Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011613530.1 TERY_RS20190 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000014265.1:WP_011613530.1 Length = 527 Score = 167 bits (422), Expect = 1e-45 Identities = 104/344 (30%), Positives = 184/344 (53%), Gaps = 7/344 (2%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 VL+ +++ G+ I+ Q V++ + EEL + I + IRS T++TK+++E A Sbjct: 4 VLVSDSIDQNGINILSQVA-QVDI-KIGLPVEELVKIIPEYDGLMIRSGTKVTKEIIEAA 61 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354 ++L +G +G + +D++ KGI V N+P NT + E A++ ++ + R++ + Sbjct: 62 DKLKIIGRAGVGVDNVDVQAATRKGIVVVNSPEGNTIAAAEHALAMMLSMSRHVPEANQS 121 Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412 + W++ EV K LG++G G IG+ ++ +A+ MGM + YD I E A Sbjct: 122 IINAQWDRKKFVGVEVYKKTLGVVGLGKIGSHVAKVAKAMGMKILAYDPFISEERAEQLG 181 Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472 + LD L++ D I+LH+ E + +N E KMK A ++N SRG ++D AL Sbjct: 182 CSLVDLDLLVQESDYITLHIPKTDETYHSINAETFAKMKPTARIINCSRGGIIDEVALSK 241 Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532 AL+ G +AGAA+DV+ EP + P +G ++TPH+G ST EAQ N+A V + Sbjct: 242 ALKEGKIAGAALDVYENEPLEVESPLRD--LG-QKIVMTPHLGASTAEAQVNVAIDVAEQ 298 Query: 533 IIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKI 576 I + + ++VN P + LK + + + +++++ Sbjct: 299 IRDVLLGLPARSAVNIPGMYPDTLKKLKPYLRLAETLGNLVSQL 342 Score = 31.2 bits (69), Expect = 1e-04 Identities = 16/65 (24%), Positives = 37/65 (56%), Gaps = 7/65 (10%) Query: 560 HRLIHIHQNAPGVLAKINQVLASYKINI----VGQYLKTNEKIGYVITDIDKRYSNDVI- 614 + L+ +H++ PG++ KI +L S+ +NI VG+ + + + ++ +D +++ Sbjct: 454 YMLLTLHRDMPGIIGKIGSLLGSFNVNIASMQVGRKIVRGDAV--MVLSVDDPLPEEILT 511 Query: 615 DALKE 619 + LKE Sbjct: 512 EILKE 516 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: 684 Number of extensions: 35 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: 2 Length of query: 630 Length of database: 527 Length adjustment: 36 Effective length of query: 594 Effective length of database: 491 Effective search space: 291654 Effective search space used: 291654 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 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