Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate CCNA_02230 CCNA_02230 gluconate 2-dehydrogenase
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__Caulo:CCNA_02230 Length = 319 Score = 144 bits (364), Expect = 2e-39 Identities = 101/317 (31%), Positives = 159/317 (50%), Gaps = 13/317 (4%) Query: 2 KRPRVFVTREVFPEALELLSKYYDVE-VWDKYQPPPYETLLSKAREADALYTLLTDRIDC 60 ++P++ ++ E+ LL Y V +WD P L + A+ + Sbjct: 7 EKPQILLSHEMLMPLQPLLEGAYIVHRLWD--YPDRMAFLEGPGQSIRAIVHAGEMALSR 64 Query: 61 DLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRV 120 D+L++ PRL ++A ++VG+D +DV GI VT++ G+ A+ L+LAA R + Sbjct: 65 DMLAEMPRLGLIACVSVGYDGVDVPWCKAHGIAVTHSTGLNAADVADHAVGLVLAAWRGI 124 Query: 121 VEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYH 180 VE D +R G W M LRG+ G++G+G IG VA KAF M++ + Sbjct: 125 VEGDQRLRGGHWSHAER-----MAPRPGLRGRKAGVVGLGHIGEAVAARLKAFDMKVAWW 179 Query: 181 SRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNT 240 + R +E + SL L R+SD+L + D RHLI + ++ + ++VN Sbjct: 180 A-PRPKETDYPRAD---SLMALARDSDVLIVCARPDDSNRHLINKPVIEAVGAQGLIVNV 235 Query: 241 GRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRETRL 300 RG+++D AL++ALR G + AALDVFE+EP P VL PH A AT ++ Sbjct: 236 ARGSLIDEDALIQALRAGTLGMAALDVFEQEP-TPAARWADVPRTVLTPHTAGATLDSLP 294 Query: 301 RMAMMAAENLVAFAQGK 317 M + ENL + G+ Sbjct: 295 AMVSLTLENLRRYFHGE 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: 243 Number of extensions: 9 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: 319 Length adjustment: 28 Effective length of query: 307 Effective length of database: 291 Effective search space: 89337 Effective search space used: 89337 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