Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate WP_086510868.1 BZY95_RS15845 aldehyde oxidase
Query= metacyc::MONOMER-12746 (434 letters) >NCBI__GCF_002151265.1:WP_086510868.1 Length = 999 Score = 213 bits (543), Expect = 2e-59 Identities = 136/389 (34%), Positives = 207/389 (53%), Gaps = 22/389 (5%) Query: 16 AANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPDK- 74 AAN A+ +++G +A AGDC ACHTA+ G+ AGG +TP G +YSTN+TPD+ Sbjct: 597 AANLYSAET---IERGRLVAAAGDCAACHTAEGGQENAGGRAFDTPFGTLYSTNLTPDEE 653 Query: 75 TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARD 134 TGIG +S+ F++A+RHG+++ G LYPA P+ ++A++SDADMQALYAY M A V+ + Sbjct: 654 TGIGRWSYAAFERAMRHGISRDGKHLYPAFPYTAFAKISDADMQALYAYLMAQPA-VSAE 712 Query: 135 NQDSDIPWPLSMRWPLSIWRWMF-APSVETPAPAAGSDPVISRGAYLVEGLGHCGACHTP 193 + + +P + R ++ W ++ P+ P P G + +RGAYL EGLGHC ACH+P Sbjct: 713 TPANALSFPFNFRPLMAGWNALYHDPNPFEPDP--GQSDLYNRGAYLAEGLGHCSACHSP 770 Query: 194 RALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDR 253 R A+ A + A ++GW A L + + WSE L +L+ G S Sbjct: 771 R------NAMGAEQRGEHSLAGAMVDGWEAPPLNRLSRSPI-PWSETSLYDYLRHGASSL 823 Query: 254 SAVFGGMSDVVVHSMQYMTDADLTAIARYL---KSLPANDPKDQPHQYDKQVAQALWNGD 310 V G VV + + + D+ A+A Y+ PA D + ++A A Sbjct: 824 HGVASGPMAPVVAGLGELPEYDVRALAHYVAVQMDAPAGDSETVRADAAVRIATAQSGPA 883 Query: 311 DSKPGAAVYIDNCAACHRTDG-HGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATH 369 + G ++ CA+CH +G +T +LA N L S ++I +L G + A H Sbjct: 884 GMEEGERLFEGACASCHMENGTPSFTSAQTSLALNTNLHSQHPDNVIQSIL--GGVHADH 941 Query: 370 SAPSTFTMPAFAWRLSDQEVADVVNFIRS 398 P MP FA SD +V + ++R+ Sbjct: 942 -VPGLGNMPGFADSFSDSQVVTLTAYLRA 969 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: 1231 Number of extensions: 84 Number of successful extensions: 6 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: 999 Length adjustment: 38 Effective length of query: 396 Effective length of database: 961 Effective search space: 380556 Effective search space used: 380556 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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