Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AO353_03380 AO353_03380 sugar ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03380 Length = 386 Score = 184 bits (466), Expect = 4e-51 Identities = 111/317 (35%), Positives = 172/317 (54%), Gaps = 10/317 (3%) Query: 2 LELRNAAKMVGADYH--IYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIH 59 LELRN K G+ + +L ++ G +L+GP+ GK++LM +AGL+ +GG+I Sbjct: 4 LELRNVNKTYGSGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLENISGGAIL 63 Query: 60 FDGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELL 119 D D++GM + R++AMV+Q + YP ++V +NIA ++I AA ID EV + A+LL Sbjct: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPAAEIDEEVARVAKLL 123 Query: 120 KLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFA 179 ++ L R P LSGGQQQR A+ RAL + + L DEPL+NLD KLR E+R E+ + Sbjct: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 Query: 180 QSGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNT 239 + VY T + EA+ LG A + G + QFG ++Y P NL A PP+N Sbjct: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKQIYNDPANLFVASFIGSPPMNF 243 Query: 240 LDV---TKSGNVF----TRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLA-PQTGDAAR 291 + + K G + + + +P+ A + D V + P + LA + Sbjct: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGMRPEQIVLANGEANGLPT 303 Query: 292 LQARTLVSEITGSESFV 308 ++A V+E TG ++ V Sbjct: 304 IRAEVQVTEPTGPDTLV 320 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: 343 Number of extensions: 23 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: 386 Length adjustment: 30 Effective length of query: 328 Effective length of database: 356 Effective search space: 116768 Effective search space used: 116768 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