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_111607209.1 DK187_RS09960 ABC transporter ATP-binding protein
Query= TCDB::P21629 (255 letters) >NCBI__GCF_003259225.1:WP_111607209.1 Length = 249 Score = 161 bits (408), Expect = 1e-44 Identities = 89/253 (35%), Positives = 141/253 (55%), Gaps = 15/253 (5%) Query: 1 MSRPILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGG 60 +S P++ SG+ +G ++GV+ + + V ++GPNGAGKTT+F L G P+ G Sbjct: 5 LSTPVITGSGIDKHYGAFQVLHGVDFSANKGEAVGIVGPNGAGKTTLFGVLAGATAPSAG 64 Query: 61 LIRLDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKT 120 + GE+I + G+ RT Q R F MT ENLL A AGL Sbjct: 65 SVIYQGEDITTTNAAQRCHAGIARTHQVPRPFLGMTVFENLLTAAQNG------AGL--- 115 Query: 121 PAFRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180 S +A +YA H L++ ++ ANR L ++RLE+AR + T P++L+LDE Sbjct: 116 -----SGDDAEKYAVHALQQADIAHLANRPTSALGLLDRKRLELARALATAPKVLLLDEI 170 Query: 181 AAGLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQ 240 GL E L ALI++L+++ +T++ IEH + ++ + D +V +++G +A+G P Sbjct: 171 GGGLTEGELHQLIALISELKAD-GLTIIWIEHILHALLKVIDRLVCMSEGRVIAEGAPSD 229 Query: 241 IRDNPDVIKAYLG 253 + +NPDV+KAYLG Sbjct: 230 VMNNPDVMKAYLG 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: 160 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: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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