Align aquaglyceroporin (characterized)
to candidate GFF1100 PS417_05580 glycerol uptake facilitator GlpF
Query= CharProtDB::CH_024677 (281 letters) >FitnessBrowser__WCS417:GFF1100 Length = 285 Score = 403 bits (1035), Expect = e-117 Identities = 197/279 (70%), Positives = 233/279 (83%) Query: 3 QTSTLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGV 62 Q +L QC+AEFLGT LLIFFG GCVAALKVAGASFG WEIS+IWG+GV+MAIYL+AG+ Sbjct: 6 QQPSLSSQCMAEFLGTALLIFFGTGCVAALKVAGASFGLWEISIIWGVGVSMAIYLSAGI 65 Query: 63 SGAHLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIV 122 SGAHLNPAV+IAL +FA FDKRK+ +I++Q+AGAFC+AALVY LY NLFFD+EQTHH+V Sbjct: 66 SGAHLNPAVSIALCIFADFDKRKLPFYILAQIAGAFCSAALVYTLYSNLFFDYEQTHHMV 125 Query: 123 RGSVESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLL 182 RGS S++LA FSTYP+ ++ QAF VEMVITAILMG+I+ALTDD NG+PRGPLAPLL Sbjct: 126 RGSQASLELASVFSTYPHALLSTAQAFLVEMVITAILMGVIMALTDDNNGLPRGPLAPLL 185 Query: 183 IGLLIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIV 242 IGLLIAVIG++MGPLTGFAMNPARDFGPK+ + AGWG +AFTGGRDIPYFLVP+F PIV Sbjct: 186 IGLLIAVIGSAMGPLTGFAMNPARDFGPKLMTFFAGWGEMAFTGGRDIPYFLVPIFAPIV 245 Query: 243 GAIVGAFAYRKLIGRHLPCDICVVEEKETTTPSEQKASL 281 GA +GA AYR LI RHLP ++E+ T K + Sbjct: 246 GACLGAAAYRGLIARHLPSAAPAIDEETPDTAVNGKTRI 284 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: 332 Number of extensions: 10 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: 281 Length of database: 285 Length adjustment: 26 Effective length of query: 255 Effective length of database: 259 Effective search space: 66045 Effective search space used: 66045 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