Align Glycerol uptake facilitator protein 3 (characterized)
to candidate CA265_RS07865 CA265_RS07865 aquaporin
Query= SwissProt::F9UTW9 (240 letters) >FitnessBrowser__Pedo557:CA265_RS07865 Length = 246 Score = 229 bits (583), Expect = 5e-65 Identities = 115/237 (48%), Positives = 146/237 (61%), Gaps = 11/237 (4%) Query: 11 LGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGVYASSFMSPAHLN 70 L EF+GT ++ILLG+GVVA V L +K N+GW+ IT W AV +GV + S AHLN Sbjct: 5 LAEFIGTALMILLGNGVVANVVLKGTKGNNSGWIVITTAWALAVFVGVVVAGPYSGAHLN 64 Query: 71 PAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATKDAGAILGIFATG 130 P V+LG+A+ F WA Y AQ+AG + G +VWL Y H+ AT D G FAT Sbjct: 65 PIVTLGLAIGKGFSWALAPFYIIAQLAGAMTGSFLVWLIYKDHFDATDDQGLKAAPFATA 124 Query: 131 PGIRRYFWNFISEVIGTFVLVFGLLAFTKGQF-----------TAGLNPIVVGILIIAIG 179 P IR N +SE+IGTFVL+F + FT + I V L+ IG Sbjct: 125 PAIRNISSNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGAIPVAFLVWVIG 184 Query: 180 LSLGGTTGYAINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALLF 236 L+LGGTTGYAINPARDLGPRI H ++P+ KG SDW+Y+WVPI GP++G L A+ F Sbjct: 185 LALGGTTGYAINPARDLGPRIIHFLIPMKGKGGSDWSYAWVPIVGPIIGSVLAAVAF 241 Score = 23.5 bits (49), Expect = 0.004 Identities = 26/114 (22%), Positives = 40/114 (35%), Gaps = 11/114 (9%) Query: 6 LALQLLGEFLGTFILILL-------GDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGV 58 ++ LL E +GTF+LI + G VT L W + +G Sbjct: 130 ISSNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGAIPVAFLVWVIGLALGG 189 Query: 59 YASSFMSPAH-LNPAV---SLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWL 108 ++PA L P + + M G W+Y I G V+ + L Sbjct: 190 TTGYAINPARDLGPRIIHFLIPMKGKGGSDWSYAWVPIVGPIIGSVLAAVAFLL 243 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: 260 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 246 Length adjustment: 23 Effective length of query: 217 Effective length of database: 223 Effective search space: 48391 Effective search space used: 48391 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 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