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_041096493.1 SUTH_RS01370 ABC transporter ATP-binding protein
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000828635.1:WP_041096493.1 Length = 350 Score = 255 bits (652), Expect = 1e-72 Identities = 164/349 (46%), Positives = 207/349 (59%), Gaps = 42/349 (12%) Query: 96 LALVVVAFV-WPF-FASRGA--VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVG 151 LAL+ VA + PF AS G V I +++V+L +GLNIVVG AGLLDLGYV FYAVG Sbjct: 10 LALIAVALIALPFVLASAGTAWVRITNFAVLFVLLSLGLNIVVGYAGLLDLGYVAFYAVG 69 Query: 152 AYTYALLAEYAGFG----FWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEII 207 AY YALLA FG FW LPI +A + G +LG P LRLRGDYLAIVTLGFGEI+ Sbjct: 70 AYVYALLAS-PHFGLHLPFWVILPIGAAVACVAGVILGAPTLRLRGDYLAIVTLGFGEIV 128 Query: 208 RILLRNMT---EITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVIL 264 RI + N++ +T GP GI I P G P + G+A++ K Sbjct: 129 RIFMNNLSAPVNLTNGPKGINRID-PFQIG-------PVNFSSTDTLAGLAFSGPIK--- 177 Query: 265 LYVVALLLVLLALFVINR-LMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASF 323 Y LLLVLLA+ VINR L IGRAW A+REDE+A +A G+N +KL AF +GASF Sbjct: 178 -YYYFLLLVLLAVIVINRRLQDSRIGRAWVAIREDEIAAKASGINTRNIKLLAFAMGASF 236 Query: 324 AGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEMRGF- 382 G AG FAA Q V+PESF ES M+LA+VVLGGMG+ GVI A+++ + E+ + Sbjct: 237 GGIAGGMFAAMQTFVSPESFVLNESIMVLAMVVLGGMGNIWGVIAGALLLSFVPELLRYT 296 Query: 383 ----------------NEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLEL 415 RML+FG+ +++ M +RP GL P R E+ Sbjct: 297 VEPAQRALFGKLLVDPEVLRMLVFGVALVLTMRFRPAGLWPETRHRREM 345 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: 400 Number of extensions: 17 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: 350 Length adjustment: 30 Effective length of query: 387 Effective length of database: 320 Effective search space: 123840 Effective search space used: 123840 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 Apr 09 2024. 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