Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate N515DRAFT_0557 N515DRAFT_0557 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >FitnessBrowser__Dyella79:N515DRAFT_0557 Length = 246 Score = 123 bits (309), Expect = 3e-33 Identities = 89/250 (35%), Positives = 129/250 (51%), Gaps = 14/250 (5%) Query: 15 SLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIAT-EASEALCNEVAAAGHPKPLFR 73 SL GK +TGG GIGAAIV A+ GA VAF +++ + ++AL E+ AAG ++ Sbjct: 3 SLDGKVALVTGGSRGIGAAIVRRLARDGATVAFTYVSSPDKAQALVQEIEAAGGKARAYQ 62 Query: 74 HCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRPSFF 133 D D A QA + + A+ G D+LVNNA E+ TLE + +A+N R F Sbjct: 63 -ADAADTAALQAAVDRVAAESGRLDILVNNAGIFLGGAFEDTTLEDFERTMAVNVRAVFV 121 Query: 134 AVQSVVEGMKRRGGGSIINFSS-ISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHKIR 192 A Q+ V M GG I++ S ++ G +Y+ +K++ TRGLARDLGP I Sbjct: 122 ASQAAVRHM--GDGGRIVSIGSCLADRVPSAGMTLYSMSKSALSAFTRGLARDLGPRGIT 179 Query: 193 VNTVTPGWVMTERQIKLWL---DEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMC 249 VN V PG T+ ++ G+ AI R GD ++A MV +LA+++ Sbjct: 180 VNVVQPGSTDTDMNPADGAHAEEQRGRMAIKR----YGDAS--NIAGMVAWLASEEGRFA 233 Query: 250 TAQEFIVDAG 259 F +D G Sbjct: 234 NGAAFTIDGG 243 Lambda K H 0.321 0.134 0.411 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: 111 Number of extensions: 3 Number of successful extensions: 2 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: 261 Length of database: 246 Length adjustment: 24 Effective length of query: 237 Effective length of database: 222 Effective search space: 52614 Effective search space used: 52614 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 46 (22.3 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