Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b20713 SM_b20713 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Smeli:SM_b20713 Length = 513 Score = 378 bits (970), Expect = e-109 Identities = 207/505 (40%), Positives = 317/505 (62%), Gaps = 17/505 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L + K FPGV AL++V K+K G +HAL+GENGAGKSTLMK+L+G+Y +GE+ Sbjct: 23 LLTAEGVRKEFPGVVALDDVEFKLKRGTVHALMGENGAGKSTLMKILAGIYYPD--QGEV 80 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123 GA ++ D+ + GI +IHQEL L+P +++AENI++ E + G + + Sbjct: 81 KLRGAGIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNRFGFVDHGEMRRM 140 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 T +L +++ + PE + + V +Q+VEIAKA+S +LI+DEPT++L E + L Sbjct: 141 TAKLFERLKIDLDPEIEVRHLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVAHLF 200 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCH-QEEISEDVIIRNMV 242 ++ + R+QG+ + ITHK+NE+ ++AD+ +V RDG + T H E++ D IIR MV Sbjct: 201 EIIRDLRSQGIGIVYITHKMNELFEIADEFSVFRDGKYIGT---HLSNEVTRDDIIRMMV 257 Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302 GR++ +P +VPIG+ +L VKN V D++ VR GE++G+AGL+G+G Sbjct: 258 GREITQMFPKEEVPIGDVVLSVKNLTL-------NGVFRDVSFDVRAGEILGVAGLVGSG 310 Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362 R+ A ++FG + +G + IDGK V + + KAI +A++TEDRK G +L +IL Sbjct: 311 RSNVAETLFGVTPAS--SGTIAIDGKEVVIDSANKAIRHRMAFLTEDRKDTGCLLILDIL 368 Query: 363 HNTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N +A L K + + + + +LR+++ + + NLSGGNQQKV++ + Sbjct: 369 ENMQIAVLQDKFVKRGFVSEREVTAACEEMSRKLRVKTPNLQERVENLSGGNQQKVLIGR 428 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL +NP +LILDEPTRGIDVGAK EI+ ++ +LA +G V+MISSEMPE+LG DRI VM Sbjct: 429 WLLTNPRILILDEPTRGIDVGAKAEIHRLVTELARNGVAVIMISSEMPEVLGMSDRIMVM 488 Query: 482 NEGRIVAELPKGEASQESIMRAIMR 506 +EGR+ L + EA+Q +M R Sbjct: 489 HEGRVTGILDRAEATQIKVMELAAR 513 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: 662 Number of extensions: 38 Number of successful extensions: 10 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: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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