Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_038202510.1 Q392_RS05395 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >NCBI__GCF_000745855.1:WP_038202510.1 Length = 380 Score = 346 bits (888), Expect = e-100 Identities = 182/371 (49%), Positives = 243/371 (65%), Gaps = 5/371 (1%) Query: 7 LTVVAAIAA--AAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTI 64 L +AA AA AAG A+AQE V IGH P+SGA A GKDNENG R+AIE+LNA+ + Sbjct: 10 LAALAAAAAFCAAGPAAAQELTVPIGHTGPLSGANAFAGKDNENGVRLAIEDLNARQLKA 69 Query: 65 GGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124 GG+ +KFEL +EDD D K G A AQK D V VVG SG IPAS+VY+D G Sbjct: 70 GGRTLKFELRSEDDQCDAKTGVAVAQKFVDDNVKFVVGPYCSGVAIPASRVYSDGGTLMS 129 Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184 T TNP +T GY FRIIA+D +GA +A YA + LK+K V IIDDR+A+GQG+AD Sbjct: 130 T-VGTNPKITAAGYTNVFRIIASDAQIGASMASYAANVLKVKNVGIIDDRSAFGQGLADE 188 Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244 F K A G+ +V ++FTT+K+ DF AILT +KAKNP+ +F+GG PQG PMLRQM+QLG Sbjct: 189 FGKEARRLGLTIVGQEFTTEKSVDFNAILTRLKAKNPEVVFFGGYAPQGAPMLRQMKQLG 248 Query: 245 MGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304 + + GGD +C+ E+ K+ G+ V CA+GG+ L K PGG ++KA++ K+ Sbjct: 249 F-DARLLGGDTLCSPEMGKI-GGSAVNDTVFCAQGGAVLDKTPGGPSFKARFKQKFNADP 306 Query: 305 QVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITL 364 VY+PY YD T + +A+ R + DP+ +L KSS+KGV T +++ G +KN T+ Sbjct: 307 DVYAPYYYDQTLFLGEAIARVGAADPEKVAADLRKSSYKGVAGTYSYDDKGNLKNAPTTV 366 Query: 365 YVYKDGKKTPL 375 + +K K TPL Sbjct: 367 FTFKGEKLTPL 377 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: 473 Number of extensions: 16 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 375 Length of database: 380 Length adjustment: 30 Effective length of query: 345 Effective length of database: 350 Effective search space: 120750 Effective search space used: 120750 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