Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate WP_092482462.1 BM299_RS05460 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >NCBI__GCF_900115975.1:WP_092482462.1 Length = 285 Score = 132 bits (333), Expect = 6e-36 Identities = 73/224 (32%), Positives = 123/224 (54%), Gaps = 6/224 (2%) Query: 27 LKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKVECEVVTSDWDGIIPALNAKKFD 86 + +G++ + P +D +GQ+VGFD D+G ++ V+ E + +DW G+ ALN+KKFD Sbjct: 54 MTIGLDDTFRPMGFRDENGQLVGFDIDMGKEFEKRLGVKMEWIPTDWSGVTGALNSKKFD 113 Query: 87 FLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFKTDKDSLKGKVIGAQRAT----L 142 +I+ +SITEERK+ +DF+ PY + + K +D LKGK + Q + Sbjct: 114 VVINGMSITEERKKVIDFSIPYVNASIGMAVQKDNNDIKTRDDLKGKTVATQAGSSGYEA 173 Query: 143 AGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILADKYVNYDWLKTEAGRAYEFKGD 202 +ED + + K Y+ A+ DL GRVD ++ D D++ Y+ + Sbjct: 174 CKKLVEDGIIDETNLKQYNQYPEAFQDLAFGRVDVVVVDVTTAQDFVNKRPD-TYKVVEE 232 Query: 203 PVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKINDKYF 246 P+VE D I +RK D +L+ L+ L+E++ DGT +I+ ++F Sbjct: 233 PLVE-DFYAIGLRKEDKDLKEVLDKTLREMMEDGTLVEISKRWF 275 Lambda K H 0.316 0.133 0.381 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: 182 Number of extensions: 4 Number of successful extensions: 3 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: 251 Length of database: 285 Length adjustment: 25 Effective length of query: 226 Effective length of database: 260 Effective search space: 58760 Effective search space used: 58760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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