Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS05195 HSERO_RS05195 xylose ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS05195 Length = 518 Score = 696 bits (1795), Expect = 0.0 Identities = 347/505 (68%), Positives = 418/505 (82%) Query: 3 NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62 + ILEMR I K+FPGVKAL NVNL V+EGEIHA+VGENGAGKSTLMKVLSGVYP G+Y G Sbjct: 2 SNILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSG 61 Query: 63 EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122 +I Y+G VR F+ I DSE +GIIIIHQELALVPLLS+ EN+FLGNE A GVI W+Q++ Sbjct: 62 DIVYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNEQARGGVIDWEQSYV 121 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 R +ELL KVGLKESP T + D+GVGKQQL+EIAKALSK VKLLILDEPTASLNESDS+AL Sbjct: 122 RAKELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDAL 181 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 L LL+E + QG+ SI+I+HKLNE+ KVAD ITVLRDG TV T DC E ISED II++MV Sbjct: 182 LELLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHMV 241 Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 GR++ DRYP RD IGE I EV++W +H H DR + D+N++VR GE+VGIAGLMGAG Sbjct: 242 GREMADRYPQRDPQIGEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGAG 301 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362 RTE A S+FG++YG +ITG + GK VD+ST+ KAI G+AYVTEDRK GLVL ++I Sbjct: 302 RTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKAIAKGIAYVTEDRKGDGLVLEEDIK 361 Query: 363 HNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422 N +LANL GVS+ ++ID+ +E K+A+DF+ ++RIR S + Q+ VNLSGGNQQKVVLSKW Sbjct: 362 KNISLANLGGVSERTVIDEAREYKIAADFKQQMRIRCSSVLQKVVNLSGGNQQKVVLSKW 421 Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482 LFS P+VLILDEPTRGIDVGAK+EIY II++LAA+GK ++MISSEMPELLG CDRIYVMN Sbjct: 422 LFSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELLGMCDRIYVMN 481 Query: 483 EGRIVAELPKGEASQESIMRAIMRS 507 EG+ V LPK EA+QE+IMRAIMR+ Sbjct: 482 EGQFVGHLPKAEATQENIMRAIMRN 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: 787 Number of extensions: 23 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: 518 Length adjustment: 35 Effective length of query: 477 Effective length of database: 483 Effective search space: 230391 Effective search space used: 230391 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 17 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