Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate AO356_30205 AO356_30205 alcohol dehydrogenase
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30205 Length = 444 Score = 398 bits (1023), Expect = e-115 Identities = 211/410 (51%), Positives = 269/410 (65%), Gaps = 8/410 (1%) Query: 17 ANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPDK-T 75 A+A AD Q LVQ+GEY+AR DCVACH+ G PFAGGL M TP+G IY+TNITPDK T Sbjct: 35 ASAPSADAQ-LVQRGEYVARLSDCVACHSTPKGAPFAGGLEMATPMGSIYATNITPDKQT 93 Query: 76 GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVARDN 135 GIG+YS DFD+AVR GVA G LYPAMP+PSYA++SD D++ALYA+FM GV P + N Sbjct: 94 GIGNYSLADFDRAVRSGVAADGHRLYPAMPYPSYAKLSDDDVRALYAFFMAGVKPAQQQN 153 Query: 136 QDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHTPRA 195 Q S IPWPL+MRWPL++W F A + D + +RGAY+V+G GHCG+CHTPR+ Sbjct: 154 QQSHIPWPLNMRWPLALWNTAFVDDGAYQAKPS-EDALWNRGAYIVQGAGHCGSCHTPRS 212 Query: 196 LTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRSDRSA 255 LTM EK+L S + FLSGS L+GW A SLR D GLG WSE+++V +LKTGR+ S Sbjct: 213 LTMNEKSLDESSAT-FLSGSL-LDGWYAPSLRQDPNTGLGRWSEQEIVDYLKTGRNAHSV 270 Query: 256 VFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDDSKPG 315 V G M++V +S QYM+D DL AIA YL SLP + +D P + A L S PG Sbjct: 271 VVGTMAEVFNNSTQYMSDPDLKAIAHYLVSLPGDPKRDGP---PWKPAAKLAEQPLSTPG 327 Query: 316 AAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSAPSTF 375 AA Y+ C++CH +DG G P LAG + + I+ L G + P ++ Sbjct: 328 AANYMAKCSSCHGSDGSGQAPWIPPLAGASSSMVKEGATSINATLNGSERVVANGIPDSY 387 Query: 376 TMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALRNGDLQSTSN 425 MP + +LSDQEVADV+ F+R+SWGNQ AVK +V LR ++SN Sbjct: 388 RMPPYRNQLSDQEVADVLTFVRTSWGNQGGAVKADEVKELRERTNPASSN 437 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: 615 Number of extensions: 31 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: 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