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Conserved domains on  [gi|19705545|ref|NP_599238|]
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guanine nucleotide exchange factor for Rab-3A [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rab11BD_RAB3IP_like super family cl41767
Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 ...
 216-373 2.14e-103

Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 (RAB3IL1) and similar proteins; The family includes RAB3IP and RAB3IL1, as well as Rab guanine nucleotide exchange factor SEC2 from yeast. RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. SEC2 is a guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. SEC2 binds the Rab GTPase YPT32 but does not have exchange activity on YPT32. The model corresponds to the Rab11a/Rab11b-binding region of family members which lies within the carboxy-terminus, a region distinct from their GEF domain and Rab3a-binding region.


The actual alignment was detected with superfamily member cd21069:

Pssm-ID: 425398  Cd Length: 163  Bit Score: 301.78  E-value: 2.14e-103
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 216 EGKEVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLPNV-----E 290
Cdd:cd21069   1 EGKEVDTVLFAEFQAWKESPTLDRSCPFLSRIYREDIGPCLDFTKRELSDLVQSAVENNTLTIEPVASQALPVVkasavE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 291 CNNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVRQDAEPMFWEIMRLRKGMSLAKL 370
Cdd:cd21069  81 CGGPKKCALSGLSRTCRHRIKLGDSGNYYYISPSCRARITAVCNFFTYIRYIQQGLVRQDAEQMFWEVMRLRREMSLAKL 160


                ...
gi 19705545 371 GFF 373
Cdd:cd21069 161 GFY 163
Sec2p super family cl05764
GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor ...
 92-160 4.87e-11

GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.


The actual alignment was detected with superfamily member pfam06428:

Pssm-ID: 428938 [Multi-domain]  Cd Length: 92  Bit Score: 58.74  E-value: 4.87e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19705545    92 KLKDEECERLC--KVRAQLEQELEELTASLFEEAHKMVREANMKQAASEK-------QLKEAWGKIDMLQAEVTALKT 160
Cdd:pfam06428   1 ELKEEKKKRLEaeKEKKKLEKELEDLTASLFEEANKMVAAARREKHAVEIkndqlkeQLKEKETLLESLQEQLKELKQ 78
 
Name Accession Description Interval E-value
Rab11BD_RAB3IL1 cd21069
Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called ...
 216-373 2.14e-103

Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IL1 lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region.


Pssm-ID: 411033  Cd Length: 163  Bit Score: 301.78  E-value: 2.14e-103
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 216 EGKEVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLPNV-----E 290
Cdd:cd21069   1 EGKEVDTVLFAEFQAWKESPTLDRSCPFLSRIYREDIGPCLDFTKRELSDLVQSAVENNTLTIEPVASQALPVVkasavE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 291 CNNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVRQDAEPMFWEIMRLRKGMSLAKL 370
Cdd:cd21069  81 CGGPKKCALSGLSRTCRHRIKLGDSGNYYYISPSCRARITAVCNFFTYIRYIQQGLVRQDAEQMFWEVMRLRREMSLAKL 160


                ...
gi 19705545 371 GFF 373
Cdd:cd21069 161 GFY 163
Sec2p pfam06428
GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor ...
 92-160 4.87e-11

GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.


Pssm-ID: 428938 [Multi-domain]  Cd Length: 92  Bit Score: 58.74  E-value: 4.87e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19705545    92 KLKDEECERLC--KVRAQLEQELEELTASLFEEAHKMVREANMKQAASEK-------QLKEAWGKIDMLQAEVTALKT 160
Cdd:pfam06428   1 ELKEEKKKRLEaeKEKKKLEKELEDLTASLFEEANKMVAAARREKHAVEIkndqlkeQLKEKETLLESLQEQLKELKQ 78
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
80-160 4.85e-05

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 44.89  E-value: 4.85e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  80 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLfEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTALK 159
Cdd:COG4372  43 LQEELEQLREELEQAREELEQLEEELEQARSELEQLEEEL-EELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQ 121


                .
gi 19705545 160 T 160
Cdd:COG4372 122 K 122
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 78-159 9.99e-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: 41.20  E-value: 9.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545     78 EFLKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTA 157
Cdd:TIGR02168  192 EDILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEE 271


                   ..
gi 19705545    158 LK 159
Cdd:TIGR02168  272 LR 273
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 80-159 2.45e-03

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: 36.56  E-value: 2.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  80 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELT-----ASLFEEAHKMVREANMKQAASEKQLKEawgKIDMLQAE 154
Cdd:cd09803   6 LAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPvlkaqAEIYKSDFEAERAAREKLHQEKEQLAE---QLEYLQRE 82


                ....*
gi 19705545 155 VTALK 159
Cdd:cd09803  83 NQELK 87
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
68-159 5.65e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.89  E-value: 5.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545   68 SSMEIREKGSEFLKEELYKAQKELKLKDEECERLckvraqlEQELEELTASLFEEAHKMVREANMKQ----AASEKQLKE 143
Cdd:PRK03918 612 KELEREEKELKKLEEELDKAFEELAETEKRLEEL-------RKELEELEKKYSEEEYEELREEYLELsrelAGLRAELEE 684

                         90
                 ....*....|....*.
gi 19705545  144 AWGKIDMLQAEVTALK 159
Cdd:PRK03918 685 LEKRREEIKKTLEKLK 700
 
Name Accession Description Interval E-value
Rab11BD_RAB3IL1 cd21069
Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called ...
 216-373 2.14e-103

Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1); RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IL1 lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region.


Pssm-ID: 411033  Cd Length: 163  Bit Score: 301.78  E-value: 2.14e-103
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 216 EGKEVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVRTAVEDNTLTIEPVASQTLPNV-----E 290
Cdd:cd21069   1 EGKEVDTVLFAEFQAWKESPTLDRSCPFLSRIYREDIGPCLDFTKRELSDLVQSAVENNTLTIEPVASQALPVVkasavE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 291 CNNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQQGLVRQDAEPMFWEIMRLRKGMSLAKL 370
Cdd:cd21069  81 CGGPKKCALSGLSRTCRHRIKLGDSGNYYYISPSCRARITAVCNFFTYIRYIQQGLVRQDAEQMFWEVMRLRREMSLAKL 160


                ...
gi 19705545 371 GFF 373
Cdd:cd21069 161 GFY 163
Rab11BD_RAB3IP cd21068
Rab11 binding domain of Rab-3A-interacting protein (RAB3IP); RAB3IP, also called Rabin-3, or ...
 189-373 4.34e-79

Rab11 binding domain of Rab-3A-interacting protein (RAB3IP); RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IP lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region.


Pssm-ID: 411032  Cd Length: 193  Bit Score: 241.36  E-value: 4.34e-79
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 189 GHSRQKSTSSLCPVVCPTAGHIPTPDKEGKEVDTTLFAEFQAWRASPTLDKNCPFLERVYREDVGPCLDFTVQELSALVR 268
Cdd:cd21068   1 GHARNKSTSSAMSGSHQDLSVIQPIVKDCKEADLSLYNEFRLWKEEPTMDRTCPFLDRIYQEDIFPCLTFSKSELASAVL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 269 TAVEDNTLTIEPVASQTLP-----NVECNNTNTCALSGLARTCHHRIRLGDSDGHYYISPSSRARITAVCNFFTYVRYIQ 343
Cdd:cd21068  81 EAVENNTLSIEPVGLQPLRfvkasAVECGGPKKCALSGQTKSCKHRIKLGDSSNYYYISPFCRYRITSVCNFFTYIRYIQ 160

                       170       180       190
                ....*....|....*....|....*....|.
gi 19705545 344 QGLVR-QDAEPMFWEIMRLRKGMSLAKLGFF 373
Cdd:cd21068 161 QGLVKqQDVDQMFWEVMQLRKEMSLAKLGYY 191
Rab11BD_RAB3IP_like cd21044
Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 ...
 218-371 3.41e-55

Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 (RAB3IL1) and similar proteins; The family includes RAB3IP and RAB3IL1, as well as Rab guanine nucleotide exchange factor SEC2 from yeast. RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. SEC2 is a guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. SEC2 binds the Rab GTPase YPT32 but does not have exchange activity on YPT32. The model corresponds to the Rab11a/Rab11b-binding region of family members which lies within the carboxy-terminus, a region distinct from their GEF domain and Rab3a-binding region.


Pssm-ID: 411031  Cd Length: 178  Bit Score: 179.48  E-value: 3.41e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 218 KEVDTTLFAEFQAWRASP-----TLDKNCPFLERVYREDVGPCLDFTVQELSAL----VRTAVEDNTLTIEPVASQTLPN 288
Cdd:cd21044   1 FEVDLVLFEEFQEFLKAPsslslSLLKSSPFLKRILAEDIEPCLRFDPALLNWLlkkrLLAAILENTLEIEPISGSTETS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545 289 VECNNTN-----------TCALSGLART--CHHRIRLGDSDGH-YYISPSSRARITAVCNFFTYVRYIQQGLVRQ-DAEP 353
Cdd:cd21044  81 SSSNNTApvsspppaspkKCALCGESRLdaCLYRLRLSDSDSEwYPICSYCRNRLRAVCDFFAYLRYIRQGLVKSrSIEK 160

                       170
                ....*....|....*...
gi 19705545 354 MFWEIMRLRKGMSLAKLG 371
Cdd:cd21044 161 LYLEILRLRLRMFLARLG 178
Sec2p pfam06428
GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor ...
 92-160 4.87e-11

GDP/GTP exchange factor Sec2p; In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.


Pssm-ID: 428938 [Multi-domain]  Cd Length: 92  Bit Score: 58.74  E-value: 4.87e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19705545    92 KLKDEECERLC--KVRAQLEQELEELTASLFEEAHKMVREANMKQAASEK-------QLKEAWGKIDMLQAEVTALKT 160
Cdd:pfam06428   1 ELKEEKKKRLEaeKEKKKLEKELEDLTASLFEEANKMVAAARREKHAVEIkndqlkeQLKEKETLLESLQEQLKELKQ 78
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
80-160 4.85e-05

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 44.89  E-value: 4.85e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  80 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLfEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTALK 159
Cdd:COG4372  43 LQEELEQLREELEQAREELEQLEEELEQARSELEQLEEEL-EELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQ 121


                .
gi 19705545 160 T 160
Cdd:COG4372 122 K 122
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 80-162 6.89e-05

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: 44.37  E-value: 6.89e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  80 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLfEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTALK 159
Cdd:COG4942  25 AEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRI-AALARRIRALEQELAALEAELAELEKEIAELRAELEAQK 103


                ...
gi 19705545 160 TLV 162
Cdd:COG4942 104 EEL 106
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
63-174 4.16e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 42.20  E-value: 4.16e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  63 SRLRSSSMEIREKGSEF--LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASlfeeahkmVREANMKQAASEKQ 140
Cdd:COG4372  80 EELEELNEQLQAAQAELaqAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQ--------IAELQSEIAEREEE 151

                        90       100       110
                ....*....|....*....|....*....|....
gi 19705545 141 LKEAWGKIDMLQAEVTALKTLVITSTPASPNREL 174
Cdd:COG4372 152 LKELEEQLESLQEELAALEQELQALSEAEAEQAL 185
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 78-159 9.99e-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: 41.20  E-value: 9.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545     78 EFLKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVTA 157
Cdd:TIGR02168  192 EDILNELERQLKSLERQAEKAERYKELKAELRELELALLVLRLEELREELEELQEELKEAEEELEELTAELQELEEKLEE 271


                   ..
gi 19705545    158 LK 159
Cdd:TIGR02168  272 LR 273
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
80-160 1.60e-03

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 40.52  E-value: 1.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  80 LKEELYKAQKELKLKDEECERL---CKVRAQLEQELEELTASLFEEAHKMVREANMKQAASEKQLKEAWGKIDMLQAEVT 156
Cdd:COG4717 130 LYQELEALEAELAELPERLEELeerLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLA 209


                ....
gi 19705545 157 ALKT 160
Cdd:COG4717 210 ELEE 213
UBAN cd09803
polyubiquitin binding domain of NEMO and related proteins; NEMO (NF-kappaB essential modulator) ...
 80-159 2.45e-03

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: 36.56  E-value: 2.45e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545  80 LKEELYKAQKELKLKDEECERLCKVRAQLEQELEELT-----ASLFEEAHKMVREANMKQAASEKQLKEawgKIDMLQAE 154
Cdd:cd09803   6 LAARLQEAEEALALKQEDIDELKEEIAQQEADLETIPvlkaqAEIYKSDFEAERAAREKLHQEKEQLAE---QLEYLQRE 82


                ....*
gi 19705545 155 VTALK 159
Cdd:cd09803  83 NQELK 87
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 61-159 4.62e-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: 39.27  E-value: 4.62e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545     61 DVSRLRSSSMEIREKgSEFLKEELYKAQKELKLKDEECERLCKVRAQLEQELEELTASLfEEAHKMVREANMKQAASEKQ 140
Cdd:TIGR02168  268 KLEELRLEVSELEEE-IEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQL-EELESKLDELAEELAELEEK 345

                           90
                   ....*....|....*....
gi 19705545    141 LKEAWGKIDMLQAEVTALK 159
Cdd:TIGR02168  346 LEELKEELESLEAELEELE 364
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
68-159 5.65e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 38.89  E-value: 5.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545   68 SSMEIREKGSEFLKEELYKAQKELKLKDEECERLckvraqlEQELEELTASLFEEAHKMVREANMKQ----AASEKQLKE 143
Cdd:PRK03918 612 KELEREEKELKKLEEELDKAFEELAETEKRLEEL-------RKELEELEKKYSEEEYEELREEYLELsrelAGLRAELEE 684

                         90
                 ....*....|....*.
gi 19705545  144 AWGKIDMLQAEVTALK 159
Cdd:PRK03918 685 LEKRREEIKKTLEKLK 700
PRK12704 PRK12704
phosphodiesterase; Provisional
 66-138 6.15e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 38.61  E-value: 6.15e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19705545   66 RSSSMEIREKGSEFLKEELYKAQKELKLKDEECERLckvRAQLEQELEE---LTAslfEEAHKMVREaNMKQAASE 138
Cdd:PRK12704 101 KLELLEKREEELEKKEKELEQKQQELEKKEEELEEL---IEEQLQELERisgLTA---EEAKEILLE-KVEEEARH 169
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 81-160 7.65e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 36.01  E-value: 7.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19705545    81 KEELYKAQKELKLKDEECERLCKV----RAQLEQELEELTASLFE------EAHKMVREAnMKQAASEKQLKEAWGK-ID 149
Cdd:pfam13863   5 KREMFLVQLALDAKREEIERLEELlkqrEEELEKKEQELKEDLIKfdkflkENDAKRRRA-LKKAEEETKLKKEKEKeIK 83

                          90
                  ....*....|.
gi 19705545   150 MLQAEVTALKT 160
Cdd:pfam13863  84 KLTAQIEELKS 94
 
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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