Updated Annotations for Shewanella oneidensis MR-1

Updated annotations for Shewanella oneidensis MR-1

46 genes with updated (or confirmed) annotations:

SO0095 hutI : Imidazolonepropionase (EC 3.5.2.7)
Original description: imidazolonepropionase (NCBI ptt file)
SEED: Imidazolonepropionase (EC 3.5.2.7)
KEGG: imidazolonepropionase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (IMIDAZOLONEPROPIONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO0344 prpC : 2-methylcitrate synthase (EC 2.3.3.5)
Original description: methylcitrate synthase (NCBI ptt file)
SEED: 2-methylcitrate synthase (EC 2.3.3.5)
KEGG: 2-methylcitrate synthase
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (2.3.3.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SO0619 astD : Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
Original description: succinylglutamic semialdehyde dehydrogenase (NCBI ptt file)
SEED: Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
KEGG: succinylglutamic semialdehyde dehydrogenase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCGLUALDDEHYD-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO0827 lldP : propionate/L-lactate/D-lactate transporter
Original description: L-lactate permease (NCBI ptt file)
SEED: L-lactate permease
KEGG: lactate transporter, LctP family
Rationale: Specifically important for propionate utilization. Another study named it lctP2 and found that it was involved in utilization of both L- and D-lactate (PMC5603553)

SO1115 pepD : dipeptidase (EC 3.4.13.-)
Original description: aminoacyl-histidine dipeptidase (NCBI ptt file)
SEED: Aminoacyl-histidine dipeptidase (Peptidase D) (EC 3.4.13.3)
KEGG: aminoacylhistidine dipeptidase
Rationale: Specific phenotype: utilization of Gly-DL-Asp

SO1219 deoB : Phosphopentomutase (EC 5.4.2.7)
Original description: phosphopentomutase (NCBI ptt file)
SEED: Phosphopentomutase (EC 5.4.2.7)
KEGG: phosphopentomutase
Rationale: Specifically important for utilizing Adenosine. Automated validation from mutant phenotype: the predicted function (PPENTOMUT-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1267 : Gamma-glutamyl-gamma-aminobutyrate hydrolase (EC 3.5.1.94)
Original description: hypothetical Glutamine amidotransferase (NCBI ptt file)
SEED: Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
KEGG: putative glutamine amidotransferase
Rationale: Specifically important for utilizing Putrescine Dihydrochloride. Automated validation from mutant phenotype: the predicted function (RXN0-3942) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1268 : Glutamate--putrescine ligase (EC 6.3.1.11)
Original description: glutamine synthetase (NCBI ptt file)
SEED: Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
KEGG: glutamine synthetase
Rationale: Specifically important for utilizing Putrescine Dihydrochloride. Automated validation from mutant phenotype: the predicted function (RXN0-3901) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1275 gabD : succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16]
Original description: succinate-semialdehyde dehydrogenase (NCBI ptt file)
SEED: Aldehyde dehydrogenase B (EC 1.2.1.22)
KEGG: succinate-semialdehyde dehydrogenase (NADP+)
Rationale: Specifically important for: L-Isoleucine. Also very important with putrescine as the N source. The more specific KEGG annotation is consistent its role on N putrescine (which is converted to 4-aminobutyrate and then to succinate semialdehyde). Its role on isoleucine is unclear but a close homolog, Shewana3_3092, also has this phenotype (albeit milder). Also note that isoleucine is catabolized to propionyl-CoA and Shewana3_3092 is very important for propionate utilization. The annotation of son:SO_1275 in KEGG has been updated to list glutarate-semialdehyde as an additional substrate. (KEGG_correct)

SO1319 : putative transporter, required for glycine utilization
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: Putative inner membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

SO1483 aceB : Malate synthase (EC 2.3.3.9)
Original description: malate synthase A (NCBI ptt file)
SEED: Malate synthase (EC 2.3.3.9)
KEGG: malate synthase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (MALSYN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1484 aceA : Isocitrate lyase (EC 4.1.3.1)
Original description: isocitrate lyase (NCBI ptt file)
SEED: Isocitrate lyase (EC 4.1.3.1)
KEGG: isocitrate lyase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1522 : D,L-lactate/pyruvate symporter LctP2
Original description: L-lactate permease, putative (NCBI ptt file)
SEED: L-lactate permease
KEGG: lactate transporter, LctP family
Rationale: Important for utilization of L-lactate, D,L-lactate, or pyruvate. Has phenotypes in many nitrogen source experiments with D,L-lactate as the carbon source. Also see PMID:28285200 for evidence that LctP2 transports D-lactate.

SO1666 phhA : Phenylalanine 4-monooxygenase (EC 1.14.16.1)
Original description: phenylalanine-4-hydroxylase (NCBI ptt file)
SEED: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
KEGG: phenylalanine-4-hydroxylase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.14.16.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SO1670 : fumarylacetoacetate hydrolase (EC 3.7.1.2)
Original description: fumarylacetoacetate hydrolase family protein (NCBI ptt file)
SEED: Fumarylacetoacetate hydrolase family protein
KEGG: no annotation
Rationale: # Important for utilization of phenylalanine (which is catabolized via tyrosine due to phenylalanine-4-hydroxylase SO1666) , gelatin, or CASamino acids. This protein encodes the missing fumarylacetaectate hydrolase.

SO1671 : Maleylacetoacetate isomerase (EC 5.2.1.2)
Original description: glutathione S-transferase family protein (NCBI ptt file)
SEED: Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
KEGG: maleylacetoacetate isomerase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (5.2.1.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SO1677 atoB : 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16)
Original description: acetyl-CoA acetyltransferase (NCBI ptt file)
SEED: 3-ketoacyl-CoA thiolase [isoleucine degradation] (EC 2.3.1.16)
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (METHYLACETOACETYLCOATHIOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1679 : 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5)
Original description: acyl-CoA dehydrogenase family protein (NCBI ptt file)
SEED: Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12)
KEGG:
Rationale: # Specifically important in carbon source L-Isoleucine; nitrogen source L-Isoleucine (EC 1.3.8.5). Similar to ACAD8_HUMAN (Isobutyryl-CoA dehydrogenase, mitochondrial).

SO1683 : 3-hydroxy-2-methylbutyryl-CoA dehydrogenase IvdG (EC:1.1.1.178)
Original description: 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)
SEED: 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
KEGG: 3-oxoacyl-[acyl-carrier protein] reductase
Rationale: Important for utilization of L-isoleucine as a carbon or nitrogen source. SO1683 is expected to be the 3-hydroxy-2-methylbutyryl-CoA dehydrogenase for isoleucine degradation (PMC2612455), and this is confirmed by its mutants' phenotype. (Also see data from an independent set of transposon mutants in PMC3219624.) Mutants in SO1683 have many other phenotypes which are not explained.

SO1812 mdeA : Methionine gamma-lyase (EC 4.4.1.11)
Original description: methionine gamma-lyase (NCBI ptt file)
SEED: Methionine gamma-lyase (EC 4.4.1.11)
KEGG: methionine-gamma-lyase
Rationale: Specifically important for utilizing L-Methionine. Automated validation from mutant phenotype: the predicted function (4.4.1.11) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SO1962 : 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Original description: 4-hydroxyphenylpyruvate dioxygenase (NCBI ptt file)
SEED: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
KEGG: 4-hydroxyphenylpyruvate dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (RXN-10815) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SO1963 : Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
KEGG: homogentisate 1,2-dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.13.11.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SO2395 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: acyl-CoA dehydrogenase family protein (NCBI ptt file)
SEED: no annotation
KEGG: no annotation
Rationale: Specific phenotype: utilization of Tween 20. Not sure about preferred substrate length

SO2492 : acyl-CoA dehydrogenase (1.3.8.-)
Original description: oxidoreductase, acyl-CoA dehydrogenase family (NCBI ptt file)
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG:
Rationale: Specifically important for: Tween 20. Tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation. Similar to fadE from E. coli. The specific SEED annotation as butyryl-CoA dehydrogenase seems questionable but could still be correct

SO2706 astB : Succinylarginine dihydrolase (EC 3.5.3.23)
Original description: succinylarginine dihydrolase (NCBI ptt file)
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.

SO2744 : DNA damage response helicase (yejH or radD)
Original description: helicase (NCBI ptt file)
SEED: ATP-dependent RNA helicase YejH
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also important for resisting ionizing radiation and UV radiation in E. coli (PMID:25425430)

SO2791 cdd : Cytidine deaminase (EC 3.5.4.5)
Original description: cytidine deaminase (NCBI ptt file)
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.

SO2882 : yeaG component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: hypothetical Ser protein kinas (NCBI ptt file)
SEED: Serine protein kinase (prkA protein), P-loop containing
KEGG: no annotation
Rationale: conserved cofitness; yeaG is a protein kinase

SO2883 : yeaH component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: UPF0229 protein YeaH
KEGG: hypothetical protein
Rationale: PFam PF04285.8 (DUF444). conserved cofitness; yeaG is a protein kinase

SO2884 : ycgB component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: FIG004684: SpoVR-like protein
KEGG: no annotation
Rationale: conserved cofitness; yeaG is a protein kinase

SO3342 : putative transporter, required for L-alanine utilization
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: Putative inner membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

SO3365 glsA : Glutaminase (EC 3.5.1.2)
Original description: glutaminase A (NCBI ptt file)
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.

SO3461 : Fatty acid transporter
Original description: transporter, putative (NCBI ptt file)
SEED: TRANSPORTER
KEGG: no annotation
Rationale: Specific phenotype on Tween-20, which is hydrolyzed extracellularly to fatty acids (typically around 12 carbons). This protein is distantly related (PF03547) to auxin efflux transporters in plants and to the malate permease mleT of Lactobacillus casei (PMID: 23835171)

SO3503 : N-acetyl glucosamine transporter, NagP
Original description: glucose/galactose transporter (NCBI ptt file)
SEED: N-acetyl glucosamine transporter, NagP
KEGG: no annotation
Rationale: Specific phenotype on NAG. Also see PMID:16857666 (SEED_correct)

SO3505 nagA : N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Original description: N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)
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.

SO3506 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: SIS domain protein (NCBI ptt file)
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.

SO3507 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59)
KEGG: no annotation
Rationale: Specifically important for: N-Acetyl-D-Glucosamine. First step in NAG catabolism; (SEED_correct); see PMID 16857666

SO3749 : Acetylornithine deacetylase (EC:3.5.1.16)
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG160851: peptidase
KEGG: no annotation
Rationale: see Deutschbauer et al 2011, PMID:22125499 (auxotroph)

SO3774 : proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.5.2; EC 1.2.1.88)
Original description: proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, putative (NCBI ptt file)
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: Specific phenotype: utilization of Gelatin (gelatin contains a lot of proline)

SO3900 : yqiA-like hydrolase, affects the cell envelope
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: Putative esterase, FIGfam005057
KEGG: no annotation
Rationale: PFam PF05728.8 (UPF0227). conserved phenotypes: important for resisting fusidic acid and carbenicillin

SO4006 : predicted chromosome partitioning protein (with smc-like SO4008)
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG020568: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (SO4008)

SO4007 : predicted chromosome partitioning protein (with smc-like SO4008)
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG020042: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (SO4008)

SO4008 : smc-like chromosome partitioning protein (DUF3584)
Original description: hypothetical protein (NCBI ptt file)
SEED: FIG020374: hypothetical protein
KEGG: no annotation
Rationale: Conserved phenotypes: important for motility and cisplatin resistance. DUF3584 is distantly related to smc proteins.

SO4133 udp : Uridine phosphorylase (EC 2.4.2.3)
Original description: uridine phosphorylase (NCBI ptt file)
SEED: Uridine phosphorylase (EC 2.4.2.3)
KEGG: uridine phosphorylase
Rationale: Specifically important for utilizing Cytidine. 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.

SO4164 : predicted FeS cluster maintenance protein
Original description: conserved hypothetical protein (NCBI ptt file)
SEED: FIG028220: hypothetical protein co-occurring with HEAT repeat protein
KEGG: no annotation
Rationale: PFam PF06155.8 (DUF971). conserved cofitness with mrp/apbC (SO2618) and perhaps bolA

SO4731 add : Adenosine deaminase (EC 3.5.4.4)
Original description: adenosine deaminase (NCBI ptt file)
SEED: Adenosine deaminase (EC 3.5.4.4)
KEGG: adenosine deaminase
Rationale: Specifically important for utilizing Adenosine. Automated validation from mutant phenotype: the predicted function (ADENODEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Shewanella oneidensis MR-1 or for all organisms as tab-delimited tables