Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate BWI76_RS12790 BWI76_RS12790 lactate dehydrogenase
Query= metacyc::MONOMER-20569 (394 letters) >FitnessBrowser__Koxy:BWI76_RS12790 Length = 329 Score = 119 bits (297), Expect = 2e-31 Identities = 80/251 (31%), Positives = 130/251 (51%), Gaps = 6/251 (2%) Query: 60 ARALSLIIRAGAGVNTIDVNAASNHGVLVTNTPGQNNDAVAELAFGHIIACDRCIPQNTM 119 A + I AG N +D++AA G+ V P + +AVAE A G +++ +R I + Sbjct: 66 AHGVKYIALRCAGFNNVDLDAAKELGLRVVRVPAYSPEAVAEHAIGMMMSLNRRIHRAYQ 125 Query: 120 HIKNGEWRKKLFLNSTGLRDRTLGLVGCGNISHSMIHIAKGFNMNVAVYSIPFSPEEAKS 179 ++ + + T + +T G++G G I + + I KGF M + + P+ A Sbjct: 126 RTRDANFSLEGLTGFT-MHGKTAGVIGTGKIGVAALRILKGFGMRLLAFD-PYPSAAALD 183 Query: 180 LGVQYCGTLEELAKIADVVSVHVPYMKETHHLINKQFFDAMKKKAIFINTSRGEIVDTVA 239 +GV+Y LE L + +DV+S+H P E +HL+N F+ MK + INTSRG ++D+ A Sbjct: 184 MGVEYVD-LETLYRESDVISLHCPLTDENYHLLNHAAFERMKDGVMIINTSRGALIDSQA 242 Query: 240 MIEAIKEKGI-KVGLDVYENEPAGSFGTFQNNQIAEVV--TSATCHIGASTQQASERIAD 296 I+A+K + I +G+DVYENE F N+ I + V + CH T + A+ Sbjct: 243 AIDALKHQKIGALGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLTAE 302 Query: 297 ETIRIVNTFVE 307 I I T ++ Sbjct: 303 ALISISQTTLD 313 Lambda K H 0.319 0.134 0.384 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: 282 Number of extensions: 15 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: 394 Length of database: 329 Length adjustment: 29 Effective length of query: 365 Effective length of database: 300 Effective search space: 109500 Effective search space used: 109500 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: 49 (23.5 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