Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF3198 PS417_16375 2-hydroxyacid dehydrogenase
Query= metacyc::MONOMER-20569 (394 letters) >FitnessBrowser__WCS417:GFF3198 Length = 329 Score = 107 bits (266), Expect = 6e-28 Identities = 79/245 (32%), Positives = 124/245 (50%), Gaps = 13/245 (5%) Query: 65 LIIRAGAGVNTIDVNAASNHGVLVTNTPGQNNDAVAELAFGHIIACDRCIPQNTMHIKNG 124 LI AG N +D+ A G+ + P + AVAE A I+A +R + + ++G Sbjct: 71 LIALRSAGYNHVDLACAKRLGLTIVRVPAYSPHAVAEHAVALILALNRRLHRAYNRTRDG 130 Query: 125 EWRKKLFLNSTGLRDRTLGLVGCGNISHSMIHIAKGFNMNVAVYSIPFSPEEAKSLGVQY 184 ++ L L +T+G+VG G I + I GF + Y PF + ++LG +Y Sbjct: 131 DFSLH-GLTGFDLVGKTVGVVGTGQIGATFAKIMAGFGCQLLAYD-PFPNPQVQALGTRY 188 Query: 185 CGTLEELAKIADVVSVHVPYMKETHHLINKQFFDAMKKKAIFINTSRGEIVDTVAMIEAI 244 +L EL A ++S+H P ++ HLIN + M+ A+ INT RG +VDT A+IEA+ Sbjct: 189 V-SLPELLAQAQIISLHCPLTADSKHLINARSLAQMQPGAMLINTGRGGLVDTPALIEAL 247 Query: 245 KEKGI-KVGLDVYENEPAGSFG-----TFQNNQIAEVVT----SATCHIGASTQQASERI 294 K+ + +GLDVYE E F Q++ +A ++T T H T++A I Sbjct: 248 KDGQLGYLGLDVYEEEAQLFFEDRSDLPLQDDVLARLLTFPNVIITAHQAFLTREALAAI 307 Query: 295 ADETI 299 A T+ Sbjct: 308 AGTTL 312 Lambda K H 0.319 0.134 0.384 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: 260 Number of extensions: 14 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: 394 Length of database: 329 Length adjustment: 29 Effective length of query: 365 Effective length of database: 300 Effective search space: 109500 Effective search space used: 109500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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