Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate 6938941 Sama_3039 D-isomer specific 2-hydroxyacid dehydrogenase family protein (RefSeq)
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__SB2B:6938941 Length = 308 Score = 615 bits (1587), Expect = 0.0 Identities = 308/308 (100%), Positives = 308/308 (100%) Query: 1 MRHKLLLLTRENERYRSLLASCHLPELELLDDNPANIRLADIWLAEPGLAAPLVNHASGL 60 MRHKLLLLTRENERYRSLLASCHLPELELLDDNPANIRLADIWLAEPGLAAPLVNHASGL Sbjct: 1 MRHKLLLLTRENERYRSLLASCHLPELELLDDNPANIRLADIWLAEPGLAAPLVNHASGL 60 Query: 61 RWMQSTFAGVDLLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQK 120 RWMQSTFAGVDLLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQK Sbjct: 61 RWMQSTFAGVDLLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQK 120 Query: 121 LWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEAL 180 LWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEAL Sbjct: 121 LWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEAL 180 Query: 181 PTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHP 240 PTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHP Sbjct: 181 PTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRGDVLDLDALERQLRQHP 240 Query: 241 QQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSH 300 QQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSH Sbjct: 241 QQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSH 300 Query: 301 RVNFERGY 308 RVNFERGY Sbjct: 301 RVNFERGY 308 Lambda K H 0.320 0.137 0.404 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: 506 Number of extensions: 11 Number of successful extensions: 1 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: 308 Length of database: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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