L-histidine catabolism in Herbaspirillum seropedicae SmR1

Best path

PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'

Also see fitness data for the top candidates

Rules

Overview: Histidine utilization in GapMind is based on MetaCyc pathways L-histidine degradation I (link) or II (link). These pathways are very similar. Other pathways in MetaCyc (III-VI) are not complete or are not reported in prokaryotes, so they are not included.

• all:
  • histidine-transport, hutH, hutU, hutI and hutG
  • or histidine-transport, hutH, hutU, hutI, hutH, hutF and hutG'
  • Comment: In pathway I, hutH deaminates histidine to urocanate, hutU hydrates it to 4-imidazolone-5-propanoate, hutI hydrolyzes it to N-formiminoglutamate, and hutG hydrolyzes it to formamide and glutamate. Formamide can be cleaved to formate and ammonia, but it could also be secreted, so this is not described. Similarly, formate may be oxidized to CO2 or secreted. Pathway II also involves conversion to N-formiminoglutamate, but then it is deaminated to N-formylglutamate by hutF, and hydrolyzed to formate and glutamate by hutG'.
• histidine-transport:
  • hisP, hisM, hisQ and hisJ
  • or PA5503, PA5504 and PA5505
  • or Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555 and Ac3H11_2554
  • or natA, natB, natC, natD and natE
  • or aapJ, aapQ, aapM and aapP
  • or braC, braD, braE, braF and braG
  • or hutV, hutW and hutX
  • or bgtA and bgtB
  • or BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010 and BPHYT_RS24015
  • or permease
  • or Ga0059261_1577
  • or S15A3
  • or LAT2
  • or LHT
  • or SLC38A3
  • or PTR2
  • Comment: Transporters were identified using query: transporter:histidine:L-histidine:his

48 steps (32 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
PA5503	L-histidine ABC transporter, ATPase component	HSERO_RS07850	HSERO_RS04980
PA5504	L-histidine ABC transporter, permease component	HSERO_RS07845	HSERO_RS11635
PA5505	L-histidine ABC transporter, substrate-binding component	HSERO_RS07840	HSERO_RS04970
hutH	histidine ammonia-lyase	HSERO_RS22680	HSERO_RS18505
hutU	urocanase
hutI	imidazole-5-propionate hydrolase
hutF	N-formiminoglutamate deiminase	HSERO_RS11455
hutG'	N-formylglutamate amidohydrolase
Alternative steps:
aapJ	L-histidine ABC transporter, substrate-binding component AapJ
aapM	L-histidine ABC transporter, permease component 2 (AapM)	HSERO_RS07530	HSERO_RS23030
aapP	L-histidine ABC transporter, ATPase component AapP	HSERO_RS17555	HSERO_RS19240
aapQ	L-histidine ABC transporter, permease component 1 (AapQ)	HSERO_RS19340	HSERO_RS17565
Ac3H11_2554	ABC transporter for L-Histidine, permease component 2	HSERO_RS11445	HSERO_RS05830
Ac3H11_2555	L-histidine ABC transporter, substrate-binding component 2	HSERO_RS11440	HSERO_RS17550
Ac3H11_2560	L-histidine ABC transporter, ATPase component	HSERO_RS01865	HSERO_RS16975
Ac3H11_2561	L-histidine ABC transporter, permease component 1	HSERO_RS01860
Ac3H11_2562	L-histidine ABC transporter, substrate-binding component 1
bgtA	L-histidine ABC transporter, ATPase component BgtA	HSERO_RS00320	HSERO_RS21250
bgtB	L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000	L-histidine ABC transporter, substrate-binding component	HSERO_RS10775
BPHYT_RS24005	L-histidine ABC transporter, permease component 1	HSERO_RS11445	HSERO_RS05830
BPHYT_RS24010	L-histidine ABC transporter, permease component 2	HSERO_RS11445	HSERO_RS10770
BPHYT_RS24015	L-histidine ABC transporter, ATPase component	HSERO_RS00320	HSERO_RS05835
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	HSERO_RS08270	HSERO_RS17350
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	HSERO_RS08275	HSERO_RS05960
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	HSERO_RS08280	HSERO_RS05965
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	HSERO_RS08285	HSERO_RS20055
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	HSERO_RS08290	HSERO_RS05975
Ga0059261_1577	L-histidine transporter
hisJ	L-histidine ABC transporter, substrate-binding component HisJ	HSERO_RS10775	HSERO_RS21615
hisM	L-histidine ABC transporter, permease component 1 (HisM)	HSERO_RS11445	HSERO_RS23035
hisP	L-histidine ABC transporter, ATPase component HisP	HSERO_RS00320	HSERO_RS05835
hisQ	L-histidine ABC transporter, permease component 2 (HisQ)	HSERO_RS05830	HSERO_RS00315
hutG	N-formiminoglutamate formiminohydrolase	HSERO_RS08555	HSERO_RS00305
hutV	L-histidine ABC transporter, ATPase component HutV	HSERO_RS08545	HSERO_RS04980
hutW	L-histidine ABC transporter, permease component HutW	HSERO_RS08540	HSERO_RS07845
hutX	L-histidine ABC transporter, substrate-binding component HutX
LAT2	L-histidine transporter
LHT	L-histidine transporter
natA	L-histidine ABC transporter, ATPase component 1 (NatA)	HSERO_RS14705	HSERO_RS08285
natB	L-histidine ABC transporter, substrate-binding component NatB
natC	L-histidine ABC transporter, permease component 1 (NatC)
natD	L-histidine ABC transporter, permease component 2 (NatD)	HSERO_RS08275	HSERO_RS05960
natE	L-histidine ABC transporter, ATPase component 2 (NatE)	HSERO_RS06785	HSERO_RS08925
permease	L-histidine permease
PTR2	L-histidine:H+ symporter
S15A3	L-histidine transporter
SLC38A3	L-histidine:Na+ symporter

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.