Align D-sorbitol dehydrogenase (EC 1.1.1.14; EC 1.1.1.9) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase
Query= metacyc::MONOMER-13193 (363 letters) >FitnessBrowser__HerbieS:HSERO_RS04830 Length = 341 Score = 112 bits (281), Expect = 1e-29 Identities = 91/305 (29%), Positives = 141/305 (46%), Gaps = 17/305 (5%) Query: 24 VTFEERPKPTITDPNDVLVAVNYTGICGSDVHYWVHGAIGHFVVKD--PMVLGHESAGTV 81 ++ E+ P PT P +LV +G+C +D+H A G + VK P + GHE G V Sbjct: 17 LSIEQVPVPTPA-PGQILVKFEASGVCHTDLH----AAHGDWPVKPTPPFIPGHEGTGYV 71 Query: 82 VEVGPAVKSLKPGDRVALEPGYP-CRRCSFCRAGKYNLCPDMVFAATPPYHGTLTGLWAA 140 VG VK +K GDRV + + C CS CR G LC + +G+ A Sbjct: 72 AAVGAGVKHVKEGDRVGVPWLHTACGCCSPCRTGWETLCAEQQNTGYS-VNGSFAEYGLA 130 Query: 141 PADFCYKLPDGVSLQEGALIEPLAVAVHI-VKQARVQPGQSVVVMGAGPVGLLCAAVAKA 199 F LPD + A + V V+ +K+ V+PG+ VV+ G G +G + AKA Sbjct: 131 DPKFVGHLPDNLDFGPAAPVLCAGVTVYKGLKETEVRPGEWVVISGIGGLGHMAVQYAKA 190 Query: 200 YGASTIVSVDIVQSKLDFARGFCSTHTYVSQRISAEDNAKAIKELAGLPGGADVVIDASG 259 G +V+ DI + KL A+ + T + N A+ E+ + GGA + + Sbjct: 191 MGMH-VVAADIHEDKLALAKKLGADLTVDGR------NHNAVAEVQRIIGGAHGALVTAV 243 Query: 260 AEPSIQTSIHVVRMGGTYVQGGMGKSDITFPIMAMCLKEVTVRGSFRYGAGDYELAVELV 319 + +++ + +R GT G+ DI+ P+ LK +TVRGS D E ++ Sbjct: 244 SPKAMEQAFGFLRARGTMALVGLPPGDISLPVFNTVLKRITVRGSIVGTRQDLEESLVFA 303 Query: 320 RTGRV 324 G+V Sbjct: 304 AEGKV 308 Lambda K H 0.319 0.136 0.406 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: 340 Number of extensions: 21 Number of successful extensions: 6 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: 363 Length of database: 341 Length adjustment: 29 Effective length of query: 334 Effective length of database: 312 Effective search space: 104208 Effective search space used: 104208 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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