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)