Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_043536170.1 SACCYDRAFT_RS05055 phosphoglycerate dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000244975.1:WP_043536170.1 Length = 306 Score = 117 bits (294), Expect = 3e-31 Identities = 82/281 (29%), Positives = 136/281 (48%), Gaps = 11/281 (3%) Query: 29 LLDDNPANIRLADIWL--AEPGLAAPLVNHASGLRWMQSTFAGVDLLVKPRQRRDYLLTN 86 L + PA A++ + A+P PL++ LR +Q AG + + LL+ Sbjct: 32 LAEGVPAEAAEAEVLIPGAKPAALLPLLDAMPRLRLIQLLSAGAENWTD-QVPDGVLLST 90 Query: 87 VRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQKLWLPGSYKTLQGSELLLLGTGSIAKH 146 RG G +E++ LL+ R + Q+ + W P + +TLQGS +L++G G + Sbjct: 91 CRGAHGGSTAEWVMAVLLSTYRGLPEFAEAQRARTWSPSTGRTLQGSRVLVVGAGDVGNE 150 Query: 147 LAQTAKHFGMKVAGINRSAKATEGFDEVATLEALPTLMARADAIASILPSTEATRGILNE 206 L + F V + + + + V +E LP L+ D + + P T TRG+++ Sbjct: 151 LRRRLVPFDAWVTMVGFTPR-----EGVHGVEELPELLPDTDVVVLVTPLTSHTRGMVDA 205 Query: 207 NILARMKPDAVLFNLGRGDVLDLDALERQLRQHPQQQAVLDVFNQEPLPEDHPIWGLGNV 266 LA + A+L N RG V+D DAL +L + A LDV + EPLP DHP+W NV Sbjct: 206 AFLAALPDGALLVNASRGPVVDTDALLAELTT-GRLSAALDVTDPEPLPADHPLWTAPNV 264 Query: 267 IVTPHI--AAPSFPEQVAEIFSSNYHKFLLGETLSHRVNFE 305 ++TPH+ A + + ++ +++ GE + V E Sbjct: 265 VITPHVGGAVRDARRRSYRVVAAEIERYVRGELPDNLVQGE 305 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: 238 Number of extensions: 13 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: 308 Length of database: 306 Length adjustment: 27 Effective length of query: 281 Effective length of database: 279 Effective search space: 78399 Effective search space used: 78399 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 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