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_028310571.1 H566_RS0104990 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000482785.1:WP_028310571.1 Length = 306 Score = 177 bits (450), Expect = 2e-49 Identities = 97/303 (32%), Positives = 172/303 (56%), Gaps = 8/303 (2%) Query: 9 QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDSV 68 QQL NG+ +G+ YA++A+G+T+ +G++ +I F+HG+V +G + A + L+ +G++S Sbjct: 8 QQLWNGVMLGTIYAMVAVGFTLFFGVLDVIKFSHGDVLTLGVFAALATLGGLSALGVEST 67 Query: 69 PLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD-- 126 + ++AA A + + G I R PLR I L+ + + ++ + L Sbjct: 68 AVRLVAATLAGVGGMALLGAGIARAFILPLREAPSFIVLLVTLMVGTVIREGIRLFYPGG 127 Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186 S ++ P LLP G + GV + + +++ + + L I+R+RLG A RA Sbjct: 128 SNPQSFPHLLPS----GGIELGGVTLRFDSLILLAAGLGTICAVHLLITRTRLGLAIRAV 183 Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246 A+D + ++GI+ ++ TF +G+ LAA+A ++ G+ Y +N G G + G+ F+AAV Sbjct: 184 AQDGETARVMGIDFTRVVLFTFALGSGLAALAGLINGLYYSEVNFGTGLMLGVIGFSAAV 243 Query: 247 LGGIGSIPGAMLGGLLLGVAE--AFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEV 304 +GG+G++ GA+LGG L + A A +YKDVVAF +I ++ +PTG++G Sbjct: 244 VGGLGNLYGAILGGFLFAALQMLAVVALPLASEYKDVVAFAAVIALIGLKPTGLIGERAY 303 Query: 305 EKV 307 E+V Sbjct: 304 ERV 306 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: 299 Number of extensions: 15 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: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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