RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14379
(120 letters)
>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 = 31.4 bits (70), Expect = 0.051
Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 15/68 (22%)
Query: 47 NDLQNLSP-----EEQEKQKAEWTQELARVEEEINTL-------KHVLASKTKTAQDLKK 94
ND Q + + + + EL R + + + K +A + ++
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQALLEL-RPAKNV-LIDGVLGSGKTWVALDVCLSYKVQC 178
Query: 95 KLGFTV-W 101
K+ F + W
Sbjct: 179 KMDFKIFW 186
Score = 30.6 bits (68), Expect = 0.095
Identities = 23/112 (20%), Positives = 38/112 (33%), Gaps = 30/112 (26%)
Query: 13 KCCLEMQDVLTIIRSFHVVGEEANN---LDL----SPDSGINDLQNL----SPEEQEKQK 61
K + L + S+ V + L+L SP++ + LQ L P +
Sbjct: 163 KTWV----ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218
Query: 62 AEWTQELARVEEEINTLKHVLASKT-KTA-------QDLKKKLGFTVWKEFN 105
+L R+ L+ +L SK + Q+ K W FN
Sbjct: 219 HSSNIKL-RIHSIQAELRRLLKSKPYENCLLVLLNVQNAK------AWNAFN 263
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 30.0 bits (68), Expect = 0.17
Identities = 9/59 (15%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L++L+ E+ + + E + + ++ L + + +L K+F D+
Sbjct: 690 LRHLAKLEEMEIRHE----QDELSAKAAIIREQLENPESLKNLIISELK-EDAKKFGDE 743
>3u24_A Putative lipoprotein; COG4805, DUF885, structural genomics,
PSI-biology, midwest C structural genomics, MCSG, lipid
BIND protein; 2.25A {Shewanella oneidensis}
Length = 572
Score = 29.9 bits (67), Expect = 0.19
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 8/44 (18%)
Query: 38 LDLSPDS----GIND----LQNLSPEEQEKQKAEWTQELARVEE 73
LSP G + L+ + K A + A++++
Sbjct: 37 WQLSPTWALYSGKHVNDGYLEIPDEAGRVKTLAFVKAQQAKLKQ 80
>1zvu_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling,
decatenation, DNA bindi topology; 3.00A {Escherichia
coli}
Length = 716
Score = 29.9 bits (68), Expect = 0.20
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L++L+ E+ K + E + +E+E + L+ +LAS+ K LKK+L + + DD
Sbjct: 396 LRHLAKLEEMKIRGE----QSELEKERDQLQGILASERKMNNLLKKELQ-ADAQAYGDD 449
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 29.7 bits (67), Expect = 0.22
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 33 EEANNLDLSPDSGINDLQNLSPE--EQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQ 90
E+ NNL+++ + L++ E++ T + ++EEI L+ L +
Sbjct: 949 EKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKK 1008
Query: 91 DLKKKL 96
+++
Sbjct: 1009 TIEEWA 1014
Score = 25.5 bits (56), Expect = 6.0
Identities = 9/62 (14%), Positives = 22/62 (35%), Gaps = 5/62 (8%)
Query: 58 EKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKNVKE 117
E + + +++ +E +L + + T +KL + + L S + K
Sbjct: 927 ENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTETEKL-----RSDVERLRMSEEEAKN 981
Query: 118 TQ 119
Sbjct: 982 AT 983
>3iuk_A Uncharacterized protein; PF05960.1, DUF885, M32
carboxypeptidase-like fold, PSI, MCSG structural
genomics, protein structure initiative; 1.85A
{Arthrobacter aurescens}
Length = 562
Score = 29.2 bits (65), Expect = 0.34
Identities = 7/44 (15%), Positives = 13/44 (29%), Gaps = 8/44 (18%)
Query: 38 LDLSPDS----GIND----LQNLSPEEQEKQKAEWTQELARVEE 73
++L+P G+ Q+ SP L +
Sbjct: 29 IELNPSFATTLGLPGHETEYQDYSPAGAAAHAEATRLALEALAG 72
>1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural
genomics/proteomics INIT RSGI, structural genomics; HET:
SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1
Length = 194
Score = 27.9 bits (63), Expect = 0.59
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 44 SGINDLQNLSPEEQEKQKAEWTQ 66
+G+ D L PE +K A+W +
Sbjct: 171 AGLYDRPRLDPELYQKVLADWLR 193
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 28.3 bits (63), Expect = 0.76
Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 55 EEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKN 114
E Q + T+E +EE ++ L LA + + A++L K + +L +K
Sbjct: 993 LIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTKLK--NKHESMISELEVRLKK 1050
Query: 115 VKETQ 119
++++
Sbjct: 1051 EEKSR 1055
Score = 26.0 bits (57), Expect = 3.9
Identities = 10/65 (15%), Positives = 25/65 (38%), Gaps = 5/65 (7%)
Query: 55 EEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKN 114
K+ E ++ ++E++ + K K +DL ++L + +L ++
Sbjct: 1112 NNALKKIRELESHISDLQEDLESEKAARNKAEKQKRDLSEEL-----EALKTELEDTLDT 1166
Query: 115 VKETQ 119
Q
Sbjct: 1167 TATQQ 1171
>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell
division inhibitor, MINC, MINE, cell hydrolase; HET:
ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*
Length = 260
Score = 27.6 bits (62), Expect = 0.84
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 13/67 (19%)
Query: 1 MQNIHIKHPIIPKCCLEMQDVLT--------IIRSFHVVGEEANNLDLSPDSGINDLQNL 52
++N+ + + + +V+ +I+ + NL + P S D L
Sbjct: 43 LRNLDLIMGCERRVVYDFVNVIQGDATLNQALIK-----DKRTENLYILPASQTRDKDAL 97
Query: 53 SPEEQEK 59
+ E K
Sbjct: 98 TREGVAK 104
>2inr_A DNA topoisomerase 4 subunit A; topoisomerase II fold; HET: DNA;
2.80A {Staphylococcus aureus}
Length = 514
Score = 27.1 bits (61), Expect = 1.5
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L L+ + + E +E I L+H+L + +K++L + K+F +
Sbjct: 448 LYRLTNTDIVALEGE----HKELEALIKQLRHILDNHDALLNVIKEEL-NEIKKKFKSE 501
>1urj_A Major DNA-binding protein; SSB, ICP8, HSV-1, DNA replication,
zinc-finger, nuclear protein.; 3.0A {Human herpesvirus
1} SCOP: e.58.1.1
Length = 1136
Score = 27.0 bits (59), Expect = 1.7
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 11 IPKCCL--EMQDVLTIIRSFHVVGEEANNLDLSPDS 44
+P L E + + I+ F + N ++L+P++
Sbjct: 852 LPARLLSREDIETIAFIKKFSLDYGAINFINLAPNN 887
>2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV,
GRAM-positive bacteria, quinolone target, DNA binding,
DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae}
PDB: 3foe_A* 3fof_A* 3k9f_A* 3ksa_A* 3ksb_A* 3ltn_A*
3rad_A* 3rae_A* 3raf_A*
Length = 496
Score = 26.7 bits (60), Expect = 2.1
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L L+ + + E A + E+I L ++ + +KK+L V K+F
Sbjct: 424 LYRLTNTDVVVLQEE----EAELREKIAMLAAIIGDERTMYNLMKKEL-REVKKKFATP 477
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.7 bits (58), Expect = 2.1
Identities = 10/67 (14%), Positives = 27/67 (40%), Gaps = 9/67 (13%)
Query: 54 PEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVW-KEFNDDLTQSI 112
PE K + E + L ++ ++ + K +DL++ W + ++ + ++
Sbjct: 84 PESIRKWREEQRKRLQELDAASKVMEQEW--REKAKKDLEE------WNQRQSEQVEKNK 135
Query: 113 KNVKETQ 119
N +
Sbjct: 136 INNRIAD 142
>1g9g_A Cellulase CEL48F; processive-endo, hydrolase; 1.90A {Clostridium
cellulolyticum} SCOP: a.102.1.2 PDB: 1f9o_A* 1fbo_A*
1fce_A* 1fae_A 1fbw_A* 1f9d_A* 2qno_A* 1g9j_A*
Length = 629
Score = 26.4 bits (58), Expect = 2.4
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 62 AEWTQELARVEEEINTLKHVLA-SKTKTAQDLKKKLGFTVWKEFNDDL 108
+ +L NTL + A S +T++ +KL +W ++D
Sbjct: 489 VNYGTDLGCASSLANTLTYYAAKSGDETSRQNAQKLLDAMWNNYSDSK 536
>3lpx_A GYRA, DNA gyrase, A subunit; topoisomraseii, ATP-binding,
isomerase, nucleo binding; HET: DNA; 2.60A {Colwellia
psychrerythraea} PDB: 2wl2_A* 2y3p_A* 3nuh_A* 1ab4_A
Length = 500
Score = 26.4 bits (59), Expect = 2.5
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L LS E +K E + + I L H+LA+ + + + ++L + EF D+
Sbjct: 433 LYKLSGMEHDK----ILSEYKALLDLIAELMHILATPARLMEVICEEL-VAIRDEFGDE 486
>3ilw_A DNA gyrase subunit A; DNA topology, topoisomerase, antibiotic
resistance, breakage-reunion domain, struct genomics;
HET: DNA; 1.60A {Mycobacterium tuberculosis} PDB:
3ifz_A*
Length = 470
Score = 26.3 bits (59), Expect = 2.7
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L+ L+ E+++ + LA++E EI L+ +LA + ++ +L + DD
Sbjct: 410 LRRLAALERQRIIDD----LAKIEAEIADLEDILAKPERQRGIVRDELA-EIVDRHGDD 463
>1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying
enzyme, topological knot; 1.85A {Aquifex aeolicus}
Length = 211
Score = 26.0 bits (58), Expect = 3.0
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 44 SGINDLQNLSPEEQEKQKAEWTQ-ELARV 71
G+ +LS EE +K +W ++ +
Sbjct: 175 KGMYSRPSLSEEEIQKILKKWAYEDVIKE 203
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xct_B* 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 26.1 bits (58), Expect = 3.2
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 49 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 107
L+ L+ E++K +AE + I+ L+ +LA + Q ++ +L + F DD
Sbjct: 631 LRRLTGLERDKIEAE----YNELLNYISELETILADEEVLLQLVRDELT-EIRDRFGDD 684
>2faf_A Phosphoenolpyruvate carboxykinase; pepck, phosphoryl transfer,
lyase; HET: 20S EPE 1PE; 1.70A {Gallus gallus} PDB:
2fah_A* 2qzy_A*
Length = 608
Score = 25.5 bits (55), Expect = 5.3
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 48 DLQNLSPEEQEKQ----KAEWTQELARVEE 73
DL L + + K W +E ++ E
Sbjct: 551 DLGGLPGVDYSQLFPMEKGFWEEECRQLRE 580
>3f79_A Probable two-component response regulator; adaptor, signaling
protein; 2.80A {Pseudomonas aeruginosa} PDB: 3es2_A
Length = 255
Score = 25.3 bits (56), Expect = 6.0
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 78 LKHVLASKTKTAQDLKKKLGFTVWKEFNDDLT 109
L +A+ T L++ G E DD+
Sbjct: 215 LPEQVAAAGGTLDGLRQVFGLANLAEMPDDIA 246
>3eq2_A Probable two-component response regulator; adaptor sigmas,
signaling protein; 3.40A {Pseudomonas aeruginosa} PDB:
3f7a_A
Length = 394
Score = 25.2 bits (55), Expect = 6.5
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 78 LKHVLASKTKTAQDLKKKLGFTVWKEFNDDLT 109
L +A+ T L++ G E DD+
Sbjct: 354 LPEQVAAAGGTLDGLRQVFGLANLAEMPDDIA 385
>2jjq_A Uncharacterized RNA methyltransferase pyrab10780; metal-binding,
tRNA methyltransferase, S-adenosyl-L-methionine, iron,
4Fe-4S, iron-sulfur; HET: SAH; 1.8A {Pyrococcus abyssi}
PDB: 2vs1_A*
Length = 425
Score = 24.8 bits (55), Expect = 8.6
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 48 DLQNLSPEEQEKQKAEWTQELARVEEEI 75
LQ+L+ + Q + K + + + E E+
Sbjct: 91 TLQHLNYDYQLEFKRKKLKRILGFEVEV 118
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 24.8 bits (54), Expect = 9.0
Identities = 6/43 (13%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 85 KTKTAQDLKKKLGFTVWK-------EFNDDLTQSIKNVKETQV 120
KTK ++ G + + +++ +S +N++ ++
Sbjct: 186 KTKDFIAAMQRWGLDPAEKSLFFLMDLVENVEKSGRNIRTLKL 228
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
0.312 0.129 0.364
Gapped
Lambda K H
0.267 0.0509 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,755,004
Number of extensions: 90463
Number of successful extensions: 275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 270
Number of HSP's successfully gapped: 70
Length of query: 120
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,412,271
Effective search space: 167666298
Effective search space used: 167666298
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 (23.9 bits)