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Conserved domains on  [gi|365192541|ref|NP_001242944|]
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homologous-pairing protein 2 homolog isoform 4 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LZ3wCH pfam18517
Leucine zipper with capping helix domain; This domain is found at the C-terminal region of ...
 75-131 1.43e-15

Leucine zipper with capping helix domain; This domain is found at the C-terminal region of Hop2 and Mnd1 proteins. In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (for homologous pairing; also known as TBPIP) is expressed specifically during meiosis, same as Mnd1 (for meiotic nuclear divisions 1). The C-terminal region of both Hop2 and Mnd1, folds into three alpha-helices that are interrupted by two short non-helical regions. These alpha-helices of the two proteins together form a parallel coiled coil that provides the major interface for heterodimer formation. The non-helical regions form substantially kinked junctions between adjacent leucine zippers: the LZ1-LZ2 and LZ2-LZ3 junctions.This domain is the C-terminal segment of Hop2 and Mnd1 which folds back onto the C-terminal leucine zipper (LZ3) to form a helical bundle-like structure, hence designated LZ3wCH (for LZ3 with capping helices). The LZ3wCH region plays a role in interacting with the Dmc1 nucleofilament.


:

Pssm-ID: 465789  Cd Length: 55  Bit Score: 66.03  E-value: 1.43e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 365192541   75 VTPEEKEQVYRERQKYCKEWRKrkrMATELSDAILEGYPKSKKQFFEEVGIETDEDY 131
Cdd:pfam18517   1 ETPEEKKKATKVAKEAANRWTD---NIFDIKSWIKEKFPKSKKELNEEFGIETDEDY 54
SMC_N super family cl47134
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 5-129 7.04e-03

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


The actual alignment was detected with superfamily member TIGR02169:

Pssm-ID: 481474 [Multi-domain]  Cd Length: 1164  Bit Score: 35.43  E-value: 7.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365192541     5 ADLQVLDGKIVALTAKVQSLQQSCRYMEAELKELSSALT-----TPEMQKEIQELKKECAGYRERLKNIKAATNHvTPEE 79
Cdd:TIGR02169  674 AELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSdasrkIGEIEKEIEQLEQEEEKLKERLEELEEDLSS-LEQE 752

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 365192541    80 KEQVYRERQKYCKEWRKRKRMATELSDAILEGYPKSKKQFFEEVGIETDE 129
Cdd:TIGR02169  753 IENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSK 802
 
Name Accession Description Interval E-value
LZ3wCH pfam18517
Leucine zipper with capping helix domain; This domain is found at the C-terminal region of ...
 75-131 1.43e-15

Leucine zipper with capping helix domain; This domain is found at the C-terminal region of Hop2 and Mnd1 proteins. In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (for homologous pairing; also known as TBPIP) is expressed specifically during meiosis, same as Mnd1 (for meiotic nuclear divisions 1). The C-terminal region of both Hop2 and Mnd1, folds into three alpha-helices that are interrupted by two short non-helical regions. These alpha-helices of the two proteins together form a parallel coiled coil that provides the major interface for heterodimer formation. The non-helical regions form substantially kinked junctions between adjacent leucine zippers: the LZ1-LZ2 and LZ2-LZ3 junctions.This domain is the C-terminal segment of Hop2 and Mnd1 which folds back onto the C-terminal leucine zipper (LZ3) to form a helical bundle-like structure, hence designated LZ3wCH (for LZ3 with capping helices). The LZ3wCH region plays a role in interacting with the Dmc1 nucleofilament.


Pssm-ID: 465789  Cd Length: 55  Bit Score: 66.03  E-value: 1.43e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 365192541   75 VTPEEKEQVYRERQKYCKEWRKrkrMATELSDAILEGYPKSKKQFFEEVGIETDEDY 131
Cdd:pfam18517   1 ETPEEKKKATKVAKEAANRWTD---NIFDIKSWIKEKFPKSKKELNEEFGIETDEDY 54
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 5-129 7.04e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 35.43  E-value: 7.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365192541     5 ADLQVLDGKIVALTAKVQSLQQSCRYMEAELKELSSALT-----TPEMQKEIQELKKECAGYRERLKNIKAATNHvTPEE 79
Cdd:TIGR02169  674 AELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSdasrkIGEIEKEIEQLEQEEEKLKERLEELEEDLSS-LEQE 752

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 365192541    80 KEQVYRERQKYCKEWRKRKRMATELSDAILEGYPKSKKQFFEEVGIETDE 129
Cdd:TIGR02169  753 IENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSK 802
 
Name Accession Description Interval E-value
LZ3wCH pfam18517
Leucine zipper with capping helix domain; This domain is found at the C-terminal region of ...
 75-131 1.43e-15

Leucine zipper with capping helix domain; This domain is found at the C-terminal region of Hop2 and Mnd1 proteins. In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (for homologous pairing; also known as TBPIP) is expressed specifically during meiosis, same as Mnd1 (for meiotic nuclear divisions 1). The C-terminal region of both Hop2 and Mnd1, folds into three alpha-helices that are interrupted by two short non-helical regions. These alpha-helices of the two proteins together form a parallel coiled coil that provides the major interface for heterodimer formation. The non-helical regions form substantially kinked junctions between adjacent leucine zippers: the LZ1-LZ2 and LZ2-LZ3 junctions.This domain is the C-terminal segment of Hop2 and Mnd1 which folds back onto the C-terminal leucine zipper (LZ3) to form a helical bundle-like structure, hence designated LZ3wCH (for LZ3 with capping helices). The LZ3wCH region plays a role in interacting with the Dmc1 nucleofilament.


Pssm-ID: 465789  Cd Length: 55  Bit Score: 66.03  E-value: 1.43e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 365192541   75 VTPEEKEQVYRERQKYCKEWRKrkrMATELSDAILEGYPKSKKQFFEEVGIETDEDY 131
Cdd:pfam18517   1 ETPEEKKKATKVAKEAANRWTD---NIFDIKSWIKEKFPKSKKELNEEFGIETDEDY 54
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 5-129 7.04e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 35.43  E-value: 7.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 365192541     5 ADLQVLDGKIVALTAKVQSLQQSCRYMEAELKELSSALT-----TPEMQKEIQELKKECAGYRERLKNIKAATNHvTPEE 79
Cdd:TIGR02169  674 AELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSdasrkIGEIEKEIEQLEQEEEKLKERLEELEEDLSS-LEQE 752

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 365192541    80 KEQVYRERQKYCKEWRKRKRMATELSDAILEGYPKSKKQFFEEVGIETDE 129
Cdd:TIGR02169  753 IENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSK 802
 
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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