Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_084545052.1 H566_RS24850 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000482785.1:WP_084545052.1 Length = 344 Score = 134 bits (337), Expect = 4e-36 Identities = 108/337 (32%), Positives = 165/337 (48%), Gaps = 31/337 (9%) Query: 79 SGLKNF-LSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLA 137 SGL F LS + +LALV + P A VD+ +L+ + + L ++VG Sbjct: 11 SGLPWFRLSRGAFDAGLLLALVAL----PLLAPGWQVDLVLKVLVLALFAVSLELLVGHT 66 Query: 138 GLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL-FGFLLGFPVLRLRGDYL 196 GL+ LG+ F+ +GAY ALLA + G L A M+AA + +G LR +G Y Sbjct: 67 GLVSLGHAAFFGIGAYVPALLASDSEPGSLLLLGGAAMLAAAGYALAVGLLTLRSQGIYF 126 Query: 197 AIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAY 256 +VTL FG++ + + T++ GG +GI +P L G T Sbjct: 127 IMVTLAFGQMAYHVAHD-TKLAGGTDGIYLYLRPLL---------AVGSATL-------V 169 Query: 257 NTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSA 316 +T +V L ++V LV A+ +N ++ GRA +R +E RA G K++ Sbjct: 170 DTEDRVQLYWLVLGTLVA-AIGCLNLVLHSRFGRALAGVRVNETRMRATGYATYPYKVAI 228 Query: 317 FTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL 376 F + A A AG F + G V+PES ++ +S +L + +LGG+GS G +L AV V L Sbjct: 229 FVLAAVLAALAGFFQTVKDGFVSPESLSWHQSGAVLVMCILGGLGSLRGAVLGAVAFVGL 288 Query: 377 QEM-------RGFNEYRMLIFGLTMIVMMIWRPQGLL 406 QE+ F + L FGL +IV + P+GL+ Sbjct: 289 QELFQSEALFGDFARHWQLGFGLAIIVCVALMPRGLV 325 Lambda K H 0.330 0.146 0.439 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: 392 Number of extensions: 29 Number of successful extensions: 4 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: 417 Length of database: 344 Length adjustment: 30 Effective length of query: 387 Effective length of database: 314 Effective search space: 121518 Effective search space used: 121518 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 50 (23.9 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