Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate RR42_RS10775 RR42_RS10775 alcohol dehydrogenase
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__Cup4G11:RR42_RS10775 Length = 434 Score = 353 bits (906), Expect = e-102 Identities = 185/414 (44%), Positives = 249/414 (60%), Gaps = 10/414 (2%) Query: 2 MINRLKAALGAVAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGG 61 + R +A A AV LLA A A +++G Y+A++ +C ACHTS+ G +AGG Sbjct: 3 LATRRFSATVAFAVLLLAPCFAAAADAPGAAQVERGRYLAKVANCAACHTSVGGAPFAGG 62 Query: 62 LSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQ 121 L +KT +GT+YSTNITPD GIG Y+F+EFD A+R GV + G LYPAMPYPS+AR+ + Sbjct: 63 LPLKTGVGTVYSTNITPDVDSGIGAYSFEEFDRALREGVARHGKRLYPAMPYPSYARLAE 122 Query: 122 DDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVF---APAPKDFTPAPGTD 178 D++ALYAY V+ + Q ++ WP MRW L +W +F P P + G Sbjct: 123 PDVQALYAYLRTEVKAVRQATAEPEMRWPFGMRWLLRVWNWLFLESGPVPAN----AGQS 178 Query: 179 AEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPV 238 E RG YLV HCGACHTPRG M EK LD FL G V + W + +LR DP Sbjct: 179 VEWNRGAYLVQAVAHCGACHTPRGMLMAEKGLD-ERSRHFLAGASV-EGWASTNLRGDPR 236 Query: 239 LGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPP 298 GLG WS ED+ +L +GR H+ +FG M++V+ STQ+ T DL A+ Y+KS+P Sbjct: 237 TGLGTWSREDIAEYLHTGRNAHATSFGPMSEVIASSTQFMTRPDLDAVAVYLKSVPGARS 296 Query: 299 ARGDYSYDASTAQMLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSD 358 Y+YDA TA L F GA+ Y E C CH +G G AR+FPPLAGNP VV Sbjct: 297 DETPYAYDAHTADALAQGRFDA-TGARQYAEFCMPCHGANGKGFARVFPPLAGNPTVVDP 355 Query: 359 NPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRA 412 +P+S+A++++DG V A + MP Y L +Q++A+V+ FIR+ WGN+A Sbjct: 356 DPSSLANLLLDGAVTAHVGTAATDYHMPGYGWTLDNQELANVLTFIRTGWGNQA 409 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: 650 Number of extensions: 37 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: 472 Length of database: 434 Length adjustment: 33 Effective length of query: 439 Effective length of database: 401 Effective search space: 176039 Effective search space used: 176039 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