RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6355
(83 letters)
>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 = 57.3 bits (139), Expect = 1e-12
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGT-IPKGSNEPITVKFANSPSSS 52
++G + F++F EA+ AI L+G+ G++ + VKFA++ S
Sbjct: 48 LRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100
>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 = 57.6 bits (140), Expect = 3e-12
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+G F+R+++R EA+ AI LN IP+G ++P++V+ A
Sbjct: 131 RGV-------AFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 37.6 bits (88), Expect = 8e-05
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
T + F+ F ++++RAI+ LNG + + V +A S K
Sbjct: 41 TGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNK--RLKVSYARPGGESIK 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 = 56.8 bits (138), Expect = 5e-12
Identities = 27/45 (60%), Positives = 31/45 (68%), Gaps = 7/45 (15%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+G GFIRFD+RIEAE AI+ LNG P G+ EPITVKFA
Sbjct: 130 RGV-------GFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 37.6 bits (88), Expect = 8e-05
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 5 TDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKV 55
T GF+ + +AE+AI LNG + I V +A S+S +
Sbjct: 40 TGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK--TIKVSYARPSSASIRD 88
>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 = 55.7 bits (135), Expect = 5e-12
Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 13/55 (23%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKG------SNEPITVKFANSPS 50
+G GF R + + E I NG K EP+ KF+ S
Sbjct: 66 RGV-------GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113
>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 = 55.3 bits (134), Expect = 2e-11
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGT-IPKGSNEPITVKFAN 47
+G F+ F R A+ AI+ ++ +G + P+ VKFA+
Sbjct: 136 RGC-------AFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
Score = 34.9 bits (81), Expect = 7e-04
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 12 GFIRFDQRIEAERAIQELNGT-IPKGSNEPITVKFANSPSS 51
F+ F R A A L+ + G + PI +K A+S +
Sbjct: 50 CFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKN 90
>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 = 50.4 bits (121), Expect = 4e-09
Identities = 19/71 (26%), Positives = 27/71 (38%), Gaps = 12/71 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAA 61
KGF + ++ AE A Q+ +G GS + V F + LAA
Sbjct: 226 KGF-------AVLEYETAEMAEEAQQQADGLSLGGS--HLRVSFCAPGPPGR---SMLAA 273
Query: 62 YLTPQAAAARR 72
+ QA A R
Sbjct: 274 LIAAQATALNR 284
Score = 42.3 bits (100), Expect = 2e-06
Identities = 10/51 (19%), Positives = 20/51 (39%), Gaps = 9/51 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSS 52
KG+ GF + ++ A RA +L G + V + ++ +
Sbjct: 137 KGY-------GFAEYMKKDSAARAKSDLLGKPLGPR--TLYVHWTDAGQLT 178
Score = 36.1 bits (84), Expect = 4e-04
Identities = 6/39 (15%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
F+ +AE AI + + + ++V+ + +
Sbjct: 60 AFVTLLNGEQAEAAINAFHQSRLRER--ELSVQLQPTDA 96
>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 = 47.3 bits (113), Expect = 8e-09
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNG-TIPKGSNEPITVKFANSPS 50
KG F+ + +R A +A L+ G N PI VK A+S S
Sbjct: 55 KGC-------AFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES 97
>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 = 48.0 bits (115), Expect = 1e-08
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 11/75 (14%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAA 61
KG+ GF+ F+ + AERAI+++NG + ++ + V S + A
Sbjct: 143 KGY-------GFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFKSRKEREAELGARAK 193
Query: 62 YLTPQAAAARRFGGP 76
P + G
Sbjct: 194 EFYPY--DVPDYAGS 206
Score = 38.4 bits (90), Expect = 5e-05
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKV 55
++ F Q +AERA+ +N + KG P+ + ++ S K
Sbjct: 60 AYVNFQQPADAERALDTMNFDVIKGK--PVRIMWSQRDPSLRKS 101
>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 = 43.0 bits (102), Expect = 3e-07
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 9/50 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSS 51
KGF GFIR + R AE A EL+ +G + V+FA +S
Sbjct: 51 KGF-------GFIRLETRTLAEIAKVELDNMPLRGK--QLRVRFACHSAS 91
>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 = 42.6 bits (101), Expect = 4e-07
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSS 52
+I+++ A+ A ++ G G + + V FA S SS
Sbjct: 56 AYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96
>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 = 42.7 bits (101), Expect = 4e-07
Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
KG+ F+RF A AI +NGT +G + +
Sbjct: 61 KGY-------SFVRFSTHESAAHAIVSVNGTTIEGH--VVKCYWGKESPDMTS 104
>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 = 42.1 bits (100), Expect = 2e-06
Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+G+ GF+ F + +A+ A+ + G + P+ + +A
Sbjct: 129 RGY-------GFVSFTSQDDAQNAMDSMQGQDL--NGRPLRINWA 164
Score = 38.3 bits (90), Expect = 5e-05
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
F+ + Q +A A+Q LNG + + + + +A S+
Sbjct: 44 AFVEYHQSHDANIALQTLNGKQIENN--IVKINWAFQSQQSSS 84
>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 = 42.2 bits (99), Expect = 2e-06
Identities = 10/71 (14%), Positives = 21/71 (29%), Gaps = 8/71 (11%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAAYLTPQAA 68
+ ++ +A+ A+ LNG G PI + + +
Sbjct: 41 KENALVQMADGNQAQLAMSHLNGHKLHGK--PIRITLSKHQNVQLPREGQ------EDQG 92
Query: 69 AARRFGGPIHH 79
+ +G H
Sbjct: 93 LTKDYGNSPLH 103
Score = 36.8 bits (85), Expect = 2e-04
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
F R + I+ EA +A+ +L+ G N + V F+ S
Sbjct: 150 GFKFFQKDRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVSFSKST 197
>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 = 42.4 bits (100), Expect = 2e-06
Identities = 14/84 (16%), Positives = 25/84 (29%), Gaps = 10/84 (11%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGT--IPKGSNEPITVKFANSPSSSNKVIAPL 59
G GF+ F + A +A++ + + P+ V+ + + L
Sbjct: 137 TGK-------GFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKL 189
Query: 60 AAYLTPQAAAARRFGGPIHHAGRF 83
T Q R G F
Sbjct: 190 MQK-TQQYHKEREQPPRFAQPGTF 212
Score = 39.7 bits (93), Expect = 2e-05
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 9/49 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+GF GFIR + R AE A EL+GTI K P+ ++FA +
Sbjct: 58 RGF-------GFIRLESRTLAEIAKAELDGTILKSR--PLRIRFATHGA 97
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 40.7 bits (96), Expect = 3e-06
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+ GF F+ F++ A +AI+E++G +P+ V ++ P+
Sbjct: 64 LNGF-------AFVEFEEAESAAKAIEEVHGKSFAN--QPLEVVYSKLPA 104
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dk2_A
Length = 103
Score = 40.3 bits (95), Expect = 3e-06
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 9/54 (16%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+K + FI FD+R A +A++E+NG +G I + FA P K
Sbjct: 44 LKDY-------AFIHFDERDGAVKAMEEMNGKDLEGE--NIEIVFAKPPDQKRK 88
>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 = 40.2 bits (94), Expect = 4e-06
Identities = 10/63 (15%), Positives = 17/63 (26%), Gaps = 5/63 (7%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS-----PSSSNKV 55
R F+ ++ A A ++L + I V +A V
Sbjct: 44 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 103
Query: 56 IAP 58
P
Sbjct: 104 SGP 106
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 39.2 bits (92), Expect = 9e-06
Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
KG FI++D +A I L +G + +
Sbjct: 63 KGC-------CFIKYDTHEQAAVCIVALANFPFQGR--NLRTGWGKE 100
>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 = 39.2 bits (92), Expect = 1e-05
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
F+ F + +A A+ +NG G + V +A +PSS
Sbjct: 58 CFVEFYEHRDAAAALAAMNGRKILGK--EVKVNWATTPSSQKS 98
>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 = 38.7 bits (91), Expect = 1e-05
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+K + F+ ++ +A+ AI +LNG KG + I V+ +
Sbjct: 42 VKDY-------AFVHMEKEADAKAAIAQLNGKEVKG--KRINVELSTKGQ 82
>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 = 38.4 bits (90), Expect = 2e-05
Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 9/52 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
+ F+ +++ A++A+ ELNGT + + V A +
Sbjct: 49 RNC-------AFVTYEKMESADQAVAELNGTQVESV--QLKVNIARKQPMLD 91
>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 = 40.0 bits (93), Expect = 2e-05
Identities = 11/69 (15%), Positives = 21/69 (30%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAAYLTPQA 67
+ ++ +A+ A+ LNG G IT+ + +
Sbjct: 71 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 130
Query: 68 AAARRFGGP 76
+ RF P
Sbjct: 131 SPLHRFKKP 139
Score = 33.8 bits (77), Expect = 0.003
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 4 FTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
F R + I+ EA +A+ +L+ G N + V F+ S
Sbjct: 184 FFQKDRKMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVSFSKST 228
>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 = 38.6 bits (90), Expect = 2e-05
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+ F+ +++ A++A+ ELNGT + + V A +
Sbjct: 73 RNC-------AFVTYEKMESADQAVAELNGTQVESV--QLKVNIARKQPMLDA 116
>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 = 38.5 bits (90), Expect = 2e-05
Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 9/54 (16%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
KG+ F+++ A A+ NG + G + + + A P
Sbjct: 61 HKGY-------AFVQYSNERHARAAVLGENGRVLAG--QTLDINMAGEPKPDRS 105
>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 = 38.0 bits (89), Expect = 3e-05
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
++ + F+ F R +A A++ LNG + GS PI V A
Sbjct: 50 IRDY-------AFVHFSNREDAVEAMKALNGKVLDGS--PIEVTLA 86
>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 = 38.0 bits (89), Expect = 3e-05
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
M+G FI F + A +A+ +NG G + + ++F +
Sbjct: 66 MRGQ-------AFITFPNKEIAWQALHLVNGYKLYG--KILVIEFGKNKK 106
>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 = 38.0 bits (89), Expect = 3e-05
Identities = 9/47 (19%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
G + F+++ +A +A+++ NG G P+ ++ S
Sbjct: 70 LGT-------ADVHFERKADALKAMKQYNGVPLDG--RPMNIQLVTS 107
>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 = 37.6 bits (88), Expect = 4e-05
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+K + F+ ++ +A AI+ L+ T +G + + V+ + S
Sbjct: 43 VKDY-------AFVHMERAEDAVEAIRGLDNTEFQG--KRMHVQLSTSRL 83
>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 = 37.4 bits (87), Expect = 4e-05
Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 4 FTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAP 58
+ D + F+ +A+ AIQ + +G + V+ P+ + P
Sbjct: 35 YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGK--DLIVQLQ--PTDALLCSGP 85
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 37.6 bits (88), Expect = 4e-05
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KG+ GF++F +E +RA+ E G + GS P+ + A
Sbjct: 51 KGY-------GFVKFTDELEQKRALTECQGAVGLGSK-PVRLSVAI 88
>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 = 37.2 bits (87), Expect = 5e-05
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
K F GF+ F AI LNG G PI V +S
Sbjct: 57 KSF-------GFVCFKHPESVSYAIALLNGIRLYGR--PINVSGPSS 94
>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 = 37.2 bits (87), Expect = 5e-05
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+K + GF+ + + AE AI+ L+ G I V+ + + S ++
Sbjct: 41 IKNY-------GFVHIEDKTAAEDAIRNLHHYKLHG--VNINVEASKNKSKASS 85
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 36.8 bits (86), Expect = 7e-05
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
F GFI+FD AI+ + + G + + ++ ++S +
Sbjct: 44 KNAF-------GFIQFDNPQSVRDAIECESQEMNFG--KKLILEVSSSNA 84
>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 = 36.8 bits (86), Expect = 7e-05
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KG+ GF+ F + +AE AIQ++ G G I +A
Sbjct: 48 KGY-------GFVSFFNKWDAENAIQQMGGQWLGG--RQIRTNWAT 84
>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 = 36.5 bits (85), Expect = 9e-05
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 12 GFIRFDQRIEAERAIQE-LNGTIPKGSNEPITVKFA 46
FI+F R AE A ++ N I G + VK+
Sbjct: 51 AFIQFATRQAAEVAAEKSFNKLIVNG--RRLNVKWG 84
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 36.1 bits (84), Expect = 1e-04
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
F GFI+FD AI+ + + G + + ++ ++S +
Sbjct: 56 KNAF-------GFIQFDNPQSVRDAIEXESQEMNFG--KKLILEVSSSNA 96
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 36.1 bits (84), Expect = 2e-04
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
KGF GF+ F+ +A+RA ++L+GT+ +G I V A + +N
Sbjct: 55 KGF-------GFVTFENSADADRAREKLHGTVVEG--RKIEVNNATARVMTNS 98
>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 = 36.1 bits (84), Expect = 2e-04
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
M+G F+ F + A A++ + G P+ +++A + S
Sbjct: 50 MRGQ-------AFVIFKEVSSATNALRSMQGFPFYDK--PMRIQYAKTDS 90
>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 = 35.7 bits (83), Expect = 2e-04
Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
GF GF+ + + +A++A+++L G G + V+ +
Sbjct: 50 MGF-------GFVEYKKPEQAQKALKQLQGHTVDGH--KLEVRISE 86
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 36.2 bits (84), Expect = 2e-04
Identities = 11/67 (16%), Positives = 19/67 (28%), Gaps = 10/67 (14%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAA 61
G + F A+ ++ L+ T G+ I + K +
Sbjct: 48 LGL-------ARVLFTSTRGAKETVKNLHLTSVMGN--IIHAQLDIKGQQRMKYYELIVN 98
Query: 62 YL-TPQA 67
TPQ
Sbjct: 99 GSYTPQT 105
>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 = 36.8 bits (86), Expect = 2e-04
Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 9/47 (19%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KG +I F +AE+ ++E G G +++ +
Sbjct: 135 SKGI-------AYIEFKSEADAEKNLEEKQGAEIDGR--SVSLYYTG 172
Score = 28.0 bits (63), Expect = 0.24
Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 10/53 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+ F G++ F+ + E+A+ EL G G+ I ++ S
Sbjct: 54 RKF-------GYVDFESAEDLEKAL-ELTGLKVFGN--EIKLEKPKGRDSKKV 96
>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 = 35.8 bits (83), Expect = 2e-04
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNE--PITVKFANSPSSSN 53
F+ F AE+ + ++NG G+ + +A S+
Sbjct: 55 CFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSS 98
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 35.7 bits (83), Expect = 2e-04
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 9/51 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSS 52
KG ++ ++ +A +A+ +++G K I V +NS SS
Sbjct: 58 KGL-------AYVEYENESQASQAVMKMDGMTIKE--NIIKVAISNSGPSS 99
>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 = 35.8 bits (83), Expect = 2e-04
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
K F GF+ +D + A+ AIQ +NG + + V+ S + S
Sbjct: 67 KCF-------GFVSYDNPVSAQAAIQSMNGFQIGM--KRLKVQLKRSKNDSKS 110
>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 = 36.3 bits (84), Expect = 2e-04
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
MKG FI A +A++E NG + G +P+ V+FA S
Sbjct: 91 MKGQ-------AFIGLPNEKAAAKALKEANGYVLFG--KPMVVQFARSAR 131
>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 = 35.7 bits (83), Expect = 3e-04
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
+G G + F+Q IEA +AI NG + P+ VK
Sbjct: 56 RGI-------GTVTFEQSIEAVQAISMFNGQLLFD--RPMHVKMDERA 94
>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 = 36.8 bits (84), Expect = 3e-04
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
M+G F+ F + A A++ + G P+ +++A + S
Sbjct: 51 MRGQ-------AFVIFKEVSSATNALRSMQGFPFYDK--PMRIQYAKTDS 91
Score = 32.2 bits (72), Expect = 0.009
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
F+ FD ++A A L G N + + FA
Sbjct: 247 AFVEFDNEVQAGAARDALQGF-KITQNNAMKISFA 280
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 35.2 bits (82), Expect = 3e-04
Identities = 10/46 (21%), Positives = 21/46 (45%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
+G+ GF+ F + +A+ A+ + G G P+ + +A
Sbjct: 43 RGY-------GFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWAA 79
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 35.4 bits (82), Expect = 3e-04
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
KG+ GF+ F + +AE AIQ++ G G I +A + K
Sbjct: 57 KGY-------GFVSFFNKWDAENAIQQMGGQWLGG--RQIRTNWATRKPPAPK 100
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 35.0 bits (81), Expect = 3e-04
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 9/49 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGS--NEPITVKFANS 48
+GF F++ ++A + +Q L P + I V FA S
Sbjct: 53 RGF-------AFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 35.4 bits (82), Expect = 3e-04
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KGF GF+ F+ +A+RA ++L+GT+ +G I V A
Sbjct: 69 KGF-------GFVTFENSADADRAREKLHGTVVEG--RKIEVNNAT 105
>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 = 34.9 bits (81), Expect = 3e-04
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 10/51 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIP-KGSNEPITVKFANSPSS 51
G+ F+ + + A RAI+ L+G + G + + V ++ S
Sbjct: 44 SGY-------AFVDYPDQNWAIRAIETLSGKVELHG--KIMEVDYSVSKKL 85
>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 = 36.1 bits (84), Expect = 3e-04
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+ F +I + +A +++LNG +G + K +N S +
Sbjct: 159 RRF-------AYIDVTSKEDARYCVEKLNGLKIEG--YTLVTKVSNPLEKSKR 202
Score = 35.7 bits (83), Expect = 5e-04
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 10/45 (22%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
F+ F+ + AERA+ ++N ++ I+V A
Sbjct: 254 NCC-------AFMVFENKDSAERAL-QMNRSLLGNR--EISVSLA 288
Score = 29.6 bits (67), Expect = 0.085
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 12 GFIRFDQRIEAERAIQELNGTI 33
I F + A AI + + +
Sbjct: 84 ARIEFARYDGALAAITKTHKVV 105
>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 = 36.2 bits (83), Expect = 4e-04
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 2/41 (4%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSN--EPITVKFA 46
G + +D + +A + LN K N P T+K
Sbjct: 164 RSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204
Score = 30.4 bits (68), Expect = 0.034
Identities = 7/38 (18%), Positives = 12/38 (31%), Gaps = 2/38 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
+ +RAI LN + + V + P
Sbjct: 45 AMVEMADGYAVDRAITHLNNN--FMFGQKMNVCVSKQP 80
>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 = 35.4 bits (82), Expect = 4e-04
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
G + F++R +A +A+++ G G P+ ++ S
Sbjct: 76 LGT-------ADVHFERRADALKAMKQYKGVPLDG--RPMDIQLVAS 113
>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 = 34.9 bits (81), Expect = 4e-04
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KGF GF+ F EA +A+ E+NG I +P+ V A
Sbjct: 55 KGF-------GFVCFSSPEEATKAVTEMNGRIVAT--KPLYVALAQ 91
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 35.0 bits (81), Expect = 5e-04
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
K F GF+ FD A+ AI+ +NG + V+
Sbjct: 82 KCF-------GFVSFDNPDSAQVAIKAMNGFQVGTK--RLKVQLK 117
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 34.5 bits (80), Expect = 6e-04
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
KG G ++F+ AERA + +NG G I V+ + S
Sbjct: 48 KGC-------GVVKFESPEVAERACRMMNGMKLSG--REIDVRIDRNAS 87
>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 = 34.1 bits (79), Expect = 7e-04
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+GF F+ F+ +A+ A + NG G I V +S
Sbjct: 57 RGF-------AFVYFENVDDAKEAKERANGMELDG--RRIRVSGPSS 94
>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 = 34.5 bits (80), Expect = 7e-04
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
KG+ GF+ F+ + AERAI+++NG + + V S
Sbjct: 45 KGY-------GFVHFETQEAAERAIEKMNGMLLNDR--KVFVGRFKS 82
>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 = 34.0 bits (79), Expect = 7e-04
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKG 36
KG+ GF+ FD A++A+ L + +
Sbjct: 47 KGY-------GFVDFDSPSAAQKAVTALKASGVQA 74
>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 = 34.6 bits (80), Expect = 8e-04
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+GF FI F+ +A+ A +++NG G + I V+ A PS
Sbjct: 48 RGF-------AFITFENPADAKNAAKDMNGKSLHG--KAIKVEQAKKPS 87
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 34.1 bits (79), Expect = 8e-04
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
+GF GF+ F+ +A+ A+ +NG G I V A S +
Sbjct: 54 RGF-------GFVTFENIDDAKDAMMAMNGKSVDG--RQIRVDQAGKSSDNR 96
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 34.5 bits (79), Expect = 8e-04
Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+I F + A+ ++ G +G+ P+ + F+ +P
Sbjct: 75 AYIVFATQESAQAFVEAFQGYPFQGN--PLVITFSETPQ 111
>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 = 33.8 bits (78), Expect = 0.001
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+G+ GF+ F +A+ AI+ ++ G +PI V A++ + +
Sbjct: 57 QGY-------GFVEFLSEEDADYAIKIMDMIKLYG--KPIRVNKASAHNKNLS 100
>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 = 33.8 bits (78), Expect = 0.001
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
F+ F+ +AE A+ +G G + V+F S +
Sbjct: 64 AFVEFEDPRDAEDAVYGRDGYDYDG--YRLRVEFPRSGRGTGS 104
>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 = 34.1 bits (78), Expect = 0.001
Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 12 GFIRFDQRIEAERAIQELNGTIP---KGSNEPITVKFANS 48
F R+ E++RA LNG G + + F
Sbjct: 66 SFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105
>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 = 33.8 bits (78), Expect = 0.001
Identities = 9/52 (17%), Positives = 19/52 (36%), Gaps = 9/52 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
KG +I F +AE+ ++E G G +++ + +
Sbjct: 53 KGI-------AYIEFKSEADAEKNLEEKQGAEIDGR--SVSLYYTGEKGGTR 95
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 34.4 bits (79), Expect = 0.001
Identities = 8/37 (21%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ F++R +A +A+++ G G P+ ++ S
Sbjct: 132 ADVHFERRADALKAMKQYKGVPLDGR--PMDIQLVAS 166
>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 = 34.3 bits (78), Expect = 0.002
Identities = 11/81 (13%), Positives = 22/81 (27%), Gaps = 9/81 (11%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAA 61
KGF + +++ + L G + V N S +
Sbjct: 112 KGF-------ALVGVGSEASSKKLMDLLPKRELHG--QNPVVTPVNKQFLSQFEMQSRKT 162
Query: 62 YLTPQAAAARRFGGPIHHAGR 82
+ Q + + G P +
Sbjct: 163 TQSGQMSGEGKAGPPGGSSRA 183
>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 = 34.1 bits (78), Expect = 0.002
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
F+ F+ +A A++EL+G G + V+ +N
Sbjct: 113 AFVEFEDPRDAADAVRELDGRTLCG--CRVRVELSNGE 148
>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 = 33.3 bits (77), Expect = 0.002
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 7/31 (22%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGT 32
KGF FI F +R +A RAI ++G
Sbjct: 57 KGF-------AFISFHRREDAARAIAGVSGF 80
>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 = 33.0 bits (76), Expect = 0.002
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSS 51
+ F+ R EA A+ +LN + + + PSS
Sbjct: 60 AMVAFESRDEATAAVIDLNDRPIGSR--KVKLVLGSGPSS 97
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 34.2 bits (79), Expect = 0.002
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
KG+ GFI +++ ++ A+ +N G + + V A +P
Sbjct: 167 KGY-------GFIEYEKAQSSQDAVSSMNLFDLGG--QYLRVGKAVTP 205
Score = 32.7 bits (75), Expect = 0.006
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAA 61
KGF F+ ++ A+ A++++N + G I V ++ + +I LA
Sbjct: 70 KGF-------AFVEYEVPEAAQLALEQMNSVMLGGR--NIKVGRPSNIGQAQPIIDQLAE 120
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 33.2 bits (76), Expect = 0.002
Identities = 6/41 (14%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSS 52
+ + + +A +A+ +LNG + + V + ++
Sbjct: 57 VNVTYSSKDQARQALDKLNGFQLENF--TLKVAYIPDEMAA 95
>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 = 32.9 bits (76), Expect = 0.002
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSP 49
KG+ ++ F+ EAE+A++ ++G G IT +P
Sbjct: 47 KGY-------AYVEFENPDEAEKALKHMDGGQIDGQ--EITATAVLAP 85
>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 = 32.9 bits (76), Expect = 0.002
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
KG+ FI F ++ AI+ +NG N PITV +A
Sbjct: 48 KGY-------AFINFASFDASDAAIEAMNGQYL--CNRPITVSYAFK 85
>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 = 32.6 bits (75), Expect = 0.003
Identities = 7/47 (14%), Positives = 14/47 (29%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
KGF + +++ + L G + V +N
Sbjct: 45 KGF-------ALVGVGSEASSKKLMDLLPKRELHG--QNPVVTPSNK 82
>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 = 32.6 bits (75), Expect = 0.003
Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG FI F + A+ + +N G I A
Sbjct: 58 KGV-------AFILFLDKDSAQNCTRAINNKQLFGR--VIKASIA 93
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 32.9 bits (75), Expect = 0.003
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
G + F A++ LN +GS ITV+ ++P +
Sbjct: 70 GALEFPSEEILVEALERLNNIEFRGS--VITVERDDNPPPIRR 110
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 32.7 bits (75), Expect = 0.004
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
F+ F+ +AE A++ L+G + GS + V+ +
Sbjct: 40 AFVEFEDPRDAEDAVRGLDGKVICGSR--VRVELSTGMP 76
>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 = 32.5 bits (74), Expect = 0.004
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 8/50 (16%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA------NSPSSS 52
++ + + +A RAIQ +N + G + S SS
Sbjct: 63 SASAYVTYIRSEDALRAIQCVNNVVVDG--RTLKASLGTTKYCSYSGPSS 110
>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 = 32.2 bits (74), Expect = 0.004
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
KGF F+ F A +A E++G + +G + V + +++
Sbjct: 50 KGF-------AFVTFMFPEHAVKAYAEVDGQVFQG--RMLHVLPSTIKKEASQ 93
>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 = 33.1 bits (76), Expect = 0.004
Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 9/51 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSS 52
KG+ F + ++AI LNG + V+ A+ + +
Sbjct: 156 KGY-------AFCEYVDINVTDQAIAGLNGMQLGDK--KLLVQRASVGAKN 197
>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 = 32.2 bits (74), Expect = 0.004
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KGF GF+ F+ +A+ A + + G+ +T+ +A
Sbjct: 54 KGF-------GFVDFNSEEDAKAAKEAMEDGEIDGN--KVTLDWAK 90
>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 = 32.1 bits (74), Expect = 0.004
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KG+ GFI F A RA+++LNG G P+ V
Sbjct: 47 KGY-------GFITFSDSECARRALEQLNGFELAG--RPMRVGHVT 83
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 32.4 bits (74), Expect = 0.005
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+GF F+RF + +AE A+ ++G + G + V+ A
Sbjct: 89 RGF-------AFVRFHDKRDAEDAMDAMDGAVLDGRE--LRVQMA 124
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 31.7 bits (72), Expect = 0.006
Identities = 7/40 (17%), Positives = 13/40 (32%), Gaps = 2/40 (5%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSS 51
F+ + A++A+ L G + V A
Sbjct: 59 AFLHYPDSAAAQQAVSCLQGLRLGTD--TLRVALARQQRD 96
>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 = 32.4 bits (74), Expect = 0.006
Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+G+ GF++F A++AI LNG + + V A S
Sbjct: 84 RGY-------GFVKFQSGSSAQQAIAGLNGFNILN--KRLKVALAAS 121
>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 = 31.8 bits (73), Expect = 0.006
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+GF F+RF R +A+ A ++G G + V+ A
Sbjct: 55 RGF-------AFVRFHDRRDAQDAEAAMDGAELDG--RELRVQVA 90
>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 = 32.0 bits (73), Expect = 0.006
Identities = 8/54 (14%), Positives = 21/54 (38%), Gaps = 9/54 (16%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
+G ++ ++ +A+ A+ L+G + V + N+ + K
Sbjct: 46 TRGT-------AYVVYEDIFDAKNAVDHLSGFNVSN--RYLVVLYYNANRAFQK 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 = 32.2 bits (73), Expect = 0.006
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 9/51 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSS 52
KG+ + + ++ L G + G E + V+ A + S
Sbjct: 99 KGY-------AEVVVASENSVHKLLELLPGKVLNG--EKVDVRPATRQNLS 140
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 32.5 bits (73), Expect = 0.006
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 10/50 (20%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGT----------IPKGSNEPITVKFANS 48
+ GF++F + AE A + ++ + + VK+AN
Sbjct: 179 KNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANE 228
>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 = 32.7 bits (74), Expect = 0.008
Identities = 10/71 (14%), Positives = 24/71 (33%), Gaps = 11/71 (15%)
Query: 19 RIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAPLAAYLTPQAAAARRFGGP-- 76
+ + + + + N +P + + + + N N V++ L R+ P
Sbjct: 346 QEQVQDYVNKTNSHLP--AGKQVEISLVNGA--KNLVVSGPPQSLYGLNLTLRKAKAPSG 401
Query: 77 -----IHHAGR 82
I + R
Sbjct: 402 LDQSRIPFSER 412
Score = 30.0 bits (67), Expect = 0.063
Identities = 14/86 (16%), Positives = 31/86 (36%), Gaps = 18/86 (20%)
Query: 9 RYLGFIRFDQRIEAER----------AIQELNGTIPKGSNEPI---TVKF-ANSPSSSNK 54
++LG++ +E + + E +G++ I K + ++ K
Sbjct: 63 KFLGYV--SSLVEPSKVGQFDQVLNLCLTEFENCYLEGND--IHALAAKLLQENDTTLVK 118
Query: 55 VIAPLAAYLTPQAAAARRFGGPIHHA 80
+ Y+T + A R F + A
Sbjct: 119 TKELIKNYITARIMAKRPFDKKSNSA 144
>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 = 32.1 bits (73), Expect = 0.008
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+GF F+RF + +AE A+ ++G + G + V+ A
Sbjct: 112 RGF-------AFVRFHDKRDAEDAMDAMDGAVLDGRE--LRVQMA 147
>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 = 31.5 bits (72), Expect = 0.008
Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 9/52 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
KG+ FI F +A+ A+ N +G I ++ S N
Sbjct: 53 KGY-------AFIEFASFEDAKEALNSCNKREIEG--RAIRLELQGPRGSPN 95
>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 = 31.8 bits (73), Expect = 0.010
Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KG+ F + ++AI LNG + V+ A+
Sbjct: 136 KGY-------AFCEYVDINVTDQAIAGLNGMQLGDK--KLLVQRAS 172
>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 = 31.6 bits (72), Expect = 0.010
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+GF F+ F+ +A+ A + NG G I V F+
Sbjct: 88 RGF-------AFVYFENVDDAKEAKERANGMELDG--RRIRVDFS 123
>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 = 31.3 bits (71), Expect = 0.010
Identities = 7/39 (17%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+ F + +EA +A + L + P+ +++A
Sbjct: 45 GGITAIVEFLEPLEARKAFRHLAYSKFHHV--PLYLEWA 81
>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 = 31.7 bits (72), Expect = 0.011
Identities = 11/53 (20%), Positives = 19/53 (35%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
GF F+ + R +AE A++ +NGT I + +
Sbjct: 81 CGF-------CFVEYYSRADAENAMRYINGTRLDD--RIIRTDWDAGFKEGRQ 124
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 31.1 bits (71), Expect = 0.011
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 9/46 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFAN 47
KG+ GFI F A++A+++LNG G P+ V
Sbjct: 68 KGY-------GFITFSDSECAKKALEQLNGFELAG--RPMKVGHVT 104
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 31.2 bits (71), Expect = 0.014
Identities = 15/53 (28%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNK 54
KG + FD A+ AI +G G+ PI V FA + N+
Sbjct: 57 KGE-------ATVSFDDPPSAKAAIDWFDGKEFSGN--PIKVSFATRRADFNR 100
>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 = 30.7 bits (70), Expect = 0.014
Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG + FD A+ AI +G G+ PI V FA
Sbjct: 63 KGE-------ATVSFDDPPSAKAAIDWFDGKEFSGN--PIKVSFA 98
>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 = 30.7 bits (70), Expect = 0.016
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 9/52 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
+GF F+ F+ +A AI +N + G I V A
Sbjct: 54 RGF-------AFVEFELAEDAAAAIDNMNESELFG--RTIRVNLAKPMRIKE 96
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 31.3 bits (71), Expect = 0.016
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+GF F+ F+ +A AI +N + G I V A
Sbjct: 105 RGF-------AFVEFELAEDAAAAIDNMNESELFG--RTIRVNLA 140
>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 = 30.2 bits (69), Expect = 0.022
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
+GF F+ F+ +A AI +N + G I V A
Sbjct: 49 RGF-------AFVEFELAEDAAAAIDNMNESELFG--RTIRVNLA 84
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 29.9 bits (68), Expect = 0.031
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG+ + ++ EA+ A++ LNG G +PI+V +
Sbjct: 65 KGY-------TLVEYETYKEAQAAMEGLNGQDLMG--QPISVDWC 100
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing,
mRNA splicing, mRNA transport, nonsense-mediated mRNA
decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB:
2j0q_D*
Length = 126
Score = 30.4 bits (69), Expect = 0.032
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG+ + ++ EA+ A++ LNG G +PI+V +
Sbjct: 64 KGY-------TLVEYETYKEAQAAMEGLNGQDLMG--QPISVDWC 99
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 30.2 bits (68), Expect = 0.032
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ FI + A + P +PI ++F+N
Sbjct: 51 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 30.0 bits (68), Expect = 0.037
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 10/55 (18%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQEL-NGTIPKGSNEPITVKFANSPSSSNK 54
+GF GF+ F + +A++A L + T G + +++A+S +
Sbjct: 57 HRGF-------GFVDFITKQDAKKAFNALCHSTHLYGR--RLVLEWADSEVTVQS 102
>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 = 29.5 bits (67), Expect = 0.039
Identities = 10/52 (19%), Positives = 19/52 (36%), Gaps = 9/52 (17%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
KG+ FI F + A++ LNG + ++++ S
Sbjct: 44 KGY-------AFIEFRDLESSASAVRNLNGYQLGS--RFLKCGYSSNSDISG 86
>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 = 29.6 bits (67), Expect = 0.045
Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG+ + ++ +A A + LNG G + I V +
Sbjct: 68 KGY-------ALVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 103
>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 = 29.3 bits (66), Expect = 0.067
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG + ++ A+ A++ +G +GS + V A
Sbjct: 65 KGD-------ATVSYEDPPTAKAAVEWFDGKDFQGS--KLKVSLA 100
>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 = 29.4 bits (66), Expect = 0.072
Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFA 46
KG+ + ++ +A A + LNG G + I V +
Sbjct: 114 KGY-------ALVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 149
>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 = 29.0 bits (65), Expect = 0.074
Identities = 5/25 (20%), Positives = 14/25 (56%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKG 36
G + F ++ + A+++L+ T +
Sbjct: 53 GVVEFVRKEDMTYAVRKLDNTKFRS 77
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 29.1 bits (65), Expect = 0.092
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ FI + A + P +PI ++F+N
Sbjct: 66 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106
>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 = 28.8 bits (65), Expect = 0.096
Identities = 8/57 (14%), Positives = 18/57 (31%), Gaps = 11/57 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNE----PITVKFANSPSSSNK 54
KG F +F + A++ + + G + + V A + +
Sbjct: 57 KGC-------AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
>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 = 28.3 bits (64), Expect = 0.11
Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 10/52 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSN 53
KGF GF+ + AI +L+ T G I V AN S
Sbjct: 43 KGF-------GFVEMQEE-SVSEAIAKLDNTDFMGR--TIRVTEANPKKSLE 84
>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 = 28.6 bits (64), Expect = 0.11
Identities = 7/41 (17%), Positives = 16/41 (39%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ F+ A + + P N+PI ++++N
Sbjct: 50 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH 90
>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 = 28.6 bits (64), Expect = 0.12
Identities = 3/40 (7%), Positives = 12/40 (30%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ + F+ A+ + + + ++ S
Sbjct: 51 KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS 90
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 28.0 bits (63), Expect = 0.15
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 10/47 (21%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ F G++ F+ + E+A+ EL G G+ I ++
Sbjct: 58 RKF-------GYVDFESAEDLEKAL-ELTGLKVFGN--EIKLEKPKG 94
>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 = 28.1 bits (63), Expect = 0.17
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 13 FIRFDQRIEAERAIQELNG 31
+ F EA+ IQ L+G
Sbjct: 68 SVSFRDPEEADYCIQTLDG 86
>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 = 28.1 bits (63), Expect = 0.18
Identities = 4/19 (21%), Positives = 9/19 (47%)
Query: 13 FIRFDQRIEAERAIQELNG 31
+++ A A+ L+G
Sbjct: 59 YVKCPSIAAAIAAVNALHG 77
>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 = 0.18
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 12 GFIRFDQRIEAERAIQELNG 31
+ F+ R EA A+ +LN
Sbjct: 60 AMVAFESRDEATAAVIDLND 79
>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 = 0.19
Identities = 8/50 (16%), Positives = 21/50 (42%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+ FT ++ +++ + A+ A L+G + + + F+ S
Sbjct: 58 IITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition
motif, C-terminal helix, N-terminal helix, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 28.0 bits (63), Expect = 0.20
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 9/47 (19%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
KG+ GF + + A A++ LNG G + V A S
Sbjct: 50 KGY-------GFCEYQDQETALSAMRNLNGREFSG--RALRVDNAAS 87
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 27.7 bits (61), Expect = 0.24
Identities = 11/47 (23%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKVIAP 58
+RF + AERA + + G+ I V F + P
Sbjct: 49 AILRFINQDSAERAQKRMENEDVFGN--RIIVSFTPKNRELCETSGP 93
>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 = 27.8 bits (62), Expect = 0.24
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 12 GFIRFDQRIEAERAIQELNG 31
F+ F + ++A+Q L G
Sbjct: 62 IFVEFTSVFDCQKAMQGLTG 81
>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 = 27.9 bits (62), Expect = 0.24
Identities = 5/25 (20%), Positives = 14/25 (56%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKG 36
G + F ++ + A+++L+ T +
Sbjct: 54 GVVEFVRKEDMTYAVRKLDNTKFRS 78
>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 = 27.8 bits (62), Expect = 0.25
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 13 FIRFDQRIEAERAIQELNG 31
F+ F E +AIQ LNG
Sbjct: 75 FVEFSIASETHKAIQALNG 93
>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 = 0.34
Identities = 9/55 (16%), Positives = 23/55 (41%)
Query: 1 MKGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPSSSNKV 55
+ FT ++ +++ + A+ A L+G + + + F+ S + K
Sbjct: 76 IITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKY 130
>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 = 27.1 bits (60), Expect = 0.37
Identities = 6/19 (31%), Positives = 14/19 (73%)
Query: 13 FIRFDQRIEAERAIQELNG 31
+++F + +AE+A+ +LN
Sbjct: 72 YVKFRREEDAEKAVIDLNN 90
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 26.6 bits (59), Expect = 0.40
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 7/31 (22%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGT 32
KG+ F+ + A A++ +G
Sbjct: 47 KGY-------IFLEYASPAHAVDAVKNADGY 70
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 27.0 bits (60), Expect = 0.43
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 7/31 (22%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGT 32
KG+ F+ + A A++ +G
Sbjct: 61 KGY-------IFLEYASPAHAVDAVKNADGY 84
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 27.5 bits (61), Expect = 0.45
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 13 FIRFDQRIEAERAIQELNG 31
F+ F E +AIQ LNG
Sbjct: 179 FVEFSIASETHKAIQALNG 197
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 27.0 bits (60), Expect = 0.45
Identities = 6/37 (16%), Positives = 13/37 (35%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+ F+ + A A+ + P V ++ S
Sbjct: 60 ALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96
>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 = 26.5 bits (59), Expect = 0.67
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 10/47 (21%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
+G+ GF+ R AERA ++ N I V A
Sbjct: 59 RGY-------GFVTMADRAAAERACKDPNPII---DGRKANVNLAYL 95
>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure
initiative, NE structural genomix research consortium,
nysgxrc; 2.35A {Pichia guilliermondii}
Length = 132
Score = 26.6 bits (58), Expect = 0.85
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 1/24 (4%)
Query: 14 IRFDQRIEAERAIQELNGTIPKGS 37
I +D A A+ E NG + G
Sbjct: 67 ITYDNPASAVDALLE-NGAVFNGV 89
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 26.2 bits (58), Expect = 0.89
Identities = 4/21 (19%), Positives = 10/21 (47%)
Query: 12 GFIRFDQRIEAERAIQELNGT 32
F+ +A++ I+ +G
Sbjct: 57 LFVECGSMNDAKKIIKSFHGK 77
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI,
protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 25.8 bits (56), Expect = 1.5
Identities = 7/24 (29%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 14 IRFDQRIEAERAIQELNGTIPKGS 37
IR+ +++A +A+ + +G I S
Sbjct: 64 IRYQSKLQARKALSK-DGRIFGES 86
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 25.4 bits (55), Expect = 1.9
Identities = 7/43 (16%), Positives = 16/43 (37%)
Query: 8 CRYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANSPS 50
+ F+ + A++A LNG + +++A
Sbjct: 61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR 103
>3go6_A Ribokinase RBSK; phosphofructokinase, carbohydrate kinase,
transferase; HET: RIB ADP; 1.98A {Mycobacterium
tuberculosis} PDB: 3go7_A*
Length = 310
Score = 24.9 bits (55), Expect = 3.9
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 66 QAAAARRFGGPIHHAGR 82
QA AA R G + +G
Sbjct: 62 QAVAAARAGAQVQFSGA 78
>1nx8_A CARC, carbapenem synthase; jelly roll, unknown function; HET: AKG
N7P; 2.30A {Pectobacterium carotovorum} SCOP: b.82.2.8
PDB: 1nx4_A*
Length = 273
Score = 24.6 bits (54), Expect = 4.0
Identities = 2/23 (8%), Positives = 6/23 (26%), Gaps = 2/23 (8%)
Query: 63 LTP--QAAAARRFGGPIHHAGRF 83
+ +G + +A
Sbjct: 49 IDSDTFRDIYSAYGTIVEYADEK 71
>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 = 24.1 bits (53), Expect = 4.2
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 10/33 (30%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQ---ELNG 31
KG+ GF+ F ++ ++ ++ +G
Sbjct: 50 KGY-------GFVSFYNDVDVQKIVESQINFHG 75
>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 = 24.4 bits (54), Expect = 4.4
Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 17/57 (29%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQ---ELNGTIPKGSNEPITVKFANSPSSSNKV 55
+GF GF+ F++ + ++ L+G I K A +K
Sbjct: 45 RGF-------GFLSFEKPSSVDEVVKTQHILDGK-------VIDPKRAIPRDEQDKT 87
>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 = 23.9 bits (52), Expect = 4.8
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 12 GFIRFDQRIEAERAIQELNGTIPKG 36
F+ F E +A+ +G I +G
Sbjct: 56 AFLEFRSVDETTQAMA-FDGIIFQG 79
>2rbc_A Sugar kinase, AGR_C_4560P; ribokinase family, ATP-binding site,
structura genomics, PSI-2, protein structu initiative;
HET: MSE GOL; 1.90A {Agrobacterium tumefaciens str}
Length = 343
Score = 24.5 bits (54), Expect = 4.9
Identities = 6/17 (35%), Positives = 6/17 (35%)
Query: 66 QAAAARRFGGPIHHAGR 82
A A R GG G
Sbjct: 72 AAYAVHRMGGRASLWGA 88
>3ikh_A Carbohydrate kinase; transferase,kinase,SAD,ribose,D-ribose
metabolic process,ATP ribokinase, PFKB
family,11206L1,PSI-II,nysgxrc; HET: ATP; 1.88A
{Klebsiella pneumoniae subsp} PDB: 3i3y_A*
Length = 299
Score = 24.4 bits (54), Expect = 5.7
Identities = 4/17 (23%), Positives = 4/17 (23%)
Query: 66 QAAAARRFGGPIHHAGR 82
QA R G
Sbjct: 45 QAIILSRCGIETRLIAA 61
>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase,
phosphoprotein, nitrogen FIX PER-ARNT-SIM,
metal-binding, PAS, iron, heme; HET: HEM; 1.5A
{Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A*
2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A*
1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A*
2owj_A*
Length = 119
Score = 23.6 bits (52), Expect = 6.7
Identities = 7/22 (31%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 10 YLGFIRFD--QRIEAERAIQEL 29
+ GF+R D + + + +QEL
Sbjct: 99 FTGFVR-DLTEHQQTQARLQEL 119
>1pgl_2 Bean POD mottle virus large (L) subunit; comovirus, viral coat
protein, bean POD mottle virus (BPMV), icosahedral
virus, virus/RNA complex; 2.80A {Bean-pod mottle virus}
SCOP: b.121.4.2 b.121.4.2 PDB: 1bmv_2 1pgw_2
Length = 370
Score = 24.0 bits (51), Expect = 7.9
Identities = 8/40 (20%), Positives = 15/40 (37%)
Query: 9 RYLGFIRFDQRIEAERAIQELNGTIPKGSNEPITVKFANS 48
R++G + F Q L+ G+ I + N+
Sbjct: 195 RWMGKLTFPQGTSRSVKRMPLSIGGGAGAKSAILMNMPNA 234
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM,
RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 23.3 bits (51), Expect = 8.0
Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 17/50 (34%)
Query: 2 KGFTDFCRYLGFIRFDQRIEAERAIQ---ELNGTIPKGSNEPITVKFANS 48
KGF GF+RF + + + ++G K NS
Sbjct: 57 KGF-------GFVRFTEYETQVKVMSQRHMIDGRW-------CDCKLPNS 92
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.137 0.411
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: 1,374,343
Number of extensions: 68799
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 320
Number of HSP's successfully gapped: 175
Length of query: 83
Length of database: 6,701,793
Length adjustment: 51
Effective length of query: 32
Effective length of database: 5,277,822
Effective search space: 168890304
Effective search space used: 168890304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.4 bits)