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Conserved domains on  [gi|30684467|ref|NP_196860|]
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structural maintenance of chromosomes protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
COG4913 super family cl25907
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
268-433 1.85e-06

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


The actual alignment was detected with superfamily member COG4913:

Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 51.45  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  268 ETLAKIR-LCSRLEGLLIRKRQLSNGDSP---DIHAQKVDKLRVLLESLANSTSKAEKRISENRLQKEEA----LKARVV 339
Cdd:COG4913  252 ELLEPIReLAERYAAARERLAELEYLRAAlrlWFAQRRLELLEAELEELRAELARLEAELERLEARLDALreelDELEAQ 331
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  340 KANETGEKEKELGAEIAQLEKQRDE-------LEADLKRVNLSLAAAQARFRNATEERDQFGEANNQIIAHLKTKDDDLS 412
Cdd:COG4913  332 IRGNGGDRLEQLEREIERLERELEErerrrarLEALLAALGLPLPASAEEFAALRAEAAALLEALEEELEALEEALAEAE 411
                        170       180
                 ....*....|....*....|.
gi 30684467  413 KSVVACKKEAEVIKTWINFLE 433
Cdd:COG4913  412 AALRDLRRELRELEAEIASLE 432
 
Name Accession Description Interval E-value
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
268-433 1.85e-06

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 51.45  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  268 ETLAKIR-LCSRLEGLLIRKRQLSNGDSP---DIHAQKVDKLRVLLESLANSTSKAEKRISENRLQKEEA----LKARVV 339
Cdd:COG4913  252 ELLEPIReLAERYAAARERLAELEYLRAAlrlWFAQRRLELLEAELEELRAELARLEAELERLEARLDALreelDELEAQ 331
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  340 KANETGEKEKELGAEIAQLEKQRDE-------LEADLKRVNLSLAAAQARFRNATEERDQFGEANNQIIAHLKTKDDDLS 412
Cdd:COG4913  332 IRGNGGDRLEQLEREIERLERELEErerrrarLEALLAALGLPLPASAEEFAALRAEAAALLEALEEELEALEEALAEAE 411
                        170       180
                 ....*....|....*....|.
gi 30684467  413 KSVVACKKEAEVIKTWINFLE 433
Cdd:COG4913  412 AALRDLRRELRELEAEIASLE 432
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
221-391 1.96e-04

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: 44.67  E-value: 1.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    221 INAEMLRIDAEASDLRKKLEKMNA--SQIPQESEDKEHKETPLT--IEAFKETLAKIRLcsRLEGLlirKRQLSNGDSPD 296
Cdd:TIGR02169  721 IEKEIEQLEQEEEKLKERLEELEEdlSSLEQEIENVKSELKELEarIEELEEDLHKLEE--ALNDL---EARLSHSRIPE 795
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    297 I--HAQKVDKLRVLLESLANSTSKAEKRISENRLQKEEALKARVVKANETGEKEKELGAEIAQLEKQRDELEADLKRVNL 374
Cdd:TIGR02169  796 IqaELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEA 875
                          170
                   ....*....|....*..
gi 30684467    375 SLAAAQARFRNATEERD 391
Cdd:TIGR02169  876 ALRDLESRLGDLKKERD 892
PRK05431 PRK05431
seryl-tRNA synthetase; Provisional
283-376 9.16e-03

seryl-tRNA synthetase; Provisional


Pssm-ID: 235461 [Multi-domain]  Cd Length: 425  Bit Score: 38.90  E-value: 9.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  283 LIRKRQLSNGDSPDIHA-QKVDKLR----VLLESL---ANSTSKAekrISENRLQKEEA--LKARVvkanetgekeKELG 352
Cdd:PRK05431  13 AVKEALAKRGFPLDVDElLELDEERrelqTELEELqaeRNALSKE---IGQAKRKGEDAeaLIAEV----------KELK 79
                         90       100
                 ....*....|....*....|....
gi 30684467  353 AEIAQLEKQRDELEADLKRVNLSL 376
Cdd:PRK05431  80 EEIKALEAELDELEAELEELLLRI 103
 
Name Accession Description Interval E-value
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
268-433 1.85e-06

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 51.45  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  268 ETLAKIR-LCSRLEGLLIRKRQLSNGDSP---DIHAQKVDKLRVLLESLANSTSKAEKRISENRLQKEEA----LKARVV 339
Cdd:COG4913  252 ELLEPIReLAERYAAARERLAELEYLRAAlrlWFAQRRLELLEAELEELRAELARLEAELERLEARLDALreelDELEAQ 331
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  340 KANETGEKEKELGAEIAQLEKQRDE-------LEADLKRVNLSLAAAQARFRNATEERDQFGEANNQIIAHLKTKDDDLS 412
Cdd:COG4913  332 IRGNGGDRLEQLEREIERLERELEErerrrarLEALLAALGLPLPASAEEFAALRAEAAALLEALEEELEALEEALAEAE 411
                        170       180
                 ....*....|....*....|.
gi 30684467  413 KSVVACKKEAEVIKTWINFLE 433
Cdd:COG4913  412 AALRDLRRELRELEAEIASLE 432
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
221-391 1.96e-04

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: 44.67  E-value: 1.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    221 INAEMLRIDAEASDLRKKLEKMNA--SQIPQESEDKEHKETPLT--IEAFKETLAKIRLcsRLEGLlirKRQLSNGDSPD 296
Cdd:TIGR02169  721 IEKEIEQLEQEEEKLKERLEELEEdlSSLEQEIENVKSELKELEarIEELEEDLHKLEE--ALNDL---EARLSHSRIPE 795
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    297 I--HAQKVDKLRVLLESLANSTSKAEKRISENRLQKEEALKARVVKANETGEKEKELGAEIAQLEKQRDELEADLKRVNL 374
Cdd:TIGR02169  796 IqaELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEA 875
                          170
                   ....*....|....*..
gi 30684467    375 SLAAAQARFRNATEERD 391
Cdd:TIGR02169  876 ALRDLESRLGDLKKERD 892
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
267-576 1.58e-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: 41.97  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    267 KETLAKIRLC----SRLEGLLI-RKRQLsngDSPDIHAQKVDKLRVLLESLanstSKAEKRISENRL-QKEEALKARVVK 340
Cdd:TIGR02168  175 KETERKLERTrenlDRLEDILNeLERQL---KSLERQAEKAERYKELKAEL----RELELALLVLRLeELREELEELQEE 247
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    341 ANETGEKEKELGAEIAQLEKQRDELEADLKRVNLSLAAAQARFRNATE-------------ERDQFGEANNQ----IIAH 403
Cdd:TIGR02168  248 LKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANeisrleqqkqilrERLANLERQLEeleaQLEE 327
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    404 LKTKDDDLSKSVVACKKEAEVIKTWINFLEDtwLLQCSHIETKD-KQTLDELEKHEDYF-SDVAL---------NILSVY 472
Cdd:TIGR02168  328 LESKLDELAEELAELEEKLEELKEELESLEA--ELEELEAELEElESRLEELEEQLETLrSKVAQlelqiaslnNEIERL 405
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    473 KKEVAPLISRIENYVENLKNLGPgSEKPPNADQGDNQVSNPRKILEEEYIDYETKIITTFSIvdnvKEQFQVLQSKLD-- 550
Cdd:TIGR02168  406 EARLERLEDRRERLQQEIEELLK-KLEEAELKELQAELEELEEELEELQEELERLEEALEEL----REELEEAEQALDaa 480
                          330       340
                   ....*....|....*....|....*.
gi 30684467    551 KKDDRRVKELFDDMEKMRQQFESIAR 576
Cdd:TIGR02168  481 ERELAQLQARLDSLERLQENLEGFSE 506
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
299-423 2.51e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 41.08  E-value: 2.51e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467 299 AQKVDKLRVLLESLANSTSKAEKRISENRLQKEEALKArvvkANETGEKEKELGAEIAQLEKQRDELEADLKRVNLSLAA 378
Cdd:COG1196 245 EAELEELEAELEELEAELAELEAELEELRLELEELELE----LEEAQAEEYELLAELARLEQDIARLEERRRELEERLEE 320
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 30684467 379 AQARFRNATEERDQFGEANNQIIAHLKTKDDDLSKSVVACKKEAE 423
Cdd:COG1196 321 LEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEE 365
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
282-455 2.78e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 41.11  E-value: 2.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    282 LLIRKRQLSNGDSPDIHAQKVDKLRVLLESLAN-STSKAEKRISENRL-QKEEALKARVVKANETGE---KEKELGAEIA 356
Cdd:TIGR00618  198 LLTLRSQLLTLCTPCMPDTYHERKQVLEKELKHlREALQQTQQSHAYLtQKREAQEEQLKKQQLLKQlraRIEELRAQEA 277
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467    357 QLEKQRDELeaDLKRVNLSLAAAQARFrnaTEERDQFGEANNQIIAHLKTKDDDLSKSVVACKKEAEVIKTwiNFLEDTW 436
Cdd:TIGR00618  278 VLEETQERI--NRARKAAPLAAHIKAV---TQIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQ--RRLLQTL 350
                          170
                   ....*....|....*....
gi 30684467    437 LLQCSHIETKDKQTLDELE 455
Cdd:TIGR00618  351 HSQEIHIRDAHEVATSIRE 369
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
300-427 3.65e-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: 39.52  E-value: 3.65e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467 300 QKVDKLRVLLESLANSTSKAEKRISENRLQKE------EALKARVVKANE---TGEKEKELGA---EIAQLEKQRDELEA 367
Cdd:COG1579  31 AELAELEDELAALEARLEAAKTELEDLEKEIKrleleiEEVEARIKKYEEqlgNVRNNKEYEAlqkEIESLKRRISDLED 110
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467 368 DLKRVNLSLAAAQARFRNATEERDQFGEANNQIIAHLKTKDDDLSKSVVACKKEAEVIKT 427
Cdd:COG1579 111 EILELMERIEELEEELAELEAELAELEAELEEKKAELDEELAELEAELEELEAEREELAA 170
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
300-412 4.01e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 40.69  E-value: 4.01e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467 300 QKVDKLRVLLESLANSTSKAEKRISenrlQKEEALKARVVKANETGEKEKELGAEIAQLEKQRDELEADLKRVNLSLAAA 379
Cdd:COG1196 274 LELEELELELEEAQAEEYELLAELA----RLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEA 349
                        90       100       110
                ....*....|....*....|....*....|...
gi 30684467 380 QARFRNATEERDQFGEANNQIIAHLKTKDDDLS 412
Cdd:COG1196 350 EEELEEAEAELAEAEEALLEAEAELAEAEEELE 382
PRK05431 PRK05431
seryl-tRNA synthetase; Provisional
283-376 9.16e-03

seryl-tRNA synthetase; Provisional


Pssm-ID: 235461 [Multi-domain]  Cd Length: 425  Bit Score: 38.90  E-value: 9.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30684467  283 LIRKRQLSNGDSPDIHA-QKVDKLR----VLLESL---ANSTSKAekrISENRLQKEEA--LKARVvkanetgekeKELG 352
Cdd:PRK05431  13 AVKEALAKRGFPLDVDElLELDEERrelqTELEELqaeRNALSKE---IGQAKRKGEDAeaLIAEV----------KELK 79
                         90       100
                 ....*....|....*....|....
gi 30684467  353 AEIAQLEKQRDELEADLKRVNLSL 376
Cdd:PRK05431  80 EEIKALEAELDELEAELEELLLRI 103
 
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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