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_007726703.1 C1M55_RS06865 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_002893965.1:WP_007726703.1 Length = 285 Score = 152 bits (384), Expect = 8e-42 Identities = 94/286 (32%), Positives = 154/286 (53%), Gaps = 6/286 (2%) Query: 8 LVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVALIV 67 L +GL LG+VY L+A+GY +V+ NFA + M+G F+ Y + + ++ V ++ Sbjct: 4 LWSGLALGAVYVLVAIGYNIVFVSSNTFNFAQAQLMMVGTFVAYTGLVTLKLPVLVVAVM 63 Query: 68 AMLATAILGVVIEFLAYRPLR-HSTRIAVLITAIGVSFLLEYGMVYLVGANTRAFPQAIQ 126 A + +L V E +A RP+ H + L+T +GV+ LL + G+ P Sbjct: 64 ATVTVMLLASVEEIVAIRPVADHQNQ---LVTTLGVATLLNGATQLIWGSEPLTVPFFGS 120 Query: 127 TVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMGINVN 186 L V++ +L ++ L++ L + +KT G A+ +S D +AA L G+NV Sbjct: 121 NEPITLLGGRTYPVEIALLVAAIALVVGLSYVSKKTMTGLALIGISEDREAAMLRGVNVR 180 Query: 187 RTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAALGGF 246 R FA ALAG G+ + ++ L G LK FVA +GG G +PGA +GG Sbjct: 181 RLALGAFAFSGALAGVLGLFVGPKTFAVATL-GAALALKGFVALAIGGFGSLPGALIGGL 239 Query: 247 VIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 +GL+E+F + S + + V+ +L++IL+V+PAG+ G NV+E+V Sbjct: 240 TVGLVESFTALWAGSQYSNIAVFTVLIVILMVKPAGLFG-NVRERV 284 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: 204 Number of extensions: 13 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: 285 Length adjustment: 26 Effective length of query: 266 Effective length of database: 259 Effective search space: 68894 Effective search space used: 68894 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