RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781190|ref|YP_003065603.1| hypothetical protein
CLIBASIA_05485 [Candidatus Liberibacter asiaticus str. psy62]
         (233 letters)



>gnl|CDD|80309 cd04859, Prim_Pol, Prim_Pol: Primase-polymerase (primpol) domain of
           the type found in bifunctional replicases from archaeal
           plasmids, including ORF904 protein of the crenarchaeal
           plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol).
           These primpol domains belong to the archaeal/eukaryal
           primase (AEP) superfamily. This group includes archaeal
           plasmids and bacteriophage AEPs. The ORF904 protein is a
           multifunctional protein having ATPase, primase and DNA
           polymerase activity, and may play a role in the
           replication of the archaeal plasmid. The pRN1 primpol
           domain exhibits DNA polymerase and primase activities; a
           cluster of active site residues (three acidic residues,
           and a histidine) is required for both these activities.
           For pRN1 primpol, the primase activity prefers dNTPs to
           rNTPs; incorporation of dNTPs requires rNTP as cofactor.
           The pRN1 primpol contains an unusual zinc-binding stem,
           which is not conserved in other members of this group..
          Length = 152

 Score = 31.6 bits (71), Expect = 0.19
 Identities = 19/118 (16%), Positives = 34/118 (28%), Gaps = 11/118 (9%)

Query: 7   DHYVYNGFGILCGIGTHPVYAFDVDVLDEQVVDRFN-NEFQSCCGKPISRVGQAPKTLML 65
           D    N  G+  G     +   D+DV  +         E        ++    +    + 
Sbjct: 36  DGPDAN-IGLRTG--PSGLVVIDIDVKHDGAAALAALAELGKLPPLTLTVRTGSGGRHLY 92

Query: 66  FRMQETNLKKQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWS------IAPHAL 117
           FR+ +  +  +  + K    ++    G   VA          Y W        AP  L
Sbjct: 93  FRVPDG-VPVKSVKGKGGPGIDIRGGGGYVVAPPSVHPGGGYYVWKSTVDPAPAPEWL 149


>gnl|CDD|36414 KOG1200, KOG1200, KOG1200, Mitochondrial/plastidial
           beta-ketoacyl-ACP reductase [Lipid transport and
           metabolism].
          Length = 256

 Score = 29.6 bits (66), Expect = 0.78
 Identities = 18/64 (28%), Positives = 23/64 (35%), Gaps = 4/64 (6%)

Query: 15  GILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQA--PKTLMLFRMQETN 72
           G L G G H   AF  DV     V     E +   G P   V  A   +  +L RM++  
Sbjct: 56  GDLGGYGDH--SAFSCDVSKAHDVQNTLEEMEKSLGTPSVLVNCAGITRDGLLLRMKQEQ 113

Query: 73  LKKQ 76
               
Sbjct: 114 WDSV 117


>gnl|CDD|31439 COG1246, ArgA, N-acetylglutamate synthase and related
           acetyltransferases [Amino acid transport and
           metabolism].
          Length = 153

 Score = 26.8 bits (59), Expect = 5.4
 Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 4/41 (9%)

Query: 115 HALKVEELPLLTPDEVEYF----FEFFDTITTPRDKEKSYR 151
             L ++EL +LT    E+F    F   D    P +   SY 
Sbjct: 95  RELGIKELFVLTTRSPEFFAERGFTRVDKDELPEEVWSSYN 135


>gnl|CDD|146980 pfam04599, Pox_G5, Poxvirus G5 protein.  This protein has been
           predicted to be related to the FEN-1 endonuclease.
          Length = 426

 Score = 26.1 bits (58), Expect = 7.3
 Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 139 TITTPRD--KEKSYRKL-SKIWKSHNNRRYTNIEIRAFLSCFGEEFYNGS 185
            I  P+     K  RKL   I K+   ++ T  +I++ +S FG E  N S
Sbjct: 348 CILEPKKEISVKEIRKLCKIIDKNKRYKKVTINDIKSVISIFGYEINNTS 397


>gnl|CDD|38106 KOG2895, KOG2895, KOG2895, Uncharacterized conserved protein
           [Function unknown].
          Length = 408

 Score = 26.1 bits (57), Expect = 7.9
 Identities = 20/120 (16%), Positives = 40/120 (33%), Gaps = 12/120 (10%)

Query: 87  EFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKVEELPLLTPDEVEYFFEFFDTITTPRDK 146
            F A+  +F    +     + Y  S    + K  +       + +         +    +
Sbjct: 21  SFDAFKDRFKDKVVS----KYYHGSHLSRSKKKVQTREGLSRQKDSHHPHHLNRSRSFLQ 76

Query: 147 EKSYRKLSK-----IWKSHNNRRYTNIEIR---AFLSCFGEEFYNGSHDEWIPVVMAIHY 198
            ++   LSK       ++  + R+ N ++      L   G  F  G+  E I +V  I Y
Sbjct: 77  LQTREILSKQAVKIAKQAEEHERFINEKVTHLVGVLGFGGFCFLLGARPEDIHLVYTIFY 136


>gnl|CDD|37249 KOG2038, KOG2038, KOG2038, CAATT-binding transcription factor/60S
           ribosomal subunit biogenesis protein [Translation,
           ribosomal structure and biogenesis, Transcription].
          Length = 988

 Score = 26.2 bits (57), Expect = 8.3
 Identities = 8/42 (19%), Positives = 17/42 (40%)

Query: 130 VEYFFEFFDTITTPRDKEKSYRKLSKIWKSHNNRRYTNIEIR 171
           +  +F  F T+   +DK+          K  +N++    E+ 
Sbjct: 421 ISIYFSLFKTLVGKKDKDNRKDDKGAAKKKKSNKKDKKEEVS 462


>gnl|CDD|32655 COG2827, COG2827, Predicted endonuclease containing a URI domain
           [DNA replication, recombination, and repair].
          Length = 95

 Score = 26.0 bits (57), Expect = 8.4
 Identities = 8/26 (30%), Positives = 15/26 (57%)

Query: 133 FFEFFDTITTPRDKEKSYRKLSKIWK 158
           ++E FD  +    +EK  +KL++  K
Sbjct: 51  WYEEFDDKSEALRREKRIKKLTRKQK 76


>gnl|CDD|36897 KOG1684, KOG1684, KOG1684, Enoyl-CoA hydratase [Lipid transport and
           metabolism].
          Length = 401

 Score = 26.0 bits (57), Expect = 9.8
 Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 1/105 (0%)

Query: 16  ILCGIGTHPVYAFDVDVLDEQVVDRFNNEFQSCCGKPISRVGQAPKTLMLFRMQETNL-K 74
           + CG+ TH V +  +  L+E+++   N++ QS   + + +     K        + ++  
Sbjct: 211 LRCGLATHYVPSEKLPSLEERLLKNLNDDPQSVINETLEKYASPAKDESFSLSLKLDVIN 270

Query: 75  KQKSEEKIQGHLEFLAYGQQFVAYNIHPKTQRAYTWSIAPHALKV 119
           K  S   ++  +E L   QQ    +   K        ++P +LKV
Sbjct: 271 KCFSANTVEEIIEALKNYQQSADGSEWAKETLKTLKKMSPTSLKV 315


  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
   0.321    0.137    0.431 

Gapped
Lambda     K      H
   0.267   0.0715    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,039,082
Number of extensions: 156466
Number of successful extensions: 363
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 15
Length of query: 233
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 142
Effective length of database: 4,297,318
Effective search space: 610219156
Effective search space used: 610219156
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 (21.9 bits)
S2: 56 (25.4 bits)