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_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 114 bits (284), Expect = 3e-30 Identities = 73/222 (32%), Positives = 124/222 (55%), Gaps = 5/222 (2%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 +L++E+++V G Q + D++ EV EGE ++G G GKT IL T++G+ RP G I F Sbjct: 1 MLRLEHVTVKLGEFQLL-DINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRF 59 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 + + + ++ G + Q +FP LTV EN+ GA ++K ++ + Sbjct: 60 KERNLATLAPEQRKVGFVYQ---DYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVA 116 Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182 + N+ +TLSGGEQQ A+ RAL+ +P++LLLDEP L P + + ++ I Sbjct: 117 MLGIGHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKI 176 Query: 183 -QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223 Q TT L + + N+A+ ++D+ V+ G+I+ GT +E+ Sbjct: 177 HQTLKTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEI 218 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: 176 Number of extensions: 7 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: 344 Length adjustment: 26 Effective length of query: 210 Effective length of database: 318 Effective search space: 66780 Effective search space used: 66780 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