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_085635672.1 MGEO_RS05255 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_002115805.1:WP_085635672.1 Length = 245 Score = 185 bits (469), Expect = 9e-52 Identities = 106/253 (41%), Positives = 150/253 (59%), Gaps = 20/253 (7%) Query: 5 ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64 +L + G T RFGGL+AVN ++ V E +V+ +IGPNG+GK+T N ++G +PT G I L Sbjct: 7 VLSLRGATKRFGGLVAVNDMDFDVTEHEVLGLIGPNGSGKSTTLNLISGALKPTEGTISL 66 Query: 65 DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL---LVAQHRHLNTNFLAGLFKTP 121 G I L IAR+G+ RTFQ VRL MT +EN+ V HR Sbjct: 67 RGTPISHLSAADIARRGIARTFQLVRLLPSMTVLENVRAGAVFGHR-------------- 112 Query: 122 AFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPA 181 RR EA +A L V L AN G L Y +R+E+AR + + P++L+LDE Sbjct: 113 --RRWGAEADAHAMRMLALVGLDRRANAHVGELTYIDTKRVELARVLASEPKVLLLDEWL 170 Query: 182 AGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQI 241 AGLNP E ++ ALI +LR E T++L+EH M + S+ D VV++ G +A+GTPE++ Sbjct: 171 AGLNPTELEEGIALIKRLRDEGR-TIILVEHVMDAIRSLCDRCVVMSTGTKIAEGTPEEV 229 Query: 242 RDNPDVIKAYLGE 254 +P+VI+AYLG+ Sbjct: 230 LSDPEVIRAYLGD 242 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: 159 Number of extensions: 6 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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 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