Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate GFF1452 PS417_07385 2-hydroxyacid dehydrogenase
Query= reanno::SB2B:6938941 (308 letters) >FitnessBrowser__WCS417:GFF1452 Length = 310 Score = 179 bits (454), Expect = 7e-50 Identities = 106/311 (34%), Positives = 173/311 (55%), Gaps = 8/311 (2%) Query: 4 KLLLLTRENERYRSLLASCHLPELELLD--DNPANIRLA---DIWLAEPGLAAPLVNHAS 58 ++L+ +++ Y LL P+LE+L D+ RLA +WL +P L A L+ Sbjct: 2 RVLIAEQDHPLYAQLLGEA-APDLEVLTSGDSAELSRLAADCPVWLGQPDLLATLLRQGH 60 Query: 59 GLRWMQSTFAGVDLLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQ 118 +W+QST+AG+ L+ RDY LT GIFG +M+E++ Y+L +RE Q Sbjct: 61 RPQWLQSTWAGITPLLAEGLPRDYRLTRAVGIFGQVMAEFVLTYMLGHEREVLARLVSQV 120 Query: 119 QKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLE 178 ++ W ++L G + L++GTG I + +A+ FG+K+ GI +A+ F EVA L+ Sbjct: 121 ERKWDNRMGQSLAGRKALIVGTGDIGQRVAEFLVPFGVKLYGIASTAREQAPFIEVAGLD 180 Query: 179 ALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRG-DVLDLDALERQLR 237 L ++ D + ++LP+T +T + + + + KP + N+GRG V+D D +E L+ Sbjct: 181 QLGRMVGEVDYVINLLPNTPSTHDLYDAALFKQFKPTGLFINVGRGVAVVDADLVEA-LK 239 Query: 238 QHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGET 297 + AV+DV QEPLP+ HP W +++T H +AP+ PE + E+F N + + Sbjct: 240 EGHLAGAVIDVCRQEPLPQRHPFWTAWGLLLTGHSSAPTSPELMVELFVQNLRAYQAKQA 299 Query: 298 LSHRVNFERGY 308 L V+FERGY Sbjct: 300 LRGEVDFERGY 310 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: 255 Number of extensions: 13 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: 310 Length adjustment: 27 Effective length of query: 281 Effective length of database: 283 Effective search space: 79523 Effective search space used: 79523 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