Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
113  structures 4611  species 1  interaction 5133  sequences 17  architectures

# Summary: Thymidylate kinase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Thymidylate kinase". More...

# Thymidylate kinase

Thymidylate kinase
Identifiers
Symbol Thymidylate_kin
Pfam PF02223
InterPro IPR000062
PROSITE PDOC01034

Thymidylate kinase (EC 2.7.4.9; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium:

ATP + thymidine 5'-phosphate $\rightleftharpoons$ ADP + thymidine 5'-diphosphate

Thymidylate kinase is a ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages.[1]

## References

1. ^ Li C, Huang SH, Tang A, Drisco B, Zhang SQ, Seeger R, Jong A (1994). "Human dTMP kinase: gene expression and enzymatic activity coinciding with cell cycle progression and cell growth". DNA Cell Biol. 13 (5): 461–471. doi:10.1089/dna.1994.13.461. PMID 8024690.

This article incorporates text from the public domain Pfam and InterPro IPR000062

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.

# Thymidylate kinase

No Pfam abstract.

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

# Domain organisation

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

# 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(25)
Full
(5133)
Representative proteomes NCBI
(4369)
Meta
(2991)
RP15
(460)
RP35
(873)
RP55
(1164)
RP75
(1395)
Jalview View  View  View  View  View  View  View  View
HTML View    View  View  View  View
PP/heatmap 1   View  View  View  View
Pfam viewer View  View

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

Key: available, not generated, not available.

## Format an alignment

Seed
(25)
Full
(5133)
Representative proteomes NCBI
(4369)
Meta
(2991)
RP15
(460)
RP35
(873)
RP55
(1164)
RP75
(1395)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(25)
Full
(5133)
Representative proteomes NCBI
(4369)
Meta
(2991)
RP15
(460)
RP35
(873)
RP55
(1164)
RP75
(1395)

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

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

# 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.

# 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

 Seed source: Pfam-B_484 (release 5.2) Previous IDs: none Type: Domain Author: Bateman A Number in seed: 25 Number in full: 5133 Average length of the domain: 185.50 aa Average identity of full alignment: 31 % Average coverage of the sequence by the domain: 82.85 %

## HMM information

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 186
Family (HMM) version: 12

# Species distribution

### Sunburst controls

Show

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...

### Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...