Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_1937 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1937 Length = 279 Score = 210 bits (535), Expect = 2e-59 Identities = 106/257 (41%), Positives = 165/257 (64%), Gaps = 6/257 (2%) Query: 2 SQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGT 61 + TLL +++S RFGG+ A+N V + RG+++ LIGPNGAGKTT FN+I+ +Y P TGT Sbjct: 3 NDTLLSAQNLSVRFGGVLAVNNVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYTPTTGT 62 Query: 62 FELDGK-----PYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGA 116 G P + PH+VA GIARTFQNI LF +VL N+++G H + +++ Sbjct: 63 IAYAGPGGAMLPLTDQPPHKVASLGIARTFQNIELFEHASVLHNLLIGRHTQQHSSLWAE 122 Query: 117 VFRHKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLA 176 +F + RE E REK+++++DF+ + + L YG ++ +E+ARAL T+P+LL Sbjct: 123 MFFTRKVREGEIQAREKAEQIIDFLDLQHYRDTMVAGLPYGVRKVVELARALCTEPKLLL 182 Query: 177 LDEPAAGMNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEG 235 LDEP++G+N E + + IQ E G T+L++EHD+ L+ + +R+ ++ G+ +A G Sbjct: 183 LDEPSSGLNVEETDDMAFWIQDIQHELGITVLMVEHDMSLVSKVSDRVLAMNQGEVVAMG 242 Query: 236 VPADVQKNPAVIEAYLG 252 P +VQ +P V+EAYLG Sbjct: 243 TPREVQTHPGVVEAYLG 259 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: 194 Number of extensions: 9 Number of successful extensions: 3 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: 279 Length adjustment: 25 Effective length of query: 230 Effective length of database: 254 Effective search space: 58420 Effective search space used: 58420 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