Protein NP_349919.1 in Clostridium acetobutylicum ATCC 824
Annotation: NCBI__GCF_000008765.1:NP_349919.1
Length: 247 amino acids
Source: GCF_000008765.1 in NCBI
Candidate for 25 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 54% | 100% | 264.6 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-asparagine catabolism | glnQ | med | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 55% | 97% | 259.6 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-glutamate catabolism | gltL | med | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 55% | 97% | 259.6 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 51% | 95% | 256.1 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-histidine catabolism | hisP | med | histidine transport ATP-binding protein hisP (characterized) | 52% | 96% | 251.1 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-lysine catabolism | hisP | med | histidine transport ATP-binding protein hisP (characterized) | 52% | 96% | 251.1 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 50% | 97% | 247.7 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 53% | 98% | 243.4 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 53% | 98% | 243.4 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 50% | 93% | 238 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 50% | 91% | 237.3 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 50% | 91% | 237.3 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 49% | 92% | 230.3 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 49% | 90% | 229.9 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 49% | 90% | 229.9 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-citrulline catabolism | PS417_17605 | med | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 49% | 89% | 229.9 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 48% | 97% | 228 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-asparagine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 226.5 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-aspartate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 226.5 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-glutamate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 226.5 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-leucine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 226.5 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-proline catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 47% | 93% | 226.5 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 31% | 95% | 114 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 92% | 113.2 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 92% | 113.2 | TcyC (YckI), component of Uptake system for L-cystine | 58% | 295.4 |
Sequence Analysis Tools
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MITISNLHKSFGNTEILKGIDLNVNKGETTVIIGPSGSGKTTLLRCINLLETPNKGSITV
GNSSIDFDNNNSFYTSDVINLRKKTGMVFQSFNLFPHMTVLQNIMEGQVTVLKRSKSEAR
KKALLLLEKVGLSEKQDQYPHELSGGQQQRVAIARAMAMDPEVLLFDEPTSALDPELEAE
VLKVMKELSNEGMTMIVVTHKMSFAKDAAHRVIFMDNGTIIEAGTPEHVFTASTNPRVKQ
FLNIVSD
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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