Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 194 bits (494), Expect = 2e-54 Identities = 116/353 (32%), Positives = 180/353 (50%), Gaps = 11/353 (3%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 L+LR K G I DL +++G V +GP+ GK++L+RL+AGL+ GGS+ D Sbjct: 4 LQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSLMLD 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKL 121 G D+T P KR++AMV+Q + YP ++VY N++ ++++ D ID +V+ AA +L L Sbjct: 64 GRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARILNL 123 Query: 122 TPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQS 181 T YL RTP LSGGQ+QR A+ RA+V+ + L DEPL+NLD LR + R E+ K+ Sbjct: 124 TQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHRDL 183 Query: 182 GAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLD 241 GA +Y T + EA+ L L G + Q G +E+Y +P N A P +N + Sbjct: 184 GATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMNVVP 243 Query: 242 VTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGLAPQTGDAARLQARTLVSEI 301 V K + PV P G A + +T A + + + E Sbjct: 244 VDK----------LPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEA 293 Query: 302 TGSESFVHLEY-DGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAIA 353 G+E+ +++ G ++V + D+ V +D F + GR +A Sbjct: 294 LGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGRVVA 346 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: 311 Number of extensions: 11 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: 350 Length adjustment: 29 Effective length of query: 329 Effective length of database: 321 Effective search space: 105609 Effective search space used: 105609 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