Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_084058845.1 B9A12_RS14615 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_900176285.1:WP_084058845.1 Length = 236 Score = 239 bits (610), Expect = 3e-68 Identities = 123/235 (52%), Positives = 166/235 (70%), Gaps = 2/235 (0%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64 ML + YG I+ LH ++L + +GEIVT++GANGAGK+T L T+ G + SG + + Sbjct: 1 MLQLVDLRVKYGNIEVLHGINLEVKEGEIVTILGANGAGKSTTLLTISGLVKPASGAVYY 60 Query: 65 DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFA-ERDQFQERIKWVYEL 123 + K++ +A VPEGRR+F +TV+ENL +G F + + ++ +W+YEL Sbjct: 61 HKTSLHKRPPHKVVEAGIAHVPEGRRIFGTLTVQENLNLGAFTCRDAGRIRKTQEWIYEL 120 Query: 124 FPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQL 183 FP L ERR Q AGT+SGGEQQMLAIGR LMS+P++LLLDEPSLGLAP++++ IF TI+++ Sbjct: 121 FPVLAERRNQLAGTLSGGEQQMLAIGRGLMSHPKILLLDEPSLGLAPLLVKTIFQTIQEI 180 Query: 184 REQ-GMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLGG 237 + G+TI LVEQNA ALKLA RGYVLE G++VL DT LLAN V+ AYLGG Sbjct: 181 NQSGGVTIVLVEQNARAALKLAHRGYVLEVGNIVLEDTAQGLLANSDVQKAYLGG 235 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: 169 Number of extensions: 6 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: 237 Length of database: 236 Length adjustment: 23 Effective length of query: 214 Effective length of database: 213 Effective search space: 45582 Effective search space used: 45582 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