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 7025915 Shewana3_3064 aquaporin Z (RefSeq)
Query= TCDB::Q9C4Z5 (246 letters) >FitnessBrowser__ANA3:7025915 Length = 231 Score = 153 bits (387), Expect = 3e-42 Identities = 96/248 (38%), Positives = 138/248 (55%), Gaps = 29/248 (11%) Query: 2 VSLTKRCIAEFIGTFILVFFGAGSAAVTLMIASGGTSPNPFNIGIGLLGGLGDWVAIGLA 61 ++++++ AEF+GT LV G GSA + +GIGLLG + LA Sbjct: 1 MNMSQKMAAEFLGTLWLVLGGCGSAVLAAAFPE---------VGIGLLG-------VALA 44 Query: 62 FGFAIAASIYALGNISGCHINPAVTIGLWSVKKFPGREVVPYIIAQLLGAAFGSFIFLQC 121 FG + +A+G+ISGCH+NPAV+ GLW+ +FP E++PYIIAQ+ G G+ + Sbjct: 45 FGLTVLTMAFAIGHISGCHLNPAVSFGLWAGGRFPASELLPYIIAQVAGGIVGAGVLYAI 104 Query: 122 A----GIGAA---TVGGLGATAPFPGISYWQAMLAEVVGTFLLMITIMGIAVDERAPKGF 174 A G A G G +P G S ++ E+V T ++ I+G A DERAPKGF Sbjct: 105 ASGQEGFSLAAGFASNGFGEHSP-GGYSMMSVLICEIVMTLFFLLVILG-ATDERAPKGF 162 Query: 175 AGIIIGLTVAGIITTLGNISGSSLNPARTFGPYLNDMIFAGTDLWNYYSIYVIGPIVGAV 234 A I IGL + I +S +S+NPAR+ GP L +A + LW I+ + PIVGA+ Sbjct: 163 APIAIGLCLTLIHLISIPVSNTSVNPARSTGPALFVGDWAVSQLW----IFWVAPIVGAI 218 Query: 235 LAALTYQY 242 LA + Y+Y Sbjct: 219 LAGMIYRY 226 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: 223 Number of extensions: 18 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 246 Length of database: 231 Length adjustment: 23 Effective length of query: 223 Effective length of database: 208 Effective search space: 46384 Effective search space used: 46384 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