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_011867836.1 MMARC5_RS00300 ATP-binding cassette domain-containing protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000016125.1:WP_011867836.1 Length = 312 Score = 95.9 bits (237), Expect = 8e-25 Identities = 62/190 (32%), Positives = 111/190 (58%), Gaps = 8/190 (4%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +LK+E L + Q ++ V+ ++++ + L+G +GAGK+ I++ ++G+++P SG+I F Sbjct: 1 MLKLEKLCKSWKEFQ-LKSVNLDIDDNYCI-LLGPSGAGKSVIIQCITGILKPDSGRIYF 58 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 G++I +P +K G VP+ +FP + V N+ G L+K + + Sbjct: 59 DGEDITDIPPEKRNFG---YVPQNYALFPHMNVYNNIAYGMKLRKCPKLEIEKKITEIAE 115 Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182 F ++ N+ TLSGGEQQ +A+ RAL+ PK+LLLDEP+ L I+E ++I ++ Sbjct: 116 FLKITHILNRKPTTLSGGEQQRVAIARALVLDPKILLLDEPTSAL-DTNIKE--NVISEL 172 Query: 183 QKQGTTVLLI 192 ++ G V +I Sbjct: 173 KRIGELVPII 182 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: 156 Number of extensions: 8 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: 236 Length of database: 312 Length adjustment: 25 Effective length of query: 211 Effective length of database: 287 Effective search space: 60557 Effective search space used: 60557 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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