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 SM_b20402 SM_b20402 alcohol dehydrogenase cytochrome c subunit precursor
Query= SwissProt::Q47945 (478 letters) >FitnessBrowser__Smeli:SM_b20402 Length = 462 Score = 213 bits (541), Expect = 1e-59 Identities = 150/414 (36%), Positives = 212/414 (51%), Gaps = 49/414 (11%) Query: 33 AAHAQDADEALIKRGEYVARLSDCIACHTALHGQPYAGGLEIKSPIGTIYSTNITPDPEH 92 AA A+ A E L+ +G +A L +CIACHT +AGGL + +P GTIYSTNITPD E Sbjct: 36 AAEARFAAE-LVAKGAQLAALGNCIACHTVPGRPAFAGGLALPTPFGTIYSTNITPDRET 94 Query: 93 GIGNYTLEDFTKALRKGIRKDGATVYPAMPYPEFARLSDDDIRAMYAFFMH--GVKPVAL 150 GIG ++ F +A+R+G+ ++G+ +YPA PY F R+S DD RA+YAF M VK AL Sbjct: 95 GIGGWSEAAFERAMREGVDREGSHLYPAFPYEHFTRVSADDNRALYAFLMTRVAVKAEAL 154 Query: 151 QNKAPDISWPLSMRWPLGMWRAMFVPSMTPGVDKSISDPEVARGEYLVNGPGHCGECHTP 210 +N D+ +PL R L W+ +F+ S D SD RG YL G GHCG CHTP Sbjct: 155 EN---DLPFPLKFRPLLAGWKLLFLDSGEREPDPGQSD-AWNRGRYLAEGLGHCGACHTP 210 Query: 211 RG-FGMQVKAYGTAGGNAYLAGGAPIDNWIAPSLRSNSDTGLGRWSEDDIVTFLKSGRID 269 R FG + + GG A + W A ++ + S + W E + +L++G + Sbjct: 211 RNPFGAEDRDRHFGGGEA--------EGWQAYAINTESKAPI-PWDEQSLAFYLRNGWHE 261 Query: 270 HSAVFGGMADVVAYSTQHWSDDDLRATAKYLKSMPAVP---------------EGKNLGQ 314 V G V + D D+ A A Y++S+ P EG+ Q Sbjct: 262 FHGVSRGPMAEVTGNLAFLPDSDIAAIATYVRSIMGAPTPEREQRAAQLREAFEGQRPEQ 321 Query: 315 -DDGQTTALLNKGGQGNAGAEVYLHNCAICHMNDGTGVNRMFPPLAG-----NPVVITDD 368 D Q + + G Q G +YL CA CH G R P G + V + Sbjct: 322 AADSQRSPVSASGSQ--PGEAIYLAACASCH----EGGRRQ--PFGGLNFELSTAVNAPN 373 Query: 369 PTSLANVVAFGGILPPTNSAPSAVAMPGFKNHLSDQEMADVVNFMRKGWGNNAP 422 P ++ NVV FG LPP + SAV MP F++ L+DQ++AD++ +MR+ + P Sbjct: 374 PQNIVNVVLFG--LPPADGEASAV-MPAFRHLLNDQQVADLLAYMRERFSEEPP 424 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: 660 Number of extensions: 42 Number of successful extensions: 8 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: 462 Length adjustment: 33 Effective length of query: 445 Effective length of database: 429 Effective search space: 190905 Effective search space used: 190905 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: 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