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 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein
Query= TCDB::P21627 (307 letters) >MicrobesOnline__882:208249 Length = 306 Score = 214 bits (545), Expect = 2e-60 Identities = 118/307 (38%), Positives = 191/307 (62%), Gaps = 10/307 (3%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAF-IAITLLAMMGL 65 ++Q + N L GS YALIA+GYT+VYG++ +INFAHG+++M+G+YI+F +A LL +G Sbjct: 4 FIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQIGG 63 Query: 66 D---SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLR--GGNRLIPLISAIGMSIFLQNA 120 S P+ + ++++T+ G ++ERVAYRPLR G +RL +I+A+ I L+N Sbjct: 64 FFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIMLENG 123 Query: 121 VMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLG 180 + + KA+P ++ V+ ++ V ++ +++++ V FLV L ++R+R+G Sbjct: 124 NLALLGASRKALPEMID-KVVY---TIGTVSVTNLKLMVIVTAFLVFALLQFIVTRTRIG 179 Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240 A RA A D L+GI ++II TFV+G+ A +A +L M Y +++P +G + G K Sbjct: 180 MAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWK 239 Query: 241 AFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILG 300 AF AAV+GGIG I GA +GG LL E A VF ++D+ AF +L+ ++ RPTG+ G Sbjct: 240 AFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTGLFG 299 Query: 301 RPEVEKV 307 + K+ Sbjct: 300 VAKTTKI 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: 273 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: 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 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