Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate AZOBR_RS28580 AZOBR_RS28580 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__azobra:AZOBR_RS28580 Length = 387 Score = 196 bits (497), Expect = 1e-54 Identities = 127/376 (33%), Positives = 196/376 (52%), Gaps = 11/376 (2%) Query: 15 GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPL 74 G GA +QL ++ A + V+ DP L + ++ L G ++ V+T + PEP Sbjct: 18 GVGAHEQLPDVLREWNATRLFVLLDPALADSAIFRRIEGLLTSNGVALSVFTGIEPEPGD 77 Query: 75 ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134 T + A R+ ++ +GGGS +D+AK +L + G +ADY G + L Sbjct: 78 RTVQAAYERCREQDAQALLAIGGGSTIDVAKAVGILMTNGGRIADY---EGIEKFAIRPL 134 Query: 135 PKILIPTTSGTGSEVTNISVLS--LETTKDVVTHD-YLLADVAIVDPQLTVSVPPRVTAA 191 P I +PTT+GTGSEV+ V++ TK + H + A VAI+DP S+P V A Sbjct: 135 PLIAVPTTAGTGSEVSGACVITDTARKTKMAIRHAAFSPAQVAILDPLAVGSMPAHVAAH 194 Query: 192 TGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLA 251 GIDA HA E+Y+S A+ SD + + A+ LI+ S+R VA+ ++ A +DM GS LA Sbjct: 195 AGIDAFVHAFESYLSKRATVFSDAVNLHAMTLIAGSIRPFVADRTNVPAALDMLCGSALA 254 Query: 252 GLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGN 311 ++F G+ VH +A +G F + HG +NAV LPY + + +RMA I LG + Sbjct: 255 AMSFGVTGLGNVHCMAMSVGALFPVPHGLANAVCLPYAAAFNVSAKPERMARIAEILGVD 314 Query: 312 SSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKD--AVQQKRLLARSP 369 ++ L +A+ V+ L AD+GIP L G+ E L+ + + A R +P Sbjct: 315 TAGLPLDQAAEAAVDGLRTLCADLGIPPRLRDVGVTEDRLDEMARRSYAADYNRW---NP 371 Query: 370 LPLLEADIRAIYEAAF 385 E D + ++ AAF Sbjct: 372 RHTSEPDFQDLFRAAF 387 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: 368 Number of extensions: 16 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: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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