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_041098464.1 SUTH_RS08250 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000828635.1:WP_041098464.1 Length = 288 Score = 144 bits (363), Expect = 2e-39 Identities = 97/299 (32%), Positives = 156/299 (52%), Gaps = 21/299 (7%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 +L QL+NGL G L+A G T+++GI+G+IN AHG YM+G+Y+A+ L Sbjct: 6 FLIQLLNGLQYGLLLFLVASGLTLIFGIMGIINLAHGSFYMVGAYLAW---------SLS 56 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQ--NAVMLS 124 S+ + AA +I +T G ++ER+ +R L + L ++ G+ + + +V+ Sbjct: 57 SLTGSLTAAILLAIPLTVILGMALERLLFRHLYQRDHLYQVLLTYGLILVFEELRSVIWG 116 Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISY--MQILIFVVTFLVMFGLTLFISRSRLGRA 182 D A+P LL + E+ +SY ++ I V L+ L I ++RLG Sbjct: 117 DDVHGVAVPALLSHSIPLTEN------LSYPVYRLAISGVCLLLAACLYFLIQKTRLGMM 170 Query: 183 CRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAF 242 RA A + +M LGI+ I L F +G LAA A ++ + P +G I F Sbjct: 171 IRAGASNREMVQSLGIDIKLIYTLVFALGIVLAAFAG-MINAPLSSVFPNMGSQVLIICF 229 Query: 243 TAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 V+GGIGS+ GAM L++G+AE FG V + ++ + L+ +VL++RP G+ GR Sbjct: 230 VVVVIGGIGSVKGAMAASLMIGLAETFG-QVLVPEVAGMIVYVLMAIVLVWRPEGLFGR 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: 274 Number of extensions: 18 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: 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 Apr 09 2024. 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