Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_058932692.1 AU252_RS01705 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_001484605.1:WP_058932692.1 Length = 510 Score = 344 bits (882), Expect = 5e-99 Identities = 204/505 (40%), Positives = 296/505 (58%), Gaps = 13/505 (2%) Query: 2 ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61 A + LE R I K F GV L+ V+L ++ G I AL GENGAGKSTLMK+ SG Y + Sbjct: 13 APSTLECRGIEKAFGGVPVLKGVSLTLEAGTITALAGENGAGKSTLMKIASGQYRPDS-- 70 Query: 62 GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTF 121 GE+ G + + +G+ I+ QELA VP LS+ ENIF+G E+ + + Sbjct: 71 GEVFVRGEDLHAGNTQMAHRLGVSIVPQELASVPDLSVYENIFIGREIRGVFGLQRKAMI 130 Query: 122 NRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181 R+ L+ G+ P + + VG +Q+VEI KA + K ++LDEP++++ E + E Sbjct: 131 EEARKNLEVFGVNVDPTARMGSLPVGIRQIVEIIKATNTGAKAILLDEPSSAIAEREVER 190 Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNM 241 L++++ R++G+ + THK+ E+R VAD++ VLRDG V LD +++D I+ M Sbjct: 191 LISVMRHLRDRGVALLFTTHKMEEIRAVADRVVVLRDGNLV--LDQPLALLTDDDIVTAM 248 Query: 242 VGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301 +GR+LED +P R+ P ETILE+ N ++++VR+GE+VG+AGL+GA Sbjct: 249 IGRELEDLFPDRNTPGEETILEIDNLEVDGAGG-------PVSLSVRRGEIVGLAGLVGA 301 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 GRTE +VFG + G+V + G+ V + AI A +A V EDRK G +L+ ++ Sbjct: 302 GRTELLETVFG--IRRPLGGEVRVSGRVVKKHSPSAAIAAKIAIVPEDRKGAGAILSMDV 359 Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 L N +L LA S AS++ +R++S G+ Q LSGGNQQKVVL++ Sbjct: 360 LDNASLPRLASFSTASLLKQGARRAAVRKATESVRLKSRGLNQSMETLSGGNQQKVVLAR 419 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL DVLILDEPTRG+DVGA+ EIY II LA+ G VLM SS+MPE+L R VM Sbjct: 420 WLTGPVDVLILDEPTRGVDVGARSEIYRIIVALASQGMAVLMASSDMPEVLSLSHRALVM 479 Query: 482 NEGRIVAELPKGEASQESIMRAIMR 506 G + AEL + + + + I R Sbjct: 480 RGGEVAAELSRDDLDRTDVQDKIFR 504 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: 631 Number of extensions: 33 Number of successful extensions: 9 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