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 5210164 Shew_2608 inner-membrane translocator (RefSeq)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__PV4:5210164 Length = 357 Score = 125 bits (313), Expect = 3e-33 Identities = 94/311 (30%), Positives = 147/311 (47%), Gaps = 46/311 (14%) Query: 118 TLILIYVMLGI---GLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAG 174 TL + LGI GLNI+VG G + LG+ F+ GA+ A L +P+AG Sbjct: 52 TLFIQISYLGIAALGLNILVGFTGQISLGHGAFFGFGAFASAWLNTSFNIPVVFCIPLAG 111 Query: 175 MMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFG 234 + G + G P R++G YLAI TL II+ +GG +G + P +LFG Sbjct: 112 FLTMGVGMMFGMPAARIKGLYLAIATLAAQFIIQDFFGRAEWFSGGSSGAMAAPV-SLFG 170 Query: 235 LTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEA 294 F+ T F+ IA + ++ +Y+ LMR GRA+ A Sbjct: 171 FDFD--------TDMSFYFIAL---FALVFMYIWGC-----------NLMRSRDGRAFVA 208 Query: 295 LREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAI 354 +R+ ++ +G+ +L +F I + +AG G+ +A G V+ E FT + S LA+ Sbjct: 209 VRDHYLSAEIMGVKLNKYRLLSFGISSFYAGIGGALYAHYLGYVSSEGFTILMSIQFLAM 268 Query: 355 VVLGGMGSQLGVILAAVVMVLLQE----MRGFNEY----------------RMLIFGLTM 394 V++GG+GS G ++ V MVLL E M G +Y + + GL + Sbjct: 269 VIIGGLGSIKGTLMGVVFMVLLPEVLEGMVGLMKYTDYGNLPMVTDGLAYIKEMAIGLVI 328 Query: 395 IVMMIWRPQGL 405 I+ +I+ P+GL Sbjct: 329 ILFLIFEPEGL 339 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: 427 Number of extensions: 29 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: 417 Length of database: 357 Length adjustment: 30 Effective length of query: 387 Effective length of database: 327 Effective search space: 126549 Effective search space used: 126549 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