RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780553|ref|YP_003064966.1| Holliday junction DNA helicase
RuvA [Candidatus Liberibacter asiaticus str. psy62]
         (207 letters)



>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
           recombination, helicase; 1.90A {Escherichia coli} SCOP:
           a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A
           1d8l_A
          Length = 203

 Score =  190 bits (484), Expect = 2e-49
 Identities = 56/204 (27%), Positives = 99/204 (48%), Gaps = 3/204 (1%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MIG+++G I       VLI+V GV Y ++ P+     L + G    +F    +R+D   L
Sbjct: 1   MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLL 60

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           +GF +  +R  F  L    GVG ++A+ +LS ++A + V ++  +    + ++PGI  K 
Sbjct: 61  YGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKT 120

Query: 121 ASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTA 180
           A R++ E+K +   L   +    + +        +       A++ LV LGY   +A+  
Sbjct: 121 AERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVARLVALGYKPQEASRM 180

Query: 181 VVSVLKKEKNIADDSQIIRLALRA 204
           V  + + +   A    +IR ALRA
Sbjct: 181 VSKIARPD---ASSETLIREALRA 201


>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
           octameric RUVA, AAA-ATPase domain, complex with
           nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
           thermophilus} SCOP: a.60.2.1 b.40.4.2
          Length = 191

 Score =  157 bits (397), Expect = 2e-39
 Identities = 49/205 (23%), Positives = 94/205 (45%), Gaps = 15/205 (7%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MI  ++G +        ++   GV + +  P   L  L + G    +     ++++ + L
Sbjct: 1   MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQAL-EEGKEVGVHTHLLLKEEGLSL 59

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           +GF  + +   F LL SV GVG +VA+ +LS +    L  +++  +++++    G+  ++
Sbjct: 60  YGFPDEENLALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRL 119

Query: 121 ASRIMTELKGKAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQATTA 180
           A RI  ELKGK        ++  S   +E             A+ AL  LG+ + QA   
Sbjct: 120 AERIALELKGKVPPHLLAGEKVESEAAEE-------------AVMALAALGFKEAQARAV 166

Query: 181 VVSVLKKEKNIADDSQIIRLALRAI 205
           V+ +L +    A    +I+ AL+ +
Sbjct: 167 VLDLLAQNPK-ARAQDLIKEALKRL 190


>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination,
           branch migration, DNA binding, oligomerization, acidic
           PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A
           2zte_A 2h5x_A 1bvs_A
          Length = 212

 Score =  129 bits (324), Expect = 7e-31
 Identities = 57/208 (27%), Positives = 92/208 (44%), Gaps = 17/208 (8%)

Query: 1   MIGKIKGNIEGLYEDYVLIDVQGVCYIIYCPIRTLSCLGKIGDFCTLFVETHMRQDQIRL 60
           MI  ++G +  +  D+V+I+  GV Y +     TL+ L + G    L     +R+D + L
Sbjct: 17  MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATL-RQGTEARLITAMIVREDSMTL 75

Query: 61  FGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKI 120
           +GF     R  F+ L SV GVG R+AM  L+   A  L + +   N   + ++PGI  + 
Sbjct: 76  YGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRG 135

Query: 121 ASRIMTELKG--KAISLSSVVQQDMSCVNKEQAHICSMPSFAINAISALVNLGYGQDQAT 178
           A R++ EL+      +    +  +   V                 + ALV LG+   QA 
Sbjct: 136 AERMVLELRDKVGVAATGGALSTNGHAVRSP-------------VVEALVGLGFAAKQAE 182

Query: 179 TAVVSVLKKEKNIADDSQIIRLALRAIS 206
            A  +VL    + A  S  +R AL  + 
Sbjct: 183 EATDTVLAANHD-ATTSSALRSALSLLG 209


>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex,
           RNA-RNA complex, protein-RNA complex, peptidyl
           transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
           2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB:
           1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y*
           1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y*
           1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
          Length = 241

 Score = 42.4 bits (99), Expect = 7e-05
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 68  DRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTE 127
             + +  L  + GVG   A  +       E VE +   +   +A + GI   +A+RI  +
Sbjct: 10  AEEEYTELTDISGVGPSKAESLRE--AGFESVEDVRGADQSALADVSGIGNALAARIKAD 67

Query: 128 LKGK 131
           + G 
Sbjct: 68  VGGL 71


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 38/220 (17%), Positives = 72/220 (32%), Gaps = 87/220 (39%)

Query: 7   GNIEGLYEDYV--LIDVQGVCYIIYCP-IRTLSCLGKIGDFCTL--FVETHMRQDQIRLF 61
           GN +    DY   L D+    Y  Y   +  L  +    +  TL   + T +  +++   
Sbjct: 164 GNTD----DYFEELRDL----YQTYHVLVGDL--IKFSAE--TLSELIRTTLDAEKVFTQ 211

Query: 62  GFLSDLDRQWFMLLQSVQG----VGARVAM---GVLS----RITATELVESIILQNSKVI 110
           G   ++  +W     +       +   ++    GV+      +TA            K++
Sbjct: 212 GL--NI-LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTA------------KLL 256

Query: 111 AQIPGISMKIASRIMTELKGK---------AISLSSVVQQDMSCVNKEQAHICSMPSFAI 161
              PG   ++ S     LKG          A++++     D            S  SF +
Sbjct: 257 GFTPG---ELRSY----LKGATGHSQGLVTAVAIAET---D------------SWESFFV 294

Query: 162 NAISALVNL---GY-GQDQA--TTAVVSVLKKEKNIADDS 195
           +   A+  L   G    +    T+   S+L+       DS
Sbjct: 295 SVRKAITVLFFIGVRCYEAYPNTSLPPSILE-------DS 327



 Score = 30.3 bits (68), Expect = 0.32
 Identities = 20/79 (25%), Positives = 26/79 (32%), Gaps = 25/79 (31%)

Query: 27  IIYCPIRTLSCLGKIGDF--CTLFVETHMRQDQIRLF--GFLSDLDRQWFMLLQSVQGVG 82
           I+ C I  L        +   T F  TH     I  F  G  S L     +  ++  G G
Sbjct: 479 IVDC-IIRLPV-----KWETTTQFKATH-----ILDFGPGGASGLGV---LTHRNKDGTG 524

Query: 83  ARVAMGVLSRITATELVES 101
            RV       I A  L  +
Sbjct: 525 VRV-------IVAGTLDIN 536


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 35.7 bits (81), Expect = 0.008
 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 12/35 (34%)

Query: 174 QDQATTAVVSVLKK-EKNI---ADDSQIIRLALRA 204
           + QA       LKK + ++   ADDS    LA++A
Sbjct: 18  EKQA-------LKKLQASLKLYADDSAPA-LAIKA 44



 Score = 29.2 bits (64), Expect = 0.65
 Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 8/29 (27%)

Query: 140 QQDMSCVNKEQAHIC-----SMPSFAINA 163
           +Q    + K QA +      S P+ AI A
Sbjct: 19  KQ---ALKKLQASLKLYADDSAPALAIKA 44


>1ixs_A Holliday junction DNA helicase RUVA; heterodimeric protein complex,
           AAA-ATPase domain, complex with nucleotide, hydrolase;
           HET: ANP; 3.20A {Thermus thermophilus} SCOP: a.5.1.1
          Length = 62

 Score = 30.0 bits (67), Expect = 0.36
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 162 NAISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI 205
            A+ AL  LG+ + QA   V+ +L +    A    +I+ AL+ +
Sbjct: 19  EAVMALAALGFKEAQARAVVLDLLAQNPK-ARAQDLIKEALKRL 61


>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
           domain, homodimer, hydrolase; 1.45A {Pyrococcus
           furiosus} SCOP: a.60.2.5
          Length = 75

 Score = 28.7 bits (64), Expect = 0.84
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 64  LSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASR 123
           L+  +RQ   +++ +  V A +A  +L        VE +   +   + ++ GI  KIA  
Sbjct: 6   LTLAERQRL-IVEGLPHVSATLARRLLKHF---GSVERVFTASVAELMKVEGIGEKIAKE 61

Query: 124 IMTELKGK 131
           I   +   
Sbjct: 62  IRRVITAP 69


>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain,
           DNA-binding domain, DNA binding protein; NMR
           {Escherichia coli} SCOP: a.60.2.3
          Length = 78

 Score = 28.2 bits (63), Expect = 1.3
 Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 75  LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129
           L++++GVG +    +L  +     ++ +   + + IA++PGIS  +A +I   LK
Sbjct: 26  LETIEGVGPKRRQMLLKYM---GGLQGLRNASVEEIAKVPGISQGLAEKIFWSLK 77


>1fnb_A Ferredoxin-NADP+ reductase; oxidoreductase
           (NADP+(A),ferredoxin(A)); HET: FAD; 1.70A {Spinacia
           oleracea} SCOP: b.43.4.2 c.25.1.1 PDB: 1fnc_A* 1fnd_A*
           1bx1_A* 1frq_A* 1frn_A* 1bx0_A* 1qg0_A* 1qga_A* 1qfz_A*
           1qfy_A* 1gaw_A* 1gaq_A* 1sm4_A*
          Length = 314

 Score = 27.5 bits (60), Expect = 2.5
 Identities = 6/45 (13%), Positives = 14/45 (31%)

Query: 150 QAHICSMPSFAINAISALVNLGYGQDQATTAVVSVLKKEKNIADD 194
             ++C +          +V+L   +          LKK +    +
Sbjct: 268 YVYMCGLKGMEKGIDDIMVSLAAAEGIDWIEYKRQLKKAEQWNVE 312


>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
           ATP-binding, nucleotide-binding, hydrolase; 2.20A
           {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
          Length = 574

 Score = 26.8 bits (58), Expect = 3.9
 Identities = 10/60 (16%), Positives = 22/60 (36%), Gaps = 7/60 (11%)

Query: 67  LDRQWFMLLQSVQGVGARVAMGVLSRITAT--ELVESIILQNSKVIAQIPGISMKIASRI 124
           L+R+    LQ + G+    A     R            + ++   + ++ GI    A ++
Sbjct: 6   LERRLLAGLQGL-GLTINQAQ----RAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKL 60


>1iyr_A DFF45, DNA fragmentation factor alpha subunit; apoptosis, riken
           structural genomics/proteomics initiative, RSGI,
           structural genomics; HET: DNA; NMR {Homo sapiens} SCOP:
           a.164.1.1 PDB: 1koy_A*
          Length = 111

 Score = 25.7 bits (56), Expect = 7.0
 Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 6/35 (17%)

Query: 120 IASRIMTELKGKA---ISLSSVVQQDMSCVNKEQA 151
           +AS I+T L+ K    +SLSS   QD+  V KE  
Sbjct: 17  LASHILTALREKQAPELSLSS---QDLELVTKEDP 48


>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric
           ring, heptamer, ring, oligomer, RAD51 polymerization
           motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP:
           a.60.4.1 c.37.1.11
          Length = 349

 Score = 25.9 bits (56), Expect = 7.6
 Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 75  LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTELK 129
           ++ + GVG   A  +      T  +E+I + +   + ++ GIS   A +I+   +
Sbjct: 37  IEDLPGVGPATAEKLREAGYDT--LEAIAVASPIELKEVAGISEGTALKIIQAAR 89


>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA
           damage, DNA recombinat repair, nucleotide-binding; HET:
           DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*
          Length = 400

 Score = 25.9 bits (56), Expect = 7.6
 Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 99  VESIILQNSKVIAQIPGISMKIASRIMTELKGKAISLSSVVQQDMSCVNKEQAHI 153
            E++     K + +I GIS   A +++ E   + + +  V   D      E   +
Sbjct: 107 AEAVAYAPRKDLLEIKGISEAKADKLLNEAA-RLVPMGFVTAADFHMRRSELICL 160


>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP),
           dimer, inactive(APO, unliganded) form, allostery, DNA
           binding; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A*
           3i59_A*
          Length = 227

 Score = 25.6 bits (55), Expect = 7.9
 Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 10/79 (12%)

Query: 55  QDQIRLFGFLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIP 114
            + +    F     R    LLQ  Q  G +    +      T+          + IAQ+ 
Sbjct: 138 NNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQ----------EEIAQLV 187

Query: 115 GISMKIASRIMTELKGKAI 133
           G S +  ++ + +   +  
Sbjct: 188 GASRETVNKALADFAHRGW 206


>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural
           genomics, joint center for structural genomics, JCSG;
           HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}
          Length = 231

 Score = 25.4 bits (54), Expect = 9.2
 Identities = 11/84 (13%), Positives = 29/84 (34%), Gaps = 2/84 (2%)

Query: 52  HMRQDQIRLFG-FLSDLDRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSK-V 109
            +  +   +    ++ L+ +     Q+ +     V   +  +  A  + +  +L      
Sbjct: 121 RVLWNLAEMLARRVTFLNDELIAFGQNTEAALTHVFANLYRQRLAAGVPQPEVLPLGTQD 180

Query: 110 IAQIPGISMKIASRIMTELKGKAI 133
           I      S +  SR++  L+   I
Sbjct: 181 IMARTSSSRETVSRVLKRLEAHNI 204


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.324    0.137    0.390 

Gapped
Lambda     K      H
   0.267   0.0502    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,584,628
Number of extensions: 65143
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 278
Number of HSP's successfully gapped: 23
Length of query: 207
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 119
Effective length of database: 3,559,758
Effective search space: 423611202
Effective search space used: 423611202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.1 bits)