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_013135598.1 ARNIT_RS08960 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_000092245.1:WP_013135598.1 Length = 300 Score = 259 bits (661), Expect = 7e-74 Identities = 127/300 (42%), Positives = 197/300 (65%), Gaps = 8/300 (2%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQ-- 58 M+ +LQQL+NGL +GS+YAL+ALGYTMVYG++KLINFAHGD+ A++G L F Sbjct: 1 MDTLLQQLINGLTVGSLYALVALGYTMVYGVMKLINFAHGDLVAFSAYVGLTLFTQFYGS 60 Query: 59 -----MNFFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYL 113 +N + + + A +GV++E LAYRPLR + R++ +++A+G S +++ G++ + Sbjct: 61 NALTLVNIIIVFTLTAIIVAFVGVLLERLAYRPLRTAPRLSAVVSALGASLVIQNGIMLI 120 Query: 114 VGANTRAFPQAI-QTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVS 172 G N FP + + ++ G + ++ QL+IL +S +LM+ L + + KTKMG A+RA + Sbjct: 121 WGPNMEIFPANVFPSTSWNFGGVIISFTQLVILALSAVLMVALYLFINKTKMGTAIRATA 180 Query: 173 VDSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVL 232 +D DAA+LMGINVNR I F +GS L G+ I +YY L MG GL +F+AA++ Sbjct: 181 IDQDAAKLMGINVNRVIMTIFIIGSMLGAIGGLFIGMYYRGLTFDMGWLYGLNAFIAAII 240 Query: 233 GGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 GGIG IPGA LGG ++GL + + +++ + + +L++ILIV+P G+ G+N EKV Sbjct: 241 GGIGSIPGAMLGGLLLGLFNALISGYISTEWAETFTFILLIIILIVKPTGLFGENTAEKV 300 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: 264 Number of extensions: 19 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: 300 Length adjustment: 26 Effective length of query: 266 Effective length of database: 274 Effective search space: 72884 Effective search space used: 72884 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