Align ABC transporter for D-glucosamine, permease component 1 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21715 (220 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 132 bits (333), Expect = 5e-36 Identities = 76/221 (34%), Positives = 122/221 (55%), Gaps = 14/221 (6%) Query: 14 FDTLLAGLGLGLELALVSIAIGCVIGLLMAFALLSKHRALRVLASVYVTVIRNTPILVLI 73 F + G+G+ + +A+VS + ++G+ A LSK+ LR LA+ YV ++R P+LV + Sbjct: 53 FKYVWVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIPLLVQL 112 Query: 74 LLIYFALP----SLGIRLDKLPSF----------IITLSLYAGAYLTEVFRGGLLSIPKG 119 + YFA P S+G L+ P I ++ GAY++E++R G+ SIPKG Sbjct: 113 IWWYFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKG 172 Query: 120 LREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARK 179 EA ++G+ Q YV +P LR VLP + N FI+L KDTSL + +AV ++ R+ Sbjct: 173 QMEAARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMVRLGRE 232 Query: 180 INVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRLAIRR 220 ++ IE W + LY+ L + L+ Y+E++ A R Sbjct: 233 FTATNFNPIEVWTMIGLLYLILTLLSSRLINYIEKKTAFSR 273 Lambda K H 0.329 0.143 0.416 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: 162 Number of extensions: 8 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: 220 Length of database: 273 Length adjustment: 24 Effective length of query: 196 Effective length of database: 249 Effective search space: 48804 Effective search space used: 48804 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: 46 (22.3 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