RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781145|ref|YP_003065558.1| hypothetical protein
CLIBASIA_05245 [Candidatus Liberibacter asiaticus str. psy62]
         (350 letters)



>gnl|CDD|180577 PRK06464, PRK06464, phosphoenolpyruvate synthase; Validated.
          Length = 795

 Score = 33.2 bits (77), Expect = 0.12
 Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 3/42 (7%)

Query: 49  AVSPDEFLIHPDSVDIEKSPIVGRKLYLTRSDLISMGYDRES 90
           AV+PDEF +H  ++   K  IV R L    S  I M YD   
Sbjct: 232 AVNPDEFYVHKPTLKAGKPAIVRRTL---GSKKIKMVYDDGG 270


>gnl|CDD|129629 TIGR00538, hemN, oxygen-independent coproporphyrinogen III oxidase.
            This model represents HemN, the oxygen-independent
           coproporphyrinogen III oxidase that replaces HemF
           function under anaerobic conditions. Several species,
           including E. coli, Helicobacter pylori, and Aquifex
           aeolicus, have both a member of this family and a member
           of another, closely related family for which there is no
           evidence of coproporphyrinogen III oxidase activity.
           Members of this family have a perfectly conserved motif
           PYRT[SC]YP in a region N-terminal to the region of
           homology with the related uncharacterized protein.
          Length = 455

 Score = 32.8 bits (75), Expect = 0.12
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 61  SVDIEKSPIVGRKLYLTRSDLISMGYDRESINNLPIISSQNIENTWKFPKNQYSDKALEM 120
           +VD   +P V R + L++ D I     +  + N  +     IE  +      Y  K LE+
Sbjct: 347 AVDEGGNP-VERGIALSQDDCIRREVIKSLMCNFKL-DYSKIEEKFDLDFADYFAKELEL 404

Query: 121 IEYYELYVTIDYDGDGI 137
           ++  E    +D D  GI
Sbjct: 405 LKPLEEDGLLDVDEKGI 421


>gnl|CDD|152853 pfam12419, DUF3670, SNF2 Helicase protein.  This domain family is
           found in bacteria, archaea and eukaryotes, and is
           approximately 140 amino acids in length. The family is
           found in association with pfam00271, pfam00176. Most of
           the proteins in this family are annotated as SNF2
           helicases but there is little accompanying literature to
           confirm this.
          Length = 140

 Score = 29.9 bits (68), Expect = 1.0
 Identities = 10/17 (58%), Positives = 11/17 (64%)

Query: 333 KVRMVRLRDQWVSFDPR 349
           K  +VRLR QWV  DP 
Sbjct: 96  KRPLVRLRGQWVELDPE 112


>gnl|CDD|149960 pfam09090, MIF4G_like_2, MIF4G like.  Members of this family are
           involved in mediating U snRNA export from the nucleus.
           They adopt a highly helical structure, wherein the
           polypeptide chain forms a right-handed solenoid. At the
           tertiary level, the domain is composed of a superhelical
           arrangement of successive antiparallel pairs of helices.
          Length = 248

 Score = 29.7 bits (67), Expect = 1.2
 Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 16/63 (25%)

Query: 181 SLAASIIE--IQKIKTVLL------RQTLDNL--YWQNQPQTIV------QEGSIIDPES 224
           S A S IE   + +KT+        +  ++ +  YW+NQPQ             II P +
Sbjct: 69  SHAFSAIERYKEVLKTLSAESEEKQQWIIEAVFEYWKNQPQMGFVILDKLLNYGIISPIA 128

Query: 225 VLN 227
           ++ 
Sbjct: 129 IIT 131


>gnl|CDD|171835 PRK13016, PRK13016, dihydroxy-acid dehydratase; Provisional.
          Length = 577

 Score = 29.7 bits (67), Expect = 1.3
 Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 3/29 (10%)

Query: 78  RSDLISMGYDRESINNLPIISSQNIENTW 106
           RS ++ MGY  E  +  P+I+   I NTW
Sbjct: 26  RSRMMQMGYAPEDFDGKPVIA---ILNTW 51


>gnl|CDD|162349 TIGR01418, PEP_synth, phosphoenolpyruvate synthase.  Also called
           pyruvate,water dikinase and PEP synthase. The member
           from Methanococcus jannaschii contains a large intein.
           This enzyme generates phosphoenolpyruvate (PEP) from
           pyruvate, hydrolyzing ATP to AMP and releasing inorganic
           phosphate in the process. The enzyme shows extensive
           homology to other enzymes that use PEP as substrate or
           product. This enzyme may provide PEP for
           gluconeogenesis, for PTS-type carbohydrate transport
           systems, or for other processes.
          Length = 782

 Score = 28.5 bits (64), Expect = 2.4
 Identities = 9/26 (34%), Positives = 17/26 (65%)

Query: 49  AVSPDEFLIHPDSVDIEKSPIVGRKL 74
           AV+PDE+++   +++  K  I+ R L
Sbjct: 229 AVTPDEYVVFKPTLEQGKKAILERTL 254


>gnl|CDD|171815 PRK12911, PRK12911, bifunctional preprotein translocase subunit
           SecD/SecF; Reviewed.
          Length = 1403

 Score = 27.9 bits (62), Expect = 3.9
 Identities = 17/81 (20%), Positives = 36/81 (44%)

Query: 239 GMDIRSVLGIHSVPMIEKSFSMLHYLDQELVDRTGISDISSGFSPEILQNMTATATSLIE 298
           G  +  V G     + EK FS + Y D++      + ++++    E  +  +    S+ +
Sbjct: 129 GETVVQVSGSLVTSLTEKDFSFVSYEDEDETVSQELENLATNLFIESERPCSCGYPSIWD 188

Query: 299 QSGVGQVELIVRTLAQGLEIL 319
            + + +V  + R L  GL +L
Sbjct: 189 TAPIEKVIQVARNLCSGLRLL 209


>gnl|CDD|152738 pfam12303, SNDH, Membrane bound L-sorbosone dehydrogenase.  This
           domain family is found in bacteria, and is approximately
           140 amino acids in length. There are two conserved
           sequence motifs: LPNGD and LLRD. SNDH converts
           L-sorbosone to 2-keto-L-gulonic acid.
          Length = 140

 Score = 27.3 bits (61), Expect = 6.3
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 131 DYDGDGIAELRRVIMAG 147
           D DGDG+AE R V + G
Sbjct: 119 DADGDGVAEQRTVFLEG 135


>gnl|CDD|180416 PRK06131, PRK06131, dihydroxy-acid dehydratase; Validated.
          Length = 571

 Score = 27.1 bits (61), Expect = 7.0
 Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 3/36 (8%)

Query: 71  GRKLYLTRSDLISMGYDRESINNLPIISSQNIENTW 106
             + +  RS + + GY  E  +  PII    I NTW
Sbjct: 15  DFRAFYHRSFMKNQGYPDELFDGRPIIG---ICNTW 47


>gnl|CDD|184795 PRK14698, PRK14698, V-type ATP synthase subunit A; Provisional.
          Length = 1017

 Score = 26.9 bits (59), Expect = 7.2
 Identities = 30/113 (26%), Positives = 55/113 (48%), Gaps = 21/113 (18%)

Query: 94  LPIISSQNIENTWKFPKNQYSDKAL-------EMIEYYELYVTIDYDGDGIAELRRVIMA 146
           +P+I+ Q + +T+ FP+ +    A+       + ++   L +T ++    I +L  ++  
Sbjct: 209 VPLITGQRVIDTF-FPQAKGGTAAIPGPFGSGKCVDGDTLILTKEFGLIKIKDLYEIL-- 265

Query: 147 GGTGKDNILCNEEWNEL--PFTC-------LRAMRAPHCFIGESLAASIIEIQ 190
            G GK  +  NEEW EL  P T        +  ++A H + G S  A +IEI+
Sbjct: 266 DGKGKKTVEGNEEWTELEEPITLYGYKDGKIVEIKATHVYKGAS--AGMIEIK 316


>gnl|CDD|152175 pfam11739, DctA-YdbH, Dicarboxylate transport.  In certain
           bacterial families this protein is expressed from the
           ydbH gene, and there is a suggestion that this is a form
           of DctA or dicarboxylate transport protein.
           Dicarboxylate transport proteins are found in aerobic
           bacteria which grow on succinate or other
           C4-dicarboxylates.
          Length = 207

 Score = 26.8 bits (60), Expect = 9.8
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 116 KALEMIEYYELYVTIDYDGDGIAELR 141
            ALE + Y +L  ++DYD DG   L 
Sbjct: 138 DALENLHYSQLSSSLDYDPDGELVLG 163


  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
   0.321    0.138    0.402 

Gapped
Lambda     K      H
   0.267   0.0673    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,915,255
Number of extensions: 388979
Number of successful extensions: 706
Number of sequences better than 10.0: 1
Number of HSP's gapped: 706
Number of HSP's successfully gapped: 16
Length of query: 350
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 256
Effective length of database: 3,963,321
Effective search space: 1014610176
Effective search space used: 1014610176
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: 58 (26.2 bits)