Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Pf1N1B4_3215 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3215 Length = 255 Score = 231 bits (590), Expect = 8e-66 Identities = 116/253 (45%), Positives = 166/253 (65%), Gaps = 1/253 (0%) Query: 1 MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60 MS+ +LK+ D+S RFGGL A+N V +T++ Q+ +IGPNGAGKTT FN +TG YQP G Sbjct: 1 MSREILKVTDLSMRFGGLLAVNSVALTVKEKQVVSMIGPNGAGKTTVFNCLTGFYQPTAG 60 Query: 61 TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120 + LDG+ H++A G+ RTFQN+RLF +MT +EN+++ H N +F+ Sbjct: 61 SIVLDGEQIQGLPGHKIALKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFLAGLFKT 120 Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180 A R E E ++ L+ V + +FA R A L+YG QRRLEIAR + T P++L LDEP Sbjct: 121 PAFRRSEREAMEYAEYWLEKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 Query: 181 AAGMNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239 AAG+N E L+ L+ ++ E T+LLIEHD+KL+M + + I V++ G P+A+G P Sbjct: 181 AAGLNPRETEDLKALIGILREEHDVTVLLIEHDMKLVMSISDHIFVINQGTPLADGTPEQ 240 Query: 240 VQKNPAVIEAYLG 252 ++ NP VI+AYLG Sbjct: 241 IRDNPEVIKAYLG 253 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: 183 Number of extensions: 8 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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