Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate AO353_27065 AO353_27065 cytochrome C oxidase Cbb3
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27065 Length = 415 Score = 257 bits (657), Expect = 5e-73 Identities = 160/429 (37%), Positives = 232/429 (54%), Gaps = 26/429 (6%) Query: 3 INRLKAALGAVAVGLLAGT-SLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGG 61 + RL ++LG AVGL ++ AQ AD+ IK+GEY+AR DC+ACHT+ G YAGG Sbjct: 1 MKRLLSSLGT-AVGLAVSLMAIQQAQAADQQQIKRGEYLARAADCMACHTAPGGAPYAGG 59 Query: 62 LSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQ 121 L I +P GTIY TNITPD +GIG Y+ EF A+ G R+DGA LYPAMPY S+ M + Sbjct: 60 LPIVSPFGTIYGTNITPDKDHGIGQYSDDEFFAALTEGKRRDGANLYPAMPYTSYHLMPR 119 Query: 122 DDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEI 181 +D A++AY + V PI + T +S+P ++R L W ++ K TPA G + Sbjct: 120 EDSDAIHAY-LQTVAPINRAAPVTRLSFPFNVRLGLMGWNMLYGKDVK-LTPAEGKSEDW 177 Query: 182 ARGEYLVTGPGHCGACHTPRGFG---MQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPV 238 RG+YLV GHCG CHTPRG Q+K L GG+++ ++APSL + + Sbjct: 178 KRGQYLVDVLGHCGECHTPRGLPGAMQQDKRLT----------GGLLNGYLAPSLLANDL 227 Query: 239 LGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPVPP 298 G W+ +DL FLK G + F M V STQ + DL +M ++ PP P Sbjct: 228 AARG-WTHQDLSSFLKHGMSAQGTMFNEMFPVFHNSTQNLNEPDLASMATFLLGDPP-PQ 285 Query: 299 ARGDYSYDASTAQMLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSD 358 AR + LD S G + Y+ CA CH +G G + + GN + + Sbjct: 286 AR------VLSEVPLDKMTESARRGRQDYLNVCAGCHGVNGEGKPHIAVAMQGNTTLRLE 339 Query: 359 NPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTA 418 +P ++ ++ DG MP + + LS+QQ+ D+++++R AWG + PA+ Sbjct: 340 DPRNLLRVIEDGIGEQKFAGFERMQPMPGFADKLSNQQMTDLISYLRQAWGGQ-PADLLI 398 Query: 419 ADIQKLRLD 427 I++L+ D Sbjct: 399 GQIEQLKAD 407 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: 586 Number of extensions: 36 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: 472 Length of database: 415 Length adjustment: 32 Effective length of query: 440 Effective length of database: 383 Effective search space: 168520 Effective search space used: 168520 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