Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate BPHYT_RS20960 BPHYT_RS20960 dihydrofolate reductase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__BFirm:BPHYT_RS20960 Length = 320 Score = 177 bits (448), Expect = 4e-49 Identities = 101/243 (41%), Positives = 144/243 (59%), Gaps = 6/243 (2%) Query: 68 LKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVEADAFVR 127 +KIIA + G+D++D+ A +RGI VTN P LT+ TAD + L+LA RR E + +R Sbjct: 73 VKIIANASAGFDHMDVAAARERGIVVTNAPDALTECTADFSLLLVLAACRRASEYERIMR 132 Query: 128 SGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYSRTRKPEA 187 +G W KS + LG + GKTLGIVGFGRIG+A+AKRA+GFGM++IY R + Sbjct: 133 NG-WGKS---FGMTEMLGTRVNGKTLGIVGFGRIGRAVAKRAQGFGMRVIYTDINRAAAS 188 Query: 188 EEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTSRGAVVDT 247 E Y + +L ++LHVP ++ ++E L+ A+ +N +RGA+VD Sbjct: 189 LENGATFYNSLDEMLPHCQVLTLHVP--GGGVPLMTKREFALLPAGAVFVNAARGALVDE 246 Query: 248 NALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGMAELVAKN 307 +AL +AL G + GAGLDV+ EP ++ L NV L PH+ SAT E R+ M N Sbjct: 247 DALYEALTSGHLFGAGLDVYRNEPNVDKRFAGLDNVFLTPHMASATMETRDQMGFTALDN 306 Query: 308 LIA 310 + A Sbjct: 307 VAA 309 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: 234 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: 331 Length of database: 320 Length adjustment: 28 Effective length of query: 303 Effective length of database: 292 Effective search space: 88476 Effective search space used: 88476 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: 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