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)