Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_020173790.1 A3OQ_RS0102580 hypothetical protein
Query= curated2:O27051 (525 letters) >NCBI__GCF_000385335.1:WP_020173790.1 Length = 319 Score = 174 bits (442), Expect = 3e-48 Identities = 105/291 (36%), Positives = 162/291 (55%), Gaps = 21/291 (7%) Query: 33 TPEELLDAIKDFDAIVVRSRTKVTREVIEAAPRLKIIARAGVGVDNVDVKAATDRGIMVI 92 +PE++++ + D D ++ ++ +V +E P+LK+IA A G D VD I VI Sbjct: 37 SPEQIVERLADADIAII-NKVQVRTASLEKLPKLKMIAVAATGTDCVDKAYCKAHNIPVI 95 Query: 93 NAPESTSITVAEHSIGLMLALARKIAIADRSVKEGKWEK-NRFMGIE-----LNGKTLGI 146 N TV EH++ L+ AL R + V++GKW+ ++F + ++G TLG+ Sbjct: 96 NIRNYAVNTVPEHTLALIFALRRSLIPYTLDVRKGKWQTIDQFCYFDHPIRDISGSTLGL 155 Query: 147 IGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEMGVTVTDLETLLRESDIVTIHVPLT 206 IG G +G V R +A GM ++ D Y DL+T+L+ESDIV++H PLT Sbjct: 156 IGYGALGKSVATRAEALGMKVIATDVYDFPGKV--------DLDTILKESDIVSLHCPLT 207 Query: 207 PETRHLISEDEFKLMKDTAFIVNCARGGIIDEDALYRALKDGEIAGAALDVFEEEPPEGS 266 TR++I E K MK A ++N ARGG++DE AL ALK GEI GA DV EPP+ Sbjct: 208 DGTRNIIGAAELKKMKKDAILINTARGGLVDEAALVDALKTGEIGGAGFDVLTVEPPKNG 267 Query: 267 PLL-----ELENVVLTPHIGASTSEAQRDAAIIVANEIKTVFQGGAPRNVL 312 +L +L N+++TPH+ ++ EA A + I+ ++ G PRN++ Sbjct: 268 NVLLDQGADLPNLIITPHVAWASHEAMTGLANQLVENIE-LWVAGTPRNLV 317 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: 412 Number of extensions: 26 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: 319 Length adjustment: 31 Effective length of query: 494 Effective length of database: 288 Effective search space: 142272 Effective search space used: 142272 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