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)