Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_057687611.1 ABB28_RS17405 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_001431535.1:WP_057687611.1 Length = 587 Score = 97.1 bits (240), Expect = 7e-25 Identities = 72/231 (31%), Positives = 117/231 (50%), Gaps = 13/231 (5%) Query: 2 LQFENVSTFYGK---IQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSI 58 ++F++V Y + AL ++ VR GE V L+G +GAGKST+L L SG++ Sbjct: 347 IRFDDVVFHYPQRPDTAALEHFSLHVRHGETVALVGPSGAGKSTVLQLLLRFHDPRSGAL 406 Query: 59 RYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQ-----EQM 113 G +L D + +R +A+VP+ +FA + +N+ G + + + Sbjct: 407 SVDGIDLRAMDPA-ALRAQLALVPQQPTLFA-ASARDNIRYGRLDASDAEVEAAARAAEA 464 Query: 114 DKVLHLFP-RLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQI 172 D+ L P +RG +SGG+QQ +AI RAL+ +LLLDE + L + + Sbjct: 465 DEFLRALPDGYDSELGERGARLSGGQQQRIAIARALLKDAPILLLDEATSALDAQSERAV 524 Query: 173 FDIIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTD 223 +E+L G T ++ LK ADR V+++GR++ QGT E LL + Sbjct: 525 QQALERLMA-GRTTLVIAHRLATILK-ADRIVVMDHGRIIAQGTHEQLLAE 573 Lambda K H 0.320 0.137 0.381 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: 281 Number of extensions: 14 Number of successful extensions: 3 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: 233 Length of database: 587 Length adjustment: 30 Effective length of query: 203 Effective length of database: 557 Effective search space: 113071 Effective search space used: 113071 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 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