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 GFF521 PS417_02655 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__WCS417:GFF521 Length = 378 Score = 321 bits (823), Expect = 2e-92 Identities = 177/363 (48%), Positives = 231/363 (63%), Gaps = 6/363 (1%) Query: 2 KKSLLSAVALTAMLAFSGNAWADVLIAVAGPLTGPNAAFGAQLQKGAEQAAADINAAGGI 61 KK L A+A+ A L S ADV I VAGP+TG NAAFG Q KGA+ AA IN AGGI Sbjct: 7 KKGFL-ALAVAAALGVSTFVQADVKIGVAGPMTGANAAFGEQYMKGAQAAADVINKAGGI 65 Query: 62 NGEQIKIELGDDVSDPKQGISVANKFA-ADGVKFVIGHFNSGVSIPASEVYAENGILRNH 120 NGE+I + GDD +PKQ ++VAN+ A D V V+GHF S +IPASEVY E GI+ Sbjct: 66 NGEKIVLVAGDDACEPKQAVAVANRLADQDKVIGVVGHFCSSNTIPASEVYDEAGIIAIT 125 Query: 121 PGRDEPDLHGTGLWNTFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLADET 180 PG P + GL FR CGRDDQQG +AG Y+ D K K+AV++DK YG+GLAD T Sbjct: 126 PGSTNPQVTERGLGAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVINDKDTYGKGLADAT 185 Query: 181 KKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAADQGL 240 + GV V+ EG+ G+KDFSAL+ K++ G ++Y+GGLH EAG ++RQ + GL Sbjct: 186 AAQLTKRGVKPVLEEGLTRGEKDFSALVTKIRSTGADVVYFGGLHPEAGPLVRQIREAGL 245 Query: 241 K-ATLVSGDGIVSNELASIAGDA--VAGTLNTFGPDPTANPANKELVEKFKAAGFNPEAY 297 K +S DG+V++EL + AG A V G TFG DP P +K +VE+F+ G PE Y Sbjct: 246 KDVKFMSDDGVVTDELVATAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKNGTEPEGY 305 Query: 298 TLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYIMYE 357 TLY+YA++Q +A A S E AK +K P TV+G+ ++D KGD KI Y++Y+ Sbjct: 306 TLYAYASVQALAAGFNGAKSNKGEDAAKWLKAH-PVKTVMGEKAWDSKGDLKISDYVVYQ 364 Query: 358 WKK 360 W K Sbjct: 365 WDK 367 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: 451 Number of extensions: 20 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