Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_013419867.1 RVAN_RS11390 D-glycerate dehydrogenase
Query= curated2:O27051 (525 letters) >NCBI__GCF_000166055.1:WP_013419867.1 Length = 329 Score = 192 bits (488), Expect = 2e-53 Identities = 116/315 (36%), Positives = 183/315 (58%), Gaps = 10/315 (3%) Query: 4 MKVLIADSINEKGISELEEVAEVVVNTTITP---EELLDAIKDFDAIVVRSRTKVTREVI 60 +KV++ + E + + E+ +V +N + P ++L A++ +V ++ + ++ Sbjct: 6 VKVVVTRKLPELVEARMRELFDVTLNASDAPMTRDQLAAAMRTATVLVPTVTDRIDKTLL 65 Query: 61 EAA-PRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAI 119 +A P+LK+IA G GVDN+D++ A +RGI+V N P + A+ ++ L+L++ R++ Sbjct: 66 SSAGPQLKLIANYGTGVDNIDLETARNRGIIVTNTPGILTEDTADMTMALILSVPRRLVE 125 Query: 120 ADRSVKEGK----WEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYIS 175 +++GK W +G + GK LGIIGMGRIG V R KAFG+ I ++ Sbjct: 126 GADYLQDGKEWHGWSPTWMLGHRIWGKKLGIIGMGRIGRAVARRAKAFGLSINYHNRRRV 185 Query: 176 KEAAE-EMGVTVTD-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARG 233 A E E+G T + L+ +L DI++++ P TP T HL+S KL+K TA+IVN ARG Sbjct: 186 PGAVEAELGATYWESLDQMLAHMDIISVNCPHTPATFHLLSARRLKLLKPTAYIVNTARG 245 Query: 234 GIIDEDALYRALKDGEIAGAALDVFEEEPPEGSPLLELENVVLTPHIGASTSEAQRDAAI 293 +IDE+AL R ++ GE+AGA LDVFE EP LL VV+ PH+G++T E + D Sbjct: 246 EVIDENALSRMVEAGEVAGAGLDVFENEPAINPKLLRNPKVVVLPHLGSATIEGRLDMGE 305 Query: 294 IVANEIKTVFQGGAP 308 V I+T G P Sbjct: 306 KVIINIRTFLDGHNP 320 Lambda K H 0.316 0.135 0.366 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: 370 Number of extensions: 21 Number of successful extensions: 3 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: 525 Length of database: 329 Length adjustment: 31 Effective length of query: 494 Effective length of database: 298 Effective search space: 147212 Effective search space used: 147212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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