Align aquaglyceroporin (characterized)
to candidate N515DRAFT_3908 N515DRAFT_3908 glycerol uptake facilitator protein
Query= CharProtDB::CH_024677 (281 letters) >FitnessBrowser__Dyella79:N515DRAFT_3908 Length = 282 Score = 181 bits (460), Expect = 1e-50 Identities = 105/263 (39%), Positives = 156/263 (59%), Gaps = 9/263 (3%) Query: 9 GQCIAEFLGTGLLIFFG--VGCVAAL-KVAGASFGQWEISVIWGLGVAMAIYLTAGVSGA 65 G+ I+E L ++I G V C+ L + W + + WGL V +AIY TA +SG Sbjct: 6 GELISEALAMFIIIGLGDSVACMYVLYDPSPYQNAYWGVCIAWGLAVTIAIYATASISGT 65 Query: 66 HLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGS 125 H NPAVT+AL +F F +KV+P+ V+QV GAF AA+VY L+ + + Q H + R Sbjct: 66 HANPAVTLALAIFRGFPWKKVLPYTVAQVIGAFLGAAIVYVLFGPVIDHYNQAHGLTR-- 123 Query: 126 VESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGV-PRGPLAPLLIG 184 E+ AG F T+P + + A ++++TA L+ I A+T+ N + P L+IG Sbjct: 124 -EAGGAAGVFFTHPGLAVTPMHALLDQVILTAFLLFGIFAITERFNEMAPGANSGALMIG 182 Query: 185 LLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGA 244 LL+A IGA MG L +A+NPARDFGP++FA+ AGWG A + Y+ +P+ GP++G Sbjct: 183 LLVATIGACMGYLEAWAINPARDFGPRLFAFFAGWGQSALPSPDN--YWWIPIVGPLIGG 240 Query: 245 IVGAFAYRKLIGRHLPCDICVVE 267 +VGA AY+ L+ LP + +E Sbjct: 241 VVGAGAYQLLVHPFLPARLRELE 263 Lambda K H 0.327 0.143 0.451 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: 265 Number of extensions: 20 Number of successful extensions: 4 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: 281 Length of database: 282 Length adjustment: 26 Effective length of query: 255 Effective length of database: 256 Effective search space: 65280 Effective search space used: 65280 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: 47 (22.7 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