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_050464418.1 AKL27_RS18990 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_001189915.1:WP_050464418.1 Length = 306 Score = 161 bits (407), Expect = 2e-44 Identities = 97/304 (31%), Positives = 170/304 (55%), Gaps = 17/304 (5%) Query: 4 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYF----------- 52 + Q L +GL LG YAL+ALG+++ + K +NF+HGD G+FIG+ Sbjct: 5 LFQALFSGLALGGAYALVALGFSITFTTTKTLNFSHGDFVSAGSFIGFTAMLLLTGAPLG 64 Query: 53 -LINSFQMNFFVALIVAMLATAI---LGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEY 108 +I+ ++ LI +LA A+ LG+V+ A RP +A +++ IG +L+ Sbjct: 65 SVIDVLAVHGSEQLIAVLLAVAVMGVLGIVLYLSAVRPFAGKPGMAWVMSTIGFGIILQS 124 Query: 109 GMVYLVGANTRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAM 168 + + G P + + + + +L+++ ++L++M++ +++KT +GKAM Sbjct: 125 VGLAIWGPAPVKVPAPLGEDVIRIFGAGVRSQELLLIAVALVIMVVFDWVMRKTMIGKAM 184 Query: 169 RAVSVDSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFV 228 RAV+ D + A LMGINVN + F + S LAG +G L+A S MG+ LK F Sbjct: 185 RAVAHDRNIASLMGINVNAIMLGAFFISSGLAGLSGYLLA-PIASASLFMGLGIALKGFS 243 Query: 229 AAVLGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNV 288 A++GG+ G +GGF++G+LE+ + + +R+ +++G+++L+L RP G+ GK + Sbjct: 244 GAMVGGLTNPRGCVIGGFMMGILESMINLW-QAQWREIVLFGLVILVLAFRPNGLFGKKL 302 Query: 289 KEKV 292 EKV Sbjct: 303 VEKV 306 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: 237 Number of extensions: 16 Number of successful extensions: 5 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: 306 Length adjustment: 27 Effective length of query: 265 Effective length of database: 279 Effective search space: 73935 Effective search space used: 73935 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