Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 3608606 Dshi_1999 inner-membrane translocator (RefSeq)
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Dino:3608606 Length = 435 Score = 215 bits (548), Expect = 2e-60 Identities = 145/440 (32%), Positives = 225/440 (51%), Gaps = 50/440 (11%) Query: 1 MSSANTTNEESNVISVGSYIRS---NIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNL 57 MS A+ T + S++++ + R GM+ A V + + F T G N+ NL Sbjct: 1 MSDASPTESRLPSRAKRSFLQTLELDTRLLGMIGAFVLVCLVFNLLTDGRFLTARNIFNL 60 Query: 58 ILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAI-----AAILTVQWGMN------P 106 +Q + IMA GM+ +IV HIDL+VG+++A A AIL +G+ P Sbjct: 61 SIQTVSVAIMATGMVFIIVTRHIDLAVGALLATCSAAMAMTQTAILPQVFGLELGHPAIP 120 Query: 107 FLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDF 166 ++A L+ LV G +IGA QGY + Y IP+FIVTL G+LV+R + ++ G+ IGP F Sbjct: 121 WIAMLVGLVTGTVIGAFQGYLVGYLMIPAFIVTLGGLLVWRNVAWYMTNGQTIGPLDPTF 180 Query: 167 QVISTGFLPDIGGIEGL--NTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIV 224 + GGI G T S I+ ++ VA + W R + H V+P + Sbjct: 181 MTL--------GGINGTLGATLSWIVGLVAVVAACWALWSGRKNKIAHDAPVKPVWAELT 232 Query: 225 QNLLISGAILFL-----GYQLSTYR--------------------GLPNVLIVMLVLIAL 259 ++S AIL Y++ T R G+P +++++ + Sbjct: 233 VMGVVSVAILGFVAILNSYEVPTARLRRLFEARGEVMPEGYTEVYGIPYSVLLLIAVAVA 292 Query: 260 YSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSA 319 + + ++T GR ++A GGN A +LSGINT L+ F MG L ++ ++ + RL + Sbjct: 293 MTVIAKKTRFGRYIFATGGNPDAAELSGINTRMLTVKVFALMGALCAISAIVASARLTNH 352 Query: 320 TPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMV 379 + G EL VIAA IGG + +GG+G I GA++GA IM + +GM++VG+ Q +V Sbjct: 353 SNDIGTLDELRVIAAAVIGGTALAGGIGTIYGAILGALIMQSLQSGMAMVGVDAPLQNIV 412 Query: 380 KGLVLLAAVFFDV-YNKNKG 398 G VL+AAV D+ Y K G Sbjct: 413 VGTVLVAAVLIDILYRKRMG 432 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: 536 Number of extensions: 26 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: 435 Length adjustment: 31 Effective length of query: 367 Effective length of database: 404 Effective search space: 148268 Effective search space used: 148268 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