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 GFF1121 HP15_1099 inner-membrane translocator
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Marino:GFF1121 Length = 287 Score = 140 bits (354), Expect = 3e-38 Identities = 91/298 (30%), Positives = 153/298 (51%), Gaps = 19/298 (6%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 + QL+NGL G LIA G T+V G++G++N AHG +YM+G+Y+ + + + + Sbjct: 6 FFVQLINGLQYGLLLFLIASGLTLVLGVMGILNLAHGSLYMVGAYLMWYFVGVTGSFTVS 65 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAV---ML 123 ++ S ++ A G IER+ + L N L ++ IGM IF+ N+V + Sbjct: 66 AI---------LSAVIALALGILIERLLIQRLYKRNHLDQVLLTIGM-IFVFNSVQSILW 115 Query: 124 SQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRAC 183 D ++P L G+ F ++S V +I ++ + L L +S++RLG Sbjct: 116 GNDPYGVSVPEALSGSVPFTDNSSYPV----YRIFAALICIAIAAALYLVVSKTRLGMLI 171 Query: 184 RACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFT 243 RA + +M LG+N ++ + F IG LAA++ ++ ++ PG+G I F Sbjct: 172 RAGESNREMVEALGVNIKSLYTIVFAIGVMLAAISGIIAAPMRSIV-PGMGESVLITCFV 230 Query: 244 AAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 V+GG+GSI GA + L +GV F A V ++V + +ILVLL +P G+ + Sbjct: 231 VVVIGGMGSIKGAFVSALWVGVITTFAA-VLTPTMSNMVIYLFMILVLLVKPQGLFAK 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: 246 Number of extensions: 18 Number of successful extensions: 5 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: 287 Length adjustment: 26 Effective length of query: 281 Effective length of database: 261 Effective search space: 73341 Effective search space used: 73341 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