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)