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_092349194.1 BLU87_RS12680 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_900107645.1:WP_092349194.1 Length = 298 Score = 272 bits (695), Expect = 8e-78 Identities = 138/298 (46%), Positives = 205/298 (68%), Gaps = 6/298 (2%) Query: 1 MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSF--Q 58 M++ LQQL NGL +GS++AL+ALGYTMVYG++KLINFAHGD+ AF+G + Q Sbjct: 1 MDIFLQQLANGLTIGSMFALVALGYTMVYGVMKLINFAHGDMVAASAFVGLTIYTQVLGQ 60 Query: 59 MNFFVALIVAMLATAIL----GVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLV 114 +A+I L +A++ G+++E LAYRPLR + R++ +++A+G S +++ G++ + Sbjct: 61 ATSLIAVIAIFLLSAMVMACVGILLERLAYRPLREAPRLSAVVSALGASLVIQNGIMLIW 120 Query: 115 GANTRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVD 174 G R FP+ + V +DLG + ++ +Q++IL SL+LMI L + V+KT+MG A+RA ++D Sbjct: 121 GPQMRIFPELVPQVYWDLGGVVISLIQVLILVFSLVLMIALYLFVEKTRMGAAIRASAID 180 Query: 175 SDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGG 234 DAA+LMGINVN I+ F +GS+L G+ I LYY + MG GL +F+AA+LGG Sbjct: 181 QDAARLMGINVNSVIALIFIIGSSLGAVGGLFIGLYYRGITFNMGWQYGLYAFIAAILGG 240 Query: 235 IGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKNVKEKV 292 IG IPGA LGG ++GL + F + S + DA + +L+LILIVRP G+LG+ V EKV Sbjct: 241 IGNIPGAMLGGMLLGLFQAFIAGYISSTWADAFTFILLILILIVRPTGLLGERVAEKV 298 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: 245 Number of extensions: 11 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: 298 Length adjustment: 26 Effective length of query: 266 Effective length of database: 272 Effective search space: 72352 Effective search space used: 72352 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