The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands .
This clan contains 45 families and the total number of domains in the clan is 210543. The clan was built by DJ Studholme and A Bateman.
- Murzin AG; , EMBO J 1993;12:861-867.: OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. PUBMED:8458342 EPMC:8458342
This clan contains the following 45 member families:BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind
External database links
Below is a listing of the unique domain organisations or architectures from this clan. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by
clicking on the graphic. You can also choose to see all sequences which
have a given architecture by clicking on the
in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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The table below shows the number of occurrences of each domain throughout the sequence database. More...
In brackets beside each number is the percentage of the total number of sequence hits for the clan that are represented by this domain. The rightmost column provides a link to the alignments tab for each domain. Finally, the last row in the table provides a link to the HTML representation of the alignment for the seed alignments for all members of this clan.
Please note: the clan alignment can be extremely large and the resulting HTML file is often too large to be rendered by web-browsers. Please consider downloading the alignment (by right-clicking the link) rather than viewing it in your browser.
|Pfam family||Num. domains||Alignment|
|S1 (PF00575)||46862 (22.3%)||View|
|tRNA_anti-codon (PF01336)||22969 (10.9%)||View|
|CSD (PF00313)||14886 (7.1%)||View|
|TOBE_2 (PF08402)||14426 (6.9%)||View|
|tRNA_bind (PF01588)||10729 (5.1%)||View|
|SSB (PF00436)||10092 (4.8%)||View|
|TRAM (PF01938)||8506 (4.0%)||View|
|Ribosom_S12_S23 (PF00164)||6678 (3.2%)||View|
|Ribosomal_L2 (PF00181)||6547 (3.1%)||View|
|TOBE (PF03459)||5980 (2.8%)||View|
|eIF-1a (PF01176)||5916 (2.8%)||View|
|EFP (PF01132)||5656 (2.7%)||View|
|Ribosomal_S17 (PF00366)||5324 (2.5%)||View|
|OB_RNB (PF08206)||5260 (2.5%)||View|
|OB_NTP_bind (PF07717)||5209 (2.5%)||View|
|DNA_ligase_OB (PF03120)||5111 (2.4%)||View|
|RuvA_N (PF01330)||4290 (2.0%)||View|
|tRNA_anti_2 (PF13742)||4104 (1.9%)||View|
|RecO_N (PF11967)||4019 (1.9%)||View|
|Rho_RNA_bind (PF07497)||3771 (1.8%)||View|
|S1_2 (PF13509)||2158 (1.0%)||View|
|DUF35 (PF01796)||1861 (0.9%)||View|
|BOF (PF04076)||1522 (0.7%)||View|
|Pfam family||Num. domains||Alignment|
|EutN_CcmL (PF03319)||1340 (0.6%)||View|
|OmdA (PF13376)||1185 (0.6%)||View|
|TOBE_3 (PF12857)||1134 (0.5%)||View|
|eIF-5a (PF01287)||832 (0.4%)||View|
|DUF223 (PF02721)||441 (0.2%)||View|
|Rep-A_N (PF04057)||381 (0.2%)||View|
|mRNA_cap_C (PF03919)||377 (0.2%)||View|
|RNA_pol_Rpb8 (PF03870)||366 (0.2%)||View|
|EXOSC1 (PF10447)||355 (0.2%)||View|
|POT1 (PF02765)||329 (0.2%)||View|
|RNA_pol_Rbc25 (PF08292)||328 (0.2%)||View|
|Rep_fac-A_3 (PF08661)||305 (0.1%)||View|
|DUF3127 (PF11325)||271 (0.1%)||View|
|tRNA_anti-like (PF12869)||205 (0.1%)||View|
|RecO_N_2 (PF13114)||198 (0.1%)||View|
|S1-like (PF14444)||185 (0.1%)||View|
|Stn1 (PF10451)||123 (0.1%)||View|
|Ten1 (PF12658)||90 (0.0%)||View|
|Ten1_2 (PF15490)||82 (0.0%)||View|
|Phage_DNA_bind (PF02303)||81 (0.0%)||View|
|DUF2110 (PF09883)||44 (0.0%)||View|
|TEBP_beta (PF07404)||15 (0.0%)||View|
|Total: 45||Total: 210543||Clan alignment|
Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.
This diagram shows the relationships between members of this clan. More...
Relationships between families in a clan are determined using HHsearch. Families are deemed to be closely related if their E-value is less than 10-3 and these relationships are shown with a solid line. Less closely related family pairs, with an E-value of between 10-3 and 10-1, are shown with a dashed line.
The E-value for each pair of closely or partially related families is shown next to the line linking the families. Clicking on the E-value will take you to the pairwise HMM-logo for that relationship. You can see the information regarding a Pfam family by clicking on the family box.
We could not retrieve a family relationship diagram for this clan.
This tree shows the occurrence of the domains in this clan across different species. More...
For all of the domain matches in a full alignment we count the number of domains that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There are 44 interactions for this clan. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.
Loading structure mapping...