Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF3404 PS417_17420 alcohol dehydrogenase
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__WCS417:GFF3404 Length = 387 Score = 193 bits (490), Expect = 8e-54 Identities = 122/386 (31%), Positives = 199/386 (51%), Gaps = 6/386 (1%) Query: 1 MSVARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGY 60 +S+ R P G G + K GA+ +LV++DP ++ G V V + L+ G Sbjct: 5 LSLLRKFVSPEIIFGAGCRHNVGNYAKTFGARKVLVVSDPGVIAAGWVADVEASLQAIGI 64 Query: 61 SVHVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADY 120 +Y+ V P P +E R+ D+++ +GGGS +D K ++ H + ++ Sbjct: 65 DYCLYSAVSPNPRVEEVMLGAEVYRENHCDVIVAIGGGSPMDCGKAIGIVVAHGRCILEF 124 Query: 121 LNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDP 178 G T+ P ILIPTT+GT ++V+ ++S E K + ++ DV+++DP Sbjct: 125 ---EGVDTIRVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLIDP 181 Query: 179 QLTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDK 238 + T S+ P ++A TGIDAL HA+EA+VS P +D A+ A+RLI+ +L + +AN D Sbjct: 182 ETTASMDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPGDI 241 Query: 239 QARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCT 298 R + GS AGLAF NA + VHA+++ LGG + HG NAVL+ +V+ + S Sbjct: 242 ALREKIMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAP 301 Query: 299 KRMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDA 358 +R I G + LS + R VE L +G +TLG G+ + + L++ A Sbjct: 302 ERFKVIAETFGIDCRGLSHRQVCARLVEHLIALKHAIGFHETLGLHGVRVADIPFLSRHA 361 Query: 359 VQQKRLLARSPLPLLEADIRAIYEAA 384 + +L +P + D+ +Y A Sbjct: 362 MHDPCILT-NPRESSQRDVEVVYGEA 386 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: 408 Number of extensions: 16 Number of successful extensions: 3 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