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Conserved domains on  [gi|870870015|gb|KMT20760|]
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hypothetical protein BVRB_1g007300 isoform A [Beta vulgaris subsp. vulgaris]

Protein Classification

coiled-coil domain-containing protein( domain architecture ID 1000037)

coiled-coil domain-containing protein contains a region with alpha-helical coiled-coil sequence signatures that is being annotated by a variety of protein family models, not necessarily indicating family membership

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CCDC66 super family cl37891
Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil ...
 1296-1365 9.48e-04

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.


The actual alignment was detected with superfamily member pfam15236:

Pssm-ID: 434558 [Multi-domain]  Cd Length: 154  Bit Score: 41.32  E-value: 9.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1296 RRQKYLEEAALREAECLQELDRQRTLELEK---DIERQRLLELERA---KTNELRHNLD-----MEKEKQTQReiQRDLE 1364
Cdd:pfam15236   69 ERQKKLEEERRRQEEQEEEERLRREREEEQkqfEEERRKQKEKEEAmtrKTQALLQAMQkaqelAQRLKQEQR--IRELA 146


                   .
gi 870870015  1365 Q 1365
Cdd:pfam15236  147 E 147
SMC_N super family cl47134
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 1148-1368 4.27e-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: 41.98  E-value: 4.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1148 RVGEMEK---RICQALSKIKCEEDEAKKALEEALSTCQSKEFDPQFGNTRESVLQvlANLTSVQSYLDIFAEKIdqeare 1224
Cdd:TIGR02169  682 RLEGLKRelsSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLK--ERLEELEEDLSSLEQEI------ 753

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1225 lEEAELEMDILQKEVPLLEISDHHHEVAVPS-SDRKGVHCLQQIKDDIRSLEKSRIREEIIERR-QKKLMLRHRRQKYLE 1302
Cdd:TIGR02169  754 -ENVKSELKELEARIEELEEDLHKLEEALNDlEARLSHSRIPEIQAELSKLEEEVSRIEARLREiEQKLNRLTLEKEYLE 832

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 870870015  1303 EA-----ALREAECLQELDRQRTLE-LEKDIER-QRLLELERAKTNELRHNL-DMEKE----KQTQREIQRDLEQVES 1368
Cdd:TIGR02169  833 KEiqelqEQRIDLKEQIKSIEKEIEnLNGKKEElEEELEELEAALRDLESRLgDLKKErdelEAQLRELERKIEELEA 910
 
Name Accession Description Interval E-value
CCDC66 pfam15236
Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil ...
 1296-1365 9.48e-04

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.


Pssm-ID: 434558 [Multi-domain]  Cd Length: 154  Bit Score: 41.32  E-value: 9.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1296 RRQKYLEEAALREAECLQELDRQRTLELEK---DIERQRLLELERA---KTNELRHNLD-----MEKEKQTQReiQRDLE 1364
Cdd:pfam15236   69 ERQKKLEEERRRQEEQEEEERLRREREEEQkqfEEERRKQKEKEEAmtrKTQALLQAMQkaqelAQRLKQEQR--IRELA 146


                   .
gi 870870015  1365 Q 1365
Cdd:pfam15236  147 E 147
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 1148-1368 4.27e-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: 41.98  E-value: 4.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1148 RVGEMEK---RICQALSKIKCEEDEAKKALEEALSTCQSKEFDPQFGNTRESVLQvlANLTSVQSYLDIFAEKIdqeare 1224
Cdd:TIGR02169  682 RLEGLKRelsSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLK--ERLEELEEDLSSLEQEI------ 753

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1225 lEEAELEMDILQKEVPLLEISDHHHEVAVPS-SDRKGVHCLQQIKDDIRSLEKSRIREEIIERR-QKKLMLRHRRQKYLE 1302
Cdd:TIGR02169  754 -ENVKSELKELEARIEELEEDLHKLEEALNDlEARLSHSRIPEIQAELSKLEEEVSRIEARLREiEQKLNRLTLEKEYLE 832

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 870870015  1303 EA-----ALREAECLQELDRQRTLE-LEKDIER-QRLLELERAKTNELRHNL-DMEKE----KQTQREIQRDLEQVES 1368
Cdd:TIGR02169  833 KEiqelqEQRIDLKEQIKSIEKEIEnLNGKKEElEEELEELEAALRDLESRLgDLKKErdelEAQLRELERKIEELEA 910
 
Name Accession Description Interval E-value
CCDC66 pfam15236
Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil ...
 1296-1365 9.48e-04

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.


Pssm-ID: 434558 [Multi-domain]  Cd Length: 154  Bit Score: 41.32  E-value: 9.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1296 RRQKYLEEAALREAECLQELDRQRTLELEK---DIERQRLLELERA---KTNELRHNLD-----MEKEKQTQReiQRDLE 1364
Cdd:pfam15236   69 ERQKKLEEERRRQEEQEEEERLRREREEEQkqfEEERRKQKEKEEAmtrKTQALLQAMQkaqelAQRLKQEQR--IRELA 146


                   .
gi 870870015  1365 Q 1365
Cdd:pfam15236  147 E 147
MAP7 pfam05672
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ...
 1288-1371 3.59e-03

MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.


Pssm-ID: 461709 [Multi-domain]  Cd Length: 153  Bit Score: 39.64  E-value: 3.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1288 QKKLMLRHRRQKYLEEAALREAEcLQELDRQRTLELEkdiERQRLLELERAKtnelrhnlDMEKEKQTQREIQRDLEQVE 1367
Cdd:pfam05672   40 EERLRKEELRRRAEEERARREEE-ARRLEEERRREEE---ERQRKAEEEAEE--------REQREQEEQERLQKQKEEAE 107


                   ....
gi 870870015  1368 SGSR 1371
Cdd:pfam05672  108 AKAR 111
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 1288-1393 3.86e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 41.65  E-value: 3.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1288 QKKLMLRHRRQKYLEEAALREAE-CLQELDRQRTLELE----KDIERQRLLELERAKTNELRHNLD-MEKEKQTQREIqr 1361
Cdd:pfam17380  504 RKQAMIEEERKRKLLEKEMEERQkAIYEEERRREAEEErrkqQEMEERRRIQEQMRKATEERSRLEaMEREREMMRQI-- 581

                           90       100       110
                   ....*....|....*....|....*....|..
gi 870870015  1362 dleqVESGSRppRREFSSSTHSSRPRDRYRDR 1393
Cdd:pfam17380  582 ----VESEKA--RAEYEATTPITTIKPIYRPR 607
CALCOCO1 pfam07888
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ...
 1288-1388 3.99e-03

Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.


Pssm-ID: 462303 [Multi-domain]  Cd Length: 488  Bit Score: 41.42  E-value: 3.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1288 QKKLMLRHRRQKYLEEAALREAECL---QELDRQRTLELEKDIE--RQRLL----ELERAKtNELRHNLDMEKEKQTQRE 1358
Cdd:pfam07888   96 HEELEEKYKELSASSEELSEEKDALlaqRAAHEARIRELEEDIKtlTQRVLeretELERMK-ERAKKAGAQRKEEEAERK 174

                           90       100       110
                   ....*....|....*....|....*....|.
gi 870870015  1359 -IQRDLEQVESGSRPPRREFSSSTHSSRPRD 1388
Cdd:pfam07888  175 qLQAKLQQTEEELRSLSKEFQELRNSLAQRD 205
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 1148-1368 4.27e-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: 41.98  E-value: 4.27e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1148 RVGEMEK---RICQALSKIKCEEDEAKKALEEALSTCQSKEFDPQFGNTRESVLQvlANLTSVQSYLDIFAEKIdqeare 1224
Cdd:TIGR02169  682 RLEGLKRelsSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLK--ERLEELEEDLSSLEQEI------ 753

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 870870015  1225 lEEAELEMDILQKEVPLLEISDHHHEVAVPS-SDRKGVHCLQQIKDDIRSLEKSRIREEIIERR-QKKLMLRHRRQKYLE 1302
Cdd:TIGR02169  754 -ENVKSELKELEARIEELEEDLHKLEEALNDlEARLSHSRIPEIQAELSKLEEEVSRIEARLREiEQKLNRLTLEKEYLE 832

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 870870015  1303 EA-----ALREAECLQELDRQRTLE-LEKDIER-QRLLELERAKTNELRHNL-DMEKE----KQTQREIQRDLEQVES 1368
Cdd:TIGR02169  833 KEiqelqEQRIDLKEQIKSIEKEIEnLNGKKEElEEELEELEAALRDLESRLgDLKKErdelEAQLRELERKIEELEA 910
 
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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