Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate RR42_RS10775 RR42_RS10775 alcohol dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__Cup4G11:RR42_RS10775 Length = 434 Score = 392 bits (1006), Expect = e-113 Identities = 197/415 (47%), Positives = 263/415 (63%), Gaps = 4/415 (0%) Query: 3 ALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPI 62 A V + LL A AA+A A V++G YLA+ +C ACHT+ G PFAGGLP++T + Sbjct: 10 ATVAFAVLLLAPCFAAAADAPGAAQVERGRYLAKVANCAACHTSVGGAPFAGGLPLKTGV 69 Query: 63 GVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALY 121 G +YSTNITPD +GIG YSFE+FD+A+R GVA+ G LYPAMP+PSYAR+++ D+QALY Sbjct: 70 GTVYSTNITPDVDSGIGAYSFEEFDRALREGVARHGKRLYPAMPYPSYARLAEPDVQALY 129 Query: 122 AYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLV 181 AY V V + + ++ WP MRW L +W W+F S PA A G +RGAYLV Sbjct: 130 AYLRTEVKAVRQATAEPEMRWPFGMRWLLRVWNWLFLESGPVPANA-GQSVEWNRGAYLV 188 Query: 182 EGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQ 241 + + HCGACHTPR + M EK L FL+G A +EGW + +LRGD + GLG+WS E Sbjct: 189 QAVAHCGACHTPRGMLMAEKGLDERS-RHFLAG-ASVEGWASTNLRGDPRTGLGTWSRED 246 Query: 242 LVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQ 301 + ++L TGR+ + FG MS+V+ S Q+MT DL A+A YLKS+P + P+ YD Sbjct: 247 IAEYLHTGRNAHATSFGPMSEVIASSTQFMTRPDLDAVAVYLKSVPGARSDETPYAYDAH 306 Query: 302 VAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLK 361 A AL G GA Y + C CH +G G+ RVFP LAGNP + D +SL +++L Sbjct: 307 TADALAQGRFDATGARQYAEFCMPCHGANGKGFARVFPPLAGNPTVVDPDPSSLANLLLD 366 Query: 362 GGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 G +A + + MP + W L +QE+A+V+ FIR+ WGNQAS VK VAA R Sbjct: 367 GAVTAHVGTAATDYHMPGYGWTLDNQELANVLTFIRTGWGNQASQVKEATVAARR 421 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: 549 Number of extensions: 32 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: 434 Length adjustment: 32 Effective length of query: 402 Effective length of database: 402 Effective search space: 161604 Effective search space used: 161604 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