Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_011382583.1 AMB_RS00685 phosphoglycerate dehydrogenase
Query= curated2:A1RYE4 (339 letters) >NCBI__GCF_000009985.1:WP_011382583.1 Length = 318 Score = 145 bits (366), Expect = 1e-39 Identities = 88/253 (34%), Positives = 136/253 (53%), Gaps = 8/253 (3%) Query: 57 DKIDAEVMDAAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILA 116 +K+D V+ P+LKV+ Y VG D ID+ ++ G + T GV +V+E + +A Sbjct: 61 EKLDEAVLSRLPDLKVVGKYGVGLDMIDLAAMSRLGKRLGWTGGVNRRSVSELVIAFAIA 120 Query: 117 VTRRIVEADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKIL 176 + R I + + +IR G W + L G +L +T+G+VG G IG ++ L +F ++L Sbjct: 121 LLRHIPQGNALIRDGGWRQ------LMGRQLSERTVGIVGCGHIGKDLSRLLKAFGCRVL 174 Query: 177 YYDIERRWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYL 236 +DI R + +E DL+ LL ++DIV++H+P T ++++ ERL M+ A L Sbjct: 175 AHDI-RDFPEFYAATGVEKMDLEPLLAEADIVTLHLPFDASTRNILSAERLALMRSDAIL 233 Query: 237 INTARGPVVDTEALVKALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIE 296 IN ARG +VD AL L G +A AA DVF EP P + L + N + PH+ + E Sbjct: 234 INAARGGLVDEAALRVMLATGRLAAAAFDVFATEP-PEDRALIELPNFLCTPHVGGSAEE 292 Query: 297 ARQRMAELAARNL 309 A M A L Sbjct: 293 AVLAMGRAAIAGL 305 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: 206 Number of extensions: 11 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: 318 Length adjustment: 28 Effective length of query: 311 Effective length of database: 290 Effective search space: 90190 Effective search space used: 90190 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