Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_001484605.1:WP_058929663.1 Length = 345 Score = 127 bits (320), Expect = 2e-34 Identities = 79/244 (32%), Positives = 129/244 (52%), Gaps = 17/244 (6%) Query: 5 ENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYMGEE 64 ENV+ +G I A+ +E+ + +I LIG NGAGK+TL L G +SG ++ G Sbjct: 42 ENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKWQFEGNS 101 Query: 65 LVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD---------KG-------D 108 L G + R + + +V +LTV EN+ +GG KG + Sbjct: 102 LAGISPYKVARMGMVRTFQLTKVMGKLTVMENMRLGGSEQPGERLSKALFKGLWGGREKE 161 Query: 109 YQEQMDKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPII 168 Q + +L F +L + ++SGG++++L + R+LM +PKL++LDEP G+ P + Sbjct: 162 ITAQANVLLEKF-KLDAKKDDYAASLSGGQRKLLEMARSLMVRPKLVMLDEPMAGVNPAL 220 Query: 169 IQQIFDIIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVRE 228 Q + D I+ L+ +G+TV VE + N IAD V+ G++V +G ++ +P V + Sbjct: 221 TQSLLDHIKNLKAEGMTVLFVEHDMNMVRHIADWVVVMAEGKIVAEGPPGEVMKNPAVID 280 Query: 229 AYLG 232 AYLG Sbjct: 281 AYLG 284 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: 154 Number of extensions: 5 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: 233 Length of database: 345 Length adjustment: 26 Effective length of query: 207 Effective length of database: 319 Effective search space: 66033 Effective search space used: 66033 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