Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_061938416.1 CPter91_RS06295 sugar ABC transporter permease
Query= TCDB::O05177 (398 letters) >NCBI__GCF_001584185.1:WP_061938416.1 Length = 379 Score = 271 bits (692), Expect = 3e-77 Identities = 154/376 (40%), Positives = 224/376 (59%), Gaps = 11/376 (2%) Query: 20 IRSNIREY---GMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIV 76 ++ R+Y +LIA+ I FF + T G P NL+NL+ Q S ++A GM+LVI+ Sbjct: 6 LKQLFRQYKIMALLIAIALIWAFFSWKTEGGFVTPRNLSNLLRQMSITGVLACGMVLVII 65 Query: 77 AGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSF 136 AG IDLSVGS++ +G +AA+L V + L L+ L+ G +G GY AY RIPSF Sbjct: 66 AGEIDLSVGSMLGLLGGVAAVLDVTHHLPLSLNLLLVLLAGLALGLFNGYLTAYMRIPSF 125 Query: 137 IVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITV 196 IV L GML FRG+ L V GG I P ++ + G+LP GI L + + Sbjct: 126 IVGLGGMLAFRGILLGVTGGLTIAPVSSEMVYLGQGYLPPQLGIA--------LGIGLFA 177 Query: 197 ALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVL 256 L+WRRR +HG+ V V+ LLI +L L+TY G+P ++++L L Sbjct: 178 LALVLSWRRRSNRQQHGLPVPSVWRDAVRVLLIGAVLLAFVRTLNTYDGIPVPVLLLLAL 237 Query: 257 IALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRL 316 + L+S++T +T GRR+Y++G N +AT+LSG+N + + F MGV+ LAG++ RL Sbjct: 238 LGLFSYLTTQTVFGRRIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARL 297 Query: 317 NSATPKAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQ 376 + +P AG ELD IAACFIGG S GG G + GA+IGA +M ++NGMS++ + +Q Sbjct: 298 AAGSPSAGNMGELDAIAACFIGGTSMRGGYGTVYGALIGALVMASLDNGMSMLDVDTYWQ 357 Query: 377 QMVKGLVLLAAVFFDV 392 +VKG +L+ AV+ DV Sbjct: 358 MIVKGGILMLAVWVDV 373 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: 551 Number of extensions: 36 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: 379 Length adjustment: 30 Effective length of query: 368 Effective length of database: 349 Effective search space: 128432 Effective search space used: 128432 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