RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17596
(105 letters)
>2y69_G Cytochrome C oxidase polypeptide 6A2; electron transport, complex
IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK
PGV DMU; 1.95A {Bos taurus}
Length = 97
Score = 116 bits (291), Expect = 1e-35
Identities = 39/94 (41%), Positives = 49/94 (52%), Gaps = 7/94 (7%)
Query: 14 STSPAMKSAAGN---PDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKR 70
S S + SAA + WR LT+ ALP AL + +L H RP F+
Sbjct: 7 SLSRGLASAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHS----GHRERPAFIPY 62
Query: 71 EYLYIRNRRFPWGDGNHSLFHNKHVNALPEGYEE 104
+L IR + F WGDGNH+ FHN VN LP GYE+
Sbjct: 63 HHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYEK 96
>1v54_G Cytochrome C oxidase polypeptide VIA-heart; oxidoreductase; HET:
FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos
taurus} SCOP: f.23.2.1 PDB: 1v55_G* 2dyr_G* 2dys_G*
2eij_G* 2eik_G* 2eil_G* 2eim_G* 2ein_G* 2zxw_G* 3abk_G*
3abl_G* 3abm_G* 3ag1_G* 3ag2_G* 3ag3_G* 3ag4_G* 3asn_G*
3aso_G* 2occ_G* 1oco_G* ...
Length = 85
Score = 115 bits (290), Expect = 1e-35
Identities = 34/87 (39%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 18 AMKSAAGNPDAVKLWRNLTYFGALPCCALVGVYVYLEHQAEEEHHVRPEFVKREYLYIRN 77
+ + WR LT+ ALP AL + +L H RP F+ +L IR
Sbjct: 2 SAAKGDHGGTGARTWRFLTFGLALPSVALCTLNSWLHS----GHRERPAFIPYHHLRIRT 57
Query: 78 RRFPWGDGNHSLFHNKHVNALPEGYEE 104
+ F WGDGNH+ FHN VN LP GYE+
Sbjct: 58 KPFSWGDGNHTFFHNPRVNPLPTGYEK 84
>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA
binding, DNA repair, mismatch recognition; HET: DNA ADP;
2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12
c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A*
1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*
Length = 800
Score = 26.7 bits (60), Expect = 1.8
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 49 VYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFP 81
V V L +A ++ P F+ + + I R P
Sbjct: 554 VLVNLAERAYTLNYTCPTFIDKPGIRITEGRHP 586
>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 = 26.4 bits (57), Expect = 2.2
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 50 YVYLEHQAEEEHHVRPEFVKREYLYIRNRRFPWGDGNHSLFHNKHVN 96
Y +L + E +P + R Y+ R+R + D +F +V+
Sbjct: 91 YKFLMSPIKTEQR-QPSMMTRMYIEQRDRL--YNDN--QVFAKYNVS 132
>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase;
ssgcid, seattle structural genomics center for in
disease; HET: FK5; 1.50A {Burkholderia pseudomallei}
PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A*
1euv_B 3v60_A 3v61_A 3v62_A*
Length = 209
Score = 25.2 bits (55), Expect = 4.0
Identities = 9/46 (19%), Positives = 12/46 (26%)
Query: 59 EEHHVRPEFVKREYLYIRNRRFPWGDGNHSLFHNKHVNALPEGYEE 104
HH VK E + DG+ +F E
Sbjct: 3 HHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLME 48
>1k20_A Manganese-dependent inorganic pyrophosphatase; family II ppase,
binuclear metal centre, hydrolas; 1.50A {Streptococcus
gordonii} SCOP: c.107.1.1 PDB: 1wpp_A 2enx_A* 1i74_A
Length = 310
Score = 25.1 bits (55), Expect = 5.7
Identities = 8/23 (34%), Positives = 9/23 (39%), Gaps = 2/23 (8%)
Query: 61 HHVRPEFVKREYLYIRNRRFPWG 83
HH F LY+R P G
Sbjct: 98 HHRVANFETANPLYMRLE--PVG 118
>3a2b_A Serine palmitoyltransferase; vitamin B6-dependent enzyme fold type
I, acyltransferase, PY phosphate; HET: PLP; 2.30A
{Sphingobacterium multivorum}
Length = 398
Score = 24.8 bits (55), Expect = 6.8
Identities = 11/37 (29%), Positives = 13/37 (35%), Gaps = 11/37 (29%)
Query: 13 FSTSPAMKSAAGNPDAV-----------KLWRNLTYF 38
FS S S A A+ KLW+N Y
Sbjct: 271 FSASMTPASVASTLKALEIIQNEPEHIEKLWKNTDYA 307
>1vlo_A Aminomethyltransferase; NP417381, tetrahydrofolat dependent) of
glycine cleavage system, structural genomics, protein
structure initiative; HET: MSE; 1.70A {Escherichia coli
K12} SCOP: b.44.2.1 d.250.1.1 PDB: 3a8j_A* 3a8i_A*
3a8k_A*
Length = 381
Score = 24.8 bits (55), Expect = 7.1
Identities = 8/19 (42%), Positives = 8/19 (42%)
Query: 25 NPDAVKLWRNLTYFGALPC 43
N A WR L G PC
Sbjct: 213 NEKAADFWRALVEAGVKPC 231
>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch
recognition, mismatched unpaired DNA binding protein-DNA
complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B*
3thy_B* 3thz_B*
Length = 918
Score = 24.9 bits (55), Expect = 7.7
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 57 AEEEHHVRPEFVKREYLYIRNRRFP 81
A++ + RP + + I+N R P
Sbjct: 625 AKQGDYCRPTVQEERKIVIKNGRHP 649
>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein,
mostly mixed alpha-beta structures, one domain is
entirely helical; HET: DNA; 2.20A {Thermus aquaticus}
SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A*
1fw6_A* 1ewr_A*
Length = 765
Score = 24.4 bits (54), Expect = 9.4
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 49 VYVYLEHQAEEEHHVRPEFVKREYLYIRNRRFP 81
VY L A +VRP F + L IR R P
Sbjct: 529 VYAALAEVAVRYGYVRPRFG--DRLQIRAGRHP 559
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 0.136 0.438
Gapped
Lambda K H
0.267 0.0481 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,748,200
Number of extensions: 94152
Number of successful extensions: 142
Number of sequences better than 10.0: 1
Number of HSP's gapped: 140
Number of HSP's successfully gapped: 15
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
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 (24.0 bits)