Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate GFF2557 PS417_13035 aldehyde dehydrogenase
Query= BRENDA::C7G3B8 (472 letters) >FitnessBrowser__WCS417:GFF2557 Length = 1175 Score = 223 bits (568), Expect = 3e-62 Identities = 135/386 (34%), Positives = 206/386 (53%), Gaps = 32/386 (8%) Query: 34 IKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFD 93 +++G +A +GDC CHT+ G AGGL+++TP GT+YS+NITPD GIG +++ F+ Sbjct: 797 LERGRLLAAVGDCAVCHTAPGGATNAGGLAMQTPFGTLYSSNITPDVKTGIGAWSYPAFE 856 Query: 94 EAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQPIAQKNHPTDISWPMSM 153 A+R G+ +DG LYPA PY +F + + DM+ALYAY M P++Q P + +P ++ Sbjct: 857 RAMRDGIGRDGRNLYPAFPYTAFRNINEADMQALYAYLM-SQVPVSQAPTPNAMRFPFNI 915 Query: 154 RWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDAS 213 R ++ W ++ + +P P + RG YLV G GHC ACH+PR EK Sbjct: 916 RPLMAGWNALNL-RRGEISPQPERSEQWNRGNYLVNGLGHCAACHSPRNLMGAEK----- 969 Query: 214 GGPDFLGGGGVIDNWIAPSLRNDPVLGLGR----WSDEDLFLFLKSGRTD-HSAAFGGMA 268 GG FL GG +D W AP+L GL + W+++ LF +L +G +D H A G M Sbjct: 970 GGKSFL-AGGTVDGWEAPALN-----GLSKASTPWTEDQLFTYLSTGYSDAHGVAAGPMG 1023 Query: 269 DVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQMLDSNNISGNAGAKTYV 328 VV AD+ AM Y+ SL +GD A+ A + + N+ G + + Sbjct: 1024 PVVS-ELSKLPKADIRAMAVYLASL------KGD---AAAEAPAVTAANVPNPDGRRVFE 1073 Query: 329 DQCAICHRND-GGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPD 387 C CH + G + + P A N V SD P ++ +++ G P T MP Sbjct: 1074 GACKACHADGLGPKLFGVSPSFATNTNVHSDQPDNLIKVILQGISKPATQ---DLGYMPG 1130 Query: 388 YKNILSDQQIADVVNFIRSAWGNRAP 413 +K+ LS+ Q+AD+ ++R+ + AP Sbjct: 1131 FKDSLSNSQVADLAAYLRAQFAPNAP 1156 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: 1562 Number of extensions: 94 Number of successful extensions: 9 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: 1175 Length adjustment: 40 Effective length of query: 432 Effective length of database: 1135 Effective search space: 490320 Effective search space used: 490320 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: 55 (25.8 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