Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_018231704.1 THITHI_RS0103560 hypothetical protein
Query= curated2:O27051 (525 letters) >NCBI__GCF_000378965.1:WP_018231704.1 Length = 308 Score = 217 bits (553), Expect = 4e-61 Identities = 117/301 (38%), Positives = 181/301 (60%), Gaps = 6/301 (1%) Query: 5 KVLIADSINEKGISELEEVAEVVVNTTIT--PEELLDAIKDFDAIVVRSRTKVTREVIEA 62 +++I + ++ + L + T+ P++L + D +A++VR+RT+V E++E Sbjct: 3 RIVITEFMDTDAVEWLSSRLDTHYGPTLVDEPDKLAPLLADCEALIVRNRTQVRPELLEQ 62 Query: 63 APRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADR 122 AP LK++ R GVG+DN+D A +RG+ VI A + ++ VAE+ I + L R ++ Sbjct: 63 APGLKVVGRLGVGLDNIDQPACAERGVQVIPATGANALAVAEYVICTAMMLLRGAYLSSD 122 Query: 123 SVKEGKWEKNRFM-GIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAA-- 179 V G+W + G EL GKTLG+ G G IG + GM+ + YDPYI +A Sbjct: 123 RVAAGEWPRPALSRGRELAGKTLGLAGFGGIGQLTAKLARGLGMETVAYDPYIEADAPVL 182 Query: 180 EEMGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDED 239 + G + D++ LL ESD++++H+PLT ETR+L + M+ A ++N ARGGIIDE Sbjct: 183 AQTGTRLLDMDGLLAESDVISLHIPLTDETRNLFDAERIAAMRGGAVLINSARGGIIDEF 242 Query: 240 ALYRALKDGEIAGAALDVFEEEP-PEGSPLLELENVVLTPHIGASTSEAQRDAAIIVANE 298 AL RALKDG +AGAALDVF++EP GS L ++ N+VLTPHI T E+ + ++A Sbjct: 243 ALARALKDGHLAGAALDVFDKEPLAAGSVLADVPNLVLTPHIAGVTEESNTRVSRLIAER 302 Query: 299 I 299 + Sbjct: 303 V 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: 374 Number of extensions: 16 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: 308 Length adjustment: 31 Effective length of query: 494 Effective length of database: 277 Effective search space: 136838 Effective search space used: 136838 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