RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780814|ref|YP_003065227.1| DNA gyrase subunit B [Candidatus Liberibacter asiaticus str. psy62] (803 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 = 834 bits (2157), Expect = 0.0 Identities = 336/571 (58%), Positives = 429/571 (75%), Gaps = 5/571 (0%) Query: 5 IQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADII 64 + ++YDA SIQ+L+GL+AV+KRP MYIG T GLHH+++EV+DN+IDE+L GYAD I Sbjct: 1 SKTNNYDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRI 60 Query: 65 TVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124 VTL+ DGS +V DNGRGIP D+H +E +SA EVI T LHAGGKF+ SYKVSGGLHGVG Sbjct: 61 DVTLHEDGSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFDNDSYKVSGGLHGVG 120 Query: 125 VSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGND-TGTEVTFLPSSDIFS 183 VSVVNALS+WL++ +KR+G IY F G+ PL V GS TGT+V F P +IF Sbjct: 121 VSVVNALSTWLEVEVKRDGKIYRQRFERGVPVTPLEVIGSTDTKKTGTKVRFKPDPEIFG 180 Query: 184 VQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPL 243 +F+Y+ L+ RLREL+FLN V+I+L D+R+ E + Y+GG++ +V YL++ K PL Sbjct: 181 ETEFDYEILKRRLRELAFLNKGVKITLTDERTGEE-KKEFHYEGGLKDYVEYLNKGKTPL 239 Query: 244 MQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSY 303 + G +D I++++A++WNDGY EN+L F NNIP ++GGTH +G RSALTR I Y Sbjct: 240 HEEIFYFNGEKDGIAVEVALQWNDGYSENILSFVNNIPTREGGTHEAGFRSALTRAINEY 299 Query: 304 VEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDG 363 +K K+ + GDD REG T+V+S+K+PDP+F QTKEKL +SEVRS+VE V++ Sbjct: 300 AKKKNLLKEGD--LTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLVSEA 357 Query: 364 LSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPK 423 S +LEE+P EAK IV+K + A+ R+AAR+AR+LTRRK LDI LPGKLADC+ +DP+ Sbjct: 358 FSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSKDPE 417 Query: 424 KSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGT 483 KSELFLVEGDSAGGSAKQGR RE QAILPLRGKILNVE+AR DK+L ++EI T+ITALGT Sbjct: 418 KSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIQTIITALGT 477 Query: 484 GIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYG 543 GIG+D FD+ KLRYHKIIIMTDADVDGAHIRTLLLTFF+R MP LI NG +YI +PPLY Sbjct: 478 GIGKD-FDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYIAQPPLYK 536 Query: 544 ITRGKSLQYVKDEESLEDYLINQSLSEEIEL 574 + +GK Y D+E LE L + E+ Sbjct: 537 VKKGKKTFYAYDDEELEKLLERLGKKKGYEI 567 Score = 119 bits (301), Expect = 2e-27 Identities = 48/74 (64%), Positives = 60/74 (81%), Gaps = 1/74 (1%) Query: 731 RKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRRE 790 +KG +QRYKGLGEMN QLWETT++P+TR LL+V I DA +AD++FS LMGD+VEPRR Sbjct: 562 KKGYEIQRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFSTLMGDKVEPRRN 621 Query: 791 FIQENSL-PSALDI 803 FI+EN+L LDI Sbjct: 622 FIEENALFVENLDI 635 >gnl|CDD|35576 KOG0355, KOG0355, KOG0355, DNA topoisomerase type II [Chromatin structure and dynamics]. Length = 842 Score = 262 bits (670), Expect = 3e-70 Identities = 144/603 (23%), Positives = 250/603 (41%), Gaps = 48/603 (7%) Query: 18 LKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNM-DGSCTV 76 L + ++KR + GL+ + E+L NA D+ + + I VT++ +V Sbjct: 34 LMWVYDMEKRKMVQR---TYVPGLYKIFDEILVNAADKQRDPKMNTIKVTIDKEKNEISV 90 Query: 77 SDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGG--LHGVGVSVVNALSSW 134 +NG+GIP +HK E + E+I L ++ KV+GG +G + + + Sbjct: 91 YNNGKGIPVTIHKVEKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFT 150 Query: 135 LKLRIKREGNIYEMSFING-ILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDTLQ 193 ++ + ++ ++IN D + S D T++TF P + F +++ + D + Sbjct: 151 VETADREYKMAFKQTWINNMTRDEEPKIVPSTDED-YTKITFSPDLEKFKMKELDDDIVA 209 Query: 194 HRLRELSFLNS---SVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRH-KKPLMQSPIR 249 R L SV++ L K P ++ F Y+ + + + ++ Sbjct: 210 LMARRAYDLAGSVKSVKVELNGKNIP------------VKGFYDYVKMYLEVLWLNDDLK 257 Query: 250 IQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFG 309 N ++A+ +D + V F N+I GGTH+ + + ++ V+K Sbjct: 258 PLHEVLNFRWEVALALSDVGFQQV-SFVNSIATTKGGTHVDYVVDQIVAKLIDVVKKKKV 316 Query: 310 SKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLE 369 K SV + ++ + +P F SQTKE+L R + +++ + +E Sbjct: 317 KKD--ISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTKAIE 374 Query: 370 EHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFL 429 + I+ K L+ A +R + +R KG+ + SE K L L Sbjct: 375 LKGVVESIL-SKSLNKYKDDLAKKRGKLTSRSKGIPKLEDANDAGTKTSE----KCTLIL 429 Query: 430 VEGDSA---GGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIG 486 EGDSA S R+ + PLRGK+LNV A ++L + EI +I LG Sbjct: 430 TEGDSAKSLAVSGLSVVGRDYYGVFPLRGKLLNVREASHKQILKNAEINAIIKILGLQYK 489 Query: 487 QDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITR 546 + FD+ LRY K++IMTD D DG+HI+ LL+ F PSL+ FL P+ T+ Sbjct: 490 KKYFDVESLRYGKLMIMTDQDHDGSHIKGLLINFIHHFWPSLLQIPFLEEFITPIVKATK 549 Query: 547 GKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFYP 606 GK E + N S + L K+++ Sbjct: 550 GKQEVSFYSLPEYEKWKKNTD-------NWKSWKIKYYKGLGTSTSKEA------KEYFS 596 Query: 607 NHD 609 + D Sbjct: 597 DLD 599 Score = 34.9 bits (80), Expect = 0.091 Identities = 9/64 (14%), Positives = 18/64 (28%) Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789 K ++ YKGLG + + E + D +L + + Sbjct: 571 NWKSWKIKYYKGLGTSTSKEAKEYFSDLDRHRILFKYDGGIDDEAIDMAFSKKKIDARKE 630 Query: 790 EFIQ 793 + Sbjct: 631 WLRK 634 >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 = 228 bits (584), Expect = 4e-60 Identities = 90/115 (78%), Positives = 100/115 (86%), Gaps = 1/115 (0%) Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484 SEL++VEGDSAGGSAKQGR R QAILPLRGKILNVE+AR DK+L ++EI LITALGTG Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60 Query: 485 IGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKP 539 IG+D FD+ KLRYHKIIIMTDADVDGAHIRTLLLTFFFR M LI NG +YI +P Sbjct: 61 IGED-FDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114 >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 = 220 bits (561), Expect = 2e-57 Identities = 86/172 (50%), Positives = 125/172 (72%) Query: 227 GGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGG 286 GG++ FV L++ K+PL + PI I+G +D + +++A++W D Y EN+L F NNIP +GG Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGG 60 Query: 287 THLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEK 346 TH +G R+ALTR I Y +K+ KK + GDD REG T+V+S+K+P+P+F QTK+K Sbjct: 61 THETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDK 120 Query: 347 LVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDL 398 L +SEVRS+VES V + L WLEE+P EAK I++K + A+ R+AAR+AR+L Sbjct: 121 LGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172 >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 = 217 bits (556), Expect = 9e-57 Identities = 81/115 (70%), Positives = 94/115 (81%) Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484 EL LVEGDSAGGSAKQGR R QA+ PLRGKILNVE+A K+L ++EI +I ALG G Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60 Query: 485 IGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKP 539 IG+D FD++KLRY KIIIMTDADVDG+HIRTLLLTFF+R PSL+ NGFLYI + Sbjct: 61 IGKDDFDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115 >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 = 195 bits (499), Expect = 3e-50 Identities = 82/174 (47%), Positives = 118/174 (67%), Gaps = 4/174 (2%) Query: 228 GIEAFVSYLDRHKKPLMQSPIRIQGSR---DNISIDLAMRWNDGYHENVLCFTNNIPQKD 284 G++ +V L++ K PL I +G D I +++A++WND Y EN++ F NNIP D Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDSYSENIVSFVNNIPTPD 60 Query: 285 GGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTK 344 GGTH+ G R+ALTR + Y +K G K K + GDD REG T+V+S+K+P+P+F QTK Sbjct: 61 GGTHVDGFRAALTRALNEYAKKK-GLLKKKDKITGDDIREGLTAVVSVKIPNPQFEGQTK 119 Query: 345 EKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDL 398 EKL +SEVRS VES V++ + +LE++P AK I++K L A+ R AAR+AR+L Sbjct: 120 EKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 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 = 124 bits (315), Expect = 7e-29 Identities = 41/64 (64%), Positives = 53/64 (82%) Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789 G K + +QR+KGLGEMN QLWETT++P+TR LL+V I DA +AD++FS LMG +VEPRR Sbjct: 2 GNKKVEIQRFKGLGEMNPEQLWETTMDPETRRLLQVTIEDAEEADEMFSTLMGKDVEPRR 61 Query: 790 EFIQ 793 EFI+ Sbjct: 62 EFIE 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 = 103 bits (258), Expect = 2e-22 Identities = 46/113 (40%), Positives = 63/113 (55%), Gaps = 5/113 (4%) Query: 427 LFLVEGDSAGGSAKQGRS---RENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGT 483 L L EGDSA A G S R+ + PLRGK+LNV A +++ + EI + LG Sbjct: 3 LILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGL 62 Query: 484 GIGQDSF-DINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLI-HNGFL 534 G+ + LRY +++IMTD D DG+HI+ LL+ F PSL+ GFL Sbjct: 63 QHGKSDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKIPGFL 115 >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 = 67.7 bits (166), Expect = 1e-11 Identities = 34/111 (30%), Positives = 45/111 (40%), Gaps = 18/111 (16%) Query: 38 ESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDG---SCTVSDNGRGIPTDLHKEEGIS 94 E L ++ +LDNAI + G I VTL DG TV DNG GIP Sbjct: 3 EDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIP---------- 50 Query: 95 AAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNI 145 E + + ++ S KV G G+G+S+V L I E Sbjct: 51 -PEDLPKIFEPFFRTDKDSRKVGG--TGLGLSIVRKLVELHGGTITVESEP 98 >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 = 57.3 bits (138), Expect = 2e-08 Identities = 29/125 (23%), Positives = 53/125 (42%), Gaps = 25/125 (20%) Query: 229 IEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWND---GYHENVLCFTNNIPQKDG 285 ++ ++ + K + I ++G D ++ A+ + D + F N P ++G Sbjct: 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREG 58 Query: 286 GTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPD--PRFS-SQ 342 GTH+ +R A TR + GDD R +VLS+K+P + Sbjct: 59 GTHVKAVREAYTRAL-----------------NGDDVRRYPVAVLSLKIPPSLVDVNVHP 101 Query: 343 TKEKL 347 TKE++ Sbjct: 102 TKEEV 106 >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 = 54.2 bits (130), Expect = 1e-07 Identities = 29/102 (28%), Positives = 43/102 (42%), Gaps = 18/102 (17%) Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG---SCTVSDNGRGIPTDLHKEEGISAAE 97 L ++ +L NAI + EG IT+++ DG V DNG GIP + + Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDLE-------- 51 Query: 98 VIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139 +F+ S GG G+G+S+V L RI Sbjct: 52 ------RIFERFSDGSRSRKGGGTGLGLSIVKKLVELHGGRI 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 = 45.9 bits (109), Expect = 5e-05 Identities = 23/109 (21%), Positives = 34/109 (31%), Gaps = 26/109 (23%) Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484 +L +VEG S + Q A++ L G LN R ++L Sbjct: 1 KKLIIVEGPSDALALAQAGGY-GGAVVALGGHALNKTRELLKRLLG-------------- 45 Query: 485 IGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGF 533 ++II TDAD +G I LL + Sbjct: 46 -----------EAKEVIIATDADREGEAIALRLLELLKSLGKKVRRLLL 83 >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 = 39.8 bits (93), Expect = 0.003 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 3/74 (4%) Query: 276 FTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMP 335 F N+I GGTH+ + + +++ V+K K +V + ++ + Sbjct: 49 FVNSIATTKGGTHVDYVADQIVKKLDEVVKK---KNKGGINVKPFQVKNHLWIFVNCLIE 105 Query: 336 DPRFSSQTKEKLVS 349 +P F SQTKE L + Sbjct: 106 NPSFDSQTKETLTT 119 >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 = 39.2 bits (92), Expect = 0.004 Identities = 19/105 (18%), Positives = 32/105 (30%), Gaps = 25/105 (23%) Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484 L +VEG S + + + + L G + D + ++E Sbjct: 1 KVLIIVEGPSDAIALAKAGGYKGNVV-ALLGHLS-------DVIPLTKEQ---------- 42 Query: 485 IGQDSFDINKLRYHK--IIIMTDADVDGAHIRTLLLTFFFRQMPS 527 + K K +I+ TD D +G I LL Sbjct: 43 -----LKLLKKLAKKDEVILATDPDREGEAIAWKLLELLKPLGKK 82 >gnl|CDD|109760 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21). Length = 326 Score = 32.4 bits (74), Expect = 0.48 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 10/72 (13%) Query: 337 PRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRAR 396 S +E L+S +++ G SAW P + +++ K +DA +RD R Sbjct: 140 RDLSPAEREALLSLAKQAL-------GDSAWEPSFPSDTYVLLAKAVDAMFIRD---RLP 189 Query: 397 DLTRRKGVLDIA 408 L + V I Sbjct: 190 KLKTDRRVAGIK 201 >gnl|CDD|36006 KOG0787, KOG0787, KOG0787, Dehydrogenase kinase [Signal transduction mechanisms]. Length = 414 Score = 32.2 bits (73), Expect = 0.51 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 14/70 (20%) Query: 26 KRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYAD--------IITVTLN-MDGSCTV 76 ++Y+ S L++M++E+ NA+ ++E + D +TV D + Sbjct: 251 LSFTVYV-----PSHLYYMLFELFKNAMRATVEHHGDDGDELPPIKVTVAKGDEDLLIKI 305 Query: 77 SDNGRGIPTD 86 SD G G+P Sbjct: 306 SDRGGGVPHR 315 >gnl|CDD|33640 COG3850, NarQ, Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]. Length = 574 Score = 29.9 bits (67), Expect = 2.6 Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 5/76 (6%) Query: 43 HMIY---EVLDNAIDESLEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEE--GISAAE 97 H++ E L NAI + + + + TV DNG GI G++ Sbjct: 481 HLLQIVREALSNAIKHAQASEIKVTVSQNDGQVTLTVEDNGVGIDEAAEPSGHYGLNIMR 540 Query: 98 VIMTRLHAGGKFNQKS 113 RL + ++ Sbjct: 541 ERAQRLGGQLRIRRRE 556 >gnl|CDD|30987 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]. Length = 336 Score = 29.8 bits (65), Expect = 3.0 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 1/68 (1%) Query: 19 KGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSD 78 KG++ P + D L ++ +L NAI + G I + + +V D Sbjct: 208 KGIELAVDLPELPYVLGD-PERLRQVLVNLLSNAIKYTPGGEITISVRQDDEQVTISVED 266 Query: 79 NGRGIPTD 86 G GIP + Sbjct: 267 TGPGIPEE 274 >gnl|CDD|33099 COG3290, CitA, Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]. Length = 537 Score = 29.4 bits (66), Expect = 3.8 Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 4/44 (9%) Query: 48 VLDNAIDESLEGYAD-IITVTLNMDGS---CTVSDNGRGIPTDL 87 ++DNA++ L + I ++L+ G V+D G GIP ++ Sbjct: 435 LIDNALEALLAPEENKEIELSLSDRGDELVIEVADTGPGIPPEV 478 >gnl|CDD|173777 cd01027, TOPRIM_RNase_M5_like, TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. 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 nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 81 Score = 29.5 bits (67), Expect = 4.0 Identities = 14/40 (35%), Positives = 22/40 (55%) Query: 478 ITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLL 517 I G+ I +++ ++ K Y +II+TD D G IR L Sbjct: 26 IETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKL 65 >gnl|CDD|31579 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]. Length = 538 Score = 29.5 bits (66), Expect = 4.0 Identities = 30/109 (27%), Positives = 46/109 (42%), Gaps = 16/109 (14%) Query: 25 KKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLE-GYADIITVTLNMDG----SCTVSDN 79 +K M +G L ++E++ N++D E G I V + G V DN Sbjct: 22 RKNKEM-LGFDGPIRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDN 80 Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVV 128 G GIP EE I + ++ G KF++ S G G+G+S Sbjct: 81 GPGIP-----EEQIPK---VFGKMLYGSKFHRN--IQSRGQQGIGISAA 119 >gnl|CDD|173934 cd08175, G1PDH, Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. This family is bacteria specific. Length = 348 Score = 29.5 bits (67), Expect = 4.2 Identities = 7/26 (26%), Positives = 15/26 (57%) Query: 383 LDASMVRDAARRARDLTRRKGVLDIA 408 +D + R + A+++ R +LD+A Sbjct: 317 IDKELFRKSLILAKEIRDRYTLLDLA 342 >gnl|CDD|37391 KOG2180, KOG2180, KOG2180, Late Golgi protein sorting complex, subunit Vps53 [Intracellular trafficking, secretion, and vesicular transport]. Length = 793 Score = 29.2 bits (65), Expect = 4.3 Identities = 13/96 (13%), Positives = 32/96 (33%), Gaps = 2/96 (2%) Query: 289 LSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLV 348 + L+ +L QI + +F + + V+ P R + + Sbjct: 181 IDKLKKSLLSQIFQDFKAAFSGGETHEEALLLQKLSDACLVVDALEPSVR--EELIKWFC 238 Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD 384 S ++ + F + +A L++ + + D Sbjct: 239 SQQLEEYEQIFRENEEAASLDKLDRRYAWFKRLLRD 274 >gnl|CDD|146633 pfam04100, Vps53_N, Vps53-like, N-terminal. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events. Length = 375 Score = 29.0 bits (65), Expect = 4.8 Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 2/96 (2%) Query: 289 LSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLV 348 +S L+ +L QI + +FGS+ + R+ + V P R + + Sbjct: 166 ISKLKGSLLSQIFQDFKSAFGSQGEHRTGLLLQKLSDACLVADALDPSVR--EELIKWFC 223 Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD 384 S ++ + F + +AWL++ + + D Sbjct: 224 SQQLEEYEQIFRENEEAAWLDKIDRRYAWFKRLLRD 259 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 0.135 0.383 Gapped Lambda K H 0.267 0.0649 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 9,319,454 Number of extensions: 501084 Number of successful extensions: 1207 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1187 Number of HSP's successfully gapped: 36 Length of query: 803 Length of database: 6,263,737 Length adjustment: 102 Effective length of query: 701 Effective length of database: 4,059,619 Effective search space: 2845792919 Effective search space used: 2845792919 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 (27.4 bits)