Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_004204908.1 KVAR_RS20300 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000025465.1:WP_004204908.1 Length = 231 Score = 237 bits (605), Expect = 1e-67 Identities = 124/233 (53%), Positives = 165/233 (70%), Gaps = 2/233 (0%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 ML + FYG IQ L V+++V EIVTLIG+NGAGK++ L + ++ SG + + Sbjct: 1 MLNARELKVFYGVIQGLKGVDIDVYDREIVTLIGSNGAGKTSTLNGIVNLVRS-SGRVSF 59 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120 + +++ + I+R+ +A+VPEGRRVF LT+EENL MG + G Y D++ LF Sbjct: 60 LNDDISRSQTHQIVRRGLALVPEGRRVFTNLTIEENLRMGAYNNLAG-YTRLRDRMYALF 118 Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180 PRLKER Q GTMSGGEQQMLAI RALMS+P LL+LDEPSLGLAP I+ ++F II+QLR Sbjct: 119 PRLKERRHQMAGTMSGGEQQMLAIARALMSEPVLLMLDEPSLGLAPKIVGELFGIIKQLR 178 Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLGG 233 ++ +TV LVEQNA AL IADRAYVLENGR+ + G +LT+P+++ YLGG Sbjct: 179 EENMTVLLVEQNATAALAIADRAYVLENGRITLSGAAREMLTNPEIKRMYLGG 231 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: 168 Number of extensions: 5 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: 231 Length adjustment: 23 Effective length of query: 210 Effective length of database: 208 Effective search space: 43680 Effective search space used: 43680 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