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 GFF2762 HP15_2706 inner-membrane translocator
Query= TCDB::P21627 (307 letters) >FitnessBrowser__Marino:GFF2762 Length = 291 Score = 169 bits (428), Expect = 7e-47 Identities = 94/301 (31%), Positives = 165/301 (54%), Gaps = 14/301 (4%) Query: 7 YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66 +LQ L G+T+G+TYALIA+G+T++Y +INFA GE MIG +A + L Sbjct: 5 FLQYLFTGITIGATYALIALGFTLIYNASHVINFAQGEFLMIGG---------MATVSLT 55 Query: 67 SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126 ++ + M+ A ++I+ G +++R A P + + + +I IG SIF++ + Sbjct: 56 AMGVPMILAVVLAVILAGILGVALQRFAIAPAKQADVVTLIIITIGASIFIRGIAQVVWG 115 Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186 + + + + G V++ + + + +++ GL LF +++ +G+A A Sbjct: 116 KEYHVMQNFSTDQPI----EVFGAVLNSQSLWVLGIGAILVVGLVLFFTKTLIGKAILAT 171 Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246 + + + L+GI + ++ L F++ A L +VA +++ + IG + G+K F AA Sbjct: 172 SMNKEAARLVGIRTQMVLMLAFMVSALLGSVAGIVVA-PITFTSYDIGIILGLKGFVAAA 230 Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVEK 306 +GG+GS GA++GGL LG+ EA A YKD VAF +++LVL F P G+ G VE+ Sbjct: 231 IGGLGSGVGAVVGGLSLGIVEAMAAGYISSDYKDAVAFSMILLVLFFMPRGLFGAKVVER 290 Query: 307 V 307 V Sbjct: 291 V 291 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: 275 Number of extensions: 12 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: 291 Length adjustment: 27 Effective length of query: 280 Effective length of database: 264 Effective search space: 73920 Effective search space used: 73920 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