Align ABC transporter for D-glucosamine, permease component 2 (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21720 (220 letters) >NCBI__GCF_000186245.1:WP_013554635.1 Length = 384 Score = 70.9 bits (172), Expect = 3e-17 Identities = 37/120 (30%), Positives = 70/120 (58%), Gaps = 1/120 (0%) Query: 91 FQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASKAIGLTFYQALAYVLLPQALRQILP 150 F A + L+++ + +AE +R ++A+P+GQ EA+ ++GL+ Q L V+LPQA+R +P Sbjct: 252 FLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIAIP 311 Query: 151 TWVNSSTEIVKASTLLSVIGVAELL-LSTQQIIARTFMTLEFYLFAGFLFFIINYAIELL 209 + +N ++K S+L + IG EL+ + + +T LE L + +I+ + L+ Sbjct: 312 SIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYLLISLIVSLI 371 Lambda K H 0.330 0.142 0.440 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: 247 Number of extensions: 20 Number of successful extensions: 3 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: 220 Length of database: 384 Length adjustment: 26 Effective length of query: 194 Effective length of database: 358 Effective search space: 69452 Effective search space used: 69452 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 (21.9 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