Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate AZOBR_RS29680 AZOBR_RS29680 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >FitnessBrowser__azobra:AZOBR_RS29680 Length = 272 Score = 224 bits (572), Expect = 1e-63 Identities = 119/254 (46%), Positives = 161/254 (63%), Gaps = 1/254 (0%) Query: 1 MSQPLLSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGG 60 ++ P+L V + + F GL+A+ +++ + EIVSLIGPNGAGKTT FN +TGF KPTGG Sbjct: 13 LAGPVLEVREVAVHFSGLIAIASMSFAVPEGEIVSLIGPNGAGKTTAFNVITGFLKPTGG 72 Query: 61 TILLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKT 120 +L R L L +IA +GVVRTFQ +F TV +N+L H+Q + + LL+ Sbjct: 73 KVLFRGTDLTRLSSNRIAGLGVVRTFQRTSIFAGCTVFDNVLTGMHRQGRAETWGALLRL 132 Query: 121 PSFRRAQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEP 180 S R A L +GL A+ A NLAYG+QR L IA + P++L+LDEP Sbjct: 133 ASVRAETERMRAAVAEILAFVGLSHRADELAGNLAYGEQRLLGIAIALAADPKLLLLDEP 192 Query: 181 AAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQ 240 AAGLNP ET+ ++ +R+ TILL+EHDM++VM ISDR+ V+N G +A G PE Sbjct: 193 AAGLNPSETEAFMGVVQRIRD-RGVTILLVEHDMRMVMTISDRVVVLNHGRIIAEGPPEV 251 Query: 241 IRNNPDVIRAYLGE 254 IR NPDVI+AYLG+ Sbjct: 252 IRANPDVIQAYLGQ 265 Lambda K H 0.320 0.137 0.395 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: 207 Number of extensions: 13 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: 255 Length of database: 272 Length adjustment: 25 Effective length of query: 230 Effective length of database: 247 Effective search space: 56810 Effective search space used: 56810 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: 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