RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780134|ref|YP_003064547.1| phage-related
integrase/recombinase [Candidatus Liberibacter asiaticus str. psy62]
         (348 letters)



>gnl|CDD|162771 TIGR02224, recomb_XerC, tyrosine recombinase XerC.  The phage
           integrase family describes a number of recombinases with
           tyrosine active sites that transiently bind covalently
           to DNA. Many are associated with mobile DNA elements,
           including phage, transposons, and phase variation loci.
           This model represents XerC, one of two closely related
           chromosomal proteins along with XerD (TIGR02225). XerC
           and XerD are site-specific recombinases which help
           resolve chromosome dimers to monomers for cell division
           after DNA replication. In species with a large
           chromosome and homologs of XerC on other replicons, the
           chomosomal copy was preferred for building this model.
           This model does not detect all XerC, as some apparent
           XerC examples score in the gray zone between trusted
           (450) and noise (410) cutoffs, along with some XerD
           examples. XerC and XerD interact with cell division
           protein FtsK.
          Length = 295

 Score = 54.5 bits (132), Expect = 4e-08
 Identities = 35/159 (22%), Positives = 68/159 (42%), Gaps = 14/159 (8%)

Query: 71  LKWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSGDFDYRKITTKHIRSGVES---RK 127
           L++L  E   S H        R   +++ + +  + G     ++T   +RS +     R 
Sbjct: 4   LEYLRVERNYSPH---TVRAYRRDLKAFLEFLEEEGGLASLAEVTAADLRSFLAELHARG 60

Query: 128 HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWS 187
            +  S  + L+++R  +++ VR+  +  NP   V  PK+  +  +  ++++M+       
Sbjct: 61  LSRRSLARKLSALRSFYRFLVRRGLIKANPAAGVRAPKQPKKLPKFLSEDEMEALLDAPD 120

Query: 188 EGSQPRLA------FEFLLY-SGLRCSDSCRAGVQHLQN 219
           E  +  LA       E LLY SGLR S+     +  L  
Sbjct: 121 EDDEDWLALRDRAILE-LLYSSGLRVSELVGLDLDDLDL 158


>gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD.  The phage
           integrase family describes a number of recombinases with
           tyrosine active sites that transiently bind covalently
           to DNA. Many are associated with mobile DNA elements,
           including phage, transposons, and phase variation loci.
           This model represents XerD, one of two closely related
           chromosomal proteins along with XerC (TIGR02224). XerC
           and XerD are site-specific recombinases which help
           resolve chromosome dimers to monomers for cell division
           after DNA replication. In species with a large
           chromosome and with homologs of XerD on other replicons,
           the chomosomal copy was preferred for building this
           model. This model does not detect all XerD, as some
           apparent XerD examples score below the trusted and noise
           cutoff scores. XerC and XerD interact with cell division
           protein FtsK.
          Length = 291

 Score = 46.8 bits (112), Expect = 8e-06
 Identities = 39/224 (17%), Positives = 80/224 (35%), Gaps = 29/224 (12%)

Query: 95  FESYFDQIIRKSGDFDYRKITTKHIRSGVESRK---HTPSSAIQFLTSMRVLFKWAVRQE 151
           F  + ++        D  ++    I   +   K    +  S  + L+++R  +++ +R+ 
Sbjct: 28  FLEFLEER-----GIDLEEVDRGDIVDFLAELKEAGLSARSIARALSALRSFYRFLLREG 82

Query: 152 YVAINPCLSVERPKRKTEGIRPWTKEDMQQFKSFWSEGSQP-----RLAFEFLLYSGLRC 206
               +P   +E PK   +  +  T E+++   +   +   P     R   E L  +GLR 
Sbjct: 83  IREDDPSALIEPPKVARKLPKVLTVEEVEALLAA-PDVDTPLGLRDRAMLELLYATGLRV 141

Query: 207 SDSC--RAGVQHLQNNIFSIK-----------TQKTGTIITVELPDGFMKLLAMTPIGKE 253
           S+    R    +L      ++            ++    +   L +    LL       +
Sbjct: 142 SELVGLRLEDVNLDEGFVRVRGKGNKERLVPLGEEAIEALERYLKEARPLLLKKKVKESD 201

Query: 254 TFFINNDKQKMNATQFSIWFKAKATKAGVNK--SAHGVRKFSAT 295
             F+N     ++        K  A +AG+ K  S H +R   AT
Sbjct: 202 ALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFAT 245


>gnl|CDD|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed.
          Length = 299

 Score = 42.1 bits (100), Expect = 2e-04
 Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 87  LAVNSRISFE---SYFDQIIRKSGDFDYRKITTKHIRSGVESRKH---TPSSAIQFLTSM 140
           LA N+  S+      F + +   G     + T   +++ +          +S+ + L+++
Sbjct: 22  LAENTLSSYRRDLELFAEWLAARGL-SLAEATRDDLQAFLAELAEGGYKATSSARRLSAL 80

Query: 141 RVLFKWAVRQEYVAINPCLSVERPK 165
           R  F++ +R+     +P   ++ PK
Sbjct: 81  RRFFQFLLREGLREDDPSALLDSPK 105


>gnl|CDD|178942 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.
          Length = 297

 Score = 35.5 bits (83), Expect = 0.023
 Identities = 29/157 (18%), Positives = 54/157 (34%), Gaps = 31/157 (19%)

Query: 71  LKWLISEYRKSAHWGSLAVNSRISFESYFDQI--------IRKSGDFDYRKITTKHIRSG 122
           L++L  E   S H          +  +Y   +                   +    +RS 
Sbjct: 14  LEYLRVERGLSPH----------TLRAYRRDLRAFLAFLEEHGISSLQ--DLDAADLRSF 61

Query: 123 VESRK---HTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPKRKTEGIRPWTKEDM 179
           +  R+    +  S  + L+++R  ++W VR+  +  NP   +  PK      +P   +  
Sbjct: 62  LARRRRQGLSARSLARRLSALRSFYRWLVRRGLLKANPAAGLRAPKIPKRLPKPLDVDQA 121

Query: 180 QQFKSFWSEGSQPRLA------FEFLLYSGLRCSDSC 210
           ++     +      LA       E L  SGLR S+  
Sbjct: 122 KRL--LDAIDEDDPLALRDRAILELLYGSGLRLSELV 156


>gnl|CDD|152161 pfam11725, AvrE, Pathogenicity factor.  This family is secreted by
            gram-negative Gammaproteobacteria such as Pseudomonas
            syringae of tomato and the fire blight plant pathogen
            Erwinia amylovora, amongst others. It is an essential
            pathogenicity factor of approximately 198 kDa. Its
            injection into the host-plant is dependent upon the
            bacterial type III or Hrp secretion system. The family is
            long and carries a number of predicted functional
            regions, including an ERMS or endoplasmic reticulum
            membrane retention signal at both the C- and the
            N-termini, a leucine-zipper motif from residues 539-560,
            and a nuclear localisation signal at 1358-1361. this
            conserved AvrE-family of effectors is among the few that
            are required for full virulence of many phytopathogenic
            pseudomonads, erwinias and pantoeas.
          Length = 1771

 Score = 33.6 bits (77), Expect = 0.071
 Identities = 29/116 (25%), Positives = 49/116 (42%), Gaps = 10/116 (8%)

Query: 226  TQKTGTIITV--ELPDGFMKLL---AMTPIGKETFFINNDKQKMNATQFSIWFKAKAT-K 279
            TQ+ G   TV  E  DGF+  L    + P+      I ++ ++     F +   A    +
Sbjct: 1312 TQRNGLNFTVPDEEIDGFVDGLFEGKLNPLDLLKKGIEHEMKQGKRFNFDLTAGAALDLR 1371

Query: 280  AGVNKSAHGVRKFSATISADAGATAHELMATYGWKTV----DQAETYTKGADRIRL 331
            AG+N +  G +  +AT  A  G  A   +A+Y   +     D++ T     +R R 
Sbjct: 1372 AGINLTEPGSKPLTATARAGVGLNASANLASYTDYSSTQKNDKSSTREASDNRPRF 1427


>gnl|CDD|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed.
          Length = 358

 Score = 30.9 bits (70), Expect = 0.49
 Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 9/57 (15%)

Query: 109 FDYRKITTKHIRSGVESRKHTPSSAIQFLTSMRVLFKWAVRQEYVAINPCLSVERPK 165
           + YRK   + +         +  +    L+ +RV F+W +++ ++  NP   +E PK
Sbjct: 80  YGYRKANGEPL---------STRTQRTQLSPLRVWFRWLLKRHHILYNPAEDLELPK 127


>gnl|CDD|181403 PRK08367, porA, pyruvate ferredoxin oxidoreductase subunit alpha;
           Reviewed.
          Length = 394

 Score = 29.1 bits (65), Expect = 1.6
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 10/73 (13%)

Query: 243 KLLAMTPIGKETF-------FINNDKQKMNATQFSIWFKAKATKAGVNKSAHGVRKFSAT 295
           K++A  PI   T        F+ N +  ++A    +  +  A  A V  SA GVR F+AT
Sbjct: 23  KVIAAFPITPSTLVPEKISEFVANGE--LDAEFIKVESEHSAISACVGASAAGVRTFTAT 80

Query: 296 ISADAGATAHELM 308
            S    A  HE++
Sbjct: 81  ASQGL-ALMHEVL 92


>gnl|CDD|180751 PRK06922, PRK06922, hypothetical protein; Provisional.
          Length = 677

 Score = 27.9 bits (62), Expect = 4.1
 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 1/60 (1%)

Query: 72  KWLISEYRKSAHWGSLAVNSRISFESYFDQIIRKSG-DFDYRKITTKHIRSGVESRKHTP 130
           K +I +Y +          + +SF+   D+ ++ +   F +  +    I   VE+ K   
Sbjct: 311 KRVIEKYLREYRENEKPNTTHVSFQVKVDEDMKTAYVSFRFSAVGEALITFCVEAEKIDM 370


>gnl|CDD|178220 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
          Length = 801

 Score = 27.4 bits (61), Expect = 5.4
 Identities = 26/110 (23%), Positives = 40/110 (36%), Gaps = 22/110 (20%)

Query: 244 LLAMTPIGKETFFINNDKQKMNATQF----------SIWFKAKATKAGVNKSAHGVRKFS 293
           LL   P   +T F   D Q    ++            + F AK   AG          + 
Sbjct: 376 LLTNRPEVSDTLFTWADLQAKLNSELLNNLGNFINRVLSFIAKPPGAG----------YG 425

Query: 294 ATISADAGATAHELMATYGWKTVDQAETYTKGADRIRL--GIKNSRRISS 341
           + I    GA +H L      K     E Y +  ++++L  G+K +  ISS
Sbjct: 426 SVIPDAPGAESHPLTKKLAEKVGKLVEQYVEAMEKVKLKQGLKTAMSISS 475


>gnl|CDD|183690 PRK12698, flgH, flagellar basal body L-ring protein; Reviewed.
          Length = 224

 Score = 27.4 bits (61), Expect = 5.7
 Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)

Query: 216 HLQNNIFS-IKTQKTGTIITVEL 237
              N+++S IK  K G IITV L
Sbjct: 52  SQANSLYSDIKAHKVGDIITVVL 74


>gnl|CDD|178415 PLN02820, PLN02820, 3-methylcrotonyl-CoA carboxylase, beta chain.
          Length = 569

 Score = 27.5 bits (61), Expect = 5.8
 Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 161 VERPKRKTEGIRPWTKEDMQQFKS 184
           +ER  +K +GI  W+KE+ + FK+
Sbjct: 491 IERENKKRQGI-QWSKEEEEAFKA 513


>gnl|CDD|184758 PRK14596, PRK14596, peptide deformylase; Provisional.
          Length = 199

 Score = 27.1 bits (60), Expect = 6.9
 Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 3/28 (10%)

Query: 145 KWAVRQEYVAINPCLSVERPKRK--TEG 170
           +  V +EYV +NP ++  R   +   EG
Sbjct: 78  RSRVLREYVMVNPVITY-RKGDQSGQEG 104


>gnl|CDD|129541 TIGR00449, tgt_general, tRNA-guanine transglycosylases, various
          specificities.  Different tRNA-guanine
          transglycosylases catalyze different tRNA base
          modifications. Two guanine base substitutions by
          different enzymes described by the model are involved
          in generating queuosine at position 34 in bacterial
          tRNAs and archaeosine at position 15 in archaeal tRNAs.
          This model is designed for fragment searching, so the
          superfamily is used loosely.
          Length = 367

 Score = 27.0 bits (60), Expect = 8.6
 Identities = 13/30 (43%), Positives = 14/30 (46%)

Query: 28 GHGRRIRLPYPHESTFIPAYMSALTGSTPK 57
          GH R  RL  PH S   P +M   T  T K
Sbjct: 8  GHARVGRLKTPHGSVETPVFMPVGTLGTVK 37


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.320    0.132    0.399 

Gapped
Lambda     K      H
   0.267   0.0789    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,577,515
Number of extensions: 339420
Number of successful extensions: 574
Number of sequences better than 10.0: 1
Number of HSP's gapped: 573
Number of HSP's successfully gapped: 16
Length of query: 348
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 254
Effective length of database: 3,963,321
Effective search space: 1006683534
Effective search space used: 1006683534
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: 58 (26.0 bits)