Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_015887793.1 NGR_RS08250 iron-containing alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >NCBI__GCF_000018545.1:WP_015887793.1 Length = 377 Score = 219 bits (559), Expect = 8e-62 Identities = 139/386 (36%), Positives = 212/386 (54%), Gaps = 24/386 (6%) Query: 6 IVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVK----IGLVDQVTSPLRQEGYS 61 +V P L G G ++L + G + +LVI+D +GL +VT Sbjct: 10 MVRPGLIEFGTGVAERLGTWAESKGFRRVLVISDAFNASRTDVLGLTGEVT--------- 60 Query: 62 VHVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYL 121 VY DV EP + ++ A + DL++G GGGSA+DLAKL AVL+ +AD + Sbjct: 61 --VYGDVKAEPDTGDLDCVLSAAEGARADLIVGFGGGSAMDLAKLVAVLSGSSQRLADVV 118 Query: 122 NLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETTKD--VVTHDYLLADVAIVDPQ 179 + + + +PTTSGTGSE ++++ TK V ++LAD+A++DP Sbjct: 119 G--AGKVAGPREIALAQVPTTSGTGSEAGIRALVTDPETKAKLAVESIHMLADIAVIDPA 176 Query: 180 LTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQ 239 LT +VPP+VTAATG+DA+ H VEA+ + A P D A+ +RL+ R L +AV +G D + Sbjct: 177 LTFTVPPKVTAATGVDAMAHCVEAFTNRKAHPAVDIYAIEGVRLVGRYLARAVHDGKDAE 236 Query: 240 ARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTK 299 AR ++ S G AG HALAYPLG ++H+AHG +NA++ P+V+ + + + Sbjct: 237 ARAGLSLASLYGGYCLGPVNTAGGHALAYPLGTRWHVAHGAANALIFPHVLAFNTPAVPE 296 Query: 300 RMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAV 359 + + + ALG ++S E+++ + E F A +GI L G+ + L ++ DA Sbjct: 297 KTSAVLEALGLSAS--QEIKSVFDAAHE---FCASLGIEMKLRQLGVLANDLGTMADDAF 351 Query: 360 QQKRLLARSPLPLLEADIRAIYEAAF 385 +RLL +P L ADI AIYEAAF Sbjct: 352 AIRRLLDNNPRDLSRADILAIYEAAF 377 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: 369 Number of extensions: 15 Number of successful extensions: 5 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: 377 Length adjustment: 30 Effective length of query: 365 Effective length of database: 347 Effective search space: 126655 Effective search space used: 126655 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 Apr 09 2024. 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