Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 188 bits (478), Expect = 2e-52 Identities = 117/349 (33%), Positives = 178/349 (51%), Gaps = 8/349 (2%) Query: 4 LRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGT 63 L + K G I+ DL ++ G V +GP+ GK++L+R++AGL+ T G+I G Sbjct: 6 LESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTIRIGGR 65 Query: 64 DVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTP 123 DVT + R V+MV+Q + YP +TV N+ ++++G A I +V +A+ +LKL Sbjct: 66 DVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRILKLDD 125 Query: 124 YLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGA 183 YL R P LSGGQ+QR A+ RA+V+ + L DEPL+NLD +LR E+R E+ ++ + GA Sbjct: 126 YLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLHKEIGA 185 Query: 184 IFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVT 243 +Y T + EA+ L L GR+ Q G +E+YR P N AG P +N + Sbjct: 186 TMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMNFIRGR 245 Query: 244 KSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEITG 303 G G+ V + V I P HL L P G + R+ ++E G Sbjct: 246 VQGGEVV-SDGLVHSVSKTASAQEGQEVLIGLRPEHLELRP--GSSHRVD----LTESLG 298 Query: 304 SESFVHL-EYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRA 351 S+ HL DG + ++ G H V+ +D H+ F + A Sbjct: 299 GVSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDAKTEA 347 Lambda K H 0.319 0.136 0.392 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: 306 Number of extensions: 8 Number of successful extensions: 1 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: 358 Length of database: 350 Length adjustment: 29 Effective length of query: 329 Effective length of database: 321 Effective search space: 105609 Effective search space used: 105609 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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