Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate AO356_26030 AO356_26030 hydroxyacid dehydrogenase
Query= BRENDA::O08651 (533 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26030 Length = 320 Score = 132 bits (333), Expect = 1e-35 Identities = 87/255 (34%), Positives = 137/255 (53%), Gaps = 5/255 (1%) Query: 38 KEELIAELQDCEGL-IVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGVLVM 96 ++ L LQ E + ++R T ++ L+++ G +DL+AA G+ V Sbjct: 40 RDTLAERLQHFEVICVMRERTVFDEGLLRRLPNLKLLLTGGMRNAALDLKAAAELGIQVC 99 Query: 97 NTPNGNSLSAAELTCGMLMCLARQIPQATASMKDGKWDRKKFMGTELNGKTLGILGLGRI 156 T + +A ELT ++M LAR + Q +++ G W + +G +L+GKTL ILGLG I Sbjct: 100 GTDSYKH-AAPELTWTLIMALARNLVQEANALRAGLWQQG--LGGDLHGKTLAILGLGSI 156 Query: 157 GREVAARMQAFGMKTVGYDPIISPEVAASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGL 216 G VA Q FGM+ + + +S E AA GV + + ++ D +++H L T GL Sbjct: 157 GTRVAQFGQVFGMRVIAWSQNLSAERAAEVGVTYVSKQALFEQADILSIHLVLGERTRGL 216 Query: 217 LNDSTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEP-PRDRALVDH 275 ++ K +VN +RG IVDE AL+ AL+ + AGAALDVF +EP P Sbjct: 217 VDAQALGWMKPEALLVNTSRGPIVDEAALIDALRHRRLAGAALDVFAQEPLPLAHPFRTL 276 Query: 276 ENVISCPHLGASTKE 290 ENV++ PH+G +++ Sbjct: 277 ENVLATPHVGYVSRQ 291 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: 351 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 533 Length of database: 320 Length adjustment: 31 Effective length of query: 502 Effective length of database: 289 Effective search space: 145078 Effective search space used: 145078 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