Updated Annotations for Shewanella sp. ANA-3

Updated annotations for Shewanella sp. ANA-3

37 genes with updated (or confirmed) annotations:

Shewana3_0023 fadA : Acetyl-CoA C-acyltransferase (EC 2.3.1.16)
Original description: 3-ketoacyl-CoA thiolase (RefSeq)
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
KEGG: acetyl-CoA acyltransferase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (KETOACYLCOATHIOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_0024 fadB : Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
Original description: multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
SEED: Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
KEGG: 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase / enoyl-CoA isomerase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ENOYL-COA-HYDRAT-RXN, OHACYL-COA-DEHYDROG-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_0067 : sucrose permease scrT
Original description: major facilitator transporter (RefSeq)
SEED: Predicted sucrose permease, MFS family, FucP subfamily
KEGG: no annotation
Rationale: specific phenotype on sucrose; 82% identical to the sucrose transporter scrTII or Sfri_3989, which was validated by complementation (PMCID:PMC2996990); SEED_correct

Shewana3_0069 : Fructokinase (EC 2.7.1.4)
Original description: ribokinase-like domain-containing protein (RefSeq)
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing Sucrose. Automated validation from mutant phenotype: the predicted function (FRUCTOKINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_0611 : Arginine N-succinyltransferase (EC 2.3.1.109)
Original description: arginine succinyltransferase (RefSeq)
SEED: Arginine N-succinyltransferase (EC 2.3.1.109)
KEGG: arginine N-succinyltransferase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ARGININE-N-SUCCINYLTRANSFERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_0638 : smc-like chromosome partitioning protein (DUF3584)
Original description: hypothetical protein (RefSeq)
SEED: FIG020374: hypothetical protein
KEGG: no annotation
Rationale: This gene has a conserved motility defect. and some close homologs are important for resisting cisplatin. DUF3584 is distantly related to smc proteins.

Shewana3_0639 : predicted chromosome partitioning protein (with smc-like Shewana3_0638)
Original description: hypothetical protein (RefSeq)
SEED: FIG020042: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (Shewana3_0638)

Shewana3_0640 : predicted chromosome partitioning protein (with smc-like Shewana3_0638)
Original description: hypothetical protein (RefSeq)
SEED: FIG020568: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (Shewana3_0638)

Shewana3_0819 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
SEED: Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88)
KEGG: proline dehydrogenase / delta 1-pyrroline-5-carboxylate dehydrogenase
Rationale: Specifically important for utilizing L-Proline. Automated validation from mutant phenotype: the predicted function (1.2.1.88, 1.5.5.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Shewana3_1039 : nucleoside permease (cytidine, inosine, uridine, or thymidine)
Original description: Na+ dependent nucleoside transporter (RefSeq)
SEED: Na+ dependent nucleoside transporter NupC
KEGG: concentrative nucleoside transporter, CNT family
Rationale: Specifically important for utilization of cytidine, inosine, uridine, and thymidine.

Shewana3_1184 : Glutaminase (EC 3.5.1.2)
Original description: glutaminase (RefSeq)
SEED: Glutaminase (EC 3.5.1.2)
KEGG: glutaminase
Rationale: Specifically important for utilizing L-Glutamine. Automated validation from mutant phenotype: the predicted function (GLUTAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_1204 : putative transporter, required for glycine and L-alanine utilization
Original description: hypothetical protein (RefSeq)
SEED: Putative inner membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). Substrates are from the conserved specific phenotypes of UPF0126

Shewana3_1672 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: isovaleryl-CoA dehydrogenase (RefSeq)
SEED: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
KEGG: isovaleryl-CoA dehydrogenase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (RXN0-2301) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_1728 : Succinylarginine dihydrolase (EC 3.5.3.23)
Original description: succinylarginine dihydrolase (RefSeq)
SEED: Succinylarginine dihydrolase (EC 3.5.3.23)
KEGG: succinylarginine dihydrolase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCARGDIHYDRO-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_2065 araD : L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
Original description: L-ribulose-5-phosphate 4-epimerase (RefSeq)
SEED: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
KEGG: L-ribulose-5-phosphate 4-epimerase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (RIBULPEPIM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_2066 : L-arabinose isomerase (EC 5.3.1.4)
Original description: L-arabinose isomerase (RefSeq)
SEED: L-arabinose isomerase (EC 5.3.1.4)
KEGG: L-arabinose isomerase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (ARABISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_2070 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: dihydroxy-acid dehydratase (RefSeq)
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct)

Shewana3_2071 : L-arabinose 1-dehydrogenase (EC 1.1.1.46)
Original description: short-chain dehydrogenase/reductase SDR (RefSeq)
SEED: Putative oxidoreductase in arabinose utilization cluster
KEGG: no annotation
Rationale: Specifically important for: L-Arabinose. Also, was correctly annotated by PMID:20836887

Shewana3_2072 : L-arabinose 1-epimerase (mutarotase) (EC 5.1.3.3)
Original description: aldose 1-epimerase (RefSeq)
SEED: L-arabinose-specific 1-epimerase (mutarotase)
KEGG: aldose 1-epimerase
Rationale: Specifically important for: L-Arabinose. Was correctly annotated by PMID:20836887 (more specific than EC number); (SEED_correct)

Shewana3_2073 : L-arabinose ABC transporter, substrate-binding component AraU
Original description: periplasmic binding protein/LacI transcriptional regulator (RefSeq)
SEED: Predicted L-arabinose ABC transport system, periplasmic arabinose-binding protein
KEGG: simple sugar transport system substrate-binding protein
Rationale: Specifically important for L-arabinose utilization; the gene name is from PMC2996990

Shewana3_2074 : L-arabinose ABC transporter, ATPase component AraV
Original description: ABC transporter related (RefSeq)
SEED: Predicted L-arabinose ABC transport system, ATP-binding protein
KEGG: simple sugar transport system ATP-binding protein
Rationale: Specifically important for L-arabinose utilization; the gene name is from PMC2996990

Shewana3_2075 : L-arabinose ABC transporter, permease component 1 AraW
Original description: inner-membrane translocator (RefSeq)
SEED: Predicted L-arabinose ABC transport system, permease protein 1
KEGG: simple sugar transport system permease protein
Rationale: Specifically important for L-arabinose utilization; the gene name is from PMC2996990

Shewana3_2076 : L-arabinose ABC transporter, permease component 2 AraZ
Original description: inner membrane ABC transporter permease protein YjfF (RefSeq)
SEED: Predicted L-arabinose ABC transport system, permease protein 2
KEGG: simple sugar transport system permease protein
Rationale: Specifically important for L-arabinose utilization; the gene name is from PMC2996990

Shewana3_2088 : L-arabinolactonase (EC 3.1.1.15)
Original description: hypothetical protein (RefSeq)
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: no annotation
Rationale: Important on L-arabinose; Was correctly annotated by PMID:20836887 (SEED_correct)

Shewana3_2311 : Alpha-glucosidase (EC 3.2.1.20)
Original description: alpha amylase, catalytic region (RefSeq)
SEED: Maltodextrin glucosidase (EC 3.2.1.20)
KEGG: alpha-glucosidase
Rationale: Specifically important for utilizing D-Maltose monohydrate. Automated validation from mutant phenotype: the predicted function (3.2.1.20) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Shewana3_2573 : Cytidine deaminase (EC 3.5.4.5)
Original description: cytidine deaminase (RefSeq)
SEED: Cytidine deaminase (EC 3.5.4.5)
KEGG: cytidine deaminase
Rationale: Specifically important for utilizing Cytidine. Automated validation from mutant phenotype: the predicted function (CYTIDEAM2-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_2769 : Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12)
Original description: acyl-CoA dehydrogenase domain-containing protein (RefSeq)
SEED: Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12)
KEGG:
Rationale: Specifically important for: L-Isoleucine. specificity for isoleucine indicates that 2-methylbutanoyl-CoA is a substrate (SEED_correct)

Shewana3_2904 : propionate/L-lactate/D-lactate transporter
Original description: L-lactate permease (RefSeq)
SEED: L-lactate permease
KEGG: lactate transporter, LctP family
Rationale: Specifically important for propionate utilization. Shewana3_2904 and its orthologs in other Shewanellas also have mild phenotypes during L-lactate or D,L-lactate utilization. 95% identical to SO1522 (lctP1), which is involved in utilization of both L- and D-lactate (PMC5603553)

Shewana3_3110 : N-acetylglucosamine transporter nagP
Original description: glucose/galactose transporter (RefSeq)
SEED: N-acetyl glucosamine transporter, NagP
KEGG: no annotation
Rationale: specific phenotype on NAG and D-glucosamine. This protein is similar to SO3503, which was named nagP (PMID:16857666). There is another putative glucosamine transporter (nagX, Shewana3_3111) but the phenotype of 3110 on glucosamine does not seem to be a polar effect. (It is observed on both strands, conserved in S. amazonensis SB2B, and 3110 is downstream of nagX). It apears that both nagP and nagX might be required for glucosamine utilization. NagX has weak similarity to acyltransferases (Q3UDW8, or possibly opgC from Rhodobacter sphaeroides) so nagX might convert glucosamine into another compound before transport by nagP. (SEED_correct)

Shewana3_3111 : transmembrane glucosamine N-acetyltransferase NagX
Original description: hypothetical protein (RefSeq)
SEED: N-acetylglucosamine related transporter, NagX
KEGG: no annotation
Rationale: Specifically important for glucosamine utilization. NagX proteins are distantly related to human HGSNAT (uniprot:Q68CP4), which is a transmembrane acetyl-CoA:alpha-glucosaminide N-acetyltransferase.

Shewana3_3112 : N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Original description: N-acetylglucosamine 6-phosphate deacetylase (RefSeq)
SEED: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
KEGG: N-acetylglucosamine-6-phosphate deacetylase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (NAG6PDEACET-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_3113 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: sugar isomerase (SIS) (RefSeq)
SEED: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
KEGG: glucosamine--fructose-6-phosphate aminotransferase (isomerizing)
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (GLUCOSAMINE-6-P-DEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_3114 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: ATPase, BadF/BadG/BcrA/BcrD type (RefSeq)
SEED: N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59)
KEGG: no annotation
Rationale: Specifically important for: D-Glucosamine Hydrochloride; N-Acetyl-D-Glucosamine. The first step in NAG catabolism. The phenotype on glucosamine is strong and is present on both strands, but is not conserved. It may be a polar effect. (SEED_correct)

Shewana3_3279 : Vitamin B12 transporter, permease component (fecCD-like)
Original description: transport system permease protein (RefSeq)
SEED: ABC transporter (iron.B12.siderophore.hemin) , permease component
KEGG: iron complex transport system permease protein
Rationale: This protein is cofit with the B12-dependent methionine synthase MetH and is FecCD-like. It probably works with Shewana3_3280 (ABC transporter domain protein with similar phenotypes) and Shewana3_3272 (periplasmic binding protein). This protein is similar to SO_1033 which is also involved in B12 uptake (it is strongly cofit with metH; also see PMCid:PMC3219624)

Shewana3_3579 : Aldose 1-epimerase (EC 5.1.3.3)
Original description: aldose 1-epimerase (RefSeq)
SEED: Aldose 1-epimerase (EC 5.1.3.3)
KEGG: aldose 1-epimerase
Rationale: Specifically important for utilizing D-Maltose monohydrate. Automated validation from mutant phenotype: the predicted function (5.1.3.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Shewana3_3680 : Uridine phosphorylase (EC 2.4.2.3)
Original description: uridine phosphorylase (RefSeq)
SEED: Uridine phosphorylase (EC 2.4.2.3)
KEGG: uridine phosphorylase
Rationale: Specifically important for utilizing Cytidine and Uridine. Automated validation from mutant phenotype: the predicted function (URPHOS-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shewana3_4104 : 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
Original description: 2-amino-3-ketobutyrate coenzyme A ligase (RefSeq)
SEED: 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
KEGG: glycine C-acetyltransferase
Rationale: Specifically important for utilizing L-Threonine. Automated validation from mutant phenotype: the predicted function (AKBLIG-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Shewanella sp. ANA-3 or for all organisms as tab-delimited tables