Annotation: NCBI__GCF_000191585.1:WP_013644025.1
Length: 525 amino acids
Source: GCF_000191585.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-cysteine biosynthesis | serA | hi | D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale) | 47% | 100% | 492.3 | |||
| L-cysteine biosynthesis | serA | hi | serA: phosphoglycerate dehydrogenase (EC 1.1.1.95) (TIGR01327) | 100% | 660.8 | ||||
| L-serine biosynthesis | serA | hi | D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale) | 47% | 100% | 492.3 | |||
| L-serine biosynthesis | serA | hi | serA: phosphoglycerate dehydrogenase (EC 1.1.1.95) (TIGR01327) | 100% | 660.8 | ||||
| L-serine biosynthesis | serB | lo | fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized) | 32% | 50% | 178.7 | glycerate dehydrogenase (EC 1.1.1.29) | 42% | 419.9 |
View WP_013644025.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
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Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MDKKVLIADQINEKGIDELKDVAEIVSNFTISKEELVKEIADYDAIIVRSRTKVTREVIE AADKLKIIARAGVGVDNVDVQAATERGIMVINAPESTSITVAEHTMGLILSLSRKISIAD SSVKDGKWEKSRFMGIELNGKTLGVIGMGRIGSQVVTRSKAFGMETVVYDPYITEKSASE LGVTVVDLETLLKESDVMTIHVPLTPETKHLISKPQFEIMKENAIIINCARGGIINEEDL YEALSNNRIRGAGLDVYEVEPPENSPLFTLDNVVLTPHIAASTSEAQRDAAIIVANEIKK VFQGRSPKNVLNMPVLDPETFSMVKPYFGLIEKIGKFMIQTAKGNIKEIDVTYCGDLSEL RKHDILTRMILQEVLNPILTEPVNLVNATSVAEKRGIIVTEGKRCDAKGYKNLIKVEMKS DFNDVSIEGIMADEPKIIMINGYQVDVETEGTMLISKYKDKPGVIGAIGTKIGKHNINIA KMQVGRKELGGEAVMVLKVDQQVPLNVIEELKQLEDVNDAVAVNL
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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