Align Aquaporin-3, Aqp-3 of 271 aas (characterized)
to candidate 354244 BT4718 putative aquaporin (NCBI ptt file)
Query= TCDB::729057658 (271 letters) >FitnessBrowser__Btheta:354244 Length = 222 Score = 90.1 bits (222), Expect = 4e-23 Identities = 60/194 (30%), Positives = 102/194 (52%), Gaps = 15/194 (7%) Query: 46 GPVPAAFVVGLTLAWIAWVFGPVSGAHVNPVVSLMMLLVRKVWFLDALIYIVAQLLGSMA 105 G V A GL++ +A+ G +SG H+NP ++L + L ++ DA +Y++ Q++G++ Sbjct: 30 GTVGVALAFGLSVVAMAYAIGGISGCHINPAITLGVFLSGRMNGKDAGMYMLFQVIGAII 89 Query: 106 GSWIGTLAVPAVDAGNTLGMTTISAN----ITVGQAIGLEIVATALLLLVILSAVDELRP 161 GS + V G G T +N + QA E+V T + +LV+L + D P Sbjct: 90 GS---AILYALVTTGGHDGPTATGSNGFGDGEMLQAFIAEVVFTFIFVLVVLGSTD---P 143 Query: 162 KPWNVGNVTIFPFIFGATLALLASLLGDLTGASMNPARSFGPAVVNNN--FTDLWVYIVG 219 K G G +L L+ + +TG S+NPARS GPA+ + LW++IV Sbjct: 144 KK---GAGAFAGLAIGLSLVLVHIVCIPITGTSVNPARSIGPALFQGGEALSQLWLFIVA 200 Query: 220 PFIGALLATVLYEF 233 PF+GA ++ +++ + Sbjct: 201 PFVGAAVSALVWNY 214 Lambda K H 0.326 0.140 0.433 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: 178 Number of extensions: 12 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: 271 Length of database: 222 Length adjustment: 24 Effective length of query: 247 Effective length of database: 198 Effective search space: 48906 Effective search space used: 48906 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