Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000020045.1:WP_012402388.1 Length = 594 Score = 213 bits (542), Expect = 7e-60 Identities = 115/250 (46%), Positives = 160/250 (64%), Gaps = 2/250 (0%) Query: 3 QTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTF 62 + LL + K+FGGL A+N V ++ GQI GLIGPNGAGK+T FN++TG+ Q +G Sbjct: 344 EPLLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGAI 403 Query: 63 ELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122 G+ E+ K GI RTFQ+++L MTVLENV +G H+R + V+ +V R Sbjct: 404 TFRGERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGGHLRGRAGVWRSVARLNG 463 Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182 A EE + ++ + + VG+ + A L+ G QR LEIARAL DP LL LDEPAA Sbjct: 464 A--EEGRLMAEAARQIRRVGLEEHMYDEAGSLALGKQRILEIARALCCDPTLLLLDEPAA 521 Query: 183 GMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 G+ EK L LL K++ EG ++LL+EHD+ +M L +R+ V+++G IAEG+P DVQ Sbjct: 522 GLRYQEKQQLATLLRKLREEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQDVQN 581 Query: 243 NPAVIEAYLG 252 +PAV+EAYLG Sbjct: 582 DPAVLEAYLG 591 Lambda K H 0.320 0.138 0.394 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: 370 Number of extensions: 16 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: 255 Length of database: 594 Length adjustment: 30 Effective length of query: 225 Effective length of database: 564 Effective search space: 126900 Effective search space used: 126900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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