Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_061534007.1 CAter10_RS14805 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >NCBI__GCF_001584165.1:WP_061534007.1 Length = 402 Score = 515 bits (1326), Expect = e-150 Identities = 247/379 (65%), Positives = 317/379 (83%) Query: 19 YIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAG 78 ++++N+REYGML++L+AIM FFQ+ T G L +P+NLTNL+LQNS+IVIMALGML+VIVAG Sbjct: 24 FLKNNMREYGMLMSLIAIMAFFQYMTDGTLMQPLNLTNLVLQNSYIVIMALGMLMVIVAG 83 Query: 79 HIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIV 138 HIDLSVGS+V F+GA+AA+L V MN LA+++CL+ GG IGAAQGYW+A+ +IPSFIV Sbjct: 84 HIDLSVGSVVGFIGALAAVLIVNLHMNFVLASILCLLAGGAIGAAQGYWVAFFKIPSFIV 143 Query: 139 TLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVAL 198 TLAGMLVF+GLTL +L G+++GPFP DFQ++S+GF+PD G L TS+++ VL+ + Sbjct: 144 TLAGMLVFKGLTLALLQGQSVGPFPDDFQMLSSGFIPDFFGGADLRITSLLVGVLVAAVM 203 Query: 199 FYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIA 258 + R R VKHG++ EP FF+++N + + I+F Y L++Y+G+PNVLIVM +L+ Sbjct: 204 IVVKVRHRAKQVKHGMEDEPQLFFVLKNGVFAAVIIFFSYLLASYKGMPNVLIVMFLLMV 263 Query: 259 LYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNS 318 Y+F+ RTTIGRR+YA+GGNEKA KLSGI T R+SF TF+NMG+LA LAG+I A RLN+ Sbjct: 264 AYTFIANRTTIGRRIYAVGGNEKAAKLSGIKTSRVSFYTFINMGMLAALAGLIFAARLNT 323 Query: 319 ATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQM 378 ATPKAG GFELDVIAACFIGGASASGGVGK+ GAVIGAF+MGVMNNGMSI+G+GID+QQ+ Sbjct: 324 ATPKAGTGFELDVIAACFIGGASASGGVGKVMGAVIGAFVMGVMNNGMSIMGIGIDYQQV 383 Query: 379 VKGLVLLAAVFFDVYNKNK 397 +KGLVLLAAVF DVYNKNK Sbjct: 384 IKGLVLLAAVFVDVYNKNK 402 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: 642 Number of extensions: 24 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: 402 Length adjustment: 31 Effective length of query: 367 Effective length of database: 371 Effective search space: 136157 Effective search space used: 136157 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