The Daily SEED


PUBSEED ANNOTATIONS

In 22 genomes
OLD: 1,4-lactonase (EC 3.1.1.25)
NEW: L-ascorbate-6-phosphate lactonase UlaG # predicted from context

In 18 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter large permease protein yiaN
NEW: 2,3-diketo-L-gulonate TRAP transporter, large permease protein YiaN

In 94 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter large permease protein yiaN
NEW: 2,3-diketo-L-gulonate TRAP transporter, large permease protein YiaN

In 103 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter large permease protein yiaN based on FIGfams
NEW: 2,3-diketo-L-gulonate TRAP transporter, large permease protein YiaN

In 19 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter small permease protein yiaM
NEW: 2,3-diketo-L-gulonate TRAP transporter, small permease protein YiaM

In 97 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter small permease protein yiaM
NEW: 2,3-diketo-L-gulonate TRAP transporter, small permease protein YiaM

In 2 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter small permease protein yiaM based on FIGfams
NEW: TRAP-type C4-dicarboxylate transport system, small permease component

In 129 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter small permease protein yiaM based on FIGfams
NEW: 2,3-diketo-L-gulonate TRAP transporter, small permease protein YiaM

In 7 genomes
OLD: 2,3-diketo-L-gulonate TRAP transporter small permease protein yiaM based on unreliable automated assignments
NEW: 2,3-diketo-L-gulonate TRAP transporter, small permease protein YiaM

In 1 genome
OLD: 2,3-diketo-L-gulonate-binding periplasmic protein yiaO precursor
NEW: 2,3-diketo-L-gulonate TRAP transporter, substrate-binding protein YiaO

In 23 genomes
OLD: 2,3-diketo-L-gulonate-binding periplasmic protein yiaO precursor
NEW: 2,3-diketo-L-gulonate TRAP transporter, substrate-binding protein YiaO

In 62 genomes
OLD: 2,3-diketo-L-gulonate-binding periplasmic protein yiaO precursor based on FIGfams
NEW: 2,3-diketo-L-gulonate TRAP transporter, substrate-binding protein YiaO

In 1 genome
OLD: 2,3-diketo-L-gulonate-binding periplasmic protein yiaO precursor based on unreliable automated assignments
NEW: 2,3-diketo-L-gulonate TRAP transporter, substrate-binding protein YiaO

In 2 genomes
OLD: 2,3-diketo-L-gulonate-binding periplasmic protein yiaO precursor based on unreliable automated assignments
NEW: TRAP-type C4-dicarboxylate transport system, periplasmic component

In 46 genomes
OLD: 2-ketoarginine decarboxylase AruI
NEW: 5-guanidino-2-oxopentanoate decarboxylase AruI (EC 4.1.1.75)

In 2 genomes
OLD: 2-ketoarginine decarboxylase like
NEW: 5-guanidino-2-oxopentanoate decarboxylase AruI (EC 4.1.1.75)

In 1 genome
OLD: 3-dehydro-L-gulonate 2-dehydrogenase (EC 1.1.1.130)
NEW: Malate/L-lactate dehydrogenase-like protein

In 2 genomes
OLD: 3-dehydro-L-gulonate 2-dehydrogenase (EC 1.1.1.130)
NEW: Malate/L-lactate dehydrogenase-like protein

In 2 genomes
OLD: 3-dehydro-L-gulonate 2-dehydrogenase (EC 1.1.1.130) based on FIGfams
NEW: Malate/L-lactate dehydrogenase-like protein

In 1 genome
OLD: 3-dehydro-L-gulonate 2-dehydrogenase (EC 1.1.1.130) based on unreliable automated assignments
NEW: Malate/L-lactate dehydrogenase-like protein

In 1 genome
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase
NEW: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)

In 5 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 23 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase
NEW: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)

In 707 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 2 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)
NEW: 3-keto-L-gulonate 6-phosphate decarboxylase homolog

In 631 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)

In 8 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase based on FIGfams
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 94 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase based on FIGfams
NEW: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)

In 1 genome
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase based on unreliable automated assignments
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 3 genomes
OLD: 3-keto-L-gulonate 6-phosphate decarboxylase homolog
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)

In 158 genomes
OLD: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 1 genome
OLD: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)

In 3 genomes
OLD: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 14 genomes
OLD: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)
NEW: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)

In 4 genomes
OLD: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)

In 1 genome
OLD: Aldehyde dehydrogenase (NAD(+)) (EC 1.2.1.3)
NEW: Aldehyde dehydrogenase B (EC 1.2.1.22)

In 1 genome
OLD: Aromatic amino acid transport protein
NEW: Tyrosine-specific transport protein

In 1 genome
OLD: Ascorbate utilization transcriptional regulator UlaR, DeoR family
NEW: Ascorbate utilization transcriptional regulator, DeoR family # based on context

In 2 genomes
OLD: Ascorbate utilization transcriptional regulator UlaR, HTH-type
NEW: Ascorbate utilization transcriptional regulator UlaR, DeoR family

In 417 genomes
OLD: Ascorbate utilization transcriptional regulator YiaJ, IclR family
NEW: Transcriptional regulator YiaJ, IclR family

In 1 genome
OLD: COG0187: Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit
NEW: Uncharacterized protein STM3670

In 1 genome
OLD: COG3533 secreted protein
NEW: Putative glycosyl hydrolase of unknown function (DUF1680)

In 2 genomes
OLD: Histidine kinase
NEW: Aerobic respiration control sensor protein ArcB (EC 2.7.13.3)

In 3 genomes
OLD: Integral membrane protein based on FIGfams
NEW: YjjP-like membrane protein

In 1 genome
OLD: Integral membrane protein based on unreliable automated assignments
NEW: YjjP-like membrane protein

In 14 genomes
OLD: L-ribulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.22)
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 137 genomes
OLD: L-ribulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.22)
NEW: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)

In 7 genomes
OLD: L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22)
NEW: L-ribulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.22)

In 6 genomes
OLD: L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22)
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 302 genomes
OLD: L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22)
NEW: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)

In 24 genomes
OLD: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)
NEW: L-ribulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.22)

In 46 genomes
OLD: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 2 genomes
OLD: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)
NEW: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)

In 106 genomes
OLD: L-ribulose-5-phosphate 3-epimerase-like protein
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 2 genomes
OLD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase SgbE (EC 5.1.3.4)

In 1 genome
OLD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)

In 7 genomes
OLD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase SgbE (EC 5.1.3.4)

In 16 genomes
OLD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)

In 54 genomes
OLD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) based on FIGfams
NEW: L-ribulose-5-phosphate 4-epimerase SgbE (EC 5.1.3.4)

In 89 genomes
OLD: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) based on FIGfams
NEW: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)

In 155 genomes
OLD: L-ribulose-5-phosphate 4-epimerase SgbE (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)

In 4 genomes
OLD: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase SgbE (EC 5.1.3.4)

In 3 genomes
OLD: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)
NEW: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)

In 1 genome
OLD: L-xylulokinase (EC 2.7.1.53) @ 3-keto-L-gulonate kinase
NEW: L-xylulose kinase (EC 2.7.1.53) @ 3-keto-L-gulonate kinase

In 4 genomes
OLD: L-xylulokinase (EC 2.7.1.53) @ 3-keto-L-gulonate kinase
NEW: Xylulose kinase (EC 2.7.1.17)

In 116 genomes
OLD: L-xylulose 5-phosphate 3-epimerase
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 308 genomes
OLD: L-xylulose 5-phosphate 3-epimerase
NEW: L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22)

In 24 genomes
OLD: L-xylulose 5-phosphate 3-epimerase
NEW: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)

In 1 genome
OLD: L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.-)
NEW: L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22)

In 1 genome
OLD: L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.-) based on FIGfams
NEW: L-ribulose-5-phosphate 3-epimerase (EC 5.1.3.22)

In 5 genomes
OLD: L-xylulose 5-phosphate 3-epimerase (EC 5.1.3.22)
NEW: L-xylulose 5-phosphate 3-epimerase homolog SgbU

In 435 genomes
OLD: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)
NEW: L-ribulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.22)

In 8 genomes
OLD: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)
NEW: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)

In 12 genomes
OLD: L-xylulose 5-phosphate 3-epimerase homolog
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 22 genomes
OLD: L-xylulose 5-phosphate 3-epimerase homolog
NEW: L-ribulose-5-phosphate 3-epimerase UlaE (EC 5.1.3.22)

In 179 genomes
OLD: L-xylulose 5-phosphate 3-epimerase homolog SgbU
NEW: L-xylulose 5-phosphate 3-epimerase SgbU (EC 5.1.3.2.2)

In 4 genomes
OLD: None
NEW: PTS system, IIB component

In 256 genomes
OLD: None
NEW: 2,3-diketo-L-gulonate TRAP transporter, substrate-binding protein YiaO

In 106 genomes
OLD: None
NEW: L-ribulose-5-phosphate 4-epimerase SgbE (EC 5.1.3.4)

In 1 genome
OLD: None
NEW: Malate/L-lactate dehydrogenase-like protein

In 1 genome
OLD: None
NEW: Transcriptional regulator STM2345, LacI family

In 25 genomes
OLD: None
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase SgbH (EC 4.1.1.85)

In 348 genomes
OLD: None
NEW: L-ribulose-5-phosphate 4-epimerase UlaF (EC 5.1.3.4)

In 579 genomes
OLD: None
NEW: 2,3-diketo-L-gulonate TRAP transporter, large permease protein YiaN

In 2 genomes
OLD: None
NEW: 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC 4.1.1.85)

In 170 genomes
OLD: None
NEW: Uncharacterized protein STM3670

In 1 genome
OLD: None
NEW: L-xylulose kinase (EC 2.7.1.53) @ 3-keto-L-gulonate kinase

In 593 genomes
OLD: None
NEW: 3-keto-L-gulonate 6-phosphate decarboxylase (EC 4.1.1.85)

In 7 genomes
OLD: None
NEW: Uncharacterized protein YjfN

In 1 genome
OLD: None
NEW: PTS system, ascorbate-specific IIB component (EC 2.7.1.194)

In 787 genomes
OLD: None
NEW: 2,3-diketo-L-gulonate TRAP transporter, small permease protein YiaM

In 1 genome
OLD: PTS system, 3-keto-L-gulonate/L-ascorbate specific IIA component (PtxA) based on FIGfams
NEW: PTS system, ascorbate-specific IIA component

In 1 genome
OLD: PTS system, 3-keto-L-gulonate/L-ascorbate specific IIB component (SgaB)
NEW: PTS system, ascorbate-specific IIB component (EC 2.7.1.194)

In 3 genomes
OLD: PTS system, 3-keto-L-gulonate/L-ascorbate specific IIB component (SgaB) based on FIGfams
NEW: PTS system, ascorbate-specific IIB component (EC 2.7.1.194)

In 3 genomes
OLD: PTS system, 3-keto-L-gulonate/L-ascorbate specific IIB component (SgaB) based on unreliable automated assignments
NEW: PTS system, ascorbate-specific IIB component (EC 2.7.1.194)

In 1 genome
OLD: PTS system, IIA component
NEW: PTS system, ascorbate-specific IIA component

In 252 genomes
OLD: PTS system, IIB component
NEW: PTS system, ascorbate-specific IIB component (EC 2.7.1.194)

In 4 genomes
OLD: PTS system, ascorbate-specific IIA component
NEW: PTS system, IIA component

In 4 genomes
OLD: PTS system, ascorbate-specific IIB component (EC 2.7.1.194)
NEW: PTS system, IIB component

In 2 genomes
OLD: PTS system, lactose/cellobiose specific IIB subunit based on unreliable automated assignments
NEW: PTS system, IIB component

In 2 genomes
OLD: Probable L-ascorbate-6-phosphate lactonase UlaG (EC 3.1.1.-) (L-ascorbate utilization protein G)
NEW: L-ascorbate-6-phosphate lactonase UlaG

In 2 genomes
OLD: Putative chemotaxis protein, resembles cheA
NEW: Uncharacterized protein STM3670

In 6 genomes
OLD: Putative chemotaxis protein, resembles cheA
NEW: Uncharacterized protein STM3670

In 36 genomes
OLD: Putative chemotaxis protein, resembles cheA based on FIGfams
NEW: Uncharacterized protein STM3670

In 2 genomes
OLD: Putative chemotaxis protein, resembles cheA based on unreliable automated assignments
NEW: Uncharacterized protein STM3670

In 1 genome
OLD: Putative uncharacterized protein YjfN
NEW: Uncharacterized protein YjfN

In 10 genomes
OLD: Putative uncharacterized protein YjfN
NEW: Uncharacterized protein YjfN

In 2 genomes
OLD: TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein based on FIGfams
NEW: TRAP-type C4-dicarboxylate transport system, periplasmic component

In 1 genome
OLD: TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter
NEW: TRAP-type C4-dicarboxylate transport system, small permease component

In 1 genome
OLD: ThrE-like protein
NEW: YjjP-like membrane protein CPF_1842

In 979 genomes
OLD: Transcriptional regulator YiaJ, IclR family
NEW: Ascorbate utilization transcriptional regulator YiaJ, IclR family

In 979 genomes
OLD: Transcriptional regulator yiaJ, IclR family
NEW: Transcriptional regulator YiaJ, IclR family

In 194 genomes
OLD: Transcriptional regulator, DeoR family
NEW: Ascorbate utilization transcriptional regulator, DeoR family # based on context

In 3 genomes
OLD: Transcriptional regulator, IclR family
NEW: Ascorbate utilization transcriptional regulator YiaJ, IclR family

In 3 genomes
OLD: Transcriptional regulator, LacI family
NEW: Transcriptional regulator STM2345, LacI family

In 1 genome
OLD: Transcriptional regulator, LacI family based on FIGfams
NEW: Transcriptional regulator STM2345, LacI family

In 1 genome
OLD: Transcriptional regulator, LacI family based on unreliable automated assignments
NEW: Transcriptional regulator STM2345, LacI family

In 1 genome
OLD: Transcriptional repressor of the fructose operon, DeoR family based on FIGfams
NEW: Ascorbate utilization transcriptional regulator UlaR, DeoR family

In 2 genomes
OLD: Two-component system response regulator protein
NEW: Arginine utilization regulatory protein RocR

In 339 genomes
OLD: Uncharacterized BhsA-like protein
NEW: Uncharacterized protein YjfN

In 999 genomes
OLD: Uncharacterized BhsA-like protein
NEW: Uncharacterized BhsA-like protein YjfY

In 7 genomes
OLD: Uncharacterized MFS-type transporter
NEW: 2,3-diketo-L-gulonate MFS-type transporter # based on context

In 1 genome
OLD: Xylulose kinase (EC 2.7.1.17) based on FIGfams
NEW: L-xylulose kinase (EC 2.7.1.53) @ 3-keto-L-gulonate kinase

RAST NEWS

(RAST Citations)


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PUBSEED GENOMES WEEKLY ANNOTATION ACTIVITY

Genome Name (# Annotations)

Mycobacterium ulcerans Agy99 (272)
Streptomyces scabiei 87.22 (259)
Calothrix sp. PCC 7507 (250)
Vibrio parahaemolyticus RIMD 2210633 (235)
Brucella abortus biovar 1 str. 9-941 (235)
Brucella melitensis 16M (229)
Rivularia sp. PCC 7116 (223)
Micromonospora sp. ATCC 39149 (221)
Zobellia galactanivorans (214)
Flavobacteriales bacterium HTCC2170 (211)
Vibrio parahaemolyticus AN-5034 (211)
Vibrio parahaemolyticus K5030 (207)
Vibrio parahaemolyticus Peru-466 (205)
Dickeya chrysanthemi NCPPB 3533 (204)
Verrucosispora maris AB-18-032 (203)
Acinetobacter calcoaceticus PHEA-2 (196)
Kitasatospora setae KM-6054 (195)
Vibrio coralliilyticus ATCC BAA-450 (194)
Ochrobactrum anthropi ATCC 49188 (191)
Thermotoga naphthophila RKU-10 (184)
Marinitoga piezophila KA3 (184)
Photobacterium angustum S14 (179)
Leptospira broomii str. 5399 (173)
Vibrio parahaemolyticus RIMD 2210633 (173)
Deinococcus geothermalis DSM 11300 (173)
Brucella abortus bv. 1 str. 9-941 (173)
Actinoplanes sp. SE50/110 (172)
Brucella abortus S19 (171)
Cronobacter sakazakii ATCC BAA-894 (170)
Brucella abortus bv. 4 str. 292 (169)
Brucella abortus str. 2308 A (169)
Brucella melitensis bv. 1 str. 16M (167)
Brucella melitensis biovar Abortus 2308 (167)
Cellulophaga algicola DSM 14237 (165)
Brucella abortus NCTC 8038 (165)
Thermotoga petrophila RKU-1 (164)
Deinococcus deserti VCD115 (163)
Cronobacter turicensis z3032 (163)
Brucella abortus S19 (162)
Brucella melitensis bv. 1 str. Rev.1 (162)
Rhizobium leguminosarum bv. viciae 3841 (162)
Dickeya zeae Ech1591 (162)
Acinetobacter baylyi DSM 14961 = CIP 107474 (160)
Photobacterium damselae subsp. damselae CIP 102761 (160)
Cronobacter turicensis (159)
Flavobacteriales bacterium HTCC2170 (157)
Acinetobacter baylyi TG19579 (156)
Bacteroides salanitronis DSM 18170 (152)
Brucella abortus bv. 9 str. C68 (152)
Gloeocapsa sp. PCC 7428 (152)
Brevundimonas sp. BAL3 (149)
Brucella abortus bv. 6 str. 870 (149)