Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 189 bits (479), Expect = 1e-52 Identities = 120/363 (33%), Positives = 189/363 (52%), Gaps = 19/363 (5%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 + +RN AK + + +L +E G V +GP+ GK++L+R++AGL+ + G + Sbjct: 4 VSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDLDIG 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 + +P KR VAMV+Q + YP +++Y+N+A ++I+GK A ID V+ AA++L + Sbjct: 64 ARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKILHI 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 LDR P LSGGQ+QR A+ RA+ + S+ L DEPL+NLD LR ++R E K+ Sbjct: 124 DHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLHDDL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 +Y T + EA+ L L++GR+ Q G ++Y P N AG P +N +D Sbjct: 184 KTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKMNFID 243 Query: 242 VTKSGNVFTRPSGVTIPVPS---HLAVVPDG-------PVTIAFHPHHLGLAPQTGDAAR 291 T + + GV + +P A V DG VT+ P HL +A G AA Sbjct: 244 GTVAA---IQADGVQVQLPGGGLQWAAV-DGSTLQVGQKVTLGVRPEHLNIA--QGQAA- 296 Query: 292 LQARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDP--DMEVEAFLDTRHLMAFGSDG 349 LQAR E+ G S+++ Y+G ++ +D + D FG+DG Sbjct: 297 LQARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHLFGADG 356 Query: 350 RAI 352 +A+ Sbjct: 357 QAL 359 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: 339 Number of extensions: 15 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: 372 Length adjustment: 30 Effective length of query: 328 Effective length of database: 342 Effective search space: 112176 Effective search space used: 112176 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