RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780399|ref|YP_003064812.1| DNA mismatch repair protein
[Candidatus Liberibacter asiaticus str. psy62]
(594 letters)
>gnl|CDD|178860 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 698 bits (1805), Expect = 0.0
Identities = 255/622 (40%), Positives = 379/622 (60%), Gaps = 34/622 (5%)
Query: 1 MKIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNG 60
M I+ L ++ NQIAAGE++ERP+ +KEL+EN+LDA ++R++ I GG ++ DNG
Sbjct: 1 MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNG 60
Query: 61 FGMTSEEIPMAVQRHCTSKIS--DDFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTG 118
G++ E++ +A+ RH TSKI+ DD I T GFRGEALPSI +VS LTL SR G
Sbjct: 61 CGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEG 120
Query: 119 AQIAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAIA 178
QI G +I V+P A GT +EVRDLFF PAR FLKSE+ E I DV+ R+A+A
Sbjct: 121 WQIVYEGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKTELGHIDDVVNRLALA 180
Query: 179 YPKVSFTFSTIKSNRYKMNFQ-STNGNFPERISQVIGEDFINNAVELNEKSNEITLQGYT 237
+P V+FT + N K+ Q G +R++ ++G +F NA+ ++ + ++ L GY
Sbjct: 181 HPDVAFTLT---HNG-KLVLQTRGAGQLLQRLAAILGREFAENALPIDAEHGDLRLSGYV 236
Query: 238 GIPTFNRGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQVDV 297
G+PT +R N + Y+F+NGR V+DK + IR AY + +P GRYP VL LE+DP QVDV
Sbjct: 237 GLPTLSRANRDYQYLFVNGRYVRDKLLNHAIRQAYHDLLPRGRYPAFVLFLELDPHQVDV 296
Query: 298 NVHPAKSYIRFRNPTIIRNFIIQSIQKAINKKGISTSSVLSKKMISSFHQDNAPKTHLPK 357
NVHPAK +RFR+ ++ + I+Q+IQ+A+ + G+ ++ + +++ + P P
Sbjct: 297 NVHPAKHEVRFRDERLVHDLIVQAIQEALAQSGLIPAAAGANQVLEPAEPEPLPLQQTPL 356
Query: 358 YA---------------TSLTNTQEKLFLQENRLSTNDLLPSDDPTYSED---------- 392
YA +QE+ ++N L N S +
Sbjct: 357 YASGSSPPASSPSSAPPEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAAAPAAAP 416
Query: 393 NDPVEESEATHYQLGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKI 452
EA + LG A Q+H YI+++ DGL +VDQHAAHERL++E+++ +
Sbjct: 417 EPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQHAAHERLLYEQLKDKLAEVGL 476
Query: 453 TSQTLLTPEIIDLLEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQL 512
SQ LL P +++L E E + EH E L RLG++ E FGPN+ A+RE+PA+L ++ + +L
Sbjct: 477 ASQPLLIPLVLELSEDEADRLEEHKELLARLGLELEPFGPNSFAVREVPALLGQQELEEL 536
Query: 513 LRDIIDEIIDSSTTYTLQDRIENILATMACYGSIRSGRKMQSIEMNRLLREMEKNPNSSQ 572
+RD++DE+ + + TL++R +LATMAC+G+IR+GR++ EMN LLR++E N
Sbjct: 537 IRDLLDELAEEGDSDTLKER--ELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGT 594
Query: 573 CNHGRPTFIKLKLSDIEKLFGR 594
C HGRPT+I+L LSD+EKLF R
Sbjct: 595 CPHGRPTYIELSLSDLEKLFKR 616
>gnl|CDD|161941 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in
this family for which the functions are known are
involved in the process of generalized mismatch repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University).
Length = 312
Score = 299 bits (769), Expect = 1e-81
Identities = 126/312 (40%), Positives = 182/312 (58%), Gaps = 5/312 (1%)
Query: 1 MKIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNG 60
M I+ L +++N+IAAGE+IERP+ +KEL+ENSLDA ++R++ I GG +++DNG
Sbjct: 1 MTIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNG 60
Query: 61 FGMTSEEIPMAVQRHCTSKISD--DFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNN-T 117
G+ E++P+A +RH TSKI D I T GFRGEAL SI +VS LT+ ++ +
Sbjct: 61 SGIDKEDLPLACERHATSKIQSFEDLERIETLGFRGEALASISSVSRLTITTKTSAADGL 120
Query: 118 GAQIAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAI 177
Q + G I ++P GT VEVRDLF+ +P R FLKS + E I D++ R A+
Sbjct: 121 AWQALLEGGMIEEIKPAPRPVGTTVEVRDLFYNLPVRRKFLKSPKKEFRKILDLLNRYAL 180
Query: 178 AYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFINNAVELNE-KSNEITLQGY 236
+P VSF+ + +++ + RI V G ++ L E + ++ L+G+
Sbjct: 181 IHPDVSFSLTHDGKKVLQLSTKPNQSLKERRIRSVFGTAVLSKLFPLLEWEDGDLQLEGF 240
Query: 237 TGIPTFNRGNA-NQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQV 295
P R ++FINGR V+ K +L IR Y E +P G+YPV VL LEIDP V
Sbjct: 241 ISEPNVTRSRRSGWQFLFINGRPVELKLLLKAIREVYHEYLPKGQYPVFVLNLEIDPELV 300
Query: 296 DVNVHPAKSYIR 307
DVNVHP K +R
Sbjct: 301 DVNVHPDKKEVR 312
>gnl|CDD|149660 pfam08676, MutL_C, MutL C terminal dimerization domain. MutL and
MutS are key components of the DNA repair machinery that
corrects replication errors. MutS recognizes mispaired
or unpaired bases in a DNA duplex and in the presence of
ATP, recruits MutL to form a DNA signaling complex for
repair. The N terminal region of MutL contains the
ATPase domain and the C terminal is involved in
dimerization.
Length = 142
Score = 172 bits (438), Expect = 3e-43
Identities = 62/147 (42%), Positives = 101/147 (68%), Gaps = 6/147 (4%)
Query: 406 LGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKITSQTLLTPEIIDL 465
LG A Q+H YI+++ DGL +VDQHAAHER+++EK++ + SQ LL P ++L
Sbjct: 2 LGKALGQVHGTYILAENEDGLYLVDQHAAHERILYEKLKSKLKE-GLQSQPLLIPLTLEL 60
Query: 466 LEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIIDSST 525
E AL+ EH E L RLG + E FGPN++ +R +PA+L ++N+ +L+R+++DE+ +
Sbjct: 61 SPEEAALLEEHKELLARLGFELEEFGPNSLIVRSVPALLRQQNLEELIRELLDELAEKG- 119
Query: 526 TYTLQDRIENILATMACYGSIRSGRKM 552
++ +E +LATMAC+ +IR+GR++
Sbjct: 120 ----EELLEELLATMACHSAIRAGRRL 142
>gnl|CDD|129086 smart00853, MutL_C, MutL C terminal dimerisation domain. MutL and
MutS are key components of the DNA repair machinery that
corrects replication errors. MutS recognises mispaired
or unpaired bases in a DNA duplex and in the presence of
ATP, recruits MutL to form a DNA signaling complex for
repair. The N terminal region of MutL contains the
ATPase domain and the C terminal is involved in
dimerisation.
Length = 136
Score = 150 bits (380), Expect = 1e-36
Identities = 52/137 (37%), Positives = 92/137 (67%), Gaps = 2/137 (1%)
Query: 406 LGIACAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKIT-SQTLLTPEIID 464
LG Q+H YI++++ DGLV++DQHAAHER+++E+++ + + SQ LL P I++
Sbjct: 1 LGRVLGQVHGTYILAESEDGLVLIDQHAAHERILYEQLKAKLQAGLLEKSQPLLIPVILE 60
Query: 465 LLEGECALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIIDSS 524
L E AL+ EH E L RLG + E FG ++ +R +PA+L ++N+ +L+ +++D + +
Sbjct: 61 LSPEEAALLEEHQELLARLGFELEIFGGQSVILRSVPALLRQQNLQELIPELLDLLAEGG 120
Query: 525 TTYTLQDRIENILATMA 541
+T +L +E +LA++A
Sbjct: 121 ST-SLPQLVEALLASLA 136
>gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 38.7 bits (91), Expect = 0.005
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 9/56 (16%)
Query: 25 IAIKELIENSLDA-ESS------RVETVIAGGGKSFFQIT--DNGFGMTSEEIPMA 71
+KEL++NSLDA E + ++E GK +++T DNG G+ EEIP
Sbjct: 39 TTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVEDNGPGIPPEEIPKV 94
>gnl|CDD|184494 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 36.8 bits (86), Expect = 0.014
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 14/58 (24%)
Query: 23 PSIAIKELIENSLDAESSR------------VETVIAGGGKSFFQITDNGFGMTSEEI 68
P + ++EL++N++DA ++R +E AGGG + DNG G+T EE+
Sbjct: 24 PRVYVRELLQNAVDAITARRALDPTAPGRIRIELTDAGGGT--LIVEDNGIGLTEEEV 79
>gnl|CDD|128669 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 31.9 bits (73), Expect = 0.44
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 26 AIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEIP 69
+ L++N++ E R+ T+ G + DNG G+ E++
Sbjct: 9 VLSNLLDNAIKYTPEGGRITVTLERDGDHLEITVEDNGPGIPPEDLE 55
>gnl|CDD|162176 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase).
Length = 488
Score = 30.9 bits (70), Expect = 0.91
Identities = 18/54 (33%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 25 IAIKELIENSLDAESS-------RVETVIAGGGKSFFQITDNGFGMTSEEIPMA 71
I EL+ NSLDA +VE G + DNG G+ E IP
Sbjct: 31 TVIHELVTNSLDACEEAGILPDIKVEIEKIGKDHYKVTVEDNGPGIPEEYIPKV 84
>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
Length = 974
Score = 30.5 bits (69), Expect = 1.3
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 58 DNGFGMTSEEIPMAVQRHCTSKISDDFS-NIHTFGFRGEALPSIGAVSHLTLMSRPPQN- 115
D G ++ E+ A + S I+ + I F RG ++ G HL ++S+PP
Sbjct: 631 DGGRLTSAWELYKAQE--RLSNIARQYGVEIRFFHGRGGSVSRGGGPQHLAILSQPPNTI 688
Query: 116 NTGAQIAISGEKISS 130
+ +I I GE I+
Sbjct: 689 KSYLRITIQGETITQ 703
>gnl|CDD|163071 TIGR02916, PEP_his_kin, putative PEP-CTERM system histidine kinase.
Members of this protein family have a novel N-terminal
domain, a single predicted membrane-spanning helix, and
a predicted cystosolic histidine kinase domain. We
designate this protein PrsK, and its companion
DNA-binding response regulator protein (TIGR02915) PrsR.
These predicted signal-transducing proteins appear to
enable enhancer-dependent transcriptional activation.
The prsK gene is often associated with exopolysaccharide
biosynthesis genes.
Length = 679
Score = 29.7 bits (67), Expect = 2.3
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 21 ERPSIAIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEI 68
ER + L++N+L+A RV V G + +I D+G GM+ I
Sbjct: 578 ERLERVLGHLVQNALEATPGEGRVAIRVERECGAARIEIEDSGCGMSPAFI 628
>gnl|CDD|184870 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional.
Length = 795
Score = 29.0 bits (65), Expect = 3.3
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%)
Query: 26 AIKELIENSLDAESSR-------VETVIAGGGKSF-FQITDNGFGMTSEEIP 69
A+KE ++N+LDA VE I G + + DNG G+T E+IP
Sbjct: 50 AVKEAVDNALDATEEAGILPDIYVE--IEEVGDYYRLVVEDNGPGITKEQIP 99
>gnl|CDD|179965 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 28.9 bits (66), Expect = 3.4
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 17/61 (27%)
Query: 25 IAIKELIENSLDA------ESSRVETVIAGGGK-----SF------FQITDNGFGMTSEE 67
I ++ELI N+ DA E+ + G G SF I+DNG GMT EE
Sbjct: 29 IFLRELISNASDAIDKLRFEALTDPALYEGDGDLKIRISFDKEARTLTISDNGIGMTREE 88
Query: 68 I 68
+
Sbjct: 89 V 89
>gnl|CDD|181750 PRK09277, PRK09277, aconitate hydratase; Validated.
Length = 888
Score = 28.6 bits (65), Expect = 4.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 322 IQKAINKKGISTSSVLS 338
I+KAIN + ++VLS
Sbjct: 510 IEKAINDNDLVVTAVLS 526
>gnl|CDD|179380 PRK02190, PRK02190, agmatinase; Provisional.
Length = 301
Score = 27.9 bits (63), Expect = 7.3
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 16/64 (25%)
Query: 489 RFGPNAIAIREIPAILSKKNIP-QLLRDIIDE--IID-----------SSTTYTLQDRIE 534
RFGP AIR+ L+ ++ D+ + ++D L+ E
Sbjct: 47 RFGPA--AIRQASTNLAWEDRRYPWNFDLFERLAVVDYGDLVFDYGDAEDFPEALEAHAE 104
Query: 535 NILA 538
ILA
Sbjct: 105 KILA 108
>gnl|CDD|185569 PTZ00345, PTZ00345, glycerol-3-phosphate dehydrogenase;
Provisional.
Length = 365
Score = 28.1 bits (63), Expect = 7.6
Identities = 9/37 (24%), Positives = 16/37 (43%)
Query: 486 KAERFGPNAIAIREIPAILSKKNIPQLLRDIIDEIID 522
+ +A AI I+ + P L D+I+E +
Sbjct: 115 ENNNLKKHARAISLTKGIIVENGKPVLCSDVIEEELG 151
>gnl|CDD|161754 TIGR00189, tesB, acyl-CoA thioesterase II. Subunit: homotetramer.
Length = 271
Score = 27.7 bits (62), Expect = 9.0
Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 5/61 (8%)
Query: 315 RNFIIQSIQKAINKKGISTSSVLSKKMISSF-HQDNAPKTHLPK----YATSLTNTQEKL 369
R+FI + ++ + K I T + S HQ PK P+ L
Sbjct: 74 RSFITRRVKAVQHGKTIFTLQASFQAEESGIEHQSTMPKVPAPESELPRENQLATKYPAT 133
Query: 370 F 370
Sbjct: 134 L 134
>gnl|CDD|177398 PHA02569, 39, DNA topoisomerase II large subunit; Provisional.
Length = 602
Score = 27.4 bits (61), Expect = 10.0
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 11/57 (19%)
Query: 162 QVETNLITDVIRRMAIAYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFI 218
Q ++I D ++ +A+ +P + FTF N + +G F + Q G+D I
Sbjct: 196 QQYLDIILDRLQTLAVVFPDIKFTF----------NGKKVSGKFKKYAKQ-FGDDTI 241
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.318 0.134 0.372
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 9,676,415
Number of extensions: 638959
Number of successful extensions: 1319
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1304
Number of HSP's successfully gapped: 28
Length of query: 594
Length of database: 5,994,473
Length adjustment: 99
Effective length of query: 495
Effective length of database: 3,855,281
Effective search space: 1908364095
Effective search space used: 1908364095
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.0 bits)