Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_013723128.1 ALIDE2_RS21510 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000204645.1:WP_013723128.1 Length = 511 Score = 328 bits (842), Expect = 2e-94 Identities = 194/504 (38%), Positives = 296/504 (58%), Gaps = 17/504 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ++++ I K+FPGV+AL++V+L + GE+H ++GENGAGKSTLMK++ G Y A EG Sbjct: 19 LIKLCGIGKSFPGVRALQDVSLSLWPGEVHMIMGENGAGKSTLMKIMCGAYKAD--EGHF 76 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN--GVISWQQTFN 122 Y+G R D+ +G+ +I QE +LVP L++A+NIFLG E + G+I + Sbjct: 77 EYQGRQVAVRGAADARKLGVAVIFQEYSLVPYLNVAQNIFLGREPMRHIPGLIDHARMHR 136 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 LL+++G ++ ++ V + Q+VEIAKALS+ K+L+LDEPTA+L+ ++E L Sbjct: 137 EAAALLQRLGSDIDTRAMVENLSVAQHQVVEIAKALSQDAKVLVLDEPTAALSVREAEQL 196 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 L+ + R QG+ I+H+++EV + D+++V+RDG V TL +Q + D ++ MV Sbjct: 197 FKLVGDLREQGVAMAYISHRMDEVFALGDRVSVMRDGKMVATLTANQA--TPDELVSLMV 254 Query: 243 GRDLEDRYPPRDVPI-GETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301 GR + Y + P G+ +L+V+N + L ++ VR E+VGIAGL+G+ Sbjct: 255 GRKVNMSYSRGERPSPGDVVLQVENLAGTNG-------LAQASLQVRAREIVGIAGLVGS 307 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 GRTE ++FG G V I G P A GLA + EDRK GL L + Sbjct: 308 GRTELVRTIFGAD--PVAAGTVTIRGMPF-AGGPADARRRGLALIPEDRKRQGLALERTV 364 Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N +L +A + ++A +L I ++G + LSGGNQQK+V+ K Sbjct: 365 GDNLIATSLPRHFRAGWFVPSRADRLARSKIEQLSIATAGPRKPAGKLSGGNQQKIVIGK 424 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL + ++ I DEPTRGIDVGAK +I+ ++ L G+ VLMISSEM E++ CDR YVM Sbjct: 425 WLLDDAELFIFDEPTRGIDVGAKEQIFALMGGLVRQGRAVLMISSEMGEIVRVCDRAYVM 484 Query: 482 NEGRIVAELPKGEASQESIMRAIM 505 + RIV E+P + S+ S++ M Sbjct: 485 KDMRIVGEVPHEQLSESSLVSLAM 508 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: 562 Number of extensions: 23 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: 511 Length adjustment: 35 Effective length of query: 477 Effective length of database: 476 Effective search space: 227052 Effective search space used: 227052 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 24 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