Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate HSERO_RS17020 HSERO_RS17020 sugar ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS17020 Length = 406 Score = 190 bits (482), Expect = 6e-53 Identities = 116/304 (38%), Positives = 169/304 (55%), Gaps = 17/304 (5%) Query: 17 IYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVA 76 ++P DL + G VLLGP+ GK++++R++AGL+ +GG++ GT V +P ++RNVA Sbjct: 20 LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79 Query: 77 MVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQ 136 MV+Q + YP ++VY+NIA +R + AA IDR VR+ A LL L L+R P +SGGQ Sbjct: 80 MVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQ 139 Query: 137 QQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEAL 196 QQR A+ARA++K S+ L DEPL+NLD KLR +LR ++ ++ + VY T + EA+ Sbjct: 140 QQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAM 199 Query: 197 LLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVTKSGNVFTRPSGVT 256 L + GR+ Q G E+YR P NL AG P +N L SG V R G Sbjct: 200 TLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFL----SGTV-QRQDGQL 254 Query: 257 IPVPSHLAVVPDG----------PVTIAFHPHHLGLAPQTGDAARLQARTLVS--EITGS 304 +H G V +A P H+ +A + AA L V EI G+ Sbjct: 255 FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGA 314 Query: 305 ESFV 308 ++ + Sbjct: 315 DALL 318 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: 397 Number of extensions: 17 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: 406 Length adjustment: 30 Effective length of query: 328 Effective length of database: 376 Effective search space: 123328 Effective search space used: 123328 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