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)