Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 125 bits (313), Expect = 2e-33 Identities = 76/243 (31%), Positives = 131/243 (53%), Gaps = 19/243 (7%) Query: 3 QTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTF 62 + LLKI VSK F ++A++ V +TI +G+I+ L+G +G+GK+T ++ G +P G Sbjct: 18 EVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRI 77 Query: 63 ELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122 LDG+ + P+E I FQ+ LF MTV +N+ G K Sbjct: 78 YLDGQDITDLPPYE---RPINMMFQSYALFPHMTVEQNIAFGL---------------KQ 119 Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182 + +A I ++ Q++L V + Q+AKR LS G ++R+ +AR+LA P+LL LDEP Sbjct: 120 DKMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMG 179 Query: 183 GMNATEKLGLR-ELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241 ++ + ++ E++ ++ G T +++ HD + M + RI ++ G G P D+ Sbjct: 180 ALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIY 239 Query: 242 KNP 244 ++P Sbjct: 240 ESP 242 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: 186 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: 255 Length of database: 378 Length adjustment: 27 Effective length of query: 228 Effective length of database: 351 Effective search space: 80028 Effective search space used: 80028 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: 48 (23.1 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