Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate H281DRAFT_04220 H281DRAFT_04220 Cytochrome c, mono- and diheme variants
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Burk376:H281DRAFT_04220 Length = 432 Score = 342 bits (876), Expect = 2e-98 Identities = 196/438 (44%), Positives = 261/438 (59%), Gaps = 40/438 (9%) Query: 4 LVIATLALL------------GSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKP 51 +V+AT AL+ GSA A A ADQ ALV++GEYLARAGDC+ACHT + GK Sbjct: 13 VVVATAALVPVLWSGGDNLHNGSAVA-ATPADQAALVKKGEYLARAGDCIACHTVRGGKQ 71 Query: 52 FAGGLPMETPIGVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYA 110 FAGGLPM TP G +++ NITPD + GIG ++ +DF +A+ G +K GS LYP PF SY Sbjct: 72 FAGGLPMATPFGTMFTPNITPDDQYGIGKWTQDDFYRAMHTGRSKDGSLLYPGFPFTSYT 131 Query: 111 RVSDADMQALYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGS 170 +V+ AD A+YAY ++ V PV ++ ++ +P + R L WR +F E A Sbjct: 132 KVTRADSDAIYAY-LRSVTPVNVASRPHELKFPFNQRNMLIGWRTLFFREGEYKA----- 185 Query: 171 DPVIS----RGAYLVEGLGHCGACHTPRALTMQEKALSASGG----SDFLSGSAPLEGWI 222 DP S RGAYL+EGLGHCG CHT +++A GG + F G PL+ W Sbjct: 186 DPTKSVEWNRGAYLIEGLGHCGMCHT---------SINAMGGPVSSAAFAGGLIPLQNWY 236 Query: 223 AKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARY 282 A SL + + GLG W + + LKTG S+R AVFG M++VV +S+QYMTDAD+ A+A Y Sbjct: 237 APSLTSNKEAGLGDWETKDIADLLKTGVSNRGAVFGPMAEVVHNSLQYMTDADINAMATY 296 Query: 283 LKSLPANDPKDQPHQYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALA 342 LK++P +P Q + + G+ K G +Y DNCA CH +G G FP LA Sbjct: 297 LKTIPQKSEAPEPLQLE---TSEKFGGELLKQGQKIYADNCAKCHADNGLGQPPAFPPLA 353 Query: 343 GNPVLQSADATSLIHIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGN 402 N +Q A + I +VL GG P+T + P + MP FA LS+QEVA VV +IR SWGN Sbjct: 354 NNQSIQMPSAVNPIRMVLNGGYPPSTDANPHPYGMPPFAQSLSNQEVAAVVTYIRMSWGN 413 Query: 403 QASAVKPGDVAALRNGDL 420 +AV P V+ LR+ L Sbjct: 414 HGTAVSPQQVSDLRSAPL 431 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: 619 Number of extensions: 47 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: 432 Length adjustment: 32 Effective length of query: 402 Effective length of database: 400 Effective search space: 160800 Effective search space used: 160800 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