Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041097906.1 SUTH_RS06105 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000828635.1:WP_041097906.1 Length = 593 Score = 212 bits (540), Expect = 1e-59 Identities = 112/248 (45%), Positives = 156/248 (62%), Gaps = 2/248 (0%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 VL V ++KRFGGL A + + +T++ G+V LIGPNGAGK+T FN I+G+ G Sbjct: 344 VLLVRNVTKRFGGLVANNAMNLTVRAGEVMALIGPNGAGKSTLFNCISGVSPASEGEIHF 403 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 + + A E+AK GI+RTFQ++RL +MT LEN +G H+R + +R + Sbjct: 404 MDQRIDALASREIAKLGISRTFQHVRLNQDMTVLENAAIGAHLRGRKNFVQSAWRLD--R 461 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 EE + A L G+G+ A +L G QR +EIARAL +DP L+ LDEPAAG+ Sbjct: 462 EEERRLLWEAAHQLQRCGLGEHLFDAAGSLPLGKQRIVEIARALCSDPTLLLLDEPAAGL 521 Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248 EK L EL+D++R + ILL+EHD+ VMGL DRV V+++G+ +AEG P E+Q N Sbjct: 522 RHLEKRALAELLDKLRGEGMAILLVEHDMDFVMGLADRVVVMEFGEHLAEGLPQEIQANP 581 Query: 249 KVIEAYLG 256 KV+EAYLG Sbjct: 582 KVLEAYLG 589 Lambda K H 0.319 0.137 0.384 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: 370 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: 260 Length of database: 593 Length adjustment: 30 Effective length of query: 230 Effective length of database: 563 Effective search space: 129490 Effective search space used: 129490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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