Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 203044 SO3960 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= TCDB::P21629 (255 letters) >FitnessBrowser__MR1:203044 Length = 243 Score = 142 bits (357), Expect = 8e-39 Identities = 81/256 (31%), Positives = 142/256 (55%), Gaps = 19/256 (7%) Query: 1 MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60 M++ L+ L + V V+L V+ QVV ++GPNGAGKTT F + G + G Sbjct: 1 MTQITLKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKG 60 Query: 61 LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLL--VAQHRHLNTNFLAGLF 118 I +D +++ P H ARKG+ Q +F+++T +N++ + + LN++ Sbjct: 61 HIFIDDDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRKELNSD------ 114 Query: 119 KTPAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLD 178 EA+E LEE ++T + +L+ G++RR+EIAR + P+ ++LD Sbjct: 115 -------QREEALE---QLLEEFHITHIRDSQGMSLSGGERRRVEIARALAANPKFILLD 164 Query: 179 EPAAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTP 238 EP AG++P D+K +I +L+S + VL+ +H+++ + + +H +++ G+ +A+GTP Sbjct: 165 EPFAGVDPISVIDIKKIIEQLKS-RGLGVLITDHNVRETLDVCEHAYIVSHGSLIAEGTP 223 Query: 239 EQIRDNPDVIKAYLGE 254 +I DN V YLGE Sbjct: 224 AEILDNQQVRAVYLGE 239 Lambda K H 0.320 0.137 0.391 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: 156 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: 243 Length adjustment: 24 Effective length of query: 231 Effective length of database: 219 Effective search space: 50589 Effective search space used: 50589 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