RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780995|ref|YP_003065408.1|
Endonuclease/exonuclease/phosphatase [Candidatus Liberibacter
asiaticus str. psy62]
         (125 letters)



>gnl|CDD|146159 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase
           family.  This large family of proteins includes
           magnesium dependent endonucleases and a large number of
           phosphatases involved in intracellular signalling. This
           family includes: AP endonuclease proteins EC:4.2.99.18,
           DNase I proteins EC:3.1.21.1, Synaptojanin an
           inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56,
           Sphingomyelinase EC:3.1.4.12 and Nocturnin.
          Length = 255

 Score = 33.0 bits (75), Expect = 0.020
 Identities = 22/126 (17%), Positives = 32/126 (25%), Gaps = 25/126 (19%)

Query: 9   LKKWADQKIKTGIPFVIAGDFNRKINSIG---------DTDDFWQKMDPDGLLIRFPQEK 59
           L   +D +I    P ++ GDFN + +S            T     + D            
Sbjct: 139 LDFLSDLRIPKSDPVILCGDFNARPDSWDSALLKSIGKSTLFLLLERDLVFDGFDELPIG 198

Query: 60  -------ESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHC 112
                      +  K   S LD           L+  S        S L       S H 
Sbjct: 199 FPPTWWSYRNSSEKKNTGSRLDR---------ILVSGSLLRRVVILSLLLLVIFTGSDHR 249

Query: 113 PLTIEY 118
           P+    
Sbjct: 250 PVLATL 255


>gnl|CDD|31052 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
           repair].
          Length = 261

 Score = 30.6 bits (69), Expect = 0.12
 Identities = 29/143 (20%), Positives = 51/143 (35%), Gaps = 37/143 (25%)

Query: 7   EWLKKWADQKIKTGIPFVIAGDFN--RKINSIGDTDDFWQKMDPDGLLIR---------- 54
           + L+ + ++ +K G P V+ GDFN   +   + +    W      G L            
Sbjct: 127 DALRNYLEELLKKGKPVVLCGDFNIAPEEIDVANPKKRWLNEGNSGFLPEERAWFRRLLN 186

Query: 55  ----------FPQEKESTC-----NVIKRNKSS-LDYFVIDRDNKNFLIDNSFSIVSYDQ 98
                      P+ ++ T      N  +RN+   +DY ++     + L D          
Sbjct: 187 AGFVDTFRLFHPEPEKYTWWDYRANAARRNRGWRIDYILVSPALADRLKDAGI------- 239

Query: 99  SDLDTRR-SKLSTHCPLTIEYDF 120
            D + R   K S H P+ +E D 
Sbjct: 240 -DREVRGWEKPSDHAPVWVELDL 261


>gnl|CDD|88569 cd05129, RasGAP_RAP6, Rab5-activating protein 6 (RAP6) is an
           endosomal protein with a role in the regulation of
           receptor-mediated endocytosis. RAP6 contains a Vps9
           domain, which is involved in the activation of Rab5, and
           a Ras GAP domain (RGD). Rab5 is a small GTPase required
           for the control of the endocystic route, and its
           activity is regulated by guanine nucleotide exchange
           factor, such as Rabex5, and GAPs, such as RN-tre. Human
           Rap6 protein is localized on the plasma membrane and on
           the endosome. RAP6 binds to Rab5 and Ras through the
           Vps9 and RGD domains, respectively..
          Length = 353

 Score = 28.3 bits (63), Expect = 0.62
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 40  DDFWQKMDPDGLLIRFP---QEKESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSF 91
           D+FW  +DPD L+ RF    +EK       K  +  +  +  + + K   + N F
Sbjct: 118 DEFWLDIDPDKLMERFSPDEREKRFGEKGTKEYERRVQEYRAEVEAKLVALVNKF 172


>gnl|CDD|33370 COG3568, ElsH, Metal-dependent hydrolase [General function
           prediction only].
          Length = 259

 Score = 27.6 bits (61), Expect = 0.89
 Identities = 23/122 (18%), Positives = 34/122 (27%), Gaps = 17/122 (13%)

Query: 3   SQQGEWLKKWADQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDP-----DGLLIRFPQ 57
           S+  +     A   +    P V+ GDFN +      + ++             L   F  
Sbjct: 147 SRLRQAAALLALAGLPALNPTVLMGDFNNE----PGSAEYRLAARSPLNAQAALTGAFAP 202

Query: 58  EKESTCNVIKRNKSSLDYFVIDRDNKNFLIDNSFSIVSYDQSDLDTRRSKLSTHCPLTIE 117
               T      N   L    +DR      +    +I S      D      S H PL  E
Sbjct: 203 AVGRTIRTFPSNTPLLR---LDR----IFVSKELAIRSVHVLT-DRLARVASDHLPLLAE 254

Query: 118 YD 119
             
Sbjct: 255 LR 256


>gnl|CDD|37661 KOG2450, KOG2450, KOG2450, Aldehyde dehydrogenase [Energy
           production and conversion].
          Length = 501

 Score = 26.7 bits (59), Expect = 1.9
 Identities = 7/18 (38%), Positives = 9/18 (50%)

Query: 6   GEWLKKWADQKIKTGIPF 23
            E     A +K+K G PF
Sbjct: 319 VEKFVAAAKKKLKVGDPF 336


>gnl|CDD|34040 COG4318, COG4318, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 221

 Score = 26.1 bits (57), Expect = 2.6
 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 6/39 (15%)

Query: 14  DQKIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLL 52
            + +K G+P V+A        S    DDFW+ MD +  +
Sbjct: 92  REGVKQGLPVVVAD------LSPLAKDDFWEVMDENHWV 124


>gnl|CDD|147340 pfam05112, Baculo_p47, Baculovirus P47 protein.  This family
           consists of several Baculovirus P47 proteins which is
           one of the primary components of Baculovirus encoded RNA
           polymerase, which initiates transcription from late and
           very late promoters.
          Length = 313

 Score = 26.1 bits (58), Expect = 2.9
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 6/46 (13%)

Query: 61  STCNVIKRNKSSLDYFV--IDRDNK----NFLIDNSFSIVSYDQSD 100
           S  +VIKR+KSS  Y V  +D +N       L+ N+F+++     D
Sbjct: 191 SISDVIKRHKSSKKYIVLELDPNNAAELVKLLLKNNFTVIENAHID 236


>gnl|CDD|176468 cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and
           fumarase class II enzymes.  This group contains
           aspartase (L-aspartate ammonia-lyase), fumarase class II
           enzymes, and related proteins. It is a member of the
           Lyase class I family. Members of this family for the
           most part catalyze similar beta-elimination reactions in
           which a C-N or C-O bond is cleaved with the release of
           fumarate as one of the products. These proteins are
           active as tetramers. The four active sites of the
           homotetrameric enzyme are each formed by residues from
           three different subunits. Aspartase catalyzes the
           reversible deamination of aspartic acid. Fumarase
           catalyzes the reversible hydration/dehydration of
           fumarate to L-malate during the Krebs cycle.
          Length = 450

 Score = 25.1 bits (56), Expect = 5.3
 Identities = 7/24 (29%), Positives = 10/24 (41%), Gaps = 3/24 (12%)

Query: 19  TGIPFVIAGDFNRKINSIGDTDDF 42
           TG+PFV A +      +    D  
Sbjct: 249 TGLPFVTAPN---LFEATAAHDAL 269


>gnl|CDD|31981 COG1796, POL4, DNA polymerase IV (family X) [DNA replication,
           recombination, and repair].
          Length = 326

 Score = 24.4 bits (53), Expect = 7.5
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 11/77 (14%)

Query: 16  KIKTGIPFVIAGDFNRKINSIGDTDDFWQKMDPDGLLIRFPQ-----------EKESTCN 64
           ++   I   IAG   R   ++GD D       P+ +L    +           E + +  
Sbjct: 176 ELTPIIQASIAGSLRRGRETVGDIDILISTSHPESVLEELLEMPNVQEVIAKGETKVSML 235

Query: 65  VIKRNKSSLDYFVIDRD 81
           +I    +S+D+ V+  +
Sbjct: 236 LILDEGTSVDFRVVPPE 252


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.319    0.137    0.416 

Gapped
Lambda     K      H
   0.267   0.0757    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,568,367
Number of extensions: 74458
Number of successful extensions: 180
Number of sequences better than 10.0: 1
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 21
Length of query: 125
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 43
Effective length of database: 4,491,799
Effective search space: 193147357
Effective search space used: 193147357
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 (21.7 bits)
S2: 51 (23.4 bits)