Align ABC transporter for Glycerol, permease component 1 (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_793 (298 letters) >NCBI__GCF_000018545.1:WP_015888140.1 Length = 307 Score = 145 bits (365), Expect = 1e-39 Identities = 87/268 (32%), Positives = 146/268 (54%), Gaps = 5/268 (1%) Query: 13 WFLILPVIICVAFSAILPLMTVVNYSVQDIISPERRV---FVGTEWFAAVMRDEELHAAL 69 + ++ P ++ + I P + + Y+ ISP + FVG FA ++ D + H AL Sbjct: 29 YLMLAPTVLILLALTIFPSIYMF-YAAVHRISPNPDLPWEFVGVGNFARLLSDPQFHVAL 87 Query: 70 WRQLTFSLAVLAVEIPLGILLALSMPAQGWKSSAVLVVVALSLLIPWNVVGTIWQIYGRA 129 + F+L +A+E LG+ LAL + + S + V+ + +++P V W++ Sbjct: 88 RNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAITWKLIYEP 147 Query: 130 DIGLMGRMLQEMGIEY-SYTGNATQAWLTVLLMDVWHWTPLVALLAFAGLRSIPDAYYQA 188 G++ ++ +G+ ++ G+ A ++++ DVW WTP V LL AGL S+P Y+A Sbjct: 148 QFGVLNEIMFLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASLPVEPYEA 207 Query: 189 ARIDGASKFAVFRYIQLPKMRGVLMIAVLLRFMDSFMIYTEPFVLTGGGPGNATTFLSQY 248 A +DGAS + F + LP ++ V+ IA+LLR MD+ ++ F+LTGGGP + T LS Y Sbjct: 208 AALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADRTKVLSLY 267 Query: 249 LTTKAVGQFDLGPAAAFSLIYFFIILLL 276 + A D G AAA SL F+ ++L Sbjct: 268 IYQVAYRFADPGYAAAISLFVLFVTIVL 295 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: 241 Number of extensions: 13 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: 298 Length of database: 307 Length adjustment: 27 Effective length of query: 271 Effective length of database: 280 Effective search space: 75880 Effective search space used: 75880 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