Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 130 bits (328), Expect = 4e-35 Identities = 74/228 (32%), Positives = 130/228 (57%), Gaps = 12/228 (5%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 +++++D+ K F G+ A + V + +++G+I+ L+G NGAGK+T NV+ GLYQP+ G + Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 GKP + P+ + GI Q+ L + TV EN+++G + G + KAA+ Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILG----KEPTAGGKINIKKAAK 119 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 E ++ + + +AK + +S G Q+R+EI + L ++L DEP A + Sbjct: 120 AVETISKQYG------LAVDPYAK--IQDISVGMQQRVEILKTLYRGAEILIFDEPTAAL 171 Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPI 232 E L +++ K+ +EGK+I+LI H +K +M +C+R TV+ G+ I Sbjct: 172 TPQEITELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGI 219 Score = 89.7 bits (221), Expect = 1e-22 Identities = 64/234 (27%), Positives = 122/234 (52%), Gaps = 13/234 (5%) Query: 5 LLKIRD-VSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63 +L+I+D V K + A+N + + + G+I G+ G +G G+T ITGL +P G + Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315 Query: 64 LDGKPYSPSAPHEVAKAGIARTFQNIRLFG---EMTVLENVMVGCHVRTKQNVFGAVFRH 120 L+G+ + P ++ AG+ Q+ G + TV EN+++ + + + G + + Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFN 375 Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRT-ARHLSYGDQRRLEIARALATDPQLLALDE 179 + I +K+ +L++ + ++ T AR LS G+Q++ IAR + P LL + Sbjct: 376 E--------IYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQ 427 Query: 180 PAAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIA 233 P G++ + LVK + +GK +LLI ++ ++ + +RI V+ GK +A Sbjct: 428 PTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVA 481 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: 309 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 255 Length of database: 509 Length adjustment: 29 Effective length of query: 226 Effective length of database: 480 Effective search space: 108480 Effective search space used: 108480 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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