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Conserved domains on  [gi|47077687|dbj|BAD18724|]
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FLJ00352 protein, partial [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CYHR1_C cd22861
C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins; Cysteine and ...
 134-289 2.37e-112

C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins; Cysteine and histidine-rich protein 1 (CYHR1) was first identified as an interaction partner of murine galectin-3. Its biological function is still unknown, but it has been shown to be a prognostic marker for esophageal squamous cell carcinoma and a biomarker in hemodialysis patients for the response to erythropoietin. CYHR1 contains an N-terminal C3HC4-type RING-HC finger. This model represents the conserved C-terminal domain of unknown function.


:

Pssm-ID: 439370  Cd Length: 156  Bit Score: 320.83  E-value: 2.37e-112
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077687 134 DQSHRKEMQLYNSIFSLLSFEKIGYTEVQFRPYRTDDFITRLYYETPRFTVLNQTWVLKARVNDSERNPNLSCKRTLSFQ 213
Cdd:cd22861   1 DQTHKEEMKLYNSIFSLLSFEKITFNDLQLRPYRTDDFITKLYYETSRFTALNQQWVLKARVNDSERNPNLSCKRTLSYQ 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077687 214 LLLKSKVTAPLECSFLLLKGPYDDVRISPVIYHFVFTNESNETDYVPLPIIDSVECNKLLAAKNINLRLFLFQIQK 289
Cdd:cd22861  81 LILKSKITSPMECSFLLLKGPYGDMKVSPVIYHFEFTNESNETEYVPLPIIDSVECNKLLAAKNINLRLFMFQIQK 156
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
 9-46 1.85e-19

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


The actual alignment was detected with superfamily member cd16505:

Pssm-ID: 473075  Cd Length: 62  Bit Score: 80.19  E-value: 1.85e-19
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077687   9 QCTNGHLMCAGCFIHLLADARLKEEQATCPNCRCEISK 46
Cdd:cd16505  25 QCTNGHLMCAGCFNHLLADARLKDEQATCPNCRCEISK 62
Sina super family cl47795
Seven in absentia protein family; The seven in absentia (sina) gene was first identified in ...
 51-112 3.73e-04

Seven in absentia protein family; The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.


The actual alignment was detected with superfamily member pfam03145:

Pssm-ID: 460824 [Multi-domain]  Cd Length: 198  Bit Score: 40.66  E-value: 3.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077687    51 RNLAVEKAVSELPSECGF----CLRQFPRSLLERHQkEECQDRVTQCKYKRIGCPWHGPFHELTVH 112
Cdd:pfam03145   2 RNLALEKVAESLLFPCKYassgCSETLPYTEKADHE-ERCEFRPYSCPCPGSSCTWQGSLDAVMPH 66
 
Name Accession Description Interval E-value
CYHR1_C cd22861
C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins; Cysteine and ...
 134-289 2.37e-112

C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins; Cysteine and histidine-rich protein 1 (CYHR1) was first identified as an interaction partner of murine galectin-3. Its biological function is still unknown, but it has been shown to be a prognostic marker for esophageal squamous cell carcinoma and a biomarker in hemodialysis patients for the response to erythropoietin. CYHR1 contains an N-terminal C3HC4-type RING-HC finger. This model represents the conserved C-terminal domain of unknown function.


Pssm-ID: 439370  Cd Length: 156  Bit Score: 320.83  E-value: 2.37e-112
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077687 134 DQSHRKEMQLYNSIFSLLSFEKIGYTEVQFRPYRTDDFITRLYYETPRFTVLNQTWVLKARVNDSERNPNLSCKRTLSFQ 213
Cdd:cd22861   1 DQTHKEEMKLYNSIFSLLSFEKITFNDLQLRPYRTDDFITKLYYETSRFTALNQQWVLKARVNDSERNPNLSCKRTLSYQ 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077687 214 LLLKSKVTAPLECSFLLLKGPYDDVRISPVIYHFVFTNESNETDYVPLPIIDSVECNKLLAAKNINLRLFLFQIQK 289
Cdd:cd22861  81 LILKSKITSPMECSFLLLKGPYGDMKVSPVIYHFEFTNESNETEYVPLPIIDSVECNKLLAAKNINLRLFMFQIQK 156
RING-HC_CYHR1 cd16505
RING finger, HC subclass, found in cysteine and histidine-rich protein 1 (CYHR1) and similar ...
 9-46 1.85e-19

RING finger, HC subclass, found in cysteine and histidine-rich protein 1 (CYHR1) and similar proteins; CYHR1, also known as cysteine/histidine-rich protein (Chrp), shows sequence similarity with the Drosophila RING finger protein Seven-in-Absentia (sina) and its murine and human siah homologs. It is a novel prognostic marker that may work as a therapeutic target in patients with esophageal squamous cell carcinoma. It is also a biomarker of the response to erythropoietin in hemodialysis patients. CYHR1 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD).


Pssm-ID: 438168  Cd Length: 62  Bit Score: 80.19  E-value: 1.85e-19
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077687   9 QCTNGHLMCAGCFIHLLADARLKEEQATCPNCRCEISK 46
Cdd:cd16505  25 QCTNGHLMCAGCFNHLLADARLKDEQATCPNCRCEISK 62
Sina pfam03145
Seven in absentia protein family; The seven in absentia (sina) gene was first identified in ...
 51-112 3.73e-04

Seven in absentia protein family; The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.


Pssm-ID: 460824 [Multi-domain]  Cd Length: 198  Bit Score: 40.66  E-value: 3.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077687    51 RNLAVEKAVSELPSECGF----CLRQFPRSLLERHQkEECQDRVTQCKYKRIGCPWHGPFHELTVH 112
Cdd:pfam03145   2 RNLALEKVAESLLFPCKYassgCSETLPYTEKADHE-ERCEFRPYSCPCPGSSCTWQGSLDAVMPH 66
 
Name Accession Description Interval E-value
CYHR1_C cd22861
C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins; Cysteine and ...
 134-289 2.37e-112

C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins; Cysteine and histidine-rich protein 1 (CYHR1) was first identified as an interaction partner of murine galectin-3. Its biological function is still unknown, but it has been shown to be a prognostic marker for esophageal squamous cell carcinoma and a biomarker in hemodialysis patients for the response to erythropoietin. CYHR1 contains an N-terminal C3HC4-type RING-HC finger. This model represents the conserved C-terminal domain of unknown function.


Pssm-ID: 439370  Cd Length: 156  Bit Score: 320.83  E-value: 2.37e-112
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47077687 134 DQSHRKEMQLYNSIFSLLSFEKIGYTEVQFRPYRTDDFITRLYYETPRFTVLNQTWVLKARVNDSERNPNLSCKRTLSFQ 213
Cdd:cd22861   1 DQTHKEEMKLYNSIFSLLSFEKITFNDLQLRPYRTDDFITKLYYETSRFTALNQQWVLKARVNDSERNPNLSCKRTLSYQ 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077687 214 LLLKSKVTAPLECSFLLLKGPYDDVRISPVIYHFVFTNESNETDYVPLPIIDSVECNKLLAAKNINLRLFLFQIQK 289
Cdd:cd22861  81 LILKSKITSPMECSFLLLKGPYGDMKVSPVIYHFEFTNESNETEYVPLPIIDSVECNKLLAAKNINLRLFMFQIQK 156
RING-HC_CYHR1 cd16505
RING finger, HC subclass, found in cysteine and histidine-rich protein 1 (CYHR1) and similar ...
 9-46 1.85e-19

RING finger, HC subclass, found in cysteine and histidine-rich protein 1 (CYHR1) and similar proteins; CYHR1, also known as cysteine/histidine-rich protein (Chrp), shows sequence similarity with the Drosophila RING finger protein Seven-in-Absentia (sina) and its murine and human siah homologs. It is a novel prognostic marker that may work as a therapeutic target in patients with esophageal squamous cell carcinoma. It is also a biomarker of the response to erythropoietin in hemodialysis patients. CYHR1 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD).


Pssm-ID: 438168  Cd Length: 62  Bit Score: 80.19  E-value: 1.85e-19
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 47077687   9 QCTNGHLMCAGCFIHLLADARLKEEQATCPNCRCEISK 46
Cdd:cd16505  25 QCTNGHLMCAGCFNHLLADARLKDEQATCPNCRCEISK 62
Sina pfam03145
Seven in absentia protein family; The seven in absentia (sina) gene was first identified in ...
 51-112 3.73e-04

Seven in absentia protein family; The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana.


Pssm-ID: 460824 [Multi-domain]  Cd Length: 198  Bit Score: 40.66  E-value: 3.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 47077687    51 RNLAVEKAVSELPSECGF----CLRQFPRSLLERHQkEECQDRVTQCKYKRIGCPWHGPFHELTVH 112
Cdd:pfam03145   2 RNLALEKVAESLLFPCKYassgCSETLPYTEKADHE-ERCEFRPYSCPCPGSSCTWQGSLDAVMPH 66
 
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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