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 3607331 Dshi_0746 MIP family channel protein (RefSeq)
Query= TCDB::Q9C4Z5 (246 letters) >FitnessBrowser__Dino:3607331 Length = 228 Score = 128 bits (322), Expect = 9e-35 Identities = 89/239 (37%), Positives = 130/239 (54%), Gaps = 25/239 (10%) Query: 6 KRCIAEFIGTFILVFFGAGSAAVTLMIASGGTSPNPFNIGIGLLGGLGDWVAIGLAFGFA 65 KR +AEFIGT+ LVF G G+A ++A+G +GIG WV + LAFG + Sbjct: 3 KRTLAEFIGTYWLVFGGCGAA----LLAAGVPE-----VGIG-------WVGVSLAFGLS 46 Query: 66 IAASIYALGNISGCHINPAVTIGLWSVKKFPGREVVPYIIAQLLG--AAFGSFIFL---- 119 + YA+G ISG H NPAVT+GL +F +++ PY IAQLLG AA G+ + Sbjct: 47 VLTMAYAVGGISGGHFNPAVTLGLTIAGRFEAKDIPPYWIAQLLGGAAAAGTLFVIMSGQ 106 Query: 120 -QCAGIGAATVGGLGATAPFPGISYWQAMLAEVVGTFLLMITIMGIAVDERAPKGFAGII 178 + A +G+ G G +P G M+AEVV T + +I I+G A P+GFA I Sbjct: 107 AEFASVGSFASNGYGVASP-GGFGMMSGMIAEVVLTAVFVIVILG-ATSHMVPEGFAPIA 164 Query: 179 IGLTVAGIITTLGNISGSSLNPARTFGPYLNDMIFAGTDLWNYYSIYVIGPIVGAVLAA 237 IGL + I I+ +S+NPAR+ + A LW +++ + G ++GA++ A Sbjct: 165 IGLCLTLIHLISIPITNTSVNPARSTAMAIYADGPALGQLWLFWAAPLAGAVIGALIWA 223 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: 214 Number of extensions: 17 Number of successful extensions: 5 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: 228 Length adjustment: 23 Effective length of query: 223 Effective length of database: 205 Effective search space: 45715 Effective search space used: 45715 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