Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_029133953.1 A3GO_RS0114190 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000428045.1:WP_029133953.1 Length = 364 Score = 162 bits (409), Expect = 2e-44 Identities = 113/370 (30%), Positives = 172/370 (46%), Gaps = 11/370 (2%) Query: 1 MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60 M+ KL+V+AA + VA A + G P++G A +G + GA A+ +LNA Sbjct: 1 MKKTFKLSVMAAAMSFGSVALADIMIATAG---PMTGQYASFGAQMKAGAEQAVADLNAA 57 Query: 61 GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120 G +G K + L DDA DPKQ A A ++ + V + GH SG++IPASKVY + G Sbjct: 58 GGVLGEKLV---LEVGDDACDPKQAVAVANQMVNKGVVFMAGHFCSGSSIPASKVYEEEG 114 Query: 121 IPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQG 180 I ++ A+TNP LT+ G FR+ D+ GA + + + +A I D+TAYG+G Sbjct: 115 IVMISPASTNPKLTEEGADNVFRVCGRDDQQGAVAGKFLKENFADQKIAFIHDKTAYGKG 174 Query: 181 VADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQM 240 +AD G + + T D+ A+++ +K N ++ GG +GG ++RQM Sbjct: 175 LADATMAEYKKLGGEPAMYEAITAGEKDYTALVSKMKQSNIGVMYLGGYHTEGGLIVRQM 234 Query: 241 EQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKY 300 + GM V GD + T+E + A G K P K+ +K Sbjct: 235 REQGMDTV-LVSGDALVTNEYWSITGPA---GEGTLMTFSPDPRKNPVAAPLVEKFRSK- 289 Query: 301 PNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNP 360 + + Y YTY A A A S D L F V +F+ G++ P Sbjct: 290 GIEPEGYVLYTYGAVQAWAQAANAAGSTDTAKVVAALKSGEFDTVLGKFSFDGKGDVTAP 349 Query: 361 AITLYVYKDG 370 LY + +G Sbjct: 350 GYVLYKWTNG 359 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: 381 Number of extensions: 23 Number of successful extensions: 2 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: 364 Length adjustment: 30 Effective length of query: 345 Effective length of database: 334 Effective search space: 115230 Effective search space used: 115230 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: 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