RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 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} (A:101-290)
          Length = 190

 Score =  125 bits (315), Expect = 5e-30
 Identities = 81/197 (41%), Positives = 121/197 (61%), Gaps = 7/197 (3%)

Query: 90  PKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTL 149
           PK    LPK L +  +  LL+   I+       Q   +R   ++E+LYATG+RVSELV L
Sbjct: 1   PKLPQRLPKDLSEAQVERLLQAPLID-------QPLELRDKAMLEVLYATGLRVSELVGL 53

Query: 150 SAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKT 209
           +   ++L +  + + GKGNKERLV L   A++ L+ Y +      + G  + +   S + 
Sbjct: 54  TMSDISLRQGVVRVIGKGNKERLVPLGEEAVYWLETYLEHGRPWLLNGVSIDVLFPSQRA 113

Query: 210 GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDIST 269
             ++RQ F   +K  A  AGI  + +SPH++RHAFA+HLL  GADLR +Q+LLGH+D+ST
Sbjct: 114 QQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLST 173

Query: 270 TQIYTHLLPDKLQKLVQ 286
           TQIYTH+  ++L++L Q
Sbjct: 174 TQIYTHVATERLRQLHQ 190


>1ae9_A Lambda integrase; DNA recombination, site-specific
           recombination; 1.90A {Bacteriophage lambda} (A:)
          Length = 179

 Score = 97.9 bits (242), Expect = 1e-21
 Identities = 24/188 (12%), Positives = 53/188 (28%), Gaps = 11/188 (5%)

Query: 98  KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLT 157
             L  D    + + A+               + L +EL   TG RV +L  +    +   
Sbjct: 2   SRLTADEYLKIYQAAE----------SSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDG 51

Query: 158 ERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKTGHLSRQVF 217
              +     G K  +          + M +      ++ G +  +  +  +         
Sbjct: 52  YLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSR 111

Query: 218 ARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQIYTHLL 277
                  A+     + +        + ++ L E     +  Q LLGH   +    +    
Sbjct: 112 YFMRARKASGLSF-EGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQFRDDR 170

Query: 278 PDKLQKLV 285
             +  K+ 
Sbjct: 171 GREWDKIE 178


>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA
           complex; HET: PTR; 3.80A {Enterobacteria phage lambda}
           (A:167-356)
          Length = 190

 Score = 96.7 bits (239), Expect = 3e-21
 Identities = 29/194 (14%), Positives = 59/194 (30%), Gaps = 11/194 (5%)

Query: 90  PKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTL 149
             K+ +    L  D    + + A+               + L +EL   TG RV +L  +
Sbjct: 4   AAKSKVRRSRLTADEYLKIYQAAE----------SSPCWLRLAMELAVVTGQRVGDLCEM 53

Query: 150 SAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKT 209
               +      +     G K  +          + M +      ++ G +  +  S+ + 
Sbjct: 54  KWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGE-TIIASTRRE 112

Query: 210 GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDIST 269
              S  V    ++A  A     + +        + ++ L E     +  Q LLGH   + 
Sbjct: 113 PLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTM 172

Query: 270 TQIYTHLLPDKLQK 283
                     +  K
Sbjct: 173 ASQXRDDRGREWDK 186


>1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA
           complex; HET: PTR; 2.80A {Enterobacteria phage lambda}
           PDB: 1p7d_A* (A:94-283)
          Length = 190

 Score = 96.7 bits (239), Expect = 4e-21
 Identities = 27/198 (13%), Positives = 57/198 (28%), Gaps = 12/198 (6%)

Query: 90  PKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTL 149
             K+ +    L  D    + + A+               + L  EL   TG RV +L   
Sbjct: 4   AAKSKVRRSRLTADEYLKIYQAAESSPC----------WLRLAXELAVVTGQRVGDLCEX 53

Query: 150 SAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSSTKT 209
               +      +     G K  +          +   +      ++ G +  +  S+ + 
Sbjct: 54  KWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISXKETLDKCKEILGGE-TIIASTRRE 112

Query: 210 GHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDIST 269
              S  V     +A  A     + +        + ++ L E     +  Q LLGH   + 
Sbjct: 113 PLSSGTVSRYFXRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTX 172

Query: 270 TQI-YTHLLPDKLQKLVQ 286
                     +  +  ++
Sbjct: 173 ASQXRDDRGREWDKIEIK 190


>1aih_A HP1 integrase; DNA integration, recombination; 2.50A
           {Bacteriophage HP1} (A:1-49,A:87-170)
          Length = 133

 Score = 88.0 bits (218), Expect = 1e-18
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 213 SRQVFARDLKALAARAGIQK-KNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQ 271
                    +    RA I+  K    H++RH FASH +  G ++  ++ +LGH+ I  T 
Sbjct: 50  LFNDAYESFENAVLRAEIELPKGQLTHVLRHTFASHFMMNGGNILVLKEILGHSTIEMTM 109

Query: 272 IYTHLLPDKLQKLVQDYHPLAKKEK 296
            Y H  P  L+  V+ ++PL+   +
Sbjct: 110 RYAHFAPSHLESAVK-FNPLSNPAQ 133


>1xo0_A Recombinase CRE; CRE recombinase, holliday junction,
           recombination,complex (recombinase/DNA), hydrolase,
           ligase/DNA complex; 2.00A {Enterobacteria phage P1}
           (A:1-114)
          Length = 114

 Score = 82.3 bits (203), Expect = 7e-17
 Identities = 12/103 (11%), Positives = 27/103 (26%), Gaps = 1/103 (0%)

Query: 1   MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60
           M    +A S +T        +    +          A    +  YL +L  R L   + +
Sbjct: 11  MFRDRQAFSEHTWKMLLSVCRSWAAWCKLNNRKWFPAEPEDVRDYLLYLQARGLAVKTIQ 70

Query: 61  RKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKD 103
           + +  +   +           N    L + +          + 
Sbjct: 71  QHLGQLNMLHRRSGLPRPSDSNAVS-LVMRRIRKENVDAGERA 112


>1a0p_A Site-specific recombinase XERD; DNA binding, DNA
          recombination; 2.50A {Escherichia coli} (A:1-100)
          Length = 100

 Score = 79.6 bits (196), Expect = 5e-16
 Identities = 26/88 (29%), Positives = 50/88 (56%)

Query: 1  MMSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQR 60
           +  E+  + NTL+AY+RDL  M  +L+++ ++L+ A ++ L + L    +     +S  
Sbjct: 12 ALWLEKNLAENTLNAYRRDLSMMVEWLHHRGLTLATAQSDDLQALLAERLEGGYKATSSA 71

Query: 61 RKISVIRQFYNFLCYEGLRKDNPSDTLE 88
          R +S +R+ + +L  E  R+D+PS  L 
Sbjct: 72 RLLSAVRRLFQYLYREKFREDDPSAHLA 99


>2a3v_A Site-specific recombinase INTI4; protein-DNA complex,
           recombination; HET: DNA; 2.80A {Vibrio cholerae o1
           biovar eltor str} (A:95-144,A:243-320)
          Length = 128

 Score = 77.2 bits (190), Expect = 2e-15
 Identities = 35/80 (43%), Positives = 52/80 (65%), Gaps = 1/80 (1%)

Query: 212 LSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLRTIQILLGHTDISTTQ 271
           ++  V  + ++  A  AGI +K ++ H +RH+FA+HLLE GAD+RT+Q  LGHTD+ TTQ
Sbjct: 50  VNETVLQKAVRRSAQEAGI-EKTVTCHTLRHSFATHLLEVGADIRTVQEQLGHTDVKTTQ 108

Query: 272 IYTHLLPDKLQKLVQDYHPL 291
           IYTH+L      ++     L
Sbjct: 109 IYTHVLDRGASGVLSPLSRL 128



 Score = 46.4 bits (110), Expect = 5e-06
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 13/60 (21%)

Query: 90  PKKNHILPKTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTL 149
            +    LP  L +D I  LLE                 +  L I+LLY +G+R+ E + L
Sbjct: 2   SQLERKLPVVLTRDEIRRLLEIV-------------DPKHQLPIKLLYGSGLRLMECMRL 48


>1xo0_A Recombinase CRE; CRE recombinase, holliday junction,
           recombination,complex (recombinase/DNA), hydrolase,
           ligase/DNA complex; 2.00A {Enterobacteria phage P1}
           (A:115-310)
          Length = 196

 Score = 71.2 bits (172), Expect = 2e-13
 Identities = 19/201 (9%), Positives = 46/201 (22%), Gaps = 28/201 (13%)

Query: 98  KTLHKDTIANLLEQAKIEAENPAPGQWKRVRIFLLIELLYATGMRVSELVTLSAHTLNLT 157
               +     +    +         + + +R    + + Y T ++++E+  +    ++ T
Sbjct: 2   LAFERTDFDQVRSLME------NSDRCQDIRNLAFLGIAYNTLLKIAEIARIRVKDISRT 55

Query: 158 ERTMIIQGK-------GNKERLVILSPS--------------ALHALQMYKKTCSSMKMT 196
           +   ++                  LS                A               + 
Sbjct: 56  DGGRMLIHIGRTKTLVSTAGVEKALSLGVTKLVERWISVSGVADDPNNYLFCRVRKNGVA 115

Query: 197 GNDLWLFPSSTKTGHLSRQVFARDLKALAARAGIQKKNISPHIIRHAFASHLLEGGADLR 256
                   S+     +          A              H  R   A  +   G  + 
Sbjct: 116 APSATSQLSTRALEGIFEATHRLIYGAKDDSGQRYLAWS-GHSARVGAARDMARAGVSIP 174

Query: 257 TIQILLGHTDISTTQIYTHLL 277
            I    G T+++    Y   L
Sbjct: 175 EIMQAGGWTNVNIVMNYIRNL 195


>2kkp_A Phage integrase; SAM-like domain, alpha-helical bundle,
           structural genomics, PSI-2, protein structure
           initiative; NMR {Moorella thermoacetica atcc 39073}
           (A:27-117)
          Length = 91

 Score = 69.5 bits (170), Expect = 4e-13
 Identities = 14/91 (15%), Positives = 28/91 (30%), Gaps = 1/91 (1%)

Query: 11  NTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVIRQFY 70
           +T  +Y+  L+          I L       +        +  L  +  R    V+ +  
Sbjct: 2   STWESYETVLRLHVIPTL-GSIPLKKLQPADIQRLYASKLESGLSPTRVRYIHVVLHEAM 60

Query: 71  NFLCYEGLRKDNPSDTLELPKKNHILPKTLH 101
           +     GL   NP++  + P+         H
Sbjct: 61  SQARESGLLLQNPTEAAKPPRHPLEHHHHHH 91


>2kd1_A DNA integration/recombination/invertion protein; protein
           structure initiative, structural genomics, unknown
           function, PSI-2; HET: DNA; NMR {Bacillus cereus atcc
           14579} (A:)
          Length = 118

 Score = 68.8 bits (168), Expect = 8e-13
 Identities = 20/96 (20%), Positives = 33/96 (34%), Gaps = 1/96 (1%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
             +  I T    K  L           I L+  ++ H+ +Y+N L    L   +  + I 
Sbjct: 20  RHSVGIQTAKVLKGYLNSRIIPSL-GNIKLAKLTSLHMQNYVNSLRDEGLKRGTIEKIIK 78

Query: 65  VIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTL 100
           VIR          L   N +   +LPK +    +  
Sbjct: 79  VIRNSLEHAIDLELITKNVAAKTKLPKADKEELEHH 114


>2a3v_A Site-specific recombinase INTI4; protein-DNA complex,
          recombination; HET: DNA; 2.80A {Vibrio cholerae o1
          biovar eltor str} (A:1-94)
          Length = 94

 Score = 65.7 bits (160), Expect = 7e-12
 Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 5  ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQR-KLVTSSQRRKI 63
           R  +  T+ AY   +    +F N K    S      +  +L +L+ + K+ T +Q   +
Sbjct: 15 TRYYAKKTIEAYLHWITRYIHFHNKK--HPSLMGDKEVEEFLTYLAVQGKVATKTQSLAL 72

Query: 64 SVIRQFYNFLCYEGLRKDNP 83
          + +   Y  +    L  +  
Sbjct: 73 NSLSFLYKEILKTPLSLEIR 92


>2kiw_A INT protein; alpha, structural genomics, PSI-2, protein
           structure initiative, northeast structural genomics
           consortium; NMR {Staphylococcus haemolyticus JCSC1435}
           (A:)
          Length = 111

 Score = 64.6 bits (157), Expect = 2e-11
 Identities = 12/99 (12%), Positives = 36/99 (36%), Gaps = 3/99 (3%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
                ++++ A ++ ++      N K   +     +    +++ +S +    +     ++
Sbjct: 14  ANDVKVSSVRAREKAIQHAIERFNTK--PIQTIKKHDYQRFVDDISAQY-SKNYVDSIVA 70

Query: 65  VIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHKD 103
                + +     L K  PS+ ++ PKK   +    H  
Sbjct: 71  STNMIFKYAYDTRLIKAMPSEGIKRPKKKVSVELEHHHH 109


>2kob_A Uncharacterized protein; alpha beta, structural genomics,
           PSI-2, protein structure initiative; NMR {Clostridium
           leptum dsm 753} (A:)
          Length = 108

 Score = 62.7 bits (152), Expect = 5e-11
 Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 5/97 (5%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
               S++ L++YK   +   + L  K  SLS      + S +N     KL  ++ +   +
Sbjct: 17  ADGVSVSQLNSYKNYCRNHLSPLYMK--SLSEILPADIQSIINE---TKLAKNTLKAIRN 71

Query: 65  VIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLH 101
              Q +           NP+D + +PK         H
Sbjct: 72  TASQIFRLAIENRAIDFNPADYVRIPKIALEHHHHHH 108



 Score = 26.9 bits (59), Expect = 3.7
 Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 5/83 (6%)

Query: 45  YLNHLSQRKLVTSSQRRKISVIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPKTLHK-- 102
           +L       +  S      +  R   + L  + L +  P+D   +  +  +   TL    
Sbjct: 11  FLKSKEADGVSVSQLNSYKNYCRNHLSPLYMKSLSEILPADIQSIINETKLAKNTLKAIR 70

Query: 103 ---DTIANLLEQAKIEAENPAPG 122
                I  L  + +    NPA  
Sbjct: 71  NTASQIFRLAIENRAIDFNPADY 93


>2oxo_A Integrase; DNA-binding protein, four-helix bundle, DNA
           binding protein; 2.00A {Unidentified phage} (A:)
          Length = 103

 Score = 62.3 bits (151), Expect = 8e-11
 Identities = 16/88 (18%), Positives = 27/88 (30%), Gaps = 3/88 (3%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
            R     TL  Y   +K ++  L +    L   +T  + + LN         +S +   S
Sbjct: 16  SRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGYIDE-GKAASAKLIRS 72

Query: 65  VIRQFYNFLCYEGLRKDNPSDTLELPKK 92
            +   +     EG    N        K 
Sbjct: 73  TLSDAFREAIAEGHITTNHVAATRAAKS 100


>2key_A Putative phage integrase; protein structure, PSI, NESG,
           structural genomics, unknown function, protein structure
           initiative; NMR {Bacteroides fragilis nctc 9343} (A:)
          Length = 112

 Score = 61.5 bits (149), Expect = 1e-10
 Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 3/89 (3%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHL-SQRKLVTSSQRRKI 63
            R   I T   +K  +++ + +           + + L  YL ++        S+ +R +
Sbjct: 22  SRRLEIGTFRHHKSCMRKFKEYCEGL--QFHELTEDFLRDYLIYMKKTLCNADSTAQRNL 79

Query: 64  SVIRQFYNFLCYEGLRKDNPSDTLELPKK 92
           S I+ + +    +G  +++P     L   
Sbjct: 80  STIKIYVSAAIKKGYMENDPFKDFGLEHH 108


>2khq_A Integrase; all-alpha, structural genomics, PSI-2, protein
           structure initiative, northeast structural genomics
           consortium; NMR {Staphylococcus saprophyticus subsp}
           (A:)
          Length = 110

 Score = 60.7 bits (147), Expect = 2e-10
 Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 3/89 (3%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
               S +T   Y+   K +++   +K   L          +LN          + R+  S
Sbjct: 17  LPHVSESTKRHYESAYKHIKDHFRHK--LLKDIKRTEYQKFLNEYGLT-HSYETIRKLNS 73

Query: 65  VIRQFYNFLCYEGLRKDNPSDTLELPKKN 93
            IR  ++   +EG    NP+   EL    
Sbjct: 74  YIRNAFDDAIHEGYVIKNPTYKAELHASV 102


>1z1b_A Integrase; protein-DNA complex, DNA binding protein/DNA
          complex; HET: PTR; 3.80A {Enterobacteria phage lambda}
          (A:75-166)
          Length = 92

 Score = 59.1 bits (143), Expect = 7e-10
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 3/79 (3%)

Query: 5  ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
           R     TL  Y   +K ++  L +    L   +T  + + LN     +   +S +   S
Sbjct: 15 SRGIKQKTLINYMSKIKAIRRGLPDA--PLEDITTKEIAAMLNGY-IDEGKAASAKLIRS 71

Query: 65 VIRQFYNFLCYEGLRKDNP 83
           +   +     EG    N 
Sbjct: 72 TLSDAFREAIAEGHITTNH 90


>1z19_A Integrase; protein-DNA complex, DNA binding protein/DNA
          complex; HET: PTR; 2.80A {Enterobacteria phage lambda}
          PDB: 1p7d_A* (A:1-93)
          Length = 93

 Score = 57.2 bits (138), Expect = 3e-09
 Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 3/79 (3%)

Query: 5  ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
           R     TL  Y   +K ++  L +    L   +T  + + LN     +   +S +   S
Sbjct: 16 SRGIKQKTLINYXSKIKAIRRGLPDA--PLEDITTKEIAAXLNGY-IDEGKAASAKLIRS 72

Query: 65 VIRQFYNFLCYEGLRKDNP 83
           +   +     EG    N 
Sbjct: 73 TLSDAFREAIAEGHITTNH 91


>2kj5_A Phage integrase; GFT NMR, PSI-2, NESG, structural genomics,
           protein structure initiative; NMR {Nitrosospira
           multiformis atcc 25196} (A:)
          Length = 116

 Score = 54.9 bits (132), Expect = 1e-08
 Identities = 8/93 (8%), Positives = 28/93 (30%), Gaps = 2/93 (2%)

Query: 2   MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRR 61
                A      +  +  +++         + +      H+   L  + +R    S    
Sbjct: 17  FERMIAGRWKHPNIVRSRIEKDIKPAI-GSLKVEDVKPRHIDDVLKAVMKR-GAPSIAND 74

Query: 62  KISVIRQFYNFLCYEGLRKDNPSDTLELPKKNH 94
            +  +++ +N+     + + NP+   +      
Sbjct: 75  TLRWLKRMFNYAIKRHIIEYNPAAAFDPGDAGG 107


>2kkv_A Integrase; protein structure, PSI, nesgc, structural
           genomics, protein structure initiative, northeast
           structural genomics consortium; NMR {Salmonella enterica
           subsp} (A:)
          Length = 121

 Score = 53.0 bits (127), Expect = 4e-08
 Identities = 13/106 (12%), Positives = 27/106 (25%), Gaps = 4/106 (3%)

Query: 2   MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRR 61
             S +  S +  S   R L+            +    T+HL++ +  +          +R
Sbjct: 17  HESNKRWSEDHRSRVLRYLELYIFPHI-GSSDIRQLKTSHLLAPIKEVDTS-GKHDVAQR 74

Query: 62  KISVIRQFYNFLCYEGLRKDNPSDTLE--LPKKNHILPKTLHKDTI 105
               +     +         NP+  +   L           H    
Sbjct: 75  LQQRVTAIMRYAVQNDYIDSNPASDMAGALSTTKARHYPLEHHHHH 120


>2kj9_A Integrase; DNA_BRE_C superfamily, INTB, PSI-2, structural
           genomics, protein structure initiative; NMR
           {Pectobacterium atrosepticum} (A:)
          Length = 118

 Score = 53.0 bits (127), Expect = 5e-08
 Identities = 9/93 (9%), Positives = 28/93 (30%), Gaps = 2/93 (2%)

Query: 2   MSSERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRR 61
            +++   S +   +    L+            ++   T  L+  +  + ++        R
Sbjct: 21  FATKTTWSEDYQRSVWTRLETYLFPDI-GNKDIAELDTGDLLVPIKKI-EKLGYLEIAMR 78

Query: 62  KISVIRQFYNFLCYEGLRKDNPSDTLELPKKNH 94
                     +   + + + NP+  LE   +  
Sbjct: 79  VKQYATAIMRYAVQQKMIRFNPAYDLEGAVQKL 111


>2kj8_A Putative prophage CPS-53 integrase; INTS, INTC, YFDB, DNA
           integration, DNA recombination, structural genomics,
           protein structure initiative; NMR {Escherichia coli
           k-12} (A:)
          Length = 118

 Score = 50.0 bits (119), Expect = 4e-07
 Identities = 9/94 (9%), Positives = 26/94 (27%), Gaps = 2/94 (2%)

Query: 5   ERASSINTLSAYKRDLKEMQNFLNNKEISLSAASTNHLISYLNHLSQRKLVTSSQRRKIS 64
           ++  S+   +   +   +    +    + +       L+  +     R        +   
Sbjct: 19  KQVWSVGYATELAKMFDDDILPIIGG-LEIQDIEPMQLLEVIRRFEDR-GAMERANKARR 76

Query: 65  VIRQFYNFLCYEGLRKDNPSDTLELPKKNHILPK 98
              + + +    G  K NP+  L    K +    
Sbjct: 77  RCGEVFRYAIVTGRAKYNPAPDLADAMKGYRKKN 110


>2khv_A Phage integrase; solution structure, GFT, NESG, structural
           genomics, unknown function, PSI-2, protein structure
           initiative; NMR {Nitrosospira multiformis atcc 25196}
           (A:)
          Length = 106

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 11/88 (12%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 9   SINTLSAYKRDLKEMQNFLNNK--EISLSAASTNHLISYLNHLSQRKLVTSSQRRKISVI 66
           +      +   +K    +       +S+    T  ++  L+ + ++K  T+   R    I
Sbjct: 20  NTKHADQWTNTIK---TYCGPVIGPLSVQDVDTKLIMKVLDPIWEQKPETA--SRLRGRI 74

Query: 67  RQFYNFLCYEGLRKDNPSDTLELPKKNH 94
               ++    G R+ +         ++H
Sbjct: 75  ESVLDWATVRGYREGDNPARWRGYLEHH 102


>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
           translation termination, ATP-binding, cytoplasm,
           hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
           (A:1-326)
          Length = 326

 Score = 30.1 bits (67), Expect = 0.38
 Identities = 24/157 (15%), Positives = 44/157 (28%), Gaps = 32/157 (20%)

Query: 148 TLSAHTLNLTERTMIIQGKGNKERLVILSPSALHALQMYKKTCSSMKMTGNDLWLFPSST 207
           T  A  L +  R         K + + L+PS   A Q+        K T          +
Sbjct: 172 TA-AFALTMLSRVD---ASVPKPQAICLAPSRELARQIMDVVTEMGKYTEVKTAFGIKDS 227

Query: 208 KTGHLSRQVF------ARDLKALAARAGIQKKNISPHIIRHAFASHLLEGG--ADLRTI- 258
                              +  L  R  +  ++I    +     + L + G       I 
Sbjct: 228 VPKGAKIDAQIVIGTPGT-VMDLMKRRQLDARDI-KVFVLDEADNMLDQQGLGDQSMRIK 285

Query: 259 -------QILLGHTDISTTQIYTHLLPDKLQKLVQDY 288
                  QI+L     S T        ++++K  + +
Sbjct: 286 HLLPRNTQIVL----FSAT------FSERVEKYAERF 312


>3il6_A 3-oxoacyl-[acyl-carrier-protein] synthase 3; FABH, fatty
           acid biosynthesis, antibiotic, acyltransferase,
           cytoplasm, lipid synthesis; HET: B83; 2.50A
           {Enterococcus faecalis} PDB: 3il5_A* 3il4_A*
           (A:1-15,A:50-172)
          Length = 138

 Score = 28.1 bits (62), Expect = 1.5
 Identities = 8/53 (15%), Positives = 16/53 (30%), Gaps = 3/53 (5%)

Query: 218 ARDLKALAARAGIQKKNISPHIIRHAF---ASHLLEGGADLRTIQILLGHTDI 267
             DL    A+  ++K       I        +      +    +Q  +G T+ 
Sbjct: 18  TSDLCHQVAKQLLEKSGKQASEIDFILVATVTPDFNMPSVACQVQGAIGATEA 70


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.318    0.131    0.369 

Gapped
Lambda     K      H
   0.267   0.0534    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,058,858
Number of extensions: 87320
Number of successful extensions: 267
Number of sequences better than 10.0: 1
Number of HSP's gapped: 243
Number of HSP's successfully gapped: 39
Length of query: 300
Length of database: 4,956,049
Length adjustment: 88
Effective length of query: 212
Effective length of database: 1,981,209
Effective search space: 420016308
Effective search space used: 420016308
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: 54 (25.0 bits)