Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate SM_b20972 SM_b20972 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Smeli:SM_b20972 Length = 391 Score = 210 bits (535), Expect = 4e-59 Identities = 128/363 (35%), Positives = 191/363 (52%), Gaps = 15/363 (4%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 + + N K G+ + DL + G LGP+ GK++L+R +AGL+ GGSI Sbjct: 4 IRIDNLRKSFGSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENLDGGSIRLG 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 D+T +P +R++AMV+Q + YP + V N++ + ++G IDR V AAE+L++ Sbjct: 64 DRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALNGMKRNEIDRRVNNAAEILRI 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 T LDR P LSGGQ+QR A+ RA+V+ L L+DEPL+NLD LR +R EL + + Sbjct: 124 TELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRVELAALHERL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 G +Y T + EA+ L L++GRV+QFG +E++ RP NL AG P +N L Sbjct: 184 GVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFIGSPRMNFLP 243 Query: 242 ----------VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAAR 291 VT +G +RP VT+ S ++ D PVT+ P L L + + A Sbjct: 244 AGVAEQAATRVTLAGGGLSRP--VTLDTRSSESLNRDRPVTLGIRPDKLELT--SPEEAH 299 Query: 292 LQARTLVSEITGSESFVHLEYD-GVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGR 350 L + E G+ES VH+ + G + G H + +V L H F ++G Sbjct: 300 LAGTVRLVERLGTESHVHIRVEGGGDLTAVVRGTHPVASRDQVHLRLPPEHCHLFDAEGT 359 Query: 351 AIA 353 AIA Sbjct: 360 AIA 362 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: 358 Number of extensions: 19 Number of successful extensions: 3 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: 391 Length adjustment: 30 Effective length of query: 328 Effective length of database: 361 Effective search space: 118408 Effective search space used: 118408 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: 50 (23.9 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