Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_017599110.1 D471_RS0113565 D-2-hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000341125.1:WP_017599110.1 Length = 339 Score = 118 bits (295), Expect = 2e-31 Identities = 82/269 (30%), Positives = 129/269 (47%), Gaps = 20/269 (7%) Query: 57 ASGLRWMQSTFAGVDLLVKPRQ-RRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKS 115 A L W+ + GVD L+ P D +LTN RGIF ++EY+ G ++A ++ Sbjct: 71 ADTLTWVHAATTGVDNLIFPGMVDSDVVLTNSRGIFEQPIAEYVVGQVIAFAKDFHHTWD 130 Query: 116 QQQQKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKV--------------AGI 161 Q+ W + + G L++GTG I + +A+ GM+V + Sbjct: 131 LQRAHRWRHRETERVAGRRALVVGTGPIGRTIARGLSAVGMEVHASGSRARSGDPDFRSV 190 Query: 162 NRSAKATEGFDEVATLEALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNL 221 S+ A G D TL A + AD + P T+ATRG+++ L MKP A L N+ Sbjct: 191 VESSLADRGADGAPTLAAA---LPEADYVVVAAPLTDATRGLVDRRFLQLMKPTARLLNV 247 Query: 222 GRGDVLDLDALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAP--SFPE 279 RG ++ L L++ A LDVF EPL D P+W L +V+PH++ + + Sbjct: 248 ARGPIVVQSDLVAALQKGRIAGAALDVFEDEPLAVDSPLWELPGSVVSPHMSGDVVGWRD 307 Query: 280 QVAEIFSSNYHKFLLGETLSHRVNFERGY 308 + ++F N ++L G L + V+ RGY Sbjct: 308 DLVDLFLDNLARYLDGRELLNVVDKGRGY 336 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: 259 Number of extensions: 7 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: 308 Length of database: 339 Length adjustment: 28 Effective length of query: 280 Effective length of database: 311 Effective search space: 87080 Effective search space used: 87080 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 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