Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate WP_088754101.1 CEJ45_RS04945 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >NCBI__GCF_002213425.1:WP_088754101.1 Length = 373 Score = 293 bits (750), Expect = 5e-84 Identities = 153/355 (43%), Positives = 221/355 (62%), Gaps = 3/355 (0%) Query: 7 LLVAVAATAMTASVAKAD-IAVATAGPITGQYATFGEQMKKGIEQAVADINAAGGVLGQK 65 + +A A A A VA A+ + +A AGP+TG A +G+ +K G A+ INAAGG G K Sbjct: 10 IALAAATFAAFAGVAHAETVKIAIAGPLTGAVAQYGDMVKAGALTAIEQINAAGGANGNK 69 Query: 66 LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGVLQISPASTN 125 + + DDAC+PKQAVAVAN++ G+K+V GH CSGS+IPAS +Y EGV+ I+P++T Sbjct: 70 FEAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGVVMITPSATA 129 Query: 126 PKLTEQNL-KNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKGLADETQKAL 184 P+LTE K +FR GRDDQQG A +Y++E K K VA+LHDK +YG+G+A + AL Sbjct: 130 PQLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQGVASSVKSAL 189 Query: 185 NAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQMKDQGLNAPI 244 +A ++E AG+ DYSA+V+KLK + VD VY GGYH E GL+ RQ ++QG+ A Sbjct: 190 DAAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQAREQGVKAVF 249 Query: 245 VSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEKFRKAGYEPEG-YTLYTYA 303 + + + + AI GPA E ++T D P V+ F A + G + + Y+ Sbjct: 250 MGPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDANGPFQMPAYS 309 Query: 304 ALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGKIGFDAKGDVTSPAYVWYRWN 358 A++I A+A A STD K+A + NS+ T IG + +D KGD+ + +V + W+ Sbjct: 310 AVKIIADAITGAKSTDPDKVAAYIHGNSFKTPIGNVEYDKKGDLKAFKFVVFTWH 364 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: 403 Number of extensions: 22 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: 373 Length adjustment: 30 Effective length of query: 336 Effective length of database: 343 Effective search space: 115248 Effective search space used: 115248 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 24 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