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 BWI76_RS26345 BWI76_RS26345 branched-chain amino acid ABC transporter permease LivH
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Koxy:BWI76_RS26345 Length = 308 Score = 404 bits (1037), Expect = e-117 Identities = 204/305 (66%), Positives = 249/305 (81%) Query: 3 EIYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAM 62 + ++LQQ+ NG+T+GSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY++F+ I L M Sbjct: 4 QFLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMM 63 Query: 63 MGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVM 122 MG+D+ L++ A F +I++ SA+G+SIERVAYRP+R RLI LISAIGMSIFLQN V Sbjct: 64 MGIDTSWLLVAAGFVGAIVIASAYGWSIERVAYRPVRSSKRLIALISAIGMSIFLQNYVS 123 Query: 123 LSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRA 182 L++ S++ A+P+L G + G S I+ MQ++I+VVTF+ M LTLFI SR+GRA Sbjct: 124 LTEGSRDVALPSLFNGQWTVGSSDNFSATITTMQLVIWVVTFIAMLALTLFIRYSRMGRA 183 Query: 183 CRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAF 242 CRACAEDLKM +LLGIN++ +IALTFVIGAA+AAVA VLLG YGVINP IGF+AG+KAF Sbjct: 184 CRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAF 243 Query: 243 TAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRP 302 TAAVLGGIGSIPGAM+GGL+LG+AEA + +YKDVV+F LLILVLL PTGILGRP Sbjct: 244 TAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRP 303 Query: 303 EVEKV 307 EVEKV Sbjct: 304 EVEKV 308 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: 376 Number of extensions: 12 Number of successful extensions: 1 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: 308 Length adjustment: 27 Effective length of query: 280 Effective length of database: 281 Effective search space: 78680 Effective search space used: 78680 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