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 GFF1289 Psest_1322 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases
Query= BRENDA::Q9LSV0 (289 letters) >FitnessBrowser__psRCH2:GFF1289 Length = 295 Score = 125 bits (313), Expect = 1e-33 Identities = 85/282 (30%), Positives = 139/282 (49%), Gaps = 2/282 (0%) Query: 3 VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62 + F G+G+MG M LL G+++ VWNR+ KC+ LV GA +PAE+ + + Sbjct: 7 LAFAGIGLMGLPMCRRLLAAGYRLVVWNRSPEKCEPLVALGARAVATPAELCAEADIVLL 66 Query: 63 MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVD-AETSLKINEAITGKGGRFVEGPVS 121 L+D A V+F KGG+ E GK +D S+++ A T E G R+V+ PVS Sbjct: 67 CLADTAAVREVLFGKGGIAEGGKAGKLLVDHSSLEPAATRDMAAELEFRSGMRWVDAPVS 126 Query: 122 GSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMM 181 G AE G L+I+A G E P LG+R ++G+VG G K+ MI+ Sbjct: 127 GGTPGAEAGSLVIMAGGRVEDVERVRPVLMNLGQRLTHMGEVGAGQVTKVCNQMIVACNA 186 Query: 182 NAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPA-FPLKHQQKDM 240 +E + LA+++G+ + L L G + + P M S + P + ++ KD+ Sbjct: 187 LVIAEVVALAERAGVDASLLAPALAGGFADSRPLQILAPQMAASEFEPVKWHVRTLLKDL 246 Query: 241 RLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIE 282 A+ L E + P++ A + + S G + D + +++ Sbjct: 247 DTAVKLSREQGSATPLSGLAAQLMRLHGSQGNLERDPATLVQ 288 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: 178 Number of extensions: 7 Number of successful extensions: 2 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: 295 Length adjustment: 26 Effective length of query: 263 Effective length of database: 269 Effective search space: 70747 Effective search space used: 70747 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