RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780229|ref|YP_003064642.1| hypothetical protein
CLIBASIA_00570 [Candidatus Liberibacter asiaticus str. psy62]
         (1775 letters)



>gnl|CDD|31309 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
            subunits [DNA replication, recombination, and repair].
          Length = 767

 Score =  123 bits (310), Expect = 3e-28
 Identities = 115/585 (19%), Positives = 217/585 (37%), Gaps = 33/585 (5%)

Query: 1047 KEDEILLQEAQEFSAKLHKIREKNIV--LAEESLIKKFFGEEIKLSVFDSNTKESNKSLA 1104
            K    L     E+  +L K+ +K I   L E+  ++    E +         +   + L+
Sbjct: 176  KIKSELAGLLIEYLKRLRKVLDKIIPPPLFEKEEVRVDIVENLLELSESILLRRELELLS 235

Query: 1105 VINSTLEFAHSIRERVLFDELIQGINHIDDHTIYNSFIKDLKNLRMIWQQQVKTQEDFIE 1164
                 L+        +L  + +  I  +D         K+L N + +  +++ +  D   
Sbjct: 236  KFALILKRLLESLFEILRGKDLP-IKLLDVELELVEINKELDNEQKLAVKRLLSLNDLFL 294

Query: 1165 DTQLDMAQWAARCNDELVKLISRNSEAIKKPRWLNGWVN--LMHMVQDMQDKGLKEIQAA 1222
              Q        R    +++LI    E  K         N  + ++++ ++   +K     
Sbjct: 295  IHQGPFGTGKTRSVT-ILELIIELLENNKLKILPTAESNAAVDNLLRRLKRTVIKVELLR 353

Query: 1223 IFNNSLDVKYLESSLLAAIYHQLSQEILTEKPHLMHYSAVQFTAKQERFREYDKRLQFLQ 1282
            I + S  +K L+   L  +  +  +    +   L           +   RE  K  + L+
Sbjct: 354  IGHPSRVLKKLKLDTLEELLEKH-EIPGNKIAALDKVIRELREEGERIIREIAKLRERLE 412

Query: 1283 RQRIASVIGNQKIAQGISGGLKSDYTELSLIRSELGKKNRNIPIRQLISRAKNSLLQLKP 1342
            R+R+  +       +GI   L         +  +  K  + +    L  +A   +L+   
Sbjct: 413  RKRLDKISHLNVALRGILPALNKSEALWISLEEKQKKILKELRR--LKKKAVTKILEAAD 470

Query: 1343 CFMMSPMSVANYLEPKDVKFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRF 1402
              + S +S+A +   K  +FD VI+DE+SQ     AL  ++R K++++VGD KQLPPT F
Sbjct: 471  VVL-STLSIAGFSILKKYEFDYVIIDEASQATEPSALIALSRAKKVILVGDHKQLPPTVF 529

Query: 1403 FDHDNDQEDYDEEVAAVSQTESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYDNSL 1462
            F   + +         +S +            +  L+  YR ++ ++IA S+  FY+  L
Sbjct: 530  FKESSPEG--------LSASLFERLIDNGPEVVYLLRVQYR-MHPDIIAFSSKVFYNGRL 580

Query: 1463 IVFPSP--YTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDHALRYPEESLGVIAM 1520
             V  S   +T +D               D    EE       + +      +    VI  
Sbjct: 581  EVHTSFLAFTLLDGEIPEVVISNPLEFYDTLGAEEFFESKSKLNELEAEIVK----VIVD 636

Query: 1521 NAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFTYGP 1580
               +  L E+ I  +    ++V      L        +  ++  QG E+D I +S     
Sbjct: 637  ELLKDGLEENDIGVISPYRAQVSLIRRLLNEAGKGVEVGTVDGFQGREKDVIILSLVRSN 696

Query: 1581 HEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625
             + G   F            RRLNV  TR++R++ V  +   L+ 
Sbjct: 697  DDKGEIGFLG--------DPRRLNVALTRAKRKLIVVGSSSTLES 733


>gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication,
            recombination and repair].
          Length = 1100

 Score = 65.4 bits (159), Expect = 1e-10
 Identities = 66/314 (21%), Positives = 112/314 (35%), Gaps = 71/314 (22%)

Query: 1361 KFDLVIMDESSQIKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVAAVS 1420
            +FD  I+DE+SQI     LG ++   + V+VGD  QLPP              +E  + S
Sbjct: 796  QFDYCIIDEASQILLPLCLGPLSFSNKFVLVGDHYQLPPLVRSSEAR------QEGLSES 849

Query: 1421 QTESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYDNSLI----------------- 1463
              + + +      S   LQ  YR +N  ++  SN   Y N L                  
Sbjct: 850  LFKRLSEKHPEAVSSLTLQ--YR-MNREIMRLSNKLIYGNRLKCGSKEVSRASELDRKGA 906

Query: 1464 -VFPSPYTSVDRYGVGFTHVKNGVVV-------------DQG---NPEEARVIALAVKDH 1506
                   +S D +          V               ++G   N  EA++I+  V+D 
Sbjct: 907  LSVYMDDSSSDHWLQAVLEPTRDVCFVNTDTCSTIESQGEKGGITNHGEAKLISELVEDF 966

Query: 1507 ALR-YPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQ 1565
                     +G+I+    Q +LI   ++                        I  ++  Q
Sbjct: 967  VKSGVKPSDIGIISPYRAQVELIRKILSS-------------------AVLEINTVDRYQ 1007

Query: 1566 GDERDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDV 1625
            G ++D I +SF     +       + G +  D  WRRLNV  TR+++++ +  +   L+ 
Sbjct: 1008 GRDKDCIIVSFVRSNKK------SKVGELLKD--WRRLNVALTRAKKKLILVGSKSTLES 1059

Query: 1626 VVDIDSKLGIRVMR 1639
                   L +   R
Sbjct: 1060 YPPFRQLLKLLENR 1073



 Score = 46.1 bits (109), Expect = 9e-05
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 409 QHSAVIDVINGKN-LIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRL 467
           Q  A++  +  ++  +I G PGTGK+ TI+ +I   +  GKK+L  +   +A++ +  +L
Sbjct: 674 QRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGKKVLLTSYTHSAVDNILIKL 733

Query: 468 EKAGLGEFCLELHSHKVHK 486
           +  G+    L     K+H 
Sbjct: 734 KGFGIYILRLG-SEEKIHP 751


>gnl|CDD|37014 KOG1803, KOG1803, KOG1803, DNA helicase [Replication, recombination
           and repair].
          Length = 649

 Score = 60.8 bits (147), Expect = 4e-09
 Identities = 41/132 (31%), Positives = 67/132 (50%), Gaps = 4/132 (3%)

Query: 393 EDIHQRCPLIDDSDSSQHSAVIDVINGKNL-IIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
            +I +      + +SSQ +AV   IN K+L II GPPGTGK++T+  II+  +   K++L
Sbjct: 174 IEIKKITFFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKKRVL 233

Query: 452 FCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAI--LDDLRKRIDN-RNIKTVPQE 508
            CA    A++ +  RL    L    +   +  +   A   LD L    DN +N K + ++
Sbjct: 234 VCAPSNVAVDNIVERLTHLKLNLVRVGHPARLLESVADHSLDLLSNTKDNSQNAKDISKD 293

Query: 509 IDVEITRYEELK 520
           ID+   +  + K
Sbjct: 294 IDILFQKNTKTK 305



 Score = 60.0 bits (145), Expect = 6e-09
 Identities = 81/339 (23%), Positives = 127/339 (37%), Gaps = 81/339 (23%)

Query: 1304 KSDYTELSLIRSELGKKNRNIPIRQLISRAKNSLLQLKPCFMMSPMSVANYLEPKDVKFD 1363
            K    E+ L+R +L K+ R           K  +   +  F     ++   L  +   FD
Sbjct: 311  KGIRKEIKLLRKDLRKRER--------KTVKEIISNSRVVFATLGGALDRLL--RKRTFD 360

Query: 1364 LVIMDESSQ-IKPEDALGVIARGKQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVAAVSQT 1422
            LVI+DE++Q ++P+  + V+  GK+ ++ GDPKQLPPT   D              VS  
Sbjct: 361  LVIIDEAAQAMEPQCWIPVLK-GKKFILAGDPKQLPPTVLSDKAKRGGLQ------VSLL 413

Query: 1423 ESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYDN-----------SLIVFP----- 1466
            E + +      S   L   YR  NE ++  SN  FY+             L   P     
Sbjct: 414  ERLAE-KFGNLSKILLNEQYRM-NEKIMNWSNEVFYNGQLKAASSVASHLLRDLPNVLAT 471

Query: 1467 ----SPYTSVDRYGVGFTHVKN--GVVVDQGNPEEARVIALAVKDHALRY---PEESLGV 1517
                SP   VD  G      +     +  + N  EA+++   VK   L         + V
Sbjct: 472  ESTKSPLVLVDTQGEKDEEKRGEEEELGSKYNEGEAKIVMEHVK--RLLEAGVQPSDIAV 529

Query: 1518 IAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFT 1577
            I+    Q  L+     +  R   +VE              +  ++  QG E+D +  S  
Sbjct: 530  ISPYNAQVSLLREEDEEDFR---DVE--------------VGTVDGFQGREKDVVIFSLV 572

Query: 1578 YGPHEPGGRVFQRFGPINSDIGW----RRLNVLFTRSRR 1612
                    R   +      ++G+    RRLNV  TR+RR
Sbjct: 573  --------RSNDKG-----EVGFLGETRRLNVAITRARR 598


>gnl|CDD|37013 KOG1802, KOG1802, KOG1802, RNA helicase nonsense mRNA reducing
           factor (pNORF1) [RNA processing and modification].
          Length = 935

 Score = 53.5 bits (128), Expect = 6e-07
 Identities = 36/173 (20%), Positives = 61/173 (35%), Gaps = 41/173 (23%)

Query: 379 ASSNQNIEYKI------DEIEDIHQRCPL--------IDDSDSSQHSAVIDVINGKNLII 424
           A   + +   +        +ED   +  L        +   ++SQ +AV  V+     +I
Sbjct: 371 AVDEKKVSGYLYHKLLGHPVEDSSLKKLLPRRFSVPNLPKLNASQSNAVKHVLQRPLSLI 430

Query: 425 EGPPGTGKSQTITNII-AAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLG---------- 473
           +GPPGTGK+ T   I+   A  H   +L CA    A++ +  ++ K GL           
Sbjct: 431 QGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKTGLKVVRLCAKSRE 490

Query: 474 ------EFCLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELK 520
                  F       +   +  L  L K  D             E++  +E K
Sbjct: 491 DIESDVSFLSLHEQLRNMDKPELQKLLKLKDEGG----------ELSSSDEKK 533



 Score = 50.4 bits (120), Expect = 4e-06
 Identities = 89/399 (22%), Positives = 142/399 (35%), Gaps = 75/399 (18%)

Query: 1250 LTEKPHLMHYSAVQFTAKQERFREYDKRLQFLQRQ-RIASVIGNQKIAQGISGGLKSDYT 1308
            L EK H      V+  AK     E D     L  Q R       QK+ +     LK +  
Sbjct: 470  LAEKIHKTGLKVVRLCAKSREDIESDVSFLSLHEQLRNMDKPELQKLLK-----LKDEGG 524

Query: 1309 ELSLIRSELGKKNRNIPIRQLISRAKNSLLQLKPCFMMSPMSVANYLEPKDVKFDLVIMD 1368
            ELS         +     R+L   A+  LL        + +   +       KF  V++D
Sbjct: 525  ELS--------SSDEKKYRKLKRAAEKELLNQADVICCTCVGAGD-RRLSKFKFRTVLID 575

Query: 1369 ESSQIKPEDALGVIARG-KQIVVVGDPKQLPPTRFFDHDNDQEDYDEEVAAVSQTESILD 1427
            E++Q    + L  +  G KQ+V+VGD KQL P              ++ A    ++S+ +
Sbjct: 576  EATQATEPECLIPLVLGAKQLVLVGDHKQLGPVIM----------CKKAATAGLSQSLFE 625

Query: 1428 ALLPLF-SMRRLQWHYRSLNENLIACSNYYFYDNSL-------------IVFPSPYTSVD 1473
             L+ L     RLQ  YR ++  L    +  FY+  L             + FP P     
Sbjct: 626  RLISLGIKPIRLQVQYR-MHPALSEFPSNMFYEGELQNGVTEIERSPLGVDFPWPQPDKP 684

Query: 1474 RYGVGFTHVKNGVVVDQG-----NPEEA----RVIALAVKDHALRYPEESLGVIAMNAKQ 1524
               + F        +        N  EA    ++I   +K          +GVI     Q
Sbjct: 685  ---LFFYVCYGQEEISASGTSFLNRTEAANCEKIITKLLKSGV---KPSQIGVITPYEGQ 738

Query: 1525 RDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFTYGPHEPG 1584
            R  I   +N +    S  +    ++        + +++  QG E+D I +S         
Sbjct: 739  RSYI---VNYMQTNGSLHKDLYKEVE-------VASVDAFQGREKDFIILSCVR------ 782

Query: 1585 GRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYL 1623
                Q  G +N     RRLNV  TR++  + +    + L
Sbjct: 783  SNEHQGIGFLNDP---RRLNVALTRAKYGLVIVGNPKVL 818


>gnl|CDD|29956 cd00221, Vsr, Very Short Patch Repair (Vsr) Endonuclease.
            Endonucleases in DNA repair that recognize damaged DNA
            and cleave the phosphodiester backbone. Vsr endonucleases
            have a common endonuclease topology that has been
            tailored for recognition of TG mismatches..
          Length = 115

 Score = 48.8 bits (116), Expect = 1e-05
 Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 25/107 (23%)

Query: 1660 KQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIECDGAMYN--- 1716
             +D+    +V + L + G+    Q  D+    D+VV     PG Y + I  DG  ++   
Sbjct: 15   SKDTKPERAVRSALWELGYRFRKQDKDLPGKPDIVV-----PG-YRLAIFVDGCFWHGHP 68

Query: 1717 --------------SAKSAR--DRDRLRQEVLERMGWRIRRIWSVDW 1747
                            K  R  +RDR  Q  LER+GWR+ R+W  + 
Sbjct: 69   CHKRKPPPKNTEFWLEKIERNVERDRRVQAALERLGWRVLRVWECEL 115


>gnl|CDD|32680 COG2852, COG2852, Uncharacterized protein conserved in bacteria
            [Function unknown].
          Length = 129

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELRELIS 1767
            +E DG  +   +   + D  R   LE  G+ + R W+ +   N D V+E I+  L E   
Sbjct: 69   VELDGGQH---EEREEYDAERDAFLESQGFTVLRFWNDEVLQNIDRVLEEILAVLEERRP 125

Query: 1768 Q 1768
             
Sbjct: 126  P 126


>gnl|CDD|37017 KOG1806, KOG1806, KOG1806, DEAD box containing helicases
            [Replication, recombination and repair].
          Length = 1320

 Score = 40.4 bits (94), Expect = 0.005
 Identities = 76/353 (21%), Positives = 124/353 (35%), Gaps = 69/353 (19%)

Query: 1294 KIAQGISGGLKSDYTELSLIR-SELGKKNRNIPIRQLISRAKNSLLQLKPCFMMSPMSVA 1352
              A G    L+  + +L   R  EL        +R    R    L++      M+    A
Sbjct: 928  DYATGCFRHLEYIFQQLEEFRAFEL--------LRSGEDRELYLLVKQAKIIAMTCTHAA 979

Query: 1353 ---NYLEPKDVKFDLVIMDESSQI------------KPEDALGVIARGKQIVVVGDPKQL 1397
                 L     K+D ++M+ES+QI             P+D      R K+ +++GD  QL
Sbjct: 980  LRRGDLVKLGFKYDNLLMEESAQILEIETFIPLLLQNPQDGH---NRLKRWILIGDHHQL 1036

Query: 1398 PPT----RFFDHDNDQEDYDEEVAAVSQTESILDA-------LLPLFSMRRLQWHYRSLN 1446
            PP      F  + N ++     +  +      L+A       +  L+      W Y  L 
Sbjct: 1037 PPVVKNQAFQKYSNMEQSLFTRLVRLGVPIIDLNAQGRARASIASLY-----NWRYPLLG 1091

Query: 1447 ENLIACSNYYF-YDNSLIVFPSPYTSVDRY-GVGFTHVKNGVVVDQGNPEEARVIALAVK 1504
                      F Y N+   +   + +V  + G G T    G   + G  E A  +AL   
Sbjct: 1092 NLPHVSPLPRFQYANAGFAYEFQFINVPDFKGSGETEPSPGFYQNLGEAEYA--VALFQY 1149

Query: 1505 DHALRYPEESLGVIAMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENV 1564
               L YP   + ++     Q+ LI   IN+ C  +  +            P  +  ++  
Sbjct: 1150 MRLLGYPANKISILTTYNGQKSLIRDIINRRCSHNPFI----------GQPAKVTTVDKF 1199

Query: 1565 QGDERDRIFISFTYGPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVF 1617
            QG + D I +S           V  R      D+  RRL V  +R+R  + V 
Sbjct: 1200 QGQQNDFIILSL----------VRTREVGHLRDV--RRLVVAMSRARLGLYVL 1240


>gnl|CDD|113256 pfam04480, DUF559, Protein of unknown function (DUF559). 
          Length = 109

 Score = 38.9 bits (91), Expect = 0.012
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELR 1763
            +E DG  ++      + D  R   LE  G+ + R W+ +   NP+ V+E I+ EL 
Sbjct: 57   VELDGGQHDEQ---EEYDARRTAWLESQGFTVLRFWNDEVLKNPEGVLEEILLELE 109


>gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit. 
          Length = 103

 Score = 38.4 bits (90), Expect = 0.017
 Identities = 14/44 (31%), Positives = 24/44 (54%)

Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
           Q  A+ +++  K  +I    G+GK+ T   +IA  +   KK+LF
Sbjct: 8   QIEAIRNLLEKKRGLIVMATGSGKTLTAAKLIARLLKGKKKVLF 51


>gnl|CDD|29960 cd01038, Endonuclease_DUF559, Domain of unknown function, appears to
            be related to a diverse group of endonucleases..
          Length = 108

 Score = 38.3 bits (89), Expect = 0.019
 Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 3/56 (5%)

Query: 1708 IECDGAMYNSAKSARDRDRLRQEVLERMGWRIRRIWSVDWFSNPDEVIEPIIRELR 1763
            +E DG            D  R   LE  G+R+ R W+ +   N + V+E I+  L 
Sbjct: 56   VELDGG---QHDEQIAYDAERDAWLEARGFRVLRFWNNEVLRNIEAVLEAILAALA 108


>gnl|CDD|36346 KOG1131, KOG1131, KOG1131, RNA polymerase II transcription
           initiation/nucleotide excision repair factor TFIIH,
           5'-3' helicase subunit RAD3 [Transcription, Replication,
           recombination and repair].
          Length = 755

 Score = 34.2 bits (78), Expect = 0.31
 Identities = 15/56 (26%), Positives = 31/56 (55%), Gaps = 4/56 (7%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGK----KILFCAQKMAAIEVVRHRLEK 469
              + ++E P GTGK+ ++ ++I A  LH      K+++C++ +  IE     L++
Sbjct: 34  AKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR 89


>gnl|CDD|37012 KOG1801, KOG1801, KOG1801, tRNA-splicing endonuclease positive
            effector (SEN1) [RNA processing and modification].
          Length = 827

 Score = 33.9 bits (77), Expect = 0.41
 Identities = 58/295 (19%), Positives = 87/295 (29%), Gaps = 50/295 (16%)

Query: 1360 VKFDLVIMDESSQIK-PEDALGVIARGKQ-IVVVGDPKQLPPTRFFDHDNDQEDYDEEVA 1417
               D V++DE++Q   P     +   G Q  ++VGD  QLP T    H +    +     
Sbjct: 535  PPLDTVVIDEAAQKYEPSSLEPLQLAGYQHCILVGDLAQLPATV---HSSPAGCF----- 586

Query: 1418 AVSQTESILDALLPLFSMRRLQWHYRSLNENLIACSNYYFYD--------------NSLI 1463
                  S+ + L        L      ++  +    +  FY                 L 
Sbjct: 587  --KYMTSLFERLELAGHKTLLLTVQYRMHPEISRFPSKEFYGGRLKDVNNVSESNTVKLW 644

Query: 1464 VFPSPYTSVDRYGVGFTHVKNGVVVDQGNPEEARVIALAVKDH-----ALRYPEESLGVI 1518
                 +     + V +   + G      N EE R +                   S+GVI
Sbjct: 645  HSGETFGPYPFFNVHYGKERAGGGKSPVNNEEVRFVGAIYSRLYKVSQPQVSVPGSVGVI 704

Query: 1519 AMNAKQRDLIESTINKLCRKDSEVEKAISKLRMHADPFFIKNLENVQGDERDRIFISFTY 1578
            +    Q   +     +           +S      D F        QG ERD I IS   
Sbjct: 705  SPYKNQVKALRERFPEAYSLLLANNVDLS--VSTVDSF--------QGGERDIIIISTVR 754

Query: 1579 GPHEPGGRVFQRFGPINSDIGWRRLNVLFTRSRRRIEVFSTMRYLDVVVDIDSKL 1633
               E         G I  +   RRLNV  TR+R    +      L     I + L
Sbjct: 755  SIDE---------GSIGFECNLRRLNVALTRARTCFWLVGNEITLAPSCSIWASL 800


>gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein.  This protein
           contains an ATP/GTP binding P-loop motif. It is found
           associated with IS21 family insertion sequences. The
           function of this protein is unknown, but it may perform
           a transposase function.
          Length = 178

 Score = 33.4 bits (77), Expect = 0.52
 Identities = 12/35 (34%), Positives = 18/35 (51%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
             +NL++ GPPG GK+     +   A   G  +LF
Sbjct: 46  QAENLLLLGPPGVGKTHLACALGHQACRAGYSVLF 80


>gnl|CDD|36207 KOG0989, KOG0989, KOG0989, Replication factor C, subunit RFC4
           [Replication, recombination and repair].
          Length = 346

 Score = 33.4 bits (76), Expect = 0.58
 Identities = 23/108 (21%), Positives = 42/108 (38%), Gaps = 22/108 (20%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL------FCAQKMAAIEVVRHRL---E 468
              + +  GPPGTGK+ T   +  A  L+ +++         A     I VVR ++    
Sbjct: 56  ILPHYLFYGPPGTGKTSTA--LAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFA 113

Query: 469 KAGLGEFCLELHSHKVHKRAILDD-----------LRKRIDNRNIKTV 505
           K  +     + +     K  ILD+           LR+ +++ +  T 
Sbjct: 114 KLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTR 161


>gnl|CDD|36209 KOG0991, KOG0991, KOG0991, Replication factor C, subunit RFC2
           [Replication, recombination and repair].
          Length = 333

 Score = 33.0 bits (75), Expect = 0.74
 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 8/79 (10%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKK----ILFCAQKMAAIEVVRHRLEKAGLG 473
           N  NLII GPPGTGK+ +I   +A  +L        +   A     I+VVR++++     
Sbjct: 47  NMPNLIISGPPGTGKTTSIL-CLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQK 105

Query: 474 EFCLELHSHKVHKRAILDD 492
           +  L    HK+    ILD+
Sbjct: 106 KVTLPPGRHKI---IILDE 121


>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
           the NTP binding domain of F1 and V1 H+ATPases, DnaB and
           related helicases as well as bacterial RecA and related
           eukaryotic and archaeal recombinases. This group also
           includes bacterial conjugation proteins and related DNA
           transfer proteins involved in type II and type IV
           secretion..
          Length = 165

 Score = 32.8 bits (74), Expect = 0.90
 Identities = 7/32 (21%), Positives = 16/32 (50%)

Query: 421 NLIIEGPPGTGKSQTITNIIAAAMLHGKKILF 452
            +++ GP G+GK+     +       G K+++
Sbjct: 1   LILVFGPTGSGKTTLALQLALNIATKGGKVVY 32


>gnl|CDD|38148 KOG2937, KOG2937, KOG2937, Decapping enzyme complex, predicted
            pyrophosphatase DCP2 [RNA processing and modification].
          Length = 348

 Score = 32.3 bits (73), Expect = 1.3
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 1655 KTKTNKQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIECD 1711
            + K +K +SD   ++    E+TGF    QL D    I+  +RD       + G+  D
Sbjct: 112  RGKISKDESDSDCAIREVTEETGFDYSKQLQDNEG-IETNIRDQLVRLFIINGVSED 167


>gnl|CDD|31392 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
           replication, recombination, and repair].
          Length = 654

 Score = 32.0 bits (72), Expect = 1.6
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 5/53 (9%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAA---AMLHGKKILFCAQKMAAIEVVRHRL 467
            G+ L+IE P GTGK  T+  ++ A   A   GKK++   +  A  E +    
Sbjct: 33  GGEGLLIEAPTGTGK--TLAYLLPALAYAREEGKKVIISTRTKALQEQLLEED 83


>gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction
           only].
          Length = 329

 Score = 32.0 bits (72), Expect = 1.6
 Identities = 12/52 (23%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 412 AVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVV 463
           A++ ++ G ++++EGPPG GK+  +   +A A+      + C   +   +++
Sbjct: 36  ALLALLAGGHVLLEGPPGVGKT-LLARALARALGLPFVRIQCTPDLLPSDLL 86


>gnl|CDD|39016 KOG3812, KOG3812, KOG3812, L-type voltage-dependent Ca2+ channel,
           beta subunit [Inorganic ion transport and metabolism,
           Signal transduction mechanisms].
          Length = 475

 Score = 32.0 bits (72), Expect = 1.7
 Identities = 30/131 (22%), Positives = 55/131 (41%), Gaps = 19/131 (14%)

Query: 486 KRAILDDLRKRIDNR-NIKTVPQEIDVE------------ITRYEELKGQLNQYAQEINQ 532
           ++A+ D L+ R D R +I  V  +I +             I      +  L +   EI +
Sbjct: 195 QKALFDFLKHRFDGRISITRVTADISLAKRSVLNNPSKRAIIERSNTRSSLAEVQSEIER 254

Query: 533 IWKNTELSIHQILMGAARYRH-----NLPLDPVQLHVEGLSGENADRLLRSRLEDQIKAF 587
           I++    S+  +++ A    H        L P+ ++++  S +   RL+RSR + Q K  
Sbjct: 255 IFELAR-SLQLVVLDADTINHPAQLAKTSLAPIIVYIKVSSPKVLQRLIRSRGKSQSKHL 313

Query: 588 KDVIVEFHKQA 598
              +V   K A
Sbjct: 314 NVQMVAADKLA 324


>gnl|CDD|73237 cd00820, PEPCK_HprK, Phosphoenolpyruvate carboxykinase (PEPCK), a
           critical gluconeogenic enzyme, catalyzes the first
           committed step in the diversion of tricarboxylic acid
           cycle intermediates toward gluconeogenesis. It catalyzes
           the reversible decarboxylation and phosphorylation of
           oxaloacetate to yield phosphoenolpyruvate and carbon
           dioxide, using a nucleotide molecule (ATP  or GTP) for
           the phosphoryl transfer, and has a strict requirement
           for divalent metal ions for activity.  PEPCK's separate
           into two phylogenetic groups based on their nucleotide
           substrate specificity (the ATP-, and GTP-dependent
           groups).HprK/P, the bifunctional histidine-containing
           protein kinase/phosphatase, controls the phosphorylation
           state of the phosphocarrier protein HPr and regulates
           the utilization of carbon sources by gram-positive
           bacteria. It catalyzes both the ATP-dependent
           phosphorylation of HPr and its dephosphorylation by
           phosphorolysis. PEPCK and the C-terminal catalytic
           domain of HprK/P are structurally similar with conserved
           active site residues suggesting that these two
           phosphotransferases have related functions..
          Length = 107

 Score = 31.9 bits (72), Expect = 1.8
 Identities = 10/34 (29%), Positives = 18/34 (52%)

Query: 407 SSQHSAVIDVINGKNLIIEGPPGTGKSQTITNII 440
           +S H  ++DV     ++I G  G GK++    +I
Sbjct: 3   TSLHGVLVDVYGKVGVLITGDSGIGKTELALELI 36


>gnl|CDD|37015 KOG1804, KOG1804, KOG1804, RNA helicase [RNA processing and
           modification].
          Length = 775

 Score = 31.5 bits (71), Expect = 2.2
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 423 IIEGPPGTGKSQTITNIIAAAMLHGKK--ILFCAQKMAAIEVVRHRL 467
           I+ GPPGTGK++     IA          IL CA   A+ +   HRL
Sbjct: 330 IVFGPPGTGKTENYREAIAIVSFTSPHFYILVCAPSNASGKQPAHRL 376


>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. 
          Length = 168

 Score = 31.4 bits (72), Expect = 2.3
 Identities = 10/30 (33%), Positives = 15/30 (50%)

Query: 421 NLIIEGPPGTGKSQTITNIIAAAMLHGKKI 450
            + I GPPG GK+  +  +I      G K+
Sbjct: 1   RIFITGPPGVGKTTLVKKVIELLKSEGVKV 30


>gnl|CDD|31860 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
           proteins [Cell division and chromosome partitioning].
          Length = 858

 Score = 31.3 bits (70), Expect = 2.3
 Identities = 26/139 (18%), Positives = 47/139 (33%), Gaps = 16/139 (11%)

Query: 389 IDEIEDIHQRCPLIDDSDSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHGK 448
           +DE  +      +    D  Q   VID+    +L+I G  G+GKS  +  +I + +    
Sbjct: 500 LDEFLERFPLGVIDLPKDIRQEPIVIDLAKAGHLLIAGATGSGKSVALNTMILSLLYTHS 559

Query: 449 K-------ILFCAQKMAAIEVVRHRLEKAGLGEFCLELHSHKVHKRAILDDLRKRIDNRN 501
                   I     ++AA + + H  +              K      L +L   ++ R 
Sbjct: 560 PEEVRFYIIDPKMLELAAYDGLPHLGDPVV--------TDEKEKAEKALAELVAEMERRY 611

Query: 502 IKTVPQEIDVEITRYEELK 520
                + +   I  Y E  
Sbjct: 612 KLFSEKGVRN-IEGYNEKI 629


>gnl|CDD|132846 cd07207, Pat_ExoU_VipD_like, ExoU and VipD-like proteins; homologus
           to patatin, cPLA2, and iPLA2.  ExoU, a 74-kDa enzyme, is
           a potent virulence factor of Pseudomonas aeruginosa. One
           of the pathogenic mechanisms of P. aeruginosa is to
           induce cytotoxicity by the injection of effector
           proteins (e.g. ExoU) using the type III secretion (T3S)
           system. ExoU is homologus to patatin and also has the
           conserved catalytic residues of mammalian
           calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2.
           In vitro, ExoU cytotoxity is blocked by the inhibitor of
           cytosolic and Ca2-independent phospholipase A2 (cPLA2
           and iPLA2) enzymes, suggesting that phospholipase A2
           inhibitors may represent a novel mode of treatment for
           acute P. aeruginosa infections. ExoU requires eukaryotic
           superoxide dismutase as a cofactor and cleaves
           phosphatidylcholine and phosphatidylethanolamine in
           vitro. VipD, a 69-kDa cytosolic protein, belongs to the
           members of Legionella pneumophila family and is
           homologus to ExoU from Pseudomonas. Even though VipD
           shows high sequence similarity with several functional
           regions of ExoU (e.g. oxyanion hole, active site serine,
           active site aspartate), it has been shown to have no
           phospholipase activity. This family includes ExoU from
           Pseudomonas aeruginosa and VipD of Legionella
           pneumophila.
          Length = 194

 Score = 31.5 bits (72), Expect = 2.4
 Identities = 25/136 (18%), Positives = 45/136 (33%), Gaps = 26/136 (19%)

Query: 162 GY--ADIEDLERAIKENKPLKPPHFQ----NNLSDNQI--QTAYFQDKLESILRLINEKS 213
           GY  ADI+D+ +     K L  P        +L       +    ++ L  +L+     S
Sbjct: 47  GYSAADIKDILKETDFAKLLDSPVGLLFLLPSLFKEGGLYKGDALEEWLRELLKEKTGNS 106

Query: 214 QISIKET-----GTSILYIV-----LGFLEWYEIDDYDNPRLAPLFTIPVALEKRSSTSQ 263
             +             L +V      G L  +  +   +        +PVA   R+S S 
Sbjct: 107 FATSLLRDLDDDLGKDLKVVATDLTTGALVVFSAETTPD--------MPVAKAVRASMSI 158

Query: 264 PGLTQYHLRYTGEEII 279
           P + +      G+  +
Sbjct: 159 PFVFKPVRLAKGDVYV 174


>gnl|CDD|29833 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
           protein kinase/phosphatase, controls the phosphorylation
           state of the phosphocarrier protein HPr and regulates
           the utilization of carbon sources by gram-positive
           bacteria. It catalyzes both the ATP-dependent
           phosphorylation of Ser-46 of HPr and its
           dephosphorylation by phosphorolysis. The latter reaction
           uses inorganic phosphate as substrate and produces
           pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK)
           and the C-terminal catalytic domain of HprK/P are
           structurally similar with conserved active site residues
           suggesting these two phosphotransferases have related
           functions.  The HprK/P N-terminal domain is structurally
           similar to the N-terminal domains of the MurE and MurF
           amino acid ligases..
          Length = 149

 Score = 31.4 bits (71), Expect = 2.4
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 410 HSAVIDVINGKNLIIEGPPGTGKSQTITNII-AAAMLHGKKILFCAQKM-----AAIEVV 463
           H  +++V  G  ++I GP G GKS+    +I     L     +   ++       A E +
Sbjct: 6   HGVLVEV-GGIGVLITGPSGIGKSELALELIKRGHRLVADDRVVVKREGGRLVGRAPEAL 64

Query: 464 RHRLEKAGLG 473
           +  +E  GLG
Sbjct: 65  KGLIEIRGLG 74


>gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase.  Members of this family
           include the DEAD and DEAH box helicases. Helicases are
           involved in unwinding nucleic acids. The DEAD box
           helicases are involved in various aspects of RNA
           metabolism, including nuclear transcription, pre mRNA
           splicing, ribosome biogenesis, nucleocytoplasmic
           transport, translation, RNA decay and organellar gene
           expression.
          Length = 167

 Score = 31.1 bits (71), Expect = 2.6
 Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 7/37 (18%)

Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAML 445
           Q  A+  ++ GK+++++ P G+GK+        A +L
Sbjct: 4   QAEAIPAILEGKDVLVQAPTGSGKT-------LAFLL 33


>gnl|CDD|48371 cd02117, NifH_like, This family contains the NifH (iron protein) of
           nitrogenase, L subunit (BchL/ChlL) of the
           protochlorophyllide reductase and the BchX subunit of
           the Chlorophyllide reductase. Members of this family use
           energey from ATP hydrolysis and transfer electrons
           through a Fe4-S4 cluster to other subunit for reduction
           of substrate..
          Length = 212

 Score = 31.3 bits (71), Expect = 2.6
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           + + I G  G GKS T  N+ AA    GKK+L
Sbjct: 1   RQIAIYGKGGIGKSTTSQNLSAALAEMGKKVL 32


>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
           Magnesium-chelatase is a three-component enzyme that
           catalyses the insertion of Mg2+ into protoporphyrin IX.
           This is the first unique step in the synthesis of
           (bacterio)chlorophyll. Due to this, it is thought that
           Mg-chelatase has an important role in channelling inter-
           mediates into the (bacterio)chlorophyll branch in
           response to conditions suitable for photosynthetic
           growth. ChlI and BchD have molecular weight between
           38-42 kDa.
          Length = 207

 Score = 31.3 bits (72), Expect = 2.7
 Identities = 9/15 (60%), Positives = 13/15 (86%)

Query: 419 GKNLIIEGPPGTGKS 433
           G NL++ GPPG+GK+
Sbjct: 22  GHNLLMIGPPGSGKT 36


>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
           transduction [Signal transduction mechanisms].
          Length = 260

 Score = 30.8 bits (69), Expect = 3.2
 Identities = 17/116 (14%), Positives = 41/116 (35%), Gaps = 15/116 (12%)

Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFCLE 478
           G  ++I GPPGTGK+      +      G+ +L+ + + +  E++               
Sbjct: 23  GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPEELLE-------------N 69

Query: 479 LHSHKVHKRAILDDLRKRIDNRNIKTVPQ--EIDVEITRYEELKGQLNQYAQEINQ 532
             S        ++  +  I +  +        +  +    EEL  ++ +  ++   
Sbjct: 70  ARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEKEGA 125


>gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication,
           recombination, and repair].
          Length = 254

 Score = 30.7 bits (69), Expect = 3.4
 Identities = 22/124 (17%), Positives = 44/124 (35%), Gaps = 7/124 (5%)

Query: 418 NGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILF--CAQKMAAIEVVRHRLEKAGLGEF 475
            G+NL++ GPPG GK+     I    +  G  +LF      ++ ++              
Sbjct: 104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLE----- 158

Query: 476 CLELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWK 535
              L   K     I+DD+     ++    +  ++         L    N    E ++++ 
Sbjct: 159 EKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRYESRSLIITSNLSFGEWDELFG 218

Query: 536 NTEL 539
           +  L
Sbjct: 219 DDAL 222


>gnl|CDD|177096 CHL00204, ycf1, Ycf1; Provisional.
          Length = 1832

 Score = 30.8 bits (70), Expect = 3.7
 Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 108 YDSDDEKKNYQVLQKVRDLIVEDIKTSNDLVDIREIEKKIEISLQKLTSIIQNYGYADIE 167
            +S++E K ++ L         D       + I+EI KK+     KL          ++E
Sbjct: 558 INSEEEIKIFKFLFDAVITDPNDQTIIKKSIGIKEISKKVPRWSYKLID--------ELE 609

Query: 168 DLERAIKENKPLKP 181
            LE   +EN P   
Sbjct: 610 QLEGENEENVPSDH 623


>gnl|CDD|29370 cd00288, Pyruvate_Kinase, Pyruvate kinase (PK):  Large allosteric
           enzyme that regulates glycolysis through binding of the
           substrate, phosphoenolpyruvate, and one or more
           allosteric effectors.  Like other allosteric enzymes, PK
           has a high substrate affinity R state and a low affinity
           T state.  PK exists as several different isozymes,
           depending on organism and tissue type.  In mammals,
           there are four PK isozymes: R, found in red blood cells,
           L, found in liver, M1, found in skeletal muscle, and M2,
           found in kidney, adipose tissue, and lung.  PK forms a
           homotetramer, with each subunit containing three
           domains.  The T state to R state transition of PK is
           more complex than in most allosteric enzymes, involving
           a concerted rotation of all 3 domains of each monomer in
           the homotetramer..
          Length = 480

 Score = 30.6 bits (69), Expect = 3.7
 Identities = 22/107 (20%), Positives = 45/107 (42%), Gaps = 8/107 (7%)

Query: 69  TKKQAQAYGFADTGNHHTIDESTWIEKLGLSINYDLPIEYDSDDEKKNYQVLQKVRDLIV 128
             K        +  N   +     +   G  +  DLP   + D     + V Q V  +  
Sbjct: 136 LSKDDDKTLVCEVLNGGVLGSRKGVNLPGTDV--DLPALSEKDKADLRFGVEQGVDMIFA 193

Query: 129 EDIKTSNDLVDIREI--EKKIEISLQKLTSIIQNY-GYADIEDLERA 172
             ++ ++D+++IRE+  EK  +I   K+ + I+N  G  + +++  A
Sbjct: 194 SFVRKASDVLEIREVLGEKGKDI---KIIAKIENQEGVNNFDEILEA 237


>gnl|CDD|30853 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha subunit
            - helicase superfamily I member [DNA replication,
            recombination, and repair].
          Length = 696

 Score = 30.9 bits (69), Expect = 3.9
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 3/40 (7%)

Query: 1363 DLVIMDESSQIKPEDALGV---IARGKQIVVVGDPKQLPP 1399
            DL+I+DE+S +    A G+   I +  ++++VGD  QLP 
Sbjct: 409  DLLIIDEASMLDTSLAFGLLSAIGKLAKVILVGDVDQLPS 448


>gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family.  FtsK has extensive
           sequence similarity to wide variety of proteins from
           prokaryotes and plasmids, termed the FtsK/SpoIIIE
           family. This domain contains a putative ATP binding
           P-loop motif.  It is found in the FtsK cell division
           protein from E. coli and the stage III sporulation
           protein E SpoIIIE which has roles in regulation of
           prespore specific gene expression in B. subtilis. A
           mutation in FtsK causes a temperature sensitive block in
           cell division and it is involved in peptidoglycan
           synthesis or modification. The SpoIIIE protein is
           implicated in intercellular chromosomal DNA transfer.
          Length = 202

 Score = 30.8 bits (70), Expect = 4.0
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 406 DSSQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAA 443
           D S +  V D++   +L+I G  G+GKS  +  +I + 
Sbjct: 25  DISGNPVVADLVKMPHLLIAGATGSGKSTFLNTLILSL 62


>gnl|CDD|32863 COG3049, COG3049, Penicillin V acylase and related amidases [Cell
           envelope biogenesis, outer membrane].
          Length = 353

 Score = 30.7 bits (69), Expect = 4.1
 Identities = 12/25 (48%), Positives = 18/25 (72%)

Query: 405 SDSSQHSAVIDVINGKNLIIEGPPG 429
           SD+S  SA+I+ I+GK +I + P G
Sbjct: 168 SDASGDSAIIEPIDGKLVIHDNPYG 192


>gnl|CDD|30559 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA
           replication, recombination, and repair].
          Length = 655

 Score = 30.5 bits (68), Expect = 4.1
 Identities = 29/123 (23%), Positives = 47/123 (38%), Gaps = 7/123 (5%)

Query: 408 SQHSAVIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHG----KKILFCAQKMAAIEVV 463
            +    +   +G  L++ G  G+GK++ +T  IA  +  G    ++IL       A   +
Sbjct: 5   PEQREAVLHPDGPLLVLAGA-GSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEM 63

Query: 464 RHRLEKAGLGEFCLELHSHKVHKRA--ILDDLRKRIDNRNIKTVPQEIDVEITRYEELKG 521
           R RL K         L     H  A  IL    +R+      T+    D      E L+ 
Sbjct: 64  RERLLKLLGLPAAEGLTVGTFHSFALRILRRHGERLGLNANFTILDSDDQLALIKELLRR 123

Query: 522 QLN 524
           +LN
Sbjct: 124 ELN 126


>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein.  IVa2 protein can
           interact with the adenoviral packaging signal and that
           this interaction involves DNA sequences that have
           previously been demonstrated to be required for
           packaging. During the course of lytic infection, the
           adenovirus major late promoter (MLP) is induced to high
           levels after replication of viral DNA has started. IVa2
           is a transcriptional activator of the major late
           promoter.
          Length = 370

 Score = 30.4 bits (69), Expect = 4.5
 Identities = 8/23 (34%), Positives = 16/23 (69%)

Query: 423 IIEGPPGTGKSQTITNIIAAAML 445
           ++ GP G GKSQ + N+++  ++
Sbjct: 91  VVYGPTGCGKSQLLRNLLSCQLI 113


>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
           cellular Activities) superfamily represents an ancient
           group of ATPases belonging to the ASCE (for additional
           strand, catalytic E) division of the P-loop NTPase fold.
           The ASCE division also includes ABC, RecA-like,
           VirD4-like, PilT-like, and SF1/2 helicases. Members of
           the AAA+ ATPases function as molecular chaperons, ATPase
           subunits of proteases, helicases, or nucleic-acid
           stimulated ATPases. The AAA+ proteins contain several
           distinct features in addition to the conserved
           alpha-beta-alpha core domain structure and the Walker A
           and B motifs of the P-loop NTPases..
          Length = 151

 Score = 30.6 bits (69), Expect = 4.5
 Identities = 13/33 (39%), Positives = 16/33 (48%)

Query: 419 GKNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
            KNL++ GPPGTGK+     I       G   L
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPFL 51


>gnl|CDD|31829 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
           and repair].
          Length = 845

 Score = 30.3 bits (68), Expect = 4.7
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 2/43 (4%)

Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQ--KMAAIEV 462
           +II G  G+GK+  +   +    L     + C Q  ++AA  V
Sbjct: 68  VIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSV 110


>gnl|CDD|144246 pfam00580, UvrD-helicase, UvrD/REP helicase.  The Rep family
           helicases are composed of four structural domains. The
           Rep family function as dimers. REP helicases catalyse
           ATP dependent unwinding of double stranded DNA to single
           stranded DNA. Bacillus subtilis addA and Escherichia
           coli exodeoxyribonuclease V beta have large insertions
           near to the carboxy-terminus relative to other members
           of the family.
          Length = 494

 Score = 30.4 bits (69), Expect = 4.8
 Identities = 46/191 (24%), Positives = 75/191 (39%), Gaps = 38/191 (19%)

Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLHG----KKIL---FCAQKMAAIEVVRHRLEK 469
           + G  L++ G  GTGK++ +T  IA  +L G    ++IL   F     AA E ++ R+ K
Sbjct: 12  LGGPLLVLAGA-GTGKTRVLTERIAYLILEGGIDPEEILAVTF--TNKAARE-MKERILK 67

Query: 470 AGLGEFCLE------LHS--HKVHKRAI--LDDLRKR---IDNRNIKTVPQEIDVEITRY 516
             LG+           HS   ++ ++    + DL      +D  +   + +EI ++  R 
Sbjct: 68  L-LGKAEASELNISTFHSFCLRILRKYANRIGDLLPNFSILDELDQLALLKEI-LKKDRL 125

Query: 517 EELKGQLNQYAQEINQI--WKNTELSIHQILMGAARYRHNLPLDPV----QLHVEGLSGE 570
           +     L    +    I   KN  LS  ++    A Y             Q + E L   
Sbjct: 126 DLDSKLLRPLLELKELISKAKNELLSPEELQ--QASYAATPRDKLAAEFYQEYQERLKEN 183

Query: 571 NA----DRLLR 577
           NA    D LL 
Sbjct: 184 NALDFDDLLLL 194


>gnl|CDD|143847 pfam00063, Myosin_head, Myosin head (motor domain). 
          Length = 679

 Score = 30.3 bits (69), Expect = 5.0
 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 23/102 (22%)

Query: 482 HKVHKRAILDDLRKRIDNRNIKTVPQEIDVEITRYEELKGQLNQYAQEINQIWKNTELSI 541
            ++++ ++L +L+KR     I T    + + +  Y+    +L  Y +E    ++      
Sbjct: 8   TQLNETSVLHNLKKRYTGDLIYTYSGLVLISVNPYK----RLPIYTEEPIGEYR------ 57

Query: 542 HQILMGAARYRHNLPLDPVQLHVEGLSGENADRLLRSRLEDQ 583
                   + R  LP  P   H+  L+ + A R +    E+Q
Sbjct: 58  -------GKRRGELP--P---HIFALA-DRAYRHMLRDKENQ 86


>gnl|CDD|28927 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
           of proteins involved in ATP-dependent RNA or DNA
           unwinding. This domain contains the ATP-binding region..
          Length = 144

 Score = 30.1 bits (67), Expect = 5.2
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 2/81 (2%)

Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRHRLEKAGLGEFCL 477
           +++++  P G+GK+      I   +    G ++L  A        V  RL++       +
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60

Query: 478 ELHSHKVHKRAILDDLRKRID 498
                    +     L  + D
Sbjct: 61  GYLIGGTSIKQQEKLLSGKTD 81


>gnl|CDD|36134 KOG0916, KOG0916, KOG0916, 1,3-beta-glucan synthase/callose
           synthase catalytic subunit [Cell wall/membrane/envelope
           biogenesis].
          Length = 1679

 Score = 30.3 bits (68), Expect = 5.4
 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)

Query: 827 SVLEELFERLDSLKILQESLDDVFNMKKLPD 857
           ++   L +R+ S KIL   L+  F  K LP 
Sbjct: 715 NIFSRLPKRIYS-KILATDLEIEFKPKVLPS 744


>gnl|CDD|30951 COG0606, COG0606, Predicted ATPase with chaperone activity
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 490

 Score = 30.2 bits (68), Expect = 5.7
 Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 11/60 (18%)

Query: 393 EDIHQRCPLIDDSD-SSQHSA----VIDVINGKNLIIEGPPGTGKSQTITNIIAAAMLHG 447
           E I       D  D   Q  A     I    G NL++ GPPGTGK+      + A+ L G
Sbjct: 167 EVIESFSLAPDFKDVKGQEQAKRALEIAAAGGHNLLLVGPPGTGKT------MLASRLPG 220


>gnl|CDD|38888 KOG3684, KOG3684, KOG3684, Ca2+-activated K+ channel proteins
            (intermediate/small conductance classes) [Inorganic ion
            transport and metabolism].
          Length = 489

 Score = 29.9 bits (67), Expect = 6.5
 Identities = 22/110 (20%), Positives = 46/110 (41%), Gaps = 11/110 (10%)

Query: 907  LPNAYQFAVEKEKLEKRNFGNTLGEHYRGLSTDIVALKNIREWYRKVHQIWKDNSSLDDA 966
            L   +      + + K +    L +H R     I   ++++   RK+ +  + NS +D A
Sbjct: 370  LQETWLIYKHTKLVSKGDQAR-LRKHQRKFLQAIHQFRSVKWEQRKLSE--QANSLVDLA 426

Query: 967  LINGFLMLDSQLFKRIQKLHC--DELSKKITKVFGRIQELEQFLPKQKEL 1014
                     + ++  +Q+LH   +EL K+I  +  +++ L   L     L
Sbjct: 427  ------KTQNDMYDLLQELHSRQEELEKQIDTLESKLEALTASLSSLPGL 470


>gnl|CDD|48369 cd02040, NifH, NifH gene encodes component II (iron protein) of
           nitrogenase. Nitrogenase is responsible for the
           biological nitrogen fixation, i.e. reduction of
           molecular nitrogen to ammonia. NifH consists of two
           oxygen-sensitive metallosulfur proteins: the
           mollybdenum-iron (alternatively, vanadium-iron or
           iron-iron) protein (commonly referred to as component
           1), and the iron protein (commonly referred to as
           component 2). The iron protein is a homodimer, with an
           Fe4S4 cluster bound between the subunits and two
           ATP-binding domains. It supplies energy by ATP
           hydrolysis, and transfers electrons from reduced
           ferredoxin or flavodoxin to component 1 for the
           reduction of molecular nitrogen to ammonia..
          Length = 270

 Score = 29.8 bits (67), Expect = 6.7
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 420 KNLIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           + + I G  G GKS T  N+ AA    GKK++
Sbjct: 2   RQIAIYGKGGIGKSTTTQNLSAALAEMGKKVM 33


>gnl|CDD|73296 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
           reversible phosphorylation of cytidine monophosphate
           (CMP) to produce cytidine diphosphate (CDP), using ATP
           as the preferred phosphoryl donor..
          Length = 147

 Score = 29.7 bits (67), Expect = 6.9
 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 10/55 (18%)

Query: 424 IEGPPGTGKSQTITNIIAAAM---------LHGKKILFCAQKMAAIEVVRHRLEK 469
           I+GP G+GKS T+  ++A  +         +  +++   A ++AAI  VR  L++
Sbjct: 4   IDGPAGSGKS-TVAKLLAKKLGLPYLDTGGIRTEEVGKLASEVAAIPEVRKALDE 57


>gnl|CDD|35549 KOG0328, KOG0328, KOG0328, Predicted ATP-dependent RNA helicase
           FAL1, involved in rRNA maturation, DEAD-box superfamily
           [Translation, ribosomal structure and biogenesis].
          Length = 400

 Score = 29.9 bits (67), Expect = 7.2
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 409 QHSAVIDVINGKNLIIEGPPGTGKSQTIT 437
           Q  A+  ++ G+++I +   GTGK+ T +
Sbjct: 54  QQRAIPQILKGRDVIAQAQSGTGKTATFS 82


>gnl|CDD|31498 COG1307, DegV, Uncharacterized protein conserved in bacteria
            [Function unknown].
          Length = 282

 Score = 29.8 bits (67), Expect = 7.2
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 1075 EESLIKKFFGEEIKLSVFDSNTKESNKSLAVINSTLEFAHSIRERVLFDELIQGINHIDD 1134
            + + +     E  K+ V DS     + S+ +    LE A   +    F+E+++ +  I +
Sbjct: 98   QSAQLAAELVEGAKVHVIDS----KSVSMGLGFLVLEAAELAKAGKSFEEILKKLEEIRE 153

Query: 1135 HTIYNSFIKDLKNLR 1149
             T     + DL NL 
Sbjct: 154  KTKAYFVVDDLDNLV 168


>gnl|CDD|37153 KOG1942, KOG1942, KOG1942, DNA helicase, TBP-interacting protein
           [Replication, recombination and repair].
          Length = 456

 Score = 29.5 bits (66), Expect = 7.6
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 14/64 (21%)

Query: 413 VIDVIN-----GKNLIIEGPPGTGKSQTITNIIAAAMLH--GKKILFCAQKMAAIEVVRH 465
           ++D+I      G+ +++ GPPGTGK+      +A A+    G K+ FC   M   EV  +
Sbjct: 53  IVDLIKSKKMAGRAVLLAGPPGTGKTA-----LALAISQELGPKVPFCP--MVGSEVYSN 105

Query: 466 RLEK 469
            ++K
Sbjct: 106 EVKK 109


>gnl|CDD|48362 cd02032, Bchl_like, This family of proteins contains bchL and chlL.
           Protochlorophyllide reductase catalyzes the reductive
           formation of chlorophyllide from protochlorophyllide
           during biosynthesis of chlorophylls and
           bacteriochlorophylls. Three genes, bchL, bchN and bchB,
           are involved in light-independent protochlorophyllide
           reduction in bacteriochlorophyll biosynthesis. In
           cyanobacteria, algae, and gymnosperms, three similar
           genes, chlL, chlN and chlB are involved in
           protochlorophyllide reduction during chlorophylls
           biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit
           significant sequence similarity to the nifH, nifD and
           nifK subunits of nitrogenase, respectively. Nitrogenase
           catalyzes the reductive formation of ammonia from
           dinitrogen..
          Length = 267

 Score = 29.5 bits (66), Expect = 8.2
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 422 LIIEGPPGTGKSQTITNIIAAAMLHGKKIL 451
           L + G  G GKS T +N+  A    GKK+L
Sbjct: 3   LAVYGKGGIGKSTTSSNLSVALAKRGKKVL 32


>gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing
           and modification].
          Length = 674

 Score = 29.5 bits (66), Expect = 8.2
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 416 VINGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQ--KMAAIEVVR 464
           V + + LI+ G  G+GKS  I   +A A       + C Q  ++AA+ + +
Sbjct: 63  VEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAK 113


>gnl|CDD|110585 pfam01591, 6PF2K, 6-phosphofructo-2-kinase.  This enzyme occurs as a
            bifunctional enzyme with fructose-2,6-bisphosphatase. The
            bifunctional enzyme catalyses both the synthesis and
            degradation of fructose-2,6-bisphosphate, a potent
            regulator of glycolysis. This enzyme contains a P-loop
            motif.
          Length = 223

 Score = 29.6 bits (67), Expect = 8.4
 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 13/90 (14%)

Query: 1059 FSAKLHKIREKNIVLAEESLIKKFFGEEIKLSVFDS--NTKESNKSLAVINSTLEFAHSI 1116
             + +  KIRE+  + A + ++     E  ++++FD+   T+E  K++      L+FA   
Sbjct: 69   DNTEAMKIREQCALAALKDVLAYLNEESGQVAIFDATNTTRERRKNI------LDFAEEN 122

Query: 1117 RERVLFDELIQGINHIDDHTIYNSFIKDLK 1146
              +V F E I      DD  I    IK +K
Sbjct: 123  GLKVFFLESI-----CDDPEIIARNIKLVK 147


>gnl|CDD|31417 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
           [Transcription].
          Length = 450

 Score = 29.5 bits (66), Expect = 9.9
 Identities = 26/116 (22%), Positives = 46/116 (39%), Gaps = 24/116 (20%)

Query: 417 INGKNLIIEGPPGTGKSQTITNIIAAAMLHGKKILFCAQKMAAIEVVRHRLEKAGLGEFC 476
           + G+ ++I GPPGTGK+      +  A   G+ + F A  ++  E+    ++K       
Sbjct: 63  MAGRGILIVGPPGTGKTAL---AMGIARELGEDVPFVA--ISGSEIYSLEVKKT------ 111

Query: 477 LELHSHKVHKRAILDDLRKRIDNRNIKTVPQEIDVEIT--RYEELKGQLNQYAQEI 530
                      A+   LR+ I  R IK   +  + E+        +  LN Y +  
Sbjct: 112 ----------EALTQALRRAIGVR-IKETREVYEGEVVELEIRRARNPLNPYGKVP 156


>gnl|CDD|35520 KOG0299, KOG0299, KOG0299, U3 snoRNP-associated protein (contains
            WD40 repeats) [RNA processing and modification].
          Length = 479

 Score = 29.2 bits (65), Expect = 9.9
 Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 4/94 (4%)

Query: 1651 EHSLKTKTNKQDSDFAVSVVNELEKTGFACDSQLGDMGFSIDVVVRDPNNPGHYLMGIEC 1710
            E   + K N+ D + A  + ++ E+   A + +  D         +       YL  I  
Sbjct: 29   EEEAERKKNRDDDEDAEEIESDEEENSLAGEEEEEDEFEEETAGEKRLRLAEEYLDEIRE 88

Query: 1711 DGAMYNSAKSARDR---DRLRQEVLERMGWRIRR 1741
                   A    D     RL+++VLE+ G R+RR
Sbjct: 89   IEEDNFDADDLDDELVASRLKEDVLEQSG-RVRR 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
   0.319    0.136    0.397 

Gapped
Lambda     K      H
   0.267   0.0868    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 21,966,357
Number of extensions: 1226416
Number of successful extensions: 3701
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3685
Number of HSP's successfully gapped: 91
Length of query: 1775
Length of database: 6,263,737
Length adjustment: 108
Effective length of query: 1667
Effective length of database: 3,929,965
Effective search space: 6551251655
Effective search space used: 6551251655
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 65 (28.6 bits)