RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780952|ref|YP_003065365.1| DNA helicase II [Candidatus
Liberibacter asiaticus str. psy62]
         (685 letters)



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

 Score =  499 bits (1286), Expect = e-142
 Identities = 246/650 (37%), Positives = 363/650 (55%), Gaps = 32/650 (4%)

Query: 28  KGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQA 87
             LN +Q  AV  PD  PLL+LAGAG+GKT VL  R+ +LI    + P +ILA+TFTN+A
Sbjct: 1   SKLNPEQREAVLHPDG-PLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKA 59

Query: 88  IQEMKNRLACYLG---EKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQ 144
             EM+ RL   LG    +   + TFHSF   ILR+HGE +GL  +F ILDS +   +IK+
Sbjct: 60  AAEMRERLLKLLGLPAAEGLTVGTFHSFALRILRRHGERLGLNANFTILDSDDQLALIKE 119

Query: 145 LLKDLQ-IDDKDYDPHEVIEKIDYWQNRGWNPKDIP----QSSLTEDAEIPKAIYIQYVA 199
           LL+    +DDK+  P E +  I   +N   +P +       +  +E  +    +Y +Y  
Sbjct: 120 LLRRELNLDDKELLPREALRYISEAKNALLSPLEASALLLAAIKSEAEKKLAELYEEYQE 179

Query: 200 YLQKTKSCDFGGLIIKTIEVL-HHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQK 258
            L+   + DF  L++  + +L  +P VL+    +  YI+VDE+QD N  QY LL+LL   
Sbjct: 180 LLRLNNALDFDDLLLLALRLLEENPEVLEALQARFRYILVDEFQDTNPLQYELLKLLAGN 239

Query: 259 EDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNTAN 318
                 A +  VGD++Q IY +RGA   +IL+F+KDF  A +IKLEQNYRST +IL  AN
Sbjct: 240 -----AANLFVVGDDDQSIYGFRGADPENILDFEKDFPAAKVIKLEQNYRSTPNILAAAN 294

Query: 319 KLISHNKQRFDKKLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIIN-IQNTGMSLNNIA 377
           K+I++NK+R  K L T+ +     KV + ++  +  E   I  EI   I+   ++ ++IA
Sbjct: 295 KVIANNKKRQAKTLRTEVE-GSGEKVVLLLANDEEDEARWIASEIDALIEIGKVNYSDIA 353

Query: 378 ILVRTSWQTRKFEDAFLEQEIPHKVIGG--SFYDRQEIRDALAYFRLVCQEHRDEDFKRI 435
           IL RT+ Q+R  E+A     IP++++ G  SF++R+EI+D LAY RLV     D  F RI
Sbjct: 354 ILYRTNAQSRLIEEALRAAGIPYRIVIGGTSFFERKEIKDLLAYLRLVLNPDDDAAFLRI 413

Query: 436 INCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNN 495
           +N PKRGIG  +L K+   A + ++SLL+A + L+   +   +    L +F + I     
Sbjct: 414 LNLPKRGIGDATLKKLLELARERNLSLLEALKALLSFIRLSERGLALLLDFAELIEELRE 473

Query: 496 CSKKMDPAPIANMILEQSGYMAMWKNNKSSEKSQERLDNLRELLSII----EKHETLEGF 551
                    +   +LE  GY+       S   +++RL+NL ELL ++    E  E+L  F
Sbjct: 474 AILLSTALELIRELLEALGYLEALLEAGSLVAAEDRLENLEELLDVLKRYAEPRESLRAF 533

Query: 552 VLQAPLRENLGSF--IPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGN-- 607
           + +  L  N        +   + +MT+HAAKGLEF  VF+ G E+GL P   S++EG+  
Sbjct: 534 LSELSLLANDEEEEEPDEDGQVNLMTIHAAKGLEFPYVFLVGLEEGLFPADRSLDEGDEP 593

Query: 608 VEGERRLAYVGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLEL 657
           +E ERRL YV ITRAKKK +L Y  +R+       E       S+F+ EL
Sbjct: 594 LEEERRLLYVAITRAKKKLYLTYAASRKLWGKEVEEEP-----SRFVSEL 638


>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 =  392 bits (1008), Expect = e-109
 Identities = 195/505 (38%), Positives = 285/505 (56%), Gaps = 30/505 (5%)

Query: 30  LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89
           LN +Q  AVT     PLL+LAGAGTGKT VL  R+ +LI    I P +ILA+TFTN+A +
Sbjct: 1   LNPEQRKAVT-HLGGPLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAR 59

Query: 90  EMKNRLACYLGEKIPR---IQTFHSFCASILRKHGEVVG-LPTDFAILDSAESRTIIKQL 145
           EMK R+   LG+       I TFHSFC  ILRK+   +G L  +F+ILD  +   ++K++
Sbjct: 60  EMKERILKLLGKAEASELNISTFHSFCLRILRKYANRIGDLLPNFSILDELDQLALLKEI 119

Query: 146 LKDLQIDDKDYDPH------EVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKA--IYIQY 197
           LK    D  D D        E+ E I   +N   +P+++ Q+S         A   Y +Y
Sbjct: 120 LKK---DRLDLDSKLLRPLLELKELISKAKNELLSPEELQQASYAATPRDKLAAEFYQEY 176

Query: 198 VAYLQKTKSCDFGGLIIKTIEVLH-HPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLC 256
              L++  + DF  L++ T+E+L   P +L+ Y E+  YI+VDE+QD N  QY LL+LL 
Sbjct: 177 QERLKENNALDFDDLLLLTLELLRSDPELLEAYRERFKYILVDEFQDTNPIQYELLKLLA 236

Query: 257 QKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYRSTTHILNT 316
                     +  VGD +Q IY +RGA   +IL F+KDF  A +I LEQNYRST  ILN 
Sbjct: 237 -----GGHPNLFLVGDPDQSIYGFRGADIENILKFEKDFPAAKVITLEQNYRSTPEILNA 291

Query: 317 ANKLISHNKQRFDK-KLFTQRDCHDDAKVSIHVSQSDNSELSTIIQEIINIQNTG--MSL 373
           ANKLIS+N  R +K  L++Q+      KV+++ ++++  E   I  EI  +  +G  +  
Sbjct: 292 ANKLISNNTARKEKRLLWSQKG--SGEKVTVYEAETEQEEAEFIADEIKALHKSGAAIPF 349

Query: 374 NNIAILVRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDALAYFRLVCQEHRDEDF 432
            +IA+LVR++ Q+R  E+A L+  IP+K++GG SF+DR+EI+D LA  RL+     D   
Sbjct: 350 GDIAVLVRSNSQSRAIEEALLKAGIPYKILGGLSFFDRKEIKDLLALLRLIDNPKDDLAL 409

Query: 433 KRIINCPKRGIGKESLHKIQYHASQHHISLLQASEKLIDSGQFRPQIR--QSLQNFVKDI 490
            RI+N PKRGIG  +L K++  A    ISL +A  +L++        R  + L  F+  I
Sbjct: 410 LRILNTPKRGIGPTTLDKLRNLAKDRQISLFKALNQLLEKLNELLSARAYKKLLLFLALI 469

Query: 491 RRWNNCSKKMDPAPIANMILEQSGY 515
                   ++    + + +LE  GY
Sbjct: 470 EELEKLLLEILLEALLDEVLELLGY 494


>gnl|CDD|31272 COG1074, RecB, ATP-dependent exoDNAse (exonuclease V) beta subunit
           (contains helicase and exonuclease domains) [DNA
           replication, recombination, and repair].
          Length = 1139

 Score =  144 bits (365), Expect = 6e-35
 Identities = 104/528 (19%), Positives = 174/528 (32%), Gaps = 100/528 (18%)

Query: 191 KAIYIQYVAYLQKTKSCDFGGLIIKTIEVLHHPH--VLKKYHEKIPYIMVDEYQDINTPQ 248
           + +  +Y A  ++  + DF  LI +  ++L      + +   E+ P+I++DE+QD +  Q
Sbjct: 335 EELIERYDAEKRQRNALDFDDLIHRLAKLLTSEGEELAESLREQYPHILIDEFQDTDPQQ 394

Query: 249 YLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDANIIKLEQNYR 308
           + +L  L     +        VGD  Q IY +RGA     L      K    I LE NYR
Sbjct: 395 WRILSRLFAGFKAGNRTLFL-VGDPKQSIYRFRGADIFTFLEAASSEKAFARITLETNYR 453

Query: 309 STTHILNTANKLISHNKQRFDK---------------------------KLFTQRDCHDD 341
           ST  +LN  N L       +                               F + +    
Sbjct: 454 STPELLNAVNALFKQAMFAYPGEIDYDPVAELGARNGSPGSVNGEPLPALKFWEEEDDWT 513

Query: 342 AKVSIHVSQSDN-SELSTIIQEIINIQNTG--------MSLNNIAILVRTSWQTRKFEDA 392
           A  +    +     E   I   +  +            +   +IA+LVR+  +    E A
Sbjct: 514 APENEEDEREIADLEARQIAAWLRELIEGEAVLDGERPIRAGDIAVLVRSRNEAAAIERA 573

Query: 393 FLEQEIPHKVIGG---SFYDRQEIRDALAYFRLVCQEHRDEDFKRIINCPKRGIGKESLH 449
             +  I   V      S ++  E +D LA  R +     D     ++  P  G+ ++ L 
Sbjct: 574 LKKAGII-PVYLSNRSSLFETLEAQDLLALLRAILNPEDDLPLAALLRSPLFGLTEDDLA 632

Query: 450 KIQYHASQHHISLLQASEKLIDSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMI 509
                        L   E   +      +    +  F   +  W   +K      +    
Sbjct: 633 ------------ALAQDEAEWEFLWENLRQLADIWRFRGVLAMWRALAKITPLHDLIAER 680

Query: 510 LEQSGYMAMWKNNKSSEKSQERLDNLRELLSIIEKHET-----LEGFVLQAPLRENLGSF 564
           L  +        N          + L+ELL+    +E      LE F+       +    
Sbjct: 681 LLSTNLGERDLTNGL-----HAQELLQELLTRALSYEHGLLRWLERFI-ALIENNDEEQA 734

Query: 565 I---PDSNCIQIMTLHAAKGLEFDTVFISG-------------------------WEQGL 596
                D + ++IMT+H +KGLEF  VF+                            +   
Sbjct: 735 RRLESDRDLVRIMTIHKSKGLEFPIVFLPFILSKRFNDSDVPLLVYYDGLRFELFDDLKS 794

Query: 597 LPHQLS------INEGNVEGERRLAYVGITRAKKKCHLFYTINRRTHD 638
            P   S        E  +  E RL YV +TRAK++  L    ++R   
Sbjct: 795 YPTPESQANKELAEEEALAEELRLLYVALTRAKEQLILIGAPSKREKS 842



 Score = 75.9 bits (186), Expect = 3e-14
 Identities = 41/163 (25%), Positives = 62/163 (38%), Gaps = 43/163 (26%)

Query: 46  LLILAGAGTGKTTVLIARMLHLICHKE-IPPSKILAMTFTNQAIQEMKNRLACYLGEKIP 104
           +L+ A AGTGKT VL  R+L L+     +   +IL +TFT  A  EMK R+   L E + 
Sbjct: 19  VLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLKEALQ 78

Query: 105 ----------------------------------------RIQTFHSFCASILRKHGEVV 124
                                                    I T H FC  ILR+     
Sbjct: 79  ENDEKLASDDELLEALAALIQALIQAIRLFALALETNDEAAIFTIHGFCQRILRQFALEA 138

Query: 125 GLPTDFAILDSAESRTIIKQLLKDLQIDDKDYDPHEVIEKIDY 167
           G+  DF +L+  +   +  +L++D         P E+ + +  
Sbjct: 139 GISFDFELLE--DESDLFLELVEDFWRRRFYPLPAELAQLVAQ 179


>gnl|CDD|37319 KOG2108, KOG2108, KOG2108, 3'-5' DNA helicase [Replication,
           recombination and repair].
          Length = 853

 Score =  143 bits (363), Expect = 1e-34
 Identities = 147/643 (22%), Positives = 229/643 (35%), Gaps = 70/643 (10%)

Query: 26  YLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTN 85
               LN  Q  +   P      ++AG G+GKT VL  R+ +LI    I P +IL  T TN
Sbjct: 10  LYSLLNKSQRFSALSPLRR-KRVIAGPGSGKTLVLTERVAYLINFNNIKPDEILINTGTN 68

Query: 86  QAIQEMKNRLACYLG-----EKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRT 140
           +A   +K  L   L      ++I  I TFHS       + G ++ L  +  I D  ++  
Sbjct: 69  KAADSIKLNLIAILRTSKCSKEI--IGTFHSIAVKYSLRDGPLLPLSENCRIQDLPDTYA 126

Query: 141 IIKQLLKDL--QIDD---------KDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEI 189
           I+   +  L  +I           +   P    +      N       I    L    E 
Sbjct: 127 ILGDNIWALLAKIKLPSSSSNRKQRLLFPLRRPDSTVTKPNVTETLYSIAVLLLAMFEEG 186

Query: 190 PK-----AIYIQYVAYLQKTKSCDFGGLIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDI 244
                     I Y  YLQ  +  D   L + +++VL  P V      KI +++VDE+QDI
Sbjct: 187 INVSNRDDYEIYYYLYLQTLE--DSCTLAMNSLKVLQRPRVCSN---KITHVLVDEFQDI 241

Query: 245 NTPQYLLLRLLCQKEDSKQGARICCVGDENQCIYEWRGAQFSHILNFQKDFKDAN---II 301
              Q   L++L       +       GD +Q IY++ G   + I      F         
Sbjct: 242 LKIQLEPLQVL-------KIKAFAGTGDTDQSIYKFAGKW-AEIRILYVTFNKFIATQAE 293

Query: 302 KLEQNYRSTTHILNTANKLISHNKQRFDKK-LFTQRDCHDDAKVSIHVSQSDNSELSTII 360
           +L  N RS   I + A   I    Q   K  L        +    +   +    +     
Sbjct: 294 RLFPNNRSCKTIHSLAYGAIGRQYQEKKKLLLRKLTPS--ELNSVLAEFKGGFPKAKLKC 351

Query: 361 QEIINIQNTGMSL---NNIAILVRTSWQTRKFEDAFLEQEIPHKVIGG-SFYDRQEIRDA 416
           +   N           N+ AIL  +S Q   FE   +EQ   +K+I   SF D  E R  
Sbjct: 352 RTEENFLVAADIEFTINDHAILWCSSSQLSSFESVLVEQREKYKLIAVASFLDSNERRLG 411

Query: 417 LAYFRLVCQEHRDEDFKRIINCPKRGIGKESLHKIQYHASQ------HHISLLQASEKLI 470
           L Y +L      D   K ++  P+R  G      I    +Q       ++ L+Q     +
Sbjct: 412 LNYEKLHANMTPDGYLK-LLQLPERPNGLAKFDYIILDEAQDCTPCIQNLILIQKHNIKV 470

Query: 471 DSGQFRPQIRQSLQNFVKDIRRWNNCSKKMDPAPIANMILEQSGYMAMWKNNKSSEKSQE 530
             G F   I           R  N+    +   P   +      +    +  K  E   E
Sbjct: 471 FVGDFHQSI--------YSFRGANSALFNLATLPDTLVECLTKSFRFGNEVAKVKETILE 522

Query: 531 RLDNLRELLSIIEKHETLEGFVLQAPLRENLGSFIPDSNC-----IQIMTLHAAKGLEFD 585
           +   +R+L  +   H            ++ L S    +       +QI TLH+AKGLE+ 
Sbjct: 523 KKKRVRKLTLVSNNHFYFLSIPGDVSGQKFLLSRTLSNLTQEEEELQISTLHSAKGLEWP 582

Query: 586 TVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHL 628
            V I    + ++P          + + +   V  TRA++  HL
Sbjct: 583 VVSIGLCRENIIPILFQ---DEEDEDGQNLVVKDTRARRLLHL 622



 Score = 31.1 bits (70), Expect = 1.0
 Identities = 24/75 (32%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 559 ENLGSFIPDS-NCIQIMTLHAAKGLEFDTVFIS-------GWEQGLLPHQLSINEGNVEG 610
           EN      D    + + T+H AKGLEFD V +        G             E   E 
Sbjct: 662 ENFHIRDLDKAENVILGTIHQAKGLEFDNVHLQNDFVKVFGSVSNFERLPSFRVETYNED 721

Query: 611 ERRLAYVGITRAKKK 625
           E    YV +TRAKK+
Sbjct: 722 EWNFLYVAVTRAKKR 736


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

 Score = 42.3 bits (99), Expect = 5e-04
 Identities = 29/133 (21%), Positives = 55/133 (41%), Gaps = 7/133 (5%)

Query: 25  NYLKGLNAQQTHAVT--IPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMT 82
            + K LN+ Q  AV+  I +   L+I    GTGKT  L+  +  L+  K+    ++L   
Sbjct: 181 FFNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKK----RVLVCA 236

Query: 83  FTNQAIQEMKNRLACYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTII 142
            +N A+  +  RL  +L   + R+        S+     +++    D +      S+ I 
Sbjct: 237 PSNVAVDNIVERLT-HLKLNLVRVGHPARLLESVADHSLDLLSNTKDNSQNAKDISKDID 295

Query: 143 KQLLKDLQIDDKD 155
               K+ +  +  
Sbjct: 296 ILFQKNTKTKNDK 308


>gnl|CDD|110446 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
           Helicase activity for this family has been demonstrated
           and NTPase activity. This helicase has multiple roles at
           different stages of viral RNA replication, as dissected
           by mutational analysis.
          Length = 226

 Score = 37.4 bits (87), Expect = 0.014
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 9/59 (15%)

Query: 571 IQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629
           ++  T+H  +GL FD+V +               +     +  L YV +TR +K  H+ 
Sbjct: 176 VRATTVHEVQGLTFDSVTL---------VLDKDTDLLSISDPELLYVALTRHRKSLHIL 225


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

 Score = 36.6 bits (84), Expect = 0.022
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 12/56 (21%)

Query: 574 MTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLF 629
           MT+H ++G EFD V +      LLP        +    R L Y  ITRA+ +  L+
Sbjct: 625 MTIHKSQGSEFDRVIV------LLP------SHSPMLSRELLYTAITRARDRLILY 668


>gnl|CDD|33753 COG3972, COG3972, Superfamily I DNA and RNA helicases [General
           function prediction only].
          Length = 660

 Score = 35.4 bits (81), Expect = 0.048
 Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 30  LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQ 89
            +  QT A          I   AG+GKT +L  +   L  H + P S+I    FT     
Sbjct: 163 FDTDQTKAAFQSGFGKQRIRGLAGSGKTELLAHKAAEL--HSKNPDSRIAFTFFTKILAS 220

Query: 90  EMKNRL 95
            M+  +
Sbjct: 221 TMRTLV 226


>gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA
           processing and modification].
          Length = 673

 Score = 32.7 bits (74), Expect = 0.39
 Identities = 23/106 (21%), Positives = 40/106 (37%), Gaps = 12/106 (11%)

Query: 46  LLILAGAGTGKTTVLIARMLHLICH--------KEIPPSKILAMTFTN---QAIQEMKNR 94
            + +A  G+GKT   +  +L  I            I     + +  T    Q I+E  N+
Sbjct: 285 PIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNK 344

Query: 95  LACYLGEKIPRIQTFHSFCASILR-KHGEVVGLPTDFAILDSAESR 139
               LG +   +    SF     +   G  + + T   ++DS E+R
Sbjct: 345 FGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENR 390


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

 Score = 32.0 bits (72), Expect = 0.48
 Identities = 35/261 (13%), Positives = 64/261 (24%), Gaps = 46/261 (17%)

Query: 37  AVTIPDDTPLLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQEMKNRLA 96
           A  +     LLI A  GTGKT   +   L    +      K++  T T    +++     
Sbjct: 28  AEALKGGEGLLIEAPTGTGKTLAYLLPALA---YAREEGKKVIISTRTKALQEQLLEED- 83

Query: 97  CYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAE-----SRTIIKQLLKDLQI 151
                               L  H  +  L   FA+L         SR      L     
Sbjct: 84  --------------------LPIHKLLKKLGGKFALLKGRSNYLCLSRLERLAQLGGDDD 123

Query: 152 DDKDYDPHEVIEKIDYWQNRGWNPKDIPQSSLTEDAEIPKAIYIQYVAYLQKTKSCDFGG 211
           D       + +  +  W            +    D  +     +         + C +  
Sbjct: 124 DYLQSLALKALADLLVWLTETKTGDLRELTPKALDDPLWTL--VTDDKDSCLGEDCPY-- 179

Query: 212 LIIKTIEVLHHPHVLKKYHEKIPYIMVDEYQDINTPQYLLLRLLCQKEDSKQGARICCVG 271
                       +    Y          +   +     LL  +  ++           V 
Sbjct: 180 ------------YTECFYFPARKEAENADLV-VTNHALLLADVALEESRILLPENDVVVF 226

Query: 272 DENQCIYEWRGAQFSHILNFQ 292
           DE   + +   +  S  L+ +
Sbjct: 227 DEAHNLPDIARSALSIRLSER 247


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

 Score = 31.9 bits (72), Expect = 0.66
 Identities = 27/85 (31%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 23  VPNYLKGLNAQQTHAVTIPDDTPLLILAGA-GTGKTTVLIARMLHLICHKEIPPSKILAM 81
           VPN  K LNA Q++AV      PL ++ G  GTGKT      + HL      P   +L  
Sbjct: 405 VPNLPK-LNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGP---VLVC 460

Query: 82  TFTNQAIQEMKNRLACYLGEKIPRI 106
             +N A+ ++  ++    G K+ R+
Sbjct: 461 APSNIAVDQLAEKIH-KTGLKVVRL 484


>gnl|CDD|33754 COG3973, COG3973, Superfamily I DNA and RNA helicases [General
           function prediction only].
          Length = 747

 Score = 31.1 bits (70), Expect = 0.91
 Identities = 21/89 (23%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 30  LNAQQTHAVTIPDDTPLLILAGAGTGKTTVLIARMLHLIC-HKEIPPSKILAMTFTNQAI 88
           +  +Q   +    +  L++   AG+GKTT+ + R+ +L+  ++    +K + +   N+  
Sbjct: 213 IQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVF 272

Query: 89  QEMKNRLACYLGEKIPRIQTFHSFCASIL 117
            E  +R+   LGE+    +TF  +  +IL
Sbjct: 273 LEYISRVLPELGEEGVVQETFEEWALAIL 301



 Score = 31.1 bits (70), Expect = 0.95
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 10/59 (16%)

Query: 573 IMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAYVGITRAKKKCHLFYT 631
           ++ ++ AKGLEFD V +            SI E   E + R  YV +TRA    ++F  
Sbjct: 697 VIPVYDAKGLEFDHVIV---------VDPSIVE-ETEQDLRDLYVAVTRALHSLYIFGE 745


>gnl|CDD|153410 cd07956, Anticodon_Ia_Arg, Anticodon-binding domain of arginyl tRNA
           synthetases.  This domain is found in arginyl tRNA
           synthetases (ArgRS), which belong to the class Ia
           aminoacyl tRNA synthetases. It lies C-terminal to the
           catalytic core domain, and recognizes and specifically
           binds to the tRNA anticodon. ArgRS catalyzes the
           transfer of arginine to the 3'-end of its tRNA.
          Length = 156

 Score = 31.0 bits (71), Expect = 1.2
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 100 GEKIPRIQTFHSFCASILRKHGEVVGLPTDFAI--LDSAESRTIIKQLLK 147
           G+  P +Q  H+   SILRK GE +    D  +  L   + R +I  L K
Sbjct: 33  GDTGPYLQYAHARLCSILRKAGETIEAEADADLSLLPEPDERDLILLLAK 82


>gnl|CDD|30368 COG0018, ArgS, Arginyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 577

 Score = 30.6 bits (69), Expect = 1.4
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 100 GEKIPRIQTFHSFCASILRKHGE--VVGLPTDFAILDSAESRTIIKQLLK---DLQIDDK 154
           G   P +Q  H+   SILRK GE  +       A+L   E R ++K+LL+    L+   +
Sbjct: 453 GNTAPYVQYAHARICSILRKAGEDELDLSTEADALLTELEERELVKKLLEFPEVLEEAAE 512

Query: 155 DYDPH 159
           + +PH
Sbjct: 513 ELEPH 517


>gnl|CDD|37246 KOG2035, KOG2035, KOG2035, Replication factor C, subunit RFC3
           [Energy production and conversion, Replication,
           recombination and repair].
          Length = 351

 Score = 30.3 bits (68), Expect = 1.9
 Identities = 29/132 (21%), Positives = 55/132 (41%), Gaps = 23/132 (17%)

Query: 32  AQQTHAVTIPDDTPLLILAG-AGTGKTTVLIARMLHLICHKEIPPSKILAMTFTNQAIQE 90
           A    +++   D P L++ G +G GK T ++  +L  +    +   KI   TFT  +   
Sbjct: 22  ANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMC-LLRELYGVGVEKLKIETRTFTTPS--- 77

Query: 91  MKNRLACYLGEKIPRIQTFHSFCASILRKHGEVVGLPTDFAILDSAESRTIIKQLLKDLQ 150
                     +K+  I T  S        H E+   P+D    D    + ++K++ +  Q
Sbjct: 78  ---------KKKL-EISTVSS------NYHLEIT--PSDAGNYDRVVIQELLKEVAQTQQ 119

Query: 151 IDDKDYDPHEVI 162
           I+ +   P +V+
Sbjct: 120 IETQGQRPFKVV 131


>gnl|CDD|147737 pfam05746, DALR_1, DALR anticodon binding domain.  This all alpha
           helical domain is the anticodon binding domain in
           Arginyl and glycyl tRNA synthetase. This domain is known
           as the DALR domain after characteristic conserved amino
           acids.
          Length = 117

 Score = 29.9 bits (68), Expect = 2.1
 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 110 HSFCASILRKHGE-VVGLPTDFAILDSAESRTIIKQLLK 147
           H+   SILRK GE  + L  D  +L   E + ++K LL+
Sbjct: 5   HARICSILRKAGELGINLDIDALLLLEEEEKELLKALLQ 43


>gnl|CDD|31414 COG1221, PspF, Transcriptional regulators containing an AAA-type
           ATPase domain and a DNA-binding domain [Transcription /
           Signal transduction mechanisms].
          Length = 403

 Score = 29.6 bits (66), Expect = 3.3
 Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 41  PDDTPLLILAGAGTGKTTVLIARMLHLICHK 71
           P   P+LI+   GTGK   L AR++H +  +
Sbjct: 99  PSGLPVLIIGETGTGKE--LFARLIHALSAR 127


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

 Score = 29.2 bits (65), Expect = 3.9
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 10/81 (12%)

Query: 20  PSCVPNYLKGLNAQQTHAV--TIPDDTPLLILAGAGTGKTTVL--IARMLHLICHKEIPP 75
           P      L  LN  Q  A+   +  +   LIL   GTGKTT +  + ++L  +       
Sbjct: 660 PKIKKIILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVAL------G 713

Query: 76  SKILAMTFTNQAIQEMKNRLA 96
            K+L  ++T+ A+  +  +L 
Sbjct: 714 KKVLLTSYTHSAVDNILIKLK 734


>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 = 28.9 bits (64), Expect = 4.3
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 46 LLILAGAGTGKTTVLIARMLHLICHKEIPPSKILAMT--FTNQAIQEMKNRLACYL 99
          +L+ A  G+GKT   +  +L L+   +     +LA T    NQ  + +K      +
Sbjct: 3  VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGI 58


>gnl|CDD|30845 COG0499, SAM1, S-adenosylhomocysteine hydrolase [Coenzyme
           metabolism].
          Length = 420

 Score = 29.0 bits (65), Expect = 4.3
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 9/58 (15%)

Query: 36  HAVTIPDDTPLLILAGAGTGKTTVLIA--RMLHLIC---HKEIPPSKILAMTFTNQAI 88
            AV   +  P +       GK  +L+A  R+++L     H    PS+++ M+F NQA+
Sbjct: 310 LAVEKREVRPQVDEYELPDGKRIILLAEGRLVNLAAATGH----PSEVMDMSFANQAL 363


>gnl|CDD|33289 COG3486, IucD, Lysine/ornithine N-monooxygenase [Secondary
           metabolites biosynthesis, transport, and catabolism].
          Length = 436

 Score = 28.7 bits (64), Expect = 5.7
 Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 18/83 (21%)

Query: 608 VEGERRLAYVGITRAKKKC--HLFYTINRRTHD---FTRVERYQPSQVSQFLLELYDPSH 662
           +  +R +  +G  ++  +    L  +   + +     TR   + P   S+F LE + P  
Sbjct: 184 LLQKRSVTVIGSGQSAAEIFLDLLNSQPPQDYQLNWITRSSGFLPMDYSKFGLEYFSPE- 242

Query: 663 TQEIIYDDIYGTFSEHWNQIPEP 685
                       +++++  +P  
Sbjct: 243 ------------YTDYFYGLPPE 253


>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
          transporters homologous to the Drosophila white gene,
          which acts as a dimeric importer for eye pigment
          precursors.  The eye pigmentation of Drosophila is
          developed from the synthesis and deposition in the
          cells of red pigments, which are synthesized from
          guanine, and brown pigments, which are synthesized from
          tryptophan.  The pigment precursors are encoded by the
          white, brown, and scarlet genes, respectively.
          Evidence from genetic and biochemical studies suggest
          that the White and Brown proteins function as
          heterodimers to import guanine, while the White and
          Scarlet proteins function to import tryptophan.
          However, a recent study also suggests that White may be
          involved in the transport of a metabolite, such as
          3-hydroxykynurenine, across intracellular membranes.
          Mammalian ABC transporters belonging to the White
          subfamily (ABCG1, ABCG5, and ABCG8) have been shown to
          be involved in the regulation of lipid-trafficking
          mechanisms in macrophages, hepatocytes, and intestinal
          mucosa cells.  ABCG1 (ABC8), the human homolog of the
          Drosophila white gene is induced in monocyte-derived
          macrophages during cholesterol influx mediated by
          acetylated low-density lipoprotein.  It is possible
          that human ABCG1 forms heterodimers with several
          heterologous partners..
          Length = 226

 Score = 28.7 bits (64), Expect = 5.8
 Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 19 VPSCVPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTVL--IARMLH 66
          V     N+ K        ++ +     + IL  +G+GKTT+L  I+  + 
Sbjct: 9  VGLKAKNWNKYARILNDVSLHVESGQVMAILGSSGSGKTTLLDAISGRVE 58


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

 Score = 28.4 bits (62), Expect = 6.6
 Identities = 20/117 (17%), Positives = 41/117 (35%), Gaps = 10/117 (8%)

Query: 557 LRENLGSFIPDSNCIQIMTLHAAKGLEFDTVFISGWEQGLLPHQLSINEGNVEGERRLAY 616
           +R  L         +++ T+   +G E D + +S     L+       E    G+ R   
Sbjct: 661 IRRLLNEAGKG---VEVGTVDGFQGREKDVIILS-----LVRSNDDKGEIGFLGDPRRLN 712

Query: 617 VGITRAKKKCHLFYTINRRTHDFTRVERYQPSQVSQFLLELYDPSHTQEIIYDDIYG 673
           V +TRAK+K  +    +  T +   + +   + + +  L          +   D   
Sbjct: 713 VALTRAKRKLIVVG--SSSTLESDPLYKRLINDLKRKGLLAELNLLDLRLTDLDDES 767


>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
          nucleotide-binding domain.  This family includes the
          ATP synthase alpha and beta subunits, the ATP synthase
          associated with flagella and the termination factor
          Rho.
          Length = 213

 Score = 28.6 bits (65), Expect = 6.6
 Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)

Query: 46 LLILAGAGTGKTTVL--IAR 63
          + I  G+GTGKT +L  IAR
Sbjct: 18 IGIFGGSGTGKTVLLGMIAR 37


>gnl|CDD|176246 cd08286, FDH_like_ADH2, formaldehyde dehydrogenase (FDH)-like.
          This group is related to formaldehyde dehydrogenase
          (FDH), which  is a member of the zinc-dependent/medium
          chain alcohol dehydrogenase family.  This family uses
          NAD(H) as a cofactor in the interconversion of alcohols
          and aldehydes, or ketones. Another member is identified
          as a dihydroxyacetone reductase. Like the
          zinc-dependent alcohol dehydrogenases (ADH) of the
          medium chain alcohol dehydrogenase/reductase family
          (MDR), tetrameric FDHs have a catalytic zinc that
          resides between the catalytic and NAD(H)binding domains
          and a structural zinc in a lobe of the catalytic
          domain. Unlike ADH, where NAD(P)(H) acts as a cofactor,
          NADH in FDH is a tightly bound redox cofactor (similar
          to nicotinamide proteins). The medium chain alcohol
          dehydrogenase family (MDR) has a NAD(P)(H)-binding
          domain in a Rossmann fold of a beta-alpha form. The
          N-terminal region typically has an all-beta catalytic
          domain. These proteins typically form dimers (typically
          higher plants, mammals) or tetramers (yeast, bacteria),
          and have 2 tightly bound zinc atoms per subunit.
          Length = 345

 Score = 28.4 bits (64), Expect = 7.0
 Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 1/13 (7%)

Query: 12 HILKGDFVPSCVP 24
          HILKGD VP+  P
Sbjct: 43 HILKGD-VPTVTP 54


>gnl|CDD|147761 pfam05785, CNF1, Rho-activating domain of cytotoxic necrotizing
           factor.  This family consists of several bacterial
           cytotoxic necrotizing factor proteins as well as related
           dermonecrotic toxin (DNT) from Bordetella species.
           Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of
           rabbit skin and re-organisation of the actin
           cytoskeleton in cultured cells. Bordetella dermonecrotic
           toxin (DNT) stimulates the assembly of actin stress
           fibres and focal adhesions by deamidating or
           polyaminating Gln63 of the small GTPase Rho. DNT is an
           A-B toxin which is composed of an N-terminal
           receptor-binding (B) domain and a C-terminal
           enzymatically active (A) domain.
          Length = 281

 Score = 28.1 bits (63), Expect = 7.5
 Identities = 14/37 (37%), Positives = 21/37 (56%)

Query: 23  VPNYLKGLNAQQTHAVTIPDDTPLLILAGAGTGKTTV 59
           V N  +G N  +     +P+  PL+I +GA +G TTV
Sbjct: 101 VSNGARGTNGIKIALSEVPEGKPLIITSGALSGCTTV 137


  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
   0.321    0.136    0.409 

Gapped
Lambda     K      H
   0.267   0.0706    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 8,468,239
Number of extensions: 455795
Number of successful extensions: 1334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1305
Number of HSP's successfully gapped: 39
Length of query: 685
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 585
Effective length of database: 4,102,837
Effective search space: 2400159645
Effective search space used: 2400159645
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: 61 (27.3 bits)