Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF3640 PGA1_262p00440 xylose transport system permease protein XylH
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Phaeo:GFF3640 Length = 433 Score = 215 bits (547), Expect = 2e-60 Identities = 144/415 (34%), Positives = 211/415 (50%), Gaps = 47/415 (11%) Query: 23 NIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDL 82 ++R GM+ A V + + F T G P N+ NL +Q + IMA GM+ VIV HIDL Sbjct: 24 DVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVFVIVTRHIDL 83 Query: 83 SVGSIVAFVGAIAAILTVQ-------WGMNP----FLAALICLVIGGIIGAAQGYWIAYH 131 SVG+++A A+ A++ G+N + + L IG +IGA QG+ + + Sbjct: 84 SVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGAFQGWMVGFL 143 Query: 132 RIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILT 191 IP+FIVTL G LV+R + ++ G+ IGP + F V GG G T++ Sbjct: 144 TIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLVF--------GGTSGTLGTTLSWV 195 Query: 192 VLITVALFYLA--WRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYR----- 244 V I L LA W R HG V+P V I+ +IL L+ Y+ Sbjct: 196 VGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAILNAYQIPARR 255 Query: 245 --------------------GLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATK 284 GLP +++++ + + + RRT +GR ++A GGN A + Sbjct: 256 LKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDAAE 315 Query: 285 LSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASG 344 LSGINT L+ F MG L L+ ++ + RL + + G EL VIAA IGG + SG Sbjct: 316 LSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTALSG 375 Query: 345 GVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDV-YNKNKG 398 G G I GA++GA IM + +GM++VG+ FQ +V G VL+AAV+ D+ Y K G Sbjct: 376 GFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKRVG 430 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: 553 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: 398 Length of database: 433 Length adjustment: 31 Effective length of query: 367 Effective length of database: 402 Effective search space: 147534 Effective search space used: 147534 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