Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011320405.1 AVA_RS18775 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000204075.1:WP_011320405.1 Length = 260 Score = 196 bits (498), Expect = 4e-55 Identities = 103/252 (40%), Positives = 158/252 (62%), Gaps = 7/252 (2%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L +G+ K FGG++A+ + I + +G + GLIGPNGAGKTT FN+++ PD G Sbjct: 11 LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 G+P + H++A+ G+ RTFQ R ++++ LEN+++ +TG + + + Sbjct: 71 DGEPIQQLQPHQIAQQGMVRTFQVARTLSKLSVLENMLLAAQKQTGENFWQVQLQPQVVA 130 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 EE + ++A LL+ VG+ K A A LS G ++ LE+ RAL T+P+LI LDEPAAG+ Sbjct: 131 KEEKQLQEQAMFLLESVGLAKKAYDYAGCLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190 Query: 189 NATEKVQLRELIDRI----RNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244 N + ++ DRI R D T L+IEH++ ++M LCDRV VL G+ +A+G PAE+ Sbjct: 191 NPR---LIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEI 247 Query: 245 QKNEKVIEAYLG 256 Q N +V+EAYLG Sbjct: 248 QTNSQVLEAYLG 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: 174 Number of extensions: 5 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: 260 Length adjustment: 24 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 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