NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|767942580|ref|XP_011534024|]
View 

E3 ubiquitin-protein ligase SHPRH isoform X9 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 702-832 3.71e-66

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18070:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 257  Bit Score: 221.45  E-value: 3.71e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 702 YCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKDGFLQ---PHFLAEQDIVIITYDVLRSE 778
Cdd:cd18070   57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767942580 779 LNYVDIPHSNsedgRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKGT 832
Cdd:cd18070  136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAA 185
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 660-706 1.97e-25

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


:

Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 99.41  E-value: 1.97e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767942580 660 ECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15547    1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 440-508 9.53e-21

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


:

Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 86.81  E-value: 9.53e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRY-DVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTF 508
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 304-409 1.87e-18

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18070:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 257  Bit Score: 85.86  E-value: 1.87e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLqqecfrsspatesalhflwreivtseglklyynpytgciireypnsgpqLLGGILADEMGLGKTVEV 383
Cdd:cd18070    1 LLPYQRRAVNWML-------------------------------------------------VPGGILADEMGLGKTVEV 31

                         90       100
                 ....*....|....*....|....*.
gi 767942580 384 LALILTHTRQDVKQDALTLPEGKVVN 409
Cdd:cd18070   32 LALILLHPRPDNDLDAADDDSDEMVC 57
HepA super family cl33945
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 298-388 2.05e-09

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


The actual alignment was detected with superfamily member COG0553:

Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 61.01  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 298 PALIPVLRPYQREAVNWMLqqecfrsspatesalhFLWReivtseglklyynpytgciireypnsgpQLLGGILADEMGL 377
Cdd:COG0553  236 AGLKATLRPYQLEGAAWLL----------------FLRR----------------------------LGLGGLLADDMGL 271

                         90
                 ....*....|.
gi 767942580 378 GKTVEVLALIL 388
Cdd:COG0553  272 GKTIQALALLL 282
 
Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 702-832 3.71e-66

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 221.45  E-value: 3.71e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 702 YCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKDGFLQ---PHFLAEQDIVIITYDVLRSE 778
Cdd:cd18070   57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767942580 779 LNYVDIPHSNsedgRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKGT 832
Cdd:cd18070  136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAA 185
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 660-706 1.97e-25

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 99.41  E-value: 1.97e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767942580 660 ECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15547    1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 707-830 3.11e-23

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 100.84  E-value: 3.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  707 LVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDG---FLQPHFLAEQDIVIITYDVLRselnyvd 783
Cdd:pfam00176  41 LKHVDKNWGGPTLIVVPLSLLHNWMNEFERWVSPPALRVVVLHGNKRPQerwKNDPNFLADFDVVITTYETLR------- 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 767942580  784 iphsnsedgrrlrnqKRYMAIPSplvaVEWWRICLDEAQMVECPTVK 830
Cdd:pfam00176 114 ---------------KHKELLKK----VHWHRIVLDEGHRLKNSKSK 141
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 440-508 9.53e-21

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 86.81  E-value: 9.53e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRY-DVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTF 508
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 304-409 1.87e-18

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 85.86  E-value: 1.87e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLqqecfrsspatesalhflwreivtseglklyynpytgciireypnsgpqLLGGILADEMGLGKTVEV 383
Cdd:cd18070    1 LLPYQRRAVNWML-------------------------------------------------VPGGILADEMGLGKTVEV 31

                         90       100
                 ....*....|....*....|....*.
gi 767942580 384 LALILTHTRQDVKQDALTLPEGKVVN 409
Cdd:cd18070   32 LALILLHPRPDNDLDAADDDSDEMVC 57
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 440-512 2.40e-14

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 69.19  E-value: 2.40e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767942580 440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGK 512
Cdd:cd00073    5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSK 77
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 716-824 6.35e-10

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 62.94  E-value: 6.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 716 RATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGvKKDGFLQPHFLAEQDIVIITYDVLRSelnyvDIPHsnsedgrrl 795
Cdd:COG0553  291 RPVLIVAPTSLVGNWQRELAKF--APGLRVLVLDG-TRERAKGANPFEDADLVITSYGLLRR-----DIEL--------- 353

                         90       100
                 ....*....|....*....|....*....
gi 767942580 796 rnqkrymaipspLVAVEWWRICLDEAQMV 824
Cdd:COG0553  354 ------------LAAVDWDLVILDEAQHI 370
H15 smart00526
Domain in histone families 1 and 5;
440-501 1.30e-09

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 54.89  E-value: 1.30e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767942580   440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKG 501
Cdd:smart00526   5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVKG 66
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 298-388 2.05e-09

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 61.01  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 298 PALIPVLRPYQREAVNWMLqqecfrsspatesalhFLWReivtseglklyynpytgciireypnsgpQLLGGILADEMGL 377
Cdd:COG0553  236 AGLKATLRPYQLEGAAWLL----------------FLRR----------------------------LGLGGLLADDMGL 271

                         90
                 ....*....|.
gi 767942580 378 GKTVEVLALIL 388
Cdd:COG0553  272 GKTIQALALLL 282
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 307-389 9.83e-08

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 54.61  E-value: 9.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  307 YQREAVNWMLQQECFRSSpatesalhflwreivtseglklyynpytgciireypnsgpqllGGILADEMGLGKTVEVLAL 386
Cdd:pfam00176   1 YQIEGVNWMLSLENNLGR-------------------------------------------GGILADEMGLGKTLQTISL 37


                  ...
gi 767942580  387 ILT 389
Cdd:pfam00176  38 LLY 40
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 661-709 3.43e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 42.09  E-value: 3.43e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767942580  661 CICGELDqiDRKPRVQCLKCHLWQHAKCVNY--DEKNLKIKPFYCPHCLVA 709
Cdd:pfam00628   3 AVCGKSD--DGGELVQCDGCDDWFHLACLGPplDPAEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 675-706 6.81e-05

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 41.04  E-value: 6.81e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 767942580   675 VQCLKCHLWQHAKCVNY-DEKNLKIKPFYCPHC 706
Cdd:smart00249  15 LQCDGCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47
DEXDc smart00487
DEAD-like helicases superfamily;
718-824 7.42e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 38.63  E-value: 7.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580   718 TLIISPS-SICHQWVDEINRHVRSSSLR-VLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELnyvdiphsnSEDGRRL 795
Cdd:smart00487  57 VLVLVPTrELAEQWAEELKKLGPSLGLKvVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLL---------ENDKLSL 127

                           90       100
                   ....*....|....*....|....*....
gi 767942580   796 RNqkrymaipsplvaveWWRICLDEAQMV 824
Cdd:smart00487 128 SN---------------VDLVILDEAHRL 141
 
Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 702-832 3.71e-66

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 221.45  E-value: 3.71e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 702 YCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKDGFLQ---PHFLAEQDIVIITYDVLRSE 778
Cdd:cd18070   57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767942580 779 LNYVDIPHSNsedgRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKGT 832
Cdd:cd18070  136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAA 185
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 693-832 2.86e-29

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 117.00  E-value: 2.86e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 693 EKNLKIKPFYCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFlqPHFLAEQDIVIITY 772
Cdd:cd18008   40 PQDPKIPEELEENSSDPKKLYLSKTTLIVVPLSLLSQWKDEIEKHTKPGSLKVYVYHGSKRIKS--IEELSDYDIVITTY 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 773 DVLRSELNYVDIPHSNSEdgrrlrnqkrYMAIPSPLVAVEWWRICLDEAQMVECPTVKGT 832
Cdd:cd18008  118 GTLASEFPKNKKGGGRDS----------KEKEASPLHRIRWYRVILDEAHNIKNRSTKTS 167
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 660-706 1.97e-25

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 99.41  E-value: 1.97e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767942580 660 ECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15547    1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 707-830 3.11e-23

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 100.84  E-value: 3.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  707 LVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDG---FLQPHFLAEQDIVIITYDVLRselnyvd 783
Cdd:pfam00176  41 LKHVDKNWGGPTLIVVPLSLLHNWMNEFERWVSPPALRVVVLHGNKRPQerwKNDPNFLADFDVVITTYETLR------- 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 767942580  784 iphsnsedgrrlrnqKRYMAIPSplvaVEWWRICLDEAQMVECPTVK 830
Cdd:pfam00176 114 ---------------KHKELLKK----VHWHRIVLDEGHRLKNSKSK 141
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 440-508 9.53e-21

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 86.81  E-value: 9.53e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRY-DVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTF 508
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 304-409 1.87e-18

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 85.86  E-value: 1.87e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLqqecfrsspatesalhflwreivtseglklyynpytgciireypnsgpqLLGGILADEMGLGKTVEV 383
Cdd:cd18070    1 LLPYQRRAVNWML-------------------------------------------------VPGGILADEMGLGKTVEV 31

                         90       100
                 ....*....|....*....|....*.
gi 767942580 384 LALILTHTRQDVKQDALTLPEGKVVN 409
Cdd:cd18070   32 LALILLHPRPDNDLDAADDDSDEMVC 57
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 713-830 7.38e-16

DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350830 [Multi-domain]  Cd Length: 241  Bit Score: 77.91  E-value: 7.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 713 VSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGflQPHFLAEQDIVIITYDVLRSELNyvdiphSNSEDG 792
Cdd:cd18072   71 VPSAGTLVVCPASLVHQWKNEVESRVASNKLRVCLYHGPNRER--IGEVLRDYDIVITTYSLVAKEIP------TYKEES 142

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 767942580 793 RrlrnqkrymaiPSPLVAVEWWRICLDEAQMVECPTVK 830
Cdd:cd18072  143 R-----------SSPLFRIAWARIILDEAHNIKNPKVQ 169
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 707-832 1.14e-14

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 74.43  E-value: 1.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 707 LVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDgfLQPHFLAEQDIVIITYDVLRSElnyvdipH 786
Cdd:cd18071   63 LTTISLILANFTLIVCPLSVLSNWETQFEEHVKPGQLKVYTYHGGERN--RDPKLLSKYDIVLTTYNTLASD-------F 133

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 767942580 787 SNSEDgrrlrnqkrymaipSPLVAVEWWRICLDEAQMVECPTVKGT 832
Cdd:cd18071  134 GAKGD--------------SPLHTINWLRVVLDEGHQIRNPNAQQT 165
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 440-512 2.40e-14

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 69.19  E-value: 2.40e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767942580 440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGK 512
Cdd:cd00073    5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSK 77
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 304-394 2.93e-10

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 61.53  E-value: 2.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLqqecfrsspatesalhflWReivtseglklyynpytgciireypnsgpqllGGILADEMGLGKTVEV 383
Cdd:cd18008    1 LLPYQKQGLAWML------------------PR-------------------------------GGILADEMGLGKTIQA 31

                         90
                 ....*....|.
gi 767942580 384 LALILTHTRQD 394
Cdd:cd18008   32 LALILATRPQD 42
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 304-400 4.21e-10

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 60.66  E-value: 4.21e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMlqqecfrsspatesalHFLWReivtseglklyYNpytgciireypnsgpqlLGGILADEMGLGKTVEV 383
Cdd:cd18012    5 LRPYQKEGFNWL----------------SFLRH-----------YG-----------------LGGILADDMGLGKTLQT 40

                         90
                 ....*....|....*..
gi 767942580 384 LALILTHTRQDVKQDAL 400
Cdd:cd18012   41 LALLLSRKEEGRKGPSL 57
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 716-824 6.35e-10

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 62.94  E-value: 6.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 716 RATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGvKKDGFLQPHFLAEQDIVIITYDVLRSelnyvDIPHsnsedgrrl 795
Cdd:COG0553  291 RPVLIVAPTSLVGNWQRELAKF--APGLRVLVLDG-TRERAKGANPFEDADLVITSYGLLRR-----DIEL--------- 353

                         90       100
                 ....*....|....*....|....*....
gi 767942580 796 rnqkrymaipspLVAVEWWRICLDEAQMV 824
Cdd:COG0553  354 ------------LAAVDWDLVILDEAQHI 370
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 718-824 8.68e-10

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 58.73  E-value: 8.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 718 TLIISPSSICHQWVDEINRHVRssSLRVLVYQGVKKDGFLQPHF--LAEQDIVIITYDVLRSELNYvdiphsnsedgrrl 795
Cdd:cd17919   53 VLVVCPLSVLENWEREFEKWTP--DLRVVVYHGSQRERAQIRAKekLDKFDVVLTTYETLRRDKAS-------------- 116

                         90       100
                 ....*....|....*....|....*....
gi 767942580 796 rnqkrymaipspLVAVEWWRICLDEAQMV 824
Cdd:cd17919  117 ------------LRKFRWDLVVVDEAHRL 133
H15 smart00526
Domain in histone families 1 and 5;
440-501 1.30e-09

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 54.89  E-value: 1.30e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767942580   440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKG 501
Cdd:smart00526   5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVKG 66
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 304-389 2.00e-09

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 59.02  E-value: 2.00e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLQQEcfrSSPATESAlhflWREIVtseglKLYYNPYTGCIIREYPNSGpqlLGGILADEMGLGKTVEV 383
Cdd:cd18071    1 LLPHQKQALAWMVSRE---NSQDLPPF----WEEAV-----GLFLNTITNFSQKKRPELV---RGGILADDMGLGKTLTT 65


                 ....*.
gi 767942580 384 LALILT 389
Cdd:cd18071   66 ISLILA 71
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 298-388 2.05e-09

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 61.01  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 298 PALIPVLRPYQREAVNWMLqqecfrsspatesalhFLWReivtseglklyynpytgciireypnsgpQLLGGILADEMGL 377
Cdd:COG0553  236 AGLKATLRPYQLEGAAWLL----------------FLRR----------------------------LGLGGLLADDMGL 271

                         90
                 ....*....|.
gi 767942580 378 GKTVEVLALIL 388
Cdd:COG0553  272 GKTIQALALLL 282
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 304-398 5.92e-09

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 56.42  E-value: 5.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLQqecfrsspatesalhflwreivtseglkLYYNPYtgciireypnsgpqllGGILADEMGLGKTVEV 383
Cdd:cd17919    1 LRPYQLEGLNFLLE----------------------------LYENGP----------------GGILADEMGLGKTLQA 36

                         90
                 ....*....|....*
gi 767942580 384 LALILTHTRQDVKQD 398
Cdd:cd17919   37 IAFLAYLLKEGKERG 51
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 716-849 6.75e-09

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 56.81  E-value: 6.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 716 RATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKDgFLQPHFLAEQDIVIITYDVLRSELNYvdiphsnsedgrrl 795
Cdd:cd18012   54 GPSLVVAPTSLIYNWEEEAAKF--APELKVLVIHGTKRK-REKLRALEDYDLVITSYGLLRRDIEL-------------- 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767942580 796 rnqkrymaipspLVAVEWWRICLDEAQMVECPTVK-----------------GTawqpPTnENHCTGRWSI 849
Cdd:cd18012  117 ------------LKEVKFHYLVLDEAQNIKNPQTKtakavkalkadhrlaltGT----PI-ENHLGELWSI 170
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
 705-781 2.24e-08

DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350757 [Multi-domain]  Cd Length: 232  Bit Score: 55.82  E-value: 2.24e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767942580 705 HCLVAMEPVST-RATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELNY 781
Cdd:cd17999   44 HHKRANSFNSEnLPSLVVCPPTLVGHWVAEIKKYFPNAFLKPLAYVGPPQERRRLREQGEKHNVIVASYDVLRNDIEV 121
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 307-389 9.83e-08

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 54.61  E-value: 9.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580  307 YQREAVNWMLQQECFRSSpatesalhflwreivtseglklyynpytgciireypnsgpqllGGILADEMGLGKTVEVLAL 386
Cdd:pfam00176   1 YQIEGVNWMLSLENNLGR-------------------------------------------GGILADEMGLGKTLQTISL 37


                  ...
gi 767942580  387 ILT 389
Cdd:pfam00176  38 LLY 40
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
 304-397 1.63e-06

DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350753 [Multi-domain]  Cd Length: 223  Bit Score: 49.94  E-value: 1.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLqqecfrsspatesalhFLWREivtseglklyynpYTGCIireypnsgpqllggiLADEMGLGKTVEV 383
Cdd:cd17995    1 LRDYQLEGVNWLL----------------FNWYN-------------RRNCI---------------LADEMGLGKTIQS 36

                         90
                 ....*....|....
gi 767942580 384 LALiLTHTRQDVKQ 397
Cdd:cd17995   37 IAF-LEHLYQVEGI 49
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 662-706 4.28e-06

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 44.46  E-value: 4.28e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 767942580 662 ICGELDQIDRKPRVQCLKCHLWQHAKCVNYD-EKNLKIKPFYCPHC 706
Cdd:cd15517    4 ICNLETAAVDELWVQCDGCDKWFHQFCLGLSnERYADEDKFKCPNC 49
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 661-706 4.77e-06

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 44.23  E-value: 4.77e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 767942580 661 CICGELDqiDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKpFYCPHC 706
Cdd:cd15550    2 CICGFEH--DDGFMICCDKCSVWQHGDCMGIDRENIPDS-YLCEQC 44
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 304-396 1.38e-05

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 47.37  E-value: 1.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLQqecfrsspatesalhflwreivtseglkLYYNPYtgciireypnsgpqllGGILADEMGLGKTVEV 383
Cdd:cd18005    1 LRDYQREGVEFMYD----------------------------LYKNGR----------------GGILGDDMGLGKTVQV 36

                         90
                 ....*....|....*...
gi 767942580 384 LALIL-----THTRQDVK 396
Cdd:cd18005   37 IAFLAavlgkTGTRRDRE 54
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 304-415 1.41e-05

DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350830 [Multi-domain]  Cd Length: 241  Bit Score: 47.47  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLqqecfrsspatesalhflWREivtseglklyynpytgciireypNSGPQllGGILADEMGLGKTVEV 383
Cdd:cd18072    1 LLLHQKQALAWLL------------------WRE-----------------------RQKPR--GGILADDMGLGKTLTM 37

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 767942580 384 LALILT-----HTRQDVKQDALTLPEGKVVNYFIPSH 415
Cdd:cd18072   38 IALILAqkntqNRKEEEKEKALTEWESKKDSTLVPSA 74
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
 661-706 1.50e-05

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 42.75  E-value: 1.50e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767942580 661 CICGELDqIDRKpRVQCLKCHLWQHAKCVNYDEKNLK-IKPFYCPHC 706
Cdd:cd15553    2 CICRSSD-ISRF-MIGCDNCEEWYHGDCINITEKEAKaIKEWYCQQC 46
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 661-706 2.11e-05

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 42.30  E-value: 2.11e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767942580 661 CICGELDQiDRKPRVQCLKCHLWQHAKCVNYDEK-NLKIKPFYCPHC 706
Cdd:cd15489    3 IVCGKGGD-LGGELLQCDGCGKWFHADCLGPPLSsFVPNGKWICPVC 48
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 365-387 2.69e-05

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 45.78  E-value: 2.69e-05
                         10        20
                 ....*....|....*....|...
gi 767942580 365 QLLGGILADEMGLGKTVEVLALI 387
Cdd:cd18000   18 QRVGGILGDEMGLGKTIQIIAFL 40
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 661-709 3.43e-05

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 42.09  E-value: 3.43e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767942580  661 CICGELDqiDRKPRVQCLKCHLWQHAKCVNY--DEKNLKIKPFYCPHCLVA 709
Cdd:pfam00628   3 AVCGKSD--DGGELVQCDGCDDWFHLACLGPplDPAEIPSGEWLCPECKPK 51
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 710-779 3.46e-05

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 46.22  E-value: 3.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767942580 710 MEPVSTRA--TLIISPSSICHQWVDEINRHvrsSSLRVLVYQGVKKDGFLQPHFLAEQ-DIVIITYDVLRSEL 779
Cdd:cd18005   63 KPPASSAKkpVLIVAPLSVLYNWKDELDTW---GHFEVGVYHGSRKDDELEGRLKAGRlEVVVTTYDTLRRCI 132
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 303-387 4.24e-05

DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350767 [Multi-domain]  Cd Length: 236  Bit Score: 45.84  E-value: 4.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 303 VLRPYQREAVNWMLqqecfrsspatesalhflwreivtseglKLYYNPytgciireypnsgpqlLGGILADEMGLGKTVE 382
Cdd:cd18009    3 VMRPYQLEGMEWLR----------------------------MLWENG----------------INGILADEMGLGKTIQ 38


                 ....*
gi 767942580 383 VLALI 387
Cdd:cd18009   39 TIALL 43
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
 367-387 5.65e-05

DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350754 [Multi-domain]  Cd Length: 233  Bit Score: 45.44  E-value: 5.65e-05
                         10        20
                 ....*....|....*....|.
gi 767942580 367 LGGILADEMGLGKTVEVLALI 387
Cdd:cd17996   23 LNGILADEMGLGKTIQTISLI 43
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 675-706 6.81e-05

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 41.04  E-value: 6.81e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 767942580   675 VQCLKCHLWQHAKCVNY-DEKNLKIKPFYCPHC 706
Cdd:smart00249  15 LQCDGCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 304-393 8.03e-05

DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350762 [Multi-domain]  Cd Length: 240  Bit Score: 44.97  E-value: 8.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVNWMLQqecfrsspatesalhflwreivtseglklyynpytgCIIReypNSGPQLLGGILADEMGLGKTVEV 383
Cdd:cd18004    1 LRPHQREGVQFLYD------------------------------------CLTG---RRGYGGGGAILADEMGLGKTLQA 41

                         90
                 ....*....|
gi 767942580 384 LALILTHTRQ 393
Cdd:cd18004   42 IALVWTLLKQ 51
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 662-706 1.88e-04

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 39.58  E-value: 1.88e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 767942580 662 ICGELDqiDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15522    4 ICKKPD--DGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
PHD_HAC_like cd15614
PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar ...
 675-706 3.06e-04

PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar proteins; This family includes A. thaliana HACs (HAC1/2/4/5/12), which are histone acetyltransferases of the p300/CREB-binding protein (CBP) co-activator family. CBP-type HAT proteins are also found in animals, but absent in fungi. The domain architecture of CBP-type HAT proteins differs between plants and animals. Members in this family contain an N-terminal partially conserved KIX domain, a Zf-TAZ domain, a Cysteine rich CBP-type HAT domain that harbors a plant homeodomain (PHD) finger, a Zf-ZZ domain, and a Zf-TAZ domain. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277086  Cd Length: 73  Bit Score: 40.03  E-value: 3.06e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 767942580 675 VQCLKCHLWQHAKCVNYDEKNLKIK--PFYCPHC 706
Cdd:cd15614   40 VQCDKCERWQHQICGLYNGRRNADEtaEYVCPLC 73
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
 369-393 3.44e-04

DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350751 [Multi-domain]  Cd Length: 218  Bit Score: 42.73  E-value: 3.44e-04
                         10        20
                 ....*....|....*....|....*..
gi 767942580 369 GILADEMGLGKTVEVLALI--LTHTRQ 393
Cdd:cd17993   23 GILADEMGLGKTVQTISFLsyLFHSQQ 49
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 356-390 5.89e-04

DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350761 [Multi-domain]  Cd Length: 223  Bit Score: 42.34  E-value: 5.89e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 767942580 356 IREYPNSGPQLL--------GGILADEMGLGKTVEVLALiLTH 390
Cdd:cd18003    1 LREYQHIGLDWLatlyeknlNGILADEMGLGKTIQTIAL-LAH 42
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 304-393 7.58e-04

DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350765 [Multi-domain]  Cd Length: 239  Bit Score: 41.89  E-value: 7.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580 304 LRPYQREAVnwmlqqecfrsspatesalHFLWREIVTSEGLklyYNPYTGCIireypnsgpqllggiLADEMGLGKTVEV 383
Cdd:cd18007    1 LKPHQVEGV-------------------RFLWSNLVGTDVG---SDEGGGCI---------------LAHTMGLGKTLQV 43

                         90
                 ....*....|
gi 767942580 384 LALILTHTRQ 393
Cdd:cd18007   44 ITFLHTYLAA 53
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
 342-393 8.02e-04

DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350825 [Multi-domain]  Cd Length: 243  Bit Score: 42.07  E-value: 8.02e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 767942580 342 EGLKLYYNPYTGCIIreyPNSGpqllGGILADEMGLGKTVEVLALILTHTRQ 393
Cdd:cd18067    7 EGVKFLYRCVTGRRI---RGSH----GCIMADEMGLGKTLQCITLMWTLLRQ 51
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
 661-706 8.89e-04

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.


Pssm-ID: 277045  Cd Length: 50  Bit Score: 37.82  E-value: 8.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 767942580 661 CICGELDQIDRKprVQCLKCHLWQHAKCVNYDEKNLKIKP-----FYCPHC 706
Cdd:cd15570    2 CPCGSSMEDGSM--IQCEGCKTWQHMDCVLIPDKPADGLPelpskFYCELC 50
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 367-393 1.85e-03

DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350756 [Multi-domain]  Cd Length: 187  Bit Score: 40.45  E-value: 1.85e-03
                         10        20
                 ....*....|....*....|....*..
gi 767942580 367 LGGILADEMGLGKTVEVLALiLTHTRQ 393
Cdd:cd17998   20 LSGILADEMGLGKTIQVIAF-LAYLKE 45
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
 660-706 1.91e-03

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 36.97  E-value: 1.91e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 767942580 660 ECICGELDQiDRKPRVQCLKCHLWQHAKCVNYDEkNLKIKP-FYCPHC 706
Cdd:cd15556    1 DCSCGTRDD-DGERMIACDVCEVWQHTRCVGIAD-NEEPPDhFLCRRC 46
PHD_ash2p_like cd15583
PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and ...
 661-706 2.17e-03

PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and similar proteins; spAsh2p, also termed Set1C component ash2, or COMPASS component ash2, or complex proteins associated with set1 protein ash2, or Lid2 complex component ash2, or Lid2C component ash2, is orthologous to Drosophila melanogaster Ash2 protein. Both spAsh2p and D. melanogaster Ash2 contain a plant homeodomain (PHD) finger and a SPRY domain. In contrast, its counterpart in Saccharomyces cerevisiae, Bre2p, has no PHD finger and is not included in this family. spAsh2p shows histone H3 Lys4 (H3K4) methyltransferase activity through its PHD finger. It also interacts with Lid2p in S. pombe. Human Ash2L contains an atypical PHD finger that lacks part of the Cys4HisCys3 signature characteristic of PHD fingers, it binds to only one zinc ion through the second half of the motif and does not have histone tail binding activity.


Pssm-ID: 277058  Cd Length: 50  Bit Score: 36.94  E-value: 2.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 767942580 661 CICGElDQIDRKPRVQCLKCHLWQHAKCVNYDekNLKIKP------FYCPHC 706
Cdd:cd15583    2 CYCGK-DRNLGEVELQCSICLKWFHAKCVSID--NGSCLPfmtnyqFVCKRC 50
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 368-385 3.07e-03

DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350759 [Multi-domain]  Cd Length: 232  Bit Score: 40.05  E-value: 3.07e-03
                         10
                 ....*....|....*...
gi 767942580 368 GGILADEMGLGKTVEVLA 385
Cdd:cd18001   21 GGILADDMGLGKTVQICA 38
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 367-393 4.41e-03

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 39.61  E-value: 4.41e-03
                         10        20
                 ....*....|....*....|....*....
gi 767942580 367 LGGILADEMGLGKTVEVLALI--LTHTRQ 393
Cdd:cd17997   23 INGILADEMGLGKTLQTISLLgyLKHYKN 51
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 719-778 6.23e-03

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 38.81  E-value: 6.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767942580 719 LIISPSSICHQWVDEINRH-------VRSSSLRVLVYQGVKkdgflqphFLAEQDIVIITYDVLRSE 778
Cdd:cd18011   51 LILCPASLVEQWQDELQDKfglpfliLDRETAAQLRRLIGN--------PFEEFPIVIVSLDLLKRS 109
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
 368-395 6.79e-03

DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350824 [Multi-domain]  Cd Length: 235  Bit Score: 39.06  E-value: 6.79e-03
                         10        20
                 ....*....|....*....|....*...
gi 767942580 368 GGILADEMGLGKTVEVLALILTHTRQDV 395
Cdd:cd18066   26 GAILADEMGLGKTLQCISLIWTLLRQGP 53
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 661-706 6.83e-03

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.


Pssm-ID: 277029  Cd Length: 47  Bit Score: 35.44  E-value: 6.83e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 767942580 661 CICGELDQIDRKpRVQCLKCHLWQHAKCVNYDEKNLK-IKPFYCPHC 706
Cdd:cd15554    2 CICRQPYDVTRF-MIECDVCKDWFHGSCVGVEEHQANdIERYHCPNC 47
DEXDc smart00487
DEAD-like helicases superfamily;
718-824 7.42e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 38.63  E-value: 7.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767942580   718 TLIISPS-SICHQWVDEINRHVRSSSLR-VLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELnyvdiphsnSEDGRRL 795
Cdd:smart00487  57 VLVLVPTrELAEQWAEELKKLGPSLGLKvVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLL---------ENDKLSL 127

                           90       100
                   ....*....|....*....|....*....
gi 767942580   796 RNqkrymaipsplvaveWWRICLDEAQMV 824
Cdd:smart00487 128 SN---------------VDLVILDEAHRL 141
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH