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 RR42_RS29445 RR42_RS29445 ABC transporter permease
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Cup4G11:RR42_RS29445 Length = 358 Score = 157 bits (398), Expect = 4e-43 Identities = 100/335 (29%), Positives = 170/335 (50%), Gaps = 39/335 (11%) Query: 98 LVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYAL 157 L+ + P +AS + +LIY + G+GL ++ G GLL +G+ F VGAYT A Sbjct: 28 LMACLLIAPGWASSYWIAQLGFVLIYAIAGLGLMVLSGYTGLLSIGHAAFLGVGAYTQAW 87 Query: 158 LAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEI 217 L + G F AL A ++AL G ++G P LR++G YLAI TL FG I+ +L + Sbjct: 88 LTSH-GVPFVPALLAAAALSALTGVVVGLPALRVKGIYLAIATLAFGLIVEEILARWESV 146 Query: 218 TGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLAL 277 TGG G+ + P L+G + + Y ++L + LLA Sbjct: 147 TGGNAGL-PVAAPQLWGYVLDGP----------------------VAFYYLSLAVCLLAT 183 Query: 278 FVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGL 337 + L+R GRA+ A+R+ E++ +++G++ K +F + A+ G AG+ +A + Sbjct: 184 LAVLNLLRSATGRAFIAIRDSEISAQSMGIHLARYKTLSFALSAALVGIAGALYAHKLRY 243 Query: 338 VTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEM------------RGFNEY 385 ++PE F +S +L +VV+GG+GS G L A+ ++++ +M + Sbjct: 244 ISPEQFGIAQSIDLLLLVVVGGLGSVHGAFLGAIFLIVMPQMIVLAKDLLPPAIGQASGM 303 Query: 386 RMLIFGLTMIVMMIWRPQGLLPMQ---RPHLELKP 417 + L++GL ++ +++ P GL R +LEL P Sbjct: 304 QALVYGLVLMAFVLFEPMGLYGRWRKIRTYLELFP 338 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: 378 Number of extensions: 24 Number of successful extensions: 5 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: 358 Length adjustment: 30 Effective length of query: 387 Effective length of database: 328 Effective search space: 126936 Effective search space used: 126936 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