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 WP_092349201.1 BLU87_RS12690 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_900107645.1:WP_092349201.1 Length = 258 Score = 234 bits (598), Expect = 1e-66 Identities = 122/253 (48%), Positives = 169/253 (66%), Gaps = 1/253 (0%) Query: 1 MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60 M+ L ++ +T RFGGL AV+ +++KV+E Q+ +IGPNGAGKTTVFNC+TG Y+ G Sbjct: 1 MAHNELILTNVTKRFGGLTAVDDLSMKVKEGQIYGVIGPNGAGKTTVFNCITGIYKSEEG 60 Query: 61 LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120 + +GEEI+G+ ++I +G+VRTFQ +RLF +M+ EN++ +H G+ T Sbjct: 61 SVNWNGEEIRGMTPYQIVDRGIVRTFQTIRLFSQMSVAENIMSGRHIKSKQKMWHGIVHT 120 Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 PA RR E + LE L+EFA +L YG QRR+E+AR M P +L+LDEP Sbjct: 121 PASRRDELDNWCKVEEQLEFFQLSEFAATPTKSLPYGIQRRVEMARAMAVEPTLLILDEP 180 Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240 AAGLN KET L I K+R E VTVLLIEHDM +VM ++D++ VIN G +A+GTP + Sbjct: 181 AAGLNDKETLGLLETIYKIR-EKGVTVLLIEHDMDMVMEVTDYLTVINFGKKIAEGTPAE 239 Query: 241 IRDNPDVIKAYLG 253 ++ NP VI+AYLG Sbjct: 240 VQKNPAVIEAYLG 252 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: 187 Number of extensions: 5 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: 258 Length adjustment: 24 Effective length of query: 231 Effective length of database: 234 Effective search space: 54054 Effective search space used: 54054 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 24 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