Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Dsui_2061 Dsui_2061 ABC-type branched-chain amino acid transport system, periplasmic component
Query= TCDB::Q8DQI1 (386 letters) >FitnessBrowser__PS:Dsui_2061 Length = 384 Score = 171 bits (434), Expect = 2e-47 Identities = 117/342 (34%), Positives = 172/342 (50%), Gaps = 14/342 (4%) Query: 27 GAVNTAGNSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGIDGKQIEVVD 86 GA+ AG + + IKIG +G A YG A + G QLA DEINA GG++G +I++V Sbjct: 12 GALAAAGLA-QAADIKIGVAAALTGGAAQYGVAIRNGFQLAADEINAKGGVNGNKIQLVV 70 Query: 87 KDNKSETAEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLT 146 +D + + E +V L+ Q KV V GP S + AA A A + S T +G+T Sbjct: 71 EDEQGKKEEGINVFKKLIFQDKVLMVFGPTLSNSMFAAGPVANGAKTVVFGTSVTANGIT 130 Query: 147 KGQDYLFIGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKG---IAKSFRESYKG 203 Y+F + +S + ++ K+V + N + K + K E K Sbjct: 131 DIGPYVFRNSVMESDVLPVTVATATKHYKLKQVAVIYGNDDAFTKSGYDVFKKVLEDQKL 190 Query: 204 EIVADETFVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGDG 263 + ET+V GD DF+A LTK+K + DA++ EA I+ QARG+GI P +GG+G Sbjct: 191 PVTTTETYVKGDVDFKAQLTKIKASNPDAVICSCLAEEAANIMLQARGLGIKVPFIGGNG 250 Query: 264 FNGEEFVQQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYNEEPSTFAALAYDSV 323 FN + + ++ A F+ + + KAF+ AY KYN EP+ FAA A+D++ Sbjct: 251 FNSPKLFE--ISKLAGEGTFVGSPWSNTNPAPANKAFVAAYVKKYNAEPNQFAAQAFDAL 308 Query: 324 HLVANAAKGAKNSGEI-------KNNLAKTKDFEGVTGQTSF 358 H+ A A + K SG+I KN L K G TG F Sbjct: 309 HVAAAALQEVKLSGDIAADREALKNALPKA-TINGATGPFKF 349 Lambda K H 0.310 0.126 0.337 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: 333 Number of extensions: 17 Number of successful extensions: 3 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: 386 Length of database: 384 Length adjustment: 30 Effective length of query: 356 Effective length of database: 354 Effective search space: 126024 Effective search space used: 126024 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 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