RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8717
(69 letters)
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex,
single-stranded DNA, isomerase/DNA complex; HET: DNA;
2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A*
2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*
Length = 659
Score = 49.9 bits (120), Expect = 3e-09
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 15 QGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
Y + +S G QTP LG V R ++I F + ++ + + +
Sbjct: 186 NAGYQGV----LSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPAD 233
>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga
maritima} PDB: 2gaj_A*
Length = 633
Score = 34.1 bits (79), Expect = 0.001
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 32 QTPTLGFCVERHDKIRTFKPEPYWLLDLTLN 62
Q+ TL +R +I F P+ Y + + +
Sbjct: 169 QSATLKLVCDREREILRFVPKKYHRITVNFD 199
>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA;
1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X*
1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A*
3pwt_A* 3px7_A* 1ecl_A 1cy9_A* 1cyy_A*
Length = 592
Score = 33.3 bits (77), Expect = 0.003
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 32 QTPTLGFCVERHDKIRTFKPEPYWLLDLTL 61
Q+ + VER +I+ F PE +W +D +
Sbjct: 197 QSVAVRLVVEREREIKAFVPEEFWEVDAST 226
>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 = 32.2 bits (72), Expect = 0.004
Identities = 11/38 (28%), Positives = 13/38 (34%), Gaps = 11/38 (28%)
Query: 6 KLNLKEADYQGKYGDLDASLISYGPCQTPTLGF--CVE 41
K LK+ L ASL Y P L +E
Sbjct: 19 KQALKK---------LQASLKLYADDSAPALAIKATME 47
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 29.7 bits (67), Expect = 0.042
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 32 QTPTLGFCVERHDKIRTFKP-EPYWLLDLTLNLNGE 66
QT LG+ ++R + R + DL L + E
Sbjct: 717 QTLVLGWIIDRFQESRERRKIAIVRDFDLVLEHDEE 752
>1qp2_A Protein (PSAE protein); mainly beta, roll, pleckstrin topology,
SH3-like, electron T; NMR {Nostoc SP} SCOP: b.34.4.2
PDB: 1qp3_A
Length = 70
Score = 26.3 bits (57), Expect = 0.36
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 40 VERHDKIRTFKPEPYWLLDL 59
V+R K+R +PE YW D+
Sbjct: 2 VQRGSKVRILRPESYWFQDV 21
>1gxi_E Photosystem I reaction center subunit IV; photosynthesis, PSAE
SUB-UNIT, thylakoid; NMR {Synechocystis SP} SCOP:
b.34.4.2 PDB: 1pse_A 1psf_A
Length = 73
Score = 26.4 bits (57), Expect = 0.37
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 40 VERHDKIRTFKPEPYWLLDL 59
+ R DK+R + E YW D+
Sbjct: 2 LNRGDKVRIKRTESYWYGDV 21
>1jb0_E Photosystem 1 reaction centre subunit IV; membrane protein,
multiprotein-pigment complex, photosynthes; HET: CL1
PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP:
b.34.4.2 PDB: 3pcq_E*
Length = 75
Score = 26.3 bits (57), Expect = 0.44
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 40 VERHDKIRTFKPEPYWLLDL 59
V+R K++ +PE YW ++
Sbjct: 1 VQRGSKVKILRPESYWYNEV 20
>3hrz_B Cobra venom factor; serine protease, glycosilated, multi-domain,
complement SYST convertase, complement alternate
pathway; HET: NAG P6G; 2.20A {Naja kaouthia} PDB:
3frp_G* 3hs0_B*
Length = 252
Score = 24.8 bits (53), Expect = 2.3
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 31 CQTPTLGFCVERHDKIRTFKP 51
TPT G CV +IR K
Sbjct: 61 SFTPTKGICVAEPYEIRVMKV 81
>2hr0_B Complement C3 alpha' chain; complement component C3B, immune
system; HET: THC; 2.26A {Homo sapiens} PDB: 2icf_B*
2wii_B* 2win_B* 3g6j_B 3l5n_B* 2a73_B* 2i07_B* 2xwj_B*
2xwb_B* 2a74_C* 2ice_C* 2qki_C* 3l3o_F* 3nms_C* 3nsa_C*
3ohx_C* 3t4a_C 2ice_B* 3l3o_B* 3nms_B* ...
Length = 915
Score = 25.1 bits (53), Expect = 2.4
Identities = 3/21 (14%), Positives = 7/21 (33%)
Query: 31 CQTPTLGFCVERHDKIRTFKP 51
+ G CV ++ +
Sbjct: 60 SMSDKKGICVADPFEVTVMQD 80
>1fep_A FEPA, ferric enterobactin receptor; outer membrane, iron transport,
transport, TONB, signal, membrane protein; 2.40A
{Escherichia coli K12} SCOP: f.4.3.3
Length = 724
Score = 24.2 bits (52), Expect = 4.9
Identities = 10/59 (16%), Positives = 20/59 (33%), Gaps = 2/59 (3%)
Query: 5 LKLNLKEADYQGKYG-DLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN 62
LN +Q + + + YG Q + + T + PY ++ L+
Sbjct: 605 YTLNST-LSWQAREDLSMQTTFTWYGKQQPKKYNYKGQPAVGPETKEISPYSIVGLSAT 662
>1e4e_A Vancomycin/teicoplanin A-type resistance protein; ligase, cell
WALL, antibiotic resistance, membrane, peptidog
synthesis; HET: ADP PHY; 2.5A {Enterococcus faecium}
SCOP: c.30.1.2 d.142.1.1 PDB: 1e4e_B*
Length = 343
Score = 23.7 bits (52), Expect = 5.3
Identities = 2/16 (12%), Positives = 7/16 (43%)
Query: 11 EADYQGKYGDLDASLI 26
+ + + G +A +
Sbjct: 244 HQEVEPEKGSENAVIT 259
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
0.320 0.142 0.456
Gapped
Lambda K H
0.267 0.0483 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,080,948
Number of extensions: 47943
Number of successful extensions: 130
Number of sequences better than 10.0: 1
Number of HSP's gapped: 130
Number of HSP's successfully gapped: 13
Length of query: 69
Length of database: 6,701,793
Length adjustment: 39
Effective length of query: 30
Effective length of database: 5,612,874
Effective search space: 168386220
Effective search space used: 168386220
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 (21.7 bits)
S2: 51 (24.0 bits)