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 GFF1059 Psest_1092 Branched-chain amino acid ABC-type transport system, permease components
Query= TCDB::P21627 (307 letters) >FitnessBrowser__psRCH2:GFF1059 Length = 295 Score = 144 bits (362), Expect = 3e-39 Identities = 93/296 (31%), Positives = 154/296 (52%), Gaps = 17/296 (5%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 L QL+ GL G+ YAL+++G +++G++ +INFAHG YM+G+++AF +GL+ Sbjct: 13 LGQLLLGLINGAFYALLSLGLAIIFGLLRIINFAHGAQYMLGAFVAF--------LGLNY 64 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAV--MLSQ 125 + + A + +V G +IER R + G + L L+ G+++ ++ + + Sbjct: 65 LGVSYWFALVLAPLVVGCLGMAIERGLLRRIAGEDHLYGLLLTFGLALIVEGSFVKLFGV 124 Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 +P LL G F ++ + + + + V +V I R+RLG RA Sbjct: 125 SGSSYPMPELLRGGF-----NLGFMFLPTYRAWVIVAALVVCLATWYVIERTRLGSYLRA 179 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 E+ K+ GIN ++ LT+ G ALAA A VL Y V PG+G I F Sbjct: 180 GTENPKLMQGFGINVPLLVTLTYGYGVALAAFAGVLAAPIYAV-TPGMGSNLLIVVFAVV 238 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301 V+GG+GSI GA++ G+ +G+ E VF + + V F +++ VLL RP G+ G+ Sbjct: 239 VIGGMGSILGAIVTGIAMGLIEGL-TKVFYPEAANTVVFLVMVAVLLIRPAGLFGK 293 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: 330 Number of extensions: 20 Number of successful extensions: 6 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: 295 Length adjustment: 27 Effective length of query: 280 Effective length of database: 268 Effective search space: 75040 Effective search space used: 75040 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