Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Length = 517 Score = 311 bits (797), Expect = 4e-89 Identities = 186/509 (36%), Positives = 290/509 (56%), Gaps = 13/509 (2%) Query: 3 NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62 N +L + I KT+ L ++L + GE+ AL GENGAGKSTL K++ G+ T G Sbjct: 7 NAVLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTT--G 63 Query: 63 EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122 ++ ++G + + +E++GI ++ QEL L+P LS+AEN+FL N + G IS +Q Sbjct: 64 QMRFQGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRK 123 Query: 123 RTRELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181 E + +VGL P+TL+ ++G+G QQ+VEIA+ L +LILDEPTA L + E Sbjct: 124 AAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEM 183 Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNM 241 L + + +G++ I I+H+L E+ +VA +I VLRDG V + + ++ M Sbjct: 184 LFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEP--MANYNSEQLVTLM 241 Query: 242 VGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301 VGR+L + IG L VK + + D++ VR GE+ GI+GL+GA Sbjct: 242 VGRELGEHIDMGPRKIGAPALTVKGLTRSDK-------VRDVSFEVRAGEIFGISGLIGA 294 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 GRTE +FG T + + V + + A+ G+A +TEDRK GL+L +I Sbjct: 295 GRTELLRLIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSI 354 Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N L N+ +S +++ EM +A +RIRSS Q LSGGNQQKVV+ + Sbjct: 355 SANIALGNMPVISSGGFVNNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGR 414 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL + V++ DEPTRGIDVGAK++IY ++ +L GK ++++SS++ EL+ CDRI V+ Sbjct: 415 WLERDCTVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVL 474 Query: 482 NEGRIVAELPKGEASQESIMRAIMRSGEK 510 + GR++ + +Q+ ++ A +K Sbjct: 475 SAGRLIDTFERDSWTQDDLLAAAFAGYQK 503 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: 594 Number of extensions: 29 Number of successful extensions: 8 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: 517 Length adjustment: 35 Effective length of query: 477 Effective length of database: 482 Effective search space: 229914 Effective search space used: 229914 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