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 GFF247 PGA1_c02590 putative high-affinity branched-chain amino acid transport system permease protein LivH
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Phaeo:GFF247 Length = 291 Score = 159 bits (402), Expect = 7e-44 Identities = 99/303 (32%), Positives = 155/303 (51%), Gaps = 18/303 (5%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 +Q LV+GL G Y LIA+G+ ++Y +NFA G+ M+G+++ L + + Sbjct: 4 VQLLVSGLANGCVYGLIALGFVLIYKATEAVNFAQGDFMMLGAFVT------LGLTNAEY 57 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSI---FLQNAVMLS 124 + L A SI + + GY ++ V R L G N+ +I I + F A+ Sbjct: 58 LHLPFWLAAPLSIAIMAGLGYLLDLVILRHLFGQNQTAVVILTIALGFVIRFFAGAIWGH 117 Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184 + P L G+ + GVV+ + I +VT L+ + L F R++LG A + Sbjct: 118 E-------PQTLESPLALGDVQLAGVVLGLADLAIIIVTVLLTWSLYQFFQRTKLGLAMQ 170 Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244 A +++ +GI + L + + A AAVA +L + G I+P G L GIKAF A Sbjct: 171 AASQNQMAAYFMGIPVKRVQGLIWGLSGATAAVAGILFASK-GAIDPNAGLL-GIKAFAA 228 Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEV 304 AV+GG GS+PGA+ GGL++GV E F A Y + + LL+ VL+FRP G+ + Sbjct: 229 AVIGGFGSLPGALAGGLIVGVIEPFAARYLAAGYSQIAPYVLLLAVLVFRPHGLFSQVRT 288 Query: 305 EKV 307 +KV Sbjct: 289 KKV 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: 235 Number of extensions: 13 Number of successful extensions: 3 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