Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate RR42_RS30145 RR42_RS30145 3-oxoacyl-ACP reductase
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >FitnessBrowser__Cup4G11:RR42_RS30145 Length = 255 Score = 213 bits (543), Expect = 2e-60 Identities = 115/250 (46%), Positives = 148/250 (59%), Gaps = 1/250 (0%) Query: 11 ASFPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKP 70 A +PSLK K V ITGGG GIGA +V AFA+QGAHV F+D+ + L + + A G Sbjct: 4 AIYPSLKEKSVVITGGGGGIGAEMVGAFARQGAHVHFIDVCEVGARQLQDALTAEGL-HT 62 Query: 71 LFRHCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRP 130 +F CDLRDI A A + G VLVNNA D RH+++ VT W + IA+N R Sbjct: 63 VFHPCDLRDIGATTAVFDRIAQACGPIGVLVNNAGRDDRHQVDAVTPSDWEECIAVNLRH 122 Query: 131 SFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHK 190 FF Q GM+ G I+N S SWH + +Y TAKA GLTRGLARDLG Sbjct: 123 QFFCAQLAAAGMRTARTGVILNLGSASWHVAVPDLSIYMTAKAGIEGLTRGLARDLGRDG 182 Query: 191 IRVNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMCT 250 IRVN + PG V T RQ LW + + + ++QCL + P H+A M LFLA+DD+ C+ Sbjct: 183 IRVNCIVPGAVRTPRQTLLWQTAQSEARLLQSQCLPARIEPRHVAAMALFLASDDAERCS 242 Query: 251 AQEFIVDAGW 260 +E+ VDAG+ Sbjct: 243 GREYFVDAGY 252 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: 155 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: 255 Length adjustment: 24 Effective length of query: 237 Effective length of database: 231 Effective search space: 54747 Effective search space used: 54747 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