Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate CA265_RS12240 CA265_RS12240 phosphoglycerate dehydrogenase
Query= curated2:O27051 (525 letters) >FitnessBrowser__Pedo557:CA265_RS12240 Length = 311 Score = 199 bits (506), Expect = 1e-55 Identities = 114/310 (36%), Positives = 179/310 (57%), Gaps = 16/310 (5%) Query: 3 RMKVLIADSINEKGISELEEVAEVVVNTTITPEELLDAIKDFD--AIVVRSRTKVTREVI 60 R VL+ ++I E+ ++ L+E V V T L D + + + AI+ R + + + ++ Sbjct: 2 RKNVLLLETIAEEALALLQE--NVNVFTGYDEAGLKDTLNNVEVHAIITRGKKHIDKTLM 59 Query: 61 EAAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIA 120 +A P L++ AR GVG+DNVDV A+ R I VINAP S + T+AEH++ LML L R + + Sbjct: 60 DACPHLEVAARCGVGLDNVDVDEASARKIRVINAPGSNAATIAEHTLALMLMLMRDMHRS 119 Query: 121 DRSVKEGKWE-KNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAA 179 VK+ W +N++ G ELNGKTLGI+G+G IG +V AFGM ++ + Sbjct: 120 VNHVKQNNWNWRNQYAGDELNGKTLGILGLGNIGKRVAKLGDAFGMKVLCW--------- 170 Query: 180 EEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDED 239 V L+ +L++SD+V++H+PL+ ET +I + LMK AF++N ARG +ID Sbjct: 171 -SRSVQDLPLDEVLQQSDVVSLHLPLSNETNEIIGASQLALMKPKAFLINTARGALIDHA 229 Query: 240 ALYRALKDGEIAGAALDVFEEEPP-EGSPLLELENVVLTPHIGASTSEAQRDAAIIVANE 298 AL AL G IAG A DV +EPP + +++ N ++TPH + T+ + ++ Sbjct: 230 ALLDALNAGTIAGFAADVLPDEPPLQSLAVVQHPNALVTPHAASLTASTYKQMCLLTVRN 289 Query: 299 IKTVFQGGAP 308 + +V G P Sbjct: 290 VLSVLAGQQP 299 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: 328 Number of extensions: 20 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: 311 Length adjustment: 31 Effective length of query: 494 Effective length of database: 280 Effective search space: 138320 Effective search space used: 138320 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