Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate SM_b20402 SM_b20402 alcohol dehydrogenase cytochrome c subunit precursor
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__Smeli:SM_b20402 Length = 462 Score = 219 bits (557), Expect = 2e-61 Identities = 150/440 (34%), Positives = 230/440 (52%), Gaps = 51/440 (11%) Query: 6 LKAALGAVAVGLLAG---------------TSLAHAQNADEDLIKKGEYVARLGDCVACH 50 L+ A+G AV L+A T+ A A+ A E L+ KG +A LG+C+ACH Sbjct: 4 LRVAIGIAAVILVAAAAFFLFAWRSEIPEDTTAAEARFAAE-LVAKGAQLAALGNCIACH 62 Query: 51 TSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPA 110 T +AGGL++ TP GTIYSTNITPD GIG ++ F+ A+R GV ++G+ LYPA Sbjct: 63 TVPGRPAFAGGLALPTPFGTIYSTNITPDRETGIGGWSEAAFERAMREGVDREGSHLYPA 122 Query: 111 MPYPSFARMTQDDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKD 170 PY F R++ DD +ALYA+ M V A+ D+ +P+ R L+ W+ +F + + Sbjct: 123 FPYEHFTRVSADDNRALYAFLMTRVAVKAEALE-NDLPFPLKFRPLLAGWKLLFLDS-GE 180 Query: 171 FTPAPGTDAEIARGEYLVTGPGHCGACHTPRG-FGMQEKALDASGGPDFLGGGGVIDNWI 229 P PG RG YL G GHCGACHTPR FG +++ D GGG + W Sbjct: 181 REPDPGQSDAWNRGRYLAEGLGHCGACHTPRNPFGAEDR--------DRHFGGGEAEGWQ 232 Query: 230 APSLRNDPVLGLGRWSDEDLFLFLKSGRTD-HSAAFGGMADVVGWSTQYYTDADLHAMVK 288 A ++ + + W ++ L +L++G + H + G MA+V G + + D+D+ A+ Sbjct: 233 AYAINTESKAPI-PWDEQSLAFYLRNGWHEFHGVSRGPMAEVTG-NLAFLPDSDIAAIAT 290 Query: 289 YIKSLPPVP-PAR------------GDYSYDASTAQMLDSNNFSGNAGAKTYVEQCAICH 335 Y++S+ P P R G A+ +Q + G Y+ CA CH Sbjct: 291 YVRSIMGAPTPEREQRAAQLREAFEGQRPEQAADSQRSPVSASGSQPGEAIYLAACASCH 350 Query: 336 RNDGGGVARMFPPL--AGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILS 393 GG + F L + V + NP ++ ++V+ G LPP + SAV MP ++++L+ Sbjct: 351 E---GGRRQPFGGLNFELSTAVNAPNPQNIVNVVLFG--LPPADGEASAV-MPAFRHLLN 404 Query: 394 DQQIADVVNFIRSAWGNRAP 413 DQQ+AD++ ++R + P Sbjct: 405 DQQVADLLAYMRERFSEEPP 424 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: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 472 Length of database: 462 Length adjustment: 33 Effective length of query: 439 Effective length of database: 429 Effective search space: 188331 Effective search space used: 188331 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