Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate RR42_RS00210 RR42_RS00210 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__Cup4G11:RR42_RS00210 Length = 241 Score = 230 bits (587), Expect = 2e-65 Identities = 113/232 (48%), Positives = 163/232 (70%), Gaps = 1/232 (0%) Query: 2 LQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYM 61 L + ++T Y K+ LH V+++V G+I ++GANGAGKSTL+ + G G + + Sbjct: 10 LSVKGLTTGYDKVNVLHDVSIDVAPGKITCILGANGAGKSTLIRAILGLTPPRQGQVLWD 69 Query: 62 GEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFF-TDKGDYQEQMDKVLHLF 120 G++L G+ + +I+ IA +PEGR++F R+TV ENLA+G + TD ++++ KV +F Sbjct: 70 GKDLAGEKTHNIIATGIACIPEGRKIFPRMTVAENLALGAYLETDAARVRDRLAKVYDIF 129 Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180 PRLKER TQ GTMSGGEQ M++IGR LM++PKLL++DEPSLGL+P+ +++ F +I+Q+ Sbjct: 130 PRLKERATQLAGTMSGGEQAMVSIGRGLMAEPKLLVIDEPSLGLSPLYVKENFKVIKQIN 189 Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 G+TV LVEQNA Q L I+ YVL GRVV QGT EAL ++ +VR AY G Sbjct: 190 ALGITVLLVEQNARQTLAISHYGYVLSQGRVVAQGTAEALASNDEVRSAYFG 241 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: 166 Number of extensions: 3 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: 241 Length adjustment: 23 Effective length of query: 210 Effective length of database: 218 Effective search space: 45780 Effective search space used: 45780 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