Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 342 bits (876), Expect = 2e-98 Identities = 200/516 (38%), Positives = 309/516 (59%), Gaps = 28/516 (5%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 MA + M I K+F V AL++VNL V GEIHAL+GENGAGKSTLMKVLSG++ Sbjct: 1 MATPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPT-- 58 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN----GVIS 116 +G I N + +GI II+QEL+++ L++ EN+++G + +I Sbjct: 59 KGTITINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIID 118 Query: 117 WQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNE 176 W++ R +L +VGLK + + ++ + +Q++EIAK L K++I+DEPT+SL Sbjct: 119 WREMRVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTN 178 Query: 177 SDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQ--EEISE 234 + + L ++ + R +G + I+HKL E+R++ D+ TV++DG +V C ++S Sbjct: 179 KEVDYLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSV----CSGIVSDVSN 234 Query: 235 DVIIRNMVGRDLEDRYPPRDVPIG----ETILEVKNWNAYHQQHRDRQVLHDINVTVRKG 290 D I+R MVGR+L++R+ + ET+ EV+N + RDR+ + DI+ +V +G Sbjct: 235 DDIVRLMVGRELQNRFNAMKENVSNLAHETVFEVRNVTS-----RDRKKVRDISFSVCRG 289 Query: 291 EVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDR 350 E++G AGL+G+GRTE +FG R G++ ++GK + + A+ G+AY+TE R Sbjct: 290 EILGFAGLVGSGRTELMNCLFGVD--KRAGGEIRLNGKDISPRSPLDAVKKGMAYITESR 347 Query: 351 KHLGLVLNDNILHNTTLANL---AGVSKA-SIIDDIKEMKVASDFRTRLRIRSSGIFQET 406 + G N +I N ++ G A + ++ E + A + R L ++ + Q Sbjct: 348 RDNGFFPNFSIAQNMAISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNI 407 Query: 407 VNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISS 466 LSGGNQQKV++SKWL P+V+I DEPTRGIDVGAK EIY ++ QLA DGK +LM+SS Sbjct: 408 TELSGGNQQKVLISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSS 467 Query: 467 EMPELLGNCDRIYVMNEGRIVAELP-KGEASQESIM 501 E+PE++ CDRI V EGR+ L + + S+E IM Sbjct: 468 ELPEIITVCDRIAVFCEGRLTQILTNRDDMSEEEIM 503 Score = 66.6 bits (161), Expect = 2e-15 Identities = 58/232 (25%), Positives = 110/232 (47%), Gaps = 16/232 (6%) Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRIT-GDVLIDGKPVDVSTVRKA 338 L +N+TV GE+ + G GAG++ + G H T G + I+ + + A Sbjct: 21 LKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGI---HEPTKGTITINNISYNKLDHKLA 77 Query: 339 IDAGLAYVTEDRKHLG--LVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDF---RT 393 G+ + ++ + VL + + + GV+ I D +EM+V + R Sbjct: 78 AQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVN----IIDWREMRVRAAMMLLRV 133 Query: 394 RLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQ 453 L++ + ++ NLS ++Q + ++K L + V+I+DEPT + ++ I+NQ Sbjct: 134 GLKV---DLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLFLIMNQ 190 Query: 454 LAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 L +G ++ IS ++ E+ CDR VM +G V + S + I+R ++ Sbjct: 191 LRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMV 242 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: 659 Number of extensions: 35 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