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Conserved domains on  [gi|1207184627|ref|XP_021334300|]
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sciellin isoform X2 [Danio rerio]

Protein Classification

LIM domain-containing protein( domain architecture ID 10639037)

LIM (LIN-11, Isl1 and MEC-3) domain-containing protein; LIM is a small protein-protein interaction domain containing two zinc fingers; similar to mammalian sciellin and zinc finger protein 185

CATH:  2.10.110.10
Gene Ontology:  GO:0046872|GO:0005515
SCOP:  4003634

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
477-516 2.41e-06

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


:

Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 44.68  E-value: 2.41e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1207184627  477 ICTYCNQSMYTDEKFILDdMNINCHARCFKCGVCNTSLGN 516
Cdd:smart00132   1 KCAGCGKPIYGTERVLRA-LGKVWHPECFKCATCGKPLSG 39
 
Name Accession Description Interval E-value
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
477-516 2.41e-06

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 44.68  E-value: 2.41e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1207184627  477 ICTYCNQSMYTDEKFILDdMNINCHARCFKCGVCNTSLGN 516
Cdd:smart00132   1 KCAGCGKPIYGTERVLRA-LGKVWHPECFKCATCGKPLSG 39
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
478-536 1.46e-04

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


Pssm-ID: 259829 [Multi-domain]  Cd Length: 53  Bit Score: 39.61  E-value: 1.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184627 478 CTYCNQSMYtdEKFILDDMNINCHARCFKCGVCNTSLGnlraGDSLWVYQCAIHCASCF 536
Cdd:cd08368     1 CAGCGKPIE--GRELLRALGKKWHPECFKCAECGKPLG----GDSFYEKDGKPYCEKCY 53
 
Name Accession Description Interval E-value
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
477-516 2.41e-06

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 44.68  E-value: 2.41e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1207184627  477 ICTYCNQSMYTDEKFILDdMNINCHARCFKCGVCNTSLGN 516
Cdd:smart00132   1 KCAGCGKPIYGTERVLRA-LGKVWHPECFKCATCGKPLSG 39
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
478-536 1.46e-04

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


Pssm-ID: 259829 [Multi-domain]  Cd Length: 53  Bit Score: 39.61  E-value: 1.46e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184627 478 CTYCNQSMYtdEKFILDDMNINCHARCFKCGVCNTSLGnlraGDSLWVYQCAIHCASCF 536
Cdd:cd08368     1 CAGCGKPIE--GRELLRALGKKWHPECFKCAECGKPLG----GDSFYEKDGKPYCEKCY 53
LIM1_LIMK1 cd09462
The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain ...
469-527 3.02e-04

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188846 [Multi-domain]  Cd Length: 74  Bit Score: 39.48  E-value: 3.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184627 469 ERKVNAKDICTYCNQSMYtDEKFiLDDMNINCHARCFKCGVCNTSLgnlragdSLWVYQ 527
Cdd:cd09462    13 EEEGNVLPVCASCGQSIY-DGQY-LQALNSDWHADCFRCCECGASL-------SHWYYE 62
LIM_CRP_like cd09326
The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich ...
478-514 4.25e-03

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188712  Cd Length: 53  Bit Score: 35.65  E-value: 4.25e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1207184627 478 CTYCNQSMYTDEKFILDdmNINCHARCFKCGVCNTSL 514
Cdd:cd09326     1 CPRCGKSVYAAEEVIAA--GKSWHKSCFTCAVCNKRL 35
LIM_Eplin_like cd09442
The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins; The Lim domain of ...
478-516 4.69e-03

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188826 [Multi-domain]  Cd Length: 53  Bit Score: 35.53  E-value: 4.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1207184627 478 CTYCNQSMYTDEKFILDDMNIncHARCFKCGVCNT--SLGN 516
Cdd:cd09442     1 CTVCQKRVYPMERLIADKQNF--HKSCFRCEHCNSklSLGN 39
LIM3_Lrg1p_like cd09393
The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM ...
478-535 5.87e-03

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188779  Cd Length: 56  Bit Score: 35.37  E-value: 5.87e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207184627 478 CTYCNQSMytdEKFILDDMNINCHARCFKCGVCNTSLGNLRAGDSLWVYQCAIHCASC 535
Cdd:cd09393     1 CASCGKSI---EDECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
LIM_Ltd-1 cd09443
The LIM domain of LIM and transglutaminase domains protein (Ltd-1); The LIM domain of LIM and ...
478-531 6.19e-03

The LIM domain of LIM and transglutaminase domains protein (Ltd-1); The LIM domain of LIM and transglutaminase domains protein (Ltd-1): This family includes mouse Ky protein and Caenorhabditis elegans Ltd-1 protein. The members of this family consists a N-terminal Lim domain and a C-terminal transglutaminase domain. The mouse Ky protein has putative function in muscle development. The mouse with ky mutant exhibits combined posterior and lateral curvature of the spine. The Ltd-1 gene in C. elegans is expressed in developing hypodermal cells from the twofold stage embryo through adulthood. These data define the ltd-1 gene as a novel marker for C. elegans epithelial cell development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188827 [Multi-domain]  Cd Length: 55  Bit Score: 35.09  E-value: 6.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184627 478 CTYCNQSMYTDEKFILDDMNIncHARCFKCGVCNTSLG-----NLRAGDSLWvyqCAIH 531
Cdd:cd09443     1 CPRCGKTAYPAESVDKDGTFY--HKGCFKCRECGTRLSlktftFVQGDGEVY---CARH 54
LIM1_MLP84B_like cd09404
The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A ...
477-535 7.31e-03

The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188788  Cd Length: 54  Bit Score: 34.77  E-value: 7.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207184627 477 ICTYCNQSMYTDEKFILDDMNIncHARCFKCGVCNTSLgnlragDSLWV--YQCAIHCASC 535
Cdd:cd09404     1 KCPKCGKSVYAAEERLAGGYKW--HKMCFKCGMCNKLL------DSTNCaeHEGELYCKQC 53
LIM1_LIMK cd09364
The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain ...
478-516 7.48e-03

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188750 [Multi-domain]  Cd Length: 53  Bit Score: 34.77  E-value: 7.48e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207184627 478 CTYCNQSMYtdEKFILDDMNINCHARCFKCGVCNTSLGN 516
Cdd:cd09364     1 CAGCRGKIL--DSQYVQALNQDWHCDCFRCSVCSDSLSN 37
LIM1_Lhx7_Lhx8 cd09381
The first LIM domain of Lhx7 and Lhx8; The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 ...
477-515 8.92e-03

The first LIM domain of Lhx7 and Lhx8; The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188767 [Multi-domain]  Cd Length: 56  Bit Score: 34.95  E-value: 8.92e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207184627 477 ICTYCNQSMYtdEKFILDDMNINCHARCFKCGVCNTSLG 515
Cdd:cd09381     1 VCSSCGLEIV--DKYLLKVNDLCWHVRCLSCSVCRTSLG 37
LIM1_Lhx3b cd09467
The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein ...
477-524 9.59e-03

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188851 [Multi-domain]  Cd Length: 55  Bit Score: 34.53  E-value: 9.59e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1207184627 477 ICTYCNQSMYtdEKFILDDMNINCHARCFKCGVCNTSLGN--LRAGDSLW 524
Cdd:cd09467     3 LCAGCNQHIV--DRFILKVLDRHWHSKCLKCSDCQTQLAEkcFSRGDSVY 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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