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 WP_012967797.1 KVAR_RS09620 high-affinity branched-chain amino acid ABC transporter permease LivM
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000025465.1:WP_012967797.1 Length = 428 Score = 413 bits (1061), Expect = e-120 Identities = 229/429 (53%), Positives = 292/429 (68%), Gaps = 28/429 (6%) Query: 2 SQSLKRALFSALLV----ILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVW 57 ++ +K AL ++L ++V PI+G+ L+ G +T+A A +A+ V Sbjct: 9 ARDIKSALIDSVLAGLCALIVFGPIVGVVLKGYG-------------FTLAPARVAILVA 55 Query: 58 QLFRDRIPLKL------GRGVGYKVNGSGLKNFLSLP---STQRWAVLALVVVAFVWPFF 108 + R+ L L G+ + G+ ++ P S RW + L V+A +PF Sbjct: 56 VVMAGRLALSLLLQSRRGKAFIARFEGADDGVYVRPPGYRSRLRWIMPLLAVLAIAFPFL 115 Query: 109 ASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWT 168 AS+ + +A L LIYV+LG+GLNIVVGLAGLLDLGYV FYA+GAY AL +Y G GFW Sbjct: 116 ASKYLLTVAILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWA 175 Query: 169 ALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIP 228 LP+ +MAAL G LLGFPVLR+ GDYLAIVTLGFGEIIR++L N TGGPNG+ +P Sbjct: 176 MLPLGAVMAALAGALLGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWVSFTGGPNGV-PVP 234 Query: 229 KPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPI 288 PTLFGL F RRA +G HEFF ++YN N K I LY V L+V+L L V +RL RMPI Sbjct: 235 SPTLFGLEFTRRARDGGIPIHEFFHVSYNPNLKFIFLYAVLCLVVMLVLLVKHRLTRMPI 294 Query: 289 GRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIES 348 GRAWEALREDE+ACRA+GLN +VKLSAF +GAS AG AG FFA+ QG V P SFTF ES Sbjct: 295 GRAWEALREDEIACRAMGLNHVLVKLSAFMLGASTAGIAGVFFASYQGFVNPTSFTFFES 354 Query: 349 AMILAIVVLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLP 407 A+ILAIVVLGGMGS LGV+LAA V+ + E +RGF+EYR+L+FG+ M+VMMIWRP+GL+ Sbjct: 355 ALILAIVVLGGMGSTLGVVLAAFVLTVTPELLRGFDEYRVLLFGVLMVVMMIWRPRGLVR 414 Query: 408 MQRPHLELK 416 R + L+ Sbjct: 415 TSRSGVALR 423 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: 622 Number of extensions: 40 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: 428 Length adjustment: 32 Effective length of query: 385 Effective length of database: 396 Effective search space: 152460 Effective search space used: 152460 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 24 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