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Conserved domains on  [gi|578801610|ref|XP_006711646|]
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protein maelstrom homolog isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Maelstrom super family cl16028
piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown ...
 115-309 1.33e-45

piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species. The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, pfam00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed, in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteriztics of both 3'-5' exonuclease and Maelstrom domains.


The actual alignment was detected with superfamily member pfam13017:

Pssm-ID: 404040  Cd Length: 212  Bit Score: 156.70  E-value: 1.33e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578801610  115 CEQRFLPCEIGCVKYSLQEGIMADFHSFINPGEIPRGFRFHCQAASDSSHKIPISNFERGH-NQATVLQNLYRFIHPNPG 193
Cdd:pfam13017   4 TDDKYVPAEIAIVEYSLKEGIIDSYHTFINPGQLPLGQAYDAQHHSDETHQLPLPPNALGEsDYGKLYREILSFLKPNSG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578801610  194 --NWPPIYCKSDDRTRVNWCLKHMakASEIRQDLQLLTVEDLVVGIYQQKFLKE---------PSKTWIRSLLDVAMWDY 262
Cdd:pfam13017  84 ygKPLPVFTDEEDIPMVKSCLRYL--ASDADEEDEKIRVYDFQYLFFVLKKEVEdyagsiqtiPNKHITDALLNKDFFEY 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 578801610  263 SSNTRCKWHEENDI-LFCALAVCKKIAYCISNSLATLFGIQLT-EAHVP 309
Cdd:pfam13017 162 TSGISCEYHEDNDRsKYCALSTVKRWAYTFSDYMCSDLAIKLIpGKHLP 210
HMG-box_SF super family cl00082
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 2-58 1.65e-18

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


The actual alignment was detected with superfamily member pfam09011:

Pssm-ID: 469606 [Multi-domain]  Cd Length: 72  Bit Score: 79.37  E-value: 1.65e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 578801610    2 EKIPELRRRgLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGPSE 58
Cdd:pfam09011  17 EMIPEHKRQ-NPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTYD 72
 
Name Accession Description Interval E-value
Maelstrom pfam13017
piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown ...
 115-309 1.33e-45

piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species. The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, pfam00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed, in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteriztics of both 3'-5' exonuclease and Maelstrom domains.


Pssm-ID: 404040  Cd Length: 212  Bit Score: 156.70  E-value: 1.33e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578801610  115 CEQRFLPCEIGCVKYSLQEGIMADFHSFINPGEIPRGFRFHCQAASDSSHKIPISNFERGH-NQATVLQNLYRFIHPNPG 193
Cdd:pfam13017   4 TDDKYVPAEIAIVEYSLKEGIIDSYHTFINPGQLPLGQAYDAQHHSDETHQLPLPPNALGEsDYGKLYREILSFLKPNSG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578801610  194 --NWPPIYCKSDDRTRVNWCLKHMakASEIRQDLQLLTVEDLVVGIYQQKFLKE---------PSKTWIRSLLDVAMWDY 262
Cdd:pfam13017  84 ygKPLPVFTDEEDIPMVKSCLRYL--ASDADEEDEKIRVYDFQYLFFVLKKEVEdyagsiqtiPNKHITDALLNKDFFEY 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 578801610  263 SSNTRCKWHEENDI-LFCALAVCKKIAYCISNSLATLFGIQLT-EAHVP 309
Cdd:pfam13017 162 TSGISCEYHEDNDRsKYCALSTVKRWAYTFSDYMCSDLAIKLIpGKHLP 210
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 2-58 1.65e-18

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 79.37  E-value: 1.65e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 578801610    2 EKIPELRRRgLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGPSE 58
Cdd:pfam09011  17 EMIPEHKRQ-NPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTYD 72
HMG-box_MAEL cd21992
high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins; MAEL is ...
 1-50 5.88e-15

high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins; MAEL is an RNA-binding protein that has evolved from an ancient nuclease active in protists. It plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons.


Pssm-ID: 438808 [Multi-domain]  Cd Length: 61  Bit Score: 68.80  E-value: 5.88e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 578801610   1 MEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQ 50
Cdd:cd21992   12 LELKPELERKGKNFPGMAEAAPLASPKWKSLSPEEKEPYEEMAKEEKENQ 61
 
Name Accession Description Interval E-value
Maelstrom pfam13017
piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown ...
 115-309 1.33e-45

piRNA pathway germ-plasm component; Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species. The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, pfam00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed, in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteriztics of both 3'-5' exonuclease and Maelstrom domains.


Pssm-ID: 404040  Cd Length: 212  Bit Score: 156.70  E-value: 1.33e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578801610  115 CEQRFLPCEIGCVKYSLQEGIMADFHSFINPGEIPRGFRFHCQAASDSSHKIPISNFERGH-NQATVLQNLYRFIHPNPG 193
Cdd:pfam13017   4 TDDKYVPAEIAIVEYSLKEGIIDSYHTFINPGQLPLGQAYDAQHHSDETHQLPLPPNALGEsDYGKLYREILSFLKPNSG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578801610  194 --NWPPIYCKSDDRTRVNWCLKHMakASEIRQDLQLLTVEDLVVGIYQQKFLKE---------PSKTWIRSLLDVAMWDY 262
Cdd:pfam13017  84 ygKPLPVFTDEEDIPMVKSCLRYL--ASDADEEDEKIRVYDFQYLFFVLKKEVEdyagsiqtiPNKHITDALLNKDFFEY 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 578801610  263 SSNTRCKWHEENDI-LFCALAVCKKIAYCISNSLATLFGIQLT-EAHVP 309
Cdd:pfam13017 162 TSGISCEYHEDNDRsKYCALSTVKRWAYTFSDYMCSDLAIKLIpGKHLP 210
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 2-58 1.65e-18

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 79.37  E-value: 1.65e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 578801610    2 EKIPELRRRgLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGPSE 58
Cdd:pfam09011  17 EMIPEHKRQ-NPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRYDREMGTYD 72
HMG-box_MAEL cd21992
high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins; MAEL is ...
 1-50 5.88e-15

high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins; MAEL is an RNA-binding protein that has evolved from an ancient nuclease active in protists. It plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons.


Pssm-ID: 438808 [Multi-domain]  Cd Length: 61  Bit Score: 68.80  E-value: 5.88e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 578801610   1 MEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQ 50
Cdd:cd21992   12 LELKPELERKGKNFPGMAEAAPLASPKWKSLSPEEKEPYEEMAKEEKENQ 61
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1-48 4.96e-03

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 35.19  E-value: 4.96e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 578801610   1 MEKIPELRRRGlPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRA 48
Cdd:cd00084   11 KEKRPKLKKEN-PDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKE 57
 
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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