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Conserved domains on  [gi|300825688|gb|ADK35877|]
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gag protein [Porcine endogenous retrovirus C]

Protein Classification

Gag_MA and ZnF_C2HC domain-containing protein( domain architecture ID 10471595)

protein containing domains Gag_MA, Gag_p30, and ZnF_C2HC

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Gag_p30 super family cl03444
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ...
 212-417 1.26e-115

Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.


The actual alignment was detected with superfamily member pfam02093:

Pssm-ID: 426597  Cd Length: 208  Bit Score: 340.10  E-value: 1.26e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688  212 QYWPFSSADLYNWKTNHPPFSEDPQRLTGLVESLMFSHQPTWDDCQQLLQTLFTTEERERILLEARKNVPGADGRPTQLQ 291
Cdd:pfam02093   1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688  292 NEIDMGFPLTRPGWDYNTAEGRESLKIYRQALVAGLRGASRRPTNLAKVREVMQGPNEPPSVFLERLMEAFRRFTPFDPT 371
Cdd:pfam02093  81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 300825688  372 SEAQKASVALAFIGQSALDIRKKLQRLEGLQEAELRDLVREAEKVY 417
Cdd:pfam02093 161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIF 206
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 2-109 5.15e-38

Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.


:

Pssm-ID: 426076 [Multi-domain]  Cd Length: 126  Bit Score: 135.59  E-value: 5.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688    2 GQTVTTPLSLTLDHWTEVRSRAHNLSVQVKKGPWQTFCASEWPTFDVGWPSEGTFNSEIILAVKAIIFQTGPGSHPDQEP 81
Cdd:pfam01140   1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                          90       100
                  ....*....|....*....|....*...
gi 300825688   82 YILTWQDLAEDPPPWVKPWLNkPRKPGP 109
Cdd:pfam01140  81 YIVTWEALAADPPPWVRPFLT-PKPPPP 107
ZnF_C2HC smart00343
zinc finger;
492-508 2.39e-04

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.19  E-value: 2.39e-04
                           10
                   ....*....|....*..
gi 300825688   492 QCAYCKEKGHWARNCPK 508
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
 
Name Accession Description Interval E-value
Gag_p30 pfam02093
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ...
 212-417 1.26e-115

Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.


Pssm-ID: 426597  Cd Length: 208  Bit Score: 340.10  E-value: 1.26e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688  212 QYWPFSSADLYNWKTNHPPFSEDPQRLTGLVESLMFSHQPTWDDCQQLLQTLFTTEERERILLEARKNVPGADGRPTQLQ 291
Cdd:pfam02093   1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688  292 NEIDMGFPLTRPGWDYNTAEGRESLKIYRQALVAGLRGASRRPTNLAKVREVMQGPNEPPSVFLERLMEAFRRFTPFDPT 371
Cdd:pfam02093  81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 300825688  372 SEAQKASVALAFIGQSALDIRKKLQRLEGLQEAELRDLVREAEKVY 417
Cdd:pfam02093 161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIF 206
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 2-109 5.15e-38

Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.


Pssm-ID: 426076 [Multi-domain]  Cd Length: 126  Bit Score: 135.59  E-value: 5.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688    2 GQTVTTPLSLTLDHWTEVRSRAHNLSVQVKKGPWQTFCASEWPTFDVGWPSEGTFNSEIILAVKAIIFQTGPGSHPDQEP 81
Cdd:pfam01140   1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                          90       100
                  ....*....|....*....|....*...
gi 300825688   82 YILTWQDLAEDPPPWVKPWLNkPRKPGP 109
Cdd:pfam01140  81 YIVTWEALAADPPPWVRPFLT-PKPPPP 107
ZnF_C2HC smart00343
zinc finger;
492-508 2.39e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.19  E-value: 2.39e-04
                           10
                   ....*....|....*..
gi 300825688   492 QCAYCKEKGHWARNCPK 508
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 491-508 1.68e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.97  E-value: 1.68e-03
                          10
                  ....*....|....*...
gi 300825688  491 DQCAYCKEKGHWARNCPK 508
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
Gag_p30 pfam02093
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ...
 212-417 1.26e-115

Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.


Pssm-ID: 426597  Cd Length: 208  Bit Score: 340.10  E-value: 1.26e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688  212 QYWPFSSADLYNWKTNHPPFSEDPQRLTGLVESLMFSHQPTWDDCQQLLQTLFTTEERERILLEARKNVPGADGRPTQLQ 291
Cdd:pfam02093   1 QYWPFSSSDLYNWKNNNPSFSEDPGKLTALIESVLVTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGNDGRPTQLP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688  292 NEIDMGFPLTRPGWDYNTAEGRESLKIYRQALVAGLRGASRRPTNLAKVREVMQGPNEPPSVFLERLMEAFRRFTPFDPT 371
Cdd:pfam02093  81 NEVDAAFPLERPDWDYTTPAGRNHLVLYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPE 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 300825688  372 SEAQKASVALAFIGQSALDIRKKLQRLEGLQEAELRDLVREAEKVY 417
Cdd:pfam02093 161 DPGQETNVSMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIF 206
Gag_MA pfam01140
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ...
 2-109 5.15e-38

Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity.


Pssm-ID: 426076 [Multi-domain]  Cd Length: 126  Bit Score: 135.59  E-value: 5.15e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300825688    2 GQTVTTPLSLTLDHWTEVRSRAHNLSVQVKKGPWQTFCASEWPTFDVGWPSEGTFNSEIILAVKAIIFQTGPGSHPDQEP 81
Cdd:pfam01140   1 GQTVTTPLSLTLGHWSDVPSRACNQSVDVKKRRWVTFCSAEWPTLNVGWPRDGTFNLTTILQVKTRVFAPGPHGHPDQVP 80

                          90       100
                  ....*....|....*....|....*...
gi 300825688   82 YILTWQDLAEDPPPWVKPWLNkPRKPGP 109
Cdd:pfam01140  81 YIVTWEALAADPPPWVRPFLT-PKPPPP 107
ZnF_C2HC smart00343
zinc finger;
492-508 2.39e-04

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 38.19  E-value: 2.39e-04
                           10
                   ....*....|....*..
gi 300825688   492 QCAYCKEKGHWARNCPK 508
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 491-508 1.68e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 35.97  E-value: 1.68e-03
                          10
                  ....*....|....*...
gi 300825688  491 DQCAYCKEKGHWARNCPK 508
Cdd:pfam00098   1 GKCYNCGEPGHIARDCPK 18
 
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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