Protein WP_109970253.1 in Methanospirillum lacunae Ki8-1
Annotation: NCBI__GCF_003173355.1:WP_109970253.1
Length: 362 amino acids
Source: GCF_003173355.1 in NCBI
Candidate for 37 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 34% | 89% | 176 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 99% | 169.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 99% | 169.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 95% | 167.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 95% | 167.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 95% | 167.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 95% | 167.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 79% | 164.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-cellobiose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-glucose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| lactose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-maltose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| sucrose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| trehalose catabolism | gtsD | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 31% | 94% | 162.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 31% | 97% | 160.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 37% | 88% | 154.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 37% | 88% | 154.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 74% | 149.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 34% | 65% | 149.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 81% | 139.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 33% | 98% | 133.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 33% | 98% | 133.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 96% | 110.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 96% | 110.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 96% | 110.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 96% | 110.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 96% | 110.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 96% | 110.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 35% | 213.0 |
Sequence Analysis Tools
View WP_109970253.1 at NCBI
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
Fitness BLAST: loading...
Sequence
MIKLDHISKSFGDRLILDNISVEIPSGKIFTIIGPSGQGKTTLMRLINLLDTPSSGQIIF
NGTSLEHIKNITEIRRQMGMVFQTPIAFNETVYANLAMGLKFRGVSKDEIKKRVEEKINE
IGLSGYEHRKARTLSGGEMQRVSLARVMITNPDLLLLDEPTANLDPVSTAKIEELIRYYN
RTCGTTVIMSSHDLYQGQRLADIIAVMMGGRFVQSGETNQVFSEPCSADVARFIGIRNIL
PGVATQLENGLIQIDLGGIIIYAVSSMTEKEVMVAIRPEEITVHTNESGKTSARNVLTGI
ITEIEPYGIINHVLVSCNGIILASQVTLQSVREMNLRPGLEVQLSFKAPSVHLMSQCPGY
HI
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