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 Ac3H11_4644 Aquaporin Z
Query= TCDB::P08995 (271 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4644 Length = 248 Score = 145 bits (367), Expect = 6e-40 Identities = 90/221 (40%), Positives = 124/221 (56%), Gaps = 14/221 (6%) Query: 37 LQKLVAEAVGTYFLIFAGCASLVVNENYYNM-ITFPGIAIVWGLVLTVLVYTVGHISGGH 95 LQK AE +GT++L F GC S V+ + + I F G+++ +GL + Y +G ISGGH Sbjct: 22 LQKWSAEFLGTFWLTFGGCGSAVLAAAFPQLGIGFLGVSLAFGLTVLTGAYALGPISGGH 81 Query: 96 FNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHD-QFSGTVPNGTN- 153 FNPAV++ A RF + ++P YVVAQ+LG+I+A+G L L+ G G NG Sbjct: 82 FNPAVSVGLALGGRFKVSELPGYVVAQVLGAIVAAGVLYLIATGKPGADIGGFATNGYGE 141 Query: 154 --------LQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTG 205 L A V E ++T + VI GV T RA G+AIG L L +I PVT Sbjct: 142 HSPGGYGLLAAVVAEVVLTAVFLIVILGV-TSRRAAEGVGGMAIGLCLTLIHLISIPVTN 200 Query: 206 ASMNPARSLGPAFVHGEY--EGIWIYLLAPVVGAIAGAWVY 244 S+NPARS GPA Y +W++ AP+ GA+ GA +Y Sbjct: 201 TSVNPARSTGPALFGPSYALSELWVFWAAPIAGALLGAAIY 241 Score = 50.4 bits (119), Expect = 4e-11 Identities = 43/115 (37%), Positives = 58/115 (50%), Gaps = 14/115 (12%) Query: 149 PNGTNLQAFVFEFIMTFFLMFVICGVATDNRAVGE----FAGI--AIGSTLLLNVIIGGP 202 P T+LQ + EF+ TF+L F CG A A + F G+ A G T+L GP Sbjct: 17 PMPTSLQKWSAEFLGTFWLTFGGCGSAVLAAAFPQLGIGFLGVSLAFGLTVLTGAYALGP 76 Query: 203 VTGASMNPARSLGPA----FVHGEYEGIWIYLLAPVVGAIAGAWVYNIVRYTDKP 253 ++G NPA S+G A F E G Y++A V+GAI A V ++ T KP Sbjct: 77 ISGGHFNPAVSVGLALGGRFKVSELPG---YVVAQVLGAIVAAGVLYLIA-TGKP 127 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: 207 Number of extensions: 18 Number of successful extensions: 6 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: 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