Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate PP_3382 PP_3382 gluconate 2-dehydrogenase cytochrome c subunit
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__Putida:PP_3382 Length = 417 Score = 448 bits (1153), Expect = e-130 Identities = 221/413 (53%), Positives = 286/413 (69%), Gaps = 3/413 (0%) Query: 13 VAVGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIY 72 +A +L + A A D+ ++ GEY+AR GDCVACHT+ G+ +AGGL ++TPIGT+Y Sbjct: 8 IATLVLGAGAAAQAVANDDAQVRLGEYLARAGDCVACHTAKGGKPFAGGLPMETPIGTVY 67 Query: 73 STNITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFM 132 STNITP + GIG Y+F++FD+AVR G+ KDG+TLYPAMPYPS+AR+++ DM+ALYAYFM Sbjct: 68 STNITPAAS-GIGQYSFEDFDQAVRRGIGKDGSTLYPAMPYPSYARVSEQDMQALYAYFM 126 Query: 133 HGAQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPG 192 G P+ Q N +DI WP+SMRWPL+IWR VFAP K + + D + RG YLV G G Sbjct: 127 KGVAPVEQANKASDIPWPLSMRWPLAIWRGVFAPEAKPWQASATADPVVNRGAYLVEGLG 186 Query: 193 HCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLF 252 HCGACHTPR MQEKAL A+ G FL G ++ WIA +LR D GLG WS+ L F Sbjct: 187 HCGACHTPRALTMQEKALSAADGEQFLAGSAPLEGWIAKNLRGDHKDGLGSWSEAQLVQF 246 Query: 253 LKSGRTDHSAAFGGMADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQM 312 LK+GR+D SA FGGM+DVV S Q+ +DADL A+ +Y+K+LPP P + YD A Sbjct: 247 LKTGRSDRSAVFGGMSDVVEHSMQHMSDADLTAIARYLKTLPPSNPDDQLHVYDKQVADA 306 Query: 313 LDSNNISGNAGAKTYVDQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGV 372 L + S GA Y+D CA CHR DG G R+FP LAGNPVV + + TS+ H+V+ GG Sbjct: 307 LWKGDDS-KPGAAVYIDNCAACHRTDGQGYTRVFPALAGNPVVQTADATSLIHVVLAGGT 365 Query: 373 LPPTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425 +P T+ APS MP + LSDQ++A+VVNFIRS+WGN+ A TA D++ LR Sbjct: 366 VPATHSAPSNFTMPAFGWRLSDQEVAEVVNFIRSSWGNQGSA-VTAGDVKSLR 417 Lambda K H 0.318 0.135 0.430 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: 681 Number of extensions: 44 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: 472 Length of database: 417 Length adjustment: 32 Effective length of query: 440 Effective length of database: 385 Effective search space: 169400 Effective search space used: 169400 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 (21.7 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