Testing automated annotations with RB-TnSeq data

	A	B	C	D	E	F	G
1	orgId	locusId	sysName	original_annotation	condition	class	assigned_function
2	WCS417	GFF799	PS417_04060	peptide ABC transporter permease	Gly-Glu,Gly-Glu	transporter	dipeptide transporter
3	pseudo3_N2E3	AO353_11860	AO353_11860	Fis family transcriptional regulator	Potassium acetate,Sodium Fumarate dibasic,Sodium succinate dibasic hexahydrate,Sodium Fumarate dibasic,Sodium succinate dibasic hexahydrate,L-Malic acid disodium salt monohydrate,L-Malic acid disodium salt monohydrate	other
4	Keio	14279	b0133	pantoate--beta-alanine ligase (NCBI)	D-Glucose,D-Glucose,N-Acetyl-D-Glucosamine,N-Acetyl-D-Glucosamine,L-Glutamine,L-Glutamine,D-Serine,D-Serine,D-Alanine,D-Alanine,casamino acids,Adenosine,Adenosine,Cytidine,Cytidine,Ammonium chloride,Ammonium chloride,D-Galacturonic Acid monohydrate,D-Glucose,D-Galacturonic Acid monohydrate,D-Glucose	nonspec
5	pseudo1_N1B4	Pf1N1B4_1226		FIG01201438: hypothetical protein	Sucrose	other
6	pseudo1_N1B4	Pf1N1B4_2255		Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)	Sodium octanoate	nonspec
7	pseudo13_GW456_L13	PfGW456L13_3987		tRNA dihydrouridine synthase A	Putrescine Dihydrochloride	nonspec
8	psRCH2	GFF566	Psest_0571	Transcriptional regulators	L-Isoleucine,L-Isoleucine,L-Valine	nonspec
9	Koxy	BWI76_RS15135	BWI76_RS15135	hypothetical protein	Sodium D,L-Lactate	other
10	pseudo13_GW456_L13	PfGW456L13_2016		Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate	Sodium succinate dibasic hexahydrate,L-Malic acid disodium salt monohydrate,Tween 20	transporter	C4-dicarboxylate transporter
11	BFirm	BPHYT_RS02520	BPHYT_RS02520	Fis family transcriptional regulator	Sodium succinate dibasic hexahydrate,L-Malic acid disodium salt monohydrate	other
12	Phaeo	GFF1707	PGA1_c17310	putative fatty acid desaturase	Sodium propionate	nonspec
13	pseudo3_N2E3	AO353_10815	AO353_10815	carbonate dehydratase	Potassium acetate,Potassium acetate	nonspec
14	Putida	PP_1401	PP_1401	C4-dicarboxylate transport transcriptional regulatory protein	a-Ketoglutaric acid disodium salt hydrate	other
15	psRCH2	GFF3724	Psest_3793	Glycine/D-amino acid oxidases (deaminating)	L-Alanine,D-Alanine,L-Alanine,L-Alanine,D-Alanine,D-Alanine,L-Alanine,L-Alanine,D-Alanine,D-Alanine,Putrescine Dihydrochloride	enzyme	D-alanine dehydrogenase (EC 1.4.99.-)
16	pseudo3_N2E3	AO353_18585	AO353_18585	phenylalanine 4-monooxygenase	L-Phenylalanine,L-Phenylalanine	enzyme	Phenylalanine 4-monooxygenase (EC 1.14.16.1)
17	pseudo5_N2C3_1	AO356_17550	AO356_17550	N-acetylglucosamine-6-phosphate deacetylase	N-Acetyl-D-Glucosamine	enzyme	N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
18	pseudo5_N2C3_1	AO356_17440	AO356_17440	nucleoid-associated protein	L-Lysine	other
19	Cup4G11	RR42_RS31785	RR42_RS31785	nitrite reductase	Sodium nitrate,Sodium nitrite	enzyme	Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
20	Keio	18233	b4208	D-alanine/D-serine/glycine transporter (NCBI)	D-Galacturonic Acid monohydrate,D-Galacturonic Acid monohydrate,D-Glucose,D-Glucose	nonspec
21	Cola	Echvi_0403	Echvi_0403	Endoglucanase	L-Rhamnose monohydrate,L-Rhamnose monohydrate,L-Rhamnose monohydrate	nonspec
22	pseudo13_GW456_L13	PfGW456L13_161		putative membrane protein	Glycine	transporter	putative transporter, required for glycine utilization
23	pseudo13_GW456_L13	PfGW456L13_179		Putative esterase, FIGfam005057	Sodium octanoate	nonspec
24	BFirm	BPHYT_RS18580	BPHYT_RS18580	short-chain dehydrogenase	D-Alanine	nonspec
25	pseudo3_N2E3	AO353_21340	AO353_21340	myo-inosose-2 dehydratase	m-Inositol,m-Inositol	enzyme	Myo-inosose-2 dehydratase (EC 4.2.1.44)
26	Cup4G11	RR42_RS20305	RR42_RS20305	metal ABC transporter ATPase	Glycine	nonspec
27	Marino	GFF3193	HP15_3135	iron-containing alcohol dehydrogenase	Ethanol,Ethanol,D-Trehalose dihydrate	enzyme	ethanol oxidation regulatory protein ercA
28	SB2B	6936355	Sama_0544	outer membrane porin, putative (RefSeq)	a-Ketoglutaric acid disodium salt hydrate,a-Ketoglutaric acid disodium salt hydrate	nonspec
29	Smeli	SM_b20483	SM_b20483	catabolite repressor protein	L-Fucose,Uridine	other
30	Dino	3607308	Dshi_0723	Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)	Sodium propionate,Sodium propionate	enzyme	Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3)
31	MR1	203162	SO4078	pmba protein (NCBI ptt file)	Sodium D,L-Lactate	other
32	Phaeo	GFF3393	PGA1_c34460	hypothetical protein	L-Glutamine,L-Glutamine	nonspec
33	Smeli	SM_b21124	SM_b21124	methylcrotonoyl-CoA carboxylase biotinylated subunit	L-Leucine	enzyme	3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit (EC 6.4.1.4)
34	pseudo5_N2C3_1	AO356_15710	AO356_15710	GntR family transcriptional regulator	L-Histidine	other
35	pseudo3_N2E3	AO353_15995	AO353_15995	PTS mannose transporter subunit IIC	D-Trehalose dihydrate,D-Trehalose dihydrate	transporter	trehalose-specific PTS system, I, HPr, and IIA components
36	Cup4G11	RR42_RS15375	RR42_RS15375	AsnC family transcriptional regulator	L-Tryptophan,L-Tryptophan	other
37	Koxy	BWI76_RS15695	BWI76_RS15695	hypothetical protein	a-Cyclodextrin,a-Cyclodextrin	nonspec
38	pseudo5_N2C3_1	AO356_09645	AO356_09645	N-formimino-L-glutamate deiminase	L-Histidine,L-Histidine	enzyme	Formiminoglutamic iminohydrolase (EC 3.5.3.13)
39	MR1	201728	SO2588	protein-methionine-S-oxide reductase, PilB family (NCBI ptt file)	L-Isoleucine	nonspec
40	pseudo3_N2E3	AO353_11100	AO353_11100	acyl-CoA dehydrogenase	L-Valine	other
41	pseudo6_N2E2	Pf6N2E2_512		5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain	m-Inositol,m-Inositol	enzyme	5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29)
42	Phaeo	GFF717	PGA1_c07320	sugar ABC transporter, ATP-binding protein	m-Inositol,m-Inositol,m-Inositol	transporter	Inositol transport system ATP-binding protein
43	pseudo1_N1B4	Pf1N1B4_1693		Cystine ABC transporter, periplasmic cystine-binding protein FliY	L-Methionine,Cytidine	nonspec
44	Koxy	BWI76_RS12370	BWI76_RS12370	hypothetical protein	a-Cyclodextrin,a-Cyclodextrin	nonspec
45	pseudo5_N2C3_1	AO356_05235	AO356_05235	glycerol-3-phosphate ABC transporter substrate-binding protein	Ethanol,N-Acetyl-D-Glucosamine	other
46	Putida	PP_3728	PP_3728	Sensor histidine kinase/response regulator	L-Arginine	other
47	Phaeo	GFF1010	PGA1_c10270	hypothetical protein	casamino acids	other
48	Putida	PP_2211	PP_2211	Transcriptional regulator, AraC family	DL-2-Aminobutyric acid,DL-2-Aminobutyric acid,L-Isoleucine,L-Isoleucine	other
49	Cola	Echvi_3406	Echvi_3406	TonB-dependent siderophore receptor	L-Serine	nonspec
50	psRCH2	GFF2308	Psest_2356	Fatty acid desaturase	L-Arginine,L-Citrulline,L-Citrulline	nonspec
51	Phaeo	GFF2753	PGA1_c27960	putative oxidoreductase	N-Acetyl-D-Glucosamine,N-Acetyl-D-Glucosamine,N-Acetyl-D-Glucosamine	nonspec	role unknown
52	pseudo5_N2C3_1	AO356_20280	AO356_20280	2-dehydro-3-deoxygalactonokinase	D-Galactose	enzyme	2-dehydro-3-deoxygalactonokinase DgoK (EC 2.7.1.58)
53	pseudo6_N2E2	Pf6N2E2_4704		Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF	Carnitine Hydrochloride,Carnitine Hydrochloride,Glycine	enzyme	DgcB Dimethylglycine demethylase subunit B (EC 1.5.3.-)
54	Cola	Echvi_2512	Echvi_2512	phospho-2-dehydro-3-deoxyheptonate aldolase	L-Phenylalanine,L-Phenylalanine	nonspec
55	HerbieS	HSERO_RS20590	HSERO_RS20590	enoyl-CoA hydratase	Phenylacetic acid,Phenylacetic acid	enzyme	fused 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase and oxepin-CoA hydrolase (EC 3.3.2.12; EC 1.2.1.91; EC 4.2.1.55)
56	azobra	AZOBR_RS03325	AZOBR_RS03325	hypothetical protein	Glycerol,Glycerol	nonspec
57	pseudo6_N2E2	Pf6N2E2_496		Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)	Uridine,Cytosine,Uridine,Cytosine	enzyme	Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
58	DvH	207693	DVU2209	conserved hypothetical protein (TIGR)	L-Alanine	nonspec
59	pseudo6_N2E2	Pf6N2E2_2847		Glutamate synthase [NADPH] large chain (EC 1.4.1.13)	Putrescine Dihydrochloride	nonspec
60	Korea	Ga0059261_0152	Ga0059261_0152	Protein of unknown function (DUF2794)	L-Glutamine	nonspec
61	Putida	PP_2323	PP_2323	conserved protein of unknown function	L-Leucine	nonspec
62	DvH	209488	DVU0549	high-affinity branched-chain amino acid ABC transporter, permease protein (TIGR)	L-Glutamine,L-Glutamine,L-Threonine,L-Proline,L-Proline,L-Proline,L-Arginine	transporter	proline and maybe arginine uptake
63	Keio	17665	b3604	DNA-binding transcriptional repressor (NCBI)	Sodium D-Lactate,Sodium D-Lactate,Sodium D,L-Lactate,Sodium D,L-Lactate	other
64	ANA3	7026258	Shewana3_3400	phosphoribulokinase/uridine kinase (RefSeq)	Glycine,Glycine	nonspec
65	pseudo13_GW456_L13	PfGW456L13_3909		Ribose operon repressor	L-Arabinose,L-Arabinose,Gly-DL-Asp	nonspec
66	MR1	203724	SO4654	sulfate ABC transporter, permease protein (NCBI ptt file)	Sodium D,L-Lactate	nonspec
67	Putida	PP_2329	PP_2329	aminodeoxychorismate synthase / para-aminobenzoate synthase multi-enzyme complex	L-Phenylalanine,L-Phenylalanine	nonspec
68	pseudo5_N2C3_1	AO356_26025	AO356_26025	glycogen synthase	Cytidine	nonspec
69	pseudo5_N2C3_1	AO356_19660	AO356_19660	hypothetical protein	Sodium D-Lactate	nonspec	pyruvate transporter?
70	pseudo6_N2E2	Pf6N2E2_2376		Nitrate/nitrite transporter	Sodium nitrate,Sodium nitrate	transporter	nitrate transporter only, probably (see B.subtilis nasA, defect on nitrate only, like this)
71	Btheta	351860	BT2332	conserved hypothetical protein (NCBI ptt file)	amylopectin from maize,L-Aspartic Acid	other
72	Btheta	349800	BT0272	putative outer membrane protein, probably involved in nutrient binding (NCBI ptt file)	(+)-Arabinogalactan,(+)-Arabinogalactan	transporter	TonB-dependent receptor for (+)-arabinogalactan (SusC-like)
73	Btheta	352054	BT2526	hypothetical protein (NCBI ptt file)	Hyaluronic acid sodium salt from Streptococcus equi,Hyaluronic acid sodium salt from Streptococcus equi,Hyaluronic acid sodium salt from Streptococcus equi	other
74	Putida	PP_0294	PP_0294	choline / betaine / carnitine ABC transporter - ATP binding subunit	Choline chloride,Choline chloride,Carnitine Hydrochloride,Carnitine Hydrochloride	transporter	transport of carnitine & choline (and probably betaine as well), ATPase component
75	acidovorax_3H11	Ac3H11_968		Cytochrome c oxidase subunit CcoN (EC 1.9.3.1)	L-Isoleucine,D-Alanine,Ammonium chloride	nonspec
76	Caulo	CCNA_00650	CCNA_00650	MFS superfamily nitrate/nitrite transporter NarK	Sodium nitrate,Sodium nitrate	transporter	prob. Nitrate transport only (similar to nasA) but could be nitrate/nitrite antiporter (29% id to Q9RA46)
77	PV4	5207583	Shew_0117	protoheme IX farnesyltransferase (RefSeq)	L-Glutamine	nonspec
78	Smeli	SMc00832	SMc00832	glycolate oxidase subunit protein	Sodium D,L-Lactate	enzyme	D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6)
79	Putida	PP_3713	PP_3713	catechol 1,2-dioxygenase	benzoic acid	enzyme	Catechol 1,2-dioxygenase (EC 1.13.11.1)
80	pseudo6_N2E2	Pf6N2E2_4337		Uncharacterized protein ImpI/VasC	L-Serine,L-Serine	other
81	pseudo6_N2E2	Pf6N2E2_1678		Major facilitator family transporter	Cytidine,Cytidine	nonspec
82	ANA3	7025965	Shewana3_3113	sugar isomerase (SIS) (RefSeq)	N-Acetyl-D-Glucosamine,D-Glucosamine Hydrochloride,N-Acetyl-D-Glucosamine,D-Glucosamine Hydrochloride	enzyme	Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
83	pseudo5_N2C3_1	AO356_09615	AO356_09615	ABC transporter permease	L-Histidine	transporter	ABC transporter for L-Histidine, permease component
84	pseudo13_GW456_L13	PfGW456L13_1738		Ferric iron ABC transporter, ATP-binding protein	Sodium D-Lactate	nonspec	Fe(III) uptake
85	pseudo5_N2C3_1	AO356_07325	AO356_07325	PTS fructose transporter subunit IIBC	D-Fructose,D-Fructose	transporter	fructose PTS, IIB/IIC components
86	WCS417	GFF1090	PS417_05530	membrane protein	Inosine,Urea	nonspec	apparently involved in alginate synthesis, thought it might be a urea transporter but phenotype is not so conserved
87	pseudo3_N2E3	AO353_05990	AO353_05990	methylmalonate-semialdehyde dehydrogenase	L-Valine	enzyme	Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
88	pseudo1_N1B4	Pf1N1B4_1240		LysR family transcriptional regulator PA0133	Uridine,Uridine	other
89	pseudo6_N2E2	Pf6N2E2_6061		Methylisocitrate lyase (EC 4.1.3.30)	Sodium propionate,L-Isoleucine,Sodium propionate,L-Isoleucine,L-Isoleucine	enzyme	Methylisocitrate lyase (EC 4.1.3.30)
90	Koxy	BWI76_RS15590	BWI76_RS15590	hypothetical protein	a-Cyclodextrin,a-Cyclodextrin	nonspec
91	BFirm	BPHYT_RS15715	BPHYT_RS15715	ATP-dependent Clp protease adapter protein ClpS	Deoxyribonucleic acid from herring sperm	nonspec
92	WCS417	GFF1424	PS417_07240	GntR family transcriptional regulator	2-Deoxy-D-Ribose,2-Deoxy-D-Ribose,2-Deoxy-D-ribonic acid lithium salt,2-Deoxy-D-ribonic acid lithium salt	other
93	MR1	201736	SO2596	conserved hypothetical protein (NCBI ptt file)	L-Isoleucine	other
94	pseudo3_N2E3	AO353_05935	AO353_05935	kynureninase	L-Tryptophan,L-Tryptophan	enzyme	Kynureninase (EC 3.7.1.3)
95	Pedo557	CA265_RS06575	CA265_RS06575	MFS transporter	L-Valine	nonspec	may be a valine transporter, but not weak phenotype is not conserved, and also a phenotype on D-cycloserine stress
96	Putida	PP_3492	PP_3492	short-chain acyl-CoA dehydrogenase	L-Valine,L-Valine	enzyme	isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (modest phenotype, but conserved, and some homologs have a much stronger phenotype)
97	psRCH2	GFF561	Psest_0566	urea ABC transporter, permease protein UrtB	Parabanic Acid,Parabanic Acid,Parabanic Acid	transporter	urea transporter (parabanic acid might be hydrolyzed before transport?)
98	pseudo3_N2E3	AO353_01225	AO353_01225	ABC transporter substrate-binding protein	Sodium propionate	nonspec
99	Korea	Ga0059261_2421	Ga0059261_2421	Sterol desaturase	L-Glutamine	nonspec
100	Caulo	CCNA_02548	CCNA_02548	hypothetical protein	D-Mannose	other