Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate AO353_10800 AO353_10800 alcohol dehydrogenase
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10800 Length = 435 Score = 469 bits (1206), Expect = e-136 Identities = 232/413 (56%), Positives = 293/413 (70%), Gaps = 3/413 (0%) Query: 15 VGLLAGTSLAHAQNADEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYST 74 + LL S++ A++A + LIK+GEY+AR GDCVACHT+ G+ +AGGL ++TPIGTIYST Sbjct: 9 LALLGSCSISAAEDASQALIKQGEYLARAGDCVACHTAKGGKPFAGGLPMETPIGTIYST 68 Query: 75 NITPDPTYGIGTYTFKEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHG 134 NITPD T G+G Y+F +FD+AVRHGV K+G+TLYPAMPYPS+AR++ DMKALYAYFM G Sbjct: 69 NITPDKT-GLGDYSFDDFDKAVRHGVAKNGSTLYPAMPYPSYARVSDADMKALYAYFMKG 127 Query: 135 AQPIAQKNHPTDISWPMSMRWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHC 194 P+ Q+N +DI WP+SMRWPL+ WR +FAP+ + PA G +A I+RG YLV G GHC Sbjct: 128 VAPVTQENKGSDIPWPLSMRWPLTGWRWMFAPSVVAYQPADGKEAAISRGAYLVEGLGHC 187 Query: 195 GACHTPRGFGMQEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLK 254 GACHTPR MQEKAL A+ G FL G ++ WIA SLR D GLG WS+E L FLK Sbjct: 188 GACHTPRALTMQEKALSANEGSAFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLK 247 Query: 255 SGRTDHSAAFGGMADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQMLD 314 +GR+D SA FGGM+DVV S QY +D DL A+ +Y+KSLP P + YD AQ L Sbjct: 248 TGRSDRSAVFGGMSDVVEHSMQYMSDDDLTAIARYLKSLPANDPNDQPHPYDPQVAQALW 307 Query: 315 SNNISGNAGAKTYVDQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLP 374 + S GA Y+D CA CHR DG G R+FP LAGNPV+ SD+P S+ +IV+ G LP Sbjct: 308 KGDDS-KPGASVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSDDPVSLINIVLKGATLP 366 Query: 375 PTNWAPSAVAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLRLD 427 T+ APS MP + LSDQ++ADVVNFIR++WGN+ A AD+ +R D Sbjct: 367 ATHTAPSTFTMPAFAWRLSDQEVADVVNFIRTSWGNKG-AQIKPADVADVRKD 418 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: 750 Number of extensions: 43 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: 435 Length adjustment: 33 Effective length of query: 439 Effective length of database: 402 Effective search space: 176478 Effective search space used: 176478 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