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Conserved domains on  [gi|490998979|ref|WP_004860702|]
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MULTISPECIES: DUF2058 domain-containing protein [Raoultella]

Protein Classification

DUF2058 domain-containing protein( domain architecture ID 10006941)

DUF2058 domain-containing protein similar to Escherichia coli YaiL

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
YaiL COG3122
Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown];
3-179 1.44e-68

Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown];


:

Pssm-ID: 442356  Cd Length: 180  Bit Score: 206.24  E-value: 1.44e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979   3 KLTLQEQLLKAGLVTSKKVAKVQRTAKKSRVQAR--------EAREAVEENKKAQLERDKQLGEQQKQAALAKEYKAQVK 74
Cdd:COG3122    2 ANSLQDQLLKAGLVDKKKAKKAKKEKRKQRKQARkkgaeavdEAKAAAERAQAEKAERDRELNRQRQAEAERKAIAAQIR 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979  75 QLIEMNRIVPAKGDIGFNFTDNNLIKKIFVDKLIQAQLISGRLAIARLvpdssgESVYAIIPANVADKIAQRDADSIVLH 154
Cdd:COG3122   82 QLIEQNRLNRKDGEIAYNFTDGGKIKRIYVTAAQRKQLAAGRLAIVRL------DGRYELVPAAVAEKIAERDPSAVVLL 155
                        170       180
                 ....*....|....*....|....*
gi 490998979 155 SALSQEEQDEDDPYADFKVPDDLMW 179
Cdd:COG3122  156 NDASEAEPDEDDPYADYQIPDDLMW 180
 
Name Accession Description Interval E-value
YaiL COG3122
Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown];
3-179 1.44e-68

Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown];


Pssm-ID: 442356  Cd Length: 180  Bit Score: 206.24  E-value: 1.44e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979   3 KLTLQEQLLKAGLVTSKKVAKVQRTAKKSRVQAR--------EAREAVEENKKAQLERDKQLGEQQKQAALAKEYKAQVK 74
Cdd:COG3122    2 ANSLQDQLLKAGLVDKKKAKKAKKEKRKQRKQARkkgaeavdEAKAAAERAQAEKAERDRELNRQRQAEAERKAIAAQIR 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979  75 QLIEMNRIVPAKGDIGFNFTDNNLIKKIFVDKLIQAQLISGRLAIARLvpdssgESVYAIIPANVADKIAQRDADSIVLH 154
Cdd:COG3122   82 QLIEQNRLNRKDGEIAYNFTDGGKIKRIYVTAAQRKQLAAGRLAIVRL------DGRYELVPAAVAEKIAERDPSAVVLL 155
                        170       180
                 ....*....|....*....|....*
gi 490998979 155 SALSQEEQDEDDPYADFKVPDDLMW 179
Cdd:COG3122  156 NDASEAEPDEDDPYADYQIPDDLMW 180
DUF2058 pfam09831
Uncharacterized protein conserved in bacteria (DUF2058); This domain, found in various ...
5-179 3.68e-68

Uncharacterized protein conserved in bacteria (DUF2058); This domain, found in various prokaryotic proteins, has no known function.


Pssm-ID: 430862 [Multi-domain]  Cd Length: 174  Bit Score: 205.12  E-value: 3.68e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979    5 TLQEQLLKAGLVTSKKVAKVQRTAKKSRVQAR------EAREAVEENKKAQLERDKQLGEQQKQAALAKEYKAQVKQLIE 78
Cdd:pfam09831   1 SLQEQLLKAGLVDKKKAKQAKKEKRKQRKQKRkkgavdEAKAAAEEAKAEKAERDRELNRQRQAEAEQKALAAQIRQLIE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979   79 MNRIVPAKGDIGFNFTDNNLIKKIFVDKLIQAQLISGRLAIARLvpdssgESVYAIIPANVADKIAQRDADSIVLHSAlS 158
Cdd:pfam09831  81 QNRIPRYDGEIAYNFTDGNKVKRIYVDAALQAQLVAGRLAIVRL------EGGYELVPREVAEKIAERDPSAVVLLND-E 153
                         170       180
                  ....*....|....*....|.
gi 490998979  159 QEEQDEDDPYADFKVPDDLMW 179
Cdd:pfam09831 154 AEEPDEDDPYADYQIPDDLMW 174
MPSS6 cd23673
mitochondrial 3' processome (MPsome) subunit 6; MPSS6 is a subunit of the mitochondrial 3' ...
17-86 4.21e-03

mitochondrial 3' processome (MPsome) subunit 6; MPSS6 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS6 is predicted (AlphaFold) to contain a C-terminal oligonucleotide/oligosaccharide binding (OB) fold-like domain.


Pssm-ID: 467890  Cd Length: 243  Bit Score: 36.61  E-value: 4.21e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979  17 TSKKVAKVQRTAKKSRVQAREAREAVEENKKAQLERdkQLGEQQKQAALAKEYKAQVKQLIEMNRIVPAK 86
Cdd:cd23673   25 SKDPFATVSTSVPSNSPSSEDAKIRLEESKQKRLQR--QLKDVEEELAALKNESERKTAAVRSARYVPAP 92
 
Name Accession Description Interval E-value
YaiL COG3122
Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown];
3-179 1.44e-68

Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown];


Pssm-ID: 442356  Cd Length: 180  Bit Score: 206.24  E-value: 1.44e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979   3 KLTLQEQLLKAGLVTSKKVAKVQRTAKKSRVQAR--------EAREAVEENKKAQLERDKQLGEQQKQAALAKEYKAQVK 74
Cdd:COG3122    2 ANSLQDQLLKAGLVDKKKAKKAKKEKRKQRKQARkkgaeavdEAKAAAERAQAEKAERDRELNRQRQAEAERKAIAAQIR 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979  75 QLIEMNRIVPAKGDIGFNFTDNNLIKKIFVDKLIQAQLISGRLAIARLvpdssgESVYAIIPANVADKIAQRDADSIVLH 154
Cdd:COG3122   82 QLIEQNRLNRKDGEIAYNFTDGGKIKRIYVTAAQRKQLAAGRLAIVRL------DGRYELVPAAVAEKIAERDPSAVVLL 155
                        170       180
                 ....*....|....*....|....*
gi 490998979 155 SALSQEEQDEDDPYADFKVPDDLMW 179
Cdd:COG3122  156 NDASEAEPDEDDPYADYQIPDDLMW 180
DUF2058 pfam09831
Uncharacterized protein conserved in bacteria (DUF2058); This domain, found in various ...
5-179 3.68e-68

Uncharacterized protein conserved in bacteria (DUF2058); This domain, found in various prokaryotic proteins, has no known function.


Pssm-ID: 430862 [Multi-domain]  Cd Length: 174  Bit Score: 205.12  E-value: 3.68e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979    5 TLQEQLLKAGLVTSKKVAKVQRTAKKSRVQAR------EAREAVEENKKAQLERDKQLGEQQKQAALAKEYKAQVKQLIE 78
Cdd:pfam09831   1 SLQEQLLKAGLVDKKKAKQAKKEKRKQRKQKRkkgavdEAKAAAEEAKAEKAERDRELNRQRQAEAEQKALAAQIRQLIE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979   79 MNRIVPAKGDIGFNFTDNNLIKKIFVDKLIQAQLISGRLAIARLvpdssgESVYAIIPANVADKIAQRDADSIVLHSAlS 158
Cdd:pfam09831  81 QNRIPRYDGEIAYNFTDGNKVKRIYVDAALQAQLVAGRLAIVRL------EGGYELVPREVAEKIAERDPSAVVLLND-E 153
                         170       180
                  ....*....|....*....|.
gi 490998979  159 QEEQDEDDPYADFKVPDDLMW 179
Cdd:pfam09831 154 AEEPDEDDPYADYQIPDDLMW 174
MPSS6 cd23673
mitochondrial 3' processome (MPsome) subunit 6; MPSS6 is a subunit of the mitochondrial 3' ...
17-86 4.21e-03

mitochondrial 3' processome (MPsome) subunit 6; MPSS6 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS6 is predicted (AlphaFold) to contain a C-terminal oligonucleotide/oligosaccharide binding (OB) fold-like domain.


Pssm-ID: 467890  Cd Length: 243  Bit Score: 36.61  E-value: 4.21e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490998979  17 TSKKVAKVQRTAKKSRVQAREAREAVEENKKAQLERdkQLGEQQKQAALAKEYKAQVKQLIEMNRIVPAK 86
Cdd:cd23673   25 SKDPFATVSTSVPSNSPSSEDAKIRLEESKQKRLQR--QLKDVEEELAALKNESERKTAAVRSARYVPAP 92
 
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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