Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Echvi_3161 Echvi_3161 Lactate dehydrogenase and related dehydrogenases
Query= metacyc::MONOMER-20569 (394 letters) >FitnessBrowser__Cola:Echvi_3161 Length = 331 Score = 112 bits (279), Expect = 2e-29 Identities = 83/255 (32%), Positives = 123/255 (48%), Gaps = 16/255 (6%) Query: 63 LSLIIRAGAGVNTIDVNAASNHGVLVTNTPGQNNDAVAELAFGHIIACDRCIPQNTMHIK 122 + I AG N +D+ A+ + V P + A+AE I+A +R + + ++ Sbjct: 68 IKFIALRSAGFNHVDLEKAAELNIKVARVPAYSPYAIAEHTMALILALNRRLIKAHNRVR 127 Query: 123 NGEWRKKLFLNSTGLRDRTLGLVGCGNISHSMIHIAKGFNMNVAVYSIPFSPEEAKSLGV 182 + L L +T+G++G G I ++ I GF N+ I S + G+ Sbjct: 128 EQNFSLN-GLTGFDLNGKTVGVIGTGKIGSVLVKILHGFGCNILAQDIEESKDLIDKYGL 186 Query: 183 QY--CGTLEELAKIADVVSVHVPYMKETHHLINKQFFDAMKKKAIFINTSRGEIVDTVAM 240 Y C TL K AD++S+HVP T HLINK+ MK + INTSRG +VDT A+ Sbjct: 187 IYSDCATL---CKHADIISLHVPLKASTKHLINKEHIALMKSGVMLINTSRGGLVDTKAV 243 Query: 241 IEAIKEKGI-KVGLDVYENEPAGSF-----GTFQNNQIAEVVT----SATCHIGASTQQA 290 IE +K K I +GLDVYE E F Q++ IA ++T T H T+ A Sbjct: 244 IEGLKTKKIGYLGLDVYEEEEGLFFEDHSDDILQDDVIARLMTFNNVLITSHQAFLTKTA 303 Query: 291 SERIADETIRIVNTF 305 IA+ TI ++ F Sbjct: 304 LTNIAETTIYNLDCF 318 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: 276 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 394 Length of database: 331 Length adjustment: 29 Effective length of query: 365 Effective length of database: 302 Effective search space: 110230 Effective search space used: 110230 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