Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_03879 H281DRAFT_03879 xylose ABC transporter membrane protein
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Burk376:H281DRAFT_03879 Length = 399 Score = 262 bits (670), Expect = 1e-74 Identities = 141/366 (38%), Positives = 221/366 (60%), Gaps = 12/366 (3%) Query: 29 MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88 +LIA+ AI +FF T G P NL+NL+ Q S ++A GM+ VI+AG IDLSVGS++ Sbjct: 37 LLIAVAAIWIFFSVLTHGAFVTPRNLSNLLRQMSITGMLACGMVFVIIAGEIDLSVGSLL 96 Query: 89 AFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRG 148 +G +AAIL V + + +++G ++G G+W Y R+PSFIV L GML +RG Sbjct: 97 GLLGGVAAILDVNRHWPIGVTLPVVMLLGVLVGVFNGWWSTYRRVPSFIVGLGGMLAYRG 156 Query: 149 LTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVV 208 + L V GG I P F + G+LP + G +T +++L VL+ +L R+R Sbjct: 157 ILLGVTGGSTIAPVSDGFVFVGQGYLPTLAG----DTLAVVLFVLLA----FLTLRQRRN 208 Query: 209 NVKHGIDVEPFGFFIVQNLLISGAILFLGY--QLSTYRGLPNVLIVMLVLIALYSFVTRR 266 ++ + V P + + +I ++ G+ L Y G+P ++++L L+ +++++ + Sbjct: 209 RERYQLSVVPVWQDVAK--VIGAGVILAGFVATLDRYGGIPVPVLLLLALLGIFTWIATQ 266 Query: 267 TTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVG 326 T GRR+YA+G N +AT+LSG+NT R+ F MG++ AG++ RL + +P AG Sbjct: 267 TVFGRRIYAVGSNLEATRLSGVNTNRVKLAIFALMGLMCAFAGIVNTARLAAGSPSAGSM 326 Query: 327 FELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLA 386 ELD IAACFIGG S GG G + GA+IGA +M ++NGMS++ + +Q +VKG +L+ Sbjct: 327 GELDAIAACFIGGTSMRGGSGTVYGALIGALVMASLDNGMSMLDVDAYWQMIVKGSILVL 386 Query: 387 AVFFDV 392 AV+ DV Sbjct: 387 AVWIDV 392 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: 560 Number of extensions: 39 Number of successful extensions: 3 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: 399 Length adjustment: 31 Effective length of query: 367 Effective length of database: 368 Effective search space: 135056 Effective search space used: 135056 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