Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AZOBR_RS32415 AZOBR_RS32415 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >FitnessBrowser__azobra:AZOBR_RS32415 Length = 305 Score = 207 bits (527), Expect = 2e-58 Identities = 105/292 (35%), Positives = 178/292 (60%), Gaps = 11/292 (3%) Query: 5 LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64 LQQ++NGL +G VYAL+A+G+T+++G++ ++NFAHG++Y +GAF+G +I + Sbjct: 8 LQQVINGLSIGCVYALMAIGFTLIFGVLNVVNFAHGEVYTIGAFVGLMVITAMAPPLLAV 67 Query: 65 LIVAMLATAILGVVIEFLAYRPLRHST----------RIAVLITAIGVSFLLEYGMVYLV 114 + + + A+ GV +E +A+RP R T R A L++++ VS + M+++ Sbjct: 68 VPLVLAVGAVSGVGLERIAFRPFRRFTDEASQKSRAMREATLLSSLAVSIMTREIMMHIF 127 Query: 115 GANTRAFPQAIQTVR-YDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSV 173 G + + P + +GPI + + L+I S +++ LQ ++ +T+ G +RAVS Sbjct: 128 GGDMQGIPSGYLLQQPVAIGPIMVASGSLVIFATSAVMLGALQFLLYRTQTGLGIRAVSN 187 Query: 174 DSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLG 233 + A+ +GIN +RTI TFA+GS L AG+L+ LY ++ P MG PG+K+FVA V+G Sbjct: 188 NQLGARYVGINTDRTIVTTFAVGSMLGATAGILVGLYDGAISPHMGFAPGVKAFVAMVMG 247 Query: 234 GIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285 G+ IPGA ++G+ E+ AT F S ++D I Y +L++ L+ P G+ G Sbjct: 248 GLSSIPGAVACALLLGVSESIATEFLSSGWKDLITYSLLVITLVFFPQGLFG 299 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: 226 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: 292 Length of database: 305 Length adjustment: 27 Effective length of query: 265 Effective length of database: 278 Effective search space: 73670 Effective search space used: 73670 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 17 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