Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_022948006.1 H035_RS18360 formate dehydrogenase
Query= BRENDA::O58256 (333 letters) >NCBI__GCF_000421465.1:WP_022948006.1 Length = 393 Score = 125 bits (315), Expect = 1e-33 Identities = 83/258 (32%), Positives = 136/258 (52%), Gaps = 28/258 (10%) Query: 54 ITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLM 113 +T E + A +LK+ G D++DL+ A + G+ V +V+ S +VAE V +I+ L+ Sbjct: 104 LTAERIAKAPKLKLAITAGIGSDHVDLKAAIEHGVTVAEVTYSNSISVAEHVVMMILGLV 163 Query: 114 RKIHYADKFIRRGEWESHAKIW--TG---------FKRIESLYGKKVGILGMGAIGKAIA 162 R ++ +W + +W TG R L G +VG + G IG A+ Sbjct: 164 RN------YLPSYQWVVNKNLWDTTGGQGWNIADCISRAYDLEGMEVGTVAAGRIGLAVL 217 Query: 163 RRLIPFGVKLYYWSRHRKVN-VEKELKARYM-DIDELLEKSDIVILALPLTRDTYHIINE 220 RRL PF V+L+Y +HR VE+EL + D++ ++ D+V + PL +T H+ ++ Sbjct: 218 RRLQPFDVQLHYTDKHRLPEAVERELNLTFHPDVESMIRVCDVVTINCPLHPETEHLFDD 277 Query: 221 ERVKKLE-GKYLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWET 279 + K++ G YL+N RG + D AV A++ G+L GYA DV+ +P + + W T Sbjct: 278 NLLGKMKRGAYLINTARGKICDRDAVARALESGQLAGYAGDVWFPQPAPK----DHPWRT 333 Query: 280 V----LTPHYAGLALEAQ 293 + +TPH +G L AQ Sbjct: 334 MPHHGMTPHVSGTTLSAQ 351 Lambda K H 0.319 0.139 0.393 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: 314 Number of extensions: 12 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: 333 Length of database: 393 Length adjustment: 29 Effective length of query: 304 Effective length of database: 364 Effective search space: 110656 Effective search space used: 110656 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 (21.7 bits) S2: 49 (23.5 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