Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Dsui_0124 Dsui_0124 lactate dehydrogenase-like oxidoreductase
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__PS:Dsui_0124 Length = 322 Score = 192 bits (487), Expect = 1e-53 Identities = 106/272 (38%), Positives = 160/272 (58%), Gaps = 17/272 (6%) Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 L+ P+LK++A A G +N+D+E A ++GI V+N G + F+LLLA++R ++ Sbjct: 57 LMARLPQLKMVAVAATGTNNVDLEAARRQGIVVSNIQGYAVHTVPEHVFSLLLALSRNLL 116 Query: 121 EADAFVRSGEWKKSEVGW---HPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKII 177 V G W+++E HP+ L G TLG+VG G +GQ + + A+ FGMK++ Sbjct: 117 AYRQSVAEGRWQRAEQFCFFDHPIR----DLHGATLGVVGGGSLGQGVVRLAQAFGMKVL 172 Query: 178 YYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILI 237 R + + Y F T+L E+D +SLH PLT ET H+IG EL+ MKP+A+LI Sbjct: 173 QAER----KGAAVVRPGYTAFATVLAEADALSLHCPLTAETRHLIGAAELQAMKPSALLI 228 Query: 238 NTSRGAVVDTNALIKALKEGWIAGAGLDVF------EEEPYYNEELFKLKNVVLAPHIGS 291 NT+RG +VD AL +AL+EGWIAGAG DV ++ P + +L N +L PH+ Sbjct: 229 NTARGGLVDEAALARALREGWIAGAGFDVLTAEPPTDDHPLLSPDLLAAPNFLLTPHVAW 288 Query: 292 ATHEAREGMAELVAKNLIAFAKGEIPPNLVNK 323 A+ A + +A+ + NL AFA+G + P N+ Sbjct: 289 ASAPAMQALADQLIDNLEAFARGAMTPGAANR 320 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: 227 Number of extensions: 8 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: 331 Length of database: 322 Length adjustment: 28 Effective length of query: 303 Effective length of database: 294 Effective search space: 89082 Effective search space used: 89082 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