RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780595|ref|YP_003065008.1| nucleoside-diphosphate-sugar
epimerase protein [Candidatus Liberibacter asiaticus str. psy62]
         (289 letters)



>gnl|CDD|162758 TIGR02197, heptose_epim, ADP-L-glycero-D-manno-heptose-6-epimerase.
            This family consists of examples of
           ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme
           involved in biosynthesis of the inner core of
           lipopolysaccharide (LPS) for Gram-negative bacteria.
           This enzyme is homologous to UDP-glucose 4-epimerase
           (TIGR01179) and belongs to the NAD dependent
           epimerase/dehydratase family (pfam01370).
          Length = 314

 Score = 34.6 bits (80), Expect = 0.028
 Identities = 29/131 (22%), Positives = 60/131 (45%), Gaps = 22/131 (16%)

Query: 101 YLSSTSIYGNREGQWVDEHSFVHPISCVATQRFNAEKEWL---AITKKLNIKLAVLRLSG 157
           Y SS + YG+ E  + +      P++     +F  + +++    + + L+ ++  LR   
Sbjct: 111 YASSAATYGDGEAGFREGRELERPLNVYGYSKFLFD-QYVRRRVLPEALSAQVVGLRYFN 169

Query: 158 IYGPKRN-----------PFIKIRQKNSLRLVK-----KNQVFNR--IRVEDVARCVIFL 199
           +YGP+              F +I+   +++L K     K+    R  + V+DV    ++L
Sbjct: 170 VYGPREYHKGKMASVAFHLFNQIKAGGNVKLFKSSEGFKDGEQLRDFVYVKDVVDVNLWL 229

Query: 200 MTHHLGGIFNL 210
           + + + GIFNL
Sbjct: 230 LENGVSGIFNL 240


>gnl|CDD|182998 PRK11150, rfaD, ADP-L-glycero-D-mannoheptose-6-epimerase;
           Provisional.
          Length = 308

 Score = 32.8 bits (75), Expect = 0.10
 Identities = 27/123 (21%), Positives = 54/123 (43%), Gaps = 13/123 (10%)

Query: 101 YLSSTSIYGNREGQWVDEHSFVHPISCVATQRFNAEKEWLAITKKLNIKLAVLRLSGIYG 160
           Y SS + YG R   +++E  +  P++     +F  ++    I  + N ++   R   +YG
Sbjct: 113 YASSAATYGGRTDDFIEEREYEKPLNVYGYSKFLFDEYVRQILPEANSQICGFRYFNVYG 172

Query: 161 PKRN--------PF---IKIRQKNSLRLVKKNQVFNR--IRVEDVARCVIFLMTHHLGGI 207
           P+           F    ++    + +L + ++ F R  + V DVA   ++   + + GI
Sbjct: 173 PREGHKGSMASVAFHLNNQLNNGENPKLFEGSENFKRDFVYVGDVAAVNLWFWENGVSGI 232

Query: 208 FNL 210
           FN 
Sbjct: 233 FNC 235


>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
          Length = 2033

 Score = 31.4 bits (70), Expect = 0.26
 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 199 LMTHHLGGIFNLSDDEPAPPQNVIMEAASLMKITPPLEQC 238
           ++  H   +F  SD   A PQ V M+ ASL   TPP+  C
Sbjct: 84  ILPEHSQDLFAFSDPTSASPQPVPMD-ASLSLFTPPVPDC 122


>gnl|CDD|162529 TIGR01777, yfcH, conserved hypothetical protein TIGR01777.  This
           model represents a clade of proteins of unknown function
           including the E. coli yfcH protein.
          Length = 292

 Score = 31.5 bits (72), Expect = 0.27
 Identities = 29/123 (23%), Positives = 49/123 (39%), Gaps = 16/123 (13%)

Query: 103 SSTSIYGNREGQWVDEHSFVHPISCVATQRFNAE--KEWLAITK---KLNIKLAVLRLSG 157
           S+   YG  E +   E          A   F AE  ++W    +    L  ++ +LR   
Sbjct: 111 SAVGYYGTSEDRVFTEED------SPAGDDFLAELCRDWEEAAQAAEDLGTRVVLLRTGI 164

Query: 158 IYGPKRNPFIKIRQKNSL----RLVKKNQVFNRIRVEDVARCVIFLMTH-HLGGIFNLSD 212
           + GPK     K+     L     L    Q F+ I +ED+ + ++F + +  + G  N + 
Sbjct: 165 VLGPKGGALAKMLPPFRLGLGGPLGSGRQWFSWIHIEDLVQLILFALENASISGPVNATA 224

Query: 213 DEP 215
            EP
Sbjct: 225 PEP 227


>gnl|CDD|163088 TIGR02964, xanthine_xdhC, xanthine dehydrogenase accessory protein
           XdhC.  Members of this protein family are the accessory
           protein XdhC for insertion of the molybdenum cofactor
           into the xanthine dehydrogenase large chain, XdhB, in
           bacteria. This protein is not part of the mature
           xanthine dehydrogenase. Xanthine dehydrogenase is an
           enzyme for purine catabolism, from other purines to
           xanthine to urate to further breakdown products.
          Length = 246

 Score = 30.0 bits (68), Expect = 0.68
 Identities = 7/18 (38%), Positives = 13/18 (72%)

Query: 1   MHLMIFGAGYTGKFIADA 18
            H+++FGAG+ G+ +  A
Sbjct: 101 PHVVLFGAGHVGRALVRA 118


>gnl|CDD|178326 PLN02725, PLN02725,
           GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase.
          Length = 306

 Score = 26.6 bits (59), Expect = 8.1
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 30/103 (29%)

Query: 187 IRVEDVARCVIFLMTHHLGGIFNLSDDEPAPPQNV-------IMEAASLMK--ITPPLEQ 237
           + V+D+A  V+FLM  + G          A   NV       I E A L+K  +    E 
Sbjct: 206 LHVDDLADAVVFLMRRYSG----------AEHVNVGSGDEVTIKELAELVKEVVGFEGEL 255

Query: 238 CFDTANISPFTRFFYADNKRISNAKIKSLGFQLLYPNYRISLK 280
            +DT+      R      K + ++K++SLG      + + SLK
Sbjct: 256 VWDTSKPDGTPR------KLMDSSKLRSLG-----WDPKFSLK 287


>gnl|CDD|178494 PLN02906, PLN02906, xanthine dehydrogenase.
          Length = 1319

 Score = 26.6 bits (59), Expect = 8.9
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 6    FGAGYTGKFIADAALKVGVYTCGT 29
            FG  +T KF+  A   V VYT GT
Sbjct: 1001 FGISFTTKFMNQAGALVHVYTDGT 1024


  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
   0.324    0.138    0.423 

Gapped
Lambda     K      H
   0.267   0.0735    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,717,820
Number of extensions: 291156
Number of successful extensions: 664
Number of sequences better than 10.0: 1
Number of HSP's gapped: 662
Number of HSP's successfully gapped: 13
Length of query: 289
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 197
Effective length of database: 4,006,537
Effective search space: 789287789
Effective search space used: 789287789
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 57 (25.7 bits)