Align Hg2+-inhibitable aquaporin, AqpM (transports both water and glycerol as well as CO2) (Kozono et al., 2003; Araya-Secchi et al., 2011). Its 3-d structure has been determined to 1.7 Å. In AqpM, isoleucine replaces a key histidine residue found in the lumen of water channels, which becomes a glycine residue in aquaglyceroporins. As a result of this and other side-chain substituents in the walls of the channel, the channel is intermediate in size and exhibits differentially tuned electrostatics when compared with the other subfamilies (characterized)
to candidate Ga0059261_1307 Ga0059261_1307 MIP family channel proteins
Query= TCDB::Q9C4Z5 (246 letters) >FitnessBrowser__Korea:Ga0059261_1307 Length = 243 Score = 145 bits (366), Expect = 7e-40 Identities = 96/249 (38%), Positives = 139/249 (55%), Gaps = 30/249 (12%) Query: 6 KRCIAEFIGTFILVFFGAGSAAVTLMIASGGTSPNPFNIGIGLLGGLGDWVAIGLAFGFA 65 +R +AE +GTF LVF G GSA + +GIGLLG + AFG Sbjct: 5 QRGLAELVGTFWLVFGGCGSAVLAAAFPE---------VGIGLLG-------VSFAFGLT 48 Query: 66 IAASIYALGNISGCHINPAVTIGLWSVKKFPGREVVPYIIAQLLGAAFGSFIFLQCAGIG 125 + Y++G+ISGCH+NPAVT GLW+ +F G+++ Y++AQ++GA +++ L C G Sbjct: 49 VLTMAYSIGHISGCHLNPAVTFGLWAGGRFAGKDIPLYVVAQVIGAVIAAWL-LYCIASG 107 Query: 126 AA----TVGGLGATA---PFPGISYWQAMLA-EVVGTFLLMITIMGIAVDERAPKGFAGI 177 A GGL A PG Q+ LA EVV TF+ ++ IMG + D RAP GFA I Sbjct: 108 APGGYDLAGGLAANGFGEHSPGKFNLQSALAIEVVLTFMFVVIIMG-STDSRAPAGFAPI 166 Query: 178 IIGLTVAGIITTLGNISGSSLNPARTFGPYLNDMIFAGTDLWNYYSIYVIGPIVGAVLAA 237 IGL + I ++ +S+NPAR+ GP L +A + LW ++ + PIVG VL Sbjct: 167 AIGLALMLIHLISIPVTNTSVNPARSTGPALIVGGWAISQLW----LFWVAPIVGGVLGG 222 Query: 238 LTYQYLTSE 246 + Y+ L ++ Sbjct: 223 IFYKALGAD 231 Lambda K H 0.326 0.144 0.441 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: 229 Number of extensions: 16 Number of successful extensions: 8 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: 246 Length of database: 243 Length adjustment: 24 Effective length of query: 222 Effective length of database: 219 Effective search space: 48618 Effective search space used: 48618 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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