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 GFF1479 PGA1_c14980 putative major intrinsic protein
Query= TCDB::P08995 (271 letters) >FitnessBrowser__Phaeo:GFF1479 Length = 218 Score = 77.8 bits (190), Expect = 2e-19 Identities = 54/139 (38%), Positives = 73/139 (52%), Gaps = 4/139 (2%) Query: 38 QKLVAEAVGTYFLIFAGCASLVVNENYYNM---ITFPGIAIVWGLVLTVLVYTVGHISGG 94 QKL+AEA+GT FL+ S ++ E + A+ G +L V++ T+G ISG Sbjct: 4 QKLIAEALGTGFLLIGVVGSGIMAETLSGGNIGLALLANAVATGAMLYVIITTLGPISGA 63 Query: 95 HFNPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHDQFSGTVPNGTNL 154 HFNPAVT+AFA VP YV AQ++G IL ++F Q S T+ Sbjct: 64 HFNPAVTLAFALRGDHSWAAVPPYVAAQIIGGILGVWASHVMFDLTILQTSTTMHRTGGA 123 Query: 155 QAFVFEFIMTFFLMFVICG 173 Q F E + TF L+FVI G Sbjct: 124 QWF-SEILATFGLLFVIFG 141 Score = 37.4 bits (85), Expect = 3e-07 Identities = 26/103 (25%), Positives = 50/103 (48%), Gaps = 11/103 (10%) Query: 155 QAFVFEFIMTFFLMFVICG--VATDNRAVGEFA------GIAIGSTLLLNVIIGGPVTGA 206 Q + E + T FL+ + G + + + G +A G+ L + + GP++GA Sbjct: 4 QKLIAEALGTGFLLIGVVGSGIMAETLSGGNIGLALLANAVATGAMLYVIITTLGPISGA 63 Query: 207 SMNPARSLGPAFVHGEYEGIWI--YLLAPVVGAIAGAWVYNIV 247 NPA +L A + G++ + Y+ A ++G I G W +++ Sbjct: 64 HFNPAVTLAFA-LRGDHSWAAVPPYVAAQIIGGILGVWASHVM 105 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: 174 Number of extensions: 13 Number of successful extensions: 4 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: 218 Length adjustment: 23 Effective length of query: 248 Effective length of database: 195 Effective search space: 48360 Effective search space used: 48360 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