Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Cup4G11:RR42_RS30800 Length = 530 Score = 229 bits (583), Expect = 2e-64 Identities = 165/523 (31%), Positives = 266/523 (50%), Gaps = 24/523 (4%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M IL + ITK F + A ++++L+++ GE+ AL+GENGAGKSTL+ +L G Y A Sbjct: 1 MPTPILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADA- 59 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 G + +G + GI ++HQ L LS+ +NI LG + + Sbjct: 60 -GTVEVDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAA 118 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 + L ++ GL P+ + ++ VG++Q VEI KAL + ++LILDEPTA L ++E Sbjct: 119 RGKVLALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAE 178 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L + L + +G++ I I+HKL+EV +V+D+I VLR G V C + ++ + Sbjct: 179 TLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVAL--CAAAQTTKAELAEL 236 Query: 241 MVGR--DLEDRYPPRDVPIGET------ILEVKNWNAYHQQHRDRQVLHDINVTVRKGEV 292 MVGR + +R R G +L +++ A + R +L ++++ VR GE+ Sbjct: 237 MVGRVVAMPERVARRSAEDGANGNAAPPVLALEHVGA--RAANGRALLREVSLQVRAGEI 294 Query: 293 VGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKH 352 VGIAG+ G G+ A G G + + GKP+ R I AG+A V EDR Sbjct: 295 VGIAGVSGNGQAALAELASGMLEASE--GRITLAGKPMSAKP-RAWIGAGVARVPEDRHA 351 Query: 353 LGLVLNDNILHNTTLANLA--GVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLS 410 +G+V + + N L+ S+ +I + A D R +R++GI +S Sbjct: 352 IGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMS 411 Query: 411 GGNQQKVVLSKWLF-----SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMIS 465 GGN QK++L + L S P +++ +PT G+D+GA + + A +G VL+IS Sbjct: 412 GGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLIS 471 Query: 466 SEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSG 508 ++ EL DRI VM+ G + P + + A+ SG Sbjct: 472 EDLDELHALADRIAVMHAGHLTEARPTAAWTLGELGLAMAGSG 514 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: 603 Number of extensions: 33 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: 530 Length adjustment: 35 Effective length of query: 477 Effective length of database: 495 Effective search space: 236115 Effective search space used: 236115 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