Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate BPHYT_RS04435 BPHYT_RS04435 ABC transporter
Query= TCDB::P21628 (417 letters) >FitnessBrowser__BFirm:BPHYT_RS04435 Length = 646 Score = 164 bits (416), Expect = 6e-45 Identities = 97/286 (33%), Positives = 158/286 (55%), Gaps = 24/286 (8%) Query: 94 AVLALVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAY 153 + LAL+ +A + + + I+IY +L GL+IVVG G + LG+ G + VGAY Sbjct: 9 SALALIALAVFPVLSGNPYYIHLLETIMIYAILLFGLDIVVGYTGQVSLGHAGLFGVGAY 68 Query: 154 TYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRN 213 T +L G F P+A ++ A FG +L P LR+ G YLA+VTL FG I++IL+ Sbjct: 69 TAGVLFFKLGMPFIVTAPLAILITAAFGAILALPALRVSGPYLAMVTLAFGTILQILINE 128 Query: 214 MTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLV 273 M +T GP G+ IPKP+L G +V ++VA LLV Sbjct: 129 MDFLTNGPMGV-KIPKPSLAGRPMN----------------------EVEYYWLVAALLV 165 Query: 274 LLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAA 333 +L V++R++R +GRA+EALR+ +A +G++ K+ AF I A FAG AG ++ Sbjct: 166 -ASLIVVHRVLRSHLGRAFEALRDSPIASDCMGVSVYRYKVYAFVISAGFAGLAGCLYSY 224 Query: 334 RQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQEM 379 + ++P ++ F + + L +++GG ++ G +L + ++VLL ++ Sbjct: 225 SEQYISPNTYNFELTILFLLAIIMGGRKTRTGALLGSAIIVLLPKL 270 Lambda K H 0.330 0.146 0.439 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: 605 Number of extensions: 33 Number of successful extensions: 2 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: 417 Length of database: 646 Length adjustment: 35 Effective length of query: 382 Effective length of database: 611 Effective search space: 233402 Effective search space used: 233402 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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