Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_050465010.1 AKL27_RS21975 2-hydroxyacid dehydrogenase
Query= BRENDA::C3SVM7 (410 letters) >NCBI__GCF_001189915.1:WP_050465010.1 Length = 314 Score = 125 bits (314), Expect = 2e-33 Identities = 85/263 (32%), Positives = 130/263 (49%), Gaps = 18/263 (6%) Query: 63 THLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLL 122 T L++ + A +L I F G +DL AA + GI V +AP +N +VA+ + +L Sbjct: 56 TGLSQAQMQAMPQLRLISAFGAGYENIDLAAARQAGIAVTHAPGANNATVADHAMALMLG 115 Query: 123 LLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFY-- 180 L RG+ ++ G W A GK+LGI+G G+IG Q+ A M + ++ Sbjct: 116 LTRGLHVLDSAVKAGGWEHNRAARPTVNGKRLGILGLGNIGAQIARRAAGFDMQIAYHAR 175 Query: 181 DIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASR 240 D + +P L SD + L P P+T+ ++ ++ + P LIN +R Sbjct: 176 DARSDVPYQYCATA---GALAQYSDYLILACPGGPATRGIVNRDLLARLGPQGFLINVAR 232 Query: 241 GTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEA 300 G+VVD PAL +AL +AGAA+DV EPA + DN+LLTPHI G + EA Sbjct: 233 GSVVDTPALIEALQQHTIAGAALDVVDGEPA-----LPAAFHALDNLLLTPHISGRSPEA 287 Query: 301 Q--------ENIGLEVAGKLIKY 315 +N+ AGK +++ Sbjct: 288 MATQLRMFTDNVAASYAGKPLQH 310 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: 276 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: 410 Length of database: 314 Length adjustment: 29 Effective length of query: 381 Effective length of database: 285 Effective search space: 108585 Effective search space used: 108585 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