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_011384209.1 AMB_RS09130 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000009985.1:WP_011384209.1 Length = 415 Score = 419 bits (1077), Expect = e-122 Identities = 221/415 (53%), Positives = 291/415 (70%), Gaps = 23/415 (5%) Query: 8 ALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLFRDRIPLK 67 AL ++ ++ P+LG++L L + G W + A A + L R + Sbjct: 13 ALLGGVVAAAMALPMLGVRLEDGSTGLSLSGRLDWVAWAAGSVAGARLLIGLLRLGLA-- 70 Query: 68 LGRGVGYKVNGSGLKNFLSLPSTQRWAVL----ALVVVAFVWPF--FASRGAVDIATLIL 121 GRG SLP+ R ++ A+V A + PF F+ R VD ATL+L Sbjct: 71 -GRGP-------------SLPAPPRAMMVYVGWAMVAFALILPFLPFSGRNLVDKATLVL 116 Query: 122 IYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFG 181 IYVMLG GLNIVVGLAGLLDLG+V FYAVGAY+YALL++ G FW LP+AG++AA FG Sbjct: 117 IYVMLGWGLNIVVGLAGLLDLGFVAFYAVGAYSYALLSQTFGLSFWVCLPLAGLLAAAFG 176 Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRA 241 +LGFPVLRLRGDY+AIVT+G GEI+R++L+N ++TGGPNGI I +P+LFGL+F+ Sbjct: 177 MVLGFPVLRLRGDYIAIVTMGLGEIVRVVLQNWQDVTGGPNGISGIERPSLFGLSFKMVP 236 Query: 242 PEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVA 301 PEG QTF EFFG+ Y+ +++VI LY + L L LL + R+ R+P+GRAWEALREDE+A Sbjct: 237 PEGSQTFAEFFGLDYSADHRVIFLYFLILALALLTNVITLRIRRLPVGRAWEALREDEIA 296 Query: 302 CRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMG 361 CR+LG+NPT+VKLSAF GA FAGFAGSFFA RQG ++PESFTFIESA+ILAIVVLGGMG Sbjct: 297 CRSLGINPTLVKLSAFATGAMFAGFAGSFFATRQGFISPESFTFIESAVILAIVVLGGMG 356 Query: 362 SQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLEL 415 SQ+G++LAA+++V L E R ++RML FG M+++M+W+P GLL + P + L Sbjct: 357 SQIGIVLAALLLVGLPEWFRELQQFRMLAFGGAMVLIMLWKPAGLLSTREPTIRL 411 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: 625 Number of extensions: 38 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: 417 Length of database: 415 Length adjustment: 31 Effective length of query: 386 Effective length of database: 384 Effective search space: 148224 Effective search space used: 148224 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 17 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