Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate WP_011842345.1 RSPH17029_RS17170 sugar ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_793 (298 letters) >NCBI__GCF_000015985.1:WP_011842345.1 Length = 308 Score = 115 bits (288), Expect = 1e-30 Identities = 82/276 (29%), Positives = 134/276 (48%), Gaps = 14/276 (5%) Query: 15 LILPVIICVAFSAILPLMTVVNYSVQDII--SPERRVFVGTEWFAAVMRDEELHAALWRQ 72 L+ P ++ P++ S+ D + P++ +VG + +AA+++DE W Sbjct: 29 LLSPAVLVTLAIVFFPMVQTAWMSLHDYVLFRPKKFDWVGLKHYAAILQDE----VFWIS 84 Query: 73 LTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWN----VVGTIWQIYGR 128 L ++ +A+ +P LL L+ + V ++IPW V+ +W Sbjct: 85 LRHTVLWIAITVPAQALLGLATALLLNQKFPWRPVARALIIIPWALPSVVIALMWAWIYD 144 Query: 129 ADIGLMGRMLQEMGI---EYSYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAY 185 ++ G++ +L +GI + N A ++L W P A++ AGL+SIP +Y Sbjct: 145 SNYGVLNDLLLRVGILEQSIPWLANPGTALYAIILTLTWQGFPFFAVMILAGLQSIPRSY 204 Query: 186 YQAARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFL 245 Y+AA +DGAS F +I LP + GVL A+LLR + FV+TGGGPG AT L Sbjct: 205 YEAASLDGASSLRQFWHITLPGISGVLFTAILLRTIWVANSMDVIFVMTGGGPGYATYTL 264 Query: 246 SQYLTTKAVGQFDLGPAAAFSLIYFFIILLLCFILY 281 Y +A D G +A ++ F ++LL ILY Sbjct: 265 PLYAFLEARTNLDFGYGSALAMT-FTLLLLGIVILY 299 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: 257 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 298 Length of database: 308 Length adjustment: 27 Effective length of query: 271 Effective length of database: 281 Effective search space: 76151 Effective search space used: 76151 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 10 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