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 3610403 Dshi_3784 Gluconate 2-dehydrogenase (acceptor) (RefSeq)
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Dino:3610403 Length = 305 Score = 175 bits (443), Expect = 2e-48 Identities = 113/292 (38%), Positives = 150/292 (51%), Gaps = 16/292 (5%) Query: 21 AAAIGLM-AVSFGAAHAQDADEALIKRGEYVARLSDCIACHTALH--GQPYAGGLEIKSP 77 AA++G++ A G+A A E + RG Y+AR S CIACHT G P AGG +++P Sbjct: 16 AASLGVVIAWPVGSAVTPIAIEGNVDRGAYLARASGCIACHTNFEAGGAPLAGGAPLETP 75 Query: 78 IGTIYSTNITPDPEHGIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAM 137 GT Y N+T DPEHG+G +T E F KA+R+GI DG YP+ PY +A SD DI + Sbjct: 76 FGTFYPPNLTTDPEHGMGEWTAEQFAKAVRQGIGPDGTPYYPSFPYTFYADFSDQDIADL 135 Query: 138 YAFFMHGVKPVALQNKAPDISWPLSMRWPLGMWRAMFV--PSMTPGVDKSISDPEVARGE 195 +A F V PV D+S+P RW L +WRA F P P +S RG Sbjct: 136 WAAF-QTVPPVDEPAPENDVSFPFDQRWGLKLWRAAFFYDPDTEPIEGRS---DAWNRGR 191 Query: 196 YLVNGPGHCGECHTPRGFGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWS 255 LV G HCG CHTPR + GNA L GG+ AP++R D W+ Sbjct: 192 ELVRGAAHCGACHTPRNLAGGRDIGASFAGNAQLPGGSK-----APAIRP-KDLVKNDWT 245 Query: 256 EDDIVTFLKSGRIDHSAVFGG-MADVVAYSTQHWSDDDLRATAKYLKSMPAV 306 ++ L++G FGG MA+VV T+ + D A A +L + V Sbjct: 246 VSNLAYALQTGITPSGDAFGGSMAEVVREGTRFLTPADREAMALFLLNKDTV 297 Lambda K H 0.317 0.134 0.421 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: 528 Number of extensions: 35 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: 478 Length of database: 305 Length adjustment: 30 Effective length of query: 448 Effective length of database: 275 Effective search space: 123200 Effective search space used: 123200 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