Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 394 bits (1012), Expect = e-114 Identities = 220/501 (43%), Positives = 330/501 (65%), Gaps = 8/501 (1%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L ++NITK F GVKAL++V+L+++ G + A++GENGAGKSTLMK+LSGVYP Y+G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYP--DYKGTI 58 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123 +Y G F+ D+++ GI IIHQEL L+P LSI ENIFLG E + G++ + Sbjct: 59 YYNGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKE 118 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 +LL ++ L PET ++ + VG+QQLVEIAKALS +++I+DEPT+++++ + E L Sbjct: 119 AAQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILF 178 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 ++ R +G I+HKL+E+ +AD+ VLRDG +++ + E ++E+ +I+ MVG Sbjct: 179 GIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGE--MEGMTEEALIQKMVG 236 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R++ ET+L VK+ H + D+ +L DIN + KGEV+GI GLMGAGR Sbjct: 237 REIVIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGR 296 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TE ++FG H+ ++ + GK + ++A+DAGLA V EDRK GLVL ++ Sbjct: 297 TELMEALFGV-LPHQ-GAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCT 354 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 N++L + + ++DD KE +A + L+I++S Q LSGGNQQKVVL+KWL Sbjct: 355 NSSLTVVDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWL 414 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 + P VL+LDEPTRGID+ AK EIY +I QLA +G G++++SSE+PE+L DR+ VM E Sbjct: 415 ATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAE 474 Query: 484 GRIVAELP-KGEASQESIMRA 503 GR+ A +P + S++ I++A Sbjct: 475 GRLTANIPIDAQTSEDEILQA 495 Score = 72.0 bits (175), Expect = 5e-17 Identities = 59/230 (25%), Positives = 109/230 (47%), Gaps = 11/230 (4%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L D+++ ++ G V I G GAG++ + G ++ G + +G PV R Sbjct: 15 KALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYK--GTIYYNGDPVKFQNTRD 72 Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRI 397 A + G+ + ++ L L+ +I N L + ++D K K A+ RL++ Sbjct: 73 AQEKGINIIHQE---LNLIPYLSIRENIFLGR-EPETPMGLLDVAKMHKEAAQLLHRLKL 128 Query: 398 RSSGIFQETV--NLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLA 455 + ET L G QQ V ++K L V+I+DEPT I ++ II L Sbjct: 129 N---VDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALR 185 Query: 456 ADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 A+GK + IS ++ EL DR V+ +G+++ ++E++++ ++ Sbjct: 186 AEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235 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: 645 Number of extensions: 38 Number of successful extensions: 8 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: 502 Length adjustment: 34 Effective length of query: 478 Effective length of database: 468 Effective search space: 223704 Effective search space used: 223704 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