Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 208042 DVU2545 alcohol dehydrogenase, iron-containing
Query= BRENDA::A4IP64 (395 letters) >MicrobesOnline__882:208042 Length = 386 Score = 192 bits (487), Expect = 2e-53 Identities = 125/362 (34%), Positives = 191/362 (52%), Gaps = 8/362 (2%) Query: 26 VKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEP-PLETGEKAVAFA 84 V LG LV+TDP +++ G D V L G + V+ D+ P P +E A+ Sbjct: 29 VHNLGGTRCLVVTDPGVMRNGHADTVIGSLTAYGIAHAVFQDISPNPRDVEVQRGVEAYH 88 Query: 85 RDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPKILIPTTSG 144 R+G D ++ VGGGS +D AK ++A + GS++ Y G + K P + +PTT+G Sbjct: 89 REG-CDAIVAVGGGSPIDCAKGIGIVASNGGSISLY---EGVDAIPKPMPPLVCVPTTAG 144 Query: 145 TGSEVTNISVLSLET--TKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGIDALTHAVE 202 + ++V+ ++++ T K + +ADV+++DP T S+ +TAATGID LTHA+E Sbjct: 145 SAADVSQFAIITDTTRMVKIAIVSKAAVADVSLIDPSTTKSMSRDLTAATGIDTLTHAIE 204 Query: 203 AYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLAFFNAGVAG 262 A+ S + P +D A+ AI L++ L + +A+G D AR MA AGLAF NA + Sbjct: 205 AFASNASGPITDMFALEAISLVNTHLPQVLADGDDDTAREGMALACLNAGLAFSNAILGA 264 Query: 263 VHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNSSFLSEVEASY 322 VHA+A+ LGG + HGE NA+LLP+V+ + R A + NALG + Sbjct: 265 VHAMAHSLGGLLDLPHGECNAILLPFVVRRNFDAAPVRYARVANALGIDVGGTPATAIRD 324 Query: 323 RCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLLEADIRAIYE 382 + L G + L FG+ + L + AV+ LA +P L ADI ++Y Sbjct: 325 ALFDRLMTLRTAAGFTRGLSAFGVTREQIGRLARLAVEDP-CLATNPEALDIADIESLYA 383 Query: 383 AA 384 A Sbjct: 384 EA 385 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: 414 Number of extensions: 20 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: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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