Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate H281DRAFT_02833 H281DRAFT_02833 Cytochrome c, mono- and diheme variants
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__Burk376:H281DRAFT_02833 Length = 438 Score = 308 bits (788), Expect = 3e-88 Identities = 166/409 (40%), Positives = 243/409 (59%), Gaps = 19/409 (4%) Query: 30 DEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTP-IGTIYSTNITPDPTYGIGTYT 88 D LIK+GEY+A GDC+ACHT+ G+ +AGGL +K P +GTIYS+NITPDP GIGT++ Sbjct: 36 DAALIKRGEYLATAGDCMACHTTAKGKPFAGGLPLKVPMLGTIYSSNITPDPQTGIGTWS 95 Query: 89 FKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQPIAQKNHPTDIS 148 ++FD A+R GV KDG LYPAMPY S+A+++ D+KALYAYF +G P+ Q +DI+ Sbjct: 96 LEDFDRALRKGVSKDGHNLYPAMPYVSYAKVSDGDVKALYAYFRYGVVPVQQATRASDIA 155 Query: 149 WPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEK 208 WP++MRWPL++W +F + + P AE RG YLV G HC CHTPRGF MQE+ Sbjct: 156 WPLNMRWPLTVWNWMFLKS-GPYQAKPQQSAEWNRGAYLVQGLAHCSTCHTPRGFAMQEQ 214 Query: 209 ALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSA-AFGGM 267 ALD +G FL GG V+ +W ++ + P G+G WS L +L++G A A G M Sbjct: 215 ALDETGS-GFL-GGSVLADWDGYNITSSPDSGIGGWSHTQLVQYLQTGSVPGLAQAAGPM 272 Query: 268 ADVVGWSTQYFTDADLHAMVKYIKSLPPV------PPARGDYSYDASTAQMLDSNNISGN 321 A+ V S +DAD+ A+ Y++++PPV +R ++ + + ++ N Sbjct: 273 AEAVEHSFSKMSDADIGAIATYVRTVPPVNDGGAQSGSRSRSAWGKPSTDVARLRGVAMN 332 Query: 322 AG----AKTYVDQCAICHRNDGGGVA-RMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPT 376 G A+ Y+ CA CH+ G G +PPL N V + NP ++ +++ G Sbjct: 333 DGTLDPARLYLGNCATCHQASGKGTPDGYYPPLLHNSTVGASNPGNLMQVILHG---VQR 389 Query: 377 NWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425 A + V MP + L+D QIA + N++ + +GN A + D+ +LR Sbjct: 390 KAAGNDVGMPAFAAQLNDAQIAALTNYVTTQFGNPAAQRVSEKDVARLR 438 Score = 40.8 bits (94), Expect = 9e-08 Identities = 42/133 (31%), Positives = 53/133 (39%), Gaps = 30/133 (22%) Query: 169 KDFTPAPGTDAE-IARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGG------ 221 +D G DA I RGEYL T G C ACHT + G F GG Sbjct: 27 QDAKAVDGNDAALIKRGEYLATA-GDCMACHT------------TAKGKPFAGGLPLKVP 73 Query: 222 --GGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSG-RTDHSAAFGGMADVVGWSTQYF 278 G + + I P DP G+G WS ED L+ G D + M V S Sbjct: 74 MLGTIYSSNITP----DPQTGIGTWSLEDFDRALRKGVSKDGHNLYPAMPYV---SYAKV 126 Query: 279 TDADLHAMVKYIK 291 +D D+ A+ Y + Sbjct: 127 SDGDVKALYAYFR 139 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: 684 Number of extensions: 46 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 472 Length of database: 438 Length adjustment: 33 Effective length of query: 439 Effective length of database: 405 Effective search space: 177795 Effective search space used: 177795 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