Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_011382583.1 AMB_RS00685 phosphoglycerate dehydrogenase
Query= BRENDA::O08651 (533 letters) >NCBI__GCF_000009985.1:WP_011382583.1 Length = 318 Score = 168 bits (426), Expect = 2e-46 Identities = 94/257 (36%), Positives = 150/257 (58%), Gaps = 3/257 (1%) Query: 35 NLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGVL 94 +LS ++L+A L + + + K+ V++ L+VVG+ G G+D +DL A +R G Sbjct: 40 SLSGDDLVAFLLGHDKAVT-ALEKLDEAVLSRLPDLKVVGKYGVGLDMIDLAAMSRLGKR 98 Query: 95 VMNTPNGNSLSAAELTCGMLMCLARQIPQATASMKDGKWDRKKFMGTELNGKTLGILGLG 154 + T N S +EL + L R IPQ A ++DG W ++ MG +L+ +T+GI+G G Sbjct: 99 LGWTGGVNRRSVSELVIAFAIALLRHIPQGNALIRDGGW--RQLMGRQLSERTVGIVGCG 156 Query: 155 RIGREVAARMQAFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLLPSTT 214 IG++++ ++AFG + + +D PE A+ GV+++ LE + D +T+H P ST Sbjct: 157 HIGKDLSRLLKAFGCRVLAHDIRDFPEFYAATGVEKMDLEPLLAEADIVTLHLPFDASTR 216 Query: 215 GLLNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVD 274 +L+ A + ++N ARGG+VDE AL L +G+ A AA DVF EPP DRAL++ Sbjct: 217 NILSAERLALMRSDAILINAARGGLVDEAALRVMLATGRLAAAAFDVFATEPPEDRALIE 276 Query: 275 HENVISCPHLGASTKEA 291 N + PH+G S +EA Sbjct: 277 LPNFLCTPHVGGSAEEA 293 Lambda K H 0.318 0.134 0.394 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: 321 Number of extensions: 10 Number of successful extensions: 2 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: 533 Length of database: 318 Length adjustment: 31 Effective length of query: 502 Effective length of database: 287 Effective search space: 144074 Effective search space used: 144074 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 (21.7 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