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_012567013.1 RC1_RS08785 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000016185.1:WP_012567013.1 Length = 435 Score = 412 bits (1058), Expect = e-119 Identities = 222/423 (52%), Positives = 295/423 (69%), Gaps = 16/423 (3%) Query: 1 MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWT-IAAAALAMFVWQL 59 ++ LK A +A + +L++ P +GL TV G T W + A A+F +L Sbjct: 7 LAARLKDAGLAAGVALLLAIPFIGLT--TVNTDQ---GLSVATRWPWVGYAVAAVFAGRL 61 Query: 60 FRDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWA----VLALVVVAFVWPF--FASRGA 113 + L G + +N L T R V+A + A V PF F+ R Sbjct: 62 LAGYLRDALA---GRASAATSARNVLPTGETARRLGRGFVIAGIGFAAVMPFLPFSDRYI 118 Query: 114 VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIA 173 +D+ T LIYV+LG+GLN+ VGLAGLLDLG+V FYA+GAYT+ALLA++AG GFW +LP++ Sbjct: 119 LDLGTTALIYVLLGMGLNVTVGLAGLLDLGFVAFYAIGAYTFALLAKFAGLGFWLSLPLS 178 Query: 174 GMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLF 233 G++AALF LL P+LRLRGDYLAIVTLGFGEI RI++ N +TGGPNG+ IP+P+LF Sbjct: 179 GLVAALFAVLLSLPILRLRGDYLAIVTLGFGEITRIVILNWQSLTGGPNGVAGIPRPSLF 238 Query: 234 GLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWE 293 G++FERR PEG +FHE GIA+++ ++++ LY + L+LVL A + + RL R+PIGRAWE Sbjct: 239 GISFERRPPEGQVSFHELTGIAFSSEHRMMFLYFIILVLVLAASWAVWRLRRLPIGRAWE 298 Query: 294 ALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILA 353 ALREDE+ACR+LG+NPT K+SA+ GA G AG FF+ARQG V+PESFTFIESA+ILA Sbjct: 299 ALREDEIACRSLGINPTAAKVSAYATGAMLGGLAGCFFSARQGFVSPESFTFIESAIILA 358 Query: 354 IVVLGGMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPH 412 IVVLGGMGSQ+GV++AA+ +VLL E R F +YRML+FG MI++M+WRP GLL + P Sbjct: 359 IVVLGGMGSQIGVVIAALFIVLLPEFAREFADYRMLLFGAAMILIMVWRPGGLLSGRDPT 418 Query: 413 LEL 415 L L Sbjct: 419 LRL 421 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: 632 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: 435 Length adjustment: 32 Effective length of query: 385 Effective length of database: 403 Effective search space: 155155 Effective search space used: 155155 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: 51 (24.3 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