RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780134|ref|YP_003064547.1| phage-related integrase/recombinase [Candidatus Liberibacter asiaticus str. psy62] (348 letters) >1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 3.80A {Enterobacteria phage lambda} SCOP: d.10.1.4 d.163.1.1 PDB: 1z1g_A 1kjk_A 2wcc_3* Length = 356 Score = 68.0 bits (164), Expect = 3e-12 Identities = 65/349 (18%), Positives = 120/349 (34%), Gaps = 25/349 (7%) Query: 7 LPPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTF---IPAYMSALTGSTPKREYINS 63 LPP + R+ Y G+ L I A + +G K Sbjct: 12 LPPNLYI---RNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARI 68 Query: 64 PRKKPTTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGV 123 TL + Y K + + I++ S I R D ITTK I + + Sbjct: 69 NSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAML 128 Query: 124 ESR--KHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQ 181 + +SA +++ F+ A+ + ++ N + K K R E ++ Sbjct: 129 NGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKI 188 Query: 182 FKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGF 241 +++ S RLA E + +G R D C + + ++ KTG I + Sbjct: 189 YQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHI 248 Query: 242 MKLLA---------MTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNK-----SAH 287 L +G ET + ++ +++ S +F +G++ + H Sbjct: 249 DALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFH 308 Query: 288 GVRKFSATISADAGATAHELMATYGWKTVDQAETYTK--GADRIRLGIK 334 +R SA + + + G K+ A Y G + ++ IK Sbjct: 309 ELRSLSARL-YEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 356 >1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Length = 283 Score = 60.7 bits (145), Expect = 5e-10 Identities = 54/283 (19%), Positives = 104/283 (36%), Gaps = 19/283 (6%) Query: 70 TLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESR--K 127 TL + Y K + + I++ S I R D ITTK I + + + Sbjct: 2 TLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDE 61 Query: 128 HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWS 187 +SA +++ F+ A+ + ++ N + K K R E ++ +++ S Sbjct: 62 GKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKIYQAAES 121 Query: 188 EGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLA- 246 RLA E + +G R D C + + ++ KTG I + L Sbjct: 122 SPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGIS 181 Query: 247 --------MTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNK-----SAHGVRKFS 293 +G ET + ++ +++ S +F +G++ + H +R S Sbjct: 182 MKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLS 241 Query: 294 ATISADAGATAHELMATYGWKTVDQAETYTK--GADRIRLGIK 334 A + + + G K+ A Y G + ++ IK Sbjct: 242 ARL-YEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 283 >2kiw_A INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435} Length = 111 Score = 49.8 bits (118), Expect = 8e-07 Identities = 19/100 (19%), Positives = 42/100 (42%), Gaps = 3/100 (3%) Query: 70 TLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVE--SRK 127 T K + ++ K + + V+S + E I + + I + V+ S + Sbjct: 1 TFKQVADDWLKQ-YANDVKVSSVRAREKAIQHAIERFNTKPIQTIKKHDYQRFVDDISAQ 59 Query: 128 HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRK 167 ++ + + S ++FK+A + P ++RPK+K Sbjct: 60 YSKNYVDSIVASTNMIFKYAYDTRLIKAMPSEGIKRPKKK 99 >2kd1_A DNA integration/recombination/invertion protein; protein structure initiative, structural genomics, unknown function, PSI-2; HET: DNA; NMR {Bacillus cereus atcc 14579} Length = 118 Score = 48.6 bits (115), Expect = 2e-06 Identities = 16/102 (15%), Positives = 40/102 (39%), Gaps = 5/102 (4%) Query: 70 TLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKS-GDFDYRKITTKHIRSGVESRKH 128 + + + + S+ + + + Y + I S G+ K+T+ H+++ V S + Sbjct: 7 SYGEYLESWFNT-KRHSVGIQTAKVLKGYLNSRIIPSLGNIKLAKLTSLHMQNYVNSLRD 65 Query: 129 T---PSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRK 167 + + + +R + A+ E + N + PK Sbjct: 66 EGLKRGTIEKIIKVIRNSLEHAIDLELITKNVAAKTKLPKAD 107 >2kob_A Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} Length = 108 Score = 47.0 bits (110), Expect = 6e-06 Identities = 17/101 (16%), Positives = 37/101 (36%) Query: 69 TTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKH 128 + ++ KS ++V+ S+++Y + +I I+S + K Sbjct: 2 DSFGDWAEKFLKSKEADGVSVSQLNSYKNYCRNHLSPLYMKSLSEILPADIQSIINETKL 61 Query: 129 TPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTE 169 ++ + +F+ A+ + NP V PK E Sbjct: 62 AKNTLKAIRNTASQIFRLAIENRAIDFNPADYVRIPKIALE 102 >2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage} Length = 103 Score = 45.6 bits (107), Expect = 2e-05 Identities = 20/100 (20%), Positives = 39/100 (39%), Gaps = 2/100 (2%) Query: 70 TLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVES--RK 127 TL + Y K + + I++ S I R D ITTK I + + + Sbjct: 2 TLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDE 61 Query: 128 HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRK 167 +SA +++ F+ A+ + ++ N + K + Sbjct: 62 GKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSE 101 >2kkp_A Phage integrase; SAM-like domain, alpha-helical bundle, structural genomics, PSI-2, protein structure initiative; NMR {Moorella thermoacetica atcc 39073} Length = 117 Score = 44.9 bits (105), Expect = 2e-05 Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 4/105 (3%) Query: 69 TTLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKS-GDFDYRKITTKHIRSGVESRK 127 T++ ++ + L ++ S+E+ + + G +K+ I+ S+ Sbjct: 7 ITVEQWLNRWLTDYAKPHLRQSTWESYETVLRLHVIPTLGSIPLKKLQPADIQRLYASKL 66 Query: 128 HTPSSAIQF---LTSMRVLFKWAVRQEYVAINPCLSVERPKRKTE 169 + S + + A + NP + + P+ E Sbjct: 67 ESGLSPTRVRYIHVVLHEAMSQARESGLLLQNPTEAAKPPRHPLE 111 >2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp} Length = 110 Score = 42.2 bits (98), Expect = 2e-04 Identities = 15/102 (14%), Positives = 35/102 (34%), Gaps = 2/102 (1%) Query: 70 TLKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVES--RK 127 T ++ + ++ +++ +ES + I + I + + Sbjct: 3 TFADYFYQWYEVNKLPHVSESTKRHYESAYKHIKDHFRHKLLKDIKRTEYQKFLNEYGLT 62 Query: 128 HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTE 169 H+ + + + +R F A+ + YV NP E E Sbjct: 63 HSYETIRKLNSYIRNAFDDAIHEGYVIKNPTYKAELHASVLE 104 >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 = 41.9 bits (98), Expect = 2e-04 Identities = 68/443 (15%), Positives = 120/443 (27%), Gaps = 172/443 (38%) Query: 6 RLPPFV-TKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPA--------YMSAL---TG 53 +L T I Y + S A A+ G Sbjct: 107 KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV--AIFGGQG 164 Query: 54 STPKREYINSPRKKPTTLKWLISEY--RKSAHWGSLAVNSRISFESYFDQIIRKSGDFDY 111 +T +Y R T L+ + + L + + E F Q G + Sbjct: 165 NT--DDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTT-LDAEKVFTQ-----G-LN- 214 Query: 112 RKITTKHIRSGVESRKHTPSSAIQFLTSMRV------LFKWAVRQEYVAINPCLSVERPK 165 I +E+ +TP +L S+ + + + A V Sbjct: 215 -------ILEWLENPSNTPDKD--YLLSIPISCPLIGVIQLA--HYVVT---A------- 253 Query: 166 RKTEGIRPWTKEDMQQFKSF--WSEG-SQ--------------------PRLAFEFLLYS 202 K G P + +S+ + G SQ R A L + Sbjct: 254 -KLLGFTP------GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFI 306 Query: 203 GLRC--------------SDSCRAG---------VQHLQNNIFSIKT-QKTGTIITV--- 235 G+RC DS + +L + + Q + Sbjct: 307 GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL-----TQEQVQD---YVNKTNS 358 Query: 236 ELPDGFMKLLAMTPIGKETFFINNDKQKMNATQF------------SIWF-KAKATKAGV 282 LP G K + I +N A ++ KAKA +G+ Sbjct: 359 HLPAG--KQVE---IS----LVN------GAKNLVVSGPPQSLYGLNLTLRKAKAP-SGL 402 Query: 283 NKSA--HGVRK--FSAT---ISA--------DAGATAHELMATYG--WKTVDQA----ET 321 ++S RK FS +++ A ++ + + D +T Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDT 462 Query: 322 YTKGADRIRLGIKNSRRISSVVD 344 + G+D +R+ + +VD Sbjct: 463 FD-GSD-LRVLSGSI--SERIVD 481 Score = 38.0 bits (88), Expect = 0.003 Identities = 38/213 (17%), Positives = 62/213 (29%), Gaps = 69/213 (32%) Query: 3 PSLRLPPFVTKERTRHGKIIYYFRKGHGR-----RIR-LPYPHESTFIPAYMSALTGSTP 56 P+ LPP + ++ + G I L ++ S L P Sbjct: 315 PNTSLPPSILEDSLEN---------NEGVPSPMLSISNLTQEQVQDYVNKTNSHL----P 361 Query: 57 --KREYI---NSPRK-----KPTTLKWLISEYRK-SAHWGSLAVN-SRISFESYFDQIIR 104 K+ I N + P +L L RK A G ++ SRI F + R Sbjct: 362 AGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG---LDQSRIP----FSE--R 412 Query: 105 KSGDFDYR--KITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPC-LSV 161 K F R + + H+ L L + + V+ N + + Sbjct: 413 KL-KFSNRFLPVASPF---------HSH-----LLVPASDLINKDLVKNNVSFNAKDIQI 457 Query: 162 ERPKRKTEGIRPWTKEDMQQFKSFWSEGSQPRL 194 P T D++ S R+ Sbjct: 458 --PVYDTF-----DGSDLRVL----SGSISERI 479 Score = 27.6 bits (61), Expect = 4.0 Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 16/80 (20%) Query: 148 VRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEG--------SQPRL----- 194 +R+ Y A+ ++ K KTE I E + +F SE +QP L Sbjct: 1684 IRENYSAM-IFETIVDGKLKTEKIFKEINEHSTSY-TFRSEKGLLSATQFTQPALTLMEK 1741 Query: 195 -AFEFLLYSGLRCSDSCRAG 213 AFE L GL +D+ AG Sbjct: 1742 AAFEDLKSKGLIPADATFAG 1761 Score = 26.8 bits (59), Expect = 8.1 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 19/83 (22%) Query: 231 TIITVELPDGFMKLLAMTPIGKE------TFFINNDKQKMNATQFSIWFKAKATKAGVNK 284 TI+ DG +K I KE ++ ++K ++ATQF+ + + K Sbjct: 1695 TIV-----DGKLK---TEKIFKEINEHSTSYTFRSEKGLLSATQFT-----QPALTLMEK 1741 Query: 285 SAHGVRKFSATISADAGATAHEL 307 +A K I ADA H L Sbjct: 1742 AAFEDLKSKGLIPADATFAGHSL 1764 >3nrw_A Phage integrase/site-specific recombinase; alpha-helical domain, structural genomics, PSI-2, protein ST initiative; 1.70A {Haloarcula marismortui} Length = 117 Score = 40.8 bits (95), Expect = 5e-04 Identities = 8/60 (13%), Positives = 22/60 (36%), Gaps = 3/60 (5%) Query: 109 FDYRKITTKHIRSGVESR---KHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPK 165 R++T + R +P++ + +++ ++ R + V + V P Sbjct: 49 TAMRELTGWKLDEYETFRRGSDVSPATLNGEMQTLKNWLEYLARIDVVDEDLPEKVHVPT 108 >3lys_A Prophage PI2 protein 01, integrase; helical N-terminal domain, structural genomics, PSI-2, protein structure initiative; 2.80A {Lactococcus lactis} Length = 112 Score = 39.8 bits (93), Expect = 0.001 Identities = 11/98 (11%), Positives = 30/98 (30%), Gaps = 7/98 (7%) Query: 72 KWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVESRKHTPS 131 W+ Y+K ++ + +E + + +IT + + T + Sbjct: 14 DWM-ELYKK----NAIDEMTYKGYEQTLKYLKTYMPNVLISEITASSYQRALNKFAETHA 68 Query: 132 --SAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRK 167 S F T +R + + + + + + Sbjct: 69 KASTKGFHTRVRASIQCLIEEGRLQKDFTTRAVVKGLE 106 >1a0p_A Site-specific recombinase XERD; DNA binding, DNA recombination; 2.50A {Escherichia coli} SCOP: a.60.9.1 d.163.1.1 Length = 290 Score = 37.5 bits (85), Expect = 0.005 Identities = 39/261 (14%), Positives = 84/261 (32%), Gaps = 23/261 (8%) Query: 87 LAVNSRISFESYFDQIIR--KSGDFDYRKITTKHIRSGVESRKHTP---SSAIQFLTSMR 141 LA N+ ++ ++ + +++ + R +S+ + L+++R Sbjct: 19 LAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSARLLSAVR 78 Query: 142 VLFKWAVRQEYVAINPCLSVERPKRK----TEGIRPWTKEDMQQFKSFWSEGSQPRLAFE 197 LF++ R+++ +P + PK + + +Q + + E Sbjct: 79 RLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQVERLLQAPLIDQPLELRDKAMLE 138 Query: 198 FLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFI 257 L +GLR S+ + + ++ G + T + ++ Sbjct: 139 VLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWL 198 Query: 258 NNDKQK-----------MNATQFSIWFKAKATKAGVNK---SAHGVRKFSATISADAGAT 303 N M F K A AG++ S H +R AT + GA Sbjct: 199 LNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGAD 258 Query: 304 AHELMATYGWKTVDQAETYTK 324 + G + + YT Sbjct: 259 LRVVQMLLGHSDLSTTQIYTH 279 >1ae9_A Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda} SCOP: d.163.1.1 Length = 179 Score = 36.4 bits (82), Expect = 0.009 Identities = 21/164 (12%), Positives = 44/164 (26%), Gaps = 14/164 (8%) Query: 175 TKEDMQQ-FKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTGTII 233 T ++ + +++ S RLA E + +G R D C + + ++ KTG I Sbjct: 5 TADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKI 64 Query: 234 TVELPDGFMKLLAMTPIGKETFFINNDKQ-------------KMNATQFSIWFKAKATKA 280 + L + + + F KA Sbjct: 65 AIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSF 124 Query: 281 GVNKSAHGVRKFSATISADAGATAHELMATYGWKTVDQAETYTK 324 + + + + + G K+ A + Sbjct: 125 EGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQFRD 168 >2kj5_A Phage integrase; GFT NMR, PSI-2, NESG, structural genomics, protein structure initiative; NMR {Nitrosospira multiformis atcc 25196} Length = 116 Score = 35.5 bits (81), Expect = 0.017 Identities = 21/104 (20%), Positives = 39/104 (37%), Gaps = 7/104 (6%) Query: 66 KKPTTLKWLISEY--RKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGV 123 K T+ L EY R A R E I G + +HI + Sbjct: 4 KNAYTVAQLADEYFERMIAGRWKHPNIVRSRIEKD---IKPAIGSLKVEDVKPRHIDDVL 60 Query: 124 ES--RKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPK 165 ++ ++ PS A L ++ +F +A+++ + NP + + Sbjct: 61 KAVMKRGAPSIANDTLRWLKRMFNYAIKRHIIEYNPAAAFDPGD 104 >1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1} SCOP: d.163.1.1 Length = 170 Score = 34.4 bits (77), Expect = 0.041 Identities = 22/159 (13%), Positives = 41/159 (25%), Gaps = 11/159 (6%) Query: 171 IRPWTKEDMQQFKSFWSEGSQP--RLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQK 228 + + D+ + + P L L +G R S++ + + K Sbjct: 4 LAFLYERDIYRLLAECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFTNTK 63 Query: 229 TGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAHG 288 + TV + D +L F + + H Sbjct: 64 SKKNRTVPISDELFDML---------PKKRGRLFNDAYESFENAVLRAEIELPKGQLTHV 114 Query: 289 VRKFSATISADAGATAHELMATYGWKTVDQAETYTKGAD 327 +R A+ G L G T++ Y A Sbjct: 115 LRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAP 153 >2key_A Putative phage integrase; protein structure, PSI, NESG, structural genomics, unknown function, protein structure initiative; NMR {Bacteroides fragilis nctc 9343} Length = 112 Score = 33.7 bits (76), Expect = 0.071 Identities = 14/105 (13%), Positives = 42/105 (40%), Gaps = 12/105 (11%) Query: 61 INSPRKKPTTLKWL---ISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTK 117 +N+P + ++ + Y + L + + +S + + ++T Sbjct: 1 MNNPSDFKSFHDFVASYMKTYSRR-----LEIGTFRHHKSCMRKFKEYCEGLQFHELTED 55 Query: 118 HIRSGVESRKH----TPSSAIQFLTSMRVLFKWAVRQEYVAINPC 158 +R + K S+A + L+++++ A+++ Y+ +P Sbjct: 56 FLRDYLIYMKKTLCNADSTAQRNLSTIKIYVSAAIKKGYMENDPF 100 >1xo0_A Recombinase CRE; CRE recombinase, holliday junction, recombination,complex (recombinase/DNA), hydrolase, ligase/DNA complex; 2.00A {Enterobacteria phage P1} SCOP: a.60.9.1 d.163.1.1 PDB: 3crx_A* 1kbu_A 1ma7_A 1q3u_A* 1q3v_A* 2crx_A* 1ouq_A* 1nzb_A* 1xns_A 5crx_A* 1f44_A* 2hof_A 2hoi_A 4crx_A* 1drg_A 3c29_A* 3c28_A 1crx_A* 1pvr_A 1pvq_A ... Length = 324 Score = 33.3 bits (74), Expect = 0.077 Identities = 15/77 (19%), Positives = 24/77 (31%), Gaps = 3/77 (3%) Query: 255 FFINNDKQKMNATQFSIWFKAKATKAGVNK---SAHGVRKFSATISADAGATAHELMATY 311 ++ + +G S H R +A A AG + E+M Sbjct: 235 SQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAG 294 Query: 312 GWKTVDQAETYTKGADR 328 GW V+ Y + D Sbjct: 295 GWTNVNIVMNYIRNLDS 311 >2kj8_A Putative prophage CPS-53 integrase; INTS, INTC, YFDB, DNA integration, DNA recombination, structural genomics, protein structure initiative; NMR {Escherichia coli k-12} Length = 118 Score = 33.5 bits (76), Expect = 0.078 Identities = 15/102 (14%), Positives = 32/102 (31%), Gaps = 9/102 (8%) Query: 72 KWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVE--SRKHT 129 +W E++K A F+ II G + + I + + + Sbjct: 13 EWY--EHKKQVWSVGYATELAKMFDDDILPII---GGLEIQDIEPMQLLEVIRRFEDRGA 67 Query: 130 PSSAIQFLTSMRVLFKWAVRQEYVAINPC--LSVERPKRKTE 169 A + +F++A+ NP L+ + + Sbjct: 68 MERANKARRRCGEVFRYAIVTGRAKYNPAPDLADAMKGYRKK 109 >2kj9_A Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Length = 118 Score = 33.1 bits (75), Expect = 0.11 Identities = 14/84 (16%), Positives = 32/84 (38%), Gaps = 10/84 (11%) Query: 96 ESYFDQIIR--------KSGDFDYRKITTKHIRSGVE--SRKHTPSSAIQFLTSMRVLFK 145 E Y + G+ D ++ T + ++ + A++ + + Sbjct: 29 EDYQRSVWTRLETYLFPDIGNKDIAELDTGDLLVPIKKIEKLGYLEIAMRVKQYATAIMR 88 Query: 146 WAVRQEYVAINPCLSVERPKRKTE 169 +AV+Q+ + NP +E +K E Sbjct: 89 YAVQQKMIRFNPAYDLEGAVQKLE 112 >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 = 32.7 bits (73), Expect = 0.11 Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 4/29 (13%) Query: 284 KSAHGVRKFSATIS--ADAGATAHELMAT 310 K A ++K A++ AD A A + AT Sbjct: 19 KQA--LKKLQASLKLYADDSAPALAIKAT 45 Score = 29.2 bits (64), Expect = 1.2 Identities = 5/25 (20%), Positives = 15/25 (60%), Gaps = 3/25 (12%) Query: 176 KEDMQQFKS---FWSEGSQPRLAFE 197 K+ +++ ++ +++ S P LA + Sbjct: 19 KQALKKLQASLKLYADDSAPALAIK 43 >2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Length = 320 Score = 32.5 bits (72), Expect = 0.17 Identities = 21/97 (21%), Positives = 35/97 (36%), Gaps = 2/97 (2%) Query: 241 FMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNK--SAHGVRKFSATISA 298 + L + + + MN T + A +AG+ K + H +R AT Sbjct: 219 WHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVRRSAQEAGIEKTVTCHTLRHSFATHLL 278 Query: 299 DAGATAHELMATYGWKTVDQAETYTKGADRIRLGIKN 335 + GA + G V + YT DR G+ + Sbjct: 279 EVGADIRTVQEQLGHTDVKTTQIYTHVLDRGASGVLS 315 >2kkv_A Integrase; protein structure, PSI, nesgc, structural genomics, protein structure initiative, northeast structural genomics consortium; NMR {Salmonella enterica subsp} Length = 121 Score = 29.3 bits (65), Expect = 1.3 Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 4/72 (5%) Query: 102 IIRKSGDFDYRKITTKHIRSGVE--SRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCL 159 I G D R++ T H+ + ++ A + + + ++AV+ +Y+ NP Sbjct: 39 IFPHIGSSDIRQLKTSHLLAPIKEVDTSGKHDVAQRLQQRVTAIMRYAVQNDYIDSNPAS 98 Query: 160 SVER--PKRKTE 169 + K Sbjct: 99 DMAGALSTTKAR 110 >2b2a_A Telomerase reverse transcriptase; TERT, RT, transferase; 2.22A {Tetrahymena thermophila} Length = 199 Score = 29.3 bits (65), Expect = 1.5 Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 2/49 (4%) Query: 222 FSIKTQKTGTIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFS 270 F + T+K + T EL F + L T I E + N KQK N FS Sbjct: 47 FLLATEKI--VQTSELDTQFQEFLTTTIIASEQNLVENYKQKYNQPNFS 93 >3nkh_A Integrase; alpha-fold, MRSA protein, structural genomics, PSI-2, protei structure initiative; 2.50A {Staphylococcus aureus subsp} Length = 244 Score = 28.7 bits (63), Expect = 2.1 Identities = 24/168 (14%), Positives = 45/168 (26%), Gaps = 36/168 (21%) Query: 193 RLAFEFLLYSGLRCS-------------------DSCRAGVQHLQNNIFSIKTQKTGTII 233 L EF +G+R + T KT + Sbjct: 58 ALMTEFQALNGMRIGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGGFGVKDTTKTESSY 117 Query: 234 -TVELPD-------------GFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATK 279 T+ L + + F N+ M +F+ + A Sbjct: 118 RTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKD 177 Query: 280 AGVNK--SAHGVRKFSATISADAGATAHELMATYGWKTVDQ-AETYTK 324 G++K S+H +R ++ + G + +M G Y+ Sbjct: 178 VGIDKEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSH 225 >1on0_A YYCN protein; structural genomics, alpha-beta protein with anti-parallel beta strands, PSI, protein structure initiative; 2.20A {Bacillus subtilis} SCOP: d.108.1.1 Length = 158 Score = 28.3 bits (62), Expect = 2.5 Identities = 21/157 (13%), Positives = 48/157 (30%), Gaps = 22/157 (14%) Query: 171 IRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTG 230 + P E+ + + ++ ++ A E + D+ Q + + Sbjct: 5 LTPMQTEEFRSYLTYTTKH----YAEEKVKAGTWLPEDAQLLSKQVFTDLLPRGLETPHH 60 Query: 231 TIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKS----- 285 + +++L + +G + + A + G K Sbjct: 61 HLWSLKLNEK-------DIVGWLWIHAEPEHPQQEAFIYDFGLYEPYRGKGYAKQALAAL 113 Query: 286 -----AHGVRKFSATISADAGATAHELMATYGWKTVD 317 + G+RK S + A TA +L G++ D Sbjct: 114 DQAARSMGIRKLSLHVFAH-NQTARKLYEQTGFQETD 149 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 27.2 bits (59), Expect = 5.9 Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 10/43 (23%) Query: 162 ERPKRKTEGIRPWTKEDMQQFKSF----------WSEGSQPRL 194 +R ++ E IR W +E ++ + W E ++ L Sbjct: 78 DRLTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDL 120 >2waw_A MOBA relate protein; unknown function; HET: PGE; 1.60A {Mycobacterium SP} Length = 199 Score = 26.5 bits (58), Expect = 8.3 Identities = 20/124 (16%), Positives = 31/124 (25%), Gaps = 17/124 (13%) Query: 8 PPFVTKERTRHGKIIYYFRKGHGRRIRLPYPHESTFIPAYMSALTGSTPKREYIN----- 62 + + + G I L + SALT P E I Sbjct: 46 FDQLIVTLGGAADEVLEKVELDGLDIVLVDDAGLGCSSSLKSALTWVDPTAEGIVLMLGD 105 Query: 63 SPRKKPTTLKWLISEYRKSA--------HWGSLAVNSRISFESYFDQIIRKSGDFDYRKI 114 P + + LI+ R + G SR F + GD ++ Sbjct: 106 QPGITASAVASLIAGGRGATIAVCEYANGIGHPFWVSR----GVFGDLAELHGDKGVWRL 161 Query: 115 TTKH 118 Sbjct: 162 IESG 165 >1ufh_A YYCN protein; alpha and beta, fold, acetyltransferase, structural genomics, PSI, protein structure initiative; 2.20A {Bacillus subtilis subsp} SCOP: d.108.1.1 Length = 180 Score = 26.4 bits (57), Expect = 9.6 Identities = 22/157 (14%), Positives = 48/157 (30%), Gaps = 22/157 (14%) Query: 171 IRPWTKEDMQQFKSFWSEGSQPRLAFEFLLYSGLRCSDSCRAGVQHLQNNIFSIKTQKTG 230 + P E+ + + ++ ++ A E + D+ Q + + Sbjct: 29 LTPMQTEEFRSYLTYTTKH----YAEEKVKAGTWLPEDAQLLSKQVFTDLLPRGLETPHH 84 Query: 231 TIITVELPDGFMKLLAMTPIGKETFFINNDKQKMNATQFSIWFKAKATKAGVNKSAH--- 287 + +++L + +G + + A + G K A Sbjct: 85 HLWSLKLNEK-------DIVGWLWIHAEPEHPQQEAFIYDFGLYEPYRGKGYAKQALAAL 137 Query: 288 -------GVRKFSATISADAGATAHELMATYGWKTVD 317 G+RK S + A TA +L G++ D Sbjct: 138 DQAARSMGIRKLSLHVFAH-NQTARKLYEQTGFQETD 173 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 0.320 0.132 0.399 Gapped Lambda K H 0.267 0.0548 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,958,021 Number of extensions: 132897 Number of successful extensions: 342 Number of sequences better than 10.0: 1 Number of HSP's gapped: 334 Number of HSP's successfully gapped: 37 Length of query: 348 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 255 Effective length of database: 3,438,538 Effective search space: 876827190 Effective search space used: 876827190 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 (21.8 bits) S2: 57 (26.1 bits)