Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate SMc00086 SMc00086 diheme cytochrome C-type signal peptide protein
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Smeli:SMc00086 Length = 304 Score = 162 bits (409), Expect = 2e-44 Identities = 111/315 (35%), Positives = 157/315 (49%), Gaps = 35/315 (11%) Query: 1 MINRLKVTFSAAAFSLLAGTALA---QTPDADSAL---------VQKGAYVARLGDCVAC 48 M R + S ++AG +LA PD A + G + G CV+C Sbjct: 1 MGRRARYLLSGLVLLVVAGASLAWWLTKPDRWDAAHWEGLGGPDLANGEQIFWAGGCVSC 60 Query: 49 HTALHGQS-----YAGGLEIKSPIGTIYSTNITPDPTYGIGRYTFAEFDEAVRHGIRKDG 103 H+A + GG +KSP GT Y NI+PD T GIG +T AEF +A+ G+ KDG Sbjct: 61 HSAPGAKDDQRLVLTGGRTLKSPFGTFYPPNISPDETVGIGNWTLAEFGDAMTRGVGKDG 120 Query: 104 STLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQPDKQPDISWPLSMRWPLGIWRMMF 163 LYP+ PY S+ RMT +D+ L+ FM + + D+++P ++R LG W++++ Sbjct: 121 EHLYPSFPYGSYIRMTAKDVNDLWG-FMQTLPKSSNATPPHDLAFPYNVRLALGAWKLLY 179 Query: 164 -SPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPR----GFAMQEKALDAAGGPDFL 218 S P+ T D ++ARG YLV GPGHCG CHTPR GF E+ AG P+ Sbjct: 180 LSDEPR--TQVNTADTKLARGQYLVEGPGHCGECHTPRDALGGF---EEDRWLAGAPNPE 234 Query: 219 SGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRIDHSAVFGGMGDVVAWSTQYFT 278 G D + PS ++ +G WS DI ++L++G GG V + Sbjct: 235 GEGRIPD--ITPSSKS-----IGDWSASDIASYLETGFTPDFDTVGGSMVEVQKNMAELP 287 Query: 279 DDDLHAIAKYLKSLP 293 D AIA YLK+LP Sbjct: 288 ASDRDAIAAYLKALP 302 Lambda K H 0.317 0.134 0.425 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: 537 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: 468 Length of database: 304 Length adjustment: 30 Effective length of query: 438 Effective length of database: 274 Effective search space: 120012 Effective search space used: 120012 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 (21.6 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