Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_083988482.1 BBI00_RS11725 LPS export ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_001684965.1:WP_083988482.1 Length = 353 Score = 117 bits (292), Expect = 4e-31 Identities = 70/224 (31%), Positives = 117/224 (52%), Gaps = 4/224 (1%) Query: 21 YGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPT 80 YG + + GV V V +GEIV L+G NGAGK+T I G + +G + + ++IT Sbjct: 12 YGPKKVVKGVSVQVQQGEIVGLLGPNGAGKTTSFYMIVGLVKPTSGKIFLDKQEITTDAM 71 Query: 81 HEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFPRLKERHAQ- 139 + A+ I + +F +++V EN+ L L + + K L +H + Sbjct: 72 YRRAQKGIGYLAQEASVFRKLSVEENIMGVLQLTKLSKREQQI-KCDELIEEFSLQHVRK 130 Query: 140 -RGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEGLTVF 198 RG LSGGE++ I R L P +LLDEP G+ P+ V+ I + +R L + + + + Sbjct: 131 NRGDLLSGGERRRTEIARCLATSPNFILLDEPFAGVDPIAVEDIQKIVRSLVD-KNIGIL 189 Query: 199 LVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 + + N L ++++ Y+M GK+ G ++L +P+VR AYL Sbjct: 190 ITDHNVQQTLAITNKTYIMFEGKILKEGLPEDLANDPQVREAYL 233 Lambda K H 0.320 0.137 0.387 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: 204 Number of extensions: 10 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: 247 Length of database: 353 Length adjustment: 26 Effective length of query: 221 Effective length of database: 327 Effective search space: 72267 Effective search space used: 72267 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 (21.8 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