Align Glycerol uptake facilitator protein 3 (characterized)
to candidate WP_028311916.1 H566_RS0113940 aquaporin family protein
Query= SwissProt::F9UTW9 (240 letters) >NCBI__GCF_000482785.1:WP_028311916.1 Length = 238 Score = 230 bits (587), Expect = 2e-65 Identities = 111/230 (48%), Positives = 151/230 (65%), Gaps = 1/230 (0%) Query: 10 LLGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGVYASSFMSPAHL 69 LL EF+GT L+LLGDG VA V L ++K + + + I GW AV +GV+ ++ S AHL Sbjct: 4 LLAEFIGTAALVLLGDGAVANVLLARTKGRGSDLIVIVFGWAVAVFVGVFIAASYSGAHL 63 Query: 70 NPAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATKDAGAILGIFAT 129 NP VS+ +A+ GKF WA V Y AAQ+AGG G +VWL Y H+ A ++A L +F T Sbjct: 64 NPVVSVALALTGKFDWARVPGYVAAQMAGGAFGAFIVWLAYRQHFAAEENADLKLAVFCT 123 Query: 130 GPGIRRYFWNFISEVIGTFVLVFGLLAFTKGQFTAG-LNPIVVGILIIAIGLSLGGTTGY 188 GP IR N ++E I TF LVF +L Q G + + V +L++ +G+SLGG TGY Sbjct: 124 GPAIRSVPHNLLTEAIATFALVFAVLCMASPQVGLGAMGALPVALLVLGLGISLGGPTGY 183 Query: 189 AINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALLFNV 238 A++PARDLGPR+ HA+LPI K SDW YSW+P+ GPL+GG AL++ + Sbjct: 184 AMSPARDLGPRLVHALLPIPGKRDSDWGYSWIPVVGPLLGGGGAALVYQM 233 Lambda K H 0.325 0.143 0.459 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: 238 Number of extensions: 16 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: 240 Length of database: 238 Length adjustment: 23 Effective length of query: 217 Effective length of database: 215 Effective search space: 46655 Effective search space used: 46655 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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