Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_011653086.1 RL_RS18630 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000009265.1:WP_011653086.1 Length = 512 Score = 887 bits (2293), Expect = 0.0 Identities = 443/510 (86%), Positives = 484/510 (94%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M NTILEMR+ITKTFPGVKALENVNLKV++GEIHALVGENGAGKSTLMKVLSGVYP G+Y Sbjct: 1 MDNTILEMRSITKTFPGVKALENVNLKVRQGEIHALVGENGAGKSTLMKVLSGVYPTGSY 60 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 EG+I YEG RNF+ + DSE+IGI+IIHQELALVPLLSI ENIFLGNE A NGVISW++T Sbjct: 61 EGDIVYEGETRNFKVLKDSEEIGIVIIHQELALVPLLSIGENIFLGNENAKNGVISWEET 120 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 FNRT++LL KVGL+ESP TL+TDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNE DS+ Sbjct: 121 FNRTKKLLTKVGLRESPNTLVTDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNEKDSD 180 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 ALLNLL+EFRNQG+TSIII+HKLNE+RKVADQITVLRDGMTVKTLDCH +EISED+II+N Sbjct: 181 ALLNLLIEFRNQGITSIIISHKLNEIRKVADQITVLRDGMTVKTLDCHTDEISEDIIIKN 240 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGRDL DRYPPR VPIGETI VKNWNAYHQQHRDRQVLHDINV VRKGEVVGIAGLMG Sbjct: 241 MVGRDLADRYPPRSVPIGETIFAVKNWNAYHQQHRDRQVLHDINVNVRKGEVVGIAGLMG 300 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGRTEFAMSVFGKSYGH+++G+V ++GK VDVSTVRKAIDAGLAYVTEDRK LGLVL+D+ Sbjct: 301 AGRTEFAMSVFGKSYGHKVSGEVFVNGKAVDVSTVRKAIDAGLAYVTEDRKQLGLVLSDS 360 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 ILHNTTLANL G+S S+IDDIKEMKVA+D+R++LRIRSSG+FQETVNLSGGNQQKVVLS Sbjct: 361 ILHNTTLANLNGISSNSVIDDIKEMKVATDYRSKLRIRSSGVFQETVNLSGGNQQKVVLS 420 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KWLFS+PD+LILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLG CDRIYV Sbjct: 421 KWLFSDPDILILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGTCDRIYV 480 Query: 481 MNEGRIVAELPKGEASQESIMRAIMRSGEK 510 MNEGRIVAELPKGEASQE+IMRAIMRSGEK Sbjct: 481 MNEGRIVAELPKGEASQETIMRAIMRSGEK 510 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: 940 Number of extensions: 30 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: 512 Length adjustment: 35 Effective length of query: 477 Effective length of database: 477 Effective search space: 227529 Effective search space used: 227529 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