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 Ac3H11_552 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_552 Length = 384 Score = 164 bits (416), Expect = 3e-45 Identities = 120/364 (32%), Positives = 173/364 (47%), Gaps = 10/364 (2%) Query: 4 SLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GIN 62 S L+AVAL A +A S V IA AGP++G A G + G A D+NA I Sbjct: 15 SALTAVALAASVA-SAQDVQTVKIAHAGPVSGGIAHIGKDTENGVRLAIDDLNAQNLVIG 73 Query: 63 GEQIKIELG--DDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120 G++IK E+ DD DP+Q +VA K V V+GH SG SIPAS +YA+ + Sbjct: 74 GKKIKFEIAAEDDAGDPRQATAVAQKLCDQKVAGVVGHLQSGTSIPASAIYAKCDLPHIT 133 Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180 PDL G TFR D+ GA + ADH K +A++ D+T YGQG+A Sbjct: 134 ASASNPDLTKPGHKTTFRLIANDNALGAALALFGADHQKLKSVAIIDDRTAYGQGVASVF 193 Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240 K G+ V E N DF A++ +K I++GGL +AG ++RQ GL Sbjct: 194 KATAQQKGLKVVAEEFTNDKATDFMAILTAIKNKKPDAIFYGGLDAQAGPMLRQMEQLGL 253 Query: 241 -KATLVSGDGIVSNELASIAGDAVA---GTLNTFGPDPTANPANKELVEKFKAAGFNP-E 295 GD + + +L ++G A T T G + +++ A + Sbjct: 254 GNVKYFGGDALCTEKLPELSGKTPALKNVTCATGGASVDKMQGGADWKKRYDAKFPGQFQ 313 Query: 296 AYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIM 355 Y+ Y+Y A +A A K A S+DP+ A + K + V +I+F KG+ P + Sbjct: 314 IYSPYAYDAAMVLADAMKRANSVDPKVFAPFL-AKTEYKGVTANIAFTAKGELTTPAVTL 372 Query: 356 YEWK 359 Y +K Sbjct: 373 YTFK 376 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: 371 Number of extensions: 25 Number of successful extensions: 3 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: 384 Length adjustment: 30 Effective length of query: 351 Effective length of database: 354 Effective search space: 124254 Effective search space used: 124254 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