Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_093395386.1 BM091_RS09805 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_900114975.1:WP_093395386.1 Length = 528 Score = 197 bits (501), Expect = 1e-54 Identities = 126/381 (33%), Positives = 203/381 (53%), Gaps = 26/381 (6%) Query: 235 VLLLENVHPIGVE-IMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLEN 293 +L+ + + G+E +M + VEV +++++ EEL E +K + IRS T++T+ V+E Sbjct: 4 ILVSDPLAEAGIEKLMSVPEFEVEV-NTSLTHEELREVVKECDALVIRSSTKVTRDVIEA 62 Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353 +RL + IG + +D++ KGI V N P N + E I+ ++ + RN+ Sbjct: 63 GDRLKVIARAGIGLDNVDIDAATRKGIVVMNTPEGNVITTAEHTIALLLAVSRNIPQADA 122 Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYY------DIVERL 407 + G W K EV K LGIIG G IG ++ A+ + M V Y D+VERL Sbjct: 123 SLKAGKWEKKKFRGKEVFNKVLGIIGVGRIGRVVADRAKGLKMQVIAYDPYISSDVVERL 182 Query: 408 ALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDV 467 + + SLDELL D I++H E +N+LNK+ KMKKG ++N +RG +V+ Sbjct: 183 GI----EAVSLDELLARSDYITVHTPLTQETRNLLNKDAFKKMKKGVFIINCARGGIVNE 238 Query: 468 PALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQ 527 L +A++ G +AGAA+DVF EP D P L+ +LTPH+G ST EAQEN+A Sbjct: 239 EDLAEAIKEGIVAGAAIDVFTVEPPPPDHP----LLNLEKVVLTPHLGASTDEAQENVAI 294 Query: 528 FVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINI 587 V ++I+Y+ G N++N P I L + + + + G L ++Q+ + I Sbjct: 295 AVADQVIDYLLKGTIRNAINAPTIDGEVLANLRPYLTLSEKL-GCL--VSQITRGAPVEI 351 Query: 588 VGQYLKTNEKIGYVITDIDKR 608 +Y+ +TD+D++ Sbjct: 352 GIEYVGD-------VTDLDRQ 365 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: 739 Number of extensions: 36 Number of successful extensions: 4 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: 528 Length adjustment: 36 Effective length of query: 594 Effective length of database: 492 Effective search space: 292248 Effective search space used: 292248 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 Jul 25 2024. The underlying query database was built on Jul 25 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