Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_011384429.1 AMB_RS10230 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000009985.1:WP_011384429.1 Length = 234 Score = 232 bits (592), Expect = 4e-66 Identities = 115/233 (49%), Positives = 162/233 (69%), Gaps = 1/233 (0%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 ML+ ++ YG QAL V+++V +GE+V +IGANGAGK++L+ + G + GSIR+ Sbjct: 1 MLEVRDLDLHYGDAQALDGVSLDVAEGEVVAIIGANGAGKTSLIRAIAGMKKPSRGSIRF 60 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD-KGDYQEQMDKVLHL 119 G ++ G+ SS I +A V EGR++F ++V ENL MG + +E +++ + Sbjct: 61 EGHDIAGRASSRICDLGVAQVAEGRQIFPSMSVRENLEMGAVLPRARSKRKETLERCYEM 120 Query: 120 FPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQL 179 FP+LK R Q GT+SGGEQQMLAIGR LM +P+L++ DEPSLGLAP ++ ++F II+ L Sbjct: 121 FPKLKVRSDQAAGTLSGGEQQMLAIGRCLMGQPRLMMFDEPSLGLAPAVVSEMFKIIKTL 180 Query: 180 RKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 +G+TV LVEQN + +LK+ADR YVLENGRVV+ GTG LL D VR+AYLG Sbjct: 181 HAEGMTVILVEQNVSASLKLADRGYVLENGRVVLSGTGSGLLNDDGVRQAYLG 233 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: 183 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: 234 Length adjustment: 23 Effective length of query: 210 Effective length of database: 211 Effective search space: 44310 Effective search space used: 44310 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 17 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