Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_082181234.1 A1QA_RS0111365 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000295095.1:WP_082181234.1 Length = 352 Score = 130 bits (327), Expect = 4e-35 Identities = 80/249 (32%), Positives = 130/249 (52%), Gaps = 24/249 (9%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 ++V G+ KR+G L A+ + + I RGQ+ GL+GPNG+GKTT + + L T D G + Sbjct: 35 VEVTGLVKRYGDLTAVDGLSLRIPRGQILGLLGPNGSGKTTTISCLLQLLTYDRGEVRVF 94 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 GK TA + G+ Q + + E+T EN+ F A++ T + Sbjct: 95 GKKMAATAYGLKRRIGLIP--QEVAVIDELTVRENI----------DAFCALYVTDRARR 142 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 E +E + +VG+ +F + + LS G RRL IA +A P+LI LDEP ++ Sbjct: 143 RELV-----EEAIAFVGLERFTKFHPKKLSGGLLRRLNIACGIAHKPELIILDEPTVAVD 197 Query: 190 ATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNEK 249 + + + I R+ D TI+ H ++ V LCDR+ ++D+G+++A G AE Sbjct: 198 PQSRESILQGIRRLNADGATIIYTSHYMEEVEELCDRIVIMDHGREVASGTSAE------ 251 Query: 250 VIEAYLGTG 258 ++A +GTG Sbjct: 252 -LKAMIGTG 259 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: 210 Number of extensions: 11 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: 352 Length adjustment: 27 Effective length of query: 233 Effective length of database: 325 Effective search space: 75725 Effective search space used: 75725 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: 48 (23.1 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