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)