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 RR42_RS14425 RR42_RS14425 leucine ABC transporter substrate-binding protein
Query= TCDB::Q9L3M3 (381 letters) >FitnessBrowser__Cup4G11:RR42_RS14425 Length = 371 Score = 265 bits (677), Expect = 2e-75 Identities = 148/373 (39%), Positives = 220/373 (58%), Gaps = 9/373 (2%) Query: 1 MKKSLLSAVAL-TAMLAFSGNAWADVL-IAVAGPLTGPNAAFGAQLQKGAEQAAADINAA 58 M S L++++L TA+ A A A+ + IA+AGP++G A +G ++ GA A INAA Sbjct: 1 MTLSRLTSISLATALCALGAAANAETIKIAIAGPMSGSVAQYGDMVKAGALTAIEQINAA 60 Query: 59 GGINGEQIKIELGDDVSDPKQGISVANKFAADGVKFVIGHFNSGVSIPASEVYAENGILR 118 GG G + ++ + DD +PKQ ++VANK + + +VIGH SG +IPAS++Y GI+ Sbjct: 61 GGAGGNKFEVVMMDDACEPKQAVAVANKIVSQKIHYVIGHVCSGSTIPASDIYENEGIVM 120 Query: 119 NHPGRDEPDLHGTGLWN-TFRTCGRDDQQGAIAGKYLADHFKDAKIAVVHDKTPYGQGLA 177 P P L FRT GRDDQQG A +Y+ K K+A++HDK YGQG+A Sbjct: 121 VTPSATAPQLTENKKRKFIFRTIGRDDQQGPAAAQYIITKIKPKKVAILHDKQSYGQGIA 180 Query: 178 DETKKAMNAAGVTEVIYEGINVGDKDFSALIAKMKEAGVSIIYWGGLHTEAGLIIRQAAD 237 KK + AA + ++EG+N GD D+SA+I K+K GV +Y+GG H E GL++RQA + Sbjct: 181 SSVKKDLEAAKIPVAVFEGVNAGDSDYSAVITKLKSQGVDFVYFGGYHPEMGLLLRQARE 240 Query: 238 QGLKATLVSGDGIVSNELASIAGDAVAGTLNTFGPDPTANPANKELVEKF---KAAGFNP 294 QG+KAT + +G+ + ++ +IAG + G L T D +A+P+N LV+ F K P Sbjct: 241 QGVKATFMGPEGVGNKDVTAIAGASSEGMLVTLPADFSADPSNAALVKAFADKKRDANGP 300 Query: 295 EAYTLYSYAAMQTIAGAAKAAGSLDPEAVAKAMKEKGPFPTVLGDISFDEKGDPKIPGYI 354 + + +YAA+Q I A A S DP VA A K F T +G + +D +GD K ++ Sbjct: 301 --FQMPAYAAVQIIGDAIAGAKSTDPTKVA-AYMHKNAFQTPIGKVEYDAQGDLKSFKFV 357 Query: 355 MYEWKKVRTASTA 367 ++ W K T + A Sbjct: 358 VFTWHKDATKTAA 370 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: 438 Number of extensions: 23 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: 371 Length adjustment: 30 Effective length of query: 351 Effective length of database: 341 Effective search space: 119691 Effective search space used: 119691 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