Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate RR42_RS14425 RR42_RS14425 leucine ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Cup4G11:RR42_RS14425 Length = 371 Score = 287 bits (734), Expect = 4e-82 Identities = 147/355 (41%), Positives = 218/355 (61%), Gaps = 2/355 (0%) Query: 6 SLLVAVAATAMTASVAKADIAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65 S+ +A A A+ A+ I +A AGP++G A +G+ +K G A+ INAAGG G K Sbjct: 8 SISLATALCALGAAANAETIKIAIAGPMSGSVAQYGDMVKAGALTAIEQINAAGGAGGNK 67 Query: 66 LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125 ++ + DDAC+PKQAVAVAN++ + +V GH CSGS+IPAS +Y EG++ ++P++T Sbjct: 68 FEVVMMDDACEPKQAVAVANKIVSQKIHYVIGHVCSGSTIPASDIYENEGIVMVTPSATA 127 Query: 126 PKLTE-QNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL 184 P+LTE + K +FR GRDDQQG A +Y++ K K VAILHDK +YG+G+A +K L Sbjct: 128 PQLTENKKRKFIFRTIGRDDQQGPAAAQYIITKIKPKKVAILHDKQSYGQGIASSVKKDL 187 Query: 185 NAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPI 244 A ++E AG+ DYSA+++KLK + VD VY GGYH E GLL RQ ++QG+ A Sbjct: 188 EAAKIPVAVFEGVNAGDSDYSAVITKLKSQGVDFVYFGGYHPEMGLLLRQAREQGVKATF 247 Query: 245 VSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYTYA 303 + + + + AI G + E ++T D P V+ F + G + + YA Sbjct: 248 MGPEGVGNKDVTAIAGASSEGMLVTLPADFSADPSNAALVKAFADKKRDANGPFQMPAYA 307 Query: 304 ALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358 A+QI +A A STD K+A + KN++ T IGK+ +DA+GD+ S +V + W+ Sbjct: 308 AVQIIGDAIAGAKSTDPTKVAAYMHKNAFQTPIGKVEYDAQGDLKSFKFVVFTWH 362 Lambda K H 0.312 0.129 0.366 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: 376 Number of extensions: 16 Number of successful extensions: 3 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: 366 Length of database: 371 Length adjustment: 30 Effective length of query: 336 Effective length of database: 341 Effective search space: 114576 Effective search space used: 114576 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 (21.9 bits) S2: 49 (23.5 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