Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate CA265_RS23175 CA265_RS23175 phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__Pedo557:CA265_RS23175 Length = 309 Score = 199 bits (505), Expect = 2e-55 Identities = 110/306 (35%), Positives = 174/306 (56%), Gaps = 16/306 (5%) Query: 5 KVLIADSIN----EKGISELEEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVI 60 K+LI D ++ E+ I+ EV + IT ++ LD IKD+ I VR++ ++ E+ Sbjct: 3 KILIVDDLHPAFKEQAIAMGYEVDD---EPQITRQQTLDKIKDYTGIAVRTKFRIDAEIF 59 Query: 61 EAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIA 120 AAP LK +ARAG G+DN+D K A +R I +INAPE V EH+ GL+L+L A Sbjct: 60 AAAPNLKFVARAGAGLDNIDDKIAFERNIELINAPEGNCDAVGEHATGLLLSLMNNFRRA 119 Query: 121 DRSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAE 180 D ++ G W++ G EL GK +GIIG G +G + F +D+M YD Y K Sbjct: 120 DIEIRNGVWDREGNRGYELKGKKVGIIGYGFMGQSFAKKLAGFEVDVMAYDKY--KTGFS 177 Query: 181 EMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDA 240 + +E +++ SD++++H+PLT ET+ ++ ++ F K F +N ARG I++ A Sbjct: 178 DAFAREVSMEEIVKHSDVLSLHIPLTAETKQMVDDEYFYHFKKPIFFINTARGEIVNTPA 237 Query: 241 LYRALKDGEIAGAALDVFEEE--PPEG-----SPLLELENVVLTPHIGASTSEAQRDAAI 293 + A+K G+I GA LDV + E P G + L + V+LTPH+G T ++ R + Sbjct: 238 VLNAIKSGKILGAGLDVLQTEKFPALGEQAWYNELKNNDKVILTPHVGGWTFDSYRKISE 297 Query: 294 IVANEI 299 ++A ++ Sbjct: 298 VLAEKL 303 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: 373 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 525 Length of database: 309 Length adjustment: 31 Effective length of query: 494 Effective length of database: 278 Effective search space: 137332 Effective search space used: 137332 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 09 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