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_011842825.1 RSPH17029_RS20325 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000015985.1:WP_011842825.1 Length = 295 Score = 159 bits (402), Expect = 7e-44 Identities = 97/282 (34%), Positives = 162/282 (57%), Gaps = 3/282 (1%) Query: 7 QLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVALI 66 QL+ GLI GS YALL+LG +++G++++INFAHG YM GAF L+ + ++ ALI Sbjct: 15 QLLVGLINGSFYALLSLGLAVIFGLLRVINFAHGAQYMAGAFAALLLLTQTGIGYWPALI 74 Query: 67 VAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAF-PQAI 125 +A L + G +IE L + L+ G++ LE + G + + + P A Sbjct: 75 LAPLIVGLGGALIERTMLSRLYKLDPLYGLLFTFGLALTLEGTFRWFFGTSGQPYSPPAA 134 Query: 126 QTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGINV 185 T +LG + L + ++ SL + + + ++++KTK+G +RA + + Q G+NV Sbjct: 135 LTGAVNLGFMFLPIYRGWVVVASLAVCVGVWLLIEKTKLGAYLRAATENPVLVQSFGVNV 194 Query: 186 NRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAALGG 245 ++FT+ LG+ALAG AGVL A Y + PLMG + F V+GG+G I GA + G Sbjct: 195 PLLLTFTYGLGAALAGFAGVLAAPVY-QVSPLMGSNLIIVVFAVVVVGGMGSILGAIVTG 253 Query: 246 FVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKN 287 +++G+ E F + + +++ I+ ++LI+RPAG+ GK+ Sbjct: 254 YLLGIAEGLTKVF-YPEASNIVIFVIMAIVLILRPAGLFGKD 294 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: 224 Number of extensions: 14 Number of successful extensions: 4 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: 295 Length adjustment: 26 Effective length of query: 266 Effective length of database: 269 Effective search space: 71554 Effective search space used: 71554 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 Apr 10 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