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Conserved domains on  [gi|1789133021|ref|NP_001364243|]
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NF-kappa-B essential modulator isoform e [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 206-292 1.43e-19

polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.


:

Pssm-ID: 197361 [Multi-domain]  Cd Length: 87  Bit Score: 82.40  E-value: 1.43e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 206 MQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQ 285
Cdd:cd09803     1 GEIDELAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPVLKAQAEIYKSDFEAERAAREKLHQEKEQLAEQLEYLQ 80


                  ....*..
gi 1789133021 286 REYSKLK 292
Cdd:cd09803    81 RENQELK 87
NEMO pfam11577
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK ...
 44-110 3.22e-17

NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.


:

Pssm-ID: 431942 [Multi-domain]  Cd Length: 67  Bit Score: 75.21  E-value: 3.22e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789133021  44 EQGAPETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLE 110
Cdd:pfam11577   1 DEETLEQMKELLTENHQLKEAMKQSNQAMKERCEELSAWQEKQKEEREFLECRFREARELLRRLSLE 67
zf_C2H2_10 super family cl39752
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin ...
 341-366 3.83e-11

C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.


The actual alignment was detected with superfamily member pfam18414:

Pssm-ID: 436483  Cd Length: 26  Bit Score: 57.22  E-value: 3.83e-11
                          10        20
                  ....*....|....*....|....*.
gi 1789133021 341 PDFCCPKCQYQAPDMDTLQIHVMECI 366
Cdd:pfam18414   1 PKHCCPKCQEQLPDIDTLQIHVMDCI 26
EnvC super family cl34844
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 113-330 7.75e-06

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


The actual alignment was detected with superfamily member COG4942:

Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 47.45  E-value: 7.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 113 DLKRQKEQALREVEhlKRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGR------------RKLAQLQV 180
Cdd:COG4942    20 DAAAEAEAELEQLQ--QEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQElaaleaelaeleKEIAELRA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 181 AYHQLFQEYDNHIKSSVVGSER----------------KRGMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVME 244
Cdd:COG4942    98 ELEAQKEELAELLRALYRLGRQpplalllspedfldavRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELE 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 245 TvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREysKLKASCQESARIEDMRKRHVEVSQAPLPPAPAYLS 324
Cdd:COG4942   178 A---LLAELEEERAALEALKAERQKLLARLEKELAELAAELAE--LQQEAEELEALIARLEAEAAAAAERTPAAGFAALK 252


                  ....*.
gi 1789133021 325 SPLALP 330
Cdd:COG4942   253 GKLPWP 258
 
Name Accession Description Interval E-value
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 206-292 1.43e-19

polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.


Pssm-ID: 197361 [Multi-domain]  Cd Length: 87  Bit Score: 82.40  E-value: 1.43e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 206 MQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQ 285
Cdd:cd09803     1 GEIDELAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPVLKAQAEIYKSDFEAERAAREKLHQEKEQLAEQLEYLQ 80


                  ....*..
gi 1789133021 286 REYSKLK 292
Cdd:cd09803    81 RENQELK 87
CC2-LZ pfam16516
Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a ...
 207-292 4.59e-19

Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a leucine-zipper domain associated with the CC2 coiled-coil region of NF-kappa-B essential modulator, NEMO. It plays a regulatory role, along with the very C-terminal zinc-finger; it contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerization. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated.


Pssm-ID: 465155 [Multi-domain]  Cd Length: 100  Bit Score: 81.18  E-value: 4.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 207 QLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQR 286
Cdd:pfam16516  15 EIDCLQAQLQAAEEALAAKQREIDELKQEIAQKEEDLETISVLKAQAEVYRSDFEAERAAREKLHEEKEQLAAQLEYLQR 94


                  ....*.
gi 1789133021 287 EYSKLK 292
Cdd:pfam16516  95 QNQQLK 100
NEMO pfam11577
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK ...
 44-110 3.22e-17

NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.


Pssm-ID: 431942 [Multi-domain]  Cd Length: 67  Bit Score: 75.21  E-value: 3.22e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789133021  44 EQGAPETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLE 110
Cdd:pfam11577   1 DEETLEQMKELLTENHQLKEAMKQSNQAMKERCEELSAWQEKQKEEREFLECRFREARELLRRLSLE 67
zf_C2H2_10 pfam18414
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin ...
 341-366 3.83e-11

C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.


Pssm-ID: 436483  Cd Length: 26  Bit Score: 57.22  E-value: 3.83e-11
                          10        20
                  ....*....|....*....|....*.
gi 1789133021 341 PDFCCPKCQYQAPDMDTLQIHVMECI 366
Cdd:pfam18414   1 PKHCCPKCQEQLPDIDTLQIHVMDCI 26
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 49-270 1.17e-07

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: 53.91  E-value: 1.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   49 ETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQRE---EKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREV 125
Cdd:TIGR02168  260 AELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRleqQKQILRERLANLERQLEELEAQLEELESKLDELAEEL 339

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  126 EHLK-RCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQLQVAYHQL-FQEYDNHIKSSvvgsERK 203
Cdd:TIGR02168  340 AELEeKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNeIERLEARLERL----EDR 415

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789133021  204 RGMQLEDLKQQLQQAEEAlvAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKL 270
Cdd:TIGR02168  416 RERLQQEIEELLKKLEEA--ELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALDAA 480
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 49-319 7.22e-06

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 48.01  E-value: 7.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  49 ETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREVEHL 128
Cdd:COG1196   270 EELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEA 349

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 129 -KRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQLQVayhqlfQEYDNHIKSSVVGSERKRGMQ 207
Cdd:COG1196   350 eEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQL------EELEEAEEALLERLERLEEEL 423

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 208 LEDLKQQLQQAEEALVAKQEVIDKLKEEAEQhkivmetvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQRE 287
Cdd:COG1196   424 EELEEALAELEEEEEEEEEALEEAAEEEAEL----------EEEEEALLELLAELLEEAALLEAALAELLEELAEAAARL 493

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1789133021 288 YSKLKASCQESARIEDMRKRHVEVSQAPLPPA 319
Cdd:COG1196   494 LLLLEAEADYEGFLEGVKAALLLAGLRGLAGA 525
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 113-330 7.75e-06

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: 47.45  E-value: 7.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 113 DLKRQKEQALREVEhlKRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGR------------RKLAQLQV 180
Cdd:COG4942    20 DAAAEAEAELEQLQ--QEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQElaaleaelaeleKEIAELRA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 181 AYHQLFQEYDNHIKSSVVGSER----------------KRGMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVME 244
Cdd:COG4942    98 ELEAQKEELAELLRALYRLGRQpplalllspedfldavRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELE 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 245 TvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREysKLKASCQESARIEDMRKRHVEVSQAPLPPAPAYLS 324
Cdd:COG4942   178 A---LLAELEEERAALEALKAERQKLLARLEKELAELAAELAE--LQQEAEELEALIARLEAEAAAAAERTPAAGFAALK 252


                  ....*.
gi 1789133021 325 SPLALP 330
Cdd:COG4942   253 GKLPWP 258
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 51-239 2.20e-04

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: 43.51  E-value: 2.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   51 LQRCLEENQELRDAIRQsnqiLRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREVEHLKR 130
Cdd:TIGR02168  700 LAELRKELEELEEELEQ----LRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEE 775

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  131 CQQMAEDK-ASVKAQVTSLLGELQESQSRLEAATKECQALegRRKLAQLQVAYHQLFQEYDNHIKSSVVGSERKRGM--- 206
Cdd:TIGR02168  776 ELAEAEAEiEELEAQIEQLKEELKALREALDELRAELTLL--NEEAANLRERLESLERRIAATERRLEDLEEQIEELsed 853

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1789133021  207 --------------------QLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQH 239
Cdd:TIGR02168  854 ieslaaeieeleelieelesELEALLNERASLEEALALLRSELEELSEELREL 906
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 56-293 6.80e-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.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 38.41  E-value: 6.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   56 EENQELRDAIRQSNQILRERCEELLHFQASQREEKEflmckfqEARKLVErlgLEKLDLKRQKEQALREVEHLKRCQQMA 135
Cdd:pfam02463  173 EALKKLIEETENLAELIIDLEELKLQELKLKEQAKK-------ALEYYQL---KEKLELEEEYLLYLDYLKLNEERIDLL 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  136 EDKASVKAQVTSLLGELQESQSRLEAATKECQALEGR-RKLAQLQVAYHQLFQEYDNHIKSSVVGSERKRGMQLEDLKQQ 214
Cdd:pfam02463  243 QELLRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKeKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKE 322

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1789133021  215 LQQAEEALVAKQEVIDKLKEEAEQHKIVMETvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREYSKLKA 293
Cdd:pfam02463  323 KKKAEKELKKEKEEIEELEKELKELEIKREA---EEEEEEELEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELE 398
 
Name Accession Description Interval E-value
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 206-292 1.43e-19

polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well.


Pssm-ID: 197361 [Multi-domain]  Cd Length: 87  Bit Score: 82.40  E-value: 1.43e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 206 MQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQ 285
Cdd:cd09803     1 GEIDELAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPVLKAQAEIYKSDFEAERAAREKLHQEKEQLAEQLEYLQ 80


                  ....*..
gi 1789133021 286 REYSKLK 292
Cdd:cd09803    81 RENQELK 87
CC2-LZ pfam16516
Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a ...
 207-292 4.59e-19

Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator; CC2-LZ is a leucine-zipper domain associated with the CC2 coiled-coil region of NF-kappa-B essential modulator, NEMO. It plays a regulatory role, along with the very C-terminal zinc-finger; it contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerization. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated.


Pssm-ID: 465155 [Multi-domain]  Cd Length: 100  Bit Score: 81.18  E-value: 4.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 207 QLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQR 286
Cdd:pfam16516  15 EIDCLQAQLQAAEEALAAKQREIDELKQEIAQKEEDLETISVLKAQAEVYRSDFEAERAAREKLHEEKEQLAAQLEYLQR 94


                  ....*.
gi 1789133021 287 EYSKLK 292
Cdd:pfam16516  95 QNQQLK 100
NEMO pfam11577
NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK ...
 44-110 3.22e-17

NF-kappa-B essential modulator NEMO; NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.


Pssm-ID: 431942 [Multi-domain]  Cd Length: 67  Bit Score: 75.21  E-value: 3.22e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789133021  44 EQGAPETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLE 110
Cdd:pfam11577   1 DEETLEQMKELLTENHQLKEAMKQSNQAMKERCEELSAWQEKQKEEREFLECRFREARELLRRLSLE 67
zf_C2H2_10 pfam18414
C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin ...
 341-366 3.83e-11

C2H2 type zinc-finger; This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction.


Pssm-ID: 436483  Cd Length: 26  Bit Score: 57.22  E-value: 3.83e-11
                          10        20
                  ....*....|....*....|....*.
gi 1789133021 341 PDFCCPKCQYQAPDMDTLQIHVMECI 366
Cdd:pfam18414   1 PKHCCPKCQEQLPDIDTLQIHVMDCI 26
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 49-270 1.17e-07

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: 53.91  E-value: 1.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   49 ETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQRE---EKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREV 125
Cdd:TIGR02168  260 AELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRleqQKQILRERLANLERQLEELEAQLEELESKLDELAEEL 339

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  126 EHLK-RCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQLQVAYHQL-FQEYDNHIKSSvvgsERK 203
Cdd:TIGR02168  340 AELEeKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNeIERLEARLERL----EDR 415

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1789133021  204 RGMQLEDLKQQLQQAEEAlvAKQEVIDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAERQAREKL 270
Cdd:TIGR02168  416 RERLQQEIEELLKKLEEA--ELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALDAA 480
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 47-311 1.07e-06

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: 50.84  E-value: 1.07e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   47 APETLQRCLEENQELRDAIRQ-----SNQILRERcEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLDLKRQKEqa 121
Cdd:TIGR02169  260 ISELEKRLEEIEQLLEELNKKikdlgEEEQLRVK-EKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLA-- 336

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  122 lrEVEHLKR-CQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALegRRKLAQLQVAYHQLFQEYDNHIKSSVVGS 200
Cdd:TIGR02169  337 --EIEELEReIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAET--RDELKDYREKLEKLKREINELKRELDRLQ 412

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  201 ERKR--GMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETVpvlkaqadiyKADFQAERQAREKLAEKKELLQ 278
Cdd:TIGR02169  413 EELQrlSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQL----------AADLSKYEQELYDLKEEYDRVE 482

                          250       260       270
                   ....*....|....*....|....*....|...
gi 1789133021  279 EQLEQLQREYSKLKASCQESARIEDMRKRHVEV 311
Cdd:TIGR02169  483 KELSKLQRELAEAEAQARASEERVRGGRAVEEV 515
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 49-319 7.22e-06

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 48.01  E-value: 7.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  49 ETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREVEHL 128
Cdd:COG1196   270 EELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEA 349

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 129 -KRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQLQVayhqlfQEYDNHIKSSVVGSERKRGMQ 207
Cdd:COG1196   350 eEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQL------EELEEAEEALLERLERLEEEL 423

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 208 LEDLKQQLQQAEEALVAKQEVIDKLKEEAEQhkivmetvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQRE 287
Cdd:COG1196   424 EELEEALAELEEEEEEEEEALEEAAEEEAEL----------EEEEEALLELLAELLEEAALLEAALAELLEELAEAAARL 493

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1789133021 288 YSKLKASCQESARIEDMRKRHVEVSQAPLPPA 319
Cdd:COG1196   494 LLLLEAEADYEGFLEGVKAALLLAGLRGLAGA 525
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 113-330 7.75e-06

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: 47.45  E-value: 7.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 113 DLKRQKEQALREVEhlKRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGR------------RKLAQLQV 180
Cdd:COG4942    20 DAAAEAEAELEQLQ--QEIAELEKELAALKKEEKALLKQLAALERRIAALARRIRALEQElaaleaelaeleKEIAELRA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 181 AYHQLFQEYDNHIKSSVVGSER----------------KRGMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVME 244
Cdd:COG4942    98 ELEAQKEELAELLRALYRLGRQpplalllspedfldavRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELE 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 245 TvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREysKLKASCQESARIEDMRKRHVEVSQAPLPPAPAYLS 324
Cdd:COG4942   178 A---LLAELEEERAALEALKAERQKLLARLEKELAELAAELAE--LQQEAEELEALIARLEAEAAAAAERTPAAGFAALK 252


                  ....*.
gi 1789133021 325 SPLALP 330
Cdd:COG4942   253 GKLPWP 258
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
49-227 1.90e-05

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 46.83  E-value: 1.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   49 ETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLD-----LKRQKEQALR 123
Cdd:COG4913    620 AELEEELAEAEERLEALEAELDALQERREALQRLAEYSWDEIDVASAEREIAELEAELERLDASSddlaaLEEQLEELEA 699

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  124 EVEHL-KRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQA-----LEGRRKLAQLQVAYHQLFQEYDNhikssv 197
Cdd:COG4913    700 ELEELeEELDELKGEIGRLEKELEQAEEELDELQDRLEAAEDLARLelralLEERFAAALGDAVERELRENLEE------ 773

                          170       180       190
                   ....*....|....*....|....*....|
gi 1789133021  198 vgserkrgmQLEDLKQQLQQAEEALVAKQE 227
Cdd:COG4913    774 ---------RIDALRARLNRAEEELERAMR 794
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 51-239 2.20e-04

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: 43.51  E-value: 2.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   51 LQRCLEENQELRDAIRQsnqiLRERCEELLHFQASQREEKEFLMCKFQEARKLVERLGLEKLDLKRQKEQALREVEHLKR 130
Cdd:TIGR02168  700 LAELRKELEELEEELEQ----LRKELEELSRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEE 775

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  131 CQQMAEDK-ASVKAQVTSLLGELQESQSRLEAATKECQALegRRKLAQLQVAYHQLFQEYDNHIKSSVVGSERKRGM--- 206
Cdd:TIGR02168  776 ELAEAEAEiEELEAQIEQLKEELKALREALDELRAELTLL--NEEAANLRERLESLERRIAATERRLEDLEEQIEELsed 853

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1789133021  207 --------------------QLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQH 239
Cdd:TIGR02168  854 ieslaaeieeleelieelesELEALLNERASLEEALALLRSELEELSEELREL 906
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 110-314 2.76e-04

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 43.00  E-value: 2.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 110 EKLDLKRQKEQALREVEHLKRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEgrRKLAQLQVAYHQLFQEY 189
Cdd:COG1196   220 EELKELEAELLLLKLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELE--LELEEAQAEEYELLAEL 297

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 190 DNHIKSSVVGSERKR--GMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMETvpVLKAQADIYKADFQAERQAR 267
Cdd:COG1196   298 ARLEQDIARLEERRRelEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEE--AEAELAEAEEALLEAEAELA 375

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1789133021 268 EKLAEKKELLQEQLEQLQREYSKLKASCQESARIEDMRKRHVEVSQA 314
Cdd:COG1196   376 EAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEE 422
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
101-240 2.59e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.90  E-value: 2.59e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  101 RKLVERLGLEKLDLKRQKEQALREVEHLKRCQQMAEDkasVKAQVTsLLGELQESQSRLEAATKECQALEGRRKLAQLQV 180
Cdd:COG4913    210 DDFVREYMLEEPDTFEAADALVEHFDDLERAHEALED---AREQIE-LLEPIRELAERYAAARERLAELEYLRAALRLWF 285

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  181 AYHQLfQEYDNhikssvvgserkrgmQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHK 240
Cdd:COG4913    286 AQRRL-ELLEA---------------ELEELRAELARLEAELERLEARLDALREELDELE 329
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
33-253 2.84e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 39.75  E-value: 2.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  33 LGKPAMLHLPSEQGAPETLQRCLEENQELRDAIRQSNQI-LRERCEELLH-FQASQREEKEFLMCKFQEARKLVERLgle 110
Cdd:COG4717   328 LGLPPDLSPEELLELLDRIEELQELLREAEELEEELQLEeLEQEIAALLAeAGVEDEEELRAALEQAEEYQELKEEL--- 404

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 111 kLDLKRQKEQALREVEHLKRcqqmAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQLQVAYHQLFQEYd 190
Cdd:COG4717   405 -EELEEQLEELLGELEELLE----ALDEEELEEELEELEEELEELEEELEELREELAELEAELEQLEEDGELAELLQEL- 478

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1789133021 191 nhikssvvgserkrgmqlEDLKQQLQQAEE---ALVAKQEVIDKLKEEAEQhkivmETVPVLKAQA 253
Cdd:COG4717   479 ------------------EELKAELRELAEewaALKLALELLEEAREEYRE-----ERLPPVLERA 521
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 70-263 4.99e-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: 38.90  E-value: 4.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   70 QILRERCEELlhfqasqREEKEFLMCKFQEARKLVErlglEKLDLKRQKEQALREVEhlKRCQQMAEDKASVKAQVTSLL 149
Cdd:TIGR02169  677 QRLRERLEGL-------KRELSSLQSELRRIENRLD----ELSQELSDASRKIGEIE--KEIEQLEQEEEKLKERLEELE 743

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  150 GELQESQSRLEAATKECQALEGRrkLAQLQVAYHQLfQEYDNHIKSSVVGSE-RKRGMQLEDLKQQLQQAEEALVAKQEV 228
Cdd:TIGR02169  744 EDLSSLEQEIENVKSELKELEAR--IEELEEDLHKL-EEALNDLEARLSHSRiPEIQAELSKLEEEVSRIEARLREIEQK 820

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1789133021  229 IDKLKEEAEQHKIVMETVPVLKAQADIYKADFQAE 263
Cdd:TIGR02169  821 LNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKE 855
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 41-261 6.70e-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: 38.51  E-value: 6.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   41 LPSEQGAPETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEflmckfqearklverlgleklDLKRQKEQ 120
Cdd:TIGR02169  345 IEEERKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLE---------------------KLKREINE 403

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  121 ALREVEHL-KRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQlqvayhqlfqeydnhiksSVVG 199
Cdd:TIGR02169  404 LKRELDRLqEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQLA------------------ADLS 465

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1789133021  200 SERKrgmQLEDLKQQLQQAEEALVAKQEVIDKLKEEAeqhKIVMETVPVLKAQADIYKADFQ 261
Cdd:TIGR02169  466 KYEQ---ELYDLKEEYDRVEKELSKLQRELAEAEAQA---RASEERVRGGRAVEEVLKASIQ 521
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 56-293 6.80e-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.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 38.41  E-value: 6.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   56 EENQELRDAIRQSNQILRERCEELLHFQASQREEKEflmckfqEARKLVErlgLEKLDLKRQKEQALREVEHLKRCQQMA 135
Cdd:pfam02463  173 EALKKLIEETENLAELIIDLEELKLQELKLKEQAKK-------ALEYYQL---KEKLELEEEYLLYLDYLKLNEERIDLL 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  136 EDKASVKAQVTSLLGELQESQSRLEAATKECQALEGR-RKLAQLQVAYHQLFQEYDNHIKSSVVGSERKRGMQLEDLKQQ 214
Cdd:pfam02463  243 QELLRDEQEEIESSKQEIEKEEEKLAQVLKENKEEEKeKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKE 322

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1789133021  215 LQQAEEALVAKQEVIDKLKEEAEQHKIVMETvpvLKAQADIYKADFQAERQAREKLAEKKELLQEQLEQLQREYSKLKA 293
Cdd:pfam02463  323 KKKAEKELKKEKEEIEELEKELKELEIKREA---EEEEEEELEKLQEKLEQLEEELLAKKKLESERLSSAAKLKEEELE 398
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
112-319 8.12e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 38.36  E-value: 8.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  112 LDLKRQKEQALREVEHLKRCQQMAEDKASVKAQVTSLlgELQESQSRLEAATKECQALegRRKLAQLQVAYHQLFQEYDN 191
Cdd:COG4913    245 EDAREQIELLEPIRELAERYAAARERLAELEYLRAAL--RLWFAQRRLELLEAELEEL--RAELARLEAELERLEARLDA 320

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  192 HiKSSVVGSERKR----GMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQ--------HKIVMETVPVLKAQADIYKAD 259
Cdd:COG4913    321 L-REELDELEAQIrgngGDRLEQLEREIERLERELEERERRRARLEALLAAlglplpasAEEFAALRAEAAALLEALEEE 399

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1789133021  260 FQAERQAREKLAEKKELLQEQLEQLQREYSKLKAscQES---ARIEDMRK---RHVEVSQAPLPPA 319
Cdd:COG4913    400 LEALEEALAEAEAALRDLRRELRELEAEIASLER--RKSnipARLLALRDalaEALGLDEAELPFV 463
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 114-307 9.72e-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: 38.11  E-value: 9.72e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  114 LKRQKEQALR------EVEHLKRcQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEG-----RRKLAQLQVAY 182
Cdd:TIGR02168  205 LERQAEKAERykelkaELRELEL-ALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEkleelRLEVSELEEEI 283

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021  183 HQLFQEYDNH--IKSSVVGSERKRGMQLEDLKQQLQQAEEALVAKQEVIDKLKEEAEQHKIVMEtvpVLKAQADIYKADF 260
Cdd:TIGR02168  284 EELQKELYALanEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLE---ELKEELESLEAEL 360

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1789133021  261 QAERQAREKLAEKKELLQEQLEQLQREYSKLKASC-QESARIEDMRKR 307
Cdd:TIGR02168  361 EELEAELEELESRLEELEEQLETLRSKVAQLELQIaSLNNEIERLEAR 408
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
103-270 9.88e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 37.82  E-value: 9.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 103 LVERLGLEKLDL-KRQKEQALREVEHLKRCQQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRKLAQLQVA 181
Cdd:COG4717    47 LLERLEKEADELfKPQGRKPELNLKELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLLQ 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021 182 YHQLFQEYDNH-----IKSSVVGSERKRGMQLEDLKQQLQQAEEALVAKQEVIDKLKEE-----AEQHKIVMETVPVLKA 251
Cdd:COG4717   127 LLPLYQELEALeaelaELPERLEELEERLEELRELEEELEELEAELAELQEELEELLEQlslatEEELQDLAEELEELQQ 206

                         170
                  ....*....|....*....
gi 1789133021 252 QADIYKADFQAERQAREKL 270
Cdd:COG4717   207 RLAELEEELEEAQEELEEL 225
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
49-174 9.99e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 37.97  E-value: 9.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1789133021   49 ETLQRCLEENQELRDAIRQSNQILRERCEELLHFQASQREEKEflmCKFQEARKLVERLGL----EKLDLKRQKEQALRE 124
Cdd:COG4913    316 ARLDALREELDELEAQIRGNGGDRLEQLEREIERLERELEERE---RRRARLEALLAALGLplpaSAEEFAALRAEAAAL 392

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1789133021  125 VEhlkrcqQMAEDKASVKAQVTSLLGELQESQSRLEAATKECQALEGRRK 174
Cdd:COG4913    393 LE------ALEEELEALEEALAEAEAALRDLRRELRELEAEIASLERRKS 436
 
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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