RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764515|ref|YP_003065608.2| SNF2 related [Candidatus
Liberibacter asiaticus str. psy62]
         (458 letters)



>gnl|CDD|30899 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
           [Transcription / DNA replication, recombination, and
           repair].
          Length = 866

 Score = 93.7 bits (231), Expect = 9e-20
 Identities = 94/523 (17%), Positives = 179/523 (34%), Gaps = 77/523 (14%)

Query: 2   NLAPHQTKIVDWILD-----HKRCAIWASMGSGKTVSVLTALSYIHLWGE---KSVLVIA 53
            L P+Q + V+W+ +          +   MG GKTV  +  L  +    +      L++ 
Sbjct: 338 ELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVV 397

Query: 54  PLRVAQSVWTSEVQRWSNFSHMNISVI---TGTVKQRTKVLKTPAVLYVINFE----NLG 106
           P  +  S W  E ++++    + +      +   K+R  +     +  VI F+       
Sbjct: 398 PASLL-SNWKREFEKFAPDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYE 456

Query: 107 WLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGL 166
            L + L        I  D     ++ R++   +++   A    ++   ++LTGTP  N L
Sbjct: 457 LLRRFLVDHGGLKKIEWDRVVLDEAHRIK-NDQSSEGKALQFLKALNRLDLTGTPLENRL 515

Query: 167 IDLWGQIWFLDKGKRLGRVFQSFVARWFNTTQIGSHIGAV--RYTAKETAQKEIEAQLSD 224
            +LW  +        LG  F  F   +    Q    IG +  R    E  +K +   +  
Sbjct: 516 GELWSLLQEFLNPGLLGTSFAIFTRLFEKPIQAEEDIGPLEARELGIELLRKLLSPFILR 575

Query: 225 CCLSLDIADYQNIDKPILITKKVPLPQPVMKQY--------------------------- 257
                D+   + +   I    +  L +   + Y                           
Sbjct: 576 -RTKEDVEVLKELPPKIEKVLECELSEEQRELYEALLEGAEKNQQLLEDLEKADSDENRI 634

Query: 258 ---------HKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEKHWKEVHDEK 308
                       +    C+      E   +    +  L   +    Y ++   +    + 
Sbjct: 635 GDSELNILALLTRLRQICNHPALVDEGLEATFDRIVLLLREDKDFDYLKKPLIQLSKGKL 694

Query: 309 IKALEVI----IEKANAAPIIVAYHFNSDLARLQK---------AFPQGRTLDKDPC-TI 354
               E++    +E+ +   +++   F   L  L+              G T  K     I
Sbjct: 695 QALDELLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELI 754

Query: 355 QEWNEGKIPLLF-AHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAG 413
             +N  +   +F     + G GLNL    + ++ F  WW+     Q I+R    R  Q  
Sbjct: 755 DRFNADEEEKVFLLSLKAGGLGLNLTG-ADTVILFDPWWNPAVELQAIDRA--HRIGQ-- 809

Query: 414 FKRAVFVYYLIAQNTIDELVLQRLRTKSTIQDLLLNALKKETI 456
            KR V VY LI + TI+E +L+    K  + D L++A  ++ +
Sbjct: 810 -KRPVKVYRLITRGTIEEKILELQEKKQELLDSLIDAEGEKEL 851


>gnl|CDD|36218 KOG1000, KOG1000, KOG1000, Chromatin remodeling protein
           HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure
           and dynamics].
          Length = 689

 Score = 76.2 bits (187), Expect = 2e-14
 Identities = 98/468 (20%), Positives = 166/468 (35%), Gaps = 78/468 (16%)

Query: 2   NLAPHQTKIVDWILDHK-RCAIWASMGSGKTVSVLT-ALSYIHLWGEKSVLVIAPLRVAQ 59
            L P Q + V + L+   R  +   MG GKT+  L  A  Y   W    +L++ P  V  
Sbjct: 198 RLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAEW---PLLIVCPASVRF 254

Query: 60  SVWTSEVQRWSNFSHMNISVITGTVKQRTKVLKTPAVLYVINFENLGWLVQELKGTWPFA 119
           + W   + R+    H    V           + T   + ++++E L  L   LK    + 
Sbjct: 255 T-WAKALNRFLPSIHPIFVVDKS--SDPLPDVCTSNTVAIVSYEQLSLLHDILK-KEKYR 310

Query: 120 TIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKG 179
            ++ DES  LK  + ++ +K A  L K A   +  I L+GTP+ +   +L+ QI  +D  
Sbjct: 311 VVIFDESHMLKDSKTKR-TKAATDLLKVA---KHVILLSGTPAVSRPSELYTQIRAVD-- 364

Query: 180 KRLGRVFQSFVARWFNTTQI--------GSHIGAVRYTAKETA-----QKEIEAQLSD-- 224
             L   F  F  R+ +  Q+         +++  +     +       + ++  QL    
Sbjct: 365 HTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLKQLPPKR 424

Query: 225 -----CCLSLDIADYQNIDKPILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNSA 279
                       A   ++ K      KV      M++ H+     Y         A    
Sbjct: 425 REVVYVSGGRIDARMDDLVKAAADYTKV----NSMERKHESLLLFYSLTGIAKAAAV--- 477

Query: 280 SKTVKCLQLANGAVYYDEEKHWKEV---HDEKIKALEVIIEKANAAPIIVAYHFNSDLAR 336
                C  +       D       V   H   +  ++V + K     I           R
Sbjct: 478 -----CEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSI-----------R 521

Query: 337 LQ-KAFPQGRTLDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWD-- 393
           +        RTL     + Q   E ++ +L     + G GL L     + VF  L W+  
Sbjct: 522 IDGSTPSHRRTLLCQ--SFQTSEEVRVAVLSI--TAAGVGLTLTAASVV-VFAELHWNPG 576

Query: 394 -LEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVLQRLRTK 440
            L + +    RIG           +VFV YL+A+ T D+ +   L+ K
Sbjct: 577 VLLQAEDRAHRIGQK--------SSVFVQYLVAKGTADDYMWPMLQQK 616


>gnl|CDD|143942 pfam00176, SNF2_N, SNF2 family N-terminal domain.  This domain is
           found in proteins involved in a variety of processes
           including transcription regulation (e.g., SNF2, STH1,
           brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5),
           DNA recombination (e.g., RAD54), and chromatin unwinding
           (e.g., ISWI) as well as a variety of other proteins with
           little functional information (e.g., lodestar, ETL1).
          Length = 295

 Score = 67.3 bits (165), Expect = 8e-12
 Identities = 72/300 (24%), Positives = 123/300 (41%), Gaps = 53/300 (17%)

Query: 6   HQTKIVDWILD----HKRCAIWASMGSGKTVSVLTALSYIHLWGEKS--VLVIAPLRVAQ 59
           +Q + V+W++          +   MG GKT+  ++ L+Y+      +   LV+ PL    
Sbjct: 1   YQLEGVNWLISLYNNGLGGILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLSTLD 60

Query: 60  SVWTSEVQRWSNFSHMNISVITGTVKQRTKVLKTPAVLY-----VINFENLGWLVQELKG 114
           + W +E ++W     +NI V  G    R+++L+           + ++E +     EL  
Sbjct: 61  N-WLNEFEKW--APDLNIVVYYGDGDSRSELLRNVLRTGKFDVLITSYEYIRRDKDELHK 117

Query: 115 T-WPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQI 173
             W +  +++DE  ++K+ +    SK + AL     ++   + LTGTP  N L +LW  +
Sbjct: 118 ANWRY--VILDEGHRIKNAK----SKLSLALKS--LKTNNRLLLTGTPIQNNLAELWSLL 169

Query: 174 WFLDKGKRLGRVFQSF--VARWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSLDI 231
            FL  G      F SF    +WF    +          +  T +K  EA L        I
Sbjct: 170 NFLRPGI-----FGSFKEFDKWFVNPILNGG------CSDAT-EKLEEAGL------KLI 211

Query: 232 ADYQNIDKPILI--TKKV---PLPQPVMKQYH----KFQRELYCD-LQGENIEAFNSASK 281
                I KP L+   KK     LP            K Q+ELY   L  ++++  N  + 
Sbjct: 212 NRLHKILKPFLLRRLKKDVEKSLPPKTEYVLFCNLSKLQKELYKKFLTSKDVKFINDGNG 271


>gnl|CDD|35606 KOG0385, KOG0385, KOG0385, Chromatin remodeling complex WSTF-ISWI,
           small subunit [Transcription].
          Length = 971

 Score = 58.1 bits (140), Expect = 4e-09
 Identities = 58/296 (19%), Positives = 121/296 (40%), Gaps = 46/296 (15%)

Query: 3   LAPHQTKIVDWILDHKRCAIWA----SMGSGKTVSVLTALSYIH--LWGEKSVLVIAPLR 56
           L  +Q + ++W++      I       MG GKT+  ++ L Y+          LVIAP  
Sbjct: 168 LRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKS 227

Query: 57  VAQSVWTSEVQRWSNFSHMNISVITGTVKQRTKVLK-----TPAVLYVINFENLGWLVQE 111
              + W +E +R++    +N+ V  G  ++R  + +         + + ++E +    + 
Sbjct: 228 TLDN-WMNEFKRFT--PSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYE-IAIKDKS 283

Query: 112 LKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWG 171
               + +  +V+DE+ ++K+    + SK ++ L +  ++++  + LTGTP  N L +LW 
Sbjct: 284 FLKKFNWRYLVIDEAHRIKN----EKSKLSKILRE--FKTDNRLLLTGTPLQNNLHELWA 337

Query: 172 QIWFLDKGKRLGRVFQSF--VARWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSL 229
            + FL     L  +F S      WF+ T              +     +   L    L  
Sbjct: 338 LLNFL-----LPDIFNSAEDFDSWFDFTNC---------EGDQELVSRLHKVLRPFLLRR 383

Query: 230 DIADYQ-NIDKPILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNSASKTVK 284
             +D + ++     +   V +           Q++ Y  +  ++++A N   K  K
Sbjct: 384 IKSDVEKSLPPKKELIIYVGMSSM--------QKKWYKAILMKDLDALNGEGKGEK 431



 Score = 33.8 bits (77), Expect = 0.10
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 12/79 (15%)

Query: 373 GHGLNLQYGGNILVFFSLW---WDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTI 429
           G G+NL     ++++ S W    DL+       RIG  +         V VY LI +NT+
Sbjct: 551 GLGINLTAADTVILYDSDWNPQVDLQA-MDRAHRIGQKKP--------VVVYRLITENTV 601

Query: 430 DELVLQRLRTKSTIQDLLL 448
           +E +++R   K  +  L++
Sbjct: 602 EEKIVERAAAKLRLDKLVI 620


>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 = 54.7 bits (131), Expect = 5e-08
 Identities = 25/148 (16%), Positives = 54/148 (36%), Gaps = 8/148 (5%)

Query: 18  KRCAIWASMGSGKT-VSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMN 76
           +   + A  GSGKT  ++L  L  +       VLV+AP R   +   +E  +      + 
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTREL-ANQVAERLKELFGEGIK 59

Query: 77  ISVITGTV---KQRTKVLKTPAVLYVINFENLGWLVQELKGTWPFATIVVDESTKLKSFR 133
           +  + G     +Q   +     ++       L  L +          +++DE+ +L +  
Sbjct: 60  VGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLN-- 117

Query: 134 LRQGSKTARALAKPAWESERFIELTGTP 161
            +        +     +  + + L+ TP
Sbjct: 118 -QGFGLLGLKILLKLPKDRQVLLLSATP 144


>gnl|CDD|35608 KOG0387, KOG0387, KOG0387, Transcription-coupled repair protein
           CSB/RAD26 (contains SNF2 family DNA-dependent ATPase
           domain) [Transcription, Replication, recombination and
           repair].
          Length = 923

 Score = 51.9 bits (124), Expect = 4e-07
 Identities = 47/199 (23%), Positives = 81/199 (40%), Gaps = 31/199 (15%)

Query: 3   LAPHQTKIVDWIL---DHKRCAIWA-SMGSGKTVSVLTALSYIHLWG--EKSVLVIAPLR 56
           L P+Q + V W+      +   I    MG GKT+ +++ L+ +H  G   K  L++ P  
Sbjct: 206 LFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPAT 265

Query: 57  VAQSVWTSEVQRWSNFSHMNISVITGTV-------------KQRTKVLKTPAVLYVINFE 103
           +    W  E Q W     + I   TG+              K   + + T   + +  ++
Sbjct: 266 IIHQ-WMKEFQTWWPPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYD 324

Query: 104 NLGWLVQELKG-TWPFATIVVDESTKLKSFRLRQGSKTARALA-KPAWESERFIELTGTP 161
                  +L G  W +   ++DE  ++++        +  +LA K      R I L+GTP
Sbjct: 325 GFRIQGDDLLGILWDYV--ILDEGHRIRN------PNSKISLACKKIRTVHRII-LSGTP 375

Query: 162 SPNGLIDLWGQIWFLDKGK 180
             N L +LW    F+  GK
Sbjct: 376 IQNNLTELWSLFDFVFPGK 394



 Score = 32.7 bits (74), Expect = 0.22
 Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 351 PCTIQEWNEGK-IPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQ 409
              +  +NE + I +        G GLNL  G N ++ F   W+     Q  ER      
Sbjct: 587 QKLVDRFNEDESIFVFLLTTRVGGLGLNLT-GANRVIIFDPDWNPSTDNQARERA----- 640

Query: 410 RQAGFKRAVFVYYLIAQNTIDELVLQR 436
            + G K+ V VY L+   TI+E +  R
Sbjct: 641 WRIGQKKDVVVYRLMTAGTIEEKIYHR 667


>gnl|CDD|35605 KOG0384, KOG0384, KOG0384, Chromodomain-helicase DNA-binding
           protein [Transcription].
          Length = 1373

 Score = 49.6 bits (118), Expect = 2e-06
 Identities = 51/170 (30%), Positives = 76/170 (44%), Gaps = 28/170 (16%)

Query: 26  MGSGKTVSVLTALSYIHLWGEK--SVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITG- 82
           MG GKTV  +T LSY+    +     LV+ PL    + W  E + W++   MN+ V  G 
Sbjct: 398 MGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITA-WEREFETWTD---MNVIVYHGN 453

Query: 83  ------------TVKQRTKVLKTPAVLYVINFENLGWLVQELKGTWPFATIVVDESTKLK 130
                            TK LK  A+L    +E +     EL    P+  ++VDE+ +LK
Sbjct: 454 LESRQLIRQYEFYHSSNTKKLKFNALL--TTYEIVLKDKAEL-SKIPWRYLLVDEAHRLK 510

Query: 131 SFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGK 180
           +      SK   +L    ++    + +TGTP  N L +LW  + FL  GK
Sbjct: 511 N----DESKLYESLN--QFKMNHRLLITGTPLQNSLKELWSLLHFLMPGK 554


>gnl|CDD|35607 KOG0386, KOG0386, KOG0386, Chromatin remodeling complex SWI/SNF,
           component SWI2 and related ATPases (DNA/RNA helicase
           superfamily) [Chromatin structure and dynamics,
           Transcription].
          Length = 1157

 Score = 47.7 bits (113), Expect = 7e-06
 Identities = 47/182 (25%), Positives = 83/182 (45%), Gaps = 28/182 (15%)

Query: 26  MGSGKTVSVLTALSYI--HLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITGT 83
           MG GKT+  ++ ++Y+  H   +   L+I PL      W+SE  +W+    +      GT
Sbjct: 422 MGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTL-VNWSSEFPKWA--PSVQKIQYKGT 478

Query: 84  VKQRTKVLKTPAVL----YVINFENLGW---LVQELKGTWPFATIVVDESTKLKSFRLRQ 136
            +QR+ + K          +  +E +     L+ ++   W +  +++DE  ++K+     
Sbjct: 479 PQQRSGLTKQQRHGKFNVLLTTYEYIIKDKALLSKIS--WKY--MIIDEGHRMKN----A 530

Query: 137 GSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLGRVFQSFVA--RWF 194
             K    L    + ++R + LTGTP  N L +LW  + FL     L  +F S  A  +WF
Sbjct: 531 ICKLTDTL-NTHYRAQRRLLLTGTPLQNNLPELWALLNFL-----LPNIFNSCKAFEQWF 584

Query: 195 NT 196
           N 
Sbjct: 585 NQ 586


>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 = 47.2 bits (113), Expect = 9e-06
 Identities = 35/134 (26%), Positives = 58/134 (43%), Gaps = 21/134 (15%)

Query: 5   PHQTKIVDWILDHKRCAIWASMGSGKT-VSVLTALSYI-HLWGEKSVLVIAPLR--VAQS 60
           P Q + +  IL+ K   + A  GSGKT   +L AL  +         LV+AP R    Q 
Sbjct: 2   PIQAEAIPAILEGKDVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQI 61

Query: 61  VWTSEVQRWSNFSHMNISVITGTV---KQRTKVLKTPAVLYV------INFENLGWLVQE 111
               E+++   +  + ++++ G     +Q  K+ K P +L           E  G L++ 
Sbjct: 62  Y--EELKKLGKYLGLKVALLYGGDSPKEQLRKLKKGPDILVGTPGRLLDLLERGGLLLKN 119

Query: 112 LKGTWPFATIVVDE 125
           LK       +V+DE
Sbjct: 120 LK------LLVLDE 127


>gnl|CDD|35611 KOG0390, KOG0390, KOG0390, DNA repair protein, SNF2 family
           [Replication, recombination and repair].
          Length = 776

 Score = 46.2 bits (109), Expect = 2e-05
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 358 NEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA 417
            E    +      + G GLNL  G + L+ F   W+    QQ + R       + G K+ 
Sbjct: 644 PESPSFVFLLSSKAGGEGLNL-IGASRLILFDPDWNPAVDQQAMARA-----WRDGQKKP 697

Query: 418 VFVYYLIAQNTIDELVLQRLRTKSTI 443
           V++Y L+A  TI+E + QR   K  +
Sbjct: 698 VYIYRLLATGTIEEKIYQRQTHKEGL 723


>gnl|CDD|36233 KOG1015, KOG1015, KOG1015, Transcription regulator XNP/ATRX,
           DEAD-box superfamily [Transcription].
          Length = 1567

 Score = 42.4 bits (99), Expect = 2e-04
 Identities = 55/210 (26%), Positives = 92/210 (43%), Gaps = 37/210 (17%)

Query: 20  CAIWASMGSGKTVSVLTALSYIHL---WGEKSVLVIAPLRVAQSVWTSEVQRW----SNF 72
           C +   MG GKT+ V+T L  + L    G K+ LV+ PL  A + W +E ++W     + 
Sbjct: 699 CILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPLNTALN-WMNEFEKWMEGLEDD 757

Query: 73  SHMNISVITGTVK---QRTKVLK---TPAVLYVINFENLGWLVQE-----LKGTWPFAT- 120
             + +S +  TVK   +R+ +L+       + +I ++    L Q       K    F   
Sbjct: 758 EKLEVSEL-ATVKRPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKA 816

Query: 121 --------IVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQ 172
                   +V DE   LK+    + S  ++A+      ++R I LTGTP  N L++    
Sbjct: 817 LVDPGPDFVVCDEGHILKN----EKSAVSKAMNS--IRTKRRIILTGTPLQNNLMEYHCM 870

Query: 173 IWFLDKGKRLGRVFQSFVARWFNTTQIGSH 202
           + F+ +   LG   + F  R+ N  Q G  
Sbjct: 871 VNFVKEN-LLG-SIKEFRNRFVNPIQNGQC 898



 Score = 34.0 bits (77), Expect = 0.079
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 375  GLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVL 434
            G+NL    N ++ F   W+     Q I R+      + G  + V++Y  IAQ T++E + 
Sbjct: 1231 GINL-VAANRVIIFDASWNPSYDTQSIFRV-----YRFGQTKPVYIYRFIAQGTMEEKIY 1284

Query: 435  QRLRTK 440
            +R  TK
Sbjct: 1285 KRQVTK 1290


>gnl|CDD|35612 KOG0391, KOG0391, KOG0391, SNF2 family DNA-dependent ATPase
           [General function prediction only].
          Length = 1958

 Score = 42.4 bits (99), Expect = 3e-04
 Identities = 50/190 (26%), Positives = 88/190 (46%), Gaps = 29/190 (15%)

Query: 2   NLAPHQTKIVDWIL---DHKRCAIWA-SMGSGKTVSVLTALSYI----HLWGEKSVLVIA 53
            L  +Q   +DW+    +     I A  MG GKT+  ++ L+++      WG    L++ 
Sbjct: 615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPH--LIVV 672

Query: 54  PLRVAQSVWTSEVQRWSNFSHMNISVITGTVKQRTKVLK---TPAVLYVINFENLGWLVQ 110
           P  V  + W  E++RW     + I    G+ K+R +  +    P   +V    +   + Q
Sbjct: 673 PTSVILN-WEMELKRWC--PGLKILTYYGSHKERKEKRQGWAKPNAFHVC-ITSYKLVFQ 728

Query: 111 ELKG----TWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGL 166
           +L       W +  +V+DE+  +K+F+ +      R  A   + S+R + LTGTP  N L
Sbjct: 729 DLTAFKRKRWQY--LVLDEAQNIKNFKSQ------RWQALLNFNSQRRLLLTGTPLQNSL 780

Query: 167 IDLWGQIWFL 176
           ++LW  + FL
Sbjct: 781 MELWSLMHFL 790


>gnl|CDD|35613 KOG0392, KOG0392, KOG0392, SNF2 family DNA-dependent ATPase
            domain-containing protein [Transcription].
          Length = 1549

 Score = 41.9 bits (98), Expect = 4e-04
 Identities = 79/345 (22%), Positives = 131/345 (37%), Gaps = 68/345 (19%)

Query: 26   MGSGKTVSVLT--ALSYIHLWGE------KSVLVIAPLRVAQSVWTSEVQRWSNFSHMNI 77
            MG GKT+  +   A  +     E         L++ P  +    W SEV+++  F  +  
Sbjct: 1003 MGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPSTLTGH-WKSEVKKFFPFLKVLQ 1061

Query: 78   SVITGTVKQRTKVLKTPAVLYVINFENLGWLVQEL-KGTWPFATIVVDESTKLKSFRLRQ 136
             V     ++  +     A + V +++ +   V  L K  W +   V+DE   +K+ + + 
Sbjct: 1062 YVGPPAERRELRDQYKNANIIVTSYDVVRNDVDYLIKIDWNY--CVLDEGHVIKNSKTK- 1118

Query: 137  GSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLG--RVFQSFVARWF 194
                     K    + R I L+GTP  N +++LW    FL  G  LG  + FQS      
Sbjct: 1119 ----LTKAVKQLRANHRLI-LSGTPIQNNVLELWSLFDFLMPG-FLGTEKQFQS------ 1166

Query: 195  NTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSLDIADYQNIDKPILITKKVPLPQPVM 254
               + G  I A R    +++ KE EA +    L+L+    Q +  P L+ +   L + V+
Sbjct: 1167 ---RFGKPILASRDP--KSSSKEQEAGV----LALEALHKQVL--PFLLRR---LKEDVL 1212

Query: 255  KQY-HKFQRELYCDL---QGENIEAFNSASKTVKCLQLANGAVYYDEEK----------- 299
            K    K  ++ YC+L   Q +    F   +K     Q+  G      +K           
Sbjct: 1213 KDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLR 1272

Query: 300  ----HWKEVHDEKIKALEVIIEKANAAPIIVAYHFNSDLARLQKA 340
                H   V       L  I+            HFNS L  +Q +
Sbjct: 1273 KLCNHPALVLTPVHPDLAAIVSH--------LAHFNSSLHDIQHS 1309



 Score = 39.6 bits (92), Expect = 0.002
 Identities = 36/144 (25%), Positives = 64/144 (44%), Gaps = 15/144 (10%)

Query: 308  KIKALEVIIEKANAAPIIVAYHFNSDLARLQKAFPQGRTLDKDPCTIQEWNEGK-IPLLF 366
            ++K++  ++EK     +   Y  +    RL  + P G         ++ +NE   I +L 
Sbjct: 1348 QLKSMLDLVEKD----LFKKYMPSVTYMRLDGSVPPGDRQK----IVERFNEDPTIDVLL 1399

Query: 367  AHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQ 426
                  G GLNL  G + +VF    W+     Q ++R       + G KR V VY LI +
Sbjct: 1400 LTTHVGGLGLNLT-GADTVVFVEHDWNPMRDLQAMDR-----AHRIGQKRVVNVYRLITR 1453

Query: 427  NTIDELVLQRLRTKSTIQDLLLNA 450
             T++E V+   + K  + + ++N 
Sbjct: 1454 GTLEEKVMGLQKFKMNVANTVINQ 1477


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

 Score = 38.4 bits (90), Expect = 0.004
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 1  MNLAPHQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAP 54
          + L P+Q + +  +L+ KR  I  + GSGKT+     L    L G+K VL + P
Sbjct: 2  LELRPYQIEAIRNLLEKKRGLIVMATGSGKTL-TAAKLIARLLKGKKKVLFLVP 54


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

 Score = 37.7 bits (87), Expect = 0.007
 Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 5/97 (5%)

Query: 3   LAPHQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVW 62
             P Q  +   +L  +   I A  GSGKT+  L A+    L G   V+ I PL+   ++ 
Sbjct: 33  FNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLK---ALA 89

Query: 63  TSEVQRWSNFSHMNISV--ITGTVKQRTKVLKTPAVL 97
             + + +S    + I V   TG      + L    V+
Sbjct: 90  EEKYEEFSRLEELGIRVGISTGDYDLDDERLARYDVI 126


>gnl|CDD|39640 KOG4439, KOG4439, KOG4439, RNA polymerase II transcription
           termination factor TTF2/lodestar, DEAD-box superfamily
           [Transcription, Replication, recombination and repair].
          Length = 901

 Score = 37.0 bits (85), Expect = 0.010
 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 358 NEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA 417
             G   +L +  A  G GLNL  G N L+   L W+    QQ  +RI      + G K+ 
Sbjct: 796 KGGARVMLLSLTAG-GVGLNL-IGANHLILVDLHWNPALEQQACDRI-----YRMGQKKD 848

Query: 418 VFVYYLIAQNTIDELVLQRLRTKSTIQDLLL 448
           VF++ L+ + T+++ V      K  +   +L
Sbjct: 849 VFIHRLMCKGTVEQRVKSLQDKKLDLAKGVL 879


>gnl|CDD|35610 KOG0389, KOG0389, KOG0389, SNF2 family DNA-dependent ATPase
           [Chromatin structure and dynamics].
          Length = 941

 Score = 36.5 bits (84), Expect = 0.017
 Identities = 46/190 (24%), Positives = 73/190 (38%), Gaps = 28/190 (14%)

Query: 3   LAPHQTKIVDWIL---DHKRCAIWA-SMGSGKTVSVLTALSYIHLWGEKSV-LVIAPLRV 57
           L  +Q   V+W+L     K   I A  MG GKT+ V+  L+Y+   G     LV+ P   
Sbjct: 400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSST 459

Query: 58  AQSVWTSEVQRW-----------SNFSHMNISVITGTVKQRTKVLKTPAVLYVINFENLG 106
            ++ W  E  +W           S      +       K    VL T   L   + ++  
Sbjct: 460 LEN-WLREFAKWCPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRS 518

Query: 107 WLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGL 166
           +L         F  ++ DE   LK+    + S+  + L      +   + LTGTP  N L
Sbjct: 519 FLKN-----QKFNYVIYDEGHMLKN----RTSERYKHLMSIN--ANFRLLLTGTPLQNNL 567

Query: 167 IDLWGQIWFL 176
            +L   + F+
Sbjct: 568 KELISLLAFV 577



 Score = 28.8 bits (64), Expect = 3.2
 Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 7/88 (7%)

Query: 354 IQEWNEGK-IPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQA 412
           I E+N  K I +      + G G+NL    N ++   +  D   +    ++    R  + 
Sbjct: 820 IDEFNTDKDIFVFLLSTKAGGFGINLT-CANTVIIHDI--DFNPY---DDKQAEDRCHRV 873

Query: 413 GFKRAVFVYYLIAQNTIDELVLQRLRTK 440
           G  + V VY LI ++TI+E +L+  +TK
Sbjct: 874 GQTKPVTVYRLITKSTIEEGILRLAKTK 901


>gnl|CDD|36219 KOG1001, KOG1001, KOG1001, Helicase-like transcription factor
           HLTF/DNA helicase RAD5, DEAD-box superfamily
           [Transcription, Replication, recombination and repair].
          Length = 674

 Score = 36.1 bits (83), Expect = 0.022
 Identities = 32/197 (16%), Positives = 65/197 (32%), Gaps = 28/197 (14%)

Query: 257 YHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVY----YDEEKHWKEVHDEKIKAL 312
            H F  E       ++I+   +A   +    L    +          +       KI A 
Sbjct: 472 GHDFCVECLK----KSIQQSENAPCPLCRNVLKEKKLLSANPLPSIINDLLPESSKIYAF 527

Query: 313 EVIIE--KANAAP-IIVAYHFNSDLARLQ----------KAFPQGRTLDKDPCTIQEWNE 359
             I++  + +  P I++       LA +             +     +     +  ++  
Sbjct: 528 LKILQAKEMSEQPKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPC 587

Query: 360 GKIPLLFAHPASCGH-GLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAV 418
             +          G  GLNL    ++L+    WW+    +Q I+R     Q      + V
Sbjct: 588 DPLVTALLMSLKAGKVGLNLTAASHVLLM-DPWWNPAVEEQAIDRAHRIGQT-----KPV 641

Query: 419 FVYYLIAQNTIDELVLQ 435
            V   I ++T++E +L+
Sbjct: 642 KVSRFIIKDTVEERILK 658



 Score = 33.4 bits (76), Expect = 0.15
 Identities = 39/178 (21%), Positives = 67/178 (37%), Gaps = 33/178 (18%)

Query: 16  DHKRCAIWA-SMGSGKTVSVLTALSYIHLWGE--------KSVLVIAPLRVAQSVWTSEV 66
              R  I A  MG GKTV  +  +    L  +        K+ L++ P  +    W +E+
Sbjct: 150 QSLRGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTSLLTQ-WKTEL 208

Query: 67  QRWSNFSHMNISVITGTVKQRTK------VLKTPAVLYVINFENLGWLVQELKGTWPFAT 120
           ++ +    ++I V  G  K +++      VL T  +L       + WL            
Sbjct: 209 EKVTEEDKLSIYVYHGRTKDKSELNSYDVVLTTYDILKNSPLVKIKWL------------ 256

Query: 121 IVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFLDK 178
            +V +       +  Q  K    L     +++    LTGTP  N L +L+    FL+ 
Sbjct: 257 RIVLDEAHTIKNKDTQIFKAVCQL-----DAKYRWCLTGTPIQNNLDELYSLFKFLEI 309


>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 = 35.7 bits (82), Expect = 0.030
 Identities = 25/137 (18%), Positives = 57/137 (41%), Gaps = 21/137 (15%)

Query: 298 EKHWKEVHDEKIKALEVIIEKANAAP--IIVAYHFNSDLARLQKAFP-----------QG 344
           +++   V DEK++AL  ++++       +++       L  L +               G
Sbjct: 3   KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62

Query: 345 RTLDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERI 404
              +++   ++++ EG+I +L A       G++L    ++++ + L W    + Q I R 
Sbjct: 63  SQEEREE-VLKDFREGEIVVLVATDVI-ARGIDLP-NVSVVINYDLPWSPSSYLQRIGRA 119

Query: 405 GVTRQRQAGFKRAVFVY 421
           G     +AG K    + 
Sbjct: 120 G-----RAGQKGTAILL 131


>gnl|CDD|144016 pfam00271, Helicase_C, Helicase conserved C-terminal domain.  The
           Prosite family is restricted to DEAD/H helicases,
           whereas this domain family is found in a wide variety of
           helicases and helicase related proteins. It may be that
           this is not an autonomously folding unit, but an
           integral part of the helicase.
          Length = 78

 Score = 35.2 bits (82), Expect = 0.044
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 353 TIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIG 405
            ++++  GK  +L A     G G++L    N+++ + L W+   + Q I R G
Sbjct: 25  ILEDFRNGKSKVLVA-TDVAGRGIDLP-DVNVVINYDLPWNPASYIQRIGRAG 75


>gnl|CDD|35609 KOG0388, KOG0388, KOG0388, SNF2 family DNA-dependent ATPase
           [Replication, recombination and repair].
          Length = 1185

 Score = 34.7 bits (79), Expect = 0.052
 Identities = 39/170 (22%), Positives = 75/170 (44%), Gaps = 35/170 (20%)

Query: 26  MGSGKTVSVLTALSYI----HLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVIT 81
           MG GKTV  ++ L+++    ++WG    LV+ P     + W  E+ R+       +    
Sbjct: 595 MGLGKTVQSISVLAHLAETHNIWG--PFLVVTPASTLHN-WAQEISRF--LPSFKVLPYW 649

Query: 82  GTVKQRTKVLKTPAVLYVINFENLGWLV---------------QELKGTWPFATIVVDES 126
           G+  +R K+L+       +   N  + V               Q++K  W +  +++DE+
Sbjct: 650 GSPSER-KILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQKVK--WQY--MILDEA 704

Query: 127 TKLKSFRLRQGSKTARALAKPAWESERFIELTGTPSPNGLIDLWGQIWFL 176
             +KS      S ++R     +++    + LTGTP  N + +LW  + F+
Sbjct: 705 QAIKS------SSSSRWKTLLSFKCRNRLLLTGTPIQNSMQELWALLHFI 748


>gnl|CDD|36234 KOG1016, KOG1016, KOG1016, Predicted DNA helicase, DEAD-box
           superfamily [General function prediction only].
          Length = 1387

 Score = 34.3 bits (78), Expect = 0.066
 Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 20  CAIWASMGSGKTVSVLTALS-YIHLWGEKSVLVIAPLRVAQSVWTSEVQRW 69
           C +  SMG GKT+ V++    ++     K+VLVI P+   Q+ W SE   W
Sbjct: 285 CILAHSMGLGKTLQVISFSDIFLRHTKAKTVLVIVPINTLQN-WLSEFNMW 334


>gnl|CDD|31261 COG1061, SSL2, DNA or RNA helicases of superfamily II
           [Transcription / DNA replication, recombination, and
           repair].
          Length = 442

 Score = 33.5 bits (76), Expect = 0.12
 Identities = 33/165 (20%), Positives = 62/165 (37%), Gaps = 20/165 (12%)

Query: 1   MNLAPHQTKIVD----WILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLR 56
             L P+Q + +D         +R  I    G+GKTV    A++ +    ++S LV+ P +
Sbjct: 35  FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL----KRSTLVLVPTK 90

Query: 57  VAQSVWTSEVQRWSNFSHMNISVITGTVKQRTKVLKTPAVLYVINFENLGWLVQELKGTW 116
                W   ++++   +   I +  G  K+      T A +  +    L       +   
Sbjct: 91  ELLDQWAEALKKFLLLND-EIGIYGGGEKELEPAKVTVATVQTLARRQLLDEFLGNE--- 146

Query: 117 PFATIVVDESTKLKSFRLRQGSKTARALAKPAWESERFIELTGTP 161
            F  I+ DE   L        + + R + +    +   + LT TP
Sbjct: 147 -FGLIIFDEVHHL-------PAPSYRRILELLSAAYPRLGLTATP 183


>gnl|CDD|36339 KOG1123, KOG1123, KOG1123, RNA polymerase II transcription
           initiation/nucleotide excision repair factor TFIIH,
           3'-5' helicase subunit SSL2 [Transcription, Replication,
           recombination and repair].
          Length = 776

 Score = 33.4 bits (76), Expect = 0.12
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 27  GSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSEVQRWSNFSHMNISVITGTVKQ 86
           G+GKT+  +TA   I    +KS LV+    V+   W  + ++WS      I   T   K+
Sbjct: 330 GAGKTLVGVTAACTI----KKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQICRFTSDAKE 385

Query: 87  RTK 89
           R  
Sbjct: 386 RFP 388


>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 = 32.8 bits (74), Expect = 0.21
 Identities = 29/127 (22%), Positives = 53/127 (41%), Gaps = 21/127 (16%)

Query: 5   PHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEK---SVLVIAPLRVAQS 60
           P Q   +  IL  +     A  G+GKT + +L  L  I    E+   S L++AP R    
Sbjct: 54  PIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAV 113

Query: 61  VWTSEVQRWS-NFSHMNISVITG--TVKQRTKVLK--------TPAVL------YVINFE 103
               E+++   N   + ++V+ G  +++++ + LK        TP  L        ++  
Sbjct: 114 QIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLS 173

Query: 104 NLGWLVQ 110
            +  LV 
Sbjct: 174 GVETLVL 180


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

 Score = 32.1 bits (73), Expect = 0.31
 Identities = 30/140 (21%), Positives = 54/140 (38%), Gaps = 22/140 (15%)

Query: 3   LAPHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEK------SVLVIAPL 55
           L P Q   +  I   +   I A  GSGKT +  L  ++ +   G+         L I+PL
Sbjct: 23  LTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPL 82

Query: 56  RVAQSVWTSEVQRWSNFSHMNISVITGTV--KQRTKVLKTPAVLYVINFENLGWLVQELK 113
           +   +     ++       + ++V  G     ++ K+LK P  + +   E+L  L+    
Sbjct: 83  KALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILL---- 138

Query: 114 GTWPFA--------TIVVDE 125
              P           ++VDE
Sbjct: 139 -NSPKFRELLRDVRYVIVDE 157


>gnl|CDD|33166 COG3358, COG3358, Uncharacterized conserved protein [Function
           unknown].
          Length = 262

 Score = 30.0 bits (67), Expect = 1.5
 Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 148 AWESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLGRVFQSFVARWFN--TTQIGSHIGA 205
           AW   R  E     S  G   L    W      +    F S   RW+      +G+H+  
Sbjct: 18  AWHFSRNKEAI---SRTGATSLSATEWISATTLKDAHTFPSLPGRWYKRGGGVVGAHLP- 73

Query: 206 VRYTAKETAQKEIEAQLSD 224
             +T   TAQ+   A    
Sbjct: 74  PPFTTTGTAQRRRGALFRA 92


>gnl|CDD|31398 COG1205, COG1205, Distinct helicase family with a unique C-terminal
           domain including a metal-binding cysteine cluster
           [General function prediction only].
          Length = 851

 Score = 29.6 bits (66), Expect = 1.8
 Identities = 35/159 (22%), Positives = 60/159 (37%), Gaps = 31/159 (19%)

Query: 2   NLAPHQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSV-LVIAPLRVAQS 60
            L  HQ   +  I + +   +    GSGKT S L  +    L    +  L++ P     +
Sbjct: 70  RLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTN---A 126

Query: 61  VWTSEVQRWSNFSH-----MNISVITGTVKQRTK----------VLKTPAVLYVI---NF 102
           +   + +R           +     TG      +          +L  P +L+ +   N 
Sbjct: 127 LANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNH 186

Query: 103 ENLGWLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTA 141
           +   WL++ LK       +VVDE   L ++R  QGS+ A
Sbjct: 187 DAWLWLLRNLK------YLVVDE---LHTYRGVQGSEVA 216


>gnl|CDD|33957 COG4232, COG4232, Thiol:disulfide interchange protein
           [Posttranslational modification, protein turnover,
           chaperones / Energy production and conversion].
          Length = 569

 Score = 29.5 bits (66), Expect = 1.8
 Identities = 21/108 (19%), Positives = 34/108 (31%), Gaps = 9/108 (8%)

Query: 144 LAKPAWESERFIELTGTPSPNGLIDLWGQIWFL---DKGKRLGRVFQS-----FVARWFN 195
           LA   W   R +   G  +  GL+ L    W        KR   VF        +     
Sbjct: 373 LATAIWLLWRVLPEVGALALWGLLLLAFGAWLFGRWLAAKRGPWVFALVLILALLGALVG 432

Query: 196 TTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLSLDIADYQNIDKPILI 243
              + +        A+  +  E    +S     LD A  +   KP+++
Sbjct: 433 VQPLQAKAFLNPEAAQSVSHGEFWQPISPLAE-LDQALAEAKAKPVML 479


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

 Score = 29.6 bits (66), Expect = 1.9
 Identities = 27/131 (20%), Positives = 49/131 (37%), Gaps = 24/131 (18%)

Query: 3   LAPHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEK-------SVLVIAP 54
             P Q +     L  +     A  GSGKT++ +L A+ +++    K        VLV+AP
Sbjct: 114 PTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAP 173

Query: 55  LRVAQSVWTSEVQRWSNFSHMNISVITGTVKQRTK----------VLKTPAVLY------ 98
            R       +E + +     +  + + G   +  +          V+ TP  L       
Sbjct: 174 TRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEG 233

Query: 99  VINFENLGWLV 109
            +N   + +LV
Sbjct: 234 SLNLSRVTYLV 244


>gnl|CDD|39131 KOG3928, KOG3928, KOG3928, Mitochondrial ribosome small subunit
           component, mediator of apoptosis DAP3 [Translation,
           ribosomal structure and biogenesis].
          Length = 461

 Score = 29.2 bits (65), Expect = 2.6
 Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 5/66 (7%)

Query: 6   HQTKIVDWILDHKRCAIWASMGSGKTVSVLTALSYIHLWGEKSVLVIAPLRVAQSVWTSE 65
              ++VD +   KR  +    G+GK++    AL+    +      +I  +  A+  WT+ 
Sbjct: 168 LYKRLVDPMHPVKRFVLDGEPGTGKSI----ALAQAVHYAADQKWLILHIPYAEL-WTNG 222

Query: 66  VQRWSN 71
            + +S 
Sbjct: 223 RKDYSY 228


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

 Score = 28.8 bits (64), Expect = 3.4
 Identities = 31/141 (21%), Positives = 54/141 (38%), Gaps = 18/141 (12%)

Query: 1   MNLAPHQTKIVDWILDHKRCAIWASMGSGKTVS-VLTALSYIHLWGEKS---VLVIAPLR 56
                 Q++ +   L  +     A  GSGKT +  L  L    L  E      LV+ P R
Sbjct: 82  KKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQ--RLLQEPKLFFALVLTPTR 139

Query: 57  VAQSVWTSEVQRWSNFSHMNISVITG---TVKQRTKVLKTPAVLYVINFENLGWLVQELK 113
                   + +   +   + ++V+ G    + Q  ++ K P +L        G L   L+
Sbjct: 140 ELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVA----TPGRLWDHLE 195

Query: 114 GTWPFAT-----IVVDESTKL 129
            T  F+      +V+DE+ +L
Sbjct: 196 NTKGFSLEQLKFLVLDEADRL 216


>gnl|CDD|145508 pfam02399, Herpes_ori_bp, Origin of replication binding protein. 
          This Pfam family represents the herpesvirus origin of
          replication binding protein, probably involved in DNA
          replication.
          Length = 829

 Score = 28.5 bits (64), Expect = 3.6
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 24 ASMGSGKTVSVLTALSYIHLWGEKSVLVI 52
          A MGSGKT +++  L       + SVLV+
Sbjct: 56 APMGSGKTTALIEWLRAALDSPDTSVLVV 84


>gnl|CDD|35519 KOG0298, KOG0298, KOG0298, DEAD box-containing helicase-like
            transcription factor/DNA repair protein [Replication,
            recombination and repair].
          Length = 1394

 Score = 28.4 bits (63), Expect = 3.7
 Identities = 12/47 (25%), Positives = 20/47 (42%)

Query: 401  IERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVLQRLRTKSTIQDLL 447
             E   + R  + G KR  FV+  I   T++E +L  + +K       
Sbjct: 1300 DEAQAIGRVHRIGQKRPTFVHRFIVNETVEENILSLITSKEETLTKS 1346


>gnl|CDD|33398 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
           and repair].
          Length = 402

 Score = 28.1 bits (62), Expect = 5.0
 Identities = 18/93 (19%), Positives = 32/93 (34%), Gaps = 8/93 (8%)

Query: 179 GKRLGRVFQSFVA----RWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCC--LSLDIA 232
           GK    ++           F         G V Y + E  +++I  +L      + L  A
Sbjct: 101 GKTTLLLYLCIALAAGKNLFGNKVKEP--GKVLYVSLELYREDILERLEPVRARMGLSPA 158

Query: 233 DYQNIDKPILITKKVPLPQPVMKQYHKFQRELY 265
           D +N+D   +            K Y +F++ L 
Sbjct: 159 DVRNMDLTDVSGAADESDVLSPKLYRRFEKILE 191


>gnl|CDD|30596 COG0247, GlpC, Fe-S oxidoreductase [Energy production and
           conversion].
          Length = 388

 Score = 28.0 bits (61), Expect = 5.1
 Identities = 22/105 (20%), Positives = 33/105 (31%), Gaps = 13/105 (12%)

Query: 256 QYHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEKHWKEVHDEKIKALEVI 315
            Y     E    L  +NIEAF    +    +     A Y   +K + E+  E+   +  +
Sbjct: 193 AYRSGFLERAKKLAKKNIEAFKKLIEGGDPIVTVCPACYGALKKEYPELLGERALKVVDL 252

Query: 316 IE-------------KANAAPIIVAYHFNSDLARLQKAFPQGRTL 347
           +E                    IV YH    L R      + R L
Sbjct: 253 VELLAELLREGKLKLLPKLKGKIVTYHDPCHLRRGGGVVDEPREL 297


>gnl|CDD|35900 KOG0681, KOG0681, KOG0681, Actin-related protein - Arp5p
           [Cytoskeleton].
          Length = 645

 Score = 27.7 bits (61), Expect = 7.9
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 232 ADYQNIDKPILITKKVPLPQPVMKQYHKFQRELY 265
            D Q ID PI++T+ +  P     +  +   E Y
Sbjct: 110 VDGQGIDHPIILTEALANPVYSRSEMVELLFETY 143


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

 Score = 27.7 bits (61), Expect = 7.9
 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)

Query: 298 EKHWKEV-HDEKIKALEVIIEKANAAPIIV 326
           E+  + V  DEK K L  I+E     PII+
Sbjct: 493 EQKVEMVSEDEKRKKLIEILESNFDPPIII 522


>gnl|CDD|147517 pfam05373, Pro_3_hydrox_C, L-proline 3-hydroxylase, C-terminal.
           Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases
           catalyse oxidative reactions in a range of metabolic
           processes. Proline 3-hydroxylase hydroxylates proline at
           position 3, the first of a 2-OG oxygenase catalysing
           oxidation of a free alpha-amino acid. The structure
           contains conserved motifs present in other 2-OG
           oxygenases including a jelly roll strand core and
           residues binding iron and 2-oxoglutarate, consistent
           with divergent evolution within the extended family. The
           structure differs significantly from many other 2-OG
           oxygenases in possessing a discrete C-terminal helical
           domain.
          Length = 101

 Score = 27.1 bits (60), Expect = 9.3
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 3/43 (6%)

Query: 295 YDEEKHWKEVHDEKIKALEVIIEKANAAPIIV---AYHFNSDL 334
            DE K + +   E+I A   II +AN   I+      HF   +
Sbjct: 19  VDERKPFTDETKERILAFSGIISEANFRDIVFILSKLHFTYKV 61


  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    0.135    0.416 

Gapped
Lambda     K      H
   0.267   0.0630    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,622,220
Number of extensions: 294740
Number of successful extensions: 735
Number of sequences better than 10.0: 1
Number of HSP's gapped: 723
Number of HSP's successfully gapped: 52
Length of query: 458
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 361
Effective length of database: 4,167,664
Effective search space: 1504526704
Effective search space used: 1504526704
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: 59 (26.7 bits)