Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate HSERO_RS10090 HSERO_RS10090 oxidoreductase
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__HerbieS:HSERO_RS10090 Length = 282 Score = 129 bits (325), Expect = 6e-35 Identities = 86/275 (31%), Positives = 140/275 (50%), Gaps = 3/275 (1%) Query: 11 MGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIAMLSDPCAA 70 MG M+ NL++ G+ V WNR+ + + L GA +PAE I+ML+D A Sbjct: 1 MGFPMAANLVRAGYAVRAWNRSPAPVERLAALGAQAAATPAEAAADADVLISMLADDDAT 60 Query: 71 LSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSGSKKPAEDG 130 + + D G L + G +++M+T+ +L++ +G +V PV G AE G Sbjct: 61 ETSLLD-AGALAALRPGAIHVNMATISVALALRLAGLHQARGVAYVAAPVLGRVNVAEAG 119 Query: 131 QLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAK-MKLIVNMIMGSMMNAFSEGLV 189 QL ILAAG++ P DVLG++++ LG+ A KL +N ++ S + A SE + Sbjct: 120 QLNILAAGEEQALAAVQPLLDVLGQKTWRLGRQPEQANAAKLAMNFMIASAIGAMSEAVA 179 Query: 190 LADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPA-FPLKHQQKDMRLALALGD 248 L GL +++ A P++KG G ++ + PA F L KD+RLAL G+ Sbjct: 180 LVQGYGLDKAGFIELATSTAFAAPVYKGYGQAIADDRFEPAGFKLALGLKDVRLALEAGE 239 Query: 249 ENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEA 283 + V + +A+A + + G G LD++A+ A Sbjct: 240 QAHVPLSLASALRDLHIDGLAHGEGHLDWAALSRA 274 Lambda K H 0.317 0.134 0.379 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: 164 Number of extensions: 5 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: 289 Length of database: 282 Length adjustment: 26 Effective length of query: 263 Effective length of database: 256 Effective search space: 67328 Effective search space used: 67328 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: 47 (22.7 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