Align Glycerol uptake facilitator protein 2 (characterized)
to candidate WP_089136227.1 CES79_RS02655 aquaporin family protein
Query= SwissProt::F9USY3 (235 letters) >NCBI__GCF_002217945.1:WP_089136227.1 Length = 236 Score = 342 bits (876), Expect = 5e-99 Identities = 159/235 (67%), Positives = 190/235 (80%) Query: 1 MHGFLGEFLGTMVLIVFGVGSGAAMNLKGNYARHQNWTFICLAWGLAVTFGVYVAGQFGS 60 M+GF+GEF GTMVLI G G+GA+ NL YA+ NW ++ L+WGLAVT GVY AG GS Sbjct: 1 MNGFIGEFFGTMVLITLGAGTGASFNLNKAYAQGANWLYVSLSWGLAVTMGVYTAGVLGS 60 Query: 61 DGHLNPAVTVGFALFGYLPMANVWPYLLGQFLGAFIGAVIVIIQYYPHFQAAKTAADGNQ 120 DGHLNPAVT+GFA G + V PYLLGQFLGAF+GA IVI+ +YPHF+A KT +GNQ Sbjct: 61 DGHLNPAVTIGFACAGLFKWSLVIPYLLGQFLGAFVGAAIVIVHFYPHFKATKTEEEGNQ 120 Query: 121 VGIFATGPAISNPVFNFLSETIATFFFIFVLLNLGNFTQGLKPLMVGLLIVVVGQTLGGT 180 VGIFAT PAI+ P++NFLSE IATFFF+F+LLNLGNFTQGLKPL+VGL+I VVG LG T Sbjct: 121 VGIFATVPAINAPIWNFLSEVIATFFFVFILLNLGNFTQGLKPLIVGLVITVVGTALGST 180 Query: 181 TGFAINPARDWAPRLAYTILPVPNKGLANWGYAWVPMFGPLLGGILAAGLETIIS 235 TGFA+NPARDW PR AYT+LPVPN+G +W YAWVPM GPL+GGI+A+ LE ++ Sbjct: 181 TGFALNPARDWGPRFAYTVLPVPNRGRTHWEYAWVPMCGPLVGGIIASLLEVSLT 235 Lambda K H 0.328 0.145 0.471 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: 318 Number of extensions: 13 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: 235 Length of database: 236 Length adjustment: 23 Effective length of query: 212 Effective length of database: 213 Effective search space: 45156 Effective search space used: 45156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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