NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1034584720|ref|XP_016876162|]
View 

centromere protein J isoform X4 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ClpA super family cl33938
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 888-979 2.34e-04

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


The actual alignment was detected with superfamily member COG0542:

Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 45.07  E-value: 2.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  888 KLNISQDQPPgdnARSQVLREKIIELETEIEKFKAENASLAKLRieresaLEKLRKEIADFEQQKAKELARIEEfKKEEM 967
Cdd:COG0542    401 RVRMEIDSKP---EELDELERRLEQLEIEKEALKKEQDEASFER------LAELRDELAELEEELEALKARWEA-EKELI 470

                           90
                   ....*....|..
gi 1034584720  968 RKLQKERKVFEK 979
Cdd:COG0542    471 EEIQELKEELEQ 482
 
Name Accession Description Interval E-value
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 888-979 2.34e-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: 2.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  888 KLNISQDQPPgdnARSQVLREKIIELETEIEKFKAENASLAKLRieresaLEKLRKEIADFEQQKAKELARIEEfKKEEM 967
Cdd:COG0542    401 RVRMEIDSKP---EELDELERRLEQLEIEKEALKKEQDEASFER------LAELRDELAELEEELEALKARWEA-EKELI 470

                           90
                   ....*....|..
gi 1034584720  968 RKLQKERKVFEK 979
Cdd:COG0542    471 EEIQELKEELEQ 482
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 886-998 1.17e-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: 43.13  E-value: 1.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  886 ELKLNISQDQPPGDNARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKElaRIEEfKKE 965
Cdd:TIGR02169  722 EKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHS--RIPE-IQA 798

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1034584720  966 EMRKLQKERKVFEKYT------TAARTFPDKKEREEIQH 998
Cdd:TIGR02169  799 ELSKLEEEVSRIEARLreieqkLNRLTLEKEYLEKEIQE 837
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 900-973 2.67e-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: 2.67e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELariEEFKKEEMRKLQKE 973
Cdd:pfam03938   29 KKRQAELEAKQKELQKLYEELQKDGALLEEEREEKEQELQKKEQELQQLQQKAQQEL---QKKQQELLQPIQDK 99
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
906-979 6.29e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.43  E-value: 6.29e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034584720  906 LREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEqQKAKELARIEEfKKEEMRKLQKERKVFEK 979
Cdd:PRK03918   236 LKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELE-EKVKELKELKE-KAEEYIKLSEFYEEYLD 307
 
Name Accession Description Interval E-value
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 888-979 2.34e-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: 2.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  888 KLNISQDQPPgdnARSQVLREKIIELETEIEKFKAENASLAKLRieresaLEKLRKEIADFEQQKAKELARIEEfKKEEM 967
Cdd:COG0542    401 RVRMEIDSKP---EELDELERRLEQLEIEKEALKKEQDEASFER------LAELRDELAELEEELEALKARWEA-EKELI 470

                           90
                   ....*....|..
gi 1034584720  968 RKLQKERKVFEK 979
Cdd:COG0542    471 EEIQELKEELEQ 482
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
901-976 4.19e-04

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


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 44.08  E-value: 4.19e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034584720  901 ARSQVLREKIIELETEIEKFKAENASLaklrierESALEKLRKEIADFEqqkakelARIEEFKKEEMRKLQKERKV 976
Cdd:COG2433    406 RELTEEEEEIRRLEEQVERLEAEVEEL-------EAELEEKDERIERLE-------RELSEARSEERREIRKDREI 467
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 900-993 1.07e-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: 1.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADfEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG4942    163 AALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAE-LAAELAELQQEAEELEALIARLEAEAAAAAE 241

                           90
                   ....*....|....
gi 1034584720  980 yTTAARTFPDKKER 993
Cdd:COG4942    242 -RTPAAGFAALKGK 254
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 886-998 1.17e-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: 43.13  E-value: 1.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  886 ELKLNISQDQPPGDNARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKElaRIEEfKKE 965
Cdd:TIGR02169  722 EKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHS--RIPE-IQA 798

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1034584720  966 EMRKLQKERKVFEKYT------TAARTFPDKKEREEIQH 998
Cdd:TIGR02169  799 ELSKLEEEVSRIEARLreieqkLNRLTLEKEYLEKEIQE 837
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-995 1.70e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 42.62  E-value: 1.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG1196    287 QAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEA 366

                           90
                   ....*....|....*.
gi 1034584720  980 YTTAARTFPDKKEREE 995
Cdd:COG1196    367 LLEAEAELAEAEEELE 382
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 885-997 2.28e-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: 41.67  E-value: 2.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  885 NELKLNISQDQPPGDNARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKaKELARIEEFKK 964
Cdd:COG4942    120 PPLALLLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEER-AALEALKAERQ 198

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1034584720  965 EEMRKLQKERKVFEKYTTAArtfpdKKEREEIQ 997
Cdd:COG4942    199 KLLARLEKELAELAAELAEL-----QQEAEELE 226
HlpA COG2825
Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope ...
 901-973 2.38e-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: 2.38e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034584720  901 ARSQVLREKIIELETEIEKFKAENASL-AKLRIERESALEKLRKEIADFEQQKAKELARIEEfkkEEMRKLQKE 973
Cdd:COG2825     54 KRQAELQKLEKELQALQEKLQKEAATLsEEERQKKERELQKKQQELQRKQQEAQQDLQKRQQ---ELLQPILEK 124
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 901-997 2.45e-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: 2.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  901 ARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFkKEEMRKLQKERKVFEKY 980
Cdd:TIGR02168  344 EKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERL-EARLERLEDRRERLQQE 422

                           90
                   ....*....|....*..
gi 1034584720  981 TTAARTFPDKKEREEIQ 997
Cdd:TIGR02168  423 IEELLKKLEEAELKELQ 439
OmpH pfam03938
Outer membrane protein (OmpH-like); This family includes outer membrane proteins such as OmpH ...
 900-973 2.67e-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: 2.67e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELariEEFKKEEMRKLQKE 973
Cdd:pfam03938   29 KKRQAELEAKQKELQKLYEELQKDGALLEEEREEKEQELQKKEQELQQLQQKAQQEL---QKKQQELLQPIQDK 99
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-995 3.65e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 41.46  E-value: 3.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG1196    280 ELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAE 359

                           90
                   ....*....|....*.
gi 1034584720  980 YTTAARTFPDKKEREE 995
Cdd:COG1196    360 LAEAEEALLEAEAELA 375
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-974 4.01e-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: 4.01e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKER 974
Cdd:COG1196    238 EAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRR 312
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
906-979 6.29e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.43  E-value: 6.29e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034584720  906 LREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEqQKAKELARIEEfKKEEMRKLQKERKVFEK 979
Cdd:PRK03918   236 LKEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELE-EKVKELKELKE-KAEEYIKLSEFYEEYLD 307
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 900-1002 7.83e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 40.31  E-value: 7.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034584720  900 NARSQVLREKIIELETEIEKFKAENASLAKLRIERESALEKLRKEIADFEQQKAKELARIEEFKKEEMRKLQKERKVFEK 979
Cdd:COG1196    308 EERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEE 387

                           90       100
                   ....*....|....*....|...
gi 1034584720  980 YTTAARTfpDKKEREEIQHMATE 1002
Cdd:COG1196    388 LLEALRA--AAELAAQLEELEEA 408
MRP-S26 pfam14943
Mitochondrial ribosome subunit S26; This family of proteins corresponds to mitochondrial ...
 922-977 9.13e-03

Mitochondrial ribosome subunit S26; This family of proteins corresponds to mitochondrial ribosomal subunit S26 in eukaryotes


Pssm-ID: 464391 [Multi-domain]  Cd Length: 168  Bit Score: 37.99  E-value: 9.13e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034584720  922 AENASLAKLRIERESALEKLRKE-----IADFEQQKAKELARIEefkkEEMRKLQKERKVF 977
Cdd:pfam14943   82 EWNAEIAKLREERLAKEAEEREEeilerIEEKEEKEEEKKERAE----EEVRQEKEESKTF 138
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH