Summary: Kinesin motor domain
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Kinesin Edit Wikipedia article
A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule filaments, and are powered by the hydrolysis of 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 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 microtubules' minus end.
Kinesins were discovered as microtubule (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 – a long, central alpha-helical coiled-coil domain – 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|
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 related structurally 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 domains.
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 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.
Direction of motion
Motor proteins travel in a specific direction along a microtubule. This is because the microtubule is polar and the heads only bind to the microtubule in one orientation, while ATP binding gives each step its direction through a process known as neck linker zippering.
Most kinesins walk towards the plus end of a microtubule which, in most cells, entails transporting cargo from the centre of the cell towards the periphery. This form of transport is known as anterograde transport/orthrograde transport. Kinesin-14 family proteins, such as Drosophila melanogaster NCD, budding yeast KAR3, and Arabidopsis thaliana ATK5, walk in the opposite direction, toward microtubule minus ends.
A different 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 centre, for example from the terminal boutons of a neuronal axon to the cell body (soma). This is known as retrograde transport.
Cin8, a member of the Kinesin-5 family, has the novel ability to switch directionality. It has been shown to be minus-end-directed (contrary to the rest of the known Kinesins) when bound to a single microtubule, but plus-end-directed when cross-linking antiparallel microtubules (pushing the minus ends further apart and pulling the plus ends towards each other). 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. 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.
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.
Theoretical modeling of kinesin
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, 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.
Kinesin and mitosis
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 – KIF1A, 1B – KIF1B = kinesin-3
- 2A – KIF2A, 2C – KIF2C = kinesin-13
- 3B – KIF3B, 3C – KIF3C = kinesin-2
- 4A – KIF4A, 4B – KIF4B = kinesin-4
- 5A – KIF5A, 5B – KIF5B, 5C – KIF5C = kinesin-1
- 6 – KIF6 = kinesin-9
- 7 – KIF7 = kinesin-4
- 9 – KIF9 = kinesin-9
- 11 – KIF11 = kinesin-5
- 12 – KIF12 = kinesin-12
- 13A – KIF13A, 13B – KIF13B = kinesin-3
- 14 – KIF14 = kinesin-3
- 15 – KIF15 = kinesin-12
- 16B – KIF16B = kinesin-3
- 17 – KIF17 = kinesin-2
- 18A – KIF18A, 18B – KIF18B = kinesin-8
- 19 – KIF19 = kinesin-8
- 20A – KIF20A, 20B – KIF20B = kinesin-6
- 21A – KIF21A, 21B – KIF21B = kinesin-4
- 22 – KIF22 = kinesin-10
- 23 – KIF23 = kinesin-6
- 24 – KIF24 = kinesin-13
- 25 – KIF25 = kinesin-14
- 26A – KIF26A, 26B – KIF26B = kinesin-11
- 27 – KIF27 = kinesin-4
- C1 – KIFC1, C2 – KIFC2, C3 – KIFC3 = kinesin-14
kinesin-1 light chains:
kinesin-2 associated protein:
- KAP-1, KAP3 or KIFAP3
- Axoplasmic transport
- Intraflagellar transport along cilia
- Kinesin 8
- Kinesin 13
- Molecular motors
- Transport by Multiple Kinesin
- Vale RD (February 2003). "The molecular motor toolbox for intracellular transport". Cell 112 (4): 467–80. doi:10.1016/S0092-8674(03)00111-9. PMID 12600311.
- Vale RD, Reese TS, Sheetz MP (August 1985). "Identification of a novel force-generating protein, kinesin, involved in microtubule-based motility". Cell 42 (1): 39–50. doi:10.1016/S0092-8674(85)80099-4. PMC 2851632. PMID 3926325.
- Cole DG, Chinn SW, Wedaman KP, Hall K, Vuong T, Scholey JM (November 1993). "Novel heterotrimeric kinesin-related protein purified from sea urchin eggs". Nature 366 (6452): 268–70. Bibcode:1993Natur.366..268C. doi:10.1038/366268a0. PMID 8232586.
- Rosenbaum JL, Witman GB (November 2002). "Intraflagellar transport". Nat. Rev. Mol. Cell Biol. 3 (11): 813–25. doi:10.1038/nrm952. PMID 12415299.
- Yang JT, Laymon RA, Goldstein LS (March 1989). "A three-domain structure of kinesin heavy chain revealed by DNA sequence and microtubule binding analyses". Cell 56 (5): 879–89. doi:10.1016/0092-8674(89)90692-2. PMID 2522352.
- Aizawa H, Sekine Y, Takemura R, Zhang Z, Nangaku M, Hirokawa N (December 1992). "Kinesin family in murine central nervous system". J. Cell Biol. 119 (5): 1287–96. doi:10.1083/jcb.119.5.1287. PMC 2289715. PMID 1447303.
- Enos AP, Morris NR (March 1990). "Mutation of a gene that encodes a kinesin-like protein blocks nuclear division in A. nidulans". Cell 60 (6): 1019–27. doi:10.1016/0092-8674(90)90350-N. PMID 2138511.
- Meluh PB, Rose MD (March 1990). "KAR3, a kinesin-related gene required for yeast nuclear fusion". Cell 60 (6): 1029–41. doi:10.1016/0092-8674(90)90351-E. PMID 2138512.
- Hirokawa N, Noda Y, Tanaka Y, Niwa S (October 2009). "Kinesin superfamily motor proteins and intracellular transport". Nat. Rev. Mol. Cell Biol. 10 (10): 682–96. doi:10.1038/nrm2774. PMID 19773780.
- 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". J. Cell Biol. 167 (1): 19–22. doi:10.1083/jcb.200408113. PMC 2041940. PMID 15479732.
- Hirokawa N, Pfister KK, Yorifuji H, Wagner MC, Brady ST, Bloom GS (March 1989). "Submolecular domains of bovine brain kinesin identified by electron microscopy and monoclonal antibody decoration". Cell 56 (5): 867–78. doi:10.1016/0092-8674(89)90691-0. PMID 2522351.
- PDB 1BG2; Kull FJ, Sablin EP, Lau R, Fletterick RJ, Vale RD (April 1996). "Crystal structure of the kinesin motor domain reveals a structural similarity to myosin". Nature 380 (6574): 550–5. Bibcode:1996Natur.380..550J. doi:10.1038/380550a0. PMC 2851642. PMID 8606779.
- Schnitzer MJ, Block SM (1997). "Kinesin hydrolyses one ATP per 8-nm step". Nature 388 (6640): 386–390. Bibcode:1997Natur.388..386S. doi:10.1038/41111. PMID 9237757.
- Vale RD, Milligan RA (April 2000). "The way things move: looking under the hood of molecular motor proteins". Science 288 (5463): 88–95. Bibcode:2000Sci...288...88V. doi:10.1126/science.288.5463.88. PMID 10753125.
- Mather WH, Fox RF (October 2006). "Kinesin's biased stepping mechanism: amplification of neck linker zippering". Biophys. J. 91 (7): 2416–26. Bibcode:2006BpJ....91.2416M. doi:10.1529/biophysj.106.087049. PMC 1562392. PMID 16844749.
- Gross SP, Vershinin M, Shubeita GT (June 2007). "Cargo transport: two motors are sometimes better than one". Current Biology : CB 17 (12): R478–86. doi:10.1016/j.cub.2007.04.025. PMID 17580082.
- Hancock WO (August 2008). "Intracellular transport: kinesins working together". Current Biology : CB 18 (16): R715–7. doi:10.1016/j.cub.2008.07.068. PMID 18727910.
- Kunwar A, Vershinin M, Xu J, Gross SP (August 2008). "Stepping, strain gating, and an unexpected force-velocity curve for multiple-motor-based transport". Current Biology : CB 18 (16): 1173–83. doi:10.1016/j.cub.2008.07.027. PMC 3385514. PMID 18701289.
- 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): 17284–9. 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): 778–84. Bibcode:1999Natur.402..778R. doi:10.1038/45483. PMID 10617199.
- 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". Mol. Biol. Cell 16 (4): 1584–92. doi:10.1091/mbc.E04-10-0935. PMC 1073643. PMID 15659646.
- Roostalu, J.; Hentrich, C.; Bieling, P.; Telley, I. A.; Schiebel, E.; Surrey, T. (2011). "Directional Switching of the Kinesin Cin8 Through Motor Coupling". Science 332 (6025): 94–99. doi:10.1126/science.1199945.
- Yildiz A, Tomishige M, Vale RD, Selvin PR (2004). "Kinesin Walks Hand-Over-Hand". Science 303 (5658): 676–8. Bibcode:2004Sci...303..676Y. doi:10.1126/science.1093753. PMID 14684828.
- Asbury CL (2005). "Kinesin: world’s tiniest biped". Current Opinion in Cell Biology 17 (1): 89–97. doi:10.1016/j.ceb.2004.12.002. PMID 15661524.
- Sindelar CV, Downing KH (February 2010). "An atomic-level mechanism for activation of the kinesin molecular motors". Proc Natl Acad Sci U S A 107 (9): 4111–6. Bibcode:2010PNAS..107.4111S. doi:10.1073/pnas.0911208107. PMC 2840164. PMID 20160108.
- Lay Summary (18 February 2010). "Life’s smallest motor, cargo carrier of the cells, moves like a seesaw". PhysOrg.com. Retrieved 31 May 2013.
- Atzberger PJ, Peskin CS (January 2006). "A Brownian Dynamics model of kinesin in three dimensions incorporating the force-extension profile of the coiled-coil cargo tether". Bull. Math. Biol. 68 (1): 131–60. doi:10.1007/s11538-005-9003-6. PMID 16794924.
- Peskin CS, Oster G (April 1995). "Coordinated hydrolysis explains the mechanical behavior of kinesin". Biophys. J. 68 (4 Suppl): 202S–210S; discussion 210S–211S. PMC 1281917. PMID 7787069.
- Mogilner A, Fisher AJ, Baskin RJ (July 2001). "Structural changes in the neck linker of kinesin explain the load dependence of the motor's mechanical cycle". J. Theor. Biol. 211 (2): 143–57. doi:10.1006/jtbi.2001.2336. PMID 11419956.
- Goshima G, Vale RD (August 2005). "Cell cycle-dependent dynamics and regulation of mitotic kinesins in Drosophila S2 cells". Mol. Biol. Cell 16 (8): 3896–907. doi:10.1091/mbc.E05-02-0118. PMC 1182325. PMID 15958489.
- 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". J. Cell Biol. 167 (1): 19–22. doi:10.1083/jcb.200408113. PMC 2041940. PMID 15479732.
- MBInfo - Kinesin transports cargo along microtubules
- Animated model of kinesin walking
- Ron Vale's seminar:"Cytoskeletal Motor Proteins"
- Animation of kinesin movement[dead link] ASCB image library
- Kinesin and Dynein Microtubule Movement
- The Inner Life of a Cell, 3D animation featuring a Kinesin transporting a vesicle
- The Kinesin Homepage[dead link]
- Kinesin at the US National Library of Medicine Medical Subject Headings (MeSH)
- EC 184.108.40.206
- EC 220.127.116.11
- 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
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.
- 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)|
|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:
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AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes .
The clan contains the following 198 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_4 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_2 Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arch_ATPase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 Bac_DnaA CbiA CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1253 DUF1611 DUF2075 DUF2478 DUF258 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GTP_EFTU GTP_EFTU_D2 GTP_EFTU_D4 Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK IIGP IPPT IPT IstB_IS21 KaiC KAP_NTPase Kinesin Kinesin-relat_1 Kinesin-related KTI12 LpxK MCM MEDS Mg_chelatase Mg_chelatase_2 MipZ Miro MMR_HSR1 MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SE 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 UPF0079 UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YhjQ 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family:
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- 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.
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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.
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 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:||84|
|Number in full:||9740|
|Average length of the domain:||290.90 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||34.34 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|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 3 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 149 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 seqence.
Loading structure mapping...