Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate 16552 b2453 ethanolamine utilization; homolog of Salmonella enzyme, similar to iron-containing alcohol dehydrogenase (VIMSS)
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Keio:16552 Length = 395 Score = 219 bits (557), Expect = 1e-61 Identities = 147/379 (38%), Positives = 213/379 (56%), Gaps = 14/379 (3%) Query: 9 PPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68 PP++ G G++ + + G KH+ V+ D L + G+ +T L +G ++ ++ Sbjct: 27 PPVTLCGPGSVSSCGQQAQTRGLKHLFVMADSFLHQAGMTAGLTRSLTVKGIAMTLWPCP 86 Query: 69 VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVH-DGSVADYLNLTGTR 127 V EP + AVA R+ D VI GGGS LD AK +L + D ++A+ ++ T Sbjct: 87 VGEPCITDVCAAVAQLRESGCDGVIAFGGGSVLDAAKAVTLLVTNPDSTLAE---MSETS 143 Query: 128 TLEKKGLPKILIPTTSGTGSEVTNISVL--SLETTKDVVTHDYLLADVAIVDPQLTVSVP 185 L+ + LP I IPTT+GTGSE TN++V+ ++ K V+ H L+ DVAI+D LT VP Sbjct: 144 VLQPR-LPLIAIPTTAGTGSETTNVTVIIDAVSGRKQVLAHASLMPDVAILDAALTEGVP 202 Query: 186 PRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMA 245 VTA TGIDALTHA+EAY ++NA+P +D LA+ AI +I +SL KAV G D AR M Sbjct: 203 SHVTAMTGIDALTHAIEAYSALNATPFTDSLAIGAIAMIGKSLPKAVGYGHDLAARESML 262 Query: 246 NGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIF 305 S +AG+AF +AG+ HA+A+ G HI HG +NA+LLP VM + R C +R + I Sbjct: 263 LASCMAGMAFSSAGLGLCHAMAHQPGAALHIPHGLANAMLLPTVMEFNRMVCRERFSQIG 322 Query: 306 NALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLL 365 AL S+ + V EL +A+VGI K LG G + + + A++ L Sbjct: 323 RALRTKK---SDDRDAINAVSEL---IAEVGIGKRLGDVGATSAHYGAWAQAALEDICLR 376 Query: 366 ARSPLPLLEADIRAIYEAA 384 + LE I +Y AA Sbjct: 377 SNPRTASLE-QIVGLYAAA 394 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: 332 Number of extensions: 13 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: 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