Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate H281DRAFT_01762 H281DRAFT_01762 Cytochrome c, mono- and diheme variants
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__Burk376:H281DRAFT_01762 Length = 450 Score = 332 bits (851), Expect = 2e-95 Identities = 184/419 (43%), Positives = 241/419 (57%), Gaps = 21/419 (5%) Query: 10 LGAVAVGLLAGTSLAHAQN---------ADEDLIKKGEYVARLGDCVACHT-SLNGQKYA 59 L V L SLA + + +D LI +G Y+A+LGDC CHT G +A Sbjct: 20 LAMTMVAALCAHSLAQSDSPSVDDEVSLSDPALISRGAYLAKLGDCAGCHTVPKQGAPFA 79 Query: 60 GGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARM 119 GGL + +P GTIYSTNITPDP GIG Y++ +F+ A+R GV G LYPAMPY SF ++ Sbjct: 80 GGLPMGSPFGTIYSTNITPDPQTGIGRYSYADFERALRDGVAPGGKRLYPAMPYASFTKI 139 Query: 120 TQDDMKALYAYFMHGAQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDA 179 DM ALYAYFMHG QP+A + T + +P S RW L+ W F + F P DA Sbjct: 140 NDSDMHALYAYFMHGVQPVAHRPPETKLPFPFSQRWGLAFWDFAFVQHER-FIPDGKRDA 198 Query: 180 EIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVL 239 RG Y+V GHCGACHTPRG G +E+ D S GG D+W AP+L DP Sbjct: 199 LWNRGAYIVQSLGHCGACHTPRGPGFEERGYDESS--KLYLTGGTNDHWFAPNLTGDPGS 256 Query: 240 GLGRWSDEDLFLFLKSGR--TDHSAAFGGMADVVGWSTQYFTDADLHAMVKYIKSLPPVP 297 GLGR S D+ FLKSG H FG M +VV S QYF+D DL+A+ +Y+KSL P Sbjct: 257 GLGRLSPRDIASFLKSGHGVDVHVVTFGSMVEVVEDSGQYFSDDDLNAVARYLKSL-PAR 315 Query: 298 PARGDYSYDA----STAQMLDSNNISGNAGAKTYVDQCAICHRNDGGGVARMFPPLAGNP 353 + G Y + TA L + + GA Y+ CA CH+ DG G FP LAGNP Sbjct: 316 QSSGAYKPNTQKLQETAVSLKAGEVE-RPGAGLYMSFCAKCHQADGRGEPHKFPALAGNP 374 Query: 354 VVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRA 412 V++ + +S+ +V++GG P T P MP ++N +D++IA V++F+R+AWGN A Sbjct: 375 AVLAPDTSSLIRLVLEGGTSPQTENGPIHREMPAFRNQFTDREIARVLSFVRTAWGNEA 433 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: 676 Number of extensions: 45 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: 472 Length of database: 450 Length adjustment: 33 Effective length of query: 439 Effective length of database: 417 Effective search space: 183063 Effective search space used: 183063 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