Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_089215766.1 CHB69_RS09450 FAD-binding protein
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_900188185.1:WP_089215766.1 Length = 528 Score = 472 bits (1215), Expect = e-137 Identities = 254/523 (48%), Positives = 326/523 (62%), Gaps = 3/523 (0%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 +FD +++G GSAG A RL+ D VCL+EAG + + TP G +P + NW Sbjct: 3 QFDIIVIGGGSAGSAAAGRLAGDGRRRVCLVEAGGTNDIVRVKTP-GFMPFIP-KASNWQ 60 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 + T PQ GL GR+GYQPRG+ LGGSS+IN M+YIRG D++ W LG GW + DVLP+ Sbjct: 61 YDTVPQRGLNGRIGYQPRGRGLGGSSAINAMVYIRGTAFDYDQWAELGATGWSYADVLPW 120 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAG 180 F++SE + G+ E+HG DG L V + S FVESA DFN + EG G Sbjct: 121 FKRSEGNERGADEWHGADGPLNVMDQRWPNVTSRRFVESAAALQLPRTADFNRPSNEGFG 180 Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240 Y VT + G RWS A A+++P+R R+N + T VE I++ +A GV G R L Sbjct: 181 LYQVTQKAGERWSAARAYVEPLRGRANFDIRTGALVEKILIEKGRAVGVAIRRGGRRETL 240 Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKS 300 RA VILSAGAFGSP +LMLSG+G AA L GI + GVG NLQDH D V +++ Sbjct: 241 RAAGGVILSAGAFGSPQILMLSGVGPAAHLREHGIEVVRDRAGVGANLQDHIDYVSSWET 300 Query: 301 NDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIG 360 T G SL G +M KA+F++ HR G + + AEAG F K+ P L PD+Q H V Sbjct: 301 RSTEPFGDSLGGTWRMVKAIFEHRLHRTGILTTCFAEAGGFWKSRPDLPAPDVQYHFVPA 360 Query: 361 TVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKG 420 ++DH R GHGFSCH CVLRP+S GSV LAS DP AP IDP FL D D+ATL G Sbjct: 361 MLEDHGRTRVKGHGFSCHACVLRPESRGSVTLASADPAAAPLIDPGFLTDDRDMATLRAG 420 Query: 421 YRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVV 480 R+ I+A P+A +G D + L +D L L+R R DT+YHP+G+C+MG D AVV Sbjct: 421 VRMMHRIVATPPLADYGGVDRHPVDLDDDAALDALIRDRADTVYHPVGSCRMGSDADAVV 480 Query: 481 DSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 D L+++GIEGL V DASIMP LV GNTNA +IMI ERAA+++ Sbjct: 481 DPALKLNGIEGLWVADASIMPRLVSGNTNAPSIMIGERAADFV 523 Lambda K H 0.319 0.137 0.419 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: 885 Number of extensions: 48 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: 526 Length of database: 528 Length adjustment: 35 Effective length of query: 491 Effective length of database: 493 Effective search space: 242063 Effective search space used: 242063 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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