Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 341 bits (875), Expect = 3e-98 Identities = 203/500 (40%), Positives = 311/500 (62%), Gaps = 18/500 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +LEM+ I+KTF G++ L+ V LKV GEIHAL+GENGAGKSTLMK+LSG Y A GEI Sbjct: 6 LLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADP-GGEI 64 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 G + ++ +GI +I+QEL+L P LS+AENI+LG E+ I + Sbjct: 65 RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 E+L+++G + +P T ++ + + ++QLVEIA+AL K+L++DEPT L+ +++ L Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 L+ + R+QG+ I I+H++ E+ ++D+++VLRDG + L ++ +S + +++ MVGR Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELT--RDALSAEALVKMMVGR 242 Query: 245 DLEDRYPPRDVPI--GETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 DL Y G ++ V++ D + + + + GEV+GIAGL+GAG Sbjct: 243 DLSGFYKKEHAAYNPGNVVMRVRDM-------ADGKRVRHCSFDLHAGEVLGIAGLVGAG 295 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVD-VSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 RTE A +F R +G + + GK V + T AI AG+ Y+TEDRK GL L+ ++ Sbjct: 296 RTELARLIFAAD--PRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSV 353 Query: 362 LHNTTL-ANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 N + A + ++D ++ ++D L IR + LSGGNQQKV+L+ Sbjct: 354 ADNINVCACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLA 413 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 + L P VLILDEPTRG+D+G+K EIY IINQLA G G+++ISSE+PE++G CDR+ + Sbjct: 414 RLLEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLI 473 Query: 481 MNEGRIVAELPKGEASQESI 500 M EG++VAE+ G AS ++I Sbjct: 474 MREGQLVAEV--GGASGQAI 491 Score = 65.9 bits (159), Expect = 3e-15 Identities = 54/237 (22%), Positives = 112/237 (47%), Gaps = 25/237 (10%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 +VL + + V GE+ + G GAG++ M + +Y G++ I G+ + Sbjct: 20 RVLKTVGLKVYPGEIHALMGENGAGKSTL-MKILSGAYQADPGGEIRIAGQLIPTFDPAT 78 Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLA---------NLAGVSKASIIDDIKEMKVA 388 A G+A + ++ L L N ++ N L + G+ +A I+ ++ ++ Sbjct: 79 AKALGIAVIYQE---LSLCPNLSVAENIYLGRELRRGWTIDRKGM-EAGCIEVLQ--RLG 132 Query: 389 SDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIY 448 ++F R+ S LS +Q V +++ L ++ +L++DEPT + ++ Sbjct: 133 AEFTPATRVSS---------LSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLF 183 Query: 449 TIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 +I QL + G ++ IS M E+ DR+ V+ +G + EL + S E++++ ++ Sbjct: 184 ALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMV 240 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: 611 Number of extensions: 42 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 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