Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate PfGW456L13_2028 D-lactate dehydrogenase (EC 1.1.1.28)
Query= curated2:B1L765 (332 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2028 Length = 330 Score = 163 bits (413), Expect = 5e-45 Identities = 102/288 (35%), Positives = 154/288 (53%), Gaps = 21/288 (7%) Query: 47 DALVSLLTDPIDAEVFE--AAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETT 104 +A+ + + D + A V E AA R++A + GY+++D+ A + G+ + P Sbjct: 46 EAVCAFINDDLGAAVLERLAAGGTRLIALRSAGYNHVDLPTAKRLGLAIVRVPAYSPHAV 105 Query: 105 ADFAFALLMAAARRVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVAR 164 A+ A AL++A RR+ A REG +++ + G+D+ G+T+G+VG G+IGA A+ Sbjct: 106 AEHAVALILALNRRLPRAYNRTREGDFRLQG----LTGFDLVGKTVGVVGTGQIGATFAK 161 Query: 165 RAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQL 224 GFG R+L YD E LG Y+ L +LL ES +SLH PL E++ H+I E L Sbjct: 162 IMSGFGCRLLAYDPYPDPQVEA-LGARYLSLPQLLAESQIISLHCPLNEQSKHLINRESL 220 Query: 225 RRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQE---------PIPPDDP- 274 M+ A+L+NT RG +VD AL ALK+G + GLDV+E+E +P D Sbjct: 221 AHMQPGAMLINTGRGGLVDTPALIDALKDGRLGYLGLDVYEEEAQLFFEDRSDLPLQDDV 280 Query: 275 ---LLKLENVVLAPHAASASHETRSRMAEMVAENLIAFKRGEIPPNLV 319 LL NV++ H A + E +A N+ A+ G P NLV Sbjct: 281 LARLLTFPNVIVTAHQAFLTREALDAIAATTLHNIAAWTAG-TPENLV 327 Lambda K H 0.319 0.137 0.398 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: 232 Number of extensions: 14 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: 332 Length of database: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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: 49 (23.5 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