We are sorry, but NCBI web applications do not support your browser and may not function properly. More information

Results: 4

1.
Fig. 3

Fig. 3. From: A survey of integral ?-helical membrane proteins.

Target selection for membrane protein structural genomics. Structural coverage of the known IMG (Integral Membrane Genome) sequence space was defined by taking sequences from 598 IM Pfam families and clustering them at 30% sequence identity

Libusha Kelly, et al. J Struct Funct Genomics. 2009 December;10(4):269-280.
2.
Fig. 4

Fig. 4. From: A survey of integral ?-helical membrane proteins.

Links between the transmembrane domains of human ABC transporters. The transmembrane domains of 48 human ABC transporter proteins were excised from their complete sequences. Profiles were generated for each transmembrane domain and run against the membrane protein profile database (Methods). Significantly related profiles are linked and colored according to organism with red, blue, and yellow representing eukaryotes, bacteria, and archaea, respectively. The two major clusters represent ABCA and G family members (dark and light green); and ABCB, C, and D family members (purple)

Libusha Kelly, et al. J Struct Funct Genomics. 2009 December;10(4):269-280.
3.
Fig. 2

Fig. 2. From: A survey of integral ?-helical membrane proteins.

PFAM membrane protein families in 34 organisms. Organism names are listed horizontally at the top (columns). 476 Pfam membrane protein families are on the vertical axis (rows). Colors indicate binning for the number of times a particular family appears in an organism. White indicates a particular family is not found in an organism; light blue means the family appears once; medium blue, between two and 49 times; and dark blue means the family is found 50 or more times. The red and yellow bars show the clustering of eukaryotes and prokaryotes, respectively. The heatmap was constructed using the R function “heatmap.2” with hierarchical clustering and default parameters [37]

Libusha Kelly, et al. J Struct Funct Genomics. 2009 December;10(4):269-280.
4.
Fig. 1

Fig. 1. From: A survey of integral ?-helical membrane proteins.

Membrane protein annotation pipeline. All Pfam-A families with at least three predicted transmembrane helices (TMH) were used to identify membrane protein families in 34 genomes (cyan). Sequences predicted to have three or more TMHs in each genome were collected (red). In parallel, Pfam family membership was defined where available for each sequence profile (yellow). Automated multiple sequence alignment profiles were generated for each sequence. A database of profiles was constructed, and each profile was compared to all other profiles in the database to link membrane proteins (blue). The annotation pipeline can be generally used as input to an experimental structure determination pipeline. Finally, resulting structures can be used as templates to generate comparative models for all homologous sequences. The five steps are detailed in Methods

Libusha Kelly, et al. J Struct Funct Genomics. 2009 December;10(4):269-280.

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Write to the Help Desk