RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781187|ref|YP_003065600.1| putative phage terminase,
large subunit [Candidatus Liberibacter asiaticus str. psy62]
         (367 letters)



>gnl|CDD|146059 pfam03237, Terminase_6, Terminase-like family.  This family
           represents a group of terminase proteins.
          Length = 380

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 44/267 (16%), Positives = 80/267 (29%), Gaps = 36/267 (13%)

Query: 82  ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPH-RHW 140
           I   R  GKT   A   L         + I ++ S+ Q +      + +    L      
Sbjct: 2   ILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEITFE 61

Query: 141 FEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA 200
            +  +  + P+G               ++         E   T  G        ++ DEA
Sbjct: 62  EKNGNPIILPNGAKL------------YF------LGLESETTAQGYRGASIAGIYFDEA 103

Query: 201 SGTP-DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVE 259
           +  P    ++ +          R    +        W YD +   L+D  +       VE
Sbjct: 104 TWLPKFQESELVRRLRATKGKWRKTFFS-TPPSPGHWVYDFWTGWLDDKGKRTFIPADVE 162

Query: 260 G-------IDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAID 312
                   +   + E + + Y  D + AR  ++G++     + F      E        +
Sbjct: 163 VTIEDARALGPEYKEELRALYS-DEEFAR-LLMGEWVDTSGSIF---KRFELERCDVDEE 217

Query: 313 DLYA--PLIMGCDIA-GEGGDKTVVVF 336
                  +I G D A   GGD   +V 
Sbjct: 218 RPPEHREVIGGVDPAASRGGDYAALVV 244


>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
           nucleotide-binding domain (P-loop) near the N-terminus,
           participates in the maturation of the nickel center of
           carbon monoxide dehydrogenase (CODH). CODH from
           Rhodospirillum rubrum catalyzes the reversible oxidation
           of CO to CO2. CODH contains a nickel-iron-sulfur cluster
           (C-center) and an iron-sulfur cluster (B-center). CO
           oxidation occurs at the C-center. Three accessory
           proteins encoded by cooCTJ genes are involved in nickel
           incorporation into a nickel site. CooC functions as a
           nickel insertase that mobilizes nickel to apoCODH using
           energy released from ATP hydrolysis. CooC is a homodimer
           and has NTPase activities. Mutation at the P-loop
           abolishs its function..
          Length = 116

 Score = 27.9 bits (62), Expect = 4.7
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)

Query: 79  KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113
           K AI+   G+GKTT+ A +  +L     G  ++ I
Sbjct: 1   KIAITGKGGVGKTTIAALLARYL--AEKGKPVLAI 33


>gnl|CDD|145816 pfam02863, Arg_repressor_C, Arginine repressor, C-terminal domain. 
          Length = 70

 Score = 27.8 bits (63), Expect = 5.1
 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 5/40 (12%)

Query: 310 AIDDLYAPLIMGCDIAGEGGDKTV-VVFRRGNIIEHIFDW 348
            ID L  P I+G  IA   GD T+ V+ R     E + + 
Sbjct: 31  LIDSLKLPEILGT-IA---GDDTILVICRSEEDAEELAEK 66


>gnl|CDD|31671 COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and
           metabolism].
          Length = 312

 Score = 27.5 bits (61), Expect = 6.4
 Identities = 21/106 (19%), Positives = 36/106 (33%), Gaps = 18/106 (16%)

Query: 99  LWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEM--------QSLSL-- 148
           LW  +   G S +     + +  + L A+  + L        F +          LS+  
Sbjct: 36  LWAGAHPNGPSTVANGPGQGKSLSELIADPRELLGN-KSFDRFPLLFKILDANDPLSIQV 94

Query: 149 HPSGWYAELLEQSMGIDSKHYTITCRTY--SEERPDTFVGPHNTHG 192
           HPS  YAE  E+ +   +      C  Y  +  +P+   G      
Sbjct: 95  HPSDEYAEEGEEGILGKT-----ECWYYKDANHKPELIYGLTPAKS 135


>gnl|CDD|39697 KOG4497, KOG4497, KOG4497, Uncharacterized conserved protein WDR8,
           contains WD repeats [General function prediction only].
          Length = 447

 Score = 27.3 bits (60), Expect = 6.5
 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 116 SETQLKNTLWAEVSKWLSMLPH-RHWFEMQSLSLHPSGWYAELLEQ 160
           SE  L+ T+W+  ++   +LPH +    ++  + HP G +  +L +
Sbjct: 110 SEFDLRITVWSLNTQKGYLLPHPKT--NVKGYAFHPDGQFCAILSR 153


>gnl|CDD|112181 pfam03354, Terminase_1, Phage Terminase.  The majority of the
           members of this family are bacteriophage proteins,
           several of which are thought to be terminase large
           subunit proteins. There are also a number of bacterial
           proteins of unknown function.
          Length = 473

 Score = 27.4 bits (61), Expect = 7.3
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 82  ISAGRGIGKTTLNAWMMLW--LISTRPGMSIICIANSETQ 119
           +S GR  GK+ L A  +L+  L+  +    I+  A +  Q
Sbjct: 27  VSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQ 66


  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
   0.322    0.137    0.440 

Gapped
Lambda     K      H
   0.267   0.0795    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,817,766
Number of extensions: 260753
Number of successful extensions: 576
Number of sequences better than 10.0: 1
Number of HSP's gapped: 575
Number of HSP's successfully gapped: 13
Length of query: 367
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 272
Effective length of database: 4,210,882
Effective search space: 1145359904
Effective search space used: 1145359904
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: 58 (26.0 bits)