RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

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



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

 Score =  139 bits (351), Expect = 3e-34
 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


>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
          recombination, helicase; 1.90A {Escherichia coli}
          (A:1-65)
          Length = 65

 Score = 82.4 bits (204), Expect = 4e-17
 Identities = 21/65 (32%), Positives = 34/65 (52%)

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

Query: 61 FGFLS 65
          +GF +
Sbjct: 61 YGFNN 65


>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
           recombination, helicase; 1.90A {Escherichia coli}
           (A:66-144)
          Length = 79

 Score = 77.4 bits (191), Expect = 1e-15
 Identities = 20/71 (28%), Positives = 38/71 (53%)

Query: 68  DRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTE 127
           +R  F  L    GVG ++A+ +LS ++A + V ++  +    + ++PGI  K A R++ E
Sbjct: 3   ERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVE 62

Query: 128 LKGKAISLSSV 138
           +K +   L   
Sbjct: 63  MKDRFKGLHGD 73


>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
           (A:80-154)
          Length = 75

 Score = 76.6 bits (189), Expect = 2e-15
 Identities = 23/70 (32%), Positives = 37/70 (52%)

Query: 68  DRQWFMLLQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTE 127
            R  F+ L SV GVG R+AM  L+   A  L + +   N   + ++PGI  + A R++ E
Sbjct: 4   TRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLE 63

Query: 128 LKGKAISLSS 137
           L+ K    ++
Sbjct: 64  LRDKVGVAAT 73


>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 (A:1-79)
          Length = 79

 Score = 75.9 bits (187), Expect = 4e-15
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

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 FGF 63
          +GF
Sbjct: 76 YGF 78


>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
           (A:155-212)
          Length = 58

 Score = 47.4 bits (113), Expect = 2e-06
 Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 163 AISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAIS 206
            + ALV LG+   QA  A  +VL    + A  S  +R AL  + 
Sbjct: 13  VVEALVGLGFAAKQAEEATDTVLAANHD-ATTSSALRSALSLLG 55


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

 Score = 47.0 bits (112), Expect = 2e-06
 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 163 AISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRAI 205
           A+ AL  LG+ + QA   V+ +L +    A    +I+ AL+ +
Sbjct: 20  AVMALAALGFKEAQARAVVLDLLAQNPK-ARAQDLIKEALKRL 61


>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
           recombination, helicase; 1.90A {Escherichia coli}
           (A:145-203)
          Length = 59

 Score = 40.1 bits (94), Expect = 2e-04
 Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 163 AISALVNLGYGQDQATTAVVSVLKKEKNIADDSQIIRLALRA 204
           A++ LV LGY   +A+  V  + + +   A    +IR ALRA
Sbjct: 19  AVARLVALGYKPQEASRMVSKIARPD---ASSETLIREALRA 57


>3h0l_B Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B;
           multi protein complex, ligase, protein biosynthesis;
           HET: ADP; 2.30A {Aquifex aeolicus} PDB: 3h0m_B 3h0r_B*
           (B:297-478)
          Length = 182

 Score = 26.8 bits (59), Expect = 2.2
 Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 89  VLSRITATELVESIILQNSKVIAQIPGISMK----IASRIMTELKGKA 132
           +       ELV+ I  ++ K + ++     K       ++M E +GKA
Sbjct: 119 ITDENQIKELVKKIFEKHPKEVERLKQGEEKLIGFFVGQVMRETRGKA 166


>1iyr_A DFF45, DNA fragmentation factor alpha subunit; apoptosis,
           riken structural genomics/proteomics initiative, RSGI,
           structural genomics; HET: DNA; NMR {Homo sapiens} (A:)
          Length = 111

 Score = 26.1 bits (57), Expect = 3.7
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 120 IASRIMTELKGKAISLSSVVQQDMSCVNKEQA 151
           +AS I+T L+ K     S+  QD+  V KE  
Sbjct: 17  LASHILTALREKQAPELSLSSQDLELVTKEDP 48


>1wcn_A Transcription elongation protein NUSA; RNA-binding protein,
           escherichia coli NUSA, transcription regulation,
           regulation of RNA binding; NMR {Escherichia coli} PDB:
           2jzb_B (A:)
          Length = 70

 Score = 25.7 bits (57), Expect = 4.1
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 75  LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRIMTE 127
           L +++GV   +A  + +R   T  +E +  Q    +A I G++ + A  ++  
Sbjct: 9   LLNLEGVDRDLAFKLAARGVCT--LEDLAEQGIDDLADIEGLTDEKAGALIMA 59


>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix,
           hydrolase; HET: DNA; NMR {Homo sapiens} (A:)
          Length = 89

 Score = 25.5 bits (56), Expect = 5.5
 Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 75  LQSVQGVGARVAMGVLSRITATELVESIILQNSKVIAQIPGISMKIASRI 124
           L +V+ V    +  +L+       +E +I  + + +A  PG+  + A R+
Sbjct: 21  LTTVKSVNKTDSQTLLTTF---GSLEQLIAASREDLALCPGLGPQKARRL 67


>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA;
           heptameric ring, heptamer, ring, oligomer, RAD51
           polymerization motif; HET: DNA; 2.85A {Pyrococcus
           furiosus} (A:1-95)
          Length = 95

 Score = 25.1 bits (55), Expect = 6.5
 Identities = 7/31 (22%), Positives = 17/31 (54%)

Query: 99  VESIILQNSKVIAQIPGISMKIASRIMTELK 129
           +E+I + +   + ++ GIS   A +I+   +
Sbjct: 59  LEAIAVASPIELKEVAGISEGTALKIIQAAR 89


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.324    0.137    0.390 

Gapped
Lambda     K      H
   0.267   0.0606    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,379,218
Number of extensions: 53820
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 20
Length of query: 207
Length of database: 4,956,049
Length adjustment: 84
Effective length of query: 123
Effective length of database: 2,116,429
Effective search space: 260320767
Effective search space used: 260320767
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: 52 (24.1 bits)