RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3930
(299 letters)
>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 = 109 bits (272), Expect = 4e-29
Identities = 43/167 (25%), Positives = 76/167 (45%), Gaps = 11/167 (6%)
Query: 101 GGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE-IEVSVFLKCNKLARLTHD 159
G + L +I + +E+Y D NL +D+F + ++ + + + +K N+L RLT D
Sbjct: 4 GDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTD 63
Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTV---------VVQDKPDVDECTIYVEKLPPEAEH 210
+ +V+AL KSK + K + + K DV ++Y++ P +A
Sbjct: 64 FNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATL 123
Query: 211 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
D I+ G+V + + + KG FV F + E A K +E
Sbjct: 124 DDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 169
Score = 47.1 bits (111), Expect = 1e-06
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 1 MEFYLSDSNLRKDRFFSQLLQESPE-IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEV 59
+E+Y D NL +D+F + ++ + + + +K N+L RLT D + +V+AL KSK +
Sbjct: 20 IEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELM 79
Query: 60 TEDG 63
Sbjct: 80 EISE 83
>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA
binding protein; 1.60A {Trypanosoma brucei} SCOP:
a.4.5.46
Length = 92
Score = 86.7 bits (215), Expect = 6e-22
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVK 165
+ Q++ +EFY SD N+++D F + E+ E + + L ++ +T D +VV+
Sbjct: 9 ENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVE 68
Query: 166 ALRKSKLLEVTEDGTKVRR 184
A+R S+ L ++EDG VRR
Sbjct: 69 AIRPSEKLVLSEDGLMVRR 87
Score = 78.3 bits (193), Expect = 9e-19
Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 1 MEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLE 58
+EFY SD N+++D F + E+ E + + L ++ +T D +VV+A+R S+ L
Sbjct: 18 VEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLV 77
Query: 59 VTEDGTKVK 67
++EDG V+
Sbjct: 78 LSEDGLMVR 86
>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: a.4.5.46
Length = 101
Score = 84.5 bits (209), Expect = 7e-21
Identities = 23/80 (28%), Positives = 39/80 (48%)
Query: 105 RKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVV 164
+ L + + +EF S NL KD + + I + ++ +LT DPD ++
Sbjct: 10 STEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLIL 69
Query: 165 KALRKSKLLEVTEDGTKVRR 184
+ LR S +++V E G KVR
Sbjct: 70 EVLRSSPMVQVDEKGEKVRP 89
Score = 74.9 bits (184), Expect = 3e-17
Identities = 24/79 (30%), Positives = 39/79 (49%)
Query: 1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 60
+EF S NL KD + + I + ++ +LT DPD +++ LR S +++V
Sbjct: 22 LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVD 81
Query: 61 EDGTKVKGNIIRHFLVPIS 79
E G KV+ + R P S
Sbjct: 82 EKGEKVRPSHKRCISGPSS 100
>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 = 77.6 bits (192), Expect = 2e-18
Identities = 23/66 (34%), Positives = 35/66 (53%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
+ D +IYV + A + +E+ F G V V++ K +G KGFA++EFS KE
Sbjct: 2 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
Query: 252 AKALEL 257
+L L
Sbjct: 62 RTSLAL 67
>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 = 77.6 bits (192), Expect = 3e-18
Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
D TI V L + ++ +F +G ++ + L K K+TG+ KGFAF+ F +E+AA+A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 255 LELGLN 260
+ G++
Sbjct: 74 IA-GVS 78
>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 = 77.1 bits (190), Expect = 7e-18
Identities = 16/69 (23%), Positives = 39/69 (56%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
++K ++D+ ++YV + + +E+ FS G + +++ K +G KG+A++EF+ +
Sbjct: 29 EEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER 88
Query: 249 EEAAKALEL 257
A+ +
Sbjct: 89 NSVDAAVAM 97
>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 = 76.6 bits (189), Expect = 7e-18
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFST 247
Q I V +P +A I +FS +G++ V LPK TG +GF FV+F T
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 248 KEEAAKALE 256
K++A KA
Sbjct: 68 KQDAKKAFN 76
>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 = 74.9 bits (185), Expect = 2e-17
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ +YV L E + + + F +G +T + +P T K +GFAFVEF E+AA A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 255 LELGLN 260
++ +N
Sbjct: 66 ID-NMN 70
>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 = 75.4 bits (186), Expect = 2e-17
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
+ D T++ +L +E FS GKV V + +++ + KG A+VEF +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 251 AAKALEL 257
A+ L
Sbjct: 80 VPLAIGL 86
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 75.0 bits (185), Expect = 2e-17
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
+ V+ ++V + EA + I F++YG++ + L + TG LKG+ VE+ T +
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
Query: 250 EAAKALELGLN 260
EA A+E GLN
Sbjct: 77 EAQAAME-GLN 86
>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 = 74.2 bits (183), Expect = 4e-17
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ +YV L E + + + F +G +T + +P T K +GFAFVEF E+AA A
Sbjct: 11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 255 LELGLN 260
++ +N
Sbjct: 71 ID-NMN 75
>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 = 74.2 bits (183), Expect = 4e-17
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 192 PDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
PDVD T+ V+ L D + VF KYG+V V +P+ T +GFAFV F + +
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67
Query: 251 AAKALELGLN 260
A A ++
Sbjct: 68 AQDAEA-AMD 76
>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 = 73.8 bits (182), Expect = 5e-17
Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ T+YV LP ++ + +FSKYGKV V++ K K T K KG AF+ F K+ A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 255 LELGLN 260
+N
Sbjct: 75 TR-AIN 79
>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 = 74.3 bits (183), Expect = 6e-17
Identities = 18/62 (29%), Positives = 32/62 (51%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ T+++ L ++E + + V ++G + YV + T KG AF +F T+E A K
Sbjct: 14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
Query: 255 LE 256
L
Sbjct: 74 LA 75
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 74.8 bits (184), Expect = 6e-17
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ +YV L E + + + F +G +T + +P T K +GFAFVEF E+AA A
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 255 LELGLN 260
++ +N
Sbjct: 122 ID-NMN 126
>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 = 73.9 bits (182), Expect = 8e-17
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
+ V+ ++V + EA+ D I+ F YG++ + L + TG KG+A VE+ T +
Sbjct: 20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
Query: 250 EAAKALELGLN 260
+A A E LN
Sbjct: 80 QALAAKE-ALN 89
>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 = 73.6 bits (181), Expect = 1e-16
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
+ V+ ++V + EA + I F++YG++ + L + TG LKG+ VE+ T +
Sbjct: 16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
Query: 250 EAAKALELGLN 260
EA A+E GLN
Sbjct: 76 EAQAAME-GLN 85
>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 = 72.6 bits (179), Expect = 1e-16
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+YV L D + +F +GK+ + L K TG+ KG+ F+ FS E A +A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 255 LELGLN 260
LE LN
Sbjct: 64 LE-QLN 68
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 72.3 bits (178), Expect = 2e-16
Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 184 RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFV 243
+ V + +++ +++ LP + +E + +G V + L + GK KG A+V
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63
Query: 244 EFSTKEEAAKALELGLN 260
E+ + +A++A+ ++
Sbjct: 64 EYENESQASQAVM-KMD 79
>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 = 72.2 bits (178), Expect = 2e-16
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
++V L + + +E +FS YG ++ + P T K KGFAFV F E
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 250 EAAKALELGLN 260
A KA ++
Sbjct: 62 HAVKAYA-EVD 71
>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 = 71.0 bits (175), Expect = 4e-16
Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEAAKAL 255
+++ +L D+I +FS YGK+ + +P + KG+A+VEF +EA KAL
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 256 ELGLN 260
+ ++
Sbjct: 65 K-HMD 68
>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 = 73.3 bits (180), Expect = 5e-16
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
V+ ++V + EA+ D I+ F YG++ + L + TG KG+A VE+ T ++A
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129
Query: 254 ALELGLN 260
A E LN
Sbjct: 130 AKE-ALN 135
>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 = 70.8 bits (174), Expect = 8e-16
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ T+YV L + + +F + G V +PK + TG+ +G+ FVEF ++E+A A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 255 LELGLN 260
++ ++
Sbjct: 74 IK-IMD 78
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 71.7 bits (176), Expect = 9e-16
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
++ V+ L D + VF KYG+V V +P+ + T + +GFAFV F K +A A
Sbjct: 46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105
Query: 255 LELGLN 260
++ ++
Sbjct: 106 MD-AMD 110
>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 = 70.4 bits (173), Expect = 1e-15
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
K +YV L D + +F +G++ + L TG+ KG+ F+ FS E
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 251 AAKALELGLN 260
A KALE LN
Sbjct: 81 AKKALE-QLN 89
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 70.2 bits (172), Expect = 1e-15
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
K DV ++Y++ P +A D I+ G+V + + + KG FV F + E
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIES 64
Query: 251 AAKALEL 257
A K +E
Sbjct: 65 AKKFVET 71
>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 = 70.0 bits (172), Expect = 2e-15
Identities = 17/68 (25%), Positives = 36/68 (52%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
D D +++ ++P + ++ +F ++GK+ +++ K + TG KG AF+ + +
Sbjct: 6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65
Query: 249 EEAAKALE 256
E A KA
Sbjct: 66 ESALKAQS 73
>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 = 71.4 bits (176), Expect = 2e-15
Identities = 20/99 (20%), Positives = 39/99 (39%), Gaps = 4/99 (4%)
Query: 159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
P V + ++ +L DG + + I+V + P+ E FS
Sbjct: 54 KPSSVDEVVKTQHIL----DGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFS 109
Query: 219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
++G + L K TG+ +GF FV + + + + +
Sbjct: 110 QWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148
Score = 55.2 bits (134), Expect = 1e-09
Identities = 16/62 (25%), Positives = 31/62 (50%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ C +++ L + D + F KYG VT + + K +TG+ +GF F+ F +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 255 LE 256
++
Sbjct: 62 VK 63
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 71.0 bits (174), Expect = 2e-15
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 164 VKALRKSKLLEVTED-GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGK 222
+KALR +E+++ R Q+K CT+YV L + I +FSK G
Sbjct: 6 LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGD 65
Query: 223 VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ + + K GF FVE+ ++ +A A+
Sbjct: 66 IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
>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 = 2e-15
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
++ V+ L D + VF KYG+V V +P+ + T + +GFAFV F K +A A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 255 LELGLN 260
++ ++
Sbjct: 129 MD-AMD 133
>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 = 69.2 bits (170), Expect = 3e-15
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
DE ++V L + +E VFSKYG+++ V + K + T + +GF FV F ++A A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 255 LELGLN 260
+ +N
Sbjct: 71 MM-AMN 75
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 69.3 bits (170), Expect = 4e-15
Identities = 13/59 (22%), Positives = 26/59 (44%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ +L +++ + KYG+V V + T K G A V F++ A + ++
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
>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 = 68.4 bits (168), Expect = 4e-15
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+Y+ +P + + I + S G V + + TG+ KG+AF+EF E +A A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 257 LGLN 260
LN
Sbjct: 63 -NLN 65
>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 = 68.8 bits (169), Expect = 5e-15
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
D +++V +P EA + ++ +FS+ G V L + TGK KG+ F E+ +E A
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 252 AKALELGLN 260
A+ LN
Sbjct: 64 LSAMR-NLN 71
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 72.3 bits (178), Expect = 7e-15
Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 10/100 (10%)
Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVR-RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESV 216
+ + A+ +++R R + VQ +P + + V LPP E +
Sbjct: 65 LNGEQAEAAINAF-------HQSRLRERELSVQLQPT--DALLCVANLPPSLTQQQFEEL 115
Query: 217 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+G + L + TG+ KG+ F E+ K+ AA+A
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155
Score = 70.4 bits (173), Expect = 3e-14
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 198 TIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ V++LPP + D + S T+ L G+LKGFA +E+ T E A +A +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC-GQDGQLKGFAVLEYETAEMAEEAQQ 244
Score = 56.1 bits (136), Expect = 3e-09
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 7/79 (8%)
Query: 178 DGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL 237
D ++R+ + ++ + I + LP + + + + S Y K+ K
Sbjct: 4 DPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKY 56
Query: 238 KGFAFVEFSTKEEAAKALE 256
KG AFV E+A A+
Sbjct: 57 KGTAFVTLLNGEQAEAAIN 75
>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 = 68.1 bits (167), Expect = 7e-15
Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+K ++V LPP+ + + +F KYGK V + K KGF F+ T+
Sbjct: 8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETR 61
Query: 249 EEAAKALELGLN 260
A A L+
Sbjct: 62 TLAEIAKV-ELD 72
>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 = 1e-14
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+++ L E +++VF K+G ++ V L K + T K +GFAF+ F +A A
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64
Query: 255 LELGLN 260
+ +N
Sbjct: 65 AK-DMN 69
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 70.1 bits (172), Expect = 1e-14
Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 1/87 (1%)
Query: 174 EVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS 233
+ V VV +++ LP D ++ + + +G + +L K +
Sbjct: 92 PGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA 151
Query: 234 TGKLKGFAFVEFSTKEEAAKALELGLN 260
TG KG+AF E+ +A+ GLN
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIA-GLN 177
Score = 61.6 bits (150), Expect = 1e-11
Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 5/66 (7%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEA 251
+YV +P + + F+ ++ ++ + K FAF+EF + +E
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 252 AKALEL 257
+A+
Sbjct: 65 TQAMAF 70
>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 = 68.1 bits (167), Expect = 1e-14
Identities = 21/68 (30%), Positives = 38/68 (55%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
Q K + ++V L PE + I++ F+ +G+++ + K +TGK KG+ FV F K
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 249 EEAAKALE 256
+A A++
Sbjct: 68 WDAENAIQ 75
>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 = 67.8 bits (166), Expect = 2e-14
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 183 RRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAF 242
R V + PD C + V L + VFSKYG + VS+ + + + +GFAF
Sbjct: 34 SRHVGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92
Query: 243 VEFSTKEEAAKALELGLN 260
V F ++A +A E N
Sbjct: 93 VYFENVDDAKEAKE-RAN 109
>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 = 67.3 bits (165), Expect = 2e-14
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
++C IYV LPP+ IE VF KYG + + L K+ FAFVEF +A
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDA 74
Query: 252 AKALELGLN 260
A+ G +
Sbjct: 75 EDAVY-GRD 82
>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 = 66.9 bits (164), Expect = 2e-14
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 1/70 (1%)
Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
V+ +++ L P ++ S+ +++ TG + F +V+F +
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFES 67
Query: 248 KEEAAKALEL 257
E+ KALEL
Sbjct: 68 AEDLEKALEL 77
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 68.8 bits (169), Expect = 2e-14
Identities = 24/106 (22%), Positives = 45/106 (42%), Gaps = 10/106 (9%)
Query: 158 HDPDDVVKALRKSKLLEVTEDGT--KVRRTVVVQDKPDVDECT-IYVEKLPPEAEHDYIE 214
D+ +A+ + G K+RR D + +++ LP D ++
Sbjct: 59 RSVDETTQAM---AFDGIIFQGQSLKIRRP---HDYQPLPGAHKLFIGGLPNYLNDDQVK 112
Query: 215 SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
+ + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 113 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 157
Score = 54.9 bits (133), Expect = 2e-09
Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEAA 252
+YV +P + + F+ ++ ++ + K FAF+EF + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 253 KALEL 257
+A+
Sbjct: 66 QAMAF 70
>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 = 66.4 bits (163), Expect = 2e-14
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+Y+ L P + + YGK+ K+T K KG+ FV+F + A KA
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 255 LELGLN 260
+ L
Sbjct: 64 VT-ALK 68
>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 = 66.5 bits (163), Expect = 2e-14
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ PD C + V L + VFSKYG + VS+ + + + +GFAFV F
Sbjct: 9 RANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Query: 249 EEAAKALELGLN 260
++A +A E N
Sbjct: 68 DDAKEAKE-RAN 78
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 68.8 bits (169), Expect = 2e-14
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 10/100 (10%)
Query: 159 DPDDVVKALRKSKLLEVTEDGTKVR--RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESV 216
+D+ KAL +L + G +++ + K T+ + L D ++ V
Sbjct: 63 SAEDLEKAL---ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEV 119
Query: 217 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
F ++ V GK KG A++EF ++ +A K LE
Sbjct: 120 FEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 154
Score = 63.4 bits (155), Expect = 2e-12
Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 1/70 (1%)
Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
V+ +++ L P ++ S+ +++ TG + F +V+F +
Sbjct: 5 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFES 63
Query: 248 KEEAAKALEL 257
E+ KALEL
Sbjct: 64 AEDLEKALEL 73
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 66.9 bits (164), Expect = 2e-14
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
++ P T YV LP I+++F + V L + K T K KGF +VEF
Sbjct: 8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEV 66
Query: 249 EEAAKALEL 257
+ +AL
Sbjct: 67 DSLKEALTY 75
>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 = 70.0 bits (172), Expect = 5e-14
Identities = 18/99 (18%), Positives = 34/99 (34%), Gaps = 6/99 (6%)
Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVF 217
H D + L + + + + T+ V+ LP + + F
Sbjct: 7 HARPDSKRPLDEGSPAAAGL----TSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYF 62
Query: 218 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
G + +V + S K FA +EF+ + A A+
Sbjct: 63 KHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAIT 99
Score = 69.2 bits (170), Expect = 9e-14
Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 190 DKPDVDECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFST 247
D ++ I + L E + + + F +G + +++P K AF+ F
Sbjct: 204 DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN 263
Query: 248 KEEAAKALEL 257
K+ A +AL++
Sbjct: 264 KDSAERALQM 273
Score = 66.9 bits (164), Expect = 5e-13
Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 12/99 (12%)
Query: 159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
D + A+ K+ + ++V + ECT+++ PP I +
Sbjct: 90 RYDGALAAITKTH-------KVVGQNEIIVSH---LTECTLWMTNFPPSYTQRNIRDLLQ 139
Query: 219 KYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
V + LP + FA+++ ++KE+A +E
Sbjct: 140 DINVVALSIRLPS-LRFNTSRRFAYIDVTSKEDARYCVE 177
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 68.5 bits (168), Expect = 6e-14
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
IYV + + D I+SVF +GK+ +L + +TGK KG+ F+E+ + + A+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Score = 66.2 bits (162), Expect = 5e-13
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 179 GTKVRRTVVVQDKPDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL 237
G ++ R Q + + +YV + E D I F+ +G + + + T K
Sbjct: 10 GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKH 69
Query: 238 KGFAFVEFSTKEEAAKALE 256
KGFAFVE+ E A ALE
Sbjct: 70 KGFAFVEYEVPEAAQLALE 88
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 66.3 bits (162), Expect = 6e-14
Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFA 241
++ + D TI+V+ L + + F + G + ++L + TGKLKG A
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 242 FVEFSTKEEAAKALEL 257
V F A A++
Sbjct: 61 TVSFDDPPSAKAAIDW 76
>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 = 65.4 bits (160), Expect = 7e-14
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 8/77 (10%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGF 240
D TI+V+ L + + F + G + ++L + TGKLKG
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
Query: 241 AFVEFSTKEEAAKALEL 257
A V F A A++
Sbjct: 66 ATVSFDDPPSAKAAIDW 82
>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 = 65.3 bits (160), Expect = 7e-14
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
+ + T++V L + + +F + G +T V++ K + GK K F FV F E
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPES 69
Query: 251 AAKALELGLN 260
+ A+ L LN
Sbjct: 70 VSYAIAL-LN 78
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 65.0 bits (159), Expect = 7e-14
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFST 247
TI + + P D I + S Y V + L K K T + +GFAFV+ S+
Sbjct: 3 HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS 62
Query: 248 KEEAAKALE 256
+A++ L+
Sbjct: 63 AMDASQLLQ 71
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 66.3 bits (162), Expect = 8e-14
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ V +P + + +F +YG + V + + T + +G+ FV+F + A +A
Sbjct: 41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100
Query: 255 LELGLN 260
+ GLN
Sbjct: 101 IA-GLN 105
>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 = 65.0 bits (159), Expect = 1e-13
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ + ++V L + + + +F +G + ++ + G KG AFV+FS+
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSH 66
Query: 249 EEAAKALELGLN 260
EA A+ L+
Sbjct: 67 TEAQAAIH-ALH 77
>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 = 67.3 bits (165), Expect = 1e-13
Identities = 22/105 (20%), Positives = 43/105 (40%), Gaps = 11/105 (10%)
Query: 159 DPDDVVKALR-KSKLLEVTEDGTKVR------RTVVVQDKPDVDECTIYVEKLPPEAEHD 211
++V A+ + + DG V R + + I+V + + E
Sbjct: 64 TVEEVDAAMNARPHKV----DGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 212 YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Score = 55.8 bits (135), Expect = 1e-09
Identities = 15/62 (24%), Positives = 31/62 (50%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+++ L E + + S F ++G +T + + +T + +GF FV ++T EE A
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 255 LE 256
+
Sbjct: 72 MN 73
>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 = 64.5 bits (158), Expect = 1e-13
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
IYV L A + ++ +FS++GKV V L + T K KGF FVE E ++A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA- 60
Query: 258 GLN 260
L+
Sbjct: 61 KLD 63
>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 = 65.1 bits (159), Expect = 1e-13
Identities = 21/77 (27%), Positives = 28/77 (36%), Gaps = 8/77 (10%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGF 240
D D IYV+ L D + F + G V + + K TGK KG
Sbjct: 8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67
Query: 241 AFVEFSTKEEAAKALEL 257
A V + A A+E
Sbjct: 68 ATVSYEDPPTAKAAVEW 84
>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 = 64.6 bits (158), Expect = 2e-13
Identities = 16/60 (26%), Positives = 31/60 (51%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+Y++ L P + S+F+++ + + TG+++G AF+ F KE A +AL
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
>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 = 63.3 bits (155), Expect = 2e-13
Identities = 11/62 (17%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
++V L + + + + F + + TG +G+ FV F+++++A A++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD-S 62
Query: 259 LN 260
+
Sbjct: 63 MQ 64
>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 = 63.3 bits (155), Expect = 3e-13
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
P ++V L PE I + F+ +G+++ + K +TGK KG+ FV F K +A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 252 AKALE 256
A++
Sbjct: 62 ENAIQ 66
>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 = 63.9 bits (156), Expect = 3e-13
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 176 TEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG 235
+ TK R V ++ CT+Y + + FS +G++ + +
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP----- 59
Query: 236 KLKGFAFVEFSTKEEAAKALELGLN 260
KG++FV FST E AA A+ +N
Sbjct: 60 -EKGYSFVRFSTHESAAHAIV-SVN 82
>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 = 66.3 bits (161), Expect = 3e-13
Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 1/91 (1%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+++ ++ P E + + + G S+ F + +E+ +K
Sbjct: 116 KNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSK 175
Query: 249 EEAAKALELGLNPCPPDYQSSILTTTSRLSF 279
+A + L LN + T +L F
Sbjct: 176 SDALETLGF-LNHYQMKNPNGPYPYTLKLCF 205
Score = 46.2 bits (109), Expect = 3e-06
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 6/63 (9%)
Query: 195 DECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
D + V L D + +VF YG V V K K G A VE + +
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57
Query: 254 ALE 256
A+
Sbjct: 58 AIT 60
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 63.1 bits (154), Expect = 6e-13
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 9/72 (12%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ + ++ ++V P + + + +F +G + V + GFAFVEF
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEA 75
Query: 249 EEAAKALELGLN 260
E AAKA+E ++
Sbjct: 76 ESAAKAIE-EVH 86
>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 = 62.6 bits (153), Expect = 6e-13
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEE 250
P T ++ LP + + I+ F ++ V LP+ S +LKGF + EF +
Sbjct: 15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS 73
Query: 251 AAKALEL 257
AL L
Sbjct: 74 LLSALSL 80
>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 = 64.5 bits (158), Expect = 7e-13
Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 12/104 (11%)
Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVR-RTVVV----QDKPDVDECTIYVEKLPPEAEHDY 212
D +A++ +G VR + + V + + +YV LP D
Sbjct: 53 TSEMDSQRAIK-------VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQ 105
Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++++F KYG + ++ + K TG+ +G AFV ++ +EEA +A+
Sbjct: 106 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Score = 61.8 bits (151), Expect = 7e-12
Identities = 13/59 (22%), Positives = 31/59 (52%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ V LP + + ++F G + + + TG G+AFV+F+++ ++ +A++
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 62.3 bits (152), Expect = 1e-12
Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 7/73 (9%)
Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
+ T Y+ +P A + +F +G + KG F+++ T
Sbjct: 19 IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDT 72
Query: 248 KEEAAKALELGLN 260
E+AA + L
Sbjct: 73 HEQAAVCIV-ALA 84
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL---KGFAFVEFSTKEEA 251
++++ L + ++ VFSK G + ++ K K+ + GF FVE+ E+A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 252 AKALE 256
KAL+
Sbjct: 64 QKALK 68
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ T+ + L A + ++ VF K + GK KG+AF+EF++
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQ----NQNGKSKGYAFIEFASF 63
Query: 249 EEAAKALELGLN 260
E+A +AL N
Sbjct: 64 EDAKEALN-SCN 74
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFST 247
P T ++ LP + + I+ F ++ V LP+ S +LKGF + EF
Sbjct: 8 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 66
Query: 248 KEEAAKALEL 257
+ AL L
Sbjct: 67 LDSLLSALSL 76
>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 = 62.0 bits (151), Expect = 1e-12
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 12/71 (16%)
Query: 192 PDVDECTIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
P +++ L + D +E++FSKYG+V S+ K G+AFV++S +
Sbjct: 23 PKSINSRVFIGNLNTALVKKSD-VETIFSKYGRVAGCSVHK--------GYAFVQYSNER 73
Query: 250 EAAKALELGLN 260
A A+ G N
Sbjct: 74 HARAAVL-GEN 83
>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 = 61.5 bits (150), Expect = 2e-12
Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
K T+ + L D ++ VF ++ V GK KG A++EF ++
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEA 64
Query: 250 EAAKALE 256
+A K LE
Sbjct: 65 DAEKNLE 71
>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 = 61.4 bits (150), Expect = 2e-12
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 9/66 (13%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+++ LP EA I S+F +YGKV + +K + FV K A A
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDA 58
Query: 255 LELGLN 260
+ L+
Sbjct: 59 IR-NLH 63
>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 = 61.6 bits (150), Expect = 2e-12
Identities = 16/62 (25%), Positives = 24/62 (38%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
I V+ +P D I F Y + K+ G G A V F +++EA A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 255 LE 256
+
Sbjct: 74 VI 75
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 62.0 bits (151), Expect = 2e-12
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 1/64 (1%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+++ LP E + +F +G V + K T K F FV + A A++
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 257 LGLN 260
+N
Sbjct: 86 -SMN 88
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 62.0 bits (151), Expect = 2e-12
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
C +++ LP E + S F +G V + K T K F FV F + A A++
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 257 LGLN 260
+N
Sbjct: 101 -AMN 103
>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 = 60.8 bits (148), Expect = 3e-12
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
++++ L P + ++I F+ G V V + + + TG G+ FVEF+ A K L
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 256 ELGLN 260
+N
Sbjct: 70 H-KIN 73
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 60.9 bits (148), Expect = 3e-12
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 184 RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFV 243
+ +VV P + + S+FSK GKV + P ++TGK KGF FV
Sbjct: 7 QYIVVNGAP-------VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
Query: 244 EFSTKEEAAKALE 256
E + +A K ++
Sbjct: 60 ECGSMNDAKKIIK 72
>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 = 60.7 bits (148), Expect = 3e-12
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
++V + P + + + F +YG V + K +AFV E+A
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDA 57
Query: 252 AKALELGLN 260
+A+ GL+
Sbjct: 58 VEAIR-GLD 65
>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 = 60.7 bits (148), Expect = 4e-12
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ D T+YV L + I +FS+ G + ++ + FVEF
Sbjct: 8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEH 65
Query: 249 EEAAKALELGLN 260
+AA AL +N
Sbjct: 66 RDAAAALA-AMN 76
>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 = 60.7 bits (148), Expect = 4e-12
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++V + + I S F++YG V V + TG KG+ FV F + K +E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSFYNDVDVQKIVE 68
>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 = 60.8 bits (148), Expect = 5e-12
Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+Y+ LP + + + +F KYG + + + T + +G A+V + +A A++
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65
>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 = 60.4 bits (147), Expect = 5e-12
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ ++V +P + +F ++GK+ V + + K GF FV F
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENS 65
Query: 249 EEAAKALELGLN 260
+A +A E L+
Sbjct: 66 ADADRARE-KLH 76
>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 = 60.0 bits (146), Expect = 6e-12
Identities = 16/62 (25%), Positives = 24/62 (38%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
I V+ +P D I F Y + K+ G G A V F +++EA A
Sbjct: 14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
Query: 255 LE 256
+
Sbjct: 74 VI 75
>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 = 59.9 bits (146), Expect = 6e-12
Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 9/66 (13%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ I+V + + S+F + G+V + +K +AFV + +A A
Sbjct: 8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAA 59
Query: 255 LELGLN 260
+ LN
Sbjct: 60 IA-QLN 64
>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 = 61.9 bits (151), Expect = 7e-12
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL--KGFAFVEFSTKEEAA 252
D ++V ++P + +F +YG V +++ + +S KG FV F T++ A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 253 KALE 256
+A
Sbjct: 62 EAQN 65
Score = 61.1 bits (149), Expect = 1e-11
Identities = 20/107 (18%), Positives = 42/107 (39%), Gaps = 17/107 (15%)
Query: 159 DPDDVVKALRKSKLLEVTEDGTKV--RRTVVVQDKP-------DVDECTIYVEKLPPEAE 209
++A KV +Q KP V++ +++ + +
Sbjct: 56 TRKAALEAQN-------ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCT 108
Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ I +FS +G++ + + G +G AFV F+T+ A A++
Sbjct: 109 ENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTTRAMAQTAIK 154
>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 = 62.3 bits (152), Expect = 8e-12
Identities = 16/68 (23%), Positives = 30/68 (44%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
P ++YV L P+ + FS G + + + + T + G+A+V F
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 249 EEAAKALE 256
+A +AL+
Sbjct: 68 ADAERALD 75
Score = 58.1 bits (141), Expect = 3e-10
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
I+++ L ++ + FS +G + + KG+ FV F T+E A
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAE 157
Query: 253 KALE 256
+A+E
Sbjct: 158 RAIE 161
>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 = 59.9 bits (145), Expect = 1e-11
Identities = 18/69 (26%), Positives = 28/69 (40%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
++ + + LP + I FS V GK+ G AFV+F+++
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94
Query: 249 EEAAKALEL 257
E A KAL
Sbjct: 95 ELAEKALGK 103
>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 = 58.8 bits (143), Expect = 1e-11
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++V L P + F ++G + + K FA++++ + + A A
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 59.2 bits (144), Expect = 1e-11
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++V L + +E FS++GK+ V KLK +AF+ F ++ A KA+E
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAME 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 = 59.0 bits (143), Expect = 2e-11
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGK-VTYVSLPK-FKSTGKLKGFAFVEFSTKE 249
C +++ +P + + I +K + V V + K +GFAFVE+ +
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 250 EAAKALE 256
AA A
Sbjct: 64 AAAMARR 70
>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 = 59.5 bits (144), Expect = 2e-11
Identities = 19/69 (27%), Positives = 28/69 (40%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
P +Y++ LP EAE+ ++ F K V + GK G FVEF +
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
Query: 249 EEAAKALEL 257
+ AL
Sbjct: 78 ADYKAALCR 86
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 59.3 bits (144), Expect = 2e-11
Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ V L I+ +F+++G + ++ + +G+ G A V F + +A KA++
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 58.6 bits (142), Expect = 2e-11
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 11/79 (13%)
Query: 187 VVQDKPDVDE---CTIYVEKLP--PEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKL 237
V++D+P + I V+ +P + I +FSK+GK+T P+ GK
Sbjct: 3 VLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKT 60
Query: 238 KGFAFVEFSTKEEAAKALE 256
KG+ F+E+++ A A++
Sbjct: 61 KGYIFLEYASPAHAVDAVK 79
>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 = 58.0 bits (141), Expect = 2e-11
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 7/63 (11%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
+Y+ L P D + +F G+AFV++ + A +A+E
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE- 62
Query: 258 GLN 260
L+
Sbjct: 63 TLS 65
>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 = 58.6 bits (142), Expect = 2e-11
Identities = 9/69 (13%), Positives = 23/69 (33%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ + + ++ +P + + G+ G A V+F +
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67
Query: 249 EEAAKALEL 257
++A K+ L
Sbjct: 68 DDARKSERL 76
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+Y+ L + + G + + + ++ G+ KGFA V ++ + K ++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 257 LGLN 260
L
Sbjct: 64 -LLP 66
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 189 QDKPDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
D+ + +YV+ L + + + FS +G +T + G+ KGF FV FS+
Sbjct: 7 GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSS 64
Query: 248 KEEAAKALE 256
EEA KA+
Sbjct: 65 PEEATKAVT 73
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 197 CTIYVEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
TIY+ L + + D + ++FS++G++ + + + + K++G AFV F A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65
Query: 253 KALE 256
AL
Sbjct: 66 NALR 69
>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 = 58.5 bits (142), Expect = 3e-11
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
T++V L + ++ VFS G V + + K GK +G V F EA +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 57.8 bits (140), Expect = 3e-11
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 196 ECTIYVEKLP--PEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
+ I V+ +P + I +FSK+GK+T P+ GK KG+ F+E+++
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPA 58
Query: 250 EAAKALE 256
A A++
Sbjct: 59 HAVDAVK 65
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ V L I+ +F+++G + ++ + +G+ G A V F K +A KA++
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 88
>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 = 59.9 bits (146), Expect = 3e-11
Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 2/99 (2%)
Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVF 217
DP D KA+ L + ++ + + + +YV LP +E +F
Sbjct: 52 IDPKDAEKAINTLNGLRL--QTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLF 109
Query: 218 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
S+YG++ + + TG +G F+ F + EA +A++
Sbjct: 110 SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Score = 58.0 bits (141), Expect = 1e-10
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ V LP + S+F G++ L + K TG+ G+ FV + ++A KA+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
>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 = 58.0 bits (141), Expect = 3e-11
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ T++V+ L + + ++ F + + + TG KGF FV+F+++
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSE 64
Query: 249 EEAAKALELGLN 260
E+A A E +
Sbjct: 65 EDAKAAKE-AME 75
>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 = 59.8 bits (146), Expect = 3e-11
Identities = 11/59 (18%), Positives = 28/59 (47%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++V L + + + + F + + TG +G+ FV F+++++A A++
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147
Score = 56.4 bits (137), Expect = 5e-10
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+YV L D ++ F G + + + K K +AFVE+ +A AL+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 57.6 bits (140), Expect = 3e-11
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
C I+V LP + ++ F++ G V Y + GK KG V+F + E A +A
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR 66
Query: 257 LGLN 260
+N
Sbjct: 67 -MMN 69
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 58.1 bits (141), Expect = 4e-11
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 3/82 (3%)
Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK 238
V R + + ++V +P + +F ++GK+ V + + K
Sbjct: 12 SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK-- 69
Query: 239 GFAFVEFSTKEEAAKALELGLN 260
GF FV F +A +A E L+
Sbjct: 70 GFGFVTFENSADADRARE-KLH 90
>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 = 58.2 bits (141), Expect = 5e-11
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 9/82 (10%)
Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK 238
G R + + T+YV + + FS +G + +S+ +
Sbjct: 22 GPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP------PR 73
Query: 239 GFAFVEFSTKEEAAKALELGLN 260
AFV + E A +A+ LN
Sbjct: 74 NCAFVTYEKMESADQAVA-ELN 94
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 57.2 bits (139), Expect = 5e-11
Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 12/68 (17%)
Query: 195 DECTIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
+ +++ LP + + D + +FS YG + +++ F F++F +
Sbjct: 9 PKSRLFIGNLPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVR 59
Query: 253 KALELGLN 260
A+E +
Sbjct: 60 DAIE-CES 66
>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 = 58.7 bits (142), Expect = 5e-11
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+++ LP +A + I + FS V V + G++ G A VEF+T
Sbjct: 39 FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEI-GPDGRVTGEADVEFATH 96
Query: 249 EEAAKALEL 257
EEA A+
Sbjct: 97 EEAVAAMSK 105
>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 = 56.9 bits (138), Expect = 6e-11
Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
D T+YV L + + F ++G++ +++ + + AF++F+T++ A
Sbjct: 9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAE 62
Query: 253 KALELGLN 260
A E N
Sbjct: 63 VAAEKSFN 70
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 57.3 bits (139), Expect = 6e-11
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
+YV L A +E FS YG + V + + GFAFVEF +A A+ G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIAR-----NPPGFAFVEFEDPRDAEDAVR-G 56
Query: 259 LN 260
L+
Sbjct: 57 LD 58
>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 = 57.6 bits (140), Expect = 7e-11
Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
+ + D +Y+ LP + +E++ +G+V + + S+G +G F + E+
Sbjct: 20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEK 78
Query: 251 AAKALELGLN 260
+ N
Sbjct: 79 CEAVIG-HFN 87
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 56.4 bits (137), Expect = 8e-11
Identities = 19/58 (32%), Positives = 29/58 (50%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
I+V L P+ + I F +G+V + LP T K +GF F+ F +E K +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 56.6 bits (137), Expect = 1e-10
Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 191 KPDVDECTIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ + +++ LP + + D + +FS YG + +++ F F++F
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67
Query: 249 EEAAKALE 256
+ A+E
Sbjct: 68 QSVRDAIE 75
>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 = 58.0 bits (140), Expect = 1e-10
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
+C +YV L +E F YG + V + + GFAFVEF +A
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDA 123
Query: 252 AKALELGLN 260
A A+ L+
Sbjct: 124 ADAVR-ELD 131
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 57.9 bits (140), Expect = 2e-10
Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
+ V L I+ +F+++G + ++ + +G+ G A V F + +A KA+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV-DYDRSGRSLGTADVHFERRADALKAM 146
Query: 256 E 256
+
Sbjct: 147 K 147
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+YV L + IE F+ + K ++ +AFV FS +E+A +A++
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMK 69
>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 = 55.9 bits (135), Expect = 2e-10
Identities = 17/63 (26%), Positives = 28/63 (44%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
++ + + LP + I FS V G+ G AFV+F+++E A KA
Sbjct: 14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73
Query: 255 LEL 257
L+
Sbjct: 74 LKK 76
>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 = 14/59 (23%), Positives = 27/59 (45%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
I+V +P + F K+G VT V + + +GF F+ F ++ +A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>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 = 58.6 bits (141), Expect = 2e-10
Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
+Y+ L + + G + + + ++ G+ KGFA V ++ + K +
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 256 E 256
+
Sbjct: 130 D 130
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 55.5 bits (134), Expect = 2e-10
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ + +PP + + ++S+ +YG V S V +S+K++A +A
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQA 70
Query: 255 LELGLN 260
L+ LN
Sbjct: 71 LD-KLN 75
>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 = 59.1 bits (142), Expect = 3e-10
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 197 CTIYVEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
TIY+ L + + D + ++FS++G++ + + + + K++G AFV F A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 253 KALE 256
AL
Sbjct: 67 NALR 70
Score = 49.1 bits (116), Expect = 6e-07
Identities = 13/60 (21%), Positives = 25/60 (41%), Gaps = 5/60 (8%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+++ LP E + +F+++ V L + AFVEF + +A A +
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262
>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 = 55.2 bits (133), Expect = 4e-10
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ I + LP I+ FS++G + V LP+ A VEF EA KA
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKA 62
Query: 255 LE 256
Sbjct: 63 FR 64
>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 = 54.5 bits (132), Expect = 5e-10
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF---KSTGKLKGFAFVEFSTKEEAAKA 254
I++ L PE + + FS +G + + PK TG KG+AF+ F++ + + A
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 255 LELGLN 260
+E +N
Sbjct: 65 IE-AMN 69
>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 = 54.9 bits (133), Expect = 6e-10
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
I+++ L ++ + FS +G + +S KG+ FV F T+E A +A
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERA 61
Query: 255 LELGLN 260
+E +N
Sbjct: 62 IE-KMN 66
>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 = 54.2 bits (131), Expect = 7e-10
Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 8/68 (11%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ + T+YV + + FS +G + +S+ + AFV +
Sbjct: 8 ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKM 59
Query: 249 EEAAKALE 256
E A +A+
Sbjct: 60 ESADQAVA 67
>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 = 54.3 bits (131), Expect = 8e-10
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+++ LP A + I + FS V + G++ G A VEF+T
Sbjct: 8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEI-GPDGRVTGEADVEFATH 65
Query: 249 EEAAKALEL 257
E+A A+
Sbjct: 66 EDAVAAMAK 74
>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 = 57.9 bits (139), Expect = 9e-10
Identities = 25/159 (15%), Positives = 53/159 (33%), Gaps = 9/159 (5%)
Query: 144 VSVFLKCNKLARLTHDPDDVVKAL--RKSKLLEVTEDGTKVRRTVVVQDKPDVD------ 195
++ +++ + R P + K E E + T + P D
Sbjct: 41 IAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGD 100
Query: 196 -ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
T++V ++ + + F YG + + + K +GK +G+AF+E+ + + A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 255 LELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWF 293
+ + + R G P G
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 55.3 bits (133), Expect = 1e-09
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 3/65 (4%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
+YV + V G V + + ++ G+ KG+A V +++ K L
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 256 ELGLN 260
E L
Sbjct: 117 E-LLP 120
>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 = 54.0 bits (130), Expect = 1e-09
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
E + V LPP ++ + G V Y + + G VEF KE+ A+
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAV 67
Query: 256 E 256
Sbjct: 68 R 68
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 53.5 bits (129), Expect = 1e-09
Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 5/61 (8%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
+++V P + + F +G V V + K K FA VE L
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLSQ 64
Query: 258 G 258
Sbjct: 65 S 65
>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 = 53.6 bits (129), Expect = 1e-09
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
D+ + V +P A + + F +V V L K G+ G V+F + ++ +A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLK-DHVGRNNGNGLVKFLSPQDTFEA 72
Query: 255 LEL 257
L+
Sbjct: 73 LKR 75
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 53.3 bits (128), Expect = 2e-09
Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 6/82 (7%)
Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK 238
+ + +YV LP +A ++ + G V P + +
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPR 56
Query: 239 GFAFVEFSTKEEAAKALELGLN 260
AF+ + A +A+ L
Sbjct: 57 RRAFLHYPDSAAAQQAVS-CLQ 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 = 55.4 bits (133), Expect = 3e-09
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
T+++ +PP + ++ +FS G V V KF + A ++ + EEA +AL
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGV--VKGFKFFQKDR--KMALIQMGSVEEAVQALI 207
Score = 45.8 bits (108), Expect = 4e-06
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 6/61 (9%)
Query: 197 CTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
+ V L PE + +F YG V V K K A V+ + +A A+
Sbjct: 35 SVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLAM 89
Query: 256 E 256
Sbjct: 90 S 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 = 52.3 bits (126), Expect = 3e-09
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
T+ + P + + K + + + + G G+ FV+FS +EE +AL+
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVR-NAHGNKTGYIFVDFSNEEEVKQALKC 69
>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 = 52.7 bits (127), Expect = 3e-09
Identities = 15/68 (22%), Positives = 28/68 (41%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ D I+V LP + F +G + + + TGK +G+ FV + +
Sbjct: 10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 69
Query: 249 EEAAKALE 256
A +A +
Sbjct: 70 AAAERACK 77
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 53.0 bits (127), Expect = 3e-09
Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 197 CTIYVEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
+ + + PE + + ++ S G + + + + G A++ F+T+E A
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQ 86
Query: 253 KALE 256
+E
Sbjct: 87 AFVE 90
>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 = 52.6 bits (126), Expect = 5e-09
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 194 VDECTIYVEKLPP---EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK---GFAFVEFST 247
V + ++V L + E F K+GK+ V + S + A+V +
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72
Query: 248 KEEAAKALE 256
E+A +A++
Sbjct: 73 SEDALRAIQ 81
>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 = 6e-09
Identities = 17/58 (29%), Positives = 29/58 (50%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
I+V L + ++ F ++GKV L K+T + +GF FV F +++ K E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 51.3 bits (123), Expect = 7e-09
Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEAAK 253
+YV +P + + F+ ++ ++ + K FAF+EF + +E +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 254 ALEL 257
A+
Sbjct: 69 AMAF 72
>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 = 53.7 bits (129), Expect = 8e-09
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
T+++ +PP + ++ +FS G V FK K + A ++ + EEA +AL
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVV----KGFKFFQKDRKMALIQMGSVEEAVQALI 176
Score = 44.9 bits (106), Expect = 6e-06
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 194 VDECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
+ + V L PE + +F YG V V K K A V+ + +A
Sbjct: 1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQ 55
Query: 253 KALE 256
A+
Sbjct: 56 LAMS 59
>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 = 54.3 bits (131), Expect = 8e-09
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ V+ L P ++ +E FS++G V + G+ G FVEF+ K A KALE
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV-DDRGRATGKGFVEFAAKPPARKALE 155
Score = 53.5 bits (129), Expect = 1e-08
Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 181 KVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGF 240
++ + +K C ++V LP + + + +F +YG+ + V + + + GF
Sbjct: 7 DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GF 60
Query: 241 AFVEFSTKEEAAKALE 256
F+ ++ A A
Sbjct: 61 GFIRLESRTLAEIAKA 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 = 51.4 bits (123), Expect = 1e-08
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
E + V LPP ++ + G V Y + + G VEF KE+ A
Sbjct: 15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYA 67
Query: 255 LE 256
+
Sbjct: 68 VR 69
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 51.8 bits (124), Expect = 1e-08
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY----VSLPKFKSTGKLKGFAFVE 244
Q ++ + + LP A + + + F ++ +T + G+ G AFV
Sbjct: 16 QFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT-YPDGRPTGDAFVL 74
Query: 245 FSTKEEAAKALEL 257
F+ +E A AL
Sbjct: 75 FACEEYAQNALRK 87
>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 = 51.8 bits (124), Expect = 1e-08
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLP-----KFKSTGKLKGFAFVEFSTKEEA 251
C IYV+ L + ++ +F +Y + + + G++KG AF+ ++ A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 252 AKALE 256
AKAL+
Sbjct: 106 AKALK 110
>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 = 50.6 bits (121), Expect = 2e-08
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 6/59 (10%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++V L + K+G + YV + F K A VEF + A + +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVT 69
>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 = 49.7 bits (119), Expect = 2e-08
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
I V+ LP ++ + + Y K+ + K AFV E+A A
Sbjct: 4 GSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA 56
Query: 255 LE 256
++
Sbjct: 57 IQ 58
>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 = 49.9 bits (120), Expect = 3e-08
Identities = 19/66 (28%), Positives = 29/66 (43%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
+ + V LP + ++ FS +G+V V + K TG KGF FV F+ E
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 251 AAKALE 256
K +
Sbjct: 70 QVKVMS 75
>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 = 50.4 bits (120), Expect = 3e-08
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 4/82 (4%)
Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTG 235
G ++ R ++ + + + LP + +++ S V G
Sbjct: 27 GQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY-TREG 85
Query: 236 KLKGFAFVEFSTKEEAAKALEL 257
+ G AFVE ++++ AL+
Sbjct: 86 RQSGEAFVELGSEDDVKMALKK 107
>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 = 53.3 bits (127), Expect = 5e-08
Identities = 53/322 (16%), Positives = 96/322 (29%), Gaps = 81/322 (25%)
Query: 7 DSNLRKDRFF--SQLLQES--PEIEVSVFLKC-NKLARLTH--DPDDV-----VKALRKS 54
+ LR + F S + E P + ++++ ++L +V LR+
Sbjct: 84 EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ- 142
Query: 55 KLLEVTEDGTKVKGNIIRHFLVPISM-----ETEASDNVDKDLSDLQRKDG-------GG 102
LLE+ + N++ + A D V + D
Sbjct: 143 ALLEL-----RPAKNVLID-----GVLGSGKTWVALD-VCLSYKVQCKMDFKIFWLNLKN 191
Query: 103 RHRKKQLYQQIMNLMEFYLSDSNL--RKDRFFS-QLLQESPEIEVSVFLKCNKLAR---- 155
+ + + + + L Y D N R D + +L S + E+ LK
Sbjct: 192 CNSPETVLEMLQKL--LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249
Query: 156 LTHDPDDV-----VKALR-KSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAE 209
L +V A K+L +T T R V I ++
Sbjct: 250 L----LNVQNAKAWNAFNLSCKIL-LT---T--RFKQVTDFLSAATTTHISLDHHSMTLT 299
Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTG---KLKGFA-----------FVEFSTKEEAAKAL 255
D ++S+ KY LP+ T +L A + ++ +
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII 359
Query: 256 ELGLNPCPPD-----YQS-SIL 271
E LN P + S+
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVF 381
Score = 36.0 bits (82), Expect = 0.017
Identities = 43/238 (18%), Positives = 71/238 (29%), Gaps = 62/238 (26%)
Query: 5 LSDSNLRKDRFFSQL--LQESPEIEVSVFLKCNKLARL-----THDPDDVVKALRKSKLL 57
L + RK F +L S I + L+ + D VV L K L+
Sbjct: 366 LEPAEYRK--MFDRLSVFPPSAHIPTIL------LSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 58 EV-TEDGTKVKGNIIRHFLVPISMETE------ASDNVDK--DLSDL--QRKDG-----G 101
E ++ T +I V + E N+ K D DL D
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477
Query: 102 GRHRKKQLYQQIMNLME-FYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDP 160
G H K + + M L +L + R FL+ K+ R
Sbjct: 478 GHHLKNIEHPERMTLFRMVFL---DFR-------------------FLE-QKI-RHDSTA 513
Query: 161 DDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
+ +L + + + D P + + P+ E + I S ++
Sbjct: 514 WNAS-----GSILNTLQQLKFYKPYICDND-PKYERLVNAILDFLPKIEENLICSKYT 565
>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 = 49.2 bits (118), Expect = 6e-08
Identities = 14/74 (18%), Positives = 28/74 (37%)
Query: 183 RRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAF 242
V C +++ L + + + F ++G+V + + T + +GF F
Sbjct: 12 SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 243 VEFSTKEEAAKALE 256
V F + K L
Sbjct: 72 VTFMDQAGVDKVLA 85
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 49.0 bits (117), Expect = 6e-08
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+++ L + ++G ++YV + K A VEF A A+
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVN 75
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 48.8 bits (117), Expect = 7e-08
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFST 247
E +++V L P+ + + F K Y + + TG KG+ FV+F+
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60
Query: 248 KEEAAKALE 256
+ E +AL
Sbjct: 61 ELEQKRALT 69
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 47.9 bits (115), Expect = 8e-08
Identities = 13/60 (21%), Positives = 27/60 (45%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
C +++ L + + + F ++G+V + + T + +GF FV F + K L
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
>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 = 47.9 bits (115), Expect = 8e-08
Identities = 16/66 (24%), Positives = 32/66 (48%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
K + D ++V L + ++ F+K+G+V ++ +TG+ +GF F+ F
Sbjct: 6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAAS 65
Query: 251 AAKALE 256
K L+
Sbjct: 66 VEKVLD 71
>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 = 49.7 bits (118), Expect = 1e-07
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
I VE L D + +FSK+G V + + + A ++++ A A
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 102
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 48.9 bits (116), Expect = 1e-07
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
I VE L D + +FSK+G V + + + A ++++ A A
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 84
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 47.5 bits (113), Expect = 2e-07
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
I++ KLP + + S+ +GKVT + + K K AF+E +T+E A +
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 48.0 bits (114), Expect = 2e-07
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
I++ KLP + + S+ +GKVT + + K K AF+E +T+E A +
Sbjct: 33 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 85
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
++V + + D + FS+YG V V +PK + FAFV F+ + A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60
>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 = 47.2 bits (113), Expect = 3e-07
Identities = 17/67 (25%), Positives = 30/67 (44%)
Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
+ + ++V L + + S FS+YG+V + K K+T + +GF FV+F
Sbjct: 10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69
Query: 250 EAAKALE 256
L
Sbjct: 70 CVGTVLA 76
>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 = 47.6 bits (113), Expect = 3e-07
Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 4/70 (5%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFST 247
+ + + LP + +++ S V V G+ G AFVE +
Sbjct: 12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIY-TREGRQSGEAFVELES 70
Query: 248 KEEAAKALEL 257
+++ AL+
Sbjct: 71 EDDVKLALKK 80
>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 = 46.8 bits (111), Expect = 4e-07
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ L + + V K G V + +P K ++F + T EE+ +A
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYV 81
>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 = 46.1 bits (110), Expect = 4e-07
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
++V + + + ++ F +YG+V V +PK + FAFV F+
Sbjct: 4 SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADD 58
Query: 249 EEAAKALE 256
+ A
Sbjct: 59 KVAQSLCG 66
>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 = 46.4 bits (110), Expect = 5e-07
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVE 244
++++ D D I + LP + + + FS + GK +G A +E
Sbjct: 4 LEEEVD-DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLL-NRDGKRRGDALIE 61
Query: 245 FSTKEEAAKALEL 257
++++ KALE
Sbjct: 62 MESEQDVQKALEK 74
>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 = 46.5 bits (111), Expect = 6e-07
Identities = 13/68 (19%), Positives = 33/68 (48%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
+ + +++ L E + + + + ++GK+T + + ++ + +GF FV FS+
Sbjct: 20 KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79
Query: 249 EEAAKALE 256
E A+
Sbjct: 80 AEVDAAMA 87
>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 = 45.6 bits (108), Expect = 8e-07
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+++ KLP E + ++ +GKVT + + K K AF+E +T+E A +
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVN 69
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 43.3 bits (102), Expect = 8e-06
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
K I ++ LP ++ + + + T+ S+ +T G +EF ++E
Sbjct: 23 KLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV----NTRDFDGTGALEFPSEE 78
Query: 250 EAAKALE 256
+ALE
Sbjct: 79 ILVEALE 85
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 43.0 bits (101), Expect = 9e-06
Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTK 248
++V LPP+ + D I + F ++G + + + KS KG+AF+ F +
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 249 EEAAKALE 256
++
Sbjct: 63 SSVQALID 70
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 41.7 bits (97), Expect = 2e-05
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL--ELGLNPCP 263
D + + KYG+V + L K G A VEF+T + A A+ E+GL P
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEVGLVDNP 81
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 41.2 bits (96), Expect = 3e-05
Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ ++ L + + + ++ ++G + + G A +++T+EEA KA +
Sbjct: 8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ------GIALCKYTTREEANKA-Q 60
Query: 257 LGLNPCP 263
+ LN C
Sbjct: 61 MALNNCV 67
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 42.0 bits (98), Expect = 3e-05
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
+ ++ D + +V + GKV + + A VEF + A KA
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKA 80
>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 = 40.3 bits (94), Expect = 1e-04
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 198 TIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
I++ LP + + + YGK+ L ++K AF+E T+E+A +
Sbjct: 27 VIHLSNLPHSGYSDSA-VLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMV 79
Query: 256 E 256
+
Sbjct: 80 D 80
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 41.7 bits (97), Expect = 1e-04
Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 15/74 (20%)
Query: 192 PDVDECTIYVEKLPPEAEHDYIES---------VFSKYGKVTYVSLPKFKSTGKLKGFAF 242
T+YV + +++ VFS+ G + + + K F
Sbjct: 130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGF 183
Query: 243 VEFSTKEEAAKALE 256
V+F + A A E
Sbjct: 184 VKFKYQANAEFAKE 197
>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 = 39.5 bits (92), Expect = 1e-04
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 207 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
E + + KYG+V +++ L G +V+F +E+A KA+ LN
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKFRREEDAEKAVI-DLN 89
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 206 PEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
+ + + V +K+G V ++ + K + G +V+ + A A+ L+
Sbjct: 24 VGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVN-ALH 76
>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 = 40.8 bits (95), Expect = 5e-04
Identities = 50/268 (18%), Positives = 79/268 (29%), Gaps = 92/268 (34%)
Query: 68 GNIIRHFLVPISM--------------ETEASDNVDKD----------------LSDLQR 97
G++ LVP + E ++ D +S L
Sbjct: 14 GSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVE 73
Query: 98 KDGGGRHRKKQLYQQIMN--LMEF---YLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKC 150
G+ + Q++N L EF YL +++ ++LLQ ++ ++ +K
Sbjct: 74 PSKVGQ------FDQVLNLCLTEFENCYLEGNDIHA--LAAKLLQENDTTLVKTKELIKN 125
Query: 151 NKLAR-LTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV---QDKPDVDECTIYVEKLPP 206
AR + P S L +G + V + Q D Y E+L
Sbjct: 126 YITARIMAKRP---FDKKSNSALFRAVGEGNA--QLVAIFGGQGNTDD-----YFEEL-- 173
Query: 207 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN------ 260
++ Y V S L T +A K GLN
Sbjct: 174 -------RDLYQTYH--VLVGDLIKFSAETLSELI----RTTLDAEKVFTQGLNILEWLE 220
Query: 261 ---PCPP-DYQSSILTTTSRLSFGITPL 284
P DY SI +S PL
Sbjct: 221 NPSNTPDKDYLLSIP-----ISC---PL 240
Score = 28.5 bits (63), Expect = 3.2
Identities = 22/112 (19%), Positives = 35/112 (31%), Gaps = 38/112 (33%)
Query: 15 FFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKL-LEV--TEDGT---KVKG 68
F S LL + + + D + + + V T DG+ + G
Sbjct: 427 FHSHLLVPASD-------------LINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSG 473
Query: 69 NIIRHFLV------PISMETEASDN----VD------KDLSDL--QRKDGGG 102
+I +V P+ ET +D L L + KDG G
Sbjct: 474 SIS-ERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTG 524
>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 = 38.1 bits (89), Expect = 5e-04
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 8/58 (13%)
Query: 206 PEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
P ++ E + SK+G++ + L G A V F EEA ++ L+
Sbjct: 33 PLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQ-TLD 85
>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 = 36.7 bits (85), Expect = 0.002
Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 205 PPEAEHDYIESVF---SKYGKVTYVSLPK----FKSTGKLKGFAFVEFSTKEEAAKALE 256
P + + D V K+G V V + + + ++ FVEFS E KA++
Sbjct: 31 PKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 89
>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 = 35.5 bits (82), Expect = 0.004
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 213 IESVFSKYGKVTYVSLPKFK--STGKLKGFAFVEFSTKEEAAKALE 256
+ SKYG V + +P+ G FVEF++ + KA++
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQ 77
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 35.3 bits (81), Expect = 0.004
Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 13/87 (14%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
+ V LPP + + F + + ++ +L + F +A +
Sbjct: 7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ---RLGCGGVLTFREPADAERV 63
Query: 255 LE----------LGLNPCPPDYQSSIL 271
L L L P PP + +L
Sbjct: 64 LAQADHELHGAQLSLRPAPPRAPARLL 90
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 34.1 bits (78), Expect = 0.011
Identities = 8/61 (13%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 198 TIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
+++ + + + +G ++ + + AF+E +T E+A A+
Sbjct: 17 VVHIMDFQRGKNLRYQ-LLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQAAV 69
Query: 256 E 256
+
Sbjct: 70 D 70
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 34.4 bits (78), Expect = 0.038
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP 264
+ V K G V + +P K ++F + T EE+ +A LN
Sbjct: 37 LLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYV-TLNGKEV 81
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 30.6 bits (69), Expect = 0.19
Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 205 PPEAEHDYIESVF---SKYGKVTYVSLPKFKSTGK-LKGFAFVEFSTKEEAAKALE 256
E + D KYGKV + + F+EF E A KA+
Sbjct: 19 AGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVV 74
>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 = 30.0 bits (67), Expect = 0.24
Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 7/63 (11%)
Query: 198 TIYVEKLPPEAE----HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
+ V + ++ F+++GKV V L + A V+ ++A
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVEL---SPHTDYQLKAVVQMENLQDAIG 67
Query: 254 ALE 256
A+
Sbjct: 68 AVN 70
>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling
protein-metal binding protein COM; HET: TRE; 1.70A {Homo
sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A
2y5b_B
Length = 152
Score = 29.2 bits (65), Expect = 1.0
Identities = 19/91 (20%), Positives = 44/91 (48%)
Query: 78 ISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ 137
I++E E SD ++ + +Q K+G +++ ++ LSD N++K+ +L+
Sbjct: 13 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
Query: 138 ESPEIEVSVFLKCNKLARLTHDPDDVVKALR 168
+++ V K L +P D ++ ++
Sbjct: 73 LRGGMQIFVKTLTGKTITLEVEPSDTIENVK 103
>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}
Length = 172
Score = 28.1 bits (62), Expect = 2.7
Identities = 19/91 (20%), Positives = 44/91 (48%)
Query: 78 ISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ 137
I++E E SD ++ + +Q K+G +++ ++ LSD N++K+ +L+
Sbjct: 33 ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 92
Query: 138 ESPEIEVSVFLKCNKLARLTHDPDDVVKALR 168
+++ V K L +P D ++ ++
Sbjct: 93 LRGGMQIFVKTLTGKTITLEVEPSDTIENVK 123
>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 = 27.6 bits (60), Expect = 3.1
Identities = 8/31 (25%), Positives = 17/31 (54%), Gaps = 9/31 (29%)
Query: 227 SLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
+L K +++ LK +A +++A AL +
Sbjct: 21 ALKKLQAS--LKLYA-------DDSAPALAI 42
Score = 26.5 bits (57), Expect = 7.7
Identities = 5/18 (27%), Positives = 9/18 (50%)
Query: 248 KEEAAKALELGLNPCPPD 265
+++A K L+ L D
Sbjct: 18 EKQALKKLQASLKLYADD 35
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein
structure initiati midwest center for structural
genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Length = 382
Score = 28.0 bits (63), Expect = 3.7
Identities = 12/65 (18%), Positives = 18/65 (27%), Gaps = 5/65 (7%)
Query: 150 CNKL----ARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLP 205
N L A L D+V+A+ + G + + D I L
Sbjct: 280 TNDLIKQGATLITSASDIVEAVASILERPIELPGREPEHAPPEGEPDTGDRTRIL-ALLG 338
Query: 206 PEAEH 210
P
Sbjct: 339 PSPVG 343
>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold,
hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4}
PDB: 2o0h_A* 2o0k_A*
Length = 385
Score = 28.2 bits (61), Expect = 4.1
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNK 152
Q Y+ N Y+ NL++ +Q +E V + KC
Sbjct: 100 QTYKDKNNKRSRYMGLPNLKRANIKTQWTRE----MVEEWKKCRD 140
>2v1u_A Cell division control protein 6 homolog; DNA replication,
nucleotide-binding, replication, archaea; HET: ADP;
3.10A {Aeropyrum pernix}
Length = 387
Score = 27.9 bits (61), Expect = 4.3
Identities = 22/153 (14%), Positives = 45/153 (29%), Gaps = 16/153 (10%)
Query: 36 KLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIR-----HFLVPISMETEASDNVDK 90
AR D + LR + + +V+ + +S K
Sbjct: 234 LAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIERDRVSEVVRTLPLHAK 293
Query: 91 DL--SDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFL 148
+ S + +DGG ++Y++ L + R S ++ E + +
Sbjct: 294 LVLLSIMMLEDGGRPASTGEIYERYKELTSTLGLEH--VTLRRVSGIISELDMLGIVKSR 351
Query: 149 KCNK-------LARLTHDPDDVVKALRKSKLLE 174
++ L D V AL + +
Sbjct: 352 VVSRGRYGKTREVSLDADRLAVENALSEDPFVA 384
>2nvu_B Maltose binding protein/NEDD8-activating enzyme E1 catalytic
subunit chimera; multifunction macromolecular complex,
ubiquitin, ATP, conformational change, thioester,
switch, adenylation, protein turnover, ligase; HET: ATP;
2.80A {Homo sapiens} SCOP: c.111.1.2 c.94.1.1
Length = 805
Score = 28.0 bits (62), Expect = 5.5
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 8/76 (10%)
Query: 33 KCNKLA-RLTHDPD----DVVKALRKSKLLEVTEDG---TKVKGNIIRHFLVPISMETEA 84
C++L + P +V+ L S L++ T N + S+E
Sbjct: 708 ACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERT 767
Query: 85 SDNVDKDLSDLQRKDG 100
N+ K L +L DG
Sbjct: 768 RPNLSKTLKELGLVDG 783
>3q8d_A DNA repair protein RECO; OB-fold, recombination initation, recom
initiation, SSB, RECR; HET: DNA CPS; 2.30A {Escherichia
coli}
Length = 242
Score = 27.1 bits (60), Expect = 6.1
Identities = 7/51 (13%), Positives = 17/51 (33%)
Query: 90 KDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESP 140
+ L L ++ + + ++ YL L+ F Q + +
Sbjct: 186 RQLKALNAREFPDADTLRAAKRFTRMALKPYLGGKPLKSRELFRQFMPKRT 236
>2i9x_A Putative septation protein spovg; APC86317.1, staphylococcus
epidermidis ATCC 12228, ST genomics, PSI-2, protein
structure initiative; 1.80A {Staphylococcus epidermidis}
SCOP: d.366.1.1
Length = 87
Score = 25.5 bits (56), Expect = 7.3
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 222 KVTYVSLPKFKSTGKLKGFAFVEF 245
KVT V L K ++ G++K +
Sbjct: 5 KVTDVRLRKIQTDGRMKALVSITL 28
>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative
initiation, ATP-binding, DNA- binding, hydrolase,
nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB:
3ezk_A*
Length = 592
Score = 27.2 bits (59), Expect = 8.4
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNK 152
Q Y+ N Y+ NL++ +Q +E V + KC
Sbjct: 100 QTYKDKNNKRSRYMGLPNLKRANIKTQWTRE----MVEEWKKCRD 140
>2ia9_A Putative septation protein spovg; APC85465, bacillus subtilis
subsp. subtilis STR. 168, structural genomics, PSI-2;
3.00A {Bacillus subtilis} SCOP: d.366.1.1
Length = 100
Score = 25.6 bits (56), Expect = 9.4
Identities = 6/24 (25%), Positives = 13/24 (54%)
Query: 222 KVTYVSLPKFKSTGKLKGFAFVEF 245
+VT V L + + G+++ A +
Sbjct: 5 EVTDVRLRRVNTDGRMRAIASITL 28
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
0.317 0.135 0.384
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,631,181
Number of extensions: 278703
Number of successful extensions: 1146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1024
Number of HSP's successfully gapped: 254
Length of query: 299
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 206
Effective length of database: 4,105,140
Effective search space: 845658840
Effective search space used: 845658840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.7 bits)