RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781148|ref|YP_003065561.1| hypothetical protein
CLIBASIA_05275 [Candidatus Liberibacter asiaticus str. psy62]
         (69 letters)



>gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
          HK022 subfamily.  Members of this family are phage (or
          prophage-region) homologs of the bacterial
          homohexameric replicative helicase DnaB. Some phage may
          rely on host DnaB, while others encode their own
          verions. This model describes the largest
          phage-specific clade among the close homologs of DnaB,
          but there are, or course, other DnaB homologs from
          phage that fall outside the scope of this model.
          Length = 421

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 21 IGLEQEILGSLLLK-GNLQPIISFLDAQHFIDPIHSEVFRAITR 63
          I  EQ +LG LLL    ++ +++ L  +HF    H  +F A+  
Sbjct: 2  IEAEQAVLGGLLLDNDFIERVMAILKPEHFYSQDHRIIFEAMLD 45


>gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase.  This model describes
          the helicase DnaB, a homohexameric protein required for
          DNA replication. The homohexamer can form a ring around
          a single strand of DNA near a replication fork. An
          intein of > 400 residues is found at a conserved
          location in DnaB of Synechocystis PCC6803, Rhodothermus
          marinus (both experimentally confirmed), and
          Mycobacterium tuberculosis. The intein removes itself
          by a self-splicing reaction. The seed alignment
          contains inteins so that the model built from the seed
          alignment will model a low cost at common intein
          insertion sites.
          Length = 434

 Score = 35.5 bits (83), Expect = 0.003
 Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 21 IGLEQEILGSLLLKGNLQP-IISFLDAQHFIDPIHSEVFRAITR 63
          I  EQ +LG++LL       +   L  + F  P H  +F+AI  
Sbjct: 6  IEAEQAVLGAILLDNEAIDDVAEILKPEDFYRPAHQLIFQAILD 49


>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
          Length = 497

 Score = 33.7 bits (78), Expect = 0.010
 Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)

Query: 24 EQEILGSLLLKGNLQPIIS-FLDAQHFIDPIHSEVFRAITR 63
          EQ +LG++L+       +S FL  +HF +P+H  ++ AI +
Sbjct: 28 EQALLGAILINNRALDRVSDFLKPEHFFEPLHQRIYEAIAK 68


>gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated.
          Length = 886

 Score = 30.9 bits (70), Expect = 0.083
 Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 1/44 (2%)

Query: 21 IGLEQEILGSLLL-KGNLQPIISFLDAQHFIDPIHSEVFRAITR 63
          +  EQ +LG +LL K  +  ++  L    F  P H  ++ AI  
Sbjct: 28 LAAEQSVLGGMLLSKEAIARVLERLRPGAFYRPAHQNIYDAILD 71


>gnl|CDD|168658 PRK06749, PRK06749, replicative DNA helicase; Provisional.
          Length = 428

 Score = 29.9 bits (67), Expect = 0.15
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 2/45 (4%)

Query: 24 EQEILGSLLLKGNLQPIISFLDAQHFIDPIHSEVFRAITRKTTNE 68
          E+ +LGSLLL G L      L  Q+F  P+H  +F+ + RK  +E
Sbjct: 9  EKTVLGSLLLDGELIKECR-LTEQYFSMPVHKSIFQLM-RKMEDE 51


>gnl|CDD|177919 PLN02280, PLN02280, IAA-amino acid hydrolase.
          Length = 478

 Score = 26.5 bits (58), Expect = 1.5
 Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 2/27 (7%)

Query: 4   DFSKKYYSRNNNSIYYFIGLEQEILGS 30
           DFS  +YS+   + +Y+IG+  E LGS
Sbjct: 419 DFS--FYSQVVPAAFYYIGIRNETLGS 443


>gnl|CDD|183174 PRK11521, PRK11521, hypothetical protein; Provisional.
          Length = 124

 Score = 24.7 bits (54), Expect = 5.6
 Identities = 11/18 (61%), Positives = 12/18 (66%)

Query: 27 ILGSLLLKGNLQPIISFL 44
          ILGSLLL+G  Q   SF 
Sbjct: 7  ILGSLLLQGMNQQQRSFA 24


>gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
          Length = 819

 Score = 23.9 bits (52), Expect = 8.8
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 10  YSRNNNSIYYFIGLEQEILGSLLLK 34
            S+N   I + +G E+ IL  LL K
Sbjct: 417 LSKNFFCITHEVGAEEIILYFLLKK 441


  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
   0.323    0.140    0.403 

Gapped
Lambda     K      H
   0.267   0.0684    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,096,379
Number of extensions: 54733
Number of successful extensions: 117
Number of sequences better than 10.0: 1
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 17
Length of query: 69
Length of database: 5,994,473
Length adjustment: 40
Effective length of query: 29
Effective length of database: 5,130,153
Effective search space: 148774437
Effective search space used: 148774437
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.1 bits)