Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Echvi_2777 Echvi_2777 Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__Cola:Echvi_2777 Length = 630 Score = 159 bits (403), Expect = 1e-43 Identities = 97/289 (33%), Positives = 154/289 (53%), Gaps = 14/289 (4%) Query: 39 LLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPG 98 L EK++ V + ++ K++LENA +L + + +G + ID+E ++GI V N P Sbjct: 268 LCEKIKNVSIIGIRSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPF 327 Query: 99 VLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGF 158 T + +LA + ++ + R + + + G W KS G + ++GK LGI+G+ Sbjct: 328 SNTRSVVELAISEIIFLMRNLHDKTLKMHQGIWNKSASG-------SFEVRGKKLGIIGY 380 Query: 159 GRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKET 218 G IG L+ A+ GM + YY + + +D LL+ D ISLHV E Sbjct: 381 GNIGAQLSVLAENMGMNVFYYDIVERLALGNATKIDSLD--ELLETCDIISLHVDGRTEN 438 Query: 219 YHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELF 278 +++ ++++ MK AIL+N SRG VVD AL AL+ G +AGA +DVF EP N+E F Sbjct: 439 KNILNKEKIFKMKKGAILVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPF 498 Query: 279 KLK-----NVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPNLVN 322 + + N +L PHIG +T EA+E +A+ V +I + N VN Sbjct: 499 ESELIGCPNTILTPHIGGSTLEAQENIAQFVPGKIIEYINSGNTFNSVN 547 Lambda K H 0.317 0.137 0.392 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: 465 Number of extensions: 23 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: 331 Length of database: 630 Length adjustment: 33 Effective length of query: 298 Effective length of database: 597 Effective search space: 177906 Effective search space used: 177906 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. 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