Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_012047223.1 BBTA_RS34980 2-hydroxyacid dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000015165.1:WP_012047223.1 Length = 327 Score = 142 bits (357), Expect = 2e-38 Identities = 96/277 (34%), Positives = 147/277 (53%), Gaps = 10/277 (3%) Query: 39 VIGRFDGIIVS-PTTKITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLL 97 V GR G+ V+ T K V+ + RL++I+ GYD+I A + GI VT +L Sbjct: 47 VKGRIRGVAVTFHTVKTDAAVMASLPRLEIIASFGVGYDHIAAAHAGQHGIVVTNTPDVL 106 Query: 98 SEAVAEFTVGLIINLMRKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAI 157 +E VA+ +GL+I R+ AD+F+R GEW S + + SL + VG++GMG I Sbjct: 107 TEEVADVALGLLIATCREFIKADRFVRSGEWTSKPYPLS----VGSLRDRTVGMVGMGRI 162 Query: 158 GKAIARRLIPFGVKLYYWSRHRKVNVEKELKARYMDIDELLEKSDIVILALPLTRDTYHI 217 G+AIARRL V + Y SR+ V + Y D+ ++ + D +++ +P T I Sbjct: 163 GQAIARRLEASLVPVVYHSRNAAAGVANK---HYPDLLQMAKDVDTLVVIVPGGASTNKI 219 Query: 218 INEERVKKLEGK-YLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYE 276 +N E +K L + +VN+ RG+++DE A+ +A+K G + DVFEKEP EL K Sbjct: 220 VNAEVLKALGPRGVVVNVARGSVIDEAALVDALKSGTILAAGLDVFEKEPAVPDEL-KAM 278 Query: 277 WETVLTPHYAGLALEAQEDVGFRAVENLLKVLRGEVP 313 VL PH A+ + + V+NL G+ P Sbjct: 279 DNVVLLPHIGSAAIVTRNAMDQLVVDNLKVWFAGKPP 315 Lambda K H 0.319 0.139 0.393 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 282 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 327 Length adjustment: 28 Effective length of query: 305 Effective length of database: 299 Effective search space: 91195 Effective search space used: 91195 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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