Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF1423 HP15_1388 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Marino:GFF1423 Length = 395 Score = 192 bits (488), Expect = 1e-53 Identities = 121/382 (31%), Positives = 203/382 (53%), Gaps = 13/382 (3%) Query: 15 GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVH-VYTDVVPEPP 73 G AL+ + E+ + AK +++TD + GL++ V + + G + +Y DV P+ Sbjct: 17 GKAALEHIPYELTGMAAKRPMIVTDKGVRAAGLLEPVIAACEESGLEITTIYDDVPPDSS 76 Query: 74 LETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKG 133 R K D +I VGGGSA+D K +L G D +G L+ Sbjct: 77 TTVVRDIAGIYRQEKCDSIIAVGGGSAIDTGKAVNILVSEGGD--DIAKYSGAGVLKHPL 134 Query: 134 LPKILIPTTSGTGSEVTNISVLSLET--TKDVVTHDYLLADVAIVDPQLTVSVPPRVTAA 191 P ++PTT+GTGSEVT+++V++ E K T +LL + AI+DP++T+++PP +TAA Sbjct: 135 KPFFVVPTTAGTGSEVTSVAVITDEAKGVKLPFTSSFLLPNAAIIDPRMTLTLPPHITAA 194 Query: 192 TGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLA 251 T +DA+THA EA+ + +P SD A AAI+ IS+SL + + N D R+++A S +A Sbjct: 195 TAMDAMTHATEAFTCMAKNPLSDAYATAAIKKISQSLLQVMDNPKDSDGRLELAQASTMA 254 Query: 252 GLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGN 311 G+AF N+ V VHAL + G H+ HG ++ LPY + Y ++ + + ++ L G Sbjct: 255 GIAFSNSMVGLVHALGHATGAVCHLPHGLCMSLYLPYALEYNLETIREPLGELLLYLEGP 314 Query: 312 SSFLS-----EVEASYRCVEEL-ERFVADVGIPKTLGGFG-IPESALESLTKDAVQQKRL 364 F + EAS + +L + +P+TL G + E+ L+ + + A+ + Sbjct: 315 EVFAATPASRRAEASISAIRKLRDALYKRCQLPRTLKETGKVTEAQLDHIAEMALDDGSI 374 Query: 365 LARSPLPLLEADIRAIYEAAFA 386 + +P + D R++ A+A Sbjct: 375 MF-NPKEVTLEDARSVLRRAWA 395 Lambda K H 0.318 0.135 0.381 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: 346 Number of extensions: 18 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: 395 Length of database: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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