Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_012336126.1 M446_RS31400 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000019365.1:WP_012336126.1 Length = 244 Score = 209 bits (533), Expect = 3e-59 Identities = 108/238 (45%), Positives = 158/238 (66%), Gaps = 7/238 (2%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64 +L ++ YG+I+A+ VS + GE+VTL+G+NGAGK+T L T+ G + G ++F Sbjct: 3 LLEIRDLTVRYGEIEAVRGVSFAVEPGEVVTLLGSNGAGKSTTLKTISGLVKPAGGEVLF 62 Query: 65 DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMG-----GFFAERDQFQERIKW 119 + + + + +I+R VA VPEGRRVF +TV EN+ +G G A R ++ + Sbjct: 63 EGQPLVGLKPEEIVRRGVAHVPEGRRVFPGLTVRENIMLGASNRTGLSARR--IRDEAEG 120 Query: 120 VYELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDT 179 ++ELFP + T+SGG+ QM+A+ R LM+ PR+LLLDEPSLGLAP+I+Q +F Sbjct: 121 MFELFPDIRRFGDALGWTLSGGQLQMVALARGLMAKPRILLLDEPSLGLAPVIVQAVFSI 180 Query: 180 IEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLGG 237 I ++R +G T+ LVEQNA L +ADRGYVLE G +VLS + D+L AN+ +R+AYLGG Sbjct: 181 IAEVRRRGTTVLLVEQNARMGLSVADRGYVLETGQLVLSGSPDSLWANDDIRAAYLGG 238 Lambda K H 0.321 0.137 0.390 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: 154 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: 237 Length of database: 244 Length adjustment: 23 Effective length of query: 214 Effective length of database: 221 Effective search space: 47294 Effective search space used: 47294 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