RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2111
(63 letters)
>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 = 58.9 bits (143), Expect = 1e-13
Identities = 16/44 (36%), Positives = 20/44 (45%)
Query: 11 RAYRTLHGAWFNSKLVTVKYLRYERYHERFPQAKALVAPLKPSN 54
A LHG WF K++T Y+ YH FP + L PS
Sbjct: 70 AAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSR 113
>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 = 33.6 bits (77), Expect = 9e-04
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 10 RRAYRTLHGAWFNSKLVTVKYLRYERYHER 39
++A + L G F +++V KY + YH R
Sbjct: 73 QKAMQGLTGRKFANRVVVTKYCDPDSYHRR 102
>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 = 33.1 bits (76), Expect = 0.001
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 11 RAYRTLHGAWFNSKLVTVKYLRYERYHERFPQA 43
+TL G WF + +T + ++ P +
Sbjct: 79 YCIQTLDGRWFGGRQITAQAWDGTTDYQSGPSS 111
>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 = 31.6 bits (72), Expect = 0.004
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 10 RRAYRTLHGAWFNSKLVTVKYLRYERYHER 39
+A + L+G WF + V + ER+
Sbjct: 85 HKAIQALNGRWFAGRKVVAEVYDQERFDNS 114
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 27.5 bits (61), Expect = 0.17
Identities = 5/30 (16%), Positives = 14/30 (46%)
Query: 10 RRAYRTLHGAWFNSKLVTVKYLRYERYHER 39
+A L+G +F ++V + +++
Sbjct: 70 IKAVVDLNGRYFGGRVVKACFYNLDKFRVL 99
>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 = 26.0 bits (57), Expect = 0.49
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 11 RAYRTLHGAWFNSKLVTVKY 30
+A L+ WFN + + +
Sbjct: 83 KAVIDLNNRWFNGQPIHAEL 102
>3qzb_A SOR, putative superoxide reductase; immunoglobulin-like
beta-sandwich, structural genomics, JOIN for structural
genomics, JCSG; 1.10A {Thermotoga maritima} PDB: 2amu_A
Length = 143
Score = 25.9 bits (56), Expect = 0.68
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 11 RAYRTLHGAWFNSKLVTVK 29
+Y +HG W +S+ +TV+
Sbjct: 124 LSYCNIHGLWESSQKITVE 142
>3m6i_A L-arabinitol 4-dehydrogenase; medium chain dehydrogenase/reductase,
oxidoreductase; HET: NAD; 2.60A {Neurospora crassa}
Length = 363
Score = 25.3 bits (56), Expect = 1.4
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 4/33 (12%)
Query: 35 RYHERFPQAKALVA----PLKPSNDRRYSLQQA 63
RY +P+A LV L R+ L+ A
Sbjct: 308 RYCNTWPRAIRLVENGLVDLTRLVTHRFPLEDA 340
>1pl8_A Human sorbitol dehydrogenase; NAD, oxidoreductase; HET: NAD; 1.90A
{Homo sapiens} SCOP: b.35.1.2 c.2.1.1 PDB: 1pl7_A
1pl6_A* 3qe3_A
Length = 356
Score = 24.9 bits (55), Expect = 1.8
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 35 RYHERFPQAKALVA----PLKPSNDRRYSLQQA 63
RY +P A +++A +KP R+ L++A
Sbjct: 298 RYCNTWPVAISMLASKSVNVKPLVTHRFPLEKA 330
>2dq4_A L-threonine 3-dehydrogenase; NAD-dependent, oxidoreductase,
structural genomics, NPPSFA; HET: MES; 2.50A {Thermus
thermophilus} PDB: 2ejv_A*
Length = 343
Score = 24.5 bits (54), Expect = 2.4
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 4/42 (9%)
Query: 26 VTVKYLRYERYHERFPQAKALVA----PLKPSNDRRYSLQQA 63
+T + R + + Q ALV L P R L +
Sbjct: 281 ITAFGIAGRRLWQTWMQGTALVYSGRVDLSPLLTHRLPLSRY 322
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 24.3 bits (53), Expect = 2.8
Identities = 2/33 (6%), Positives = 11/33 (33%)
Query: 10 RRAYRTLHGAWFNSKLVTVKYLRYERYHERFPQ 42
+ + LH ++ + + ++ +
Sbjct: 62 KETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYE 94
>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 = 24.1 bits (52), Expect = 4.0
Identities = 7/55 (12%), Positives = 19/55 (34%), Gaps = 2/55 (3%)
Query: 11 RAYRTLHGAWFNSKLVTVKYLRYE--RYHERFPQAKALVAPLKPSNDRRYSLQQA 63
A L+G + K + + +++ + + + L S R+ +
Sbjct: 56 LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 110
>2y35_A LD22664P; hydrolase-DNA complex, RNA degradation, exonuclease
5'-3', R interference; 3.20A {Drosophila melanogaster}
Length = 1140
Score = 24.2 bits (51), Expect = 4.3
Identities = 8/45 (17%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 14 RTLHGAWFNSKLVTVKYLRYERYHERFPQAKALVAPLKPSNDRRY 58
+ W+ S L V +R Y +R+P + +
Sbjct: 930 FRTNNQWYYSSL-AVDLMR--NYCQRYPDVIDFFGDSNDRAEFVF 971
>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 = 23.4 bits (51), Expect = 6.0
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 2/49 (4%)
Query: 11 RAYRTLHGAWFNSKLVTVKYLRYERYHERFPQAKALVAPLKPSNDRRYS 59
RA ++G N + V V ++ ER + A P + Y+
Sbjct: 158 RAIEKMNGMLLNDRKVFVGR--FKSRKEREAELGARAKEFYPYDVPDYA 204
>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 = 23.2 bits (50), Expect = 6.7
Identities = 9/32 (28%), Positives = 11/32 (34%)
Query: 10 RRAYRTLHGAWFNSKLVTVKYLRYERYHERFP 41
A R L F S Y+R + R P
Sbjct: 64 TYAVRKLDNTKFRSHEGETAYIRVKVDGPRSP 95
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
0.321 0.133 0.418
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 985,401
Number of extensions: 41814
Number of successful extensions: 100
Number of sequences better than 10.0: 1
Number of HSP's gapped: 100
Number of HSP's successfully gapped: 18
Length of query: 63
Length of database: 6,701,793
Length adjustment: 34
Effective length of query: 29
Effective length of database: 5,752,479
Effective search space: 166821891
Effective search space used: 166821891
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)