Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_019615558.1 G327_RS0114705 iron-containing alcohol dehydrogenase
Query= BRENDA::U6CL97 (387 letters) >NCBI__GCF_000381745.1:WP_019615558.1 Length = 383 Score = 441 bits (1133), Expect = e-128 Identities = 228/386 (59%), Positives = 287/386 (74%), Gaps = 4/386 (1%) Query: 1 MLNFTLHTPTKILFGEGQIAELGKEIPADARILITYGGGSVKHNGVLDQVYRALEGRNVR 60 M NFT + T+I FGEGQI+ + EIP + ++L+ YGGGS+K+NGV +QV AL + Sbjct: 1 MNNFTFYNNTRIHFGEGQISAIASEIPQNKKVLVLYGGGSIKNNGVYEQVQTALTDHDWD 60 Query: 61 EFSGIEPNPTYETLMKAVEVVRAEKIDFLLAVGGGSVVDGTKFIAAAADYQAAQDPWHIL 120 EFSGIEPNP Y+TLMKAVE + E D+LLAVGGGSV+DGTKFIAAAA ++ DPW I+ Sbjct: 61 EFSGIEPNPQYDTLMKAVEKINNEGFDYLLAVGGGSVIDGTKFIAAAACFKG-NDPWDIV 119 Query: 121 QTGGAEIDRGVALAAVLTLPATGSESNNGAVITRKSTNDKLAFRSPHTQPLFAVLDPVVT 180 A +D + L +VLTLPATGSESN GAVITR DKL F SP +P FAVLDP T Sbjct: 120 SKY-APVDTALPLGSVLTLPATGSESNGGAVITRGQ--DKLGFGSPLVRPAFAVLDPTTT 176 Query: 181 YTLPARQIANGVVDAFVHTVEQYLTYSVDAKVQDRFAEGLLLTLVEEGPRALAEPENYKV 240 +L ARQ ANGVVDAFVH +EQYLTY V+AKVQDRFAE LLL L+EEGP+ L P++ +V Sbjct: 177 LSLSARQSANGVVDAFVHVMEQYLTYPVNAKVQDRFAEALLLNLIEEGPKVLRTPDDLEV 236 Query: 241 RANVMWSATMALNGLIGAGVPQDWSTHMLGHELTALHGLDHAQTLAIVLPAMLAARKSQK 300 RAN+MWSAT ALNGLIGAGVP DW++HM+GHELT G+DHA++L+IVLPA++ + +K Sbjct: 237 RANIMWSATQALNGLIGAGVPNDWTSHMIGHELTGNFGIDHARSLSIVLPAVMDVCRVEK 296 Query: 301 RDKLLQYAERVWNLRDGSEDQRIDGAIAATRDFFEKMGVPTRLSDYQLDGSSIPTLVAKL 360 KLLQYA+R++ + +GS ++RI+ AI +T FF+ MGVPT LS+ LD SSI L+ L Sbjct: 297 EAKLLQYAQRIFGINEGSTEERIEQAIGSTIAFFKSMGVPTTLSEVDLDISSIEVLLNSL 356 Query: 361 SEHGLTALGEHRDITLEESQKIYEAA 386 HG+TALGEH L +++ I E A Sbjct: 357 EAHGMTALGEHGKNDLIKARAILETA 382 Lambda K H 0.317 0.134 0.383 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: 441 Number of extensions: 13 Number of successful extensions: 3 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: 383 Length adjustment: 30 Effective length of query: 357 Effective length of database: 353 Effective search space: 126021 Effective search space used: 126021 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