Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_028744164.1 RL_RS28050 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >NCBI__GCF_000009265.1:WP_028744164.1 Length = 386 Score = 261 bits (666), Expect = 3e-74 Identities = 156/379 (41%), Positives = 227/379 (59%), Gaps = 7/379 (1%) Query: 10 PLSHVGWGALDQLVPEVK-RLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDV 68 P + WG ++ + R A+ +L++TD LVK G++ + + L G+SV ++ V Sbjct: 12 PSMEMAWGGAKRIGQIIAARFAARKVLLVTDAGLVKAGMIAPIAASLEAAGFSVAIFDKV 71 Query: 69 VPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRT 128 V +PP V AR D+VIG+GGGS+LD+AKLAAVL + S+AD + G Sbjct: 72 VADPPESVLYGCVEEARQVAADIVIGLGGGSSLDIAKLAAVLLSSEQSLAD---MYGVGK 128 Query: 129 LEKKGLPKILIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPR 187 ++ P +L+PTT+GTGSEVTNIS+++ ETTK V L AD ++D +LTV +P Sbjct: 129 VQGARFPLVLVPTTAGTGSEVTNISIITTGETTKMGVVSPELYADFVLLDAELTVGLPQV 188 Query: 188 VTAATGIDALTHAVEAYVSVNA-SPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMAN 246 TAATGIDA+ HA+EAY S + +P SD LA A+RL+ R+L A S++ AR M Sbjct: 189 HTAATGIDAMVHAIEAYTSKHKKNPLSDALAREALRLLGRNLIAACKEPSNRDAREGMLL 248 Query: 247 GSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFN 306 G+ LAG AF N+ VA VHALAYPLGG +HI HG SNA++L V+ Y Q+ A++ + Sbjct: 249 GATLAGQAFSNSPVAAVHALAYPLGGHYHIPHGLSNALMLGPVLRYNAQAAAPLYAELAD 308 Query: 307 ALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLA 366 LG S + + Y V ++ + + G P+ L G+ +++L L DA++Q RLL Sbjct: 309 VLGVTGSGDATARSEY-FVAHMQVLMDESGAPRRLRDVGVTDNSLAMLAADAMKQTRLLV 367 Query: 367 RSPLPLLEADIRAIYEAAF 385 +P+ + E D A+Y AF Sbjct: 368 NNPVEVREEDALALYREAF 386 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: 374 Number of extensions: 20 Number of successful extensions: 6 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 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