Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_043458529.1 H537_RS0110495 C-terminal binding protein
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_000430725.1:WP_043458529.1 Length = 317 Score = 130 bits (328), Expect = 4e-35 Identities = 82/260 (31%), Positives = 128/260 (49%), Gaps = 12/260 (4%) Query: 70 INAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPE 129 +NA+ +L +G +G + +D+ A RG+PV N P V++ +G L RG+ Sbjct: 67 VNASSRLQHVGRIGVGLDNIDVAACTARGLPVTNVPDYCVEEVSDHAVGFALAWTRGLVA 126 Query: 130 ANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKL-PL 188 + H G W+ A +G++GYG IG + G V + N L P Sbjct: 127 FDRDVHAGRWDPAKARLRRLSALTVGLVGYGRIGQASARKFAAFGCRV----LANTLTPP 182 Query: 189 GNATQVQ--HLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDI 246 +T V+ L LL SD+V LH+P P + +++ I+ MKPG+LL+N SRG +VD Sbjct: 183 ARSTGVEFTELDTLLTQSDIVVLHLPLTPESHHLINRSRINAMKPGALLVNVSRGGIVDT 242 Query: 247 PALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGL 306 A+ +ALAS HL GAA+DV +EP + P LLTPH+ S+ + + Sbjct: 243 DAVVEALASGHLGGAALDVIESEPQVPAALLAQP-----GALLTPHVAFSSDASLAELRR 297 Query: 307 EVAGKLIKYSDNGSTLSAVN 326 A + ++ + L+ N Sbjct: 298 RAAEETVRVLSGRAPLNRCN 317 Lambda K H 0.318 0.135 0.383 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: 295 Number of extensions: 14 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: 410 Length of database: 317 Length adjustment: 29 Effective length of query: 381 Effective length of database: 288 Effective search space: 109728 Effective search space used: 109728 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: 49 (23.5 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