Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2143 PS417_10930 D-xylose ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__WCS417:GFF2143 Length = 378 Score = 266 bits (679), Expect = 1e-75 Identities = 154/365 (42%), Positives = 222/365 (60%), Gaps = 10/365 (2%) Query: 29 MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88 ++IA+ I VFF + T G P NL+NL+ Q S I+A GM+LVI++G IDLSVGS++ Sbjct: 16 LVIAVAVIWVFFSWQTEGGFLTPRNLSNLLRQMSITGILACGMVLVIISGEIDLSVGSLL 75 Query: 89 AFVGAIAAILTVQWGMNPFLAALICLVIGGI-IGAAQGYWIAYHRIPSFIVTLAGMLVFR 147 +G +AAIL V + + P LA L + + G+ IG A GY AY RIPSFIV L GML FR Sbjct: 76 GLLGGLAAILDVVYHI-PLLANLSLVALCGLMIGLANGYMTAYLRIPSFIVGLGGMLAFR 134 Query: 148 GLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRV 207 G+ L + GG I P + G+LP GI GL LTV +T W++R Sbjct: 135 GILLGITGGTTIAPVSPSLVYVGQGYLPHSVGI-GLGVLLFSLTVFLT-------WKQRR 186 Query: 208 VNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRT 267 HG+ +V+ +I + L++Y G+P ++++LVL+ ++S+VT +T Sbjct: 187 NRALHGLAAHSLVRDLVRVAVIGAVLAGFVTTLNSYDGIPVPVLLLLVLLGVFSYVTSQT 246 Query: 268 TIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGF 327 GRRVYA+G N +AT+LSGIN + + F MGV+ LAG++ RL + +P AG Sbjct: 247 VFGRRVYAVGSNMEATRLSGINVQAVKLWIFGIMGVMCALAGLVNTARLAAGSPSAGNMG 306 Query: 328 ELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAA 387 ELD IAACFIGG S GG G + GA++GA ++ ++NGMS++ + +Q +VKG +L+ A Sbjct: 307 ELDAIAACFIGGTSMRGGSGTVYGALLGALVITSLDNGMSMLDVDSYWQMIVKGSILVLA 366 Query: 388 VFFDV 392 V+ DV Sbjct: 367 VWVDV 371 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: 527 Number of extensions: 37 Number of successful extensions: 2 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: 378 Length adjustment: 30 Effective length of query: 368 Effective length of database: 348 Effective search space: 128064 Effective search space used: 128064 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