Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_003470113.1 J416_RS10100 iron-containing alcohol dehydrogenase
Query= BRENDA::A4ISB9 (387 letters) >NCBI__GCF_000359605.1:WP_003470113.1 Length = 388 Score = 539 bits (1389), Expect = e-158 Identities = 253/388 (65%), Positives = 316/388 (81%), Gaps = 1/388 (0%) Query: 1 MQNFTFRNPTKLIFGRGQIEQLKEEVPKYGKKVLLVYGGGSIKRNGLYDEVMSLLTDIGA 60 M+NF F NPTKL FG QIEQLK E+ +YG+ +L+VYGGGSIKRNGLYDEV ++L D G Sbjct: 1 MENFAFYNPTKLYFGSDQIEQLKHEIEQYGQNILMVYGGGSIKRNGLYDEVTNILKDAGK 60 Query: 61 EVVELPGVEPNPRLSTVKKGVDICRREGIEFLLAVGGGSVIDCTKAIAAGAKFDGDPWEF 120 + EL GVEPNPR++T +KG+++C+ E I+F+LAVGGGS IDCTKAIAAGA D D W+ Sbjct: 61 HIFELSGVEPNPRVTTARKGIELCKSENIDFILAVGGGSTIDCTKAIAAGAVTDADIWDI 120 Query: 121 ITKKATVTEALPFGTVLTLAATGSEMNAGSVITNWETKEKYGWGSPVTFPQFSILDPTYT 180 +TKK T +LPFGT+LTLAATGSEMNAGSVITNWETKEK+GWGSP +FP FSILDP YT Sbjct: 121 VTKKEQATGSLPFGTILTLAATGSEMNAGSVITNWETKEKHGWGSPYSFPAFSILDPAYT 180 Query: 181 MTVPKDHTVYGIVDMMSHVFEQYFHHTPNTPLQDRMCEAVLKTVIEAAPKLVDDLENYEL 240 +VP+ TVYG+VD+MSH E YFHH NT LQDRM E +L+TVIE APKL++DLEN Sbjct: 181 KSVPEHQTVYGMVDIMSHALEHYFHHEENTLLQDRMVEGILQTVIETAPKLLEDLENETH 240 Query: 241 RETIMYSGTIALNGFLQMGVRGDWATHDIEHAVSAVYDIPHAGGLAILFPNWMKHVLDEN 300 R TI+Y+GT+ALNG + MG +GDWATH++EHAVSAV+DIPH GGLAILFP+WM++ +DEN Sbjct: 241 RATILYNGTMALNGMVNMGYKGDWATHNLEHAVSAVHDIPHGGGLAILFPHWMEYAIDEN 300 Query: 301 VSRFAQLAVRVFDVDPTGKTERDVALEGIERLRAFWSSLGAPSRLADYGIGEENLELMAD 360 V RF QLAVRVFDVD GK+++++ LEGI++LR FW+SLGAPS L DY I E+++ MAD Sbjct: 301 VDRFKQLAVRVFDVDTEGKSDKEIGLEGIQKLRDFWNSLGAPSSLGDYDITEDSIPEMAD 360 Query: 361 K-AMAFGEFGRFKTLNRDDVLAILRASL 387 + +A +FG FK+LNR+D +AI + +L Sbjct: 361 RTVIARDQFGNFKSLNREDAVAIYQKAL 388 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: 569 Number of extensions: 14 Number of successful extensions: 2 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: 388 Length adjustment: 30 Effective length of query: 357 Effective length of database: 358 Effective search space: 127806 Effective search space used: 127806 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