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_086511955.1 BZY95_RS21625 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_002151265.1:WP_086511955.1 Length = 295 Score = 135 bits (340), Expect = 1e-36 Identities = 91/297 (30%), Positives = 152/297 (51%), Gaps = 17/297 (5%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 ++ QL+ GL G+ YAL+++G +++G++ ++NFAHG +YM+G++ A++G+ Sbjct: 12 FMGQLLLGLINGAFYALLSLGLAVIFGLLKIVNFAHGAMYMLGAF--------AALLGMR 63 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVM--LS 124 + + AA + +V FG +ER+ R + + L L+ G+++ + ++ Sbjct: 64 YLGINYWAALLLAPLVVGLFGMLLERIMLRRIAHLDHLYGLLLTFGLALIFEGTLVNFFG 123 Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184 P L G F G + + + + V +V F I R+RLG R Sbjct: 124 VSGARYPTPEALQGGFQTG-----FMFLPTYRAWVLVAAIVVCFFTWYMIERTRLGAYLR 178 Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244 A E+ + G+N +I LT+ G ALAA A VL Y V +P +G I F Sbjct: 179 AGTENPALMQAFGVNVPLLITLTYGFGVALAAFAGVLAAPLYPV-SPTMGSNLLIVVFAV 237 Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 V+GG+GSI GA+L GL +G+ E V+ + + V F ++ILVLL RP G+ G+ Sbjct: 238 VVIGGMGSILGAVLTGLGMGLIEGL-TKVYYPEAANTVIFLVMILVLLTRPAGLFGK 293 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: 327 Number of extensions: 18 Number of successful extensions: 6 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: 295 Length adjustment: 27 Effective length of query: 280 Effective length of database: 268 Effective search space: 75040 Effective search space used: 75040 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