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_RS34790 RR42_RS34790 ABC transporter permease
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Cup4G11:RR42_RS34790 Length = 348 Score = 157 bits (397), Expect = 5e-43 Identities = 97/318 (30%), Positives = 171/318 (53%), Gaps = 29/318 (9%) Query: 93 WAVLALVVVAFVWPFFASRGA-VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVG 151 WA+L + +AF P + + TL IY + +GLN++ G G L+L + GF A+G Sbjct: 11 WALLLALAIAF--PLVTPNSYYLTVMTLAFIYAIATLGLNLITGYTGQLNLAHGGFMAIG 68 Query: 152 AYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILL 211 AYT +L FW A ++G++ + G+ +G LRL+G Y +I TL G II +L+ Sbjct: 69 AYTLGILTVDHQVPFWAAFVLSGVVCMMVGYFVGVVSLRLKGHYFSIFTLCIGYIIYLLI 128 Query: 212 RNMTEITGGPNGIGSIPKPTLFG-LTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVAL 270 +T G G+ IP P G L F+ Y ++L ++VA Sbjct: 129 EKWESLTHGTVGLIGIPVPASVGPLAFDN----------------VQAQYYLVLFFLVA- 171 Query: 271 LLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSF 330 F+++R++ +GR++ A+R + ALG+N K+ +F + +AGFAG+ Sbjct: 172 -----GTFLMHRIVTSLLGRSFMAVRNSDALAEALGINLMRTKVLSFVLSVGYAGFAGAL 226 Query: 331 FAARQGLVTPE-SFTFIESAMILAIVVLGGMGSQLGVILAAVVMV-LLQEMRGFNEYRML 388 +A + + P+ + T + M++A++V GG G+ LG +L AV++ + Q ++ +YRML Sbjct: 227 YAGQVRFLGPDIARTDLTFEMVMAMLV-GGTGTLLGPLLGAVLVPWVTQTLQFLQDYRML 285 Query: 389 IFGLTMIVMMIWRPQGLL 406 +FG +++++I+ P G++ Sbjct: 286 VFGPVLVLLIIFVPDGIV 303 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: 352 Number of extensions: 26 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: 348 Length adjustment: 30 Effective length of query: 387 Effective length of database: 318 Effective search space: 123066 Effective search space used: 123066 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