Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate 207685 DVU2201 alcohol dehydrogenase, iron-containing
Query= BRENDA::U6CL97 (387 letters) >MicrobesOnline__882:207685 Length = 385 Score = 395 bits (1014), Expect = e-114 Identities = 205/388 (52%), Positives = 265/388 (68%), Gaps = 6/388 (1%) Query: 1 MLNFTLHTPTKILFGEGQIAELGKEIPADARILITYGGGSVKHNGVLDQVYRALEGRNVR 60 M F + PT I+FG+ ++ E+ + +P DAR+LI YGGGS K G +D V +AL R V Sbjct: 1 MYPFDFYNPTHIVFGKDRLPEIDRLVPKDARVLILYGGGSAKRFGTIDAVKKALGDRFVM 60 Query: 61 EFSGIEPNPTYETLMKAVEVVRAEKIDFLLAVGGGSVVDGTKFIAAAADYQAAQDPWHIL 120 F GIE NP + TLM+AV + R IDFLLAVGGGSV+DGTKF+A A Y+ D +L Sbjct: 61 AFGGIEANPQFTTLMRAVALTRENDIDFLLAVGGGSVMDGTKFVALAHGYEG--DEQGLL 118 Query: 121 QTG--GAEIDRGVALAAVLTLPATGSESNNGAVITRKSTNDKLAFRSPHTQPLFAVLDPV 178 + G I++ + L V+TLPATGSE N G VI+ N K T P F++LDP Sbjct: 119 KHGLNPIPIEKALPLGTVVTLPATGSEMNMGGVISHG--NGKYPVLCAATFPRFSILDPT 176 Query: 179 VTYTLPARQIANGVVDAFVHTVEQYLTYSVDAKVQDRFAEGLLLTLVEEGPRALAEPENY 238 +TYTLPA Q+ANGVVD FVH +EQYLT+ + + QDR AEG+LLTL E G L + +Y Sbjct: 177 LTYTLPAAQVANGVVDTFVHVMEQYLTFPAEGRFQDRTAEGILLTLTEVGYATLEDRADY 236 Query: 239 KVRANVMWSATMALNGLIGAGVPQDWSTHMLGHELTALHGLDHAQTLAIVLPAMLAARKS 298 RAN+MW ATMALNGLIGAGVPQDW++HM+GHE+TALHG+DH +TLA++LPA++ R+ Sbjct: 237 DPRANLMWCATMALNGLIGAGVPQDWTSHMIGHEITALHGVDHGRTLAVILPAVMRVRRE 296 Query: 299 QKRDKLLQYAERVWNLRDGSEDQRIDGAIAATRDFFEKMGVPTRLSDYQLDGSSIPTLVA 358 QKR+KLLQY RVW + E+ ID AIA T FFE +GVPTRLS Y + + ++A Sbjct: 297 QKREKLLQYGRRVWGVTAKDENAAIDEAIARTEFFFESLGVPTRLSAYGIGEEAFDAIIA 356 Query: 359 KLSEHGLTALGEHRDITLEESQKIYEAA 386 L E G TA+ E D+TLE+S+ I +AA Sbjct: 357 GLKEKGHTAMSERGDLTLEDSRNILKAA 384 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: 460 Number of extensions: 15 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: 385 Length adjustment: 30 Effective length of query: 357 Effective length of database: 355 Effective search space: 126735 Effective search space used: 126735 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 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