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 H281DRAFT_01194 H281DRAFT_01194 amino acid/amide ABC transporter substrate-binding protein, HAAT family (TC 3.A.1.4.-)
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Burk376:H281DRAFT_01194 Length = 383 Score = 205 bits (521), Expect = 2e-57 Identities = 130/374 (34%), Positives = 191/374 (51%), Gaps = 15/374 (4%) Query: 7 SAVALTAMLAFSGNAWA----DVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGIN 62 SA+ + LA + ++A DV I A PLTG A +GA + G + A D+N + Sbjct: 10 SAIVMGLALAGAPCSYAATPVDVKIGFAAPLTGGQAHYGADFRSGVQLAIEDMNGTNPVI 69 Query: 63 GEQ---IKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRN 119 G + ++ DD +DP+ G +VA K DGV VIGH+NSG SIPA+ +YA+ G + Sbjct: 70 GGKPVHFVLDAQDDQADPRTGTTVAQKLVDDGVVAVIGHYNSGTSIPAAPIYAKAGTPQV 129 Query: 120 HPGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADE 179 P GL TFR D Q GA+ G + K ++A+V D+T YGQG+A+E Sbjct: 130 AMAT-APSYTRLGLPTTFRLLTSDTQLGAVLGDFAVKGLKFKRLAIVDDRTAYGQGVAEE 188 Query: 180 TKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQG 239 KA AAG T V E N DF A++ K+K+A V +++GG T+A +++Q Sbjct: 189 FAKAAKAAGATVVTEEYTNDKAVDFRAILTKIKQANVDAVFYGGADTQAAPMLKQMRSLA 248 Query: 240 LKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTAN-PANKELVEKFKAAGFNP-EAY 297 +K+TL+ D + S+ L IAG+A GTL P + P K E+++ P E Y Sbjct: 249 IKSTLLGPDMLQSDNLIKIAGEASEGTLAASEGSPLSQMPGGKAFAERYQKRFNQPVELY 308 Query: 298 TLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYE 357 Y+Y + A K A S DP A+K ++S+D+ GD K G +Y+ Sbjct: 309 APYAYDGTMAVFNAMKKADSTDPHVFLSALKATNMKGVTTSELSYDQYGDLKYGGVTVYK 368 Query: 358 -----WKKVRTAST 366 WK ++T T Sbjct: 369 VVNGTWKPLQTVGT 382 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: 358 Number of extensions: 14 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: 383 Length adjustment: 30 Effective length of query: 351 Effective length of database: 353 Effective search space: 123903 Effective search space used: 123903 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