Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS08920 Length = 655 Score = 254 bits (650), Expect = 2e-72 Identities = 126/251 (50%), Positives = 171/251 (68%) Query: 4 TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63 TLLK+ + +FGGL+ALN V + + +G ++GLIGPNG+GK+T NV+TG+Y+P G E Sbjct: 391 TLLKVNQILMQFGGLKALNRVDLDVRKGTVHGLIGPNGSGKSTMMNVLTGIYRPTDGVVE 450 Query: 64 LDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAA 123 DG+P S + P +A G+ARTFQN++LFGEMT ENV+VG H NV + Sbjct: 451 YDGRPISGNVPSAIALGGVARTFQNVQLFGEMTATENVLVGLHHTFNSNVVDVMANTPRY 510 Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183 EE A RE++ +L+FVG+ A AR+L YG QR LEI RAL +P LL LDEPAAG Sbjct: 511 VREEQAARERAAAILEFVGLANLANEEARNLPYGKQRLLEIGRALGLNPSLLLLDEPAAG 570 Query: 184 MNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243 + A + L ++ KI+ G TI+LIEH + ++M +C+ +TVLD+G+ IAEG PA VQ + Sbjct: 571 LTAPDIKELVAIIRKIREAGITIILIEHHMDVVMSICDTVTVLDFGQKIAEGKPAQVQAD 630 Query: 244 PAVIEAYLGAG 254 P VIEAYLG+G Sbjct: 631 PKVIEAYLGSG 641 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: 441 Number of extensions: 23 Number of successful extensions: 1 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: 655 Length adjustment: 31 Effective length of query: 224 Effective length of database: 624 Effective search space: 139776 Effective search space used: 139776 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 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