Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Pf6N2E2_1705 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1705 Length = 256 Score = 199 bits (507), Expect = 4e-56 Identities = 101/252 (40%), Positives = 157/252 (62%), Gaps = 1/252 (0%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL++R+VS F G++A++ + +++ G+I LIGPNGAGK++ N++ G+Y+ D G Sbjct: 4 LLEVRNVSLSFRGVKAISDLSFSVKLGEICALIGPNGAGKSSLLNILNGVYRADAGQLFF 63 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 +P P + A+ GI RTFQN LF +M+V++N++ G + AR Sbjct: 64 AAEPLHRPHPLKAARLGIGRTFQNNALFKKMSVVDNLLTGLSRFQRTFFLEQALGLPRAR 123 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 E A E+++++L+F+ + + L+YG Q+R+E+ RAL P LL LDEP AGM Sbjct: 124 REARAFAERAERVLEFLELQAWRDVAVGSLAYGLQKRVELGRALIAQPTLLLLDEPMAGM 183 Query: 185 NATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243 NA EK + + I + G T++LIEHD++++MGL + + VLDYG+ + +G PA+VQ N Sbjct: 184 NAEEKQDMSRFITDINRDLGTTVILIEHDIQVVMGLSSHVVVLDYGRKVGDGSPAEVQVN 243 Query: 244 PAVIEAYLGAGH 255 P VI AYLGA H Sbjct: 244 PEVIAAYLGASH 255 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: 166 Number of extensions: 7 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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