Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate GFF4128 PS417_21145 oxidoreductase
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >FitnessBrowser__WCS417:GFF4128 Length = 248 Score = 117 bits (294), Expect = 2e-31 Identities = 92/252 (36%), Positives = 125/252 (49%), Gaps = 16/252 (6%) Query: 15 SLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEA-SEALCNEVAAAGHPKPLFR 73 +L GK I GG GIGAAIV+ A QGA VAF +++ A +E L N V + G K L Sbjct: 5 NLSGKVALIQGGSRGIGAAIVKRLAAQGAAVAFTYVSSVAKAEELQNSVISEG-GKALAI 63 Query: 74 HCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRPSFF 133 H D D A + + G D+LVNNA LE+ LE ++ +AIN R F Sbjct: 64 HADSADAGAIRNAVNATVEAFGRLDILVNNAGVLAIAPLEDFKLEDFDQTLAINVRSVFI 123 Query: 134 AVQSVVEGMKRRGGGSIINFSSISWHQS--GGGFPVYTTAKASTLGLTRGLARDLGPHKI 191 A Q + M GG +IN S + + GGG P Y +KA+ +GLT+GLARDLGP I Sbjct: 124 ATQEAAKHM--ADGGRVINIGSTNAERMPFGGGGP-YAMSKAALVGLTKGLARDLGPRGI 180 Query: 192 RVNTVTPGWVMTERQIKLWLDEE---GKKAIARNQCLQGDLLPWHLARMVLFLAADDSAM 248 +N V PG V T+ E G A+ R ++ +A V +LA ++ Sbjct: 181 TINNVQPGPVDTDMNPANSDFAESLIGLMAVGRYGHVE------EIASFVAYLAGPEAGY 234 Query: 249 CTAQEFIVDAGW 260 T +D G+ Sbjct: 235 ITGASLTIDGGF 246 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: 123 Number of extensions: 6 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: 248 Length adjustment: 24 Effective length of query: 237 Effective length of database: 224 Effective search space: 53088 Effective search space used: 53088 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