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 3608584 Dshi_1978 inner-membrane translocator (RefSeq)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Dino:3608584 Length = 317 Score = 142 bits (357), Expect = 2e-38 Identities = 100/316 (31%), Positives = 151/316 (47%), Gaps = 42/316 (13%) Query: 114 VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALL------AEYAGFGFW 167 V AT+ I + +GLN+ G GL + G V F+ G Y +L A GFG Sbjct: 9 VFFATIASILAIAVLGLNLHWGNTGLFNGGVVAFFGAGGYATLILGGTPQAAHLGGFGLP 68 Query: 168 TALPIAG--MMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIG 225 L + G ++A L +L+G +RLR DYLAI T G L+RN + GG +G+ Sbjct: 69 YGLALLGGLVIAGLLAWLVGLLTIRLRHDYLAIATFGVAVAFENLVRNAQRLAGGASGLR 128 Query: 226 SIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMR 285 FER + + G+AYN + +L AL+ L L RL+R Sbjct: 129 G----------FERPLADTIPP-----GLAYNAAFFAFVL--AALIATYLGL---ERLIR 168 Query: 286 MPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTF 345 P GR A+REDE A RALG +P ++L+AF IG+ G AG+ +A ++P+ Sbjct: 169 GPFGRLLRAIREDETAARALGKSPDRIRLTAFVIGSVILGLAGALYATFYAFISPQDVLP 228 Query: 346 IESAMILAIVVLGGMGSQLGVILAAVVMVLLQEMRGF--------------NEYRMLIFG 391 I + I A++++GG G+ G I A ++ G+ + ++ G Sbjct: 229 ILTFQIWAMLIVGGAGNNRGAIAGAFLIWGAWTASGWALSRFAPIEVQLYTGSIQFVLIG 288 Query: 392 LTMIVMMIWRPQGLLP 407 ++ M++WRPQGL P Sbjct: 289 CVIVGMLLWRPQGLFP 304 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: 420 Number of extensions: 23 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: 317 Length adjustment: 29 Effective length of query: 388 Effective length of database: 288 Effective search space: 111744 Effective search space used: 111744 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: 49 (23.5 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