Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1701 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1701 Length = 258 Score = 197 bits (500), Expect = 2e-55 Identities = 111/242 (45%), Positives = 156/242 (64%), Gaps = 9/242 (3%) Query: 1 MLQFENVSTFY-GKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHS---- 55 +L +++ Y G I A+ V++ V QG+IV L+GANGAGKST L + G QA Sbjct: 14 LLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAQVS 73 Query: 56 -GSIRYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD--KGDYQEQ 112 G I + G + G ++ + R+ I V EGR VFA LTVE+NL GGF + ++ Sbjct: 74 RGRIVFQGRDTAGVAANLLARQGIVHVLEGRHVFAHLTVEDNLRSGGFLRKPTRRALEQD 133 Query: 113 MDKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQI 172 ++++ FPRLK + + G SGGEQQMLAIGRALM+KP+L+LLDEPS+GLAP+++++I Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPLLVEEI 193 Query: 173 FDIIEQLR-KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYL 231 F I+ QL ++GV+ + EQN N AL+ A AY+LENGRVV +G AL ++ YL Sbjct: 194 FAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATALAAREDIQHFYL 253 Query: 232 GG 233 GG Sbjct: 254 GG 255 Lambda K H 0.320 0.137 0.381 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: 184 Number of extensions: 9 Number of successful extensions: 4 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: 233 Length of database: 258 Length adjustment: 24 Effective length of query: 209 Effective length of database: 234 Effective search space: 48906 Effective search space used: 48906 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: 46 (22.3 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