Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate H281DRAFT_01762 H281DRAFT_01762 Cytochrome c, mono- and diheme variants
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Burk376:H281DRAFT_01762 Length = 450 Score = 359 bits (922), Expect = e-104 Identities = 193/426 (45%), Positives = 263/426 (61%), Gaps = 16/426 (3%) Query: 5 VIATLALLGSAAANAAEADQQ------ALVQQGEYLARAGDCVACHTA-KDGKPFAGGLP 57 ++A L A +++ D + AL+ +G YLA+ GDC CHT K G PFAGGLP Sbjct: 24 MVAALCAHSLAQSDSPSVDDEVSLSDPALISRGAYLAKLGDCAGCHTVPKQGAPFAGGLP 83 Query: 58 METPIGVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDAD 116 M +P G IYSTNITPD +TGIG YS+ DF++A+R GVA GG LYPAMP+ S+ +++D+D Sbjct: 84 MGSPFGTIYSTNITPDPQTGIGRYSYADFERALRDGVAPGGKRLYPAMPYASFTKINDSD 143 Query: 117 MQALYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISR 176 M ALYAYFM GV PVA ++ +P+P S RW L+ W + F E P D + +R Sbjct: 144 MHALYAYFMHGVQPVAHRPPETKLPFPFSQRWGLAFWDFAFVQH-ERFIPDGKRDALWNR 202 Query: 177 GAYLVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGS 236 GAY+V+ LGHCGACHTPR +E+ S G+ + W A +L GD GLG Sbjct: 203 GAYIVQSLGHCGACHTPRGPGFEERGYDESSKLYLTGGTN--DHWFAPNLTGDPGSGLGR 260 Query: 237 WSEEQLVQFLKTGRSDRSAV--FGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKD- 293 S + FLK+G V FG M +VV S QY +D DL A+ARYLKSLPA Sbjct: 261 LSPRDIASFLKSGHGVDVHVVTFGSMVEVVEDSGQYFSDDDLNAVARYLKSLPARQSSGA 320 Query: 294 -QPH-QYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSAD 351 +P+ Q ++ A +L G+ +PGA +Y+ CA CH+ DG G FPALAGNP + + D Sbjct: 321 YKPNTQKLQETAVSLKAGEVERPGAGLYMSFCAKCHQADGRGEPHKFPALAGNPAVLAPD 380 Query: 352 ATSLIHIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGD 411 +SLI +VL+GGT P T + P MPAF + +D+E+A V++F+R++WGN+A V D Sbjct: 381 TSSLIRLVLEGGTSPQTENGPIHREMPAFRNQFTDREIARVLSFVRTAWGNEARPVATRD 440 Query: 412 VAALRN 417 V+ +R+ Sbjct: 441 VSTVRS 446 Lambda K H 0.316 0.131 0.404 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: 608 Number of extensions: 38 Number of successful extensions: 9 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: 434 Length of database: 450 Length adjustment: 32 Effective length of query: 402 Effective length of database: 418 Effective search space: 168036 Effective search space used: 168036 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 (21.6 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