RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8320
(119 letters)
>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU
PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1
g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A
2opf_A* 1q3b_A*
Length = 262
Score = 27.9 bits (63), Expect = 0.75
Identities = 10/56 (17%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 46 IESGG--RRIGENKALTASKARFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 94
+ G + AL RF + + E C+ C + + ++C C
Sbjct: 209 YATRGQVDENKHHGAL----FRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGC 260
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 28.1 bits (62), Expect = 0.78
Identities = 8/71 (11%), Positives = 22/71 (30%)
Query: 42 SRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGIC 101
+ I+S + + + K R N ++ +C + ++ +
Sbjct: 113 GKLKIDSSNPKFNDTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGH 172
Query: 102 AMCGKKLLDVK 112
CG ++
Sbjct: 173 GGCGAAQPTIR 183
>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair,
sequence context; HET: DNA 08Q; 1.60A {Geobacillus
stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A* 3u6m_A*
3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A* 2f5q_A*
2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A 3sau_A*
3sar_A* 3sav_A* ...
Length = 273
Score = 26.7 bits (60), Expect = 1.9
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 69 YTQKFESCKIC-----RQKVHQVGSHYCQAC 94
Y ++ CK C + V G+HYC C
Sbjct: 241 YGRQGNPCKRCGTPIEKTVVAGRGTHYCPRC 271
>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET:
VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A*
1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A
1pjj_A*
Length = 271
Score = 26.3 bits (59), Expect = 2.3
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 5/35 (14%)
Query: 65 RFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 94
Y + E C C + KV G+H+C C
Sbjct: 234 ELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVC 268
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns
helix, riken STR genomics/proteomics initiative, RSGI,
structural genomics; 1.90A {Thermus thermophilus} SCOP:
a.156.1.2 b.113.1.1 g.39.1.8
Length = 266
Score = 26.3 bits (59), Expect = 2.3
Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 5/26 (19%)
Query: 74 ESCKIC-----RQKVHQVGSHYCQAC 94
C C R+ V G+H+C C
Sbjct: 236 LPCPACGRPVERRVVAGRGTHFCPTC 261
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA
repair, beta sandwich, zinc finger, helix two-turns
helix, hydrolase/DNA complex; HET: PED; 2.10A
{Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8
Length = 268
Score = 25.5 bits (57), Expect = 4.2
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 65 RFNPYTQKFESCKIC-----RQKVHQVGSHYCQAC 94
Y +K E C++C K Q + YC+ C
Sbjct: 232 ELQVYGRKGEPCRVCGTPIVATKHAQRATFYCRQC 266
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.0 bits (56), Expect = 4.6
Identities = 10/52 (19%), Positives = 15/52 (28%), Gaps = 8/52 (15%)
Query: 65 RFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLLDVKNYKQ 116
R + F + QK+ + A I L +K YK
Sbjct: 489 RMTLFRMVFLDFRFLEQKIRHDST----AWNASGSILNT----LQQLKFYKP 532
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 25.4 bits (55), Expect = 5.1
Identities = 7/32 (21%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 76 CKICRQKVHQVGSHYCQACAYKKG--ICAMCG 105
C C+ ++ + +G +CA+CG
Sbjct: 24 CPECKVYPPKI------VERFSEGDVVCALCG 49
>3vk8_A Probable formamidopyrimidine-DNA glycosylase; DNA glycosylase,
hneil1 ortholog, DNA lesion, thymine glycol zincless
finger; HET: DNA CTG; 2.00A {Acanthamoeba polyphaga
mimivirus} PDB: 3vk7_A* 3a42_A 3a46_A* 3a45_A*
Length = 295
Score = 25.3 bits (56), Expect = 6.1
Identities = 8/46 (17%), Positives = 16/46 (34%), Gaps = 7/46 (15%)
Query: 56 NKALTASKARFNPYTQKFESC-------KICRQKVHQVGSHYCQAC 94
N T + F Y +K + KI ++ +++ A
Sbjct: 240 NIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAI 285
>3d00_A Tungsten formylmethanofuran dehydrogenase subunit; FWDE/GAPDH
domain-like fold, structural genomics, joint CENT
structural genomics; HET: MSE; 1.90A {Syntrophus
aciditrophicus}
Length = 191
Score = 25.0 bits (54), Expect = 7.3
Identities = 8/35 (22%), Positives = 11/35 (31%), Gaps = 2/35 (5%)
Query: 63 KARFNPYTQKFES--CKICRQKVHQVGSHYCQACA 95
K F K + C CR+ C +C
Sbjct: 151 KPGFLEKKHKGKIVLCPQCREAYPAQDGELCLSCQ 185
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 0.408
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,777,503
Number of extensions: 90470
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 285
Number of HSP's successfully gapped: 30
Length of query: 119
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,440,192
Effective search space: 168727296
Effective search space used: 168727296
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)