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 RR42_RS16975 RR42_RS16975 ABC transporter permease
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Cup4G11:RR42_RS16975 Length = 311 Score = 270 bits (691), Expect = 2e-77 Identities = 152/310 (49%), Positives = 208/310 (67%), Gaps = 13/310 (4%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMM--G 64 ++QQ+VNGL +GS YALIA+GYTMVYGI+G+INFAHG+V MIG+ A AI L G Sbjct: 4 FIQQIVNGLVLGSIYALIALGYTMVYGILGIINFAHGDVLMIGALTALSAILGLQKFFPG 63 Query: 65 LDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLS 124 L +++A A + V +A Y+IERVAYRPLR RL PLI+AIG+SI LQ M+ Sbjct: 64 LPEWLTLVIATLIA-MPVCAALAYTIERVAYRPLRNAPRLAPLITAIGVSIILQTLAMMI 122 Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184 P LLP + + + G I+ +I+I + +VM GL ++R++LGRA R Sbjct: 123 WSRNPLTFPQLLPSSPI--DIGSTGATITGKEIVIIGMALMVMAGLLTLVNRTKLGRAMR 180 Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244 A AE+ K+ L+G+N N +I+ TF+IGAALAA+A V++ YG + +GF+ G+KAFTA Sbjct: 181 ATAENQKVAGLMGVNPNFVISATFMIGAALAALAGVMMATNYGNAHFYMGFIPGLKAFTA 240 Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGA--------DVFGDQYKDVVAFGLLILVLLFRPT 296 AVLGGIG++ GAM+GG+LLG+ EA GA VFG Y+DV AF +LI+VL+FRP+ Sbjct: 241 AVLGGIGNLAGAMVGGMLLGLIEALGAGYIGDLTNGVFGSNYQDVFAFIVLIIVLVFRPS 300 Query: 297 GILGRPEVEK 306 GI+G E+ Sbjct: 301 GIMGERVSER 310 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: 334 Number of extensions: 13 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: 307 Length of database: 311 Length adjustment: 27 Effective length of query: 280 Effective length of database: 284 Effective search space: 79520 Effective search space used: 79520 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