Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_092487414.1 BM299_RS17355 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_900115975.1:WP_092487414.1 Length = 529 Score = 212 bits (539), Expect = 4e-59 Identities = 130/372 (34%), Positives = 207/372 (55%), Gaps = 16/372 (4%) Query: 231 SRINVLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKV 290 ++ VL ++NV G+E +++E V+ M+E+EL E I + + +RS T++T +V Sbjct: 2 AKFKVLAMDNVSEKGLEPLRKEPDIEVVIGKKMTEDELVEIIGDYDAMIVRSATKVTPRV 61 Query: 291 LENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHD 350 LENA +L VG +G + IDL + G+ V NAP NT + E I+ ++ L RN+ Sbjct: 62 LENAPKLKVVGRAGVGVDNIDLNAATQHGVLVVNAPDGNTIAATEHTIAMMLALARNIPQ 121 Query: 351 KTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLA 408 KM G+W+K A E+RGK LG+IG G IG+ ++ A+ + M++ YD I A Sbjct: 122 AVAKMKNGVWDKKAFLGVELRGKVLGVIGLGRIGSAVARRAQALEMDIVAYDPYITSEKA 181 Query: 409 LGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVP 468 K+ ++DELL D I++H+ E ++L+++ KMK G ++N +RG +VD Sbjct: 182 ESLGIKLVTMDELLPVADFITMHMPKTKETYHMLDEQAFAKMKDGVRVINCARGGIVDEE 241 Query: 469 ALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQF 528 AL ++SG +AGAA+DVF EP ES L+ N I TPH+G ST EAQ N+A Sbjct: 242 ALYKYMQSGKVAGAALDVFEKEPNT-----ESPLLALDNFIATPHLGASTAEAQLNVAID 296 Query: 529 VPGKIIEYINSGNTFNSVNFPNIQ-------LPFLKDAHRLIHIHQNAPGVLAKINQVLA 581 V +I+E + N+VN P+++ P+LK A +L A V + ++ Sbjct: 297 VAEEIVEALQGKVVRNTVNIPSVKPEVMVKIKPYLKLAEKLGKF--QAQLVEGRATKLEV 354 Query: 582 SYKINIVGQYLK 593 +Y ++ G+ +K Sbjct: 355 TYNGDLAGEEVK 366 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: 674 Number of extensions: 31 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: 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 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