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2  structures 140  species 0  interactions 6767  sequences 73  architectures

Family: LOB (PF03195)

Summary: Lateral organ boundaries (LOB) domain

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Lateral organ boundaries (LOB) domain Provide feedback

The lateral organ boundaries (LOB) gene encodes a plant-specific protein of unknown function that is expressed at the adaxial base of initiating lateral organs. The N-terminal of the LOB protein contains an approximately 100-amino acid conserved domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins as well as in proteins from a variety of other plant species. The LOB domain contains conserved blocks of amino acids that identify the LOB domain (LBD) gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is the defining feature of the LOB domain, is present in all LBD proteins [1].

Literature references

  1. Shuai B, Reynaga-Pena CG, Springer PS;, Plant Physiol. 2002;129:747-761.: The lateral organ boundaries gene defines a novel, plant-specific gene family. PUBMED:12068116 EPMC:12068116


This tab holds annotation information from the InterPro database.

InterPro entry IPR004883

The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [ PUBMED:12068116 ] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [ PUBMED:12068116 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(147)
Full
(6767)
Representative proteomes UniProt
(9833)
RP15
(620)
RP35
(3688)
RP55
(5639)
RP75
(7527)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(147)
Full
(6767)
Representative proteomes UniProt
(9833)
RP15
(620)
RP35
(3688)
RP55
(5639)
RP75
(7527)
Alignment:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(147)
Full
(6767)
Representative proteomes UniProt
(9833)
RP15
(620)
RP35
(3688)
RP55
(5639)
RP75
(7527)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_2998 (release 6.5)
Previous IDs: DUF260;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 147
Number in full: 6767
Average length of the domain: 96.70 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 43.54 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.2 24.2
Trusted cut-off 24.5 24.2
Noise cut-off 24.1 24.0
Model length: 99
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LOB domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0N7KD70 View 3D Structure Click here
A0A0N7KQN6 View 3D Structure Click here
A0A0P0UXR8 View 3D Structure Click here
A0A0P0W082 View 3D Structure Click here
A0A0P0WII3 View 3D Structure Click here
A0A0P0WKY8 View 3D Structure Click here
A0A0R0EGE3 View 3D Structure Click here
A0A0R0FN09 View 3D Structure Click here
A0A0R0FV53 View 3D Structure Click here
A0A0R0GVL9 View 3D Structure Click here
A0A0R0H4Z3 View 3D Structure Click here
A0A0R0IRH1 View 3D Structure Click here
A0A0R0J3T7 View 3D Structure Click here
A0A0R0JEY4 View 3D Structure Click here
A0A0R0JQP9 View 3D Structure Click here
A0A0R0K3S6 View 3D Structure Click here
A0A0R0K3Z9 View 3D Structure Click here
A0A0R0LBU1 View 3D Structure Click here
A0A1D6F053 View 3D Structure Click here
A0A1D6F9Z0 View 3D Structure Click here
A0A1D6FQ52 View 3D Structure Click here
A0A1D6GL54 View 3D Structure Click here
A0A1D6HSN9 View 3D Structure Click here
A0A1D6I377 View 3D Structure Click here
A0A1D6IIB9 View 3D Structure Click here
A0A1D6JZ19 View 3D Structure Click here
A0A1D6KC74 View 3D Structure Click here
A0A1D6KJL1 View 3D Structure Click here
A0A1D6KM00 View 3D Structure Click here
A0A1D6KXT4 View 3D Structure Click here
A0A1D6KXW5 View 3D Structure Click here
A0A1D6L713 View 3D Structure Click here
A0A1D6LGV7 View 3D Structure Click here
A0A1D6M2R3 View 3D Structure Click here
A0A1D6M4G5 View 3D Structure Click here
A0A1D6M9Z4 View 3D Structure Click here
A0A1D6MM36 View 3D Structure Click here
A0A1D6MV27 View 3D Structure Click here
A0A1D6PAX1 View 3D Structure Click here
A0A1D6PJV6 View 3D Structure Click here
A0A1D6Q0Q8 View 3D Structure Click here
A0A368UGU2 View 3D Structure Click here
A1YKY7 View 3D Structure Click here
A2ZUK5 View 3D Structure Click here
A2ZUL5 View 3D Structure Click here
A5H448 View 3D Structure Click here
A5H450 View 3D Structure Click here
B4FE47 View 3D Structure Click here
B4FGE2 View 3D Structure Click here
B6SPU9 View 3D Structure Click here
B6TDS9 View 3D Structure Click here
B6TET9 View 3D Structure Click here
B6U7K7 View 3D Structure Click here
C0HGH5 View 3D Structure Click here
C0P4U0 View 3D Structure Click here
C0PK80 View 3D Structure Click here
C4J6G5 View 3D Structure Click here
C6SVI6 View 3D Structure Click here
C6TJL6 View 3D Structure Click here
C7J5S5 View 3D Structure Click here
I1J7M5 View 3D Structure Click here
I1J7Y2 View 3D Structure Click here
I1J947 View 3D Structure Click here
I1J9D3 View 3D Structure Click here
I1JFY2 View 3D Structure Click here
I1JID9 View 3D Structure Click here
I1JKK9 View 3D Structure Click here
I1JP22 View 3D Structure Click here
I1JP23 View 3D Structure Click here
I1JXA7 View 3D Structure Click here
I1JY97 View 3D Structure Click here
I1K2B8 View 3D Structure Click here
I1KBA6 View 3D Structure Click here
I1KIX1 View 3D Structure Click here
I1KMA9 View 3D Structure Click here
I1KU11 View 3D Structure Click here
I1L0C8 View 3D Structure Click here
I1L6U2 View 3D Structure Click here
I1LD38 View 3D Structure Click here
I1LH74 View 3D Structure Click here
I1LLS0 View 3D Structure Click here
I1LQZ6 View 3D Structure Click here
I1LX21 View 3D Structure Click here
I1LYI0 View 3D Structure Click here
I1M5B9 View 3D Structure Click here
I1M7R0 View 3D Structure Click here
I1M7R7 View 3D Structure Click here
I1MDM7 View 3D Structure Click here
I1MG13 View 3D Structure Click here
I1MVN0 View 3D Structure Click here
I1MYZ7 View 3D Structure Click here
I1MZ09 View 3D Structure Click here
I1MZV5 View 3D Structure Click here
I1N3F1 View 3D Structure Click here
I1N5C2 View 3D Structure Click here
I1N6Q1 View 3D Structure Click here
I1N9P5 View 3D Structure Click here
I1N9P6 View 3D Structure Click here
I1NFI9 View 3D Structure Click here
I1NG19 View 3D Structure Click here
I1NHD1 View 3D Structure Click here
K7K3V1 View 3D Structure Click here
K7KAB5 View 3D Structure Click here
K7KAM4 View 3D Structure Click here
K7KBG3 View 3D Structure Click here
K7KCD7 View 3D Structure Click here
K7KJC7 View 3D Structure Click here
K7KNN7 View 3D Structure Click here
K7KNS1 View 3D Structure Click here
K7KVP4 View 3D Structure Click here
K7KXY2 View 3D Structure Click here
K7L6R9 View 3D Structure Click here
K7L7L8 View 3D Structure Click here
K7L8Z2 View 3D Structure Click here
K7LAI1 View 3D Structure Click here
K7LAX8 View 3D Structure Click here
K7LH87 View 3D Structure Click here
K7LH88 View 3D Structure Click here
K7LI56 View 3D Structure Click here
K7LLG5 View 3D Structure Click here
K7LN93 View 3D Structure Click here
K7M0L0 View 3D Structure Click here
K7M386 View 3D Structure Click here
K7M4H2 View 3D Structure Click here
K7M5B3 View 3D Structure Click here
K7M5P6 View 3D Structure Click here
K7M865 View 3D Structure Click here
K7MD92 View 3D Structure Click here
K7MKN0 View 3D Structure Click here
K7MM90 View 3D Structure Click here
K7MVP6 View 3D Structure Click here
K7MWX0 View 3D Structure Click here
K7MY04 View 3D Structure Click here
K7N0C6 View 3D Structure Click here
K7TWK5 View 3D Structure Click here
K7TYY8 View 3D Structure Click here
K7U8R9 View 3D Structure Click here
K7UU76 View 3D Structure Click here
K7V244 View 3D Structure Click here
K7VBT3 View 3D Structure Click here
K7VEV1 View 3D Structure Click here
K7VH99 View 3D Structure Click here
O04479 View 3D Structure Click here
O22131 View 3D Structure Click here
O22132 View 3D Structure Click here
O49651 View 3D Structure Click here
O64836 View 3D Structure Click here
O81322 View 3D Structure Click here
O81323 View 3D Structure Click here
O82198 View 3D Structure Click here
P59467 View 3D Structure Click here
P59468 View 3D Structure Click here
P59469 View 3D Structure Click here
Q0DPV4 View 3D Structure Click here
Q0J4G1 View 3D Structure Click here
Q0J7T3 View 3D Structure Click here
Q0JME5 View 3D Structure Click here
Q10N09 View 3D Structure Click here
Q10P52 View 3D Structure Click here
Q27YF3 View 3D Structure Click here
Q2QYU3 View 3D Structure Click here
Q32SG3 View 3D Structure Click here
Q5KQR7 View 3D Structure Click here
Q5N8Y9 View 3D Structure Click here
Q5NA79 View 3D Structure Click here
Q5QMB4 View 3D Structure Click here
Q5UG13 View 3D Structure Click here
Q6AT73 View 3D Structure Click here
Q6AV61 View 3D Structure Click here
Q6JAD1 View 3D Structure Click here
Q6K713 View 3D Structure Click here
Q6ZBW8 View 3D Structure Click here
Q75HN5 View 3D Structure Click here
Q75L85 View 3D Structure Click here
Q7EZ26 View 3D Structure Click here
Q7XGL4 View 3D Structure Click here
Q84JC7 View 3D Structure Click here
Q8L3S3 View 3D Structure Click here
Q8L5T5 View 3D Structure Click here
Q8L8Q3 View 3D Structure Click here
Q8LBW3 View 3D Structure Click here
Q8LQH4 View 3D Structure Click here
Q9AS62 View 3D Structure Click here
Q9AT61 View 3D Structure Click here
Q9C8V8 View 3D Structure Click here
Q9CA30 View 3D Structure Click here
Q9FFL3 View 3D Structure Click here
Q9FKZ3 View 3D Structure Click here
Q9FML4 View 3D Structure Click here
Q9FN11 View 3D Structure Click here
Q9LHS8 View 3D Structure Click here
Q9LIJ0 View 3D Structure Click here
Q9LNB9 View 3D Structure Click here
Q9LQR0 View 3D Structure Click here
Q9LRW1 View 3D Structure Click here
Q9M2J7 View 3D Structure Click here
Q9M886 View 3D Structure Click here
Q9SA51 View 3D Structure Click here
Q9SCS4 View 3D Structure Click here
Q9SHE9 View 3D Structure Click here
Q9SJW5 View 3D Structure Click here
Q9SK08 View 3D Structure Click here
Q9SLB6 View 3D Structure Click here
Q9SLB7 View 3D Structure Click here
Q9SN23 View 3D Structure Click here
Q9SRL8 View 3D Structure Click here
Q9SRV3 View 3D Structure Click here
Q9SSM9 View 3D Structure Click here
Q9STS6 View 3D Structure Click here
Q9SZE8 View 3D Structure Click here
Q9ZUP0 View 3D Structure Click here
Q9ZW96 View 3D Structure Click here