Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Ac3H11_608 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= TCDB::O05177 (398 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_608 Length = 409 Score = 505 bits (1301), Expect = e-148 Identities = 247/397 (62%), Positives = 318/397 (80%) Query: 1 MSSANTTNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQ 60 ++ N T + S+ +++ N+REYGMLI LVAIM FFQ+ T G L +P+NLTNL+LQ Sbjct: 12 LADGNPTTAARHDKSLLQHLQHNLREYGMLITLVAIMGFFQYMTEGTLMQPLNLTNLVLQ 71 Query: 61 NSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGII 120 NS+IVIMALGMLLVIVAGHIDLSVGS+ F+GA+AA+L V++ + A L+CL+ GG+I Sbjct: 72 NSYIVIMALGMLLVIVAGHIDLSVGSVCGFIGALAAVLMVEYNWHFVPATLVCLLCGGLI 131 Query: 121 GAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGI 180 GA QG ++A+ RIPSFIVTLAGMLVF+GL L +L G+++GPFP+ FQ++S+GF+PD+ + Sbjct: 132 GAIQGSFVAFSRIPSFIVTLAGMLVFKGLALALLAGQSVGPFPSAFQMLSSGFIPDLFSV 191 Query: 181 EGLNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQL 240 EGL TS++L + AL R+R ++HG+ EP G FI + ++ G +++ Y L Sbjct: 192 EGLRMTSLLLGAAVAAALAVGGLRQRANRLRHGVQTEPAGLFIARTVVFGGLLVYFSYLL 251 Query: 241 STYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVN 300 ++Y+GLPNVLIVM +LI L+ FVT RTTIGRR+YAMGGNEKA KLSGI TERL+ F+N Sbjct: 252 ASYKGLPNVLIVMALLIVLFDFVTSRTTIGRRIYAMGGNEKAAKLSGIKTERLTLYAFIN 311 Query: 301 MGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMG 360 MGVLA LAG++ A RLN+ATPKAG+GFELDVIAACFIGGASASGGVGK+ GAVIGAF+MG Sbjct: 312 MGVLAALAGLVFAARLNTATPKAGLGFELDVIAACFIGGASASGGVGKVMGAVIGAFVMG 371 Query: 361 VMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNK 397 VMNNGMSI+G+GID+QQ++KG+VLLAAV DVYNKNK Sbjct: 372 VMNNGMSILGIGIDYQQVIKGVVLLAAVLVDVYNKNK 408 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: 629 Number of extensions: 29 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: 409 Length adjustment: 31 Effective length of query: 367 Effective length of database: 378 Effective search space: 138726 Effective search space used: 138726 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 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