Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012047541.1 BBTA_RS36615 ABC transporter permease
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000015165.1:WP_012047541.1 Length = 330 Score = 133 bits (335), Expect = 6e-36 Identities = 108/387 (27%), Positives = 173/387 (44%), Gaps = 70/387 (18%) Query: 4 ANTTNEESNVISVGSYIRSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSF 63 A++T + + S +R R Y + IA V ++V F + L N N+ Q + Sbjct: 11 ASSTRSDRRRRILQSLLRGE-RPYMLYIAFVILLVVFSLSSPWFLSVD-NFLNIGRQTTL 68 Query: 64 IVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAA 123 + I+A+GM +I+A IDLSV S +A G AA+ Q + ++G + G Sbjct: 69 VSIIAVGMTFIIIARQIDLSVASTLALSGMAAALAMSQINNS--------WIVGAVAGLG 120 Query: 124 QGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGL 183 G L G+L G T + S FL +G + Sbjct: 121 TG-------------ALVGLLN--------------GILTTQLSIPS--FLVTLGSLSMA 151 Query: 184 NTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTY 243 +M++T + +P ++I+ F + T Sbjct: 152 RGLAMMVT-----------------------NTKP--------VIITNETYFAIFGEGTL 180 Query: 244 RGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGV 303 G+P + L + + + GRR+YA+GGN A SGINT+ ++ FV G Sbjct: 181 LGIPVPIAWTLAAMIVGILLLHYNVFGRRIYAVGGNPTAALYSGINTKLITTAAFVLTGT 240 Query: 304 LAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMN 363 LAGLA ++++ R ++A P G ELDVIAA +GG S GG G I G + G+ I+G +N Sbjct: 241 LAGLAALVLSARSHAARPDVVQGMELDVIAAVILGGCSLFGGRGYILGTLFGSLIIGTLN 300 Query: 364 NGMSIVGLGIDFQQMVKGLVLLAAVFF 390 NG+ ++G+ Q ++KG +++AAV F Sbjct: 301 NGLVLLGVSSPMQLVIKGAIIVAAVAF 327 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: 424 Number of extensions: 25 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 330 Length adjustment: 29 Effective length of query: 369 Effective length of database: 301 Effective search space: 111069 Effective search space used: 111069 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: 49 (23.5 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