RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780391|ref|YP_003064804.1| DNA polymerase III subunit chi
[Candidatus Liberibacter asiaticus str. psy62]
         (141 letters)



>gnl|CDD|180224 PRK05728, PRK05728, DNA polymerase III subunit chi; Validated.
          Length = 142

 Score = 92.6 bits (231), Expect = 3e-20
 Identities = 39/122 (31%), Positives = 60/122 (49%), Gaps = 7/122 (5%)

Query: 17  LLVLLQDEYEKGKRVSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVL 76
           L  L +     G RV VQC  E   ++L+E LWT++ + FLPHG         ++ QPVL
Sbjct: 18  LCELAEKALRAGWRVLVQCEDEEQAEALDEALWTFRDESFLPHG---LAGEGPAAGQPVL 74

Query: 77  LTISSL-NANTSTIRFLVDEASMHIGDVDYYEKVVFIINTDDQGSLEWGRAHWRSLKNSG 135
           LT     NAN   +   +D A         +E+VV  +  D+  + +  R  W++ + +G
Sbjct: 75  LTWPGKRNANHRDLLINLDGA--VPAFAAAFERVVDFVGYDEA-AKQAARERWKAYRAAG 131

Query: 136 YA 137
           YA
Sbjct: 132 YA 133


>gnl|CDD|102480 PRK06646, PRK06646, DNA polymerase III subunit chi; Provisional.
          Length = 154

 Score = 31.9 bits (72), Expect = 0.068
 Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 3/53 (5%)

Query: 41 RDSLNEYLWTWKKDGFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLV 93
          ++ LN+ LWT+ +  F+PHG  +  +      QP+ +T    N N +++  ++
Sbjct: 42 QEMLNKNLWTYSRKQFIPHGSKLDPQ---PEKQPIYITDELQNPNNASVLVII 91


>gnl|CDD|130353 TIGR01286, nifK, nitrogenase molybdenum-iron protein beta chain.
           This model represents the majority of known sequences of
           the nitrogenase molybdenum-iron protein beta subunit. A
           distinct clade in a phylogenetic tree contains
           molybdenum-iron, vanadium-iron, and iron-iron forms of
           nitrogenase beta subunit and is excluded from this
           model. Nitrogenase, also called dinitrogenase, is
           responsible for nitrogen fixation. Note: the trusted
           cutoff score has recently been lowered to include an
           additional family in which the beta subunit is shorter
           by about 50 amino acids at the N-terminus. In species
           with the shorter form of the beta subunit, the alpha
           subunit has a novel insert of similar length.
          Length = 515

 Score = 27.9 bits (62), Expect = 0.98
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 31  VSVQCGSERVRDSLNEYLWTWKKDGFLPHGVDV 63
           VS  C +E + D LN ++   KK+GF+P    V
Sbjct: 148 VSTTCMAEVIGDDLNAFIGNAKKEGFIPDDFPV 180


>gnl|CDD|177527 PHA03095, PHA03095, ankyrin-like protein; Provisional.
          Length = 471

 Score = 26.5 bits (59), Expect = 2.3
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 57  LPHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDVD 104
           L  G DV    D     P+ + + S NAN   +R L+D A   +  VD
Sbjct: 139 LRKGADVNAL-DLYGMTPLAVLLKSRNANVELLRLLID-AGADVYAVD 184


>gnl|CDD|180659 PRK06690, PRK06690, acetyl-CoA acetyltransferase; Provisional.
          Length = 361

 Score = 26.7 bits (59), Expect = 2.4
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 10/46 (21%)

Query: 72  FQPVLLTISSL----------NANTSTIRFLVDEASMHIGDVDYYE 107
           ++PVL  + S                 +  L++E +M + D+DY+E
Sbjct: 237 YKPVLRFVRSAVVGVDPNLPGTGPIFAVNKLLNEMNMKVEDIDYFE 282


>gnl|CDD|151221 pfam10740, DUF2529, Protein of unknown function (DUF2529).  This
           family is conserved in the Bacillales. The function is
           not known. Several members are annotated as being YWJG,
           a protein expressed downstream of pyrG, a gene encoding
           for cytidine triphosphate synthetase.
          Length = 172

 Score = 26.5 bits (59), Expect = 2.5
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 2   RTLLFYRFKNDWEYNLLVLLQDEYEKGKRVSVQCGSERVRDSLNEYL 48
           R LLF RF ND E   + L +  Y++G  V     + +  DSL ++ 
Sbjct: 84  RVLLFSRFSNDEE--AVALAKKLYDQGIDVVAVSPNAKEGDSLADHA 128


>gnl|CDD|165290 PHA02987, PHA02987, Ig domain OX-2-like protein; Provisional.
          Length = 189

 Score = 25.6 bits (56), Expect = 5.3
 Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 11/52 (21%)

Query: 43 SLNEYLWTWKKD-----GFLPHGVDVGDEGDFSSFQPVLLTISSLNANTSTI 89
          S N  L TWKK+     G+ P G  + D+     F+  +  +S  + N STI
Sbjct: 42 SFNSILITWKKNNKTIAGYGPCGPVIVDK-----FKNKIEYLSK-SFNESTI 87


>gnl|CDD|151517 pfam11072, DUF2859, Protein of unknown function (DUF2859).  This is
           a bacterial family of uncharacterized proteins.
          Length = 142

 Score = 25.3 bits (56), Expect = 5.4
 Identities = 12/68 (17%), Positives = 21/68 (30%), Gaps = 11/68 (16%)

Query: 73  QPVLLTISSLNANTSTIRFLVDEASMHIGDVDYYEKV--------VFIINTDDQGSLEWG 124
           +P     S            V    +  G V+   +         +F+I  D   S +W 
Sbjct: 22  EPQPSPPSPPAGALEAAMLPVRSPRLSPGVVE--RRALNLPGLQPLFLIGDDPA-SRQWL 78

Query: 125 RAHWRSLK 132
           + +   LK
Sbjct: 79  QQNADELK 86


>gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
          Length = 535

 Score = 25.2 bits (56), Expect = 6.7
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 11/46 (23%)

Query: 58  PHGVDVGDEGDFSSFQPVLLTISSLNANTSTIRFLVDEASMHIGDV 103
           PHGVD+G           L  +++     +   FLV+E S  +GD 
Sbjct: 238 PHGVDLGT----------LKRMAARTKRRTLKEFLVEEFS-RVGDK 272


>gnl|CDD|162338 TIGR01398, FlhA, flagellar biosynthesis protein FlhA.  This model
          describes flagellar biosynthesis protein FlhA, one of a
          large number of genes associated with the biosynthesis
          of functional bacterial flagella. Homologs of many such
          proteins, including FlhA, function in type III protein
          secretion systems. A separate model describes InvA
          (Salmonella enterica), LcrD (Yersinia enterocolitica),
          HrcV (Xanthomonas), etc., all of which score below the
          noise cutoff for this model.
          Length = 678

 Score = 24.5 bits (54), Expect = 9.0
 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 2/25 (8%)

Query: 68 DFSSFQPVLL--TISSLNANTSTIR 90
          DFSSF  +LL  T+  L+ N ++ R
Sbjct: 52 DFSSFPTLLLIATLFRLSLNVASTR 76


  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    0.138    0.431 

Gapped
Lambda     K      H
   0.267   0.0754    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,313,934
Number of extensions: 131649
Number of successful extensions: 242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 16
Length of query: 141
Length of database: 5,994,473
Length adjustment: 84
Effective length of query: 57
Effective length of database: 4,179,401
Effective search space: 238225857
Effective search space used: 238225857
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: 52 (23.8 bits)