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 Pf1N1B4_3394 Aquaporin Z
Query= TCDB::P08995 (271 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3394 Length = 232 Score = 143 bits (360), Expect = 4e-39 Identities = 81/221 (36%), Positives = 126/221 (57%), Gaps = 15/221 (6%) Query: 38 QKLVAEAVGTYFLIFAGCASLVVNENYYNM-ITFPGIAIVWGLVLTVLVYTVGHISGGHF 96 ++ E VGT++L+ GC S V+ + N+ I G+++ +GL + + + +GHISG H Sbjct: 5 KRSATELVGTFWLVLGGCGSAVLAAAFPNVGIGLLGVSLAFGLTVLTMAFAIGHISGCHL 64 Query: 97 NPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMG--NHDQFSGTVPNG--- 151 NPAV++ RFP ++PAY++AQ++G I+A+ L + G + SG NG Sbjct: 65 NPAVSVGLVVGGRFPAKELPAYIIAQVIGGIIAAALLYFIASGKPGFELASGLASNGYGE 124 Query: 152 ------TNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTG 205 + FV E +MT + +I G +TD RA A IAIG L L +I PVT Sbjct: 125 HSPGGYSMAAGFVSELVMTAMFILIILG-STDKRAPAGLAPIAIGLALTLIHLISIPVTN 183 Query: 206 ASMNPARSLGPAFVHGEY--EGIWIYLLAPVVGAIAGAWVY 244 S+NPARS GPA + G + + +W++ LAP++GA+ G +Y Sbjct: 184 TSVNPARSTGPALIVGGWAIQQLWLFWLAPILGAVIGGVMY 224 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: 198 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: 232 Length adjustment: 24 Effective length of query: 247 Effective length of database: 208 Effective search space: 51376 Effective search space used: 51376 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