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 WP_029133168.1 A3GO_RS0109320 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000428045.1:WP_029133168.1 Length = 288 Score = 144 bits (364), Expect = 2e-39 Identities = 99/301 (32%), Positives = 156/301 (51%), Gaps = 25/301 (8%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAF--IAITLLAMMG 64 Y QL+NG+ G L+A G T+++GI+G+IN AHG YM+G+Y+ + IT G Sbjct: 6 YFIQLLNGIQYGFLLFLMASGLTLIFGIMGIINLAHGAFYMVGAYLCYWLTGITGNLFTG 65 Query: 65 LDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQ--NAVM 122 + L A SI+V GY++ER+A L + L ++ + + +++ Sbjct: 66 I-------LLAIPLSILV----GYAVERLAISYLYRRDHLYQVLLTYALILIANELQSIL 114 Query: 123 LSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLF--ISRSRLG 180 D IP LL G+ ++ +Y +F+ ++ ++ I ++RLG Sbjct: 115 WGNDVHSVPIPELLRGSVQLTDNQ------AYPVYRLFISATCILLAAVMYWVIQKTRLG 168 Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240 RA A + +M LGIN N + A+ F +GAALAA A +L + PGIG I Sbjct: 169 MTIRAGASNREMVQALGININWLFAIVFSMGAALAAFAG-MLAAPVNTVYPGIGDNILII 227 Query: 241 AFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILG 300 +F V+GGIGSI GA +G LL+G+A+ FG V + +V + L+ VL +RP G+ G Sbjct: 228 SFVVVVIGGIGSIKGAFIGALLIGLADTFG-KVLLPEMASMVVYTLMAAVLFWRPQGLFG 286 Query: 301 R 301 + Sbjct: 287 K 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: 262 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: 288 Length adjustment: 26 Effective length of query: 281 Effective length of database: 262 Effective search space: 73622 Effective search space used: 73622 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 24 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