Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_012042355.1 BBTA_RS09965 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000015165.1:WP_012042355.1 Length = 516 Score = 642 bits (1655), Expect = 0.0 Identities = 328/503 (65%), Positives = 406/503 (80%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ILEMRN++K+F V+AL +V+ V GEIHALVGENGAGKSTLMKVLSGVYP G YEG+I Sbjct: 4 ILEMRNVSKSFGNVQALRDVSFAVAPGEIHALVGENGAGKSTLMKVLSGVYPHGRYEGQI 63 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 +EG R FR INDSE +GIIIIHQELAL+PL+SIAENIFL + + GVI + + RT Sbjct: 64 IFEGEERRFRDINDSEALGIIIIHQELALIPLMSIAENIFLSHAPSRFGVIDRDEVYRRT 123 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 ++LL +VGLKESP+TLITD+GVGKQQLVEIAKALSK VKLLILDEPTASLNE+DS+ALL+ Sbjct: 124 QQLLAQVGLKESPDTLITDLGVGKQQLVEIAKALSKRVKLLILDEPTASLNEADSQALLD 183 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 L+ FR QG++SI+ITHKLNEV +VAD+ITVLRDG +V +DC E + ED II++MV R Sbjct: 184 RLVAFREQGISSILITHKLNEVARVADRITVLRDGRSVDGIDCRAEPVLEDRIIKSMVNR 243 Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304 D+ R+P R IGE + V+NW+ +H QH DR+V+ +++ VR+GE+VGIAGLMGAGRT Sbjct: 244 DMAHRFPERQPKIGEPVFTVENWSVFHPQHPDRRVIKNVDFQVRRGEIVGIAGLMGAGRT 303 Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364 EFAMS+FG+S+G I+G ++GK V++++V AIDAGLAYVTEDRK LGL+L D++ N Sbjct: 304 EFAMSLFGRSWGVNISGRARLEGKDVNLTSVPAAIDAGLAYVTEDRKQLGLILADDVRKN 363 Query: 365 TTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424 TLA+L+ V+ +IDDI E+K AS +R R+RIR S ++QE LSGGNQQKVVLSKWL Sbjct: 364 ITLASLSQVAPKGVIDDIAELKAASGYRGRMRIRCSDVYQEAGQLSGGNQQKVVLSKWLM 423 Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484 ++P VLILDEPTRGIDVGAKYEIY II +LA G+GV++ISSEMPELLG CDRI VMN+G Sbjct: 424 TDPKVLILDEPTRGIDVGAKYEIYCIIQELADAGRGVVVISSEMPELLGICDRICVMNDG 483 Query: 485 RIVAELPKGEASQESIMRAIMRS 507 V E EA+QE IMRAIMR+ Sbjct: 484 AFVGEFAAQEATQEKIMRAIMRN 506 Lambda K H 0.316 0.135 0.374 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: 795 Number of extensions: 32 Number of successful extensions: 5 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: 512 Length of database: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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