Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate GFF3991 Psest_4064 Lactate dehydrogenase and related dehydrogenases
Query= curated2:A1RYE4 (339 letters) >FitnessBrowser__psRCH2:GFF3991 Length = 329 Score = 159 bits (401), Expect = 1e-43 Identities = 105/277 (37%), Positives = 150/277 (54%), Gaps = 21/277 (7%) Query: 55 LTDKIDAEVMD--AAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVG 112 + D + A V++ AA ++I+ S G++H+D+P A + G+ V P AVAE TV Sbjct: 52 VNDVLSAPVLERLAAGGTRLIALRSAGYNHVDLPCAKRLGLPVVRVPAYSPHAVAEHTVA 111 Query: 113 LILAVTRRIVEADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFD 172 LILA+ RR+ A IR G + LTG +L GK +G+VG G+IG A+ + F Sbjct: 112 LILALNRRLPRAYNRIREGNFSLQG----LTGFDLVGKRVGVVGSGQIGAVFARIMLGFG 167 Query: 173 VKILYYDIERRWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKK 232 ++ YD ++E + M + LD LL SDIVS+H PLT +T+HLIN++ L MK Sbjct: 168 CEVQLYDPYPNPELERL--GMRYVALDELLASSDIVSLHCPLTAQTHHLINQQSLATMKP 225 Query: 233 TAYLINTARGPVVDTEALVKALKEGWIAGAALDVFEQE-----------PLPPN--HPLT 279 A LINT RG ++DT AL+ ALK G + LDV+E+E PL + L Sbjct: 226 RAMLINTGRGALIDTPALIGALKSGQLGYLGLDVYEEEAGLFFEDHSGLPLQDDVLARLL 285 Query: 280 KFDNVVLAPHIASATIEARQRMAELAARNLIAVLKGE 316 F NV++ H A T EA +A N+ A G+ Sbjct: 286 SFPNVIVTAHQAFLTEEALSAIAGTTLGNVAAWQAGQ 322 Lambda K H 0.319 0.137 0.404 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: 224 Number of extensions: 9 Number of successful extensions: 3 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: 339 Length of database: 329 Length adjustment: 28 Effective length of query: 311 Effective length of database: 301 Effective search space: 93611 Effective search space used: 93611 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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