Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 208247 DVU2741 high-affinity branched chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >MicrobesOnline__882:208247 Length = 255 Score = 256 bits (655), Expect = 2e-73 Identities = 134/255 (52%), Positives = 178/255 (69%), Gaps = 4/255 (1%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 MALLE+K LT+ FGGL AV D +EL GEL GLIGPNGAGKTT+FNL +G Y P+EG++ Sbjct: 1 MALLEIKGLTQRFGGLQAVSDFNIELEAGELAGLIGPNGAGKTTVFNLTSGFYTPTEGSI 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHK--QHVFTSFLRL 118 T DG G P+++ +LG+ RTFQNIRL+ DL+VLDN+ IA HH+ ++ +FLR Sbjct: 61 TFDGTPTRGLRPHQVTALGIARTFQNIRLWHDLSVLDNIRIA--QHHRLGYTLWDAFLRT 118 Query: 119 PAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEP 178 + EK + A A E+L+ DL A + +NL YG QRR+EI RA++ +PK+L LDEP Sbjct: 119 RRYTAGEKAIDAIAWEMLEAMDLKEYANEVPRNLPYGMQRRVEIARAMSMKPKLLLLDEP 178 Query: 179 AAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238 AAG+N + L LIR I DEF ITI +IEH M +VM + +RI V+++G IA GTP+ Sbjct: 179 AAGLNSVDVDGLIRLIRWIHDEFDITIWMIEHQMKVVMSLCQRIKVIDFGSTIADGTPET 238 Query: 239 IKTNKRVIEAYLGGE 253 I+TN VI+AYLG + Sbjct: 239 IQTNPVVIKAYLGDD 253 Lambda K H 0.319 0.139 0.385 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: 184 Number of extensions: 3 Number of successful extensions: 1 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: 254 Length of database: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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 (21.7 bits) S2: 47 (22.7 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