Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_058859430.1 AS188_RS14460 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_001482365.1:WP_058859430.1 Length = 269 Score = 105 bits (263), Expect = 7e-28 Identities = 71/228 (31%), Positives = 122/228 (53%), Gaps = 12/228 (5%) Query: 6 VENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFLGQ 65 VE+L YG ++ ++ +S V G+VV LIG +G+GK+T+LR ++ L P G+I Sbjct: 23 VEDLHKSYGSLEVLKGISLTVAAGQVVCLIGPSGSGKSTLLRCVNLLETPQKGRITIGDV 82 Query: 66 EIQKMPAQ-KIVAGGLSQVPEGRHVFPGLTVMENLEMGAF--LKKNREENQ----ANLKK 118 E+ A + + V + ++FP L+V+EN + LK+ + E + ANL++ Sbjct: 83 EVTDPEADVDRLRRHVGMVFQQFNLFPHLSVLENCTVAQVKVLKREKAEAERIARANLER 142 Query: 119 VFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDI 178 V L E+ + LSGG+QQ +A+ RAL P L+L DEP+ L P + ++ I Sbjct: 143 V-----GLAEKADGYPDQLSGGQQQRVAIARALSMDPSLMLFDEPTSALDPETVGDVLAI 197 Query: 179 IQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASS 226 ++ + +G T+L++ A ++DR ++ G +V G E+ S Sbjct: 198 MRSLAAEGMTMLVVTHEMEFARDVADRVVFMDGGVVVEEGPAAEVIGS 245 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: 7 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: 269 Length adjustment: 24 Effective length of query: 212 Effective length of database: 245 Effective search space: 51940 Effective search space used: 51940 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 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