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_029133998.1 A3GO_RS0114445 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000428045.1:WP_029133998.1 Length = 271 Score = 201 bits (510), Expect = 2e-56 Identities = 105/240 (43%), Positives = 163/240 (67%), Gaps = 8/240 (3%) Query: 4 LKVENLSVHYG-MIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRP-----SS 57 L+V N+ V Y +I ++ VS EV +G +V+L+GANGAGK+T L+ +S L+ + Sbjct: 9 LEVNNIEVIYDHVILVLKGVSLEVPKGGIVALLGANGAGKSTTLKAISNLLGAERGDVTK 68 Query: 58 GKIEFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKN-REENQANL 116 G I + G+ ++ + +V G+ QV EGRH F LT+ ENL GA+ +++ R+ +L Sbjct: 69 GNILYKGEAVESLNPSDLVRRGVVQVMEGRHCFEHLTIEENLLTGAYTRRDGRKAIAQSL 128 Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176 + ++ FPRL ER++ A SGGEQQM A+GRA+++ P+++LLDEPSMGLAP ++EIF Sbjct: 129 EMIYDYFPRLRERRSSQAGYTSGGEQQMCAIGRAMLAQPEMILLDEPSMGLAPQLVEEIF 188 Query: 177 DIIQDI-QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 +I++ + Q +G + LL EQN N AL SD GY++E G++V+ G KEL+ +E+V++ YLG Sbjct: 189 EIVKKLNQNEGVSFLLAEQNTNVALRYSDYGYIMENGRVVMEGNAKELSENEDVKEFYLG 248 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: 174 Number of extensions: 11 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: 236 Length of database: 271 Length adjustment: 24 Effective length of query: 212 Effective length of database: 247 Effective search space: 52364 Effective search space used: 52364 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