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 SMc01870 SMc01870 aquaporin Z
Query= TCDB::P08995 (271 letters) >FitnessBrowser__Smeli:SMc01870 Length = 228 Score = 132 bits (333), Expect = 5e-36 Identities = 81/223 (36%), Positives = 123/223 (55%), Gaps = 14/223 (6%) Query: 38 QKLVAEAVGTYFLIFAGCASLVVNENYYNM-ITFPGIAIVWGLVLTVLVYTVGHISGGHF 96 +KL E +GT++L+ GC S V+ + + I G++ +GL + + Y VG ISGGHF Sbjct: 3 RKLSVEFLGTFWLVLGGCGSAVLAAAFPEVGIGLLGVSFAFGLTVLTMAYAVGGISGGHF 62 Query: 97 NPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHD-QFSGTVPNG---- 151 NPAV++ A R P + Y++AQ+ G+I A+ L ++ G D Q G NG Sbjct: 63 NPAVSVGLAVAGRMPPASLVGYILAQVTGAIAAAAVLYVIASGKADFQLGGFAANGYGEH 122 Query: 152 -----TNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGA 206 + A V E +MT F + +I G +T +R FA IAIG L L ++ PVT Sbjct: 123 SPGGYSLTAALVTEVVMTAFFLLIILG-STHSRVPVGFAPIAIGLGLTLIHLVSIPVTNT 181 Query: 207 SMNPARSLGPAFVHGEY--EGIWIYLLAPVVGAIAGAWVYNIV 247 S+NPARS G A G++ +W++ +AP++GA+ V+ IV Sbjct: 182 SVNPARSTGQALFVGDWAISQLWLFWVAPLIGAVIAGIVWKIV 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: 182 Number of extensions: 17 Number of successful extensions: 6 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: 228 Length adjustment: 24 Effective length of query: 247 Effective length of database: 204 Effective search space: 50388 Effective search space used: 50388 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