Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate YP_004142092.1 Mesci_2911 inner-membrane translocator
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000185905.1:YP_004142092.1 Length = 418 Score = 165 bits (418), Expect = 2e-45 Identities = 117/376 (31%), Positives = 192/376 (51%), Gaps = 22/376 (5%) Query: 26 EYGMLIALVAIMVFFQFYTG--GILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLS 83 + G L +V +++ + + I NL NL+ S + ++ALG++ V++ G IDLS Sbjct: 42 DLGSLPVIVGLVIIWTVFASINPIFLSSSNLVNLLFDCSTVGVIALGIVCVLMVGEIDLS 101 Query: 84 VGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRI--PSFIVTLA 141 VGSI F A+ L V G LA L + +GG IGA Y + ++R+ PSF+ TLA Sbjct: 102 VGSISGFASAMVGTLWVNQGWPVALAILAAVAVGGFIGAL--YALLFNRLGMPSFVSTLA 159 Query: 142 GMLVFRGLTLFVLGGKNIGPFPTDFQVISTG---FLPDI--GGIEGLNTTSMILTVLITV 196 G+L GL L++LG P +++ G +P + + + M++T L TV Sbjct: 160 GLLAVLGLQLYILGSTGSINLPYGSNLVNFGQLLMMPKLVSFALAAVPGIVMLITGLRTV 219 Query: 197 ALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVL 256 A RRR N + G + + ++I+ + + + L+ RG+P + + + L Sbjct: 220 A------RRRAAN----LSAPSTGGLVTRAVVITVILELIVFYLNQARGIPWMFGLFVGL 269 Query: 257 IALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRL 316 + + RT GR + A+GGN +A + +GIN + FV +LA G++ A RL Sbjct: 270 VISMHYALTRTKWGRSMSAVGGNREAARRAGINVRLIYSSAFVLCSMLAAFGGVLSAARL 329 Query: 317 NSATPKAGVG-FELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDF 375 SA+ +AG G L+ IAA IGG S GG G A++G ++ + +G++++ L Sbjct: 330 ASASQQAGTGDVNLNAIAAAVIGGTSLFGGRGSAYSALLGIIVIQSIASGLTLLDLSSSL 389 Query: 376 QQMVKGLVLLAAVFFD 391 + M+ G VL AV D Sbjct: 390 RYMITGAVLAIAVIVD 405 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: 510 Number of extensions: 36 Number of successful extensions: 4 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: 418 Length adjustment: 31 Effective length of query: 367 Effective length of database: 387 Effective search space: 142029 Effective search space used: 142029 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