Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Echvi_2777 Echvi_2777 Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Cola:Echvi_2777 Length = 630 Score = 132 bits (332), Expect = 2e-35 Identities = 91/275 (33%), Positives = 135/275 (49%), Gaps = 10/275 (3%) Query: 45 GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104 GI S +IT +LE A RL A+ +G +Q D+ +GI + N P T S + Sbjct: 279 GIRSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAI 338 Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164 S I+ R + + + G W S + +V+GK LGI+G G IG ++ A Sbjct: 339 SEIIFLMRNLHDKTLKMHQGIWNKSASGSF---EVRGKKLGIIGYGNIGAQLSVLAE-NM 394 Query: 165 NMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKK 224 M V Y + A + L ELL T D + L V E K+++ ++ MKK Sbjct: 395 GMNVFYYDIVERLALGNA--TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKK 452 Query: 225 SAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSP----LLKLANVVALP 280 AIL+N SRG VD AL +AL++G + GA +DVF TEP +D P L+ N + P Sbjct: 453 GAILVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTP 512 Query: 281 HIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 HIG +T E + +A+ ++ ++ T N VN Sbjct: 513 HIGGSTLEAQENIAQFVPGKIIEYINSGNTFNSVN 547 Lambda K H 0.317 0.131 0.366 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: 337 Number of extensions: 17 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: 321 Length of database: 630 Length adjustment: 33 Effective length of query: 288 Effective length of database: 597 Effective search space: 171936 Effective search space used: 171936 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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