Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043744206.1 AMB_RS10835 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
Query= BRENDA::P42328 (339 letters) >NCBI__GCF_000009985.1:WP_043744206.1 Length = 358 Score = 140 bits (353), Expect = 5e-38 Identities = 107/343 (31%), Positives = 160/343 (46%), Gaps = 22/343 (6%) Query: 11 EPLKIKEVEKPTISYGEVLVRIKACGVCHTDLHAAHGDWPVKPKLPLIPGHEGVGIVEEV 70 +P+ + +E GEVLV + CGVCHTDL + LPL GHE G V + Sbjct: 15 QPMVKEAMEIAAPGAGEVLVEVAGCGVCHTDLDYYYNGVRTNHALPLALGHEISGRVIQA 74 Query: 71 GPGVTHLKVGDRVGIPWLYSACGHCDYCLSGQETLCEHQKNAGYSVDGGYAEYCRAAADY 130 G G VG V I + CG CD C G+ T+C QK G + GG+A + A+ Sbjct: 75 GAGAESW-VGKAVIISAVIP-CGQCDLCKRGKGTICRSQKMPGNDLQGGFATHITVPANG 132 Query: 131 VVKIPD------NLSFEEAAPIFCAGVTTYKALKVTGAKPGEWVAIYGIGGLGHVAVQYA 184 + + + L E + + A T Y+A G G+ V + G GG+G +VQ A Sbjct: 133 LCAVDEARLKAAGLELSEVSVVADALTTPYQAAVQAGIGQGDLVIVIGCGGVGGYSVQVA 192 Query: 185 KAMGLNVVAVDIGDEKLELAKELGADLVVNPLKEDAAKFMKEKVGGVHAA---------- 234 AMG VVA+DI KLE K GA L +NP + + +K+++G A Sbjct: 193 SAMGATVVALDIDPVKLEAVKAAGAKLTLNPKDFPSTREIKKEIGAFAKAQGLRSTEWII 252 Query: 235 VVTAVSKPAFQSAYNSIRRGGACVLVGLPPEEMPIPIFDTVLNGIKIIGSIVGTRKDLQE 294 + + S P QSA++ + G +VG + + + + + +G+ G DL Sbjct: 253 MECSGSVPGQQSAFDLMVHGCTICVVGYTMNKAEFRLSNLMAFHARALGN-WGCPPDLYP 311 Query: 295 -ALQFAAEGK--VKTIIEVQPLEKINEVFDRMLKGQINGRVVL 334 AL GK VK +E +PL+ IN+ F + +++ R VL Sbjct: 312 GALDLVLSGKINVKNFVERRPLDSINDTFAAVHDHKLSRRAVL 354 Lambda K H 0.318 0.138 0.415 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: 285 Number of extensions: 17 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: 339 Length of database: 358 Length adjustment: 29 Effective length of query: 310 Effective length of database: 329 Effective search space: 101990 Effective search space used: 101990 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: 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