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 AZOBR_RS32410 AZOBR_RS32410 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >FitnessBrowser__azobra:AZOBR_RS32410 Length = 355 Score = 201 bits (511), Expect = 3e-56 Identities = 114/319 (35%), Positives = 173/319 (54%), Gaps = 27/319 (8%) Query: 93 WAVLALVVVAFVWPFF----ASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFY 148 W +L L V P S IA +I+V+L LN V G AGLL +G+ FY Sbjct: 30 WTLLLLAVAFGAVPAAIVGTGSSYLAQIAITTMIFVILSASLNHVTGTAGLLSIGHAAFY 89 Query: 149 AVGAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIR 208 +GAY ALL+ G F LP AG++AALFGFL+ P +RL Y A+ TLG GE+I Sbjct: 90 GIGAYAAALLSTKLGLPFIVTLPAAGLIAALFGFLVALPTMRLVSIYFAVATLGIGEMIY 149 Query: 209 ILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVV 268 ++L N ++T GP GI IP LFG + ++ Y+ Sbjct: 150 VVLLNWVDVTRGPMGIRGIPPIELFGWQAD----------------------TLLTRYLA 187 Query: 269 ALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAG 328 ++ + ++V++RL G A ALRED+ ++G+N +K+ +F + FAG AG Sbjct: 188 VAVIAVACVWVLHRLTHSYYGNALRALREDDQCADSMGINVERLKIESFVVATFFAGIAG 247 Query: 329 SFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRM 387 + A + P++F F+ES +ILA+VV+GG+GS G ++ A+ M++L E +R +YRM Sbjct: 248 ALLAHTSAYIAPDNFRFMESILILAMVVVGGLGSLPGAVVGALFMIVLPEALRDIGDYRM 307 Query: 388 LIFGLTMIVMMIWRPQGLL 406 + G TM + ++ P+G+L Sbjct: 308 IAVGATMFLSILLLPKGML 326 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: 409 Number of extensions: 29 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: 417 Length of database: 355 Length adjustment: 30 Effective length of query: 387 Effective length of database: 325 Effective search space: 125775 Effective search space used: 125775 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: 50 (23.9 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