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Conserved domains on  [gi|2462537544|ref|XP_054230730|]
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centromere protein J isoform X5 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG2433 super family cl43687
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
901-999 1.66e-04

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


The actual alignment was detected with superfamily member COG2433:

Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 45.62  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 901 ARSQVLREKIIELETEIEKFKAENASLaklrierESALEKLRKEIADFEqqkakelARIEEFKKEEMRKLQKERKVfeky 980
Cdd:COG2433   406 RELTEEEEEIRRLEEQVERLEAEVEEL-------EAELEEKDERIERLE-------RELSEARSEERREIRKDREI---- 467

                          90
                  ....*....|....*....
gi 2462537544 981 ttaartfpdKKEREEIQRL 999
Cdd:COG2433   468 ---------SRLDREIERL 477
 
Name Accession Description Interval E-value
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
901-999 1.66e-04

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 45.62  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 901 ARSQVLREKIIELETEIEKFKAENASLaklrierESALEKLRKEIADFEqqkakelARIEEFKKEEMRKLQKERKVfeky 980
Cdd:COG2433   406 RELTEEEEEIRRLEEQVERLEAEVEEL-------EAELEEKDERIERLE-------RELSEARSEERREIRKDREI---- 467

                          90
                  ....*....|....*....
gi 2462537544 981 ttaartfpdKKEREEIQRL 999
Cdd:COG2433   468 ---------SRLDREIERL 477
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 901-998 1.61e-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: 42.35  E-value: 1.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544  901 ARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFkKEEMRKLQKERKVFEKY 980
Cdd:TIGR02168  344 EKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERL-EARLERLEDRRERLQQE 422

                           90
                   ....*....|....*...
gi 2462537544  981 TTAARTFPDKKEREEIQR 998
Cdd:TIGR02168  423 IEELLKKLEEAELKELQA 440
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 900-973 2.81e-03

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 39.10  E-value: 2.81e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462537544 900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELariEEFKKEEMRKLQKE 973
Cdd:pfam03938  29 KKRQAELEAKQKELQKLYEELQKDGALLEEEREEKEQELQKKEQELQQLQQKAQQEL---QKKQQELLQPIQDK 99
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
906-979 7.57e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.43  E-value: 7.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462537544 906 LREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEqQKAKELARIEEfKKEEMRKLQKERKVFEK 979
Cdd:PRK03918  236 LKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELE-EKVKELKELKE-KAEEYIKLSEFYEEYLD 307
 
Name Accession Description Interval E-value
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
901-999 1.66e-04

Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 45.62  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 901 ARSQVLREKIIELETEIEKFKAENASLaklrierESALEKLRKEIADFEqqkakelARIEEFKKEEMRKLQKERKVfeky 980
Cdd:COG2433   406 RELTEEEEEIRRLEEQVERLEAEVEEL-------EAELEEKDERIERLE-------RELSEARSEERREIRKDREI---- 467

                          90
                  ....*....|....*....
gi 2462537544 981 ttaartfpdKKEREEIQRL 999
Cdd:COG2433   468 ---------SRLDREIERL 477
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 888-979 2.48e-04

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 45.07  E-value: 2.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 888 KLNISQDQPPgdnARSQVLREKIIELETEIEKFKAENASLAKLRieresaLEKLRKEIADFEQQKAKELARIEEfKKEEM 967
Cdd:COG0542   401 RVRMEIDSKP---EELDELERRLEQLEIEKEALKKEQDEASFER------LAELRDELAELEEELEALKARWEA-EKELI 470

                          90
                  ....*....|..
gi 2462537544 968 RKLQKERKVFEK 979
Cdd:COG0542   471 EEIQELKEELEQ 482
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 885-999 4.94e-04

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 43.60  E-value: 4.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 885 NELKLNISQDQPPGDNARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKaKELARIEEFKK 964
Cdd:COG4942   120 PPLALLLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEER-AALEALKAERQ 198

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2462537544 965 EEMRKLQKERKVFEKYTTAArtfpdKKEREEIQRL 999
Cdd:COG4942   199 KLLARLEKELAELAAELAEL-----QQEAEELEAL 228
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 900-993 1.11e-03

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 42.44  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADfEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG4942   163 AALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAE-LAAELAELQQEAEELEALIARLEAEAAAAAE 241

                          90
                  ....*....|....
gi 2462537544 980 yTTAARTFPDKKER 993
Cdd:COG4942   242 -RTPAAGFAALKGK 254
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 901-998 1.61e-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: 42.35  E-value: 1.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544  901 ARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFkKEEMRKLQKERKVFEKY 980
Cdd:TIGR02168  344 EKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERL-EARLERLEDRRERLQQE 422

                           90
                   ....*....|....*...
gi 2462537544  981 TTAARTFPDKKEREEIQR 998
Cdd:TIGR02168  423 IEELLKKLEEAELKELQA 440
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-995 1.76e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 42.23  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG1196   287 QAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEA 366

                          90
                  ....*....|....*.
gi 2462537544 980 YTTAARTFPDKKEREE 995
Cdd:COG1196   367 LLEAEAELAEAEEELE 382
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 886-999 2.32e-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: 2.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544  886 ELKLNISQDQPPGDNARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKElaRIEEfKKE 965
Cdd:TIGR02169  722 EKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHS--RIPE-IQA 798

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2462537544  966 EMRKLQKERKVFEKYT------TAARTFPDKKEREEIQRL 999
Cdd:TIGR02169  799 ELSKLEEEVSRIEARLreieqkLNRLTLEKEYLEKEIQEL 838
HlpA COG2825
Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope ...
 901-973 2.45e-03

Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442073 [Multi-domain]  Cd Length: 171  Bit Score: 39.82  E-value: 2.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462537544 901 ARSQVLREKIIELETEIEKFKAENASL-AKLRIERESALEKLRKEIADFEQQKAKELARIEEfkkEEMRKLQKE 973
Cdd:COG2825    54 KRQAELQKLEKELQALQEKLQKEAATLsEEERQKKERELQKKQQELQRKQQEAQQDLQKRQQ---ELLQPILEK 124
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 900-973 2.81e-03

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 39.10  E-value: 2.81e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462537544 900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELariEEFKKEEMRKLQKE 973
Cdd:pfam03938  29 KKRQAELEAKQKELQKLYEELQKDGALLEEEREEKEQELQKKEQELQQLQQKAQQEL---QKKQQELLQPIQDK 99
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-974 4.21e-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: 4.21e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462537544 900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKER 974
Cdd:COG1196   238 EAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRR 312
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-999 6.49e-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: 6.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG1196   308 EERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEE 387

                          90       100
                  ....*....|....*....|
gi 2462537544 980 YTTAARTfpDKKEREEIQRL 999
Cdd:COG1196   388 LLEALRA--AAELAAQLEEL 405
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
906-979 7.57e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.43  E-value: 7.57e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462537544 906 LREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEqQKAKELARIEEfKKEEMRKLQKERKVFEK 979
Cdd:PRK03918  236 LKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELE-EKVKELKELKE-KAEEYIKLSEFYEEYLD 307
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 908-999 7.57e-03

Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.


Pssm-ID: 461098 [Multi-domain]  Cd Length: 140  Bit Score: 37.94  E-value: 7.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 908 EKIIEletEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKERKVFEKYTTAARTF 987
Cdd:pfam03938   8 QKILE---ESPEGKAAQAQLEKKFKKRQAELEAKQKELQKLYEELQKDGALLEEEREEKEQELQKKEQELQQLQQKAQQE 84

                          90
                  ....*....|..
gi 2462537544 988 PDKKEREEIQRL 999
Cdd:pfam03938  85 LQKKQQELLQPI 96
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
883-998 8.86e-03

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 40.00  E-value: 8.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462537544 883 LGNELKLNISQDQPPGDNARSQVLREKIIELETEIekfkaenASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEF 962
Cdd:COG3206   245 LRAQLGSGPDALPELLQSPVIQQLRAQLAELEAEL-------AELSARYTPNHPDVIALRAQIAALRAQLQQEAQRILAS 317

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2462537544 963 KKEEMRKLQKE----RKVFEKYTTAARTFPDK-KEREEIQR 998
Cdd:COG3206   318 LEAELEALQAReaslQAQLAQLEARLAELPELeAELRRLER 358
 
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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