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)