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_RS00195 RR42_RS00195 ABC transporter permease
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Cup4G11:RR42_RS00195 Length = 309 Score = 182 bits (461), Expect = 1e-50 Identities = 98/308 (31%), Positives = 170/308 (55%), Gaps = 13/308 (4%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDSV 68 Q + NGL +G YA++A+G+T+ +G++ +I F+HG+ M+G++ A T + M+ + S Sbjct: 6 QYVFNGLMLGMIYAMVAVGFTLFFGVLDVIKFSHGDTLMVGAFAGLAASTGVLMLDIQSP 65 Query: 69 PLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVML--SQD 126 + +LA +I VT G +I + PLR L L++ + + ++ +V L Sbjct: 66 WIRLLAVVLCAICVTGLLGAAIAKFLILPLRKAAPLNTLLATLMLGTVMRESVRLFYPDG 125 Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186 S K P LLP + + + + +++ ++ G+ L I+R+R G A RA Sbjct: 126 SNPKPFPALLPTASI----ELGSLSLRADNLILLATGIAIIVGVHLLITRTRFGMAIRAV 181 Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246 A+D + L+GIN ++ LTF +G+ +AA+A V+ G+ Y IN +G L G+ F AA+ Sbjct: 182 AQDGETARLMGINFEAVVLLTFALGSGMAALAGVMNGLYYNEINFNVGLLLGVIGFAAAI 241 Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADV-------FGDQYKDVVAFGLLILVLLFRPTGIL 299 LGG+G+I GA+LGG L + G+ YKDV AF ++I+++ ++PTG++ Sbjct: 242 LGGLGNIYGAILGGFLFAALQVLGSATLPALIPDIPSAYKDVFAFAVVIVLMAWKPTGLI 301 Query: 300 GRPEVEKV 307 E+V Sbjct: 302 AEKSSERV 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: 291 Number of extensions: 12 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: 309 Length adjustment: 27 Effective length of query: 280 Effective length of database: 282 Effective search space: 78960 Effective search space used: 78960 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