RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16924
(94 letters)
>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 = 50.8 bits (122), Expect = 7e-10
Identities = 32/41 (78%), Positives = 32/41 (78%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPG 41
M DR AAERACKDPNPIIDGRKANVNLA LGAKPR
Sbjct: 66 MADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGF 106
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 38.0 bits (89), Expect = 5e-05
Identities = 9/39 (23%), Positives = 11/39 (28%), Gaps = 4/39 (10%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPG 41
D +DGR + PRG P G
Sbjct: 67 DPNCVGTVLASRPHTLDGRNIDPKPCT----PRGMQPSG 101
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 35.3 bits (82), Expect = 5e-04
Identities = 5/34 (14%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLAIL-GAKPR 35
D+ ++ +D + + +A A+P+
Sbjct: 76 DQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 34.5 bits (80), Expect = 8e-04
Identities = 6/26 (23%), Positives = 10/26 (38%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLA 28
D + E+ +DGR + A
Sbjct: 62 DAASVEKVLDQKEHRLDGRVIDPKKA 87
>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 = 34.5 bits (80), Expect = 9e-04
Identities = 7/42 (16%), Positives = 14/42 (33%), Gaps = 5/42 (11%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPGISH 44
+ + + +IDGR + L + + G S
Sbjct: 66 EYETQVKVMSQRH-MIDGRWCDCKLPN----SKQSQDSGPSS 102
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 33.6 bits (78), Expect = 0.001
Identities = 4/26 (15%), Positives = 8/26 (30%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLA 28
E+ C+ I+ + A
Sbjct: 50 SEDIVEKVCEIHFHEINNKMVECKKA 75
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 33.6 bits (78), Expect = 0.001
Identities = 3/26 (11%), Positives = 10/26 (38%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLA 28
D+ ++ +D + + +A
Sbjct: 51 DQAGVDKVLAQSRHELDSKTIDPKVA 76
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 99
Score = 33.3 bits (77), Expect = 0.002
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPGISH 44
D + ++A I G+K V A PR + G S
Sbjct: 59 FEDEQSVDQAVNMHFHDIMGKKVEVKRAE----PRDSKSSGPSS 98
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 32.6 bits (75), Expect = 0.006
Identities = 8/39 (20%), Positives = 10/39 (25%), Gaps = 4/39 (10%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPG 41
+ A IDGR A+ R G
Sbjct: 78 SMAEVDAAMAARPHSIDGRVVEPKRAV----AREESGSG 112
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 31.7 bits (73), Expect = 0.006
Identities = 2/26 (7%), Positives = 9/26 (34%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLA 28
+ ++ + + K + +A
Sbjct: 50 EEEPVKKIMEKKYHNVGLSKCEIKVA 75
>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 = 30.0 bits (68), Expect = 0.045
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 1/48 (2%)
Query: 1 MGDRPAAERACKDPNP-IIDGRKANVNLAILGAKPRGTLPPGISHQRS 47
+ A+ A KD N + G+ V A + G + R+
Sbjct: 55 FENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRN 102
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 28.7 bits (65), Expect = 0.11
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 5/39 (12%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPG 41
D A+ C + II G +++ A P+ G
Sbjct: 51 DDQIAQSLCGED-LIIKGISVHISNAE----PKHNSNSG 84
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 29.2 bits (66), Expect = 0.13
Identities = 7/47 (14%), Positives = 11/47 (23%), Gaps = 4/47 (8%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNLAILGAKPRGTLPPGISHQRS 47
+ A +DGR A+ R +H
Sbjct: 62 YATVEEVDAAMNARPHKVDGRVVEPKRAV----SREDSQRPGAHLTV 104
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43
inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA;
1.65A {Mus musculus}
Length = 89
Score = 28.0 bits (63), Expect = 0.23
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 5/34 (14%)
Query: 3 DRPAAERACKDPNPIIDGRKANVNLAILGAKPRG 36
D A+ C + II G +++ A P+
Sbjct: 57 DDKVAQSLCGEDL-IIKGISVHISNAE----PKH 85
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 27.2 bits (61), Expect = 0.47
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 5/42 (11%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRGTLPPG 41
+ A+RA + + +++GRK VN A R G
Sbjct: 62 FENSADADRAREKLHGTVVEGRKIEVNN----ATARVMTNSG 99
>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 = 27.1 bits (61), Expect = 0.65
Identities = 6/29 (20%), Positives = 12/29 (41%), Gaps = 1/29 (3%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNLAI 29
+ + K + I+DG+ + AI
Sbjct: 52 FEKPSSVDEVVKTQH-ILDGKVIDPKRAI 79
>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 = 26.4 bits (59), Expect = 0.94
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 1/42 (2%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRGTLPPG 41
A++A K +DG K V ++ KP G
Sbjct: 57 YKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPASGPSSG 98
>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 = 25.6 bits (57), Expect = 1.3
Identities = 4/41 (9%), Positives = 12/41 (29%), Gaps = 5/41 (12%)
Query: 1 MGDRPAAERACKD-PNPIIDGRKANVNLAILGAKPRGTLPP 40
+G ++++ P + G+ V +
Sbjct: 52 VGSEASSKKLMDLLPKRELHGQNPVVTP----SNKLEHHHH 88
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 25.7 bits (56), Expect = 2.1
Identities = 5/29 (17%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 1 MGDRPAAERACKD-PNPIIDGRKANVNLA 28
+ + + + P +++G K +V A
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRPA 134
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 25.2 bits (56), Expect = 2.3
Identities = 5/37 (13%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRG 36
+ + A + + + G+K + ++ A+P+
Sbjct: 52 FDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQF 88
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 25.0 bits (55), Expect = 2.5
Identities = 7/33 (21%), Positives = 12/33 (36%), Gaps = 5/33 (15%)
Query: 1 MGDRPAAERACK-----DPNPIIDGRKANVNLA 28
+ A + + P IDG+ V+ A
Sbjct: 60 LSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 24.9 bits (55), Expect = 2.8
Identities = 11/37 (29%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRG 36
M A+ A N + G++ NV L+ G K G
Sbjct: 50 MEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86
>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 = 25.0 bits (55), Expect = 2.9
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 1/42 (2%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRGTLPPG 41
+ A A N ++ G+ ++N+A R G
Sbjct: 69 YSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSSG 110
>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 = 25.0 bits (54), Expect = 5.0
Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 17/60 (28%)
Query: 46 RSLALGSNDFEYTGWPSFLM---IYVHMGSILTFEFNPFL-KPY--------PISGIKLL 93
R L L E+ L+ + S L +FN L +P P + +L+
Sbjct: 7 RPLTLSHGSLEH----VLLVPTASFFI-ASQLQEQFNKILPEPTEGFAADDEPTTPAELV 61
>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 = 24.1 bits (53), Expect = 5.5
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 5/42 (11%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRGTLPPG 41
A+ A + IDG K ++ AKP+G G
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDW----AKPKGEGGSG 98
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 24.1 bits (53), Expect = 5.7
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRG 36
AERAC+ N + GR+ +V + + P
Sbjct: 55 FESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSS 91
>1hkq_A REPA, replication protein; DNA binding protein, winged-helix, PPS10
plasmid, replication initiator dimer.; 2.75A
{Pseudomonas syringae PV} SCOP: a.4.5.10
Length = 132
Score = 24.4 bits (53), Expect = 6.5
Identities = 6/33 (18%), Positives = 11/33 (33%), Gaps = 1/33 (3%)
Query: 53 NDFEYTGWPSFLMIYVHMGSILTFEFNPFLKPY 85
E W + Y + F+P + P+
Sbjct: 87 KVVERMRWVFHVK-YREGQGCVELGFSPTIIPH 118
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 24.3 bits (53), Expect = 7.0
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRG 36
D+ AE A + ++DGR+ V +A G P
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDS 132
>2l1u_A MSRB2, methionine-R-sulfoxide reductase B2, mitochondria;
methionine sulfoxide reductase, oxidoreductase; NMR
{Mus musculus}
Length = 143
Score = 24.1 bits (53), Expect = 7.0
Identities = 6/6 (100%), Positives = 6/6 (100%)
Query: 58 TGWPSF 63
TGWPSF
Sbjct: 58 TGWPSF 63
>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 = 23.7 bits (52), Expect = 7.4
Identities = 4/29 (13%), Positives = 10/29 (34%), Gaps = 1/29 (3%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNLAI 29
+ ++ + G+K + AI
Sbjct: 57 FYNDVDVQKIVESQI-NFHGKKLKLGPAI 84
>2k8d_A Peptide methionine sulfoxide reductase MSRB; thermophilic, Zn
binding, metal-binding, oxidoreductase; NMR
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 151
Score = 24.1 bits (53), Expect = 7.7
Identities = 6/6 (100%), Positives = 6/6 (100%)
Query: 58 TGWPSF 63
TGWPSF
Sbjct: 82 TGWPSF 87
>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 = 23.8 bits (52), Expect = 7.9
Identities = 9/52 (17%), Positives = 15/52 (28%), Gaps = 1/52 (1%)
Query: 1 MGDRPAAERACKDPN-PIIDGRKANVNLAILGAKPRGTLPPGISHQRSLALG 51
A +A N ++ R +V + PP Q + G
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114
>1jb0_A Photosystem I P700 chlorophyll A apoprotein A1; membrane protein,
multiprotein-pigment complex, photosynthes; HET: CL1 PQN
BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP:
f.29.1.1 PDB: 3pcq_A* 2o01_A* 2wsc_A* 2wse_A* 2wsf_A*
3lw5_A*
Length = 755
Score = 24.4 bits (52), Expect = 8.1
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 5/39 (12%)
Query: 44 HQRSLALGSNDFEYTGWPSFLMIYVHMGSILTFEFNPFL 82
HQ ++L N G + + H F NP L
Sbjct: 215 HQIHVSLPINKLLDAGVAAKDIPLPH-----EFILNPSL 248
>3hcj_A MSRB, peptide methionine sulfoxide reductase; methionine
sulfoxide reductase B, oxidized form, oxidoreductase;
1.66A {Xanthomonas campestris PV} PDB: 3hci_A*
Length = 154
Score = 24.1 bits (53), Expect = 8.6
Identities = 6/6 (100%), Positives = 6/6 (100%)
Query: 58 TGWPSF 63
TGWPSF
Sbjct: 71 TGWPSF 76
>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 = 23.9 bits (51), Expect = 9.3
Identities = 7/62 (11%), Positives = 19/62 (30%), Gaps = 5/62 (8%)
Query: 1 MGDRPAAERACKD-PNPIIDGRKANVNLAILGAKPRGTLPPGISHQRSLALGSNDFEYTG 59
+G ++++ P + G+ V + + +++ G E
Sbjct: 119 VGSEASSKKLMDLLPKRELHGQNPVVTP----VNKQFLSQFEMQSRKTTQSGQMSGEGKA 174
Query: 60 WP 61
P
Sbjct: 175 GP 176
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
0.322 0.142 0.447
Gapped
Lambda K H
0.267 0.0796 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,501,760
Number of extensions: 76700
Number of successful extensions: 139
Number of sequences better than 10.0: 1
Number of HSP's gapped: 139
Number of HSP's successfully gapped: 46
Length of query: 94
Length of database: 6,701,793
Length adjustment: 61
Effective length of query: 33
Effective length of database: 4,998,612
Effective search space: 164954196
Effective search space used: 164954196
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.3 bits)