Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS16735 HSERO_RS16735 alcohol dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__HerbieS:HSERO_RS16735 Length = 444 Score = 488 bits (1257), Expect = e-142 Identities = 251/417 (60%), Positives = 306/417 (73%), Gaps = 8/417 (1%) Query: 3 ALVIATLALLGSAAANAA--EADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMET 60 A V++ AL +A +N A ADQQ LVQ+GEYLA+AGDCVACHTAK GKPFAGGL + T Sbjct: 14 AAVMSLSALTAAAQSNPAAPSADQQ-LVQRGEYLAKAGDCVACHTAKGGKPFAGGLAIAT 72 Query: 61 PIGVIYSTNITPDK-TGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQA 119 PIG +YS+NITPDK GIG+YS EDFD+A+RHG+ K G++LYPAMP+PSYA+V AD++A Sbjct: 73 PIGTVYSSNITPDKENGIGNYSEEDFDRALRHGIRKDGASLYPAMPYPSYAKVKPADVKA 132 Query: 120 LYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAY 179 LYAYFM GV N+ DI WPLSMRWPLSIWR +FAP+V P S V RG Y Sbjct: 133 LYAYFMHGVQADPAPNRGVDITWPLSMRWPLSIWRKVFAPAVAVDGPEDNSPLV--RGQY 190 Query: 180 LVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSE 239 LVEGLGHCGACHTPR + MQEKALS + S FLSG ++G++A +LRGD +DGLG+WSE Sbjct: 191 LVEGLGHCGACHTPRGVGMQEKALS-NDSSQFLSGGV-IDGYLANNLRGDGRDGLGNWSE 248 Query: 240 EQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYD 299 +V FLKTGR+ SA FGGM+DVV +S QYMT+ DL+A+A+YLKSL YD Sbjct: 249 ADIVAFLKTGRNSHSAAFGGMADVVANSTQYMTEEDLSAMAKYLKSLKPVKDGTPALAYD 308 Query: 300 KQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIV 359 + QAL G D PGA +++NCAACHR+ G GY FP+LA +P + + + SLI IV Sbjct: 309 DKTHQALRKGSDQSPGAMAFLNNCAACHRSSGKGYDETFPSLALSPTVNAENPASLIRIV 368 Query: 360 LKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 L+G +P TH AP+ F MPAF RLSDQEVA+VV FIRSSWGNQAS+V DVA +R Sbjct: 369 LEGAEMPWTHKAPTQFAMPAFGSRLSDQEVAEVVTFIRSSWGNQASSVSASDVAKVR 425 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: 679 Number of extensions: 45 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: 434 Length of database: 444 Length adjustment: 32 Effective length of query: 402 Effective length of database: 412 Effective search space: 165624 Effective search space used: 165624 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