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Conserved domains on  [gi|41629671|ref|NP_009446|]
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Sea4p [Saccharomyces cerevisiae S288C]

Protein Classification

RING finger protein( domain architecture ID 582309)

RING finger protein containing a C3H3C2-type zinc-finger; similar to Saccharomyces cerevisiae SEH-associated protein 4, which is a component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis

Gene Ontology:  GO:0008270
PubMed:  32851833|11007473

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-RING_16 super family cl24077
RING/Ubox like zinc-binding domain;
943-1036 9.99e-28

RING/Ubox like zinc-binding domain;


The actual alignment was detected with superfamily member pfam17034:

Pssm-ID: 390276  Cd Length: 125  Bit Score: 108.98  E-value: 9.99e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41629671    943 CPHCGSSFPRCAICLMPLGTSNLPfvingtqsrdpmQTEDSQDGANRELVSRKLKLNEWFSFCLSCNHGMHAGHAEEWFD 1022
Cdd:pfam17034   41 CPACSQPLPRCAVCGLSLGTSNLT------------NKDSRRKSVVKDPQDFEKLFEKWFSFCLSCGHGSHADHATEWFS 108

                           90
                   ....*....|....
gi 41629671   1023 RHNVCPTPGCTCQC 1036
Cdd:pfam17034  109 THSICPVADCNCLC 122
 
Name Accession Description Interval E-value
zinc_ribbon_16 pfam17034
Zinc-ribbon like family; This family is found at the C-terminus of WD40 repeat structures in ...
 943-1036 9.99e-28

Zinc-ribbon like family; This family is found at the C-terminus of WD40 repeat structures in eukaryotes.


Pssm-ID: 374955  Cd Length: 125  Bit Score: 108.98  E-value: 9.99e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41629671    943 CPHCGSSFPRCAICLMPLGTSNLPfvingtqsrdpmQTEDSQDGANRELVSRKLKLNEWFSFCLSCNHGMHAGHAEEWFD 1022
Cdd:pfam17034   41 CPACSQPLPRCAVCGLSLGTSNLT------------NKDSRRKSVVKDPQDFEKLFEKWFSFCLSCGHGSHADHATEWFS 108

                           90
                   ....*....|....
gi 41629671   1023 RHNVCPTPGCTCQC 1036
Cdd:pfam17034  109 THSICPVADCNCLC 122
mRING-H2-C3H3C2_Mio cd16691
Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and ...
 951-1036 5.53e-23

Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and simialr proteins; This family contains Mio,its counterpart Sea4 from yeast, and other homologs. Mio/Sea4 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea2/WDR24, and Sea3/WDR59. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. Mio interacts with endogenous RagA and RagC, and plays an essential role in the activation of mTOR Complex 1 (mTORC1) by amino acids. In GATOR2, Mio and Seh1 localize to lysosomes and autolysosomes, and form a heterodimer that is required to oppose the TORC1 inhibitory activity of the Iml1/GATOR1 complex to prevent the constitutive down-regulation of TORC1 activity in later stages of oogenesis. A tissue-specific requirement is necessary for Mio to be involved in cell growth in the female germ line. Mio contains an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type.


Pssm-ID: 438352  Cd Length: 75  Bit Score: 93.28  E-value: 5.53e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41629671  951 PRCAICLMPLGTSNLPFvingtQSRDPMQTEDSQDGAnrelvsrKLKLNEWFSFCLSCNHGMHAGHAEEWFDRHNVCPTP 1030
Cdd:cd16691    2 PRCSLCLIPMGTPSSSL-----PGATASDVDLSSDKK-------LAPFSSWFTWCQTCRHGGHAGHLQEWFRDHSECPVS 69


                 ....*.
gi 41629671 1031 GCTCQC 1036
Cdd:cd16691   70 GCDCKC 75
 
Name Accession Description Interval E-value
zinc_ribbon_16 pfam17034
Zinc-ribbon like family; This family is found at the C-terminus of WD40 repeat structures in ...
 943-1036 9.99e-28

Zinc-ribbon like family; This family is found at the C-terminus of WD40 repeat structures in eukaryotes.


Pssm-ID: 374955  Cd Length: 125  Bit Score: 108.98  E-value: 9.99e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41629671    943 CPHCGSSFPRCAICLMPLGTSNLPfvingtqsrdpmQTEDSQDGANRELVSRKLKLNEWFSFCLSCNHGMHAGHAEEWFD 1022
Cdd:pfam17034   41 CPACSQPLPRCAVCGLSLGTSNLT------------NKDSRRKSVVKDPQDFEKLFEKWFSFCLSCGHGSHADHATEWFS 108

                           90
                   ....*....|....
gi 41629671   1023 RHNVCPTPGCTCQC 1036
Cdd:pfam17034  109 THSICPVADCNCLC 122
mRING-H2-C3H3C2_Mio cd16691
Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and ...
 951-1036 5.53e-23

Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and simialr proteins; This family contains Mio,its counterpart Sea4 from yeast, and other homologs. Mio/Sea4 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea2/WDR24, and Sea3/WDR59. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. Mio interacts with endogenous RagA and RagC, and plays an essential role in the activation of mTOR Complex 1 (mTORC1) by amino acids. In GATOR2, Mio and Seh1 localize to lysosomes and autolysosomes, and form a heterodimer that is required to oppose the TORC1 inhibitory activity of the Iml1/GATOR1 complex to prevent the constitutive down-regulation of TORC1 activity in later stages of oogenesis. A tissue-specific requirement is necessary for Mio to be involved in cell growth in the female germ line. Mio contains an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type.


Pssm-ID: 438352  Cd Length: 75  Bit Score: 93.28  E-value: 5.53e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41629671  951 PRCAICLMPLGTSNLPFvingtQSRDPMQTEDSQDGAnrelvsrKLKLNEWFSFCLSCNHGMHAGHAEEWFDRHNVCPTP 1030
Cdd:cd16691    2 PRCSLCLIPMGTPSSSL-----PGATASDVDLSSDKK-------LAPFSSWFTWCQTCRHGGHAGHLQEWFRDHSECPVS 69


                 ....*.
gi 41629671 1031 GCTCQC 1036
Cdd:cd16691   70 GCDCKC 75
mRING-H2-C3H3C2_Mio-like cd16488
Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and ...
 952-1034 4.07e-14

Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and its homologs; This subfamily contains Mio, WDR24, WDR59, and their counterparts Sea4, Sea2, and Sea3 from yeast, respectively. Mio/Sea4, Sea2/WDR24, and Sea3/WDR59 are components of the GATOR2 complex, which also includes another two subunits, Seh1and Sec13. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. All subfamily members contain an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type.


Pssm-ID: 438151 [Multi-domain]  Cd Length: 44  Bit Score: 67.35  E-value: 4.07e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41629671  952 RCAICLMPLGTSnlpfvingtqsrdpmqtedsqdganrelvsrklklnewFSFCLSCNHGMHAGHAEEWFDRHNVCPTpG 1031
Cdd:cd16488    1 SCAICHLPVKGL--------------------------------------SSFCLNCGHGGHAECIREWFEDHTECPT-G 41


                 ...
gi 41629671 1032 CTC 1034
Cdd:cd16488   42 CGC 44
mRING-H2-C3H3C2_WDR59 cd16692
Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 ...
 1003-1036 7.79e-12

Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins; WDR59 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea2/WDR24, and Mio/Sea4. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. WDR59 contains an N-terminal WD40 domain followed by a RWD domain, and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type. Sea3 is the yeast counterpart of WDR59. It is not included in this subfamily.


Pssm-ID: 438353  Cd Length: 47  Bit Score: 60.86  E-value: 7.79e-12
                         10        20        30
                 ....*....|....*....|....*....|....
gi 41629671 1003 SFCLSCNHGMHAGHAEEWFDRHNVCPTpGCTCQC 1036
Cdd:cd16692   15 NFCLACGHGGHTSHMMEWFRTQDVCPT-GCGCHC 47
mRING-H2-C3H3C2_WDR24 cd16693
Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 24 ...
 1002-1036 2.46e-06

Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 24 (WDR24) and similar proteins; WDR24 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea3/WDR59, and Mio/Sea4. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. WDR24 contains an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type. Sea2 is the yeast counterpart of WDR24. It is not included in this subfamily.


Pssm-ID: 438354  Cd Length: 46  Bit Score: 45.35  E-value: 2.46e-06
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 41629671 1002 FSFCLSCNHGMHAGHAEEWFDRHNVCPTpGCTCQC 1036
Cdd:cd16693   13 YVWCQGCGHGGHLEHMKEWFSTNSHCPA-GCGHLC 46
zf-RING_16 pfam17120
RING/Ubox like zinc-binding domain;
1002-1036 2.27e-05

RING/Ubox like zinc-binding domain;


Pssm-ID: 375001  Cd Length: 57  Bit Score: 42.77  E-value: 2.27e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 41629671   1002 FSFCLSCNHGMHAGHAEEWFDR-HNVCPTpGCTCQC 1036
Cdd:pfam17120   18 VFLCGVCQHVLHASCAREWWENdDGECPS-GCGCNC 52
 
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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