Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate YP_004145035.1 Mesci_5978 inner-membrane translocator
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000185905.1:YP_004145035.1 Length = 428 Score = 473 bits (1217), Expect = e-138 Identities = 243/417 (58%), Positives = 315/417 (75%), Gaps = 25/417 (5%) Query: 5 NTTNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFI 64 N E+ I+V S + +N+REYG++IAL+ IM+FFQF T G LF+PVNL+NL+ QNSFI Sbjct: 12 NVAEEQRPRIAV-SALATNLREYGLIIALIVIMLFFQFTTSGTLFKPVNLSNLVQQNSFI 70 Query: 65 VIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGM----NPFLAALICLVIGGII 120 ++MALGMLLVIV+G+IDLSVGS+ F+GA+AA + V W + NP + ++ICLV+GG+I Sbjct: 71 IVMALGMLLVIVSGYIDLSVGSVAGFIGALAANMMVIWQLGPLSNPLVVSIICLVVGGLI 130 Query: 121 GAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGG-KNIGPFPTDFQVISTGFLPDIGG 179 GAAQGYWIAYHRIPSFIVTLAGML+FRG+ +LGG ++GP P DF+++S+GF+PD+ G Sbjct: 131 GAAQGYWIAYHRIPSFIVTLAGMLIFRGICQALLGGGSSVGPLPDDFKMLSSGFIPDVIG 190 Query: 180 ---------------IEG----LNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFG 220 I G L+ T+++L ++ +A Y R R +HG + EPF Sbjct: 191 PLTLIPPTVNAAGKTIMGSGLTLHMTTIVLGLIAVLAYAYFGVRTRRKRERHGYEAEPFA 250 Query: 221 FFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNE 280 F+V+ L+ S LFL Y+ ++YRGLP VL+VM VLI+L+ FVT+R TIGRR+YAMGGN Sbjct: 251 LFVVKTLVASALALFLVYEFASYRGLPVVLLVMGVLISLFVFVTKRMTIGRRIYAMGGNA 310 Query: 281 KATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGA 340 KA +LSGINTERL+ + F+NMGVL+ L G+IIA RL A P AG+G ELDVIAA FIGGA Sbjct: 311 KAAQLSGINTERLTLMVFINMGVLSALGGLIIAARLGQAVPAAGLGSELDVIAAVFIGGA 370 Query: 341 SASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVFFDVYNKNK 397 SA GGVG++ GAV+G FIMGVMNNGMSI+G+ +D+QQ+VKGLVLL AV FDVYNKNK Sbjct: 371 SAMGGVGQVIGAVVGGFIMGVMNNGMSIMGVNVDWQQVVKGLVLLGAVIFDVYNKNK 427 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: 676 Number of extensions: 43 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: 428 Length adjustment: 31 Effective length of query: 367 Effective length of database: 397 Effective search space: 145699 Effective search space used: 145699 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