Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 313 bits (802), Expect = 9e-90 Identities = 192/512 (37%), Positives = 292/512 (57%), Gaps = 19/512 (3%) Query: 3 NTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEG 62 N +L + I KT+ L ++L + GE+ AL GENGAGKSTL K++ G+ T G Sbjct: 7 NAVLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTT--G 63 Query: 63 EIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122 ++ ++G + +E++GI ++ QEL L+P LS+AEN+FL N ++ G IS +Q Sbjct: 64 QMQFQGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRK 123 Query: 123 RTRELLKKVGLKE-SPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181 + +VGL P+TL+ ++G+G QQ+VEIA+ L +LILDEPTA L + E Sbjct: 124 AAIAAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEM 183 Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNM 241 L + + +G+ I I+H+L E+ +VA +I VLRDG V + + ++ M Sbjct: 184 LFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEP--MANYNSEQLVNLM 241 Query: 242 VGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301 VGR+L + IG L VK + + + D++ VR GE+ GI+GL+GA Sbjct: 242 VGRELGEHIDLGPRHIGAPALTVKGLSRSDK-------VRDVSFEVRSGEIFGISGLIGA 294 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDA---GLAYVTEDRKHLGLVLN 358 GRTE +FG +G V + G P V ++R DA G+A +TEDRK GL+L Sbjct: 295 GRTELLRLIFGADAAD--SGTVAL-GSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLT 351 Query: 359 DNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418 +I N L N+ +S I++ EM +A +RIRSS Q LSGGNQQKVV Sbjct: 352 QSISANIALGNMPVISSGGIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVV 411 Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478 + +WL VL+ DEPTRGIDVGAK++IY ++ +L GK ++++SS++ EL+ CDRI Sbjct: 412 IGRWLERECSVLLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRI 471 Query: 479 YVMNEGRIVAELPKGEASQESIMRAIMRSGEK 510 V++ GR++ + +Q+ ++ A +K Sbjct: 472 GVLSAGRLIDTFERDSWTQDDLLAAAFAGYQK 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: 599 Number of extensions: 30 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: 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 Apr 09 2024. 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