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)