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 Dsui_1111 Dsui_1111 ABC-type branched-chain amino acid transport system, permease component
Query= TCDB::P21628 (417 letters) >FitnessBrowser__PS:Dsui_1111 Length = 355 Score = 132 bits (333), Expect = 1e-35 Identities = 105/328 (32%), Positives = 154/328 (46%), Gaps = 39/328 (11%) Query: 96 LALVVVAFVWPFFASRGAVDIATL-ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYT 154 L LVV A V P AS + + LI+ + +GLNI+ G AG L LG F AVGA+ Sbjct: 31 LILVVAALVVPMVASEYWIKAILIPFLIFSLAALGLNILTGYAGQLSLGSAAFMAVGAFA 90 Query: 155 -YALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRN 213 Y + G A G+ AA G L G P LR++G YLA+ TL I L Sbjct: 91 AYNFMGRIEGMPVLLAFVGGGLSAAAVGILFGLPSLRIKGFYLAVATLAAQFFIVWAL-- 148 Query: 214 MTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLV 273 T FG F + G+ T E + Y + + L +V ++ Sbjct: 149 -----------------TKFGW-FSMDSSSGVITAQEIQILGYRFDTPISLYLLVLTIVA 190 Query: 274 LLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFA- 332 ++AL N ++R +GRAW A+R+ +VA +G+ KL AF I + + G AG+ +A Sbjct: 191 VMALAAKN-MVRSSVGRAWMAVRDMDVAAEVIGIRIMHTKLLAFAISSFYCGVAGALYAY 249 Query: 333 ARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL---------QEMRGF- 382 A G V PE F S IL ++++GG+GS +G L A +VLL + G Sbjct: 250 AYLGTVEPEGFNLDLSFKILFMIIIGGVGSIMGSFLGAAFIVLLPIFLDVLIQDFLTGLL 309 Query: 383 -----NEYRMLIFGLTMIVMMIWRPQGL 405 + ++++FG +I +I P GL Sbjct: 310 PPSISSNLQLMVFGGLIIFFLIVEPHGL 337 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: 365 Number of extensions: 22 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: 355 Length adjustment: 30 Effective length of query: 387 Effective length of database: 325 Effective search space: 125775 Effective search space used: 125775 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