Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate PP_3382 PP_3382 gluconate 2-dehydrogenase cytochrome c subunit
Query= SwissProt::P0A388 (468 letters) >FitnessBrowser__Putida:PP_3382 Length = 417 Score = 465 bits (1196), Expect = e-135 Identities = 232/409 (56%), Positives = 287/409 (70%), Gaps = 3/409 (0%) Query: 16 LLAGTALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNI 75 +L A AQ D A V+ G Y+AR GDCVACHTA G+ +AGGL +++PIGT+YSTNI Sbjct: 12 VLGAGAAAQAVANDDAQVRLGEYLARAGDCVACHTAKGGKPFAGGLPMETPIGTVYSTNI 71 Query: 76 TPDPTYGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVK 135 TP + GIG+Y+F +FD+AVR GI KDGSTLYPAMPYPS++R++++DMQALYAYFM GV Sbjct: 72 TPAAS-GIGQYSFEDFDQAVRRGIGKDGSTLYPAMPYPSYARVSEQDMQALYAYFMKGVA 130 Query: 136 PVAQPDKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGA 195 PV Q +K DI WPLSMRWPL IWR +F+P K + + DP + RG YLV G GHCGA Sbjct: 131 PVEQANKASDIPWPLSMRWPLAIWRGVFAPEAKPWQASATADPVVNRGAYLVEGLGHCGA 190 Query: 196 CHTPRGFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSG 255 CHTPR MQEKAL AA G FL+G AP++ W+A +LR D GLG WSE + FLK+G Sbjct: 191 CHTPRALTMQEKALSAADGEQFLAGSAPLEGWIAKNLRGDHKDGLGSWSEAQLVQFLKTG 250 Query: 256 RIDHSAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASG 315 R D SAVFGGM DVV S Q+ +D DL AIA+YLK+LPP P + YD A+ L G Sbjct: 251 RSDRSAVFGGMSDVVEHSMQHMSDADLTAIARYLKTLPPSNPDDQLHVYDKQVADALWKG 310 Query: 316 NTASVPGADTYVKECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHGGVLPPS 375 + S PGA Y+ CA CHR DG G R+FP LAGNPVV T + TSL++V+ GG +P + Sbjct: 311 DD-SKPGAAVYIDNCAACHRTDGQGYTRVFPALAGNPVVQTADATSLIHVVLAGGTVPAT 369 Query: 376 NWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424 + APS MP + LS Q++A+VVNFIR+SWGN+ VTA DV LR Sbjct: 370 HSAPSNFTMPAFGWRLSDQEVAEVVNFIRSSWGNQG-SAVTAGDVKSLR 417 Lambda K H 0.317 0.134 0.425 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: 674 Number of extensions: 35 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: 468 Length of database: 417 Length adjustment: 32 Effective length of query: 436 Effective length of database: 385 Effective search space: 167860 Effective search space used: 167860 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