Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate PfGW456L13_3925 Putative diheme cytochrome c-553
Query= metacyc::MONOMER-12746 (434 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3925 Length = 412 Score = 241 bits (614), Expect = 4e-68 Identities = 154/418 (36%), Positives = 216/418 (51%), Gaps = 24/418 (5%) Query: 4 LVIATLAL-LGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPI 62 L+++ LAL +G AA A A V+QGEYLARA DC+ACHTA G P+AGGLP+ +P Sbjct: 3 LLLSRLALAVGLAAPVVAAHADDAQVKQGEYLARAADCMACHTAPGGAPYAGGLPIVSPF 62 Query: 63 GVIYSTNITPDKT-GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALY 121 G IY TNITP K GIG Y+ ++F A+ G + G+ LYPAMP+ SY + AD A++ Sbjct: 63 GTIYGTNITPSKEHGIGLYNDDEFFAALTEGKRRDGANLYPAMPYTSYHLIPRADSDAIH 122 Query: 122 AYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRGAYLV 181 AY +K V P+ R + + +P ++R L W M+ V+ PA G RG Y+V Sbjct: 123 AY-LKTVEPIERAAPVTSLSFPFNVRLGLMGWNMMYGKDVKL-EPAEGKSEAWKRGQYMV 180 Query: 182 EGLGHCGACHTPRAL--TMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSE 239 + LGHCG CHTPR L MQ G L G++A SL G W+ Sbjct: 181 DVLGHCGECHTPRGLPGAMQMDKRMTGG---------ILNGYLAPSLLATDLAARG-WNH 230 Query: 240 EQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYD 299 + L FLK G S + +F M V +S Q ++D DL A+A +L DQP Sbjct: 231 QDLSSFLKHGMSAQGTMFNEMFPVFHNSTQGLSDPDLAAMATFLLG-------DQPPAAK 283 Query: 300 KQVAQALWNGDDS-KPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHI 358 V L S + G Y++ CA CH G G + A+ GN L+ D +L+ + Sbjct: 284 VLVEVPLDKLSPSVQRGRQEYLNVCAGCHAPGGEGKPHIAVAMRGNTTLRLEDPRNLVRV 343 Query: 359 VLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416 + G MP F +L+D+++ D++N++R WG Q + + DV LR Sbjct: 344 IDDGIGEQKFSGFEHMQPMPGFVDKLNDEQLTDLLNYLRQGWGGQPNDLAVNDVQKLR 401 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: 560 Number of extensions: 41 Number of successful extensions: 6 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: 412 Length adjustment: 32 Effective length of query: 402 Effective length of database: 380 Effective search space: 152760 Effective search space used: 152760 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: 50 (23.9 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