Align BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_000009985.1:WP_011385357.1 Length = 366 Score = 368 bits (945), Expect = e-106 Identities = 183/359 (50%), Positives = 244/359 (67%), Gaps = 1/359 (0%) Query: 1 MKKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGG 60 M ++ ++ + L A L +G A AD+ I VAGPL+G AAFG Q ++GA +A DINA GG Sbjct: 1 MSRTGITGITLAAALLMAGAARADITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGG 60 Query: 61 INGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120 + G+++ + LGDD DPKQ ++VAN+ AA V FV GHF SG SIPASEVYAE GIL+ Sbjct: 61 VLGQKLALTLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQIS 120 Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180 P P GL N FRTCGRDDQQG IA Y+A H KD +A+VHDK+ YG+GLAD+T Sbjct: 121 PASTNPKFTERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQT 180 Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240 + A+ AG+ +YE I+ G+KD+SAL+ K+K + V ++Y+GG TEAGLI+RQ DQG+ Sbjct: 181 RDALGKAGIKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGM 240 Query: 241 KATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAYTLY 300 + L+ GD +V+ E +I G A GT+ TF PDP NPAN +LV+ ++A + PEAYTLY Sbjct: 241 QTRLMGGDALVTEEYWAITGAAGEGTMMTFSPDPRKNPANADLVKYYRAQKYEPEAYTLY 300 Query: 301 SYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359 +Y +Q A AA+ A + D + VA +K + F T +G I FD KGD PGY+MY WK Sbjct: 301 TYGTIQAWAQAAEKAKTTDWKKVAAVLKAE-KFDTAIGKIGFDAKGDVAAPGYVMYVWK 358 Lambda K H 0.314 0.132 0.383 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: 412 Number of extensions: 23 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: 381 Length of database: 366 Length adjustment: 30 Effective length of query: 351 Effective length of database: 336 Effective search space: 117936 Effective search space used: 117936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 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