Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate BPHYT_RS31960 BPHYT_RS31960 hypothetical protein
Query= curated2:A1RYE4 (339 letters) >FitnessBrowser__BFirm:BPHYT_RS31960 Length = 316 Score = 198 bits (504), Expect = 1e-55 Identities = 127/324 (39%), Positives = 179/324 (55%), Gaps = 15/324 (4%) Query: 5 KVYVTRIIPEPGLSMLKECCDVVVHESKDWPPSREELLRN-IRDKDALLCLLTDKIDAEV 63 +V T I L +L+ C++VV P EE LR + D DAL+ + ++ ++ Sbjct: 6 RVLATSPIHLSALPILEPSCELVVA-----PDDSEETLRKFVADADALIVRV--RLPDDI 58 Query: 64 MDAAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVE 123 D AP LK + VG D I + AT+ I V + P T AVAE VG ILA+ R Sbjct: 59 FDHAPRLKACVRHGVGLDFIPVERATRADIAVANLPDSNTQAVAEHVVGAILAMARGF-- 116 Query: 124 ADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLS-SFDVKILYYDIER 182 D++ R + D G EL+ +T+G+VGLGRIG+ A L F +++L D Sbjct: 117 -DRLPRAWRNDGWLVRQTFQGIELRDRTVGIVGLGRIGLQVAAALHHGFGMRVLGCDNGA 175 Query: 183 RWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARG 242 R + + + T ++ + SD +++H PL K T HL+N E L K A L+N ARG Sbjct: 176 REGLPSYVDQ---TSIENVFSGSDFITLHAPLVKSTRHLVNAELLSLAKPGALLVNAARG 232 Query: 243 PVVDTEALVKALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIEARQRMA 302 ++D +ALV AL+ G I AALDVFE EPLPP+HP DNV+L PH+A+ T E RM+ Sbjct: 233 GLIDDDALVAALRSGQIGCAALDVFEPEPLPPDHPYWSIDNVLLTPHVAAFTSEGLVRMS 292 Query: 303 ELAARNLIAVLKGEMPPALVNKEV 326 AAR ++ +L G P LVN+EV Sbjct: 293 TGAARAVVEILHGRRPEHLVNEEV 316 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: 244 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: 316 Length adjustment: 28 Effective length of query: 311 Effective length of database: 288 Effective search space: 89568 Effective search space used: 89568 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: 48 (23.1 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