Unkempt Zinc finger domain 1 (Znf1); This is CCCH zinc finger 1 domain found in Unkempt N-terminal region. Unkempt is an evolutionary conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. It carries six CCCH zinc fingers (ZnFs) forming two compact clusters, ZnF1-3 and ZnF4-6, that recognize distinct trinucleotide RNA substrates. These clusters, recognize an unexpectedly short stretch of RNA sequence-only three consecutive ribonucleotides-with a varying degree of specificity. ZnF1-3 binds to the UUA motif of RNA substrates.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 169403709   25 YRYLKEFRTEQCPLFSQHKCAQHRPFTCFHWHFLNQ 60
Cdd:pfam18384   1 YHYLKNFRVRQCPRFLQHHCPAHKPMTCFDWHFDNQ 36

Zinc finger C-x8-C-x5-C-x3-H type (and similar);

                          10        20
                  ....*....|....*....|..
gi 169403709  288 CNDMRQTGYCPRGPFCAFAHVE 309
Cdd:pfam00642   6 CRFFLRTGYCKYGDRCKFAHGQ 27

Unkempt Zinc finger domain 1 (Znf1); This is CCCH zinc finger 1 domain found in Unkempt N-terminal region. Unkempt is an evolutionary conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. It carries six CCCH zinc fingers (ZnFs) forming two compact clusters, ZnF1-3 and ZnF4-6, that recognize distinct trinucleotide RNA substrates. These clusters, recognize an unexpectedly short stretch of RNA sequence-only three consecutive ribonucleotides-with a varying degree of specificity. ZnF1-3 binds to the UUA motif of RNA substrates.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 169403709   25 YRYLKEFRTEQCPLFSQHKCAQHRPFTCFHWHFLNQ 60
Cdd:pfam18384   1 YHYLKNFRVRQCPRFLQHHCPAHKPMTCFDWHFDNQ 36

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 169403709  566 ELARVRRQLDEAKRKIRQWEESWQQVKQVCDAWQREAQEAKERARVADS---DRQLALQKKEEVEAQVIFQLRAKQ 638
Cdd:COG4913   700 ELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLELRallEERFAAALGDAVERELRENLEERI 775

type I restriction enzyme EcoKI subunit R; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169403709  532 GSIWDFVSGRFSPSPSPilsagppsSSSASPNGAELARVRRQLDEAKRKIRQWEESWQQVKQVCDAWQREAQEAKERARV 611
Cdd:PRK11448  124 GKDWDFKPGPFVPPEDP--------ENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQE 195

                          90       100
                  ....*....|....*....|....
gi 169403709  612 ADSDRQLALQKKEEVEAQVIFQLR 635
Cdd:PRK11448  196 LEAQLEQLQEKAAETSQERKQKRK 219

Unkempt Zinc finger domain 1 (Znf1); This is CCCH zinc finger 1 domain found in Unkempt N-terminal region. Unkempt is an evolutionary conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. It carries six CCCH zinc fingers (ZnFs) forming two compact clusters, ZnF1-3 and ZnF4-6, that recognize distinct trinucleotide RNA substrates. These clusters, recognize an unexpectedly short stretch of RNA sequence-only three consecutive ribonucleotides-with a varying degree of specificity. ZnF1-3 binds to the UUA motif of RNA substrates.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 169403709   25 YRYLKEFRTEQCPLFSQHKCAQHRPFTCFHWHFLNQ 60
Cdd:pfam18384   1 YHYLKNFRVRQCPRFLQHHCPAHKPMTCFDWHFDNQ 36

Zinc finger, C3HC4 type (RING finger);

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 169403709  637 KQCVACRERAHGAVLRPCQHHILCEPCA----ATAPECPYCK 674
Cdd:pfam13920   3 LLCVICLDRPRNVVLLPCGHLCLCEECAerllRKKKKCPICR 44

RING finger, HC subclass, found in RING finger protein unkempt (UNK) and similar proteins; UNK, also known as zinc finger CCCH domain-containing protein 5, is a metazoan-specific zinc finger protein enriched in embryonic brains. It may play a broad regulatory role during the formation of the central nervous system (CNS). It is a sequence-specific RNA-binding protein required for early neuronal morphology. UNK is a neurogenic component of the mTOR pathway, and functions as a negative regulator of the timing of photoreceptor differentiation. It also specifically binds to Brg/Brm-associated factor BAF60b and promotes its ubiquitination in a Rac1-dependent manner. UNK contains six tandem CCCH-type zinc fingers at the N-terminus, and a C3HC4-type RING-HC finger at its C-terminus.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 169403709 639 CVACRERahGAVLRPCQHHILCEPCaATAPECPYC 673
Cdd:cd16771    5 CLKCQEL--KRVTLPCQHALLCETC-ATSEECPIC 36

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 169403709  566 ELARVRRQLDEAKRKIRQWEESWQqvkqvcDAWQrEAQEAKERARvadsDRQLALQKKEEV-------EAQVIFQLRAKQ 638
Cdd:pfam13868 185 EIARLRAQQEKAQDEKAERDELRA------KLYQ-EEQERKERQK----EREEAEKKARQRqelqqarEEQIELKERRLA 253

                  ....*...
gi 169403709  639 CVACRERA 646
Cdd:pfam13868 254 EEAEREEE 261

RING finger, HC subclass, found in inhibitor of apoptosis proteins (IAPs); IAPs are frequently overexpressed in cancer and associated with tumor cell survival, chemoresistance, disease progression, and poor prognosis. They function primarily as negative regulators of cell death. They regulate caspases and apoptosis through the inhibition of specific members of the caspase family of cysteine proteases. In addition, IAPs has been implicated in a multitude of other cellular processes, including inflammatory signalling and immunity, mitogenic kinase signalling, proliferation and mitosis, as well as cell invasion and metastasis. IAPs in this family includes cellular inhibitor of apoptosis protein c-IAP1 (BIRC2) and c-IAP2 (BIRC3), XIAP (BIRC4), BIRC7, and BIRC8, all of which contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of polyubiquitin (polyUb), and a C3HC4-type RING-HC finger at the carboxyl terminus that is required for ubiquitin ligase activity. The UBA domain is only absent in mammalian homologs of BIRC7. Moreover, c-IAPs contains an additional caspase activation and recruitment domain (CARD) between the UBA and C3HC4-type RING-HC domains. The CARD domain may serve as a protein interaction surface.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 169403709 636 AKQCVACRERAHGAVLRPCQHHILCEPCAATAPECPYCKG 675
Cdd:cd16510    1 EKLCKICMDREVNIVFLPCGHLVTCAQCAASLRKCPICRT 40

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 169403709 566 ELARVRRQLDEAKRKIRQWEESWQQVKQVCDAWQREAQEAKERARVADSD-------RQLALQKKEEVEAQV 630
Cdd:COG4372   67 ELEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEEleelqkeRQDLEQQRKQLEAQI 138

Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 (CGRRF1), RNF156 (MGRN1), RNF157 and similar proteins; This subfamily corresponds to a group of RING finger proteins containing a modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. Cell growth regulator with RING finger domain protein 1 (CGRRF1), also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination after viral infection and promoting degradation of IRF3, another important component required for virus-triggered interferon induction. Mahogunin ring finger-1 (MGRN1), also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase MGRN1. In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 169403709 637 KQCVACRERAHGAVLRPCQHHILCEPCAATA--PECPYCK 674
Cdd:cd16649    1 GLCVVCLENPASVLLLPCRHLCLCEVCAKGLrgKTCPICR 40

RING finger, HC subclass, found in RNA-binding protein MEX3A; MEX3A, also known as RING finger and KH domain-containing protein 4 (RKHD4), is an RNA-binding phosphoprotein that localizes in P-bodies and stress granules, which are two structures involved in the storage and turnover of mRNAs. It has been implicated in the regulation of tumorigenesis. It controls the polarity and stemness of intestinal epithelial cells through the post-transcriptional regulation of the homeobox transcription factor CDX2, which plays a crucial role in intestinal cell fate specification, both during normal development and in tumorigenic processes involving intestinal reprogramming. Moreover, it exhibits a transforming activity when overexpressed in gastric epithelial cells. MEX3A contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3A shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 169403709 636 AKQCVACRERAHGAVLRPCQHHILCEPCAA-----TAPECPYC 673
Cdd:cd16720    2 GRDCMVCFESEVTAALVPCGHNLFCMECAVricerNEPECPVC 44

RING finger, HC subclass, found in RNA-binding proteins of the evolutionarily-conserved MEX-3 family; MEX-3 phosphoproteins are found in vertebrates. They are mediators of post-transcriptional regulation in different organisms, and have been implicated in many core biological processes, including embryonic development, epithelial homeostasis, immune responses, metabolism, and cancer. They contain two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. They shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The RNA-binding protein MEX-3 from nematode Caenorhabditis elegans is the founding member of the MEX-3 family. Due to the lack of a RING-HC finger, it is not included here.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 169403709 637 KQCVACRERAHGAVLRPCQHHILCEPCA-----ATAPECPYCKGQPLQ 679
Cdd:cd16518    1 RDCVVCFESEVVAALVPCGHNLFCMECAnriceKSDPECPVCHTPVTQ 48