Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 163 bits (412), Expect = 7e-45 Identities = 121/376 (32%), Positives = 182/376 (48%), Gaps = 62/376 (16%) Query: 23 NIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHIDL 82 +I ++ LIAL+ + + + L N N++ Q S + +++GM LVI+ IDL Sbjct: 3 SIAKFQSLIALIILCLVLSLLSDRFLTL-ANGWNVMRQVSVNICISVGMTLVILTAGIDL 61 Query: 83 SVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIVTLAG 142 SVGSI+A GA+ A L + Sbjct: 62 SVGSILALCGAVTASL-----------------------------------------IKN 80 Query: 143 MLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLI-TVALFYL 201 + GL L +IG P ++ G +G G T + + T+A+ + Sbjct: 81 GIAVEGLNL------HIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPFVATLAMLTI 134 Query: 202 AWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIALYS 261 A G+ + G F + L A L G+ L G+P + + V++AL Sbjct: 135 A---------RGLTMLWTGGFPINGLGEDFAFLGTGWFL----GIPMPVWITAVIVALAV 181 Query: 262 FVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNSATP 321 +T++T GR VYA+GGNE+A +LSGIN R+ + G LA + GMI+ +RL+SA P Sbjct: 182 LLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQP 241 Query: 322 KAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQMVKG 381 AG+ +ELD IAA IGG S SGG G I GAV+G I+GV+NNG+ ++ + +QQ+VKG Sbjct: 242 NAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKG 301 Query: 382 LVLLAAVFFDVYNKNK 397 V+L AV D N + Sbjct: 302 AVILLAVVIDKANSKE 317 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: 477 Number of extensions: 24 Number of successful extensions: 3 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: 318 Length adjustment: 29 Effective length of query: 369 Effective length of database: 289 Effective search space: 106641 Effective search space used: 106641 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 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