RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780919|ref|YP_003065332.1| dTDP-4-dehydrorhamnose
3,5-epimerase [Candidatus Liberibacter asiaticus str. psy62]
         (198 letters)



>1ep0_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; racemase,
           DTDP-4-dehydrorhamnose epimerase, structural genomics,
           PSI; 1.50A {Methanothermobacterthermautotrophicus} SCOP:
           b.82.1.1 PDB: 1epz_A*
          Length = 185

 Score =  220 bits (561), Expect = 2e-58
 Identities = 76/181 (41%), Positives = 101/181 (55%), Gaps = 7/181 (3%)

Query: 1   MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRG 55
                       I++   + D RG+F +T++  + +E GL+  FVQDN S S     +RG
Sbjct: 4   FRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRG-VLRG 62

Query: 56  LHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHG 115
           LHFQR    Q KLVR I G IFD+AVD+R+NS TYG W  + +S  N  + +IP GFAHG
Sbjct: 63  LHFQREK-PQGKLVRVIRGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHG 121

Query: 116 FMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQI 175
           F+ L     V YK T+ Y  E+DSG+ W D  I I WPL       +SEKD+N   L + 
Sbjct: 122 FLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLREN 181

Query: 176 D 176
            
Sbjct: 182 P 182


>1dzr_A DTDP-4-dehydrorhamnose 3,5-epimerase; isomerase, 3, 5-hexulose
           epimerase; 2.17A {Salmonella typhimurium} SCOP: b.82.1.1
           PDB: 1dzt_A*
          Length = 183

 Score =  217 bits (555), Expect = 1e-57
 Identities = 83/180 (46%), Positives = 113/180 (62%), Gaps = 9/180 (5%)

Query: 1   MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDV-FVQDNHSFSFDCGTIR 54
           M +       V IL+ + F D RG+F ++Y+ +  +EL  + V FVQDNHS S     +R
Sbjct: 2   MIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDNHSKSK-KNVLR 60

Query: 55  GLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAH 114
           GLHFQR   AQ KLVRC  G +FD+AVDIR+ SPT+G WV + +SA N  Q++IP GFAH
Sbjct: 61  GLHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWVGVNLSAENKRQLWIPEGFAH 120

Query: 115 GFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174
           GF+TL    E +YK T++YS   +  + W D++I I WP   + LP +S KD   P L+Q
Sbjct: 121 GFVTLSEYAEFLYKATNYYSPSSEGSILWNDEAIGIEWPF--SQLPELSAKDAAAPLLDQ 178


>1oi6_A PCZA361.16; epimerase, vancomycin group antibiotic, EVAD,
           isomerase; HET: TMP; 1.4A {Amycolatopsis orientalis}
           SCOP: b.82.1.1 PDB: 1ofn_A* 1wa4_A
          Length = 205

 Score =  176 bits (447), Expect = 3e-45
 Identities = 50/182 (27%), Positives = 79/182 (43%), Gaps = 10/182 (5%)

Query: 1   MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKEL--GLQDVFVQDNHSFSFDCGTI 53
           M               R F D RG     Y  +   E   G      Q  HS S   G +
Sbjct: 1   MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKR-GVV 59

Query: 54  RGLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFA 113
           RG+H+   P   AK V C  G+  DI +DIR  SPT+G W S+ +   +   +Y+P G  
Sbjct: 60  RGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVG 119

Query: 114 HGFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLN 173
           H F+ LE +T + Y ++  Y  + +  ++  D ++ +   +     P VS++D+    L 
Sbjct: 120 HAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVE--PIVSDRDRVAITLA 177

Query: 174 QI 175
           + 
Sbjct: 178 EA 179


>1nxm_A DTDP-6-deoxy-D-XYLO-4-hexulose 3,5-epimerase; jelly roll-like
           structure, beta sheet, isomerase; 1.30A {Streptococcus
           suis} SCOP: b.82.1.1 PDB: 1nyw_A* 1nzc_A* 2ixl_A*
          Length = 197

 Score =  135 bits (341), Expect = 6e-33
 Identities = 53/190 (27%), Positives = 80/190 (42%), Gaps = 18/190 (9%)

Query: 3   INPVRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVF-----VQDNHSFSFDCGTIRGLH 57
           I  +         D+RGWF + +  + +  LG  + F     +Q+N SFS     +RGLH
Sbjct: 18  IPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRK-NVLRGLH 76

Query: 58  FQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFM 117
                    K +    G          R   T+G      I A+    I++P G A+GF 
Sbjct: 77  A----EPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASK--SIFVPRGVANGFQ 130

Query: 118 TLEMNTEVIYKVTDFYSVEHD---SGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174
            L       Y V D++++E     + V + D S+DI W  L+     VSE D+N PFL  
Sbjct: 131 VLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEE--AEVSEADENHPFLKD 188

Query: 175 IDSPFEYDGL 184
           +  P   + L
Sbjct: 189 V-KPLRKEDL 197


>1upi_A DTDP-4-dehydrorhamnose 3,5-epimerase; rhamnose pathway, PSI,
           protein structure initiative, TB structural genomics
           consortium, TB; HET: CME; 1.7A {Mycobacterium
           tuberculosis} SCOP: b.82.1.1 PDB: 2ixc_A* 1pm7_A*
          Length = 225

 Score =  133 bits (335), Expect = 3e-32
 Identities = 54/184 (29%), Positives = 91/184 (49%), Gaps = 5/184 (2%)

Query: 1   MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRG 55
           M            +      DSRG F +  +    +      + V+  +      G +RG
Sbjct: 21  MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRG 80

Query: 56  LHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHG 115
           LHF + P +QAK V C++G +FD+ VDIR  SPT+G W S+ +   +   IY+  G AHG
Sbjct: 81  LHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHG 140

Query: 116 FMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQI 175
           F+ L+ N+ V+Y  +  Y+ + +  +   D ++ + WPL+D   PS+S++D   P    +
Sbjct: 141 FLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDV 200

Query: 176 DSPF 179
            +  
Sbjct: 201 RASG 204


>2ixk_A DTDP-4-dehydrorhamnose 3,5-epimerase; isomerase, lipopolysaccharide
           biosynthesis, epimerise, epimerize; HET: TDO; 1.7A
           {Pseudomonas aeruginosa} PDB: 2ixi_A* 2ixh_A* 1rtv_A*
           2ixj_A*
          Length = 184

 Score =  123 bits (310), Expect = 2e-29
 Identities = 78/182 (42%), Positives = 104/182 (57%), Gaps = 10/182 (5%)

Query: 1   MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKE-LGLQDVFVQDNHSFSFDCGTIR 54
           M         V + + R F D RG+F ++Y+ +  +E  G    FVQDNHS S   G +R
Sbjct: 4   MKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSA-RGVLR 62

Query: 55  GLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAH 114
           GLH+Q     Q KLVR   G +FD+AVD+RR SPT+G WV   +SA N  Q++IP GFAH
Sbjct: 63  GLHYQIRQA-QGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAH 121

Query: 115 GFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174
           GF+ L    E +YK TDF++ EH+  + W D  + I WPL D   P +SEKD+       
Sbjct: 122 GFVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDA--PLLSEKDRQGKAFAD 179

Query: 175 ID 176
            D
Sbjct: 180 AD 181


>1wlt_A 176AA long hypothetical DTDP-4-dehydrorhamnose 3, 5-epimerase;
           jelly roll-like topology, flattened barrel, isomerase;
           1.90A {Sulfolobus tokodaii} SCOP: b.82.1.1 PDB: 2b9u_A
          Length = 196

 Score =  123 bits (310), Expect = 2e-29
 Identities = 59/175 (33%), Positives = 101/175 (57%), Gaps = 10/175 (5%)

Query: 6   VRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPPYAQ 65
           + ++K + F D RG+F + + S+   ++ + +  +Q N SFS     +RGLH+QR P  Q
Sbjct: 32  IILIKPKVFPDKRGFFLEVFKSEDFTKMRIPN-VIQTNMSFSRKG-VVRGLHYQRTPKEQ 89

Query: 66  AKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTLEMNTEV 125
            K++    GRI D+AVD+R++SPT+G +V  E++  N   ++IP GFAHGF  LE +  +
Sbjct: 90  GKIIFVPKGRILDVAVDVRKSSPTFGKYVKAELNEENHYMLWIPPGFAHGFQALEDSIVI 149

Query: 126 IYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQIDSPFE 180
            +   + YS  H+  +++      I WP+ + I+   S+KD   P L + +  F+
Sbjct: 150 YFITHNEYSPPHERCISYS----YIDWPIKEVII---SDKDLQCPSLEKAE-VFD 196


>2c0z_A NOVW; isomerase, epimerase, antibiotic biosynthesis, RMLC-like
           cupin; 1.60A {Streptomyces sphaeroides} SCOP: b.82.1.1
          Length = 216

 Score =  119 bits (299), Expect = 4e-28
 Identities = 55/181 (30%), Positives = 78/181 (43%), Gaps = 10/181 (5%)

Query: 1   MNINP-----VRILKTRKFEDSRGWFSQTYSSKLLKE-LGLQDVFVQDNHSFSFDCGTIR 54
           M + P     V  +   +  D RG F   Y      E +G      Q N S S     +R
Sbjct: 10  MRLRPLGIEGVWEITPEQRADPRGVFLDWYHVDRFAEAIGRPLRLAQANLSVSVRG-VVR 68

Query: 55  GLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAH 114
           G+HF   P  QAK V C+ G +FD+ VD+R  SPTYGCW    +   +   +Y+  G  H
Sbjct: 69  GIHFVDVPPGQAKYVTCVRGAVFDVVVDLRVGSPTYGCWEGTRLDDVSRRAVYLSEGIGH 128

Query: 115 GFMTLEMNTEVIYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQ 174
           GF  +     + Y  +  Y    + GV   D  + I WP    +L   S +DQ+   L +
Sbjct: 129 GFCAISDEATLCYLSSGTYDPATEHGVHPLDPELAIDWPTGTPLL---SPRDQDALLLAE 185

Query: 175 I 175
            
Sbjct: 186 A 186


>3ejk_A DTDP sugar isomerase; YP_390184.1, structural genomics, joint
           center for structural genomics, JCSG; HET: CIT; 1.95A
           {Desulfovibrio desulfuricans subsp}
          Length = 174

 Score = 96.0 bits (238), Expect = 5e-21
 Identities = 22/158 (13%), Positives = 44/158 (27%), Gaps = 10/158 (6%)

Query: 1   MNINPVRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQR 60
           + +   ++ + R+     G           +       F +   S       ++      
Sbjct: 18  LPVEGAQLSELRQIPAEGGPVLHMLRLDSPQFSQ----FGEIYFSEVL-PRRVKAWKRHS 72

Query: 61  PPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQ-IYIPTGFAHGFMTL 119
                 +L     G I  +  D R  SPT G    + +   +  + + IP    +GF   
Sbjct: 73  LMT---QLFAVPVGCIHVVLYDGREKSPTSGRLAQVTLGRPDNYRLLRIPPQVWYGFAAT 129

Query: 120 EMNTEVIYKVTD-FYSVEHDSGVAWQDKSIDITWPLLD 156
                ++   TD  +              I  +W   D
Sbjct: 130 GDTPALVANCTDIPHRQGESERAPQDAPFIPFSWAGAD 167


>2pa7_A DTDP-6-deoxy-3,4-keto-hexulose isomerase; deoxysugar biosynthesis,
           S-layer biosynthesis, ketoisomerase; HET: TYD; 1.50A
           {Aneurinibacillus thermoaerophilus} SCOP: b.82.1.1 PDB:
           2pae_A* 2pak_A* 2pam_A*
          Length = 141

 Score = 61.6 bits (149), Expect = 1e-10
 Identities = 19/134 (14%), Positives = 40/134 (29%), Gaps = 19/134 (14%)

Query: 1   MNINPVRILKTRKFEDSRGWFSQTYSSKLLKELGLQDVFVQDNHSFSFDCGTIRGLHFQR 60
           M     +++  +K  DSRG       +K +          +  + F       RG H  +
Sbjct: 3   MEN---KVINFKKIIDSRGSLVAIEENKNIPF-----SIKRVYYIFDTKGEEPRGFHAHK 54

Query: 61  PPYAQAKLVRCIAGRIFDIAVDIRRNSPTYGCWVSLEISANNGLQIYIPTGFAHGFMTLE 120
                 +++ C+ G    I  D                     + +Y+     H      
Sbjct: 55  K---LEQVLVCLNGSCRVILDDGNIIQEITLDS--------PAVGLYVGPAVWHEMHDFS 103

Query: 121 MNTEVIYKVTDFYS 134
            +  ++   +D+Y 
Sbjct: 104 SDCVMMVLASDYYD 117


>2zkl_A Capsular polysaccharide synthesis enzyme CAP5F; rossmann fold,
           isomerase; 2.61A {Staphylococcus aureus}
          Length = 369

 Score = 50.3 bits (119), Expect = 3e-07
 Identities = 15/109 (13%), Positives = 34/109 (31%), Gaps = 10/109 (9%)

Query: 30  LKELGLQDVFVQDNHSFSFDCGTIRGLHFQRPPYAQAKLVRCIAGRIFDIAVDIRRNSPT 89
             E        Q + + S   G  +G H+        +    ++G+       +  +   
Sbjct: 262 FTEFIKTPDRGQVSVNISKP-GITKGNHWHHTKN---EKFLVVSGKGVIRFRHVNDDEI- 316

Query: 90  YGCWVSLEISANNGLQIYIPTGFAHGFMTL-EMNTEVIYKVTDFYSVEH 137
               +   +S +    + IP G+ H    L + +   I  V + +    
Sbjct: 317 ----IEYYVSGDKLEVVDIPVGYTHNIENLGDTDMVTIMWVNEMFDPNQ 361


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 27.6 bits (61), Expect = 1.9
 Identities = 10/85 (11%), Positives = 20/85 (23%), Gaps = 32/85 (37%)

Query: 145 DKSIDITWP-----------LLDTILPSVSEKDQNLPFLNQIDSPFE------------- 180
             S++               L +     + E  +     ++  +P E             
Sbjct: 13  HGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLV 72

Query: 181 -------YDGLPLLSLN-MERDLLC 197
                  +D +  L L   E   L 
Sbjct: 73  EPSKVGQFDQVLNLCLTEFENCYLE 97



 Score = 27.2 bits (60), Expect = 2.8
 Identities = 25/192 (13%), Positives = 50/192 (26%), Gaps = 75/192 (39%)

Query: 22  SQTYSSKLLKELGLQDV---FVQDN--HSFSFDCGTIRGL--HFQRPPYAQAKLVRC--- 71
                 ++L    L +    +++ N  H+          L            +L++    
Sbjct: 76  KVGQFDQVLNLC-LTEFENCYLEGNDIHAL------AAKLLQENDTTLVKTKELIKNYIT 128

Query: 72  ---IAGRIFDIAVDIRRNSPTYGCWVSLEISANNG-LQIYIPTGF-AHGFMTLEMNTEV- 125
              +A R         + S +     +L  +   G  Q+     F   G      NT+  
Sbjct: 129 ARIMAKR------PFDKKSNS-----ALFRAVGEGNAQLV--AIFGGQG------NTDDY 169

Query: 126 ------IYKVTDFYSVEHDSGVAWQDKSIDITWPLLDTILPSVSEKDQNLPFLNQIDSPF 179
                 +Y+    Y                    L+  ++   +E       L +     
Sbjct: 170 FEELRDLYQT---YH------------------VLVGDLIKFSAETLSE---LIRTTLDA 205

Query: 180 EY---DGLPLLS 188
           E     GL +L 
Sbjct: 206 EKVFTQGLNILE 217


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.323    0.139    0.434 

Gapped
Lambda     K      H
   0.267   0.0556    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,722,999
Number of extensions: 75556
Number of successful extensions: 192
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 15
Length of query: 198
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 110
Effective length of database: 3,559,758
Effective search space: 391573380
Effective search space used: 391573380
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 (21.9 bits)
S2: 54 (25.0 bits)