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Conserved domains on  [gi|947058604|gb|KRH08010|]
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hypothetical protein GLYMA_16G123700v4 [Glycine max]

Protein Classification

SKP1 family protein( domain architecture ID 13034557)

SKP1 family protein may be a component of E3 ubiquitin ligase SCF complex involved in ubiquitination and subsequent proteasomal degradation of target proteins; similar to Homo sapiens S-phase kinase-associated protein 1 (SKP1)

CATH:  3.30.710.10
Gene Ontology:  GO:0006511
PubMed:  35345853|12678488
SCOP:  4001926|4001139

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BTB_POZ_SKP1 cd18322
BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in ...
 6-120 1.97e-59

BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in S-phase kinase-associated protein 1 (SKP1) and similar proteins; SKP1 is also called cyclin-A/CDK2-associated protein p19 (p19A), organ of Corti protein 2 (OCP-2), organ of Corti protein II (OCP-II), RNA polymerase II elongation factor-like protein, transcription elongation factor B polypeptide 1-like, or p19skp1. It is an essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. SKP1 serves as an adaptor protein that links the F-box protein to CUL1. SKP1 and CUL1 are invariant components of all SCF complexes, while F-box proteins are variable substrate binding modules that determine specificity. SKP1 belongs to the BTB/POZ domain family; the domain is a common protein-protein interaction motif of about 100 amino acids.


:

Pssm-ID: 349631  Cd Length: 120  Bit Score: 180.10  E-value: 1.97e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604   6 KITLKSSDGEAFEVEEAVALESQTIKHMIEDDC-ADSGIPLPNVTSKILAKVIEYCKKHVEANSADEK----PSEDVLKA 80
Cdd:cd18322    1 KIKLQSSDGEIFEVDEEVARQSVTIKNMLEDLGyDDDPIPLPNVTSKILKKVIEWCEHHKDDPPPEIDldseKRTDDIPE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 947058604  81 WDVDFVNVDQATLFDLILAANYLNIKSLLDLTCQTVADMI 120
Cdd:cd18322   81 WDAEFLKVDQDTLFELILAANYLDIKGLLDLTCKTVANMI 120
Skp1 pfam01466
Skp1 family, dimerization domain;
106-153 1.93e-20

Skp1 family, dimerization domain;


:

Pssm-ID: 460222  Cd Length: 48  Bit Score: 78.70  E-value: 1.93e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 947058604  106 KSLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWA 153
Cdd:pfam01466   1 KGLLDLTCKTVADMIKGKTPEEIREIFNIENDFTPEEEEEIRKENAWA 48
 
Name Accession Description Interval E-value
BTB_POZ_SKP1 cd18322
BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in ...
 6-120 1.97e-59

BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in S-phase kinase-associated protein 1 (SKP1) and similar proteins; SKP1 is also called cyclin-A/CDK2-associated protein p19 (p19A), organ of Corti protein 2 (OCP-2), organ of Corti protein II (OCP-II), RNA polymerase II elongation factor-like protein, transcription elongation factor B polypeptide 1-like, or p19skp1. It is an essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. SKP1 serves as an adaptor protein that links the F-box protein to CUL1. SKP1 and CUL1 are invariant components of all SCF complexes, while F-box proteins are variable substrate binding modules that determine specificity. SKP1 belongs to the BTB/POZ domain family; the domain is a common protein-protein interaction motif of about 100 amino acids.


Pssm-ID: 349631  Cd Length: 120  Bit Score: 180.10  E-value: 1.97e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604   6 KITLKSSDGEAFEVEEAVALESQTIKHMIEDDC-ADSGIPLPNVTSKILAKVIEYCKKHVEANSADEK----PSEDVLKA 80
Cdd:cd18322    1 KIKLQSSDGEIFEVDEEVARQSVTIKNMLEDLGyDDDPIPLPNVTSKILKKVIEWCEHHKDDPPPEIDldseKRTDDIPE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 947058604  81 WDVDFVNVDQATLFDLILAANYLNIKSLLDLTCQTVADMI 120
Cdd:cd18322   81 WDAEFLKVDQDTLFELILAANYLDIKGLLDLTCKTVANMI 120
SKP1 COG5201
SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, ...
 4-153 4.25e-45

SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227528 [Multi-domain]  Cd Length: 158  Bit Score: 145.09  E-value: 4.25e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604   4 TKKITLKSSDGEAFEVEEAVALESQTIKHMIEDDCA-DSGIPLPNVTSKILAKVIEYCKKHVEANSADEKPSEDVLKA-- 80
Cdd:COG5201    1 MSMIELESIDGEIFRVDENIAERSILIKNMLCDSTAcNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKps 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 947058604  81 --WDVDFVNVDQATLFDLILAANYLNIKSLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWA 153
Cdd:COG5201   81 dfWDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWA 155
Skp1 smart00512
Found in Skp1 protein family; Family of Skp1 (kinetochore protein required for cell cycle ...
 5-105 1.93e-42

Found in Skp1 protein family; Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.


Pssm-ID: 214704  Cd Length: 104  Bit Score: 136.27  E-value: 1.93e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604     5 KKITLKSSDGEAFEVEEAVALESQTIKHMIEDDCADSG----IPLPNVTSKILAKVIEYCKKHVeaNSADEKPSEDVLKA 80
Cdd:smart00512   2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDEnnnpIPLPNVTSKILSKVIEYCEHHV--DDPPSVADKDDIPT 79

                           90       100
                   ....*....|....*....|....*
gi 947058604    81 WDVDFVNVDQATLFDLILAANYLNI 105
Cdd:smart00512  80 WDAEFLKIDQETLFELILAANYLDI 104
Skp1_POZ pfam03931
Skp1 family, tetramerization domain;
5-65 3.31e-28

Skp1 family, tetramerization domain;


Pssm-ID: 397838  Cd Length: 60  Bit Score: 98.91  E-value: 3.31e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 947058604    5 KKITLKSSDGEAFEVEEAVALESQTIKHMIEDDCADsGIPLPNVTSKILAKVIEYCKKHVE 65
Cdd:pfam03931   1 PKIVLQSSDGESFEVEEAVARKSKTIKHMIEDDGDD-PIPLPNVTSKILEKVIEYCKHHRV 60
Skp1 pfam01466
Skp1 family, dimerization domain;
106-153 1.93e-20

Skp1 family, dimerization domain;


Pssm-ID: 460222  Cd Length: 48  Bit Score: 78.70  E-value: 1.93e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 947058604  106 KSLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWA 153
Cdd:pfam01466   1 KGLLDLTCKTVADMIKGKTPEEIREIFNIENDFTPEEEEEIRKENAWA 48
 
Name Accession Description Interval E-value
BTB_POZ_SKP1 cd18322
BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in ...
 6-120 1.97e-59

BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in S-phase kinase-associated protein 1 (SKP1) and similar proteins; SKP1 is also called cyclin-A/CDK2-associated protein p19 (p19A), organ of Corti protein 2 (OCP-2), organ of Corti protein II (OCP-II), RNA polymerase II elongation factor-like protein, transcription elongation factor B polypeptide 1-like, or p19skp1. It is an essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. SKP1 serves as an adaptor protein that links the F-box protein to CUL1. SKP1 and CUL1 are invariant components of all SCF complexes, while F-box proteins are variable substrate binding modules that determine specificity. SKP1 belongs to the BTB/POZ domain family; the domain is a common protein-protein interaction motif of about 100 amino acids.


Pssm-ID: 349631  Cd Length: 120  Bit Score: 180.10  E-value: 1.97e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604   6 KITLKSSDGEAFEVEEAVALESQTIKHMIEDDC-ADSGIPLPNVTSKILAKVIEYCKKHVEANSADEK----PSEDVLKA 80
Cdd:cd18322    1 KIKLQSSDGEIFEVDEEVARQSVTIKNMLEDLGyDDDPIPLPNVTSKILKKVIEWCEHHKDDPPPEIDldseKRTDDIPE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 947058604  81 WDVDFVNVDQATLFDLILAANYLNIKSLLDLTCQTVADMI 120
Cdd:cd18322   81 WDAEFLKVDQDTLFELILAANYLDIKGLLDLTCKTVANMI 120
SKP1 COG5201
SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, ...
 4-153 4.25e-45

SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227528 [Multi-domain]  Cd Length: 158  Bit Score: 145.09  E-value: 4.25e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604   4 TKKITLKSSDGEAFEVEEAVALESQTIKHMIEDDCA-DSGIPLPNVTSKILAKVIEYCKKHVEANSADEKPSEDVLKA-- 80
Cdd:COG5201    1 MSMIELESIDGEIFRVDENIAERSILIKNMLCDSTAcNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKps 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 947058604  81 --WDVDFVNVDQATLFDLILAANYLNIKSLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWA 153
Cdd:COG5201   81 dfWDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWA 155
Skp1 smart00512
Found in Skp1 protein family; Family of Skp1 (kinetochore protein required for cell cycle ...
 5-105 1.93e-42

Found in Skp1 protein family; Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.


Pssm-ID: 214704  Cd Length: 104  Bit Score: 136.27  E-value: 1.93e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604     5 KKITLKSSDGEAFEVEEAVALESQTIKHMIEDDCADSG----IPLPNVTSKILAKVIEYCKKHVeaNSADEKPSEDVLKA 80
Cdd:smart00512   2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDEnnnpIPLPNVTSKILSKVIEYCEHHV--DDPPSVADKDDIPT 79

                           90       100
                   ....*....|....*....|....*
gi 947058604    81 WDVDFVNVDQATLFDLILAANYLNI 105
Cdd:smart00512  80 WDAEFLKIDQETLFELILAANYLDI 104
Skp1_POZ pfam03931
Skp1 family, tetramerization domain;
5-65 3.31e-28

Skp1 family, tetramerization domain;


Pssm-ID: 397838  Cd Length: 60  Bit Score: 98.91  E-value: 3.31e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 947058604    5 KKITLKSSDGEAFEVEEAVALESQTIKHMIEDDCADsGIPLPNVTSKILAKVIEYCKKHVE 65
Cdd:pfam03931   1 PKIVLQSSDGESFEVEEAVARKSKTIKHMIEDDGDD-PIPLPNVTSKILEKVIEYCKHHRV 60
Skp1 pfam01466
Skp1 family, dimerization domain;
106-153 1.93e-20

Skp1 family, dimerization domain;


Pssm-ID: 460222  Cd Length: 48  Bit Score: 78.70  E-value: 1.93e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 947058604  106 KSLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWA 153
Cdd:pfam01466   1 KGLLDLTCKTVADMIKGKTPEEIREIFNIENDFTPEEEEEIRKENAWA 48
BTB_POZ_EloC cd18321
BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in ...
 7-105 4.42e-14

BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Elongin-C (EloC) and similar proteins; Elongin-C is also called elongin 15 kDa subunit, RNA polymerase II transcription factor SIII subunit C, SIII p15, or transcription elongation factor B polypeptide 1 (TCEB1). It is a component of SIII (also known as elongin), which is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. It forms a regulatory complex with subunit B or elongin-B (BC) that enhances the activity of the transcriptionally active subunit A. The BC complex also functions as an adaptor protein in the proteasomal degradation of target proteins via different E3 ubiquitin ligase complexes, including the von Hippel-Lindau ubiquitination complex CBC (VHL) and the suppressors of cytokine signaling (SOCS) box ubiquitin ligase family. Elongin-C belongs to the BTB/POZ domain family; the domain is a common protein-protein interaction motif of about 100 amino acids.


Pssm-ID: 349630  Cd Length: 95  Bit Score: 63.76  E-value: 4.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604   7 ITLKSSDGEAFEVEEAVALESQTIKHMIEDDCADSG-----IPLPNVTSKILAKVIEYCKKHVE-ANSADEKPsedvlka 80
Cdd:cd18321    2 VKLISSDGHEFIVDREAAMVSGTIKAMLSGPGQFAEnetneVRFPEISSHILEKVCEYFYYKVRyTNSSTEIP------- 74

                         90       100
                 ....*....|....*....|....*
gi 947058604  81 wdvDFvNVDQATLFDLILAANYLNI 105
Cdd:cd18321   75 ---EF-PIPPEIALELLMAANFLDC 95
BTB_POZ cd01165
BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain ...
 12-103 3.41e-03

BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily; Proteins in this superfamily are characterized by the presence of a common protein-protein interaction motif of about 100 amino acids, known as the BTB/POZ domain. Members include transcription factors, oncogenic proteins, ion channel proteins, and potassium channel tetramerization domain (KCTD) proteins. They have been identified in poxviruses and many eukaryotes, and have diverse functions, such as transcriptional regulation, chromatin remodeling, protein degradation and cytoskeletal regulation. Many BTB/POZ proteins contain one or two additional domains, such as kelch repeats, zinc-finger domains, FYVE (Fab1, YOTB, Vac1, and EEA1) fingers, or ankyrin repeats, among others. These special additional domains or interaction partners provide unique characteristics and functions to BTB/POZ proteins. In ion channel proteins and KCTD proteins, the BTB/POZ domain is also called the tetramerization (T1) domain.


Pssm-ID: 349496 [Multi-domain]  Cd Length: 79  Bit Score: 34.56  E-value: 3.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 947058604  12 SDGEAFEVEEAVALESQTIKH-MIEDDCADSG---IPLPNVTSKILAKVIEYCKKHveansadekpsedvlkawdvdFVN 87
Cdd:cd01165    5 VEGEKFHVNKELLAQSSEYFRaLFRGGFRESGqaeINLRDISPEDFRALLEFLYGG---------------------KRD 63

                         90
                 ....*....|....*.
gi 947058604  88 VDQATLFDLILAANYL 103
Cdd:cd01165   64 LDASNLLELLEAANFL 79
 
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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