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 BPHYT_RS15605 BPHYT_RS15605 ABC transporter permease
Query= TCDB::P21627 (307 letters) >FitnessBrowser__BFirm:BPHYT_RS15605 Length = 316 Score = 283 bits (723), Expect = 5e-81 Identities = 155/307 (50%), Positives = 215/307 (70%), Gaps = 14/307 (4%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLA--MMG 64 ++QQ++NGL +GS YA+IA+GYTMVYGI+G+INFAHG+V M+G+ +A AI +L G Sbjct: 4 FIQQVLNGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAIGVLQNHFPG 63 Query: 65 LDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLS 124 L +VP +++A A+I V +A GY+IERVAYRPLR RL PLI+AIG+SI LQ M+ Sbjct: 64 LGNVPTLIIALIIAAI-VCAAVGYTIERVAYRPLRKAPRLAPLITAIGVSILLQTLAMMI 122 Query: 125 QDSKEKAIPTLLPG---NFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGR 181 P LLP N + + G VIS +I+I VV FLVM GL L + +++LGR Sbjct: 123 WSRNPLPFPQLLPTDPLNVIKATDTTPGAVISMTEIVIIVVAFLVMGGLLLLVHKTKLGR 182 Query: 182 ACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKA 241 A RA AE+ +L+G+N N +I+ TF+IG+ALAA+A V++ +YG + +GF+ G+KA Sbjct: 183 AMRAIAENPGNASLMGVNPNFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIPGLKA 242 Query: 242 FTAAVLGGIGSIPGAMLGGLLLGVAEAFGA--------DVFGDQYKDVVAFGLLILVLLF 293 FTAAVLGGIG++ GAM+GG++LG+ E GA VFG Y+DV AF +LI+VL+F Sbjct: 243 FTAAVLGGIGNLGGAMVGGVILGLIEQLGAGYIGNLTGGVFGSNYQDVFAFIVLIIVLVF 302 Query: 294 RPTGILG 300 RP+G+LG Sbjct: 303 RPSGLLG 309 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: 345 Number of extensions: 14 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: 307 Length of database: 316 Length adjustment: 27 Effective length of query: 280 Effective length of database: 289 Effective search space: 80920 Effective search space used: 80920 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