Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate AZOBR_RS01325 AZOBR_RS01325 2-hydroxyacid dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__azobra:AZOBR_RS01325 Length = 329 Score = 212 bits (539), Expect = 2e-59 Identities = 120/283 (42%), Positives = 174/283 (61%), Gaps = 6/283 (2%) Query: 32 ITPEELLDAIKDFDAIVVRSRTKVTREVIE-AAPRLKIIARAGVGVDNVDVKAATDRGIM 90 +T +L+D ++ D +V ++ REVIE A P+L++IA G GVD++D+KAA +RGI Sbjct: 38 LTHAQLIDVVQTADVLVPTVTDRIDREVIEKAGPQLRLIASFGTGVDHIDLKAARERGIS 97 Query: 91 VINAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWE---KNRFMGIELNGKTLGII 147 V N P + A+ ++ L+LA+ R++A +R V+ G+W+ +G + GK LGI+ Sbjct: 98 VTNTPGVLTEDTADMTMALLLAVGRRVAEGERLVRSGQWKGWGPTTMLGHRIQGKRLGIL 157 Query: 148 GMGRIGSQVVVRTKAFGMDIMVYDPY-ISKEAAEEMGVTVTD-LETLLRESDIVTIHVPL 205 GMGRIG + R +AFGM I ++ + + +E+ T + L+ +L D+V+I+ P Sbjct: 158 GMGRIGQALARRARAFGMSIHYHNRRRVYPDVEQELEATYWESLDQMLARMDVVSINCPH 217 Query: 206 TPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEG 265 TP T HL+SE KL++ FIVN +RG +IDE AL R L GEIAGA LDVFE EP Sbjct: 218 TPATYHLLSERRLKLLRPHCFIVNTSRGEVIDETALTRMLSKGEIAGAGLDVFEHEPAVN 277 Query: 266 SPLLELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAP 308 LL L+NVVL PH+G++T E + D V IKT G AP Sbjct: 278 PKLLRLDNVVLLPHMGSATIEGRIDMGEKVIINIKTFADGHAP 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: 382 Number of extensions: 17 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: 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 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