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 BWI76_RS09585 BWI76_RS09585 aquaporin
Query= TCDB::P08995 (271 letters) >FitnessBrowser__Koxy:BWI76_RS09585 Length = 231 Score = 145 bits (366), Expect = 8e-40 Identities = 87/222 (39%), Positives = 125/222 (56%), Gaps = 16/222 (7%) Query: 38 QKLVAEAVGTYFLIFAGCASLVVNENYYNM-ITFPGIAIVWGLVLTVLVYTVGHISGGHF 96 +KL AE GT++L+F GC S V+ + + I F G+A+ +GL + + Y VGHISGGHF Sbjct: 3 RKLAAECFGTFWLVFGGCGSAVLAAAFPELGIGFAGVALAFGLTVLTMAYAVGHISGGHF 62 Query: 97 NPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGN---HDQFSGTVPNG-- 151 NPAVT+ + RFP +V Y++AQ++G I+A+ L ++ G SG NG Sbjct: 63 NPAVTLGLWAGGRFPAKEVIGYIIAQVVGGIIAAAILYVVASGKAGFDAAASGFASNGYG 122 Query: 152 -------TNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVT 204 + L A V E ++T + VI G ATD A FA IAIG L L +I PVT Sbjct: 123 EHSPGGFSMLSAIVIEIVLTCGFLLVIHG-ATDKNAPAGFAPIAIGLALTLIHLISIPVT 181 Query: 205 GASMNPARSLGPAFVHGEY--EGIWIYLLAPVVGAIAGAWVY 244 S+NPARS A G + + +W++ + P++G I G +Y Sbjct: 182 NTSVNPARSTAVAIFQGGWALQQLWLFWVMPIIGGILGGVLY 223 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: 183 Number of extensions: 18 Number of successful extensions: 5 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: 231 Length adjustment: 24 Effective length of query: 247 Effective length of database: 207 Effective search space: 51129 Effective search space used: 51129 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: 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