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_011767452.1 AZO_RS18715 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >NCBI__GCF_000061505.1:WP_011767452.1 Length = 371 Score = 219 bits (558), Expect = 1e-61 Identities = 138/368 (37%), Positives = 199/368 (54%), Gaps = 13/368 (3%) Query: 1 MKKSLLSAVALTAMLAFSGNAWAD---VLIAVAGPLTGPNAAFGAQLQKGAEQAAADINA 57 MKKS+ VAL M G+A A V I PLTG A G L+ G A + NA Sbjct: 1 MKKSV---VALAVMALGIGSAQAQEQVVKIGGVAPLTGTIAHLGKDLENGTRLAVEEANA 57 Query: 58 AG-GINGEQIKIEL--GDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAEN 114 G I G+++K+E DD +DP+ G +VA + GVK V+GH NSG SIPAS +Y + Sbjct: 58 KGVTIGGKKVKLEFVGEDDQADPRTGTTVAQRLVDAGVKAVVGHLNSGTSIPASRIYDQA 117 Query: 115 GILRNHPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQ 174 GI + P P L G FRT D QQG++ GK+ A + KIA++ D+T YGQ Sbjct: 118 GIAQVTPASTNPKLTQQGYKGVFRTIANDVQQGSVLGKFAATNLGAKKIAIIDDRTAYGQ 177 Query: 175 GLADETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQ 234 GLADET+K A+G V E DF+A++ K++ +I++GG+ +AG ++RQ Sbjct: 178 GLADETEKGAKASGAQIVAREFTTDKATDFNAILTKIRATNPDVIFFGGMDAQAGPMLRQ 237 Query: 235 AADQGLKATLVSGDGIVSNELASIAGDAVAGT--LNTFGPDPTANPANKELVEKFKAA-G 291 G+ A ++GDG S E+ +AGDA++ + G P + E++K Sbjct: 238 MKQLGISAKFLTGDGGCSPEMIKLAGDAISANAYCSMAGLPIEKMPGGADFRERYKKRYN 297 Query: 292 FNPEAYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIP 351 + + Y+ Y+Y A I A + AGS +P +K K FP V+G+ISFD+KGD K Sbjct: 298 ADVQIYSPYAYDAATAIITAMQKAGSAEPAKYIPELK-KVNFPGVIGNISFDDKGDLKEG 356 Query: 352 GYIMYEWK 359 +Y++K Sbjct: 357 SITVYQFK 364 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: 392 Number of extensions: 23 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: 381 Length of database: 371 Length adjustment: 30 Effective length of query: 351 Effective length of database: 341 Effective search space: 119691 Effective search space used: 119691 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 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