Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_003463745.1 J416_RS02050 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000359605.1:WP_003463745.1 Length = 386 Score = 414 bits (1064), Expect = e-120 Identities = 201/378 (53%), Positives = 279/378 (73%) Query: 21 RSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHI 80 R+N+REYGM+IALV I F T G+ F P+NLTNLILQN FI+++A+GM+LVI+ G+I Sbjct: 9 RNNLREYGMIIALVLITGLFWILTDGVTFTPLNLTNLILQNGFILVLAVGMVLVIITGNI 68 Query: 81 DLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTL 140 DLSVGS+VAF+GAIA +L + + +LA ++ ++ G +IG QG+WIAY IPSFIVTL Sbjct: 69 DLSVGSVVAFIGAIAGVLMINHDVPVWLAVVLSILAGAVIGVWQGFWIAYIGIPSFIVTL 128 Query: 141 AGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFY 200 AGML+FRGLTL++L G+++ PFP FQ IS GFLPD+ G ++ +++ + +I++ L Y Sbjct: 129 AGMLIFRGLTLYLLNGQSLAPFPESFQNISGGFLPDLFGGSDIHILTLVFSAVISLVLIY 188 Query: 201 LAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALY 260 L + RR +++ +V P + + ++ I + YQL+ G+P VL+++L LI +Y Sbjct: 189 LEFNRRKTQLQYKFEVVPVWITLAKLAILVFVINWFAYQLALNEGMPMVLVIVLFLIVIY 248 Query: 261 SFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSAT 320 +F+ + T +GR +YA GGN+KA LSGI T+R+ F FVN G+LA LAG++ A RLNSAT Sbjct: 249 TFIMKNTVMGRHIYATGGNKKAADLSGIKTKRVVFGVFVNNGILAALAGLMFAARLNSAT 308 Query: 321 PKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVK 380 P AG ELD IAA FIGGAS +GGVG + GA++G +MGVMNNGMS++G+GID+QQ +K Sbjct: 309 PAAGEMLELDAIAAVFIGGASMAGGVGTVIGAIVGGLVMGVMNNGMSLIGIGIDWQQFIK 368 Query: 381 GLVLLAAVFFDVYNKNKG 398 G+VLL AV FDVYNKNKG Sbjct: 369 GMVLLIAVGFDVYNKNKG 386 Lambda K H 0.329 0.145 0.422 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: 619 Number of extensions: 34 Number of successful extensions: 1 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: 398 Length of database: 386 Length adjustment: 31 Effective length of query: 367 Effective length of database: 355 Effective search space: 130285 Effective search space used: 130285 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 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 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