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_041096495.1 SUTH_RS01375 branched-chain amino acid ABC transporter permease
Query= TCDB::P21627 (307 letters) >NCBI__GCF_000828635.1:WP_041096495.1 Length = 328 Score = 270 bits (691), Expect = 3e-77 Identities = 155/328 (47%), Positives = 208/328 (63%), Gaps = 34/328 (10%) Query: 8 LQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDS 67 LQQ++NGLT GS YA++A+GYTMVYG+I +INFAHGEV MIG+ +AF IT LA L Sbjct: 5 LQQIINGLTTGSVYAVVALGYTMVYGVIQLINFAHGEVVMIGAMVAFSIITSLAGSSLPP 64 Query: 68 VPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQDS 127 + ++ LA A+I GY +ERVAYRPLR RL PLI+AIGMSI LQ+ +L Sbjct: 65 LAIV-LAGVLAAIPACMLMGYLLERVAYRPLRHAPRLAPLITAIGMSIILQHLALLVWGR 123 Query: 128 KEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRACA 187 A P ++ N VF ++ G IS +Q+ I +++ +M GL+ FI R+R G A RA A Sbjct: 124 NPLAFPQIID-NRVF---AIGGAAISSVQVAIILLSLSMMAGLSWFIYRTRFGIAIRATA 179 Query: 188 EDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAVL 247 E++ + L+G+N+N +IA TFV+GA L AVA V+ G YG+ + +GF G+KAF+AAVL Sbjct: 180 ENVHVAGLMGVNANRVIAATFVVGAGLGAVAGVMYGSYYGIAHYTMGFSLGLKAFSAAVL 239 Query: 248 GGIGSIPGAMLGGLLLGVAEAFGAD-----------------------------VFGDQY 278 GGIG+I GAMLGG+LLG+ EA G +FG Y Sbjct: 240 GGIGNIAGAMLGGILLGLVEALGTGYVGELTDLCHWPIASGVLAGHCADGGNFVLFGSNY 299 Query: 279 KDVVAFGLLILVLLFRPTGILGRPEVEK 306 +DV AF +LILVL+FRP+G+LG E+ Sbjct: 300 QDVFAFLMLILVLVFRPSGLLGERVSER 327 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: 342 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 307 Length of database: 328 Length adjustment: 27 Effective length of query: 280 Effective length of database: 301 Effective search space: 84280 Effective search space used: 84280 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 Apr 09 2024. 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