Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.

                           10
                   ....*....|....*.
gi 1704602914 1045 CYNCGATGHRAQDCKQ 1060
Cdd:pfam00098    3 CYNCGEPGHIARDCPK 18

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.

                           10
                   ....*....|....*.
gi 1704602914 1045 CYNCGATGHRAQDCKQ 1060
Cdd:pfam00098    3 CYNCGEPGHIARDCPK 18

The phosphoinositide binding Phox Homology domain of Five SH protein; The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Five SH (FISH), also called Tks5, is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. FISH contains an N-terminal PX domain and five Src homology 3 (SH3) domains. FISH binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. This subfamily also includes proteins with a different number of SH3 domains than FISH, such as Tks4, which contains four SH3 domains instead of five. The Tks4 adaptor protein is required for the formation of functional podosomes. It has overlapping, but not identical, functions as FISH. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1704602914  256 EVLWSDSSITSVTKSSSEVTEFISKLCQLYPEENLEK-----LIPCLAGPDAFyvERNHV---------DLDSGLRYLAS 321
Cdd:cd06888     24 NVTWSDGSSNVIYRRYSKFFDLQMQLLDKFPIEGGQKdpsqrIIPFLPGKILF--RRSHIrdvavkrlkPIDEYCKALVR 101

                           90
                   ....*....|....*...
gi 1704602914  322 LPSHVLKNDHVRRFLSTS 339
Cdd:cd06888    102 LPPHISQCDEVLRFFEAK 119

Sterile alpha motif; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 1704602914   438 ILDWLRKLRLHKYYPVFKQ--LSMEKFLSLT-EEDLNKFESLTMGAKKKLKTQLE 489
Cdd:smart00454    9 VADWLESIGLEQYADNFRKngIDGALLLLLTsEEDLKELGITKLGHRKKILKAIQ 63

SAM (Sterile alpha motif ); SAM (sterile alpha motif) domain of Smaug-like subfamily proteins is an RNA binding domain. SAM interacts with stem-loop structures in target mRNAs. Proteins of this subfamily are post-transcriptional regulators involved in mRNA silencing and deadenylation; they can be implicated in transcript stability regulation and vacuolar protein transport as well. SAM_Smaug-like domain-containing proteins are found in metazoa from yeast to human. In animals they are active during early embryogenesis.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1704602914  437 GILDWLRKLRLHKYYPVFKQLSMEKFLSLTEEDLNKFESLTMGAKKKLKTQLELEKE 493
Cdd:cd09489      1 GIPMWLKSLRLHKYSDAFKGTTWEELLYLTEETLEKKGVLTLGARRKLLKAFGIVKE 57

SAM domain of VTS1 RNA-binding proteins; SAM (sterile alpha motif) domain of VTS1 subfamily proteins is RNA binding domain located in the C-terminal region. SAM interacts with stem-loop structures of mRNA. Proteins of this subfamily participate in regulation of transcript stability and degradation, and also may be involved in vacuolar protein transport regulation. VTS1 protein of S.cerevisiae induces mRNA degradation via the major deadenylation-dependent mRNA decay pathway; VTS1 recruits CCR4/POP2/NOT deadenylase complex to target mRNA. The recruitment is the initial step resulting in poly(A) tail removal transcripts. Potentially SAM domain may be responsible not only for RNA binding but also for deadenylase binding.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1704602914  436 NGILDWLRKLRLHKYYPVFKQLSMEKFLSLTEEDLNKFESLTMGAKKKLKTQLELEKEKSERR 498
Cdd:cd09556      7 KDIPAWLRSLRLHKYTDNLKDLSWKELIELDDEDLEDKGVSALGARRKLLKAFEIVREYKERG 69

SAM domain of BICC1 (bicaudal) subfamily; SAM (sterile alpha motif) domain of BICC1 (bicaudal) subfamily is a protein-protein interaction domain. Proteins of this group have N-terminal K homology RNA-binding vigilin-like repeats and a C-terminal SAM domain. BICC1 is involved in the regulation of embryonic differentiation. It plays a role in the regulation of Dvl (Dishevelled) signaling, particularly in the correct cilia orientation and nodal flow generation. In Drosophila, disruption of BICC1 can disturb the normal migration direction of the anterior follicle cell of oocytes; the specific function of SAM is to recruit whole protein to the periphery of P-bodies. In mammals, mutations in this gene are associated with polycystic kidney disease and it was suggested that the BICC1 protein can indirectly interact with ANKS6 protein (ANKS6 is also associated with polycystic kidney disease) through some protein and RNA intermediates.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1704602914  442 LRKLRLHKYYPVFKQ--LSMEKFLSLTEEDLNKFESLTMGAKKKL 484
Cdd:cd09520     11 LAKLGLEKYIDLFAQqeIDLQTFLTLTDQDLKELGITAFGARRKM 55

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.

                           10
                   ....*....|....*.
gi 1704602914 1045 CYNCGATGHRAQDCKQ 1060
Cdd:pfam00098    3 CYNCGEPGHIARDCPK 18

The phosphoinositide binding Phox Homology domain of Five SH protein; The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Five SH (FISH), also called Tks5, is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. FISH contains an N-terminal PX domain and five Src homology 3 (SH3) domains. FISH binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. This subfamily also includes proteins with a different number of SH3 domains than FISH, such as Tks4, which contains four SH3 domains instead of five. The Tks4 adaptor protein is required for the formation of functional podosomes. It has overlapping, but not identical, functions as FISH. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1704602914  256 EVLWSDSSITSVTKSSSEVTEFISKLCQLYPEENLEK-----LIPCLAGPDAFyvERNHV---------DLDSGLRYLAS 321
Cdd:cd06888     24 NVTWSDGSSNVIYRRYSKFFDLQMQLLDKFPIEGGQKdpsqrIIPFLPGKILF--RRSHIrdvavkrlkPIDEYCKALVR 101

                           90
                   ....*....|....*...
gi 1704602914  322 LPSHVLKNDHVRRFLSTS 339
Cdd:cd06888    102 LPPHISQCDEVLRFFEAK 119

The phosphoinositide binding Phox Homology domain of the p47phox subunit of NADPH oxidase; The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. p47phox is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox), which plays a key role in the ability of phagocytes to defend against bacterial infections. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p47phox is required for activation of NADH oxidase and plays a role in translocation. It contains an N-terminal PX domain, two Src Homology 3 (SH3) domains, and a C-terminal domain that contains PxxP motifs for binding SH3 domains. The PX domain of p47phox is unique in that it contains two distinct basic pockets on the membrane-binding surface: one preferentially binds phosphatidylinositol-3,4-bisphosphate [PI(3,4)P2] and is analogous to the PI3P-binding pocket of p40phox, while the other binds anionic phospholipids such as phosphatidic acid or phosphatidylserine. Simultaneous binding in the two pockets results in increased membrane affinity. The PX domain of p47phox is also involved in protein-protein interaction.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1704602914  255 FEVLWSDSSITSVTKSSSEVTEFISKLCQLYPEEN-----LEKLIPCLAGPDAF----YVERNHVDLDSGLRYLASLPSH 325
Cdd:cd06887     23 FLVKWQDLSEKLVYRRFTEIYEFHKTLKEMFPIEAgdinkENRIIPHLPAPKWFdgqrAAENRQGTLTEYCSTLLSLPPK 102

                           90
                   ....*....|...
gi 1704602914  326 VLKNDHVRRFLST 338
Cdd:cd06887    103 ISRCPHVLDFFKV 115