Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_075620503.1 GY23_RS17650 iron-containing alcohol dehydrogenase
Query= BRENDA::A4ISB9 (387 letters) >NCBI__GCF_001939075.1:WP_075620503.1 Length = 387 Score = 562 bits (1449), Expect = e-165 Identities = 263/387 (67%), Positives = 325/387 (83%) Query: 1 MQNFTFRNPTKLIFGRGQIEQLKEEVPKYGKKVLLVYGGGSIKRNGLYDEVMSLLTDIGA 60 M F+F NP KLIFG+GQ+E++K+E+P YG+KVL+VYGGGSIK+NGLYDEVM +L + Sbjct: 1 MNAFSFYNPVKLIFGKGQLEEIKQELPIYGQKVLVVYGGGSIKKNGLYDEVMDVLKEANL 60 Query: 61 EVVELPGVEPNPRLSTVKKGVDICRREGIEFLLAVGGGSVIDCTKAIAAGAKFDGDPWEF 120 EV EL GVEPNPR+STV++GV++C++E IE LLAVGGGSVIDCTK I+AGA +DGD W+F Sbjct: 61 EVFELSGVEPNPRISTVRRGVELCKQENIEMLLAVGGGSVIDCTKLISAGALYDGDAWDF 120 Query: 121 ITKKATVTEALPFGTVLTLAATGSEMNAGSVITNWETKEKYGWGSPVTFPQFSILDPTYT 180 +++KAT ALPFGTVLTLAATGSEMN+GSVITN ET+EKYGWG+P+ FP+FS+LDPTYT Sbjct: 121 VSRKATPKAALPFGTVLTLAATGSEMNSGSVITNEETQEKYGWGTPLVFPKFSVLDPTYT 180 Query: 181 MTVPKDHTVYGIVDMMSHVFEQYFHHTPNTPLQDRMCEAVLKTVIEAAPKLVDDLENYEL 240 +VP D TVYGIVDMMSH+FEQYF++ NTP+QD MCE VL+ ++E APKL+ DL +YE Sbjct: 181 FSVPLDQTVYGIVDMMSHIFEQYFNNATNTPVQDEMCEGVLRAIMETAPKLLKDLHSYEH 240 Query: 241 RETIMYSGTIALNGFLQMGVRGDWATHDIEHAVSAVYDIPHAGGLAILFPNWMKHVLDEN 300 RETI+++GT+ LN FLQMG RGDWATH+IEHAVSAVYDIPHAGGLAILFP+WM+H + N Sbjct: 241 RETILFAGTMGLNNFLQMGYRGDWATHNIEHAVSAVYDIPHAGGLAILFPHWMRHNVKVN 300 Query: 301 VSRFAQLAVRVFDVDPTGKTERDVALEGIERLRAFWSSLGAPSRLADYGIGEENLELMAD 360 RFA+LAV VF V+P GKT ++ALEGI+ LRA+W+SLGAP LADY I + N+ELM + Sbjct: 301 PERFARLAVYVFGVEPDGKTVEEIALEGIDNLRAYWTSLGAPQTLADYNIDDSNIELMVE 360 Query: 361 KAMAFGEFGRFKTLNRDDVLAILRASL 387 KAM +G FG F L +DV AIL+ASL Sbjct: 361 KAMVYGPFGNFTALQAEDVRAILKASL 387 Lambda K H 0.320 0.138 0.412 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: 582 Number of extensions: 21 Number of successful extensions: 1 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: 387 Length of database: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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 (21.8 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