Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011159842.1 TX73_RS21970 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000195775.1:WP_011159842.1 Length = 529 Score = 200 bits (509), Expect = 1e-55 Identities = 123/339 (36%), Positives = 187/339 (55%), Gaps = 17/339 (5%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSS-AMSEEELCEKIKNVSIIGIRSKTQITKKVLEN 293 VL+ + + V+I K G +V+ + +++L E I N + IRS T+ T K+LE Sbjct: 6 VLISDALSEAAVQIFKDRGIDVDFQPNLGKDKDKLAEIIGNYDGLAIRSATKATAKILEK 65 Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353 ANRL +G IG + +++ KGI V N PF N+ + E AI+ ++ L R + Sbjct: 66 ANRLKVIGRAGIGVDNVEIPAATAKGIIVMNTPFGNSITTAEHAITMMLSLAREIPAADA 125 Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALG 410 G W K+ E+ K LG+IG GNIG+ ++ A + M V +D ER Sbjct: 126 STQAGKWEKNRFMGVEITAKTLGVIGCGNIGSIVADRALGLKMKVIAFDPFLSPERAKDL 185 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 K++ L+++ + D I+LH + KNI++ I KMKKG ++N +RG +VD AL Sbjct: 186 GVEKVE-LEDIFKRADFITLHTPLTDKTKNIIDAAAIAKMKKGVRIINCARGGLVDENAL 244 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 +AL+SGH+AGAA DVF EP ++ L G PN I TPH+G ST EAQEN+A V Sbjct: 245 AEALKSGHVAGAAFDVFSEEPAT-----KNVLFGLPNVICTPHLGASTTEAQENVALQVA 299 Query: 531 GKIIEYINSGNTFNSVNFPNIQL-------PFLKDAHRL 562 ++ +Y+ +G N++NFP+I PF++ A +L Sbjct: 300 EQMSDYLLTGAITNAINFPSITAEEAPKLKPFIELAEKL 338 Lambda K H 0.317 0.136 0.377 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: 679 Number of extensions: 37 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: 630 Length of database: 529 Length adjustment: 36 Effective length of query: 594 Effective length of database: 493 Effective search space: 292842 Effective search space used: 292842 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 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