RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9171
(118 letters)
>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 = 71.1 bits (174), Expect = 2e-17
Identities = 13/55 (23%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 21 DRQKSDFKPSRVIHIRNIPNE-VTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
+ + RVIH+ N+P+ +++ ++ L P+G++ N ++++ K+Q + +E
Sbjct: 16 QKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEME 70
>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 = 70.7 bits (173), Expect = 2e-17
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEV-TEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
QK + RV+HI + +++ L PFG ++N L+L N+ + +
Sbjct: 6 SGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATT 62
>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 = 66.4 bits (162), Expect = 9e-16
Identities = 33/52 (63%), Positives = 40/52 (76%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
K D PSRV+HIR +P EVTE E+I LG+PFG+VTN+L+LKGKNQ L L
Sbjct: 8 DKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELA 59
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 66.0 bits (161), Expect = 1e-15
Identities = 29/52 (55%), Positives = 38/52 (73%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
PSRVIHIR +P +VTE E+I LG+PFG+VTN+L+LKGKNQ + +
Sbjct: 9 HHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMN 60
>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 = 64.2 bits (156), Expect = 9e-15
Identities = 30/56 (53%), Positives = 41/56 (73%)
Query: 19 KLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
+ +S PSRVIHIR +P +VTE E+I LG+PFG+VTN+L+LKGKNQ + +
Sbjct: 20 HMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMN 75
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 63.2 bits (154), Expect = 1e-14
Identities = 16/46 (34%), Positives = 27/46 (58%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
S V+HIR + + V EA+++ FG ++ V+V+ K Q L+ E
Sbjct: 20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFE 65
>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 = 62.9 bits (153), Expect = 2e-14
Identities = 14/46 (30%), Positives = 25/46 (54%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLE 74
S V+H+R + V EA+++ FG + V+++ K Q L+ E
Sbjct: 14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFE 59
>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 = 37.6 bits (88), Expect = 9e-05
Identities = 6/40 (15%), Positives = 16/40 (40%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
P+ + + + + A + FG + + +KG +
Sbjct: 15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS 54
>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 = 36.7 bits (85), Expect = 2e-04
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
VI +N+P AEI FG + VL+ +G
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGI 47
>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 = 36.5 bits (85), Expect = 3e-04
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ F + + N+P ++TE E+ L +G+ V + K K
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG 52
>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 = 36.1 bits (84), Expect = 4e-04
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
S +V+ +RN+ N VTE + FG++ V LK
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>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 = 36.9 bits (85), Expect = 6e-04
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 27 FKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
F PS +H+ NIP V+E ++ L G V K+
Sbjct: 148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD 188
Score = 28.8 bits (64), Expect = 0.33
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 29 PSRVIHIRNI-PNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
+ V+ + N+ P VT + L +G V V +L K
Sbjct: 33 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 71
>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 = 35.0 bits (81), Expect = 0.001
Identities = 10/45 (22%), Positives = 22/45 (48%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+S R + + + + +E +++ L PFG + VL+G +
Sbjct: 8 SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD 52
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 34.2 bits (79), Expect = 0.002
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
RQ+ + +R + +R P +V E+E+ + PFG + V +L G
Sbjct: 24 RQEGELSNTR-LFVRPFPLDVQESELNEIFGPFGPMKEVKILNG 66
>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 = 34.9 bits (80), Expect = 0.002
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 27 FKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
F PS +H+ NIP V+E ++ L G V K+
Sbjct: 117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD 157
Score = 27.2 bits (60), Expect = 1.2
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 30 SRVIHIRNI-PNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
+ V+ + N+ P VT + L +G V V +L K
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 40
>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 = 34.9 bits (81), Expect = 0.002
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 15 VVQAKL-DRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+Q K D +K++ R + I I + TE +I + FG++ +L+G +
Sbjct: 79 PIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD 132
Score = 29.9 bits (68), Expect = 0.13
Identities = 7/33 (21%), Positives = 17/33 (51%)
Query: 35 IRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ +P +E ++ L +G V + VL+ ++
Sbjct: 8 VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS 40
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 33.4 bits (77), Expect = 0.004
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 37 NIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
NIP+ TEA++I L FG + + K
Sbjct: 34 NIPHFATEADLIPLFQNFGFILDFKHYPEKG 64
>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 = 33.4 bits (77), Expect = 0.004
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
PSRV+++ +IP + TE +I+ L G V N+
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINL 32
>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 = 33.0 bits (76), Expect = 0.004
Identities = 6/40 (15%), Positives = 20/40 (50%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
K +++ + + +TE ++ + FG + + V++ +
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ 49
Score = 23.8 bits (52), Expect = 9.2
Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 74 EAEIIHLGIPFGRVTNVLVLKGKNQVSLISGYRNRQSAA 112
E ++ + FG + + V++ + + I + RQ+A
Sbjct: 26 ETDLRNHFYQFGEIRTITVVQRQQ-CAFIQ-FATRQAAE 62
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 33.7 bits (77), Expect = 0.005
Identities = 7/50 (14%), Positives = 17/50 (34%), Gaps = 4/50 (8%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIH----LGIPFGRVTNVLVLKGKN 67
Q + ++ +R +P T E++ G +L + +
Sbjct: 15 AQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64
>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 = 33.0 bits (76), Expect = 0.005
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
K S +H+ NI T E+ +G V ++K
Sbjct: 8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>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 = 33.0 bits (76), Expect = 0.005
Identities = 13/42 (30%), Positives = 20/42 (47%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
Q + + I +RNIP + + EI L FG + V + K
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPK 49
>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 = 33.1 bits (76), Expect = 0.006
Identities = 9/37 (24%), Positives = 22/37 (59%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ +R+++IRN+P ++T E+ + +G + + V
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN 42
>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 = 32.6 bits (75), Expect = 0.007
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
+ I + N+ T E+ L GRV V+K
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 32.4 bits (74), Expect = 0.010
Identities = 8/50 (16%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 19 KLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
+ + +R ++I+ P + T +I G+V N+ + + ++
Sbjct: 3 WILKNDVK---NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK 49
>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 = 32.3 bits (74), Expect = 0.011
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 37 NIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
I + +T+ + PFG++ + V K
Sbjct: 32 GIASGLTDQLMRQTFSPFGQIMEIRVFPEKG 62
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 32.0 bits (73), Expect = 0.012
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
R + IRNIP + + L + +G V + + +
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS 52
>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 = 32.0 bits (73), Expect = 0.013
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+H+R +P TE +I + P V + G +
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD 51
>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 = 32.2 bits (73), Expect = 0.014
Identities = 7/41 (17%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 29 PSRVIHIRN--IPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++ + + N + N V+ +++ + G V +L+ K
Sbjct: 24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP 64
>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 = 32.8 bits (74), Expect = 0.015
Identities = 12/42 (28%), Positives = 15/42 (35%)
Query: 27 FKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
PS V+H N P EVTE + G V +
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK 161
Score = 30.1 bits (67), Expect = 0.14
Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 29 PSRVIHIRNI-PNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
S V+ + + +++ + ++ +G V V +K K
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP 42
>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 = 31.5 bits (72), Expect = 0.019
Identities = 10/41 (24%), Positives = 18/41 (43%)
Query: 24 KSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
SD + + IRN+ + E + + FG + V V+
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVL 49
>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 = 31.4 bits (72), Expect = 0.020
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
+ I N+P E TE EI L +G+V ++K
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN 43
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 31.6 bits (72), Expect = 0.021
Identities = 7/36 (19%), Positives = 15/36 (41%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
P + + + + V E + + +G V V +L
Sbjct: 5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILL 40
>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 = 32.4 bits (74), Expect = 0.021
Identities = 8/52 (15%), Positives = 24/52 (46%)
Query: 16 VQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+++ L + + + + N+P ++TE + L +G + V + + +
Sbjct: 8 IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG 59
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 31.7 bits (72), Expect = 0.023
Identities = 9/43 (20%), Positives = 19/43 (44%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
RV+++ + EV + + IPFG +T++ +
Sbjct: 55 GSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97
>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 = 31.1 bits (71), Expect = 0.024
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 25 SDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+ + R + + NIP E TE ++ + G V +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSF 38
>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 = 31.7 bits (72), Expect = 0.028
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
++ + +I E E EI +G + N+
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 102
>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 = 31.9 bits (73), Expect = 0.028
Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 1/68 (1%)
Query: 1 MKDIGGNVKYTLVMVVQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIH-LGIPFGRVTN 59
I G T V K R S R I IRN+ E+ + ++ FG +
Sbjct: 181 GLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEK 240
Query: 60 VLVLKGKN 67
+ + G+
Sbjct: 241 INIPAGQK 248
Score = 29.2 bits (66), Expect = 0.29
Identities = 5/36 (13%), Positives = 15/36 (41%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
+ ++N+P + ++ G + +V V +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK 79
Score = 26.1 bits (58), Expect = 3.3
Identities = 7/40 (17%), Positives = 13/40 (32%), Gaps = 4/40 (10%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK----GKNQ 68
+ + N P T+ I L V + L ++
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSR 159
>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 = 31.3 bits (71), Expect = 0.029
Identities = 9/50 (18%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 19 KLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTN-VLVLKGKN 67
K R +S + ++++ +P E +I V + + + G N
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPN 63
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 31.0 bits (70), Expect = 0.037
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGI----PFGRVTNVLVLKGK 66
L +PS+V+ I NI EV + ++ L G + +++V
Sbjct: 16 SPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD 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 = 30.5 bits (69), Expect = 0.040
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVL 63
D + +R +P ++ EI+ V N + L
Sbjct: 8 NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTL 48
>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 = 30.7 bits (70), Expect = 0.041
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLV 62
P++V++++N+ VTE +++ L F +
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPI 57
>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 = 30.7 bits (70), Expect = 0.042
Identities = 6/45 (13%), Positives = 16/45 (35%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ +++++RN+ +E I V K ++
Sbjct: 8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD 52
>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 = 30.3 bits (69), Expect = 0.044
Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 26 DFKPSRVIHIRNIPNEVTEAEIIHLGI----PFGRVTNVLVLKGKN 67
+ +P+ I+I N+ ++ + E+ FG++ ++LV +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK 49
>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 = 30.7 bits (70), Expect = 0.045
Identities = 8/40 (20%), Positives = 18/40 (45%)
Query: 25 SDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
S+ +++ + +V+E + L + G V N + K
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK 49
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 31.0 bits (70), Expect = 0.048
Identities = 7/63 (11%), Positives = 18/63 (28%), Gaps = 2/63 (3%)
Query: 2 KDIGGNVKYTLVMVVQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVL 61
+ R +++ N+ N + E+ +G + +V
Sbjct: 47 DATKTFTVTEGSHHHHHHMHRDSCP--LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW 104
Query: 62 VLK 64
V +
Sbjct: 105 VAR 107
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 30.9 bits (70), Expect = 0.051
Identities = 7/43 (16%), Positives = 18/43 (41%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
R D + + + N+ + + + +GRV +V + +
Sbjct: 39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81
>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 = 31.4 bits (70), Expect = 0.051
Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 26 DFKPSRVIHIRNIPNEVTEAEIIHLGI----PFGRVTNVLVLKGKN 67
+ +P+ I+I N+ ++ + E+ FG++ ++LV +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK 50
Score = 27.1 bits (59), Expect = 1.4
Identities = 13/62 (20%), Positives = 27/62 (43%)
Query: 6 GNVKYTLVMVVQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
G + +M Q + S+ P+ ++ + N+P E E + L F V ++ G
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242
Query: 66 KN 67
++
Sbjct: 243 RH 244
>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 = 30.1 bits (68), Expect = 0.052
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 1/47 (2%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAE 76
S I ++N+P + E+ L + + V + K + L
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNG 50
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dgq_A
Length = 106
Score = 30.4 bits (69), Expect = 0.057
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 37 NIPNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
IP + E ++ L FG++ + VLK +
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDR 49
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 29.9 bits (68), Expect = 0.066
Identities = 7/42 (16%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 25 SDFKPSRVIHIRNIP-NEVTEAEIIHLGIPFGRVTNVLVLKG 65
+ P + I N+P V++ ++ + P+G + + +
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 46
>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 = 30.7 bits (70), Expect = 0.071
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 16 VQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++ +L+ + F+ R I IR +P +VT E+ L + + V K K
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG 58
Score = 29.9 bits (68), Expect = 0.14
Identities = 5/51 (9%), Positives = 15/51 (29%), Gaps = 1/51 (1%)
Query: 18 AKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIH-LGIPFGRVTNVLVLKGKN 67
+ SR + + +P + + + T + G++
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD 222
Score = 28.8 bits (65), Expect = 0.33
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 35 IRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ N+P +T+ + L PFG + ++
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVY 129
>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 = 30.0 bits (68), Expect = 0.076
Identities = 9/50 (18%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIP-NEVTEAEIIHLGIPFGRVTNVLVLKG 65
+ + + + + I N+ V ++++ + +GRV V KG
Sbjct: 14 ASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG 63
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 29.6 bits (67), Expect = 0.090
Identities = 6/32 (18%), Positives = 13/32 (40%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+ I +P T+ E+ + G V ++
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDL 47
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 29.5 bits (67), Expect = 0.091
Identities = 8/43 (18%), Positives = 18/43 (41%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ I + N+ + E ++ L PFG ++ + + K
Sbjct: 7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAK 49
>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 = 29.7 bits (67), Expect = 0.098
Identities = 6/47 (12%), Positives = 17/47 (36%)
Query: 18 AKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
L ++ R +++ N+ T ++ G + + +L
Sbjct: 24 QPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70
>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 = 29.6 bits (67), Expect = 0.11
Identities = 5/47 (10%), Positives = 19/47 (40%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ I++ N+P ++ +I + +G + ++ + +
Sbjct: 13 VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG 59
>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 = 30.2 bits (68), Expect = 0.11
Identities = 6/43 (13%), Positives = 17/43 (39%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
D + + + N+ + + + +GRV +V + +
Sbjct: 62 HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 29.7 bits (67), Expect = 0.11
Identities = 5/41 (12%), Positives = 19/41 (46%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLV 62
+++ P+ + + + TE ++ + +G + +V +
Sbjct: 38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSI 78
>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 = 29.5 bits (67), Expect = 0.11
Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
QA++ +Q + P+ ++I N+P + E E+ ++ PFG+V + +L+
Sbjct: 14 QAQMAKQ-QEQDPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILR 59
>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 = 29.0 bits (66), Expect = 0.11
Identities = 6/32 (18%), Positives = 18/32 (56%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
++IR + T+ +++ L P+G++ + +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL 39
>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 = 29.0 bits (66), Expect = 0.11
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
RV+++ + EV + + IPFG +T++ +
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 41
>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 = 29.8 bits (67), Expect = 0.12
Identities = 9/42 (21%), Positives = 20/42 (47%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLV 62
+ Q+ K S +++ N+ TE +I L G + +++
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIM 71
>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 = 29.8 bits (67), Expect = 0.13
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+H+R +P + TE +I + P V + G +
Sbjct: 37 SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD 82
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 29.2 bits (66), Expect = 0.13
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
R + + P V A++ + FG V +V++ K K
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG 45
>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 = 29.2 bits (66), Expect = 0.13
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
++ + +I E E EI +G + N+
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 56
>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 = 29.1 bits (66), Expect = 0.14
Identities = 9/43 (20%), Positives = 19/43 (44%)
Query: 25 SDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + R + + N+ V E + L + G +T V + K +
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE 53
>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 = 29.1 bits (66), Expect = 0.15
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
RV+++ + EV + + IPFG +T++ +
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 46
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 29.0 bits (65), Expect = 0.16
Identities = 6/43 (13%), Positives = 16/43 (37%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
+ +++ N+P + +++ G V L +G
Sbjct: 12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG 54
>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 = 28.9 bits (65), Expect = 0.17
Identities = 7/41 (17%), Positives = 15/41 (36%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVL 63
+ HI NIP +T+ +++ N + +
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHV 48
>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 = 29.0 bits (65), Expect = 0.18
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGR-VTNVLVLKGKN 67
+ I IP EI+ V +V+V
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA 46
>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 = 28.8 bits (65), Expect = 0.19
Identities = 7/39 (17%), Positives = 12/39 (30%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++I N+ VT ++ L VL
Sbjct: 7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG 45
>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 = 28.7 bits (65), Expect = 0.19
Identities = 7/37 (18%), Positives = 19/37 (51%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+++ N+P +T ++ + +G+V V ++K
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMK 50
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 28.8 bits (65), Expect = 0.20
Identities = 6/39 (15%), Positives = 15/39 (38%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+ +R + +N+ +TE E+ + + V
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV 46
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 29.4 bits (66), Expect = 0.21
Identities = 8/46 (17%), Positives = 18/46 (39%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + + N+ V++A+I L FG + V ++
Sbjct: 80 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 125
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 29.2 bits (66), Expect = 0.22
Identities = 6/48 (12%), Positives = 25/48 (52%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
Q +D+ + + I++ ++ ++++ +I + FG++ + + +
Sbjct: 112 QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR 159
Score = 25.7 bits (57), Expect = 3.6
Identities = 7/43 (16%), Positives = 19/43 (44%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+++ +++ +I E+ E I PFG + ++ +
Sbjct: 20 QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW 62
>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 = 28.8 bits (65), Expect = 0.23
Identities = 9/45 (20%), Positives = 18/45 (40%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
D R +++ N+ +VTE I+ L G + ++
Sbjct: 8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT 52
>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 = 28.9 bits (65), Expect = 0.24
Identities = 5/27 (18%), Positives = 13/27 (48%)
Query: 41 EVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++T + PFG + ++ + +N
Sbjct: 48 DMTPTLLRGAFSPFGNIIDLSMDPPRN 74
Score = 24.7 bits (54), Expect = 6.1
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 6/41 (14%)
Query: 74 EAEIIHLGIPFGRVTNVLVLKGKNQ--VSLISGYRNRQSAA 112
+ PFG + ++ + +N V+ Y +SA
Sbjct: 51 PTLLRGAFSPFGNIIDLSMDPPRNCAFVT----YEKMESAD 87
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 28.4 bits (64), Expect = 0.24
Identities = 6/33 (18%), Positives = 14/33 (42%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
++ + + E TE +I +G + N+
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNI 53
>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 = 27.9 bits (63), Expect = 0.29
Identities = 7/44 (15%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+R D P+ + + + TE ++ + +G + +V ++
Sbjct: 8 NRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY 49
>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 = 28.0 bits (63), Expect = 0.31
Identities = 8/38 (21%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 29 PSRVIHIRNIPNE-VTEAEIIHLGIPFGRVTNVLVLKG 65
SR + I N+P + V++ ++ + P+G + + +
Sbjct: 22 KSR-LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 58
>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 = 28.0 bits (63), Expect = 0.36
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
VI ++N+P V+ EI+ + + + LK
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLK 49
>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 = 28.3 bits (63), Expect = 0.38
Identities = 9/41 (21%), Positives = 16/41 (39%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVL 63
+D + +R +P T+ EI+ V N + L
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75
>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 = 27.5 bits (62), Expect = 0.39
Identities = 9/37 (24%), Positives = 15/37 (40%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+R I++ N+ T E+ G V V +L
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILC 40
>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 = 28.0 bits (63), Expect = 0.41
Identities = 6/43 (13%), Positives = 16/43 (37%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
D + + N+ + + + +GRV +V + +
Sbjct: 5 SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR 47
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 28.1 bits (62), Expect = 0.47
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 13 VMVVQAKLDRQKSDFKPSRV--IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
+ A +D + S V I + N+ VT + + FG V ++ NQ
Sbjct: 9 LAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ 66
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 27.7 bits (62), Expect = 0.50
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ I ++P E T+ ++ +PFG V + V K
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQ 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 = 28.0 bits (63), Expect = 0.53
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 27 FKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKG 65
+R +++ NIP +TE ++ R+ + G
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39
>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 = 27.6 bits (62), Expect = 0.53
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHL 50
P + N+P +VTE I
Sbjct: 13 SPPYTAFLGNLPYDVTEESIKEF 35
>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 = 0.54
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHL 50
R + P + N+P +VTE I
Sbjct: 10 HRSRLPKSPPYTAFLGNLPYDVTEESIKEF 39
>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 = 28.1 bits (63), Expect = 0.56
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
+R +++ NIP +TE ++ R+ + G
Sbjct: 3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN 40
Score = 27.7 bits (62), Expect = 0.75
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ I +PN + + ++ L FG + ++K
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 148
>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 = 27.7 bits (62), Expect = 0.59
Identities = 9/35 (25%), Positives = 19/35 (54%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ I ++P E + +++ + +PFG V + V K
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ 62
>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 = 27.2 bits (61), Expect = 0.60
Identities = 7/42 (16%), Positives = 19/42 (45%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ +H+ NIP + ++ + FG++ +V ++
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF 49
>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 = 27.8 bits (61), Expect = 0.60
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 2/58 (3%)
Query: 13 VMVVQAKLDRQKSDFKPSRVIH--IRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
+ A +D + S V+ + N+ VT + + FG V ++ NQ
Sbjct: 27 LAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ 84
>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 = 27.3 bits (61), Expect = 0.74
Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
Q+S ++ + + E TE +I +G + N+
Sbjct: 17 QRSV--EGWILFVTGVHEEATEEDIHDKFAEYGEIKNI 52
>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 = 27.2 bits (61), Expect = 0.75
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 25 SDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLV 62
S S + +RN+ +E ++ L +G ++ +
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHY 40
>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 = 26.9 bits (60), Expect = 0.75
Identities = 6/48 (12%), Positives = 16/48 (33%), Gaps = 5/48 (10%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFG--RVTNVLVLKGKN 67
S + +R P VTE ++ + + +++ +
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEF---LAPLKPVAIRIVRNAH 46
>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 = 26.9 bits (60), Expect = 0.76
Identities = 5/27 (18%), Positives = 13/27 (48%)
Query: 41 EVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++T + PFG + ++ + +N
Sbjct: 24 DMTPTLLRGAFSPFGNIIDLSMDPPRN 50
>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 = 27.0 bits (60), Expect = 0.77
Identities = 8/41 (19%), Positives = 14/41 (34%), Gaps = 5/41 (12%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFG--RVTNVLVLKGKN 67
+ + +P E ++ F RV V +LK
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDF---FHGLRVDAVHLLKDHV 52
>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 = 27.5 bits (62), Expect = 0.79
Identities = 5/33 (15%), Positives = 15/33 (45%)
Query: 35 IRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ +P ++T+ E+ L G + +++
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYK 40
Score = 26.0 bits (58), Expect = 3.1
Identities = 6/43 (13%), Positives = 20/43 (46%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
R + +++ N+P +T+ ++ + +G + +L+
Sbjct: 81 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 123
>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 = 26.9 bits (60), Expect = 0.80
Identities = 8/35 (22%), Positives = 17/35 (48%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+I ++N+P V+ EI+ + + + LK
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLK 49
>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 = 27.3 bits (61), Expect = 0.87
Identities = 8/46 (17%), Positives = 18/46 (39%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + + N+ V++A+I L FG + V ++
Sbjct: 27 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 72
>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 = 26.6 bits (59), Expect = 0.89
Identities = 6/24 (25%), Positives = 13/24 (54%)
Query: 27 FKPSRVIHIRNIPNEVTEAEIIHL 50
+R +++ NIP +TE ++
Sbjct: 3 LGSARRLYVGNIPFGITEEAMMDF 26
>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 = 27.2 bits (61), Expect = 0.96
Identities = 7/47 (14%), Positives = 19/47 (40%)
Query: 14 MVVQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+ ++ R + +R + +N+ +TE E+ + + V
Sbjct: 83 IKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV 129
Score = 24.9 bits (55), Expect = 7.2
Identities = 6/45 (13%), Positives = 16/45 (35%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ S+ + I N+ + AE+ ++ V+ +
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT 50
>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 = 26.8 bits (59), Expect = 1.0
Identities = 6/44 (13%), Positives = 15/44 (34%), Gaps = 5/44 (11%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIH----LGIPFGRVTNVLVLKGKN 67
V+ +R +P + ++ + I V V + +
Sbjct: 15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIH-DGVAGVHFIYTRE 57
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 26.8 bits (60), Expect = 1.0
Identities = 5/33 (15%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNV 60
+P ++ N+P + +I + + +V
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSV 44
>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 = 26.9 bits (60), Expect = 1.1
Identities = 7/48 (14%), Positives = 22/48 (45%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
A + + +++ ++ +TE + + PFGR+ ++ ++
Sbjct: 13 AAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60
>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 = 27.7 bits (61), Expect = 1.1
Identities = 13/71 (18%), Positives = 32/71 (45%), Gaps = 17/71 (23%)
Query: 39 PNEVTEAEIIHLGIPFGRVTNVLVLKG--KNQLLLHLEAEIIHLGIPFGRVTNVLVLKGK 96
P+ + ++ + G+P + +L + + Q+ ++ HL P G+
Sbjct: 321 PSILEDSLENNEGVP----SPMLSISNLTQEQVQDYVNKTNSHL--PAGKQV-------- 366
Query: 97 NQVSLISGYRN 107
++SL++G +N
Sbjct: 367 -EISLVNGAKN 376
Score = 26.6 bits (58), Expect = 2.7
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 15 VVQAKLDRQKSDFKPS---RVIHI-RNIPNEVTEAEIIHLGIPFGR 56
Q +R + FK + ++ I N P +T IH G G+
Sbjct: 1641 AAQDVWNRADNHFKDTYGFSILDIVINNPVNLT----IHFGGEKGK 1682
Score = 25.4 bits (55), Expect = 6.1
Identities = 17/78 (21%), Positives = 24/78 (30%), Gaps = 26/78 (33%)
Query: 16 VQAKLDRQKSDFKPSRVIHI--RNIPNE--VTEAEIIHLGIPFGRVTNVLVLKGKNQLLL 71
VQ +++ S + + I N V+ G P L G N L
Sbjct: 349 VQDYVNKTNSHLPAGKQVEISLVNGAKNLVVS-------GPP-------QSLYGLNLTLR 394
Query: 72 HLEAEIIHLG-----IPF 84
+A G IPF
Sbjct: 395 KAKAPS---GLDQSRIPF 409
>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 = 26.4 bits (59), Expect = 1.2
Identities = 6/34 (17%), Positives = 16/34 (47%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLV 62
+HI + VT+ I+ + +G++ + +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDM 36
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 26.5 bits (59), Expect = 1.2
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 2/38 (5%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGR--VTNVLVLK 64
I +RNI I+ P+ V N+ ++K
Sbjct: 8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIK 45
>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 = 26.5 bits (59), Expect = 1.3
Identities = 6/42 (14%), Positives = 15/42 (35%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ S+ + I N+ + AE+ ++ V+
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD 51
>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 = 26.9 bits (60), Expect = 1.4
Identities = 8/43 (18%), Positives = 20/43 (46%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ P +++ ++ +VTEA + P G + ++ V +
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR 49
>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 = 26.4 bits (59), Expect = 1.5
Identities = 8/36 (22%), Positives = 22/36 (61%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
S +++ ++ +TE + + PFG++ N++++K
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK 39
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 26.1 bits (58), Expect = 1.6
Identities = 4/32 (12%), Positives = 14/32 (43%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+++ N+ + E+ +G + V + +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIAR 34
>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 = 26.7 bits (60), Expect = 1.7
Identities = 9/38 (23%), Positives = 19/38 (50%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQ 68
RV+++ N+ +TE + G + N+ ++ KN
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN 38
>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 = 26.1 bits (58), Expect = 1.7
Identities = 8/46 (17%), Positives = 19/46 (41%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ + + + N+ V++A+I L FG + V ++
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS 66
>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 = 26.4 bits (59), Expect = 1.8
Identities = 6/33 (18%), Positives = 15/33 (45%)
Query: 35 IRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
+ +P +T+ E L G + + +++ K
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI 39
>2zo4_A Metallo-beta-lactamase family protein; hydrolase; 2.10A {Thermus
thermophilus}
Length = 317
Score = 26.6 bits (59), Expect = 2.3
Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 48 IHLGIPFG-RVTNVLVLKGKNQLLL------------HLEAEIIHLGIPFGRVTNVLV 92
+ + IP+ + N+ +L+G ++ L LE + LG+ F V +L+
Sbjct: 11 LPVPIPYPLKTVNLYLLQGAGEVALVDTALGTRAARGALELHLAELGLCFQDVKTILL 68
>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 = 25.9 bits (57), Expect = 2.4
Identities = 6/42 (14%), Positives = 19/42 (45%)
Query: 17 QAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVT 58
+ R +P+ I+++N+ V E ++ ++ + +
Sbjct: 32 TLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFS 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 = 26.0 bits (58), Expect = 2.6
Identities = 8/53 (15%), Positives = 20/53 (37%)
Query: 15 VVQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
V+ K + + + I + I +V E +G + + ++ K+
Sbjct: 72 VIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
>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 = 3.0
Identities = 8/43 (18%), Positives = 19/43 (44%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ + R + + IP V E ++ L +G + +V ++
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC 76
>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 = 26.4 bits (57), Expect = 3.2
Identities = 15/91 (16%), Positives = 28/91 (30%), Gaps = 13/91 (14%)
Query: 20 LDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKNQLLLHLEAEIIH 79
D KS + HI + V+ R+ L+ K + + +E E++
Sbjct: 39 QDMPKSILSKEEIDHIIMSKDAVSGTL---------RLFWTLLSKQEEMVQKFVE-EVLR 88
Query: 80 LGIPF--GRVTNVLVLKGKNQVSLISGYRNR 108
+ F + I R+R
Sbjct: 89 INYKFLMSPIKTEQRQPSMMTRMYIE-QRDR 118
>1qs1_A ADP-ribosyltransferase; alpha-beta protein, binary toxin,
insecticial protein; 1.50A {Bacillus cereus} SCOP:
d.166.1.1 d.166.1.1 PDB: 1qs2_A*
Length = 462
Score = 26.1 bits (56), Expect = 3.3
Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 28 KPSRVIHIRNIPNEVTEAEIIHLGIPFG---RVTNVLVLKGKNQLLLHLEAEII 78
K S ++ I +E EI+ + + V + K ++A ++
Sbjct: 410 KGSTGAYLSAIGGFASEKEIL---LDKDSKYHIDKVTEVIIKGVKRYVVDATLL 460
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 101
Score = 25.3 bits (56), Expect = 3.5
Identities = 4/29 (13%), Positives = 11/29 (37%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRV 57
S+ + + N+ TE + + +
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEKATFI 42
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 25.3 bits (55), Expect = 3.7
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 30 SRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
SR + + +P ++ E EI FG + K ++
Sbjct: 8 SRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAES 45
>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 = 25.1 bits (55), Expect = 3.9
Identities = 8/55 (14%), Positives = 22/55 (40%), Gaps = 10/55 (18%)
Query: 28 KPSRVIHIRNI--PNEVTEAEIIHL--------GIPFGRVTNVLVLKGKNQLLLH 72
P+ V+ + N+ P E+ + E +G V ++ + + + + +
Sbjct: 3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVP 57
>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 = 25.2 bits (55), Expect = 4.0
Identities = 3/30 (10%), Positives = 13/30 (43%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHL 50
+ + + +I + +P T ++++
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNF 31
>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 = 25.0 bits (55), Expect = 4.0
Identities = 4/36 (11%), Positives = 10/36 (27%)
Query: 23 QKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVT 58
+ I ++ + VT + G +
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIK 41
>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 = 25.1 bits (55), Expect = 4.3
Identities = 4/32 (12%), Positives = 11/32 (34%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ + +P + ++ G V V +
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYR 49
>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 = 25.6 bits (55), Expect = 4.6
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
R ++I+ P + T +I G+V N+ + + +
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH 146
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 25.0 bits (55), Expect = 5.2
Identities = 7/36 (19%), Positives = 19/36 (52%)
Query: 29 PSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
+ +H+ NIP + ++ + FG++ +V ++
Sbjct: 28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF 63
>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 = 24.6 bits (54), Expect = 7.2
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
QK D + + ++ E+T +I PFGR+++ V+K
Sbjct: 7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVK 49
>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 = 24.6 bits (53), Expect = 7.6
Identities = 3/30 (10%), Positives = 11/30 (36%)
Query: 21 DRQKSDFKPSRVIHIRNIPNEVTEAEIIHL 50
+ V+ +R +P + ++ +
Sbjct: 35 MMLGPEGGEGFVVKLRGLPWSCSVEDVQNF 64
>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 = 24.2 bits (53), Expect = 8.8
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 33 IHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGK 66
+ I + E E + + G ++ VL++K +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR 43
>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 = 24.2 bits (53), Expect = 8.8
Identities = 7/52 (13%), Positives = 22/52 (42%)
Query: 16 VQAKLDRQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
V+ +D + + +R + + + ++ G+V +V ++ +N
Sbjct: 11 VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 24.3 bits (53), Expect = 8.9
Identities = 5/36 (13%), Positives = 12/36 (33%)
Query: 24 KSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTN 59
+ D + I ++ + VT + G +
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKT 36
>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 = 24.1 bits (53), Expect = 9.5
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 31 RVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLK 64
R I++ N+ T ++ L FG+V NV ++
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIY 35
>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 = 24.6 bits (54), Expect = 9.7
Identities = 4/46 (8%), Positives = 17/46 (36%)
Query: 22 RQKSDFKPSRVIHIRNIPNEVTEAEIIHLGIPFGRVTNVLVLKGKN 67
++ + I + I + E + +G++ + ++ +
Sbjct: 96 QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG 141
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
0.323 0.141 0.390
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,745,159
Number of extensions: 96712
Number of successful extensions: 278
Number of sequences better than 10.0: 1
Number of HSP's gapped: 274
Number of HSP's successfully gapped: 166
Length of query: 118
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 37
Effective length of database: 4,440,192
Effective search space: 164287104
Effective search space used: 164287104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.4 bits)