Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate WP_057507640.1 ABB28_RS05325 alcohol dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >NCBI__GCF_001431535.1:WP_057507640.1 Length = 456 Score = 447 bits (1150), Expect = e-130 Identities = 218/398 (54%), Positives = 286/398 (71%), Gaps = 5/398 (1%) Query: 23 DQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPD-KTGIGDYS 81 ++ A++++G Y+A A DCVACH+ G FAGGLP+ +PIG IYSTNITPD KTGIG+YS Sbjct: 39 ERAAMIERGRYVATASDCVACHSTPGGAAFAGGLPIASPIGTIYSTNITPDRKTGIGEYS 98 Query: 82 FEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDNQDSDIP 141 +DFD+AVRHG+ G TLYPAMP+PSY R++DAD++A+Y YFM GVAP +N+ + I Sbjct: 99 LDDFDRAVRHGITPHGDTLYPAMPYPSYVRLTDADIEAMYTYFMHGVAPAQAENRPAGIR 158 Query: 142 WPLSMRWPLSIWRWMFAPSVETPAPAAGS--DPVISRGAYLVEGLGHCGACHTPRALTMQ 199 WPLSMRWPL+IWR F P GS D I+RGAYLV+G GHCG+CHTPRALT+Q Sbjct: 159 WPLSMRWPLAIWRKQFGPDPAQAGKMQGSYPDEEIARGAYLVQGPGHCGSCHTPRALTLQ 218 Query: 200 EKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVFGG 259 EKA+ SG +++L+G ++GW+A +LRG+ DGLG+WS + ++ LKTGRS+R AV G Sbjct: 219 EKAMDESG-AEYLAGGQVIDGWLAVNLRGNKADGLGNWSRQDIIDVLKTGRSERHAVVGR 277 Query: 260 -MSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDDSKPGAAV 318 M+DVV HS Q++TDADL AIA YLKSLPA + Q A L G ++ GA + Sbjct: 278 PMADVVQHSTQHLTDADLGAIAAYLKSLPATQQDPSSFVANPQTASELRAGVNNSRGAEL 337 Query: 319 YIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTFTMP 378 Y+DNCAACHR+D GY RVFP+LAGN + + D T+L+ +VL+G +P+T APS MP Sbjct: 338 YVDNCAACHRSDAEGYPRVFPSLAGNSTILAKDPTTLVRLVLEGSEMPSTVHAPSNLGMP 397 Query: 379 AFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 FA RLSD +VA++ F+R S+GN+A AV VA +R Sbjct: 398 GFAERLSDADVAELGTFLRGSFGNKAPAVTATQVAKVR 435 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: 645 Number of extensions: 35 Number of successful extensions: 5 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: 456 Length adjustment: 32 Effective length of query: 402 Effective length of database: 424 Effective search space: 170448 Effective search space used: 170448 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 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