Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_028314565.1 G491_RS0110525 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000429905.1:WP_028314565.1 Length = 526 Score = 196 bits (498), Expect = 2e-54 Identities = 123/350 (35%), Positives = 191/350 (54%), Gaps = 11/350 (3%) Query: 233 INVLLLENVHPIGVEIMKQEGYNVEV-VSSAMSEEELCEKIKNVSIIGIRSKTQITKKVL 291 + VL+ + + G+++ +E +EV V++ + EL + I + I IRS T++T+++L Sbjct: 1 MKVLVSDKLGEAGIQLF-EEAQGIEVDVNTGLEPAELKKIIGDYDAIVIRSATKVTEELL 59 Query: 292 ENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDK 351 + A L VG IG + +D+ ++G+ V N P N + E AIS ++ L RN+ Sbjct: 60 DAAPNLKVVGRAGIGLDNVDIPAATKRGVVVMNTPGGNVVTTAEHAISMMLSLTRNIPRG 119 Query: 352 TLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLA 408 T + G W+K E+ K LG+IG+GNIG+ + A + MNV D ER+ Sbjct: 120 TASLKAGKWDKKLLQGKEIFNKTLGVIGFGNIGSIAADRARGLRMNVIVADPHVTPERIE 179 Query: 409 LGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVP 468 + SLDEL E D I++HV E +LNK+ KMKKG +++N +RG +VD Sbjct: 180 KAGFEAV-SLDELYERSDYITVHVPKMKETIGLLNKDAFAKMKKGVMVINCARGGIVDEA 238 Query: 469 ALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQF 528 L DA++ G +AGAA+DVF TEP FE + N I TPH+G ST EAQ N+A Sbjct: 239 DLYDAIQEGKVAGAALDVFATEPPGVIPLFELD-----NVICTPHLGASTAEAQTNVAVA 293 Query: 529 VPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQ 578 V +II Y+ +G N+VN P++ L+ L+ + + A++ Q Sbjct: 294 VAEQIIAYLQTGTVINAVNAPSVTGDLLEKLKPLLTLGDRMGCLQAQLAQ 343 Score = 29.3 bits (64), Expect = 5e-04 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 6/79 (7%) Query: 546 VNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKINI----VGQYLKTNEKIGYV 601 V + ++ + + H L+ + + PG + + +L +NI VGQ N ++ Sbjct: 439 VRIDSFRVEMVPEGHVLLIHNIDKPGAIGSVGSMLGEASVNIARMQVGQEEDGNR--NFI 496 Query: 602 ITDIDKRYSNDVIDALKEI 620 + + D +DV+ L+E+ Sbjct: 497 VMETDTETPDDVVAKLREL 515 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: 658 Number of extensions: 34 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: 526 Length adjustment: 36 Effective length of query: 594 Effective length of database: 490 Effective search space: 291060 Effective search space used: 291060 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