Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_047094222.1 AAV99_RS11820 SDR family oxidoreductase
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >NCBI__GCF_001013305.1:WP_047094222.1 Length = 261 Score = 249 bits (637), Expect = 3e-71 Identities = 126/250 (50%), Positives = 163/250 (65%), Gaps = 2/250 (0%) Query: 11 ASFPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKP 70 A +PSL KRV I+GGG+GIGA IVE F +QGA VAFVD+ ASEALC +A A H +P Sbjct: 13 AVYPSLLDKRVIISGGGSGIGAGIVEGFVRQGARVAFVDVQDAASEALCARLADAAH-QP 71 Query: 71 LFRHCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRP 130 ++RHCD+ D + I+ L +LG DV++NNA ND RH + +VT EYW+ R+A+N + Sbjct: 72 VYRHCDITDTDGYSRCISSLVDRLGGCDVIINNAGNDDRHAIADVTSEYWDQRMAVNLKH 131 Query: 131 SFFAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHK 190 FFA ++V M+ GGG+IIN SISWH VY TAKA+ GLTR LAR+LGP Sbjct: 132 HFFAAKTVAPAMRNAGGGAIINLGSISWHLGLENLTVYQTAKAAIEGLTRSLARELGPDN 191 Query: 191 IRVNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMCT 250 IRVN + PG V T RQ + W E + I QCL G + P +A M +FLA+DD+ C+ Sbjct: 192 IRVNAILPGNVQTPRQ-QEWYTPEQEDEIVEAQCLPGRIQPADIAAMAMFLASDDARFCS 250 Query: 251 AQEFIVDAGW 260 + VDAGW Sbjct: 251 GHNYWVDAGW 260 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: 172 Number of extensions: 6 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: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 24 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