Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_084260337.1 Q394_RS0102910 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000621325.1:WP_084260337.1 Length = 375 Score = 338 bits (868), Expect = 1e-97 Identities = 185/362 (51%), Positives = 240/362 (66%), Gaps = 10/362 (2%) Query: 15 AAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKFELV 74 AAAG A VKIG +P++G QAH GKDN+NG R+AI+E+NA I GK + FE++ Sbjct: 17 AAAGENGAV--TVKIGQSSPLTGPQAHIGKDNDNGVRLAIDEINASKPVIDGKPVTFEVM 74 Query: 75 AEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNPNLT 134 +EDD ADPK T AQ++ D + GV+GHLNSG TIPASKVY+D IP ++ +AT T Sbjct: 75 SEDDQADPKTATIVAQRMIDEGIVGVIGHLNSGATIPASKVYSDNNIPQISPSATAIKYT 134 Query: 135 KPGYKTTFRIIANDNALGAGLAFYAVDTLKL-KTVAIIDDRTAYGQGVADVFKKTATAKG 193 G+KT FR++ ND G L YA KL K VAIIDD+TAYGQG+A +K A A G Sbjct: 135 DQGFKTAFRVMTNDAQQGKVLGAYAA---KLGKKVAIIDDQTAYGQGLAAEVEKAAKAAG 191 Query: 194 MKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYFGG 253 +VV + T DKA+DF AILT+IK K PD +F+GGMDPQ P+ +QM QLGM + GG Sbjct: 192 AEVVAVEHTNDKASDFTAILTSIKGKAPDVVFFGGMDPQAAPIAKQMHQLGM-TAQLLGG 250 Query: 254 DGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPYTYD 313 DG+ T + +LAA I + G + KMP G +K K++AKY Q Q+YSPY YD Sbjct: 251 DGMQTPKFIELAAA--DAEGAIASIPGLPIDKMPKGADFKQKFEAKY-GQIQLYSPYAYD 307 Query: 314 ATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDGKKT 373 A +++VDAMKRANS DP Y PEL K+SF+GVT I+F+ G++ + ITLY + G+ T Sbjct: 308 AAYVMVDAMKRANSTDPAKYLPELGKTSFEGVTGKISFDAKGDLTSGPITLYKVQAGQWT 367 Query: 374 PL 375 L Sbjct: 368 TL 369 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: 444 Number of extensions: 16 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: 375 Length adjustment: 30 Effective length of query: 345 Effective length of database: 345 Effective search space: 119025 Effective search space used: 119025 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