Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_041098945.1 SUTH_RS09885 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000828635.1:WP_041098945.1 Length = 398 Score = 172 bits (436), Expect = 2e-47 Identities = 111/355 (31%), Positives = 182/355 (51%), Gaps = 28/355 (7%) Query: 291 LENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRN--- 347 +E A ++A+G GTN I + ++G+ VFNAP +N +V EL ++ ++ RN Sbjct: 52 VEIAKSVLAIGRAGSGTNNIPVAEMSKRGVPVFNAPGANANAVKELVLAGMLLAARNIGG 111 Query: 348 -------LHDKTLKMHQGI-WNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVF 399 L +M + + K +E+ G LG++G G IG ++ A +GMNV Sbjct: 112 AMKFVAALDPSDAEMEKKVEGGKKTYAGYEISGHTLGVVGLGKIGCLVADAAIKLGMNVI 171 Query: 400 YYD----IVERLAL-GNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGA 454 YD + +L K +SL ++L + ++LHV + ++N E I +MK GA Sbjct: 172 GYDPEITVDAAWSLPSQVKKANSLGDVLRHSNFVTLHVPLVDATRKMINAESIEQMKHGA 231 Query: 455 ILVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHI 514 +L+N SR V D A+ AL++ L G V FP+ N+ P+ I PH+ Sbjct: 232 VLLNFSREGVADEAAVLAALDARRL-GCYVCDFPSARVNSH----------PHVIALPHL 280 Query: 515 GGSTLEAQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLA 574 G ST EA+EN A V ++ +Y+ GN NSVNFP + +P + A R+ + N P ++ Sbjct: 281 GASTREAEENCAIMVADQVRDYLLDGNIVNSVNFPGVAMP-RESAFRIAIANANVPNMVG 339 Query: 575 KINQVLASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRIL 629 +I+ +A ++NI K+ + + Y + D+D + VID + +IEG + R L Sbjct: 340 QISTAMADARLNIHNMMNKSKKDVAYTLVDVDSKVPKKVIDQIAKIEGVLSVRYL 394 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: 507 Number of extensions: 24 Number of successful extensions: 5 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: 398 Length adjustment: 34 Effective length of query: 596 Effective length of database: 364 Effective search space: 216944 Effective search space used: 216944 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 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