RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|255764498|ref|YP_003065000.2| site-specific tyrosine recombinase XerD [Candidatus Liberibacter asiaticus str. psy62] (300 letters) >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 = 149 bits (377), Expect = 5e-37 Identities = 105/286 (36%), Positives = 169/286 (59%), Gaps = 7/286 (2%) Query: 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60 + E+ + NTL+AY+RDL M +L+++ ++L+ A ++ L + L + +S Sbjct: 12 ALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSA 71 Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPA 120 R +S +R+ + +L E R+D+PS L PK LPK L + + + + P Sbjct: 72 RLLSAVRRLFQYLYREKFREDDPSAHLASPKLPQRLPKDLSEAQV-------ERLLQAPL 124 Query: 121 PGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSAL 180 Q +R ++E+LYATG+RVSELV L+ ++L + + + GKGNKERLV L A+ Sbjct: 125 IDQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVVRVIGKGNKERLVPLGEEAV 184 Query: 181 HALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 + L+ Y + + G + + S + ++RQ F +K A AGI + +SPH++ Sbjct: 185 YWLETYLEHGRPWLLNGVSIDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVL 244 Query: 241 RHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQ 286 RHAFA+HLL GADLR +Q+LLGH+D+STTQIYTH+ ++L++L Q Sbjct: 245 RHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQ 290 >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 = 138 bits (347), Expect = 2e-33 Identities = 33/308 (10%), Positives = 86/308 (27%), Gaps = 22/308 (7%) Query: 1 MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60 M +A S +T + + A + YL +L R L + + Sbjct: 11 MFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQ 70 Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHIL--PKTLHKDTIANLLEQAKIEAEN 118 + + + + N + + + + + + ++ + Sbjct: 71 QHLGQLNMLHRRSGLPRPSDSNAVSLVMRRIRKENVDAGERAKQALAFERTDFDQVRSLM 130 Query: 119 PAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQ-------GKGNKER 171 + + +R + + Y T ++++E+ + ++ T+ ++ Sbjct: 131 ENSDRCQDIRNLAFLGIAYNTLLKIAEIARIRVKDISRTDGGRMLIHIGRTKTLVSTAGV 190 Query: 172 LVILSPSALHALQMYKK-------------TCSSMKMTGNDLWLFPSSTKTGHLSRQVFA 218 LS ++ + ST+ + Sbjct: 191 EKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVAAPSATSQLSTRALEGIFEATH 250 Query: 219 RDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLP 278 R + +G + S H R A + G + I G T+++ Y L Sbjct: 251 RLIYGAKDDSGQRYLAWSGHSARVGAARDMARAGVSIPEIMQAGGWTNVNIVMNYIRNLD 310 Query: 279 DKLQKLVQ 286 + +V+ Sbjct: 311 SETGAMVR 318 >2a3v_A Site-specific recombinase INTI4; protein-DNA complex, recombination; HET: DNA; 2.80A {Vibrio cholerae o1 biovar eltor str} Length = 320 Score = 125 bits (313), Expect = 1e-29 Identities = 65/303 (21%), Positives = 120/303 (39%), Gaps = 25/303 (8%) Query: 5 ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLS-QRKLVTSSQRRKI 63 R + T+ AY + +F N K SL + +L +L+ Q K+ T +Q + Sbjct: 15 TRYYAKKTIEAYLHWITRYIHFHNKKHPSL--MGDKEVEEFLTYLAVQGKVATKTQSLAL 72 Query: 64 SVIRQFYNFLCYEGLRKDNPSDTLELPKKNHIL-----------PKTLHKDTIANLLEQA 112 + + Y + L + +L +K ++ LL + Sbjct: 73 NSLSFLYKEILKTPLSLEIRFQRSQLERKLPVVLTRDEIRRLLEIVDPKHQLPIKLLYGS 132 Query: 113 KIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERL 172 + + + + ++ + VTL+ + + + + L Sbjct: 133 GLRLMECMRLRVQDIDFDYGAIRIWQGKGGKNRTVTLAKELYPHLKEQIALAKRYYDRDL 192 Query: 173 VILSPSALHALQMYKKTCSSMKMTGNDLWLFPS----------STKTGHLSRQVFARDLK 222 + + K+ + +LFPS + H++ V + ++ Sbjct: 193 HQKNYGGVWLPTALKEKYPNAPYEFRWHYLFPSFQLSLDPESDVMRRHHMNETVLQKAVR 252 Query: 223 ALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQ 282 A AGI+K ++ H +RH+FA+HLLE GAD+RT+Q LGHTD+ TTQIYTH+L Sbjct: 253 RSAQEAGIEKT-VTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQIYTHVLDRGAS 311 Query: 283 KLV 285 ++ Sbjct: 312 GVL 314 >3nkh_A Integrase; alpha-fold, MRSA protein, structural genomics, PSI-2, protei structure initiative; 2.50A {Staphylococcus aureus subsp} Length = 244 Score = 106 bits (265), Expect = 6e-24 Identities = 46/227 (20%), Positives = 91/227 (40%), Gaps = 28/227 (12%) Query: 87 LELPKKNHILPKT--LHKDTIANLLEQAKIEAENPAPGQWKRVRIF--LLIELLYATGMR 142 ++L +N L + I ++++ +A+ G KR +F L+ E GMR Sbjct: 11 VDLGTENLYFQSNAYLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMR 70 Query: 143 VSELVTLSAHTLNLTERTMIIQG-------------------KGNKERLVILSPSALHAL 183 + E++ + ++ +++ I G + R + LS + L Sbjct: 71 IGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGGFGVKDTTKTESSYRTIGLSSRSCEIL 130 Query: 184 QMYKKTCSSMKMTGN---DLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHII 240 + + + ++ K + + F + L+ A GI K +S HI+ Sbjct: 131 KKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDK-EVSSHIL 189 Query: 241 RHAFASHLLEGGADLRTIQILLGHTDISTT-QIYTHLLPDKLQKLVQ 286 RH+ S L + G L+ I +GH+D TT IY+H+ + ++ Sbjct: 190 RHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQMDKDMMN 236 >1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA complex; HET: PTR; 2.80A {Enterobacteria phage lambda} PDB: 1p7d_A* Length = 283 Score = 91.5 bits (225), Expect = 2e-19 Identities = 40/281 (14%), Positives = 83/281 (29%), Gaps = 15/281 (5%) Query: 4 SERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKI 63 + R TL Y +K ++ L + L +T + + LN S++ + Sbjct: 15 ASRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGYIDEGKAASAKLIRS 72 Query: 64 SVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQ 123 ++ F + NH+ K + A + + Sbjct: 73 TLSDAFREAIAEG------------HITTNHVAATRAAKSKVRRSRLTADEYLKIYQAAE 120 Query: 124 WKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHAL 183 + L +EL TG RV +L + + + G K + + Sbjct: 121 SSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGI 180 Query: 184 QMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHA 243 M + ++ G + + + + A+ + + H +R Sbjct: 181 SMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRS- 239 Query: 244 FASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKL 284 ++ L E + Q LLGH + Y + K+ Sbjct: 240 LSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKI 280 >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 = 83.8 bits (205), Expect = 4e-17 Identities = 45/284 (15%), Positives = 87/284 (30%), Gaps = 19/284 (6%) Query: 4 SERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKI 63 + R TL Y +K ++ L + L +T + + LN +S + Sbjct: 88 ASRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGYIDEGK-AASAKLIR 144 Query: 64 SVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQ 123 S + + EG N K + + + + Sbjct: 145 STLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKI-----------YQAAE 193 Query: 124 WKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHAL 183 + L +EL TG RV +L + + + G K + + Sbjct: 194 SSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGI 253 Query: 184 QMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKK--NISPHIIR 241 M + ++ G + + ST+ LS +R +G+ + + H +R Sbjct: 254 SMKETLDKCKEILGGETIIA--STRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELR 311 Query: 242 HAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV 285 ++ L E + Q LLGH + Y + K+ Sbjct: 312 S-LSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIE 354 >3nrw_A Phage integrase/site-specific recombinase; alpha-helical domain, structural genomics, PSI-2, protein ST initiative; 1.70A {Haloarcula marismortui} Length = 117 Score = 70.1 bits (171), Expect = 6e-13 Identities = 7/88 (7%), Positives = 36/88 (40%), Gaps = 1/88 (1%) Query: 5 ERASSINTLSAYKRDLKEMQNFLNNKEI-SLSAASTNHLISYLNHLSQRKLVTSSQRRKI 63 + ++ ++ +++ LK + ++I ++ + L Y + ++ ++ Sbjct: 21 QTDAADASIKSFRYRLKHFVEWAEERDITAMRELTGWKLDEYETFRRGSDVSPATLNGEM 80 Query: 64 SVIRQFYNFLCYEGLRKDNPSDTLELPK 91 ++ + +L + ++ + + +P Sbjct: 81 QTLKNWLEYLARIDVVDEDLPEKVHVPT 108 >1ae9_A Lambda integrase; DNA recombination, site-specific recombination; 1.90A {Bacteriophage lambda} SCOP: d.163.1.1 Length = 179 Score = 69.5 bits (168), Expect = 9e-13 Identities = 26/158 (16%), Positives = 50/158 (31%), Gaps = 1/158 (0%) Query: 128 RIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYK 187 + L +EL TG RV +L + + + G K + + K Sbjct: 22 WLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVK-IAIPTALHIDALGISMK 80 Query: 188 KTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASH 247 +T K + S+ + S V ++A A + + + ++ Sbjct: 81 ETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSAR 140 Query: 248 LLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLV 285 L E + Q LLGH + + + K+ Sbjct: 141 LYEKQISDKFAQHLLGHKSDTMASQFRDDRGREWDKIE 178 >1aih_A HP1 integrase; DNA integration, recombination; 2.50A {Bacteriophage HP1} SCOP: d.163.1.1 Length = 170 Score = 69.0 bits (167), Expect = 1e-12 Identities = 37/177 (20%), Positives = 65/177 (36%), Gaps = 24/177 (13%) Query: 120 APGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLTERTMIIQGKGNKERLVILSPSA 179 + + L++ + ATG R SE TL+ + + T K K R V +S Sbjct: 18 ECDNSRNPDLGLIVRICLATGARWSEAETLTQSQVMPYKITFT-NTKSKKNRTVPISDEL 76 Query: 180 LHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHI 239 L + + + + K H+ Sbjct: 77 FDMLPKKRGRLFNDAYESFENAVLR----------------------AEIELPKGQLTHV 114 Query: 240 IRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLLPDKLQKLVQDYHPLAKKEK 296 +RH FASH + G ++ ++ +LGH+ I T Y H P L+ V+ ++PL+ + Sbjct: 115 LRHTFASHFMMNGGNILVLKEILGHSTIEMTMRYAHFAPSHLESAVK-FNPLSNPAQ 170 >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 = 63.4 bits (154), Expect = 6e-11 Identities = 53/297 (17%), Positives = 98/297 (32%), Gaps = 138/297 (46%) Query: 13 LSAYKRDL--KEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVI--RQ 68 LS +L +++Q+++N TN HL ++ +IS++ + Sbjct: 339 LSI--SNLTQEQVQDYVN---------KTNS------HLPA------GKQVEISLVNGAK 375 Query: 69 FYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVR 128 N + G P +L + L TL K + L+Q++I P ++++ Sbjct: 376 --NLVV-SG-----PPQSL------YGLNLTLRKAKAPSGLDQSRI------PFSERKLK 415 Query: 129 I---FLLIELLYATGMRVSELVTLSA--HTLNLTERTMIIQGKGNKERLVILSPSALHAL 183 FL + ++ H+ L + +I + LV Sbjct: 416 FSNRFLPV----------------ASPFHSHLLVPASDLI-----NKDLV---------- 444 Query: 184 QMYKKTCSSMKMTGNDLWLFPS-STKTGHLSRQVFARDLKALAARAGIQKKNISPHIIR- 241 +++ D+ P T G DL+ L+ +IS I+ Sbjct: 445 ------KNNVSFNAKDI-QIPVYDTFDG--------SDLRVLSG-------SISERIVDC 482 Query: 242 ------H-----AF-ASHLLE---GGA-----------D---LRTIQILLGHTDIST 269 F A+H+L+ GGA D +R I+ G DI+ Sbjct: 483 IIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRV--IVAGTLDINP 537 Score = 55.7 bits (134), Expect = 1e-08 Identities = 45/251 (17%), Positives = 72/251 (28%), Gaps = 97/251 (38%) Query: 20 LKEMQ-NFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGL 78 L E + +L +I H + L Q T + +++ I+ + Sbjct: 88 LTEFENCYLEGNDI--------H--ALAAKLLQENDTTLVKTKEL--IKNYITARIMAKR 135 Query: 79 RKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLI----- 133 D S++ L ++ + Sbjct: 136 PFDKKSNSA--------------------LFRAVGEG----------NAQLVAIFGGQGN 165 Query: 134 ------EL--LYAT--GMRVSELVTLSAHTLN----LTERTMIIQGKGNKERLVILS--- 176 EL LY T + V +L+ SA TL+ T + +G L IL Sbjct: 166 TDDYFEELRDLYQTYHVL-VGDLIKFSAETLSELIRTTLDAEKVFTQG----LNILEWLE 220 Query: 177 -----P------SA-----LHAL-QM--YKKTCSSMKMTGNDLWLFPSSTKTGHLSRQ-- 215 P S L + Q+ Y T + T +L + TGH S Q Sbjct: 221 NPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA-TGH-S-QGL 277 Query: 216 VFARDLKALAA 226 V A A+A Sbjct: 278 VTA---VAIAE 285 Score = 46.9 bits (111), Expect = 5e-06 Identities = 50/269 (18%), Positives = 78/269 (28%), Gaps = 93/269 (34%) Query: 34 LSAASTNHLISYLNH--LSQRKLVTSSQRRKISVIR-QFYNFL--CYEGLRKDN-PSDTL 87 + A ST L L+H L LV ++ S ++ QF L EG D+ P+ Sbjct: 1 MDAYSTRPLT--LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA 58 Query: 88 ELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELV 147 EL + L E GQ ++L L Sbjct: 59 EL---------------VGKFLGYVSSLVEPSKVGQ--------FDQVL--------NLC 87 Query: 148 TLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSST 207 L E L + +HAL + + Sbjct: 88 ------LTEFENC-------------YLEGNDIHAL------AAKL----------LQEN 112 Query: 208 KTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTI---QILLGH 264 T + + ++ + AR ++ A + EG A L I Q G+ Sbjct: 113 DTTLVKTKELIKN--YITARIMAKRP--FDKKSNSALFRAVGEGNAQLVAIFGGQ---GN 165 Query: 265 TDISTTQIYTHLLPDKLQKLVQDYHPLAK 293 TD + ++L+ L Q YH L Sbjct: 166 TD-------DYF--EELRDLYQTYHVLVG 185 Score = 44.9 bits (106), Expect = 2e-05 Identities = 51/308 (16%), Positives = 88/308 (28%), Gaps = 146/308 (47%) Query: 21 KEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVI------RQFYNFLC 74 E++++L +T H SQ LVT+ I F+ Sbjct: 261 GELRSYL--------KGATGH--------SQ-GLVTAV------AIAETDSWESFF---- 293 Query: 75 YEGLRKDNPSDTLEL------------PKKNHILPKTLHKDTIANLLEQAKIEAE-NPAP 121 + + + P + LP ++ +D++ N E P+P Sbjct: 294 ------VSVRKAITVLFFIGVRCYEAYPNTS--LPPSILEDSLEN--------NEGVPSP 337 Query: 122 GQWKRVRIFLLIELLYATGMRVSELVTLSAHT---LNLTERTMI--IQGKGNKERLVIL- 175 +L + + ++ T L ++ I + G N LV+ Sbjct: 338 -------------MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN---LVVSG 381 Query: 176 SPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNI 235 P +L+ L +L L R KA +G+ + I Sbjct: 382 PPQSLYGL---------------NLTL----------------RKAKA---PSGLDQSRI 407 Query: 236 SPH-----IIRH-------AFASHLLEGGADLRTIQIL--LGHTDISTTQIYTHLLPDKL 281 P + F SHLL +DL I L ++S + Sbjct: 408 -PFSERKLKFSNRFLPVASPFHSHLLVPASDL----INKDLVKNNVS-------FNAKDI 455 Query: 282 QKLVQDYH 289 Q V Y Sbjct: 456 QIPV--YD 461 >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 = 20/86 (23%), Positives = 31/86 (36%), Gaps = 1/86 (1%) Query: 9 SINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQ 68 I T K L I L+ ++ H+ +Y+N L L + + I VIR Sbjct: 24 GIQTAKVLKGYLNSRIIPSLGN-IKLAKLTSLHMQNYVNSLRDEGLKRGTIEKIIKVIRN 82 Query: 69 FYNFLCYEGLRKDNPSDTLELPKKNH 94 L N + +LPK + Sbjct: 83 SLEHAIDLELITKNVAAKTKLPKADK 108 >2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA binding protein; 2.00A {Unidentified phage} Length = 103 Score = 47.1 bits (111), Expect = 5e-06 Identities = 16/88 (18%), Positives = 28/88 (31%), Gaps = 3/88 (3%) Query: 4 SERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKI 63 + R TL Y +K ++ L + L +T + + LN +S + Sbjct: 15 ASRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGYIDEG-KAASAKLIR 71 Query: 64 SVIRQFYNFLCYEGLRKDNPSDTLELPK 91 S + + EG N K Sbjct: 72 STLSDAFREAIAEGHITTNHVAATRAAK 99 >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 = 43.4 bits (101), Expect = 7e-05 Identities = 13/87 (14%), Positives = 28/87 (32%), Gaps = 1/87 (1%) Query: 5 ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64 + +T +Y+ L+ I L + + L + R Sbjct: 22 KPHLRQSTWESYETVLRLHVIPTLGS-IPLKKLQPADIQRLYASKLESGLSPTRVRYIHV 80 Query: 65 VIRQFYNFLCYEGLRKDNPSDTLELPK 91 V+ + + GL NP++ + P+ Sbjct: 81 VLHEAMSQARESGLLLQNPTEAAKPPR 107 >2kiw_A INT protein; alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus haemolyticus JCSC1435} Length = 111 Score = 42.9 bits (100), Expect = 8e-05 Identities = 12/84 (14%), Positives = 34/84 (40%), Gaps = 3/84 (3%) Query: 9 SINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQ 68 ++++ A ++ ++ N K I + +++ +S + + ++ Sbjct: 18 KVSSVRAREKAIQHAIERFNTKPIQ--TIKKHDYQRFVDDISAQY-SKNYVDSIVASTNM 74 Query: 69 FYNFLCYEGLRKDNPSDTLELPKK 92 + + L K PS+ ++ PKK Sbjct: 75 IFKYAYDTRLIKAMPSEGIKRPKK 98 >2key_A Putative phage integrase; protein structure, PSI, NESG, structural genomics, unknown function, protein structure initiative; NMR {Bacteroides fragilis nctc 9343} Length = 112 Score = 42.5 bits (99), Expect = 1e-04 Identities = 11/85 (12%), Positives = 29/85 (34%), Gaps = 1/85 (1%) Query: 5 ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64 R I T +K +++ + + + + S+ +R +S Sbjct: 22 SRRLEIGTFRHHKSCMRKFKEYCEGLQFH-ELTEDFLRDYLIYMKKTLCNADSTAQRNLS 80 Query: 65 VIRQFYNFLCYEGLRKDNPSDTLEL 89 I+ + + +G +++P L Sbjct: 81 TIKIYVSAAIKKGYMENDPFKDFGL 105 >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 = 34.8 bits (80), Expect = 0.021 Identities = 13/84 (15%), Positives = 32/84 (38%), Gaps = 3/84 (3%) Query: 9 SINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQ 68 T Y++ LK ++ ++ N +S + + LN ++ +S + + +R Sbjct: 25 DEMTYKGYEQTLKYLKTYMPNVL--ISEITASSYQRALNKFAETH-AKASTKGFHTRVRA 81 Query: 69 FYNFLCYEGLRKDNPSDTLELPKK 92 L EG + + + + Sbjct: 82 SIQCLIEEGRLQKDFTTRAVVKGL 105 >2kob_A Uncharacterized protein; alpha beta, structural genomics, PSI-2, protein structure initiative; NMR {Clostridium leptum dsm 753} Length = 108 Score = 32.7 bits (73), Expect = 0.096 Identities = 8/47 (17%), Positives = 20/47 (42%) Query: 45 YLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPK 91 + +++ KL ++ + + Q + NP+D + +PK Sbjct: 52 IQSIINETKLAKNTLKAIRNTASQIFRLAIENRAIDFNPADYVRIPK 98 >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 = 32.3 bits (72), Expect = 0.13 Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 20/48 (41%) Query: 184 QMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQ 231 Q KK +S+K+ +D S+ ALA +A ++ Sbjct: 20 QALKKLQASLKLYADD-----SA---------------PALAIKATME 47 Score = 31.1 bits (69), Expect = 0.32 Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 16/42 (38%) Query: 102 KDTIANLLEQA--KIEAENPAPGQWKRVRIFLLIELLYATGM 141 K + L QA K+ A++ AP L I+ AT M Sbjct: 19 KQALKKL--QASLKLYADDSAPA--------LAIK---AT-M 46 >1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A {Saccharomyces cerevisiae} SCOP: e.15.1.1 Length = 223 Score = 29.3 bits (66), Expect = 1.1 Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 1/41 (2%) Query: 88 ELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVR 128 PK + + +D + NL + A + P +W +R Sbjct: 158 AHPKTGKLKRRVNPEDIVLNLSKDAPVP-PAPEGHKWGEIR 197 >2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; NMR {Staphylococcus saprophyticus subsp} Length = 110 Score = 28.7 bits (63), Expect = 1.7 Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 3/88 (3%) Query: 5 ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64 S +T Y+ K +++ +K + + + R+ S Sbjct: 17 LPHVSESTKRHYESAYKHIKDHFRHKLLK---DIKRTEYQKFLNEYGLTHSYETIRKLNS 73 Query: 65 VIRQFYNFLCYEGLRKDNPSDTLELPKK 92 IR ++ +EG NP+ EL Sbjct: 74 YIRNAFDDAIHEGYVIKNPTYKAELHAS 101 >2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA complex; HET: DNA; 2.27A {Leishmania donovani} Length = 432 Score = 28.2 bits (63), Expect = 2.1 Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 1/41 (2%) Query: 88 ELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVR 128 + P + + +D N+ E A++ PA +W V+ Sbjct: 168 KHPLMGKLKVRVQPEDITINIGETAEVP-VPPAGHKWAAVQ 207 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 28.2 bits (62), Expect = 2.2 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 5/59 (8%) Query: 75 YEGLRKDNPSDTLELPKKNHILPKTLHKDTIANLLEQAKIEAEN-PAPGQWKRVRIFLL 132 + ++ +P+ ++ K+ + + KD + N LE K+EAE P+ Q + FLL Sbjct: 1234 HSSVKYASPNLNMKYRKRQLVTREAQIKDWVENELEALKLEAEEIPSEDQNE----FLL 1288 >2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis, malonyl/palmitoyl transferase, phosphopantetheine, transferase; HET: GVL FMN; 3.10A {Saccharomyces cerevisiae} PDB: 2vkz_A* 3hmj_A* Length = 1887 Score = 27.0 bits (59), Expect = 5.3 Identities = 8/41 (19%), Positives = 16/41 (39%) Query: 92 KNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLL 132 + I+P + D + +LEQ + + VR + Sbjct: 1601 NSGIIPGNRNADNVDKILEQFEYVLYPSKTLKTDGVRAVSI 1641 >2uv9_A Fatty acid synthase alpha subunits; fungal, dehydratase, enoyl reductase, ketoacyl synthase, ketoacyl reductase; 3.1A {Thermomyces lanuginosus} PDB: 2uvb_A* Length = 1878 Score = 26.9 bits (59), Expect = 6.3 Identities = 6/41 (14%), Positives = 15/41 (36%) Query: 92 KNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLL 132 I+P + D + ++EQ + ++ F + Sbjct: 1582 NTGIVPGNRNADNVDKVMEQFDYIVYPSRSIKTDGIKAFSV 1622 >3fhd_A ORF 37; enase like PD-(D/E)XK superfamily, hydrolase; 1.85A {Human herpesvirus 8 type M} Length = 508 Score = 26.4 bits (58), Expect = 7.3 Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 20/102 (19%) Query: 180 LHALQMYKKTCSSMKMTGNDLWLFPSST---KTGH---------LSRQVFARDLKALAAR 227 L + +YKK S+M+ T LF L+ F++ LK R Sbjct: 10 LESTSLYKKAGSAMEATPTPADLFSEDYLVDTLDGLTVDDQQAVLASLSFSKFLKHAKVR 69 Query: 228 AGIQKKNISPHI--IRHAFASHLLEGGADLRTIQILLGHTDI 267 + I P + +R A+ L + +G D+ Sbjct: 70 DWCAQAKIQPSMPALRMAYNYFL------FSKVGEFIGSEDV 105 >1edy_A Alpha 1-macroglobulin; beta sandwich, pseudo-symmetric dimer, protein binding; 2.30A {Rattus norvegicus} SCOP: b.2.4.1 Length = 134 Score = 26.4 bits (58), Expect = 7.7 Identities = 7/45 (15%), Positives = 21/45 (46%) Query: 10 INTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKL 54 + +S + ++ + I + +TNH++ Y+ L+ + + Sbjct: 46 VKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVLIYIEKLTNQTM 90 >1a31_A Protein (topoisomerase I); topoisomerase I/DNA, topoisomerase I; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP: d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A* 1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A* 1lpq_A* 1rr8_C* 1ej9_A* Length = 591 Score = 26.3 bits (58), Expect = 8.6 Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%) Query: 88 ELPKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVR 128 PK + + + +D I N + AK+ P +WK VR Sbjct: 192 NHPKMGMLKRRIMPEDIIINCSKDAKVP-SPPPGHKWKEVR 231 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 0.318 0.131 0.369 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: 2,365,224 Number of extensions: 104291 Number of successful extensions: 350 Number of sequences better than 10.0: 1 Number of HSP's gapped: 329 Number of HSP's successfully gapped: 41 Length of query: 300 Length of database: 5,693,230 Length adjustment: 92 Effective length of query: 208 Effective length of database: 3,462,782 Effective search space: 720258656 Effective search space used: 720258656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (25.8 bits)