Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_075858559.1 cpu_RS03150 phosphoglycerate dehydrogenase
Query= curated2:A1RYE4 (339 letters) >NCBI__GCF_001950255.1:WP_075858559.1 Length = 525 Score = 230 bits (587), Expect = 5e-65 Identities = 133/312 (42%), Positives = 202/312 (64%), Gaps = 9/312 (2%) Query: 12 IPEPGLSMLKECCDVVVHESKDWPPSREELLRNIRDKDALLCLLTDKIDAEVMDAAPNLK 71 + E GL++L+E +V ++K S EEL++ I + DAL+ K+ A +++AA NLK Sbjct: 9 VSEKGLNILREEGFIVEEKTK---LSEEELIKIISEFDALIVRSETKVTARIIEAAENLK 65 Query: 72 VISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVEADKIIRTG 131 +I VG D+ID+ A+K+GI V ++P T A AE T L++A+ R I +A ++ G Sbjct: 66 IIGRAGVGVDNIDLAAASKKGIIVVNSPEGNTIAAAEHTFALMMALLRNIPQAHAALKEG 125 Query: 132 QWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKILYYDIERRWDVETVIP 191 +W + TG EL+GKT+G++GLGRIG A AKR+ +F+ K++ YD + ++ Sbjct: 126 KWLRKE----FTGYELRGKTVGIIGLGRIGTAVAKRVKAFETKVIGYDPFISEERAHML- 180 Query: 192 NMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARGPVVDTEALV 251 + L+ LL+K+DIV++H+PL ET +LIN ERL+ MKK+A++IN ARG ++D EAL Sbjct: 181 GITLMSLEELLQKADIVTMHLPLNNETRNLINRERLKLMKKSAFIINCARGGIIDEEALY 240 Query: 252 KALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIEARQRMAELAARNLIA 311 +ALK G IAGAALDVF +EPL + PL + NV++ PH+ ++T EA+ +A AR + Sbjct: 241 EALKTGEIAGAALDVFSKEPLTES-PLFELPNVIVTPHLGASTKEAQVNVAIDVAREIAN 299 Query: 312 VLKGEMPPALVN 323 VLKG + VN Sbjct: 300 VLKGGLAQNAVN 311 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: 410 Number of extensions: 19 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: 339 Length of database: 525 Length adjustment: 32 Effective length of query: 307 Effective length of database: 493 Effective search space: 151351 Effective search space used: 151351 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: 50 (23.9 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