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 WP_011841981.1 RSPH17029_RS14870 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000015985.1:WP_011841981.1 Length = 310 Score = 104 bits (260), Expect = 3e-27 Identities = 101/323 (31%), Positives = 140/323 (43%), Gaps = 35/323 (10%) Query: 94 AVLA-LVVVAFVWPFFASRGAVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGA 152 AVLA + + FV P + A I L+ IG NI G GLL LG+ F+A G Sbjct: 9 AVLAGIAALQFVLPAYHHTNAARI----LVLATYAIGFNIAFGYTGLLSLGHALFFAGGM 64 Query: 153 YTYALLAEYAGFGFWTAL---PIA-GMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIR 208 Y LL + G+ W AL P+A G++AA G L LR G IVTL F + Sbjct: 65 YATGLLVDQGGWQPWAALLAGPVAGGVLAAGVGLL----ALRTAGPAFMIVTLMFAQAFH 120 Query: 209 ILLRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVV 268 + + TGG G TL G R P F +A T Y Sbjct: 121 LAILYWGRFTGGDEGF------TLSGAA-RRIGP---------FDLADPTT-----RYGA 159 Query: 269 ALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAG 328 A LL AL L+R GR A+RE+E R LG + KL A + +G AG Sbjct: 160 AFLLFAAALLGCLALVRSRTGRVLIAVRENEERTRMLGYDTFRTKLLALALSGLLSGAAG 219 Query: 329 SFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVIL-AAVVMVLLQEMRGFNEYRM 387 + + G V S + L V+LGG G+ LG +L A++ L+ Sbjct: 220 ATYGLMFGYVGGSFAAIQYSILPLIWVLLGGAGTVLGPLLGTALLFYLIDWASSITTASQ 279 Query: 388 LIFGLTMIVMMIWRPQGLLPMQR 410 + G +I+++++ P+GLL + R Sbjct: 280 FVVGAVLILLVLFAPRGLLGLLR 302 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: 376 Number of extensions: 20 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: 310 Length adjustment: 29 Effective length of query: 388 Effective length of database: 281 Effective search space: 109028 Effective search space used: 109028 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: 49 (23.5 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