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_092344942.1 BLU87_RS03945 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_900107645.1:WP_092344942.1 Length = 303 Score = 209 bits (533), Expect = 5e-59 Identities = 120/312 (38%), Positives = 186/312 (59%), Gaps = 25/312 (8%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLL------- 60 +Q ++N + GS YALIA+GYT+VYG++ +INFAHG+++M+G+YI+F + L Sbjct: 5 IQNILNAMQWGSFYALIALGYTLVYGVLRLINFAHGDIFMVGAYISFFVASFLISPFTGL 64 Query: 61 --AMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLR--GGNRLIPLISAIGMSIF 116 AM + +VPL ML +TS G ++ER+AYRPLR G +RL +I+A+ + Sbjct: 65 SPAMAFIITVPLTML--------LTSLVGVTLERIAYRPLRRKGAHRLYVVITALMCGLI 116 Query: 117 LQNAVMLSQDSKEKAIPTLLPGN-FVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFIS 175 L+ + + + P L+ + FG+ V ++ +++++ V LV L ++ Sbjct: 117 LEYSNLALLGASRLKFPELIEKQVWRFGD-----VTLTNLKVMVIVTAVLVFLFLQWVVT 171 Query: 176 RSRLGRACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGF 235 R+R+G A RA + D L+GI + II +TFV+G+ A +A +L M Y V+ P +G Sbjct: 172 RTRVGMAMRAISYDKFAIPLMGIPIDRIIVVTFVLGSGFAGLAGLLFAMSYPVLEPFMGM 231 Query: 236 LAGIKAFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRP 295 L G KAF AAV+GGIG I GA +GG LLG E VF Y+D+ AF +L+L+L +P Sbjct: 232 LIGWKAFIAAVVGGIGDIKGAFVGGFLLGFIEVGVVTVFPSTYRDLFAFTILLLILWIKP 291 Query: 296 TGILGRPEVEKV 307 TG+ G P+ K+ Sbjct: 292 TGLFGIPQSTKI 303 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: 302 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: 303 Length adjustment: 27 Effective length of query: 280 Effective length of database: 276 Effective search space: 77280 Effective search space used: 77280 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 24 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