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Conserved domains on  [gi|1315970541|dbj|GAY37526|]
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hypothetical protein CUMW_029690 [Citrus unshiu]

Protein Classification

NEDD4-binding protein 2; CID family protein( domain architecture ID 10198928)

NEDD4-binding protein 2 (N4BP2) has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination| CTC-interacting domain (CID) family protein similar to Arabidopsis thaliana polyadenylate-binding protein-interacting protein 5/6

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CUE_CID7_like cd14371
CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins; ...
 221-262 2.32e-19

CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins; CID7 is encoded by ubiquitously expressed gene CID7. It contains an N-terminal PABC-interacting domain (PAM2 or PABP-interacting motif 2) which is also found in the human Paip1 and Paip2. At this point, it functions as an interaction partner of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. It also harbors an ubiquitin-associated (UBA)-like CUE domain and a C-terminal small MutS-related (SMR) domain. CID5 and CID6 are encoded by gene CID5, CID6, respectively. CID5 is only expressed in immature siliques. The biological function of CID5 and CID6 remain unclear.


:

Pssm-ID: 270554  Cd Length: 43  Bit Score: 81.54  E-value: 2.32e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1315970541 221 NPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLTQLELQ 262
Cdd:cd14371     2 ADVELLSSMFPGVSADSIAEVYEANGGDLDLTIDMLTQLESQ 43
DUF1771 pfam08590
Domain of unknown function (DUF1771); This domain is highly charged and may represent a small ...
 416-486 2.44e-18

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.


:

Pssm-ID: 462528  Cd Length: 62  Bit Score: 79.10  E-value: 2.44e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1315970541 416 ELREEARDHARLRNAYFEQqlivivflqARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRN 486
Cdd:pfam08590   1 RLRAEARKHARKRNELFQK---------AAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62
SMR smart00463
Small MutS-related domain;
498-583 2.23e-11

Small MutS-related domain;


:

Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 60.00  E-value: 2.23e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315970541  498 DRMIDLHGLHVSEAIHVLKHELSVLRSTARAagqrLQVYICVGTGHHTRGSRTPVRlpIAVQRYlLEEEGLDYTEP-QPG 576
Cdd:smart00463   1 KWSLDLHGLTVEEALTALDKFLNNARLKGLE----QKLVIITGKGKHSLGGKSGVK--PALKEH-LRVESFRFAEEgNSG 73


                   ....*..
gi 1315970541  577 LLRVVIY 583
Cdd:smart00463  74 VLVVKLK 80
 
Name Accession Description Interval E-value
CUE_CID7_like cd14371
CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins; ...
 221-262 2.32e-19

CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins; CID7 is encoded by ubiquitously expressed gene CID7. It contains an N-terminal PABC-interacting domain (PAM2 or PABP-interacting motif 2) which is also found in the human Paip1 and Paip2. At this point, it functions as an interaction partner of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. It also harbors an ubiquitin-associated (UBA)-like CUE domain and a C-terminal small MutS-related (SMR) domain. CID5 and CID6 are encoded by gene CID5, CID6, respectively. CID5 is only expressed in immature siliques. The biological function of CID5 and CID6 remain unclear.


Pssm-ID: 270554  Cd Length: 43  Bit Score: 81.54  E-value: 2.32e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1315970541 221 NPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLTQLELQ 262
Cdd:cd14371     2 ADVELLSSMFPGVSADSIAEVYEANGGDLDLTIDMLTQLESQ 43
DUF1771 pfam08590
Domain of unknown function (DUF1771); This domain is highly charged and may represent a small ...
 416-486 2.44e-18

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.


Pssm-ID: 462528  Cd Length: 62  Bit Score: 79.10  E-value: 2.44e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1315970541 416 ELREEARDHARLRNAYFEQqlivivflqARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRN 486
Cdd:pfam08590   1 RLRAEARKHARKRNELFQK---------AAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62
SMR smart00463
Small MutS-related domain;
498-583 2.23e-11

Small MutS-related domain;


Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 60.00  E-value: 2.23e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315970541  498 DRMIDLHGLHVSEAIHVLKHELSVLRSTARAagqrLQVYICVGTGHHTRGSRTPVRlpIAVQRYlLEEEGLDYTEP-QPG 576
Cdd:smart00463   1 KWSLDLHGLTVEEALTALDKFLNNARLKGLE----QKLVIITGKGKHSLGGKSGVK--PALKEH-LRVESFRFAEEgNSG 73


                   ....*..
gi 1315970541  577 LLRVVIY 583
Cdd:smart00463  74 VLVVKLK 80
Smr pfam01713
Smr domain; This family includes the Smr (Small MutS Related) proteins, and the C-terminal ...
 502-562 9.94e-04

Smr domain; This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity. The full-length Swiss:Q86UW6 also has the polynucleotide kinase activity.


Pssm-ID: 460303 [Multi-domain]  Cd Length: 76  Bit Score: 38.22  E-value: 9.94e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1315970541 502 DLHGLHVSEAIHVLKHELsvlrSTARAAGQRlQVYICVGTGHHtrgsrtPVrLPIAVQRYL 562
Cdd:pfam01713   1 DLHGMTVEEAREALDKFL----DDALLAGLR-CVLIIHGKGTH------GV-LRKAVREWL 49
 
Name Accession Description Interval E-value
CUE_CID7_like cd14371
CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins; ...
 221-262 2.32e-19

CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins; CID7 is encoded by ubiquitously expressed gene CID7. It contains an N-terminal PABC-interacting domain (PAM2 or PABP-interacting motif 2) which is also found in the human Paip1 and Paip2. At this point, it functions as an interaction partner of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. It also harbors an ubiquitin-associated (UBA)-like CUE domain and a C-terminal small MutS-related (SMR) domain. CID5 and CID6 are encoded by gene CID5, CID6, respectively. CID5 is only expressed in immature siliques. The biological function of CID5 and CID6 remain unclear.


Pssm-ID: 270554  Cd Length: 43  Bit Score: 81.54  E-value: 2.32e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1315970541 221 NPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEMLTQLELQ 262
Cdd:cd14371     2 ADVELLSSMFPGVSADSIAEVYEANGGDLDLTIDMLTQLESQ 43
DUF1771 pfam08590
Domain of unknown function (DUF1771); This domain is highly charged and may represent a small ...
 416-486 2.44e-18

Domain of unknown function (DUF1771); This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear.


Pssm-ID: 462528  Cd Length: 62  Bit Score: 79.10  E-value: 2.44e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1315970541 416 ELREEARDHARLRNAYFEQqlivivflqARQAYLIGNKALAKELSVKGQLHNMQMKAAHGKAQESIYRQRN 486
Cdd:pfam08590   1 RLRAEARKHARKRNELFQK---------AAEAYRRGDGAAAKELSEQGKEHGEKMEEANRQAAEAIFEENN 62
SMR smart00463
Small MutS-related domain;
498-583 2.23e-11

Small MutS-related domain;


Pssm-ID: 214676 [Multi-domain]  Cd Length: 80  Bit Score: 60.00  E-value: 2.23e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1315970541  498 DRMIDLHGLHVSEAIHVLKHELSVLRSTARAagqrLQVYICVGTGHHTRGSRTPVRlpIAVQRYlLEEEGLDYTEP-QPG 576
Cdd:smart00463   1 KWSLDLHGLTVEEALTALDKFLNNARLKGLE----QKLVIITGKGKHSLGGKSGVK--PALKEH-LRVESFRFAEEgNSG 73


                   ....*..
gi 1315970541  577 LLRVVIY 583
Cdd:smart00463  74 VLVVKLK 80
Smr pfam01713
Smr domain; This family includes the Smr (Small MutS Related) proteins, and the C-terminal ...
 502-562 9.94e-04

Smr domain; This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity. The full-length Swiss:Q86UW6 also has the polynucleotide kinase activity.


Pssm-ID: 460303 [Multi-domain]  Cd Length: 76  Bit Score: 38.22  E-value: 9.94e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1315970541 502 DLHGLHVSEAIHVLKHELsvlrSTARAAGQRlQVYICVGTGHHtrgsrtPVrLPIAVQRYL 562
Cdd:pfam01713   1 DLHGMTVEEAREALDKFL----DDALLAGLR-CVLIIHGKGTH------GV-LRKAVREWL 49
CUE cd14279
CUE domain found in ubiquitin-binding CUE proteins; This family includes many coupling of ...
 221-256 2.36e-03

CUE domain found in ubiquitin-binding CUE proteins; This family includes many coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domain containing proteins that are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. CUE domains form three-helix bundle structures and are distantly related to the ubiquitin-associated (UBA) domains which are widely occurring ubiquitin-binding motifs found in a broad range of cellular proteins in species ranging from yeast to human. The majority of family members contain one CUE domain, but some family members from fungi harbor two CUE domains.


Pssm-ID: 270465  Cd Length: 38  Bit Score: 35.91  E-value: 2.36e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1315970541 221 NPVEFLASQFPGFAAESLAEVYFANGCDLNLTIEML 256
Cdd:cd14279     2 EKLEQLQEMFPDLDEEVLEDVLEANNGDVEAAIDAL 37
 
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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