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 17517 b3456 leucine/isoleucine/valine transporter subunit (NCBI)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Keio:17517 Length = 425 Score = 479 bits (1233), Expect = e-140 Identities = 257/417 (61%), Positives = 313/417 (75%), Gaps = 17/417 (4%) Query: 8 ALFSALLVILVSYPILGLKLRTVGIKLEV-LGADAQTLWTIAAAALAMFVWQLFRDRIPL 66 AL SA + +++ +G++L G KL V +D + W A+ F +QL R Sbjct: 9 ALLSAAMFFVLAGVFMGVQLELDGTKLVVDTASDVRWQWVFIGTAVVFF-FQLLRPAFQK 67 Query: 67 KLGRGVGYK-----VNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLIL 121 L G K ++GS +K Q+ ++AL+V+A WPF SRG VDIATL + Sbjct: 68 GLKSVSGPKFILPAIDGSTVK--------QKLFLVALLVLAVAWPFMVSRGTVDIATLTM 119 Query: 122 IYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALFG 181 IY++LG+GLN+VVGL+GLL LGY GFYA+GAYT+ALL Y G GFWT LPIAG+MAA G Sbjct: 120 IYIILGLGLNVVVGLSGLLVLGYGGFYAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAAG 179 Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERRA 241 FLLGFPVLRLRGDYLAIVTLGFGEI+RILL N TEITGGPNGI IPKPTLFGL F R A Sbjct: 180 FLLGFPVLRLRGDYLAIVTLGFGEIVRILLLNNTEITGGPNGISQIPKPTLFGLEFSRTA 239 Query: 242 PE-GMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300 E G TF FFG+ Y+ + +VI LY+VALLLV+L+LFVINRL+RMP+GRAWEALREDE+ Sbjct: 240 REGGWDTFSNFFGLKYDPSDRVIFLYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEI 299 Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360 ACR+LGL+P +KL+AFTI A+FAGFAG+ FAARQG V+PESFTF ESA +LAIVVLGGM Sbjct: 300 ACRSLGLSPRRIKLTAFTISAAFAGFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGM 359 Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416 GSQ VILAA+++V+ +E MR FNEY ML+ G M++MMIWRPQGLLPM RP L+LK Sbjct: 360 GSQFAVILAAILLVVSRELMRDFNEYSMLMLGGLMVLMMIWRPQGLLPMTRPQLKLK 416 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: 578 Number of extensions: 30 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: 425 Length adjustment: 32 Effective length of query: 385 Effective length of database: 393 Effective search space: 151305 Effective search space used: 151305 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