Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_018371595.1 BN415_RS07285 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000341525.1:WP_018371595.1 Length = 289 Score = 472 bits (1214), Expect = e-138 Identities = 239/289 (82%), Positives = 270/289 (93%) Query: 4 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFV 63 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAF+GY+LI S MNF++ Sbjct: 1 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFMGYYLIGSLHMNFYL 60 Query: 64 ALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFPQ 123 ALIV+M+ TA LGV+IEFLAYRPLRHSTRIA LITAIGVSF LEY MV +V AN +AFPQ Sbjct: 61 ALIVSMVGTAALGVLIEFLAYRPLRHSTRIAALITAIGVSFFLEYSMVAVVSANVKAFPQ 120 Query: 124 AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGI 183 + +VR+ LGP+S+T++QL IL ++LILM+LLQ+IVQKTKMGKAMRAVSVDSDAAQLMGI Sbjct: 121 VLPSVRFVLGPVSVTSIQLTILAVALILMVLLQLIVQKTKMGKAMRAVSVDSDAAQLMGI 180 Query: 184 NVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAAL 243 NVN+TISFTFALGSALAGAAGVLIALYYNSL+PLMG+TPGLKSFVAAV+GGIGIIPGAAL Sbjct: 181 NVNQTISFTFALGSALAGAAGVLIALYYNSLDPLMGMTPGLKSFVAAVIGGIGIIPGAAL 240 Query: 244 GGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 GGFVIG+LETFAT +S++RDAIVYGIL+LIL++RPAGILGKNVKEKV Sbjct: 241 GGFVIGILETFATVINLSEYRDAIVYGILILILLIRPAGILGKNVKEKV 289 Lambda K H 0.330 0.146 0.407 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: 354 Number of extensions: 17 Number of successful extensions: 1 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: 292 Length of database: 289 Length adjustment: 26 Effective length of query: 266 Effective length of database: 263 Effective search space: 69958 Effective search space used: 69958 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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