Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Ac3H11_1938 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= TCDB::Q8DQH9 (318 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1938 Length = 358 Score = 163 bits (413), Expect = 5e-45 Identities = 97/306 (31%), Positives = 168/306 (54%), Gaps = 26/306 (8%) Query: 19 YSLI--SVLVSVGVLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYA 76 YSL+ +++ + V +++ L + I I+ +GL L+ GF+G FSLGHA F+ +GAY Sbjct: 25 YSLLGLTLVAAPWVAPEYWLAQLTFVLIYSIVGLGLMLLAGFTGLFSLGHAAFLGVGAYT 84 Query: 77 AAIIGSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFII 136 A++ + ++ A LS AV ++VG+P LR+KG YL +ATL I+ Sbjct: 85 QAVLTGMGWPFAL---SLACAAGLSAAVGVVVGLPALRVKGIYLGMATLSFGFIVEEVFA 141 Query: 137 NGGSLTNGAAGILGIP------NFTTWQMVYFF----VVITTIATLNFLRSPIGRSTLSV 186 S+T G +G +P +F + + YF V++T+A LN LRSP GR+ +++ Sbjct: 142 RWESVTGGNSGKHLVPPQMFGYSFESTESFYFLCLVIAVVSTLAILNLLRSPTGRAFVAI 201 Query: 187 REDEIAAESVGVNTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIV 246 R+ EI+A+S+G++ + K ++F A A + G+L A + + P + + SI++L+++ Sbjct: 202 RDSEISAQSMGIHLARYKTLSFSLSAALAGVGGALYAHKLQFISPDQFNILQSIDLLLMI 261 Query: 247 VFGGLGSITGAIVSAIVLGILNMLLQ-----------DVASVRMIIYALALVLVMIFRPG 295 V GGLGS+ GA + AI L + ++ ++ ++Y L+ ++F P Sbjct: 262 VIGGLGSVHGAFLGAIFLISMPQMISLSKDWLPAAIGQAPGLQAVVYGAVLIAFVLFEPM 321 Query: 296 GLLGTW 301 GL G W Sbjct: 322 GLYGRW 327 Lambda K H 0.327 0.143 0.403 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: 245 Number of extensions: 15 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: 318 Length of database: 358 Length adjustment: 28 Effective length of query: 290 Effective length of database: 330 Effective search space: 95700 Effective search space used: 95700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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