RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6947
(92 letters)
>3mea_A SAGA-associated factor 29 homolog; structural genomics consortium,
SGC, nucleus, transcription, transcription regulation,
chromosomal protein, DNA-binding; HET: M3L; 1.26A {Homo
sapiens} PDB: 3meu_A* 3met_A* 3me9_A* 3mev_A* 3lx7_A
3mew_A
Length = 180
Score = 119 bits (299), Expect = 5e-36
Identities = 54/91 (59%), Positives = 70/91 (76%)
Query: 1 KGPHQLSRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDD 60
K H LSR+++IPLP +ANPET+PEALF +V+ALYPQTTCFY+A++++ P DD
Sbjct: 89 KERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDD 148
Query: 61 YELLFEDNSYADNYAPPLGVPQRYVIAYKKS 91
Y +LFED SYAD Y+PPL V QRYV+A K+
Sbjct: 149 YSVLFEDTSYADGYSPPLNVAQRYVVACKEP 179
>3mp6_A MBP, SGF29, maltose-binding periplasmic protein, linker, SAGA
associated factor 29; histone, tudor domain, histone
binding protei; HET: MLY MAL; 1.48A {Escherichia coli}
PDB: 3mp1_A* 3mp8_A*
Length = 522
Score = 41.8 bits (98), Expect = 5e-06
Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 11/86 (12%)
Query: 7 SRKQIIPLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFE 66
+RK+++ +P +P G+ V+A YP+TT FY AIV GT L F+
Sbjct: 442 NRKELLLIPPGFPTKN------YPPGTKVLARYPETTTFYPAIVIGTKRDGT--CRLRFD 493
Query: 67 DNSYADNYAPPLGVPQRYVIAYKKSS 92
D V +R V+ +
Sbjct: 494 GEEEVDKETE---VTRRLVLPSPTAL 516
>2l8d_A Lamin-B receptor; DNA binding protein; NMR {Gallus gallus}
Length = 66
Score = 30.9 bits (69), Expect = 0.012
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 25 PEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
P + G VVM +P + +Y+ V S Y + ++D
Sbjct: 6 PNRKYADGEVVMGRWPGSVLYYEVQVTSYDDAS-HLYTVKYKD 47
>2g3r_A Tumor suppressor P53-binding protein 1; tandem tudor domains,
cell cycle-transcription complex; 1.25A {Homo sapiens}
SCOP: b.34.9.1 b.34.9.1 PDB: 2ig0_A* 3lgf_A* 3lgl_A*
3lh0_A* 1xni_A
Length = 123
Score = 31.2 bits (70), Expect = 0.019
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 31 IGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFEDNSYAD 72
+G V+A + FY + G Y+LLF+D D
Sbjct: 7 VGLRVVAKWSSNGYFYSGKITRDVGAGK--YKLLFDDGYECD 46
>2xdp_A Lysine-specific demethylase 4C; oxidoreductase, histone
modification; 1.56A {Homo sapiens}
Length = 123
Score = 30.4 bits (68), Expect = 0.041
Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 29 FPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFEDNSYADNYAP 76
+G V+ + T +Y V ++ + YE++F+D S++ + P
Sbjct: 7 ISVGQTVITKHRNTR-YYSCRVMAVTSQTF--YEVMFDDGSFSRDTFP 51
>3pnw_C Tudor domain-containing protein 3; FAB, structural genomics
consortium, antibody, SGC, protein immune system
complex; 2.05A {Homo sapiens}
Length = 77
Score = 29.4 bits (66), Expect = 0.053
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 13 PLPTKRANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
P ++ E ++ G ALY + FY+A V +L ++G + F D
Sbjct: 2 PEKILESSIPMEYAKMWKPGDECFALYWEDNKFYRAEVEALHSSG-MTAVVKFID 55
>1ssf_A Transformation related protein 53 binding protein 1; tudor
domains, tandem, SH3-like fold, beta barrel, alpha-
helix, cell cycle; NMR {Mus musculus} SCOP: b.34.9.1
b.34.9.1
Length = 156
Score = 29.1 bits (64), Expect = 0.12
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 2/51 (3%)
Query: 22 ETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFEDNSYAD 72
++ +G V+A + FY + G Y+LLF+D D
Sbjct: 2 DSSSSGNSFVGLRVVAKWSSNGYFYSGKITRDVGAGK--YKLLFDDGYECD 50
>2dig_A Lamin-B receptor; tudor domain, integral nuclear envelope inner
membrane protein, nuclear protein, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: b.34.9.1
Length = 68
Score = 27.9 bits (61), Expect = 0.16
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 25 PEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFEDNS 69
P F G VV +P ++ +Y+ + S +T Y + ++D +
Sbjct: 9 PSRKFADGEVVRGRWPGSSLYYEVEILSHDSTS-QLYTVKYKDGT 52
>3ntk_A Maternal protein tudor; tudor domain, OB-fold, GERM cell
formation, transcription; 1.80A {Drosophila
melanogaster} PDB: 3nth_A* 3nti_A*
Length = 169
Score = 28.3 bits (63), Expect = 0.29
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 18 RANPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
A + + G++ +A +P+ FY+A + + G E+ F D
Sbjct: 37 DAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGK--CEVHFID 84
>4a4f_A SurviVal of motor neuron-related-splicing factor; RNA binding
protein; HET: 2MR; NMR {Homo sapiens} PDB: 4a4h_A*
Length = 64
Score = 26.6 bits (59), Expect = 0.39
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 23 TEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
T+P + +G MA++ + Y+A + + + F
Sbjct: 3 TQPTHSWKVGDKCMAVWSEDGQCYEAEIEEIDEEN-GTAAITFAG 46
>2wac_A CG7008-PA; unknown function, tudor, beta-barrel, nuclease domain,
tudor P100, SND1, methylated arginine, SDMA, splicing;
2.10A {Drosophila melanogaster}
Length = 218
Score = 27.7 bits (61), Expect = 0.39
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 20 NPETEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
NP G +V A + +Y+A V + + +L+ D
Sbjct: 43 NPPIAGSYTPKRGDLVAAQFTLDNQWYRAKVERVQ---GSNATVLYID 87
>3s6w_A Tudor domain-containing protein 3; methylated arginine recognize,
ISO-propanol, transcri; 1.78A {Homo sapiens} PDB:
3pmt_A*
Length = 54
Score = 26.1 bits (58), Expect = 0.55
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 28 LFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
++ G ALY + FY+A V +L ++G + F D
Sbjct: 1 MWKPGDECFALYWEDNKFYRAEVEALHSSG-MTAVVKFID 39
>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 = 27.2 bits (59), Expect = 0.62
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 70 YADNYAPPLGV 80
YAD+ AP L +
Sbjct: 32 YADDSAPALAI 42
>3fdr_A Tudor and KH domain-containing protein; TDRD2, structural
genomics, structural genomics consortium, SGC,
alternative splicing, RNA-binding; 1.75A {Homo sapiens}
Length = 94
Score = 25.9 bits (57), Expect = 1.2
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 22 ETEPEALFP-IGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
+ PE L +G +V A P +Y+A V G +L F D
Sbjct: 20 NSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGN--LDLYFVD 64
>2d9t_A Tudor domain-containing protein 3; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: b.34.9.1
Length = 78
Score = 25.2 bits (55), Expect = 1.7
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 29 FPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
+ G ALY + FY+A V +L ++G + F D
Sbjct: 10 WKPGDECFALYWEDNKFYRAEVEALHSSG-MTAVVKFTD 47
>2diq_A Tudor and KH domain-containing protein; tudor domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
SCOP: b.34.9.1
Length = 110
Score = 25.6 bits (56), Expect = 1.7
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 22 ETEPEALFP-IGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
+ PE L +G +V A P +Y+A V G +L F D
Sbjct: 25 NSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGN--LDLYFVD 69
>2yxz_A Thiamin-monophosphate kinase; alpha/beta structure, transferase;
1.90A {Thermus thermophilus}
Length = 311
Score = 25.6 bits (57), Expect = 2.3
Identities = 6/30 (20%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 56 TGTDDYELLF----EDNSYADNYAPPLGVP 81
G +++E + E + + A G+P
Sbjct: 254 YGGEEFEAVLVVPQEGAAAVEARAKAKGLP 283
>3mcq_A Thiamine-monophosphate kinase; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2; HET: MSE PGE PG4 1PE; 1.91A {Methylobacillus
flagellatus}
Length = 319
Score = 25.6 bits (57), Expect = 2.8
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 56 TGTDDYELLF 65
+G DDYEL F
Sbjct: 256 SGGDDYELCF 265
>3c9u_A Thiamine monophosphate kinase; beta barrel, alpha-beta structure,
transferase; HET: TPP ADP; 1.48A {Aquifex aeolicus}
SCOP: d.79.4.1 d.139.1.1 PDB: 3c9r_A* 3c9t_A* 3c9s_A*
1vqv_A
Length = 342
Score = 25.3 bits (56), Expect = 3.8
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 56 TGTDDYELLF 65
G +DY+LLF
Sbjct: 293 FGGEDYQLLF 302
>1g5v_A SurviVal motor neuron protein 1; mRNA processing, translation;
NMR {Homo sapiens} SCOP: b.34.9.1
Length = 88
Score = 23.4 bits (50), Expect = 8.3
Identities = 6/45 (13%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 23 TEPEALFPIGSVVMALYPQTTCFYKAIVNSLPTTGTDDYELLFED 67
+ +G A++ + C Y A + S+ + +++
Sbjct: 5 AASLQQWKVGDKCSAIWSEDGCIYPATIASIDFKR-ETCVVVYTG 48
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
0.315 0.134 0.399
Gapped
Lambda K H
0.267 0.0667 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,374,590
Number of extensions: 68312
Number of successful extensions: 88
Number of sequences better than 10.0: 1
Number of HSP's gapped: 88
Number of HSP's successfully gapped: 24
Length of query: 92
Length of database: 6,701,793
Length adjustment: 59
Effective length of query: 33
Effective length of database: 5,054,454
Effective search space: 166796982
Effective search space used: 166796982
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: 42 (22.0 bits)
S2: 51 (23.6 bits)