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_108401790.1 B9Z44_RS04225 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_003063475.1:WP_108401790.1 Length = 309 Score = 255 bits (651), Expect = 1e-72 Identities = 139/303 (45%), Positives = 202/303 (66%), Gaps = 15/303 (4%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 LQQ++NGL +GS YAL+A+GYTMVYGII +INFAHGEV MIG+ ++ I LL + D+ Sbjct: 5 LQQVINGLVLGSMYALVALGYTMVYGIINLINFAHGEVLMIGALCSWSVIGLLQPLMPDT 64 Query: 68 VP-LMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126 +++L + + I +A Y+IE++AYRPLR +L PLI+AIGMSI LQ M+ Sbjct: 65 PGWVLLLISMVLASIAAAALNYAIEKIAYRPLRNAPKLAPLITAIGMSILLQTLAMIVWK 124 Query: 127 SKEKAIPTLLPGN-FVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185 K PTLLP F GE+ VI+ Q++I +T + + L+ ++R++LGRA RA Sbjct: 125 PNYKPFPTLLPTTPFEIGEA-----VITPTQLMILGLTAVALAVLSWLVNRTKLGRAMRA 179 Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245 AE+ ++ +L+G+ + +I+ TF+IGA LA +A V+ M YG + +GFL G+KAFTAA Sbjct: 180 TAENPRVASLMGVKPDVVISATFIIGAVLATIAGVMWAMNYGTAHHAMGFLPGLKAFTAA 239 Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGA--------DVFGDQYKDVVAFGLLILVLLFRPTG 297 V GGIG++ GA++GGLLLG+ E+ G+ V G Y D++AF +LI+ L RP+G Sbjct: 240 VFGGIGNLGGAVVGGLLLGLIESIGSGYLGELTGGVLGSHYTDILAFVVLIITLTLRPSG 299 Query: 298 ILG 300 +LG Sbjct: 300 LLG 302 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: 317 Number of extensions: 16 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: 309 Length adjustment: 27 Effective length of query: 280 Effective length of database: 282 Effective search space: 78960 Effective search space used: 78960 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