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Conserved domains on  [gi|240256103|ref|NP_194738|]
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golgin family A protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SMC_prok_B super family cl37069
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 44-150 1.15e-03

chromosome segregation protein SMC, common bacterial 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. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


The actual alignment was detected with superfamily member TIGR02168:

Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 41.20  E-value: 1.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103    44 LNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIdfsqfenpvkhaSEVEEKVYELQKQVFGLKREV 123
Cdd:TIGR02168  234 LEELREELEELQEELKEAEEELEELTAELQELEEKLEEL----RLEV------------SELEEEIEELQKELYALANEI 297

                           90       100
                   ....*....|....*....|....*..
gi 240256103   124 EtqrkrRLEVEAELADKKVAQLSSKLE 150
Cdd:TIGR02168  298 S-----RLEQQKQILRERLANLERQLE 319
 
Name Accession Description Interval E-value
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 44-150 1.15e-03

chromosome segregation protein SMC, common bacterial 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. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 41.20  E-value: 1.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103    44 LNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIdfsqfenpvkhaSEVEEKVYELQKQVFGLKREV 123
Cdd:TIGR02168  234 LEELREELEELQEELKEAEEELEELTAELQELEEKLEEL----RLEV------------SELEEEIEELQKELYALANEI 297

                           90       100
                   ....*....|....*....|....*..
gi 240256103   124 EtqrkrRLEVEAELADKKVAQLSSKLE 150
Cdd:TIGR02168  298 S-----RLEQQKQILRERLANLERQLE 319
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
44-152 6.18e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.89  E-value: 6.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103  44 LNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIdfSQFENPVKHASEVEEKVYE------LQKQVF 117
Cdd:PRK03918 233 LEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEEL----KKEI--EELEEKVKELKELKEKAEEyiklseFYEEYL 306

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 240256103 118 GLKREVEtQRKRRLEVEAELADKKVAQLSSKLENI 152
Cdd:PRK03918 307 DELREIE-KRLSRLEEEINGIEERIKELEEKEERL 340
Tropomyosin_1 pfam12718
Tropomyosin like; This family is a set of eukaryotic tropomyosins. Within the yeast Tpm1 and ...
 51-153 6.61e-03

Tropomyosin like; This family is a set of eukaryotic tropomyosins. Within the yeast Tpm1 and Tpm2, biochemical and sequence analyses indicate that Tpm2p spans four actin monomers along a filament, whereas Tpm1p spans five. Despite its shorter length, Tpm2p can compete with Tpm1p for binding to F-actin. Over-expression of Tpm2p in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1p. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis. The family also contains higher eukaryote Tpm3 members.


Pssm-ID: 403808 [Multi-domain]  Cd Length: 142  Bit Score: 36.90  E-value: 6.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103   51 VSALQSIIKEKNQELLSKEEKIRGLElyirEKPYLFESEIDfsQFENPVKHASEVEEKVYELQKQVFGLKRevetqRKRR 130
Cdd:pfam12718  16 AEELEEKVKELEQENLEKEQEIKSLT----HKNQQLEEEVE--KLEEQLKEAKEKAEESEKLKTNNENLTR-----KIQL 84

                          90       100
                  ....*....|....*....|...
gi 240256103  131 LEVEAELADKKVAQLSSKLENID 153
Cdd:pfam12718  85 LEEELEESDKRLKETTEKLRETD 107
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 41-152 7.05e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 37.60  E-value: 7.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103  41 NHLLNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIDfsQFENPVKHASE-----VEEKVYE-LQK 114
Cdd:COG1579   23 EHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRL----ELEIE--EVEARIKKYEEqlgnvRNNKEYEaLQK 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 240256103 115 QVFGLKREVETQRKRRLEVEAEL--ADKKVAQLSSKLENI 152
Cdd:COG1579   97 EIESLKRRISDLEDEILELMERIeeLEEELAELEAELAEL 136
 
Name Accession Description Interval E-value
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 44-150 1.15e-03

chromosome segregation protein SMC, common bacterial 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. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 41.20  E-value: 1.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103    44 LNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIdfsqfenpvkhaSEVEEKVYELQKQVFGLKREV 123
Cdd:TIGR02168  234 LEELREELEELQEELKEAEEELEELTAELQELEEKLEEL----RLEV------------SELEEEIEELQKELYALANEI 297

                           90       100
                   ....*....|....*....|....*..
gi 240256103   124 EtqrkrRLEVEAELADKKVAQLSSKLE 150
Cdd:TIGR02168  298 S-----RLEQQKQILRERLANLERQLE 319
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 44-151 4.00e-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: 39.28  E-value: 4.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103    44 LNELKSTVSALQSIIKEKNQELLSK-------EEKIRGLELYIRE---KPYLFESEIDFSQFENPvKHASEVEEK---VY 110
Cdd:TIGR02169  800 LSKLEEEVSRIEARLREIEQKLNRLtlekeylEKEIQELQEQRIDlkeQIKSIEKEIENLNGKKE-ELEEELEELeaaLR 878

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 240256103   111 ELQKQVFGLKREVET---------QRKRRLEVEAELADKKVAQLSSKLEN 151
Cdd:TIGR02169  879 DLESRLGDLKKERDEleaqlreleRKIEELEAQIEKKRKRLSELKAKLEA 928
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 46-153 4.28e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 39.23  E-value: 4.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103   46 ELKSTVSALQSIIKEKNQELLSKEEKIrgLELYIREKPYLFESEIDFSQFE-NPVKHA--------SEVEEKVYELQKQV 116
Cdd:TIGR04523 521 SLKEKIEKLESEKKEKESKISDLEDEL--NKDDFELKKENLEKEIDEKNKEiEELKQTqkslkkkqEEKQELIDQKEKEK 598

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 240256103  117 FGLKREVE--TQRKRRLEVEAELADKKVAQLSSKLENID 153
Cdd:TIGR04523 599 KDLIKEIEekEKKISSLEKELEKAKKENEKLSSIIKNIK 637
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
44-152 6.18e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.89  E-value: 6.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103  44 LNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIdfSQFENPVKHASEVEEKVYE------LQKQVF 117
Cdd:PRK03918 233 LEELKEEIEELEKELESLEGSKRKLEEKIRELEERIEEL----KKEI--EELEEKVKELKELKEKAEEyiklseFYEEYL 306

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 240256103 118 GLKREVEtQRKRRLEVEAELADKKVAQLSSKLENI 152
Cdd:PRK03918 307 DELREIE-KRLSRLEEEINGIEERIKELEEKEERL 340
Tropomyosin_1 pfam12718
Tropomyosin like; This family is a set of eukaryotic tropomyosins. Within the yeast Tpm1 and ...
 51-153 6.61e-03

Tropomyosin like; This family is a set of eukaryotic tropomyosins. Within the yeast Tpm1 and Tpm2, biochemical and sequence analyses indicate that Tpm2p spans four actin monomers along a filament, whereas Tpm1p spans five. Despite its shorter length, Tpm2p can compete with Tpm1p for binding to F-actin. Over-expression of Tpm2p in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1p. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis. The family also contains higher eukaryote Tpm3 members.


Pssm-ID: 403808 [Multi-domain]  Cd Length: 142  Bit Score: 36.90  E-value: 6.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103   51 VSALQSIIKEKNQELLSKEEKIRGLElyirEKPYLFESEIDfsQFENPVKHASEVEEKVYELQKQVFGLKRevetqRKRR 130
Cdd:pfam12718  16 AEELEEKVKELEQENLEKEQEIKSLT----HKNQQLEEEVE--KLEEQLKEAKEKAEESEKLKTNNENLTR-----KIQL 84

                          90       100
                  ....*....|....*....|...
gi 240256103  131 LEVEAELADKKVAQLSSKLENID 153
Cdd:pfam12718  85 LEEELEESDKRLKETTEKLRETD 107
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 41-152 7.05e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 37.60  E-value: 7.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 240256103  41 NHLLNELKSTVSALQSIIKEKNQELLSKEEKIRGLELYIREKpylfESEIDfsQFENPVKHASE-----VEEKVYE-LQK 114
Cdd:COG1579   23 EHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRL----ELEIE--EVEARIKKYEEqlgnvRNNKEYEaLQK 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 240256103 115 QVFGLKREVETQRKRRLEVEAEL--ADKKVAQLSSKLENI 152
Cdd:COG1579   97 EIESLKRRISDLEDEILELMERIeeLEEELAELEAELAEL 136
 
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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