Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_040659170.1 ON16_RS02715 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >NCBI__GCF_000307265.1:WP_040659170.1 Length = 404 Score = 325 bits (833), Expect = 1e-93 Identities = 174/387 (44%), Positives = 251/387 (64%), Gaps = 16/387 (4%) Query: 24 IREYGMLIALVAIMVFFQFYTGGILFRPV--------NLTNLILQNSFIVIMALGMLL-V 74 +++ M+IALV + + F+ + +PV N++NLI QNS++VI+A+GML+ + Sbjct: 17 LKKNTMVIALVLVTLLFEVLIITVAHKPVSQALLTPANISNLISQNSYVVILAVGMLMCI 76 Query: 75 IVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIP 134 + G+IDLSVGS+VA VGA+A L V MN +LA +ICL++G IGA Q YWIAY RIP Sbjct: 77 LTGGNIDLSVGSVVALVGAVAGTLIVNMHMNIYLAMVICLLVGLAIGAWQAYWIAYVRIP 136 Query: 135 SFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLI 194 FIVTLAGML++RGL +L G I +P + + ++P G +T + +T++I Sbjct: 137 PFIVTLAGMLLWRGLAQIILDGLTISGYPETYLNLFNSYIP---GASAEKSTILTVTLVI 193 Query: 195 TVAL--FYLAWR--RRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVL 250 V L YLA + R ++ + + F +N ++ +L L L ++GLP +L Sbjct: 194 GVVLCAVYLAVQLMNRAKRKRNHYETQSASMFWGKNAVLCALMLALCLMLGNHKGLPTIL 253 Query: 251 IVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGM 310 I++ V++ +Y + T+ T GR +YAMGGNEKA KLSGINT R F + NM L+ +A + Sbjct: 254 ILLAVIVLIYGYYTQNTVPGRHLYAMGGNEKAAKLSGINTNRTMFFAYTNMAFLSAVAAL 313 Query: 311 IIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVG 370 ++ R NSA P AG +E+D I ACFIGGASA GG G + GAV+GA MGV+NNGMSI+G Sbjct: 314 VVTARFNSAAPSAGTSYEMDAIGACFIGGASAYGGTGTVAGAVVGAVFMGVINNGMSILG 373 Query: 371 LGIDFQQMVKGLVLLAAVFFDVYNKNK 397 + ++Q++VKGLVLLAAV FDV +K + Sbjct: 374 IDANWQKVVKGLVLLAAVIFDVVSKRR 400 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: 547 Number of extensions: 32 Number of successful extensions: 5 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: 404 Length adjustment: 31 Effective length of query: 367 Effective length of database: 373 Effective search space: 136891 Effective search space used: 136891 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