Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 350222 BT0694 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::P0A9S7 (255 letters) >FitnessBrowser__Btheta:350222 Length = 224 Score = 90.5 bits (223), Expect = 3e-23 Identities = 65/200 (32%), Positives = 104/200 (52%), Gaps = 25/200 (12%) Query: 19 LAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEGLP----- 73 +A+N+VNLE+ E V+++GP+G GK+T+ N L PT G+ L + + GL Sbjct: 19 VALNHVNLEVKEGEFVAIMGPSGCGKSTLLNILGLLDNPTEGSYRLLGEEVAGLKEKERT 78 Query: 74 GQQIARMGVVRTFQHVRLFREMTVIENL-LVAQHQQLKTGLFSGLLKTPSFRRAQSEALD 132 G + ++G V FQ L E+ V EN+ L + +K+ S RR E + Sbjct: 79 GVRKGKLGFV--FQSFNLIDELNVFENVELPLTYLGIKS----------SERRRMVEDI- 125 Query: 133 RAATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKETKEL 192 L+R+ + A L+ G Q+R+ IAR +VT P++++ DEP L+ K E+ Sbjct: 126 -----LKRMNISHRAKHFPQQLSGGQQQRVAIARAVVTNPKLILADEPTGNLDSKNGAEV 180 Query: 193 DELIAELRNHHNTTILLIEH 212 L+ EL N TTI+++ H Sbjct: 181 MNLLTEL-NKEGTTIIMVTH 199 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: 133 Number of extensions: 6 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: 224 Length adjustment: 23 Effective length of query: 232 Effective length of database: 201 Effective search space: 46632 Effective search space used: 46632 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 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