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_092344942.1 BLU87_RS03945 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_900107645.1:WP_092344942.1 Length = 303 Score = 251 bits (641), Expect = 1e-71 Identities = 131/296 (44%), Positives = 200/296 (67%), Gaps = 11/296 (3%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYF----LINS 56 M+ ++Q ++N + GS YAL+ALGYT+VYG+++LINFAHGDI+M+GA+I +F LI+ Sbjct: 1 MDFIIQNILNAMQWGSFYALIALGYTLVYGVLRLINFAHGDIFMVGAYISFFVASFLISP 60 Query: 57 FQ-----MNFFVALIVAMLATAILGVVIEFLAYRPLRH--STRIAVLITAIGVSFLLEYG 109 F M F + + + ML T+++GV +E +AYRPLR + R+ V+ITA+ +LEY Sbjct: 61 FTGLSPAMAFIITVPLTMLLTSLVGVTLERIAYRPLRRKGAHRLYVVITALMCGLILEYS 120 Query: 110 MVYLVGANTRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMR 169 + L+GA+ FP+ I+ + G ++LTN+++M++ ++++ + LQ +V +T++G AMR Sbjct: 121 NLALLGASRLKFPELIEKQVWRFGDVTLTNLKVMVIVTAVLVFLFLQWVVTRTRVGMAMR 180 Query: 170 AVSVDSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVA 229 A+S D A LMGI ++R I TF LGS AG AG+L A+ Y LEP MG+ G K+F+A Sbjct: 181 AISYDKFAIPLMGIPIDRIIVVTFVLGSGFAGLAGLLFAMSYPVLEPFMGMLIGWKAFIA 240 Query: 230 AVLGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285 AV+GGIG I GA +GGF++G +E S +RD + ILLLIL ++P G+ G Sbjct: 241 AVVGGIGDIKGAFVGGFLLGFIEVGVVTVFPSTYRDLFAFTILLLILWIKPTGLFG 296 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: 253 Number of extensions: 13 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: 292 Length of database: 303 Length adjustment: 26 Effective length of query: 266 Effective length of database: 277 Effective search space: 73682 Effective search space used: 73682 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