RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780327|ref|YP_003064740.1| preprotein translocase subunit
SecA [Candidatus Liberibacter asiaticus str. psy62]
         (890 letters)



>gnl|CDD|30998 COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA
           helicase) [Intracellular trafficking and secretion].
          Length = 822

 Score =  996 bits (2576), Expect = 0.0
 Identities = 463/880 (52%), Positives = 587/880 (66%), Gaps = 59/880 (6%)

Query: 5   LAKLASKLLIPSNERRLRPYYAKVIAINELEKEISHLSDDSLANKTSEFKERINNGETLD 64
           L  L  KL    NER L+     V+ IN LE E+  LSD+ L  KT+EFKER+ +GE LD
Sbjct: 1   LFSLLKKLFGSGNERILKRLRKIVMQINALEAEMESLSDEELKAKTNEFKERLASGE-LD 59

Query: 65  DLLVPAFAVVREVARRTLGMRPFDVQLLGGMILHKGCVAEMKTGEGKTLAAVLPVYLNAL 124
           DLL  AFAVVRE ++R LGMR FDVQLLGG++LH G +AEM+TGEGKTL A LP YLNAL
Sbjct: 60  DLLPEAFAVVREASKRVLGMRHFDVQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNAL 119

Query: 125 SGKGVHVVTVNDYLARRDSNTMSAIYKFLGLSTGVVFHDLSDDKRRAAYACDITYITNNE 184
           +GKGVHVVTVNDYLARRD+  M  +Y+FLGLS GV+   +S +++RAAYACDITY TNNE
Sbjct: 120 AGKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGVILAGMSPEEKRAAYACDITYGTNNE 179

Query: 185 LGFDYLRDNMQYRRVDMVQRGHNFAIVDEVDSIFIDEARTPLIISGPVEDHSDLYRTIDS 244
           LGFDYLRDNM   + + VQRG NFAIVDEVDSI IDEARTPLIISGP ED S+LY+ +D 
Sbjct: 180 LGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIISGPAEDSSELYKKVDD 239

Query: 245 IIIQLHP-SDYEIDEKQRTVHFSEKGTERIEELLHGENLLKSGGLYSFENVAIVHLINNA 303
           ++  L    D+ IDEK + V  +E G E+ EELL  EN      LY  ENV +VH +N A
Sbjct: 240 LVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIEN------LYDLENVNLVHHLNQA 293

Query: 304 LKSHTLFLRNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQHQALEAKERVKIQPENQTLS 363
           L++H LF R+ DYIV   EVVI+DEFTGRMM GRR+SDG HQA+EAKE V+IQ ENQTL+
Sbjct: 294 LRAHILFFRDVDYIVRDGEVVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLA 353

Query: 364 SITFQNYFLKYRKLSGMTGTASTEAEELANIYNLDVIEVPTNVPVIRIDEHDEIYRTSEE 423
           +ITFQN F  Y KL+GMTGTA TE EE   IY LDV+ +PTN P+IR+DE D +Y+T EE
Sbjct: 354 TITFQNLFRLYPKLAGMTGTADTEEEEFDVIYGLDVVVIPTNRPIIRLDEPDLVYKTEEE 413

Query: 424 KYAAIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFTKFQILNALYHEKEAYIIS 483
           K+ AI+ +I + H+KGQPVLVGT SIEKSE L+  LRK       +LNA  H +EA II+
Sbjct: 414 KFKAIVEDIKERHEKGQPVLVGTVSIEKSELLSKLLRKAGI-PHNVLNAKNHAREAEIIA 472

Query: 484 QAGIPGAVTIATNMAGRGTDIQLGGNVAMRIEHELANISDEEIRNKRIKMIQEEVQSLKE 543
           QAG PGAVTIATNMAGRGTDI+LGGN                                 E
Sbjct: 473 QAGQPGAVTIATNMAGRGTDIKLGGNP--------------------------------E 500

Query: 544 KAIVAGGLYVISTERHESRRIDNQLRGRSGRQGDPGRSKFYLSLQDDLMRIFGSPRMESF 603
             +  GGL+VI TERHESRRIDNQLRGR+GRQGDPG S+FYLSL+DDLMR F S R+ + 
Sbjct: 501 FVMELGGLHVIGTERHESRRIDNQLRGRAGRQGDPGSSRFYLSLEDDLMRRFASDRLPAL 560

Query: 604 LRKIGLKEGEAIIHPWINKAIERAQQKVEARNFETRKNLLKYDDVLNEQRKIIFEQRLEI 663
           + K+GLKEGEAI    + +A+ERAQ+KVE RNF+ RK LL+YDDVLN+QRK+I+ QR  +
Sbjct: 561 MDKLGLKEGEAIESKMVTRAVERAQRKVEGRNFDIRKQLLEYDDVLNDQRKVIYAQRNRL 620

Query: 664 IDTENILEIIADMRHDTLHNIVEKCIPNNSYPEKWDIKKLETEIYEIFGIHFPVLEWRND 723
           ++  ++ E I+ M  D +  +V + IP     E WD++ L  E+        P+ +   +
Sbjct: 621 LEALDLSEFISKMIEDVIKALVGEYIPPPQQAELWDLEGLIDELKGTVHPDLPINKSDLE 680

Query: 724 NGIDHTEMSKRIFAKADKIAEDQENSFGTEKMQALGRHILLHTLDSFWREHMARLEHSRS 783
           +     E+++RI   AD+  + +E   G E M+   R+++L  LD  WREH+  ++  R 
Sbjct: 681 DE-AEEELAERILKAADEAYDKKEE-VGPEAMREFERYVMLQVLDYLWREHLDAMDALRE 738

Query: 784 IIGFRGYAQRDPLQEYKSEAFGFFNTLLTHLRKDVVSQIARIEPNNINNQELNNSLPYIA 843
            I  RGYAQ+DPL EYK EAF  F  +L  +++DVV ++ +++   +  ++ +       
Sbjct: 739 GIHLRGYAQKDPLIEYKREAFELFEDMLEDIKEDVVKRLFKVQVAEVEEEDRSLLA---- 794

Query: 844 ENDHGPVIQKENELDTPNVCKTSKIKRNHPCPCGSGKKYK 883
                  + +   L         KI RN PCPCGSG KYK
Sbjct: 795 ---QEKALTQARALG--------KIGRNEPCPCGSG-KYK 822


>gnl|CDD|177045 CHL00122, secA, preprotein translocase subunit SecA; Validated.
          Length = 870

 Score =  871 bits (2252), Expect = 0.0
 Identities = 375/879 (42%), Positives = 541/879 (61%), Gaps = 75/879 (8%)

Query: 13  LIPSNERRLRPYYAKVIAINELEKEISHLSDDSLANKTSEFKERINNGETLDDLLVPAFA 72
            + +N+ +L  Y   V  IN LE+E+ +L+D  L +KT++ K+R++NG+ L+ ++  +FA
Sbjct: 4   NLFNNKSKLNKYQTLVNQINLLEEELKNLTDTELRSKTNKLKKRLSNGQNLNKIIPESFA 63

Query: 73  VVREVARRTLGMRPFDVQLLGGMILHKGCVAEMKTGEGKTLAAVLPVYLNALSGKGVHVV 132
           + RE + RTLG+R FDVQL+GG++L+ G +AEMKTGEGKTL A LP YLNAL+GKGVH+V
Sbjct: 64  LTREASFRTLGLRHFDVQLIGGLVLNDGKIAEMKTGEGKTLVATLPAYLNALTGKGVHIV 123

Query: 133 TVNDYLARRDSNTMSAIYKFLGLSTGVVFHDLSDDKRRAAYACDITYITNNELGFDYLRD 192
           TVNDYLA+RD   M  IY+FLGL+ G++   +S ++R+  Y  DITY+TN+ELGFDYLRD
Sbjct: 124 TVNDYLAKRDQEWMGQIYRFLGLTVGLIQEGMSSEERKKNYLKDITYVTNSELGFDYLRD 183

Query: 193 NMQYRRVDMVQRGHNFAIVDEVDSIFIDEARTPLIISGPVEDHSDLYRTIDSIIIQLHPS 252
           NM     D+VQR  N+ I+DEVDSI IDEARTPLIISG  + + D Y   D +   L  +
Sbjct: 184 NMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLIISGQSKTNIDKYIVADELAKYLEKN 243

Query: 253 -DYEIDEKQRTVHFSEKGTERIEELLHGENLLKSGGLYSFENVAIVHLINNALKSHTLFL 311
             YE+DEK + V  +E+G   IE++L  E+      LYS  +  I   I NALK+  LF 
Sbjct: 244 VHYEVDEKNKNVILTEQGILFIEKILKIED------LYSANDPWI-PYILNALKAKELFF 296

Query: 312 RNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQHQALEAKERVKIQPENQTLSSITFQNYF 371
           +N  YIV  +E++I+DEFTGR+MPGRR+SDG HQA+EAKE + I+ E +TL+SIT+QN+F
Sbjct: 297 KNVHYIVRNNEIIIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFF 356

Query: 372 LKYRKLSGMTGTASTEAEELANIYNLDVIEVPTNVPVIRIDEHDEIYRTSEEKYAAIIAE 431
           L Y KLSGMTGTA TE  E   IYNL+V+ +PT+ P++R D  D IY+    K+ AI  E
Sbjct: 357 LLYPKLSGMTGTAKTEELEFEKIYNLEVVCIPTHRPMLRKDLPDLIYKDELSKWRAIADE 416

Query: 432 IIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFTKFQILNAL--YHEKEAYIISQAGIPG 489
            +  H+ G+P+L+GT +IEKSE L SQL K      Q+LNA      +E+ I++QAG  G
Sbjct: 417 CLQMHQTGRPILIGTTTIEKSELL-SQLLKEYRLPHQLLNAKPENVRRESEIVAQAGRKG 475

Query: 490 AVTIATNMAGRGTDIQLGGNVAMRIEHELANI-----SDEEIR----------------- 527
           ++TIATNMAGRGTDI LGGN   +++ EL ++     S+E+I                  
Sbjct: 476 SITIATNMAGRGTDIILGGNPEFKLKKELYDLLLSYKSNEKISTISQNFLNILNSLKNDL 535

Query: 528 ------------------------NKRIKMIQEEVQSL---------KEKAIV--AGGLY 552
                                   N     ++     L         KEK IV   GGLY
Sbjct: 536 KFLSLSDFENLKILNEASEISIPKNSYQLSLRFLYNELLEKYKKLQEKEKKIVKKLGGLY 595

Query: 553 VISTERHESRRIDNQLRGRSGRQGDPGRSKFYLSLQDDLMRIFGSPRMESFLRKIGLKEG 612
           VI TERHESRRIDNQLRGR+GRQGDPG S+F+LSL+D+L+RIFG  ++++ ++ + L + 
Sbjct: 596 VIGTERHESRRIDNQLRGRAGRQGDPGSSRFFLSLEDNLLRIFGGDKIQNLMQTLNLDD- 654

Query: 613 EAIIHPWINKAIERAQQKVEARNFETRKNLLKYDDVLNEQRKIIFEQRLEIIDTENILEI 672
           E +    ++K+++ AQ+KVE   ++ RK L +YD VLN+QRK I+ +R +I++++++ + 
Sbjct: 655 EPLESKLLSKSLDSAQKKVEEYYYDQRKQLFEYDQVLNKQRKAIYSERRKILESQSLRDW 714

Query: 673 IADMRHDTLHNIVEKCIPNNSYPEKWDIKKLETEIYEIFGIHFPVLEWRNDNGIDHTEMS 732
           I       + +I+       +   K     L  +  E+  +        + N ++  E+ 
Sbjct: 715 ILAYGEQVIDDIITFLKSRKNPNNK--FINLINKFKELLKLPL-CFNKSDLNTLNSGELK 771

Query: 733 KRIFAK---ADKIAEDQENSFGTEKMQALGRHILLHTLDSFWREHMARLEHSRSIIGFRG 789
           K ++ +   +  + E      GT  M+ L R +LL  +D  W+EH+ ++   R  IG+R 
Sbjct: 772 KFLYQQFWISYDLKELYLEQIGTGLMRELERSLLLQQIDKSWKEHLQKMSLLREAIGWRS 831

Query: 790 YAQRDPLQEYKSEAFGFFNTLLTHLRKDVVSQIARIEPN 828
           Y Q+DPL EYK+EAF  F  ++ H+R  V+  + R    
Sbjct: 832 YGQKDPLIEYKNEAFNLFINMINHIRHLVIYDLFRSSIL 870


>gnl|CDD|144583 pfam01043, SecA_PP_bind, SecA preprotein cross-linking domain.  The
           SecA ATPase is involved in the insertion and retraction
           of preproteins through the plasma membrane. This domain
           has been found to cross-link to preproteins, thought to
           indicate a role in preprotein binding. The pre-protein
           cross-linking domain is comprised of two sub domains
           that are inserted within the ATPase domain.
          Length = 113

 Score =  170 bits (434), Expect = 1e-42
 Identities = 63/119 (52%), Positives = 82/119 (68%), Gaps = 7/119 (5%)

Query: 231 PVEDHSDLYRTIDSIIIQLHPS-DYEIDEKQRTVHFSEKGTERIEELLHGENLLKSGGLY 289
           P ED S+LYR  + ++  L    DYE+DEK R V  +E+G E+ E+LL  ENL      Y
Sbjct: 1   PAEDSSELYRRANKLVKTLKEEEDYEVDEKSRQVELTEEGIEKAEKLLGIENL------Y 54

Query: 290 SFENVAIVHLINNALKSHTLFLRNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQHQALE 348
             EN+ ++H IN AL++H LF R+ DYIV   EVVI+DEFTGR+MPGRR+SDG HQA+E
Sbjct: 55  DPENIELLHHINQALRAHHLFKRDVDYIVRDGEVVIVDEFTGRVMPGRRWSDGLHQAIE 113


>gnl|CDD|145784 pfam02810, SEC-C, SEC-C motif.  The SEC-C motif found in the
           C-terminus of the SecA protein, in the middle of some
           SWI2 ATPases and also solo in several proteins. The
           motif is predicted to chelate zinc with the CXC and
           C[HC] pairs that constitute the most conserved feature
           of the motif. It is predicted to be a potential nucleic
           acid binding domain.
          Length = 19

 Score = 59.7 bits (146), Expect = 3e-09
 Identities = 15/18 (83%), Positives = 15/18 (83%)

Query: 870 RNHPCPCGSGKKYKHCHG 887
           RN PCPCGSGKKYK C G
Sbjct: 1   RNDPCPCGSGKKYKKCCG 18


>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 = 43.0 bits (102), Expect = 4e-04
 Identities = 27/126 (21%), Positives = 47/126 (37%), Gaps = 18/126 (14%)

Query: 98  HKGCVAEMKTGEGKTLAAVLPVYLNALSGKGVHVVTVNDY------LARRDSNTMSAIYK 151
            K  + +  TG GKTLA +LP  L AL         +         LA +    +  + K
Sbjct: 14  GKDVLVQAPTGSGKTLAFLLPA-LQALLKNPDGPQAL--VLAPTRELAEQIYEELKKLGK 70

Query: 152 FLGLSTGVVFHDLSDDKRRAAYA--CDITYITNNELGFDYLRDNMQYRRVDMVQRGHNFA 209
           +LGL   +++   S  ++        DI   T   L     R  +  + + ++       
Sbjct: 71  YLGLKVALLYGGDSPKEQLRKLKKGPDILVGTPGRLLDLLERGGLLLKNLKLL------- 123

Query: 210 IVDEVD 215
           ++DE  
Sbjct: 124 VLDEAH 129


>gnl|CDD|32829 COG3012, COG3012, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 151

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 12/15 (80%), Positives = 13/15 (86%)

Query: 873 PCPCGSGKKYKHCHG 887
           PCPCGSGKK+K C G
Sbjct: 136 PCPCGSGKKFKKCCG 150



 Score = 31.0 bits (70), Expect = 1.4
 Identities = 10/17 (58%), Positives = 11/17 (64%)

Query: 873 PCPCGSGKKYKHCHGSY 889
            CPCGSG +Y  C G Y
Sbjct: 4   LCPCGSGLEYSLCCGPY 20


>gnl|CDD|28928 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
           involved in ATP-dependent RNA unwinding, needed in a
           variety of cellular processes including splicing,
           ribosome biogenesis and RNA degradation. The name
           derives from the sequence of the Walker  B motif (motif
           II). This domain contains the ATP- binding region..
          Length = 203

 Score = 40.5 bits (95), Expect = 0.002
 Identities = 31/154 (20%), Positives = 55/154 (35%), Gaps = 22/154 (14%)

Query: 85  RPFDVQLLGGMILHKG--CVAEMKTGEGKTLAAVLPV-----YLNALSGKGVHVVTVNDY 137
           +P  +Q      L  G   + + +TG GKT A ++P+           G    ++     
Sbjct: 21  KPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRE 80

Query: 138 LARRDSNTMSAIYKFLGLSTGVVF--HDLSDDKRRAAYACDITYITNNELGFDYL-RDNM 194
           LA + +     + K   L   V++    +    R+      I   T   L  D L R  +
Sbjct: 81  LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRL-LDLLERGKL 139

Query: 195 QYRRVDMVQRGHNFAIVDEVDSI----FIDEART 224
              +V  +       ++DE D +    F D+ R 
Sbjct: 140 DLSKVKYL-------VLDEADRMLDMGFEDQIRE 166


>gnl|CDD|33127 COG3318, COG3318, Predicted metal-binding protein related to the
           C-terminal domain of SecA [General function prediction
           only].
          Length = 216

 Score = 38.1 bits (88), Expect = 0.012
 Identities = 22/81 (27%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 810 LLTHLRKDVVSQIARIEPNNINNQELNNSLPYIAENDHG---PVIQKENELDTPNVCKTS 866
              H  ++  + I  +    +  +EL +++   A + H     + +K+         +  
Sbjct: 139 GGLHDEEENFAIILTMSEELV--EELESAIEQAALDLHAYEQAIPEKKQYAKPIKEEE-- 194

Query: 867 KIKRNHPCPCGSGKKYKHCHG 887
           K  RN PCPCGSGKK+K C G
Sbjct: 195 KTGRNDPCPCGSGKKFKQCCG 215



 Score = 30.4 bits (68), Expect = 2.2
 Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 1/21 (4%)

Query: 867 KIKRNHPCPCGSG-KKYKHCH 886
           K+  N  CPC S  KKYK   
Sbjct: 3   KLNENDLCPCLSALKKYKQDG 23


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

 Score = 36.6 bits (84), Expect = 0.030
 Identities = 52/228 (22%), Positives = 91/228 (39%), Gaps = 38/228 (16%)

Query: 311 LRNRDYIVNRDEVVIIDEFTGRM---------------MPGRRYSDGQHQALEAKERVKI 355
           L NR  ++N+   V++DE   RM               MP    S       + KE  + 
Sbjct: 387 LENRYLVLNQCTYVVLDE-ADRMIDMGFEPDVQKILEQMP----SSNAKPDTDEKEGEER 441

Query: 356 QPENQTLSSITFQNYFLKYRKLSGMTGTASTEAEELANIYNLDVIEVPTNV---PVIRID 412
             +N + S    Q            T T     E LA  Y    + V       P  R++
Sbjct: 442 VRKNFSSSKKYRQTVMF--------TATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVE 493

Query: 413 EHDEIYRTSEEKYAAIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFTKFQILNA 472
           +  E   + +EK   +I EI++S     P+++   + + ++ LA  L K  +    +   
Sbjct: 494 QKVE-MVSEDEKRKKLI-EILES-NFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGG 550

Query: 473 LYHEKEAYIISQ-AGIPGAVTIATNMAGRGTDIQLGGNVAMRIEHELA 519
              E+    ++      G + +AT++AGRG DI    NV++ I +++A
Sbjct: 551 KSQEQRENALADFREGTGDILVATDVAGRGIDIP---NVSLVINYDMA 595


>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 = 36.2 bits (83), Expect = 0.041
 Identities = 28/124 (22%), Positives = 53/124 (42%), Gaps = 14/124 (11%)

Query: 99  KGCVAEMKTGEGKTLAAVLPV--YLNALSGKGVHVVTVNDYLARRDSNTMSAI---YKFL 153
           +  +    TG GKTLAA+LP+   L++L G  V V+     LA + +  +  +      +
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60

Query: 154 GLSTGVVFHDLSDDKRRAAYACDITYITNNELGFDYLRDNMQYRRVDMVQRGHNFAIVDE 213
           G   G     +   ++  +   DI   T   L  +  R  +  +++D++       I+DE
Sbjct: 61  GYLIG--GTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLL-------ILDE 111

Query: 214 VDSI 217
              +
Sbjct: 112 AHRL 115


>gnl|CDD|31397 COG1204, COG1204, Superfamily II helicase [General function
           prediction only].
          Length = 766

 Score = 35.8 bits (82), Expect = 0.053
 Identities = 31/156 (19%), Positives = 55/156 (35%), Gaps = 22/156 (14%)

Query: 311 LRNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQHQALEAKERVKIQPENQTLSSITFQNY 370
            R R   +   ++V+IDE     + G R      +++ A+ R                N 
Sbjct: 137 TRKRPSWIEEVDLVVIDEI---HLLGDRTRGPVLESIVARMRR--------------LNE 179

Query: 371 FLKYRKLSGMTGTASTEAEEL-ANIYNLDVIEVPTNVPVI----RIDEHDEIYRTSEEKY 425
            ++   LS     A   A+ L A +   D   VP    V      +    +         
Sbjct: 180 LIRIVGLSATLPNAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLID 239

Query: 426 AAIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRK 461
              +  +++S  +G  VLV   S +++E  A +LR 
Sbjct: 240 NLALELVLESLAEGGQVLVFVHSRKEAEKTAKKLRI 275


>gnl|CDD|35564 KOG0343, KOG0343, KOG0343, RNA Helicase [RNA processing and
           modification].
          Length = 758

 Score = 34.2 bits (78), Expect = 0.14
 Identities = 37/150 (24%), Positives = 64/150 (42%), Gaps = 25/150 (16%)

Query: 31  INELEKEISHLSDDSLANKTSEFKERINNGETLDDLLVPAFAVVREVARRTLGMRPFDVQ 90
           I EL+++ + +     +    +F +   + +TL  L    F  + E+ R T+ M      
Sbjct: 53  IEELKQKYAEID----STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPM-----A 103

Query: 91  LLGGMILHKGCVAEMKTGEGKTLAAVLPVYLNAL--------SGKGVHVVTVNDYLARRD 142
           L G  +L        KTG GKTLA ++PV L AL         G G  +++    LA + 
Sbjct: 104 LQGHDVL-----GAAKTGSGKTLAFLVPV-LEALYRLKWSPTDGLGALIISPTRELALQT 157

Query: 143 SNTMSAIYKFLGLSTGVVF--HDLSDDKRR 170
              ++ + K    S G++    D+  +  R
Sbjct: 158 FEVLNKVGKHHDFSAGLIIGGKDVKFELER 187


>gnl|CDD|31420 COG1227, PPX1, Inorganic pyrophosphatase/exopolyphosphatase [Energy
           production and conversion].
          Length = 311

 Score = 33.7 bits (77), Expect = 0.25
 Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 10/95 (10%)

Query: 363 SSITFQNYFLKYRKLSG----MTGTASTEAEELANIYNLDVIEVPTNV----PVIRIDEH 414
           S+I +  Y L             G  + E   + + + ++  ++  +V     VI +D H
Sbjct: 19  SAIVYA-YLLNAYGEFEAKAVRLGEPNLETAFVLDYFGVEAPKLVESVKGEKKVILVD-H 76

Query: 415 DEIYRTSEEKYAAIIAEIIDSHKKGQPVLVGTPSI 449
           +E  ++ ++   A I  IID H+           I
Sbjct: 77  NEFQQSVDDIEDAEILGIIDHHRLADFETAAPLYI 111


>gnl|CDD|28960 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
           with DEXDc-, DEAD-, and DEAH-box proteins, yeast
           initiation factor 4A, Ski2p, and Hepatitis C virus NS3
           helicases; this domain is found in a wide variety of
           helicases and helicase related proteins; may not be an
           autonomously folding unit, but an integral part of the
           helicase; 4 helicase superfamilies at present according
           to the organization of their signature motifs; all
           helicases share the ability to unwind nucleic acid
           duplexes with a distinct directional polarity; they
           utilize the free energy from nucleoside triphosphate
           hydrolysis to fuel their translocation along DNA,
           unwinding the duplex in the process.
          Length = 131

 Score = 33.4 bits (76), Expect = 0.28
 Identities = 34/172 (19%), Positives = 56/172 (32%), Gaps = 44/172 (25%)

Query: 414 HDEIYRTSEEKYAAIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFTKFQILNAL 473
              +    +EK  A++  + +  KKG  VL+  PS +  + LA  LRK       +    
Sbjct: 3   KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62

Query: 474 YHEKEAYIISQAGIPGAVT-IATNMAGRGTDIQLGGNVAMRIEHELANISDEEIRNKRIK 532
             E+   ++        V  +AT++  RG D+               N+S          
Sbjct: 63  SQEEREEVLKDFREGEIVVLVATDVIARGIDLP--------------NVS---------- 98

Query: 533 MIQEEVQSLKEKAIVAGGLYVISTERHESRRIDNQLRGRSGRQGDPGRSKFY 584
                               VI+ +   S     Q  GR+GR G  G +   
Sbjct: 99  -------------------VVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131


>gnl|CDD|35552 KOG0331, KOG0331, KOG0331, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 519

 Score = 33.0 bits (75), Expect = 0.41
 Identities = 46/233 (19%), Positives = 77/233 (33%), Gaps = 25/233 (10%)

Query: 4   HLAKLASKLLIPSNERRLRPYYAKVIAINELEKEISHLSDDSLANKTSE--FKERINNGE 61
                  K      ER+ +     V   + + K +    +     K  E   K   ++GE
Sbjct: 27  KEHPSVKKRGSAEVERKRKKNEITVKGGDSVPKPVKSFEESGFPAKVLEEIPKLSRSSGE 86

Query: 62  TLDDLLVPAFAVVREVARRTLGM---RPFDVQLLGGMILHKG--CVAEMKTGEGKTLAAV 116
           +          +  E+ +        +P  +Q  G  I   G   V   +TG GKTLA +
Sbjct: 87  SDSSAAFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYL 146

Query: 117 LP--VYLNALSGKGVH-------VVTVNDYLARRDSNTMSAIYKFLGLSTGVVFHDLSDD 167
           LP  V+LN   GK          V+     LA +         K L L +  V+      
Sbjct: 147 LPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKG 206

Query: 168 K--RRAAYACDITYITNNELGFDYLRDNMQYRRVDMVQRGHNFAIVDEVDSIF 218
              R      D+   T        L D ++   +++      + ++DE D + 
Sbjct: 207 PQLRDLERGVDVVIATP-----GRLIDLLEEGSLNL--SRVTYLVLDEADRML 252


>gnl|CDD|39145 KOG3942, KOG3942, KOG3942, MIF4G domain-containing protein
           [Translation, ribosomal structure and biogenesis].
          Length = 348

 Score = 32.7 bits (74), Expect = 0.42
 Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 4/71 (5%)

Query: 17  NERRLRPYYAKVIAINELEKEISHLSDDSLANKTSEFKERINNGETLDDLLVPAFAVVRE 76
              R RP   K++   E+   I ++S D L N T   +  IN     DD ++  F     
Sbjct: 118 ENLRARPLQGKMMKWVEIVTSICNISADLLTNLTMPMEALINP--AYDDEML--FRCGPT 173

Query: 77  VARRTLGMRPF 87
           +AR+ +     
Sbjct: 174 IARQAVEGGGG 184


>gnl|CDD|145946 pfam03063, Prismane, Prismane/CO dehydrogenase family.  This family
           includes both hybrid-cluster proteins and the beta chain
           of carbon monoxide dehydrogenase. The hybrid-cluster
           proteins contain two Fe/S centres - a [4Fe-4S] cubane
           cluster, and a hybrid [4Fe-2S-2O] cluster. The
           physiological role of this protein is as yet unknown,
           although a role in nitrate/nitrite respiration has been
           suggested. The prismane protein from Escherichia coli
           was shown to contain hydroxylamine reductase activity
           (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is
           rather low. Hydroxylamine reductase activity was also
           found in CO-dehydrogenase in which the active site Ni
           was replaced by Fe. The CO dehydrogenase contains a
           Ni-3Fe-2S-3O centre.
          Length = 477

 Score = 32.1 bits (74), Expect = 0.70
 Identities = 23/101 (22%), Positives = 35/101 (34%), Gaps = 23/101 (22%)

Query: 372 LKYRKLSGMTGTA-STEAEELANIYNLDVIEVPTN--VPVI-RIDE--HDEIYRTS---- 421
           LKYR   G  G A   E  E       D I V TN  +P +  + E     +  TS    
Sbjct: 186 LKYRHGVGNYGNAWQQELVEFTGA--PDAIVVDTNCIMPPLASVAECYKTRVITTSPVGK 243

Query: 422 -----------EEKYAAIIAEIIDSHKKGQPVLVGTPSIEK 451
                      ++  + II + I++    +   V  P  + 
Sbjct: 244 IPGAEHIEEKADKDASEIIEKAIEAFGFREDEKVTIPKGKG 284


>gnl|CDD|33855 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
           uptake (late competence protein) [DNA replication,
           recombination, and repair].
          Length = 441

 Score = 31.5 bits (71), Expect = 0.97
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 427 AIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFTKFQI 469
            +   +    K G+PVL+  P IE  E +A+ L+K K  K  I
Sbjct: 293 KLKRWLEKQRKTGRPVLIFFPEIETMEQVAAALKK-KLPKETI 334


>gnl|CDD|35566 KOG0345, KOG0345, KOG0345, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 567

 Score = 30.3 bits (68), Expect = 2.2
 Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 63  LDDLLVPAFAVVREVARRTLGMRPFDVQLLGGMIL--HKGCVAEMKTGEGKTLAAVLPV 119
              L  P    + E    +   +   VQ     +L  +K  V E  TG GKTLA +LP+
Sbjct: 6   FSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPM 64


>gnl|CDD|37008 KOG1797, KOG1797, KOG1797, Uncharacterized conserved protein
            (Neuroblastoma-amplified protein) [Function unknown].
          Length = 1660

 Score = 29.3 bits (65), Expect = 4.3
 Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 11/73 (15%)

Query: 315  DYIVNRDEVVIIDEFTGRMMPG-------RRYSDGQHQALEAKERVKIQPENQTLSSITF 367
            D I    + VI+   T  + P        RR+ +  H+A E  E       N +  S   
Sbjct: 1576 DEIAYLFQAVILLHNTPSLPPLLLDAIKLRRHLEKMHRATETPE--PATASNGS--STGL 1631

Query: 368  QNYFLKYRKLSGM 380
             +YF   R  SGM
Sbjct: 1632 SSYFSNLRDNSGM 1644


>gnl|CDD|35561 KOG0340, KOG0340, KOG0340, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 442

 Score = 29.1 bits (65), Expect = 4.8
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 8/88 (9%)

Query: 80  RTLGMR-PFDVQL--LGGMILHKGCVAEMKTGEGKTLAAVLPVYLNALS----GKGVHVV 132
           + LG++ P  +Q   +  ++  + C+   KTG GKT A  LP+ LN LS    G    V+
Sbjct: 23  KALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPI-LNRLSEDPYGIFALVL 81

Query: 133 TVNDYLARRDSNTMSAIYKFLGLSTGVV 160
           T    LA + +    A+ K L L   V+
Sbjct: 82  TPTRELALQIAEQFIALGKLLNLKVSVI 109


>gnl|CDD|31393 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
           and repair / Transcription].
          Length = 677

 Score = 29.0 bits (65), Expect = 5.2
 Identities = 13/67 (19%), Positives = 28/67 (41%)

Query: 108 GEGKTLAAVLPVYLNALSGKGVHVVTVNDYLARRDSNTMSAIYKFLGLSTGVVFHDLSDD 167
           G GKT+ A+L +     +G    ++   + LA +   ++    + LG+   ++   L   
Sbjct: 293 GSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGK 352

Query: 168 KRRAAYA 174
            R+    
Sbjct: 353 ARKEILE 359


>gnl|CDD|30859 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
           replication, recombination, and repair / Transcription /
           Translation, ribosomal structure and biogenesis].
          Length = 513

 Score = 29.0 bits (64), Expect = 5.3
 Identities = 48/289 (16%), Positives = 90/289 (31%), Gaps = 22/289 (7%)

Query: 383 TASTEAEELANIYNLDVIEV-----PTNVPVIRIDEHDEIYRTSEEKYAAIIAEIIDSHK 437
           T   +  ELA  Y  D +E+          + +I +      + EEK   ++ +++    
Sbjct: 214 TMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLL-KLLKDED 272

Query: 438 KGQPVLVGTPSIEKSEYLASQLRKHKFTKFQILNALYHEKEAYIISQ-AGIPGAVTIATN 496
           +G+ V+V   +    E LA  LRK  F    +   L  E+    + +       V +AT+
Sbjct: 273 EGR-VIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATD 331

Query: 497 MAGRGTDIQLGGNVAMRIEHELANISDEEI-------RNKR----IKMIQEEVQSLKEKA 545
           +A RG DI    +V+  I ++L    ++ +       R  R    I  + EE +  K K 
Sbjct: 332 VAARGLDIP---DVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKR 388

Query: 546 IVAGGLYVISTERHESRRIDNQLRGRSGRQGDPGRSKFYLSLQDDLMRIFGSPRMESFLR 605
           I       + +            +     +               L     +      +R
Sbjct: 389 IEKRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEESDISDEIKKLKSSKKALLRGLGVR 448

Query: 606 KIGLKEGEAIIHPWINKAIERAQQKVEARNFETRKNLLKYDDVLNEQRK 654
               K    +                  R      + ++Y       R 
Sbjct: 449 FTLSKLLANLGKEIPGAGDAVTIDPELERRSPNSADDIEYILKGLSYRA 497


>gnl|CDD|31394 COG1201, Lhr, Lhr-like helicases [General function prediction
           only].
          Length = 814

 Score = 29.1 bits (65), Expect = 5.4
 Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 20/78 (25%)

Query: 107 TGEGKTLAAVLPVYLNAL-------SGKGVHVVTV-------NDYLARRDSNTMSAIYKF 152
           TG GKT AA LPV +N L          G++ + +       ND   R     +    + 
Sbjct: 46  TGSGKTEAAFLPV-INELLSLGKGKLEDGIYALYISPLKALNNDIRRR-----LEEPLRE 99

Query: 153 LGLSTGVVFHDLSDDKRR 170
           LG+   V   D    +++
Sbjct: 100 LGIEVAVRHGDTPQSEKQ 117



 Score = 29.1 bits (65), Expect = 6.1
 Identities = 31/141 (21%), Positives = 52/141 (36%), Gaps = 17/141 (12%)

Query: 322 EVVIIDEFTGRMMPGRRYSDGQHQALEAKERVKIQPENQTLS-SITFQNYFLKYRKLSGM 380
             VI+DE        R    G   AL  +   ++  + Q +  S T        + L G 
Sbjct: 151 RYVIVDEIHALAESKR----GVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFLVGF 206

Query: 381 TGTASTEAEELANIYNLDVIEVPTNVPVIRIDEHDEIYRTSEEKYAAIIAEIIDSHKKGQ 440
                      A    + VI      PV  +   +E++    E+    IAE++  H+   
Sbjct: 207 GDPCEIVDVSAAKKLEIKVI-----SPVEDLIYDEELWAALYER----IAELVKKHRT-- 255

Query: 441 PVLVGTPSIEKSEYLASQLRK 461
             L+ T +   +E LA +L+K
Sbjct: 256 -TLIFTNTRSGAERLAFRLKK 275


>gnl|CDD|35551 KOG0330, KOG0330, KOG0330, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 476

 Score = 28.8 bits (64), Expect = 6.2
 Identities = 51/269 (18%), Positives = 96/269 (35%), Gaps = 49/269 (18%)

Query: 76  EVARRTLGMRPFDVQLLGGMILHKG--CVAEMKTGEGKTLAAVLPVYLNALSGKG----V 129
           E  +     +P  +Q     +   G   +   +TG GKT A  LP+ L  L  +      
Sbjct: 74  EACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPI-LQRLLQEPKLFFA 132

Query: 130 HVVTVNDYLARRDSNTMSAIYKFLGLSTGVVF--HDLSDDKRRAAYACDITYITNNELGF 187
            V+T    LA++ +    A+   +GL   V+    D+     + +    I   T   L +
Sbjct: 133 LVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRL-W 191

Query: 188 DYLRDNMQYRRVDMVQRGHNFAIVDEVDSIFIDEARTPLIISGPVEDHSDLYRTIDSIII 247
           D+L +   +           F ++DE D +                   D    +D I+ 
Sbjct: 192 DHLENTKGFS-----LEQLKFLVLDEADRLLDM----------------DFEEELDYILK 230

Query: 248 QLHPSDYEIDEKQRTVHFSEKGTERIEELLHGENLLKSGGLYSFENVAIVHL--INNALK 305
            +         +++T  FS   T+++ +L           L +   VA+       + LK
Sbjct: 231 VIPR-------ERQTFLFSATMTKKVRKLQ-------RASLDNPVKVAVSSKYQTVDHLK 276

Query: 306 SHTLFLRNRDYIVNRDEVVIIDEFTGRMM 334
              LF+  +D   +   V +++E  G  +
Sbjct: 277 QTYLFVPGKDK--DTYLVYLLNELAGNSV 303


>gnl|CDD|146126 pfam03331, LpxC, UDP-3-O-acyl N-acetylglycosamine deacetylase.  The
           enzymes in this family catalyse the second step in the
           biosynthetic pathway for lipid A.
          Length = 276

 Score = 28.8 bits (65), Expect = 6.6
 Identities = 10/41 (24%), Positives = 17/41 (41%)

Query: 498 AGRGTDIQLGGNVAMRIEHELANISDEEIRNKRIKMIQEEV 538
               T +   G     +EH LA ++   I N  I++   E+
Sbjct: 59  TMLSTTLGNDGARISTVEHLLAALAGLGIDNLIIEVDGPEI 99


>gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only].
          Length = 365

 Score = 28.6 bits (64), Expect = 8.0
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 439 GQPVLVGTPSIEKSEYLA------SQLRKHKFTKFQILNALYHEKEAYIISQAGIPGAVT 492
               LVG PS+ KS  L       S++  + FT  + +  +   K A  I    +PG + 
Sbjct: 64  ATVALVGFPSVGKSTLLNKLTNTKSEVADYPFTTLEPVPGMLEYKGAQ-IQLLDLPGIIE 122

Query: 493 IATNMAGRGTDI 504
            A++  GRG  +
Sbjct: 123 GASSGRGRGRQV 134


>gnl|CDD|35574 KOG0353, KOG0353, KOG0353, ATP-dependent DNA helicase [General
           function prediction only].
          Length = 695

 Score = 28.6 bits (63), Expect = 8.4
 Identities = 35/175 (20%), Positives = 62/175 (35%), Gaps = 9/175 (5%)

Query: 420 TSEEKYAAIIAEIIDSHKKGQPVLVGTPSIEKSEYLASQLRKHKFTKFQILNALYHEKEA 479
            +E+     IA++I     GQ  ++   S +  E +A  L+ H        +A    ++ 
Sbjct: 298 GNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGI-HAGAYHANLEPEDK 356

Query: 480 YIISQAGIPGA--VTIATNMAGRGTDIQLGGNVAMRIEHELANISD---EEIRNKRIKMI 534
               Q  I G   V +AT   G G D     +V   I H L    +   +      ++M 
Sbjct: 357 SGAHQGWIAGEIQVIVATVAFGMGID---KPDVRFVIHHSLPKSIENYYQASARILLRMT 413

Query: 535 QEEVQSLKEKAIVAGGLYVISTERHESRRIDNQLRGRSGRQGDPGRSKFYLSLQD 589
           +++ +S    +     L V +  +        +  GR+GR         Y    D
Sbjct: 414 KQKNKSDTGGSTQINILEVCTNFKIFFAVFSEKESGRAGRDDMKADCILYYGFAD 468


  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
   0.318    0.136    0.387 

Gapped
Lambda     K      H
   0.267   0.0643    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 10,820,072
Number of extensions: 603296
Number of successful extensions: 1663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1644
Number of HSP's successfully gapped: 58
Length of query: 890
Length of database: 6,263,737
Length adjustment: 102
Effective length of query: 788
Effective length of database: 4,059,619
Effective search space: 3198979772
Effective search space used: 3198979772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 62 (27.8 bits)