Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_013554637.1 NITSA_RS08645 amino acid ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000186245.1:WP_013554637.1 Length = 287 Score = 126 bits (317), Expect = 4e-34 Identities = 70/229 (30%), Positives = 129/229 (56%), Gaps = 5/229 (2%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 ++Q +NV+ +YG L +N++V++GEIV + G +G+GKST++ + + GSI+ Sbjct: 46 IIQLQNVNKWYGDFHVLKDINLDVKKGEIVVVAGPSGSGKSTMIRCINRLEEYQEGSIKV 105 Query: 61 MGEELVGQDSSHI--MRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLH 118 G E V D ++ +R ++A+V + +F LT+ ENL + + K +E ++ +H Sbjct: 106 NGIE-VNNDVKNLRQVRSNVAMVFQHFNLFPHLTILENLTLAPVWVYKKPKKEAIETAMH 164 Query: 119 LFPRLK--ERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDII 176 ++ E+ + +SGG+QQ +AI RAL P ++L DEP+ L P +I ++ D++ Sbjct: 165 YLEKVNIAEQANKYPNQLSGGQQQRVAIARALCKNPDIMLFDEPTSALDPEMIGEVLDVM 224 Query: 177 EQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPK 225 +L ++G T+ V A K+ADR ++ G++V + E P+ Sbjct: 225 MKLAEEGKTMVTVTHEMGFARKVADRVIFMDAGQIVEENDPETFFHHPE 273 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: 145 Number of extensions: 9 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: 287 Length adjustment: 24 Effective length of query: 209 Effective length of database: 263 Effective search space: 54967 Effective search space used: 54967 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 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