Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Echvi_2777 Echvi_2777 Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like
Query= BRENDA::P0A9T0 (410 letters) >FitnessBrowser__Cola:Echvi_2777 Length = 630 Score = 427 bits (1098), Expect = e-124 Identities = 211/409 (51%), Positives = 289/409 (70%), Gaps = 4/409 (0%) Query: 3 KVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSR 62 K S K +I LL+E VH +E ++ GY N+E A+ +E+L E I++ IG+RS+ Sbjct: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283 Query: 63 THLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLL 122 T +T+ V+ A +L+A+G FCIGTNQ+DL+ ++GI VFNAPFSNTRSV EL I E++ Sbjct: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343 Query: 123 LLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDI 182 L+R + + K H+G+WNK A+GSFE RGKKLGIIGYG+IG QL +LAE++GM V++YDI Sbjct: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403 Query: 183 ENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGT 242 +L LGNAT++ L +LL D++SLHV KN++ ++I MK G++L+N SRG Sbjct: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463 Query: 243 VVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQE 302 VVD+PAL DAL S HLAGAA+DVFPTEP N +PF S L N +LTPHIGGST EAQE Sbjct: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523 Query: 303 NIGLEVAGKLIKYSDNGSTLSAVNFPEVSLP-LHGGRRLMHIHENRPGVLTALNKIFAEQ 361 NI V GK+I+Y ++G+T ++VNFP + LP L RL+HIH+N PGVL +N++ A Sbjct: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583 Query: 362 GVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY 410 +NI QYL+T+ ++GYV+ DI D+ + + A+K I GTIR R+LY Sbjct: 584 KINIVGQYLKTNEKIGYVITDI--DKRYSNDVIDALKEIEGTIRFRILY 630 Lambda K H 0.318 0.135 0.383 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: 627 Number of extensions: 21 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: 410 Length of database: 630 Length adjustment: 34 Effective length of query: 376 Effective length of database: 596 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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