Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_008804341.1 KVAR_RS09630 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000025465.1:WP_008804341.1 Length = 239 Score = 251 bits (642), Expect = 7e-72 Identities = 129/232 (55%), Positives = 165/232 (71%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +L F V FYG IQAL V++ V +GE V LIGANGAGKSTLLM++ G P+ G I Y Sbjct: 5 LLAFNEVDVFYGPIQALKQVSLTVNEGETVALIGANGAGKSTLLMSVFGQPRIAGGEIFY 64 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120 GE + + + I IA PEGRR+F +TVEENL MG E ++ LF Sbjct: 65 RGEAISRKSTHFIASNGIAQAPEGRRIFPDMTVEENLLMGTIAIGNRYQAEDKARMYQLF 124 Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180 PRL+ER QR T+SGGEQQMLAI RALMS+P+LLLLDEPSLGLAP++++QIF I+ +L Sbjct: 125 PRLEERRGQRAMTLSGGEQQMLAIARALMSRPRLLLLDEPSLGLAPLVVKQIFQILRELT 184 Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 G+T+FLVEQNA AL ++DRAYV+ NG++ + G+G+ALL DP+VR+AYLG Sbjct: 185 AQGMTLFLVEQNARHALNLSDRAYVMVNGQIRLSGSGQALLNDPEVRKAYLG 236 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: 199 Number of extensions: 6 Number of successful extensions: 1 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: 239 Length adjustment: 23 Effective length of query: 210 Effective length of database: 216 Effective search space: 45360 Effective search space used: 45360 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: 46 (22.3 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