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)