Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_013722844.1 ALIDE2_RS18220 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000204645.1:WP_013722844.1 Length = 377 Score = 327 bits (838), Expect = 3e-94 Identities = 178/373 (47%), Positives = 234/373 (62%), Gaps = 4/373 (1%) Query: 3 LKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGV 62 LK L AA+A AAG A AQEQ+VKIGH P+SG G+DN+NG R+AIEELNA+ + Sbjct: 6 LKSTLVAAAALACAAG-ALAQEQIVKIGHSGPLSGPNTFAGRDNDNGVRLAIEELNARKI 64 Query: 63 TIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIP 122 ++GGK +KFELV+EDD D K G A AQK D+ V V+G SG TIPAS+ Y+ G+ Sbjct: 65 SVGGKTLKFELVSEDDQCDAKTGVAVAQKFVDSGVRYVMGPYCSGVTIPASREYDKGGVM 124 Query: 123 HVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVA 182 V+ TNP +T+ GYK FRI+A+D GA +A YA + LK K VA+IDDRTA+GQG+A Sbjct: 125 -VSTVGTNPKITQAGYKNLFRIVASDVQAGASMATYAANVLKAKKVAVIDDRTAFGQGLA 183 Query: 183 DVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQ 242 D F K A GM V +FTTDKATDFMAILT IKAK P+AIFYGG PQ PM RQ++Q Sbjct: 184 DEFAKEAQKLGMTVAGREFTTDKATDFMAILTNIKAKQPEAIFYGGYAPQAAPMARQIKQ 243 Query: 243 LGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPN 302 LG+ N K GGD +C+ E+ KL A G V CA G + G A++ K+ ++ Sbjct: 244 LGI-NAKLLGGDTLCSPEMPKLGGDAVN-GVVYCAYAGMLMESDAGARAFQDKFKKRFNQ 301 Query: 303 QFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAI 362 VY P+ YD I +AM+R+ S+D + + ++KGV A++ G + Sbjct: 302 APDVYGPFYYDQVMNIGEAMQRSGSIDVNKVGAYMHQHTYKGVMGEYAYDDKGNRVKAPV 361 Query: 363 TLYVYKDGKKTPL 375 + ++ GK PL Sbjct: 362 VVMTFEGGKAKPL 374 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: 407 Number of extensions: 18 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: 375 Length of database: 377 Length adjustment: 30 Effective length of query: 345 Effective length of database: 347 Effective search space: 119715 Effective search space used: 119715 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