Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AO353_25895 AO353_25895 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25895 Length = 367 Score = 199 bits (505), Expect = 1e-55 Identities = 126/359 (35%), Positives = 191/359 (53%), Gaps = 9/359 (2%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 L+++N K I DL + V +GP+ GK++L+RL+AGL+ T G+I D Sbjct: 4 LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 G D+T + KR++AMV+Q + YP ++V N++ + ++G + A ++++V +AA +L+L Sbjct: 64 GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARILEL 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 P L+R P LSGGQ+QR A+ RA+V+N + L DEPL+NLD LR ++R EL ++ + Sbjct: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKEL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 A +Y T + EA+ L LN GR+ Q G +E+Y +P NL AG P + L Sbjct: 184 QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLK 243 Query: 242 -----VTKSGNVFTRPSGVTIPVP-SHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQAR 295 V + +G I +P S + G VT+ P HL LA GD LQ Sbjct: 244 GKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLA-LPGDCT-LQVT 301 Query: 296 TLVSEITGSESFVH-LEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIA 353 VSE GS++F H L G M G ++ LD H F ++G A+A Sbjct: 302 ADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHLFDANGVAVA 360 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: 307 Number of extensions: 14 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: 367 Length adjustment: 29 Effective length of query: 329 Effective length of database: 338 Effective search space: 111202 Effective search space used: 111202 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