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_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000009985.1:WP_043743902.1 Length = 291 Score = 152 bits (383), Expect = 1e-41 Identities = 93/303 (30%), Positives = 163/303 (53%), Gaps = 18/303 (5%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 +LQ L +GLT G+ YAL +G+ ++Y +INFA GE MIG +A + G+ Sbjct: 5 FLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGG----MATATMVAAGVP 60 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126 + L + A AAS++V G ++E+ A P R + + +I IG SIF++ A L D Sbjct: 61 -IYLAIPLAMAASMLV----GVAMEKFAIEPARNADVVTIIIITIGASIFMRGAAQLIWD 115 Query: 127 SKEKAIPTLLPGNFVFGES--SMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184 + ++P GE+ ++ G + + +F ++ + + L F +R+ G+A Sbjct: 116 KEFHSLPAFS------GETPIAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAML 169 Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244 + + L+G+ ++ +F + A L AV +++ N G + G+K F+A Sbjct: 170 GTSHNRLAAQLVGVAVKRVLLASFALSALLGAVGGIVV-TPITFTNYEAGIMLGLKGFSA 228 Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEV 304 AVLGG+G+ GA++GGL++G+AEA + YKD +AF +++ VL F P+G+ G+ Sbjct: 229 AVLGGLGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGKRGT 288 Query: 305 EKV 307 ++V Sbjct: 289 DRV 291 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: 14 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: 291 Length adjustment: 27 Effective length of query: 280 Effective length of database: 264 Effective search space: 73920 Effective search space used: 73920 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