Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= TCDB::P21627 (307 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 196 bits (498), Expect = 5e-55 Identities = 115/296 (38%), Positives = 170/296 (57%), Gaps = 15/296 (5%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDSV 68 QQL+N LT+GS YAL A+G+T+V+G++ +IN +HG V+M+GSY A LAM+ + Sbjct: 4 QQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAA------LAMVSHLNA 57 Query: 69 PLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGN--RLIPLISAIGMSIFLQNAVMLSQD 126 PL + A +++V+ G ++ + +PLR N LIP+I+ IG+ I L +A Sbjct: 58 PLWV--AMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFG 115 Query: 127 SKEKAIPT-LLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 ++ P ++P GE + V + ++I I + FL+M L + R++LGRA RA Sbjct: 116 AEVLRFPEDVMPA----GEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRA 171 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 AE K LLGIN + +T + AAL +A VL+G+ + I P +G K Sbjct: 172 IAESPKAAYLLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVI 231 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 +LGG+G I GA++GGL LG AE Q D VAFGLL L+LL RP+G+ GR Sbjct: 232 ILGGMGDIRGALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLFGR 287 Lambda K H 0.328 0.145 0.413 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: 272 Number of extensions: 17 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: 307 Length of database: 293 Length adjustment: 27 Effective length of query: 280 Effective length of database: 266 Effective search space: 74480 Effective search space used: 74480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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