Align alcohol dehydrogenase (NADP+) (EC 1.1.1.2); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate Echvi_1168 Echvi_1168 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family
Query= BRENDA::U6CL97 (387 letters) >FitnessBrowser__Cola:Echvi_1168 Length = 386 Score = 369 bits (946), Expect = e-106 Identities = 184/387 (47%), Positives = 257/387 (66%), Gaps = 3/387 (0%) Query: 1 MLNFTLHTPTKILFGEGQIAELGKEIPADARILITYGGGSVKHNGVLDQVYRALEGRNVR 60 MLNF PTKI+FG+GQ A++ EIPA A++L+TYGGGS+K NG+ D V AL+ V Sbjct: 1 MLNFEFKNPTKIIFGQGQTAKIADEIPAGAKVLMTYGGGSIKKNGIYDAVKDALKDFEVI 60 Query: 61 EFSGIEPNPTYETLMKAVEVVRAEKIDFLLAVGGGSVVDGTKFIAAAADYQAAQDPWHIL 120 EF GI NP Y L+ A+++++ E I F+LAVGGGSV+D TKF+++AA Y ++PW IL Sbjct: 61 EFGGIPANPAYHQLLDALKIIKEEGITFMLAVGGGSVIDATKFLSSAALYDG-EEPWDIL 119 Query: 121 QTGGAEIDRGVALAAVLTLPATGSESNNGAVITRKSTNDKLAFRSPHTQPLFAVLDPVVT 180 + G+ VLT+PATGSESN+GAVI+ T +K + P P F++LDP V Sbjct: 120 AKK-IRTEEGLPFGTVLTIPATGSESNSGAVISNHQTGEKFSMGGPGLFPQFSLLDPTVI 178 Query: 181 YTLPARQIANGVVDAFVHTVEQYLTYSVDAKVQDRFAEGLLLTLVEEGPRALAEPENYKV 240 TLP RQ+ANG++DAF H +EQY+TY V A +QDRFAE ++ TL+E GP+ + +P +Y Sbjct: 179 RTLPQRQLANGIMDAFSHALEQYMTYPVKAGLQDRFAESIMQTLIEVGPQVMKDPSDYDA 238 Query: 241 RANVMWSATMALNGLIGAGVPQDWSTHMLGHELTALHGLDHAQTLAIVLPAMLAARKSQK 300 + MW TMALNGLI GVP DW+ H +GHELTAL+G+DHA+TLAIV + +K Sbjct: 239 AGDFMWCCTMALNGLIQKGVPTDWAIHAMGHELTALYGIDHARTLAIVAGSHYRYNLDRK 298 Query: 301 RDKLLQYAERVWNLRDGSEDQRIDGAIAATRDFFEKMGVPTRLSDY-QLDGSSIPTLVAK 359 + KL QYAERVW + DG+ +++ I T F + +G+ T+LS Y ++ + + Sbjct: 299 KAKLAQYAERVWGIVDGTAEEKALAGIKKTEAFIQSLGIETQLSAYTDTYKTAAKEIADR 358 Query: 360 LSEHGLTALGEHRDITLEESQKIYEAA 386 + G T LGEH+D++ + +KI E A Sbjct: 359 FTSRGWTGLGEHKDLSPADVEKIVEMA 385 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: 440 Number of extensions: 26 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: 386 Length adjustment: 30 Effective length of query: 357 Effective length of database: 356 Effective search space: 127092 Effective search space used: 127092 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