Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_027699619.1 TT13_RS08680 (S)-acetoin forming diacetyl reductase
Query= BRENDA::Q4J9F2 (255 letters) >NCBI__GCF_000691805.2:WP_027699619.1 Length = 257 Score = 127 bits (318), Expect = 3e-34 Identities = 84/255 (32%), Positives = 131/255 (51%), Gaps = 14/255 (5%) Query: 9 KVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEV-LGVKADVS 67 +V VTGAG GIG AI K+ A + V V +L ++ E+ + L V ADV+ Sbjct: 3 EVAFVTGAGQGIGEAIVKRLADDGFKVAVVGRTLSKLERVANEINAIHPNAALPVLADVA 62 Query: 68 KKKDVEEFVRRTFETYSRIDVLCNNAGIMDGVTPVAEVSDELWERVLAVNLYSAFYSSRA 127 K++DV V +T E + + V+ NNAG+ TP+ EV +E + +N+ + +A Sbjct: 63 KREDVFAGVAKTIEAFGDLTVMINNAGVAP-TTPIMEVDEETIDWTFDINIKGTVWGIQA 121 Query: 128 VIPIM--LKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAVA 185 + LK G G I+N S AG+ G Y +K + G+T++ A GI A Sbjct: 122 AVEAFKQLKHG-GKIINATSQAGVEGNPNLTVYGASKFAIRGITQTTAKELAPLGITVNA 180 Query: 186 VLPGTVKT--------NIGLGSSKPSELGMRTLTKLMSLSSRLAEPEDIANVIVFLASDE 237 PG VKT +G + K E GM + ++L RL+EPE++A+ + FLA + Sbjct: 181 FAPGIVKTPMMFDIAHEVGQNAGKSDEWGMEQFSDGIALG-RLSEPEEVASGVAFLAGHD 239 Query: 238 ASFVNGDAVVVDGGL 252 +S++ G +V DGG+ Sbjct: 240 SSYMTGQTLVTDGGM 254 Lambda K H 0.318 0.135 0.369 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: 162 Number of extensions: 10 Number of successful extensions: 4 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: 255 Length of database: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 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: 47 (22.7 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