Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate H281DRAFT_05401 H281DRAFT_05401 Cytochrome c, mono- and diheme variants
Query= BRENDA::D2SZY5 (472 letters) >FitnessBrowser__Burk376:H281DRAFT_05401 Length = 431 Score = 396 bits (1018), Expect = e-115 Identities = 212/433 (48%), Positives = 274/433 (63%), Gaps = 18/433 (4%) Query: 2 MINRLKAALGAVAVGL--LAGTSLAHA--QNADEDLIKKGEYVARLGDCVACHTSLNGQK 57 M N LK A+ V L LA TS A A AD+ L+++G Y+A+ GDC ACHT+ G+ Sbjct: 1 MKNTLKGFGAALCVALPFLAQTSPASAAASAADQALVQRGAYLAKAGDCAACHTAPKGKP 60 Query: 58 YAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFA 117 +AGGL + TP+G IY+TNITPD GIG+YT ++F A+R GV KDG LYPAMPYPS+A Sbjct: 61 FAGGLPMNTPMGQIYTTNITPDAQTGIGSYTEQDFARAMREGVAKDGHNLYPAMPYPSYA 120 Query: 118 RMTQDDMKALYAYFMHGVQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGT 177 ++ +DMKALYA+FM GV P+ Q N +DI WPM+MRWPL +W VF + PG Sbjct: 121 KVNDEDMKALYAFFMSGVAPVQQANRESDIKWPMNMRWPLKLWNMVFLEKGV-YQNKPGK 179 Query: 178 DAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDP 237 D RG YL+ G GHCG+CHTPRG QEKALD +G FL GG++DNW A +L + Sbjct: 180 DVAWNRGAYLIQGLGHCGSCHTPRGIAFQEKALDETGSA-FL-TGGLLDNWYATNLTGEH 237 Query: 238 VLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYYTDADLHAMVKYIKSLPPV- 296 +GLGRWSD+DL FLK+G H++AFG M V+ STQ D D+ AM Y+KSLP V Sbjct: 238 NVGLGRWSDQDLQAFLKTGANRHASAFGSMTSVINNSTQNLNDGDIAAMTTYLKSLPAVG 297 Query: 297 ----PPARGDYSYDASTAQMLDSNNFSGNAGAKTYVEQCAICHRNDGGGVARMFPPLAGN 352 PP Y YD T + + N + +AGA+ Y C CH DG G A M PLAGN Sbjct: 298 GNGAPP----YKYDPQTTK-VSLNRPANDAGARVYTAYCMHCHGVDGRGFAPMLAPLAGN 352 Query: 353 PVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRA 412 P V+ + +S+ ++ ++G P+ MP Y +L+DQQIADV+ F+R+ W N A Sbjct: 353 PNVLEKDASSLINVTLNGTEDLVIGGIPAPYPMPKYAPVLNDQQIADVLTFVRAGWNNGA 412 Query: 413 PANTTAADIQKLR 425 PA TAAD+ KLR Sbjct: 413 PA-VTAADVTKLR 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: 706 Number of extensions: 31 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: 431 Length adjustment: 33 Effective length of query: 439 Effective length of database: 398 Effective search space: 174722 Effective search space used: 174722 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