RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5032
(193 letters)
>3q5d_A Atlastin-1; G protein, GTPase, GDP/GTP binding, hydrolase; HET:
GDP; 2.70A {Homo sapiens} PDB: 3q5e_A* 3qnu_A* 3qof_A*
Length = 447
Score = 132 bits (332), Expect = 5e-37
Identities = 101/153 (66%), Positives = 122/153 (79%), Gaps = 5/153 (3%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
AFRKGKSFL+DF+LRYM S DW+G + PL GFSWRGGSER+TTGI +WS +
Sbjct: 75 AFRKGKSFLMDFMLRYMY-----NQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEI 129
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQH 143
++ P G+K AV+L+DTQGTFDS+ST+RD ATVFALSTM+SSIQ+YNLSQN+QEDDLQH
Sbjct: 130 FLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQH 189
Query: 144 LQLFTEYGRLALADTGTKPFQRLQFLAVNNNNP 176
LQLFTEYGRLA+ +T KPFQ L FL + + P
Sbjct: 190 LQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFP 222
>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP
hydrolysis, GDP, GMP, dynamin related, large GTPase
family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens}
SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A*
2bc9_A* 2d4h_A*
Length = 592
Score = 105 bits (263), Expect = 6e-27
Identities = 34/142 (23%), Positives = 54/142 (38%), Gaps = 26/142 (18%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
+R GKS+L++ L GFS + T GI MW
Sbjct: 46 LYRTGKSYLMNKLAGKKK---------------------GFSLGSTVQSHTKGIWMWCV- 83
Query: 84 YIATLPTGEKAAVILLDTQGTFDSE-STVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQ 142
P ++LLDT+G D E ++ + +FAL+ +LSS +YN I + +
Sbjct: 84 ---PHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMD 140
Query: 143 HLQLFTEYGRLALADTGTKPFQ 164
L TE + + +
Sbjct: 141 QLYYVTELTHRIRSKSSPDENE 162
>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 = 32.6 bits (75), Expect = 0.017
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 121 STMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALADTGTK 161
S+ ++ + I NLS + DDL+ QLF + K
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLR--QLFGDRKLPLAGQVLLK 43
>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 = 32.6 bits (75), Expect = 0.020
Identities = 11/29 (37%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
++I++ NLS++ +E DLQ +LF +G +
Sbjct: 16 ATIRVTNLSEDTRETDLQ--ELFRPFGSI 42
>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 = 31.6 bits (72), Expect = 0.069
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
+ + + E L+ QLF YG
Sbjct: 47 VNYIPTTVDEVQLR--QLFERYG 67
>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 = 30.6 bits (70), Expect = 0.077
Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 2/24 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGR 152
I L + DL +L YG+
Sbjct: 10 IRGLQPGTTDQDLV--KLCQPYGK 31
>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 = 30.8 bits (70), Expect = 0.12
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
IY+L Q + DL Q+F +G
Sbjct: 30 IYHLPQEFGDQDLL--QMFMPFG 50
>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 = 29.9 bits (68), Expect = 0.14
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 121 STMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALAD 157
S I + N+S +L+ LF GR+ D
Sbjct: 6 SGNTWKIFVGNVSAACTSQELR--SLFERRGRVIECD 40
>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 = 29.9 bits (68), Expect = 0.17
Identities = 8/35 (22%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALAD 157
++++ NL + E +++ LF +YG++ D
Sbjct: 7 GMVKLFIGNLPREATEQEIR--SLFEQYGKVLECD 39
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 30.0 bits (68), Expect = 0.17
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
IY+L Q + DL F +G
Sbjct: 45 IYHLPQEFTDTDLA--STFLPFG 65
>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 = 29.5 bits (67), Expect = 0.19
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALAD 157
+S +++ N+S +L+ F EYG + D
Sbjct: 9 ASTKLHVGNISPTCTNQELR--AKFEEYGPVIECD 41
>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 = 29.4 bits (67), Expect = 0.19
Identities = 7/35 (20%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALAD 157
+++ L++N+ +D + ++F+ YG++ + D
Sbjct: 3 KPTKVHIGRLTRNVTKDHIM--EIFSTYGKIKMID 35
>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 = 29.2 bits (66), Expect = 0.31
Identities = 9/35 (25%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 121 STMLSSIQIY--NLSQNIQEDDLQHLQLFTEYGRL 153
S M ++ NL+ + E+ L+ + F+++G+L
Sbjct: 6 SGMAKVKVLFVRNLANTVTEEILE--KAFSQFGKL 38
>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 = 0.32
Identities = 8/51 (15%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 103 GTFDSESTVRDCATVFALSTMLSSIQIY--NLSQNIQEDDLQHLQLFTEYG 151
+++ D + ++ ++ + QED++Q + F +YG
Sbjct: 3 HSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ--EKFCDYG 51
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 29.0 bits (65), Expect = 0.35
Identities = 8/28 (28%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYGRLA 154
+QI N+ ++Q + L L +YG +
Sbjct: 18 LQIRNIPPHLQWEVLD--SLLVQYGVVE 43
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 29.2 bits (66), Expect = 0.37
Identities = 5/25 (20%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
+ ++QE +L ++F +G +
Sbjct: 36 VRPFPLDVQESELN--EIFGPFGPM 58
>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 = 28.8 bits (65), Expect = 0.45
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 10/43 (23%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALA------DTG 159
+++Y +L NI ED L+ +F +GR+ +TG
Sbjct: 25 GPMRLYVGSLHFNITEDMLR--GIFEPFGRIESIQLMMDSETG 65
>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 = 28.4 bits (64), Expect = 0.57
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 12/40 (30%)
Query: 112 RDCATVFALSTMLSSIQIYNLSQNIQEDDLQHLQLFTEYG 151
RD TVF L+ I+ DL+ F+ G
Sbjct: 23 RDARTVF----------CMQLAARIRPRDLE--DFFSAVG 50
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 28.9 bits (65), Expect = 0.58
Identities = 9/31 (29%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 123 MLSSIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
++S+++ NL+ D L+ ++F +YGR+
Sbjct: 46 GMTSLKVDNLTYRTSPDTLR--RVFEKYGRV 74
>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 = 28.5 bits (64), Expect = 0.64
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 121 STMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALADTGTKPFQRL 166
+ S+I + L+ ++ DDL F + G + + +P +
Sbjct: 12 DSDNSAIYVQGLNDSVTLDDLA--DFFKQCGVVKMNKRTGQPMIHI 55
>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 = 28.4 bits (64), Expect = 0.65
Identities = 6/24 (25%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGR 152
I NL ++ E +L+ + +G+
Sbjct: 30 ISNLPLSMDEQELE--NMLKPFGQ 51
>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 = 28.4 bits (64), Expect = 0.67
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALAD 157
+ ++ NL + + D+Q +LF E+G L A
Sbjct: 28 TGGKLLVSNLDFGVSDADIQ--ELFAEFGTLKKAA 60
>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 = 28.4 bits (64), Expect = 0.67
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRL 153
+ +IY NL +I+ D++ +F +YG +
Sbjct: 21 NDCRIYVGNLPPDIRTKDIE--DVFYKYGAI 49
>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 = 28.4 bits (64), Expect = 0.73
Identities = 8/23 (34%), Positives = 11/23 (47%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
+ NLS + E DL LF +
Sbjct: 30 LKNLSPRVTERDLV--SLFARFQ 50
>2qmc_A GGT, gamma-glutamyltranspeptidase; NTN-hydrolase, transferase; HET:
GTB; 1.55A {Helicobacter pylori} PDB: 2qm6_A* 3fnm_A*
2nqo_A
Length = 377
Score = 29.1 bits (66), Expect = 0.79
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 119 ALSTMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALADTGTKPFQRLQFLA 170
L +L+ ++ +LS + +++ + E R A AD R ++
Sbjct: 286 HLIQILNVMENADLSA-LGYGASKNIHIAAEAMRQAYAD-------RSVYMG 329
>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 = 28.0 bits (63), Expect = 0.81
Identities = 8/23 (34%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 131 NLSQNIQEDDLQHLQLFTEYGRL 153
NL +I E++++ +LF +YG+
Sbjct: 22 NLPPDITEEEMR--KLFEKYGKA 42
>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 = 27.9 bits (63), Expect = 0.89
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRLALA----DTG 159
+ NL I ++ L+ + F+ +G + A + G
Sbjct: 20 VKNLDDGIDDERLR--KAFSPFGTITSAKVMMEGG 52
>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 = 28.1 bits (63), Expect = 0.93
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 125 SSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALAD 157
+ ++ NL + + D+Q +LF E+G L A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQ--ELFAEFGTLKKAA 66
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 27.7 bits (61), Expect = 0.94
Identities = 7/28 (25%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 127 IQIYNLSQNIQEDDLQHL--QLFTEYGR 152
+Q+ N+ + +LQ L + F +G+
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGK 39
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 27.9 bits (62), Expect = 1.0
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 125 SSIQIYNLSQNIQEDDLQHL--QLFTEYGR 152
+ I N++ + ++ LQ L L + G
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGD 59
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 27.6 bits (62), Expect = 1.1
Identities = 6/21 (28%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 131 NLSQNIQEDDLQHLQLFTEYG 151
+ + E+D+ F EYG
Sbjct: 30 GVHEEATEEDIH--DKFAEYG 48
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 28.3 bits (63), Expect = 1.1
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYGRLALAD 157
+ + NL + + D+Q +LF E+G L A
Sbjct: 91 LLVSNLDFGVSDADIQ--ELFAEFGTLKKAA 119
>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 = 27.9 bits (62), Expect = 1.1
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 2/30 (6%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYGRLA 154
+ I NL ++Q + F+ +G L
Sbjct: 11 TVILAKNLPAGTLAAEIQ--ETFSRFGSLG 38
>2dg5_A Gamma-glutamyltranspeptidase; gamma-glutamyltransferase, GGT,
gamma-GT, glutathione; HET: GLU; 1.60A {Escherichia coli
K12} SCOP: d.153.1.6 PDB: 2dbu_A 2dbw_A* 2dbx_A* 2e0x_A
2e0y_A 2z8i_A* 2z8j_A* 2z8k_A*
Length = 366
Score = 28.7 bits (65), Expect = 1.1
Identities = 6/39 (15%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 119 ALSTMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALAD 157
+ +L+ ++ +++ + +Q+ E + A AD
Sbjct: 275 HIVQILNILENFDMKK-YGFGSADAMQIMAEAEKYAYAD 312
>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 = 27.5 bits (62), Expect = 1.2
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 10/42 (23%)
Query: 126 SIQIY--NLSQNIQEDDLQHLQLFTEYGRLALA------DTG 159
S +Y +L NI ED L+ +F +G++ DTG
Sbjct: 5 SSGLYVGSLHFNITEDMLR--GIFEPFGKIDNIVLMKDSDTG 44
>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 = 28.3 bits (63), Expect = 1.2
Identities = 7/27 (25%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYG 151
+ + ++ + QED++Q + F +YG
Sbjct: 73 WILFVTSIHEEAQEDEIQ--EKFCDYG 97
>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 = 27.6 bits (62), Expect = 1.3
Identities = 6/25 (24%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
+ L++ E+D+ +LF +G +
Sbjct: 20 VGMLNKQQSEEDVL--RLFQPFGVI 42
>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 = 27.9 bits (62), Expect = 1.3
Identities = 8/23 (34%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
+ NL++++QE DL+ +F Y
Sbjct: 50 VKNLAKHVQEKDLK--YIFGRYV 70
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 1.5
Identities = 9/41 (21%), Positives = 11/41 (26%), Gaps = 21/41 (51%)
Query: 21 EKSAFRKGKSFLLDFLLR-YMNFTYIEEAPSGDWMGPDDVP 60
EK A +K L L+ Y D P
Sbjct: 18 EKQALKK-----LQASLKLY---------------ADDSAP 38
>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 = 1.5
Identities = 6/33 (18%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 121 STMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
+ + + N+ ++ DL+ Q+F ++G++
Sbjct: 12 KSTPKRLHVSNIPFRFRDPDLR--QMFGQFGKI 42
>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 = 27.2 bits (61), Expect = 1.6
Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 121 STMLSSIQIY--NLSQNIQEDDLQHLQLFTEYGRLALADT 158
TM S +Y NL + E+ ++ + F A+
Sbjct: 10 DTMSSVKILYVRNLMLSTSEEMIE--KEFNNIKPGAVERV 47
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 27.3 bits (61), Expect = 1.6
Identities = 6/23 (26%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
+ N+ ++ DL+ Q+F ++G
Sbjct: 34 VSNIPFRFRDPDLR--QMFGQFG 54
>2v36_A Gamma-glutamyltranspeptidase large chain; transferase, glutathione
biosynthesis, gamma-glutamyl transferase,
acyltransferase, zymogen; 1.85A {Bacillus subtilis} PDB:
3a75_A*
Length = 376
Score = 28.3 bits (64), Expect = 1.9
Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 8/52 (15%)
Query: 119 ALSTMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALADTGTKPFQRLQFLA 170
L M + +NLSQ + QL E L+ AD R +
Sbjct: 271 FLLQMPKILDHFNLSQ-YDVRSWEKYQLLAETMHLSYAD-------RASYAG 314
>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 = 27.7 bits (61), Expect = 2.0
Identities = 7/25 (28%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYG 151
+ + N+ ++ E+DL+ LF+ G
Sbjct: 154 LHLSNIPPSVSEEDLK--VLFSSNG 176
>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 = 26.8 bits (60), Expect = 2.1
Identities = 9/28 (32%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 129 IY--NLSQNIQEDDLQHL--QLFTEYGR 152
IY NL++ I++D+L+ +F+ +G+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQ 38
>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 = 27.2 bits (60), Expect = 2.1
Identities = 5/25 (20%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
I L ++ E ++ + L +G++
Sbjct: 36 IRKLPIDVTEGEV--ISLGLPFGKV 58
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 26.9 bits (60), Expect = 2.1
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
I N+ E DL LF +G +
Sbjct: 32 IGNIPHFATEADLI--PLFQNFGFI 54
>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 = 26.9 bits (60), Expect = 2.1
Identities = 5/23 (21%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 131 NLSQNIQEDDLQHLQLFTEYGRL 153
N+ + +++ +LF+ +G L
Sbjct: 22 NIPFQANQREIR--ELFSTFGEL 42
>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 = 26.8 bits (60), Expect = 2.3
Identities = 5/25 (20%), Positives = 11/25 (44%), Gaps = 4/25 (16%)
Query: 129 IY--NLSQNIQEDDLQHLQLFTEYG 151
+Y L++ + + L F +G
Sbjct: 15 LYVGGLAEEVDDKVLH--AAFIPFG 37
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 26.6 bits (59), Expect = 2.4
Identities = 6/23 (26%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
L+ N++E L+ + +YG
Sbjct: 11 FARLNDNVRETFLK--DMCRKYG 31
>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 = 26.7 bits (59), Expect = 2.4
Identities = 5/26 (19%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRLA 154
+ L +++ E DL ++ ++G +
Sbjct: 20 VRGLCESVVEADL--VEALEKFGTIC 43
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 26.7 bits (59), Expect = 2.5
Identities = 5/25 (20%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
I L ++ E ++ + L +G++
Sbjct: 21 IRKLPIDVTEGEV--ISLGLPFGKV 43
>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 = 27.0 bits (60), Expect = 2.5
Identities = 6/27 (22%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYG 151
+ + + + E+D+ F EYG
Sbjct: 23 WILFVTGVHEEATEEDIH--DKFAEYG 47
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 26.4 bits (59), Expect = 2.6
Identities = 8/29 (27%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRLALAD 157
+ NL + L+ F E G + AD
Sbjct: 13 VRNLPFDFTWKMLK--DKFNECGHVLYAD 39
>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 = 27.2 bits (60), Expect = 2.6
Identities = 7/25 (28%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYG 151
+ + N+ ++ E+DL+ LF+ G
Sbjct: 123 LHLSNIPPSVSEEDLK--VLFSSNG 145
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 26.4 bits (59), Expect = 2.7
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
+ + NLS E+DL+ +LF+ YG L
Sbjct: 9 GRLFVRNLSYTSSEEDLE--KLFSAYGPL 35
>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 = 27.4 bits (60), Expect = 2.7
Identities = 4/25 (16%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYG 151
+ +N + E++ ++ E G
Sbjct: 126 LHFFNAPLEVTEENFF--EICDELG 148
>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 = 27.1 bits (60), Expect = 2.8
Identities = 9/29 (31%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
+S+++ NL+ D L+ ++F +YGR+
Sbjct: 71 TSLKVDNLTYRTSPDTLR--RVFEKYGRV 97
>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 = 26.4 bits (59), Expect = 2.9
Identities = 8/29 (27%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 125 SSIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
++++ NL+ D L+ ++F +YGR+
Sbjct: 14 ITLKVDNLTYRTSPDSLR--RVFEKYGRV 40
>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 = 26.3 bits (58), Expect = 3.2
Identities = 5/25 (20%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
I L + E ++ + L +G++
Sbjct: 20 IRKLPGEVTETEV--IALGLPFGKV 42
>3g9k_L Capsule biosynthesis protein CAPD; CAPD protein, the great lakes
regional C excellence, GLRCE, capsule
biogenesis/degradation; HET: GLU; 1.79A {Bacillus
anthracis} PDB: 3ga9_L*
Length = 323
Score = 27.1 bits (61), Expect = 3.3
Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 8/52 (15%)
Query: 119 ALSTMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALADTGTKPFQRLQFLA 170
L ML + + + + ++ E R+A D R + L
Sbjct: 244 TLLQMLKLAEKKEVYK-DVDHTATYMSKMEEISRIAYQD-------RKKNLG 287
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 26.3 bits (58), Expect = 3.5
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
I L + E DL ++ E+G +
Sbjct: 26 IRGLIDGVVEADL--VEALQEFGPI 48
>2e0w_A Gamma-glutamyltranspeptidase; NTN hydrolase, precursor, gamma-GTP,
post-translational PROC maturation, transferase; 2.55A
{Escherichia coli K12} SCOP: d.153.1.6
Length = 556
Score = 27.1 bits (61), Expect = 3.7
Identities = 8/52 (15%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 119 ALSTMLSSIQIYNLSQNIQEDDLQHLQLFTEYGRLALADTGTKPFQRLQFLA 170
+ +L+ ++ +++ + +Q+ E + A AD R ++L
Sbjct: 275 HIVQILNILENFDMKK-YGFGSADAMQIMAEAEKYAYAD-------RSEYLG 318
>2e9f_A Argininosuccinate lyase; alpha helix bundle; HET: ARG; 2.80A
{Thermus thermophilus}
Length = 462
Score = 27.1 bits (61), Expect = 4.3
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 100 DTQGTFDSESTVRDCATVFALSTMLSSIQI 129
D + D+ +T RD + A +L ++
Sbjct: 327 DKEPLLDALATYRDSLRLLAA--LLPGLKW 354
>1tj7_A Argininosuccinate lyase; crystallin, E. coli, fumarase, ASPA lyase;
2.44A {Escherichia coli} SCOP: a.127.1.1
Length = 457
Score = 26.8 bits (60), Expect = 4.6
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 100 DTQGTFDSESTVRDCATVFALSTMLSSIQI 129
D +G FD+ T DC + AL +L IQ+
Sbjct: 324 DKEGLFDALDTWLDCLHMAAL--VLDGIQV 351
>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 = 25.7 bits (57), Expect = 4.7
Identities = 5/23 (21%), Positives = 8/23 (34%), Gaps = 2/23 (8%)
Query: 131 NLSQNIQEDDLQHLQLFTEYGRL 153
L N L + F +G +
Sbjct: 24 GLGPNTSLAALA--REFDRFGSI 44
>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 = 25.8 bits (57), Expect = 5.1
Identities = 3/24 (12%), Positives = 13/24 (54%), Gaps = 2/24 (8%)
Query: 131 NLSQNIQEDDLQHLQLFTEYGRLA 154
++ + + ++ Q F+ +G++
Sbjct: 32 GIASGLTDQLMR--QTFSPFGQIM 53
>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 = 25.4 bits (56), Expect = 6.8
Identities = 6/23 (26%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 131 NLSQNIQEDDLQHLQLFTEYGRL 153
NL I +++ +F +YG +
Sbjct: 15 NLPYKITAEEMY--DIFGKYGPI 35
>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 = 26.1 bits (58), Expect = 7.1
Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYGRL 153
+ I L + +D ++ +L T +G L
Sbjct: 117 LFIGGLPNYLNDDQVK--ELLTSFGPL 141
>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 = 25.3 bits (56), Expect = 7.6
Identities = 8/36 (22%), Positives = 13/36 (36%), Gaps = 6/36 (16%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRLALA----DTGT 160
I NL ++I L F+ +G + D
Sbjct: 10 IKNLDKSIDNKALY--DTFSAFGNILSCKVVCDENG 43
>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 = 25.0 bits (55), Expect = 8.5
Identities = 9/24 (37%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGR 152
I + +N+ E DL+ LF E+G+
Sbjct: 18 IGQIPRNLDEKDLK--PLFEEFGK 39
>1k7w_A Delta 2 crystallin; eye lens protein, argininosuccinate lyase,
enzyme mechanism; HET: AS1; 1.96A {Anas platyrhynchos}
SCOP: a.127.1.1 PDB: 1hy1_A 1tju_A 1auw_A 1tjv_A 1tjw_A*
1u16_A* 1u15_A* 1dcn_A* 1xwo_A 1hy0_A 1i0a_A 1aos_A
1k62_A
Length = 468
Score = 26.0 bits (58), Expect = 9.9
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 100 DTQGTFDSESTVRDCATVFALSTMLSSIQI 129
D + FD T+ V ++S++QI
Sbjct: 330 DKEAVFDVVDTLTAVLQVATG--VISTLQI 357
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
0.318 0.133 0.394
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,851,836
Number of extensions: 158559
Number of successful extensions: 343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 338
Number of HSP's successfully gapped: 78
Length of query: 193
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 105
Effective length of database: 4,244,745
Effective search space: 445698225
Effective search space used: 445698225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.9 bits)