RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13491
(69 letters)
>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 = 54.3 bits (131), Expect = 1e-11
Identities = 26/39 (66%), Positives = 33/39 (84%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNR 41
A+R+ V A+AMDE++FRGR IKV PKRTN PGIS+T+R
Sbjct: 86 AERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISSTDR 124
>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 = 50.6 bits (122), Expect = 1e-10
Identities = 24/31 (77%), Positives = 29/31 (93%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNPKRTNRPGI 36
+ V+T++A+DESLFRGRQIKV PKRTNRPGI
Sbjct: 59 ESVRTSLALDESLFRGRQIKVIPKRTNRPGI 89
>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 = 41.9 bits (99), Expect = 6e-07
Identities = 7/37 (18%), Positives = 13/37 (35%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG 42
V A+ + G I V + + +S + G
Sbjct: 78 QSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114
>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 = 33.1 bits (76), Expect = 0.001
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRG 42
+ A+ D F+G ++KV+ R P S + G
Sbjct: 73 EDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113
>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 = 32.3 bits (74), Expect = 0.004
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNP--KRTNRPGISTTNRGGPRGRGRGRVS 53
DE AMA D +F+G+ +K+ PG+S G V
Sbjct: 62 DETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVP 111
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 31.2 bits (71), Expect = 0.007
Identities = 11/49 (22%), Positives = 16/49 (32%), Gaps = 3/49 (6%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNP--KRTNRPGISTTNRGGPRGRG 48
+ A+ D F G IKV+ +R + RGG
Sbjct: 65 DDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHHH 113
>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 = 29.7 bits (67), Expect = 0.022
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVN 27
DE AMA D +F+G+ +K+
Sbjct: 63 VDETTQAMAFDGIIFQGQSLKIR 85
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 29.9 bits (68), Expect = 0.032
Identities = 9/36 (25%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNR 41
DE AMA D +F+G+ +K+ + + + ++
Sbjct: 62 DETTQAMAFDGIIFQGQSLKIR-RPHDYQPLPGAHK 96
>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 = 29.2 bits (66), Expect = 0.042
Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 1/27 (3%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNP 28
+ A+ D F G IKV+
Sbjct: 71 DDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 29.1 bits (66), Expect = 0.043
Identities = 6/32 (18%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNP--KRTNRPG 35
++++ A+ + G +IK+ R G
Sbjct: 69 EDLEKALELTGLKVFGNEIKLEKPKGRDGTRG 100
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 28.4 bits (64), Expect = 0.093
Identities = 7/34 (20%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVN---PKRTNRPG 35
D ++ A+ D +L R ++V+ ++ ++ G
Sbjct: 66 VDSLKEALTYDGALLGDRSLRVDIAEGRKQDKSG 99
>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 = 28.4 bits (64), Expect = 0.094
Identities = 6/36 (16%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVN---PKRTNRPG 35
D + +A++++E ++I+V+ + G
Sbjct: 65 EDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 27.7 bits (62), Expect = 0.13
Identities = 7/41 (17%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRG 46
+ ++ + G +++V P R + S ++ P+G
Sbjct: 56 GAREAVLSQSQHSLGGHRLRVRP-REQKEFQSPASK-SPKG 94
>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 = 27.6 bits (62), Expect = 0.18
Identities = 6/25 (24%), Positives = 15/25 (60%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVN 27
D + +A++++E R+I+V+
Sbjct: 69 EDLDSLLSALSLNEESLGNRRIRVD 93
>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 = 26.8 bits (60), Expect = 0.30
Identities = 8/43 (18%), Positives = 15/43 (34%)
Query: 1 MKAKRDEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGG 43
V+ +D +F+GR + V P + + G
Sbjct: 57 FMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99
>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 = 26.9 bits (60), Expect = 0.41
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 3 AKRDEVQTAMAMDESLFRGRQIKVN 27
+D + A+ M+ SL R+I V+
Sbjct: 262 ENKDSAERALQMNRSLLGNREISVS 286
>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 = 26.4 bits (59), Expect = 0.45
Identities = 5/32 (15%), Positives = 10/32 (31%), Gaps = 3/32 (9%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNP--KRTNRP 34
+ M + + G+ V P K +
Sbjct: 56 ASSKKLMDLLPKRELHGQNPVVTPSNKLEHHH 87
>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 = 26.5 bits (59), Expect = 0.48
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 3/61 (4%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGG 61
+ + A M+ G+ IKV + +P + R P R R G+ +
Sbjct: 56 ENPADAKNAAKDMNGKSLHGKAIKVE--QAKKPSFQSGGRRRPPASSRNRSPSGSLEHHH 113
Query: 62 Y 62
+
Sbjct: 114 H 114
>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 = 26.1 bits (58), Expect = 0.62
Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVN--PKRTNRPGISTTNRGGP 44
+ +AM ++ F GR ++V+ N+ + + G P
Sbjct: 61 ETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102
>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 = 26.6 bits (58), Expect = 0.70
Identities = 14/70 (20%), Positives = 22/70 (31%), Gaps = 29/70 (41%)
Query: 12 MAMD--------------------ESL-FRGRQI-KVNPKRTNRPGISTTNRGGPRGRGR 49
M MD ++ F I NP T + GG +G+ R
Sbjct: 1631 MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNL------TIHFGGEKGK-R 1683
Query: 50 GRVSRGAAMY 59
R + A ++
Sbjct: 1684 IRENYSAMIF 1693
>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 = 26.2 bits (58), Expect = 0.73
Identities = 13/51 (25%), Positives = 17/51 (33%), Gaps = 1/51 (1%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRVSRG 55
E Q AM ++ G+ I V+ P G R R R R
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRRL 125
>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 = 25.9 bits (57), Expect = 0.77
Identities = 8/48 (16%), Positives = 14/48 (29%), Gaps = 2/48 (4%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNP--KRTNRPGISTTNRGGPRGRGRG 50
D+ + + + GR+ V+ R G G G
Sbjct: 67 EDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114
>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 = 26.0 bits (58), Expect = 0.88
Identities = 5/37 (13%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNP--KRTNRPGISTTN 40
++++ A+ + G +IK+ R ++ +
Sbjct: 65 EDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAART 101
>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 = 25.6 bits (57), Expect = 0.90
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVN 27
++ A+ M+ES GR I+VN
Sbjct: 60 EDAAAAIDNMNESELFGRTIRVN 82
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 25.3 bits (56), Expect = 1.00
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNPKRT 31
+EV+ A+ + GR I+V +++
Sbjct: 60 EEEVKQALKCNREYMGGRYIEVFREKS 86
>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 = 25.9 bits (57), Expect = 1.0
Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 4/48 (8%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRGRV 52
Q A+ ++ +++KV G G G G G +
Sbjct: 95 SSAQQAIAGLNGFNILNKRLKVALA---ASGHQRPGIAGAVGDGNGYL 139
>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 = 25.8 bits (56), Expect = 1.2
Identities = 8/66 (12%), Positives = 17/66 (25%), Gaps = 3/66 (4%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNP--KRTNRPGISTTNRGGPRGRGRGRVSRGAAMYGGY 62
+ M + + G+ V P K+ + + G+ G G
Sbjct: 123 ASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSR 182
Query: 63 RPVRRA 68
+
Sbjct: 183 AAFPQG 188
>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 = 25.4 bits (56), Expect = 1.4
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 6/48 (12%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVN-----PKRTNRPGISTTNRGGP 44
+ + + A+ M GRQI+ N P S T + GP
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGP 112
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 25.5 bits (56), Expect = 1.4
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVN 27
++ A+ M+ES GR I+VN
Sbjct: 113 ELAEDAAAAIDNMNESELFGRTIRVN 138
>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 = 24.9 bits (55), Expect = 1.5
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVN---PKRTNRPG 35
++ A+ M+ES GR I+VN P R G
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNLAKPMRIKESG 98
>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 = 24.4 bits (54), Expect = 2.0
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVN 27
+D+ Q AM +M GR +++N
Sbjct: 51 TSQDDAQNAMDSMQGQDLNGRPLRIN 76
>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 = 24.5 bits (54), Expect = 2.3
Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 3/33 (9%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNP--KRTNRPG 35
+ + A+ M+ L R++ V R R
Sbjct: 56 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREA 88
>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 = 24.5 bits (54), Expect = 2.4
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNP--KRTNRP 34
A D A+ AM+ R I V+ K+ ++
Sbjct: 56 ASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG 90
>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 = 24.1 bits (53), Expect = 2.7
Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRG 42
R + A +D RG+Q++V + S + G
Sbjct: 59 ETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSSG 99
>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 = 24.1 bits (53), Expect = 2.9
Identities = 6/23 (26%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVN 27
+ V A+ ++ GR I V+
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVS 90
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 24.3 bits (53), Expect = 3.2
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNP 28
+ A+ + L R ++V+P
Sbjct: 66 PQDTFEALKRNRMLMIQRYVEVSP 89
>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 = 24.1 bits (53), Expect = 3.5
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 1 MKAKRDEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRG 42
+RD AMD + GR+++V R R +S + G
Sbjct: 62 FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103
>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 = 23.7 bits (52), Expect = 3.7
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 5 RDEVQTAM-AMDESLFRGRQIKVNPKRTNRP 34
DE + A+ MD G++I P
Sbjct: 57 PDEAEKALKHMDGGQIDGQEITATAVLAPWP 87
>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 = 23.7 bits (52), Expect = 4.2
Identities = 7/26 (26%), Positives = 11/26 (42%), Gaps = 1/26 (3%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVN 27
+D Q A++ GR IK +
Sbjct: 66 LDKDSAQNCTRAINNKQLFGRVIKAS 91
>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 = 23.8 bits (52), Expect = 4.3
Identities = 7/39 (17%), Positives = 14/39 (35%), Gaps = 6/39 (15%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVN-----PKRTNRPG 35
+ A + ++ GR+I+VN + P
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPS 101
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 23.9 bits (52), Expect = 4.3
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPR 45
++ AMA D++ + R +++ T + T+ GP
Sbjct: 65 HEDAVAAMAKDKANMQHRYVELFLNST-----AGTSGSGPS 100
>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 = 23.7 bits (52), Expect = 4.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 3 AKRDEVQTAM-AMDESLFRGRQIKVNPKRTNRP 34
+ + + A+ M GRQI+ N T +P
Sbjct: 56 FNKWDAENAIQQMGGQWLGGRQIRTN-WATRKP 87
>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 = 23.8 bits (52), Expect = 4.6
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRG 42
++ A+ MD G+ I+VN + +S + G
Sbjct: 68 EDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105
>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 = 23.7 bits (52), Expect = 4.7
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVN---PKRTNRP 34
+ V A+ +D + F GR I+V PK++
Sbjct: 53 ESVSEAIAKLDNTDFMGRTIRVTEANPKKSLEH 85
>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 = 23.7 bits (52), Expect = 4.7
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNPKRTNRPGISTTNRG 42
D+ + AM AM+ GRQI+V+ + S + G
Sbjct: 65 DDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 23.9 bits (52), Expect = 4.9
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNPKR 30
D Q A+ AM+ +++KV K+
Sbjct: 93 DSAQVAIKAMNGFQVGTKRLKVQLKK 118
>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 = 23.6 bits (51), Expect = 6.2
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 1 MKAKRDEVQTAMAMDESLFRGRQIKVNPKRTNRP 34
KRD AMD ++ GR+++V R RP
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP 152
>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 = 23.3 bits (50), Expect = 7.3
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTNRGGPRGRGRG 50
+E AM+ D + + R I++ + G S +G G
Sbjct: 96 HEEAVAAMSKDRANMQHRYIEL--FLNSTTGASNGAYSSQVMQGMG 139
>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 = 23.3 bits (50), Expect = 7.4
Identities = 4/24 (16%), Positives = 10/24 (41%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNP 28
++ + A+ + R I+V
Sbjct: 94 QELAEKALGKHKERIGHRYIEVFK 117
>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 = 22.9 bits (50), Expect = 7.4
Identities = 5/33 (15%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNP--KRTNRPG 35
+ + A+ ++ GR ++V +R +
Sbjct: 58 ECARRALEQLNGFELAGRPMRVGHVTERLDGGS 90
>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 = 23.0 bits (50), Expect = 7.6
Identities = 5/23 (21%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVN 27
+ + A+ ++ GR +KV
Sbjct: 79 ECAKKALEQLNGFELAGRPMKVG 101
>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 = 23.2 bits (50), Expect = 8.0
Identities = 3/23 (13%), Positives = 9/23 (39%)
Query: 6 DEVQTAMAMDESLFRGRQIKVNP 28
+ + A+ + R I++
Sbjct: 68 EIAEKALKKHKERIGHRYIEIFK 90
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 23.3 bits (50), Expect = 8.2
Identities = 5/47 (10%), Positives = 15/47 (31%), Gaps = 3/47 (6%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNP--KRTNRPGISTTNRGGPRGRGR 49
+ V + + + G ++ V P ++ + + R
Sbjct: 110 NSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRVPR 156
>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 = 23.4 bits (51), Expect = 8.4
Identities = 7/29 (24%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 5 RDEVQTAM-AMDESLFRGRQIKVNPKRTN 32
++ + A+ A +S R R++ V + T+
Sbjct: 67 GEQAEAAINAFHQSRLRERELSVQLQPTD 95
>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 = 23.3 bits (50), Expect = 8.5
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 5 RDEVQTAMAMDESLFRGRQIKVNP 28
+ + A+ + R I+V+P
Sbjct: 77 EADYKAALCRHKQYMGNRFIQVHP 100
>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 = 23.2 bits (50), Expect = 9.2
Identities = 12/63 (19%), Positives = 21/63 (33%), Gaps = 4/63 (6%)
Query: 5 RDEVQTAM-AMDESLFRGRQIKVN---PKRTNRPGISTTNRGGPRGRGRGRVSRGAAMYG 60
R + + AM ++ + R I+ + + R + G R R G YG
Sbjct: 91 RADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYG 150
Query: 61 GYR 63
Sbjct: 151 KLA 153
>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 = 23.0 bits (50), Expect = 9.3
Identities = 7/26 (26%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 6 DEVQTAM-AMDESLFRGRQIKVNPKR 30
Q A+ +M+ +++KV KR
Sbjct: 78 VSAQAAIQSMNGFQIGMKRLKVQLKR 103
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 22.8 bits (49), Expect = 10.0
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 1 MKAKRDEVQTAMAMDESLFRGRQIKVNPKRTNRP 34
KRD AMD ++ GR+++V R RP
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP 129
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
0.320 0.135 0.394
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,050,692
Number of extensions: 49727
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 283
Number of HSP's successfully gapped: 115
Length of query: 69
Length of database: 6,701,793
Length adjustment: 39
Effective length of query: 30
Effective length of database: 5,612,874
Effective search space: 168386220
Effective search space used: 168386220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)