Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_011766824.1 AZO_RS15545 phosphoglycerate dehydrogenase
Query= reanno::Cola:Echvi_2777 (630 letters) >NCBI__GCF_000061505.1:WP_011766824.1 Length = 410 Score = 412 bits (1059), Expect = e-119 Identities = 207/410 (50%), Positives = 279/410 (68%), Gaps = 1/410 (0%) Query: 222 MNKKFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGI 280 MN++ S K ++NV+L E +H VE + +GY +V V+ A++ EEL + + + +GI Sbjct: 1 MNQRLSVQKDKLNVVLFEGIHASAVEAFRADGYGSVTAVAKALAGEELAQALAHAHFVGI 60 Query: 281 RSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISE 340 RS+T++T +VL A +L+AVG FCIGTNQ+DL +G+ VFNAPFSNTRSV EL I+E Sbjct: 61 RSRTRLTAEVLAQAPKLVAVGCFCIGTNQVDLGAAAARGVPVFNAPFSNTRSVAELVIAE 120 Query: 341 IIFLMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFY 400 I LMR + + H+G W KSA+ ++EVRGK LGI+GYG+IG Q+ VLAE +GM+V + Sbjct: 121 TIMLMRGIPARNALQHRGGWMKSAANAWEVRGKTLGIVGYGHIGTQVGVLAEQLGMSVVF 180 Query: 401 YDIVERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLS 460 +DI RL LGNA ++ SLD LL D++SLHV N++ ++ MK G+ L+N S Sbjct: 181 HDIETRLPLGNARQLGSLDALLAVADVVSLHVPETPATMNMIAAPQLAAMKAGSFLINAS 240 Query: 461 RGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLE 520 RG VVD+ AL ALE+GHL GAA+DVFP EP+ ND+PF S L N ILTPHIGGST E Sbjct: 241 RGTVVDIDALAQALEAGHLLGAAIDVFPVEPEGNDDPFVSPLTRFDNVILTPHIGGSTAE 300 Query: 521 AQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVL 580 AQ NI + V K+I Y N+G+T +VNFP + LP R++HIH+N PG+LA+IN+ Sbjct: 301 AQANIGREVAAKLIRYSNNGSTVTAVNFPEVSLPEHAGKCRVLHIHRNVPGMLARINERF 360 Query: 581 ASYKINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630 + INI GQYL+T +GYV+ D+D S D L IEGTIR R+LY Sbjct: 361 SRAGINIAGQYLQTTPDLGYVVIDVDAAASQVAFDELCSIEGTIRCRVLY 410 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: 543 Number of extensions: 14 Number of successful extensions: 2 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: 410 Length adjustment: 34 Effective length of query: 596 Effective length of database: 376 Effective search space: 224096 Effective search space used: 224096 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