Align BadH (characterized)
to candidate HSERO_RS05565 HSERO_RS05565 short-chain dehydrogenase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS05565 Length = 249 Score = 150 bits (379), Expect = 2e-41 Identities = 98/257 (38%), Positives = 144/257 (56%), Gaps = 16/257 (6%) Query: 4 LQNKTAVITGGGG--GIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVR 61 L++K AVITGG G G+G AT R A++GA++ V DL A+ A A R G + Sbjct: 3 LKDKVAVITGGAGINGLGYATARLMAEQGARVVVLDLA--QADPAAAAAR-IGSQHLGLV 59 Query: 62 CDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTE--PGEWERLIAINLTGAL 119 D+ D+ S + A A G +DILVNNAG I +P E +++R++ ++L G L Sbjct: 60 ADVTDKASCETAAAAILQQFGRIDILVNNAG--ITQPVKTLEITGADYDRILDVSLRGTL 117 Query: 120 HMHHAVLPGMVERRHGRIVNIASDAARVGSS--GEAVYAACKGGLVAFSKTLAREHARHG 177 +M AVLP M +++G I+ I+S +A+ G G Y+A K G++ ++ +ARE G Sbjct: 118 YMSQAVLPAMRAQQNGSIICISSVSAQRGGGILGGPHYSAAKAGVLGLARAMAREFGPEG 177 Query: 178 ITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDA 237 I VN + PG T D+ G EK E + IPL RLG+ DD+ GA F GSD + Sbjct: 178 IRVNSITPGLIGT----DIIKGKLTEEKKAE-IAETIPLARLGRADDIGGACVFLGSDLS 232 Query: 238 GFITGQVLSVSGGLTMN 254 + TG L V+GG+ ++ Sbjct: 233 QYCTGITLDVNGGMLIH 249 Lambda K H 0.318 0.135 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: 163 Number of extensions: 12 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: 255 Length of database: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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: 46 (22.3 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