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 HSERO_RS00870 HSERO_RS00870 ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__HerbieS:HSERO_RS00870 Length = 378 Score = 166 bits (421), Expect = 8e-46 Identities = 116/341 (34%), Positives = 164/341 (48%), Gaps = 8/341 (2%) Query: 25 VLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAG-GINGEQIKIEL--GDDVSDPKQGI 81 V I + PLTGP A+ G Q G A +NA + G++IK ++ DD +DPK G+ Sbjct: 30 VKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGKKIKFDVIAEDDQADPKSGV 89 Query: 82 SVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILRNHPGRDEPDLHGTGLWNTFRTCG 141 +VA K A GVK ++G +NSGV+IPAS VY + GI+ + P + G FR Sbjct: 90 AVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIVVATVASN-PKITQQGFATLFRVAA 148 Query: 142 RDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADETKKAMNAAGVTEVIYEGINVGD 201 D Q G Y A K ++AV+ D+T YGQGLA E K A G+ V + N Sbjct: 149 SDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIKVAKANGIDVVSTDFTNDKA 208 Query: 202 KDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKATLVSGDGIVSNELASIAGD 261 DF+A++ +K ++ GG + G I RQ G+ L+ GDGI S E+ + GD Sbjct: 209 TDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDVPLMGGDGICSPEMGRLGGD 268 Query: 262 AVAGTLNTFGPDPTANPANKELV---EKFKAAGFNPEAYTLYSYAAMQTIAGAAKAAGSL 318 A+ ++ + A + V E K E Y + Y M IA A K A S+ Sbjct: 269 AIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAVSFYDGMMLIAQAMKQANSV 328 Query: 319 DPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYEWK 359 DP+ A+ K + V G FD D K +Y +K Sbjct: 329 DPKQFGPAL-AKISYKGVAGQYDFDANHDLKQSPVTVYRFK 368 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: 379 Number of extensions: 19 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: 378 Length adjustment: 30 Effective length of query: 351 Effective length of database: 348 Effective search space: 122148 Effective search space used: 122148 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