Align L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized)
to candidate WP_061534238.1 CAter10_RS16300 3-oxoacyl-ACP reductase FabG
Query= reanno::BFirm:BPHYT_RS28235 (260 letters) >NCBI__GCF_001584165.1:WP_061534238.1 Length = 252 Score = 149 bits (376), Expect = 6e-41 Identities = 96/257 (37%), Positives = 140/257 (54%), Gaps = 20/257 (7%) Query: 2 LLKDKVVIVTGGSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIEALG 61 +L KV + GGSRGIG A+A A +GA VA+ Y +S G R+ ++V +IEA G Sbjct: 9 VLAGKVAFIQGGSRGIGAAVAKRLARDGAAVALTY-----ISSGERAL--QMVKDIEAAG 61 Query: 62 RRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVAVN 121 R +AI+ + A E + + T+ FG++D+L +NAG+ D E + T+A+N Sbjct: 62 GRALAIKADSADAEAIKAAIGQTMTKFGRLDILVNNAGVLAIAPLADFSLEDFDRTLAIN 121 Query: 122 LNGAFYVTQAAAQQMKLQGTGGAIVATSSISA----LVGGGMQTHYTPTKAGVHSLMQSC 177 + F +Q AA+ M G GG I+ S +A GGG Y +K+ + L + Sbjct: 122 VRSVFIASQEAARHM---GGGGRIINIGSTNADRMPFAGGG---PYAMSKSALVGLTRGL 175 Query: 178 AVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLA 237 A LGP GI N+V PG + TD+N A A + +P+GR G E+VA V +LA Sbjct: 176 ARDLGPRGITINNVQPGPVDTDMNP---AGSDFAASLKAMMPVGRYGTAEEVAGFVAYLA 232 Query: 238 SDRARYVTGAALLVDGG 254 S A Y+TGA+L +DGG Sbjct: 233 SPEAAYITGASLSIDGG 249 Lambda K H 0.319 0.134 0.386 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: 178 Number of extensions: 10 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: 260 Length of database: 252 Length adjustment: 24 Effective length of query: 236 Effective length of database: 228 Effective search space: 53808 Effective search space used: 53808 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 (21.8 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