Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS32815 BPHYT_RS32815 sugar ABC transporter
Query= TCDB::O05176 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS32815 Length = 519 Score = 412 bits (1060), Expect = e-119 Identities = 228/513 (44%), Positives = 329/513 (64%), Gaps = 5/513 (0%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M ++ MR I K F GVKAL+ ++L V GE L GENGAGKSTLMKVLSGVYP GT+ Sbjct: 1 MTQALMTMRGIVKAFSGVKALDGIDLTVAPGECVGLCGENGAGKSTLMKVLSGVYPWGTW 60 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVA-SNGVISWQQ 119 +GEI +EG ++ D+E GIIIIHQEL LVP LS+AENIFLGNE+ G +++ Sbjct: 61 DGEIIWEGEPLKAASVRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAA 120 Query: 120 TFNRTRELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESD 178 + R ELL+++G+ + + + G G QQL+EIAKAL+K KLLILDEP++SL S+ Sbjct: 121 MYQRADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKRAKLLILDEPSSSLTSSE 180 Query: 179 SEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVII 238 LL+++ + + +G+ + I+HKL+EV V D I+V+RDG V T ++ D II Sbjct: 181 IRILLDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEP--MRALTTDRII 238 Query: 239 RNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGL 298 MVGR++++ +P PIG+ I E ++ + + R+ ++D++ +R GE++G+AGL Sbjct: 239 SLMVGREIKNLFPREPHPIGDVIFEARHVTCFDVTNPRRKRVNDVSFGLRHGEILGVAGL 298 Query: 299 MGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLN 358 +GAGRTE ++FG +Y V++DGKP+ + AI AG+ V EDRK G+V Sbjct: 299 VGAGRTELMQAIFG-AYPGVSEATVVMDGKPLKIRAPVDAIRAGIGMVPEDRKRHGIVPG 357 Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418 ++ HN TLA L + ID E+ + RL +R++ +LSGGNQQK V Sbjct: 358 LSVGHNITLAVLQRFASGGRIDSAAELDTINTEMKRLSVRAAHPMLSIASLSGGNQQKAV 417 Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478 L++ L +NP VLILDEPTRG+DVGAKYEIY +I QLA G ++M+SSE+PE+LG DR+ Sbjct: 418 LTRMLLTNPKVLILDEPTRGVDVGAKYEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRV 477 Query: 479 YVMNEGRIVAELPKGEASQESIMRAIMRSGEKN 511 V+ EG + + +QE I+ A +R +++ Sbjct: 478 LVIGEGELRGDFVNDGLTQEDILSAAIRPVQRS 510 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: 658 Number of extensions: 28 Number of successful extensions: 9 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: 519 Length adjustment: 35 Effective length of query: 477 Effective length of database: 484 Effective search space: 230868 Effective search space used: 230868 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