As text, or see rules and steps
# GapMind describes L-alanine uptake only. No enzymatic steps are represented # because L-alanine is a single transamination reaction # away from pyruvate, which is a central metabolic intermediate. # (L-alanine can also be converted to pyruvate by alanine dehydrogenase # or by by alanine racemase and D-alanine dehydrogenase, metacyc:ALADEG-PWY). # A sequence nearly identical to E. coli K-12's cycA (CYCA_ECOL6 / A0A0H2VDI7) is annotated as a D-alanine # transporter only, ignore. # And add DL-alanine permease SERP2_LACLM / A2RI86. # And add general amino-acid permease GAP1_YEAST / P19145, GAP2_CANAL / A0A1D8PK89. cycA L-alanine symporter CycA curated:SwissProt::P0AAE0 curated:TCDB::F2HQ24 curated:TCDB::M1IW84 curated:TCDB::Q2VQZ4 curated:reanno::WCS417:GFF1065 curated:reanno::pseudo3_N2E3:AO353_16120 curated:reanno::pseudo5_N2C3_1:AO356_17670 ignore:SwissProt::A0A0H2VDI7 curated:SwissProt::A2RI86 curated:SwissProt::P19145 curated:SwissProt::A0A1D8PK89 # ABC transporters: there's BraCDEFG (P. aeruginosa), NatABCDE (Synechocystis), LivJFGHM (S. pneumoniae) # Although TCDB suggests that LivJFGHM transports alanine and serine, this is not supported by PMID:19470745, # so this was removed. # Also, BraFG and NatAE are similar and were clustered together; # clustering at 40% separates this into BraF/NatA and BraG/NatE (P21630/P73650). # And an orthologous system to NatABCDE, TC 3.A.1.4.6, was missed initially # # Also, TC 3.A.1.4.3 from Rhizobium leguminosarum is described as BraCDEFG and as a L-alanine transporter. # However, the substrate-binding protein BraC is not required for L-alanine uptake, so is another # SBP is likely used. # # Also note: some components of the R. leguminosarum system are very similar to # BraC (SMc01946) and BraDEFG (SMc01951:SMc01948) from S. meliloti, but some are quite distant. # (In S. meliloti, these are important for utilization of some larger amino acids, and again, # BraC does not seem to be the only SBP for this system.) # braC and natB are quite distantly related and were not clustered, but both are SBP braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) curated:SwissProt::P21175 curated:TCDB::Q55387 curated:TCDB::Q8YVY4 braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) curated:TCDB::P21627 curated:TCDB::P74318 curated:TCDB::Q8YXD0 braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) curated:TCDB::P21628 curated:TCDB::P74455 curated:TCDB::Q8YY08 braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) curated:TCDB::P21629 curated:TCDB::Q55164 curated:TCDB::Q7A2H0 braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) curated:TCDB::P21630 curated:TCDB::P73650 curated:TCDB::Q8YT15 # Merge in TC 2.A.25.1.1 / P30144 (dagA from Alteromonas haloplanktis), which is similar but was # not included in the cluster because it is longer alsT L-alanine symporter AlsT/DagA curated:SwissProt::P30145 curated:SwissProt::Q6LX42 curated:TCDB::Q45068 curated:TCDB::W0WFC6 curated:TCDB::P30144 SLC1A4 L-alanine symporter SLC1A4 curated:CharProtDB::CH_091534 curated:CharProtDB::CH_091706 SLC38A3 L-alanine symporter SLC38A3 curated:CharProtDB::CH_091437 curated:SwissProt::Q9EQ25 # Structural studies show these are related to TRIC transporters TRIC TRIC-type L-alanine transporter curated:reanno::ANA3:7023996 curated:reanno::MR1:202450 AAP1 L-alanine permease AAP1 curated:CharProtDB::CH_091601 AAP24 L-alanine transporter AAP24 curated:TCDB::A4HUI4 snatA L-alanine symporter SnatA curated:TCDB::Q8J305 metP sodium-dependent methionine/alanine transporter, large subunit MetP curated:TCDB::Q8NRL8 metS sodium-dependent methionine/alanine transporter, small subunit MetS curated:TCDB::Q8NRL9 # Transporters were identified using curated clusters and # query: transporter:L-alanine:alanine alanine-transport: cycA alanine-transport: braC braD braE braF braG alanine-transport: alsT alanine-transport: SLC1A4 alanine-transport: SLC38A3 alanine-transport: TRIC alanine-transport: AAP1 alanine-transport: AAP24 alanine-transport: snatA alanine-transport: metP metS # Ignore LAT2_HUMAN / Q9UHI5 and related proteins, which are amino acid exchangers in animals. # Ignore b2670 (ALAE_ECOLI) and related proteins, which are amino acid exporters. # Ignore PA5152-PA5155, which probably transports D-alanine. # Ignore D-alanyl carrier protein DCP (P39579). # Ignore aspartate/alanine antiporter (Q8L3K8 or Q845W9). # Ignore spore germination L-alanine receptor (P07869). # Ignore likely efflux protein b4210 / YtfF. # Ignore TC 2.A.21.4.1 / Q8VM88 which has far tighter affinity for lactate/pyruvate. all: alanine-transport
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory