RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5794
(152 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 = 37.5 bits (86), Expect = 0.001
Identities = 22/154 (14%), Positives = 56/154 (36%), Gaps = 37/154 (24%)
Query: 2 EEEINTLKHVLASKTKTAQ-----DLKKKLGFTVWKEFNDDLTQS----IKNVKETQVRD 52
+EEI H++ SK + + ++F +++ + + + +T+ R
Sbjct: 48 KEEI---DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ 104
Query: 53 IHIVILRFVIPGEEANNLDLSPDSGINDLQNLSP-----EEQEKQKAEWTQELARVEEEI 107
++ ++ E+ + L ND Q + + + + EL R + +
Sbjct: 105 PSMMTRMYI---EQRDRL-------YNDNQVFAKYNVSRLQPYLKLRQALLEL-RPAKNV 153
Query: 108 NTL-------KHVLASKTKTAQDLKKKLGFTV-W 133
+ K +A + ++ K+ F + W
Sbjct: 154 -LIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186
Score = 32.9 bits (74), Expect = 0.035
Identities = 29/202 (14%), Positives = 58/202 (28%), Gaps = 69/202 (34%)
Query: 9 KHVLASKTKTAQDLKKKLGFTV-WKEF--------------------------NDDLTQS 41
K +A + ++ K+ F + W D + +
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 42 IK-NVKETQVRDIHI----------VILRFVIPGEEANNLDL-------SPDSGIND--- 80
IK + Q + ++L V + N +L + + D
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLS 282
Query: 81 ------------LQNLSPEEQEKQKAEWT----QELARVEEEINTLKHVLASKTKTAQDL 124
L+P+E + ++ Q+L R N + + +++ +D
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI--RDG 340
Query: 125 KKKLGFTVWKEFN-DDLTQSIK 145
WK N D LT I+
Sbjct: 341 LATWDN--WKHVNCDKLTTIIE 360
>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 = 30.2 bits (68), Expect = 0.26
Identities = 28/148 (18%), Positives = 54/148 (36%), Gaps = 27/148 (18%)
Query: 2 EEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKNVKETQVRDIHIVILRFV 61
EE ++ L LA + + A++L K + I ++ ++
Sbjct: 1010 EERVSDLTTNLAEEEEKAKNLTKL---------KNKHESMISELEVRLKKEEKSR----- 1055
Query: 62 IPGEEANNLDLSPDSGINDLQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTA 121
+E + + +DL E + Q AE +LA+ EEE+ L +T
Sbjct: 1056 ---QELEKIKRKLEGESSDLHE-QIAELQAQIAELKAQLAKKEEELQAALARLEDETSQK 1111
Query: 122 QDLKKKLGFTVWKEFNDDLTQSIKNVKE 149
+ KK+ +L I +++E
Sbjct: 1112 NNALKKI---------RELESHISDLQE 1130
Score = 30.2 bits (68), Expect = 0.28
Identities = 24/150 (16%), Positives = 55/150 (36%), Gaps = 16/150 (10%)
Query: 2 EEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDDLTQSIKNVKETQVRDIHIVILRFV 61
E I+ L+ L + K+ Q+L+K ++ + + + + E Q I + +
Sbjct: 1038 ESMISELEVRLKKEEKSRQELEKIK-----RKLEGESSDLHEQIAELQ-AQIAELKAQLA 1091
Query: 62 IPGEEANNLDLSPDSGINDLQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTA 121
EE + + N K+ E ++ ++E++ + K K
Sbjct: 1092 KKEEELQAALARLEDETSQKNNA-----LKKIRELESHISDLQEDLESEKAARNKAEKQK 1146
Query: 122 QDLKKKLGFTVWKEFNDDLTQSIKNVKETQ 151
+DL ++L + +L ++ Q
Sbjct: 1147 RDLSEEL-----EALKTELEDTLDTTATQQ 1171
Score = 27.5 bits (61), Expect = 2.2
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 87 EEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKK 126
E Q + T+E +EE ++ L LA + + A++L K
Sbjct: 993 LIMEDQNNKLTKERKLLEERVSDLTTNLAEEEEKAKNLTK 1032
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 29.6 bits (67), Expect = 0.37
Identities = 9/59 (15%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
L++L+ E+ + + E + + ++ L + + +L K+F D+
Sbjct: 690 LRHLAKLEEMEIRHE----QDELSAKAAIIREQLENPESLKNLIISELK-EDAKKFGDE 743
>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 = 29.5 bits (67), Expect = 0.40
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 61 VIPGEEANNLDLSPDSGINDLQNLSPEEQEK 91
+I + NL + P S D L+ E K
Sbjct: 74 LIKDKRTENLYILPASQTRDKDALTREGVAK 104
>1zvu_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling,
decatenation, DNA bindi topology; 3.00A {Escherichia
coli}
Length = 716
Score = 29.5 bits (67), Expect = 0.48
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
L++L+ E+ K + E + +E+E + L+ +LAS+ K LKK+L + + DD
Sbjct: 396 LRHLAKLEEMKIRGE----QSELEKERDQLQGILASERKMNNLLKKELQ-ADAQAYGDD 449
>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 = 29.2 bits (65), Expect = 0.53
Identities = 8/44 (18%), Positives = 16/44 (36%), Gaps = 8/44 (18%)
Query: 70 LDLSPDS----GIND----LQNLSPEEQEKQKAEWTQELARVEE 105
LSP G + L+ + K A + A++++
Sbjct: 37 WQLSPTWALYSGKHVNDGYLEIPDEAGRVKTLAFVKAQQAKLKQ 80
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 29.3 bits (66), Expect = 0.60
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 65 EEANNLDLSPDSGINDLQNLSPE--EQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQ 122
E+ NNL+++ + L++ E++ T + ++EEI L+ L +
Sbjct: 949 EKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKK 1008
Query: 123 DLKKKL 128
+++
Sbjct: 1009 TIEEWA 1014
>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 = 28.8 bits (64), Expect = 0.84
Identities = 7/44 (15%), Positives = 13/44 (29%), Gaps = 8/44 (18%)
Query: 70 LDLSPDS----GIND----LQNLSPEEQEKQKAEWTQELARVEE 105
++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 = 1.0
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 76 SGINDLQNLSPEEQEKQKAEWTQ 98
+G+ D L PE +K A+W +
Sbjct: 171 AGLYDRPRLDPELYQKVLADWLR 193
>2inr_A DNA topoisomerase 4 subunit A; topoisomerase II fold; HET: DNA;
2.80A {Staphylococcus aureus}
Length = 514
Score = 27.1 bits (61), Expect = 2.7
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
L L+ + + E +E I L+H+L + +K++L + K+F +
Sbjct: 448 LYRLTNTDIVALEGE----HKELEALIKQLRHILDNHDALLNVIKEEL-NEIKKKFKSE 501
>2x0d_A WSAF; GT4 family, transferase; HET: MSE; 2.28A {Geobacillus
stearothermophilus} PDB: 2x0f_A* 2x0e_A*
Length = 413
Score = 27.1 bits (59), Expect = 2.8
Identities = 9/53 (16%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 36 DDLTQSIKNVKETQVRDIHIVILRFVIPGEEANNLDLSPDSGINDLQNLSPEE 88
+ +++K + R + + GE+ ++ L +N L L+ E+
Sbjct: 258 TLIVEALKIFVQKYDRSNE---WKIISVGEKHKDIALGKGIHLNSLGKLTLED 307
>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 = 3.7
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
L L+ + + E A + E+I L ++ + +KK+L V K+F
Sbjct: 424 LYRLTNTDVVVLQEE----EAELREKIAMLAAIIGDERTMYNLMKKEL-REVKKKFATP 477
>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 = 4.5
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
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 = 4.7
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
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 = 5.2
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 76 SGINDLQNLSPEEQEKQKAEWTQ-ELARV 103
G+ +LS EE +K +W ++ +
Sbjct: 175 KGMYSRPSLSEEEIQKILKKWAYEDVIKE 203
>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 = 26.0 bits (57), Expect = 5.7
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 94 AEWTQELARVEEEINTLKHVLA-SKTKTAQDLKKKLGFTVWKEFNDDL 140
+ +L NTL + A S +T++ +KL +W ++D
Sbjct: 489 VNYGTDLGCASSLANTLTYYAAKSGDETSRQNAQKLLDAMWNNYSDSK 536
>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 = 5.9
Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 81 LQNLSPEEQEKQKAEWTQELARVEEEINTLKHVLASKTKTAQDLKKKLGFTVWKEFNDD 139
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 = 25.9 bits (56), Expect = 7.4
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 80 DLQNLSPEEQEKQ----KAEWTQELARVEE 105
DL L + + K W +E ++ E
Sbjct: 551 DLGGLPGVDYSQLFPMEKGFWEEECRQLRE 580
>3eq2_A Probable two-component response regulator; adaptor sigmas,
signaling protein; 3.40A {Pseudomonas aeruginosa} PDB:
3f7a_A
Length = 394
Score = 25.6 bits (56), Expect = 9.0
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 8 LKHVLASKTKTAQDLKKKLGFTVWKEFNDDLT 39
L +A+ T L++ G E DD+
Sbjct: 354 LPEQVAAAGGTLDGLRQVFGLANLAEMPDDIA 385
Score = 25.6 bits (56), Expect = 9.0
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 110 LKHVLASKTKTAQDLKKKLGFTVWKEFNDDLT 141
L +A+ T L++ G E DD+
Sbjct: 354 LPEQVAAAGGTLDGLRQVFGLANLAEMPDDIA 385
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
0.309 0.127 0.345
Gapped
Lambda K H
0.267 0.0800 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,216,399
Number of extensions: 120188
Number of successful extensions: 359
Number of sequences better than 10.0: 1
Number of HSP's gapped: 350
Number of HSP's successfully gapped: 65
Length of query: 152
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,328,508
Effective search space: 290010036
Effective search space used: 290010036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.1 bits)