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_RS15600 BPHYT_RS15600 ABC transporter ATP-binding protein
Query= TCDB::P21628 (417 letters) >FitnessBrowser__BFirm:BPHYT_RS15600 Length = 389 Score = 242 bits (617), Expect = 2e-68 Identities = 154/351 (43%), Positives = 201/351 (57%), Gaps = 49/351 (13%) Query: 95 VLALVVVAFVWPFFASRGA--VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGA 152 + A+ V+A A+ G V + ++YVML +GLN+VVG AGLLDLGY+ FYAVGA Sbjct: 28 ITAIFVIAAPMIIGAAGGNYWVRVLDFAMLYVMLALGLNVVVGFAGLLDLGYIAFYAVGA 87 Query: 153 YTYALL------------AEYAGFG----FWTALPIAGMMAALFGFLLGFPVLRLRGDYL 196 YT ALL A A G F +P A +AA FG +LG P LRLRGDYL Sbjct: 88 YTSALLSSPHLSSQFEWIAHLAPNGLHVPFLIIVPCAMAVAAFFGVILGAPTLRLRGDYL 147 Query: 197 AIVTLGFGEIIRILLRNM---TEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFG 253 AIVTLGFGEI+RI L N+ IT GP GI I P G + H FG Sbjct: 148 AIVTLGFGEIVRIFLNNLDRPVNITNGPKGITGID-PVHAG-------DFSLAQTHSLFG 199 Query: 254 IAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVK 313 + + + Y L+V+A LLV+ +V RL IGRAW A+REDE+A +A+G+N VK Sbjct: 200 LQFPSVYSYYYLFVLAALLVI---WVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVK 256 Query: 314 LSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVM 373 L AF +GASF G +G+ F + QG V+PESFT ES ++LA VVLGGMG GVIL AV++ Sbjct: 257 LLAFAMGASFGGLSGAMFGSFQGFVSPESFTLPESIVVLACVVLGGMGHIPGVILGAVLL 316 Query: 374 VLL-----------------QEMRGFNEYRMLIFGLTMIVMMIWRPQGLLP 407 +L E+ R L++ L M+++M++R +GL P Sbjct: 317 AVLPEFLRSTMGPLQNMVFGHEIVDTEVIRQLVYALAMVLIMLYRSEGLWP 367 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: 462 Number of extensions: 23 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: 389 Length adjustment: 31 Effective length of query: 386 Effective length of database: 358 Effective search space: 138188 Effective search space used: 138188 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