: 43 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKC 93
VFVGN+ +++++F G VV +V + YGF D
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 94 IKELNGMMVDGKPMKV 109
++ LNG G+ ++V
Sbjct: 67 MRNLNGREFSGRALRV 82
Score = 36.9 bits (86), Expect = 0.001
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+F+GN+ + E ++ +F + G VV +V K YGF
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFC 55
Score = 34.5 bits (80), Expect = 0.008
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
++ E +A++ LNG+ + + L+++ A S K
Sbjct: 57 YQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 56.9 bits (138), Expect = 1e-10
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFV-PYGTVVECDIVRN-------YGFVHIDSP- 88
G + P +FVG+L+ + + E FV Y + +V + YGFV
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDEL 62
Query: 89 DINKCIKELNG-MMVDGKPMKVVVA 112
+ + + E G + + KP+++ VA
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVA 87
Score = 32.6 bits (75), Expect = 0.036
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEK-YGKVVECDVV-------KNYGFV 346
+ +F+G++ P ++ F K Y VV K YGFV
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFV 56
Score = 29.9 bits (68), Expect = 0.40
Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 8 NDEEGRTAIKELNGQI-VNEKPLKIEAATSRK 38
++ E + A+ E G + + KP+++ A +
Sbjct: 60 DELEQKRALTECQGAVGLGSKPVRLSVAIPKA 91
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 11/78 (14%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGT--VVECDIVRN--------YGFVHIDSP-DINKCI 94
+++GNL+ T ++ E G ++E N + V + S K +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 95 KELNGMMVDGKPMKVVVA 112
L + G+ V +
Sbjct: 63 DLLPKRELHGQNPVVTPS 80
Score = 33.7 bits (78), Expect = 0.014
Identities = 1/32 (3%), Positives = 12/32 (37%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
+ ++ + + L + ++ + + +
Sbjct: 52 VGSEASSKKLMDLLPKRELHGQNPVVTPSNKL 83
Score = 31.0 bits (71), Expect = 0.099
Identities = 9/49 (18%), Positives = 18/49 (36%), Gaps = 10/49 (20%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKN--------YGFV 346
++IGN+ T+ E + G ++E +N + V
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 50
>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 = 19/72 (26%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---RNYGFVHIDSPDI-NKCIKE 96
++ ++ VFVG + + E+RE F YG V++ I R + FV I E
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE 61
Query: 97 ---LNGMMVDGK 105
+ G+ V
Sbjct: 62 DLIIKGISVHIS 73
Score = 48.0 bits (115), Expect = 1e-07
Identities = 10/41 (24%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK---NYGFV 346
+F+G + + +R F +YG V++ + K + FV
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFV 47
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 10/89 (11%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---------YGFV 83
++ + P +P F+GNL + ++E F + + R +G+
Sbjct: 4 GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 62
Query: 84 HIDSPDINKCIKELNGMMVDGKPMKVVVA 112
+ D LN + K ++V VA
Sbjct: 63 EFEDLDSLLSALSLNEESLGNKRIRVDVA 91
Score = 28.8 bits (65), Expect = 0.89
Identities = 6/33 (18%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E+ + +A+ LN + + K ++++ A +
Sbjct: 64 FEDLDSLLSALS-LNEESLGNKRIRVDVADQAQ 95
Score = 28.4 bits (64), Expect = 1.0
Identities = 7/48 (14%), Positives = 17/48 (35%), Gaps = 10/48 (20%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFV 346
+ F+GN+ + E I+ F + + + +G+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 62
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 56.0 bits (136), Expect = 2e-10
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDS 87
S + + K+FVG + N E+RE F +G V E ++ R +GF+ +
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 88 PDINKCIKELNGMMVDGKPMKV 109
++ + GK ++V
Sbjct: 62 EQSVDQAVNMHFHDIMGKKVEV 83
Score = 46.0 bits (110), Expect = 7e-07
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 307 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ KIF+G + +R F+K+G V E ++ + +GF+
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFI 57
>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 = 58.1 bits (140), Expect = 4e-10
Identities = 19/145 (13%), Positives = 50/145 (34%), Gaps = 40/145 (27%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE-------------------------------- 32
M + + + A+ LNG ++ KP++I
Sbjct: 78 QMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 137
Query: 33 --AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHID 86
+ + + P+ + + N+ + +++ LF G VV+ R + +
Sbjct: 138 KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMG 197
Query: 87 SPDI-NKCIKELNG-MMVDGKPMKV 109
S + + + +L+ + + ++V
Sbjct: 198 SVEEAVQALIDLHNHDLGENHHLRV 222
Score = 52.7 bits (126), Expect = 3e-08
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 5/78 (6%)
Query: 40 PNTPTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCI 94
+ + V NL+ + + LF YG V I+ N V + +
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAM 89
Query: 95 KELNGMMVDGKPMKVVVA 112
LNG + GKP+++ ++
Sbjct: 90 SHLNGHKLHGKPIRITLS 107
Score = 37.3 bits (86), Expect = 0.004
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 298 NMPGFSSVGTFKIFIGNVNPGT-SVELIRPLFEKYGKVVECDVVKN---YGFV 346
+PG + G + + N+NP + + + LF YG V ++ N V
Sbjct: 25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALV 77
Score = 36.5 bits (84), Expect = 0.006
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV----KNYGFV 346
+ + N+ P S E ++ LF G VV+ + +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALI 194
Score = 27.7 bits (61), Expect = 5.4
Identities = 7/34 (20%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 5 HMENDEEGRTAIKELNG-QIVNEKPLKIEAATSR 37
M + EE A+ +L+ + L++ + S
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 55.1 bits (133), Expect = 4e-10
Identities = 10/74 (13%), Positives = 23/74 (31%), Gaps = 5/74 (6%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK----- 95
+ V + L D ++ E +G + ++ ++ D+
Sbjct: 18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYA 77
Query: 96 ELNGMMVDGKPMKV 109
N + + G P V
Sbjct: 78 ADNQIYIAGHPAFV 91
Score = 37.8 bits (88), Expect = 6e-04
Identities = 6/39 (15%), Positives = 14/39 (35%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+ I + G + +++G + V+ K V
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALV 62
>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 = 55.2 bits (133), Expect = 6e-10
Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 4/81 (4%)
Query: 36 SRKGPNTPTT--KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-YGFVHIDSP-DIN 91
S GP + + +V V L + ++++ G V D+ R+ G V D+
Sbjct: 5 SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMT 64
Query: 92 KCIKELNGMMVDGKPMKVVVA 112
+++L+ +
Sbjct: 65 YAVRKLDNTKFRSHEGETAYI 85
Score = 38.2 bits (89), Expect = 5e-04
Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-YGFV 346
++ + + P S + ++ + G V DV ++ G V
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVV 55
Score = 26.3 bits (58), Expect = 6.3
Identities = 3/33 (9%), Positives = 10/33 (30%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E+ A+++L+ + +
Sbjct: 57 FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV 89
>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 = 54.9 bits (133), Expect = 6e-10
Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 10/82 (12%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---------YGFVHIDSPDI 90
P +P F+GNL + ++E F + + R +G+ + D
Sbjct: 15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS 73
Query: 91 NKCIKELNGMMVDGKPMKVVVA 112
LN + + ++V VA
Sbjct: 74 LLSALSLNEESLGNRRIRVDVA 95
Score = 29.1 bits (66), Expect = 0.59
Identities = 5/33 (15%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
E+ + +A+ LN + + + ++++ A +
Sbjct: 68 FEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ 99
Score = 28.4 bits (64), Expect = 1.1
Identities = 7/61 (11%), Positives = 18/61 (29%), Gaps = 10/61 (16%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGF 345
+ + F+GN+ + E I+ F + + + +G+
Sbjct: 7 HHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGY 65
Query: 346 V 346
Sbjct: 66 A 66
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 55.0 bits (133), Expect = 6e-10
Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 9/88 (10%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH 84
++ ++ P P +VGNL NT ++ +F + +VR+ + +V
Sbjct: 4 GSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVE 62
Query: 85 IDSPDINKCIKELNGMMVDGKPMKVVVA 112
D D K +G ++ + ++V +A
Sbjct: 63 FDEVDSLKEALTYDGALLGDRSLRVDIA 90
Score = 28.8 bits (65), Expect = 0.92
Identities = 6/36 (16%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 41
+ + + A+ +G ++ ++ L+++ A RK
Sbjct: 63 FDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDK 97
Score = 27.6 bits (62), Expect = 2.0
Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 9/59 (15%)
Query: 296 ARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ + + ++GN+ T I +F+ + +V K + +V
Sbjct: 4 GSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 55.1 bits (133), Expect = 7e-10
Identities = 18/91 (19%), Positives = 26/91 (28%), Gaps = 17/91 (18%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------------RNYGFVH 84
N+ +FV L +N V + F G + + V
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 85 -IDSPDINKCIKELNGMMVDGKPMKVVVAGF 114
D P I +G G P+KV A
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFATR 94
Score = 32.0 bits (73), Expect = 0.082
Identities = 5/28 (17%), Positives = 13/28 (46%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVE 336
IF+ + ++E + F++ G +
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKT 36
Score = 32.0 bits (73), Expect = 0.087
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 38
++ + AI +G+ + P+K+ AT R
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 54.8 bits (132), Expect = 9e-10
Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 4/81 (4%)
Query: 36 SRKGPNTPTT--KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-YGFVHIDSP-DIN 91
R GP + + +V V L + ++++ G V D+ R+ G V D+
Sbjct: 6 GRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMT 65
Query: 92 KCIKELNGMMVDGKPMKVVVA 112
+++L+ +
Sbjct: 66 YAVRKLDNTKFRSHEGETAYI 86
Score = 36.3 bits (84), Expect = 0.002
Identities = 8/40 (20%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 308 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-YGFV 346
++ + + P S + ++ + G V DV ++ G V
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVV 56
Score = 26.3 bits (58), Expect = 8.4
Identities = 3/38 (7%), Positives = 10/38 (26%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTP 43
E+ A+++L+ + +
Sbjct: 58 FVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRS 95
>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 = 54.0 bits (130), Expect = 1e-09
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELF-----------VPYGTVVECDIV--RNYGFVHI 85
GP +++VGN+ + + F P V+ I +N+ F+
Sbjct: 1 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
Query: 86 DSPDINKCIKELNGMMVDGKPMKV 109
S D +G++ G+ +K+
Sbjct: 61 RSVDETTQAMAFDGIIFQGQSLKI 84
Score = 29.3 bits (66), Expect = 0.38
Identities = 8/51 (15%), Positives = 19/51 (37%), Gaps = 13/51 (25%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------------KNYGFV 346
++++GN+ G + E + F ++ KN+ F+
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 58
>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 = 54.2 bits (131), Expect = 1e-09
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-IN 91
+T TK+FVG L +T +R+ F +G + E ++ + YGFV +
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 92 KCIKELNGMMVDGKPMKVVVA 112
+ K+ N ++DG+ V +A
Sbjct: 74 RACKDPNP-IIDGRKANVNLA 93
Score = 46.1 bits (110), Expect = 9e-07
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
KIF+G + T+ +R FE +G + E V+ + YGFV
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
>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 = 53.4 bits (129), Expect = 1e-09
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---RNYGFVHIDSPDI-NKCIKE--- 96
+KVFVG +++ A E+++ F YG VV+ I R + FV + E
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLI 70
Query: 97 LNGMMVDGK 105
+ G+ V
Sbjct: 71 IKGISVHIS 79
Score = 47.2 bits (113), Expect = 2e-07
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK---NYGFV 346
K+F+G + E ++ F +YG+VV+ + K + FV
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFV 53
>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 = 53.6 bits (129), Expect = 2e-09
Identities = 9/81 (11%), Positives = 29/81 (35%), Gaps = 5/81 (6%)
Query: 34 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DI 90
++ + + V V L ++ ++ E +GT+ ++ + V ++
Sbjct: 5 SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSA 64
Query: 91 NKCIKEL--NGMMVDGKPMKV 109
+C+ + + G+
Sbjct: 65 KECVTFAADVPVYIAGQQAFF 85
Score = 37.5 bits (87), Expect = 8e-04
Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+ + + + EK+G + ++ K V
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALV 56
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 53.1 bits (128), Expect = 3e-09
Identities = 17/89 (19%), Positives = 28/89 (31%), Gaps = 17/89 (19%)
Query: 41 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE--------CDIVRN--------YGFVH 84
++ +FV L +N V + F G + ++ + V
Sbjct: 10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 69
Query: 85 -IDSPDINKCIKELNGMMVDGKPMKVVVA 112
D P I +G G P+KV A
Sbjct: 70 FDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 32.3 bits (74), Expect = 0.047
Identities = 5/28 (17%), Positives = 13/28 (46%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVE 336
IF+ + ++E + F++ G +
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKT 42
Score = 31.9 bits (73), Expect = 0.065
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAAT 35
++ + AI +G+ + P+K+ AT
Sbjct: 70 FDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99
>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 = 52.5 bits (126), Expect = 4e-09
Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 5/77 (6%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK-- 95
K P+ + + L EV L +P+G V +++ ++ I
Sbjct: 9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMV 68
Query: 96 ---ELNGMMVDGKPMKV 109
+ +P+ +
Sbjct: 69 NYYSAVTPHLRNQPIYI 85
Score = 36.3 bits (84), Expect = 0.002
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+ I + + + L +GKV ++ KN F+
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFL 56
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 50.9 bits (123), Expect = 7e-09
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIK- 95
K+FVG LS NT +V+ F +G V + ++ R +GFV +S D + K +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 96 ---ELNGMMVDGK 105
E+N MV+ K
Sbjct: 61 HFHEINNKMVECK 73
Score = 45.2 bits (108), Expect = 9e-07
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
KIF+G ++ T+VE ++ FE++GKV + ++ + +GFV
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFV 46
>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 = 51.4 bits (123), Expect = 1e-08
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 15/78 (19%)
Query: 47 VFVGNLSDNTRAPEV---RELFVPYGTVVECDIVRN-----------YGFVHIDSPDI-N 91
VFV LS PEV E F +G + + I + +V +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 92 KCIKELNGMMVDGKPMKV 109
+ I+ +N ++VDG+ +K
Sbjct: 78 RAIQCVNNVVVDGRTLKA 95
Score = 30.6 bits (69), Expect = 0.24
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAAT----SRKGPNT 42
E+ AI+ +N +V+ + LK T S GP++
Sbjct: 70 YIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYCSYSGPSS 110
Score = 29.1 bits (65), Expect = 0.90
Identities = 5/36 (13%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 310 IFIGNVNPGTSVELI---RPLFEKYGKVVECDVVKN 342
+F+ ++ + + F K+GK+ + + +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNS 53
>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 = 50.2 bits (121), Expect = 1e-08
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIK- 95
K+FVG LS +T ++RE F +G V ++ R + F+ + + K ++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 96 ---ELNGMMVDGK 105
+ + K
Sbjct: 61 KYHNVGLSKCEIK 73
Score = 45.2 bits (108), Expect = 7e-07
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
KIF+G ++P T E IR F +G+V ++ + + F+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFI 46
>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 = 54.5 bits (130), Expect = 2e-08
Identities = 24/163 (14%), Positives = 47/163 (28%), Gaps = 11/163 (6%)
Query: 7 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFV 66
E E R E Q V + + +FV ++ +T ++R F
Sbjct: 65 ERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124
Query: 67 PYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVVVAGFISS 117
YG + +V + Y F+ + D++ K +G +DG+ + V V +
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184
Query: 118 ILSCLNVIFFIRCGRGGHWSKECPRAGNFRSSGCYCKSKSSHK 160
+ G + +
Sbjct: 185 KGWRPRRLGGGLGGTRRGG--ADVNIRHSGRDDTSRYDERPGP 225
Score = 39.8 bits (92), Expect = 0.001
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+F+ VN T+ +R FE YG + +V + Y F+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFI 149
>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 = 50.9 bits (122), Expect = 2e-08
Identities = 13/87 (14%), Positives = 28/87 (32%), Gaps = 17/87 (19%)
Query: 45 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------------RNYGFVHIDSP 88
+ ++V L+D+ ++ + F G V + V + P
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 89 D-INKCIKELNGMMVDGKPMKVVVAGF 114
++ +G G +KV +A
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARK 102
Score = 32.4 bits (74), Expect = 0.063
Identities = 7/41 (17%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTPTT 45
E+ + A++ +G+ LK+ A + + P++
Sbjct: 72 YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112
Score = 31.6 bits (72), Expect = 0.11
Identities = 5/28 (17%), Positives = 14/28 (50%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVE 336
I++ +N +++ + F++ G V
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKM 44
>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 = 52.8 bits (126), Expect = 2e-08
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 5/75 (6%)
Query: 43 PTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKEL 97
+ + V L V +F YG V + +++ V + +++ I L
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62
Query: 98 NGMMVDGKPMKVVVA 112
N + G+ M V V+
Sbjct: 63 NNNFMFGQKMNVCVS 77
Score = 49.7 bits (118), Expect = 2e-07
Identities = 14/150 (9%), Positives = 30/150 (20%), Gaps = 45/150 (30%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIE-------------------------------- 32
M + AI LN + + + +
Sbjct: 48 EMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNR 107
Query: 33 ----AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNY 80
++ P+ + N E+ G + +
Sbjct: 108 FSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSS 167
Query: 81 GFVHIDSPDI-NKCIKELNGMMVDGKPMKV 109
G + DS + + LN +
Sbjct: 168 GLLEWDSKSDALETLGFLNHYQMKNPNGPY 197
Score = 37.8 bits (87), Expect = 0.002
Identities = 8/111 (7%), Positives = 27/111 (24%), Gaps = 8/111 (7%)
Query: 244 RMMGGYPMKFGLILIPRSQIESLDLCGHFKQTKTTIVWSPRYQSFGTVVVIEARNMPGFS 303
+ M + + S+ ++ + + + +S +
Sbjct: 60 THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI 119
Query: 304 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFV 346
+ + N + E + ++ G V + G +
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLL 170
Score = 34.3 bits (78), Expect = 0.038
Identities = 6/41 (14%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 310 IFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKN---YGFV 346
+ + ++ + + + +F YG V + +K+ V
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMV 47
>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 = 50.3 bits (121), Expect = 3e-08
Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH 84
++ K T+ + V L T +++E F +G V+ + ++ +GFV
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 85 IDSPD-INKCIKELNGMMVDGK 105
+ K + + + M+DG+
Sbjct: 64 FTEYETQVKVMSQRH--MIDGR 83
Score = 44.1 bits (105), Expect = 4e-06
Identities = 9/46 (19%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
+ + + T+ + ++ F +G+V+ V K+ +GFV
Sbjct: 17 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV 62
>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 = 49.9 bits (120), Expect = 3e-08
Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 10/85 (11%)
Query: 34 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI 85
+ K+FVG LS +T ++++ F +G VV+C I + +GF+
Sbjct: 1 GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60
Query: 86 DSPD-INKCIKELNGMMVDGKPMKV 109
+ K + + +DG+ +
Sbjct: 61 KDAASVEKVLDQKEH-RLDGRVIDP 84
Score = 42.6 bits (101), Expect = 8e-06
Identities = 13/46 (28%), Positives = 27/46 (58%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+F+G ++ TS + ++ F K+G+VV+C + + +GF+
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFI 58
>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 = 50.0 bits (120), Expect = 3e-08
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 10/81 (12%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYG-TVVECDIVRN--------YGFVHIDSP- 88
G + +++G+L + F G TV+ I+RN Y FV
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63
Query: 89 DINKCIKELNGMMVDGKPMKV 109
KC+ ++NG + G
Sbjct: 64 TAEKCLHKINGKPLPGATPAK 84
Score = 31.5 bits (72), Expect = 0.084
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYG-KVVECDVVKN--------YGFV 346
SS +++G++ P I F G V+ +++N Y FV
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFV 57
Score = 26.5 bits (59), Expect = 4.4
Identities = 6/37 (16%), Positives = 13/37 (35%), Gaps = 4/37 (10%)
Query: 6 MENDEEGRTAIKELNGQIVN----EKPLKIEAATSRK 38
+ + ++NG+ + K K+ AT
Sbjct: 59 FADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSG 95
>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 = 48.4 bits (116), Expect = 2e-07
Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 13/94 (13%)
Query: 26 EKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------ 79
EK L+ +K K+F+G LS T +R + +G + +C ++R+
Sbjct: 9 EKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 68
Query: 80 --YGFVHIDSPD-INKCIK----ELNGMMVDGKP 106
+GFV S ++ + ++G +V+ K
Sbjct: 69 RGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR 102
Score = 43.4 bits (103), Expect = 8e-06
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R +E++GK+ +C V+++ +GFV
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 74
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 47.8 bits (114), Expect = 2e-07
Identities = 12/74 (16%), Positives = 24/74 (32%), Gaps = 7/74 (9%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDINKCIKELN 98
V++ + +++E G V+ + R FV DS + K E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 99 GMMVDGKPMKVVVA 112
G + ++
Sbjct: 73 GQKYKETDLLILFK 86
Score = 36.3 bits (84), Expect = 0.002
Identities = 7/45 (15%), Positives = 17/45 (37%), Gaps = 7/45 (15%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFV 346
++I +++ I+ E G+V+ + + FV
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFV 57
>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 = 10/80 (12%), Positives = 25/80 (31%), Gaps = 6/80 (7%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGFVHIDSP-D 89
++ + NL + ++++L V G + S
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEI 79
Query: 90 INKCIKELNGMMVDGKPMKV 109
+ + ++ LN + G + V
Sbjct: 80 LVEALERLNNIEFRGSVITV 99
Score = 29.0 bits (65), Expect = 0.78
Identities = 10/70 (14%), Positives = 21/70 (30%), Gaps = 8/70 (11%)
Query: 282 SPRYQSFGTVVVIEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV- 340
+ S G V + ++I + N+ G S + ++ L + V
Sbjct: 6 HHHHHSSGLV---PRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN 62
Query: 341 ----KNYGFV 346
G +
Sbjct: 63 TRDFDGTGAL 72
Score = 29.0 bits (65), Expect = 0.87
Identities = 5/32 (15%), Positives = 12/32 (37%)
Query: 6 MENDEEGRTAIKELNGQIVNEKPLKIEAATSR 37
++E A++ LN + +E +
Sbjct: 74 FPSEEILVEALERLNNIEFRGSVITVERDDNP 105
>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 = 46.9 bits (112), Expect = 4e-07
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 9/78 (11%)
Query: 44 TTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVHIDSPDI-NKCI 94
T + V N+ E+ + F Y + + N V +S D +
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 95 KELNGMMVDGKPMKVVVA 112
+LN + + +K+V+
Sbjct: 75 IDLNDRPIGSRKVKLVLG 92
Score = 28.0 bits (63), Expect = 1.5
Identities = 6/32 (18%), Positives = 16/32 (50%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATS 36
E+ +E A+ +LN + + + +K+ +
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94
Score = 27.3 bits (61), Expect = 2.6
Identities = 7/37 (18%), Positives = 12/37 (32%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVE 336
G I + N+ S++ I F Y +
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPG 44
>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 = 47.3 bits (113), Expect = 4e-07
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 13/82 (15%)
Query: 37 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP 88
+ K+F+G LS T +RE F +G V EC ++R+ +GFV
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 89 D-INKCIK----ELNGMMVDGK 105
++K + EL+ +D K
Sbjct: 78 AGVDKVLAQSRHELDSKTIDPK 99
Score = 44.2 bits (105), Expect = 4e-06
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 72
>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 = 46.5 bits (111), Expect = 5e-07
Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 14/95 (14%)
Query: 33 AATSRKGPNTP-TTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFV 83
+ +S P T + V N+ E+ + F Y + + N V
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 84 HIDSPDI-NKCIKELNGMMVDGKPMKVVVAGFISS 117
+S D + +LN + + +K+ S
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKL----SGPS 93
Score = 28.8 bits (65), Expect = 0.65
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATS 36
E+ +E A+ +LN + + + +K+ +S
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94
Score = 26.1 bits (58), Expect = 6.2
Identities = 7/37 (18%), Positives = 12/37 (32%)
Query: 300 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVE 336
G I + N+ S++ I F Y +
Sbjct: 8 SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPG 44
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 45.6 bits (109), Expect = 6e-07
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 13/73 (17%)
Query: 46 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIK- 95
K+F+G LS T +RE F +G V EC ++R+ +GFV ++K +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 96 ---ELNGMMVDGK 105
EL+ +D K
Sbjct: 62 SRHELDSKTIDPK 74
Score = 44.0 bits (105), Expect = 2e-06
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV 47
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 46.1 bits (110), Expect = 8e-07
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 14/88 (15%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV 83
+ + G + K+FVG L +T +R F YG VV+C I+++ +GFV
Sbjct: 5 SSGMNNSGADEIG-KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
Query: 84 HIDSPD-INKCIK----ELNGMMVDGKP 106
P+ + + L+G +D KP
Sbjct: 64 KFKDPNCVGTVLASRPHTLDGRNIDPKP 91
Score = 43.4 bits (103), Expect = 8e-06
Identities = 16/46 (34%), Positives = 29/46 (63%), Gaps = 8/46 (17%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFV 346
K+F+G ++ T+ E +R F +YG+VV+C ++K+ +GFV
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
>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 = 45.6 bits (108), Expect = 1e-06
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 13/86 (15%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------RNYGFVHIDSPD 89
++ ++F+G + + E+ E V IV R + FV +S
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 90 I-NKCIKELN--GMMVDGKPMKVVVA 112
++L + + G + V A
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIAVDWA 89
Score = 40.9 bits (96), Expect = 6e-05
Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 10/54 (18%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----------KNYGFV 346
S G ++FIG + E I K + V +V + + FV
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFV 57
>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 = 47.4 bits (112), Expect = 6e-06
Identities = 55/296 (18%), Positives = 91/296 (30%), Gaps = 96/296 (32%)
Query: 31 IEAATSRKGPNTPTTKVFV-----GNLSDNTRAPEVRELFVPYGTVVECDIVRN-----Y 80
A ++ GN + E+R+L+ Y +V D+++
Sbjct: 146 FRAVGEGN------AQLVAIFGGQGN--TDDYFEELRDLYQTYHVLVG-DLIKFSAETLS 196
Query: 81 GFVHIDSPDINKCIKELNGMMVDG---KPMKVVVAGFISSI-LSCLNVIFFIRCGRGGHW 136
+ + D K + G+ + P ++ SI +SC +I I+ H+
Sbjct: 197 ELIR-TTLDAEKVFTQ--GLNILEWLENPSNTPDKDYLLSIPISC-PLIGVIQL---AHY 249
Query: 137 SKECPRAG----NFRS--SGCYCKSKSSHKIYQDALVLWEDQDLWTGLVKGTSDLVVVIA 190
G RS G TG +G +V A
Sbjct: 250 VVTAKLLGFTPGELRSYLKGA------------------------TGHSQG-----LVTA 280
Query: 191 SPIHQAHC-DSFLCCSRRFGAVGGPGPLDRF--GYPR--EAYPRDPYPPPPPPSFLRDRM 245
I + +SF R+ V L F G R EAYP PPS L D +
Sbjct: 281 VAIAETDSWESFFVSVRKAITV-----L--FFIGV-RCYEAYPN----TSLPPSILEDSL 328
Query: 246 MGGY----PMKFGLILIPRSQIESL--DLCGHFKQTKT---TIVWSPRYQSFGTVV 292
PM + + + Q++ H K ++V + + VV
Sbjct: 329 ENNEGVPSPM-LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK--NL--VV 379
Score = 37.7 bits (87), Expect = 0.006
Identities = 33/188 (17%), Positives = 56/188 (29%), Gaps = 60/188 (31%)
Query: 77 VRNYGFVHIDSPDINKCIKEL-----------NGMMVDGKPMKVVVAGFISSILSCLNVI 125
+ N + +NK L NG +VV+G S L LN+
Sbjct: 341 ISNLTQEQVQD-YVNKTNSHLPAGKQVEISLVNG------AKNLVVSGPPQS-LYGLNLT 392
Query: 126 F-FIRCGRGG-----HWSKECPRAGN--------FRSSGCYCKSKSSHKIYQDAL---VL 168
+ G +S+ + N F S +S I +D + V
Sbjct: 393 LRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSH--LLVP-ASDLINKDLVKNNVS 449
Query: 169 WEDQDL-------WTG----LVKG--TSDLVVVIAS-PIH---QAHCDS--FLCCSRRFG 209
+ +D+ + G ++ G + +V I P+ + L G
Sbjct: 450 FNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGP--G 507
Query: 210 AVGGPGPL 217
G G L
Sbjct: 508 GASGLGVL 515
Score = 29.6 bits (66), Expect = 1.9
Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 29/100 (29%)
Query: 42 TPTTKVFVGNLSDNTRAPEVRELFVP-YGT----------------VVECDIVR------ 78
P + + +L N + +++ +P Y T +V+C I+R
Sbjct: 433 VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC-IIRLPVKWE 491
Query: 79 ---NYGFVHI-D-SPDINKCIKELNGMMVDGKPMKVVVAG 113
+ HI D P + L DG ++V+VAG
Sbjct: 492 TTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAG 531
>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 = 43.3 bits (102), Expect = 1e-05
Identities = 10/82 (12%), Positives = 24/82 (29%), Gaps = 8/82 (9%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVHIDS 87
S + V + L E+ + F V + + FV S
Sbjct: 34 SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93
Query: 88 PDINKCIKELNGMMVDGKPMKV 109
++ + + + + ++V
Sbjct: 94 QELAEKALGKHKERIGHRYIEV 115
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 42.9 bits (101), Expect = 2e-05
Identities = 12/83 (14%), Positives = 25/83 (30%), Gaps = 8/83 (9%)
Query: 35 TSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVHID 86
+ + P+ V++ L V + F V + I GFV
Sbjct: 16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75
Query: 87 SPDINKCIKELNGMMVDGKPMKV 109
+ K + + + ++V
Sbjct: 76 NEADYKAALCRHKQYMGNRFIQV 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 = 42.0 bits (99), Expect = 2e-05
Identities = 9/88 (10%), Positives = 27/88 (30%), Gaps = 8/88 (9%)
Query: 33 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVH 84
++ N+ + N+ + +V + ++ + V
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63
Query: 85 IDSPDINKCIKELNGMMVDGKPMKVVVA 112
+ D + + L+ ++G+ V V
Sbjct: 64 FKNEDDARKSERLHRKKLNGREAFVHVV 91
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 41.9 bits (98), Expect = 3e-05
Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 17/88 (19%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------RNYGFVHIDSP 88
++ + KVFVG L + E+ F +G +V + Y F+
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 89 D-----INKCIKELNGM--MVDGKPMKV 109
I+ C++E + V +K
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKD 90
Score = 38.8 bits (90), Expect = 4e-04
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 309 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
K+F+G + P + I F ++G +V K
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKA 43
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 41.6 bits (98), Expect = 3e-05
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 9/67 (13%)
Query: 48 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELN 98
+ + + LF G VV + + + FV S D K IK +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 99 GMMVDGK 105
G +D K
Sbjct: 76 GKRLDLK 82
Score = 30.5 bits (69), Expect = 0.23
Identities = 10/55 (18%), Positives = 17/55 (30%), Gaps = 12/55 (21%)
Query: 288 FGTVVVIEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN 342
+V+ P I + + + LF K GKVV + +
Sbjct: 5 SDQYIVVN--GAP----------VIPSAKVPVLKKALTSLFSKAGKVVNMEFPID 47
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 41.6 bits (98), Expect = 3e-05
Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 13/74 (17%)
Query: 45 TKVFVGNLSDNTRA------PEVRELFVPYGTVVECDIVRN------YGFVHIDSPDI-N 91
+ + V N+ + ++F +G + Y F+ SP
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 75
Query: 92 KCIKELNGMMVDGK 105
+K +G +D +
Sbjct: 76 DAVKNADGYKLDKQ 89
Score = 28.9 bits (65), Expect = 0.90
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 10/50 (20%)
Query: 301 GFSSVGTFKIFIGNV------NPGTSVELIRPLFEKYGKVVECDVVKNYG 344
G SV I + NV +I +F K+GK+ + G
Sbjct: 13 GIDSV----IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDG 58
>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 = 40.7 bits (95), Expect = 8e-05
Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 6/78 (7%)
Query: 38 KGPNTPTTKVFVGNL-SDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK- 95
+ + NL V +L PYG + ++R I+ +
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAM 78
Query: 96 ----ELNGMMVDGKPMKV 109
+ G+ +KV
Sbjct: 79 VDHCLKKALWFQGRCVKV 96
Score = 29.9 bits (67), Expect = 0.48
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 310 IFIGNV-NPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
I + N+ + G S + L E YGK+ ++ K+ F+
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFI 67
>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 = 39.5 bits (92), Expect = 2e-04
Identities = 17/98 (17%), Positives = 34/98 (34%), Gaps = 6/98 (6%)
Query: 26 EKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFV 83
L+ E + T + V G L + ++ + G V + + Y F
Sbjct: 10 HTLLRHEGIETVSYA-TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFA 68
Query: 84 HIDSP-DINKCIKELNG-MMVDGKPMKVVV-AGFISSI 118
+ + + LNG +VD K+ + F+ +
Sbjct: 69 RYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV 106
Score = 36.1 bits (83), Expect = 0.003
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 310 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFV 346
+ G + G S + P+ EK G V + K Y F
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFA 68
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 39.3 bits (92), Expect = 2e-04
Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 9/86 (10%)
Query: 35 TSRKGPNTPTTK-VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHID 86
+ + P P V V + + +VR+ F V ++++ G V
Sbjct: 6 SGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFL 64
Query: 87 SPDINKCIKELNGMMVDGKPMKVVVA 112
SP + N M++ + ++V A
Sbjct: 65 SPQDTFEALKRNRMLMIQRYVEVSPA 90
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 19/81 (23%), Positives = 27/81 (33%), Gaps = 8/81 (9%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP 88
S T V + N V E P V IVRN Y FV +
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNE 60
Query: 89 DINKCIKELNGMMVDGKPMKV 109
+ K + N + G+ ++V
Sbjct: 61 EEVKQALKCNREYMGGRYIEV 81
>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 = 39.1 bits (91), Expect = 4e-04
Identities = 10/93 (10%), Positives = 25/93 (26%), Gaps = 12/93 (12%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVH 84
+ +T V + L ++ F P V I V
Sbjct: 34 SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVE 92
Query: 85 IDSPDINKCIKELNGMMVDGKPMKVVVAGFISS 117
+ + + + + +++ F++S
Sbjct: 93 FATHEEAVAAMSKDRANMQHRYIEL----FLNS 121
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 37.4 bits (87), Expect = 6e-04
Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 13/74 (17%)
Query: 45 TKVFVGNL--SDNTRAPE----VRELFVPYGTVVECDIVRN------YGFVHIDSP-DIN 91
+ + V N+ R + + ++F +G + Y F+ SP
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 92 KCIKELNGMMVDGK 105
+K +G +D +
Sbjct: 62 DAVKNADGYKLDKQ 75
Score = 27.0 bits (60), Expect = 2.9
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 6/41 (14%)
Query: 310 IFIGNV------NPGTSVELIRPLFEKYGKVVECDVVKNYG 344
I + NV +I +F K+GK+ + G
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDG 44
>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 = 37.8 bits (88), Expect = 6e-04
Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 12/87 (13%)
Query: 35 TSRKGPNTPTTK----VFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGF 82
+S N+P T V + L E+ + F V + + F
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 83 VHIDSPDINKCIKELNGMMVDGKPMKV 109
V S +I + + + + + +++
Sbjct: 62 VQFASQEIAEKALKKHKERIGHRYIEI 88
>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 = 39.5 bits (91), Expect = 0.002
Identities = 48/355 (13%), Positives = 97/355 (27%), Gaps = 119/355 (33%)
Query: 56 TRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDI-NKCI----KELNGMMVDGKPMKV- 109
TR +V + T + + + K + ++L ++ P ++
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331
Query: 110 VVAGFISSILSCLNVIFFIRCGRGGHWSKECPRAGNFRSSGCYCKS---KSS-------- 158
++A I L+ W N++ C + +SS
Sbjct: 332 IIAESIRDGLA--------------TWD-------NWKHVNCDKLTTIIESSLNVLEPAE 370
Query: 159 -HKIYQDALVLWEDQD--------LWTGLVKGTSDLVV--------VIASP------IHQ 195
K++ V +W ++K +VV V P I
Sbjct: 371 YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 196 AHCDSFLCCS------RRFGAVGGPGPLDRFGYPREAYPRDPYPPPPPP---SFLRDRMM 246
+ + + R +D + P+ D PP S +
Sbjct: 431 IYLELKVKLENEYALHRSI--------VDHYNIPKTFDSDDLIPPYLDQYFYSHI----- 477
Query: 247 GGYPMK----------FGLILIPRSQIESLDLCGHFKQTK---TTIVWSPRYQSFGTVVV 293
G+ +K F ++ LD F + K + W+ T+
Sbjct: 478 -GHHLKNIEHPERMTLFRMVF--------LDF--RFLEQKIRHDSTAWNASGSILNTLQQ 526
Query: 294 IE------ARNMPGFSS-VGTFKIFIGNVNP----GTSVELIR-PLFEKYGKVVE 336
++ N P + V F+ + +L+R L + + E
Sbjct: 527 LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFE 581
>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 = 36.6 bits (85), Expect = 0.002
Identities = 9/87 (10%), Positives = 24/87 (27%), Gaps = 12/87 (13%)
Query: 38 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDI 90
+T V + L ++ F P + I V + +
Sbjct: 9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHED 67
Query: 91 NKCIKELNGMMVDGKPMKVVVAGFISS 117
+ + + +++ F++S
Sbjct: 68 AVAAMAKDKANMQHRYVEL----FLNS 90
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 38.2 bits (88), Expect = 0.002
Identities = 15/132 (11%), Positives = 35/132 (26%), Gaps = 15/132 (11%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP---NTPTTKVFVGNLSDNTRAP-- 59
H+ ++E+ + + G ++VG + +
Sbjct: 92 HIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHL 151
Query: 60 -------EVRELFVPYGTVVECDIV--RNYGFVH-IDSPDINKCIKELNGMMVDGKPMKV 109
+R +F G + V +N GFV + + ++ + K
Sbjct: 152 KPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKE 211
Query: 110 VVAGFISSILSC 121
+ L
Sbjct: 212 WDDRREGTGLLV 223
Score = 33.6 bits (76), Expect = 0.061
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 11/63 (17%)
Query: 295 EARNMPGFSSVGTFKIFIGNVNPGTSV---------ELIRPLFEKYGKVVECDVV--KNY 343
E G +++G ++ + IR +F + G + V KN
Sbjct: 122 EDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNC 181
Query: 344 GFV 346
GFV
Sbjct: 182 GFV 184
>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 = 35.4 bits (81), Expect = 0.007
Identities = 11/96 (11%), Positives = 24/96 (25%), Gaps = 14/96 (14%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPY---GTVVECDIVRN-------YG 81
+ V + L + +V+ +
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 82 FVHIDSPDINKCIKELNGMMVDGKPMKVVVAGFISS 117
FV + S D K + + + + ++V F S
Sbjct: 92 FVELGSEDDVKMALKKDRESMGHRYIEV----FKSH 123
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 34.9 bits (80), Expect = 0.010
Identities = 11/93 (11%), Positives = 26/93 (27%), Gaps = 15/93 (16%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECD----IVRN-------YGFVH 84
++ V + L A EV F + + V FV
Sbjct: 15 AQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVL 74
Query: 85 IDSPDINKCIKELNGMMVDGKPMKVVVAGFISS 117
+ + + ++ + +++ F S+
Sbjct: 75 FACEEYAQNALRKHKDLLGKRYIEL----FRST 103
>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 = 34.7 bits (79), Expect = 0.018
Identities = 17/116 (14%), Positives = 37/116 (31%), Gaps = 9/116 (7%)
Query: 5 HMENDEEGRTAIKELNGQIVNEKPLKIEAAT----SRKGPNTPTTKVFVGNLSDNTRAPE 60
H + + A++ +N L AA +P ++ V NL
Sbjct: 3 HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62
Query: 61 VRELFVPYGTVVECDIV----RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVVV 111
+ ++F +GTV++ + + P L+G + + +
Sbjct: 63 LHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 118
Score = 27.4 bits (60), Expect = 4.9
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 274 QTKTTIVWSPRYQSFGTVVVIEARNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGK 333
Q ++ + V M G S V +I + N+ +++++ +F K+G
Sbjct: 15 QAVNSVQSGNLALAASAAAVDAGMAMAGQSPV--LRIIVENLFYPVTLDVLHQIFSKFGT 72
Query: 334 VVEC-DVVKNYGF 345
V++ KN F
Sbjct: 73 VLKIITFTKNNQF 85
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 32.5 bits (74), Expect = 0.018
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 129 RCGRGGHWSKECPRAGNFRSSGCYC 153
CG GH+ +CP+ +S C
Sbjct: 9 TCGSPGHYQAQCPKKRKSGNSRERC 33
Score = 28.3 bits (63), Expect = 0.67
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 129 RCGRGGHWSKECP 141
C GH +K+C
Sbjct: 35 LCNGMGHNAKQCR 47
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding
protein, retrovirus, viral protein; NMR {Mason-pfizer
monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Length = 60
Score = 31.8 bits (72), Expect = 0.036
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 129 RCGRGGHWSKECPRAGNFR 147
RC RG HW+ EC + +
Sbjct: 35 RCKRGKHWANECKSKTDNQ 53
Score = 30.3 bits (68), Expect = 0.13
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 129 RCGRGGHWSKECPRAGNFRSSG 150
+CG+ GH++K C + +
Sbjct: 6 KCGKKGHFAKNCHEHAHNNAEP 27
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 32.9 bits (75), Expect = 0.037
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 8/64 (12%)
Query: 54 DNTRAPEVRELFVPYGTVVECDIVRN-----YGFVHI---DSPDINKCIKELNGMMVDGK 105
D E+ YG V E ++ N G V++ D K + +LN +G+
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 106 PMKV 109
P+
Sbjct: 97 PIHA 100
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 31.8 bits (72), Expect = 0.067
Identities = 13/73 (17%), Positives = 22/73 (30%), Gaps = 10/73 (13%)
Query: 44 TTKVFVGNLSDNTRAPEVRELF-----VPYGTVVECDIVRNYGFVHIDSP-DINKCIK-- 95
V V L + F G V+ + G + P D + +
Sbjct: 8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQA 67
Query: 96 --ELNGMMVDGKP 106
EL+G + +P
Sbjct: 68 DHELHGAQLSLRP 80
Score = 30.7 bits (69), Expect = 0.21
Identities = 10/49 (20%), Positives = 17/49 (34%), Gaps = 5/49 (10%)
Query: 303 SSVGTFKIFIGNVNPGTSVELIRPLFEKY-----GKVVECDVVKNYGFV 346
S G + + + P EL+ FE G V+ + G +
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVL 52
>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 = 32.2 bits (73), Expect = 0.071
Identities = 12/96 (12%), Positives = 25/96 (26%), Gaps = 14/96 (14%)
Query: 32 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR----------NYG 81
+ V + L + +V+ V
Sbjct: 5 SSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEA 64
Query: 82 FVHIDSPDINKCIKELNGMMVDGKPMKVVVAGFISS 117
FV ++S D K + + + + ++V F S
Sbjct: 65 FVELESEDDVKLALKKDRESMGHRYIEV----FKSH 96
>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 = 31.9 bits (73), Expect = 0.079
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 8/62 (12%)
Query: 60 EVRELFVPYGTVVECDIVRNYG----FVHIDSPDI-NKCIKELNGMMVDGKPMKVVVAGF 114
+V E +G V+ + +N +V S + L+G GK + A +
Sbjct: 33 DVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKM---ITAAY 89
Query: 115 IS 116
+
Sbjct: 90 VP 91
>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 = 31.7 bits (72), Expect = 0.10
Identities = 7/86 (8%), Positives = 24/86 (27%), Gaps = 11/86 (12%)
Query: 34 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN----------YGFV 83
+ + + + L + +V F + + +
Sbjct: 2 SKLEEEVDDVFL-IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60
Query: 84 HIDSPDINKCIKELNGMMVDGKPMKV 109
++S + E + M + + ++V
Sbjct: 61 EMESEQDVQKALEKHRMYMGQRYVEV 86
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 30.9 bits (70), Expect = 0.15
Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 14/68 (20%)
Query: 60 EVRELFVPYGTVVECDIVRNY----------GFVHIDSPDI-NKCIKELNGMMVDGKPMK 108
+VR+ YG V +I R FV S K ++ L G +
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFAN---R 87
Query: 109 VVVAGFIS 116
VVV +
Sbjct: 88 VVVTKYCD 95
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 55
Score = 29.4 bits (66), Expect = 0.19
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 129 RCGRGGHWSKECPRAGN 145
RCG+ GH+ K CP G+
Sbjct: 12 RCGKPGHYIKNCPTNGD 28
>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 = 31.7 bits (71), Expect = 0.23
Identities = 8/78 (10%), Positives = 23/78 (29%), Gaps = 9/78 (11%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY-----GFVHI---DSPDIN 91
+ V++ + +++E G V+ + R G + +
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 164
Query: 92 KCIKELNGMMVDGKPMKV 109
K ++ G + +
Sbjct: 165 KFVETP-GQKYKETDLLI 181
Score = 26.7 bits (58), Expect = 9.0
Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 7/56 (12%)
Query: 298 NMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFV 346
+ V ++I +++ I+ E G+V+ + K FV
Sbjct: 100 TDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFV 155
>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 = 30.4 bits (69), Expect = 0.26
Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 60 EVRELFVPYGTVVECDIVRNY--GFVHI---DSPDINKCIKELNGMMVDGKPMKVVVAGF 114
++R +G + + + + G + D + + CI+ L+G G+ + A
Sbjct: 42 DLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQ---ITAQA 98
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U
mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger,
NC, viral protein-RN; HET: AP7; NMR {Moloney murine
leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A
1wwg_A
Length = 56
Score = 28.9 bits (64), Expect = 0.33
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 130 CGRGGHWSKECPR 142
C GHW+K+CP+
Sbjct: 29 CKEKGHWAKDCPK 41
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 30.0 bits (67), Expect = 0.37
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 8/67 (11%)
Query: 51 NLSDNTRAPEVRELFVPYGTVVECDI-----VRNYGFVHI---DSPDINKCIKELNGMMV 102
LSD + + + E DI V ++ I DS K + LNG
Sbjct: 28 PLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQF 87
Query: 103 DGKPMKV 109
GK ++
Sbjct: 88 QGKVIRS 94
>2kvo_A Photosystem II reaction center PSB28 protein; membrane,
photosynthesis, thylakoid, structural genom 2, protein
structure initiative; NMR {Synechocystis SP}
Length = 120
Score = 29.9 bits (67), Expect = 0.46
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 9 DEEGRTAIKELNGQIVNEKPLKIEA 33
D+EG +E+ G+ +N +P IEA
Sbjct: 56 DDEGEIITREVKGKFINGRPTAIEA 80
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 29.7 bits (66), Expect = 0.64
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 5/31 (16%)
Query: 129 RCGRGGHWSKECPRAGNFRSSGCYCKSKSSH 159
C + GH K+CP YC + H
Sbjct: 9 NCSQRGHLKKDCPHI-----ICSYCGATDDH 34
Score = 27.4 bits (60), Expect = 3.6
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 129 RCGRGGHWSKECP 141
CG GH+ +C
Sbjct: 110 NCGGKGHFGDDCK 122
Score = 27.0 bits (59), Expect = 5.1
Identities = 9/40 (22%), Positives = 14/40 (35%), Gaps = 2/40 (5%)
Query: 120 SCLNVIFFIRCGRGGHWSKECPRAGNFRSSGCYCKSKSSH 159
C I +C GH+ +CP ++ C H
Sbjct: 38 HCPKAIQCSKCDEVGHYRSQCPH--KWKKVQCTLCKSKKH 75
Score = 26.7 bits (58), Expect = 6.8
Identities = 5/32 (15%), Positives = 10/32 (31%), Gaps = 2/32 (6%)
Query: 129 RCGRGGHWSKECPRAGNFRSSGCYCKSKSSHK 160
C H + CP R+ ++ +
Sbjct: 69 LCKSKKHSKERCPSIW--RAYILVDDNEKAKP 98
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 29.3 bits (66), Expect = 0.73
Identities = 17/70 (24%), Positives = 23/70 (32%), Gaps = 16/70 (22%)
Query: 60 EVRELFVPYGTVVECDIVRNYGFVHIDSPDI-------------NKCIKELNGMMVDGKP 106
EV E +G V I + D+ I +K I+ LNG G
Sbjct: 41 EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG-- 98
Query: 107 MKVVVAGFIS 116
+ VVA
Sbjct: 99 -RKVVAEVYD 107
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 28.5 bits (63), Expect = 0.90
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 3/69 (4%)
Query: 39 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI---DSPDINKCIK 95
++ + + NL+ P +R L + +G +V N G + NK
Sbjct: 2 AMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQM 61
Query: 96 ELNGMMVDG 104
LN ++
Sbjct: 62 ALNNCVLAN 70
>1dhk_B Bean lectin-like inhibitor, porcine pancreatic alpha-amylase; CO
(hydrolase-inhibitor), complex (hydrolase-inhibitor)
comple; HET: NAG; 1.85A {Phaseolus vulgaris} SCOP:
b.29.1.1 PDB: 1viw_B*
Length = 223
Score = 30.1 bits (67), Expect = 0.94
Identities = 24/161 (14%), Positives = 49/161 (30%), Gaps = 24/161 (14%)
Query: 21 GQIVNEKPLKIEAATSRKGPNTPTTKVF-VGNLSDNTRAPEVRELFVPYGTV-------V 72
+ P++I +T+ + T + A + + VP V
Sbjct: 41 SRAFYSAPIQIRDSTTGNVASFDTNFTMNIRTHRQANSAVGLDFVLVPVQPESKGDTVTV 100
Query: 73 ECDIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKVVVAGFISSILSCLNVIFFIRCGR 132
E D + + +++ DI + DG+ +V + +S +V
Sbjct: 101 EFDTFLSRISIDVNNNDIK--SVPWDVHDYDGQNAEVRIT--YNSSTKVFSV-SLSNPST 155
Query: 133 GGHWS-----------KECPRAGNFRSSGCYCKSKSSHKIY 162
G + + G +SG Y S +H +
Sbjct: 156 GKSNNVSTTVELEKEVYDWVSVGFSATSGAYQWSYETHDVL 196
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase;
1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 27.9 bits (63), Expect = 0.99
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 75 DIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKVVVA 112
I+ N +V I + +K + V GK +KV A
Sbjct: 37 TIMDNASYVEILNGKGPHVLKVMKNTTVKGKQLKVNKA 74
>2wue_A 2-hydroxy-6-OXO-6-phenylhexa-2,4-dienoate hydrolase BPHD; HET: KEK;
1.80A {Mycobacterium tuberculosis} PDB: 2wud_A* 2wuf_A*
2wug_A* 2vf2_A
Length = 291
Score = 29.2 bits (66), Expect = 1.8
Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 19/83 (22%)
Query: 206 RRFGAVGGPGPLDRFGYPREAYPRDPYPPPPPPSFLR-------------DRMMGGYPMK 252
+RF P L +++ + + DR+ P+
Sbjct: 191 QRFALASTPESLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVN---PLD 247
Query: 253 FGLIL---IPRSQIESLDLCGHF 272
L+ IPR+Q+ CGH+
Sbjct: 248 GALVALKTIPRAQLHVFGQCGHW 270
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 1.8
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 8/28 (28%)
Query: 13 RTAIKELNGQIVNEKPLKIEAATSRKGP 40
+ A+K+L + LK+ A S P
Sbjct: 19 KQALKKL------QASLKLYADDS--AP 38
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA
complex; NMR {Homo sapiens}
Length = 74
Score = 27.3 bits (60), Expect = 2.0
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 130 CGRGGHWSKECPRAGNFRSSGCYCKSKSSH 159
CG H +KEC + C+ SH
Sbjct: 30 CGGLDHHAKECKLPP--QPKKCHFCQSISH 57
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 63
Score = 26.8 bits (59), Expect = 2.3
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 130 CGRGGHWSKECPRAGNFRSSGCYCKSKSSH 159
CG H +KEC + C+ SH
Sbjct: 13 CGGLDHHAKECKLPP--QPKKCHFCQSISH 40
Score = 25.3 bits (55), Expect = 7.9
Identities = 5/22 (22%), Positives = 5/22 (22%)
Query: 129 RCGRGGHWSKECPRAGNFRSSG 150
C H CP S
Sbjct: 34 FCQSISHMVASCPLKAQQGPSA 55
>3ec8_A Putative uncharacterized protein FLJ10324; beta barrel, helix,
structural genomics, structural genomics consortium,
SGC, cell adhesion; 2.60A {Homo sapiens}
Length = 166
Score = 28.6 bits (63), Expect = 2.4
Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 19/58 (32%)
Query: 306 GTFKIFIGNVNPG------------TSVELIRPLFEKYGKVVE-------CDVVKNYG 344
G K+F +V G ++ EL++ E+Y CDVV G
Sbjct: 36 GVLKVFGDSVCTGTHYKSVLATGTSSARELVKEALERYALDPRQAGQYVLCDVVGQAG 93
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 27.7 bits (61), Expect = 3.4
Identities = 11/81 (13%), Positives = 26/81 (32%), Gaps = 5/81 (6%)
Query: 36 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHIDSPDI- 90
+P ++ V NL + ++F +GTV++ + + P
Sbjct: 20 MAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 79
Query: 91 NKCIKELNGMMVDGKPMKVVV 111
L+G + + +
Sbjct: 80 QHAKLSLDGQNIYNACCTLRI 100
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 27.3 bits (60), Expect = 3.5
Identities = 13/88 (14%), Positives = 25/88 (28%), Gaps = 6/88 (6%)
Query: 30 KIEAATSRKGPNTPTTK--VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVH 84
+I + P+ + + N + + P G V I + V
Sbjct: 9 RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVE 68
Query: 85 IDSP-DINKCIKELNGMMVDGKPMKVVV 111
+S K LNG + + +
Sbjct: 69 FESVLCAQKAKAALNGADIYAGCCTLKI 96
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 27.3 bits (60), Expect = 3.6
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 311 FIGNVNPGTSVELIRPLFEKYGKVVECDVVK 341
F G+++ T E + LF +G++ D V+
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVR 53
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide;
transcription, nucleotidyltransferase; 2.70A {Homo
sapiens} SCOP: b.40.4.5 d.230.1.1
Length = 172
Score = 28.0 bits (62), Expect = 3.7
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 7/79 (8%)
Query: 241 LRDRMMGGYPMKFGLIL-------IPRSQIESLDLCGHFKQTKTTIVWSPRYQSFGTVVV 293
L + G K+G ++ I I+ + IV+ P VV
Sbjct: 30 LFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVV 89
Query: 294 IEARNMPGFSSVGTFKIFI 312
+ + F+ +G FI
Sbjct: 90 TQVNKVGLFTEIGPMSCFI 108
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 26.5 bits (58), Expect = 3.7
Identities = 8/22 (36%), Positives = 10/22 (45%), Gaps = 3/22 (13%)
Query: 128 IRCGRGGHWSKECPRAGNFRSS 149
CG GH+ +C RSS
Sbjct: 50 YNCGGKGHFGDDCKEK---RSS 68
>1c4x_A BPHD, protein (2-hydroxy-6-OXO-6-phenylhexa-2,4-dienoat hydrolase);
PCB degradation; 2.40A {Rhodococcus SP} SCOP: c.69.1.10
Length = 285
Score = 28.0 bits (63), Expect = 4.0
Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 19/83 (22%)
Query: 206 RRFGAVGGPGPLDRFGYPREAYPRDPYPPPPPPSFLR-------------DRMMGGYPMK 252
RF P E+ PP+ L DR++ P+
Sbjct: 186 SRFEVANDPEVRRIQEVMFESMKAGMESLVIPPATLGRLPHDVLVFHGRQDRIV---PLD 242
Query: 253 FGLIL---IPRSQIESLDLCGHF 272
L L + +++ LD CGH+
Sbjct: 243 TSLYLTKHLKHAELVVLDRCGHW 265
>2r83_A Synaptotagmin-1; C2A-C2B, exocytosis, calcium, cell junction,
cytoplasmic vesicle, glycoprotein, lipoprotein,
membrane, metal-binding palmitate; 2.70A {Homo sapiens}
SCOP: b.7.1.2
Length = 284
Score = 27.8 bits (62), Expect = 4.4
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 240 FLRDRMMGGYPMKFGLILIPRSQIESLDL---CGHFKQTKTTIVWSPRYQSFG---TVVV 293
F + ++G + + + E DL ++ I +S RY TVV+
Sbjct: 97 FSKHDIIGEFKVPMNTVDFGHVTEEWRDLQSAEKEEQEKLGDICFSLRYVPTAGKLTVVI 156
Query: 294 IEARNMPGFSSVGT 307
+EA+N+ G
Sbjct: 157 LEAKNLKKMDVGGL 170
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex,
PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus
musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 27.3 bits (60), Expect = 4.4
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 129 RCGRGGHWSKECPRAGNFRSSGCYCKSKSSH 159
CG H +KEC + C+ +H
Sbjct: 102 NCGGLDHHAKECKLPP--QPKKCHFCQSINH 130
>4f0j_A Probable hydrolytic enzyme; alpha/beta hydrolase fold, structural
genomics, joint center structural genomics, JCSG; HET:
MSE; 1.50A {Pseudomonas aeruginosa}
Length = 315
Score = 27.9 bits (62), Expect = 4.6
Identities = 7/47 (14%), Positives = 14/47 (29%), Gaps = 3/47 (6%)
Query: 229 RDPYPPPPPPSFLRDRMMGGYPMKFGLIL---IPRSQIESLDLCGHF 272
+D + + G + G IP++ + GH
Sbjct: 248 KDNTAIGKDAAPAELKARLGNYAQLGKDAARRIPQATLVEFPDLGHT 294
>1j1i_A META cleavage compound hydrolase; carbazole degradation, META
cleavage product hydrolase, histidine tagged protein,
alpha/beta-hydrolase; 1.86A {Janthinobacterium} SCOP:
c.69.1.10
Length = 296
Score = 27.7 bits (62), Expect = 5.1
Identities = 12/83 (14%), Positives = 24/83 (28%), Gaps = 20/83 (24%)
Query: 206 RRFGAVGGPGPLDRFGYPREAYPRDPYPPPPPPSFLR-------------DRMMGGYPMK 252
R+ + + R+ P F+R D+++ P++
Sbjct: 184 SRYTYATDEATRKAYVATMQW-IREQGGLFYDPEFIRKVQVPTLVVQGKDDKVV---PVE 239
Query: 253 FGLIL---IPRSQIESLDLCGHF 272
I S + CGH+
Sbjct: 240 TAYKFLDLIDDSWGYIIPHCGHW 262
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA
recognition, zinc finger, viral protein; NMR {Human
immunodeficiency virus type 2} SCOP: g.40.1.1
Length = 49
Score = 25.3 bits (55), Expect = 6.3
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 9/44 (20%)
Query: 118 ILSCLNVIFFIRCGRGGHWSKECPRAGNFRSSGCYCKSKSSHKI 161
++ C N CG+ GH +++C RA R GC+ K+ H +
Sbjct: 6 VIRCWN------CGKEGHSARQC-RAP--RRQGCWKCGKTGHVM 40
>3iuu_A MLRC-like, putative metallopeptidase; YP_676511.1, structural
genomics, center for structural genomics, JCSG, protein
structure INI PSI-2; HET: PGE; 2.13A {Mesorhizobium SP}
Length = 495
Score = 27.6 bits (60), Expect = 6.9
Identities = 10/62 (16%), Positives = 15/62 (24%), Gaps = 15/62 (24%)
Query: 186 VVVIASPIH-----QAHCDSFLCCSRRFGAVGGPGPLD--RFGY--PREAYPRDPYPPPP 236
VV + H + + G +F + R YP D
Sbjct: 433 AVVARAANHYKLSFADIARTITVDT------PGLTAFKPHQFPFTQARPFYPLDIVQWSF 486
Query: 237 PP 238
P
Sbjct: 487 AP 488
>3pff_A ATP-citrate synthase; phosphohistidine, organic acid, ATP-grAsp,
lyase, transferas; HET: TLA ADP; 2.30A {Homo sapiens}
Length = 829
Score = 27.5 bits (61), Expect = 8.0
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 204 CSRRFGAVGGPGPLDRFGYPREAYPRD 230
C ++G + P P R YP EAY D
Sbjct: 229 CKVKWGDIEFPPPFGREAYPEEAYIAD 255
>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I
ABC type importer, methionine uptake transporter,
membrane protein; HET: ADP; 2.90A {Escherichia coli}
PDB: 3tuj_C 3tuz_C* 3dhw_C
Length = 366
Score = 27.3 bits (61), Expect = 9.0
Identities = 9/60 (15%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 40 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-NYGFVHIDSPDINKCIKELN 98
P TP + F+ + + +E ++R + +D+P +++ + N
Sbjct: 255 PKTPLAQKFIQSTLHLDIPEDYQERLQAEPFTDCVPMLRLEFTGQSVDAPLLSETARRFN 314
>3ip3_A Oxidoreductase, putative; structural genomics, PSI-2, protein
structure initiative, NEW YORK SGX research center for
structural genomics; 2.14A {Thermotoga maritima}
Length = 337
Score = 26.9 bits (60), Expect = 9.6
Identities = 7/30 (23%), Positives = 9/30 (30%)
Query: 219 RFGYPREAYPRDPYPPPPPPSFLRDRMMGG 248
G R + Y P F + R G
Sbjct: 146 AVGEIRLVNTQKSYKLGQRPDFYKKRETYG 175
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.140 0.445
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: 5,666,108
Number of extensions: 353099
Number of successful extensions: 1779
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1589
Number of HSP's successfully gapped: 534
Length of query: 346
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 252
Effective length of database: 4,077,219
Effective search space: 1027459188
Effective search space used: 1027459188
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)