Table I

Rodent postsynaptic density proteins identified with high confidence by LC-MS/MS

PSD constituents were grouped into functional families based on published reports. Novel proteins, which could be assigned to groups on the basis of predicted domains consistent with known functions, are denoted by (§). The “Pep” column refers to the number of unique (nonredundant) peptides found per protein, which were considered in the calculation of E-values, because some peptides were sequenced by MS/MS multiple times. When a single peptide was used to identify a protein not previously confirmed to be localized in the PSD, additional information is included in Supplemental Table 2. Included in “Notes/domains (predicted)” are homologs that were also found and in bold are the predicted domains for novel proteins. In the “Protein name” column, proteins that had not been previously localized to the PSD are shown in bold. For simplicity, in cases where no identified peptide could differentiate between closely related proteins, we only report those with the greatest number of peptides found; if the number of peptides is equal, proteins are listed in italics. An asterisk denotes proteins that are likely contaminants, such as GFAP and histones. We have removed keratins, cytokeratins, trypsin, albumin, and fibrinogen, as these are common contaminants in high-sensitivity MS protein identification experiments.

AccessionProtein nameNotes/domainsa (predicted)PepE-value
    NP_787030Spectrin β2-β fodrinAlso β1, β3, β4, and α fodrin950.0E+00
    XP_127760Neurofilament triplet L proteinAlso triplet H and M523.5E−245
    NP_006079Tubulin, βAlso α and multiple isoforms of both366.4E−181
    NP_666212Internexin α291.3E−117
    CAA31455Actin-γAnd isoforms254.6E−99
    XP_192755 MAP 1B-microtubule-associated protein Also 1A, 2, 2c, 6, and τ296.4E−98
    AAH54830Actinin α 1Isoforms 1, 2, 3, 4191.1E−72
    NP_038538Band 4.1 (4.1N or 4.1R)Also 4.1B73.7E−35
    BAC32012Ankyrin 2 isoform 1Ankyrin 1, (2 isoform 1), and 3117.4E−29
    AAA37678GFAP (glial fibrillary acidic protein)*107.0E−26
    XP_194314 CBP90 (cortactin-binding protein) 66.7E−23
    NP_004921 Capping protein β Also α 1 and α 265.9E−20
    NP_031753Contactin 185.6E−19
    XP_194251 CLIP 115-cytoplasmic linker 2 31.4E−18
    NP_057920 Tropomodulin 2 neural 42.3E−15
    AAM73705 Actin-binding LIM pro.1 long-as mKIAA0059§ 4 LIM, VHP 32.2E−13
    AAF29504Adducin αIsoforms α, β, γ36.4E−13
    AAH43123 Ankyrin-like 71.8E−12
    XP_135174 CLASP2-CLIP-associating protein 54.1E−12
    NP_808346 Actin-binding LIM protein 2§ 4 LIM, VHP 31.8E−11
    AAC52639 Lasp-1 42.1E−11
    NP_062798 Actin-related protein 2/3 complex subunit 3 Subunits 2, 3, 4, and 541.9E−10
    NP_109654 WASP homolog-binding protein 41.4E−09
    NP_114083 Wave1/scar 32.7E−09
    NP_780693Coronin 2B-(CLIPIN-c) as RIKEN E130012P22Also 2A36.5E−09
    XP_192845Cofilin 132.4E−08
    NP_005727 ARP1-centractin α Also ARP2 and ARP327.1E−06
    BAC65651 ArgBP2-like, as mKIAA0777§ Sorb, 3 SH3 47.2E−06
    NP_038542 Band 4.9 (Dematin) 21.9E−04
    NP_031861 Dynactin 1 15.8E−04
    CAA42501 Peripherin 28.1E−04
    P28660 Nck-associated protein 1 24.4E−03
    NP_780547 Desmoplakin- as RIKEN cDNA 5730453H04 25.0E−03
    AAG09753Profilin II12.4E−02
    NP_033730 Microtubule-actin crosslinking factor 1 22.5E−01
    NP_031890Dlg-4 PSD-95/SAP 90405.1E−169
    NP_035937Dlg-2 chapsyn-110291.6E−107
    BAC58120Shank-2Also Shank 1 and 3191.7E−70
    AAM95461Homer 1Also Homer 3152.2E−65
    XP_145592 Shank-2-like§ 4 ANK, SH3, PDZ, SAM 118.6E−60
    BAC65780Densin-180, as mKIAA1365149.2E−41
    BAC32772 Dlg-novel§ Similar to PSD-93, 2 PDZ87.3E−40
    BAC65756Dlg-3 SAP 102, as mKIAA1232158.2E−37
    XP_148818SAPAP 1- gKAPAlso SAPAP 2, 3, and 497.0E−34
    AAN87264Dlg-1 SAP 9762.6E−17
    XP_196170 Cask-interacting protein 1-similar Internal repeat, SAM 55.1E−17
    XP_128476 Cask-interacting pro. 1 as RIKEN 3300002N10 6 ANK, SAM 31.1E−14
    AAF69144 Kalirin-7c 7d, 9a 45.5E−13
    NP_035828Lin 7 homolog b28.5E−05
    AAL82458 Ruk(l) 3 SH3 36.3E−04
Cell adhesion/polarity
    NP_033949Catenin α 2 -α(N)-cateninAlso β, α 1, o (NPRAP),p120253.9E−100
    NP_034085 Collapsin-dihydropyrimidinase-like 2,3 TOAD-64 Also 192.1E−40
    NP_031690Cadherin 2-(N-cadherin)94.5E−31
    Q8BHL5 ELMO-2 (CED-12 homolog A) 64.0E−18
    CAD65849 Neurofascin 56.9E−16
    Q9Z2Q6 Septin 5 (CDCREL-1) Also Septin 7 (CDC10), 8, 2, 957.4E−13
    P98203 Arm repeat-velo-cardio-facial syndrome 26.4E−06
    NP_703187 Reticulon 1 Also 329.3E−06
    NP_058062 Neurexin IV 31.2E−05
    XP_139743 Afadin, similar to l-Afadin§ 22.1E−03
    NP_766520 Neuroligin 3 Also neuroligin 232.6E−03
    XP_232196 Prickle-like-as similar to hypo pro. FLJ31937§ 3 LIM, NFX 12.4E−02
    NP_034418 Connexin 43* 62.8E−18
    NP_035824VDAC-1-voltage-dependent anion channelAlso VDAC 2 and 367.8E−18
    NP_036637 ATPase, Na +K + transporting, α 1, 2, 3 31.6E−13
    AAL02217 PGRL-receptor 4 IgG, TM 35.7E−09
    AAM11474Calcium channel, L-type β 1BAlso β3 and R-type α1E25.2E−08
    NP_032193GLUR δ44.4E−07
    NP_032933 Cyclophilin A Also B31.4E−06
    AAG29338GABA-B receptor25.3E−02
    AAC40082Syngap-cAlso A, B, and D311.2E−99
    XP_126291GIT1, GPCR kinase-interactor 1177.0E−59
    NP_598530 CYFIP2-p53 inducible protein 161.5E−48
    NP_035416 Rabphilin 3A 121.2E−47
    XP_228841 KIAA 0522-like§ IQ, SEC7, PH 181.1E−46
    XP_137397 Centaurin γ-3like-as hypo pro. XP_137397§ Small GTPase, PH, ArfGAP, 2 ANK 111.1E−45
    Q9EQZ6 Rap1- GEF(cAMP-GEFII) 121.6E−39
    NP_444434 Rab6-interacting protein 2 142.3E−32
    P59281 RhoGAP-like, as KIAA1688 2 WW, MyTH4, RhoGAP 92.7E−25
    XP_204243 Arf-gef-like, as similar to KIAA0763§ SEC7, PH 105.0E−24
    NP_033053 RAS-guanine nucleotide-releasing factor 2 74.1E−20
    AAH10487 ARF, ADP-ribosylation factor 1,2,3 25.4E−15
    NP_008839 Rac-1,3 52.5E−14
    XP_203999 Ras-gef-like-as RIKEN 5830453M24§ PDZ, RA, RAS-GEF 53.1E−14
    AAK71494 Ephexin-n-GEF 49.6E−13
    NP_439894 RIM 1b 72.6E−12
    XP_222780 RAS-GAP-like§ PH, C2, RasGAP 31.1E−09
    BAC27953 RIM 2 33.3E−09
    P18873G(O), α subunit 245.6E−09
    XP_138621 RAS-similar to Di-Ras2 25.9E−09
    XP_132396 RIM-binding protein 2, as similar to KIAA0318 21.5E−08
    NP_033027 RAB3A,(3b,3c) 49.5E−08
    NP_660252 Ras-like1: DIRAS family 21.1E−07
    NP_056078 Rabconnectin-3 26.4E−05
    BAB25858 RAB 10 21.2E−04
    Q9D8S3 ARF-GAP-3 16.5E−04
    NP_059497 Guanylate cyclase 1 21.9E−03
    BAC65728 Arf-gel-like, as mKIAA1110§ IQ, SEC7, PH 21.1E−02
    NP_076343 Zinc finger protein 289 ArfGAP 21.5E−02
    NP_631892 Centaurin, γ 2, 3 Small GTPase, PH, ArfGAP, 3 ANK 22.5E−02
    XP_149500Rap1, GAP123.1E−02
    NP_038653 Miller-Dieker lissencephaly protein 13.5E−02
    XP_145005 Arf-gap-like, as similar to KIAA1110§ IQ, SEC7, PH 25.4E−02
    AAG09271 GEF-LFC, as mKIAA0651 26.5E−02
    NP_803417 Rab11 interacting protein Rip11 27.1E−02
    NP_067259 Kirsten rat sarcoma oncogene 2 (k-ras) 19.3E−02
    NP_808366 Arf-gap6-like as hypo. protein D430018P08§ PH 11.2E−01
    NP_062512 Ras homolog (RhoG) 23.4E−01
    XP_109944Myosin, heavy chain BAlso HC9, IB, LC, LC3, myh11, reg-2A, 5a, 18a604.5E−278
    NP_038708Synapsin IAlso II and III291.3E−148
    T34101 SNIP-like-P140 as hypo pro., neural-specific 321.5E−131
    NP_032766N-ethylmaleimide sensitive fusion protein-NSF261.4E−112
    NP_037170 Syntaxin binding protein 1 188.7E−88
    AAA37318Dynamin 1Also Dynamin 2189.2E−76
    NP_035870 14–3-3 ζ Also β, ε, η, γ, τ, φ135.1E−61
    B30111AP-2, α 2 α-C adaptinAlso β1, α1, μ1, and δ147.9E−46
    NP_033332 Synaptotagmin 1, 2, 5, 9 95.8E−37
    BAC38575 Dynamin-like§ Dynamin GTPase, PH, GED 101.2E−35
    XP_181312 Clathrin heavy chain as RIKEN 3110065L21 119.2E−32
    NP_035558 SNAP 25 75.6E−25
    NP_598550 Zinedin 67.0E−22
    NP_074052 Munc13–1 Also 13–263.5E−21
    NP_036832 Syntaxin 1B2; Syntaxin 2 31.2E−15
    NP_009216 GABA(A) receptor-associated protein-like 2 42.3E−15
    NP_033523 Synaptobrevin I, II, III 31.3E−14
    Q920Q4 Vacuolar protein sorting 16 Also 28, 29 and 3529.0E−13
    XP_127213 Amphiphysin as hypo. protein MGC49429 51.9E−12
    NP_080832Dynein light chain 2, potent inhibitor of nNOSAlso cyto IC1, and light IC132.2E−10
    NP_032475 Kinesin-5C Also 2A and 5B32.8E−10
    NP_038961 VAMP-associated protein A 21.1E−09
    AAH09024 Vesicle trafficking protein-like 1-SEC22 28.7E−09
    NP_034759 Kinesin-associated protein 3 32.4E−08
    NP_031486 AP-3 δ Also β (adaptic 3B)23.8E−08
    NP_032724NIPSNAP1Also NIPSNAP 221.1E−06
    XP_192828Striatin, calmodulin-binding proteinAlso isoform 321.5E−04
    NP_033798 Amphiphysin-bridging integrator 1 13.1E−04
    Q00380 AP17 (clathrin coat associated pro. AP17) 18.4E−01
    NP_037052CaMKII-αAlso β, δ, and γ436.1E−159
    NP_035232Protein kinase C γAlso α, β, and ε222.5E−89
    NP_064362 Doublecortin-like kinase, as mKIAA0369 153.6E−61
    NP_034053Cyclic nucleotide phosphodiesterase 198.5E−38
    NP_758465Protein phosphatase 1 neurabin II; spinophilinAlso catalytic β, γ, and α, also Neurabin81.5E−32
    NP_003616Liprin-α2Also α3 and α476.0E−29
    NP_082483 Dual specificity phosphatase 3 MAGUK p55 subfamily member 3/DSPc51.5E−23
    NP_663596 Vesicle-associated calmodulin-binding pro. STKc 51.9E−17
    AAH52678Protein phosphatase 2 regulatory subunit A-α48.2E−16
    NP_031954 ELKL motif kinase-MARK2 59.4E−16
    NP_062760 TANK-binding kinase 1 31.5E−15
    NP_081815 Doublecortin like kinase (RIKEN 6330415M09)§ 2 DCX, STKc 41.0E−13
    NP_067490 Adenylate kinase 1 Isoforms 1 and 5, 651.1E−09
    AAD12587Protein phosphatase-2A cat, sub-α isoform31.3E−09
    BAB47440 KIAA1811§ STKc, ZNF-NFX 35.8E−09
    NP_031694CDK5-cyclin-dependent kinase 547.7E−09
    XP_282986 Similar to partner of PIX 1 PP2Cc/PP2C-Sig 21.7E−08
    NP_071637 Phosphatidylinositol 4-kinase A 26.1E−06
    O70172 P1-4-phosphate 5-kinase type II α Also β23.8E−05
    Q9JM52MAPK/ERK kinase kinase kinase 626.2E−05
    NP_062801 Glycogen synthase kinase 3 β 27.9E−05
    AAL37401 Phosphodiesterase 4B Also 4A and 4D/HDc35.2E−04
    NP_666237IP3-kinase A15.4E−04
    BAC65637 Diacylglycerol kinase, as mKIAA0718 2 EFh, 2 C1, DAGKc, DAGKa 29.5E−04
    AAF03784 Traf2 and NCK-interacting kinase 24.7E−02
    NP_570933 GRK-1 adrenergic receptor kinase, β 1 25.3E−02
    XP_126543 Protein kinase A α, β 12.6E−01
Protein turnover
    NP_077327HSP-70 proteinAlso HSPs-74, -90, -40, 27, BiP, dnaK-type381.5E−157
    NP_031932Elongation factor 1 -α2Also EF291.8E−25
    NP_061368 Tripartite motif protein 3§ RING, BBOX, BBC, Ig_FLMN, 6 NHL 72.7E−19
    NP_033015 Purine-rich element binding protein A; Pur α 3 PUR 56.2E−16
    NP_035800 Ubiquitin carboxy-terminal hydrolase L1 UCH 52.9E−15
    NP_775545 CYLD as RIKEN 2010013M14 (mKIAA0849) 2 CAP/Gly, UGH 55.0E−13
    NP_035420Ribosomal protein L6Also 40kD, L:17, 3, 11, 12, 27a, S:16, 19, 3, 831.9E−12
    Q8C7M3 Tripartite motif protein 9§ RING, 2 BBOX, BBC, FN3, SPRY 41.2E−10
    NP_034158 DEAD or DEAD/H-RNA helicase DEXDx, HELICc 51.9E−09
    NP_082083 Cullin 5 Cullin domain 56.4E−09
    NP_038728 Ubiquitin-specific protease 5 ZNF_UBP, UCH, 2 UBA 51.8E−07
    CAA76339 HnRNP A3-like Also A116.9E−05
    BAB85526 KIAA1940§ CC, FBOX 41.8E−04
    AAH09653 Puromycin-sensitive aminopeptidase PEPM 32.9E−04
    XP_216534 Splicing factor proline/glutamine CC 17.6E−01
    NP_032110Glyceraldehyde-3-phosphate dehydrogenase242.0E−89
    NP_766024Solute carrier family, Aralar, member 12Also multiple families and members194.5E−52
    P47857 Phosphofructokinase 1 Also B-type and platelet type145.7E−52
    NP_444427 Sideroflexin 3 Also Sideroflexin 5101.7E−38
    NP_034027Creatine kinase, ubiquitousAlso brain creatine kinase111.5E−31
    XP_124890 Phosphoglycerate mutase 1, 2 102.2E−26
    XP_147267 ATPase lysosomal α Also β68.5E−25
    AAB02288ATP synthase βAlso α, δ, ε, F1 (sub O, b, f)76.2E−24
    NP_031464 Aldolase 1 a, c 66.2E−21
    0709230A Transaminase, Glu 43.1E−14
    NP_035016 NADH 1 α subcomplex, 4 Also subcomplex 9, Fe-S protein 1 and 348.2E−13
    NP_079845Microsomal glutathioneS-transferase 324.5E−12
    XP_203476 ATP citrate lyase 21.5E−09
    NP_033441 Triosephosphate isomerase 21.7E−09
    NP_780386 3-hydroxybutyrate dehydrogenase 21.6E−07
    NP_032188 Glutathione peroxidase 4 25.7E−07
    XP_126624 Fatty acid synthase 41.3E−06
    NP_033414 Transketolase 32.6E−05
    NP_062732 Mitochondrial carrier homolog 2 Presenilin associated protein?21.6E−04
    AAO38689 Acyl-CoA synthetase 23.6E−04
    NP_036702 Glutamate dehydrogenase 1 39.0E−04
    AAA17989 Glutamine synthase 25.3E−02
    NP_080175 Ubiquinol-cytochrome C 14.2E−01
    AAH09119 ATP-binding cassette-member 3 3TM, AAA 25.5E−01
    XP_129322 RIKEN cDNA 1700063D12/mKIAA0417 No domains matched with significant hit181.6E−84
    NP_570932BAI1-associated protein 2-IRTK p53202.5E−72
    Q8CAQ8 Mitofillin 131.9E−56
    NP_848893 RIKEN cDNA A930041I02 No domains matched with significant hit147.1E−51
    BAC27761 AIDA-1a 2 SAM, PTB 102.0E−33
    XP_138708 Brain-specific protein p25 α, similar to No domains matched with significant hit63.4E−27
    I38202 Squamous cell carcinoma antigen Serpin 77.8E−24
    NP_035164 Peroxiredoxin 1 Also 2 and 5/AhpC/TSA82.9E−23
    XP_141380 G2-like TM, Extensin 72.5E−21
    NP_766325 Hypothetical protein D430041B17 No domains matched with significant hit73.8E−21
    AAH48407 Rpel1 protein [Mus musculus]-KIAA 1733 3 RPEL 55.4E−19
    AAH04704Myelin basic protein52.4E−18
    XP_127105 Expressed sequence AA408451 >7 TPR 53.2E−18
    NP_033386 Transcription factor A, mitochondrial 53.7E−16
    BAC41473 MKIAA1217 CC 67.6E−16
    NP_035762TNF receptor-associated factor 367.1E−15
    XP_123431 DAPIT TM 35.2E−14
    NP_775279 RIKEN cDNA 2310035C23 CC, LISH, 2 HEAT, CRF, HEAT-PBS 43.5E−13
    XP_284234B cell receptor-associated protein 3764.8E−13
    XP_135000 RIKEN cDNA 6430514L14-novel No domains matched with significant hit47.1E−13
    NP_031817 Cys and gly-rich protein 1 as EST AA408841 2 LIM 31.1E−12
    AAL03981 TGF-β resistance-associated protein 7 WD40 57.4E−12
    NP_700448 Enaptin 57.6E−12
    NP_598768 DNA segment, Chr 10, ERATO Doi 214 ZNF-CDGSH 32.4E−11
    XP_243272 Hypothetical protein XP_243272 CC 21.6E−10
    NP_033408Thymus cell antigen 1 IGV 33.4E−10
    AAH28550 Histone-H4* Also H2B53.6E−10
    AAH51956Cerebellin 1, as Unknown (IMAGE:5684648)21.7E−09
    XP_232577 Ganglioside-ind.-diff.-AP-1-similar GST-N, GST-C, 2TM 33.3E−09
    BAC65518 MKIAA0284 FHA 46.0E−09
    NP_036116 Neurochondrin 1, 2 No domains matched with significant hit27.1E−09
    NP_620093 CDP-diacylglycerol 3TM, CDPT 57.8E−09
    NP_032857 Prohibitin 48.2E−09
    XP_225171 Similar to hypo. protein MGC10772 TM 25.4E−08
    NP_766167 RIKEN cDNA 4931426N11 RAP-GAP, PDZ, CC 46.2E−08
    BAC65679 MKIAA0893 LISH, CTLH, CC, 7 WD40 37.2E−08
    NP_038563 C10 protein No domains matched with significant hit21.4E−07
    NP_064674 Leucine-rich repeat LGI family, member 1 LPRNT, LPR, 2 LRRTYP, LPRCT, 2 EPTP 32.0E−07
    NP_084452 RIKEN cDNA 2610039E05 No domains matched with significant hit44.9E−07
    NP_783573 BAI-3-brain-specific angiogenesis inhibitor 3§ TM, 7TM2, 4 TSP1, HORMR, GPS 25.7E−07
    NP_083251 Db83 protein UPF-0121 28.7E−07
    NP_653104 RIKEN cDNA 1110031B06 CC 31.4E−06
    NP_081740 RIKEN cDNA 5730469M10 TM 44.1E−06
    XP_284190 KIAA1549-like-novel No domains matched with significant hit36.1E−06
    XP_129331 Rab11-family IP 2, as RIKEN 4930470G04 No domains matched with significant hit21.4E−05
    AAH46236 RIKEN cDNA 3110035P10 CC, 7 WD40 31.8E−05
    NP_891846 Phosphoinositol 3-phosphate-binding pro.-3 PH, 2 CC 22.2E−05
    AAH49117 WD repeat domain 1 11 WD40 22.7E−05
    NP_034094 Crystallin, α B Crystaline, HSP20 35.9E−05
    NP_705816 Myocardin-related transcription factor B 27.5E−05
    AAB60388 ABR-breakpoint cluster region protein CC, RHOGEF, C2, RHOGAP, PH, SH3 22.7E−04
    NP_035923 Barrier to autointegration factor 1 BAF 23.4E−04
    NP_081636 RIKEN cDNA 2010107E04 TM 25.1E−04
    XP_222845 SPT3-associated factor 42-similar IG, IG-like, TM 21.4E−03
    XP_144572 KIAA1786 No domains matched with significant hit24.4E−03
    XP_242579 Hypothetical protein XP_242579 CC 18.3E−03
    NP_080468 Coiled-coil transcriptional coactivator C2H2 39.1E−03
    NP_112152 Open reading frame 31 2 TM 11.4E−02
    NP_080949 RIKEN cDNA 0610008C08 TM 22.0E−02
    NP_081706 RIKEN cDNA 2610205H19 UPF-0041 32.0E−02
    NP_083156 Leucine-rich repeat TM neuronal 1 LRRNT, 6 LRR, 3 LRRTYP, LRRCT, TM 22.3E−02
    XP_109913 RhoGAP-like-as exp-seq. AU040829 BAR, RHOGAP 12.6E−02
    BAC38313 Unnamed protein product CH 13.2E−02
    BAA90768 DNA polymerase* 24.4E−02
    NP_444385 Calmin >2 CH 25.5E−02
    NP_079627 RIKEN cDNA 0710001P09 DUF-737 16.2E−02
    XP_140391 WD repeat domain 7 >4 WD40, CPR 27.1E−02
    CAA53945 Lamin A, C2 11.1E−01
    NP_083907 RIKEN cDNA 1810013B01 No domains matched with significant hit11.6E−01
    XP_235056 AIDA-similar to SAM 32.1E−01
    XP_142154 Hypothetical protein BC013576-similar to DUF-634 22.6E−01
    AAB19182 Islet cell autoantigen p69 ICA69 12.9E−01
    XP_144573 KIAA1906-similar TM 23.3E−01
    XP_225646 RIKEN cDNA 1200007O21-like No domains matched with significant hit13.5E−01
    NP_848723 DNA segment, Chr 6, ERATO Doi 253 2 TM, TB2_DP1_HVA22 13.7E−01
    NP_659140 Ganglioside-ind.-diff.-AP-1-like 1 GSTN, GSTC 13.9E−01
    NP_778156BAI1-brain-specific angiogenesis inhibitor 114.8E−01
    BAC65845 MKIAA1850 No domains matched with significant hit27.1E−01
    NP_033247 Synuclein, α 18.9E−01
  • a Domains were determined using SMART: Letunic et al. (2002) Nucleic Acids Res 30, 242–244. Domain abbreviation key: 7TM2, 7 transmembrane receptor (Secretin family); AAA, ATPases associated with a variety of cellular activities; BAF, barrier to autointegration factor; BAR, domain found in amphiphysin and clathrin binding protein; BBC, B-Box C-terminal domain; BBOX, B-Box-type zinc finger; C1, protein kinase C conserved region 1; C2, calcium binding domain of PKC; C2H2, zinc finger, C2H2 type; CAP-Gly, cytoskeleton-associated protein domain; CC, coiled coil; CDPT, CDP-alcohol phosphatidyltransferase; CH, calponin homology; CPR, clathrin propeller repeat; CTLH, C-terminal to LISH motif; DAGKa, diacylglycerol kinase accessory domain (presumed); DAGKc, diacylglycerol kinase catalytic domain (presumed); DCX, domain found in doublecortin; DEXDx, DEAD-like helicases superfamily; DSPc, dual specificity phosphatase, catalytic domain; DUF-*, domain present in uncharacterised mammalian proteins, group*; EFh, EF-hand, calcium-binding motif; EPTP, domain found in LGI/epitempin; FBOX, motif in cyclin-F; FHA, forkhead-associated domain; FN3, fibronectin type 3 domain; GED, Dynamin GTPase effector domain; GPS, G-protein-coupled receptor proteolytic site domain; GST-C, glutathione S-transferase, C-terminal domain; GST-N, glutathione S-transferase, N-terminal domain; HDc, metal dependent phosphohydrolases with conserved “HD” motif; HEAT, related to armadillo/β-catenin-like repeats; HEAT-PBS, PBS lyase HEAT-like repeat; HELICc, helicase superfamily c-terminal domain; HORMR, domain present in hormone receptors; HSP20, heat shock protein 20 domain; ICA69, islet cell autoantigen ICA69 homologue; IG & IG-like, immunoglobulin domain; IG-FLMN, filamin-type immunoglobulin domains; IGV, immunoglobulin V-type; IQ, calmodulin binding; LIM, zinc-binding domain present in Lin-11, Isl-1, Mec-3; LISH, lissencephaly type-1-like homology; LRR, leucine-rich repeats, outliers; LRRCT, leucine rich repeat C-terminal; LRRNT, leucine rich repeat N-terminal; LRR-TYP, Leucine-rich repeats, typical subfamily; MyTH4, domain in myosins; NHL, similar to WD40; PDZ, domain present in PSD95, Dlg, ZO-1; PEPM, peptidase family M1; PH, plekstrin homology; PP2Cc, serine/threonine phosphatases, family 2C, catalytic domain; PP2C-Sig, Sigma factor PP2C-like phosphatases; PTB, phosphotyrosine binding; PUR, DNA/RNA-binding repeats; RA, Ras association; RAP-GAP, GAP domain in regulators small gtpases; RHOGAP, GTPase-activating protein for RHO; RHOGEF, guanine nucleotide exchange factor for RHO; RING, ring finger; SAM, sterile α motif; SEC7, arf GEF; SERPIN, serine protease inhibitor; SH3, SRC homology 3; Sorb, Sorbin homologous domain; SPRY, spla and the ryanodine receptor domain; STKc, serine/threonine protein kinases, catalytic domain; TB2_DP1_HVA22, TB2/DP1, HVA22 family; TM, transmembrane; TPR, tetratricopeptide repeats; TSP1, thrombospondin type 1 repeats; UBA, ubiquitin-associated domain; UCH, ubiquitin carboxyl-terminal hydrolase, family 1; UPF-*, uncharacterised protein family, group*; VHP, villin head piece; WD40, WD40 repeat domain; WW, two highly conserved tryptophans; ZNF_UBP, UCH-like zinc finger; ZNF-CDGSH, CDGSH-type zinc finger; ZNF-NFX, repressor of transcription.