RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780921|ref|YP_003065334.1| dTDP-4-dehydrorhamnose
reductase [Candidatus Liberibacter asiaticus str. psy62]
         (290 letters)



>gnl|CDD|162255 TIGR01214, rmlD, dTDP-4-dehydrorhamnose reductase.  This enzyme
           catalyzes the last of 4 steps in making dTDP-rhamnose, a
           precursor of LPS core antigen, O-antigen, etc.
          Length = 287

 Score =  270 bits (693), Expect = 2e-73
 Identities = 113/290 (38%), Positives = 163/290 (56%), Gaps = 10/290 (3%)

Query: 2   KCLVIGNNGQIAQSL-SSMCVQDVEIIRVGRPDIDLLKPKDFASFFLSFSPDVIINPAAY 60
           + L+ G NGQ+ + L   +  +   ++ +    +DL  P+       +  PD ++N AAY
Sbjct: 1   RILITGANGQLGRELVQQLSPEGRVVVALTSSQLDLTDPEALERLLRAIRPDAVVNTAAY 60

Query: 61  TAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIPCIYISTDYVFDGLSRTPIDEFSPTNP 120
           T VD AE +PE AF++NA     +A+AA   G   ++ISTDYVFDG  + P  E   TNP
Sbjct: 61  TDVDGAESDPEKAFAVNALAPQNLARAAARHGARLVHISTDYVFDGEGKRPYREDDATNP 120

Query: 121 LNIYGKSKLAGEEKVASYTNNYVILRTAWVYSIFGS-NFLLSMLRLAKERREISVVCDQF 179
           LN+YG+SKLAGE+ + +   N +I+RT+W+Y   G  NF+ +MLRLA    E+ VV DQ 
Sbjct: 121 LNVYGQSKLAGEQAIRAAGPNALIVRTSWLYGGGGGRNFVRTMLRLAGRGEELRVVDDQI 180

Query: 180 GTPTSALQIARAIIQIAHNLIENSDTSLRGIFHMTADGGPVSWADFAEYIFWESAERGGP 239
           G+PT A  +AR I  +   L        RG++H+    G  SW +FA+ IF E+   G  
Sbjct: 181 GSPTYAKDLARVIAALLQRLAR-----ARGVYHLANS-GQCSWYEFAQAIFEEAGADGLL 234

Query: 240 YS--KVYRIFTKQYPTKAHRPAYSCLDCSKLANTHNIRISTWKEGVRNIL 287
               +V  I +K+YP  A RPAYS LD +KL  T    +  W+E +R  L
Sbjct: 235 LHPQEVKPISSKEYPRPARRPAYSVLDNTKLVKTLGTPLPHWREALRAYL 284


>gnl|CDD|182184 PRK09987, PRK09987, dTDP-4-dehydrorhamnose reductase; Provisional.
          Length = 299

 Score =  228 bits (582), Expect = 2e-60
 Identities = 112/297 (37%), Positives = 161/297 (54%), Gaps = 11/297 (3%)

Query: 1   MKCLVIGNNGQIAQSLSSMCVQDVEIIRVGRPDI----DLLKPKDFASFFLSFSPDVIIN 56
           M  L+ G  GQ+   L         +I +         D   P+  A       PDVI+N
Sbjct: 1   MNILLFGKTGQVGWELQRALAPLGNLIALDVHSTDYCGDFSNPEGVAETVRKIRPDVIVN 60

Query: 57  PAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIPCIYISTDYVFDGLSRTPIDEFS 116
            AA+TAVDKAE EPE A  +NA    AIAKAA+ +G   ++ STDYVF G    P  E  
Sbjct: 61  AAAHTAVDKAESEPEFAQLLNATSVEAIAKAANEVGAWVVHYSTDYVFPGTGDIPWQETD 120

Query: 117 PTNPLNIYGKSKLAGEEKVASYTNNYVILRTAWVYSIFGSNFLLSMLRLAKERREISVVC 176
            T PLN+YG++KLAGE+ +  +   ++I RT+WVY+  G+NF  +MLRLAKER E+SV+ 
Sbjct: 121 ATAPLNVYGETKLAGEKALQEHCAKHLIFRTSWVYAGKGNNFAKTMLRLAKEREELSVIN 180

Query: 177 DQFGTPTSALQIARAIIQIAHNL-IENSDTSLRGIFHMTADGGPVSWADFAEYIFWESAE 235
           DQFG PT A  +A      AH + +  +   + G++H+ A  G  +W D+A  +F E+ +
Sbjct: 181 DQFGAPTGAELLADC---TAHAIRVALNKPEVAGLYHLVA-SGTTTWHDYAALVFEEARK 236

Query: 236 RGGPYS--KVYRIFTKQYPTKAHRPAYSCLDCSKLANTHNIRISTWKEGVRNILVNI 290
            G   +  K+  + T  YPT A RP  S L+  K      + +  W+ GV+ +L  +
Sbjct: 237 AGITLALNKLNAVPTSAYPTPARRPHNSRLNTEKFQQNFALVLPDWQVGVKRMLTEL 293


>gnl|CDD|130247 TIGR01179, galE, UDP-glucose-4-epimerase.  This enzyme
           interconverts UDP-glucose and UDP-galactose. A set of
           related proteins, some of which are tentatively
           identified as UDP-glucose-4-epimerase in Thermotoga
           maritima, Bacillus halodurans, and several archaea, but
           deeply branched from this set and lacking experimental
           evidence, are excluded from this model and described
           separately.
          Length = 328

 Score = 52.0 bits (125), Expect = 2e-07
 Identities = 35/118 (29%), Positives = 51/118 (43%), Gaps = 6/118 (5%)

Query: 35  DLLKPKDFASFFLSFSPDVIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGI- 93
           DL   +     F     D +I+ A   AV ++  +P   +  N      + +A    G+ 
Sbjct: 55  DLRDRELLDRLFEEHKIDAVIHFAGLIAVGESVQDPLKYYRNNVVNTLNLLEAMQQTGVK 114

Query: 94  PCIYISTDYVFDGLSRTPIDEFSPTNPLNIYGKSKLAGEE-----KVASYTNNYVILR 146
             I+ S+  V+   S  PI E SP  P+N YG+SKL  E        A    +YVILR
Sbjct: 115 KFIFSSSAAVYGEPSSIPISEDSPLGPINPYGRSKLMSERILRDLSKADPGLSYVILR 172


>gnl|CDD|130249 TIGR01181, dTDP_gluc_dehyt, dTDP-glucose 4,6-dehydratase.  This
           protein is related to UDP-glucose 4-epimerase (GalE) and
           likewise has an NAD cofactor.
          Length = 317

 Score = 47.0 bits (112), Expect = 5e-06
 Identities = 34/128 (26%), Positives = 53/128 (41%), Gaps = 11/128 (8%)

Query: 21  VQDVEIIRVGRPDI-DLLKPKDFASFFLSFSPDVIINPAAYTAVDKAEDEPEIAFSINAE 79
           ++D    R  + DI D    +  +  F    PD +++ AA + VD++   P      N  
Sbjct: 46  LEDNPRYRFVKGDIGDR---ELVSRLFTEHQPDAVVHFAAESHVDRSISGPAAFIETNVV 102

Query: 80  GAGAIAKAA--DSIGIPCIYISTDYVFDGLSRTPIDEFSPTNPLN---IYGKSKLAGEEK 134
           G   + +A           +ISTD V+  L +   D F+ T PL     Y  SK A +  
Sbjct: 103 GTYTLLEAVRKYWHEFRFHHISTDEVYGDLEKG--DAFTETTPLAPSSPYSASKAASDHL 160

Query: 135 VASYTNNY 142
           V +Y   Y
Sbjct: 161 VRAYHRTY 168


>gnl|CDD|132628 TIGR03589, PseB, UDP-N-acetylglucosamine 4,6-dehydratase.  This
           enzyme catalyzes the first step in the biosynthesis of
           pseudaminic acid, the conversion of
           UDP-N-acetylglucosamine to
           UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences
           are members of the broader pfam01073 (3-beta
           hydroxysteroid dehydrogenase/isomerase family) family.
          Length = 324

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 27/93 (29%), Positives = 39/93 (41%), Gaps = 16/93 (17%)

Query: 52  DVIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIP-CIYISTDYVFDGLSRT 110
           D +++ AA   V  AE  P      N  GA  +  AA   G+   + +STD         
Sbjct: 76  DYVVHAAALKQVPAAEYNPFECIRTNINGAQNVIDAAIDNGVKRVVALSTD--------- 126

Query: 111 PIDEFSPTNPLNIYGKSKLAGEEKVASYTNNYV 143
                   NP+N+YG +KLA  +K+    NN  
Sbjct: 127 -----KAANPINLYGATKLA-SDKLFVAANNIS 153


>gnl|CDD|182313 PRK10217, PRK10217, dTDP-glucose 4,6-dehydratase; Provisional.
          Length = 355

 Score = 34.2 bits (78), Expect = 0.044
 Identities = 31/123 (25%), Positives = 52/123 (42%), Gaps = 16/123 (13%)

Query: 34  IDLLKPKDFASFFLSFSPDVIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSI-- 91
           +D+    + A  F    PD +++ AA + VD++ D P      N  G   + +AA +   
Sbjct: 58  VDICDRAELARVFTEHQPDCVMHLAAESHVDRSIDGPAAFIETNIVGTYTLLEAARAYWN 117

Query: 92  --------GIPCIYISTDYVFDGLSRTPIDEF----SPTNPLNIYGKSKLAGEEKVASYT 139
                        +ISTD V+  L  T  D+F    +P  P + Y  SK + +  V ++ 
Sbjct: 118 ALTEDKKSAFRFHHISTDEVYGDLHST--DDFFTETTPYAPSSPYSASKASSDHLVRAWL 175

Query: 140 NNY 142
             Y
Sbjct: 176 RTY 178


>gnl|CDD|162953 TIGR02622, CDP_4_6_dhtase, CDP-glucose 4,6-dehydratase.  Members of
           this protein family are CDP-glucose 4,6-dehydratase from
           a variety of Gram-negative and Gram-positive bacteria.
           Members typically are encoded next to a gene that
           encodes a glucose-1-phosphate cytidylyltransferase,
           which produces the substrate, CDP-D-glucose, used by
           this enzyme to produce CDP-4-keto-6-deoxyglucose.
          Length = 349

 Score = 33.8 bits (78), Expect = 0.051
 Identities = 24/105 (22%), Positives = 46/105 (43%), Gaps = 7/105 (6%)

Query: 43  ASFFLSFSPDVIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIPC--IYIST 100
                 F P+++ + AA   V K+  +P   F  N  G   + +A  +IG     + +++
Sbjct: 68  RKAIAEFKPEIVFHLAAQPLVRKSYADPLETFETNVMGTVNLLEAIRAIGSVKAVVNVTS 127

Query: 101 DYVFDGLSRTPIDEFSPTNPL---NIYGKSKLAGEEKVASYTNNY 142
           D  +       +  +  T+PL   + Y  SK   E  +ASY +++
Sbjct: 128 DKCYRNDEW--VWGYRETDPLGGHDPYSSSKACAELVIASYRSSF 170


>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 = 32.6 bits (75), Expect = 0.10
 Identities = 13/38 (34%), Positives = 17/38 (44%)

Query: 92  GIPCIYISTDYVFDGLSRTPIDEFSPTNPLNIYGKSKL 129
           GIP IY S+   +        +      PLN+YG SK 
Sbjct: 106 GIPFIYASSAATYGDGEAGFREGRELERPLNVYGYSKF 143


>gnl|CDD|185387 PRK15490, PRK15490, Vi polysaccharide biosynthesis protein TviE;
           Provisional.
          Length = 578

 Score = 32.7 bits (74), Expect = 0.12
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 165 LAKERREISVVCDQFGTPTS--ALQIARAIIQIAHNLIENSDTSLRGIFHMTADGGPVSW 222
           L  E +   VV +    P++  + ++   I Q      +++DT++ G+F    D  P +W
Sbjct: 357 LKLEAKHFQVVYNGVLPPSTEPSSEVPHKIWQQFTQKTQDADTTIGGVFRFVGDKNPFAW 416

Query: 223 ADFA 226
            DFA
Sbjct: 417 IDFA 420


>gnl|CDD|177839 PLN02187, PLN02187, rooty/superroot1.
          Length = 462

 Score = 31.6 bits (71), Expect = 0.27
 Identities = 39/156 (25%), Positives = 65/156 (41%), Gaps = 33/156 (21%)

Query: 16  LSSMCVQDVEII--RVGRPDIDLLKPKDFASFFLSFSPDVIINPAAYTAVD--KAEDEPE 71
           L++ C Q +EI+   + RP+ ++L P+     + +         AAY+ ++  K +  PE
Sbjct: 136 LTAGCNQGIEIVFESLARPNANILLPRPGFPHYDA--------RAAYSGLEVRKFDLLPE 187

Query: 72  IAFSINAEGAGAIAKAADSIGIPCIYISTDYVFDGLSRTPIDEFSPTNPL-NIYGKSKLA 130
             + I+ EG  AIA   D   +  + I+                 P NP  N+Y    L 
Sbjct: 188 KEWEIDLEGIEAIA---DENTVAMVVIN-----------------PNNPCGNVYSHDHLK 227

Query: 131 GEEKVASYTNNYVILRTAWVYSIFGSNFLLSMLRLA 166
              + A      VI    +  +IFG N  +SM + A
Sbjct: 228 KVAETARKLGIMVISDEVYDRTIFGDNPFVSMGKFA 263


>gnl|CDD|182639 PRK10675, PRK10675, UDP-galactose-4-epimerase; Provisional.
          Length = 338

 Score = 31.3 bits (71), Expect = 0.30
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 46  FLSFSPDVIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIP-CIYISTDYVF 104
               + D +I+ A   AV ++  +P   +  N  G   +  A  +  +   I+ S+  V+
Sbjct: 69  LHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNLIFSSSATVY 128

Query: 105 DGLSRTPIDEFSPT-NPLNIYGKSKLAGEE 133
               + P  E  PT  P + YGKSKL  E+
Sbjct: 129 GDQPKIPYVESFPTGTPQSPYGKSKLMVEQ 158


>gnl|CDD|169939 PRK09517, PRK09517, multifunctional thiamine-phosphate
           pyrophosphorylase/synthase/phosphomethylpyrimidine
           kinase; Provisional.
          Length = 755

 Score = 30.7 bits (69), Expect = 0.42
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 8/66 (12%)

Query: 51  PDVI-INPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIPCIYISTDYVFD--GL 107
           PDVI I P A TA      +P+   ++  +G   IA  A   GI  + I    + +   L
Sbjct: 129 PDVIGIGPVASTAT-----KPDAPPALGVDGIAEIAAVAQDHGIASVAIGGVGLRNAAEL 183

Query: 108 SRTPID 113
           + T ID
Sbjct: 184 AATGID 189


>gnl|CDD|181045 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
          Length = 199

 Score = 30.2 bits (69), Expect = 0.59
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 1  MKCLVIGNNGQIAQSLSSMCVQDVEIIRVGR 31
          MK LVIG +G I +++ +   +  E+I  GR
Sbjct: 1  MKILVIGASGTIGRAVVAELSKRHEVITAGR 31


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

 Score = 28.9 bits (65), Expect = 1.8
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 93  IPCIYISTDYVFDGLSRTPIDEFSPTNPLNIYGKSK 128
           IP +Y S+   + G +   I+E     PLN+YG SK
Sbjct: 109 IPFLYASSAATYGGRTDDFIEEREYEKPLNVYGYSK 144


>gnl|CDD|178298 PLN02695, PLN02695, GDP-D-mannose-3',5'-epimerase.
          Length = 370

 Score = 28.6 bits (64), Expect = 2.0
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 117 PTNPLNIYGKSKLAGEEKVASYTNNYVI-LRTAWVYSIFG 155
           P  P + YG  KLA EE    YT ++ I  R    ++I+G
Sbjct: 160 PAEPQDAYGLEKLATEELCKHYTKDFGIECRIGRFHNIYG 199


>gnl|CDD|129307 TIGR00203, cydB, cytochrome d oxidase, subunit II (cydB).  part of
           a two component cytochrome D terminal complex. Terminal
           reaction in the aerobic respiratory chain.
          Length = 378

 Score = 28.3 bits (63), Expect = 2.1
 Identities = 23/95 (24%), Positives = 36/95 (37%), Gaps = 12/95 (12%)

Query: 102 YVFDGLSRTPIDEFSPTNPLNIYGKSKLAGEEKVASYTNNYVILRTAWVYSIFGSNFLLS 161
           Y  DG      D  +P+NPLN     K    E  A + NN+      W++   G   +  
Sbjct: 224 YGIDGFVVRSQDHNAPSNPLN-----KEVAVEPGA-WMNNFNEEPILWIFPALG--VVCP 275

Query: 162 MLRLAKERREISVVCDQFGTPTSALQIARAIIQIA 196
           +L     R++     D +    S+L +A  I    
Sbjct: 276 LLTAVFIRKKK----DGWAFGMSSLTLAGVIGTAG 306


>gnl|CDD|180053 PRK05395, PRK05395, 3-dehydroquinate dehydratase; Provisional.
          Length = 146

 Score = 28.1 bits (64), Expect = 2.6
 Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 17/44 (38%)

Query: 53 VIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAADSIGIPCI 96
          +IINP AYT             S+      A+  A  ++ IP I
Sbjct: 71 IIINPGAYT-----------HTSV------ALRDALAAVSIPVI 97


>gnl|CDD|179859 PRK04527, PRK04527, argininosuccinate synthase; Provisional.
          Length = 400

 Score = 27.5 bits (61), Expect = 3.9
 Identities = 14/41 (34%), Positives = 17/41 (41%)

Query: 200 IENSDTSLRGIFHMTADGGPVSWADFAEYIFWESAERGGPY 240
           IE     L    H+T DGGP  W  F + + W      G Y
Sbjct: 47  IEKRAAELGAASHVTVDGGPAIWEGFVKPLVWAGEGYQGQY 87


>gnl|CDD|178119 PLN02503, PLN02503, fatty acyl-CoA reductase 2.
          Length = 605

 Score = 27.1 bits (60), Expect = 5.7
 Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 3/37 (8%)

Query: 52  DVIINPAAYTAVDKAEDEPEIAFSINAEGAGAIAKAA 88
           DVIIN AA T  D+  D   +A  IN  G   +   A
Sbjct: 221 DVIINSAANTTFDERYD---VAIDINTRGPCHLMSFA 254


>gnl|CDD|177883 PLN02240, PLN02240, UDP-glucose 4-epimerase.
          Length = 352

 Score = 26.8 bits (60), Expect = 6.5
 Identities = 10/23 (43%), Positives = 13/23 (56%)

Query: 111 PIDEFSPTNPLNIYGKSKLAGEE 133
           P  E  P +  N YG++KL  EE
Sbjct: 143 PCTEEFPLSATNPYGRTKLFIEE 165


>gnl|CDD|182912 PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional.
          Length = 330

 Score = 26.8 bits (60), Expect = 7.1
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 16/65 (24%)

Query: 72  IAFSINAEGAGAIAKAADSI--GIPCIYISTD----------YVFDGLSRTPIDEFS-PT 118
           +++ I  +GA  +  AA+S   G P  +ISTD          Y  + +S +P+D+   P 
Sbjct: 60  LSYRIADDGA--LTFAAESPLPGSP-THISTDHQGRFLFSASYNANCVSVSPLDKDGIPV 116

Query: 119 NPLNI 123
            P+ I
Sbjct: 117 APIQI 121


>gnl|CDD|151214 pfam10728, DUF2520, Domain of unknown function (DUF2520).  This
           presumed domain is found C-terminal to a Rossmann-like
           domain suggesting that these proteins are
           oxidoreductases.
          Length = 131

 Score = 26.4 bits (59), Expect = 9.4
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 8/49 (16%)

Query: 154 FGSNFLLSMLRLAKERREISVVCDQFGTPTSALQIARAIIQIAHNLIEN 202
           F SNFL+++L LA E      + ++ G P        A++ +    ++N
Sbjct: 44  FASNFLVTLLALAAE------LLEEAGIP--FEDALEALLPLIRGTLDN 84


  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    0.136    0.406 

Gapped
Lambda     K      H
   0.267   0.0686    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,771,017
Number of extensions: 307220
Number of successful extensions: 663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 26
Length of query: 290
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 197
Effective length of database: 3,984,929
Effective search space: 785031013
Effective search space used: 785031013
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: 57 (25.8 bits)