Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF3897 Psest_3967 Alcohol dehydrogenase, class IV
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__psRCH2:GFF3897 Length = 387 Score = 279 bits (713), Expect = 1e-79 Identities = 161/372 (43%), Positives = 234/372 (62%), Gaps = 4/372 (1%) Query: 17 GALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLET 76 G+ +L K GA+ +LV+TDP + + GL+++V EG +V +Y V+ +PP Sbjct: 17 GSSRRLAGLCKERGARSVLVVTDPGITRFGLLNEVLPGFENEGLAVAIYDQVIADPPEHI 76 Query: 77 GEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPK 136 AV AR + DL+IG GGGS++D+AKL A+LA H ++ G + + LP Sbjct: 77 VMAAVEQARALEADLIIGFGGGSSMDVAKLVALLA-HPSCAQSLQDIYGVGNAKGRRLPL 135 Query: 137 ILIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGID 195 I +PTT+GTGSEVT I++++ ETTK V LL D+A++D LT+ +PP VTAATGID Sbjct: 136 IQVPTTAGTGSEVTQIAIITTGETTKMGVVSPLLLPDLALLDADLTLGLPPAVTAATGID 195 Query: 196 ALTHAVEAYVS-VNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLA 254 A+ HA+EAY S + +P SD LA A+RL++ +L +AV NGS+++AR M G+ LAG A Sbjct: 196 AMVHAIEAYTSALKKNPMSDLLAREALRLLAANLDEAVHNGSNREARQAMLLGACLAGQA 255 Query: 255 FFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNSSF 314 F NA VA VHALAYPLGG FHI HG SNA++LP V+ + + + ++ + G+ Sbjct: 256 FANAPVAAVHALAYPLGGNFHIPHGLSNALVLPQVLRFNVSAASTHYGELAPIILGDRLR 315 Query: 315 LSEVEA-SYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLL 373 + + + +EE E+ A VG+P L G+PE+ L L K+A+ Q+RLL +P + Sbjct: 316 TGDPSTYAGQLIEEFEQMSARVGLPTRLRDAGVPEAMLPQLAKEAMLQQRLLVNNPREVT 375 Query: 374 EADIRAIYEAAF 385 EAD AIY+AA+ Sbjct: 376 EADALAIYQAAY 387 Lambda K H 0.318 0.135 0.381 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: 404 Number of extensions: 26 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: 395 Length of database: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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: 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