Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041099057.1 SUTH_RS10320 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000828635.1:WP_041099057.1 Length = 274 Score = 198 bits (504), Expect = 9e-56 Identities = 107/260 (41%), Positives = 159/260 (61%), Gaps = 3/260 (1%) Query: 1 MTEKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYT 60 MT +N + L++ ++ FGG++AL+ V + G + +IGPNGAGKT+ FN I+G Y Sbjct: 1 MTAAANPI-LEIDQVTLAFGGVKALNGVSFEVAPGSITSVIGPNGAGKTSLFNTISGFYR 59 Query: 61 PDAGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGA 120 P AG G+ + AK G+AR+FQNI LF MT L+N+ +GRH +G+ A Sbjct: 60 PTAGHIRFLGEDITQRPAPQRAKLGLARSFQNIALFRGMTVLDNIKLGRHCHLHTGVLDA 119 Query: 121 VFRTKGFKAEEAAIAKRAQE-LLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLI 179 +F + EE + +E ++D++ I + LSYG Q+R+E+ARALA P+++ Sbjct: 120 LFYYGKARREEVRLRADIEERIIDFLEIDHIRNAPVAALSYGLQKRVEMARALAMQPKVL 179 Query: 180 ALDEPAAGMNATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAE 238 LDEP AGMN E + I +R + TIL++EHD+ +VM + D V VL++G+ IA+ Sbjct: 180 MLDEPVAGMNREETEDMARFILDVREEWGVTILMVEHDMGMVMDISDHVVVLNFGEVIAD 239 Query: 239 GNPAEVQKNEKVIEAYLGTG 258 G PA VQ N +VI AYLG+G Sbjct: 240 GTPAAVQGNPEVIRAYLGSG 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: 194 Number of extensions: 11 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: 260 Length of database: 274 Length adjustment: 25 Effective length of query: 235 Effective length of database: 249 Effective search space: 58515 Effective search space used: 58515 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