RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780750|ref|YP_003065163.1| DNA mismatch repair protein [Candidatus Liberibacter asiaticus str. psy62] (920 letters) >gnl|CDD|30598 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]. Length = 843 Score = 813 bits (2101), Expect = 0.0 Identities = 382/885 (43%), Positives = 547/885 (61%), Gaps = 47/885 (5%) Query: 20 ENLKSSTPMMRQYIEIKSINPDSLVFYRMGDFYELFFDDALLASRCLGITLTKRGKHLGK 79 + TPMM+QY+EIK+ PD+L+F+RMGDFYELFF+DA +A+R L ITLTKRG Sbjct: 1 SSKAKLTPMMQQYLEIKAQYPDTLLFFRMGDFYELFFEDAKIAARLLDITLTKRGN---- 56 Query: 80 DIPMCGVPVHTANHYIQKLIKIGHRIAICEQIESPLEAKKRGNKSLVRRNVVRLVTPGTL 139 IPM GVP H ++Y+ KLI++G+++AICEQ+E P EAK +V R VVR+VTPGTL Sbjct: 57 -IPMAGVPYHALDYYLAKLIELGYKVAICEQLEDPAEAKG-----VVERKVVRVVTPGTL 110 Query: 140 TEDQLLSPTDSNYLMAVARIR-TEWAIAWIDISTGIFKISTSNHDRLISDIMRIDPREII 198 T++ LLS ++NYL A+A R + +A+ID+STG F +S ++L+S++ R+ P+E++ Sbjct: 111 TDEALLSDRENNYLAALAIDRDGKVGLAFIDLSTGEFFVSEFEREKLLSELKRLQPKELL 170 Query: 199 FSEKELSHAEYKSLFETLGNVAVAQPNVFFDHSISESRIADYYNITTVDTFGSFS-QVEK 257 SE LS + G V P FFD +E +++Y+ + +D FG S + Sbjct: 171 LSESLLSSTLAEIQK---GLFVVRLPASFFDEDDAEEILSEYFGVRDLDGFGLISTPLAL 227 Query: 258 TAAAAAISYIKKTQMVNKPTIGYPEREDIQSTLFIDSAARSNLEILRTLSG-SREQSLLK 316 +AA A +SY+K TQ P I +R D++ + +D+A R NLE+ L G ++ SL Sbjct: 228 SAAGALLSYLKDTQKTFLPHIQIIQRYDLEDYMVLDAATRRNLELFSNLRGNGKKGSLFW 287 Query: 317 TIDYSITGAGGRLFAERIASPLTDSTKINTRLDSINFFIQNPILINPIQKILKSSPDVPR 376 +D ++T G RL + PL D +I RLD++ NP L ++++LK PD+ R Sbjct: 288 LLDRTVTPMGSRLLKRWLLQPLLDKEEIEERLDAVEELKDNPELREKLREMLKKVPDLER 347 Query: 377 SLSRLKIGRGEPKDIAVIRDGIRSGINILNLFLKNDLPEELRGAVEKLKKLPQ--SLEKT 434 LSRL +GR P+D+ +RD + I L +L +E ++ L L + Sbjct: 348 LLSRLSLGRASPRDLLRLRDSLEKIPEIFKLLSSLKSESDLLLLLEDIESLDYLAELLEL 407 Query: 435 LSSMLSDDLPTFKRDGGFLRDGADASLDETRSLRDQSKRIIASLQLKYAEETKIKNLKIK 494 L + +++D P RDG +++G + LDE R L + +K IA L+L+ E T IK+LKIK Sbjct: 408 LETAINEDPPLAVRDG-IIKEGYNIELDELRDLLNNAKEWIAKLELEERERTGIKSLKIK 466 Query: 495 HNNNLGYFIEVTSSSASVLKKDLESKDRFIHRQTMSNLTRFTTLELIDLENRITNATNSA 554 +N GY+IEVT S+A ++ D +I RQT+ N RFTT EL +LE ++ +A Sbjct: 467 YNKVYGYYIEVTKSNAKLVPDD------YIRRQTLKNAERFTTPELKELEEKLLDAEEKI 520 Query: 555 LLIELESFEILSNAIIEQSESLDNASQVIAIIDISIALAILAKEQNYCRPIIDNSTNFIV 614 L +E E F+ L I+ L ++ +A +D+ +LA +A EQNY RP +S + + Sbjct: 521 LALEYELFDELREKILAHINELQALAKALAELDVLSSLAEIAAEQNYVRPEFVDSNDLEI 580 Query: 615 KDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALIV 674 K+GRHP+VE L F+ ND DLS + ++ L+TGPNMGGKST+LRQ ALIV Sbjct: 581 KEGRHPVVEAVLD----NGFVPNDIDLS-----GNRRIILITGPNMGGKSTYLRQVALIV 631 Query: 675 IMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFVI 734 I+AQ+GS+VPA A IGIVD++F+R+G+AD+LASGRSTFMVEM+ETA+IL+ AT +S VI Sbjct: 632 ILAQIGSFVPAEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVI 691 Query: 735 LDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQVSD 794 LDEIGRGT+T DGL+IAWA +EYLHE CR L ATH+HELT+L + L + N + + Sbjct: 692 LDEIGRGTSTYDGLAIAWAVLEYLHEKIGCRTLFATHYHELTELEEKLPQVKNYHMSAVE 751 Query: 795 SNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRAYDILKTFEKLYHHNQKDMRLYY 854 I FL+KV PGIAD SYGI V KLAGLP VI RA +IL EK + ++ Sbjct: 752 EGGDITFLYKVKPGIADKSYGIHVAKLAGLPEEVIERAREILAELEKESRSSNLELN--- 808 Query: 855 PEIQTKESKNNLSKNDKLFVEKIKCLNLDEMSPLTALKTLYAVKA 899 + +LS K+ ++ +K L+ DE++P AL LY +K Sbjct: 809 --------QKDLSLFPKV-LKALKSLDPDELTPR-ALNLLYELKK 843 >gnl|CDD|144180 pfam00488, MutS_V, MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters. Length = 234 Score = 388 bits (998), Expect = e-108 Identities = 130/241 (53%), Positives = 171/241 (70%), Gaps = 8/241 (3%) Query: 601 YCRPIIDNSTNFIVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNM 660 Y RP S ++ GRHP+VE ++ F+ ND L K ++ L+TGPNM Sbjct: 1 YVRPEFTESDALHIEGGRHPVVE----AVLAENFVPNDVSL----GKERSRILLITGPNM 52 Query: 661 GGKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIET 720 GGKST+LRQ ALIVIMAQ+GS+VPA A IGIVD++F+R+G++D+LASGRSTFMVEM+ET Sbjct: 53 GGKSTYLRQVALIVIMAQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMLET 112 Query: 721 ASILNQATNQSFVILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSK 780 A+IL+ AT++S VILDE+GRGT+T DGL+IAWA E+L E R R L ATH+HELT L++ Sbjct: 113 ANILHNATDKSLVILDELGRGTSTYDGLAIAWAVAEHLAEKIRARTLFATHYHELTKLAE 172 Query: 781 SLKRFHNATLQVSDSNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRAYDILKTFE 840 L N + ++N I+FL+KV PG AD SYGI V +LAGLP +V+ RA ++L E Sbjct: 173 KLPAVKNVHMAAVETNGDIVFLYKVKPGAADKSYGIHVAELAGLPESVVERAREVLAELE 232 Query: 841 K 841 Sbjct: 233 D 233 >gnl|CDD|35438 KOG0217, KOG0217, KOG0217, Mismatch repair ATPase MSH6 (MutS family) [Replication, recombination and repair]. Length = 1125 Score = 361 bits (927), Expect = e-100 Identities = 250/882 (28%), Positives = 395/882 (44%), Gaps = 83/882 (9%) Query: 19 EENLKSSTPMMRQYIEIKSINPDSLVFYRMGDFYELFFDDALLASRCLGITLTKRGKHLG 78 K TP +Q+ EIKS N D++VF++ G FYEL+ DAL+ +R + Sbjct: 242 PSFWKKFTPGEKQWWEIKSDNFDTIVFFKKGKFYELYEMDALVGARLFDLKFMD------ 295 Query: 79 KDIPMCGVPVHTANHYIQKLIKIGHRIAICEQIESPLEAKKRGNKS-----LVRRNVVRL 133 ++P G P + +++ + I+ G+++A EQ E+PL + R K+ +VRR V R+ Sbjct: 296 VNMPHSGFPEGSFDYWADQFIQKGYKVARVEQTETPLGKEIRERKTGKKDKVVRREVCRI 355 Query: 134 VTPGTLTEDQLLSPTDSNYLMAVARIRTE-------WAIAWIDISTGIFKISTSNHDRL- 185 +T GTLT+ LL+ + YLMA+ + + +ID STG I DR Sbjct: 356 LTNGTLTDIALLTSDLAKYLMAIKESEESYSTGEVSFGVCFIDTSTGEINIGEFCDDRHC 415 Query: 186 --ISDIM-RIDPREIIFSEKELSHAEYKSLFETLGNVAV---AQPNVFFDHSISESRI-- 237 + ++ ++ P E+I K LS + L + V + F+D + I Sbjct: 416 SKLDTLLSQVRPVELIEERKNLSDPTKVIIKLKLSSNLVENLVPKSEFWDSEKTGREIIS 475 Query: 238 ADYYNITTVD-------TFGSFSQVEKTAAAAAISYIKK-------TQMVNKPTIGYPER 283 DY+ ++ + + ++ +A Y+KK M N Y Sbjct: 476 EDYFESLGLEDSPSILKSPNTDKELALSAFGGLFYYLKKLLIDEELLSMKNFEE--YDSL 533 Query: 284 EDIQSTLFIDSAARSNLEILRTLS-GSREQSLLKTIDYSITGAGGRLFAERIASPLTDST 342 + QS + +D A NLEI G E +L ++ T G RL + +PL D Sbjct: 534 D--QSEMVLDGATLENLEIFSNSRNGGDEGTLFYAVNRCSTPFGKRLLKTWLMAPLCDKE 591 Query: 343 KINTRLDSINFFIQNPILINPIQKILKSSPDVPRSLSRL-KIGRGEPKDIA-VIR--DGI 398 I R D+++ + P+ + + LK PD+ R L R+ G K IA IR +G Sbjct: 592 DIKQRQDAVDSLGKAPMDRTKVGETLKKLPDLERLLVRIHNGGEKNKKKIADFIRVLEGF 651 Query: 399 RSGINILNLFLKNDLP-EELRGAVEKLKKLPQSLEKTLSSMLSDDLPTFKRDGGFL-RDG 456 + +L + E LR E L+ +P E+ + + D ++G + +G Sbjct: 652 KEINKLLGSLINVLKEGEGLRLISELLESMPNLSEEIENWTEAFDRVKAVKEGVIVPLEG 711 Query: 457 ADASLDETRSLRDQSKRIIASLQLKYAEETKIKNLKIKHNNNLGYFIEV------TSSSA 510 D DE D+++ + + +Y + ++ Y +EV SS Sbjct: 712 FDEEYDEAMKRVDEAENELLAYLEEYRKRLGCSSIVFVDVGKDVYQLEVPENGGVPSSLR 771 Query: 511 SVLKKDLESKDRFIHRQTMSNLTRFTTLELIDLENRITNATNSALLIELESFEILSNAII 570 L + R+ + R L + E R ++ + + + Sbjct: 772 YELMSAKKGVSRY-----YTPDLRKLIAHLDEAEERKKSSLSDLK----RRLIVRFDEHY 822 Query: 571 EQSESLDNASQVIAIIDISIALAILAK--EQNYCRPIIDNSTN----FIVKDGRHPIVEK 624 ++ + +A ID ++LA +K CRP I ST+ IVK RHP Sbjct: 823 IIWQAT---VKALASIDCLLSLAETSKGLGGPMCRPEIVESTDTPGFLIVKGLRHPCFSL 879 Query: 625 TLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVP 684 + FI ND +L + G LLTGPNMGGKST LRQ + VI+AQ+G VP Sbjct: 880 PS---TGTSFIPNDVELGGAEENREG---LLTGPNMGGKSTLLRQACIAVILAQIGCDVP 933 Query: 685 ASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFVILDEIGRGTAT 744 A + +D++F+R+G+ D++ SG STF VE+ ET IL AT S VI+DE+GRGT+T Sbjct: 934 AEVMELTPIDRIFTRLGANDDIMSGESTFFVELSETKKILKHATRHSLVIVDELGRGTST 993 Query: 745 LDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQVSDSNEG-IIFLH 803 DG +IA A +E+L E +C G +TH+H L + + E + FL+ Sbjct: 994 FDGTAIAEAVLEHLSEGIQCLGFFSTHYHSLCVDFMHHPQVRLLHMACVVDEEIDVTFLY 1053 Query: 804 KVIPGIADHSYGIQVGKLAGLPNTVISRAYDILKTFEKLYHH 845 K+ GI SYG V ++AGLP+ VI RA EK + Sbjct: 1054 KLEEGICPKSYGFNVARMAGLPDQVIDRAEIKAHELEKSSAN 1095 >gnl|CDD|35439 KOG0218, KOG0218, KOG0218, Mismatch repair MSH3 [Replication, recombination and repair]. Length = 1070 Score = 359 bits (923), Expect = 2e-99 Identities = 234/911 (25%), Positives = 409/911 (44%), Gaps = 115/911 (12%) Query: 26 TPMMRQYIEIKSINPDSLVFYRMGDFYELFFDDALLASRCLGITLTKRGKHLGKDIPMCG 85 TP+ +Q E+K + D ++ +G Y F +DA +ASR LGI H + Sbjct: 163 TPLEQQVKELKMHHRDKVLVIEVGYKYRFFGEDAEIASRVLGIYC-----HNDHNFMTAS 217 Query: 86 VPVHTANHYIQKLIKIGHRIAICEQIE-SPLEAKKRGNKSLVRRNVVRLVTPGTLTED-- 142 P N ++++L+ G ++A+ +Q E + +++ SL R + + T TL ED Sbjct: 218 FPDVRLNVHLERLVHHGLKVAVVKQTETAAIKSHGASRSSLFERKLSAVYTKATLGEDST 277 Query: 143 ------QLLSPTDSNYLMAVARIRTEWAIAWIDISTGIFKISTSN----HDRLISDIMR- 191 ++L T S++L+ V + + G+ + S +D + R Sbjct: 278 FVLRGERILGDT-SSFLLCVRDNVHKSKEKSGVVKVGLIGVQLSTGEVVYDEFQDNFARS 336 Query: 192 --------IDPREIIFSEKELS------HAEYKSLFETLGNVAVAQPNVFFDHSISESRI 237 + P E++ + + S+ V + V ++ +I Sbjct: 337 ELQTRISSLQPIELLLNTDLSPQTVALLFKDNVSVELIHKRVYRLENAVVQAIKLANEKI 396 Query: 238 ADYYNITTVDTFGSFSQVEKT--------AAAAAISYIKK---TQMVNKPTIGYPEREDI 286 ++ + + + A IS++K+ Q++ P+ P Sbjct: 397 QNFEDDKEMLEGSEIICLIMNLSHPSVICLLAKLISHLKEFNLEQVLLIPSFYSP--FSS 454 Query: 287 QSTLFIDSAARSNLEILRTLSGSREQ-SLLKTIDYSITGAGGRLFAERIASPLTDSTKIN 345 + + + +LEI + E+ SL +D++ T G R+ E + PL D +I Sbjct: 455 KEHMTLSPNTLQSLEIFTNQTDGSEKGSLFWVLDHTRTSFGLRMLREWVTKPLVDVHQIE 514 Query: 346 TRLDS---INFFIQNPILINPIQKILKSSPDVPRSLSRLKIGRGEPKD------------ 390 RLD+ I N I+ I ++L PD+ R L+R+ G P+ Sbjct: 515 ERLDAVEEITSHSSNSIVFESINQMLNRLPDLLRGLNRIYYGTCTPRKEFFFVLKQIYSA 574 Query: 391 ---------------IAVIRDGIRSGINILNLFLKNDLPEELRGAVEKLKKLPQS--LEK 433 + R G +S + + L + + P L L S +E Sbjct: 575 VSHFQMHQSYLEHFKSSDGRSGKQSPL-LRRLISELNEPLSTSQLPHFLTMLNVSAAMEG 633 Query: 434 TLSSML--SDDLPTFKRDGGFLRDGADASLDETRSLRDQSKRIIASLQLKYAEETKIKNL 491 + P + + + E+ R Q K +A ++ KY K NL Sbjct: 634 NKDDQFKDFSNFPLYDE-----SEDIIKVIRESEMSRSQLKEHLAEIR-KY---LKRPNL 684 Query: 492 KIKHNNNLGYFIEVTSSSASVLKKDLESKDRFIHRQTMSNLTRFTTLELIDLENRITNAT 551 + + + + + IEV +S + D +I + ++RF T + L + Sbjct: 685 EFRQVSGVDFLIEVKNSQIKKIPDD------WIKVNSTKMVSRFHTPRIQKLLQELEYYK 738 Query: 552 NSALLIELESFEILSNAIIEQSESLDNASQVIAIIDISIALAILAKEQNYCRP-IIDNST 610 ++ ++ N I E L A+ +A +D ++LA + NY RP +D Sbjct: 739 ELLIIESEAQYKSFLNKISEHYTELRKATLNLATLDCILSLAATSCNVNYVRPTFVDGQQ 798 Query: 611 NFIVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQN 670 I+K+GRHP++E L F+ ND LS + ++TGPNMGGKS+++RQ Sbjct: 799 EIIIKNGRHPVIESLLVDY----FVPNDIMLS----PEGERCNIITGPNMGGKSSYIRQV 850 Query: 671 ALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQ 730 ALI IMAQ+GS+VPA A + I D + +R+G++DN+ +GRSTFMVEM++T IL +AT + Sbjct: 851 ALITIMAQIGSFVPAEEARLSIFDGVLTRMGASDNIINGRSTFMVEMLDTLEILKKATKR 910 Query: 731 SFVILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSK----SLKRFH 786 S VILDE+GRGT+T DG++I++AT++Y E ++C L THF L ++ ++ +H Sbjct: 911 SLVILDELGRGTSTHDGIAISYATLKYFSELSKCLILFVTHFPMLGEIESGFPGQVRNYH 970 Query: 787 NATLQVSD----SNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRAYDILKTFEKL 842 L+ D + + FL+K++ G+A SYG+ V KLA +P ++I+RA+ I + EK Sbjct: 971 MGYLESEDKTGEDWDSVTFLYKLVRGLASRSYGLNVAKLARIPKSIINRAFSISEELEKE 1030 Query: 843 YHHNQKDMRLY 853 + +K ++L+ Sbjct: 1031 SRNERKLLKLF 1041 >gnl|CDD|73043 cd03284, ABC_MutS1, MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 216 Score = 331 bits (849), Expect = 7e-91 Identities = 125/224 (55%), Positives = 166/224 (74%), Gaps = 8/224 (3%) Query: 613 IVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNAL 672 ++ GRHP+VE+ L + PF+ ND +L ++ L+TGPNM GKST+LRQ AL Sbjct: 1 EIEGGRHPVVEQVLDNE---PFVPNDTELD-----PERQILLITGPNMAGKSTYLRQVAL 52 Query: 673 IVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSF 732 I ++AQ+GS+VPAS A IG+VD++F+R+G++D+LA GRSTFMVEM+ETA+ILN AT +S Sbjct: 53 IALLAQIGSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATERSL 112 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQV 792 V+LDEIGRGT+T DGLSIAWA +EYLHE + L ATH+HELT+L L R N + V Sbjct: 113 VLLDEIGRGTSTYDGLSIAWAIVEYLHEKIGAKTLFATHYHELTELEGKLPRVKNFHVAV 172 Query: 793 SDSNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRAYDIL 836 + G++FLHK++ G AD SYGI+V +LAGLP VI RA +IL Sbjct: 173 KEKGGGVVFLHKIVEGAADKSYGIEVARLAGLPEEVIERAREIL 216 >gnl|CDD|35440 KOG0219, KOG0219, KOG0219, Mismatch repair ATPase MSH2 (MutS family) [Replication, recombination and repair]. Length = 902 Score = 315 bits (807), Expect = 4e-86 Identities = 223/862 (25%), Positives = 374/862 (43%), Gaps = 91/862 (10%) Query: 29 MRQYIEIKSINPDSLVFYRMGDFYELFFDDALLASRCLGITLTKRGKHLGKDIPMCGVPV 88 ++ E ++ F+ G++Y + +DA +R + T K L D V Sbjct: 19 FLKFYEGLPKPTTTVRFFDRGEYYTVHGEDAEFVARNVYKTQAVI-KTLSPDNAKNTKEV 77 Query: 89 HTANHYIQKLIK-----IGHRIAICEQIESPLEAKKRGNKSLVRRNVVRLVTPGTLT--E 141 + +K+++ + +R+ + + + KRG +PG L E Sbjct: 78 SLSKGNFEKVVRELLLVLRYRVEVYSSNQGDWKLTKRG-------------SPGNLVQFE 124 Query: 142 DQLLSPTDSNYLMAVARIRTEWA-------IAWIDISTGIFKISTSNHDRLISD----IM 190 D L S D + ++ +A++D +S D S+ ++ Sbjct: 125 DLLFSNNDVPISIISLIVKHPGVDGQRRVGVAFVDTINVKIGLSEFVDDDSFSNLEALLI 184 Query: 191 RIDPREIIFSEKELSHAEYK---SLFETLGNVAVAQPNVFFDHSISESRIA----DYYNI 243 ++ P+E + E E K ++ + G + + E + + Sbjct: 185 QLGPKECVLPEGS-VAGEMKKLRNIIDRCGVLITLRKKSESSWKDVEQDLNRLLKSQEHA 243 Query: 244 TTVDTFGSFSQVEKTAAAAAISYIKKTQMVNKPTI-GYPE--REDIQSTLFIDSAARSNL 300 + Q+ +A +A I Y+ + N+ + G E + + +DSAA L Sbjct: 244 AYLPELEL--QLAMSALSALIKYL---DLENEYSNSGKYELTNHGLHQFMRLDSAAVRAL 298 Query: 301 EILR------TLSGSREQSLLKTIDYSITGAGGRLFAERIASPLTDSTKINTRLDSINFF 354 + S + SLL ++ T G RL + + PL D +IN R D + Sbjct: 299 NLFPLPYNNPEKSNNLALSLL---NHCKTLQGERLLRQWLKQPLRDIDRINERHDLVEAL 355 Query: 355 IQNPILINPIQK-ILKSSPDVPRSLSRLKIGRGEPKDIAVIRDGIRSGINILNLF----- 408 +++ + ++ +L+ PD+ R RL + +D+ I + ++ + Sbjct: 356 VEDAEIRQKLRDDLLRRIPDISRLARRLM--KANLQDVNRIYQAAKLLPTVVQVLISLSE 413 Query: 409 -LKNDLPEELRGAVEKLKKLPQSLEKTLSSMLSDDLPTFKRDGGFLRDGADASLDETRSL 467 L L ++KL+K + +E T+ DL + + +R D L E R Sbjct: 414 SHNRLLKSPLTEHLKKLEKFQEMVETTV------DLDAEEENEYRVRVDFDEELQELREK 467 Query: 468 RDQSKRIIASLQLKYAEE---TKIKNLKIKHNNNLGYFIEVTSSSASVLKKDLESKDRFI 524 D+ +R + L K + + K LK++++ G++ VT VL+K K + Sbjct: 468 LDELERKMEKLHKKVSADLGLDPKKQLKLENSAQFGWYFRVTRKEEKVLRK----KKNYT 523 Query: 525 HRQTMSNLTRFTTLELIDLENRITNATNSALLIELESFEILSNAIIEQSESLDNASQVIA 584 T +FTT +L L + + + E + + L+ +QV+A Sbjct: 524 ELSTQKGGVKFTTKKLSSLNDEFMSLQKEYDEAQNEIVREIIKIAATYTPPLEALNQVLA 583 Query: 585 IIDISIALAILAKEQ--NYCRP--IIDNSTNFIVKDGRHPIVEKTLKQQSSKPFIANDCD 640 +D+ ++ A A Y RP + S +K RHP++E Q PFI ND Sbjct: 584 HLDVFVSFAHAATVAPIPYVRPKLLPLGSKRLELKQSRHPVLE----GQDEIPFIPNDVV 639 Query: 641 LSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRV 700 L +K ++ ++TGPNMGGKST++RQ +IV+MAQ+G +VP A I IVD + +RV Sbjct: 640 L----EKGKCRMLIITGPNMGGKSTYIRQVGVIVLMAQIGCFVPCESATISIVDGILTRV 695 Query: 701 GSADNLASGRSTFMVEMIETASILNQATNQSFVILDEIGRGTATLDGLSIAWATIEYLHE 760 G+ D+ G STFM EM+ETASIL +AT S +I+DE+GRGT+T DG IAWA E++ Sbjct: 696 GAGDSQLKGISTFMAEMLETASILRRATKNSLIIIDELGRGTSTYDGFGIAWAIAEHIAT 755 Query: 761 TNRCRGLLATHFHELTDLSKSLKRFHNATLQVSDSNEGIIFLHKVIPGIADHSYGIQVGK 820 C L ATHFHELT L++ L N + N+ I L+KV G+ D S+GI V + Sbjct: 756 KIGCFCLFATHFHELTKLAEQLPTVKNLHVTAQIENDDITLLYKVFEGVCDQSFGIHVAE 815 Query: 821 LAGLPNTVISRAYDILKTFEKL 842 L G P VI A + E Sbjct: 816 LVGFPEHVIEMAKQKAEELEDE 837 >gnl|CDD|147401 pfam05192, MutS_III, MutS domain III. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in. Length = 306 Score = 263 bits (674), Expect = 2e-70 Identities = 120/313 (38%), Positives = 179/313 (57%), Gaps = 8/313 (2%) Query: 287 QSTLFIDSAARSNLEILRTLSG-SREQSLLKTIDYSITGAGGRLFAERIASPLTDSTKIN 345 + + +DSA R NLE++ LSG + SL +D ++T G RL + PL D +IN Sbjct: 1 EDYMLLDSATRRNLELVENLSGDGKNGSLFSVLDRTVTAMGSRLLRRWLLQPLRDREEIN 60 Query: 346 TRLDSINFFIQNPILINPIQKILKSSPDVPRSLSRLKIGRGEPKDIAVIRDGIRSGINIL 405 RLD++ +++P L ++++LK PD+ R LSRL +GR P+D+ +RD + I Sbjct: 61 ARLDAVEELLEDPELRQTLRELLKRVPDLERLLSRLALGRANPRDLLRLRDSLERLPTIK 120 Query: 406 NLFLKNDLPEELRGAVEKLKKLPQSLEKTLSSMLSDDLPTFKRDGGFLRDGADASLDETR 465 L + D P L+ + K L L + +++D P R+GG ++ G DA LDE R Sbjct: 121 ELLEELDSPLLLK-ELRKSIDDLSELLDLLETAINEDPPLLIREGGVIKSGYDAELDELR 179 Query: 466 SLRDQSKRIIASLQLKYAEETKIKNLKIKHNNNLGYFIEVTSSSASVLKKDLESKDRFIH 525 LRD++K IA L+ K EET I +LKI +N GY+IEVT S+A +L K FI Sbjct: 180 DLRDEAKEWIAELEAKEREETGIDSLKIGYNKVGGYYIEVTKSNADLLPKH------FIR 233 Query: 526 RQTMSNLTRFTTLELIDLENRITNATNSALLIELESFEILSNAIIEQSESLDNASQVIAI 585 RQT+ N RFTT EL +LE++I NA L +E E FE L ++E +E L ++ +A Sbjct: 234 RQTLKNAERFTTPELKELEDKILNAEERILALEKELFEELRERVVEHAEPLQALAEALAE 293 Query: 586 IDISIALAILAKE 598 +D+ ++ A LA E Sbjct: 294 LDVLVSFAELAAE 306 >gnl|CDD|35441 KOG0220, KOG0220, KOG0220, Mismatch repair ATPase MSH4 (MutS family) [Replication, recombination and repair]. Length = 867 Score = 261 bits (668), Expect = 6e-70 Identities = 199/829 (24%), Positives = 358/829 (43%), Gaps = 77/829 (9%) Query: 107 ICEQIESPLEAKKRGNKSLVRRNVVRLVTPGTL---TEDQLLSPTDSNYLMAVAR----I 159 P K + +R+ + P + +S + ++AV Sbjct: 57 SARDTNYPQTLKTPLSTGNPQRSGYKSWAPSLGYSSSNSSAISAHSPSVIVAVVEGRGLA 116 Query: 160 RTEWAIAWIDISTGIFKIS----TSNHDRLISDIMRIDPREIIFSEKELSHAEYKSLFET 215 R E +A ID+ +S ++ + ++I+ + + P EII S + K LF Sbjct: 117 RGEIGMASIDLKNPQIILSQFADSTTYAKVITKLKILSPLEIIISNTACAVGNSKLLFTL 176 Query: 216 LGNVAVAQPNV--------FFDHSISESRIADYYN--ITTVDTFGSFSQVEKTAAAAAIS 265 + NV +F+ + I +TV AAAA + Sbjct: 177 ITENF---KNVNFTTISRKYFNSTKGLEYIEQLCIAEFSTVLEEIQSKTYALGAAAALLK 233 Query: 266 YIKKTQ-MVNKPTIGYPEREDIQSTLFIDSAARSNLEILRTLSGSREQSLLKTIDYSITG 324 Y+++ Q V P + ++T IDS++ +LE++ +L ++Y+ T Sbjct: 234 YVEEIQSSVYAPKSLRICFQGSENTAMIDSSSAQSLELVINNQYKNNHTLFGVLNYTKTP 293 Query: 325 AGGRLFAERIASPLTDSTKINTRLDSINFFIQNPILINPIQKILKSSPDVPRSLSRL--- 381 G R I PLTD IN RL++I + + L ++ ++K D+ + LS L Sbjct: 294 GGYRRLRSSILQPLTDIETINMRLEAIQELLADEELFFGLRSVIKRFLDLDQLLSVLVQI 353 Query: 382 ------KIGRGEPKDIAVIRDGIRSGINILNLFLKNDLPEELRGAVEKLK-KLPQSLEKT 434 + ++ ++ + ++ L + LKN LR K K + + Sbjct: 354 PTQDTVNAAESKINNLIYLKHTLEL-VDPLKIALKNCNSNLLREYYGSFKDKRFGIILEK 412 Query: 435 LSSMLSDDLPTFK-------RDGGFLRDGADASLDETRSLRDQSKRIIASLQLKYAEETK 487 + +++DD K + ++ + LD R + IA + + E+ Sbjct: 413 IKEVINDDALYAKGCLNLRTQKCYAVKSNINGFLDIARRTYTEIVDDIAGMISQLGEKFS 472 Query: 488 IKNLKIKHNNNLGYFIEVTSSSASVLKKDLESKDRFIHRQTMSNLTRFTTLELIDLENRI 547 + NL++ ++ G+FI +T+ ++ L FI + N FT+ +LI + R+ Sbjct: 473 L-NLRLSFSSARGFFIRITTDCIALPSDTL--PSEFIKISKVKNSYSFTSADLIKMNERL 529 Query: 548 TNATNSALLIELESFEILSNAIIEQSESLDNASQVIAIIDISIALAILAKEQNYCRPIID 607 L+ L + I E L ++ ++++D+ + A +Y RP Sbjct: 530 KEVLREIFLMTEMIVCKLLDEIYEHISCLYKLAEAVSMLDMLCSFAHACTLSDYVRPEFT 589 Query: 608 NSTNFIVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFL 667 +S +K GRHPI+EK ++ IAN+ ++ ++TGPNM GKST+L Sbjct: 590 DS--LAIKQGRHPILEKISAEK----PIANNTYVT-----EGSNFLIITGPNMSGKSTYL 638 Query: 668 RQNALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQA 727 +Q AL IMAQ+GSYVPA YA + ++F+R+G+ D L STFM EM E A IL A Sbjct: 639 KQVALCQIMAQIGSYVPAEYASFRVFKRIFTRMGTNDELERNSSTFMSEMKEAAYILQNA 698 Query: 728 TNQSFVILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDL---SKSLKR 784 S ++LDE+GRGT+T +G++I +A EYL + LATHF ++ + ++ Sbjct: 699 NKNSLIVLDELGRGTSTEEGIAITYAVCEYLLSL-KAYTFLATHFLDIAAIANYYPAVDN 757 Query: 785 FHNATLQVSDSNEGIIFLHKVIPG-IADHSYGIQVGKLAGLPNTVISRAYDILKTFEKLY 843 H L +D N +K+ G + +YG++ +++ LP++++ A +I Sbjct: 758 LH--FLVQTDENSSKNKKYKLSRGLTEEKNYGLKAAEVSSLPDSIVEDAKEITTQITAQI 815 Query: 844 HHNQKDMRLYYPEIQTKESKNNLS---------KNDKLFVEKIKCLNLD 883 NQ+D PE++ + + +L+ ++ K+K L Sbjct: 816 LQNQRD----TPEMERQRAVYHLATRLVQTAGNSDEDSLRIKLKNLKKK 860 >gnl|CDD|73002 cd03243, ABC_MutS_homologs, The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 202 Score = 236 bits (603), Expect = 3e-62 Identities = 98/211 (46%), Positives = 145/211 (68%), Gaps = 10/211 (4%) Query: 614 VKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALI 673 +K GRHP++ K ++ F+ ND +L SG+L L+TGPNMGGKST+LR L Sbjct: 2 IKGGRHPVLLALTKGET---FVPNDINLG------SGRLLLITGPNMGGKSTYLRSIGLA 52 Query: 674 VIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFV 733 V++AQ+G +VPA A I +VD++F+R+G+ D+++ GRSTFM E++E IL+ AT +S V Sbjct: 53 VLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPRSLV 112 Query: 734 ILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQVS 793 ++DE+GRGT+T +GL+IA+A +E+L E CR L ATHFHEL DL + + N ++ Sbjct: 113 LIDELGRGTSTAEGLAIAYAVLEHLLEK-GCRTLFATHFHELADLPEQVPGVKNLHMEEL 171 Query: 794 DSNEGIIFLHKVIPGIADHSYGIQVGKLAGL 824 + G+ F +K+I GI D SY +Q+ +LAGL Sbjct: 172 ITTGGLTFTYKLIDGICDPSYALQIAELAGL 202 >gnl|CDD|73044 cd03285, ABC_MSH2_euk, MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 222 Score = 230 bits (589), Expect = 9e-61 Identities = 100/222 (45%), Positives = 135/222 (60%), Gaps = 10/222 (4%) Query: 613 IVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNAL 672 ++K+ RHP VE Q FI ND L + + ++TGPNMGGKST++RQ + Sbjct: 1 VLKEARHPCVE----AQDDVAFIPNDVTL----TRGKSRFLIITGPNMGGKSTYIRQIGV 52 Query: 673 IVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSF 732 IV+MAQ+G +VP A I IVD + +RVG++D+ G STFM EM+ETA+IL AT S Sbjct: 53 IVLMAQIGCFVPCDSADIPIVDCILARVGASDSQLKGVSTFMAEMLETAAILKSATENSL 112 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHN--ATL 790 +I+DE+GRGT+T DG +AWA EY+ +C L ATHFHELT L+ + N T Sbjct: 113 IIIDELGRGTSTYDGFGLAWAIAEYIATQIKCFCLFATHFHELTALADEVPNVKNLHVTA 172 Query: 791 QVSDSNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRA 832 D++ + L+KV G D S+GI V +LA P VI A Sbjct: 173 LTDDASRTLTMLYKVEKGACDQSFGIHVAELANFPKEVIEMA 214 >gnl|CDD|35442 KOG0221, KOG0221, KOG0221, Mismatch repair ATPase MSH5 (MutS family) [Replication, recombination and repair]. Length = 849 Score = 217 bits (554), Expect = 1e-56 Identities = 150/588 (25%), Positives = 270/588 (45%), Gaps = 40/588 (6%) Query: 313 SLLKTIDYSITGAGGRLFAERIASPLTDSTKINTRLDSINFFI--QNPILINPIQKILKS 370 SL ++ + G +L +P TD ++++RLD I FF+ QN + + ++L Sbjct: 268 SLFGLLNRCHSKWGEKLLRLWFTNPTTDLGELSSRLDVIQFFLLPQNADMAQMLSRLLGR 327 Query: 371 SPDVPRSLSRLKIGRGEPKDIAVIRDGIRSGINILNLFLKNDLPEELRGAVEK-----LK 425 +VP L R+K G + D V+ + S + I + +L + + L Sbjct: 328 IKNVPLILKRMKSGHTKLSDWQVLYSTVYSALGIRDACRSLPQSIQLFRDIAQEFSDDLH 387 Query: 426 KLPQSLEKTLSSMLSDDLPTFKRDGGFLRDGADASLDETRSLRDQSKRIIASLQLKYAE- 484 ++ + K + S F + G D LDE R + + K E Sbjct: 388 EIASLIGKVIDFEGSLAENRFT-----VLPGIDPELDEKRRRYMGLPSFLTEVARKELEN 442 Query: 485 -ETKIKNLKIKHNNNLGYFIEVTSSSASVLKKDLESKDRFIHRQTMSNLTR-FTTLELID 542 +++I ++ + + +G+ + + + V D E+ F+ R T EL Sbjct: 443 LDSRIPSVSVVYIPLIGFLLSIPRLPSMVEASDFENGLDFMFLSEEKLHYRNARTKELDA 502 Query: 543 LENRITNATNSALLIELESFEILSNAIIEQSESLDNASQVIAIIDISIALAILAKEQNYC 602 L I E L ++ + L + + +D+ ++LA A + Y Sbjct: 503 LLGDIYCEIRDQ---ETLIMYQLQCQVLARKAVLTRVLDLASRLDVLLSLASAAADYGYS 559 Query: 603 RP-IIDNSTNFIVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMG 661 RP ++ +++GRHP++E F+ N ++ + G++ ++TGPN Sbjct: 560 RPRLVPEVLILRIQNGRHPLMELCADT-----FVPNSTEI----GGDKGRIKVITGPNAS 610 Query: 662 GKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETA 721 GKS +L+Q LIV +A +GS+VPA A IGIVD++F+R+ S ++++ G+STFM+++ + A Sbjct: 611 GKSIYLKQVGLIVFLAHIGSFVPAEEAEIGIVDRIFTRIHSCESVSLGQSTFMIDLNQVA 670 Query: 722 SILNQATNQSFVILDEIGRGTATLDGLSIAWATIEYLHETNRC--RGLLATHFHELTDLS 779 L AT QS V++DE G+GT T DGLS+ + + + R + THFHEL + Sbjct: 671 KALRNATAQSLVLIDEFGKGTNTEDGLSLLASVMRHWLARGPTCPRIFVCTHFHELVNEQ 730 Query: 780 ----KSLKRFHNATLQVSDSNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRAYDI 835 + +F + D E I+FL++V G+A S+ + K AGLP+ V++RA ++ Sbjct: 731 LLPQNPIVQFLTMEVLREDG-EDIVFLYRVCEGLAKASFALHTAKQAGLPDKVVARAKEV 789 Query: 836 LKTFEKLYHHNQKDMRLYYPEIQTKESKNNLSKNDKLFVEKIKCLNLD 883 K ++ ++ + +N + DK ++ NLD Sbjct: 790 SDAIRS-----GKPVKPVKDLLKKNQMENCQTLVDKFMKLDLELPNLD 832 >gnl|CDD|73045 cd03286, ABC_MSH6_euk, MutS6 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 218 Score = 214 bits (545), Expect = 1e-55 Identities = 98/226 (43%), Positives = 135/226 (59%), Gaps = 14/226 (6%) Query: 613 IVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNAL 672 ++ RHP L ++ F+ ND DL S ++ +LTGPNMGGKST LR L Sbjct: 1 CFEELRHPC----LNASTASSFVPNDVDL----GATSPRILVLTGPNMGGKSTLLRTVCL 52 Query: 673 IVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSF 732 VIMAQMG VPA + +VD++F+R+G+ D++ G STFMVE+ ETA+IL AT S Sbjct: 53 AVIMAQMGMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATPDSL 112 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQV 792 VILDE+GRGT+T DG +IA A +EYL + +C L +TH+H L D + Sbjct: 113 VILDELGRGTSTHDGYAIAHAVLEYLVKKVKCLTLFSTHYHSLCDEFHEHGGVRLGHMAC 172 Query: 793 SDSNEG------IIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRA 832 + NE I FL+K++ GI SYG+ V +AG+P+ V+ RA Sbjct: 173 AVKNESDPTIRDITFLYKLVAGICPKSYGLYVALMAGIPDGVVERA 218 >gnl|CDD|73046 cd03287, ABC_MSH3_euk, MutS3 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 222 Score = 211 bits (539), Expect = 7e-55 Identities = 104/230 (45%), Positives = 156/230 (67%), Gaps = 19/230 (8%) Query: 613 IVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNAL 672 ++K+GRHP++E +L +S F+ ND LS G ++TGPNMGGKS+++RQ AL Sbjct: 2 LIKEGRHPMIE-SLLDKS---FVPNDIHLS----AEGGYCQIITGPNMGGKSSYIRQVAL 53 Query: 673 IVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSF 732 I IMAQ+GS+VPAS A + I D + +R+G++D++ G STFMVE+ ET+ IL+ T++S Sbjct: 54 ITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTSRSL 113 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSK----SLKRFH-- 786 VILDE+GRGT+T DG++IA+AT+ YL E +C L TH+ L ++ + S++ +H Sbjct: 114 VILDELGRGTSTHDGIAIAYATLHYLLEEKKCLVLFVTHYPSLGEILRRFEGSIRNYHMS 173 Query: 787 ----NATLQVSDSNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRA 832 + SDS I FL+K++ G+A S+G+ V +LAGLP ++ISRA Sbjct: 174 YLESQKDFETSDSQS-ITFLYKLVRGLASRSFGLNVARLAGLPKSIISRA 222 >gnl|CDD|73040 cd03281, ABC_MSH5_euk, MutS5 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 213 Score = 190 bits (483), Expect = 2e-48 Identities = 82/221 (37%), Positives = 131/221 (59%), Gaps = 19/221 (8%) Query: 614 VKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALI 673 ++ GRHP++E F+ ND ++ + ++TGPN GKS +L+Q ALI Sbjct: 2 IQGGRHPLLE-----LFVDSFVPNDTEI----GGGGPSIMVITGPNSSGKSVYLKQVALI 52 Query: 674 VIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFV 733 V +A +GS+VPA A IG+VDK+F+R+ S ++++SG+S FM+++ + + L AT +S V Sbjct: 53 VFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRRSLV 112 Query: 734 ILDEIGRGTATLDGLSIAWATIEYLHE--TNRCRGLLATHFHEL-----TDLSKSLKRFH 786 ++DE G+GT T DG + ATIE+L + R +++THFHEL +K Sbjct: 113 LIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRSLLPERLKIKFLT 172 Query: 787 NATLQ---VSDSNEGIIFLHKVIPGIADHSYGIQVGKLAGL 824 L + NE I +L++++PG+AD S+ I KLAG+ Sbjct: 173 MEVLLNPTSTSPNEDITYLYRLVPGLADTSFAIHCAKLAGI 213 >gnl|CDD|144998 pfam01624, MutS_I, MutS domain I. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in. Length = 113 Score = 182 bits (463), Expect = 6e-46 Identities = 66/117 (56%), Positives = 89/117 (76%), Gaps = 5/117 (4%) Query: 26 TPMMRQYIEIKSINPDSLVFYRMGDFYELFFDDALLASRCLGITLTKRGKHLGKDIPMCG 85 TPMMRQY+E+KS PD+++F+R+GDFYELF +DA +A+R LGITLT RG GK IPM G Sbjct: 1 TPMMRQYLELKSKYPDAVLFFRVGDFYELFGEDAEIAARELGITLTVRGGGSGKRIPMAG 60 Query: 86 VPVHTANHYIQKLIKIGHRIAICEQIESPLEAKKRGNKSLVRRNVVRLVTPGTLTED 142 VP H Y+++L+ G+++AICEQ E P EA K +V+R VVR++TPGTLT++ Sbjct: 61 VPEHAFETYLRRLVNKGYKVAICEQTEDPAEA-----KGVVKREVVRVITPGTLTDE 112 >gnl|CDD|73041 cd03282, ABC_MSH4_euk, MutS4 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 204 Score = 156 bits (396), Expect = 3e-38 Identities = 78/214 (36%), Positives = 121/214 (56%), Gaps = 13/214 (6%) Query: 613 IVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNAL 672 I++D RHPI+++ K FI ND L+ + S + ++TGPNM GKST+L+Q AL Sbjct: 1 IIRDSRHPILDRDKKN-----FIPNDIYLT----RGSSRFHIITGPNMSGKSTYLKQIAL 51 Query: 673 IVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSF 732 + IMAQ+G +VPA YA + I ++L SR+ + D++ STF EM ETA IL+ A S Sbjct: 52 LAIMAQIGCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGDSL 111 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQV 792 V++DE+GRGT++ DG +I+ A +E L + ATHF ++ + + + ++ Sbjct: 112 VLIDELGRGTSSADGFAISLAILECLIKK-ESTVFFATHFRDIAAILGNKSCVVHLHMKA 170 Query: 793 SDSNE-GIIFLHKVIPGIA--DHSYGIQVGKLAG 823 N GI +K++ G+ V LA Sbjct: 171 QSINSNGIEMAYKLVLGLYRIVDDGIRFVRVLAL 204 >gnl|CDD|73042 cd03283, ABC_MutS-like, MutS-like homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 199 Score = 130 bits (328), Expect = 2e-30 Identities = 61/212 (28%), Positives = 103/212 (48%), Gaps = 17/212 (8%) Query: 615 KDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALIV 674 K+ HP++ + +AND D+ N L+TG NM GKSTFLR + V Sbjct: 3 KNLGHPLIG-------REKRVANDIDMEKKN------GILITGSNMSGKSTFLRTIGVNV 49 Query: 675 IMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQ--SF 732 I+AQ G+ V AS + K+F+ + +D+L G S F E+ I+ +A Sbjct: 50 ILAQAGAPVCAS-SFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKGEPVL 108 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQV 792 +LDEI +GT + + + + A +++L G+++TH EL DL N + Sbjct: 109 FLLDEIFKGTNSRERQAASAAVLKFLKN-KNTIGIISTHDLELADLLDLDSAVRNYHFRE 167 Query: 793 SDSNEGIIFLHKVIPGIADHSYGIQVGKLAGL 824 + +IF +K+ PG++ +++ K G+ Sbjct: 168 DIDDNKLIFDYKLKPGVSPTRNALRLMKKIGI 199 >gnl|CDD|73039 cd03280, ABC_MutS2, MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.. Length = 200 Score = 110 bits (276), Expect = 2e-24 Identities = 55/212 (25%), Positives = 106/212 (50%), Gaps = 14/212 (6%) Query: 614 VKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALI 673 +++ RHP++ + + D L + ++ ++TGPN GGK+ L+ L+ Sbjct: 2 LREARHPLLPL-----QGEKVVPLDIQL-----GENKRVLVITGPNAGGKTVTLKTLGLL 51 Query: 674 VIMAQMGSYVPASY-AHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSF 732 +MAQ G +PA+ + + + + +F+ +G ++ STF M A IL A S Sbjct: 52 TLMAQSGLPIPAAEGSSLPVFENIFADIGDEQSIEQSLSTFSSHMKNIARILQHADPDSL 111 Query: 733 VILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQV 792 V+LDE+G GT ++G ++A A +E L E + TH+ EL + + NA+++ Sbjct: 112 VLLDELGSGTDPVEGAALAIAILEELLERG-ALVIATTHYGELKAYAYKREGVENASMEF 170 Query: 793 SDSNEGIIFLHKVIPGIADHSYGIQVGKLAGL 824 E + ++++ G+ S +++ + GL Sbjct: 171 DP--ETLKPTYRLLIGVPGRSNALEIARRLGL 200 >gnl|CDD|31386 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]. Length = 753 Score = 110 bits (276), Expect = 2e-24 Identities = 115/502 (22%), Positives = 202/502 (40%), Gaps = 46/502 (9%) Query: 337 PLTDSTKINTRLDSINFFIQNPILINPIQKILKSSPDVPRSLSRLKIGRGEPKDIAVIRD 396 P TD I L + IL + L DV +L RL+ G + + Sbjct: 34 PRTDLELIEEELSETAEALD--ILEDEGLPPLGGLNDVSEALGRLEKGGR------LHVE 85 Query: 397 GIRSGINILNLFLKNDLPEELRGAVEKLKKLPQSLEKTLSSM--LSDDLPTFKRDGGFLR 454 + + L F L+ A++KL+++ ++L L + L ++ D G ++ Sbjct: 86 ELLEISDFLRGF------RALKRAIKKLERIKRTLALALIELSDLELEINIPIDDDGLIK 139 Query: 455 DGADASLDETR-SLRDQSKRIIASLQLKYAEETKIKNL-KIKHNNNLGYFIEVTSSSASV 512 D A LD R LRD + I L+ + +I + + V + Sbjct: 140 DRASFELDAIRRQLRDLEEEIRDKLESLIRSKEAKYLQDRIVTTRDGREVLPVKAE---- 195 Query: 513 LKKDLESKDRFIHRQTMSNLTRFT-TLELIDLENRITNATNSALLIELESFEILSNAIIE 571 K ++ +H + S T + ++ L N + E LS + Sbjct: 196 FKGAIKGI---VHDTSSSGATLYIEPRSVVKLNNELRALLVEEDEEEERILRELSALVAP 252 Query: 572 QSESLDNASQVIAIIDISIALAILAKEQNYCRPIIDNSTNFIVKDGRHPIVEKTLKQQSS 631 L+ ++I +D A AK +P N + D RHP++++ Sbjct: 253 VIPELEILLEIIGELDFIEAKVRYAKALKGVKPDFSNDGVLELLDARHPLLKED------ 306 Query: 632 KPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVPASYAH-I 690 + ND +L D+ ++TGPN GGK+ L+ L+ +MAQ G +PA + Sbjct: 307 ---VPNDLELGEELDRL-----IITGPNTGGKTVTLKTLGLLRLMAQSGLPIPALEGSEL 358 Query: 691 GIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFVILDEIGRGTATLDGLSI 750 + K+F+ +G ++ STF M IL +A S V+ DE+G GT +G ++ Sbjct: 359 PVFVKIFADIGDEQSIEQSLSTFSSHMTNIVEILEKAD--SLVLFDELGSGTDPDEGAAL 416 Query: 751 AWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQVSDSNEGIIFLHKVIPGIA 810 A A +E L E + + TH+ EL L+ + NA+++ E + ++++ G+ Sbjct: 417 AIAILEDLLEKP-AKIVATTHYRELKALAAEREGVENASME--FDAETLRPTYRLLEGVP 473 Query: 811 DHSYGIQVGKLAGLPNTVISRA 832 S + GLP +I A Sbjct: 474 GRSNAFDIALRLGLPEPIIEEA 495 Score = 34.9 bits (80), Expect = 0.11 Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 3/86 (3%) Query: 654 LLTGPNMGGKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGR-ST 712 LLTG N GGK++ L A IV++A MG VPA A + VD++ L +G + Sbjct: 536 LLTGANSGGKTSLLELKAQIVVLAHMGLPVPAEEAKVEAVDEVKFLKKKKGILDAGAFES 595 Query: 713 FMVEMIETASILNQATNQSFVILDEI 738 + + + +L +A + + DE+ Sbjct: 596 TLKD--KKNKVLPEAKKRKLKLGDEV 619 >gnl|CDD|147399 pfam05190, MutS_IV, MutS family domain IV. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam00488. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds in part with globular domain IV, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in. Length = 92 Score = 87.7 bits (218), Expect = 1e-17 Identities = 39/95 (41%), Positives = 52/95 (54%), Gaps = 6/95 (6%) Query: 456 GADASLDETRSLRDQSKRIIASLQLKYAEETKIKNLKIKHNNNLGYFIEVTSSSASVLKK 515 G D LDE R L ++ + + L K E IK+LK+ +N GY+IEVT S A + K Sbjct: 1 GFDEELDELRDLLEELESELDELLAKERERLGIKSLKVGYNKVFGYYIEVTRSEAKKVPK 60 Query: 516 DLESKDRFIHRQTMSNLTRFTTLELIDLENRITNA 550 D +I RQT+ N RFTT EL LE+ + A Sbjct: 61 D------YIRRQTLKNGVRFTTPELKKLEDELLEA 89 >gnl|CDD|147397 pfam05188, MutS_II, MutS domain II. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075). Length = 133 Score = 80.9 bits (200), Expect = 1e-15 Identities = 33/126 (26%), Positives = 62/126 (49%), Gaps = 4/126 (3%) Query: 151 NYLMAVARIR-TEWAIAWIDISTGIFKIS-TSNHDRLISDIMRIDPREIIFSEKELS-HA 207 NYL A++R + +A++D+STG F +S + + L++++ R+ P+E++ E S Sbjct: 1 NYLAAISRGDGNRYGLAFLDLSTGEFGVSEFEDFEELLAELSRLSPKELLLPESLSSSTV 60 Query: 208 EYKSLFETLGNVAVAQPNVFFDHSISESRIADYYNITTVDTFGS-FSQVEKTAAAAAISY 266 L +P F+ + + + + + +D FG + AA A ISY Sbjct: 61 AESQKLLELRLRVGRRPTWLFELEHAYEDLNEDFGVEDLDGFGLEELPLALCAAGALISY 120 Query: 267 IKKTQM 272 +K+TQ Sbjct: 121 LKETQK 126 >gnl|CDD|72986 cd03227, ABC_Class2, ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.. Length = 162 Score = 79.6 bits (196), Expect = 4e-15 Identities = 43/142 (30%), Positives = 63/142 (44%), Gaps = 11/142 (7%) Query: 648 NSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFS--RVGSADN 705 G L ++TGPN GKST L L + AQ + S G + S + + Sbjct: 19 GEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRR-SGVKAGCIVAAVSAELIFTRLQ 77 Query: 706 LASGRSTFMVEMIETASILNQATNQ--SFVILDEIGRGTATLDGLSIAWATIEYLHETNR 763 L+ G E+ A IL A+ + ILDEI RG DG ++A A +E+L Sbjct: 78 LSGG----EKELSALALILALASLKPRPLYILDEIDRGLDPRDGQALAEAILEHL--VKG 131 Query: 764 CRGLLATHFHELTDLSKSLKRF 785 + ++ TH EL +L+ L Sbjct: 132 AQVIVITHLPELAELADKLIHI 153 >gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 157 Score = 50.3 bits (120), Expect = 3e-06 Identities = 32/132 (24%), Positives = 53/132 (40%), Gaps = 8/132 (6%) Query: 648 NSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLA 707 +G++ L GPN GKST LR A ++ + +++L R+G L+ Sbjct: 23 KAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLS 82 Query: 708 SGRSTFMVEMIETASILNQATNQSFVILDEIGRGTATLDGLSIAWATIEYLHETNRCRGL 767 G + + A L N ++LDE G + + L E R + Sbjct: 83 GG----QRQRVALARAL--LLNPDLLLLDEPTSGLDPASRERL-LELLRELAEEGR-TVI 134 Query: 768 LATHFHELTDLS 779 + TH EL +L+ Sbjct: 135 IVTHDPELAELA 146 >gnl|CDD|173971 cd08206, RuBisCO_large_I_II_III, Ribulose bisphosphate carboxylase large chain, Form I,II,III. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubico-like proteins (RLP), are missing critical active site residues. Length = 414 Score = 32.2 bits (74), Expect = 0.59 Identities = 33/126 (26%), Positives = 44/126 (34%), Gaps = 31/126 (24%) Query: 714 MVEMIETASILNQATNQSFVILDEIGRGTATLDGLSIAWATIEYLHETNRCRGLLATHFH 773 EMI+ A E+G +DG++ W I+ GL A H H Sbjct: 212 PEEMIKRAEFA-----------KELGSVIVMVDGVTAGWTAIQSARRWCPDNGL-ALHAH 259 Query: 774 ELTDLSKSLKRFHNATLQVSDSNEGIIFLHKVIPGIA-----DHSY-GIQVGKLAGLPNT 827 + H A N GI V+ +A DH + G VGKL G P+ Sbjct: 260 ---------RAGHAAF--TRQKNHGISMR--VLAKLARLIGVDHIHTGTVVGKLEGDPSE 306 Query: 828 VISRAY 833 V A Sbjct: 307 VKGIAD 312 >gnl|CDD|72988 cd03229, ABC_Class3, This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 178 Score = 32.1 bits (73), Expect = 0.70 Identities = 42/167 (25%), Positives = 70/167 (41%), Gaps = 30/167 (17%) Query: 622 VEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR--------QNALI 673 V K Q+ + ND L+ +G++ L GP+ GKST LR + I Sbjct: 6 VSKRYGQK----TVLNDVSLNIE----AGEIVALLGPSGSGKSTLLRCIAGLEEPDSGSI 57 Query: 674 VI----MAQMGSYVPASYAHIGIVDK---LFSRVGSADNLASGRSTFMVEMIETASILNQ 726 +I + + +P IG+V + LF + +N+A G S + + A L Sbjct: 58 LIDGEDLTDLEDELPPLRRRIGMVFQDFALFPHLTVLENIALGLSGGQQQRVALARAL-- 115 Query: 727 ATNQSFVILDEIGRGTATLDGLSIA--WATIEYLHETNRCRGLLATH 771 A + ++LDE T+ LD ++ A ++ L +L TH Sbjct: 116 AMDPDVLLLDE---PTSALDPITRREVRALLKSLQAQLGITVVLVTH 159 >gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.. Length = 211 Score = 31.2 bits (71), Expect = 1.4 Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 4/44 (9%) Query: 625 TLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR 668 + +D L+ G+ L+ GPN GKST LR Sbjct: 6 SFSYPDGARPALDDISLTIK----KGEFVLIVGPNGSGKSTLLR 45 >gnl|CDD|31318 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 254 Score = 31.0 bits (70), Expect = 1.8 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 648 NSGKLWLLTGPNMGGKSTFLR 668 G++ L GPN GKST L+ Sbjct: 28 EKGEITALIGPNGAGKSTLLK 48 >gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.. Length = 180 Score = 30.4 bits (69), Expect = 2.1 Identities = 35/161 (21%), Positives = 63/161 (39%), Gaps = 40/161 (24%) Query: 634 FIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR--------QNALIVI---------- 675 + +D LS +G++ + GPN GKST L+ + I++ Sbjct: 13 TVLDDLSLSIE----AGEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGKDLASLSP 68 Query: 676 --MAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFV 733 +A+ +YVP + +G+ + L+ G + + A L Q + Sbjct: 69 KELARKIAYVPQALELLGLAHLADRPF---NELSGGER----QRVLLARALAQEP--PIL 119 Query: 734 ILDEIGRGTATLDGLSIAWATIEYLHETNRCRG---LLATH 771 +LDE T+ LD ++ +E L R RG ++ H Sbjct: 120 LLDE---PTSHLD-IAHQIELLELLRRLARERGKTVVMVLH 156 >gnl|CDD|73005 cd03246, ABCC_Protease_Secretion, This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substrates ranges from inorganic ions, nutrients such as amino acids, sugars, or peptides, hydrophobic drugs, to large polypeptides, such as HlyA.. Length = 173 Score = 30.5 bits (69), Expect = 2.1 Identities = 32/137 (23%), Positives = 55/137 (40%), Gaps = 28/137 (20%) Query: 625 TLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR---------QNALIVI 675 + + ++P + + S G+ + GP+ GKST R + + Sbjct: 7 SFRYPGAEPPVLRNVSFSIE----PGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLD 62 Query: 676 MAQMGSYVPASY-AHIGIV---DKLFSRVGS-ADNLASGRSTFMVEMIETASILNQATNQ 730 A + + P H+G + D+LFS GS A+N+ SG + + A L N Sbjct: 63 GADISQWDPNELGDHVGYLPQDDELFS--GSIAENILSGGQ---RQRLGLARALYG--NP 115 Query: 731 SFVILDEIGRGTATLDG 747 ++LDE + LD Sbjct: 116 RILVLDE---PNSHLDV 129 >gnl|CDD|31316 COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]. Length = 257 Score = 30.2 bits (68), Expect = 2.6 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 9/53 (16%) Query: 648 NSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRV 700 N G+ W + GPN GK+T L L+ P S + ++ + F + Sbjct: 55 NPGEHWAIVGPNGAGKTTLLS---LLT------GEHPPSSGDVTLLGRRFGKG 98 >gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]. Length = 258 Score = 29.8 bits (67), Expect = 4.1 Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 4/37 (10%) Query: 632 KPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR 668 I +D S P G++ + GPN GKST L+ Sbjct: 14 GKPILDDLSFSIP----KGEITGILGPNGSGKSTLLK 46 >gnl|CDD|36999 KOG1788, KOG1788, KOG1788, Uncharacterized conserved protein [Function unknown]. Length = 2799 Score = 29.7 bits (66), Expect = 4.2 Identities = 44/257 (17%), Positives = 88/257 (34%), Gaps = 13/257 (5%) Query: 374 VPRSLSRLKIGRGEPKDIAVIRDGIRSGINILNLFLKNDLPEELRGAVEKLKKLPQSLEK 433 V + + IGR KD ++ G G N+L + G +K + L S K Sbjct: 117 VEQHIFSFVIGRAFVKDYEKLKAGSSHGANLL-----TAEEVLMSGPADK-QSLLDSGIK 170 Query: 434 TLSSMLSDDLPTFKRDGGFLRDGADASLDETRSLRDQSKRIIASLQLKYAEETKIKNLKI 493 + L +GA DE + ++ + + + A I Sbjct: 171 CCLIHFDLAALAYTVTSTDLTEGATEVEDEEKKNNEKVEGSVVQIMKALASFPSAAQSLI 230 Query: 494 KHNNNLGYFIEVTSSSASVLKKDLESKDRFIHRQTMSNLTRFTTLELIDLENRITNATNS 553 + ++ L F+ V + S + + Q + L L++ +N T A Sbjct: 231 EDDSLLLLFVMVANGSLMAFSRFKVGLVAEHNIQLHKLAMQILGLLLVN-DNGSTAAYIR 289 Query: 554 ALLIELESFEILSNAIIEQSESLDNASQVIAIIDISIALAILAKEQNYCRPIIDNSTNFI 613 + ++L A+ + +++ I+D+ + L+ Y + + + Sbjct: 290 KHHLI----KVLLMAVKNFDPACGDSAYTQGIVDLLLECVELSYRPEYGGVRLLD--DIR 343 Query: 614 VKDGRHPIVEKTLKQQS 630 G H +V+ LK S Sbjct: 344 NAHGYHFLVQFALKLSS 360 >gnl|CDD|31315 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]. Length = 345 Score = 29.5 bits (66), Expect = 4.8 Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 4/43 (9%) Query: 628 QQSSKPF--IANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR 668 K F D+S D SG+L L GP+ GKST LR Sbjct: 6 NNVKKRFGAFGALDDISL--DIKSGELVALLGPSGAGKSTLLR 46 >gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 213 Score = 29.3 bits (66), Expect = 5.2 Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 15/87 (17%) Query: 634 FIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNA--------LIVIMAQMGSYVPA 685 +D L+ G+ L GP+ GK+T LR A I+I + + VP Sbjct: 14 RALDDLSLTVE----PGEFLALLGPSGCGKTTLLRLIAGLERPDSGEILIDGRDVTGVPP 69 Query: 686 SYAHIGIV---DKLFSRVGSADNLASG 709 +IG+V LF + A+N+A G Sbjct: 70 ERRNIGMVFQDYALFPHLTVAENIAFG 96 >gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.. Length = 271 Score = 29.1 bits (65), Expect = 5.6 Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 1/34 (2%) Query: 650 GKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYV 683 G+L +LT GK+TFLR+ AL +I Q G V Sbjct: 30 GELIILTAGTGVGKTTFLREYALDLIT-QHGVRV 62 >gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]. Length = 692 Score = 29.0 bits (65), Expect = 7.0 Identities = 33/191 (17%), Positives = 70/191 (36%), Gaps = 9/191 (4%) Query: 450 GGFLRDGADASLDETRSLRDQSKRIIASLQLKYAEETKIKNLKIKHNNNLGYFI-EVTSS 508 GGF + S E + R + I + E +I N + + I + + Sbjct: 74 GGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSVDPENDPDILAMVGA 133 Query: 509 SASVLKKDL-------ESKDRFIHRQTMSNLTRFTTLELIDLENRITNATNSALLIELES 561 SA++ + + +I + N T LE L+ + ++ ++E E+ Sbjct: 134 SAALSLSGIPFLGPIGAVRVGYIDGIFVLNPT-LEELEESKLDLVVAGTKDAVNMVESEA 192 Query: 562 FEILSNAIIEQSESLDNASQVIAIIDISIALAILAKEQNYCRPIIDNSTNFIVKDGRHPI 621 E+ ++E E A Q + +AL + K+ P +D V+D Sbjct: 193 DELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDEELEAKVRDLAEDE 252 Query: 622 VEKTLKQQSSK 632 +++ + + + Sbjct: 253 LKEAVGIREKQ 263 >gnl|CDD|33894 COG4138, BtuD, ABC-type cobalamin transport system, ATPase component [Coenzyme metabolism]. Length = 248 Score = 28.8 bits (64), Expect = 7.1 Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 9/39 (23%) Query: 648 NSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMGSYVPAS 686 +G++ L GPN GKST L A+M S Sbjct: 23 RAGEILHLVGPNGAGKSTLL---------ARMAGMTSGS 52 >gnl|CDD|36145 KOG0927, KOG0927, KOG0927, Predicted transporter (ABC superfamily) [General function prediction only]. Length = 614 Score = 28.8 bits (64), Expect = 7.3 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 2/37 (5%) Query: 648 NSGKLWLLTGPNMGGKSTFLR--QNALIVIMAQMGSY 682 N G+ + L GPN GKSTFLR + I + Y Sbjct: 99 NRGRRYGLIGPNGSGKSTFLRAIAGREVPIPEHIDFY 135 >gnl|CDD|72994 cd03235, ABC_Metallic_Cations, ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.. Length = 213 Score = 28.6 bits (64), Expect = 8.1 Identities = 9/21 (42%), Positives = 12/21 (57%) Query: 648 NSGKLWLLTGPNMGGKSTFLR 668 G+ + GPN GKST L+ Sbjct: 23 KPGEFLAIVGPNGAGKSTLLK 43 >gnl|CDD|73055 cd03296, ABC_CysA_sulfate_importer, Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 239 Score = 28.7 bits (64), Expect = 8.2 Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 15/84 (17%) Query: 637 NDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLR--------QNALIVIMAQMGSYVPASYA 688 +D L P SG+L L GP+ GK+T LR + I+ + + VP Sbjct: 19 DDVSLDIP----SGELVALLGPSGSGKTTLLRLIAGLERPDSGTILFGGEDATDVPVQER 74 Query: 689 HIGIVDK---LFSRVGSADNLASG 709 ++G V + LF + DN+A G Sbjct: 75 NVGFVFQHYALFRHMTVFDNVAFG 98 >gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]. Length = 235 Score = 28.3 bits (63), Expect = 9.6 Identities = 11/30 (36%), Positives = 16/30 (53%) Query: 646 DKNSGKLWLLTGPNMGGKSTFLRQNALIVI 675 + G+ LL GPN GKST L+ ++ Sbjct: 26 EIEKGERVLLIGPNGSGKSTLLKLLNGLLK 55 >gnl|CDD|31247 COG1045, CysE, Serine acetyltransferase [Amino acid transport and metabolism]. Length = 194 Score = 28.3 bits (63), Expect = 9.7 Identities = 13/26 (50%), Positives = 16/26 (61%) Query: 283 REDIQSTLFIDSAARSNLEILRTLSG 308 REDI++ D AARS LE+L G Sbjct: 8 REDIRAVRERDPAARSYLEVLLYYPG 33 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 0.317 0.133 0.371 Gapped Lambda K H 0.267 0.0777 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 10,446,214 Number of extensions: 557252 Number of successful extensions: 1547 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1478 Number of HSP's successfully gapped: 66 Length of query: 920 Length of database: 6,263,737 Length adjustment: 103 Effective length of query: 817 Effective length of database: 4,038,010 Effective search space: 3299054170 Effective search space used: 3299054170 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: 62 (27.6 bits)