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)