Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS22470 HSERO_RS22470 D-xylose ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__HerbieS:HSERO_RS22470 Length = 377 Score = 263 bits (672), Expect = 6e-75 Identities = 148/368 (40%), Positives = 219/368 (59%), Gaps = 8/368 (2%) Query: 29 MLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIV 88 +LIA+ I FF F T G P NL+NL+ Q S I+A GM+LVI+AG IDLSVGS++ Sbjct: 16 LLIAIAIIWGFFSFMTDGGFVTPRNLSNLLRQMSVTGILACGMVLVIIAGEIDLSVGSLL 75 Query: 89 AFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRG 148 +G +AA+L V + L ++ L G +G GY AY IPSFIV L GML FRG Sbjct: 76 GLLGGLAALLDVSHHLPLALNLVLALGFGLALGLLNGYLTAYLGIPSFIVGLGGMLAFRG 135 Query: 149 LTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVALFYLAWRRRVV 208 + L + GG I P + + G+LP G+ L +L V +T W RV Sbjct: 136 ILLGITGGLTIAPVSDNMVYLGQGYLPPQMGV-ALGIALFVLAVALT-------WMSRVN 187 Query: 209 NVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTT 268 +HG+ + ++ ++I +L L++Y G+P ++++L L+ L+S+V+ +T Sbjct: 188 RSRHGLPLAALWRDALKVVVIGAVLLAFVRTLNSYDGIPVPVLLLLALLGLFSYVSTQTV 247 Query: 269 IGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFE 328 GRR+Y++G N +AT+LSG+N + + F MGV+ LAG++ RL + +P AG E Sbjct: 248 FGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARLAAGSPSAGNMGE 307 Query: 329 LDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAV 388 LD IAACFIGG S GG G I GA+IGA +M ++NGMS++ +G +Q +VKG +L+ AV Sbjct: 308 LDAIAACFIGGTSMRGGSGTIYGALIGALVMASLDNGMSMLDVGTYWQMIVKGSILVLAV 367 Query: 389 FFDVYNKN 396 + DV ++ Sbjct: 368 WVDVSTRS 375 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: 548 Number of extensions: 38 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: 377 Length adjustment: 30 Effective length of query: 368 Effective length of database: 347 Effective search space: 127696 Effective search space used: 127696 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