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Conserved domains on  [gi|1063729163|ref|NP_195751|]
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APRATAXIN-like protein [Arabidopsis thaliana]

Protein Classification

ATP-binding protein( domain architecture ID 12153081)

ATP-binding protein with an AAA (ATPases Associated with various cellular Activities) domain may function as an ATPase; similar to NEDD4-binding protein 2-like 1/2 (N4BP2L1 and N4BP2L2), whose functions are not clear

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DcpS_C pfam11969
Scavenger mRNA decapping enzyme C-term binding; This family consists of several scavenger mRNA ...
 524-631 3.31e-32

Scavenger mRNA decapping enzyme C-term binding; This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.


:

Pssm-ID: 463415 [Multi-domain]  Cd Length: 114  Bit Score: 120.79  E-value: 3.31e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 524 HPERHENVVLEYlDNIVVINDQYPKARKHVLVLARQeSLDGLEDVRKENLQLLQEMHNVGLKWVDRFQNEDASLIFRLGY 603
Cdd:pfam11969   9 KGEEPERVVYED-EGFVVFKDIKPKAPLHLLVIPKR-HIKSLRDLTPEHLPLLEHMREVAKKVIEEKYIGVDRDELRLGF 86

                          90       100
                  ....*....|....*....|....*...
gi 1063729163 604 HSVPSMRQLHLHVISQDFNSDSLKNKKH 631
Cdd:pfam11969  87 HYPPSVYHLHLHVISPDFESLGLGRKKG 114
COG4639 COG4639
Predicted kinase [General function prediction only];
27-165 1.28e-16

Predicted kinase [General function prediction only];


:

Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 77.18  E-value: 1.28e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFCdtamRSSHRPWSRICQD---------IVNNGKAGTKAQCLK-MATDSLREGKSVFIDRCNLDRE 96
Cdd:COG4639     4 LVVLIGLPGSGKSTFA----RRLFAPTEVVSSDdirallggdENDQSAWGDVFQLAHeIARARLRAGRLTVVDATNLQRE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063729163  97 QRSEFIKLG-GPEFEVHAVVLELPAQVCISRSVKRTGHEGnlqggraAAVVNKMLQS-KELPKVNEGFSRI 165
Cdd:COG4639    80 ARRRLLALArAYGALVVAVVLDVPLEVCLARNAARDRQVP-------EEVIRRMLRRlRRPPLPEEGFRVV 143
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 326-442 9.21e-15

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441713  Cd Length: 168  Bit Score: 72.52  E-value: 9.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 326 VGDITKLRSEgglhcnVIANATNWRLKpGGGGVNAAIFKAAGPDLETATR--VRANTLLPGKAVVVP---LPStcplhna 400
Cdd:COG2110     5 QGDITELDVD------AIVNAANSSLL-GGGGVAGAIHRAAGPELLEECRrlCKQGGCPTGEAVITPagnLPA------- 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 401 egiTHVIHVLGPNMNPNRPDNLNNdytkgcktLREAYTSLFE 442
Cdd:COG2110    71 ---KYVIHTVGPVWRGGGPSEEEL--------LASCYRNSLE 101
zf-C2HE pfam16278
C2HE / C2H2 / C2HC zinc-binding finger; zf-C2HE is an unusual zinc-binding domain found in ...
 636-690 1.51e-10

C2HE / C2H2 / C2HC zinc-binding finger; zf-C2HE is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C-terminus of HIT-domain-containing proteins, pfam01230. In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually a His. The fourth ligand is often mutated in neurogenerative disease-states.


:

Pssm-ID: 465082  Cd Length: 60  Bit Score: 57.30  E-value: 1.51e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063729163 636 TTSFFRDSVDVLEEVNSQGKANVASED--LLKGELRCNRCRSAHPNIPKLKSHVRSC 690
Cdd:pfam16278   1 NTPFFVPLDDVPEWLEEDGKIELLPSEvlLLKTPLKCHRCGNFGNNFPKLKAHLEEH 57
NACHT super family cl26020
Predicted NTPase, NACHT family domain [Signal transduction mechanisms];
10-42 3.92e-03

Predicted NTPase, NACHT family domain [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5635:

Pssm-ID: 444362 [Multi-domain]  Cd Length: 935  Bit Score: 40.56  E-value: 3.92e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063729163  10 KNQTSPESIEADKAKQIVVLLIGPPGSGKSTFC 42
Cdd:COG5635   165 ERIESLKRLELLEAKKKRLLILGEPGSGKTTLL 197
YmdB super family cl27277
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 255-296 4.16e-03

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG2110:

Pssm-ID: 441713  Cd Length: 168  Bit Score: 38.62  E-value: 4.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 255 TLAFPSISTADFQFDLEKASDIIVEKAEEFLSKLGTARLVLV 296
Cdd:COG2110   110 SIAFPAIGTGVGGFPWEEAAPIAVETLRDFLEEHPSLEEVRF 151
 
Name Accession Description Interval E-value
DcpS_C pfam11969
Scavenger mRNA decapping enzyme C-term binding; This family consists of several scavenger mRNA ...
 524-631 3.31e-32

Scavenger mRNA decapping enzyme C-term binding; This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.


Pssm-ID: 463415 [Multi-domain]  Cd Length: 114  Bit Score: 120.79  E-value: 3.31e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 524 HPERHENVVLEYlDNIVVINDQYPKARKHVLVLARQeSLDGLEDVRKENLQLLQEMHNVGLKWVDRFQNEDASLIFRLGY 603
Cdd:pfam11969   9 KGEEPERVVYED-EGFVVFKDIKPKAPLHLLVIPKR-HIKSLRDLTPEHLPLLEHMREVAKKVIEEKYIGVDRDELRLGF 86

                          90       100
                  ....*....|....*....|....*...
gi 1063729163 604 HSVPSMRQLHLHVISQDFNSDSLKNKKH 631
Cdd:pfam11969  87 HYPPSVYHLHLHVISPDFESLGLGRKKG 114
aprataxin_related cd01278
aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia ...
 531-618 6.22e-21

aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.


Pssm-ID: 238609 [Multi-domain]  Cd Length: 104  Bit Score: 88.21  E-value: 6.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 531 VVLEYLDNIVVINDQYPKARKHVLVLARQeSLDGLEDVRKENLQLLQEMHNVGLKWVDRFQNEDASLiFRLGYHSVP--S 608
Cdd:cd01278    17 DQVYEDDRVVVFKDIYPKARHHYLVIPKE-HIASLKALTKEDVPLLEHMETVGREKLLRSDNTDPSE-FRFGFHAPPftS 94

                          90
                  ....*....|
gi 1063729163 609 MRQLHLHVIS 618
Cdd:cd01278    95 VSHLHLHVIA 104
COG4639 COG4639
Predicted kinase [General function prediction only];
27-165 1.28e-16

Predicted kinase [General function prediction only];


Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 77.18  E-value: 1.28e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFCdtamRSSHRPWSRICQD---------IVNNGKAGTKAQCLK-MATDSLREGKSVFIDRCNLDRE 96
Cdd:COG4639     4 LVVLIGLPGSGKSTFA----RRLFAPTEVVSSDdirallggdENDQSAWGDVFQLAHeIARARLRAGRLTVVDATNLQRE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063729163  97 QRSEFIKLG-GPEFEVHAVVLELPAQVCISRSVKRTGHEGnlqggraAAVVNKMLQS-KELPKVNEGFSRI 165
Cdd:COG4639    80 ARRRLLALArAYGALVVAVVLDVPLEVCLARNAARDRQVP-------EEVIRRMLRRlRRPPLPEEGFRVV 143
AAA_33 pfam13671
AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the ...
 27-156 4.03e-15

AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.


Pssm-ID: 463952 [Multi-domain]  Cd Length: 143  Bit Score: 72.73  E-value: 4.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFcdtAMR-SSHRPWSRICQDIVNNGKAG---------------TKAQCLKMATDSLREGKSVFIDR 90
Cdd:pfam13671   1 LILLVGLPGSGKSTL---ARRlLEELGAVRLSSDDERKRLFGegrpsisyytdatdrTYERLHELARIALRAGRPVILDA 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063729163  91 CNLDREQRSEFIKLGGP-EFEVHAVVLELPAQVCISRSVKRtGHEGNLQGGRAAAVVNKMLQSKELP 156
Cdd:pfam13671  78 TNLRRDERARLLALAREyGVPVRIVVFEAPEEVLRERLAAR-ARAGGDPSDVPEEVLDRQKARFEPP 143
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 326-442 9.21e-15

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 72.52  E-value: 9.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 326 VGDITKLRSEgglhcnVIANATNWRLKpGGGGVNAAIFKAAGPDLETATR--VRANTLLPGKAVVVP---LPStcplhna 400
Cdd:COG2110     5 QGDITELDVD------AIVNAANSSLL-GGGGVAGAIHRAAGPELLEECRrlCKQGGCPTGEAVITPagnLPA------- 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 401 egiTHVIHVLGPNMNPNRPDNLNNdytkgcktLREAYTSLFE 442
Cdd:COG2110    71 ---KYVIHTVGPVWRGGGPSEEEL--------LASCYRNSLE 101
Macro_OAADPr_deacetylase cd02908
macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of ...
 325-433 3.27e-13

macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation.


Pssm-ID: 438955  Cd Length: 166  Bit Score: 67.92  E-value: 3.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 325 FVGDITKLrsegglHCNVIANATNWRLKpGGGGVNAAIFKAAGPDLETATRvRANTLLP-GKAVVVP---LPStcplhna 400
Cdd:cd02908     5 WRGDITKL------EVDAIVNAANSSLL-GGGGVDGAIHRAAGPELLEECR-KLGGVCPtGEAKITPgynLPA------- 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1063729163 401 egiTHVIHVLGP---NMNPNRPDNLNNDYT--------KGCKTL 433
Cdd:cd02908    70 ---KYVIHTVGPigeGGVEEEPELLASCYRsslelaleNGLKSI 110
A1pp smart00506
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...
 321-426 1.94e-11

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).


Pssm-ID: 214701  Cd Length: 133  Bit Score: 61.94  E-value: 1.94e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  321 KFFTFVGDITKLRSEgglhcnVIANATNWRLKPGGGgVNAAIFKAAGPDLETA--TRVRANTLLPGKAVVVPlpstcplH 398
Cdd:smart00506   1 ILKVVKGDITKPRAD------AIVNAANSDGAHGGG-VAGAIARAAGKALSKEevRKLAGGECPVGTAVVTE-------G 66

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1063729163  399 NAEGITHVIHVLGPN---MNPNRPDNLNNDY 426
Cdd:smart00506  67 GNLPAKYVIHAVGPRasgHSKEGFELLENAY 97
PRK00431 PRK00431
ADP-ribose-binding protein;
327-414 1.24e-10

ADP-ribose-binding protein;


Pssm-ID: 234759  Cd Length: 177  Bit Score: 61.01  E-value: 1.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 327 GDITKLRsegglhCNVIANATNWRLKpGGGGVNAAIFKAAGPDLETATR-VRANT--LLPGKAVVVP---LPstcplhna 400
Cdd:PRK00431   10 GDITELE------VDAIVNAANSSLL-GGGGVDGAIHRAAGPEILEECReLRQQQgpCPTGEAVITSagrLP-------- 74

                          90
                  ....*....|....
gi 1063729163 401 egITHVIHVLGPNM 414
Cdd:PRK00431   75 --AKYVIHTVGPVW 86
zf-C2HE pfam16278
C2HE / C2H2 / C2HC zinc-binding finger; zf-C2HE is an unusual zinc-binding domain found in ...
 636-690 1.51e-10

C2HE / C2H2 / C2HC zinc-binding finger; zf-C2HE is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C-terminus of HIT-domain-containing proteins, pfam01230. In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually a His. The fourth ligand is often mutated in neurogenerative disease-states.


Pssm-ID: 465082  Cd Length: 60  Bit Score: 57.30  E-value: 1.51e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063729163 636 TTSFFRDSVDVLEEVNSQGKANVASED--LLKGELRCNRCRSAHPNIPKLKSHVRSC 690
Cdd:pfam16278   1 NTPFFVPLDDVPEWLEEDGKIELLPSEvlLLKTPLKCHRCGNFGNNFPKLKAHLEEH 57
Macro pfam01661
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...
 345-426 1.22e-09

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.


Pssm-ID: 460286  Cd Length: 116  Bit Score: 56.42  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 345 NATNWRLKpGGGGVNAAIFKAAGPDL-ETATRVRANTLLPGKAVVVP---LPStcplhnaegiTHVIHVLGPNM----NP 416
Cdd:pfam01661   2 NAANSRLL-GGGGVAGAIHRAAGPELlEECRELKKGGCPTGEAVVTPggnLPA----------KYVIHTVGPTWrhggSH 70

                          90
                  ....*....|
gi 1063729163 417 NRPDNLNNDY 426
Cdd:pfam01661  71 GEEELLESCY 80
PNK-3'Pase TIGR01663
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ...
 15-166 1.44e-08

polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78


Pssm-ID: 130724 [Multi-domain]  Cd Length: 526  Bit Score: 57.73  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  15 PESIEADKAKQIVVLLIGPPGSGKSTFCDTAMRSSHrpwsricQDIVNNGKAGTKAQCLKMATDSLREGKSVFIDRCNLD 94
Cdd:TIGR01663 359 PDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAG-------YKHVNADTLGSTQNCLTACERALDQGKRCAIDNTNPD 431

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063729163  95 REQRSEFIKLGGPE-FEVHAVVLELP-AQVCISRSVKRTGHEGNLQggRAAAVVNKMLQSKELPKVNEGFSRIM 166
Cdd:TIGR01663 432 AASRAKFLQCARAAgIPCRCFLFNAPlAQAKHNIAFRELSDSAHIK--IKDMVFNGMKKKFEAPALAEGFIAIH 503
pseT PHA02530
polynucleotide kinase; Provisional
 27-130 5.36e-05

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 45.78  E-value: 5.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKST----FCDTA----------MRSS---HRPWS-----RICQDIVnngkagTKAQcLKMATDSLREGK 84
Cdd:PHA02530    4 IILTVGVPGSGKSTwareFAAKNpkavnvnrddLRQSlfgHGEWGeykftKEKEDLV------TKAQ-EAAALAALKSGK 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1063729163  85 SVFIDRCNL---DREQRSEFIKLGGPEFEVhaVVLELPAQVCISRSVKR 130
Cdd:PHA02530   77 SVIISDTNLnpeRRRKWKELAKELGAEFEE--KVFDVPVEELVKRNRKR 123
GPN2 cd17871
GPN-loop GTPase 2; GPN-loop GTPase 2 (GPN2) is a small GTPase required for proper localization ...
 25-62 5.48e-04

GPN-loop GTPase 2; GPN-loop GTPase 2 (GPN2) is a small GTPase required for proper localization of RNA polymerase II and III (RNAPII and RNAPIII). It forms heterodimers with GPN1 or GPN3.


Pssm-ID: 349780  Cd Length: 196  Bit Score: 41.75  E-value: 5.48e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1063729163  25 QIVvllIGPPGSGKSTFCDtAMRSSHRPWSRICQdIVN 62
Cdd:cd17871     3 QVV---IGPPGSGKTTYCK-GMQQFLSALGRKVA-VVN 35
NACHT COG5635
Predicted NTPase, NACHT family domain [Signal transduction mechanisms];
10-42 3.92e-03

Predicted NTPase, NACHT family domain [Signal transduction mechanisms];


Pssm-ID: 444362 [Multi-domain]  Cd Length: 935  Bit Score: 40.56  E-value: 3.92e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063729163  10 KNQTSPESIEADKAKQIVVLLIGPPGSGKSTFC 42
Cdd:COG5635   165 ERIESLKRLELLEAKKKRLLILGEPGSGKTTLL 197
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 255-296 4.16e-03

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 38.62  E-value: 4.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 255 TLAFPSISTADFQFDLEKASDIIVEKAEEFLSKLGTARLVLV 296
Cdd:COG2110   110 SIAFPAIGTGVGGFPWEEAAPIAVETLRDFLEEHPSLEEVRF 151
 
Name Accession Description Interval E-value
DcpS_C pfam11969
Scavenger mRNA decapping enzyme C-term binding; This family consists of several scavenger mRNA ...
 524-631 3.31e-32

Scavenger mRNA decapping enzyme C-term binding; This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function.


Pssm-ID: 463415 [Multi-domain]  Cd Length: 114  Bit Score: 120.79  E-value: 3.31e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 524 HPERHENVVLEYlDNIVVINDQYPKARKHVLVLARQeSLDGLEDVRKENLQLLQEMHNVGLKWVDRFQNEDASLIFRLGY 603
Cdd:pfam11969   9 KGEEPERVVYED-EGFVVFKDIKPKAPLHLLVIPKR-HIKSLRDLTPEHLPLLEHMREVAKKVIEEKYIGVDRDELRLGF 86

                          90       100
                  ....*....|....*....|....*...
gi 1063729163 604 HSVPSMRQLHLHVISQDFNSDSLKNKKH 631
Cdd:pfam11969  87 HYPPSVYHLHLHVISPDFESLGLGRKKG 114
aprataxin_related cd01278
aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia ...
 531-618 6.22e-21

aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin.


Pssm-ID: 238609 [Multi-domain]  Cd Length: 104  Bit Score: 88.21  E-value: 6.22e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 531 VVLEYLDNIVVINDQYPKARKHVLVLARQeSLDGLEDVRKENLQLLQEMHNVGLKWVDRFQNEDASLiFRLGYHSVP--S 608
Cdd:cd01278    17 DQVYEDDRVVVFKDIYPKARHHYLVIPKE-HIASLKALTKEDVPLLEHMETVGREKLLRSDNTDPSE-FRFGFHAPPftS 94

                          90
                  ....*....|
gi 1063729163 609 MRQLHLHVIS 618
Cdd:cd01278    95 VSHLHLHVIA 104
COG4639 COG4639
Predicted kinase [General function prediction only];
27-165 1.28e-16

Predicted kinase [General function prediction only];


Pssm-ID: 443677 [Multi-domain]  Cd Length: 145  Bit Score: 77.18  E-value: 1.28e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFCdtamRSSHRPWSRICQD---------IVNNGKAGTKAQCLK-MATDSLREGKSVFIDRCNLDRE 96
Cdd:COG4639     4 LVVLIGLPGSGKSTFA----RRLFAPTEVVSSDdirallggdENDQSAWGDVFQLAHeIARARLRAGRLTVVDATNLQRE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063729163  97 QRSEFIKLG-GPEFEVHAVVLELPAQVCISRSVKRTGHEGnlqggraAAVVNKMLQS-KELPKVNEGFSRI 165
Cdd:COG4639    80 ARRRLLALArAYGALVVAVVLDVPLEVCLARNAARDRQVP-------EEVIRRMLRRlRRPPLPEEGFRVV 143
AAA_33 pfam13671
AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the ...
 27-156 4.03e-15

AAA domain; This family of domains contain only a P-loop motif, that is characteriztic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.


Pssm-ID: 463952 [Multi-domain]  Cd Length: 143  Bit Score: 72.73  E-value: 4.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFcdtAMR-SSHRPWSRICQDIVNNGKAG---------------TKAQCLKMATDSLREGKSVFIDR 90
Cdd:pfam13671   1 LILLVGLPGSGKSTL---ARRlLEELGAVRLSSDDERKRLFGegrpsisyytdatdrTYERLHELARIALRAGRPVILDA 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1063729163  91 CNLDREQRSEFIKLGGP-EFEVHAVVLELPAQVCISRSVKRtGHEGNLQGGRAAAVVNKMLQSKELP 156
Cdd:pfam13671  78 TNLRRDERARLLALAREyGVPVRIVVFEAPEEVLRERLAAR-ARAGGDPSDVPEEVLDRQKARFEPP 143
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 326-442 9.21e-15

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 72.52  E-value: 9.21e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 326 VGDITKLRSEgglhcnVIANATNWRLKpGGGGVNAAIFKAAGPDLETATR--VRANTLLPGKAVVVP---LPStcplhna 400
Cdd:COG2110     5 QGDITELDVD------AIVNAANSSLL-GGGGVAGAIHRAAGPELLEECRrlCKQGGCPTGEAVITPagnLPA------- 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 401 egiTHVIHVLGPNMNPNRPDNLNNdytkgcktLREAYTSLFE 442
Cdd:COG2110    71 ---KYVIHTVGPVWRGGGPSEEEL--------LASCYRNSLE 101
Macro_OAADPr_deacetylase cd02908
macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of ...
 325-433 3.27e-13

macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation.


Pssm-ID: 438955  Cd Length: 166  Bit Score: 67.92  E-value: 3.27e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 325 FVGDITKLrsegglHCNVIANATNWRLKpGGGGVNAAIFKAAGPDLETATRvRANTLLP-GKAVVVP---LPStcplhna 400
Cdd:cd02908     5 WRGDITKL------EVDAIVNAANSSLL-GGGGVDGAIHRAAGPELLEECR-KLGGVCPtGEAKITPgynLPA------- 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1063729163 401 egiTHVIHVLGP---NMNPNRPDNLNNDYT--------KGCKTL 433
Cdd:cd02908    70 ---KYVIHTVGPigeGGVEEEPELLASCYRsslelaleNGLKSI 110
COG0645 COG0645
Predicted kinase, contains AAA domain [General function prediction only];
27-165 1.65e-11

Predicted kinase, contains AAA domain [General function prediction only];


Pssm-ID: 440410 [Multi-domain]  Cd Length: 164  Bit Score: 63.01  E-value: 1.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFcdtAMR-SSHRPWSRICQDIVNNGKAG---------------TKAQCLKMATDSLREGKSVFIDR 90
Cdd:COG0645     1 LILVCGLPGSGKSTL---ARAlAERLGAVRLRSDVVRKRLFGaglaplerspeatarTYARLLALARELLAAGRSVILDA 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063729163  91 CNLDREQRSEFIKL----GGPefeVHAVVLELPAQVCISRSVKRTGHEGNlqGGRAAAVVNKMLQSKELPKVNEGFSRI 165
Cdd:COG0645    78 TFLRRAQREAFRALaeeaGAP---FVLIWLDAPEEVLRERLEARNAEGGD--SDATWEVLERQLAFEEPLTEDEGFLLV 151
Macro_Af1521_BAL-like cd02907
macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse ...
 327-442 1.78e-11

macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The macrodomains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macrodomain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward ADP-ribose-1"-monophosphate (Appr-1"-p). Also included in this family are the N-terminal (or first) macrodomains of BAL (B-aggressive lymphoma) proteins which contain multiple macrodomains, such as the first macrodomain of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors.


Pssm-ID: 394877 [Multi-domain]  Cd Length: 158  Bit Score: 62.89  E-value: 1.78e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 327 GDITKLrsegglHCNVIANATNWRLKpGGGGVNAAIFKAAGPDLETATR--VRAN-TLLPGKAVVVP---LPstCplhna 400
Cdd:cd02907     9 GDITKE------KVDAIVNAANERLK-HGGGVAGAISKAGGPEIQEECDkyIKKNgKLRVGEVVVTSagkLP--C----- 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 401 egiTHVIHVLGPNMNPNRPDNLnndytkgCKTLREAYTSLFE 442
Cdd:cd02907    75 ---KYVIHAVGPRWSGGSKEEC-------EDLLYKAVLNSLE 106
A1pp smart00506
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...
 321-426 1.94e-11

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).


Pssm-ID: 214701  Cd Length: 133  Bit Score: 61.94  E-value: 1.94e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  321 KFFTFVGDITKLRSEgglhcnVIANATNWRLKPGGGgVNAAIFKAAGPDLETA--TRVRANTLLPGKAVVVPlpstcplH 398
Cdd:smart00506   1 ILKVVKGDITKPRAD------AIVNAANSDGAHGGG-VAGAIARAAGKALSKEevRKLAGGECPVGTAVVTE-------G 66

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1063729163  399 NAEGITHVIHVLGPN---MNPNRPDNLNNDY 426
Cdd:smart00506  67 GNLPAKYVIHAVGPRasgHSKEGFELLENAY 97
PRK00431 PRK00431
ADP-ribose-binding protein;
327-414 1.24e-10

ADP-ribose-binding protein;


Pssm-ID: 234759  Cd Length: 177  Bit Score: 61.01  E-value: 1.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 327 GDITKLRsegglhCNVIANATNWRLKpGGGGVNAAIFKAAGPDLETATR-VRANT--LLPGKAVVVP---LPstcplhna 400
Cdd:PRK00431   10 GDITELE------VDAIVNAANSSLL-GGGGVDGAIHRAAGPEILEECReLRQQQgpCPTGEAVITSagrLP-------- 74

                          90
                  ....*....|....
gi 1063729163 401 egITHVIHVLGPNM 414
Cdd:PRK00431   75 --AKYVIHTVGPVW 86
zf-C2HE pfam16278
C2HE / C2H2 / C2HC zinc-binding finger; zf-C2HE is an unusual zinc-binding domain found in ...
 636-690 1.51e-10

C2HE / C2H2 / C2HC zinc-binding finger; zf-C2HE is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C-terminus of HIT-domain-containing proteins, pfam01230. In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually a His. The fourth ligand is often mutated in neurogenerative disease-states.


Pssm-ID: 465082  Cd Length: 60  Bit Score: 57.30  E-value: 1.51e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1063729163 636 TTSFFRDSVDVLEEVNSQGKANVASED--LLKGELRCNRCRSAHPNIPKLKSHVRSC 690
Cdd:pfam16278   1 NTPFFVPLDDVPEWLEEDGKIELLPSEvlLLKTPLKCHRCGNFGNNFPKLKAHLEEH 57
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 340-448 3.40e-10

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


Pssm-ID: 438957  Cd Length: 127  Bit Score: 58.34  E-value: 3.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 340 CNVIANATNWRLKPGGGgVNAAIFKAAGPDL-ETATRVRAN-TLLPGKAVVVPlpstCPLhnaeGITHVIHVLGPNmnpn 417
Cdd:cd21557     1 EDVVVNAANENLKHGGG-VAGAIYKATGGAFqKESDYIKKNgPLKVGTAVLLP----GHG----LAKNIIHVVGPR---- 67

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1063729163 418 rpDNLNNDYTKgcktLREAYTSLFEGFLSVV 448
Cdd:cd21557    68 --KRKGQDDQL----LAAAYKAVNKEYGSVL 92
Macro pfam01661
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...
 345-426 1.22e-09

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.


Pssm-ID: 460286  Cd Length: 116  Bit Score: 56.42  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 345 NATNWRLKpGGGGVNAAIFKAAGPDL-ETATRVRANTLLPGKAVVVP---LPStcplhnaegiTHVIHVLGPNM----NP 416
Cdd:pfam01661   2 NAANSRLL-GGGGVAGAIHRAAGPELlEECRELKKGGCPTGEAVVTPggnLPA----------KYVIHTVGPTWrhggSH 70

                          90
                  ....*....|
gi 1063729163 417 NRPDNLNNDY 426
Cdd:pfam01661  71 GEEELLESCY 80
PNK-3'Pase TIGR01663
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ...
 15-166 1.44e-08

polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78


Pssm-ID: 130724 [Multi-domain]  Cd Length: 526  Bit Score: 57.73  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  15 PESIEADKAKQIVVLLIGPPGSGKSTFCDTAMRSSHrpwsricQDIVNNGKAGTKAQCLKMATDSLREGKSVFIDRCNLD 94
Cdd:TIGR01663 359 PDDLALDDAPCEMVIAVGFPGAGKSHFCKKFFQPAG-------YKHVNADTLGSTQNCLTACERALDQGKRCAIDNTNPD 431

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063729163  95 REQRSEFIKLGGPE-FEVHAVVLELP-AQVCISRSVKRTGHEGNLQggRAAAVVNKMLQSKELPKVNEGFSRIM 166
Cdd:TIGR01663 432 AASRAKFLQCARAAgIPCRCFLFNAPlAQAKHNIAFRELSDSAHIK--IKDMVFNGMKKKFEAPALAEGFIAIH 503
Macro_SF cd02749
macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular ...
 342-433 2.62e-06

macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response.


Pssm-ID: 394871  Cd Length: 121  Bit Score: 47.01  E-value: 2.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 342 VIANATNWRLKpGGGGVNAAIFKAAGPDLETATRVRANTLLP--GKAVVVplpstcPLHNAeGITHVIHVLGP--NMNPN 417
Cdd:cd02749     2 AIVNPANNDLY-LGGGVAKAISKKAGGDLQEECEERKKNGYLkvGEVAVT------KGGNL-PARYIIHVVGPvaSSKKK 73

                          90
                  ....*....|....*.
gi 1063729163 418 RPDNLNNDYtKGCKTL 433
Cdd:cd02749    74 TYEPLKKCV-KNCLSL 88
HIT pfam01230
HIT domain;
525-622 3.23e-05

HIT domain;


Pssm-ID: 395984 [Multi-domain]  Cd Length: 98  Bit Score: 43.07  E-value: 3.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 525 PERHENVVLEyLDNIVVINDQYPKARKHVLVLaRQESLDGLEDVRKENL-QLLQEMHNVGLKWVDRFQNEDASLIFRLGY 603
Cdd:pfam01230   2 GEIPSTVVYE-DDLVLAFLDIDPQAPGHILVI-PKKHIRELHDLTPEELgDLMSVAQKVARALGKVFKADGYRIVINNGA 79

                          90
                  ....*....|....*....
gi 1063729163 604 HSVPSMRQLHLHVISQDFN 622
Cdd:pfam01230  80 HAGQSVPHLHIHVIPRRKH 98
Macro_BAL-like cd02903
macrodomain, B-aggressive lymphoma (BAL)-like family; Macrodomains are found in a variety of ...
 327-442 3.41e-05

macrodomain, B-aggressive lymphoma (BAL)-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family show similarity to BAL (B-aggressive lymphoma) proteins, which contain one to three macrodomains. Most BAL family macrodomains belong to this family except for the most N-terminal domain in multiple-domain containing proteins. This family includes the second and third macrodomains of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors.


Pssm-ID: 394874  Cd Length: 175  Bit Score: 44.94  E-value: 3.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 327 GDITKLRSegglhcNVIANATNwRLKPGGGGVNAAIFKAAGPDLETATRVRANTLLPGKAVVVP---LPStcplhnaegi 403
Cdd:cd02903    15 GDITKEKT------DVIVNSVS-SDLLLKGGVSKAILKAAGPELQDECANQGKQPASGDVIVTSggnLPC---------- 77

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1063729163 404 THVIHVLGPNMNPNRpdnlnndytkgCKTLREAYTSLFE 442
Cdd:cd02903    78 KYVYHVVLPHYNPGN-----------EKTLKDIVRKCLE 105
pseT PHA02530
polynucleotide kinase; Provisional
 27-130 5.36e-05

polynucleotide kinase; Provisional


Pssm-ID: 222856 [Multi-domain]  Cd Length: 300  Bit Score: 45.78  E-value: 5.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKST----FCDTA----------MRSS---HRPWS-----RICQDIVnngkagTKAQcLKMATDSLREGK 84
Cdd:PHA02530    4 IILTVGVPGSGKSTwareFAAKNpkavnvnrddLRQSlfgHGEWGeykftKEKEDLV------TKAQ-EAAALAALKSGK 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1063729163  85 SVFIDRCNL---DREQRSEFIKLGGPEFEVhaVVLELPAQVCISRSVKR 130
Cdd:PHA02530   77 SVIISDTNLnpeRRRKWKELAKELGAEFEE--KVFDVPVEELVKRNRKR 123
GPN2 cd17871
GPN-loop GTPase 2; GPN-loop GTPase 2 (GPN2) is a small GTPase required for proper localization ...
 25-62 5.48e-04

GPN-loop GTPase 2; GPN-loop GTPase 2 (GPN2) is a small GTPase required for proper localization of RNA polymerase II and III (RNAPII and RNAPIII). It forms heterodimers with GPN1 or GPN3.


Pssm-ID: 349780  Cd Length: 196  Bit Score: 41.75  E-value: 5.48e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1063729163  25 QIVvllIGPPGSGKSTFCDtAMRSSHRPWSRICQdIVN 62
Cdd:cd17871     3 QVV---IGPPGSGKTTYCK-GMQQFLSALGRKVA-VVN 35
ADK cd01428
Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine ...
 27-133 8.19e-04

Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.


Pssm-ID: 238713 [Multi-domain]  Cd Length: 194  Bit Score: 41.07  E-value: 8.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  27 VVLLIGPPGSGKSTFCD------------------TAMRSSHRPWSRIcQDIVNNGKAGTKAQCLKMATDSLRE--GKSV 86
Cdd:cd01428     1 RILLLGPPGSGKGTQAErlakkyglphistgdllrEEIASGTELGKKA-KEYIDSGKLVPDEIVIKLLKERLKKpdCKKG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063729163  87 FIdrcnLD-----REQRSEFIKLGGPEFEVHAVV-LELPAQVCISRSVKRTGH 133
Cdd:cd01428    80 FI----LDgfprtVDQAEALDELLDEGIKPDKVIeLDVPDEVLIERILGRRIC 128
AAA_18 pfam13238
AAA domain;
28-147 2.10e-03

AAA domain;


Pssm-ID: 433052 [Multi-domain]  Cd Length: 128  Bit Score: 38.95  E-value: 2.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163  28 VLLIGPPGSGKSTFCDTAmrSSHRPWSRICQDIV-------------------NNGKAGTKAQCLKMAtDSLREGKSVFI 88
Cdd:pfam13238   1 ILITGTPGVGKTTLAKEL--SKRLGFGDNVRDLAlenglvlgddpetreskrlDEDKLDRLLDLLEEN-AALEEGGNLII 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063729163  89 DRCNLDREQRSEFIKlggpefevHAVVLELPAQVCISRSVKRTGHEGNLQGGRAAAVVN 147
Cdd:pfam13238  78 DGHLAELEPERAKDL--------VGIVLRASPEELLERLEKRGYEEAKIKENEEAEILG 128
Macro_GDAP2-like cd02905
macrodomain, GDAP2-like family; Macrodomains are found in a variety of proteins with diverse ...
 320-419 2.21e-03

macrodomain, GDAP2-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family contains proteins similar to human GDAP2, the ganglioside induced differentiation associated protein 2, whose gene is expressed at a higher level in differentiated Neuro2a cells compared with non-differentiated cells. GDAP2 contains an N-terminal macrodomain and a C-terminal Sec14p-like lipid binding domain. It is specifically expressed in brain and testis.


Pssm-ID: 394876  Cd Length: 169  Bit Score: 39.53  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729163 320 AKFFTFVGDITKLRsegglhCNVIANATN--WRLKPGgggVNAAIFKAAGPDL--ETATRVRANTllpGKAVVVP---LP 392
Cdd:cd02905     1 RKIVLWDGDLTLLN------VDAIVNSTNesLTDKSP---ISDRLFLAAGPELreELAKLGGCRT---GEAKLTKgynLP 68

                          90       100
                  ....*....|....*....|....*..
gi 1063729163 393 STcplhnaegitHVIHVLGPNMNPNRP 419
Cdd:cd02905    69 AR----------YVIHTVGPRYNEKYR 85
NACHT COG5635
Predicted NTPase, NACHT family domain [Signal transduction mechanisms];
10-42 3.92e-03

Predicted NTPase, NACHT family domain [Signal transduction mechanisms];


Pssm-ID: 444362 [Multi-domain]  Cd Length: 935  Bit Score: 40.56  E-value: 3.92e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1063729163  10 KNQTSPESIEADKAKQIVVLLIGPPGSGKSTFC 42
Cdd:COG5635   165 ERIESLKRLELLEAKKKRLLILGEPGSGKTTLL 197
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 255-296 4.16e-03

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 38.62  E-value: 4.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063729163 255 TLAFPSISTADFQFDLEKASDIIVEKAEEFLSKLGTARLVLV 296
Cdd:COG2110   110 SIAFPAIGTGVGGFPWEEAAPIAVETLRDFLEEHPSLEEVRF 151
 
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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