Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_077277352.1 B1C78_RS01365 3-phosphoglycerate dehydrogenase
Query= BRENDA::O08651 (533 letters) >NCBI__GCF_002000365.1:WP_077277352.1 Length = 319 Score = 156 bits (394), Expect = 1e-42 Identities = 100/285 (35%), Positives = 152/285 (53%), Gaps = 10/285 (3%) Query: 8 KILISDSLDPCCRKI-----LQDGGLQVVEKQNLSKEELIAELQDCEGLI-VRSATKVTA 61 KI+I D C R + L D + V E L +D E L+ +R T +T Sbjct: 2 KIVIPDDYQDCVRTLACFARLADHEVTVYNDTVRDVETLAERFRDAEALVLIRERTPITD 61 Query: 62 DVINAAEKLQVVGRAGTGVDNVDLEAATRKGVLVMNTPNGNSLSAAELTCGMLMCLARQI 121 +++ +L+++ + G G+ +VDLEA TR+GV V G +AAELT G+++ R I Sbjct: 62 ELLERLPRLRLISQTGKGIAHVDLEACTRRGVAVA-VGTGAPFAAAELTWGLIIAAMRHI 120 Query: 122 PQATASMKDGKWDRKKFMGTELNGKTLGILGLGRIGREVAARMQAFGMKTVGYDPIISPE 181 P A+MK GKW + +GT L G+TLGI G G+IG VA +AF M+ + + S E Sbjct: 121 PAEVAAMKAGKWQTR--LGTGLRGRTLGIFGYGKIGSLVAHYGRAFAMRVLVWGREGSLE 178 Query: 182 VAASFGVQQLPLEE-IWPLCDFITVHTPLLPSTTGLLNDSTFAQCKKGVRVVNCARGGIV 240 AA G +E ++ D +++H L T G++ A K +VN +R ++ Sbjct: 179 RAAMVGFDTAKSQEDLFARSDVLSLHLALNEGTRGIVTADHLAAMKPTALLVNTSRAELI 238 Query: 241 DEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLG 285 EGAL+ AL++G+ AA+DV+ EP RD L+ +N + PHLG Sbjct: 239 AEGALVDALKAGRPGMAAVDVYENEPVRDHPLLHLDNALCTPHLG 283 Lambda K H 0.318 0.134 0.394 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: 341 Number of extensions: 18 Number of successful extensions: 4 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: 533 Length of database: 319 Length adjustment: 31 Effective length of query: 502 Effective length of database: 288 Effective search space: 144576 Effective search space used: 144576 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: 50 (23.9 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