Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_051242907.1 H537_RS0117810 hypothetical protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000430725.1:WP_051242907.1 Length = 637 Score = 221 bits (564), Expect = 2e-62 Identities = 116/250 (46%), Positives = 168/250 (67%), Gaps = 2/250 (0%) Query: 3 QTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTF 62 Q +L+ +V+KRFGGL A N V + ++ G+I LIGPNGAGK+TFFN+I+G+ P +G Sbjct: 381 QVVLEASEVTKRFGGLVANNAVNLHVKAGEILALIGPNGAGKSTFFNMISGVDDPTSGEV 440 Query: 63 ELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122 L G+ A G++R+FQ++RL G+ TVLENV VG H+R + ++ R Sbjct: 441 RLMGQAMKGKPSRAFAALGLSRSFQHVRLLGQRTVLENVAVGAHLRASRGWIASMLR--L 498 Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182 R EEAA+ ++++ ++ G+G A A L+ G QR +EIARALA+ P +L LDEPAA Sbjct: 499 DRAEEAAVLAEARRQIERCGLGAHADTPAASLALGQQRIVEIARALASQPAVLLLDEPAA 558 Query: 183 GMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 G+ EK L +LL +++AEG IL++EHD++ +M L +RITVL++G IAEG PA+VQ Sbjct: 559 GLRHLEKQALAKLLDQLRAEGLGILVVEHDMEFVMNLADRITVLEFGTVIAEGTPAEVQG 618 Query: 243 NPAVIEAYLG 252 N V++AYLG Sbjct: 619 NQRVLDAYLG 628 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: 413 Number of extensions: 18 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: 637 Length adjustment: 31 Effective length of query: 224 Effective length of database: 606 Effective search space: 135744 Effective search space used: 135744 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 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