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 RR42_RS16970 RR42_RS16970 ABC transporter ATP-binding protein
Query= TCDB::P21628 (417 letters) >FitnessBrowser__Cup4G11:RR42_RS16970 Length = 386 Score = 256 bits (655), Expect = 6e-73 Identities = 157/363 (43%), Positives = 205/363 (56%), Gaps = 51/363 (14%) Query: 88 PSTQRWAVLALVVVAFVWPFFASRGA----VDIATLILIYVMLGIGLNIVVGLAGLLDLG 143 P+ A+L +++A PF V + LIY+ML +GLNIVVG AGLLDLG Sbjct: 19 PAKTMAALLGFLIIALCAPFLVQTLGGNYWVRVLDFALIYIMLALGLNIVVGFAGLLDLG 78 Query: 144 YVGFYAVGAYTYALLAEY----------------AGFGFWTALPIAGMMAALFGFLLGFP 187 Y+ FYAVGAY ALL W LP+A ++AA FG LLG P Sbjct: 79 YIAFYAVGAYMMALLGSPHLANQFEWIHQLFPNGLHLSMWFVLPLAVLVAATFGVLLGAP 138 Query: 188 VLRLRGDYLAIVTLGFGEIIRILLRNMTE---ITGGPNGIGSIPKPTLFGLTFERRAPEG 244 L+LRGDYLAIVTLGFGEIIRI L N+ IT GP GI ++ +FG F + Sbjct: 139 TLKLRGDYLAIVTLGFGEIIRIFLNNLDRPLNITNGPKGITAVDPVHIFGFDFSKS---- 194 Query: 245 MQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRA 304 HE FG+ + V + Y + ++LV+ +F+ RL IGRA+ A+REDE+A +A Sbjct: 195 ----HEIFGLKFTP---VFMYYYLLVVLVIAIVFICLRLQNSRIGRAFVAIREDEIAAKA 247 Query: 305 LGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQL 364 +G+N +KL AF +GASF G +G+ F A QG V+PESF ES ILAIVVLGGMG Sbjct: 248 MGINTRNIKLLAFAMGASFGGASGAVFGAFQGFVSPESFVLWESIYILAIVVLGGMGHIP 307 Query: 365 GVILAAVVMVLLQE-MRGFNE----------------YRMLIFGLTMIVMMIWRPQGLLP 407 GVIL +++V QE +R E R L+FGL ++ +M++RP GL P Sbjct: 308 GVILGGILLVGFQELLRAVAEPAQNMIFGHTIVDAEVLRQLLFGLALVGVMLYRPAGLWP 367 Query: 408 MQR 410 R Sbjct: 368 SPR 370 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: 517 Number of extensions: 36 Number of successful extensions: 6 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: 386 Length adjustment: 31 Effective length of query: 386 Effective length of database: 355 Effective search space: 137030 Effective search space used: 137030 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