Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 182 bits (463), Expect = 9e-51 Identities = 115/355 (32%), Positives = 183/355 (51%), Gaps = 12/355 (3%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 +++R K G+ I D+ + G VL+GP+ GK++L+R++AGL+ T G I Sbjct: 4 VQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEIAIG 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 V +P ++R++AMV+Q + YP +TVY+N+A ++++ D I R+V KA+ +L L Sbjct: 64 NRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAILGL 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 L+R P LSGGQ+QR A+ RA+V++ + L DEPL+NLD KLR ++R E+ ++ + Sbjct: 124 DSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELHQRL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 VY T + EA+ + + GRV Q G + +Y P NL AG P +N + Sbjct: 184 RTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMNFVP 243 Query: 242 --VTKSGN--VFTRPSGVTIPVPSHLAVV--PDGP-VTIAFHPHHLGLA-PQTGDAARLQ 293 + +SG P G +P P+ DG V P HL L P G LQ Sbjct: 244 GVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTLGMPGQG----LQ 299 Query: 294 ARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSD 348 R V E TG+ + ++ + ++ + HD + D +H F +D Sbjct: 300 TRVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAAGDILNLVPDHQHTHLFDAD 354 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: 296 Number of extensions: 9 Number of successful extensions: 2 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: 359 Length adjustment: 29 Effective length of query: 329 Effective length of database: 330 Effective search space: 108570 Effective search space used: 108570 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 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