Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate AO356_30205 AO356_30205 alcohol dehydrogenase
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30205 Length = 444 Score = 366 bits (939), Expect = e-105 Identities = 189/404 (46%), Positives = 259/404 (64%), Gaps = 12/404 (2%) Query: 24 AHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYG 83 A A +AD L+++GEYVARL DCVACH++ G +AGGL + TP+G+IY+TNITPD G Sbjct: 35 ASAPSADAQLVQRGEYVARLSDCVACHSTPKGAPFAGGLEMATPMGSIYATNITPDKQTG 94 Query: 84 IGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGVQPIAQKNH 143 IG Y+ +FD AVR GV DG LYPAMPYPS+A+++ DD++ALYA+FM GV+P Q+N Sbjct: 95 IGNYSLADFDRAVRSGVAADGHRLYPAMPYPSYAKLSDDDVRALYAFFMAGVKPAQQQNQ 154 Query: 144 PTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGF 203 + I WP++MRWPL++W + F + P DA RG Y+V G GHCG+CHTPR Sbjct: 155 QSHIPWPLNMRWPLALWNTAFVD-DGAYQAKPSEDALWNRGAYIVQGAGHCGSCHTPRSL 213 Query: 204 GMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAA 263 M EK+LD S FL G ++D W APSLR DP GLGRWS++++ +LK+GR HS Sbjct: 214 TMNEKSLDESSA-TFL-SGSLLDGWYAPSLRQDPNTGLGRWSEQEIVDYLKTGRNAHSVV 271 Query: 264 FGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPPARG-DYSYDASTAQMLDSNNFSGNA 322 G MA+V STQY +D DL A+ Y+ SLP P G + A A+ S Sbjct: 272 VGTMAEVFNNSTQYMSDPDLKAIAHYLVSLPGDPKRDGPPWKPAAKLAEQPLS-----TP 326 Query: 323 GAKTYVEQCAICHRNDGGGVARMFPPLAG-NPVVVSDNPTSVAHIVVDGGVLPPTNWAPS 381 GA Y+ +C+ CH +DG G A PPLAG + +V + TS+ + ++G N P Sbjct: 327 GAANYMAKCSSCHGSDGSGQAPWIPPLAGASSSMVKEGATSI-NATLNGSERVVANGIPD 385 Query: 382 AVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425 + MP Y+N LSDQ++ADV+ F+R++WGN+ A A ++++LR Sbjct: 386 SYRMPPYRNQLSDQEVADVLTFVRTSWGNQGGA-VKADEVKELR 428 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: 705 Number of extensions: 29 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: 444 Length adjustment: 33 Effective length of query: 439 Effective length of database: 411 Effective search space: 180429 Effective search space used: 180429 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