RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780222|ref|YP_003064635.1| DNA topoisomerase IV subunit B [Candidatus Liberibacter asiaticus str. psy62] (686 letters) >gnl|CDD|30536 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]. Length = 635 Score = 759 bits (1961), Expect = 0.0 Identities = 303/649 (46%), Positives = 414/649 (63%), Gaps = 21/649 (3%) Query: 39 SASDNYDASSIRILEGLEPVRMRPGMYIGGT-DEKALHHLFSEVIDNAMDEVIAGYANLI 97 S ++NYDASSI++LEGLE VR RPGMYIG T D + LHHL EV+DN++DE +AGYA+ I Sbjct: 1 SKTNNYDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRI 60 Query: 98 EVSLDGNGFLTVVDNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGGLHGV 157 +V+L +G ++V DNGRGIPV+ HPK S +E+I T LHAGGKFDN +Y++SGGLHGV Sbjct: 61 DVTLHEDGSISVEDNGRGIPVDIHPKE-KVSAVEVIFTVLHAGGKFDNDSYKVSGGLHGV 119 Query: 158 GISVVNALSDELHVTVARQNTIFSQKFSRGIPLSPLEK-KEKVRNKRGTRITFRPDPKIF 216 G+SVVNALS L V V R I+ Q+F RG+P++PLE K GT++ F+PDP+IF Sbjct: 120 GVSVVNALSTWLEVEVKRDGKIYRQRFERGVPVTPLEVIGSTDTKKTGTKVRFKPDPEIF 179 Query: 217 GDKAGFDAARLLKMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTK 276 G + FD L + + A+L+ VK + ++ EK+EF++ GGLK Y++ Sbjct: 180 G-ETEFDYEILKRRLRELAFLNKGVKITLTDERTG------EEKKEFHYEGGLKDYVEYL 232 Query: 277 LENRSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPE-ITSYCNTILTDEGGTHESGLR 335 + ++ + EIF EK G VE A+ W + E I S+ N I T EGGTHE+G R Sbjct: 233 NKGKTPLHEEIFYFNGEKDG---IAVEVALQWNDGYSENILSFVNNIPTREGGTHEAGFR 289 Query: 336 VALTRGIKKYAELTQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRT 395 ALTR I +YA+ + + DD+ ++SV I +P+F GQTK KL + + + Sbjct: 290 SALTRAINEYAKKKNLLKEGDLTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSI 349 Query: 396 VENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREVNRKT-AIRKLRLPGKLA 454 VE + + F +L +NP EA K++E I ++ R RK RE+ R+ A+ LPGKLA Sbjct: 350 VEKLVSEAFSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLA 409 Query: 455 DCSQNIAHGTELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIM 514 DC+ +ELF+VEGDSAGGSAKQ R+R QA+LPLRGKILNV A +KI N++I Sbjct: 410 DCTSKDPEKSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIQ 469 Query: 515 DLVQALGCRTRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFL 574 ++ ALG + E LRY K+IIMTDADVDGAHI +LLLTFFY+ M LIE H+++ Sbjct: 470 TIITALGTGIGKDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYI 529 Query: 575 ISPPLFRITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQLKETAMD 634 PPL+++ +G K+ YA+D+E +K+LE K K EI R+KGLGEM QL ET MD Sbjct: 530 AQPPLYKVKKGKKTFYAYDDEELEKLLERLGK--KKGYEIQRYKGLGEMNPDQLWETTMD 587 Query: 635 ANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQERASFIDD 683 R LL+V I + + + LMG K + R FI+E A F+++ Sbjct: 588 PETRRLLQVTI----EDADEADEIFSTLMGDKVEPRRNFIEENALFVEN 632 >gnl|CDD|35576 KOG0355, KOG0355, KOG0355, DNA topoisomerase type II [Chromatin structure and dynamics]. Length = 842 Score = 230 bits (589), Expect = 8e-61 Identities = 135/600 (22%), Positives = 238/600 (39%), Gaps = 39/600 (6%) Query: 52 LEGLEPVRMRPGMYIGGTDEKALHHLFSEVIDNAMDEVIAGYANLIEVSLD-GNGFLTVV 110 L + + R + L+ +F E++ NA D+ N I+V++D ++V Sbjct: 34 LMWVYDMEKRKMVQRTYV--PGLYKIFDEILVNAADKQRDPKMNTIKVTIDKEKNEISVY 91 Query: 111 DNGRGIPVENHPKFPNKSTLEIILTTLHAGGKFDNSTYEISGG--LHGVGISVVNALSDE 168 +NG+GIPV H E+I L +D+ +++GG +G + + + Sbjct: 92 NNGKGIPVTIHKV-EKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFT 150 Query: 169 LHVTVARQNTIFSQKFSRGIPLSPLEKKEKVRNKRGTRITFRPDPKIFGDKAGFDAARLL 228 + F Q + + K ++ T+ITF PD F L Sbjct: 151 VETADREYKMAFKQTWINNMTRDEEPKIVPSTDEDYTKITFSPD------LEKFKMKELD 204 Query: 229 KMTQSKAYLSGRVKTCWSCDKEIAEKYGIPEKEEFYFPGGLKTYLQTKLENRSLISSEIF 288 A ++ R K + + F +K YL+ N L Sbjct: 205 DDI--VALMARRAYDLAGSVKSVKVELNGKNIPVKGFYDYVKMYLEVLWLNDDL------ 256 Query: 289 TGKTEKKGTHRGTVEWAIAWCEENP--EITSYCNTILTDEGGTHESGLRVALTRGIKKYA 346 K W +A + + S+ N+I T +GGTH + + + Sbjct: 257 -----KPLHEVLNFRWEVALALSDVGFQQVSFVNSIATTKGGTHVDYVVDQIVAKLIDVV 311 Query: 347 ELTQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVENALRDPFDH 406 + + K+ IS+ + ++ I P F QTK +L + + L + F Sbjct: 312 KKKKVKKDISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTK 371 Query: 407 YLVQNPIEATKLLEWVIERSEERLRRRKQREVNRKTAIRKLR-LPGKLADCSQNIAHGTE 465 + + +L + + ++ L +++ + +R I KL S+ Sbjct: 372 AIELKGV-VESILSKSLNKYKDDLAKKRGKLTSRSKGIPKLEDANDAGTKTSEK----CT 426 Query: 466 LFIVEGDSA---GGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGC 522 L + EGDSA S R V PLRGK+LNV A ++I N +I +++ LG Sbjct: 427 LILTEGDSAKSLAVSGLSVVGRDYYGVFPLRGKLLNVREASHKQILKNAEINAIIKILGL 486 Query: 523 RTRSQYRE-EDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISPPLFR 581 + + +Y + E LRY K++IMTD D DG+HI LL+ F + L++ L P+ + Sbjct: 487 QYKKKYFDVESLRYGKLMIMTDQDHDGSHIKGLLINFIHHFWPSLLQIPFLEEFITPIVK 546 Query: 582 ITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQLKETAMDANKRTLL 641 T+G + V + +K + KI+ +KGLG + + KE D ++ +L Sbjct: 547 ATKGKQEVSFYSLPEYEKWKKNTDNWKSWKIK--YYKGLGTSTSKEAKEYFSDLDRHRIL 604 >gnl|CDD|173786 cd03366, TOPRIM_TopoIIA_GyrB, TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 114 Score = 176 bits (449), Expect = 2e-44 Identities = 68/114 (59%), Positives = 84/114 (73%) Query: 464 TELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCR 523 +EL+IVEGDSAGGSAKQ R+R QA+LPLRGKILNV A +KI N++I L+ ALG Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60 Query: 524 TRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISP 577 + E LRY K+IIMTDADVDGAHI +LLLTFF++ M LIE H+++ P Sbjct: 61 IGEDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114 >gnl|CDD|173780 cd01030, TOPRIM_TopoIIA_like, TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 115 Score = 167 bits (426), Expect = 7e-42 Identities = 62/115 (53%), Positives = 80/115 (69%), Gaps = 1/115 (0%) Query: 464 TELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCR 523 EL +VEGDSAGGSAKQ R+R QAV PLRGKILNV A +KI N++I ++++ALG Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60 Query: 524 TRSQYRE-EDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISP 577 + + LRY K+IIMTDADVDG+HI +LLLTFFY+ L+E L++ Sbjct: 61 IGKDDFDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115 >gnl|CDD|48467 cd00822, TopoII_Trans_DNA_gyrase, TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.. Length = 172 Score = 166 bits (422), Expect = 2e-41 Identities = 64/175 (36%), Positives = 98/175 (56%), Gaps = 6/175 (3%) Query: 267 GGLKTYLQTKLENRSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPE-ITSYCNTILTD 325 GGLK +++ +++ + E + EK G VE A+ W + E I S+ N I T Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDG---VEVEVALQWTDSYSENILSFVNNIPTP 57 Query: 326 EGGTHESGLRVALTRGIKKYAELTQNKRA--ISIISDDLMISAVGILSVFIREPEFAGQT 383 EGGTHE+G R ALTR I YA+ + + + DD+ ++SV + EP+F GQT Sbjct: 58 EGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQT 117 Query: 384 KTKLVSLDAQRTVENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREV 438 K KL + + + VE+A+R+ + +L +NP EA K+LE I ++ R RK RE+ Sbjct: 118 KDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172 >gnl|CDD|143961 pfam00204, DNA_gyraseB, DNA gyrase B. This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119. Length = 173 Score = 151 bits (383), Expect = 6e-37 Identities = 60/173 (34%), Positives = 95/173 (54%), Gaps = 2/173 (1%) Query: 268 GLKTYLQTKLENRSLISSEIFTGKTEKKGTHRGTVEWAIAWCEENPE-ITSYCNTILTDE 326 GLK Y++ ++++ + E+ + E+ R VE A+ W + E I S+ N I T + Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDSYSENIVSFVNNIPTPD 60 Query: 327 GGTHESGLRVALTRGIKKYAELTQ-NKRAISIISDDLMISAVGILSVFIREPEFAGQTKT 385 GGTH G R ALTR + +YA+ K+ I DD+ ++SV I P+F GQTK Sbjct: 61 GGTHVDGFRAALTRALNEYAKKKGLLKKKDKITGDDIREGLTAVVSVKIPNPQFEGQTKE 120 Query: 386 KLVSLDAQRTVENALRDPFDHYLVQNPIEATKLLEWVIERSEERLRRRKQREV 438 KL + + + VE+ + + F +L +NP A K+LE + ++ RL RK RE+ Sbjct: 121 KLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173 >gnl|CDD|144542 pfam00986, DNA_gyraseB_C, DNA gyrase B subunit, carboxyl terminus. The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyse the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,. Length = 65 Score = 86.0 bits (214), Expect = 3e-17 Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 4/69 (5%) Query: 607 HGKGKIEISRFKGLGEMLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTK 666 G K+EI RFKGLGEM QL ET MD R LL+V I ++ + + LMG Sbjct: 1 KGNKKVEIQRFKGLGEMNPEQLWETTMDPETRRLLQVTI----EDAEEADEMFSTLMGKD 56 Query: 667 ADERFKFIQ 675 + R +FI+ Sbjct: 57 VEPRREFIE 65 >gnl|CDD|173785 cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 120 Score = 85.8 bits (213), Expect = 4e-17 Identities = 39/99 (39%), Positives = 55/99 (55%), Gaps = 5/99 (5%) Query: 466 LFIVEGDSAGGSAKQARN---RSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGC 522 L + EGDSA A + R V PLRGK+LNV A ++I N +I ++ + LG Sbjct: 3 LILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGL 62 Query: 523 RTRSQYRE--EDLRYEKVIIMTDADVDGAHIASLLLTFF 559 + E + LRY +++IMTD D DG+HI LL+ F Sbjct: 63 QHGKSDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFI 101 >gnl|CDD|145582 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. Length = 111 Score = 70.0 bits (172), Expect = 2e-12 Identities = 35/149 (23%), Positives = 55/149 (36%), Gaps = 41/149 (27%) Query: 69 TDEKALHHLFSEVIDNAMDEVIAGYANLIEVSL---DGNGFLTVVDNGRGIPVENHPKFP 125 DE L + S ++DNA+ AG IEV+L G +TV DNG GIP E+ Sbjct: 1 GDEDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIPPED----- 53 Query: 126 NKSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTVARQNTIFSQKFS 185 + + D + ++ G G+G+S+V L + T+ ++ Sbjct: 54 -------LPKIFEPFFRTDKDSRKVGG--TGLGLSIVRKLVELHGGTITVESEP------ 98 Query: 186 RGIPLSPLEKKEKVRNKRGTRITFRPDPK 214 GT TF + Sbjct: 99 ----------------GGGTTFTFTLPLE 111 >gnl|CDD|28956 cd00075, HATPase_c, Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins. Length = 103 Score = 53.4 bits (128), Expect = 2e-07 Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 19/103 (18%) Query: 74 LHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGF---LTVVDNGRGIPVENHPKFPNKSTL 130 L + ++ NA+ G I +S++ +G + V DNG GIP E+ + Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDLER------- 52 Query: 131 EIILTTLHAGGKFDNSTYEISGGLHGVGISVVNALSDELHVTV 173 +F + + GG G+G+S+V L + + Sbjct: 53 --------IFERFSDGSRSRKGGGTGLGLSIVKKLVELHGGRI 87 >gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 83 Score = 47.0 bits (112), Expect = 2e-05 Identities = 28/97 (28%), Positives = 36/97 (37%), Gaps = 25/97 (25%) Query: 465 ELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRT 524 +L IVEG S + QA AV+ L G LN +T Sbjct: 2 KLIIVEGPSDALALAQAGGY-GGAVVALGGHALN------------------------KT 36 Query: 525 RSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQ 561 R + ++VII TDAD +G IA LL Sbjct: 37 RELLKRLLGEAKEVIIATDADREGEAIALRLLELLKS 73 >gnl|CDD|73195 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.. Length = 107 Score = 43.1 bits (101), Expect = 2e-04 Identities = 23/94 (24%), Positives = 35/94 (37%), Gaps = 22/94 (23%) Query: 301 TVEWAIAWCE----ENPEITSYCNTILTDEGGTHESGLRVALTRGIKKYAELTQNKRAIS 356 VE AI++ + S+ N EGGTH +R A TR + Sbjct: 28 RVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN------------- 74 Query: 357 IISDDLMISAVGILSVFI--REPEF-AGQTKTKL 387 DD+ V +LS+ I + TK ++ Sbjct: 75 --GDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEV 106 >gnl|CDD|145089 pfam01751, Toprim, Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks. Length = 89 Score = 41.1 bits (97), Expect = 0.001 Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 20/101 (19%) Query: 465 ELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRT 524 L IVEG S + +A V L G + S+ I ++ + L++ L Sbjct: 2 VLIIVEGPSDAIALAKAGGYKGNVV-ALLGHL-------SDVIPLTKEQLKLLKKL---- 49 Query: 525 RSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYD 565 + ++VI+ TD D +G IA LL Sbjct: 50 --------AKKDEVILATDPDREGEAIAWKLLELLKPLGKK 82 >gnl|CDD|34605 COG5000, NtrY, Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]. Length = 712 Score = 38.0 bits (88), Expect = 0.008 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 8/63 (12%) Query: 66 IGGTDEKALHHLFSEVIDNAMD-----EVIAGYANLIEVSLDG-NGF--LTVVDNGRGIP 117 IG D L +F ++ NA + E LI VSLD +G + V+DNG+G P Sbjct: 593 IGMADATLLGQVFGNLLKNAAEAIEAVEAEERRTALIRVSLDDADGRIVVDVIDNGKGFP 652 Query: 118 VEN 120 EN Sbjct: 653 REN 655 >gnl|CDD|31579 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]. Length = 538 Score = 34.9 bits (80), Expect = 0.067 Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 16/96 (16%) Query: 72 KALHHLFSEVIDNAMDEV-IAGYANLIEVSLDGNG----FLTVVDNGRGIPVENHPKFPN 126 ++L E++ N++D AG I+V ++ G + V DNG GIP E PK Sbjct: 35 RSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDNGPGIPEEQIPK--- 91 Query: 127 KSTLEIILTTLHAGGKFDNSTYEISGGLHGVGISVV 162 + + G KF S G G+GIS Sbjct: 92 ------VFGKMLYGSKFH--RNIQSRGQQGIGISAA 119 >gnl|CDD|48469 cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.. Length = 153 Score = 33.7 bits (77), Expect = 0.16 Identities = 29/126 (23%), Positives = 49/126 (38%), Gaps = 12/126 (9%) Query: 304 WAIAWC--EENPEITSYCNTILTDEGGTHESGLRVALTRGIKKYAELTQNKRAISIISDD 361 W +A + + S+ N+I T +GGTH + + +KK E+ + K I Sbjct: 33 WEVAVALSDGQFQQVSFVNSIATTKGGTH---VDYVADQIVKKLDEVVKKKNKGGINVKP 89 Query: 362 LMISAVGILSVFIR----EPEFAGQTKTKLVSLDAQRTVENALRDPFDHYLVQNPIEATK 417 + L +F+ P F QTK L + + L + F V++ I Sbjct: 90 FQVKNH--LWIFVNCLIENPSFDSQTKETLTTKPKSFGSKCELSEKFLKKAVKSGI-VES 146 Query: 418 LLEWVI 423 +L W Sbjct: 147 VLSWAK 152 >gnl|CDD|30671 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]. Length = 638 Score = 33.0 bits (75), Expect = 0.28 Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 6/45 (13%) Query: 80 EVIDNAMDEVIAGYANLIEVSLDGNGF--LTVVDNGRGIPVENHP 122 E+++N++D AG A I++ ++G G + V DNG GI E+ P Sbjct: 30 ELVENSLD---AG-ATRIDIEVEGGGLKLIRVRDNGSGIDKEDLP 70 >gnl|CDD|30987 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 336 Score = 31.7 bits (70), Expect = 0.66 Identities = 13/55 (23%), Positives = 22/55 (40%) Query: 69 TDEKALHHLFSEVIDNAMDEVIAGYANLIEVSLDGNGFLTVVDNGRGIPVENHPK 123 D + L + ++ NA+ G + D ++V D G GIP E + Sbjct: 224 GDPERLRQVLVNLLSNAIKYTPGGEITISVRQDDEQVTISVEDTGPGIPEEELER 278 >gnl|CDD|173859 cd08494, PBP2_NikA_DppA_OppA_like_6, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 448 Score = 31.1 bits (71), Expect = 1.2 Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 5/56 (8%) Query: 586 TKSVYAHDEEHKQKILEEFKKHGKGKI-----EISRFKGLGEMLASQLKETAMDAN 636 +Y +D + +++L E + + + +GE++ASQL E + Sbjct: 292 LTGLYPYDPDKARQLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVK 347 >gnl|CDD|36194 KOG0976, KOG0976, KOG0976, Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]. Length = 1265 Score = 29.3 bits (65), Expect = 3.8 Identities = 13/97 (13%), Positives = 34/97 (35%) Query: 581 RITQGTKSVYAHDEEHKQKILEEFKKHGKGKIEISRFKGLGEMLASQLKETAMDANKRTL 640 Q TK ++ + + ++ + + + + F L + MD Sbjct: 313 DSEQATKYLHLENMKLTRQKADIRCALLEARRKAEGFDDKLNELEKKRDMALMDVRSIQE 372 Query: 641 LRVEINKDLNSLKDTQDSINKLMGTKADERFKFIQER 677 + + ++L SL + Q + + + F+ Q + Sbjct: 373 KKENVEEELQSLLELQAERQEQIDELKNHIFRLEQGK 409 >gnl|CDD|36467 KOG1253, KOG1253, KOG1253, tRNA methyltransferase [Translation, ribosomal structure and biogenesis]. Length = 525 Score = 29.2 bits (65), Expect = 4.1 Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 11/102 (10%) Query: 590 YAHDEEHKQKILEEFKKHGKGKIEISR-FKGLGEMLASQLKETAMDANKRTLLRVEINKD 648 EE ++LE G + ++ G+ +++A+ L E A+ + +R VE+N Sbjct: 103 LLKREEKSLRVLEALSATGLRSLRYAKELPGVRQVVANDLNENAVTSIQR---NVELNGV 159 Query: 649 LNSLKDTQDSINKLMGTK--ADERFKFIQ-----ERASFIDD 683 + ++ N LM + F I + F+D Sbjct: 160 EDIVEPHHSDANVLMYEHPMVAKFFDVIDLDPYGSPSPFLDS 201 >gnl|CDD|146358 pfam03682, UPF0158, Uncharacterized protein family (UPF0158). Length = 163 Score = 29.1 bits (65), Expect = 4.6 Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 4/86 (4%) Query: 345 YAELTQNKRAISIISDDLMISAVGILSVFIREPEFAGQTKTKLVSLDAQRTVENALRDPF 404 Y EL +N +I + I+ F+ E + TK KL+++ + R+ F Sbjct: 49 YQELEENPDRYCLIPKLSFYESKKIMEDFVNEKVYDIDTKEKLLNILQSKKA----REAF 104 Query: 405 DHYLVQNPIEATKLLEWVIERSEERL 430 +L +P E K ++ ERS R+ Sbjct: 105 LEFLYDHPEEQEKWQQFYNERSRIRI 130 >gnl|CDD|34223 COG4585, COG4585, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 365 Score = 29.0 bits (64), Expect = 4.7 Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 6/56 (10%) Query: 71 EKALHHLFSEVIDNAMDEVIAGYANLIEVSL---DGNGFLTVVDNGRGIPVENHPK 123 E AL + E + NA+ A + V+L D L V+DNG G + Sbjct: 277 EDALFRIVQEALTNAIRH---AQATEVRVTLERTDDELRLEVIDNGVGFDPDKEGG 329 >gnl|CDD|111435 pfam02534, TraG, TraG/TraD family. These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. Length = 468 Score = 28.5 bits (64), Expect = 6.7 Identities = 39/157 (24%), Positives = 64/157 (40%), Gaps = 32/157 (20%) Query: 524 TRSQYREEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISPPLFRIT 583 + S + DLR +K + + + S LL F+Q + +L L+L P Sbjct: 247 SGSDFDLRDLRRDKTSVYVILNPKDLTVVSPLLRVFFQMVVEL-----LYLKLP------ 295 Query: 584 QGTKSVYAHDEEHKQK--ILEEFKKHGK-GKIEISR--FKGLGEMLA------SQLKETA 632 D K+ +L+EF GK +E + +G G L SQLKET Sbjct: 296 -------NGDGRPKEVLFLLDEFPSLGKLEILEEALATIRGYGIRLTTICQSISQLKETY 348 Query: 633 MDANKRTLL---RVEINKDLNSLKDTQDSINKLMGTK 666 +++L V I ++ ++T I+KL+G Sbjct: 349 GGEGAKSILSNHAVVICFAASNDEETAKYISKLLGKT 385 >gnl|CDD|36002 KOG0783, KOG0783, KOG0783, Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]. Length = 1267 Score = 28.5 bits (63), Expect = 6.8 Identities = 17/95 (17%), Positives = 27/95 (28%), Gaps = 6/95 (6%) Query: 473 SAGGSAKQARNRSNQAVLPLRGK--ILNVASAGSEKIRNNQQIMDLVQALGCR-TRSQYR 529 S R R+ + + L K + + + D+ Q S + Sbjct: 649 SPLKENLSQRTRTCEMLANLLEKFHLAELLPFSVSRQPLLSLTNDIAQLYNNFLVLSDHE 708 Query: 530 EEDLRYEKVIIMTDADVDGAHIASLLLTFFYQEMY 564 E + VI + D V AH L Y Sbjct: 709 ET---MDTVIKLKDGKVLKAHKCFLSARLEYFSSM 740 >gnl|CDD|32186 COG2003, RadC, DNA repair proteins [DNA replication, recombination, and repair]. Length = 224 Score = 28.3 bits (63), Expect = 8.1 Identities = 13/58 (22%), Positives = 18/58 (31%), Gaps = 3/58 (5%) Query: 613 EISRFKGLGEMLASQLKETAMDANKRTLLRVEINKDLNSLKDTQDSINKLMGTKADER 670 E+S KG+G A Q+K KR L + + L E Sbjct: 67 ELSSVKGIGLAKAIQIKAAIELG-KRILAERLREGV--VITSPEAVAEYLRAELGGEE 121 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 0.316 0.134 0.377 Gapped Lambda K H 0.267 0.0580 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 7,938,137 Number of extensions: 422939 Number of successful extensions: 1192 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1164 Number of HSP's successfully gapped: 35 Length of query: 686 Length of database: 6,263,737 Length adjustment: 100 Effective length of query: 586 Effective length of database: 4,102,837 Effective search space: 2404262482 Effective search space used: 2404262482 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 (21.6 bits) S2: 61 (27.6 bits)