Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b20855 SM_b20855 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Smeli:SM_b20855 Length = 504 Score = 375 bits (963), Expect = e-108 Identities = 217/515 (42%), Positives = 320/515 (62%), Gaps = 20/515 (3%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSG-VYPAGT 59 M + +++I+K+F G+ AL +VN V+ GE+HAL+GENGAGKSTLM+VL G + P+ Sbjct: 1 MVTELANLKSISKSFGGIHALRSVNFDVRPGEVHALLGENGAGKSTLMRVLGGEIIPS-- 58 Query: 60 YEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQ 119 +GE+ G R D+ +GI++IHQELAL P LS+AENIFLG +IS Sbjct: 59 -QGEVVINGKRTELRDPRDARALGIVVIHQELALAPDLSVAENIFLGELPT---LISRFS 114 Query: 120 TFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDS 179 R ++L+ ++G P L+ + V QQ+VEIAKALS+ +K+++ DEPTA L D+ Sbjct: 115 LRRRAKQLIDRLGFDIDPGRLVGTLSVAHQQVVEIAKALSQDIKIIVFDEPTAVLGAQDA 174 Query: 180 EALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIR 239 L ++ R++G+ + I+H+L+EV +AD++TV++DG TV T+ +I D IIR Sbjct: 175 MKLHQIIRGLRDRGVGIVYISHRLDEVFDIADRMTVMKDGETVGTVATTDVKI--DDIIR 232 Query: 240 NMVGRDLEDRYPPRDV-PIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298 MVGR + + +P R IG +L VK NA +++ D++ +VR GE+VG+ GL Sbjct: 233 MMVGRPIANMFPERSQRTIGAELLNVKKLNA-------GRMVRDVSFSVRAGEIVGLGGL 285 Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358 +G+GRTE A ++FG +G + + GK + + + R A+ AG+ V EDRK G+V++ Sbjct: 286 IGSGRTEVARAIFGAD--PLDSGTISLKGKALKLKSPRDAVKAGIGLVPEDRKEHGVVID 343 Query: 359 DNILHNTTLANLAGVSKA-SIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKV 417 I N T+A ++ V A + E + LR+++S I +LSGGNQQKV Sbjct: 344 KPIRVNATMARMSSVVNALGFLKPALERTDVTALGKSLRLKASSIDAPVSSLSGGNQQKV 403 Query: 418 VLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDR 477 VL+KW + DV+ILDEPTRG+DVGAK EIY +IN+LA DGK VL+ISSE EL G CDR Sbjct: 404 VLAKWFHAGGDVIILDEPTRGVDVGAKAEIYALINKLAEDGKAVLVISSEHQELFGLCDR 463 Query: 478 IYVMNEGRIVAELPKGEASQESIMRAIMRSGEKNS 512 + M +G+I EL S+E+++ M G + S Sbjct: 464 VLAMGQGQIRGELTPSNYSEENLLGLSMMGGARAS 498 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: 637 Number of extensions: 31 Number of successful extensions: 11 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: 504 Length adjustment: 34 Effective length of query: 478 Effective length of database: 470 Effective search space: 224660 Effective search space used: 224660 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