Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate AZOBR_RS15695 AZOBR_RS15695 dihydrofolate reductase
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__azobra:AZOBR_RS15695 Length = 312 Score = 167 bits (422), Expect = 4e-46 Identities = 106/262 (40%), Positives = 144/262 (54%), Gaps = 10/262 (3%) Query: 62 LLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRVV 121 ++ P L IVA VG D +D++ A G+ VTNTP VLT+ A+ L++A +RR++ Sbjct: 60 IMDACPNLGIVAINGVGTDAVDLKHAAGRGVRVTNTPDVLTDDVADLAIGLMIAGSRRMM 119 Query: 122 EADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHS 181 D FVR G W G P L ++ GK LGILG+GRIG +A+ FGM I Y + Sbjct: 120 VGDRFVRAGRW---PGGGLP---LARKVTGKRLGILGLGRIGMAIAQRAAGFGMDIAYTN 173 Query: 182 RSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNTG 241 R + ++ A S DL RESDIL + + R+++ + ++ + +LVN Sbjct: 174 RKPRSDVPYRFVA---SPVDLARESDILIVAASAGPDARNMVNRAVIEALGPDGLLVNVA 230 Query: 242 RGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETRLR 301 RGA+VD LV AL +G + AALDVF EP P L NVVL PH ASAT ETR+ Sbjct: 231 RGAVVDEPELVAALADGRLGGAALDVFANEPHAP-EALFGLDNVVLQPHQASATVETRMA 289 Query: 302 MAMMAAENLVAFAQGKVPPNLV 323 M + NL AF G+ P V Sbjct: 290 MGNLVLANLSAFFAGQPLPTAV 311 Lambda K H 0.322 0.136 0.406 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: 258 Number of extensions: 15 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: 335 Length of database: 312 Length adjustment: 28 Effective length of query: 307 Effective length of database: 284 Effective search space: 87188 Effective search space used: 87188 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 (21.9 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