Summary: Kinesin motor domain
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Kinesin Edit Wikipedia article
Kinesins move along microtubule (MT) filaments, and are powered by the hydrolysis of adenosine triphosphate (ATP) (thus kinesins are ATPases). The active movement of kinesins supports several cellular functions including mitosis, meiosis and transport of cellular cargo, such as in axonal transport. Most kinesins walk towards the plus end of a microtubule, which, in most cells, entails transporting cargo such as protein and membrane components from the centre of the cell towards the periphery. This form of transport is known as anterograde transport. In contrast, dyneins are motor proteins that move toward the minus end of a microtubule in retrograde transport.
- 1 Discovery of Kinesins
- 2 Structure
- 3 Cargo transport
- 4 Direction of motion
- 5 Proposed mechanisms of movement
- 6 Theoretical modeling
- 7 Mitosis
- 8 Kinesin superfamily members
- 9 See also
- 10 References
- 11 Further reading
- 12 External links
Discovery of Kinesins
Kinesins were discovered as MT-based anterograde intracellular transport motors. The founding member of this superfamily, kinesin-1, was isolated as a heterotetrameric fast axonal organelle transport motor consisting of 2 identical motor subunits (KHC) and 2 "light chains" (KLC) via microtubule affinity purification from neuronal cell extracts. Subsequently, a different, heterotrimeric plus-end-directed MT-based motor named kinesin-2, consisting of 2 distinct KHC-related motor subunits and an accessory "KAP" subunit, was purified from echinoderm egg/embryo extracts and is best known for its role in transporting protein complexes (IFT particles) along axonemes during cilium biogenesis. Molecular genetic and genomic approaches have led to the recognition that the kinesins form a diverse superfamily of motors that are responsible for multiple intracellular motility events in eukaryotic cells. For example, the genomes of mammals encode more than 40 kinesin proteins, organized into at least 14 families named kinesin-1 through kinesin-14.
Members of the kinesin superfamily vary in shape but the prototypical kinesin-1 is a heterotetramer whose motor subunits (heavy chains or KHCs) form a protein dimer (molecule pair) that binds two light chains (KLCs).
The heavy chain of kinesin-1 comprises a globular head (the motor domain) at the amino terminal end connected via a short, flexible neck linker to the stalk â€“ a long, central alpha-helical coiled coil domain â€“ that ends in a carboxy terminal tail domain which associates with the light-chains. The stalks of two KHCs intertwine to form a coiled coil that directs dimerization of the two KHCs. In most cases transported cargo binds to the kinesin light chains, at the TPR motif sequence of the KLC, but in some cases cargo binds to the C-terminal domains of the heavy chains.
Kinesin motor domain
|Kinesin motor domain|
|Symbol||Kinesin motor domain|
|SCOPe||1bg2 / SUPFAM|
The head is the signature of kinesin and its amino acid sequence is well conserved among various kinesins. Each head has two separate binding sites: one for the microtubule and the other for ATP. ATP binding and hydrolysis as well as ADP release change the conformation of the microtubule-binding domains and the orientation of the neck linker with respect to the head; this results in the motion of the kinesin. Several structural elements in the Head, including a central beta-sheet domain and the Switch I and II domains, have been implicated as mediating the interactions between the two binding sites and the neck domain. Kinesins are structurally related to G proteins, which hydrolyze GTP instead of ATP. Several structural elements are shared between the two families, notably the Switch I and Switch II domain.
Basic kinesin regulation
Kinesins tend to have low basal enzymatic activity which becomes significant when microtubule-activated. In addition, many members of the kinesin superfamily can be self-inhibited by the binding of tail domain to the motor domain. Such self-inhibition can then be relieved via additional regulation such as cargo binding.
In the cell, small molecules, such as gases and glucose, diffuse to where they are needed. Large molecules synthesised in the cell body, intracellular components such as vesicles and organelles such as mitochondria are too large (and the cytosol too crowded) to be able to diffuse to their destinations. Motor proteins fulfill the role of transporting large cargo about the cell to their required destinations. Kinesins are motor proteins that transport such cargo by walking unidirectionally along microtubule tracks hydrolysing one molecule of adenosine triphosphate (ATP) at each step. It was thought that ATP hydrolysis powered each step, the energy released propelling the head forwards to the next binding site. However, it has been proposed that the head diffuses forward and the force of binding to the microtubule is what pulls the cargo along. In addition viruses, HIV for example, exploit kinesins to allow virus particle shuttling after assembly.
Direction of motion
Motor proteins travel in a specific direction along a microtubule. Microtubules are polar; meaning, the heads only binds to the microtubule in one orientation, while ATP binding gives each step its direction through a process known as neck linker zippering.
It has been previously known that kinesin move cargo towards the plus (+) end of a microtubule, also known as anterograde transport/orthograde transport. However, it has been recently discovered that in budding yeast cells kinesin Cin8 (a member of the Kinesin-5 family) can move toward the minus end as well, or retrograde transport. This means, kinesin has the novel ability to switch directionality. Kinesin, so far, has only been shown to move toward the minus end when in a group, with motors sliding in the antiparallel direction in an attempt to separate microtubules. This dual directionality has been observed in identical conditions where free Cin8 molecules move towards the minus end, but cross-linking Cin8 move toward the plus ends of each cross-linked microtubule. One specific study tested the speed at which Cin8 motors moved, their results yielded a range of about 25-55 nm/s, in the direction of the spindle poles. On an individual basis it has been found that through the use of ionic conditions Cin8 motors can become as fast as 380 nm/s, a notable jump. This tells us that Cin 8 can easily change directions on a microtubule, and in turn led to the plus end movement of kinesin on a microtubule. It is suggested that this unique ability is a result of coupling with other Cin8 motors and helps to fulfill the role of dynein in budding yeast. This discovery in kinesin-14 family proteins (such as Drosophila melanogaster NCD, budding yeast KAR3, and Arabidopsis thaliana ATK5) allows kinesin to walk in the opposite direction, toward microtubule minus end. This is not typical of kinesin, rather, an exception to the normal direction of movement.
Another type of motor protein, known as dyneins, move towards the minus end of the microtubule. Thus, they transport cargo from the periphery of the cell towards the center. An example of this would be transport occurring from the terminal boutons of a neuronal axon to the cell body (soma). This is known as retrograde transport.
Proposed mechanisms of movement
Kinesin accomplishes transport by "walking" along a microtubule. Two mechanisms have been proposed to account for this movement.
- In the "hand-over-hand" mechanism, the kinesin heads step past one another, alternating the lead position.
- In the "inchworm" mechanism, one kinesin head always leads, moving forward a step before the trailing head catches up.
ATP binding and hydrolysis cause kinesin to travel via a "seesaw mechanism" about a pivot point. This seesaw mechanism accounts for observations that the binding of the ATP to the no-nucleotide, microtubule-bound state results in a tilting of the kinesin motor domain relative to the microtubule. Critically, prior to this tilting the neck linker is unable to adopt its motor-head docked, forward-facing conformation. The ATP-induced tilting provides the opportunity for the neck linker to dock in this forward-facing conformation. This model is based on CRYO-EM models of the microtubule-bound kinesin structure which represent the beginning and end states of the process, but cannot resolve the precise details of the transition between the structures.
A number of theoretical models of the molecular motor protein kinesin have been proposed. Many challenges are encountered in theoretical investigations given the remaining uncertainties about the roles of protein structures, the precise way energy from ATP is transformed into mechanical work, and the roles played by thermal fluctuations. This is a rather active area of research. There is a need especially for approaches which better make a link with the molecular architecture of the protein and data obtained from experimental investigations.
The single-molecule dynamics are already well described but it seems that these nano scale machines typically work in large teams. Recent experimental research has shown that kinesins, while moving along microtubules, interact with each other, the interactions being short range and weak attractive (1.6Â±0.5 KBT). One model that has been developed takes into account these particle interactions, where the dynamic rates change accordingly with the energy of interaction. If the energy is positive the rate of creating bonds (q) will be higher while the rate of breaking bonds (r) will be lower. One can understand that the rates of entrance and exit in the microtubule will be changed as well by the energy (See figure 1 in reference 30). If the second site is occupied the rate of entrance will be Î±*q and if the last but one site is occupied the rate of exit will be Î²*r. This theoretical approach agrees with the results of Monte Carlo simulations for this model, especially for the limiting case of very large negative energy. The normal totally asymmetric simple exclusion process for (or TASEP) results can be recovered from this model making the energy equal to zero.
In recent years, it has been found that microtubule-based molecular motors (including a number of kinesins) have a role in mitosis (cell division). Kinesins are important for proper spindle length and are involved in sliding microtubules apart within the spindle during prometaphase and metaphase, as well as depolymerizing microtubule minus ends at centrosomes during anaphase. Specifically, Kinesin-5 family proteins act within the spindle to slide microtubules apart, while the Kinesin 13 family act to depolymerize microtubules.
Kinesin superfamily members
Human kinesin superfamily members include the following proteins, which in the standardized nomenclature developed by the community of kinesin researchers, are organized into 14 families named kinesin-1 through kinesin-14:
- 1A â€“ KIF1A, 1B â€“ KIF1B, 1C â€“ KIF1C = kinesin-3
- 2A â€“ KIF2A, 2C â€“ KIF2C = kinesin-13
- 3B â€“ KIF3B or 3C â€“ KIF3C ï¼Œ3A - KIF3A = kinesin-2
- 4A â€“ KIF4A, 4B â€“ KIF4B = kinesin-4
- 5A â€“ KIF5A, 5B â€“ KIF5B, 5C â€“ KIF5C = kinesin-1
- 6 â€“ KIF6 = kinesin-9
- 7 â€“ KIF7 = kinesin-4
- 9 â€“ KIF9 = kinesin-9
- 11 â€“ KIF11 = kinesin-5
- 12 â€“ KIF12 = kinesin-12
- 13A â€“ KIF13A, 13B â€“ KIF13B = kinesin-3
- 14 â€“ KIF14 = kinesin-3
- 15 â€“ KIF15 = kinesin-12
- 16B â€“ KIF16B = kinesin-3
- 17 â€“ KIF17 = kinesin-2
- 18A â€“ KIF18A, 18B â€“ KIF18B = kinesin-8
- 19 â€“ KIF19 = kinesin-8
- 20A â€“ KIF20A, 20B â€“ KIF20B = kinesin-6
- 21A â€“ KIF21A, 21B â€“ KIF21B = kinesin-4
- 22 â€“ KIF22 = kinesin-10
- 23 â€“ KIF23 = kinesin-6
- 24 â€“ KIF24 = kinesin-13
- 25 â€“ KIF25 = kinesin-14
- 26A â€“ KIF26A, 26B â€“ KIF26B = kinesin-11
- 27 â€“ KIF27 = kinesin-4
- C1 â€“ KIFC1, C2 â€“ KIFC2, C3 â€“ KIFC3 = kinesin-14
kinesin-1 light chains:
kinesin-2 associated protein:
- KIFAP3 (also known as KAP-1, KAP3)
- Axonal transport
- Intraflagellar transport along cilia
- Kinesin 8
- Kinesin 13
- Molecular motor
- Transport by multiple-motor proteins
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- Gaudin R, de Alencar BC, Jouve M, BÃ¨rre S, Le Bouder E, Schindler M, Varthaman A, Gobert FX, Benaroch P (October 2012). "Critical role for the kinesin KIF3A in the HIV life cycle in primary human macrophages". The Journal of Cell Biology. 199 (3): 467â€“79. doi:10.1083/jcb.201201144. PMC 3483138. PMID 23091068.
- Gross SP, Vershinin M, Shubeita GT (June 2007). "Cargo transport: two motors are sometimes better than one". Current Biology. 17 (12): R478â€“86. doi:10.1016/j.cub.2007.04.025. PMID 17580082.
- Hancock WO (August 2008). "Intracellular transport: kinesins working together". Current Biology. 18 (16): R715â€“7. doi:10.1016/j.cub.2008.07.068. PMID 18727910.
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- Klumpp S, Lipowsky R (November 2005). "Cooperative cargo transport by several molecular motors". Proceedings of the National Academy of Sciences of the United States of America. 102 (48): 17284â€“9. arXiv:q-bio/0512011. Bibcode:2005PNAS..10217284K. doi:10.1073/pnas.0507363102. PMC 1283533. PMID 16287974.
- Rice S, Lin AW, Safer D, Hart CL, Naber N, Carragher BO, Cain SM, Pechatnikova E, Wilson-Kubalek EM, Whittaker M, Pate E, Cooke R, Taylor EW, Milligan RA, Vale RD (December 1999). "A structural change in the kinesin motor protein that drives motility". Nature. 402 (6763): 778â€“84. Bibcode:1999Natur.402..778R. doi:10.1038/45483. PMID 10617199.
- Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J (2000). "Kinesin, Dynein, and Intracellular Transport". Cite journal requires
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- Gerson-Gurwitz A, Thiede C, Movshovich N, Fridman V, Podolskaya M, Danieli T, LakÃ¤mper S, Klopfenstein DR, Schmidt CF, Gheber L (November 2011). "Directionality of individual kinesin-5 Cin8 motors is modulated by loop 8, ionic strength and microtubule geometry". The EMBO Journal. 30 (24): 4942â€“54. doi:10.1038/emboj.2011.403. PMC 3243633. PMID 22101328.
- Ambrose JC, Li W, Marcus A, Ma H, Cyr R (April 2005). "A minus-end-directed kinesin with plus-end tracking protein activity is involved in spindle morphogenesis". Molecular Biology of the Cell. 16 (4): 1584â€“92. doi:10.1091/mbc.e04-10-0935. PMC 1073643. PMID 15659646.
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- Lawrence CJ, Dawe RK, Christie KR, Cleveland DW, Dawson SC, Endow SA, Goldstein LS, Goodson HV, Hirokawa N, Howard J, Malmberg RL, McIntosh JR, Miki H, Mitchison TJ, Okada Y, Reddy AS, Saxton WM, Schliwa M, Scholey JM, Vale RD, Walczak CE, Wordeman L (October 2004). "A standardized kinesin nomenclature". The Journal of Cell Biology. 167 (1): 19â€“22. doi:10.1083/jcb.200408113. PMC 2041940. PMID 15479732.
- MBInfo - Kinesin transports cargo along microtubules
- Animated model of kinesin walking
- Ron Vale's Seminar: "Molecular Motor Proteins"
- Animation of kinesin movement ASCB image library
- Murphy, V.F. (2004-05-12). "Microtubule Based Movement". tissue.medicalengineer.co.uk. Archived from the original on 2007-07-22. Retrieved 2015-12-10.
- The Inner Life of a Cell, 3D animation featuring a Kinesin transporting a vesicle
- The Kinesin Homepage
- Kinesin at the US National Library of Medicine Medical Subject Headings (MeSH)
- EC 22.214.171.124
- EC 126.96.36.199
- 3D electron microscopy structures of kinesin from the EM Data Bank(EMDB)
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.
Kinesin motor domain Provide feedback
No Pfam abstract.
Kozielski F, Sack S, Marx A, Thormahlen M, Schonbrunn E, Biou V, Thompson A, Mandelkow EM, Mandelkow E; , Cell 1997;91:985-994.: The crystal structure of dimeric kinesin and implications for microtubule-dependent motility. PUBMED:9428521 EPMC:9428521
Internal database links
|SCOOP:||AAA AAA_16 ATPase_2 Bac_DnaA Bac_DnaA_C IstB_IS21 Microtub_bd ResIII|
|Similarity to PfamA using HHSearch:||Microtub_bd|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001752
Kinesin [PUBMED:8542443, PUBMED:2142876, PUBMED:14732151] is a microtubule-associated force-producing protein that may play a role in organelle transport. The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds.
The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles.
The kinesin motor domain comprises five motifs, namely N1 (P-loop), N2 (Switch I), N3 (Switch II), N4 and L2 (KVD finger) [PUBMED:20587735]. It has a mixed eight stranded beta-sheet core with flanking solvent exposed alpha-helices and a small three-stranded antiparallel beta-sheet in the N-terminal region [PUBMED:15236970].
- Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end.
- Homo sapiens CENP-E [PUBMED:1832505]. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation.
- H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end.
- Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis.
- S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles.
- Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division.
- A. nidulans klpA.
- Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation.
- C. elegans osm-3.
- Xenopus laevis Eg5, which may be involved in mitosis.
- Arabidopsis thaliana KatA, KatB and katC.
- Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella.
- C. elegans hypothetical protein T09A5.2.
The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section.
The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||ATP binding (GO:0005524)|
|microtubule motor activity (GO:0003777)|
|microtubule binding (GO:0008017)|
|Biological process||microtubule-based movement (GO:0007018)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. 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 Show link 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.
Loading domain graphics...
AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes .
The clan contains the following 231 members:6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE Zeta_toxin Zot
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Author:||Bateman A , Finn RD|
|Number in seed:||71|
|Number in full:||39068|
|Average length of the domain:||299.50 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||31.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||24|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number 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. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- 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
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 6 interactions for this family. 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 the 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 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 Kinesin domain has been found. There are 308 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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