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 8501894 DvMF_2609 inner-membrane translocator (RefSeq)
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Miya:8501894 Length = 415 Score = 331 bits (849), Expect = 2e-95 Identities = 183/407 (44%), Positives = 259/407 (63%), Gaps = 24/407 (5%) Query: 3 QSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQ--LF 60 Q LK+++ +L + +++P++ +++ ++ ++ + L + + FVW+ L Sbjct: 2 QGLKKSILVSLWFMFLTFPLMVIRIDSLNGTIDWRWENM--LGMGVGSFVLSFVWRFMLA 59 Query: 61 RDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLI 120 R G G+ + S P A++ L+ V P+ S +I Sbjct: 60 RKEAGRAAAAGGAMSARGAWFERLRSDPKAAVPALVVLLSAFLVLPWVVSTYQTNIMISA 119 Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180 L+YVMLG+GLNIVVGL+G L LGYV FYAVGAY+YA+L G GFW+ LPI G MAALF Sbjct: 120 LLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYSYAILNSNFGLGFWSVLPIGGAMAALF 179 Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240 G LLGFPVLRLRGDYLAIVTLGFGEIIR++L N + + GP+GI +I +P L G+ Sbjct: 180 GILLGFPVLRLRGDYLAIVTLGFGEIIRLVLENWSSFSQGPSGIANIERPGLLGMQ---- 235 Query: 241 APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300 ++ T Y +Y + L V++ + + RL IGRAW+ALREDE+ Sbjct: 236 -----------LSVSDATTY----IYYLILAAVIVTILAVTRLKNSRIGRAWQALREDEI 280 Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360 AC+A+G++ T KL+AF +GA +AGFAG FAA+ + P SFTF+ESAM+LA+VVLGGM Sbjct: 281 ACQAMGIDITTTKLTAFALGACWAGFAGVIFAAKTTFINPASFTFLESAMVLAMVVLGGM 340 Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLL 406 GS +GV + A+V++LL E +R F+EYRMLIFG TM++MM++RPQGL+ Sbjct: 341 GSVIGVSVGALVLILLPEYLRAFSEYRMLIFGATMVLMMVFRPQGLV 387 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: 573 Number of extensions: 37 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: 415 Length adjustment: 31 Effective length of query: 386 Effective length of database: 384 Effective search space: 148224 Effective search space used: 148224 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