Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate BPHYT_RS24640 BPHYT_RS24640 alcohol dehydrogenase
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__BFirm:BPHYT_RS24640 Length = 426 Score = 393 bits (1009), Expect = e-114 Identities = 208/429 (48%), Positives = 267/429 (62%), Gaps = 15/429 (3%) Query: 2 MINRLKAALGAVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGG 61 M N LK GA L + A+ AD+ L+++G Y+A+ GDCVACHT+ G+ +AGG Sbjct: 1 MKNTLKG-FGAALCLTLPLFAQTPARAADQALVQRGAYLAKAGDCVACHTAPKGKPFAGG 59 Query: 62 LSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQ 121 L + TP+G IY+TNITPDP GIG YT ++F A+R GV KDG LYPAMPYPS+A++ Sbjct: 60 LPMTTPMGQIYTTNITPDPQTGIGGYTEEDFARAMREGVAKDGHNLYPAMPYPSYAKVND 119 Query: 122 DDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEI 181 DDMKALYAYFM GV P+ Q N DI WP++MRWPL W VF + PG D Sbjct: 120 DDMKALYAYFMSGVAPVQQANREPDIKWPLNMRWPLKFWNMVFLDKGV-YQDKPGKDVAW 178 Query: 182 ARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGL 241 RG YL+ G GHCG+CHTPRG QEKALD SG FL GG++D W A +L + +GL Sbjct: 179 NRGAYLIQGLGHCGSCHTPRGIAFQEKALDESGSA-FL-TGGLLDGWFAANLTGEHNVGL 236 Query: 242 GRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPP-----V 296 GRW+D+DL FLK+G H++AFG M V+ STQ D D+ AM Y+KSLPP Sbjct: 237 GRWNDQDLQAFLKTGANRHASAFGSMTSVINNSTQGLNDTDIAAMSTYLKSLPPAGGSGA 296 Query: 297 PPARGDYSYDASTAQMLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVV 356 PP Y YD A + N + +AGA+ Y C CH DG G A M PL+GNP V+ Sbjct: 297 PP----YKYDPQ-ATKVSLNRPANDAGARVYTAYCMHCHGVDGRGFAPMLAPLSGNPNVL 351 Query: 357 SDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANT 416 +P+S+ ++ ++G P+ MP Y +L+DQQIADV+ F+R+ W N APA Sbjct: 352 EKDPSSLINVTLNGTEDLVIGGIPAPYPMPKYAPVLNDQQIADVLTFVRAGWNNGAPA-V 410 Query: 417 TAADIQKLR 425 TA D+ KLR Sbjct: 411 TADDVAKLR 419 Lambda K H 0.318 0.135 0.430 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: 736 Number of extensions: 37 Number of successful extensions: 7 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: 472 Length of database: 426 Length adjustment: 33 Effective length of query: 439 Effective length of database: 393 Effective search space: 172527 Effective search space used: 172527 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: 51 (24.3 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