Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate 3610331 Dshi_3712 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >FitnessBrowser__Dino:3610331 Length = 252 Score = 122 bits (305), Expect = 1e-32 Identities = 80/252 (31%), Positives = 131/252 (51%), Gaps = 7/252 (2%) Query: 14 PSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKPLFR 73 P L GK ITG GIGA +A A +GA V DI A + ++A G F Sbjct: 2 PRLDGKVAIITGAAQGIGAVYAQALADEGAKVMIADILDGNPTA--SRISAQGGTAD-FM 58 Query: 74 HCDLRDIPAFQATIAELQAQLGDFDVLVNNAA---NDQRHKLEEVTLEYWNDRIAINQRP 130 D+ D + A + A+ G D+L+NNAA + + E+++ E W+ +A+N + Sbjct: 59 QTDVSDESSVAAMVDATVAKWGGVDILINNAAIWASLRAKPFEDISPEEWDKLMAVNVKG 118 Query: 131 SFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHK 190 F ++VV M+ G I+N +S + ++ F Y T+K + + +TR LAR++G Sbjct: 119 PFLCARAVVPHMRAGKYGRIVNIASGTAYKGTPNFLHYVTSKGAVIAMTRALAREVGEDG 178 Query: 191 IRVNTVTPGWVMTERQI-KLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMC 249 I VNT+ PG V++E+ + L E+ + ++ ++ D LP L +LFL +DD+A Sbjct: 179 ITVNTLAPGLVLSEQVVASPELLEKLSAPVMASRAIKRDQLPQDLVGPLLFLVSDDAAFM 238 Query: 250 TAQEFIVDAGWV 261 T + ++D G V Sbjct: 239 TGEVTVIDGGSV 250 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: 109 Number of extensions: 3 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: 261 Length of database: 252 Length adjustment: 24 Effective length of query: 237 Effective length of database: 228 Effective search space: 54036 Effective search space used: 54036 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: 47 (22.7 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