RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13428
(67 letters)
>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding
loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori}
SCOP: c.37.1.20
Length = 376
Score = 75.0 bits (185), Expect = 3e-18
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 3 LVNPK-IYEYLNKHVVGQEHAKKVLSVAVYNHYKRIYNNISSSPSQSQASAKTQD 56
+ PK + L+ +V+GQE AKKV SVAVYNHYKR+ +Q S +
Sbjct: 9 IPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELE 63
>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+
molecular machine, hexamer, asymmetric,, ATP-BIN
chaperone, metal-binding; HET: ADP; 3.25A {Escherichia
coli} PDB: 3hte_A
Length = 363
Score = 73.4 bits (181), Expect = 1e-17
Identities = 24/43 (55%), Positives = 32/43 (74%), Gaps = 1/43 (2%)
Query: 3 LVNPK-IYEYLNKHVVGQEHAKKVLSVAVYNHYKRIYNNISSS 44
L P I +L+ +V+GQE AKKVL+VAVYNHYKR+ N +S+
Sbjct: 3 LPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSN 45
>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone,
hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*
Length = 310
Score = 55.7 bits (135), Expect = 2e-11
Identities = 11/33 (33%), Positives = 24/33 (72%), Gaps = 1/33 (3%)
Query: 6 PK-IYEYLNKHVVGQEHAKKVLSVAVYNHYKRI 37
P+ I L++H++GQ AK+ +++A+ N ++R+
Sbjct: 6 PREIVSELDQHIIGQADAKRAVAIALRNRWRRM 38
>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent
proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A*
1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E*
1hqy_E* 1ht1_E* 1ht2_E*
Length = 444
Score = 41.6 bits (98), Expect = 2e-06
Identities = 10/30 (33%), Positives = 22/30 (73%)
Query: 7 KIYEYLNKHVVGQEHAKKVLSVAVYNHYKR 36
+I L++H++GQ AK+ +++A+ N ++R
Sbjct: 8 EIVSELDQHIIGQADAKRAVAIALRNRWRR 37
>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop,
rossman fold, AAA+, photosynthesis, metal transport;
2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB:
2x31_G
Length = 350
Score = 27.8 bits (62), Expect = 0.18
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 16 VVGQEHAKKVLSVAV 30
+VGQE K L +
Sbjct: 26 IVGQEDMKLALLLTA 40
>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 = 27.1 bits (59), Expect = 0.34
Identities = 4/33 (12%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 8 IYEYLNKHVVGQEHAKKVLSVAVYNHYKRIYNN 40
Y ++ H+ EH ++ ++ ++ +
Sbjct: 473 FYSHIGHHLKNIEHPER------MTLFRMVFLD 499
>2qdj_A Retinoblastoma-associated protein; cyclin fold, cyclin wedge,
antitumor protein; 2.00A {Homo sapiens}
Length = 304
Score = 25.9 bits (56), Expect = 0.84
Identities = 6/41 (14%), Positives = 16/41 (39%)
Query: 21 HAKKVLSVAVYNHYKRIYNNISSSPSQSQASAKTQDISLME 61
K + A+++ +R I + S S + +++
Sbjct: 101 LKKYDVLFALFSKLERTCELIYLTQPSSSISTEINSALVLK 141
>3c3y_A Pfomt, O-methyltransferase; plant secondary metabolism; HET: SAH;
1.37A {Mesembryanthemum crystallinum}
Length = 237
Score = 25.7 bits (57), Expect = 1.0
Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 2 ILVNPKIYEYLNKHVVG-QEHAKKVLSVAVYNHYKRIYNNISSSPSQSQ 49
+L + ++ +Y+ + V +E L + + +S+SP Q
Sbjct: 14 LLQSEELCQYILRTSVYPREA--GFLKELREANESHPDSYMSTSPLAGQ 60
>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus
thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*
Length = 311
Score = 25.6 bits (57), Expect = 1.1
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 10 EYLNKHVVGQEHAKKVLSVAV 30
E L+K VVGQ+ A + ++ A+
Sbjct: 13 EELHKRVVGQDEAIRAVADAI 33
>1sui_A Caffeoyl-COA O-methyltransferase; rossmann fold,
protein-cofactor-substrate complex; HET: SAH FRE; 2.70A
{Medicago sativa} SCOP: c.66.1.1 PDB: 1sus_A*
Length = 247
Score = 25.4 bits (56), Expect = 1.3
Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 2 ILVNPKIYEYLNKHVVGQ-EHAKKVLSVAVYNHYKRIYNNISSSPSQSQ 49
+L + +Y+Y+ + V EH + + K +N +++S + Q
Sbjct: 23 LLQSDALYQYILETSVFPREH--EAMKELREVTAKHPWNIMTTSADEGQ 69
>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A
{Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20
c.37.1.20
Length = 854
Score = 24.8 bits (55), Expect = 2.2
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 10 EYLNKHVVGQEHAKKVLSVAV 30
E L+K VVGQ+ A + ++ A+
Sbjct: 554 EELHKRVVGQDEAIRAVADAI 574
>2gpy_A O-methyltransferase; structural genomics, PSI, protein structure
initiative, NEW research center for structural
genomics, nysgxrc; HET: MSE; 1.90A {Bacillus
halodurans}
Length = 233
Score = 24.1 bits (53), Expect = 3.3
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 1 MILVNPKIYEYLNKH 15
M L+ ++ YL K
Sbjct: 1 MSLIEERLKHYLEKQ 15
>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding
mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli}
SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*
Length = 758
Score = 23.7 bits (52), Expect = 5.6
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 7 KIYEYLNKHVVGQEHAKKVLSVAV 30
+ + L V GQ+ A + L+ A+
Sbjct: 451 NLGDRLKMLVFGQDKAIEALTEAI 474
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
0.313 0.125 0.336
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 901,396
Number of extensions: 37394
Number of successful extensions: 90
Number of sequences better than 10.0: 1
Number of HSP's gapped: 90
Number of HSP's successfully gapped: 13
Length of query: 67
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,640,795
Effective search space: 163583055
Effective search space used: 163583055
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.3 bits)