Align Nodulin-26 aquaporin and glycerol facilitator, NIP (de Paula Santos Martins et al. 2015). Transports NH3 5-fold better than water in Hg2+-sensitive fashion (characterized)
to candidate BPHYT_RS03080 BPHYT_RS03080 aquaporin Z
Query= TCDB::P08995 (271 letters) >FitnessBrowser__BFirm:BPHYT_RS03080 Length = 248 Score = 113 bits (283), Expect = 3e-30 Identities = 72/226 (31%), Positives = 116/226 (51%), Gaps = 18/226 (7%) Query: 38 QKLVAEAVGTYFLIFAGCASLVVNENYYNMIT-FPGIAIVWGLVLTVLVYTVGHISGGHF 96 ++L+ E VGT +L+F GC S+V+N +A+ +GL L +Y G +SGGHF Sbjct: 6 KRLLFEGVGTAWLVFVGCGSIVLNVGAIQQAGGVLEVALAFGLALATAIYCFGGVSGGHF 65 Query: 97 NPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQF----SGTVPNGT 152 NPAVT+ F +RFP+ + Y+ +Q+LG+I+A+ L L G F S NG Sbjct: 66 NPAVTVGFTVAQRFPVRDLLPYIASQILGAIVAAALL-LYVAGGRPGFDLAASEFAANGF 124 Query: 153 N---------LQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPV 203 A EF++ F + +A R + A + IG+ L+L ++ PV Sbjct: 125 GDHSPADYQLHSAVAVEFVLAFGFVMASLLIA-HRRDMAPIAPLVIGACLVLVYLVSIPV 183 Query: 204 TGASMNPARSLGPAFVHGEY--EGIWIYLLAPVVGAIAGAWVYNIV 247 T S+NPARS A G++ + +W++ AP+ G + +++ V Sbjct: 184 TNGSVNPARSTAQALFVGDWALDQLWLFWAAPLSGGVMAGALFSFV 229 Lambda K H 0.323 0.138 0.407 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: 196 Number of extensions: 14 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: 248 Length adjustment: 24 Effective length of query: 247 Effective length of database: 224 Effective search space: 55328 Effective search space used: 55328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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