Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 202770 SO_3675 hemin importer ATP-binding subunit (RefSeq)
Query= TCDB::P0A9S7 (255 letters) >FitnessBrowser__MR1:202770 Length = 272 Score = 100 bits (249), Expect = 3e-26 Identities = 74/250 (29%), Positives = 122/250 (48%), Gaps = 24/250 (9%) Query: 6 LSVNGLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLR 65 L+V+ L G +NN+ ++ P + +L+GPNGAGK+T+ L G+I L Sbjct: 20 LTVDRLSYAIGDKAVLNNIRVQFQPGSVTALLGPNGAGKSTLLKALCQEIPSAQGSIKLG 79 Query: 66 DQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRR 125 L P ++A+ V QH L TV E + + GL+ L Sbjct: 80 HCQLVDWPRAELAKSLAVLP-QHASLTFPFTVDEVVAM--------GLYPLTL------- 123 Query: 126 AQSEALDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQ------PEILMLDE 179 +Q E WL +G+L A R L+ G+++R+++AR ++TQ P IL+LDE Sbjct: 124 SQKEGQQLVTKWLAEVGVLHLARRSYPTLSGGEKQRVQLAR-VLTQLSQSPFPPILLLDE 182 Query: 180 PAAGLNPKETKELDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPE 239 P + L+ + ++ L L + H T++++ HD+ SDR+ V+ QG ++ GTP Sbjct: 183 PTSALDLAQQHKVLALAKNLAHKHAYTVIVVLHDLNQAARYSDRVIVLKQGEIVSEGTPN 242 Query: 240 QIRNNPDVIR 249 + D+IR Sbjct: 243 DAL-SIDIIR 251 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: 159 Number of extensions: 8 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: 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