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_073040761.1 BUB04_RS14545 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_900129305.1:WP_073040761.1 Length = 258 Score = 227 bits (579), Expect = 2e-64 Identities = 115/249 (46%), Positives = 162/249 (65%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +LE+ +T FGGL AV NL++E +++ +IGPNGAGKTTVFN + GFY+PT G I Sbjct: 3 LLEIRNMTHFFGGLRAVYDFNLRLEGGELMGLIGPNGAGKTTVFNLVCGFYRPTEGEILF 62 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124 +G+E GL H + G+ RTFQN+RL+ + +NL ++QH L L +T F Sbjct: 63 EGKETAGLRPHAVTAMGIARTFQNIRLWNTLPVYDNLCISQHFRLGYGLKDALLRTRRFT 122 Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 E+ + A LE + L +A G L YG QRRLEIAR + TRP++L+LDEPAAG+ Sbjct: 123 AREKNVHKTAEELLELMGLRHYAQELPGNLPYGLQRRLEIARALATRPKLLLLDEPAAGM 182 Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244 NP E D L LI +R + ++TV LIEH M++VMS+ + + V++ G +ADG+PE+I+ N Sbjct: 183 NPGEIDQLIDLIRWIREQFDLTVWLIEHHMRVVMSVCERVQVLDFGETIADGSPEEIKQN 242 Query: 245 PDVIKAYLG 253 VI+AYLG Sbjct: 243 RRVIQAYLG 251 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: 176 Number of extensions: 6 Number of successful extensions: 1 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