Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_038217021.1 Q392_RS28895 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000745855.1:WP_038217021.1 Length = 404 Score = 411 bits (1056), Expect = e-119 Identities = 209/366 (57%), Positives = 264/366 (72%), Gaps = 2/366 (0%) Query: 11 AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIK 70 AA A AA + + VVKIGHV P SG AH GKDNE GA+MAI++LNA+ V IG K K Sbjct: 36 AAPAPAAPPPAGETLVVKIGHVGPTSGPIAHLGKDNELGAKMAIDDLNAKQVKIGDKVAK 95 Query: 71 FELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130 FELVAEDDAADPKQGTA AQKL D KV GVVGHLNSGTTIPASK+Y+D G+P ++ +ATN Sbjct: 96 FELVAEDDAADPKQGTAVAQKLMDEKVNGVVGHLNSGTTIPASKIYSDAGVPQISPSATN 155 Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190 P T+ G+KTTFR++A+D LG L YAV+TLK K +A+IDDRTAYGQGVA+ F+K A Sbjct: 156 PKYTRQGFKTTFRVVADDTQLGGTLGRYAVETLKGKNIAVIDDRTAYGQGVAEEFEKAAK 215 Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250 A G +V +FTTDK+TDF AILT +K PD +F+GGMD GGPML+Q++QLG+ NVK+ Sbjct: 216 AAGATIVGHEFTTDKSTDFNAILTKLKGAKPDILFFGGMDAVGGPMLKQVKQLGL-NVKF 274 Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGG-TAWKAKYDAKYPNQFQVYSP 309 GGDG+CT E+AKLA A V CAE G + +KA + AK Q+Y+P Sbjct: 275 MGGDGLCTGELAKLAGDAVGEEMVYCAEAGGVDGEFKEPLEKFKADFKAKNGVDVQIYAP 334 Query: 310 YTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKD 369 Y YDA ++ D+M RA S DP+ Y PE+ K+++KGVT I F+ G++KN A+TLY YK Sbjct: 335 YVYDAVQVLADSMVRAGSADPEKYLPEVGKTNYKGVTGPITFDEKGDIKNGALTLYTYKG 394 Query: 370 GKKTPL 375 G++T + Sbjct: 395 GQRTQI 400 Lambda K H 0.315 0.131 0.375 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: 514 Number of extensions: 20 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: 375 Length of database: 404 Length adjustment: 30 Effective length of query: 345 Effective length of database: 374 Effective search space: 129030 Effective search space used: 129030 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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