RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780399|ref|YP_003064812.1| DNA mismatch repair protein
[Candidatus Liberibacter asiaticus str. psy62]
(594 letters)
>gnl|CDD|30671 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 551 bits (1422), Expect = e-157
Identities = 236/637 (37%), Positives = 371/637 (58%), Gaps = 46/637 (7%)
Query: 2 KIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNGF 61
KIR+L ++NQIAAGE+IERP+ +KEL+ENSLDA ++R++ + GGG ++ DNG
Sbjct: 3 KIRQLPPDLVNQIAAGEVIERPASVVKELVENSLDAGATRIDIEVEGGGLKLIRVRDNGS 62
Query: 62 GMTSEEIPMAVQRHCTSKIS--DDFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTGA 119
G+ E++P+A+ RH TSKI+ +D I T GFRGEAL SI +VS LT+ SR + + G
Sbjct: 63 GIDKEDLPLALLRHATSKIASLEDLFRIRTLGFRGEALASIASVSRLTITSRTAEASEGT 122
Query: 120 QIAISGEKIS-SVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAIA 178
QI G + +V+P A GT VEVRDLF+ PAR FLKSE+ E IT++I R A+A
Sbjct: 123 QIYAEGGGMEVTVKPAAHPVGTTVEVRDLFYNTPARRKFLKSEKTEFGHITELINRYALA 182
Query: 179 YPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFINNAVELNEKSNEITLQGYTG 238
+P +SF+ S R ++ G+ ERI+ V G +F+ NA+ + + ++ L GY
Sbjct: 183 HPDISFSLSHNGKLRIELLKLPGTGDLEERIAAVYGTEFLKNALPIENEHEDLRLSGYVS 242
Query: 239 IPTFNRGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQVDVN 298
+P F R + + Y+F+NGR V+DK + +R AYA+ +P GRYPV VL LE+DP VDVN
Sbjct: 243 LPEFTRASRDYQYLFVNGRPVRDKLLNHALREAYADYLPRGRYPVFVLFLELDPELVDVN 302
Query: 299 VHPAKSYIRFRNPTIIRNFIIQSIQKAINKKGI--------------------------- 331
VHPAK +RF + ++ + I ++I++A+ ++G+
Sbjct: 303 VHPAKKEVRFSDERLVHDLIYEAIKEALAQQGLIPPASVEAPKSASQPLPAFQEPSPLPE 362
Query: 332 -------------STSSVLSKKMISSFHQDNAPKTHLPKYATSLTNTQEKLFLQENRLST 378
S S S +S + + + ++ L+ S
Sbjct: 363 SRIQKSKVAKSGSSKSDAPSIAEPASGASPSPASPSIRPLSKNILPESSPGSLKNEDRSY 422
Query: 379 NDLLPSDDPTY-SEDNDPVEESEATHYQLGIACAQIHQNYIISQTTDGLVIVDQHAAHER 437
+DLL + ++ + + LG A Q+H YI+++ DGLV+VDQHAAHER
Sbjct: 423 DDLLEEPAESEDKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDGLVLVDQHAAHER 482
Query: 438 LIFEKMRQDFNSTKITSQTLLTPEIIDLLEGECALIMEHDEDLHRLGIKAERFGPNAIAI 497
+++EK++ + Q LL P ++L E ++ EH E+L +LG + E FG N++A+
Sbjct: 483 ILYEKLKNEL-GNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIESFGENSVAV 541
Query: 498 REIPAILSKKNIPQLLRDIIDEIIDSSTTYTLQDRIENILATMACYGSIRSGRKMQSIEM 557
R +PA+L K + +L+R+++D++++ L++ +E + ATMAC ++++GR++ + EM
Sbjct: 542 RSVPAMLGKAEVQELIRELLDDLLEGKLK-DLKELLEELAATMACRSAVKAGRELSAEEM 600
Query: 558 NRLLREMEKNPNSSQCNHGRPTFIKLKLSDIEKLFGR 594
N LLR++E PN C HGRPT+I L L+++E+LF R
Sbjct: 601 NALLRDLEACPNPWTCPHGRPTYIVLSLAELERLFKR 637
>gnl|CDD|37190 KOG1979, KOG1979, KOG1979, DNA mismatch repair protein - MLH1
family [Replication, recombination and repair].
Length = 694
Score = 227 bits (580), Expect = 7e-60
Identities = 116/335 (34%), Positives = 186/335 (55%), Gaps = 13/335 (3%)
Query: 2 KIRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNGF 61
KIR+L E ++N+IAAGE+I+RP A+KELIENSLDA S+ ++ ++ GG QI+DNG
Sbjct: 7 KIRRLDEDVVNRIAAGEVIQRPVNALKELIENSLDANSTSIDVLVKDGGLKLLQISDNGS 66
Query: 62 GMTSEEIPMAVQRHCTSKIS--DDFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTGA 119
G+ E++P+ +R TSK++ +D ++ T+GFRGEAL SI V+H+T+ ++ +
Sbjct: 67 GIRREDLPILCERFTTSKLTKFEDLFSLSTYGFRGEALASISHVAHVTVTTKTAEGKCAY 126
Query: 120 QIAIS-GEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSEQVETNLITDVIRRMAIA 178
+ + G+ I++ +P A GTI+ V DLF+ +P R L++ E I D++ R AI
Sbjct: 127 RASYRDGKMIATPKPCAGKQGTIITVEDLFYNMPTRRKALRNHAEEYRKIMDLVGRYAIH 186
Query: 179 YPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGED----FINNAVELNEKSNEITLQ 234
P+VSF+ + S + + + I + G +N + + K + + +
Sbjct: 187 NPRVSFSLRKQGDTVADLR-TSVSCSREDNIRNIYGVSVAKNLLNELSKCDSKLLKFSAE 245
Query: 235 GYTGIPTFNRGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQ 294
GY ++ + +FINGR V+ + + YA +P G +P V L L IDP
Sbjct: 246 GYISNANYS-AKKSILVLFINGRLVESDELRHALEEVYAAYLPKGHHPFVYLSLNIDPEN 304
Query: 295 VDVNVHPAKSYIRFRNPTIIRNFIIQSIQKAINKK 329
VDVNVHP K + F N II+ I + I ++
Sbjct: 305 VDVNVHPTKREVHFLNQEE----IIERICQQIEER 335
>gnl|CDD|144638 pfam01119, DNA_mis_repair, DNA mismatch repair protein, C-terminal
domain. This family represents the C-terminal domain of
the mutL/hexB/PMS1 family. This domain has a ribosomal
S5 domain 2-like fold.
Length = 118
Score = 148 bits (375), Expect = 6e-36
Identities = 49/118 (41%), Positives = 76/118 (64%)
Query: 209 ISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYVFINGRTVQDKFILSTI 268
I+ + G +F N + ++ + + L G+ P +R N + Y+F+NGR V+DK + I
Sbjct: 1 IAAIYGREFAENLLPIDAEDEGLRLSGFISKPELSRSNRDYQYLFVNGRPVRDKLLSHAI 60
Query: 269 RTAYAETIPLGRYPVVVLLLEIDPRQVDVNVHPAKSYIRFRNPTIIRNFIIQSIQKAI 326
R AY + +P GRYPV VL LEIDP VDVNVHPAK +RFR+ + +FI +++++A+
Sbjct: 61 REAYRDLLPKGRYPVAVLFLEIDPELVDVNVHPAKREVRFRDEREVHDFIEEAVREAL 118
>gnl|CDD|48470 cd03482, MutL_Trans_MutL, MutL_Trans_MutL: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to Escherichia coli MutL. EcMutL
belongs to the DNA mismatch repair (MutL/MLH1/PMS2)
family. This transducer domain is homologous to the
second domain of the DNA gyrase B subunit, which is
known to be important in nucleotide hydrolysis and the
transduction of structural signals from the ATP-binding
site to the DNA breakage/reunion regions of the enzymes.
It has been suggested that during initiation of DNA
mismatch repair in E. coli, the mismatch recognition
protein MutS recruits MutL in the presence of ATP. The
MutS(ATP)-MutL ternary complex formed, then recruits the
latent endonuclease MutH. Prokaryotic MutS and MutL are
homodimers..
Length = 123
Score = 138 bits (349), Expect = 5e-33
Identities = 51/120 (42%), Positives = 83/120 (69%)
Query: 207 ERISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYVFINGRTVQDKFILS 266
+R++ ++GEDF A+ ++E++ + L G+ +PTF R A+ Y ++NGR V+DK I
Sbjct: 3 QRLADILGEDFAEQALAIDEEAGGLRLSGWIALPTFARSQADIQYFYVNGRMVRDKLISH 62
Query: 267 TIRTAYAETIPLGRYPVVVLLLEIDPRQVDVNVHPAKSYIRFRNPTIIRNFIIQSIQKAI 326
+R AY++ + GR+P VL LE+DP QVDVNVHPAK +RFR+ ++ +FI +++KA+
Sbjct: 63 AVRQAYSDVLHGGRHPAYVLYLELDPAQVDVNVHPAKHEVRFRDSRLVHDFIYHAVKKAL 122
>gnl|CDD|37189 KOG1978, KOG1978, KOG1978, DNA mismatch repair protein -
MLH2/PMS1/Pms2 family [Replication, recombination and
repair].
Length = 672
Score = 126 bits (318), Expect = 2e-29
Identities = 90/383 (23%), Positives = 160/383 (41%), Gaps = 26/383 (6%)
Query: 3 IRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSFFQITDNGFG 62
I+++ + +++I + ++I A+KEL+ENS+DA ++ ++ + G +++DNG G
Sbjct: 1 IKQIPKDTVHRICSSQVITSLVSAVKELVENSIDAGATAIDIKVKDYGSDSIEVSDNGSG 60
Query: 63 MTSEEIPMAVQRHCTSKISD--DFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTGAQ 120
+++ + +H TSKI D + + T GFRGEAL S+ A+ + + +R G +
Sbjct: 61 ISATDFEGLALKHTTSKIVSFADLAVLFTLGFRGEALSSLCALGDVMISTRSHSAKVGTR 120
Query: 121 IAISGE-KISSVRPVAMNPGTIVEVRDLFFTIPAR-LNFLKSEQVETNLITDVIRRMAIA 178
+ + I +PVA GT V VR LF T+P R F ++ + + + +I+ A+
Sbjct: 121 LVYDHDGHIIQKKPVARGRGTTVMVRQLFSTLPVRRKEFQRNIKRKFVKLISLIQAYALI 180
Query: 179 YPKVSFTFS--TIKSNRYKMNFQSTNGNFPERISQVIGEDFINNAVELNEKSNEITLQGY 236
+ F S T+ + + G+ IS G N L S+ G
Sbjct: 181 STAIKFLVSNSTLAGKKNIILKTGGYGSDKINISSNFGSVEEENLEPLIFISSCHHGCG- 239
Query: 237 TGIPTFNRGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGRYPVVVLLLEIDPRQVD 296
R + ++ ++FIN R V I I Y L L++ +D
Sbjct: 240 -------RSSEDRQFIFINRRPVFPSDICRVINEVYKLYN-----ERQYLFLDVPEGCID 287
Query: 297 VNVHPAKSYIRFRNPTIIRNFIIQSIQKAINKKGISTSSVLSKKMISSFHQDNAPKTHLP 356
VNV P K + N + + S+ N S+ S P + L
Sbjct: 288 VNVTPDKRQVLLSNERSVLFSLRNSLVDFYN------SNCDLNFSDVSMLPVQNPSS-LT 340
Query: 357 KYATSLTNTQEKLFLQENRLSTN 379
+ + + N + TN
Sbjct: 341 ERSDPIENKLVSRTDSMIGIKTN 363
Score = 73.1 bits (179), Expect = 2e-13
Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 11/177 (6%)
Query: 410 CAQIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKITSQTLLTPEIIDLLEGE 469
Q + +II + L IVDQHA+ E+ FE+++ +T + +Q L+ P+ +DL
Sbjct: 492 IGQFNLGFIIVKLEKDLFIVDQHASDEKRNFERLQS---TTVLKAQPLICPQALDLSAIN 548
Query: 470 CALIMEHDEDLHRLGIKAERFGPNAIAIREIPAILSK---KNI---PQLLRDIIDEIIDS 523
+++++ + G K + NA + +LS KN L+++I + +
Sbjct: 549 EMVLLDNLPLFEKNGFKVK-IDENAPDG-KRVRLLSVPVSKNQTFGVSDLKELISVLKNF 606
Query: 524 STTYTLQDRIENILATMACYGSIRSGRKMQSIEMNRLLREMEKNPNSSQCNHGRPTF 580
++ +++A+ AC S+ G + +M R++R + + + C HGRPT
Sbjct: 607 PEETYRPSKVRSMIASKACRSSVMIGDPLSKDDMTRIVRSLAELEHPWNCPHGRPTM 663
>gnl|CDD|48466 cd00782, MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of DNA mismatch repair
(MutL/MLH1/PMS2) family. This transducer domain is
homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. Included in this group are
proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and
E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1
and MLH3. These three complexes have distinct functions
in meiosis. hMLH1-hPMS2 also participates in the repair
of all DNA mismatch repair (MMR) substrates. Roles for
hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been
established. Cells lacking either hMLH1 or hPMS2 have a
strong mutator phenotype and display microsatellite
instability (MSI). Mutation in hMLH1 causes
predisposition to HNPCC, Muir-Torre syndrome and Turcot
syndrome (HNPCC variant). Mutation in hPMS2 causes
predisposition to HPNCC and Turcot syndrome. Mutation in
hMLH1 accounts for a large fraction of HNPCC families.
There is no convincing evidence to support hPMS1 having
a role in HNPCC predisposition. It has been suggested
that hMLH3 may be a low risk gene for colorectal cancer;
however there is little evidence to support it having a
role in classical HNPCC. It has been suggested that
during initiation of DNA mismatch repair in E. coli, the
mismatch recognition protein MutS recruits MutL in the
presence of ATP. The MutS(ATP)-MutL ternary complex
formed, then recruits the latent endonuclease MutH..
Length = 122
Score = 126 bits (317), Expect = 2e-29
Identities = 46/120 (38%), Positives = 73/120 (60%)
Query: 207 ERISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYVFINGRTVQDKFILS 266
+RI+QV G++ N +E+ +S + + GY P F R + ++ ++F+NGR V+DK +
Sbjct: 3 DRIAQVYGKEVAKNLIEVELESGDFRISGYISKPDFGRSSKDRQFLFVNGRPVRDKLLSK 62
Query: 267 TIRTAYAETIPLGRYPVVVLLLEIDPRQVDVNVHPAKSYIRFRNPTIIRNFIIQSIQKAI 326
I AY +P GRYPV VL LE+ P VDVNVHP K +RF + + I ++++ A+
Sbjct: 63 AINEAYRSYLPKGRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREALRSAL 122
>gnl|CDD|37188 KOG1977, KOG1977, KOG1977, DNA mismatch repair protein - MLH3
family [Replication, recombination and repair].
Length = 1142
Score = 98.8 bits (245), Expect = 3e-21
Identities = 86/339 (25%), Positives = 145/339 (42%), Gaps = 42/339 (12%)
Query: 3 IRKLSEKIINQIAAGEIIERPSIAIKELIENSLDAESSRVETVIAGGGKSF-FQITDNGF 61
I+ LS ++ ++ +G I + ++EL+ NS+DAE++ V + ++F Q+ D+GF
Sbjct: 2 IKCLSVEVQAKLRSGLAISSLAQCVEELVLNSIDAEATCVAVRV--NMETFSVQVIDDGF 59
Query: 62 GMTSEEIPMAVQRHCTSKI--SDDFSNIHTFGFRGEALPSIGAVSHLTLMSRPPQNNTGA 119
GM +++ R+ TSK +D N T+GFRGEAL SI +S L ++S+
Sbjct: 60 GMGRDDLEKLGNRYFTSKCHSVNDLENPRTYGFRGEALASISDMSSLVVISKKKNRTMKT 119
Query: 120 Q----IAISGEKISSVRPVAMNPGTIVEVRDLFFTIPARLNFLKSE-QVETNLITDVIRR 174
+ S K + + GT V V DLF+ +P R + + E I I
Sbjct: 120 FVKKFQSGSALKALEIDVTRASSGTTVTVYDLFYQLPVRRRLKCMDPRKEFEKIKQRIEA 179
Query: 175 MAIAYPKVSFTFSTIKSNRYKMNFQSTNGNFPERISQVIGEDFINNAVELNEKSNEITLQ 234
+++ +P +SF+ S M Q +N + +L E +
Sbjct: 180 ISLMHPSISFSVRNDVSG--SMVLQ------------------LNKSQKLREIL--FRYK 217
Query: 235 GYTGIPTFNRGNANQFYVFINGRTVQD----KFILSTIRTAYAETIPLGRYPVVVLLLEI 290
+ + N ++F+N R V K I +R P V+ ++
Sbjct: 218 EFELSSSEAHYNKTMGFLFVNKRLVLRTKKHKLIDQLLRKESIICK-----PKYVINVQC 272
Query: 291 DPRQVDVNVHPAKSYIRFRNPTIIRNFIIQSIQKAINKK 329
DV++ PAK+ I F+N + F IQ K KK
Sbjct: 273 PFCLYDVSMEPAKTLIEFQNWDTLL-FCIQEGVKMFLKK 310
Score = 56.4 bits (135), Expect = 2e-08
Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 22/196 (11%)
Query: 412 QIHQNYIISQTTDGLVIVDQHAAHERLIFEKMRQDFNSTKITSQTLLTPEIIDLLEGECA 471
Q+ + YI + QHA+ E+ + + + S TL+ P I +L +
Sbjct: 918 QVDKKYIACVMSTKTEENGQHASDEKQQAQGSGRKK----LLSSTLIPPLEIKVLPMQRR 973
Query: 472 LIMEHDEDLHRLGIKAE----------------RFGPNAIAIREIPAILSKKNIPQLLRD 515
L+ + ++L LG + F K+I +
Sbjct: 974 LLWCYHKNLEDLGWEFVFPDTSDSLVLVGKVPLCFVEREANELRRGRSTVTKSIVEEFIR 1033
Query: 516 IIDEIIDSSTTYTLQDRIENILATMACYGSIRSGRKMQSIEMNRLLREMEKNPNSSQCNH 575
E++ ++ + TL ++ +L + AC G+I G + E RL+ + QC H
Sbjct: 1034 EQLELLQTTGSSTLPLTVQKVLNSKACRGAIMFGDGLSLQECCRLIEALSSCQLPFQCAH 1093
Query: 576 GRPTFIKLKLSDIEKL 591
GRP+ + L+D++ L
Sbjct: 1094 GRPSM--VPLADLKHL 1107
>gnl|CDD|73195 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. The GyrB
dimerizes in response to ATP binding, and is homologous
to the N-terminal half of eukaryotic Topo II and the
ATPase fragment of MutL. Type II DNA topoisomerases
catalyze the ATP-dependent transport of one DNA duplex
through another, in the process generating transient
double strand breaks via covalent attachments to both
DNA strands at the 5' positions. Included in this group
are proteins similar to human MLH1 and PMS2. MLH1 forms
a heterodimer with PMS2 which functions in meiosis and
in DNA mismatch repair (MMR). Cells lacking either hMLH1
or hPMS2 have a strong mutator phenotype and display
microsatellite instability (MSI). Mutation in hMLH1
accounts for a large fraction of Lynch syndrome (HNPCC)
families..
Length = 107
Score = 81.6 bits (201), Expect = 6e-16
Identities = 31/105 (29%), Positives = 57/105 (54%), Gaps = 4/105 (3%)
Query: 207 ERISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYVFINGR-TVQDKFIL 265
+R+++++G+ + + + +S+ ++G P R + ++ + F+NGR + +
Sbjct: 3 DRLAEILGDKVADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHV 62
Query: 266 STIRTAYAETI---PLGRYPVVVLLLEIDPRQVDVNVHPAKSYIR 307
+R AY + + RYPV VL L+I P VDVNVHP K +R
Sbjct: 63 KAVREAYTRALNGDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107
>gnl|CDD|48471 cd03483, MutL_Trans_MLH1, MutL_Trans_MLH1: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to yeast and human MLH1 (MutL homologue
1). This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. MLH1 forms
heterodimers with PMS2, PMS1 and MLH3. These three
complexes have distinct functions in meiosis.
hMLH1-hPMS2 also participates in the repair of all DNA
mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1
or hMLH1-hMLH3 in MMR have not been established. Cells
lacking hMLH1 have a strong mutator phenotype and
display microsatellite instability (MSI). Mutation in
hMLH1 causes predisposition to HNPCC, Muir-Torre
syndrome and Turcot syndrome (HNPCC variant). Mutation
in hMLH1 accounts for a large fraction of HNPCC
families..
Length = 127
Score = 70.2 bits (172), Expect = 1e-12
Identities = 41/127 (32%), Positives = 57/127 (44%), Gaps = 9/127 (7%)
Query: 207 ERISQVIGEDFINNAVELNEKSNEITL----QGYTGIPTFNRGNANQFYVFINGRTVQDK 262
+ I V G N +E+ ++ L +G ++ F +FIN R V+
Sbjct: 4 DNIRSVYGAAVANELIEVEISDDDDDLGFKVKGLISNANYS-KKKIIFILFINNRLVECS 62
Query: 263 FILSTIRTAYAETIPLGRYPVVVLLLEIDPRQVDVNVHPAKSYIRFRNPTIIRNFIIQSI 322
+ I YA +P G +P V L LEI P VDVNVHP K + F N II+ I
Sbjct: 63 ALRRAIENVYANYLPKGAHPFVYLSLEIPPENVDVNVHPTKREVHFLNEEE----IIERI 118
Query: 323 QKAINKK 329
QK + K
Sbjct: 119 QKLVEDK 125
>gnl|CDD|48472 cd03484, MutL_Trans_hPMS_2_like, MutL_Trans_hPMS2_like: transducer
domain, having a ribosomal S5 domain 2-like fold, found
in proteins similar to human PSM2 (hPSM2). hPSM2 belongs
to the DNA mismatch repair (MutL/MLH1/PMS2) family.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. Included in
this group are proteins similar to yeast PMS1. The yeast
MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a
role in meiosis. hMLH1-hPMS2 also participates in the
repair of all DNA mismatch repair (MMR) substrates.
Cells lacking hPMS2 have a strong mutator phenotype and
display microsatellite instability (MSI). Mutation in
hPMS2 causes predisposition to HPNCC and Turcot
syndrome..
Length = 142
Score = 49.9 bits (119), Expect = 2e-06
Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 3/104 (2%)
Query: 223 ELNEKSNEITLQGYTGIPTFN--RGNANQFYVFINGRTVQDKFILSTIRTAYAETIPLGR 280
+ + +E+ + GY P+ R ++++ + +INGR V K + I Y ++ +
Sbjct: 37 DEDLADSEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKKVAKLINEVY-KSFNSRQ 95
Query: 281 YPVVVLLLEIDPRQVDVNVHPAKSYIRFRNPTIIRNFIIQSIQK 324
YP +L + + DVNV P K + + + + + S+ +
Sbjct: 96 YPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSE 139
>gnl|CDD|48473 cd03485, MutL_Trans_hPMS_1_like, MutL_Trans_hPMS1_like: transducer
domain, having a ribosomal S5 domain 2-like fold, found
in proteins similar to human PSM1 (hPSM1) and yeast
MLH2. hPSM1 and yMLH2 are members of the DNA mismatch
repair (MutL/MLH1/PMS2) family. This transducer domain
is homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. PMS1 forms a heterodimer with
MLH1. The MLH1-PMS1 complex functions in meiosis. Loss
of yMLH2 results in a small but significant decrease in
spore viability and a significant increase in gene
conversion frequencies. A role for hMLH1-hPMS1 in DNA
mismatch repair has not been established. Mutation in
hMLH1 accounts for a large fraction of Lynch syndrome
(HNPCC) families, however there is no convincing
evidence to support hPMS1 having a role in HNPCC
predisposition..
Length = 132
Score = 44.1 bits (104), Expect = 1e-04
Identities = 29/129 (22%), Positives = 53/129 (41%), Gaps = 8/129 (6%)
Query: 204 NFPERISQVIGEDFINNAVELNEKSN--EITLQGYTGIPTFNRGNANQF--YVFINGRTV 259
+ E +++V+G N V + +I+L+G+ P + ++ +N R V
Sbjct: 1 DHKEALARVLGTAVAANMVPVQSTDEDPQISLEGFLPKPGSDVSKTKSDGKFISVNSRPV 60
Query: 260 -QDKFILSTIRTAYAETIPLG---RYPVVVLLLEIDPRQVDVNVHPAKSYIRFRNPTIIR 315
K I +R Y+ RYPV L + P VDVN+ P K + +N +
Sbjct: 61 SLGKDIGKLLRQYYSSAYRKSSLRRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVL 120
Query: 316 NFIIQSIQK 324
+ ++
Sbjct: 121 QAVENLLES 129
>gnl|CDD|28956 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 37.6 bits (87), Expect = 0.010
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 15/98 (15%)
Query: 26 AIKELIENSLDA---ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEIPMAVQRHCTSKIS 81
+ L+ N++ R+ +V G ++ DNG G+ E++ +R
Sbjct: 4 VLLNLLSNAIKHTPEGGGRITISVERDGDHLEIRVEDNGPGIPEEDLERIFERF------ 57
Query: 82 DDFSNIHTFGFRGEALPSIGAVS-----HLTLMSRPPQ 114
D S G G L + + + + S P
Sbjct: 58 SDGSRSRKGGGTGLGLSIVKKLVELHGGRIEVESEPGG 95
>gnl|CDD|48474 cd03486, MutL_Trans_MLH3, MutL_Trans_MLH3: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to yeast and human MLH3 (MutL homologue
3). MLH3 belongs to the DNA mismatch repair
(MutL/MLH1/PMS2) family. This transducer domain is
homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. MLH1 forms heterodimers with
MLH3. The MLH1-MLH3 complex plays a role in meiosis. A
role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has
not been established. It has been suggested that hMLH3
may be a low risk gene for colorectal cancer; however
there is little evidence to support it having a role in
classical HNPCC..
Length = 141
Score = 36.4 bits (84), Expect = 0.020
Identities = 23/136 (16%), Positives = 48/136 (35%), Gaps = 21/136 (15%)
Query: 208 RISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYVFINGRTVQDKFILST 267
Q+ G E++ K E + GY + + ++++NGR
Sbjct: 5 VFKQIYGLVLAQKLKEVSAKFQEYEVSGYISSEGH--YSKSFQFIYVNGRLYLKTRFHKL 62
Query: 268 IRTAYAET-------------------IPLGRYPVVVLLLEIDPRQVDVNVHPAKSYIRF 308
I + +T YPV VL + + D++ P+K+ I F
Sbjct: 63 INKLFRKTSAVAKNKSSPQSKSSRRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEF 122
Query: 309 RNPTIIRNFIIQSIQK 324
++ + I++ ++
Sbjct: 123 KDWKTLLPLILEVVKS 138
>gnl|CDD|145582 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine
kinase, DNA gyrase B and HSP90.
Length = 111
Score = 35.8 bits (83), Expect = 0.034
Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 26 AIKELIENSLDA--ESSRVE-TVIAGGGKSFFQITDNGFGMTSEEIPMAVQRHCTSKISD 82
+ L++N++ +E T+ GG+ + DNG G+ E++P + +
Sbjct: 9 VLSNLLDNAIKHAPAGGEIEVTLERDGGRLRITVEDNGIGIPPEDLPKIFEPFFRTDKDS 68
Query: 83 DFSNIHTFGF 92
G
Sbjct: 69 RKVGGTGLGL 78
>gnl|CDD|31579 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA
replication, recombination, and repair].
Length = 538
Score = 34.9 bits (80), Expect = 0.072
Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 25 IAIKELIENSLDA-ESSR----VETVIAGGGKSFFQIT--DNGFGMTSEEIPMA 71
+ EL+ NSLDA E + ++ I GK +++ DNG G+ E+IP
Sbjct: 39 TTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDNGPGIPEEQIPKV 92
>gnl|CDD|30674 COG0326, HtpG, Molecular chaperone, HSP90 family
[Posttranslational modification, protein turnover,
chaperones].
Length = 623
Score = 29.8 bits (67), Expect = 2.1
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 17/63 (26%)
Query: 23 PSIAIKELIENSLDA------ESSRVETVIAGGGKSFFQ-----------ITDNGFGMTS 65
I ++ELI N+ DA E+ + G + I+DNG GMT
Sbjct: 28 KEIFLRELISNASDAIDKLRFEALSDPELGEGDSDLRIRISFDKDNKTLTISDNGIGMTK 87
Query: 66 EEI 68
+E+
Sbjct: 88 DEV 90
>gnl|CDD|35749 KOG0529, KOG0529, KOG0529, Protein geranylgeranyltransferase type
II, alpha subunit [Posttranslational modification,
protein turnover, chaperones].
Length = 421
Score = 28.8 bits (64), Expect = 3.9
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 76 CTSKISDDFSNIHTFGFRGEALPSI 100
T I+D+FSN + +R L ++
Sbjct: 172 TTKLINDNFSNYSAWHYRSLLLSTL 196
>gnl|CDD|36568 KOG1354, KOG1354, KOG1354, Serine/threonine protein phosphatase 2A,
regulatory subunit [Signal transduction mechanisms].
Length = 433
Score = 27.7 bits (61), Expect = 9.1
Identities = 28/121 (23%), Positives = 45/121 (37%), Gaps = 31/121 (25%)
Query: 193 RYKMNFQSTNGNFPERISQVIGEDFINNAVELNEKSNEITLQGYTGIPTFNRGNANQFYV 252
++ FQS F D++ ++E+ EK N+I + GN +F +
Sbjct: 63 NFQTEFQSHEPEF----------DYLK-SLEIEEKINKIRW--------LDDGNLAEFLL 103
Query: 253 FINGRTVQ---------DKFILSTIRTAYAETIPLGRYPVVV---LLLEIDPRQVDVNVH 300
N +T++ K + TI R PV L +E PR+V N H
Sbjct: 104 STNDKTIKLWKIRERGSKKEGYNLPEEGPPGTITSLRLPVEGRHDLEVEASPRRVYANAH 163
Query: 301 P 301
Sbjct: 164 T 164
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.134 0.372
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,927,700
Number of extensions: 370898
Number of successful extensions: 919
Number of sequences better than 10.0: 1
Number of HSP's gapped: 896
Number of HSP's successfully gapped: 34
Length of query: 594
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 495
Effective length of database: 4,124,446
Effective search space: 2041600770
Effective search space used: 2041600770
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 (26.9 bits)