RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11609
(83 letters)
>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 = 46.0 bits (108), Expect = 1e-07
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 7/74 (9%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILG 57
IY+ + LK LY + + G++ + + R V FK+ A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 58 SHEKHFFGCKIDVS 71
F+ + +
Sbjct: 72 MQGFPFYDKPMRIQ 85
Score = 27.5 bits (60), Expect = 0.39
Identities = 7/52 (13%), Positives = 13/52 (25%), Gaps = 1/52 (1%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFG 65
+ L + + V+++ G V F A A
Sbjct: 221 ELMLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQAGAARDALQGFKITQ 271
>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 = 42.2 bits (100), Expect = 7e-07
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 7/74 (9%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILG 57
IY+ + LK L+ + + G++ + + R V FK+ A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 58 SHEKHFFGCKIDVS 71
F+ + +
Sbjct: 71 MQGFPFYDKPMRIQ 84
>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 = 41.9 bits (99), Expect = 9e-07
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 14/73 (19%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGS 58
++V V++ L+ + + GK+ VK + Y + F + D A KA+
Sbjct: 14 LFVRNLANTVTEEILEK----AFSQFGKLERVKKL----KDYAFIHFDERDGAVKAMEEM 65
Query: 59 HEKHFFGCKIDVS 71
+ K G I++
Sbjct: 66 NGKDLEGENIEIV 78
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 41.8 bits (98), Expect = 1e-06
Identities = 9/74 (12%), Positives = 23/74 (31%), Gaps = 7/74 (9%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILG 57
+ + V L+ LY G + + + + + F + A+ +
Sbjct: 32 VLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEA 91
Query: 58 SHEKHFFGCKIDVS 71
F G + ++
Sbjct: 92 FQGYPFQGNPLVIT 105
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 38.7 bits (90), Expect = 1e-05
Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 11/73 (15%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGS 58
+YV + LK L + G V +++ QG R + + + A++A+
Sbjct: 22 VYVGNLPRDARVSDLKRALR----ELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCL 76
Query: 59 HEKHFFGCKIDVS 71
+ V+
Sbjct: 77 QGLRLGTDTLRVA 89
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 38.8 bits (91), Expect = 1e-05
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 5 IYV---VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILGSHE 60
IYV D KD + + K+G + + + + G + V F+ DAE A+ G
Sbjct: 25 IYVGNLPPDIRTKD-IEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 61 KHFFGCKIDV 70
+ G ++ V
Sbjct: 84 YDYDGYRLRV 93
>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 = 38.9 bits (91), Expect = 2e-05
Identities = 10/62 (16%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
+ +Y + K+G + +++ R V ++ DA+ A+ + + V
Sbjct: 22 AEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY 81
Query: 73 YH 74
Y+
Sbjct: 82 YN 83
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 38.8 bits (91), Expect = 2e-05
Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
++V + L + G + VKI+ G + V F++A+ A KAI H K
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-NG---FAFVEFEEAESAAKAIEEVHGKS 89
Query: 63 FFGCKIDVSP 72
F ++V
Sbjct: 90 FANQPLEVVY 99
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 38.3 bits (90), Expect = 2e-05
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
+++ + + + + ++++GKV II YG V + AE AI H
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIK----NYGFVHIEDKTAAEDAIRNLHHYK 66
Query: 63 FFGCKIDV 70
G I+V
Sbjct: 67 LHGVNINV 74
>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 = 38.8 bits (91), Expect = 2e-05
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 17/79 (21%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAE 52
+F+ Y V LK+ + G V I+ D+ G V F+++ +A
Sbjct: 18 VFVANLDYKVGWKKLKE----VFSMAGVVVRADILE---DKDGKSRGIGTVTFEQSIEAV 70
Query: 53 KAILGSHEKHFFGCKIDVS 71
+AI + + F + V
Sbjct: 71 QAISMFNGQLLFDRPMHVK 89
>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 = 38.4 bits (90), Expect = 2e-05
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
++V +S T L +++++G V I+ Y V ++A+DA +AI G
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIV----KDYAFVHMERAEDAVEAIRGLDNTE 68
Query: 63 FFGCKIDV 70
F G ++ V
Sbjct: 69 FQGKRMHV 76
>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 = 38.3 bits (89), Expect = 3e-05
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 7/66 (10%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFG 65
S LKD ++ G V + + G G+V F + +D A+ F
Sbjct: 26 PSGSWQDLKD----HMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTKFRS 78
Query: 66 CKIDVS 71
+ + +
Sbjct: 79 HEGETA 84
>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 = 37.7 bits (88), Expect = 3e-05
Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
K+ L+ + +G + + I +G + F AI ++ FG K+ +
Sbjct: 37 KEDLFRIFSPYGHIMQINIKN----AFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 37.8 bits (88), Expect = 4e-05
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
+ ++D + L +K+G+V V+I+ V F A++ +
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILL---HPRTRKHLGLARVLFTSTRGAKETV 65
Query: 56 LGSHEKHFFGCKIDVS 71
H G I
Sbjct: 66 KNLHLTSVMGNIIHAQ 81
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 37.6 bits (88), Expect = 4e-05
Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 9/70 (12%)
Query: 5 IYV----VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHE 60
+++ + + S +D L+ + +G + + I +G + F AI +
Sbjct: 13 LFIGNLPLKNVSKED-LFRIFSPYGHIMQINIKN----AFGFIQFDNPQSVRDAIECESQ 67
Query: 61 KHFFGCKIDV 70
+ FG K+ +
Sbjct: 68 EMNFGKKLIL 77
>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 = 38.8 bits (90), Expect = 4e-05
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
L+ + +G V VKI+ + LV + A+ A+ + G I ++
Sbjct: 50 QSLFILFGVYGDVQRVKILFNKKE-NALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 106
Score = 34.2 bits (78), Expect = 0.002
Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 1/70 (1%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
L + + + ++ L + +G V Q + L+ ++A +A++ H
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 213
Query: 63 FF-GCKIDVS 71
+ VS
Sbjct: 214 LGENHHLRVS 223
>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 = 37.7 bits (88), Expect = 5e-05
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 10/76 (13%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
LFIY + L + G V K+ D+ +G V + A+ AI
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI---DKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 56 LGSHEKHFFGCKIDVS 71
+ ++ V
Sbjct: 85 QSMNGFQIGMKRLKVQ 100
>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 = 37.1 bits (86), Expect = 6e-05
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 7/66 (10%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFG 65
S LKD ++ G V + + G G+V F + +D A+ F
Sbjct: 25 PSGSWQDLKD----HMREAGDVCYADVYRDG---TGVVEFVRKEDMTYAVRKLDNTKFRS 77
Query: 66 CKIDVS 71
+ + +
Sbjct: 78 HEGETA 83
>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 = 36.7 bits (86), Expect = 7e-05
Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 10/78 (12%)
Query: 1 MALFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEK 53
L+I + + L + +GK+ K I D+ YG V F A+K
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL---DKTTNKCKGYGFVDFDSPSAAQK 62
Query: 54 AILGSHEKHFFGCKIDVS 71
A+ S
Sbjct: 63 AVTALKASGVQAQMAKQS 80
>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 = 36.8 bits (86), Expect = 7e-05
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 14/72 (19%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGS 58
I+V + L+ +++ G+V ++ Y V +K DA+ AI
Sbjct: 12 IFVGNVSAACTSQELRS----LFERRGRVIECDVVK----DYAFVHMEKEADAKAAIAQL 63
Query: 59 HEKHFFGCKIDV 70
+ K G +I+V
Sbjct: 64 NGKEVKGKRINV 75
>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 = 36.8 bits (86), Expect = 7e-05
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 15/82 (18%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKII----GQGGDR---YGLVCFKKAD 49
LFI + ++ +LK + K G + I G +G V +KK +
Sbjct: 6 SGLFIKNLNFSTTEETLKG----VFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 50 DAEKAILGSHEKHFFGCKIDVS 71
A+KA+ G K++V
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVR 83
>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 = 36.9 bits (86), Expect = 7e-05
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 18/77 (23%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-----YGLVCFKKADDAEK 53
++V D L+ + + GK+ V+II + +G V F+ + DA++
Sbjct: 18 LHVSNIPFRFRDPDLRQ----MFGQFGKILDVEIIF---NERGSKGFGFVTFENSADADR 70
Query: 54 AILGSHEKHFFGCKIDV 70
A H G KI+V
Sbjct: 71 AREKLHGTVVEGRKIEV 87
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 36.9 bits (86), Expect = 8e-05
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIG-QGGDR-YGLVCFKKADDAEKAIL 56
++V D L+ + + GK+ V+II + G + +G V F+ + DA++A
Sbjct: 32 LHVSNIPFRFRDPDLRQ----MFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 87
Query: 57 GSHEKHFFGCKIDVS 71
H G KI+V+
Sbjct: 88 KLHGTVVEGRKIEVN 102
>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 = 37.0 bits (86), Expect = 8e-05
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 13/76 (17%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAI 55
+ V VSD +++ + + G + + R V F++ DA KA+
Sbjct: 38 LLVSNLDFGVSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 93
Query: 56 LGSHEKHFFGCKIDVS 71
G +D+
Sbjct: 94 KQYKGVPLDGRPMDIQ 109
>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 = 37.0 bits (86), Expect = 8e-05
Identities = 10/71 (14%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 5 IYV----VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHE 60
+YV ++ T L+ + G + + + V ++K + A++A+ +
Sbjct: 42 LYVYGEDMTPTLLRG----AFSPFGNIIDLSMDPPRN--CAFVTYEKMESADQAVAELNG 95
Query: 61 KHFFGCKIDVS 71
++ V+
Sbjct: 96 TQVESVQLKVN 106
>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 = 36.8 bits (86), Expect = 1e-04
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 15 DGLYHEYKKHGKVSWVKIIG-QGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
LY + G + K++ + G + YG V F+ + AE+AI + K+ V
Sbjct: 20 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 79
Query: 73 Y 73
+
Sbjct: 80 F 80
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 36.6 bits (85), Expect = 1e-04
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
K + + K+G+V+ + +G Y V + A A+LG + + G +D++
Sbjct: 42 KSDVETIFSKYGRVAGCSVH-KG---YAFVQYSNERHARAAVLGENGRVLAGQTLDIN 95
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 37.0 bits (86), Expect = 1e-04
Identities = 16/60 (26%), Positives = 22/60 (36%), Gaps = 10/60 (16%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
LFIY + L + G V K+ D+ +G V F D A+ AI
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFI---DKQTSLSKCFGFVSFDNPDSAQVAI 99
>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 = 36.1 bits (84), Expect = 1e-04
Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 6/70 (8%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKI-IGQGGDRYGLVCFKKADDAEKAILGSHEK 61
+YV + ++ ++ + E+ + ++ + Y V F +DA +A+ + K
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---YAFVHFSNREDAVEAMKALNGK 74
Query: 62 HFFGCKIDVS 71
G I+V+
Sbjct: 75 VLDGSPIEVT 84
>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 = 36.1 bits (84), Expect = 2e-04
Identities = 10/65 (15%), Positives = 25/65 (38%), Gaps = 3/65 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSH 59
LF+ +++ ++ + ++ G + ++ G + V F +A+ AI H
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 60 EKHFF 64
Sbjct: 78 GSQTM 82
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 36.0 bits (84), Expect = 2e-04
Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGD--RYGLVCFKKADDAEKAILGSHE 60
L++ + D + L + G ++ K++ +GG +G VCF ++A KA+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 61 KHFFGCKIDVS 71
+ + V+
Sbjct: 78 RIVATKPLYVA 88
>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 = 36.2 bits (84), Expect = 2e-04
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 17/78 (21%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAE 52
LFI ++ LK + KHG +S V +I DR + + F+ DA+
Sbjct: 10 LFIGGLNRETNEKMLKA----VFGKHGPISEVLLIK---DRTSKSRGFAFITFENPADAK 62
Query: 53 KAILGSHEKHFFGCKIDV 70
A + K G I V
Sbjct: 63 NAAKDMNGKSLHGKAIKV 80
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 35.7 bits (83), Expect = 2e-04
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
+YV + + K L + +G + V I + V F+ DAE A+ G K
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-GFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 63 FFGCKIDV 70
G ++ V
Sbjct: 62 ICGSRVRV 69
>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 = 36.9 bits (86), Expect = 2e-04
Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 6/73 (8%)
Query: 5 IYV---VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGS 58
+ V + D L ++ ++ + + ++ ++ A+ AE+A +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 59 HEKHFFGCKIDVS 71
G + VS
Sbjct: 247 DGLSLGGSHLRVS 259
Score = 33.4 bits (77), Expect = 0.003
Identities = 10/62 (16%), Positives = 19/62 (30%), Gaps = 4/62 (6%)
Query: 14 KDGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKID 69
+ + G + ++ G + YG + K D A +A K +
Sbjct: 109 QQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY 168
Query: 70 VS 71
V
Sbjct: 169 VH 170
Score = 29.2 bits (66), Expect = 0.12
Identities = 7/32 (21%), Positives = 11/32 (34%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
V + AE AI H+ ++ V
Sbjct: 59 TAFVTLLNGEQAEAAINAFHQSRLRERELSVQ 90
>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 = 36.8 bits (85), Expect = 2e-04
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 1/59 (1%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
L+ + +G V VKI+ + LV + A+ A+ + G I ++
Sbjct: 18 PQSLFILFGVYGDVQRVKILFNKKE-NALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 75
Score = 31.8 bits (72), Expect = 0.010
Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 1/70 (1%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
L + + + ++ L + +G V Q + L+ ++A +A++ H
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182
Query: 63 FF-GCKIDVS 71
+ VS
Sbjct: 183 LGENHHLRVS 192
>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 = 35.7 bits (83), Expect = 2e-04
Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 19/79 (24%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAE 52
+ V VSD +++ + + G + + DR V F++ DA
Sbjct: 32 LLVSNLDFGVSDADIQE----LFAEFGTLKKAAVHY---DRSGRSLGTADVHFERKADAL 84
Query: 53 KAILGSHEKHFFGCKIDVS 71
KA+ + G +++
Sbjct: 85 KAMKQYNGVPLDGRPMNIQ 103
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 35.7 bits (82), Expect = 2e-04
Identities = 18/67 (26%), Positives = 27/67 (40%), Gaps = 1/67 (1%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQG-GDRYGLVCFKKADDAEKAILGSHEKHFF 64
Y +S L+ L + +HGKV V++ +V + DA A+ H
Sbjct: 19 YRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIG 78
Query: 65 GCKIDVS 71
KI VS
Sbjct: 79 SKKILVS 85
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 35.5 bits (82), Expect = 2e-04
Identities = 10/70 (14%), Positives = 23/70 (32%), Gaps = 1/70 (1%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGD-RYGLVCFKKADDAEKAILGSHEK 61
L I + + L ++G V + + + V + D A +A+ +
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGF 77
Query: 62 HFFGCKIDVS 71
+ V+
Sbjct: 78 QLENFTLKVA 87
>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 = 35.7 bits (83), Expect = 3e-04
Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 3/73 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSH 59
L+I + + + L + K G+V +I+ G R G + + E I +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 60 EKHFFGCKIDVSP 72
K +P
Sbjct: 88 GKFIKTPPGVSAP 100
>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 = 35.3 bits (82), Expect = 3e-04
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 11/75 (14%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAEKAIL 56
++V + ++ LY + + G ++ V I DR +G VCFK + AI
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICK---DREGKPKSFGFVCFKHPESVSYAIA 75
Query: 57 GSHEKHFFGCKIDVS 71
+ +G I+VS
Sbjct: 76 LLNGIRLYGRPINVS 90
>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 = 35.2 bits (82), Expect = 3e-04
Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 20/80 (25%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
++V V D +L++ +K ++ D YG V F DDA
Sbjct: 4 LFVGDLNVNVDDETLRN----AFKDFPSYLSGHVMW---DMQTGSSRGYGFVSFTSQDDA 56
Query: 52 EKAILGSHEKHFFGCKIDVS 71
+ A+ + G + ++
Sbjct: 57 QNAMDSMQGQDLNGRPLRIN 76
>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 = 36.0 bits (83), Expect = 3e-04
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRY-------GLVCFKKADDAEKAI 55
+ V ++ + D L ++K+G+V V I DRY V F DAE A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR---DRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 56 LGSHEKHFFGCKIDV 70
G ++ V
Sbjct: 130 DAMDGAVLDGRELRV 144
>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 = 35.0 bits (81), Expect = 3e-04
Identities = 10/71 (14%), Positives = 28/71 (39%), Gaps = 10/71 (14%)
Query: 5 IYV----VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHE 60
+YV ++ T L+ + G + + + V ++K + A++A+ +
Sbjct: 18 LYVYGEDMTPTLLRG----AFSPFGNIIDLSMDPPRN--CAFVTYEKMESADQAVAELNG 71
Query: 61 KHFFGCKIDVS 71
++ V+
Sbjct: 72 TQVESVQLKVN 82
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 34.9 bits (81), Expect = 3e-04
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAI 55
+F+ + + LKD ++ + G V + I + G + G+V F+ + AE+A
Sbjct: 11 IFVRNLPFDFTWKMLKD----KFNECGHVLYADIKMENG-KSKGCGVVKFESPEVAERAC 65
Query: 56 LGSHEKHFFGCKIDV 70
+ G +IDV
Sbjct: 66 RMMNGMKLSGREIDV 80
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 35.2 bits (81), Expect = 4e-04
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 3/65 (4%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFG 65
S LKD + + ++ + + D G + F + +A+ + F G
Sbjct: 38 EGCSWQDLKD---LARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRG 94
Query: 66 CKIDV 70
I V
Sbjct: 95 SVITV 99
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.4 bits (81), Expect = 4e-04
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFF-GC---KIDV 70
D L+ + K G V + + L+ + A+ A L ++ + C +ID
Sbjct: 43 DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 102
Query: 71 SPYHDVDFE 79
S ++ +
Sbjct: 103 SKLTSLNVK 111
>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 = 35.8 bits (82), Expect = 4e-04
Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFF--GCKIDVS 71
D L+ + K G V + + L+ + A+ A L ++ + C + +
Sbjct: 61 DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID 119
>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 = 35.0 bits (81), Expect = 5e-04
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 20/64 (31%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
++V ++ +K + G++S +++ D YG V F DA
Sbjct: 18 VFVGDLSPEITTEDIKA----AFAPFGRISDARVVK---DMATGKSKGYGFVSFFNKWDA 70
Query: 52 EKAI 55
E AI
Sbjct: 71 ENAI 74
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 35.6 bits (82), Expect = 5e-04
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 13/76 (17%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAI 55
+ V VSD +++ + + G + + R V F++ DA KA+
Sbjct: 91 LLVSNLDFGVSDADIQE----LFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 146
Query: 56 LGSHEKHFFGCKIDVS 71
G +D+
Sbjct: 147 KQYKGVPLDGRPMDIQ 162
>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 = 34.5 bits (80), Expect = 6e-04
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 7/70 (10%)
Query: 9 SDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKI 68
+TSL L E+ + G + + + GD + + ++ D A+ A G
Sbjct: 27 PNTSLAA-LAREFDRFGSIRTIDHVK--GDSFAYIQYESLDAAQAACAKMRGFPLGGPDR 83
Query: 69 DVSPYHDVDF 78
+ VDF
Sbjct: 84 RLR----VDF 89
>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 = 34.2 bits (79), Expect = 8e-04
Identities = 9/57 (15%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
+ + G++ +++ + G Y V F + A AI+ + G +
Sbjct: 40 QLMRQTFSPFGQIMEIRVFPEKG--YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 94
>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 = 34.1 bits (79), Expect = 9e-04
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 18/79 (22%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
LF+ + ++ SL+ + K+G++S V ++ DR +G V F+ DDA
Sbjct: 15 LFVGGLSFDTNEQSLEQ----VFSKYGQISEVVVVK---DRETQRSRGFGFVTFENIDDA 67
Query: 52 EKAILGSHEKHFFGCKIDV 70
+ A++ + K G +I V
Sbjct: 68 KDAMMAMNGKSVDGRQIRV 86
>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 = 35.0 bits (81), Expect = 0.001
Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 9/75 (12%)
Query: 5 IYVV---SDTSLKDGLYHEYKKHGKVSWVKII----GQGGDR-YGLVCFKKADDAEKAIL 56
I + ++ ++ L ++ G + + I + + F+ D AE+A+
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271
Query: 57 GSHEKHFFGCKIDVS 71
+ +I VS
Sbjct: 272 QMNRSLLGNREISVS 286
Score = 32.7 bits (75), Expect = 0.006
Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 3/63 (4%)
Query: 15 DGLYHEYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
+ +Y +K G + V + + R+ + F + D A AI +H K +I VS
Sbjct: 56 NKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH-KVVGQNEIIVSH 114
Query: 73 YHD 75
+
Sbjct: 115 LTE 117
Score = 31.9 bits (73), Expect = 0.010
Identities = 5/61 (8%), Positives = 16/61 (26%), Gaps = 4/61 (6%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGD----RYGLVCFKKADDAEKAILGSHEKHFFGCKID 69
+ + + V+ + R+ + +DA + + G +
Sbjct: 131 QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV 190
Query: 70 V 70
Sbjct: 191 T 191
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 33.8 bits (78), Expect = 0.001
Identities = 9/69 (13%), Positives = 22/69 (31%), Gaps = 4/69 (5%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
Y+ + + + L ++ G + K + G + + + A I+
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG--CCFIKYDTHEQAAVCIVALANFP 87
Query: 63 FFGCKIDVS 71
F G +
Sbjct: 88 FQGRNLRTG 96
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 34.3 bits (78), Expect = 0.001
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 3/60 (5%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFG--CKIDVS 71
D LY GKV +I + +V F+ A+KA + + C + +
Sbjct: 39 VDVLYTVCNPVGKV-QRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIE 97
>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 = 33.7 bits (78), Expect = 0.001
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 21/81 (25%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR--------YGLVCFKKADD 50
+++ V+ + + + +GK+ + + +R Y V F+ D+
Sbjct: 7 VHIGRLTRNVTKDHIME----IFSTYGKIKMIDMPV---ERMHPHLSKGYAYVEFENPDE 59
Query: 51 AEKAILGSHEKHFFGCKIDVS 71
AEKA+ G +I +
Sbjct: 60 AEKALKHMDGGQIDGQEITAT 80
>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 = 33.3 bits (77), Expect = 0.001
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 20/80 (25%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
+YV +++ L + K+GKV V I+ D+ + F D A
Sbjct: 19 VYVSNLPFSLTNNDLYR----IFSKYGKVVKVTIMK---DKDTRKSKGVAFILFLDKDSA 71
Query: 52 EKAILGSHEKHFFGCKIDVS 71
+ + K FG I S
Sbjct: 72 QNCTRAINNKQLFGRVIKAS 91
>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 = 33.8 bits (78), Expect = 0.001
Identities = 13/73 (17%), Positives = 29/73 (39%), Gaps = 12/73 (16%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGS 58
++V +++ ++ ++K+GK V I G +G + + AE A +
Sbjct: 18 LFVGNLPPDITEEEMRK----LFEKYGKAGEVFIHKDKG--FGFIRLETRTLAEIAKVEL 71
Query: 59 HEKHFFGCKIDVS 71
G ++ V
Sbjct: 72 DNMPLRGKQLRVR 84
>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 = 33.4 bits (77), Expect = 0.002
Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDRYGLVCFKKADDAEKAIL 56
+YV V++ + L+ + G K+I D Y V F + DA A+
Sbjct: 18 LYVGNLSRDVTEVLILQ-LFSQI---GPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALA 73
Query: 57 GSHEKHFFGCKIDVS 71
+ + G ++ V+
Sbjct: 74 AMNGRKILGKEVKVN 88
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 33.4 bits (77), Expect = 0.002
Identities = 10/72 (13%), Positives = 23/72 (31%), Gaps = 16/72 (22%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKII---------GQGGDRYGLVCFKKADDAEK 53
+Y+ +S + L + + + I GQ + F + A +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA-----FITFPNKEIAWQ 82
Query: 54 AILGSHEKHFFG 65
A+ + +G
Sbjct: 83 ALHLVNGYKLYG 94
>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 = 33.0 bits (76), Expect = 0.002
Identities = 7/33 (21%), Positives = 17/33 (51%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
+V F+ D+A A++ +++ K+ +S
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG 91
>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 = 33.6 bits (77), Expect = 0.002
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 18/82 (21%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKAD 49
L + V + L+ L+ Y G + VKI+ DR YG V F+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQ-LFERY---GPIESVKIVC---DRETRQSRGYGFVKFQSGS 95
Query: 50 DAEKAILGSHEKHFFGCKIDVS 71
A++AI G + + ++ V+
Sbjct: 96 SAQQAIAGLNGFNILNKRLKVA 117
>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 = 33.9 bits (77), Expect = 0.002
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 1/60 (1%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPYH 74
D +++ + +G V VK + +V ++AI + FG K++V
Sbjct: 20 DRVFNVFCLYGNVEKVKFMKSKPG-AAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK 78
Score = 32.4 bits (73), Expect = 0.007
Identities = 9/76 (11%), Positives = 21/76 (27%), Gaps = 5/76 (6%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKI---IGQGGDR-YGLVCFKKADDAEKAILGS 58
L + ++ + + G + G+ GL+ + DA + +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 59 HEKHFFGCKIDVSPYH 74
+ PY
Sbjct: 186 NHYQMKNPNGPY-PYT 200
>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 = 32.6 bits (75), Expect = 0.002
Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
+YV + DT + L + + + G++ + ++ + + F AE A S K
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ--CAFIQFATRQAAEVAAEKSFNKL 72
Query: 63 FF-GCKIDVS 71
G +++V
Sbjct: 73 IVNGRRLNVK 82
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 33.6 bits (77), Expect = 0.002
Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 20/80 (25%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
+YV V D L + G ++ ++I D + V F+ A+DA
Sbjct: 66 LYVGGLAEEVDDKVLHA----AFIPFGDITDIQIPL---DYETEKHRGFAFVEFELAEDA 118
Query: 52 EKAILGSHEKHFFGCKIDVS 71
AI +E FG I V+
Sbjct: 119 AAAIDNMNESELFGRTIRVN 138
>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 = 32.6 bits (75), Expect = 0.003
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFGCK 67
L + K+G ++ V I+ D+ + V F+ DDA++A ++ G +
Sbjct: 30 RDLREVFSKYGPIADVSIVY---DQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 68 IDVS 71
I VS
Sbjct: 87 IRVS 90
>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 = 32.6 bits (75), Expect = 0.003
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 18/82 (21%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKAD 49
L++ V D L + G ++ ++I D + V F+ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHA----AFIPFGDITDIQIPL---DYETEKHRGFAFVEFELAE 65
Query: 50 DAEKAILGSHEKHFFGCKIDVS 71
DA AI +E FG I V+
Sbjct: 66 DAAAAIDNMNESELFGRTIRVN 87
>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 = 33.1 bits (76), Expect = 0.003
Identities = 6/54 (11%), Positives = 19/54 (35%), Gaps = 10/54 (18%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEK 61
+ L ++ G + +V+++ F + A+K + + +
Sbjct: 30 EALGEVLQQFGDLKYVRVVL---HPDTEHSKGCAFAQFMTQEAAQKCLAAASLE 80
>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 = 32.6 bits (75), Expect = 0.003
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 21/80 (26%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAE 52
++V + +T ++ + ++G V VKII DR YG V F D +
Sbjct: 12 VFVGGIDVRMDETEIRS----FFARYGSVKEVKIIT---DRTGVSKGYGFVSFYNDVDVQ 64
Query: 53 KAILGSHEKHFFGCKIDVSP 72
K + F G K+ + P
Sbjct: 65 KIVESQIN--FHGKKLKLGP 82
>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 = 33.5 bits (76), Expect = 0.003
Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 20/85 (23%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHG--KVSWVKIIGQGGDR-------YGLVCFKK 47
+AL+I + +D L + G + +K +R + LV
Sbjct: 69 IALYIGNLTWWTTDEDLTE----AVHSLGVNDILEIKFFE---NRANGQSKGFALVGVGS 121
Query: 48 ADDAEKAILGSHEKHFFGCKIDVSP 72
++K + ++ G V+P
Sbjct: 122 EASSKKLMDLLPKRELHGQNPVVTP 146
>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 = 32.8 bits (75), Expect = 0.004
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFGCK 67
L + K+G ++ V I+ D+ + V F+ DDA++A ++ G +
Sbjct: 61 RDLREVFSKYGPIADVSIVY---DQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 68 IDV 70
I V
Sbjct: 118 IRV 120
>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 = 33.0 bits (76), Expect = 0.004
Identities = 11/75 (14%), Positives = 23/75 (30%), Gaps = 6/75 (8%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII-----GQGGDR-YGLVCFKKADDAEKAIL 56
+F+ V T + L ++++G V + ++ + V F A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 57 GSHEKHFFGCKIDVS 71
H
Sbjct: 66 ALHNMKVLPGMHHPI 80
Score = 30.3 bits (69), Expect = 0.039
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 3/65 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSH 59
LFI ++S ++ + + G++ +I+ G R V F A+ AI H
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Query: 60 EKHFF 64
+
Sbjct: 158 QAQTM 162
>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 = 33.0 bits (76), Expect = 0.004
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 5/59 (8%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQ--GGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
D L ++ ++ V G+ G + FK DAEK + G + +
Sbjct: 114 DELKEVFEDALEIRLVSQDGKSKG---IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169
Score = 31.0 bits (71), Expect = 0.020
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 4/59 (6%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
L + + + ++ +G V F+ A+D EKA+ FG +I +
Sbjct: 28 AELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKL 85
>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 = 32.0 bits (73), Expect = 0.004
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 39 RYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
R V + A+ AI H+ F G + V
Sbjct: 41 RTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ 73
>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 = 31.8 bits (73), Expect = 0.005
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 20/64 (31%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
++V ++ ++ + G++S +++ D YG V F DA
Sbjct: 9 VFVGDLSPEITTAAIAA----AFAPFGRISDARVVK---DMATGKSKGYGFVSFFNKWDA 61
Query: 52 EKAI 55
E AI
Sbjct: 62 ENAI 65
>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 = 32.4 bits (74), Expect = 0.005
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V ++ A+ A+ K F G K+ VS
Sbjct: 67 DATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL 99
>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 = 31.8 bits (72), Expect = 0.007
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 21 YKKHGKVSWVKII-------GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
+ K GK+ V I QG V + +++DA +AI + G + S
Sbjct: 39 FGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 96
>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 = 31.3 bits (72), Expect = 0.007
Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 20/80 (25%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
+YV V D L + G ++ ++I D + V F+ A+DA
Sbjct: 10 LYVGGLAEEVDDKVLHAA----FIPFGDITDIQIPL---DYETEKHRGFAFVEFELAEDA 62
Query: 52 EKAILGSHEKHFFGCKIDVS 71
AI +E FG I V+
Sbjct: 63 AAAIDNMNESELFGRTIRVN 82
>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 = 32.2 bits (74), Expect = 0.007
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 15 DGLYHEYKKHGKVSWVKII----GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
LY ++ G ++ +I+ Y V F D+++AI + ++ V
Sbjct: 18 RELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKV 77
Query: 71 S 71
S
Sbjct: 78 S 78
Score = 29.8 bits (68), Expect = 0.050
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 15 DGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAI 55
D L + K+G + I+ G R V + K ++A++AI
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
>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 = 31.9 bits (73), Expect = 0.007
Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 18/82 (21%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKAD 49
M L++ + +++ L+ ++ G++ ++++ D YG + F ++
Sbjct: 27 MRLYVGSLHFNITEDMLRG----IFEPFGRIESIQLMM---DSETGRSKGYGFITFSDSE 79
Query: 50 DAEKAILGSHEKHFFGCKIDVS 71
A+KA+ + G + V
Sbjct: 80 CAKKALEQLNGFELAGRPMKVG 101
>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 = 31.4 bits (72), Expect = 0.007
Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 18/82 (21%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKAD 49
L++ + +++ L+ ++ GK+ + ++ D YG + F ++
Sbjct: 6 SGLYVGSLHFNITEDMLRG----IFEPFGKIDNIVLMK---DSDTGRSKGYGFITFSDSE 58
Query: 50 DAEKAILGSHEKHFFGCKIDVS 71
A +A+ + G + V
Sbjct: 59 CARRALEQLNGFELAGRPMRVG 80
>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 = 31.8 bits (72), Expect = 0.010
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 5 IYV---VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEK 61
+YV ++ + + L + +G + V + + V F+ DA A+ +
Sbjct: 76 VYVGNLGNNGNKTE-LERAFGYYGPLRSVWVAR-NPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 62 HFFGCKIDV 70
GC++ V
Sbjct: 134 TLCGCRVRV 142
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 31.5 bits (72), Expect = 0.010
Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 17/79 (21%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR------YGLVCFKKADDAE 52
LFI + + L++ K HG V ++++ +R V ++ A
Sbjct: 20 LFISGLPFSCTKEELEE----ICKAHGTVKDLRLVT---NRAGKPKGLAYVEYENESQAS 72
Query: 53 KAILGSHEKHFFGCKIDVS 71
+A++ I V+
Sbjct: 73 QAVMKMDGMTIKENIIKVA 91
>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 = 30.7 bits (70), Expect = 0.014
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
+V F+ D+A A++ +++ K+ +
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL 91
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding;
1.90A {Homo sapiens} PDB: 3sde_B
Length = 261
Score = 31.6 bits (72), Expect = 0.015
Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 4/58 (6%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
+ ++++G+ S V I DR +G + + AE A + +
Sbjct: 37 EDFKRLFERYGEPSEVFINR---DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIR 91
Score = 31.2 bits (71), Expect = 0.019
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 3/68 (4%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAILGSH 59
L + +S + L + + G V ++ +G G V F A KA+
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158
Query: 60 EKHFFGCK 67
+ F
Sbjct: 159 DGAFLLTT 166
>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 = 31.5 bits (72), Expect = 0.015
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 15 DGLYHEYKKHGKVSWVKII-GQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
LY + G + K++ + G + YG V F+ + AE+AI + K+ V
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Query: 73 Y 73
+
Sbjct: 178 F 178
Score = 26.1 bits (58), Expect = 1.1
Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 17 LYHEYKKHGKVSWVKII----GQGGDRYGLVCFKKADDAEKAI 55
LY ++ G + +++ + Y V F++ DAE+A+
Sbjct: 32 LYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
>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 = 30.8 bits (70), Expect = 0.019
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 7/77 (9%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAILGS 58
LFI + + L +++ GK+ + ++ G + + + + + A KA
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 59 HEKHFF---GCKIDVSP 72
HE+ I V P
Sbjct: 76 HEQKTLPGMNRPIQVKP 92
>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 = 31.0 bits (71), Expect = 0.021
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 10/64 (15%)
Query: 15 DGLYHEYKKHGKVSWVKII-------GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCK 67
+ + G++ K++ G YG V + DAEKAI +
Sbjct: 17 EEFRSLFGSIGEIESCKLVRDKITGQSLG---YGFVNYIDPKDAEKAINTLNGLRLQTKT 73
Query: 68 IDVS 71
I VS
Sbjct: 74 IKVS 77
Score = 27.9 bits (63), Expect = 0.28
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 15 DGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAI 55
L + ++G++ +I+ G R G + F K +AE+AI
Sbjct: 103 KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>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 = 30.4 bits (69), Expect = 0.021
Identities = 17/74 (22%), Positives = 25/74 (33%)
Query: 10 DTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKID 69
DT +KD + E KHG V + + V A A+ H + F G I
Sbjct: 27 DTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMIT 86
Query: 70 VSPYHDVDFELEFR 83
+ + F
Sbjct: 87 AAYVPLPTYHNLFP 100
>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 = 30.4 bits (69), Expect = 0.021
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 14 KDGLYHEYKKHGKVSWVKII----GQGGDR-YGLVCFKKADDAEKAILG-SHEKHFFGCK 67
+ + + G++ V++ G G R +G V F DA+KA H H +G +
Sbjct: 29 QREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR 88
Query: 68 IDV 70
+ +
Sbjct: 89 LVL 91
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 30.7 bits (70), Expect = 0.026
Identities = 8/60 (13%), Positives = 21/60 (35%), Gaps = 4/60 (6%)
Query: 15 DGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
D + + G + + + + + V ++ + A+ A+ + G I V
Sbjct: 43 DTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
Score = 30.0 bits (68), Expect = 0.051
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKAI 55
IYV V D + ++ GK+ + G + YG + ++KA ++ A+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
>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 = 30.2 bits (68), Expect = 0.028
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 10 DTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSHEKHFFGC 66
D ++ +K+G+V + + GD V F++ +DAEKA++ + + F G
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 67 KIDVS 71
I
Sbjct: 97 PIHAE 101
>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 = 30.4 bits (69), Expect = 0.029
Identities = 12/63 (19%), Positives = 30/63 (47%), Gaps = 10/63 (15%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFGCK 67
+ ++ ++ ++G++ + + DR Y LV ++ +A+ A+ G + + G
Sbjct: 37 EDIHDKFAEYGEIKNIHLNL---DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 93
Query: 68 IDV 70
I V
Sbjct: 94 ISV 96
>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 = 29.9 bits (68), Expect = 0.033
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 20/64 (31%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
I V +T L++ ++ G +S + + D+ + + F + +DA
Sbjct: 18 IRVTNLSEDTRETDLQE----LFRPFGSISRIYLAK---DKTTGQSKGFAFISFHRREDA 70
Query: 52 EKAI 55
+AI
Sbjct: 71 ARAI 74
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 30.1 bits (68), Expect = 0.037
Identities = 11/33 (33%), Positives = 12/33 (36%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V F A+ AI K F G I VS
Sbjct: 59 EATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 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 = 29.5 bits (67), Expect = 0.038
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 16/83 (19%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKAD 49
+AL+I + +D L + H + +K +R + LV
Sbjct: 2 IALYIGNLTWWTTDEDLTE-AVHSLGV-NDILEIKFFE---NRANGQSKGFALVGVGSEA 56
Query: 50 DAEKAILGSHEKHFFGCKIDVSP 72
++K + ++ G V+P
Sbjct: 57 SSKKLMDLLPKRELHGQNPVVTP 79
>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 = 29.8 bits (67), Expect = 0.038
Identities = 10/62 (16%), Positives = 21/62 (33%), Gaps = 3/62 (4%)
Query: 10 DTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKID 69
T + + + + G + V + G +V F + +A KA F +
Sbjct: 21 GTLAAE-IQETFSRFGSLGRVLLPEGGI--TAIVEFLEPLEARKAFRHLAYSKFHHVPLY 77
Query: 70 VS 71
+
Sbjct: 78 LE 79
>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 = 30.2 bits (68), Expect = 0.039
Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 10/63 (15%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFGCK 67
D + ++ +G++ + + DR Y LV ++ A A + G
Sbjct: 87 DEIQEKFCDYGEIKNIHLNL---DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 143
Query: 68 IDV 70
I V
Sbjct: 144 IQV 146
>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 = 29.7 bits (67), Expect = 0.040
Identities = 12/61 (19%), Positives = 27/61 (44%)
Query: 13 LKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
+++ L E K G++ + + + D V F+ ++A+ I + F G +I
Sbjct: 39 IREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
Query: 73 Y 73
+
Sbjct: 99 W 99
>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 = 29.5 bits (67), Expect = 0.049
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 18/81 (22%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRY-------GLVCFKKAD 49
+ L + Y S SL+ ++K+G+V V I + + V F
Sbjct: 14 ITLKVDNLTYRTSPDSLRR----VFEKYGRVGDVYIPR---EPHTKAPRGFAFVRFHDRR 66
Query: 50 DAEKAILGSHEKHFFGCKIDV 70
DA+ A G ++ V
Sbjct: 67 DAQDAEAAMDGAELDGRELRV 87
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 29.7 bits (67), Expect = 0.049
Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 3/68 (4%)
Query: 13 LKDGLYHEYKKHGKVSWVKIIGQGGD--RYGLVCFKKADDAEKAILGSHEKHFFG-CKID 69
LK+ ++ + K GK++ + G Y + + A A+ +
Sbjct: 34 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR 93
Query: 70 VSPYHDVD 77
V+ + D D
Sbjct: 94 VNLFTDFD 101
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 29.5 bits (66), Expect = 0.051
Identities = 8/71 (11%), Positives = 20/71 (28%), Gaps = 4/71 (5%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAI--LGSHE 60
+ I + + + GKV+ + ++ + + A + S
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN--QAFIEMNTEEAANTMVNYYTSVT 91
Query: 61 KHFFGCKIDVS 71
G I +
Sbjct: 92 PVLRGQPIYIQ 102
>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 = 29.2 bits (66), Expect = 0.057
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 20/74 (27%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
+YV VS+ L + L+ + G V + DR YG V F +DA
Sbjct: 18 VYVGGLDEKVSEPLLWE-LFLQA---GPVVNTHMPK---DRVTGQHQGYGFVEFLSEEDA 70
Query: 52 EKAILGSHEKHFFG 65
+ AI +G
Sbjct: 71 DYAIKIMDMIKLYG 84
>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 = 29.1 bits (66), Expect = 0.062
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 18/81 (22%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
LF+ Y S+ L+ + +G +S + D + V F + A
Sbjct: 11 LFVRNLSYTSSEEDLEK----LFSAYGPLSELHYPI---DSLTKKPKGFAFVTFMFPEHA 63
Query: 52 EKAILGSHEKHFFGCKIDVSP 72
KA + F G + V P
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLP 84
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 29.8 bits (66), Expect = 0.064
Identities = 9/76 (11%), Positives = 22/76 (28%), Gaps = 2/76 (2%)
Query: 8 VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCK 67
+ ++ + + + G + ++ + G V FK +AE A +
Sbjct: 151 LKPAQIESRIRFVFSRLGDIDRIRYVESKN--CGFVKFKYQANAEFAKEAMSNQTLLLPS 208
Query: 68 IDVSPYHDVDFELEFR 83
L +
Sbjct: 209 DKEWDDRREGTGLLVK 224
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 29.3 bits (66), Expect = 0.066
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 12/75 (16%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRY-------GLVCFKKADDAEKAI 55
+ V ++ + D L ++K+G+V V I DRY V F DAE A+
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR---DRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 56 LGSHEKHFFGCKIDV 70
G ++ V
Sbjct: 107 DAMDGAVLDGRELRV 121
>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 = 29.1 bits (66), Expect = 0.068
Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 20/80 (25%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
++V ++ LKD ++ E G V +++ DR YG ++ + A
Sbjct: 11 VFVGNIPYEATEEQLKD-IFSEV---GPVVSFRLVY---DRETGKPKGYGFCEYQDQETA 63
Query: 52 EKAILGSHEKHFFGCKIDVS 71
A+ + + F G + V
Sbjct: 64 LSAMRNLNGREFSGRALRVD 83
>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 = 29.3 bits (66), Expect = 0.070
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
LV FK DDA K+ H K G + V
Sbjct: 59 QALVQFKNEDDARKS-ERLHRKKLNGREAFVHV 90
>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 = 28.8 bits (65), Expect = 0.076
Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 13/76 (17%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQ--GGDRYGLVCFKKADDAEKA 54
L + +++ LK+ ++ ++ V G+ G + FK DAEK
Sbjct: 17 RTLLAKNLSFNITEDELKE----VFEDALEIRLVSQDGKSKG---IAYIEFKSEADAEKN 69
Query: 55 ILGSHEKHFFGCKIDV 70
+ G + +
Sbjct: 70 LEEKQGAEIDGRSVSL 85
>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 = 28.8 bits (65), Expect = 0.084
Identities = 11/33 (33%), Positives = 12/33 (36%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V F A+ AI K F G I VS
Sbjct: 65 EATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 29.1 bits (65), Expect = 0.087
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 20/85 (23%)
Query: 1 MALFI----YVVSDTSLKDGLYHEYKKHG--KVSWVKIIGQGGDR-------YGLVCFKK 47
A+++ + +D L + G V +K +R Y V
Sbjct: 56 AAVYVGSFSWWTTDQQLIQ----VIRSIGVYDVVELKFAE---NRANGQSKGYAEVVVAS 108
Query: 48 ADDAEKAILGSHEKHFFGCKIDVSP 72
+ K + K G K+DV P
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRP 133
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 28.8 bits (65), Expect = 0.094
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 10/55 (18%)
Query: 23 KHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
++G++ + + DR Y LV ++ +A+ A+ G + + G I V
Sbjct: 46 EYGEIKNIHLNL---DRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
>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 = 28.8 bits (65), Expect = 0.095
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 3/44 (6%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAI 55
L + + + ++ +G V F+ A+D EKA+
Sbjct: 32 AELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75
>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 = 29.0 bits (65), Expect = 0.096
Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 11/72 (15%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSW--------VKIIGQGGDR-YGLVCFKKADDAEK 53
IYV ++ + L + + ++ S ++++ +G + + A K
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 54 AILGSHEKHFFG 65
A+ ++ FG
Sbjct: 108 ALKEANGYVLFG 119
>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 = 28.7 bits (64), Expect = 0.10
Identities = 7/59 (11%), Positives = 21/59 (35%), Gaps = 2/59 (3%)
Query: 14 KDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
++ L +K G V + + Y ++ +++++A + + K
Sbjct: 41 RNQLLPVLEKCGLVDALLMPPNKP--YSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT 97
>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 = 28.4 bits (64), Expect = 0.12
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 10/55 (18%)
Query: 23 KHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
+G++ + + DR Y LV ++ A A + G I V
Sbjct: 49 DYGEIKNIHLNL---DRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 28.1 bits (63), Expect = 0.13
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 2/55 (3%)
Query: 13 LKDGLYHEYKKHGKVSWVKIIGQGGD--RYGLVCFKKADDAEKAILGSHEKHFFG 65
LK+ ++ + K GK++ + G Y + + A A+ +
Sbjct: 20 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 74
>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 = 28.6 bits (65), Expect = 0.16
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
+ L + +K ++ D YG V F DDA+ A+
Sbjct: 102 ETLRNAFKDFPSYLSGHVMW---DMQTGSSRGYGFVSFTSQDDAQNAM 146
Score = 27.5 bits (62), Expect = 0.32
Identities = 10/57 (17%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 17 LYHEYKKHGKVSWVKII---GQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDV 70
L ++ G ++ +KI+ Y V + ++ DA A+ + K + +
Sbjct: 17 LKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKI 73
>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 = 28.3 bits (63), Expect = 0.17
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
G V F+ D + A L H+++ I V P
Sbjct: 69 EGFVEFRNEADYKAA-LCRHKQYMGNRFIQVHP 100
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 27.7 bits (62), Expect = 0.19
Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 2/70 (2%)
Query: 3 LFIYVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
+F+ L + G V+ V + G + +V E L +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG-VFAIVEMGDVGAREAV-LSQSQHS 68
Query: 63 FFGCKIDVSP 72
G ++ V P
Sbjct: 69 LGGHRLRVRP 78
>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 = 28.0 bits (63), Expect = 0.20
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 21/79 (26%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
LF+ ++ +LK+ +I+ DR +G V F +DA
Sbjct: 18 LFVKGLSEDTTEETLKESF-------DGSVRARIVT---DRETGSSKGFGFVDFNSEEDA 67
Query: 52 EKAILGSHEKHFFGCKIDV 70
+ A + G K+ +
Sbjct: 68 KAAKEAMEDGEIDGNKVTL 86
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 27.5 bits (61), Expect = 0.28
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 20 EYKKHGKVSWVKI-----IGQGGDRYGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPYH 74
E +K+GKV I + F++ + A KA++ + ++F G + Y+
Sbjct: 33 ECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYN 92
Query: 75 DVDFE 79
F
Sbjct: 93 LDKFR 97
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 27.2 bits (61), Expect = 0.29
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 12/60 (20%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKII--GQGGDR-YGLVCFKKADDAEKAI 55
++V V D L + Y K++ G + YG V F + ++A+
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVY---PSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRAL 68
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 27.0 bits (59), Expect = 0.47
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 41 GLVCFKKADDAEKAILGSHEKHFFGCKIDVS 71
++ F D AE+A + FG +I VS
Sbjct: 49 AILRFINQDSAERAQKRMENEDVFGNRIIVS 79
>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 = 27.3 bits (61), Expect = 0.47
Identities = 8/61 (13%), Positives = 23/61 (37%), Gaps = 14/61 (22%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKA 54
+++ ++D +K+ L G + ++ G + Y + + ++A
Sbjct: 117 LFIGGLPNYLNDDQVKELL----TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 55 I 55
I
Sbjct: 173 I 173
>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 = 26.4 bits (59), Expect = 0.68
Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 13/75 (17%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGS 58
+Y+ V+ L+ + +++ + G Y V + + A +AI
Sbjct: 11 LYIGNLSPAVTADDLRQ----LFGDRKLPLAGQVLLKSG--YAFVDYPDQNWAIRAIETL 64
Query: 59 HEK-HFFGCKIDVSP 72
K G ++V
Sbjct: 65 SGKVELHGKIMEVDY 79
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 26.9 bits (59), Expect = 0.68
Identities = 13/77 (16%), Positives = 24/77 (31%), Gaps = 5/77 (6%)
Query: 6 YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSHEKH 62
+ S +++ + H + V I R V DD + A L +
Sbjct: 54 WSCSVEDVQN-FLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMA-LKKDRES 111
Query: 63 FFGCKIDVSPYHDVDFE 79
I+V H + +
Sbjct: 112 MGHRYIEVFKSHRTEMD 128
>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 = 26.6 bits (59), Expect = 0.69
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 15/78 (19%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
+YV V S L + G ++ + I+ D+ Y + F + + + A+
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILC---DKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 56 -LGSHEKHFFGCKIDVSP 72
+ E F G I V P
Sbjct: 96 AM--DETVFRGRTIKVLP 111
>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 = 26.0 bits (58), Expect = 0.76
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 5/63 (7%)
Query: 15 DGLYHEYKKHGKV-SWVKII---GQGGDR-YGLVCFKKADDAEKAILGSHEKHFFGCKID 69
LY + G + KI+ G + Y + F D ++ AI + ++ I
Sbjct: 20 KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT 79
Query: 70 VSP 72
VS
Sbjct: 80 VSY 82
>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 = 26.3 bits (58), Expect = 0.88
Identities = 12/73 (16%), Positives = 23/73 (31%), Gaps = 6/73 (8%)
Query: 13 LKDGLYHEYKKHGKVSWVKIIGQGGDRY------GLVCFKKADDAEKAILGSHEKHFFGC 66
+ + + E K+G V ++I V F D +KA+ G + F
Sbjct: 28 IVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANR 87
Query: 67 KIDVSPYHDVDFE 79
+ +
Sbjct: 88 VVVTKYCDPDSYH 100
>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 = 25.7 bits (57), Expect = 1.1
Identities = 7/40 (17%), Positives = 15/40 (37%), Gaps = 10/40 (25%)
Query: 23 KHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAI 55
G V +K++ D Y + F+ + + A+
Sbjct: 25 NVGPVINLKMMF---DPQTGRSKGYAFIEFRDLESSASAV 61
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 25.8 bits (57), Expect = 1.1
Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 13 LKDGLYHEYKKHGKVSWVKIIGQGGDR----YGLVCFKKADDAEKAILGSHEKHFFG-CK 67
LK L + K GKV ++ + V +DA+K I H K +
Sbjct: 25 LKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR 84
Query: 68 IDVSPYHDVD 77
+ + DV+
Sbjct: 85 LFLYTMKDVE 94
>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 = 25.9 bits (57), Expect = 1.5
Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 12/67 (17%)
Query: 15 DGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDAEKAILGSHEKHFFG-- 65
+ +Y + K G + + + G D+ + V + DAE A+ +
Sbjct: 54 EQIYELFSKSGDIKKIIM---GLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110
Query: 66 CKIDVSP 72
+ D
Sbjct: 111 IRTDWDA 117
>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 = 25.3 bits (56), Expect = 1.8
Identities = 12/75 (16%), Positives = 32/75 (42%), Gaps = 14/75 (18%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAI 55
L + Y ++ +L++ ++K + K+ + Y + F +DA++A+
Sbjct: 18 LVLSNLSYSATEETLQE----VFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 56 LGSHEKHFFGCKIDV 70
+++ G I +
Sbjct: 71 NSCNKREIEGRAIRL 85
>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic
sequnece for R-proteins, ribonucleoprotein, ribosoma
protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A
{Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z*
3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z*
3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z*
3i56_Z* 3cpw_Y* 4adx_Z
Length = 116
Score = 25.3 bits (55), Expect = 1.9
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 5/41 (12%)
Query: 23 KHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHF 63
G+ G RYG V ++ + E +E H
Sbjct: 27 SKSGK--TGSSGRFGARYGRVSRRRVAEIESE---MNEDHA 62
>3d53_A Inorganic pyrophosphatase; seattle structural G center for
infectious disease, ssgcid, hydrolase, magnesium
binding; 2.20A {Rickettsia prowazekii} PDB: 3emj_A*
Length = 173
Score = 25.3 bits (56), Expect = 1.9
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 10/42 (23%)
Query: 21 YKKHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKH 62
YK K WVK+ G G AE I +++
Sbjct: 142 YKDLEKGKWVKVTGWGD----------KVKAETLIKEGIDRN 173
>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 = 25.3 bits (56), Expect = 2.2
Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 14/77 (18%)
Query: 5 IYV------VSDTSLKDGLYHEYKKHGKVSWVKII---GQGGDR-YGLVCFKKADDAEKA 54
+++ ++D +K+ L G + ++ G + Y + + ++A
Sbjct: 97 LFIGGLPNYLNDDQVKELL----TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 55 ILGSHEKHFFGCKIDVS 71
I G + K+ V
Sbjct: 153 IAGLNGMQLGDKKLLVQ 169
>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 = 24.8 bits (54), Expect = 2.7
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V F + AEKA LG H++ I+V
Sbjct: 86 EAFVQFASQELAEKA-LGKHKERIGHRYIEVFK 117
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 24.7 bits (54), Expect = 2.9
Identities = 9/76 (11%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 5 IYV--VSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR---YGLVCFKKADDAEKAILGSH 59
+Y+ + D + + G+V +++ V F + A+K + +
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF-VETP 72
Query: 60 EKHFFGCKIDVSPYHD 75
+ + + + D
Sbjct: 73 GQKYKETDLLILFKDD 88
>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 = 24.7 bits (54), Expect = 3.1
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V F + AEKA L H++ I++
Sbjct: 59 EAFVQFASQEIAEKA-LKKHKERIGHRYIEIFK 90
>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 = 24.7 bits (54), Expect = 3.1
Identities = 19/78 (24%), Positives = 27/78 (34%), Gaps = 8/78 (10%)
Query: 10 DTSLKDGLYHEYKKHGKVSWVKI--------IGQGGDRYGLVCFKKADDAEKAILGSHEK 61
D L+ + E K G V+ V I V F A + KAI + +
Sbjct: 35 DDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR 94
Query: 62 HFFGCKIDVSPYHDVDFE 79
F G K+ Y F+
Sbjct: 95 WFAGRKVVAEVYDQERFD 112
>3tvi_A Aspartokinase; structural genomics, ACT domains, regulatory
domains, kinase transferase, PSI-2, protein structure
initiative; HET: LYS; 3.00A {Clostridium acetobutylicum}
Length = 446
Score = 24.9 bits (55), Expect = 3.2
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 30 VKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHF 63
+++I QG ++ + D EKA+ +
Sbjct: 405 IRMIDQGSSEINVIVGVETVDFEKAVKSIYNAFN 438
>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 = 24.7 bits (54), Expect = 3.3
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSPYHDVDFE 79
GLV F D +A L + ++VSP + +
Sbjct: 58 NGLVKFLSPQDTFEA-LKRNRMLMIQRYVEVSPATERQWV 96
>3iz5_m 60S ribosomal protein L43 (L37AE); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_m 1ysh_D 2zkr_z
Length = 92
Score = 24.4 bits (53), Expect = 3.4
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 23 KHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHF 63
K K I+G+ G RYG K+ E + H K+F
Sbjct: 3 KRTKK--AGIVGKYGTRYGASLRKQIKKMEVS---QHSKYF 38
>3izc_m 60S ribosomal protein RPL43 (L37AE); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins; NMR {Saccharomyces cerevisiae} PDB:
3izs_m 3o58_g 3o5h_g 3u5e_p 3u5i_p 1s1i_9
Length = 92
Score = 24.4 bits (53), Expect = 3.5
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 23 KHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHF 63
K K V I G+ G RYG ++ E H ++
Sbjct: 3 KRTKK--VGITGKYGVRYGSSLRRQVKKLEIQ---QHARYD 38
>1elu_A L-cysteine/L-cystine C-S lyase; FES cluster biosynthesis, pyridoxal
5'-phosphate, thiocystei aminoacrylate, enzyme-product
complex; HET: PDA; 1.55A {Synechocystis SP} SCOP:
c.67.1.3 PDB: 1elq_A* 1n2t_A* 1n31_A*
Length = 390
Score = 24.8 bits (55), Expect = 4.0
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 26 KVSWVKIIGQGGDRYGLVCF 45
++ V + + GLV F
Sbjct: 315 QLPHVHCLATSAPQAGLVSF 334
>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_Y 4a1c_Y 4a1e_Y
Length = 103
Score = 24.1 bits (52), Expect = 4.5
Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 5/41 (12%)
Query: 23 KHGKVSWVKIIGQGGDRYGLVCFKKADDAEKAILGSHEKHF 63
K + V I + G RYG K E H K+
Sbjct: 3 KRTQK--VGITRKYGTRYGASLRKVVKKFEIT---QHAKYG 38
>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 = 24.4 bits (53), Expect = 5.0
Identities = 5/33 (15%), Positives = 11/33 (33%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V F ++A A + + I++
Sbjct: 88 EADVEFATHEEAVAA-MSKDRANMQHRYIELFL 119
>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur,
iron-sulfur cluster, pyruvate catabolism, TPP-dependent
enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP:
c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB:
1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A*
2pda_A* 2uza_A*
Length = 1231
Score = 24.4 bits (53), Expect = 6.3
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 37 GDRYGLVCFKKADDAEKAI--LGS 58
G Y L + A DAE+ I +GS
Sbjct: 254 GRSYKLFDYVGAPDAERVIVSMGS 277
>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 = 23.8 bits (52), Expect = 6.3
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
Y V F ++ ++A L + ++ G I+V
Sbjct: 52 YIFVDFSNEEEVKQA-LKCNREYMGGRYIEVFR 83
>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 = 23.7 bits (52), Expect = 7.0
Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 18/69 (26%)
Query: 3 LFI----YVVSDTSLKDGLYHEYKKHGKVSWVKIIGQGGDR-------YGLVCFKKADDA 51
L + + ++ LK+ + G+V V++ D +G V F + +
Sbjct: 18 LIVLGLPWKTTEQDLKE----YFSTFGEVLMVQVKK---DLKTGHSKGFGFVRFTEYETQ 70
Query: 52 EKAILGSHE 60
K + H
Sbjct: 71 VKVMSQRHM 79
>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 = 23.5 bits (51), Expect = 7.4
Identities = 5/33 (15%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 40 YGLVCFKKADDAEKAILGSHEKHFFGCKIDVSP 72
V F +DA A + + + +++
Sbjct: 57 EADVEFATHEDAVAA-MAKDKANMQHRYVELFL 88
>3n7s_C Receptor activity-modifying protein 1; GPCR, class B GPCR,
antagonist, olcegepant, telcagepant, MIG membrane
protein; HET: 3N6 3N7; 2.10A {Homo sapiens} PDB:
3n7r_C* 3n7p_D* 2yx8_A
Length = 96
Score = 23.4 bits (50), Expect = 8.6
Identities = 6/25 (24%), Positives = 10/25 (40%)
Query: 51 AEKAILGSHEKHFFGCKIDVSPYHD 75
++ L H ++F C I D
Sbjct: 68 VDRFFLAVHGRYFRSCPISGRAVRD 92
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
0.324 0.143 0.451
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: 1,366,270
Number of extensions: 69680
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 291
Number of HSP's successfully gapped: 177
Length of query: 83
Length of database: 6,701,793
Length adjustment: 51
Effective length of query: 32
Effective length of database: 5,277,822
Effective search space: 168890304
Effective search space used: 168890304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.4 bits)