dimerization/docking (D/D) domains found in the cAMP-dependent protein kinase regulatory subunit (PRKAR) and the DPY30/SDC1-like family; This hierarchy includes the dimerization/docking (D/D) domains of type I and type II cAMP-dependent protein kinase (PKA) regulatory (R) subunits, DPY30 from animals and its homologs, SDC1 from yeasts, and similar domains. PKA is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of R subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal D/D domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. Yeast SDC1 (suppressor of CDC25 protein 1) is the smallest subunit of COMPASS (COMplex of Proteins ASsociated with Set1) and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. DPY30/SDC1 contains a C-terminal helical bundle domain that directly interacts with Ash2L (in human)/Bre2 (in yeast) COMPASS through the DPY30-binding motif (DBM). The DPY30/SDC1 helical bundle domain, also called D/D domain, is formed of two alpha-helices that may be analogous to the D/D domain found in regulatory subunit of PKA.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1615743452   7 DPLLSKYVDDNYLYNVFEALVSGLSVMVPEAPRVWIVEKL 46
Cdd:cd22977     1 DPELRKYLRKHKLPDVYEALLTGLAVMCPEDPLRFIEEKL 40

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1615743452 711 NLPRLRELKIAKCYSVVDAGLEKFAQRAEHLEFIDLSFCNNLTDEGIKALSFCCRYLQVIKLASCRK 777
Cdd:cd09293    50 NCNKLKKLILPGSKLIDDEGLIALAQSCPNLQVLDLRACENITDSGIVALATNCPKLQTINLGRHRN 116

F-box domain superfamily; This short domain is commonly found at the N-terminus of various proteins, and typically co-occurs with one or more other conserved domains or motifs, such as leucine rich repeats, WD40 repeats, kelch, tub, spry, and others. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. One of the best researched roles of F-box proteins is their participation in SCF (Skp1-Cul1-F-box protein), a multi-protein complex that functions as a ubiquitin E3 ligase, where the role of the F-box protein is to recruit target substrates. Gene families containing the F-box are found greatly expanded in narrow taxonomic lineages, such as flowering plants and nematodes. In this hierarchical classification, many of the subfamilies are named according to their domain architectures.

                          10        20        30
                  ....*....|....*....|....*....|
gi 1615743452 246 PEFLRVKIFEYLNPFDVGRSAQVSHNWMSI 275
Cdd:cd22124     5 PRKAALKIFSYLDLRDLARCAQVCRSWKVI 34

dimerization/docking (D/D) domain found in F-box/LRR-repeat protein 13 (FBXL13) and similar proteins; FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6 (DRC6), is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It may also function as a substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1615743452   7 DPLLSKYVDDNYLYNVFEALVSGLSVMVPEAPRVWIVEKL 46
Cdd:cd22977     1 DPELRKYLRKHKLPDVYEALLTGLAVMCPEDPLRFIEEKL 40

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1615743452 711 NLPRLRELKIAKCYSVVDAGLEKFAQRAEHLEFIDLSFCNNLTDEGIKALSFCCRYLQVIKLASCRK 777
Cdd:cd09293    50 NCNKLKKLILPGSKLIDDEGLIALAQSCPNLQVLDLRACENITDSGIVALATNCPKLQTINLGRHRN 116

F-box domain found in F-box/LRR-repeat protein 13 (FBXL13) and similar proteins; FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6, is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It is also the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                          10        20        30
                  ....*....|....*....|....*....|
gi 1615743452 246 PEFLRVKIFEYLNPFDVGRSAQVSHNWMSI 275
Cdd:cd22124     5 PRKAALKIFSYLDLRDLARCAQVCRSWKVI 34

Leucine-rich repeat (LRR) protein [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1615743452 584 MESIRQLYMVNCSE--LTDsILRDLMVFPSLVVINLSRCtKLTDVGvkciAQSAYASKLRELYLAGCgNLTD--RSIicl 659
Cdd:COG4886   132 LANLTNLKELDLSNnqLTD-LPEPLGNLTNLKSLDLSNN-QLTDLP----EELGNLTNLKELDLSNN-QITDlpEPL--- 201

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1615743452 660 dKRLPQLAYFSVACCP--RISKPalmrLDRWKGLWQLNISGTDLDNrgLAAIGNLPRLRELKIAKCYsVVDAGLEKFAQR 737
Cdd:COG4886   202 -GNLTNLEELDLSGNQltDLPEP----LANLTNLETLDLSNNQLTD--LPELGNLTNLEELDLSNNQ-LTDLPPLANLTN 273

                         170       180
                  ....*....|....*....|...
gi 1615743452 738 aehLEFIDLSFcNNLTDEGIKAL 760
Cdd:COG4886   274 ---LKTLDLSN-NQLTDLKLKEL 292

dimerization/docking (D/D) domain found in F-box/LRR-repeat protein 13 (FBXL13) and similar proteins; FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6 (DRC6), is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It may also function as a substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1615743452   7 DPLLSKYVDDNYLYNVFEALVSGLSVMVPEAPRVWIVEKL 46
Cdd:cd22977     1 DPELRKYLRKHKLPDVYEALLTGLAVMCPEDPLRFIEEKL 40

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1615743452 711 NLPRLRELKIAKCYSVVDAGLEKFAQRAEHLEFIDLSFCNNLTDEGIKALSFCCRYLQVIKLASCRK 777
Cdd:cd09293    50 NCNKLKKLILPGSKLIDDEGLIALAQSCPNLQVLDLRACENITDSGIVALATNCPKLQTINLGRHRN 116

Antagonist of mitotic exit network protein 1; Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1615743452 310 LRYINLSGCDLVTQAGFRFLG-TCVHLQDVNLSCCNQLTDEAVMHLIWECRDIVKLDLSQTP----VTDSAVRYLSTASN 384
Cdd:cd09293    54 LKKLILPGSKLIDDEGLIALAqSCPNLQVLDLRACENITDSGIVALATNCPKLQTINLGRHRnghlITDVSLSALGKNCT 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1615743452 385 VLEHLILANCvKVSSACRVYLKETAGfRTLIYLDLSGCIQLESDALMEIFSSL--PNVRHWILNNLPQI---SSEAL-KI 458
Cdd:cd09293   134 FLQTVGFAGC-DVTDKGVWELASGCS-KSLERLSLNNCRNLTDQSIPAILASNyfPNLSVLEFRGCPLItdfSRIILfKL 211

                         170
                  ....*....|..
gi 1615743452 459 LGSCCPIIETIS 470
Cdd:cd09293   212 WQPRLNKPILVE 223

F-box domain found in F-box/LRR-repeat protein 13 (FBXL13) and similar proteins; FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6, is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It is also the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                          10        20        30
                  ....*....|....*....|....*....|
gi 1615743452 246 PEFLRVKIFEYLNPFDVGRSAQVSHNWMSI 275
Cdd:cd22124     5 PRKAALKIFSYLDLRDLARCAQVCRSWKVI 34

F-box domain found in F-box/WD repeat-containing protein 8 (FBXW8) and similar proteins; FBXW8, also called F-box and WD-40 domain-containing protein 8, or F-box only protein 29 (FBXO29), is the substrate-recognition component of a Cul7-RING ubiquitin-protein ligase complex, which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as GORASP1, IRS1, MAP4K1/HPK1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1615743452 246 PEFLRVKIFEYLNPFDVGRSAQVSHNWMSIAE 277
Cdd:cd22134     8 PRELALKIFQYLSVTDLCRCAQVSKSWKSLAE 39

Sfi1 spindle body protein; This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organizing centres.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1615743452 121 RAWKHLIRIKAARRIQKQSMI--LKANKFrnirALRCAFEAWSNWASNISKRRAVAVsrirQVHESNCIKLCIQKWRkaa 198
Cdd:pfam08457  51 AARRHILRKKYFNAWREITAVneLKAQRF----ALKRPLGAWRRRTLQIRVREEVAV----QVYQENLLKRSFWKWF--- 119

                  ....*....
gi 1615743452 199 kdaRELKER 207
Cdd:pfam08457 120 ---WEFCER 125

F-box domain found in epithelial cell-transforming sequence 2 oncogene-like (ECT2L) and similar proteins; ECT2L, also called lung-specific F-box and DH domain-containing protein, or putative guanine nucleotide exchange factor LFDH, may act as a guanine nucleotide exchange factor (GEF). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1615743452 246 PEFLRVKIFEYLNPFDVGRSAQVSHNWMSIAER 278
Cdd:cd22173     7 PRFLSLYIFSFLDPRSLCRAAQVSWHWKFLAEQ 39

Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1615743452 638 SKLRELYLAGCGnltdrsiicLDKRLPQLayfsVACCPRISKPALMRLDrwkgLWQLNISGTDLDNRGLAAIGNlPRLRE 717
Cdd:cd00116   108 SSLQELKLNNNG---------LGDRGLRL----LAKGLKDLPPALEKLV----LGRNRLEGASCEALAKALRAN-RDLKE 169

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1615743452 718 LKIAKcYSVVDAGLEKFAQ---RAEHLEFIDLSfCNNLTDEGIKALSFC---CRYLQVIKLASC 775
Cdd:cd00116   170 LNLAN-NGIGDAGIRALAEglkANCNLEVLDLN-NNGLTDEGASALAETlasLKSLEVLNLGDN 231