Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_012474970.1 CPHAMN1_RS07770 3-phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000020545.1:WP_012474970.1 Length = 387 Score = 183 bits (465), Expect = 1e-50 Identities = 133/414 (32%), Positives = 202/414 (48%), Gaps = 49/414 (11%) Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294 +L L N+ G++ + ++ Y E+ +I + I +RS +E Sbjct: 4 ILTLNNISVTGLDRLPRDNY------------EIASEIGHPDAILLRS---FKMHDMEIP 48 Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNL------ 348 + L AVG G N I +E GI VFN P +N +V EL I+ ++ RNL Sbjct: 49 DTLKAVGRAGAGVNNIPVEKMTAMGIPVFNTPGANANAVKELVIAAMLMASRNLTQAWEY 108 Query: 349 ------HDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD 402 D + K G+ E+ GK LG+IG G IG Q++ +GMNV YD Sbjct: 109 ARNLEGDDAAIAKAVEAGKKKYVGT-ELPGKTLGVIGLGAIGGQIANAVIALGMNVIGYD 167 Query: 403 IVERLALGNATKID-------SLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAI 455 + + +A K+ S +ELL D I+ HV +N+LN E I MKK AI Sbjct: 168 --PTVTIQHAWKLSAEVERALSFEELLSEADYITFHVPLIDATRNMLNAESIKHMKKNAI 225 Query: 456 LVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIG 515 ++N +RG +VD A+ AL+ +L A ++ FPT N P+ + PH+G Sbjct: 226 VLNFARGGIVDDAAIIKALDEENLY-AYINDFPTNENKNH----------PSVVSLPHLG 274 Query: 516 GSTLEAQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAK 575 STLEA++N A V ++ +Y+ +GN NSVNFP +++P A R+ + N P ++ + Sbjct: 275 ASTLEAEDNCAVMVADQVRDYLENGNITNSVNFPEMRMP-RAGASRIAISNSNVPKMVGQ 333 Query: 576 INQVLASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRIL 629 I VLA INIV K+ I Y + D+ D+ D +K+IEG + RI+ Sbjct: 334 ITSVLADSGINIVDMLNKSRGDIAYNLLDLGTEVGKDIADKIKKIEGVLAVRIM 387 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: 549 Number of extensions: 25 Number of successful extensions: 6 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: 387 Length adjustment: 34 Effective length of query: 596 Effective length of database: 353 Effective search space: 210388 Effective search space used: 210388 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: 52 (24.6 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