Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_028996962.1 H537_RS0104630 glyoxylate/hydroxypyruvate reductase A
Query= reanno::SB2B:6938941 (308 letters) >NCBI__GCF_000430725.1:WP_028996962.1 Length = 308 Score = 115 bits (288), Expect = 1e-30 Identities = 95/301 (31%), Positives = 139/301 (46%), Gaps = 10/301 (3%) Query: 13 ERYRSLLASCH-LPELELLDDNP-ANIRLADIWLAEPGLAAPLVNHASGLRWMQSTFAGV 70 ER + A H LPE + ++ P A + + + PG L GLR +QS +AGV Sbjct: 13 ERQAWMAALQHALPEAQWVEAAPGAEVDVVLVANPPPGQLQGL----KGLRLIQSLWAGV 68 Query: 71 DLLVKPRQRRDY--LLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQQKLWLPGSYK 128 D L+ + V M+E +L+ QR Y QQ++ +W + Sbjct: 69 DRLLADATLPQGVPIARMVDPAMSAAMAETALWAVLSLQRGFFDYARQQREAIWRVLPQR 128 Query: 129 TLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLEALPTLMARAD 188 + +LG G + A+ G +V G + + G D V EALP L++R+D Sbjct: 129 RADEVRVTVLGLGEMGLTAARRMVAQGYRVQGWSARPRQEPGIDSVHGEEALPALLSRSD 188 Query: 189 AIASILPSTEATRGILNENILARMKPDAVLFNLGR-GDVLDLDALERQLRQHPQQQAVLD 247 + ++LP T ATRG+ + LA + A + NL R G V++ D L L + AVLD Sbjct: 189 VVVNLLPLTAATRGLFDAQRLALLPEGACVVNLARGGHVVEADLL-AALDGGRLRHAVLD 247 Query: 248 VFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGETLSHRVNFERG 307 VF EPLP D W V + PH AA + A I ++N + G +HRV ERG Sbjct: 248 VFQAEPLPADSRFWSHPRVTLLPHAAALTDARSAAGIAAANVRAVMAGNPPAHRVEAERG 307 Query: 308 Y 308 Y Sbjct: 308 Y 308 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: 272 Number of extensions: 13 Number of successful extensions: 3 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: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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 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