RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780947|ref|YP_003065360.1| transcription-repair coupling
factor [Candidatus Liberibacter asiaticus str. psy62]
         (1187 letters)



>gnl|CDD|161938 TIGR00580, mfd, transcription-repair coupling factor (mfd).  All
            proteins in this family for which functions are known are
            DNA-dependent ATPases that function in the process of
            transcription-coupled DNA repair in which the repair of
            the transcribed strand of actively transacribed genes is
            repaired at a higher rate than the repair of
            non-transcribed regions of the genome and than the
            non-transcribed strand of the same gene. This family is
            based on the phylogenomic analysis of JA Eisen (1999,
            Ph.D. Thesis, Stanford University). This family is
            closely related to the RecG and UvrB families.
          Length = 926

 Score =  894 bits (2312), Expect = 0.0
 Identities = 383/962 (39%), Positives = 551/962 (57%), Gaps = 46/962 (4%)

Query: 150  LETNGFQRVNAVYKVGEYAVRGGILDVYEPTKKYPVRLDFFGNTIDSLRLFDSSTQRTIR 209
            L   G++RV+ V + GE++VRG ILD++ P  + PVR++FFG+ I+S+R FD  +QR++ 
Sbjct: 1    LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLE 60

Query: 210  EISIFEINTLSE-VMLTSQNISRFRENYLANFGTTTQEDPLYVAISQGRRYPGMEHWLPF 268
            E+    I    E ++L  + I+R ++N                A+S+G    G E +LP 
Sbjct: 61   ELLEITILPAKEFILLEEETIARLKDNAARVEDAKHL--ETIEALSEGTLPAGEEMFLPL 118

Query: 269  FYQSMETIFPYLSEFCIITDPLVKETARKRSQLIQDYYEARLQYSSDKKQYSVYKPIAPE 328
            F++ + ++F YL +   I     +        L ++  E        KK       I P 
Sbjct: 119  FFEDLSSLFDYLPDNTPILLDDPERFHSAARFLQRELEEFYNALEEAKK------LINPP 172

Query: 329  KLYLNYQQFDALIQTTHKLVQMTAFNQQETAHNRVV--HLNAFPGKSWVPSAVQKIESQD 386
            +L L+                  AF     + +RV   + +     S      QK    +
Sbjct: 173  RLDLD--------------PSELAFEASAISLSRVQLENEHLSLKASEAIEGAQKHSRLE 218

Query: 387  NWESGGRFDKFLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTEIN 446
              E     ++    +      G K  ++A S+   + L  L+  H          + E  
Sbjct: 219  FGEILAFKEELFRWLKA----GFKITVAAESESQAERLKSLLAEHDIA----AQVIDESC 270

Query: 447  SLLKEEIAAVI---LPINQGFETKHMILVTETDLLGKKIARR--VVRKKNVHAQSFFDSS 501
             ++   +  V+   L       T  + ++TE++L G ++ RR    R K+   +S    +
Sbjct: 271  -IIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRPKKSRLKSKPIESL---N 326

Query: 502  NIEEGAIIVHAEHGIGRFVRLYSIEVSGTFHDCLELHYADNAKLFVPVENIDLISRYS-T 560
             +  G  +VH +HGIGRF+ L ++EV G   D L L YA   KL+VPVE + LISRY   
Sbjct: 327  ELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGG 386

Query: 561  EITTVTLDKLGGSAWKTRKANLKKRLEDLAQKLVDIAAKRAIHSVPPLMVSQDLYSQFIK 620
                  LDKLGG +W+  KA +KK + ++A KL+++ AKR            +   +F  
Sbjct: 387  SGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFED 446

Query: 621  RFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVI 680
             FP  ET DQ KAI+ +  D+ S R MDRL+CGDVGFGKTE+A+RAAF AV++G QVAV+
Sbjct: 447  SFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVL 506

Query: 681  APTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTHALLN 740
             PTTLL +QHF  F ERF  F V I  +SRF   KE     K +  G++DI+IGTH LL 
Sbjct: 507  VPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQ 566

Query: 741  PKITFANLGLIIIDEEQHFGVKHKEALKETHTGVHVLTLSATPIPRTLQLAITGVRELSL 800
              + F +LGL+IIDEEQ FGVK KE LKE  T V VLTLSATPIPRTL ++++G+R+LS+
Sbjct: 567  KDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSI 626

Query: 801  ISMPPINRIACRTSISIFDPLVVRETLMREYYRGGQSFYVCPRLSDLEKCYTFLQSEVPE 860
            I+ PP +R+  RT +  +DP +VRE + RE  RGGQ FYV  R+  +EK  T L+  VPE
Sbjct: 627  IATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPE 686

Query: 861  LKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQ 920
             +IA+AHGQM+   LE+ M  FY+G++ VL+ T+I+E+G+D+P ANT+I++RAD FGLAQ
Sbjct: 687  ARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQ 746

Query: 921  LYQLRGRVGRSKIASFALFLLPENRPLTAAAQKRLRILQSLNTLGAGFQLASYDLDIRGT 980
            LYQLRGRVGRSK  ++A  L P  + LT  AQKRL  +Q  + LGAGF++A +DL+IRG 
Sbjct: 747  LYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLEIRGA 806

Query: 981  GNLLGEEQSGHIREIGFELYQKMLEETVASIKGQK-DLVESDWSPQVLIEASVMIPESYV 1039
            GNLLGEEQSGHI  IGF+LY ++LEE +  +KG K   +E +    + +  S  IP+ Y+
Sbjct: 807  GNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEE--TDIELPYSAFIPDDYI 864

Query: 1040 SDINLRLSLYRRLGNITDHADISHFKEEMVDRFGPLPIEVIHLLKVVFLKLLCRIANIDK 1099
            +D +LRL  Y+R+ +     ++   ++E++DRFGPLP E   LL V  LKLL R   I K
Sbjct: 865  ADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRK 924

Query: 1100 MD 1101
            + 
Sbjct: 925  LK 926


>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
            Provisional.
          Length = 1147

 Score =  706 bits (1823), Expect = 0.0
 Identities = 388/1088 (35%), Positives = 600/1088 (55%), Gaps = 67/1088 (6%)

Query: 65   DIRVIIFPAWDCLPYDRVSPSPYVVTRRLSCISNLVSFNSSKETIIVLTTVSAVMCRSVN 124
            D  V+    W+ LPYD  SP   +++ RLS +  L +        +++  V+ +M R   
Sbjct: 64   DQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRG----VLILPVNTLMQRVCP 119

Query: 125  IMSIKDYKLSIQSKDQIDMAKVIEKLETNGFQRVNAVYKVGEYAVRGGILDVYEPTKKYP 184
               +  + L ++   ++    +  +LE  G++ V+ V + GEYA RG +LD++    + P
Sbjct: 120  HSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSEEP 179

Query: 185  VRLDFFGNTIDSLRLFDSSTQRTIREISIFEINTL-SEVMLTSQN-ISRFRENYLANFGT 242
             R+DFF + IDSLR+FD  +QRT+ E+    IN L +    T +  I  FR  +   F  
Sbjct: 180  YRIDFFDDEIDSLRVFDVDSQRTLEEVE--AINLLPAHEFPTDKAAIELFRSQWRDTFEV 237

Query: 243  TTQEDPLYVAISQGRRYPGMEHWLP-FFYQSMETIFPYLSE--FCIITDPLVKETARKRS 299
                + +Y  +S+G    G+E+W P FF + +  +F Y       + T  L + +A +  
Sbjct: 238  KRDAEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDL-ETSAERFW 296

Query: 300  QLIQDYYEARLQYSSDKKQYSVYKPI-APEKLYLNYQQFDALIQTTHKL--VQMTAFNQQ 356
                  +E R             +P+  PE L+L     D L         VQ+   +  
Sbjct: 297  ADTLARFENR--------GVDPMRPLLPPESLWLR---VDELFSELKNWPRVQLKTEHLP 345

Query: 357  ETAHNRVVHLNAFPGKSWVPSAVQKIESQDNWESGGRFDKFLSHVAQQAQKGIKTIISAS 416
              A N  +     P  +        +++Q         D  L    +     +  + S  
Sbjct: 346  TKAANTNLGYQKLPDLA--------VQAQ----QKAPLDA-LRRFLESFDGPV--VFSVE 390

Query: 417  SQG---ALQHLIHLIESHGFKKI--KKINTLTEINSLLKEEIAAVILPINQGF--ETKHM 469
            S+G   AL  L+  I      KI  K+I  L E +         +I     GF    +++
Sbjct: 391  SEGRREALGELLARI------KIAPKRIMRLDEASD---RGRYLMIGAAEHGFIDTVRNL 441

Query: 470  ILVTETDLLGKKIARRVVRKKN---VHAQSFFDS-SNIEEGAIIVHAEHGIGRFVRLYSI 525
             L+ E+DLLG+++ARR  R+ +   ++  +   + + +  G  +VH EHG+GR+  + ++
Sbjct: 442  ALICESDLLGERVARR--RQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRYAGMTTL 499

Query: 526  EVSGTFHDCLELHYADNAKLFVPVENIDLISRYSTEI-TTVTLDKLGGSAWKTRKANLKK 584
            E  G   + L L YA++AKL+VPV ++ LISRY+        L KLGG AW   +    +
Sbjct: 500  EAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAE 559

Query: 585  RLEDLAQKLVDIAAKRAIHSVPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSG 644
            ++ D+A +L+DI A+RA          ++ Y  F   FP   T DQ +AI+AV+ D+   
Sbjct: 560  KVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQP 619

Query: 645  RLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVR 704
              MDRL+CGDVGFGKTE+A+RAAF+AV N  QVAV+ PTTLL +QH+  F +RF  + VR
Sbjct: 620  LAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVR 679

Query: 705  IASISRFVQTKEAALHKKSITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQHFGVKHK 764
            I  +SRF   KE         EG++DI+IGTH LL   + + +LGL+I+DEE  FGV+HK
Sbjct: 680  IEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHK 739

Query: 765  EALKETHTGVHVLTLSATPIPRTLQLAITGVRELSLISMPPINRIACRTSISIFDPLVVR 824
            E +K     V +LTL+ATPIPRTL +A++G+R+LS+I+ PP  R+A +T +  +D LVVR
Sbjct: 740  ERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVR 799

Query: 825  ETLMREYYRGGQSFYVCPRLSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNAFYE 884
            E ++RE  RGGQ +Y+   + +++K    L   VPE +IA+ HGQM  + LE  MN F+ 
Sbjct: 800  EAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHH 859

Query: 885  GQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLRGRVGRSKIASFALFLLPEN 944
             +++VL+ T+I+E+G+D+P ANT+I++RAD FGLAQL+QLRGRVGRS   ++A  L P  
Sbjct: 860  QRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHP 919

Query: 945  RPLTAAAQKRLRILQSLNTLGAGFQLASYDLDIRGTGNLLGEEQSGHIREIGFELYQKML 1004
            + +T  AQKRL  + SL  LGAGF LA++DL+IRG G LLGEEQSG +  IGF LY ++L
Sbjct: 920  KAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELL 979

Query: 1005 EETVASIK-GQKDLVESDWSPQVLIE--ASVMIPESYVSDINLRLSLYRRLGNITDHADI 1061
            E  V ++K G++  +E   S Q  +E     ++P+ ++ D+N RLS Y+R+ +  +  ++
Sbjct: 980  ENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENEL 1039

Query: 1062 SHFKEEMVDRFGPLPIEVIHLLKVVFLKLLCRIANIDKMDIGLKGIIIQFRHKTFSNPEA 1121
               K E++DRFG LP    +LL +  L+   +   I K++   KG  I+F  K   +P  
Sbjct: 1040 EEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAW 1099

Query: 1122 LLQYIAQQ 1129
            L+  + +Q
Sbjct: 1100 LIGLLQKQ 1107


>gnl|CDD|182836 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
          Length = 681

 Score =  339 bits (873), Expect = 2e-93
 Identities = 159/432 (36%), Positives = 246/432 (56%), Gaps = 39/432 (9%)

Query: 583 KKRL---EDLAQKLVDIAAKRAIHSV--PPLMVSQDLYSQFIKRFPHVETEDQEKAIDAV 637
           ++RL   E  A +L  +  +    S    PL    +L  +F+   P   T  Q++ +  +
Sbjct: 214 RRRLKFEELFALQLSLLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEI 273

Query: 638 IQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSER 697
           + DL+S + M+RL+ GDVG GKT +A  AA  A+  G Q A++APT +L  QH+    + 
Sbjct: 274 LADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKL 333

Query: 698 FQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQ 757
            +   +R+A ++  ++ KE     ++I  G+ DIVIGTHAL+   + F NLGL+IIDE Q
Sbjct: 334 LEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDE-Q 392

Query: 758 H-FGVKHKEALKETHTGVHVLTLSATPIPRTLQLAITGVRELSLI-SMPPINRIACRTSI 815
           H FGV+ + AL+E     HVL ++ATPIPRTL +   G  ++S+I  +PP      R  I
Sbjct: 393 HRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPP-----GRKPI 447

Query: 816 SIFDPLVVRETLMREYYR--------GGQSFYVCPR--------LSDLEKCYTFLQSEVP 859
                +V+ ++   E Y         G Q++ VCP         L   E+ Y  LQ   P
Sbjct: 448 ---TTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFP 504

Query: 860 ELKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLA 919
           EL++ + HG+M P   +  M AF  G+ D+L++T+++E G+D+P A  M+++ A+ FGLA
Sbjct: 505 ELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLA 564

Query: 920 QLYQLRGRVGRSKIASFALFLLPENRPLTAAAQKRLRIL-QSLNTLGAGFQLASYDLDIR 978
           QL+QLRGRVGR    S+ + L  +  PL+  A++RL+I+ ++ +    GF +A  DL++R
Sbjct: 565 QLHQLRGRVGRGAAQSYCVLLYKD--PLSETARERLKIMRETND----GFVIAEKDLELR 618

Query: 979 GTGNLLGEEQSG 990
           G G LLG  QSG
Sbjct: 619 GPGELLGTRQSG 630


>gnl|CDD|161975 TIGR00643, recG, ATP-dependent DNA helicase RecG. 
          Length = 630

 Score =  326 bits (838), Expect = 2e-89
 Identities = 152/419 (36%), Positives = 241/419 (57%), Gaps = 23/419 (5%)

Query: 604  SVPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIA 663
            S PP   S++L ++F+   P   T  Q++ +  ++QDL S   M+RL+ GDVG GKT +A
Sbjct: 214  SAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVA 273

Query: 664  LRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKS 723
              A   A+  G QVA++APT +L  QH+           + +A ++  ++ K      ++
Sbjct: 274  ALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLET 333

Query: 724  ITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQHFGVKHKEALKETHTG---VHVLTLS 780
            I  GQ+ +V+GTHAL+  K+ F  L L+IIDE+  FGV+ ++ L+E   G    HVL +S
Sbjct: 334  IASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGFTPHVLVMS 393

Query: 781  ATPIPRTLQLAITGVRELSLI-SMPPINRIACRTSISIFDPL-VVRETLMREYYRGGQSF 838
            ATPIPRTL L + G  + S+I  +PP  R    T +   D   +V E +  E  +G Q++
Sbjct: 394  ATPIPRTLALTVYGDLDTSIIDELPP-GRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAY 452

Query: 839  YVCPRLSDLEKC--------YTFLQSEVPELKIAMAHGQMSPKNLEDKMNAFYEGQYDVL 890
             V P + + EK         Y  L+   P+  + + HG+M     E  M  F EG+ D+L
Sbjct: 453  VVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDIL 512

Query: 891  LSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLRGRVGRSKIASFALFLLPENRPLTAA 950
            ++T+++E G+D+P A  M+++ A+ FGL+QL+QLRGRVGR    S+   L+ +N P + +
Sbjct: 513  VATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYC-LLVYKN-PKSES 570

Query: 951  AQKRLRIL-QSLNTLGAGFQLASYDLDIRGTGNLLGEEQSGHI--REIGFELYQKMLEE 1006
            A+KRLR++  +L+    GF +A  DL++RG G+LLG +QSG+   R       +++L E
Sbjct: 571  AKKRLRVMADTLD----GFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVE 625


>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. 
          Length = 201

 Score = 94.9 bits (236), Expect = 1e-19
 Identities = 49/206 (23%), Positives = 83/206 (40%), Gaps = 23/206 (11%)

Query: 618 FIKRFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGL-- 675
             K         Q++AI+A++       L D ++    G GKT  AL  A  A+  G   
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLS-----GLRDVILAAPTGSGKTLAALLPALEALKRGKGK 55

Query: 676 QVAVIAPTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGT 735
           +V V+ PT  L  Q      +      +++  +      +E     + +  G+ DI++ T
Sbjct: 56  RVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTT 112

Query: 736 -----HALLNPKITFANLGLIIIDEEQH-----FGVKHKEALKETHTGVHVLTLSATP-- 783
                  L N  +  +N+ L+I+DE        FG + ++ LK     V +L LSATP  
Sbjct: 113 PGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPE 172

Query: 784 -IPRTLQLAITGVRELSLISMPPINR 808
            I   L+L +     + +   P    
Sbjct: 173 EIENLLELFLNDPVFIDVGPTPLEPI 198


>gnl|CDD|128766 smart00490, HELICc, helicase superfamily c-terminal domain. 
          Length = 82

 Score = 66.5 bits (163), Expect = 4e-11
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 860 ELKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLA 919
            +K+A  HG +S +  E+ +  F  G+  VL++T + E GLDLP  + +I+     +  A
Sbjct: 11  GIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPA 69

Query: 920 QLYQLRGRVGR 930
              Q  GR GR
Sbjct: 70  SYIQRIGRAGR 80


>gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
          Length = 679

 Score = 59.8 bits (146), Expect = 4e-09
 Identities = 44/142 (30%), Positives = 61/142 (42%), Gaps = 32/142 (22%)

Query: 627 TEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIA-VMN-GLQVAV----I 680
             +Q  A++A+            L+ G  G GKTE+ L+A  IA V+  G Q  V    I
Sbjct: 146 NPEQAAAVEAIRAAAGFSPF---LLDGVTGSGKTEVYLQA--IAEVLAQGKQALVLVPEI 200

Query: 681 APTTLLVRQHFRLFSERFQG-FSVRIA----SISRFVQTKEAALHKKSITEGQVDIVIGT 735
           A T  ++         RF+  F   +A     +S     +     K     G+  +VIG 
Sbjct: 201 ALTPQML--------ARFRARFGAPVAVLHSGLS--DGERLDEWRK--AKRGEAKVVIGA 248

Query: 736 H-ALLNPKITFANLGLIIIDEE 756
             AL  P   F NLGLII+DEE
Sbjct: 249 RSALFLP---FKNLGLIIVDEE 267



 Score = 30.9 bits (71), Expect = 1.9
 Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 23/97 (23%)

Query: 854 LQSEVPELKIAMAHGQMS------PKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANT 907
           L    PE +I     ++          LE  +  F  G+ D+L+ T ++  G D P    
Sbjct: 446 LAELFPEARIL----RIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTL 501

Query: 908 MIVQRADMFGL-----------AQLY-QLRGRVGRSK 932
           + V  AD+ GL            QL  Q+ GR GR++
Sbjct: 502 VGVLDADL-GLFSPDFRASERTFQLLTQVAGRAGRAE 537


>gnl|CDD|180000 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
          Length = 652

 Score = 55.1 bits (134), Expect = 1e-07
 Identities = 30/130 (23%), Positives = 67/130 (51%), Gaps = 14/130 (10%)

Query: 92  RLSCISNLVSFNSSKETIIVLTTVSAVMCRSVNIMSIKDYK---LSIQSKDQIDMAKVIE 148
           R S   +L+      + I+V  +VS +      + S ++Y    LS++   +ID  +++ 
Sbjct: 123 RHSATKSLLERR---DVIVV-ASVSCIY----GLGSPEEYLKMVLSLRVGQEIDRRELLR 174

Query: 149 KLETNGFQRVNAVYKVGEYAVRGGILDVYEP--TKKYPVRLDFFGNTIDSLRLFDSSTQR 206
           +L    ++R +  ++ G + VRG +++++ P   ++  +R++FFG+ I+ +  FD  T  
Sbjct: 175 RLVDLQYERNDIDFQRGTFRVRGDVIEIF-PAYYEERAIRIEFFGDEIERISEFDPLTGE 233

Query: 207 TIREISIFEI 216
            + E+    I
Sbjct: 234 VLGELDRVTI 243


>gnl|CDD|161969 TIGR00631, uvrb, excinuclease ABC, B subunit.  This family is based
           on the phylogenomic analysis of JA Eisen (1999, Ph.D.
           Thesis, Stanford University).
          Length = 655

 Score = 52.3 bits (126), Expect = 8e-07
 Identities = 29/127 (22%), Positives = 63/127 (49%), Gaps = 8/127 (6%)

Query: 92  RLSCISNLVSFNSSKETIIVLTTVSAVMCRSVNIMSIKDYKLSIQSKDQIDMAKVIEKLE 151
           R S   +L      +  +IV+ +VS +     +        L ++   +ID  +++ +L 
Sbjct: 120 RHSATRSL----LERRDVIVVASVSCIYGLG-SPEEYLKMVLHLEVGKEIDRRELLRRLV 174

Query: 152 TNGFQRVNAVYKVGEYAVRGGILDVYEP--TKKYPVRLDFFGNTIDSLRLFDSSTQRTIR 209
              ++R +  ++ G + VRG +++++ P    ++ VR++FFG+ I+ +   D  T   +R
Sbjct: 175 ELQYERNDVDFQRGTFRVRGDVVEIF-PAYEDEFAVRIEFFGDEIERISRVDPLTGEVLR 233

Query: 210 EISIFEI 216
           E+  F I
Sbjct: 234 ELDSFTI 240


>gnl|CDD|161946 TIGR00595, priA, primosomal protein N'.  All proteins in this
           family for which functions are known are components of
           the primosome which is involved in replication, repair,
           and recombination.This family is based on the
           phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
           Stanford University).
          Length = 505

 Score = 50.1 bits (120), Expect = 3e-06
 Identities = 49/145 (33%), Positives = 64/145 (44%), Gaps = 17/145 (11%)

Query: 650 LICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASIS 709
           L+ G  G GKTE+ L+A    +  G  V V+ P   L  Q  + F  RF G  V +    
Sbjct: 1   LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRF-GSQVAVLHSG 59

Query: 710 RFVQTKEAALHKKSITEGQVDIVIGTH-ALLNPKITFANLGLIIIDEEQHFGVKHKE--- 765
                K  A  K  +  G++ +VIGT  AL  P   F NLGLII+DEE     K +E   
Sbjct: 60  LSDSEKLQAWRK--VKNGEILVVIGTRSALFLP---FKNLGLIIVDEEHDSSYKQEEGPR 114

Query: 766 ------ALKETH-TGVHVLTLSATP 783
                 A+         V+  SATP
Sbjct: 115 YHARDVAVYRAKKFNCPVVLGSATP 139



 Score = 45.5 bits (108), Expect = 8e-05
 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 13/111 (11%)

Query: 836 QSFYVCPRLSDLEKCYTFLQSEVPELKIAMAHGQM--SPKNLEDKMNAFYEGQYDVLLST 893
            S  +  +    E+    L    P  +IA             E  +N F  G+ D+L+ T
Sbjct: 260 GSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGT 319

Query: 894 SIVESGLDLPKANTMIVQRAD--MF---------GLAQLYQLRGRVGRSKI 933
            ++  G   P    + V  AD  +          G   L Q+ GR GR++ 
Sbjct: 320 QMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAED 370


>gnl|CDD|162437 TIGR01587, cas3_core, CRISPR-associated helicase Cas3.  This model
           represents the highly conserved core region of an
           alignment of Cas3, a protein found in association with
           CRISPR repeat elements in a broad range of bacteria and
           archaea. Cas3 appears to be a helicase, with regions
           found by pfam00270 (DEAD/DEAH box helicase) and
           pfam00271 (Helicase conserved C-terminal domain). Some
           but not all members have an N-terminal HD domain region
           (pfam01966) that is not included within this model.
          Length = 358

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 71/317 (22%), Positives = 123/317 (38%), Gaps = 49/317 (15%)

Query: 656 GFGKTEIALRAAFIAVMNGLQVAVI--APTTLLVRQHFRLFSERFQGFSVRIASISRFVQ 713
           G+GKTE AL  A  ++ +     VI   PT   +   +R   E F      + S S F +
Sbjct: 9   GYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKR 68

Query: 714 TKE------------------AALHKKSITEGQVDIVIG--THALLNPKITFANLG--LI 751
            KE                    L    IT   +D V+        + + T A++   L+
Sbjct: 69  IKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLL 128

Query: 752 IIDEEQHFG-------VKHKEALKETHTGVHVLTLSATPIP---RTLQLAITGVRELSLI 801
           I DE   +        +   E LK+    V +L +SAT +P   +     I  V     +
Sbjct: 129 IFDEVHFYDEYTLALILAVLEVLKDN--DVPILLMSAT-LPKFLKEYAEKIGYVEFNEPL 185

Query: 802 SMPPINRIACRTSISIFDPLVVRET----LMREYYRGGQSFYVCPRLSDLEKCYTFLQSE 857
            +    R      I I    V   +    L+    +GG+   +   +   ++ Y  L+  
Sbjct: 186 DLKEERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKEN 245

Query: 858 VPELKIAMAHGQMSPKNLEDK----MNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRA 913
            PE +I + H + + K+   K    +    + +  V+++T ++E+ LD+  A+ MI + A
Sbjct: 246 APEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDI-SADVMITELA 304

Query: 914 DMFGLAQLYQLRGRVGR 930
               +  L Q  GR+ R
Sbjct: 305 P---IDSLIQRLGRLHR 318


>gnl|CDD|181823 PRK09401, PRK09401, reverse gyrase; Reviewed.
          Length = 1176

 Score = 41.5 bits (98), Expect = 0.001
 Identities = 31/109 (28%), Positives = 47/109 (43%), Gaps = 15/109 (13%)

Query: 656 GFGKTEIALRAA-FIAVMNGLQVAVIAPTTLLVRQ---HFRLFSERFQGFSVRIASISRF 711
           G GKT   L  + ++A   G +  +I PT LLV Q       F E+  G  V+I      
Sbjct: 105 GVGKTTFGLVMSLYLAK-KGKKSYIIFPTRLLVEQVVEKLEKFGEKV-GCGVKILYYHSS 162

Query: 712 VQTKEAALHKKSITEGQVDIVIGTHALLN------PKITFANLGLIIID 754
           ++ KE     + + EG  DI++ T   L+      PK  F     + +D
Sbjct: 163 LKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKF---DFVFVD 208



 Score = 31.4 bits (72), Expect = 1.5
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 16/72 (22%)

Query: 833 RGGQSFYVCP----------RLSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNAF 882
           +G +S+ + P          +L    +           +KI   H  +  K  E+ +   
Sbjct: 122 KGKKSYIIFPTRLLVEQVVEKLEKFGEKVGC------GVKILYYHSSLKKKEKEEFLERL 175

Query: 883 YEGQYDVLLSTS 894
            EG +D+L++TS
Sbjct: 176 KEGDFDILVTTS 187


>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
          Length = 773

 Score = 41.0 bits (97), Expect = 0.002
 Identities = 31/113 (27%), Positives = 52/113 (46%), Gaps = 13/113 (11%)

Query: 650 LICGDVGFGKTEIA-LRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASI 708
           L+    G GKT IA L  A      G +V ++APT  LV QH   F +       +I   
Sbjct: 33  LVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF 92

Query: 709 SRFVQTKE-AALHKKSITEGQVDIVIGT-----HALLNPKITFANLGLIIIDE 755
           +  V  ++ A L +K+       +++ T     + L+  +I+  ++ L+I DE
Sbjct: 93  TGEVSPEKRAELWEKA------KVIVATPQVIENDLIAGRISLEDVSLLIFDE 139



 Score = 38.3 bits (90), Expect = 0.011
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 23/74 (31%)

Query: 870 MSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMI-----------VQRADMFGL 918
           MS K   + ++ F  G+++VL+STS+ E GLD+P  + +I           +QR      
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQR------ 460

Query: 919 AQLYQLRGRVGRSK 932
                 +GR GR +
Sbjct: 461 ------KGRTGRQE 468


>gnl|CDD|162177 TIGR01054, rgy, reverse gyrase.  Generally, these gyrases are
           encoded as a single polypeptide. An exception was found
           in Methanopyrus kandleri, where enzyme is split within
           the topoisomerase domain, yielding a heterodimer of gene
           products designated RgyB and RgyA.
          Length = 1171

 Score = 38.3 bits (89), Expect = 0.011
 Identities = 30/105 (28%), Positives = 42/105 (40%), Gaps = 5/105 (4%)

Query: 656 GFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQ---HFRLFSERFQGFSVRIASISRFV 712
           G GKT   L  +      G +  +I PTTLLV Q        +E+    +V I +    +
Sbjct: 103 GVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRL 162

Query: 713 QTKEAALHKKSITEGQVDIVIGTHALL--NPKITFANLGLIIIDE 755
            TKE     + I  G  DI+I T   L  N          I +D+
Sbjct: 163 PTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFVDD 207


>gnl|CDD|184796 PRK14701, PRK14701, reverse gyrase; Provisional.
          Length = 1638

 Score = 35.6 bits (82), Expect = 0.071
 Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 5/105 (4%)

Query: 656 GFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQ--GFSVRIASISRFVQ 713
           G GK+      A    + G +  +I PTTLLV+Q         +     VR+      ++
Sbjct: 104 GMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLR 163

Query: 714 TKEAALHKKSITEGQVDIVIGTHALLN---PKITFANLGLIIIDE 755
            KE     + I  G  DI++ T   L    P++       I +D+
Sbjct: 164 KKEKEEFLERIENGDFDILVTTAQFLARNFPEMKHLKFDFIFVDD 208


>gnl|CDD|162365 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit.  This
           family describes the exodeoxyribonuclease V alpha
           subunit, RecD. RecD is part of a RecBCD complex. A
           related family in the Gram-positive bacteria separates
           in a phylogenetic tree, has an additional N-terminal
           extension of about 200 residues, and is not supported as
           a member of a RecBCD complex by neighboring genes. The
           related family is consequently described by a different
           model.
          Length = 586

 Score = 35.1 bits (81), Expect = 0.095
 Identities = 36/183 (19%), Positives = 60/183 (32%), Gaps = 44/183 (24%)

Query: 587 EDLAQKLVDIAAKRAIHS-VPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSGR 645
           E LA KL  +   R   +    L             FP +  ++ +K   A+   L S  
Sbjct: 115 EKLAAKLRTLLEARKRTAPSAILENL----------FPLLNEQNWQKVAVALA--LKSNF 162

Query: 646 LMDRLICGDVGFGKTE-----IALRAAFIAVMNGLQVAVIAPT--------TLLVRQHFR 692
               LI G  G GKT      +            L++A+ APT          L +    
Sbjct: 163 S---LITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKN 219

Query: 693 LFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTHALLNPKITFANLGLII 752
           L +         IA++     T    +H+       + I   T    + +     L +++
Sbjct: 220 LAAAE-----ALIAALPSEAVT----IHR------LLGIKPDTKRFRHHERNPLPLDVLV 264

Query: 753 IDE 755
           +DE
Sbjct: 265 VDE 267



 Score = 29.4 bits (66), Expect = 5.3
 Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 404 QAQKGIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTE-INS 447
           QA    K I S +      ++  L  SH F K   I  L + INS
Sbjct: 324 QAYALCKKINSKTRNPLSDNVCFLKTSHRFGKDSGIGQLAKAINS 368


>gnl|CDD|177796 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
           Provisional.
          Length = 518

 Score = 34.8 bits (80), Expect = 0.13
 Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 6/90 (6%)

Query: 861 LKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQ 920
           LK    HG+ S K   + M +F  G+  V+++T ++  G+DL +   +I+   DM    +
Sbjct: 393 LKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVII--FDMPNTIK 450

Query: 921 LY--QLRGRVGRSKIASFA-LFLLPENRPL 947
            Y  Q+ GR  R      A +F+  E+R L
Sbjct: 451 EYIHQI-GRASRMGEKGTAIVFVNEEDRNL 479


>gnl|CDD|132282 TIGR03238, dnd_assoc_3, dnd system-associated protein 3.  cereus
           E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas
           haloplanktis TAC12, and Escherichia coli B7A.
          Length = 504

 Score = 33.7 bits (77), Expect = 0.31
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 5/47 (10%)

Query: 619 IKRFPHVETE---DQEKAIDAVIQDLSSGRLMDRLICGDVGFGKTEI 662
            K++ +V+ +   D E+ +    ++L S  L+   +CG  G GK+EI
Sbjct: 4   FKKYLYVKRKIQTDLERILVKFNKELPSSSLL--FLCGSSGDGKSEI 48


>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
          Length = 319

 Score = 33.8 bits (77), Expect = 0.31
 Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 630 QEKAIDAVIQDLSSGRL-MDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLV 687
           Q++A D  +  L +GRL    LICG  G GK  +AL  A   + +G   A    T  L+
Sbjct: 9   QQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLI 67


>gnl|CDD|181738 PRK09265, PRK09265, aminotransferase AlaT; Validated.
          Length = 404

 Score = 31.3 bits (72), Expect = 1.4
 Identities = 25/71 (35%), Positives = 30/71 (42%), Gaps = 17/71 (23%)

Query: 335 QQF--DALIQTTHKLVQMTAFNQQETAHNRVVHLNAFPGKSWVPSAVQKIESQDNWESGG 392
           +QF  D L+Q    LVQ T FN  E  H R+V L         P         D  E+ G
Sbjct: 349 EQFVLDLLLQEKVLLVQGTGFNWPEPDHFRIVTL---------PRV------DDLEEAIG 393

Query: 393 RFDKFLSHVAQ 403
           R  +FLS   Q
Sbjct: 394 RIGRFLSGYRQ 404


>gnl|CDD|152839 pfam12404, DUF3663, Peptidase.  This domain family is found in
           bacteria, and is approximately 80 amino acids in length.
           The family is found in association with pfam00883. There
           is a conserved WAF sequence motif.
          Length = 77

 Score = 31.4 bits (72), Expect = 1.4
 Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 3/42 (7%)

Query: 397 FLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGFKKIKK 438
            LS  A  A  G K ++S +  GA    IHL E    + I++
Sbjct: 4   TLSQEAAAAHWGEKALLSFNEDGA---TIHLTEDDDLRLIQR 42


>gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional.
          Length = 399

 Score = 30.8 bits (71), Expect = 2.2
 Identities = 8/18 (44%), Positives = 12/18 (66%), Gaps = 2/18 (11%)

Query: 878 KMNAFYEGQYDVLLSTSI 895
           + NA YEG+Y   L T++
Sbjct: 77  RANALYEGKY--PLGTAL 92


>gnl|CDD|181223 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
           polymerase III subunit epsilon; Validated.
          Length = 928

 Score = 30.7 bits (70), Expect = 2.3
 Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 5/37 (13%)

Query: 728 QVDIVIGTHALL-----NPKITFANLGLIIIDEEQHF 759
             D+VI  HALL     + +    +   IIIDE  HF
Sbjct: 431 FADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHF 467


>gnl|CDD|177899 PLN02257, PLN02257, phosphoribosylamine--glycine ligase.
          Length = 434

 Score = 30.5 bits (69), Expect = 2.6
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 11/52 (21%)

Query: 1087 FLKLLCRIANIDKMDIGLKGIIIQFRHKTFSNPEALLQYIAQQKGKIIIRPD 1138
            F+K LC     DK  I         +++TF++P A  +YI +Q   I+++ D
Sbjct: 105  FMKDLC-----DKYKIPTA------KYETFTDPAAAKKYIKEQGAPIVVKAD 145


>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
           activities.  AAA - ATPases associated with a variety of
           cellular activities. This profile/alignment only detects
           a fraction of this vast family. The poorly conserved
           N-terminal helix is missing from the alignment.
          Length = 148

 Score = 30.4 bits (68), Expect = 2.9
 Identities = 18/73 (24%), Positives = 22/73 (30%)

Query: 650 LICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASIS 709
           LI G  G GKT +A   A      G  V  I    +L     +L      G     +   
Sbjct: 6   LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGEL 65

Query: 710 RFVQTKEAALHKK 722
           R       A   K
Sbjct: 66  RLRLALALARKLK 78


>gnl|CDD|114848 pfam06153, DUF970, Protein of unknown function (DUF970).  Family of
           uncharacterized bacterial proteins.
          Length = 109

 Score = 30.4 bits (69), Expect = 3.1
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 11/56 (19%)

Query: 632 KAIDAVIQDLSSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLV 687
           K + A++QD  + RL D L   + GF  T++A    F+   N         TTLL+
Sbjct: 2   KLVIAIVQDQDANRLSDAL--TEKGFRATKLASTGGFLKAGN---------TTLLI 46


>gnl|CDD|183247 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
          Length = 629

 Score = 30.2 bits (68), Expect = 3.5
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 864 AMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQ 923
           A  +G M+    E  +    +G+ D+L++T +   GLD+ + +  +V   D+   ++ Y 
Sbjct: 273 AALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERIS--LVVNYDIPMDSESYV 330

Query: 924 LR-GRVGRSKIASFALFLLPENR 945
            R GR GR+  A  AL L  ENR
Sbjct: 331 HRIGRTGRAGRAGRAL-LFVENR 352


>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
          Length = 401

 Score = 29.4 bits (66), Expect = 5.4
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 6/72 (8%)

Query: 867 HGQMSPKNLEDKMNAFYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLR- 925
           HG M  K+ +  M  F  G   VL++T ++  G+D+ + + +I    D+    + Y  R 
Sbjct: 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI--NYDLPASPENYIHRI 355

Query: 926 ---GRVGRSKIA 934
              GR GR  +A
Sbjct: 356 GRSGRFGRKGVA 367


>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
          Length = 259

 Score = 29.3 bits (66), Expect = 5.5
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 622 FPHVETEDQ------EKAIDAVIQDLSSGRLMDR----LICGDVGFGKTEIALRAAFIAV 671
           FP V+T ++        A    +Q L S   ++R    ++ G  G GKT +A+   + AV
Sbjct: 68  FPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIALGYEAV 127

Query: 672 MNGLQVAVIAPTTLL 686
             G++V       LL
Sbjct: 128 RAGIKVRFTTAADLL 142


>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
          Length = 675

 Score = 29.2 bits (66), Expect = 6.1
 Identities = 20/90 (22%), Positives = 43/90 (47%), Gaps = 14/90 (15%)

Query: 853 FLQSEVPELKIAMAHGQMSPKNLEDKMNAFYEGQY-DVLLSTSIVESGLDLPKANTMI-- 909
           +L+  +P     + HG++   N+++ +   Y  +   +++ST  +ES + +  A  +   
Sbjct: 414 YLEKRLPIYDFYIIHGKV--PNIDEILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDT 471

Query: 910 --VQRADMFGLAQLY-------QLRGRVGR 930
             V   + FG  +++       Q +GRVGR
Sbjct: 472 GRVYVPEPFGGKEMFISKSMRTQRKGRVGR 501


>gnl|CDD|168145 PRK05639, PRK05639, 4-aminobutyrate aminotransferase; Provisional.
          Length = 457

 Score = 29.1 bits (65), Expect = 7.4
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 18/89 (20%)

Query: 917 GLAQLYQLRGRVGRSKI---ASFALFLLPENRP-LTAAAQKRLRILQSLNTLGAGFQLAS 972
           G+A    L G +GR ++    S +  L P   P ++AAA+  L I++  N L    ++  
Sbjct: 292 GVASGMGLSGVIGRKELMDLTSGSALLTPAANPVISAAAEATLEIIEEENLLKNALKVGE 351

Query: 973 ------------YDL--DIRGTGNLLGEE 987
                       +++  D+RG G ++G E
Sbjct: 352 FIKKRLLEMKESFEVIGDVRGKGLMIGVE 380


>gnl|CDD|179915 PRK05015, PRK05015, aminopeptidase B; Provisional.
          Length = 424

 Score = 29.1 bits (66), Expect = 8.1
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 3/42 (7%)

Query: 397 FLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGFKKIKK 438
            LS     A+ G K ++S +  GA    IHL        I++
Sbjct: 4   TLSTQPADARWGEKALLSFNEDGA---TIHLNGKDDLGLIQR 42


>gnl|CDD|131494 TIGR02441, fa_ox_alpha_mit, fatty acid oxidation complex, alpha
           subunit, mitochondrial.  Members represent alpha subunit
           of mitochondrial multifunctional fatty acid degradation
           enzyme complex. Subunit activities include: enoyl-CoA
           hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA
           dehydrogenase (EC 1.1.1.35). Some characterization in
           human, pig, and rat. The beta subunit has activity:
           acetyl-CoA C-acyltransferase (EC 2.3.1.16).
          Length = 737

 Score = 28.6 bits (64), Expect = 9.2
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 407 KGIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTEINSLLKEEIAAVILPI--NQGF 464
           KG+KT++  ++   L      +     KK+K+     +I SL ++ I + + P     GF
Sbjct: 357 KGLKTVLKDATPAGLDRGQQQVFKGLNKKVKR----KKITSLERDSILSNLTPTLDYSGF 412

Query: 465 ETKHMIL 471
           +   M++
Sbjct: 413 KNADMVI 419


>gnl|CDD|184617 PRK14317, glmM, phosphoglucosamine mutase; Provisional.
          Length = 465

 Score = 28.8 bits (65), Expect = 9.6
 Identities = 10/13 (76%), Positives = 11/13 (84%)

Query: 980 TGNLLGEEQSGHI 992
           TG +LG EQSGHI
Sbjct: 333 TGAMLGGEQSGHI 345


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.322    0.137    0.390 

Gapped
Lambda     K      H
   0.267   0.0598    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 19,330,782
Number of extensions: 1301927
Number of successful extensions: 2686
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2645
Number of HSP's successfully gapped: 50
Length of query: 1187
Length of database: 5,994,473
Length adjustment: 104
Effective length of query: 1083
Effective length of database: 3,747,241
Effective search space: 4058262003
Effective search space used: 4058262003
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 (21.9 bits)
S2: 63 (28.3 bits)