Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_02712 Length = 505 Score = 388 bits (996), Expect = e-112 Identities = 214/498 (42%), Positives = 323/498 (64%), Gaps = 9/498 (1%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 LEMRNI++TFPGVKAL+ VNL+++ GE+ AL GENGAGKSTLMK+L+G+Y A G I Sbjct: 10 LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIY-APDPGGTIL 68 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNRT 124 EG + + +G+ II+QELA+V L++ ENIFL E + G+I + + Sbjct: 69 VEGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREA 128 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 RE+L + + P T ++++ VG+QQ++EIAKAL K +I+DEPTASL+ ++ LL Sbjct: 129 REVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLG 188 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 ++ R + + + I+H+L E+ ++AD++TVLRDG TV T +++ + ++R MV R Sbjct: 189 IVKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPI--ADMTRETLVRLMVAR 246 Query: 245 DLEDRY-PPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 +L + Y P+ + +LEV+ + + + ++ DI+ T+ +GEV+GIAGL+G+GR Sbjct: 247 ELSELYGEPQSHASRDPVLEVRALSLKPVRKAEPRI-RDISFTLHRGEVLGIAGLVGSGR 305 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TE +FG TG V I+GKPV + AI +G+ +VTEDRK GL+L + Sbjct: 306 TEIMEMIFGM---RACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRE 362 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 N +L +L S + +E + F L I++ G+ Q+ VNLSGGNQQK+V++KW+ Sbjct: 363 NFSLTHLERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWV 422 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 +P VLI+DEPTRGIDVGAK E++ +I +LAA+G GV++ISS++ E+L DRI + E Sbjct: 423 ARSPKVLIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVRE 482 Query: 484 GRIVAELPKGEASQESIM 501 GRI EL + +ASQE +M Sbjct: 483 GRISGELSRAQASQEKVM 500 Score = 74.3 bits (181), Expect = 9e-18 Identities = 56/230 (24%), Positives = 108/230 (46%), Gaps = 10/230 (4%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L +N+ +R GEV+ +AG GAG++ M + Y G +L++G+ V ++ Sbjct: 23 KALDRVNLEIRAGEVLALAGENGAGKSTL-MKILTGIYAPDPGGTILVEGQEVALADSHH 81 Query: 338 AIDAGLAYVTEDRKHLG-LVLNDNI-LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRL 395 A G+ + ++ +G L + +NI L L + + + + +E+ D Sbjct: 82 ARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAREVLATIDMDIDP 141 Query: 396 RIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLA 455 R S LS G QQ + ++K L + +I+DEPT + + I+ +L Sbjct: 142 ATRVS-------ELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGIVKRLR 194 Query: 456 ADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 V+ IS + E+ DR+ V+ +GR V P + ++E+++R ++ Sbjct: 195 ERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMV 244 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: 624 Number of extensions: 34 Number of successful extensions: 9 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: 505 Length adjustment: 34 Effective length of query: 478 Effective length of database: 471 Effective search space: 225138 Effective search space used: 225138 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