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 8501892 DvMF_2607 Extracellular ligand-binding receptor (RefSeq)
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Miya:8501892 Length = 372 Score = 186 bits (473), Expect = 7e-52 Identities = 117/355 (32%), Positives = 182/355 (51%), Gaps = 7/355 (1%) Query: 8 AVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGINGEQIK 67 AVA+ A AF+ + + VAG +G A++G A+ A INA GG+ G+Q++ Sbjct: 14 AVAVMACPAFAADT---IKFGVAGAHSGDLASYGLPTVNAAKLVAKMINAKGGVLGKQVE 70 Query: 68 IELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPD 127 + DD P+ + A K +DG V+GH SG + A +Y E I+ P P Sbjct: 71 VIPQDDQCKPELATNAATKLVSDGANVVLGHICSGATKAALPIYKEANIVLMSPSATNPA 130 Query: 128 LHGTGLW-NTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNA 186 L +G + N FRT DDQQ + + D KIAV+HDK YG+G A+ K+ + Sbjct: 131 LTQSGDYPNFFRTIASDDQQAKLGVDFTIDKLGKKKIAVLHDKGDYGKGYAEYAKQFVEQ 190 Query: 187 AGV-TEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLV 245 +G T V++EG+ G D+SA++ K++ +G + +GG H EA I++Q + + V Sbjct: 191 SGKGTVVLFEGVTPGAVDYSAVVQKIRNSGAEAVMFGGYHPEASKIVQQLRKKRMDLPFV 250 Query: 246 SGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVE-KFKAAGFNPEAYTLYSYAA 304 S DG+ + +AG G + D +A P KE +E K G P A+ +YAA Sbjct: 251 SDDGVKDDTFIKVAGKDAEGVYASSSKDVSALPLYKEAIEAHVKEFGAEPGAFYKEAYAA 310 Query: 305 MQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359 + A + AGS D + A++ + T +G I FD++GD + G+ MY+ K Sbjct: 311 SLALLNAIEKAGSTDSAKIMNALRTEF-VETSVGKIKFDKRGDAEGVGFSMYQVK 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: 372 Number of extensions: 30 Number of successful extensions: 5 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: 372 Length adjustment: 30 Effective length of query: 351 Effective length of database: 342 Effective search space: 120042 Effective search space used: 120042 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