Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_013519969.1 ALIDE2_RS06395 high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG
Query= uniprot:A0A165KC86 (260 letters) >NCBI__GCF_000204645.1:WP_013519969.1 Length = 257 Score = 235 bits (599), Expect = 8e-67 Identities = 114/248 (45%), Positives = 164/248 (66%), Gaps = 1/248 (0%) Query: 10 LKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELA 69 L V G+S RFGGL A+ + +K +++ +IGPNGAGKTT FN I+G Y P G L Sbjct: 8 LHVDGLSMRFGGLLAVDGIAFDVKEREIFAIIGPNGAGKTTVFNCISGFYRPTTGNIRLQ 67 Query: 70 GKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKA 129 G+ H VA G+ RTFQN+RLF MT LEN++V +H + L +F+T+ ++ Sbjct: 68 GQDIAGQGSHSVALNGLVRTFQNVRLFKHMTVLENLLVAQHRHLSTNLLSGLFKTRSYRE 127 Query: 130 EEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMN 189 E + A LDY+G+ +F + +A L+YG QRRLEIAR + T P+++ LDEPAAG+N Sbjct: 128 SEQKALENALHWLDYMGLREFVNREAGNLAYGHQRRLEIARCMVTKPRVLMLDEPAAGLN 187 Query: 190 ATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248 EK L+ LI+++R + +LLIEHD+ LVMG+ +R+ V++YG+ IA G P +QK+E Sbjct: 188 PQEKKDLQGLIEKLRQEYGVAVLLIEHDMSLVMGVSERILVMEYGRPIALGTPDAIQKDE 247 Query: 249 KVIEAYLG 256 +VI+AYLG Sbjct: 248 RVIKAYLG 255 Lambda K H 0.319 0.137 0.384 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: 198 Number of extensions: 9 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: 260 Length of database: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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