Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000017185.1:WP_011972867.1 Length = 281 Score = 107 bits (267), Expect = 3e-28 Identities = 77/241 (31%), Positives = 127/241 (52%), Gaps = 22/241 (9%) Query: 5 LLKIRDVSKRF-GGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63 +++ +D+ ++ G AL+ I++E+G + L+GPNGAGK+T F G+ +P +G Sbjct: 3 IIEAKDIVYKYPDGTLALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGKIL 62 Query: 64 LDGKP--YSPSAPHEVAKAGIARTFQNI--RLFGEMTVLENVMVGCHVRTKQNVFGAVFR 119 L G P Y + EV K + FQN +LF TV ++V FG + Sbjct: 63 LKGAPIKYDAKSLMEVRKT-VGIVFQNSDDQLFAP-TVKQDV-----------AFGPL-- 107 Query: 120 HKAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDE 179 + +EEE + ++ ++ L VG+ F + HLS G ++R+ IA LA P+++ LDE Sbjct: 108 NLGLKEEE--VEKRVKEALKEVGMEGFENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDE 165 Query: 180 PAAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239 P AG++ + +LL K+ EG TI++ HDV L+ N+I V+ K + G + Sbjct: 166 PTAGLDPMGASKIMKLLYKLNKEGITIIISTHDVDLVPIYANKIFVMGKTKIVKSGTVEE 225 Query: 240 V 240 V Sbjct: 226 V 226 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: 151 Number of extensions: 6 Number of successful extensions: 2 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: 281 Length adjustment: 25 Effective length of query: 230 Effective length of database: 256 Effective search space: 58880 Effective search space used: 58880 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 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