Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate WP_086511669.1 BZY95_RS20105 sugar ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_793 (298 letters) >NCBI__GCF_002151265.1:WP_086511669.1 Length = 294 Score = 390 bits (1002), Expect = e-113 Identities = 185/276 (67%), Positives = 225/276 (81%) Query: 6 KPVNQKAWFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRVFVGTEWFAAVMRDEEL 65 K N +AWFLILP+++ VAFSAI+PLMTVVNYSVQD+ R F GTEWF ++ D L Sbjct: 3 KVYNNRAWFLILPMLMLVAFSAIIPLMTVVNYSVQDVFDANTRFFTGTEWFEVMLNDPAL 62 Query: 66 HAALWRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQI 125 AAL RQ FS +LA+E+PLGI +AL MP +GW++SAVL+++ L LLIPWNVVG+IWQ+ Sbjct: 63 QAALLRQFAFSFTILAIEVPLGIGIALLMPKRGWQASAVLILITLPLLIPWNVVGSIWQL 122 Query: 126 YGRADIGLMGRMLQEMGIEYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAY 185 + R DIGLMG ++E+G Y+ T N AW T++LMDVWHWTPL+ALL ++GLRSIPDAY Sbjct: 123 FTRGDIGLMGVGIRELGYAYNITRNPADAWATIILMDVWHWTPLIALLCYSGLRSIPDAY 182 Query: 186 YQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFL 245 YQAARID ASK+AVFRYIQLPK+ VL+I VLLRFM SFMIY EPFVLTGGGPG++TTFL Sbjct: 183 YQAARIDRASKWAVFRYIQLPKLTNVLVIGVLLRFMHSFMIYAEPFVLTGGGPGSSTTFL 242 Query: 246 SQYLTTKAVGQFDLGPAAAFSLIYFFIILLLCFILY 281 SQ LTT A+GQ DLGP+AAFSLIYF IILL+C++ Y Sbjct: 243 SQSLTTMAIGQQDLGPSAAFSLIYFLIILLVCWVFY 278 Lambda K H 0.328 0.140 0.439 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: 314 Number of extensions: 7 Number of successful extensions: 1 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: 298 Length of database: 294 Length adjustment: 26 Effective length of query: 272 Effective length of database: 268 Effective search space: 72896 Effective search space used: 72896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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