Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate SMa0478 SMa0478 formate dehydrogenase
Query= BRENDA::A4VGK3 (468 letters) >FitnessBrowser__Smeli:SMa0478 Length = 401 Score = 114 bits (286), Expect = 5e-30 Identities = 78/236 (33%), Positives = 120/236 (50%), Gaps = 12/236 (5%) Query: 143 IGTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAILLLRGIPEKNASCHRGGW--IK 200 IG++ VDL AA +RGI V Y N+ SV+E V+ + L R +GGW Sbjct: 125 IGSDHVDLQAAIDRGITVAEVTYCNSISVSEHVVMMILSLARNYIPSYQWVVKGGWNVAD 184 Query: 201 SAANSFEIRGKKLGIIGYGSIGTQLSVLAEALGMQVFFYDVVTKLPLGNATQIGSLY--- 257 A S++I G +G +G G IGT + + +++ + D +LP A ++G + Sbjct: 185 CVARSYDIEGMDIGTVGAGRIGTAVLRRLKPFDVKLHYTDR-HRLPDEVAKELGVTFHQT 243 Query: 258 --ELLGMCDIVSLHVPELPSTQWMIGEKEIRAMKKGAILINAARGTVVELDHLAAAIKDE 315 E++ +CD+V+++ P P T+ + E I MK+GA L+N ARG + D +A A++ Sbjct: 244 AAEMVPVCDVVTINAPLHPETENLFNEAMIGKMKRGAYLVNTARGKICNRDAVARALESG 303 Query: 316 HLIGAAIDVFPVEPKSNDEEFESPLRGLDRVILTPHIGGSTAEAQANIGLEVAEKL 371 L G A DV+ +P D P R + +TPHI GS+ AQA E L Sbjct: 304 QLAGYAGDVWFPQPAPKDH----PWRSMPHHGMTPHISGSSLSAQARYAAGTREIL 355 Lambda K H 0.318 0.135 0.385 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: 371 Number of extensions: 22 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: 468 Length of database: 401 Length adjustment: 32 Effective length of query: 436 Effective length of database: 369 Effective search space: 160884 Effective search space used: 160884 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: 51 (24.3 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