RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8255
(117 letters)
>1jmt_B Splicing factor U2AF 65 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens}
Length = 28
Score = 49.8 bits (118), Expect = 6e-10
Identities = 20/28 (71%), Positives = 24/28 (85%)
Query: 59 RRKASLYWDVPPPGFEHVSPSQYKAMQA 86
++K YWDVPPPGFEH++P QYKAMQA
Sbjct: 1 KKKVRKYWDVPPPGFEHITPMQYKAMQA 28
>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 = 40.5 bits (95), Expect = 7e-06
Identities = 14/17 (82%), Positives = 15/17 (88%)
Query: 101 RQARRLYVGNIPFGVTE 117
ARRLYVGNIPFG+TE
Sbjct: 4 GSARRLYVGNIPFGITE 20
>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 = 36.9 bits (86), Expect = 5e-04
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 102 QARRLYVGNIPFGVTE 117
ARRLYVGNIPFG+TE
Sbjct: 3 MARRLYVGNIPFGITE 18
Score = 28.8 bits (65), Expect = 0.31
Identities = 8/44 (18%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 78 PSQYKAMQA----AAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
P Y+ + + VV + + A +L++G +P + +
Sbjct: 85 PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLND 128
>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 = 35.7 bits (83), Expect = 0.001
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 102 QARRLYVGNIPFGVTE 117
ARRLYVGNIPFG+TE
Sbjct: 3 SARRLYVGNIPFGITE 18
Score = 25.3 bits (56), Expect = 4.8
Identities = 4/18 (22%), Positives = 10/18 (55%)
Query: 100 TRQARRLYVGNIPFGVTE 117
A +L++G +P + +
Sbjct: 91 LPGAHKLFIGGLPNYLND 108
>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 = 31.9 bits (73), Expect = 0.013
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 79 SQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
+ + AAA+ + RLYVG++ F +TE
Sbjct: 2 GHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITE 40
>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 = 31.8 bits (73), Expect = 0.013
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + +LY+GN+ VT
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTA 22
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 32.9 bits (75), Expect = 0.015
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSR---DRRSRSRSKDKKRAARSRSRS 50
+ ++ RS++RD+ R +RRS SRS DK + S
Sbjct: 528 SEISFRGNKNYNNRSQNRDYDDEPFRRSNNNRRSFSRSNDKNNYSSRNSNI 578
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 32.4 bits (74), Expect = 0.015
Identities = 6/41 (14%), Positives = 10/41 (24%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
+ + R LYVG + V +
Sbjct: 37 TCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDD 77
>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 = 30.3 bits (69), Expect = 0.050
Identities = 6/30 (20%), Positives = 12/30 (40%)
Query: 88 AAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
++ + R ++VGN+ V E
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVRE 30
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 29.8 bits (68), Expect = 0.061
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 99 ITRQARRLYVGNIPFGVTE 117
+ AR +YVGN+ +G T
Sbjct: 2 MEADARSIYVGNVDYGATA 20
>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 = 30.1 bits (68), Expect = 0.076
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + RL++G IP
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKR 22
>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 = 28.7 bits (65), Expect = 0.16
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 103 ARRLYVGNIPFGVTE 117
+R +Y+G+IP+ TE
Sbjct: 2 SRVVYLGSIPYDQTE 16
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 28.8 bits (65), Expect = 0.17
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 15/50 (30%)
Query: 68 VPPPGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
+PP V+P + +A + Y+GNIP TE
Sbjct: 7 LPPQ----VNPQAVDHIIRSAPP-----------RVTTAYIGNIPHFATE 41
>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 = 28.3 bits (64), Expect = 0.21
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + +L++GN+P TE
Sbjct: 1 GSSGSSGMVKLFIGNLPREATE 22
>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 = 28.3 bits (64), Expect = 0.25
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 101 RQARRLYVGNIPFGVTE 117
R LYVG + V +
Sbjct: 5 TTKRVLYVGGLAEEVDD 21
>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 = 28.3 bits (64), Expect = 0.26
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + + RL+V N+ + +E
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSE 22
>1y0e_A Putative N-acetylmannosamine-6-phosphate 2-epimer; mannac-6-P
epimerase, NANE, structural genomics, protein STR
initiative, PSI; 1.95A {Staphylococcus aureus subsp}
SCOP: c.1.2.5
Length = 223
Score = 29.1 bits (65), Expect = 0.27
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITR 101
+P YK + VVG ITR
Sbjct: 186 TPDMYKRVMDLGVHCS-VVGGAITR 209
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 28.0 bits (63), Expect = 0.30
Identities = 5/31 (16%), Positives = 16/31 (51%)
Query: 87 AAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
++ + V + + + +L++ +PF T+
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTK 31
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 28.0 bits (63), Expect = 0.32
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
+YV N+PF +T
Sbjct: 17 STVYVSNLPFSLTN 30
>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 = 28.0 bits (63), Expect = 0.36
Identities = 3/17 (17%), Positives = 6/17 (35%)
Query: 101 RQARRLYVGNIPFGVTE 117
++V + VT
Sbjct: 11 SDNNTIFVQGLGENVTI 27
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 27.9 bits (63), Expect = 0.37
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + A +++V N+PF T
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTW 22
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 28.0 bits (63), Expect = 0.37
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 101 RQARRLYVGNIPFGVTE 117
R AR L N+ F +TE
Sbjct: 14 RAARTLLAKNLSFNITE 30
>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 = 0.41
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 101 RQARRLYVGNIPFGVTE 117
R R ++VGNIP+ TE
Sbjct: 6 RSLRSVFVGNIPYEATE 22
>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 = 28.2 bits (63), Expect = 0.44
Identities = 9/41 (21%), Positives = 12/41 (29%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
+ + Q P + R L V IP V E
Sbjct: 16 TAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDE 56
>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 = 27.6 bits (62), Expect = 0.45
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 100 TRQARRLYVGNIPFGVTE 117
Q R LYVGN+ VTE
Sbjct: 12 DGQPRTLYVGNLSRDVTE 29
>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 = 27.7 bits (62), Expect = 0.47
Identities = 3/18 (16%), Positives = 9/18 (50%)
Query: 100 TRQARRLYVGNIPFGVTE 117
+ + +++ N+ F E
Sbjct: 12 VTEGKTVFIRNLSFDSEE 29
>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 = 27.6 bits (62), Expect = 0.50
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + + L+V N+ VTE
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTE 25
>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 = 27.7 bits (62), Expect = 0.53
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 104 RRLYVGNIPFGVTE 117
+Y G I G+T+
Sbjct: 26 CTVYCGGIASGLTD 39
>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 = 0.53
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 103 ARRLYVGNIPFGVTE 117
+ LYVG++ F +TE
Sbjct: 5 SSGLYVGSLHFNITE 19
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 27.8 bits (62), Expect = 0.60
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 103 ARRLYVGNIPFGVTE 117
R +YVGN+ +G T
Sbjct: 36 KRSVYVGNVDYGSTA 50
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 27.6 bits (62), Expect = 0.72
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 101 RQARRLYVGNIPFGVTE 117
R AR L N+ F +TE
Sbjct: 97 RAARTLLAKNLSFNITE 113
>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 = 27.2 bits (61), Expect = 0.74
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
S + R LYVG + V +
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDD 26
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 26.9 bits (60), Expect = 0.76
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + R ++V P GV
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDS 22
>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 = 27.6 bits (62), Expect = 0.79
Identities = 5/18 (27%), Positives = 9/18 (50%)
Query: 100 TRQARRLYVGNIPFGVTE 117
R R++ + +P VT
Sbjct: 19 FRNRRKILIRGLPGDVTN 36
Score = 24.9 bits (55), Expect = 7.9
Identities = 5/17 (29%), Positives = 8/17 (47%)
Query: 101 RQARRLYVGNIPFGVTE 117
+R L V +P G +
Sbjct: 182 LHSRCLCVDRLPPGFND 198
>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 = 26.6 bits (59), Expect = 0.83
Identities = 3/18 (16%), Positives = 7/18 (38%)
Query: 100 TRQARRLYVGNIPFGVTE 117
+ + + V N+P
Sbjct: 2 SSGSSGILVKNLPQDSNC 19
>1yxy_A Putative N-acetylmannosamine-6-phosphate 2-epimer; structural
genomics, epimerase, PSI, structure initiative; 1.60A
{Streptococcus pyogenes} SCOP: c.1.2.5
Length = 234
Score = 27.6 bits (61), Expect = 0.86
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITR 101
SP + K + A + VVG ITR
Sbjct: 197 SPEEAKKINDLGVAGI-VVGGAITR 220
>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 = 26.9 bits (60), Expect = 0.92
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
ST + +++ L + N+ + TE
Sbjct: 8 NSTWSGESKTLVLSNLSYSATE 29
>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 = 26.8 bits (60), Expect = 0.93
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 102 QARRLYVGNIPFGVTE 117
Q RL+VGN+P +TE
Sbjct: 14 QRSRLFVGNLPPDITE 29
>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 = 27.0 bits (60), Expect = 1.0
Identities = 4/17 (23%), Positives = 6/17 (35%)
Query: 101 RQARRLYVGNIPFGVTE 117
+YV + VT
Sbjct: 13 SDNSAIYVQGLNDSVTL 29
>3iot_A Maltose-binding protein, huntingtin fusion protein; HTT-EX1, HD,
sugar transport, transport, apoptosis, cytoplasm,
disease mutation; 3.50A {Escherichia coli k-12} PDB:
3io6_A 3io4_A 3ior_A 3iou_A 3iov_A 3iow_A
Length = 449
Score = 27.5 bits (61), Expect = 1.1
Identities = 8/66 (12%), Positives = 20/66 (30%)
Query: 40 KKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVVGSTI 99
+ +S + + + + ++++ PPP P Q + +
Sbjct: 380 AFESLKSFQQQQQQQQQQQQQQQQQPPPPPPPPPPPQLPQPPPQAQPLLPQQSYQITAGK 439
Query: 100 TRQARR 105
RR
Sbjct: 440 LGTGRR 445
>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear
receptor, ECR, USP, hormone/growth factor receptor
complex; HET: P1A; 3.07A {Bemisia tabaci}
Length = 310
Score = 27.5 bits (61), Expect = 1.1
Identities = 6/53 (11%), Positives = 17/53 (32%), Gaps = 4/53 (7%)
Query: 5 RDKDRERDRRRRSR----SRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRD 53
++K ++D+ + + S D K+ R + + +
Sbjct: 28 KEKKAQKDKDKPNSTTSCSPDGIKQEIDPQRLDTDSQLLSVNGVKPITPEQEE 80
>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 = 26.4 bits (59), Expect = 1.1
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 100 TRQARRLYVGNIPFGVTE 117
+ + +L+VGNI T
Sbjct: 7 GKASTKLHVGNISPTCTN 24
>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 = 27.4 bits (60), Expect = 1.2
Identities = 11/49 (22%), Positives = 19/49 (38%)
Query: 69 PPPGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
P +++ A P V T T + LY+GN+ + T+
Sbjct: 34 APEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTD 82
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 26.5 bits (59), Expect = 1.3
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
G +L V N+ FGV++
Sbjct: 22 GGAGVETGGKLLVSNLDFGVSD 43
>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 = 26.5 bits (59), Expect = 1.4
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 102 QARRLYVGNIPFGVTE 117
Q +YVG + V+E
Sbjct: 14 QDATVYVGGLDEKVSE 29
>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 = 26.0 bits (58), Expect = 1.4
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
R +YVGN+ + T
Sbjct: 2 RNIYVGNLVYSATS 15
>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 = 26.5 bits (59), Expect = 1.5
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 101 RQARRLYVGNIPFGVTE 117
+ ++ V NIPF +
Sbjct: 13 QTTSKILVRNIPFQANQ 29
>3q58_A N-acetylmannosamine-6-phosphate 2-epimerase; TIM beta/alpha barrel,
ribulose-phosphate binding barrel, carbohydrate
metabolic process; HET: BTB; 1.80A {Salmonella enterica
subsp}
Length = 229
Score = 26.9 bits (59), Expect = 1.5
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITR 101
+P+ A AV VGS ITR
Sbjct: 192 TPALAANAIEHGAWAV-TVGSAITR 215
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 26.9 bits (60), Expect = 1.5
Identities = 5/36 (13%), Positives = 14/36 (38%)
Query: 82 KAMQAAAAAAVPVVGSTITRQARRLYVGNIPFGVTE 117
+ A + + R R+YV ++ +++
Sbjct: 104 RPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSD 139
Score = 24.6 bits (54), Expect = 8.3
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 97 STITRQARRLYVGNIPFGVTE 117
R+YVG+I + + E
Sbjct: 22 QGALAIMSRVYVGSIYYELGE 42
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 26.3 bits (58), Expect = 1.6
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 100 TRQARRLYVGNIPFGVTE 117
++ R+L + NIP +
Sbjct: 12 RQRIRKLQIRNIPPHLQW 29
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 26.7 bits (59), Expect = 1.6
Identities = 13/82 (15%), Positives = 21/82 (25%)
Query: 36 RSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVV 95
S D R RR + ++ + P
Sbjct: 21 MSLDDIIKLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCG 80
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
G +L V N+ FGV++
Sbjct: 81 GGEGVETGAKLLVSNLDFGVSD 102
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 26.0 bits (58), Expect = 1.8
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 104 RRLYVGNIPFGVTE 117
++GN+P+ VTE
Sbjct: 20 YTAFLGNLPYDVTE 33
>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 = 26.1 bits (58), Expect = 1.9
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 102 QARRLYVGNIPFGVTE 117
+RL+V NIPF +
Sbjct: 14 TPKRLHVSNIPFRFRD 29
>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 = 26.1 bits (58), Expect = 2.0
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 101 RQARRLYVGNIPFGVTE 117
A +L++G IP + E
Sbjct: 11 HDAIKLFIGQIPRNLDE 27
>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 = 25.6 bits (57), Expect = 2.1
Identities = 3/13 (23%), Positives = 9/13 (69%)
Query: 105 RLYVGNIPFGVTE 117
++++G + VT+
Sbjct: 6 KVHIGRLTRNVTK 18
>2f6u_A GGGPS, (S)-3-O-geranylgeranylglyceryl phosphate synthase;
non-canonical TIM-barrel, prenyltransferase, archaeal
lipid synthesis, dimer; HET: CIT; 1.55A {Archaeoglobus
fulgidus} SCOP: c.1.4.1 PDB: 2f6x_A*
Length = 234
Score = 26.6 bits (58), Expect = 2.1
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 82 KAMQAAAAAAVPVVGSTITRQARRLYVGNIP 112
KA + A +VG+ I + ++ +P
Sbjct: 204 KAREMLRYADTIIVGNVIYEKGIDAFLETLP 234
>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 = 25.7 bits (57), Expect = 2.1
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 102 QARRLYVGNIPFGVTE 117
+ LYV N+ +E
Sbjct: 14 SVKILYVRNLMLSTSE 29
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA,
DNA-binding, phosphorylation, POL I, POLI, rpoli,
nuclear protein; 3.10A {Saccharomyces cerevisiae}
Length = 214
Score = 26.6 bits (58), Expect = 2.2
Identities = 11/54 (20%), Positives = 17/54 (31%)
Query: 23 KKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEHV 76
KR+ +R K KK+ R +LY + P E+
Sbjct: 4 VKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENP 57
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.3 bits (57), Expect = 2.3
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 11 RDRRRRSRSRDHKKRSRSRDRRSRSRSK-DKKRAARSRSRSPR-DKTKSRRRKA 62
R R R R + + S+ R K K ++ +S + +K K R A
Sbjct: 88 RKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIA 141
>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 = 25.6 bits (57), Expect = 2.3
Identities = 4/18 (22%), Positives = 9/18 (50%)
Query: 100 TRQARRLYVGNIPFGVTE 117
+ +++VGN+ T
Sbjct: 6 SGNTWKIFVGNVSAACTS 23
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 25.8 bits (57), Expect = 2.4
Identities = 6/53 (11%), Positives = 17/53 (32%), Gaps = 6/53 (11%)
Query: 71 PGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQAR------RLYVGNIPFGVTE 117
G + + A+ A+ + + L++ ++P T+
Sbjct: 2 AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTD 54
>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 = 25.7 bits (57), Expect = 2.4
Identities = 5/17 (29%), Positives = 10/17 (58%)
Query: 101 RQARRLYVGNIPFGVTE 117
+ R+L+VG + +E
Sbjct: 13 GRDRKLFVGMLNKQQSE 29
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 26.0 bits (58), Expect = 2.5
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 104 RRLYVGNIPFGVTE 117
R LYVGN+ +TE
Sbjct: 1 RVLYVGNLDKAITE 14
>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 = 26.0 bits (58), Expect = 2.5
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 102 QARRLYVGNIPFGVTE 117
+ R+L++G I TE
Sbjct: 94 EDRKLFIGMISKKCTE 109
>4pga_A Glutaminase-asparaginase; bacterial amidohydrolase; 1.70A
{Pseudomonas SP} SCOP: c.88.1.1 PDB: 1djp_A* 1djo_A*
3pga_1
Length = 337
Score = 26.4 bits (59), Expect = 2.5
Identities = 5/24 (20%), Positives = 9/24 (37%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
VS A+Q ++ S+
Sbjct: 258 SVSSRVVPALQQLRKNGTQIIRSS 281
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 25.7 bits (57), Expect = 2.6
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 100 TRQARRLYVGNIPFGVTE 117
++GN+P+ VTE
Sbjct: 12 KSPPYTAFLGNLPYDVTE 29
>2r52_A BMP-6, bone morphogenetic protein 6; TGF-beta ligand,
chondrogenesis, cleavage on PAIR of basic residues,
cytokine, developmental protein; 2.50A {Homo sapiens}
Length = 143
Score = 25.8 bits (56), Expect = 2.7
Identities = 8/45 (17%), Positives = 16/45 (35%)
Query: 7 KDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSP 51
RRR +SR+ +S+ R S + + + +
Sbjct: 2 APTSASSRRRQQSRNRSTQSQDVARVSSASDYNSSELKTACRKHE 46
Score = 25.0 bits (54), Expect = 6.3
Identities = 7/42 (16%), Positives = 15/42 (35%)
Query: 4 DRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAAR 45
R ++ R+RS + +R + S+ K +
Sbjct: 3 PTSASSRRRQQSRNRSTQSQDVARVSSASDYNSSELKTACRK 44
>1nns_A L-asparaginase II; amidrohydrolase, crystallographic comparison
hydrolase; 1.95A {Escherichia coli} SCOP: c.88.1.1 PDB:
3eca_A 1ho3_A 1jaz_A 1ihd_A 1jja_A 4eca_A*
Length = 326
Score = 26.4 bits (59), Expect = 2.8
Identities = 6/24 (25%), Positives = 11/24 (45%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
++ S + + AA VV S+
Sbjct: 248 NLYKSVFDTLATAAKTGTAVVRSS 271
>1wsa_A Asparaginase, asparagine amidohydrolase; periplasmic; 2.20A
{Wolinella succinogenes} SCOP: c.88.1.1
Length = 330
Score = 26.0 bits (58), Expect = 3.0
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
+ P A++ AA + V V S+
Sbjct: 252 NPFPLTQNALEKAAKSGVVVARSS 275
>2wlt_A L-asparaginase; hydrolase; 1.40A {Helicobacter pylori} PDB: 2wt4_A
Length = 332
Score = 26.0 bits (58), Expect = 3.1
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
+VS KAMQ A+ V +V S+
Sbjct: 255 NVSAGFLKAMQEASQMGVVIVRSS 278
>3nxk_A Cytoplasmic L-asparaginase; structural genomics, center for
structural genomics of infec diseases, csgid,
alpha-beta-alpha sandwich; 2.40A {Campylobacter jejuni
subsp}
Length = 334
Score = 26.0 bits (58), Expect = 3.1
Identities = 4/24 (16%), Positives = 10/24 (41%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
+ +Q ++ + VV S+
Sbjct: 258 SIHKNQKDVLKELLKKGLKVVVSS 281
>3uwp_A Histone-lysine N-methyltransferase, H3 lysine-79; epigenetics,
tubercidin, structu genomics, structural genomics
consortium, SGC; HET: 5ID; 2.05A {Homo sapiens} PDB:
4eqz_A* 3sx0_A* 4er0_A* 4er7_A* 1nw3_A* 4er6_A* 4er5_A*
3qow_A* 3qox_A* 4er3_A* 3sr4_A*
Length = 438
Score = 26.3 bits (57), Expect = 3.2
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 14 RRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKT 55
++ + KK S S+ R+ + K +K A R R R + T
Sbjct: 396 EEKAGAATVKKPSPSKARKKKLNKKGRKMAGRKRGRPKKMNT 437
>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 = 25.2 bits (56), Expect = 3.2
Identities = 4/13 (30%), Positives = 7/13 (53%)
Query: 105 RLYVGNIPFGVTE 117
LY+ + G T+
Sbjct: 7 GLYIRGLQPGTTD 19
>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 = 25.5 bits (56), Expect = 3.2
Identities = 4/17 (23%), Positives = 6/17 (35%)
Query: 101 RQARRLYVGNIPFGVTE 117
R + N+P G
Sbjct: 8 RSKTVILAKNLPAGTLA 24
>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 = 25.6 bits (56), Expect = 3.5
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
L++ NIP V+E
Sbjct: 121 ATLHLSNIPPSVSE 134
>1o7j_A L-asparaginase; atomic resolution, hydrolase; 1.0A {Erwinia
chrysanthemi} SCOP: c.88.1.1 PDB: 1hfj_A 1hfk_A* 1hg0_A
1hg1_A 1hfw_A* 1jsr_A* 1jsl_A 2gvn_A 1zcf_A 2hln_A*
2jk0_A
Length = 327
Score = 25.7 bits (57), Expect = 3.5
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
VS M+ A V V+ ST
Sbjct: 254 SVSVRGIAGMRKALEKGVVVMRST 277
>1lxi_A Bone morphogenetic protein 7; cystine-knot growth factor,
hormone-growth factor complex; HET: NAG; 2.00A {Homo
sapiens} SCOP: g.17.1.2 PDB: 1lx5_A* 1bmp_A* 1m4u_L*
2qcw_A 2r53_A
Length = 139
Score = 25.4 bits (55), Expect = 3.7
Identities = 5/37 (13%), Positives = 17/37 (45%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAAR 45
++ + RS++ +++ R + S S ++ +
Sbjct: 4 SKQRSQNRSKTPKNQEALRMANVAENSSSDQRQACKK 40
Score = 25.4 bits (55), Expect = 3.7
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 22 HKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEH--VSPS 79
+ RS++R ++++ R A S D+ ++ ++ LY G++ ++P
Sbjct: 2 TGSKQRSQNRSKTPKNQEALRMANVAENSSSDQRQACKKH-ELYVSFRDLGWQDWIIAPE 60
Query: 80 QYKA 83
Y A
Sbjct: 61 GYAA 64
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 25.4 bits (56), Expect = 3.8
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 102 QARRLYVGNIPFGVTE 117
Q +RL+V NIPF +
Sbjct: 28 QPKRLHVSNIPFRFRD 43
>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 = 25.2 bits (55), Expect = 3.8
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
R L++ +P VTE
Sbjct: 16 RVLHIRKLPGEVTE 29
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 25.3 bits (56), Expect = 3.9
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 100 TRQARRLYVGNIPFGVTE 117
T YVGN+PF +
Sbjct: 12 TEPPYTAYVGNLPFNTVQ 29
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 25.1 bits (55), Expect = 4.0
Identities = 3/17 (17%), Positives = 6/17 (35%)
Query: 101 RQARRLYVGNIPFGVTE 117
++V + VT
Sbjct: 5 SDNNTIFVQGLGENVTI 21
>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 = 25.1 bits (55), Expect = 4.0
Identities = 3/14 (21%), Positives = 6/14 (42%)
Query: 104 RRLYVGNIPFGVTE 117
++V + V E
Sbjct: 16 PVVHVRGLCESVVE 29
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 25.2 bits (55), Expect = 4.1
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
R +++ +P VTE
Sbjct: 17 RVIHIRKLPIDVTE 30
>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 = 24.9 bits (55), Expect = 4.1
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
S + +L+VG + F E
Sbjct: 5 SSGMASDEGKLFVGGLSFDTNE 26
>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 = 24.9 bits (55), Expect = 4.3
Identities = 5/13 (38%), Positives = 8/13 (61%)
Query: 105 RLYVGNIPFGVTE 117
L++ N+ F TE
Sbjct: 7 GLFIKNLNFSTTE 19
>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 = 25.0 bits (55), Expect = 4.4
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
G +L V N+ FGV++
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSD 49
>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 = 24.9 bits (55), Expect = 4.4
Identities = 4/14 (28%), Positives = 5/14 (35%)
Query: 104 RRLYVGNIPFGVTE 117
L V + TE
Sbjct: 16 CCLGVFGLSLYTTE 29
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 24.9 bits (55), Expect = 4.4
Identities = 4/13 (30%), Positives = 6/13 (46%)
Query: 105 RLYVGNIPFGVTE 117
L+V + TE
Sbjct: 25 ILFVTGVHEEATE 37
>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 = 25.2 bits (56), Expect = 4.7
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 106 LYVGNIPFGVTE 117
L V +P +T+
Sbjct: 6 LIVNYLPQDMTD 17
>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 = 25.0 bits (55), Expect = 4.8
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 104 RRLYVGNIPFGVTE 117
R LY+ N+P+ +T
Sbjct: 9 RILYIRNLPYKITA 22
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 25.6 bits (56), Expect = 4.8
Identities = 6/28 (21%), Positives = 11/28 (39%)
Query: 11 RDRRRRSRSRDHKKRSRSRDRRSRSRSK 38
+D + R+R + R R +K
Sbjct: 453 KDLSKLKRNRKRITNQMTDSSRERPITK 480
Score = 25.2 bits (55), Expect = 6.1
Identities = 6/30 (20%), Positives = 15/30 (50%)
Query: 7 KDRERDRRRRSRSRDHKKRSRSRDRRSRSR 36
D++ + +R+R R + + S R ++
Sbjct: 451 FDKDLSKLKRNRKRITNQMTDSSRERPITK 480
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 25.4 bits (55), Expect = 5.2
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 4 DRDKDRERDRRRRSRSRDHKKRSRSR 29
+ + + R + R +KR R +
Sbjct: 2 EYAEHQGRIKNAREAHSQIEKRRRDK 27
>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 = 25.2 bits (56), Expect = 5.4
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 106 LYVGNIPFGVTE 117
L V +P +T+
Sbjct: 5 LIVNYLPQNMTQ 16
>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 = 24.9 bits (54), Expect = 5.5
Identities = 5/14 (35%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
R +++ +P VTE
Sbjct: 32 RVIHIRKLPIDVTE 45
>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 = 24.5 bits (54), Expect = 5.6
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 101 RQARRLYVGNIPFGVTE 117
+ LYVG + +TE
Sbjct: 10 KTITTLYVGGLGDTITE 26
>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 = 24.6 bits (54), Expect = 5.7
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
G + + L+V +I E
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQE 40
>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 = 24.5 bits (54), Expect = 6.1
Identities = 2/14 (14%), Positives = 7/14 (50%)
Query: 104 RRLYVGNIPFGVTE 117
+Y+ N+ + +
Sbjct: 9 HTIYINNLNEKIKK 22
>3pe5_A Uncharacterized protein; structural genomics, PSI-biology,
protein structure initiati northeast structural
genomics consortium, NESG; 2.38A {Clostridium leptum}
Length = 403
Score = 25.3 bits (55), Expect = 6.4
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 32 RSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
+R + + R SRS +S RK
Sbjct: 3 SNRRYQEPQNRDISSRSNGKNPFKRSTGRK 32
Score = 25.3 bits (55), Expect = 6.7
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 13 RRRRSRSRDHKKRSRSRDRRSRSRSKDKKR 42
RR ++ SRS + RS +K
Sbjct: 4 NRRYQEPQNRDISSRSNGKNPFKRSTGRKV 33
>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 = 24.1 bits (53), Expect = 7.2
Identities = 5/13 (38%), Positives = 9/13 (69%)
Query: 105 RLYVGNIPFGVTE 117
LY+GN+ + T+
Sbjct: 3 ALYIGNLTWWTTD 15
>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 = 24.9 bits (55), Expect = 7.2
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 102 QARRLYVGNIPFGVTE 117
LYVG++ VTE
Sbjct: 14 PMASLYVGDLHPDVTE 29
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 24.5 bits (54), Expect = 7.7
Identities = 4/12 (33%), Positives = 6/12 (50%)
Query: 106 LYVGNIPFGVTE 117
+Y+ N G T
Sbjct: 100 VYIKNFGPGSTR 111
>3k2o_A Bifunctional arginine demethylase and lysyl-hydro JMJD6;
structural genomics consortium, SGC, chromatin
regulator, developmental protein; 1.75A {Homo sapiens}
PDB: 3ld8_A 3ldb_A*
Length = 336
Score = 25.0 bits (54), Expect = 7.8
Identities = 9/54 (16%), Positives = 20/54 (37%)
Query: 11 RDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASL 64
+ + + R R+ K+ +R + S ++ + S S + R L
Sbjct: 2 MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERADALQL 55
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 24.2 bits (53), Expect = 7.8
Identities = 3/17 (17%), Positives = 7/17 (41%)
Query: 101 RQARRLYVGNIPFGVTE 117
R AR ++ + +
Sbjct: 23 RDARTVFCMQLAARIRP 39
>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 = 24.9 bits (55), Expect = 8.1
Identities = 4/14 (28%), Positives = 7/14 (50%)
Query: 104 RRLYVGNIPFGVTE 117
L++ N P T+
Sbjct: 118 CTLWMTNFPPSYTQ 131
>2e5f_A Hypothetical protein PH0510; structural genomics, sugar binding
protein, NPPSFA, national on protein structural and
functional analyses; 1.35A {Pyrococcus horikoshii} PDB:
2dec_A* 2df8_A 2cb0_A*
Length = 325
Score = 24.8 bits (55), Expect = 8.2
Identities = 7/30 (23%), Positives = 10/30 (33%), Gaps = 1/30 (3%)
Query: 87 AAAAAVPVVGSTITRQA-RRLYVGNIPFGV 115
+ S++TR L V I V
Sbjct: 104 VKKLGITTRESSLTRMCDYSLVVPAIEESV 133
>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 = 24.4 bits (53), Expect = 9.0
Identities = 10/82 (12%), Positives = 19/82 (23%), Gaps = 9/82 (10%)
Query: 36 RSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVV 95
+ R + K R + +E V ++ +V
Sbjct: 14 EVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVE-- 71
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
L+V +I E
Sbjct: 72 -------GWILFVTSIHEEAQE 86
>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 = 24.6 bits (53), Expect = 9.2
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 104 RRLYVGNIPFGVTE 117
L++ NIP V+E
Sbjct: 152 ATLHLSNIPPSVSE 165
>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 = 24.7 bits (54), Expect = 9.8
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 102 QARRLYVGNIPFGVTE 117
Q RL+VGN+P +TE
Sbjct: 21 QRCRLFVGNLPTDITE 36
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 24.2 bits (52), Expect = 9.9
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 96 GSTITRQARRLYVGNIPFGVTE 117
GS+ + +R+++VG +P + E
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDE 22
>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 = 24.1 bits (53), Expect = 9.9
Identities = 3/18 (16%), Positives = 8/18 (44%)
Query: 100 TRQARRLYVGNIPFGVTE 117
+ L++GN+ +
Sbjct: 14 STTPFNLFIGNLNPNKSV 31
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
0.316 0.127 0.362
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,764,428
Number of extensions: 95946
Number of successful extensions: 912
Number of sequences better than 10.0: 1
Number of HSP's gapped: 845
Number of HSP's successfully gapped: 304
Length of query: 117
Length of database: 6,701,793
Length adjustment: 80
Effective length of query: 37
Effective length of database: 4,468,113
Effective search space: 165320181
Effective search space used: 165320181
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: 51 (23.3 bits)