Annotation: NCBI__GCF_000225705.1:WP_009140795.1
Length: 586 amino acids
Source: GCF_000225705.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| lactose catabolism | lacIICB | hi | PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 (characterized) | 54% | 100% | 627.9 | VC_1282 aka IIC, component of Glucosamine β(1→4) glucosamine (GlcN)2 (glucosamine dimer) transporter, VC1281-1283 (IIB; IIC; IIA, respectively) | 32% | 243.0 |
| D-cellobiose catabolism | celEIIC | lo | Permease IIC component (characterized, see rationale) | 32% | 95% | 208 | PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 | 54% | 627.9 |
| D-galactose catabolism | ptcEIIC | lo | PTS system galactose-specific EIIC component (characterized) | 31% | 96% | 170.2 | PTS system lactose-specific EIICB component; EIICB-Lac; EII-Lac; EC 2.7.1.207 | 54% | 627.9 |
View WP_009140795.1 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...
MEQLITTIEKGKPFFNAIARNKYLKAIRDGFISVIPIIIFSSIFILIDAVPNVWGFYWPA EIDAILMKAYNYSMGILALAAAATTAKHFCDAQNRDMPKNNQINFLSVMIASVVGFLILS SDAINVEVDSVSYSGFANGFLGSKGLLTAFISAFVVGIVYKFFVSRNITIKLPDQVPPNI SQTFKDLIPFSVSISVFWLFDLIFRNAFCFCFAQGVIQVFQPLFSAADSYVGLAIIYGAM SLFWFVGVHGPSIVEPAISAALVANMSANLTAYQAGEQATHVLSLSSQYFVVCLGGTGAT LVICFMFAFLAKSKEMKAIGRASIIPTLFNVNEPFLFGAPMVLNPIFFVPFVFAPICNIW ALKIFVDLIGMDGFLYTLPWTVPGPVGIIMGLGFQPLAFVFLAAVLAIDFLVYYPFFKVY DREKCAEEAAMLEEELAAKAAAKGDAMAAAFQGKINASSVADDESKPKTANTANSDCLAK LNGHRVLVLCQGGGTSGLLANALAKAAKEHSIDLETGADAYGNHIDMMKDFDLVILAPQA ASYFDDLKADCERMGIACCVTRGKQYIDLTRDGEASLRFVAEQLNL
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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