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)