Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013525179.1 MESCI_RS31065 ABC transporter ATP-binding protein
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000185905.1:WP_013525179.1 Length = 254 Score = 240 bits (613), Expect = 2e-68 Identities = 123/250 (49%), Positives = 168/250 (67%), Gaps = 1/250 (0%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L+V + FGGL+ L D+ ++++G + LIGPNGAGKT+ FN +TG Y P G+ L Sbjct: 3 LLEVRDLRLSFGGLKVLHDISFSVEKGAINSLIGPNGAGKTSLFNCLTGFYKPKGGSISL 62 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 +G+P H + G+ARTFQNIRLF EM+ LEN M G+H R+ G+ A+ + Sbjct: 63 SGRPITGLPPHRITALGLARTFQNIRLFKEMSVLENAMSGQHCRSRHGIVSAILHLPAQR 122 Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188 EE AI L +VGI + A +A LSYGDQRRLE+ARALA+ P+LI LDEPAAG+ Sbjct: 123 REEEAIRAIGMRWLGFVGIEQHAHRRAGGLSYGDQRRLELARALASAPELILLDEPAAGL 182 Query: 189 NATEKVQLRELIDRIRNDNR-TILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKN 247 N EK+ L LI RIR++ T+LLIEHD+ LVM + +++ V DYG++IA+G P V+ + Sbjct: 183 NEREKLDLIHLIRRIRDETGVTVLLIEHDMGLVMQVSEKIVVFDYGQKIADGAPEAVRAD 242 Query: 248 EKVIEAYLGT 257 +VIEAYLGT Sbjct: 243 PRVIEAYLGT 252 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: 198 Number of extensions: 9 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: 254 Length adjustment: 24 Effective length of query: 236 Effective length of database: 230 Effective search space: 54280 Effective search space used: 54280 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