Align aquaglyceroporin (characterized)
to candidate PP_1076 PP_1076 aquaglyceroporin
Query= CharProtDB::CH_024677 (281 letters) >FitnessBrowser__Putida:PP_1076 Length = 283 Score = 387 bits (993), Expect = e-112 Identities = 188/255 (73%), Positives = 221/255 (86%) Query: 6 TLKGQCIAEFLGTGLLIFFGVGCVAALKVAGASFGQWEISVIWGLGVAMAIYLTAGVSGA 65 TL QC+AEFLGT LLIFFG GCVAALKVAGASFG WEIS+IWG+GV+MAIYLTAG+SGA Sbjct: 9 TLSSQCLAEFLGTALLIFFGTGCVAALKVAGASFGLWEISIIWGVGVSMAIYLTAGISGA 68 Query: 66 HLNPAVTIALWLFACFDKRKVIPFIVSQVAGAFCAAALVYGLYYNLFFDFEQTHHIVRGS 125 HLNPAV+IAL LFA FDKRK+ ++++QV GAFC AALVY LY NLFFDFEQ H ++RGS Sbjct: 69 HLNPAVSIALTLFAGFDKRKLPFYMLAQVCGAFCGAALVYTLYSNLFFDFEQAHAMLRGS 128 Query: 126 VESVDLAGTFSTYPNPHINFVQAFAVEMVITAILMGLILALTDDGNGVPRGPLAPLLIGL 185 S++LA FSTYP+P ++ QAF VE+VITAILM +I+ALTDD NG+PRG +APLLIGL Sbjct: 129 EGSLELASVFSTYPHPSLSTSQAFLVEVVITAILMAVIMALTDDNNGLPRGAMAPLLIGL 188 Query: 186 LIAVIGASMGPLTGFAMNPARDFGPKVFAWLAGWGNVAFTGGRDIPYFLVPLFGPIVGAI 245 LIAVIG++MGPLTGFAMNPARDFGPK+ +LAGWG +AFTGGRDIPYFLVP+F PI+GA Sbjct: 189 LIAVIGSAMGPLTGFAMNPARDFGPKLMTFLAGWGEIAFTGGRDIPYFLVPVFAPILGAC 248 Query: 246 VGAFAYRKLIGRHLP 260 +GA +YR LI R+LP Sbjct: 249 LGAASYRGLIARNLP 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: 307 Number of extensions: 8 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: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 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 Apr 09 2024. 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