Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_013684189.1 ARCVE_RS07580 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000194625.1:WP_013684189.1 Length = 523 Score = 200 bits (509), Expect = 1e-55 Identities = 117/339 (34%), Positives = 191/339 (56%), Gaps = 14/339 (4%) Query: 233 INVLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLE 292 + VL+ + + ++ M+ EG V+V + +SE+EL I + +RS T++T++V+E Sbjct: 1 MKVLVTDPIPDEAIQRMRSEGLEVDV-RTGISEDELVSIIPEYEALVVRSGTKVTRRVIE 59 Query: 293 NANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKT 352 A +L +G +G + ID++ + GI V NAP N+ S E ++ I+ + R + Sbjct: 60 AAKKLRIIGRAGVGVDNIDVQAATQHGIIVVNAPGGNSVSTAEHTLALILAVARRIPQAD 119 Query: 353 LKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALG 410 + +G W + E+RGK +G+IG G +G +++ A+ + MNV YD I E A Sbjct: 120 RSVKEGRWERKKFIGMELRGKTIGVIGLGKVGFEVAKRAKALEMNVLAYDPYISEERAKE 179 Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470 K+ LDELL++ DI+++HV E + ++++EKI MK GA L+N +RG +VD AL Sbjct: 180 IGAKLVDLDELLKSSDIVTIHVPKTKETEGLISREKIAIMKDGAYLINCARGGLVDEKAL 239 Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530 DAL+ G LAGAA+DV+ EP + + P L N + TPH+G ST EAQ ++ V Sbjct: 240 YDALKEGKLAGAALDVYEKEPPDANNP----LFTLENVVTTPHLGASTKEAQISVGMTVA 295 Query: 531 GKIIEYINSGNTFNSVNFPNIQ-------LPFLKDAHRL 562 +II N+VN P++ +P+LK A ++ Sbjct: 296 NEIINMAKGLPVRNAVNLPSMDAREYEYIMPYLKLAEKM 334 Score = 42.7 bits (99), Expect = 4e-08 Identities = 21/88 (23%), Positives = 46/88 (52%), Gaps = 3/88 (3%) Query: 540 GNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIG 599 G+ + V ++ F+ + H +I +H++ PGV+ ++ + + INI G + G Sbjct: 429 GSEYRIVRIDRYKVDFVPEGHYVISLHEDKPGVIGRVGTLFGKHNINIAGMLVGRYGGRG 488 Query: 600 YV---ITDIDKRYSNDVIDALKEIEGTI 624 V + +D S++V+D + +++G I Sbjct: 489 GVQLMLLLVDDPPSDEVLDEMVKLDGII 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: 665 Number of extensions: 30 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: 523 Length adjustment: 36 Effective length of query: 594 Effective length of database: 487 Effective search space: 289278 Effective search space used: 289278 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