Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate BWI76_RS08900 BWI76_RS08900 putative short-chain dehydrogenase/reductase SDR
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Koxy:BWI76_RS08900 Length = 249 Score = 114 bits (286), Expect = 2e-30 Identities = 86/233 (36%), Positives = 121/233 (51%), Gaps = 20/233 (8%) Query: 8 VKGLVAVITGGAS--GLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADV 65 +K VA+ITG AS GLG ATA+ GAS V+LDL + +A A LG + A+V Sbjct: 3 LKDKVAIITGAASARGLGFATAKLFAENGASVVILDLNSEASKAAAAALGEGHLGLAANV 62 Query: 66 TSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGT 125 E VQ A+ K+GRVDV VN AGI K ++K+ ++ VLDV+L GT Sbjct: 63 ADEVQVQAAMEQILAKYGRVDVLVNNAGITQPLKLMDIKRA------NYDAVLDVSLRGT 116 Query: 126 FNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQ--VGQAAYSASKGGIVGMTLPIA 183 + + V M + + G I+ +SV+A G G YSA+K G++G+ +A Sbjct: 117 LLMSQAVIPTM------RAQKSGSIVCISSVSAQRGGGIFGGPHYSAAKAGVLGLARAMA 170 Query: 184 RDLAPIGIRVMTIAPGLFGTPLLTS--LPEKVCNFLASQVPFPSRLGDPAEYA 234 R+L P +RV I PGL T + + N LA +P +RLGD + A Sbjct: 171 RELGPDNVRVNCITPGLIQTDITAGKLTDDMTANILAG-IPM-NRLGDAVDIA 221 Lambda K H 0.318 0.135 0.385 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: 149 Number of extensions: 9 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: 261 Length of database: 249 Length adjustment: 24 Effective length of query: 237 Effective length of database: 225 Effective search space: 53325 Effective search space used: 53325 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 (21.7 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