Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 6938989 Sama_3087 ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__SB2B:6938989 Length = 243 Score = 138 bits (348), Expect = 9e-38 Identities = 77/234 (32%), Positives = 129/234 (55%), Gaps = 3/234 (1%) Query: 4 LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63 LK NL+ Y Q V++VS VN G+VV L+G NGAGKTT + GLV+ G I Sbjct: 6 LKASNLAKSYKNRQVVKNVSLTVNTGQVVGLLGPNGAGKTTTFYMVVGLVQSDKGSIHIN 65 Query: 64 GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK--NREENQANLKKVFS 121 ++ P G+ +P+ +F L+V +N+ ++K N +E + L+++ Sbjct: 66 DDDLTLDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQMRKELNTDEREEALEQLLE 125 Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQD 181 F R N +LSGGE++ + + RAL + P+ +LLDEP G+ PI + +I II+ Sbjct: 126 EFHITHIRDNL-GMSLSGGERRRVEIARALAANPRFILLDEPFAGVDPISVIDIKKIIEQ 184 Query: 182 IQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 ++ +G VL+ + N + L + ++ Y++ G ++ GT E+ +++VR YLG Sbjct: 185 LKNRGLGVLITDHNVRETLDVCEKAYIVSHGDLIAEGTPAEILDNQQVRAVYLG 238 Lambda K H 0.315 0.134 0.358 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: 122 Number of extensions: 5 Number of successful extensions: 2 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: 236 Length of database: 243 Length adjustment: 23 Effective length of query: 213 Effective length of database: 220 Effective search space: 46860 Effective search space used: 46860 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: 46 (22.3 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