Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_003463746.1 J416_RS02055 ATP-binding cassette domain-containing protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000359605.1:WP_003463746.1 Length = 510 Score = 623 bits (1607), Expect = 0.0 Identities = 314/510 (61%), Positives = 399/510 (78%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M++ ILEM +ITKTFPGVKAL++VNLKV+ GEIHALVGENGAGKSTLMKVLSGV+P G+Y Sbjct: 1 MSDYILEMESITKTFPGVKALDDVNLKVQHGEIHALVGENGAGKSTLMKVLSGVHPYGSY 60 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 EG I ++G FR I SE+ GI+IIHQELAL P LSIAENIFLGNE SN ++ WQ T Sbjct: 61 EGSIVFKGEKSQFRNIKQSENEGIVIIHQELALSPYLSIAENIFLGNERQSNKIMKWQDT 120 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 F+++++LL +VGL+ESPET + +IGVGKQQLVEIAKALSK+VKLLILDEPTA+LNE+DSE Sbjct: 121 FSQSQQLLDQVGLRESPETSVMNIGVGKQQLVEIAKALSKNVKLLILDEPTAALNETDSE 180 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 LLNLL++ + QG+TSI+I+HKLNEV +AD IT+LRDG T++TLD E+ISE+ II+ Sbjct: 181 NLLNLLLDLKEQGITSILISHKLNEVSSIADSITILRDGKTIETLDTRTEDISEERIIKG 240 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGR+L R+P R IGET+ EVKNW+ YH Q ++ D+N+ +RKGE+VG+AGLMG Sbjct: 241 MVGRELTSRFPERTPNIGETVFEVKNWHVYHPQRSHELLIKDVNMKIRKGEIVGLAGLMG 300 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGRTE MS+FGKSYG +I+G++ DGK + TV AI G+AYV+EDRK GL L D+ Sbjct: 301 AGRTELVMSMFGKSYGRKISGELYKDGKQIQAHTVSDAISHGMAYVSEDRKTYGLNLIDD 360 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 I N TLANL +++ ++D +E++ A L I++ I Q NLSGGNQQKVVLS Sbjct: 361 IKGNITLANLQRIARRKVVDANQEIRDAQHLTETLNIKTPSINQVAGNLSGGNQQKVVLS 420 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KW+F+ PD+LILDEPTRGIDVGAK+EIY++I+ LA GK + +ISSE+PE+LG DRIYV Sbjct: 421 KWIFTEPDILILDEPTRGIDVGAKFEIYSLIHDLAQQGKCIFVISSELPEVLGLSDRIYV 480 Query: 481 MNEGRIVAELPKGEASQESIMRAIMRSGEK 510 MNEG I E +GEA QE++M + +G K Sbjct: 481 MNEGEITGEFNRGEADQENMMHYMTGAGGK 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: 821 Number of extensions: 33 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: 510 Length adjustment: 35 Effective length of query: 477 Effective length of database: 475 Effective search space: 226575 Effective search space used: 226575 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