Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013090285.1 BC1002_RS34540 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000092885.1:WP_013090285.1 Length = 263 Score = 370 bits (950), Expect = e-107 Identities = 185/251 (73%), Positives = 216/251 (86%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 L V G++KRFGGLQALS+VG+ I+ G++YGLIGPNGAGKTTFFNVITGLYTPD+G F+L Sbjct: 13 LSVKGVNKRFGGLQALSEVGLQIRAGEIYGLIGPNGAGKTTFFNVITGLYTPDSGEFKLD 72 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 G+ Y PTAV++VAKAGIARTFQNIRLF MTALENVMVGRH+RT GL GAVF+T + Sbjct: 73 GENYTPTAVYQVAKAGIARTFQNIRLFGGMTALENVMVGRHVRTKHGLLGAVFQTPAERK 132 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 EE I +RA ELLDYVGI ++ADY +R LSYG QRRLEIARALATDP+L+ALDEPAAGMN Sbjct: 133 EEREIKERALELLDYVGITQYADYTSRNLSYGHQRRLEIARALATDPKLLALDEPAAGMN 192 Query: 190 ATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEK 249 ATEKV+L L+D+IR D +TILLIEHDVKLVMGLC+++TVLDYGK IA+G P +VQK+ K Sbjct: 193 ATEKVELTRLLDKIRADGKTILLIEHDVKLVMGLCNQMTVLDYGKVIAQGLPQDVQKDAK 252 Query: 250 VIEAYLGTGGH 260 VIEAYLG G H Sbjct: 253 VIEAYLGAGVH 263 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: 293 Number of extensions: 3 Number of successful extensions: 1 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: 263 Length adjustment: 25 Effective length of query: 235 Effective length of database: 238 Effective search space: 55930 Effective search space used: 55930 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 2021. 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