Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate RR42_RS14425 RR42_RS14425 leucine ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Cup4G11:RR42_RS14425 Length = 371 Score = 183 bits (464), Expect = 8e-51 Identities = 126/379 (33%), Positives = 195/379 (51%), Gaps = 17/379 (4%) Query: 1 MQLKLKLTVVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQ 60 M L ++ A A A A+A + +KI P+SG+ A YG + GA AIE++NA Sbjct: 1 MTLSRLTSISLATALCALGAAANAETIKIAIAGPMSGSVAQYGDMVKAGALTAIEQINAA 60 Query: 61 GVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCG 120 G G K FE+V DDA +PKQ A A K+ K+ V+GH+ SG+TIPAS +Y + G Sbjct: 61 GGAGGNK---FEVVMMDDACEPKQAVAVANKIVSQKIHYVIGHVCSGSTIPASDIYENEG 117 Query: 121 IPHVTGAATNPNLTK-PGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQ 179 I VT +AT P LT+ K FR I D+ G A Y + +K K VAI+ D+ +YGQ Sbjct: 118 IVMVTPSATAPQLTENKKRKFIFRTIGRDDQQGPAAAQYIITKIKPKKVAILHDKQSYGQ 177 Query: 180 GVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQ 239 G+A KK A + V + +D+ A++T +K++ D +++GG P+ G +LRQ Sbjct: 178 GIASSVKKDLEAAKIPVAVFEGVNAGDSDYSAVITKLKSQGVDFVYFGGYHPEMGLLLRQ 237 Query: 240 MEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKA----K 295 + G+ + G +G+ ++ + AGA + G ++ S A KA K Sbjct: 238 AREQGV-KATFMGPEGVGNKDVTAI-AGASSEGMLVTLPADFS-ADPSNAALVKAFADKK 294 Query: 296 YDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNG 355 DA P Q Y+ A +I DA+ A S DP + K++F+ + ++ G Sbjct: 295 RDANGPFQMPAYA-----AVQIIGDAIAGAKSTDPTKVAAYMHKNAFQTPIGKVEYDAQG 349 Query: 356 EMKNPAITLYV-YKDGKKT 373 ++K+ ++ +KD KT Sbjct: 350 DLKSFKFVVFTWHKDATKT 368 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: 371 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: 371 Length adjustment: 30 Effective length of query: 345 Effective length of database: 341 Effective search space: 117645 Effective search space used: 117645 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 17 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