Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_066328438.1 BLR17_RS00855 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >NCBI__GCF_900100165.1:WP_066328438.1 Length = 380 Score = 211 bits (536), Expect = 4e-59 Identities = 146/389 (37%), Positives = 218/389 (56%), Gaps = 27/389 (6%) Query: 5 RIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHV 64 R+VF G G++ + V + G K + +I L LV + L++ G +V V Sbjct: 11 RVVF------GEGSMQRFVDDFVASGLKRMFLIGISELANT-LVPYIEK-LKENGVAVFV 62 Query: 65 YTDVVPEPPL----ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADY 120 + EP E EKA+AF D V+GVGGGS LD+AKL A + S+ + Sbjct: 63 DESIKGEPTFDDFNEVLEKAIAFNADS----VVGVGGGSVLDVAKLVAAQLKNTQSLDE- 117 Query: 121 LNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETTKDV-VTHDYLLADVAIVDPQ 179 + G L+++ IPTTSGTGSEV+ ++ + V V YL+ D A +DP Sbjct: 118 --IKGIGNLKERQTYVACIPTTSGTGSEVSPNAIFVNNLGEKVGVISPYLVPDAAYIDPV 175 Query: 180 LTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQ 239 LTV +P VTAATGIDALTH +EAY + A P D A+ +RLI++ L++A +G+D + Sbjct: 176 LTVLLPKSVTAATGIDALTHCLEAYTNKFAHPFVDLYALEGVRLIAKYLKRACDDGTDIE 235 Query: 240 ARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGY-IRQSCT 298 AR +A GS G+ A VHAL+YPLG ++HI HG SNA+LLPYVM Y I + + Sbjct: 236 ARTQVALGSMYGGMCLGPVNTAAVHALSYPLGVEYHIPHGLSNALLLPYVMEYNIEEDAS 295 Query: 299 K--RMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTK 356 K R+A++ A N+S + +E V+ +++ +AD G+P +L G+ E ++ L + Sbjct: 296 KYERIAEVLGAEKKNTSRETALEG----VKIMKQLIADCGLPTSLAHAGVKEESITKLAE 351 Query: 357 DAVQQKRLLARSPLPLLEADIRAIYEAAF 385 A++ +RLL + + D AIY++AF Sbjct: 352 GAIKVQRLLKNNIREIAVEDAVAIYQSAF 380 Lambda K H 0.318 0.135 0.381 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: 333 Number of extensions: 14 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: 395 Length of database: 380 Length adjustment: 30 Effective length of query: 365 Effective length of database: 350 Effective search space: 127750 Effective search space used: 127750 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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