Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate AZOBR_RS18320 AZOBR_RS18320 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__azobra:AZOBR_RS18320 Length = 314 Score = 170 bits (431), Expect = 6e-47 Identities = 101/265 (38%), Positives = 150/265 (56%), Gaps = 5/265 (1%) Query: 24 AEVVVNTTITPEELLDAIKDFDAIVV-RSRTKVTREVIEAAPRLKIIARAGVGVDNVDVK 82 A V I EE++ + + +V+ R RT +I+A P L+++ G + +D++ Sbjct: 27 ALTVFERPIPAEEVVGTLAPYSVLVIMRERTPFPASLIDALPNLRLLVTTGGRNNAIDLE 86 Query: 83 AATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEKNRFMGIELNGK 142 A RGI V + T AE + GL+LAL ++I +R ++ G+W+ G L GK Sbjct: 87 ACKARGITVCGTGMVGTPT-AELTWGLILALTKRIPQEERGLRAGRWQAGLTQG--LAGK 143 Query: 143 TLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIH 202 LG++G+G++G+QV +AFGM++ + P ++ E A GV D L SDIV++H Sbjct: 144 RLGLVGLGKLGTQVARVGQAFGMEVAAWSPNLTDERAAAAGVARLDKRDLFATSDIVSVH 203 Query: 203 VPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEP 262 + L TR ++ D+ MK +AF VN +R G++D DAL AL + IAGA LDVF EP Sbjct: 204 LVLGERTRGVVGADDIDAMKPSAFFVNTSRAGLVDGDALLAALHEHRIAGAGLDVFPVEP 263 Query: 263 -PEGSPLLELENVVLTPHIGASTSE 286 P SP LE N VLTPH+G T E Sbjct: 264 LPVDSPWLEAPNTVLTPHLGYVTRE 288 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: 335 Number of extensions: 13 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: 525 Length of database: 314 Length adjustment: 31 Effective length of query: 494 Effective length of database: 283 Effective search space: 139802 Effective search space used: 139802 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