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Conserved domains on  [gi|672562703|gb|KFH03589|]
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PUB domain-containing protein [Toxoplasma gondii VAND]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PUB_UBA cd10462
PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The ...
 254-352 3.08e-52

PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.


:

Pssm-ID: 198420  Cd Length: 100  Bit Score: 168.43  E-value: 3.08e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 254 CNRLMKKYRKDQKEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFKDTGDFLA-ISG 332
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFiINK 80

                         90       100
                 ....*....|....*....|
gi 672562703 333 QPDGFVLGQALKFLDVLLEQ 352
Cdd:cd10462   81 IPDTFLCSQAIKFIDLILQT 100
UBA_like_SF super family cl21463
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ...
 70-118 4.72e-14

UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.


The actual alignment was detected with superfamily member cd14295:

Pssm-ID: 473871 [Multi-domain]  Cd Length: 45  Bit Score: 65.47  E-value: 4.72e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672562703  70 SMEQADQLVDFGFPRLRAEKALFHIRQqpggGGVEAAVEWLEVHAEDED 118
Cdd:cd14295    1 DQELVAQLMEMGFPKVRAEKALFFTQN----KGLEEAMEWLEEHSEDAD 45
DUF5401 super family cl38662
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 84-268 8.70e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


The actual alignment was detected with superfamily member pfam17380:

Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 47.43  E-value: 8.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703   84 RLRAE---KALFHIRQQPGGGGVEAAVEWLEVHAEDEDIDEPIKEEEKPKEKVVLTEEEAQRRAYelQKKLREDRIEREK 160
Cdd:pfam17380 352 RIRQEerkRELERIRQEEIAMEISRMRELERLQMERQQKNERVRQELEAARKVKILEEERQRKIQ--QQKVEMEQIRAEQ 429

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  161 KEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRER------ERQRQLLREEYRERFGCEMPEEDDATE 234
Cdd:pfam17380 430 EEARQREVRRLEEERAREMERVRLEEQERQQQVERLRQQEEERKRKKlelekeKRDRKRAEEQRRKILEKELEERKQAMI 509

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 672562703  235 EGAAARL---KKMNGKEKVAYWCNRLMKKYRKDQKEQ 268
Cdd:pfam17380 510 EEERKRKlleKEMEERQKAIYEEERRREAEEERRKQQ 546
 
Name Accession Description Interval E-value
PUB_UBA cd10462
PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The ...
 254-352 3.08e-52

PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.


Pssm-ID: 198420  Cd Length: 100  Bit Score: 168.43  E-value: 3.08e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 254 CNRLMKKYRKDQKEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFKDTGDFLA-ISG 332
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFiINK 80

                         90       100
                 ....*....|....*....|
gi 672562703 333 QPDGFVLGQALKFLDVLLEQ 352
Cdd:cd10462   81 IPDTFLCSQAIKFIDLILQT 100
PUB pfam09409
PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it ...
 266-322 3.05e-14

PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain. This domain is also found on other proteins linked to the ubiquitin-proteasome system.


Pssm-ID: 462790  Cd Length: 80  Bit Score: 67.30  E-value: 3.05e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672562703  266 KEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFK 322
Cdd:pfam09409   1 KEKVKEALETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFE 57
UBA1_atUBP14 cd14295
UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) ...
 70-118 4.72e-14

UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins; atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270481 [Multi-domain]  Cd Length: 45  Bit Score: 65.47  E-value: 4.72e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672562703  70 SMEQADQLVDFGFPRLRAEKALFHIRQqpggGGVEAAVEWLEVHAEDED 118
Cdd:cd14295    1 DQELVAQLMEMGFPKVRAEKALFFTQN----KGLEEAMEWLEEHSEDAD 45
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 84-268 8.70e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 47.43  E-value: 8.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703   84 RLRAE---KALFHIRQQPGGGGVEAAVEWLEVHAEDEDIDEPIKEEEKPKEKVVLTEEEAQRRAYelQKKLREDRIEREK 160
Cdd:pfam17380 352 RIRQEerkRELERIRQEEIAMEISRMRELERLQMERQQKNERVRQELEAARKVKILEEERQRKIQ--QQKVEMEQIRAEQ 429

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  161 KEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRER------ERQRQLLREEYRERFGCEMPEEDDATE 234
Cdd:pfam17380 430 EEARQREVRRLEEERAREMERVRLEEQERQQQVERLRQQEEERKRKKlelekeKRDRKRAEEQRRKILEKELEERKQAMI 509

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 672562703  235 EGAAARL---KKMNGKEKVAYWCNRLMKKYRKDQKEQ 268
Cdd:pfam17380 510 EEERKRKlleKEMEERQKAIYEEERRREAEEERRKQQ 546
PTZ00121 PTZ00121
MAEBL; Provisional
 137-271 1.95e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 46.67  E-value: 1.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQR---QL 213
Cdd:PTZ00121 1642 EAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKkaeEL 1721

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 672562703  214 LREEYRERFGCEMPEEDDATEEGAAARLKKMNG-KEKVAYWCNRLMKKYRKDQKEQLRV 271
Cdd:PTZ00121 1722 KKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEeKKKIAHLKKEEEKKAEEIRKEKEAV 1780
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 137-243 2.51e-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: 2.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 137 EEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQLLRE 216
Cdd:COG1196  315 EERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRA 394

                         90       100
                 ....*....|....*....|....*..
gi 672562703 217 EYRERFGCEMPEEDDATEEGAAARLKK 243
Cdd:COG1196  395 AAELAAQLEELEEAEEALLERLERLEE 421
cdk7 TIGR00570
CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions ...
 150-217 6.91e-04

CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129661 [Multi-domain]  Cd Length: 309  Bit Score: 40.94  E-value: 6.91e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 672562703  150 KLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQLLREE 217
Cdd:TIGR00570 119 KKKIETYQKENKDVIQKNKEKSTREQEELEEALEFEKEEEEQRRLLLQKEEEEQQMNKRKNKQALLDE 186
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 146-220 2.11e-03

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 39.48  E-value: 2.11e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 672562703 146 ELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKE-KEDHKRERERQRQLLREEYRE 220
Cdd:cd16269  192 ALTEKEKEIEAERAKAEAAEQERKLLEEQQRELEQKLEDQERSYEEHLRQLKEKmEEERENLLKEQERALESKLKE 267
UBA pfam00627
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
 72-110 2.37e-03

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.


Pssm-ID: 395502 [Multi-domain]  Cd Length: 37  Bit Score: 35.11  E-value: 2.37e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 672562703   72 EQADQLVDFGFPRLRAEKALFHirqqpGGGGVEAAVEWL 110
Cdd:pfam00627   4 EAIQRLVEMGFDREQVREALRA-----TGNNVERAAEYL 37
 
Name Accession Description Interval E-value
PUB_UBA cd10462
PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The ...
 254-352 3.08e-52

PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover.


Pssm-ID: 198420  Cd Length: 100  Bit Score: 168.43  E-value: 3.08e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 254 CNRLMKKYRKDQKEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFKDTGDFLA-ISG 332
Cdd:cd10462    1 CNNLKKEYKDTDKQGLMTCLNTLRTYISNAHDHPLEEKYKKIRKENKAFVSKVLIFEGAIEILLACGFEDTGDFLFiINK 80

                         90       100
                 ....*....|....*....|
gi 672562703 333 QPDGFVLGQALKFLDVLLEQ 352
Cdd:cd10462   81 IPDTFLCSQAIKFIDLILQT 100
PUB cd09212
PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor ...
 267-347 1.57e-15

PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97.


Pssm-ID: 198416  Cd Length: 96  Bit Score: 71.26  E-value: 1.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 267 EQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFKDTGD----FLAISGQPDGFVLGQA 342
Cdd:cd09212   11 EAFKEALKTLLKILDNILSNPTEEKYRRIRLSNKAFQEKVLPVPGGLELLLALGFVEETEsgesFLVLPDDADVDLLKDA 90


                 ....*
gi 672562703 343 LKFLD 347
Cdd:cd09212   91 KAALE 95
PUB pfam09409
PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it ...
 266-322 3.05e-14

PUB domain; The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain. This domain is also found on other proteins linked to the ubiquitin-proteasome system.


Pssm-ID: 462790  Cd Length: 80  Bit Score: 67.30  E-value: 3.05e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672562703  266 KEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFK 322
Cdd:pfam09409   1 KEKVKEALETLLKYLNNILSNPNEEKYRKIRLSNKAFQEKVLPLEGALELLLAIGFE 57
UBA1_atUBP14 cd14295
UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) ...
 70-118 4.72e-14

UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins; atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270481 [Multi-domain]  Cd Length: 45  Bit Score: 65.47  E-value: 4.72e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 672562703  70 SMEQADQLVDFGFPRLRAEKALFHIRQqpggGGVEAAVEWLEVHAEDED 118
Cdd:cd14295    1 DQELVAQLMEMGFPKVRAEKALFFTQN----KGLEEAMEWLEEHSEDAD 45
PUB_UBA_plant cd10461
PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; ...
 256-331 9.21e-13

PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. This family contains only plant UBA domain-containing proteins.


Pssm-ID: 198419  Cd Length: 107  Bit Score: 63.99  E-value: 9.21e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 672562703 256 RLMKKYRKDQKEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFK--DTGDFLAIS 331
Cdd:cd10461    2 VDLKKAHKDDPDAVKTAFQTLLTYLGNVAKNPDEEKFRRIRLTNAAFQERVGALRGGIEFLELCGFErdEGDEALVLP 79
PUB_UBXD1 cd10460
PNGase/UBA or UBX (PUB) domain of UBXD1; This PUB domain is found in p97 adaptor protein ...
 266-335 1.33e-12

PNGase/UBA or UBX (PUB) domain of UBXD1; This PUB domain is found in p97 adaptor protein UBXD1 (UBX domain-containing protein 1, also called UBXD6). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes, except for fungi, and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. UBXD1 also interacts with HRD1 and HERP, both components of the ERAD pathway, via p97. It is possibly involved in aggresome formation; aggresomes are perinuclear compartments that contain misfolded proteins colocalized with centrosome markers.


Pssm-ID: 198418  Cd Length: 102  Bit Score: 63.42  E-value: 1.33e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 672562703 266 KEQLRVCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFK--------DTGDFLAISGQPD 335
Cdd:cd10460   11 REKVEECVDTLCKYLENIIDHPDEEKYRKIRLSNKVFQEKVLPVEGALEFLEAAGFEektlpeqeDEEDFLVLSEECD 88
PUB_WLM cd10463
PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family; The PUB domain ...
 271-340 7.16e-11

PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family; The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. WLM domains are found mostly in plant proteins, belonging to the Zincin-like superfamily of Zn-dependent peptidases that are linked to the ubiquitin signaling pathway through its fusion with the ubiquitin-binding PUB, ubiquitin-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation.


Pssm-ID: 198421  Cd Length: 96  Bit Score: 58.17  E-value: 7.16e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 271 VCFTTVRVYCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFKDTGdflaiSGQPDGFVLG 340
Cdd:cd10463   16 SALQTLFKILGNAIEHPNEDKFRRLRKSNPAFQRRVARFPGAVELLLAAGFAEEG-----VSGPDTYLLL 80
UBA_UBXN1 cd14302
UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins; UBXN1, also ...
 75-116 5.79e-09

UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins; UBXN1, also called SAPK substrate protein 1 (SAKS1) or UBA/UBX 33.3 kDa protein, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (UBX) domain. It binds polyubiquitin and valosin-containing protein (VCP), and has been identified as a substrate for stress-activated protein kinases (SAPKs). Moreover, UBXN1 specifically binds to Homer2b. It may also interact with ubiquitin (Ub) and may be involved in the Ub-proteasome proteolytic pathways. In addition, UBXN1 can associate with autoubiquitinated BRCA1 tumor suppressor and inhibit its enzymatic function through its UBA domain.


Pssm-ID: 270487 [Multi-domain]  Cd Length: 41  Bit Score: 51.14  E-value: 5.79e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 672562703  75 DQLVDFGFPRLRAEKALfhirQQPGGGGVEAAVEWLEVHAED 116
Cdd:cd14302    4 QTLIEMGFSRNRAEKAL----AKTGNQGVEAAMEWLLAHEDD 41
UBA1_spUBP14_like cd14385
UBA1 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 ...
 61-120 9.71e-09

UBA1 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270568 [Multi-domain]  Cd Length: 47  Bit Score: 50.87  E-value: 9.71e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  61 NPAFVAQHISMeqadqlvdfGFPRLRAEKALFHIrqqpGGGGVEAAVEWLEVHAEDEDID 120
Cdd:cd14385    1 NAEALAQLLGM---------GFPEVRCKKALLAT----GNSDAEAAMNWLFEHMDDPDID 47
PUB_PNGase cd10459
PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase); This ...
 279-328 5.66e-08

PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase); This PUB (PNGase/UBA or UBX) domain is found in the p97 adaptor protein PNGase (Peptide:N-glycanase). The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The mammalian PNGase binds a considerable number of proteins via its PUB domain; these include ERAD E3 enzyme, the autocrine motility factor receptor (AMFR or gp78), SAKS and Derlin-1.


Pssm-ID: 198417  Cd Length: 93  Bit Score: 49.96  E-value: 5.66e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 672562703 279 YCANAKDHPLEEKYLKIRKENNAFKSRVLPFEGALELLDVCGFKDTGDFL 328
Cdd:cd10459   22 YANNILRNPNDPKYRSIRLDNPVFSTKLLPARGAIECLFEMGFVEDEDRL 71
UBA_PUB_plant cd14290
UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins; This family ...
 76-120 8.39e-07

UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins; This family includes some uncharacterized hypothetical proteins found in plants. Although their biological function remain unclear, all family members contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal PUB domain. UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins.


Pssm-ID: 270476 [Multi-domain]  Cd Length: 49  Bit Score: 45.51  E-value: 8.39e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 672562703  76 QLVDFGFPRLRAEKALFHirqqPGGGGVEAAVEWLEVHAEDEDID 120
Cdd:cd14290    9 ELEAMGFPRARAVRALHH----TGNTSVEAAVNWIVEHENDPDID 49
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 84-268 8.70e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 47.43  E-value: 8.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703   84 RLRAE---KALFHIRQQPGGGGVEAAVEWLEVHAEDEDIDEPIKEEEKPKEKVVLTEEEAQRRAYelQKKLREDRIEREK 160
Cdd:pfam17380 352 RIRQEerkRELERIRQEEIAMEISRMRELERLQMERQQKNERVRQELEAARKVKILEEERQRKIQ--QQKVEMEQIRAEQ 429

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  161 KEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRER------ERQRQLLREEYRERFGCEMPEEDDATE 234
Cdd:pfam17380 430 EEARQREVRRLEEERAREMERVRLEEQERQQQVERLRQQEEERKRKKlelekeKRDRKRAEEQRRKILEKELEERKQAMI 509

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 672562703  235 EGAAARL---KKMNGKEKVAYWCNRLMKKYRKDQKEQ 268
Cdd:pfam17380 510 EEERKRKlleKEMEERQKAIYEEERRREAEEERRKQQ 546
UBA1_UBP5_like cd14294
UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins; ...
 75-118 1.77e-05

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins; UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5. It has similar domain architecture, but functions differently from USP5 in cellular deubiquitination processes. It exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin in a non-activation manner. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270480 [Multi-domain]  Cd Length: 44  Bit Score: 41.53  E-value: 1.77e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 672562703  75 DQLVDFGFPRLRAEKALFHIrqqpGGGGVEAAVEWLEVHAEDED 118
Cdd:cd14294    5 SQLAEMGFPLEACRKAVYHT----NNSGLEAAMNWIMEHMDDPD 44
PTZ00121 PTZ00121
MAEBL; Provisional
 137-271 1.95e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 46.67  E-value: 1.95e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQR---QL 213
Cdd:PTZ00121 1642 EAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKkaeEL 1721

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 672562703  214 LREEYRERFGCEMPEEDDATEEGAAARLKKMNG-KEKVAYWCNRLMKKYRKDQKEQLRV 271
Cdd:PTZ00121 1722 KKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEeKKKIAHLKKEEEKKAEEIRKEKEAV 1780
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 137-222 4.98e-05

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 45.11  E-value: 4.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLE-QNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQLLR 215
Cdd:pfam17380 482 EKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEErQKAIYEEERRREAEEERRKQQEMEERRRIQEQMRKA 561


                  ....*..
gi 672562703  216 EEYRERF 222
Cdd:pfam17380 562 TEERSRL 568
Caldesmon pfam02029
Caldesmon;
133-244 1.74e-04

Caldesmon;


Pssm-ID: 460421 [Multi-domain]  Cd Length: 495  Bit Score: 43.32  E-value: 1.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  133 VVLTEEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEqnakLEEEQRKRQLAQLQKEKEDHKRERERQRQ 212
Cdd:pfam02029 232 QSQEREEEAEVFLEAEQKLEELRRRRQEKESEEFEKLRQKQQEAELE----LEELKKKREERRKLLEEEEQRRKQEEAER 307

                          90       100       110
                  ....*....|....*....|....*....|..
gi 672562703  213 LLREEYRERfgcEMPEEDDATEEGAAARLKKM 244
Cdd:pfam02029 308 KLREEEEKR---RMKEEIERRRAEAAEKRQKL 336
UBA_UBS3B cd14301
UBA domain found in ubiquitin-associated and SH3 domain-containing protein B (UBS3B) and ...
 75-113 2.11e-04

UBA domain found in ubiquitin-associated and SH3 domain-containing protein B (UBS3B) and similar proteins; UBS3B, or Cbl-interacting protein p70, suppressor of T-cell receptor signaling 1 (Sts-1), T-cell ubiquitin ligand 2 (TULA-2), or tyrosine-protein phosphatase STS1/TULA2, is ubiquitously expressed in mammalian tissues in a variety of cell types. It exhibits high phosphatase activity, but demonstrates no proapoptotic activity. It negatively regulates the tyrosine kinase Zap-70 activation and T cell receptor (TCR) signaling pathways that modulate T cell activation. Moreover, UBS3B acts as a Cbl- and ubiquitin-interacting protein that inhibits endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor.


Pssm-ID: 270486 [Multi-domain]  Cd Length: 38  Bit Score: 38.19  E-value: 2.11e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 672562703  75 DQLVDFGFPRLRAEKALfhirQQPGGGGVEAAVEWLEVH 113
Cdd:cd14301    4 EVLLSMGFPKHRAEKAL----AATGGRSVQLASDWLLSH 38
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 137-243 2.51e-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: 2.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 137 EEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQLLRE 216
Cdd:COG1196  315 EERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRA 394

                         90       100
                 ....*....|....*....|....*..
gi 672562703 217 EYRERFGCEMPEEDDATEEGAAARLKK 243
Cdd:COG1196  395 AAELAAQLEELEEAEEALLERLERLEE 421
MAT1 pfam06391
CDK-activating kinase assembly factor MAT1; MAT1 is an assembly/targeting factor for ...
 157-212 2.56e-04

CDK-activating kinase assembly factor MAT1; MAT1 is an assembly/targeting factor for cyclin-dependent kinase-activating kinase (CAK), which interacts with the transcription factor TFIIH. The domain found to the N-terminal side of this domain is a C3HC4 RING finger.


Pssm-ID: 461894 [Multi-domain]  Cd Length: 202  Bit Score: 41.46  E-value: 2.56e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 672562703  157 EREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQ 212
Cdd:pfam06391  74 EKENKDLILKNKMKLSQEEEELEELLELEKREKEERRKEEKQEEEEEKEKKEKAKQ 129
UBA1_scUBP14_like cd14296
UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 ...
 71-110 2.74e-04

UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins; scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270482 [Multi-domain]  Cd Length: 39  Bit Score: 38.00  E-value: 2.74e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 672562703  71 MEQADQLVDFGFPRLRAEKALFHIrqqpGGGGVEAAVEWL 110
Cdd:cd14296    1 EEAVSQLMSMGFSENAAKRALYYT----GNSSVEAAMNWL 36
ATG14 pfam10186
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are ...
 138-216 4.03e-04

Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.


Pssm-ID: 462986 [Multi-domain]  Cd Length: 347  Bit Score: 42.05  E-value: 4.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  138 EEAQRRAYELQKKLREDRIE-REKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQ---KEKED-----HKRERE 208
Cdd:pfam10186  74 AISNERLNEIKDKLDQLRREiAEKKKKIEKLRSSLKQRRSDLESASYQLEERRASQLAKLQnsiKRIKQkwtalHSKTAE 153


                  ....*...
gi 672562703  209 RQRQLLRE 216
Cdd:pfam10186 154 SRSFLCRE 161
PTZ00266 PTZ00266
NIMA-related protein kinase; Provisional
 135-218 4.36e-04

NIMA-related protein kinase; Provisional


Pssm-ID: 173502 [Multi-domain]  Cd Length: 1021  Bit Score: 42.42  E-value: 4.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  135 LTEEEAQRRAYELQ----------KKLREDRIEREKKEAIEREKLRLAQtkamLEQNAKLEEEQRKRQLAQLQKEKEDhK 204
Cdd:PTZ00266  440 IEKENAHRKALEMKilekkrierlEREERERLERERMERIERERLERER----LERERLERDRLERDRLDRLERERVD-R 514

                          90
                  ....*....|....
gi 672562703  205 RERERQRQLLREEY 218
Cdd:PTZ00266  515 LERDRLEKARRNSY 528
UBA_atUPL1_2_like cd14327
UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 ...
 72-110 4.49e-04

UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins.


Pssm-ID: 270512 [Multi-domain]  Cd Length: 38  Bit Score: 37.28  E-value: 4.49e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 672562703  72 EQADQLVDFGFPRLRAEKALFHIrqqpGGGGVEAAVEWL 110
Cdd:cd14327    1 EAVAQLVEMGFSRERAEEALRAV----GTNSVELAMEWL 35
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 137-270 5.57e-04

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 41.86  E-value: 5.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELQKKLREDRIEREKK--EAIEREKLRLAQT----KAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQ 210
Cdd:pfam15709 349 EVERKRREQEEQRRLQQEQLERAEKmrEELELEQQRRFEEirlrKQRLEEERQRQEEEERKQRLQLQAAQERARQQQEEF 428

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  211 RQLLREEYRERfgcempeEDDATEEGAAARLKKMNGKEKVAYWCNRLMKKYRKDQKEQLR 270
Cdd:pfam15709 429 RRKLQELQRKK-------QQEEAERAEAEKQRQKELEMQLAEEQKRLMEMAEEERLEYQR 481
cdk7 TIGR00570
CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions ...
 150-217 6.91e-04

CDK-activating kinase assembly factor MAT1; All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129661 [Multi-domain]  Cd Length: 309  Bit Score: 40.94  E-value: 6.91e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 672562703  150 KLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQLLREE 217
Cdd:TIGR00570 119 KKKIETYQKENKDVIQKNKEKSTREQEELEEALEFEKEEEEQRRLLLQKEEEEQQMNKRKNKQALLDE 186
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 146-220 2.11e-03

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 39.48  E-value: 2.11e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 672562703 146 ELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKE-KEDHKRERERQRQLLREEYRE 220
Cdd:cd16269  192 ALTEKEKEIEAERAKAEAAEQERKLLEEQQRELEQKLEDQERSYEEHLRQLKEKmEEERENLLKEQERALESKLKE 267
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 137-250 2.17e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 40.11  E-value: 2.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELQKKLREDRIEREKKEAIER----EKLRlAQTKAMLEQNAKLEEEQRKRQLAQ------LQKEKEDHKR- 205
Cdd:pfam17380 429 QEEARQREVRRLEEERAREMERVRLEEQERqqqvERLR-QQEEERKRKKLELEKEKRDRKRAEeqrrkiLEKELEERKQa 507

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 672562703  206 --ERERQRQLLREEYRERFGCEMPEEDDATEEGAAARLKKMNGKEKV 250
Cdd:pfam17380 508 miEEERKRKLLEKEMEERQKAIYEEERRREAEEERRKQQEMEERRRI 554
UBA pfam00627
UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes ...
 72-110 2.37e-03

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.


Pssm-ID: 395502 [Multi-domain]  Cd Length: 37  Bit Score: 35.11  E-value: 2.37e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 672562703   72 EQADQLVDFGFPRLRAEKALFHirqqpGGGGVEAAVEWL 110
Cdd:pfam00627   4 EAIQRLVEMGFDREQVREALRA-----TGNNVERAAEYL 37
UBA1_UBP5 cd14383
UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called ...
 76-118 2.43e-03

UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5); UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA1 domain.


Pssm-ID: 270566 [Multi-domain]  Cd Length: 49  Bit Score: 35.80  E-value: 2.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 672562703  76 QLVDFGFPRLRAEKALFHIrqqpGGGGVEAAVEWLEVHAEDED 118
Cdd:cd14383    9 QLVEMGFPMDACRKAVYYT----GNSGAEAAMNWVMSHMDDPD 47
COG2433 COG2433
Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only];
103-216 2.66e-03

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


Pssm-ID: 441980 [Multi-domain]  Cd Length: 644  Bit Score: 39.46  E-value: 2.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 103 VEAAVEwlevHAEDEDIDEPIKEEEKPKEKVVLTEEEAQRRAYELQKKLREDRIE--------REKKEAIEREKLRLAQT 174
Cdd:COG2433  378 IEEALE----ELIEKELPEEEPEAEREKEHEERELTEEEEEIRRLEEQVERLEAEveeleaelEEKDERIERLERELSEA 453

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 672562703 175 KAMLEQNAKLEEE--QRKRQLAQLQKEKEDHKRERERQRQLLRE 216
Cdd:COG2433  454 RSEERREIRKDREisRLDREIERLERELEEERERIEELKRKLER 497
UBA_RUP1p cd14307
UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ...
 76-110 2.73e-03

UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.


Pssm-ID: 270492  Cd Length: 38  Bit Score: 34.96  E-value: 2.73e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 672562703  76 QLVDFGFPRLRAEKALfhirqQPGGGGVEAAVEWL 110
Cdd:cd14307    6 SLLEMGIPREVAIEAL-----RETNGDVEAAANYI 35
Mitofilin pfam09731
Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. ...
 137-245 3.94e-03

Mitochondrial inner membrane protein; Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains.


Pssm-ID: 430783 [Multi-domain]  Cd Length: 618  Bit Score: 38.97  E-value: 3.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELQKKLREDRIER-EKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKrQLAQLQKEKEDHKRERER-QRQLL 214
Cdd:pfam09731 314 IERALEKQKEELDKLAEELSARlEEVRAADEAQLRLEFEREREEIRESYEEKLRT-ELERQAEAHEEHLKDVLVeQEIEL 392

                          90       100       110
                  ....*....|....*....|....*....|.
gi 672562703  215 REEYrerfgceMPEEDDATEEGAAARLKKMN 245
Cdd:pfam09731 393 QREF-------LQDIKEKVEEERAGRLLKLN 416
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
56-216 4.69e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.13  E-value: 4.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703   56 RTQGGNP-----AFVAQHI-----SMEQADQLVDFgFPRL-RAEKALFHIRQQPG--GGGVEAAVEWLEVHAEDEDIDEP 122
Cdd:COG4913   199 KTQSFKPigdldDFVREYMleepdTFEAADALVEH-FDDLeRAHEALEDAREQIEllEPIRELAERYAAARERLAELEYL 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  123 IKEEEKPKEKVVLTEEEAQRRAYELQKKLREDRIEReKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKED 202
Cdd:COG4913   278 RAALRLWFAQRRLELLEAELEELRAELARLEAELER-LEARLDALREELDELEAQIRGNGGDRLEQLEREIERLERELEE 356

                         170
                  ....*....|....
gi 672562703  203 HKRERERQRQLLRE 216
Cdd:COG4913   357 RERRRARLEALLAA 370
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 137-273 4.77e-03

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 38.78  E-value: 4.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  137 EEEAQRRAYELqkKLREDRIE-----REKKEAIEREKLRLAQTKAMLEQNA---KLEEEQRKRQLAQLQKEKEDHKRERE 208
Cdd:pfam15709 379 ELEQQRRFEEI--RLRKQRLEeerqrQEEEERKQRLQLQAAQERARQQQEEfrrKLQELQRKKQQEEAERAEAEKQRQKE 456

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 672562703  209 RQRQLLREEYRErfgCEMPEEDdateegaaaRLKKMNGKEKVAYWCNRLMKKYRKDQKEQLRVCF 273
Cdd:pfam15709 457 LEMQLAEEQKRL---MEMAEEE---------RLEYQRQKQEAEEKARLEAEERRQKEEEAARLAL 509
PTZ00121 PTZ00121
MAEBL; Provisional
 135-267 5.00e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 38.97  E-value: 5.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  135 LTEEEAQRRAYELQKKLREDRIEREKKEAIEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERErqrqlL 214
Cdd:PTZ00121 1551 LKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEE-----L 1625

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 672562703  215 REEYRERFGCEMPEEDDATEEGAAARLKKMNGKEKVAywCNRLMKKYRKDQKE 267
Cdd:PTZ00121 1626 KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIK--AAEEAKKAEEDKKK 1676
UBA1_KPC2 cd14303
UBA1 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar ...
 76-114 5.11e-03

UBA1 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins; KPC2, also called ubiquitin-associated domain-containing protein 1 (UBAC1), or glialblastoma cell differentiation-related protein 1, is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains a ubiquitin-like (UBL) domain and two ubiquitin-associated (UBA) domains. This model corresponds to the UBA1 domain.


Pssm-ID: 270488 [Multi-domain]  Cd Length: 41  Bit Score: 34.29  E-value: 5.11e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 672562703  76 QLVDFGFPRLRAEKALFHIRQQPggggvEAAVEWLEVHA 114
Cdd:cd14303    8 QLTEMGFPEARATKALLLNRMSP-----TQAMEWLLEHE 41
PTZ00121 PTZ00121
MAEBL; Provisional
 138-270 7.98e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 38.20  E-value: 7.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703  138 EEAQRRAYELQKKLREDRIEREKKEAIEREK---LRLAQTKAMLEQNAKLEEeqrKRQLAQLQKEKEDHKRERERQ-RQL 213
Cdd:PTZ00121 1493 EEAKKKADEAKKAAEAKKKADEAKKAEEAKKadeAKKAEEAKKADEAKKAEE---KKKADELKKAEELKKAEEKKKaEEA 1569

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672562703  214 LREEYRERFGCEMPEEDDATEEGAAARLKKMNGKEKVAYWCNRLMKKYRKDQKEQLR 270
Cdd:PTZ00121 1570 KKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 135-248 8.14e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.38  E-value: 8.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672562703 135 LTEEEAQRRAYELQKKLREDRIEREKKEA-IEREKLRLAQTKAMLEQNAKLEEEQRKRQLAQLQKEKEDHKRERERQRQL 213
Cdd:COG1196  218 LKEELKELEAELLLLKLRELEAELEELEAeLEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAEL 297

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 672562703 214 LREEYRERFGCEMPEEDDATEEGAAARLKKMNGKE 248
Cdd:COG1196  298 ARLEQDIARLEERRRELEERLEELEEELAELEEEL 332
 
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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