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Conserved domains on  [gi|1201872072|ref|XP_021246654|]
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E3 ubiquitin-protein ligase SHPRH isoform X7 [Numida meleagris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 718-919 6.28e-103

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: 327.76  E-value: 6.28e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  718 YCPHCLVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKHGFLQ---PHMLAEQDVVITTYDVLRTE 794
Cdd:cd18070     57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  795 LNYVDIPHSNsedgRRFRNQKRYMAIPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDL 874
Cdd:cd18070    136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDL 211

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1201872072  875 YGLVLFLGIDPYWVKHWWDQLLYRP-YCRKNSQPLYSLIAKIMWRS 919
Cdd:cd18070    212 FGLLSFLGVEPFCDSDWWARVLIRPqGRNKAREPLAALLKELLWRS 257
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 676-722 1.15e-26

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: 103.26  E-value: 1.15e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1201872072  676 ECICGELGLVDYKARVQCLKCHLWQHAECVNYKEENLKIKPFYCPHC 722
Cdd:cd15547      1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 445-514 2.38e-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: 89.12  E-value: 2.38e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1201872072  445 YPSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRY-DTQRNRRLLKRTLEKLIADQVVEQVKGHGLAGSF 514
Cdd:pfam00538    1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 307-416 2.37e-17

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: 83.55  E-value: 2.37e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLhrenftstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpqWPGGILADEMGLGK 386
Cdd:cd18070      1 LLPYQRRAVNWML-----------------------------------------------------VPGGILADEMGLGK 27

                           90       100       110
                   ....*....|....*....|....*....|
gi 1201872072  387 TVEVLALILTHTRQDIKQDDLTLPEGELVN 416
Cdd:cd18070     28 TVEVLALILLHPRPDNDLDAADDDSDEMVC 57
HepA super family cl33945
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 103-395 2.09e-07

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: 55.62  E-value: 2.09e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  103 IVVLPYHADGSWKVLLGELAFYLPSEQIVSEEFHERGFTLMRGDSDNHLLVCVHKGSEEEYSDGRKECLGAYGQIILVEP 182
Cdd:COG0553     36 ARELLLLLLAADALLLLALLLLLELLLLLAALLLLALLLLALSALALLLLRLLLALLLLALLLLLAGLLALALLLLALLG 115

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  183 TLGGEILEGLRWLQNKKIIGLYQRPGEGRALKVGIYLLEAGLSKPEFLSDGGGRPKKANQLIQKLMEKFYSFIIPDVLEE 262
Cdd:COG0553    116 LLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALLLGRLLLLALLLLALEALLLLGLLLALALLALLELALL 195

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  263 DEEESDMELERQNIEELYDFVRHTHQQDIQLLREDVQHP--ALIPILRPYQSEAVNWMLHRenftstpgggkytenalhf 340
Cdd:COG0553    196 AAEAELLLLLELLLELELLAEAAVDAFRLRRLREALESLpaGLKATLRPYQLEGAAWLLFL------------------- 256

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1201872072  341 lwrevvtldgvkiyynpftgciiREYPFagpqwpGGILADEMGLGKTVEVLALIL 395
Cdd:COG0553    257 -----------------------RRLGL------GGLLADDMGLGKTIQALALLL 282
 
Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 718-919 6.28e-103

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: 327.76  E-value: 6.28e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  718 YCPHCLVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKHGFLQ---PHMLAEQDVVITTYDVLRTE 794
Cdd:cd18070     57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  795 LNYVDIPHSNsedgRRFRNQKRYMAIPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDL 874
Cdd:cd18070    136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDL 211

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1201872072  875 YGLVLFLGIDPYWVKHWWDQLLYRP-YCRKNSQPLYSLIAKIMWRS 919
Cdd:cd18070    212 FGLLSFLGVEPFCDSDWWARVLIRPqGRNKAREPLAALLKELLWRS 257
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 723-1003 3.20e-79

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: 263.00  E-value: 3.20e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  723 LVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHG---FLQPHMLAEQDVVITTYDVLRtelnyvd 799
Cdd:pfam00176   41 LKHVDKNWGGPTLIVVPLSLLHNWMNEFERWVSPPALRVVVLHGNKRPQerwKNDPNFLADFDVVITTYETLR------- 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  800 iphsnsedgrrfrnqKRYMAIPSplvaVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVL 879
Cdd:pfam00176  114 ---------------KHKELLKK----VHWHRIVLDEGHRLKNSKSKLSKALKSLKTRNRWILTGTPLQNNLEELWALLN 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  880 FLGIDPYWV----KHWWDQLLYRPYCRKNSQPLYSLIAKIMWRSAKKDVldQIQIPPQTENVHWLHFSPVERHFYHRqhe 955
Cdd:pfam00176  175 FLRPGPFGSlstfRNWFDRPIERGGGKKGVSRLHKLLKPFLLRRTKKDV--EKSLPPKVEYILFCRLSKLQRKLYQT--- 249

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 1201872072  956 vccqdalaKLRKISDWTLKLSSLDRRTVTSILYPLLRLRQACCHPQAV 1003
Cdd:pfam00176  250 --------FLLKKDLNAIKTGEGGREIKASLLNILMRLRKICNHPGLI 289
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 734-1040 4.82e-31

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 131.50  E-value: 4.82e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  734 TLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKHgFLQPHMLAEQDVVITTYDVLRtelnyvdiphsnsedgrrfRN 813
Cdd:COG0553    293 VLIVAPTSLVGNWQRELAKF--APGLRVLVLDGTRER-AKGANPFEDADLVITSYGLLR-------------------RD 350

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  814 QKRymaipspLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFLgiDPywvkhwwd 893
Cdd:COG0553    351 IEL-------LAAVDWDLVILDEAQHIKNPATKRAKAVRALKARHRLALTGTPVENRLEELWSLLDFL--NP-------- 413

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  894 QLLYR-------------PYCRKNSQPLYSLIAKIMWRSAKKDVLDqiQIPPQTENVHWLHFSPVERHFYhrqhevccQD 960
Cdd:COG0553    414 GLLGSlkafrerfarpieKGDEEALERLRRLLRPFLLRRTKEDVLK--DLPEKTEETLYVELTPEQRALY--------EA 483

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  961 ALAKLRKIsdwtLKLSSLDRRTVTsILYPLLRLRQACCHPQAVRGEFLPLQKSTMTMEELLTSLQkkcrTECEEAHRQLV 1040
Cdd:COG0553    484 VLEYLRRE----LEGAEGIRRRGL-ILAALTRLRQICSHPALLLEEGAELSGRSAKLEALLELLE----ELLAEGEKVLV 554
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 676-722 1.15e-26

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: 103.26  E-value: 1.15e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1201872072  676 ECICGELGLVDYKARVQCLKCHLWQHAECVNYKEENLKIKPFYCPHC 722
Cdd:cd15547      1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 445-514 2.38e-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: 89.12  E-value: 2.38e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1201872072  445 YPSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRY-DTQRNRRLLKRTLEKLIADQVVEQVKGHGLAGSF 514
Cdd:pfam00538    1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 446-528 9.82e-18

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: 79.20  E-value: 9.82e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  446 PSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRYDTQRNRRLLKRTLEKLIADQVVEQVKGHGLAGSFKLGKNYKEQKR 525
Cdd:cd00073      5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSKKKKKKKK 84


                   ...
gi 1201872072  526 RER 528
Cdd:cd00073     85 PAK 87
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 307-416 2.37e-17

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: 83.55  E-value: 2.37e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLhrenftstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpqWPGGILADEMGLGK 386
Cdd:cd18070      1 LLPYQRRAVNWML-----------------------------------------------------VPGGILADEMGLGK 27

                           90       100       110
                   ....*....|....*....|....*....|
gi 1201872072  387 TVEVLALILTHTRQDIKQDDLTLPEGELVN 416
Cdd:cd18070     28 TVEVLALILLHPRPDNDLDAADDDSDEMVC 57
H15 smart00526
Domain in histone families 1 and 5;
446-507 1.13e-11

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 61.44  E-value: 1.13e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1201872072   446 PSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRYDTQRNRRLLKRTLEKLIADQVVEQVKG 507
Cdd:smart00526    5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVKG 66
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 310-403 3.74e-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: 56.54  E-value: 3.74e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  310 YQSEAVNWMLHRENFTstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpqWPGGILADEMGLGKTVE 389
Cdd:pfam00176    1 YQIEGVNWMLSLENNL-----------------------------------------------GRGGILADEMGLGKTLQ 33

                           90
                   ....*....|....
gi 1201872072  390 VLALILTHTRQDIK 403
Cdd:pfam00176   34 TISLLLYLKHVDKN 47
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 103-395 2.09e-07

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 55.62  E-value: 2.09e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  103 IVVLPYHADGSWKVLLGELAFYLPSEQIVSEEFHERGFTLMRGDSDNHLLVCVHKGSEEEYSDGRKECLGAYGQIILVEP 182
Cdd:COG0553     36 ARELLLLLLAADALLLLALLLLLELLLLLAALLLLALLLLALSALALLLLRLLLALLLLALLLLLAGLLALALLLLALLG 115

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  183 TLGGEILEGLRWLQNKKIIGLYQRPGEGRALKVGIYLLEAGLSKPEFLSDGGGRPKKANQLIQKLMEKFYSFIIPDVLEE 262
Cdd:COG0553    116 LLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALLLGRLLLLALLLLALEALLLLGLLLALALLALLELALL 195

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  263 DEEESDMELERQNIEELYDFVRHTHQQDIQLLREDVQHP--ALIPILRPYQSEAVNWMLHRenftstpgggkytenalhf 340
Cdd:COG0553    196 AAEAELLLLLELLLELELLAEAAVDAFRLRRLREALESLpaGLKATLRPYQLEGAAWLLFL------------------- 256

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1201872072  341 lwrevvtldgvkiyynpftgciiREYPFagpqwpGGILADEMGLGKTVEVLALIL 395
Cdd:COG0553    257 -----------------------RRLGL------GGLLADDMGLGKTIQALALLL 282
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 677-722 2.29e-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: 42.97  E-value: 2.29e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1201872072   677 CICGELGlvDYKARVQCLKCHLWQHAECVNYK-EENLKIKPFYCPHC 722
Cdd:smart00249    3 SVCGKPD--DGGELLQCDGCDRWYHQTCLGPPlLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 691-725 7.64e-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: 41.71  E-value: 7.64e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1201872072  691 VQCLKCHLWQHAECVNYKEENLKIKP--FYCPHCLVA 725
Cdd:pfam00628   15 VQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 361-394 4.72e-03

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 41.32  E-value: 4.72e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1201872072  361 CI---IREYPFAGPQWP--------GGILADEMGLGKTVEVLALI 394
Cdd:PLN03142   165 CIkgkMRDYQLAGLNWLirlyengiNGILADEMGLGKTLQTISLL 209
 
Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 718-919 6.28e-103

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: 327.76  E-value: 6.28e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  718 YCPHCLVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKHGFLQ---PHMLAEQDVVITTYDVLRTE 794
Cdd:cd18070     57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  795 LNYVDIPHSNsedgRRFRNQKRYMAIPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDL 874
Cdd:cd18070    136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDL 211

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1201872072  875 YGLVLFLGIDPYWVKHWWDQLLYRP-YCRKNSQPLYSLIAKIMWRS 919
Cdd:cd18070    212 FGLLSFLGVEPFCDSDWWARVLIRPqGRNKAREPLAALLKELLWRS 257
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 723-1003 3.20e-79

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: 263.00  E-value: 3.20e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  723 LVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHG---FLQPHMLAEQDVVITTYDVLRtelnyvd 799
Cdd:pfam00176   41 LKHVDKNWGGPTLIVVPLSLLHNWMNEFERWVSPPALRVVVLHGNKRPQerwKNDPNFLADFDVVITTYETLR------- 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  800 iphsnsedgrrfrnqKRYMAIPSplvaVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVL 879
Cdd:pfam00176  114 ---------------KHKELLKK----VHWHRIVLDEGHRLKNSKSKLSKALKSLKTRNRWILTGTPLQNNLEELWALLN 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  880 FLGIDPYWV----KHWWDQLLYRPYCRKNSQPLYSLIAKIMWRSAKKDVldQIQIPPQTENVHWLHFSPVERHFYHRqhe 955
Cdd:pfam00176  175 FLRPGPFGSlstfRNWFDRPIERGGGKKGVSRLHKLLKPFLLRRTKKDV--EKSLPPKVEYILFCRLSKLQRKLYQT--- 249

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 1201872072  956 vccqdalaKLRKISDWTLKLSSLDRRTVTSILYPLLRLRQACCHPQAV 1003
Cdd:pfam00176  250 --------FLLKKDLNAIKTGEGGREIKASLLNILMRLRKICNHPGLI 289
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 708-918 4.91e-57

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: 197.51  E-value: 4.91e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  708 KEENLKIKPFYCPHCLVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHGFlqPHMLAEQDVVITT 787
Cdd:cd18008     39 RPQDPKIPEELEENSSDPKKLYLSKTTLIVVPLSLLSQWKDEIEKHTKPGSLKVYVYHGSKRIKS--IEELSDYDIVITT 116

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  788 YDVLRTELNYVDIPHSNSEdgrrfrnqkrYMAIPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPV 867
Cdd:cd18008    117 YGTLASEFPKNKKGGGRDS----------KEKEASPLHRIRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPI 186

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1201872072  868 QRGLEDLYGLVLFLGIDPYWVKHWWDQLLYRPYC---RKNSQPLYSLIAKIMWR 918
Cdd:cd18008    187 QNSLDDLYSLLRFLRVEPFGDYPWFNSDISKPFSkndRKALERLQALLKPILLR 240
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 723-918 4.36e-33

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: 128.74  E-value: 4.36e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  723 LVAMKPVSTGATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHgfLQPHMLAEQDVVITTYDVLRTElnyvdipH 802
Cdd:cd18071     63 LTTISLILANFTLIVCPLSVLSNWETQFEEHVKPGQLKVYTYHGGERN--RDPKLLSKYDIVLTTYNTLASD-------F 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  803 SNSEDgrrfrnqkrymaipSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFLG 882
Cdd:cd18071    134 GAKGD--------------SPLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGSLLSFLH 199

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1201872072  883 IDPYWVKHWWDQLLYRPYCRKN---SQPLYSLIAKIMWR 918
Cdd:cd18071    200 LKPFSNPEYWRRLIQRPLTMGDptgLKRLQVLMKQITLR 238
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 734-1040 4.82e-31

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 131.50  E-value: 4.82e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  734 TLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKHgFLQPHMLAEQDVVITTYDVLRtelnyvdiphsnsedgrrfRN 813
Cdd:COG0553    293 VLIVAPTSLVGNWQRELAKF--APGLRVLVLDGTRER-AKGANPFEDADLVITSYGLLR-------------------RD 350

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  814 QKRymaipspLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFLgiDPywvkhwwd 893
Cdd:COG0553    351 IEL-------LAAVDWDLVILDEAQHIKNPATKRAKAVRALKARHRLALTGTPVENRLEELWSLLDFL--NP-------- 413

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  894 QLLYR-------------PYCRKNSQPLYSLIAKIMWRSAKKDVLDqiQIPPQTENVHWLHFSPVERHFYhrqhevccQD 960
Cdd:COG0553    414 GLLGSlkafrerfarpieKGDEEALERLRRLLRPFLLRRTKEDVLK--DLPEKTEETLYVELTPEQRALY--------EA 483

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  961 ALAKLRKIsdwtLKLSSLDRRTVTsILYPLLRLRQACCHPQAVRGEFLPLQKSTMTMEELLTSLQkkcrTECEEAHRQLV 1040
Cdd:COG0553    484 VLEYLRRE----LEGAEGIRRRGL-ILAALTRLRQICSHPALLLEEGAELSGRSAKLEALLELLE----ELLAEGEKVLV 554
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 729-918 7.87e-27

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: 110.65  E-value: 7.87e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  729 VSTGATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHGflQPHMLAEQDVVITTYDVLRTELNyvdiphSNSEDG 808
Cdd:cd18072     71 VPSAGTLVVCPASLVHQWKNEVESRVASNKLRVCLYHGPNRER--IGEVLRDYDIVITTYSLVAKEIP------TYKEES 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  809 RrfrnqkrymaiPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFLGIDPY-- 886
Cdd:cd18072    143 R-----------SSPLFRIAWARIILDEAHNIKNPKVQASIAVCKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFdd 211

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1201872072  887 ---WvKHWWDQllyrpYCRKNSQPLYSLIAKIMWR 918
Cdd:cd18072    212 lkvW-KKQVDN-----KSRKGGERLNILTKSLLLR 240
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 676-722 1.15e-26

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: 103.26  E-value: 1.15e-26
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1201872072  676 ECICGELGLVDYKARVQCLKCHLWQHAECVNYKEENLKIKPFYCPHC 722
Cdd:cd15547      1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 445-514 2.38e-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: 89.12  E-value: 2.38e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1201872072  445 YPSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRY-DTQRNRRLLKRTLEKLIADQVVEQVKGHGLAGSF 514
Cdd:pfam00538    1 HPPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 446-528 9.82e-18

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: 79.20  E-value: 9.82e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  446 PSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRYDTQRNRRLLKRTLEKLIADQVVEQVKGHGLAGSFKLGKNYKEQKR 525
Cdd:cd00073      5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSKKKKKKKK 84


                   ...
gi 1201872072  526 RER 528
Cdd:cd00073     85 PAK 87
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 307-416 2.37e-17

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: 83.55  E-value: 2.37e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLhrenftstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpqWPGGILADEMGLGK 386
Cdd:cd18070      1 LLPYQRRAVNWML-----------------------------------------------------VPGGILADEMGLGK 27

                           90       100       110
                   ....*....|....*....|....*....|
gi 1201872072  387 TVEVLALILTHTRQDIKQDDLTLPEGELVN 416
Cdd:cd18070     28 TVEVLALILLHPRPDNDLDAADDDSDEMVC 57
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 732-881 3.52e-17

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: 80.69  E-value: 3.52e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHVRssSLRVLVYQGVKKHGFLQPHM--LAEQDVVITTYDVLRTELNYvdiphsnsedgr 809
Cdd:cd17919     51 GPVLVVCPLSVLENWEREFEKWTP--DLRVVVYHGSQRERAQIRAKekLDKFDVVLTTYETLRRDKAS------------ 116

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1201872072  810 rfrnqkrymaipspLVAVEWWRICLDEAQMV---ECTTAKAAeMALRLSgiNRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd17919    117 --------------LRKFRWDLVVVDEAHRLknpKSQLSKAL-KALRAK--RRLLLTGTPLQNNLEELWALLDFL 174
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 732-881 8.48e-16

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: 77.99  E-value: 8.48e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKHgFLQPHMLAEQDVVITTYDVLRTELNYvdiphsnsedgrrf 811
Cdd:cd18012     54 GPSLVVAPTSLIYNWEEEAAKF--APELKVLVIHGTKRK-REKLRALEDYDLVITSYGLLRRDIEL-------------- 116

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  812 rnqkrymaipspLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd18012    117 ------------LKEVKFHYLVLDEAQNIKNPQTKTAKAVKALKADHRLALTGTPIENHLGELWSIFDFL 174
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
 721-881 1.23e-15

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: 77.78  E-value: 1.23e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  721 HCLVAMKPVSTGA-TLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHGFLQPHMLAEQDVVITTYDVLRTELNYvd 799
Cdd:cd17999     44 HHKRANSFNSENLpSLVVCPPTLVGHWVAEIKKYFPNAFLKPLAYVGPPQERRRLREQGEKHNVIVASYDVLRNDIEV-- 121

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  800 iphsnsedgrrfrnqkrymaipspLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVL 879
Cdd:cd17999    122 ------------------------LTKIEWNYCVLDEGHIIKNSKTKLSKAVKQLKANHRLILSGTPIQNNVLELWSLFD 177


                   ..
gi 1201872072  880 FL 881
Cdd:cd17999    178 FL 179
H15 smart00526
Domain in histone families 1 and 5;
446-507 1.13e-11

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 61.44  E-value: 1.13e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1201872072   446 PSLRVMVLAAVKEMNVKKGASIFAIFKYIGAVYRYDTQRNRRLLKRTLEKLIADQVVEQVKG 507
Cdd:smart00526    5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVKG 66
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 307-453 1.30e-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: 63.08  E-value: 1.30e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLHRenftstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpqwpGGILADEMGLGK 386
Cdd:cd18008      1 LLPYQKQGLAWMLPR-----------------------------------------------------GGILADEMGLGK 27

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  387 TVEVLALILTHTRQDIKQDDLTLPegelvnffVPPQPSQGSKKKKT-------------REmelkLKEKIQYPSLRVMVL 453
Cdd:cd18008     28 TIQALALILATRPQDPKIPEELEE--------NSSDPKKLYLSKTTlivvplsllsqwkDE----IEKHTKPGSLKVYVY 95
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 307-396 4.26e-10

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: 61.72  E-value: 4.26e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLHRENFTSTPGggkytenalhfLWrevvtLDGVKIYYNPFTGCIIREYPFAGPqwpGGILADEMGLGK 386
Cdd:cd18071      1 LLPHQKQALAWMVSRENSQDLPP-----------FW-----EEAVGLFLNTITNFSQKKRPELVR---GGILADDMGLGK 61

                           90
                   ....*....|
gi 1201872072  387 TVEVLALILT 396
Cdd:cd18071     62 TLTTISLILA 71
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 730-886 3.11e-09

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: 58.17  E-value: 3.11e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  730 STGATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKHgflQPHM-------LAEQDVVITTYDVLRtelnyvdiph 802
Cdd:cd17998     48 IPGPHLVVVPSSTLDNWLREFKRW--CPSLKVEPYYGSQEE---RKHLrydilkgLEDFDVIVTTYNLAT---------- 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  803 SNSEDGRRFRNQKRYMAIpsplvavewwricLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFLG 882
Cdd:cd17998    113 SNPDDRSFFKRLKLNYVV-------------YDEGHMLKNMTSERYRHLMTINANFRLLLTGTPLQNNLLELMSLLNFIM 179


                   ....
gi 1201872072  883 IDPY 886
Cdd:cd17998    180 PKPF 183
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
 732-881 1.22e-08

DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 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: 350760 [Multi-domain]  Cd Length: 229  Bit Score: 57.13  E-value: 1.22e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHVrsSSLRVLVYQGVKK-----HGFLQPHMLAEQD----VVITTYDVLRTELNYvdiph 802
Cdd:cd18002     51 GPFLVIAPASTLHNWQQEISRFV--PQFKVLPYWGNPKdrkvlRKFWDRKNLYTRDapfhVVITSYQLVVQDEKY----- 123

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1201872072  803 snsedgrrfrnqkrymaipspLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd18002    124 ---------------------FQRVKWQYMVLDEAQAIKSSSSSRWKTLLSFHCRNRLLLTGTPIQNSMAELWALLHFI 181
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 731-881 1.40e-08

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: 56.95  E-value: 1.40e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  731 TGATLIISPSSICHQWVDEINRHVrsSSLRVLVYQGVK--KHGFLQPHMLAEQ-DVVITTYDVLRTELNYVdiphsnsed 807
Cdd:cd17997     53 NGPHLIIVPKSTLDNWMREFKRWC--PSLRVVVLIGDKeeRADIIRDVLLPGKfDVCITSYEMVIKEKTVL--------- 121

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1201872072  808 gRRFRnqkrymaipsplvaveWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd17997    122 -KKFN----------------WRYIIIDEAHRIKNEKSKLSQIVRLFNSRNRLLLTGTPLQNNLHELWALLNFL 178
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 310-403 3.74e-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: 56.54  E-value: 3.74e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  310 YQSEAVNWMLHRENFTstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpqWPGGILADEMGLGKTVE 389
Cdd:pfam00176    1 YQIEGVNWMLSLENNL-----------------------------------------------GRGGILADEMGLGKTLQ 33

                           90
                   ....*....|....
gi 1201872072  390 VLALILTHTRQDIK 403
Cdd:pfam00176   34 TISLLLYLKHVDKN 47
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 306-410 5.06e-08

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: 54.88  E-value: 5.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  306 ILRPYQSEAVNWMlhrenftstpgggkytenalHFLwrevvtldgvkiyynpftgciiREYPFagpqwpGGILADEMGLG 385
Cdd:cd18012      4 TLRPYQKEGFNWL--------------------SFL----------------------RHYGL------GGILADDMGLG 35

                           90       100
                   ....*....|....*....|....*
gi 1201872072  386 KTVEVLALILthtrqDIKQDDLTLP 410
Cdd:cd18012     36 KTLQTLALLL-----SRKEEGRKGP 55
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 307-406 5.27e-08

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: 54.11  E-value: 5.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLHRENftstpgggkytenalhflwrevvtldgvkiyynpftgciireypfagpQWPGGILADEMGLGK 386
Cdd:cd17919      1 LRPYQLEGLNFLLELYE------------------------------------------------NGPGGILADEMGLGK 32

                           90       100
                   ....*....|....*....|
gi 1201872072  387 TVEVLALILTHTRQDIKQDD 406
Cdd:cd17919     33 TLQAIAFLAYLLKEGKERGP 52
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 734-881 7.54e-08

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: 54.68  E-value: 7.54e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  734 TLIISPSSICHQWVDEINRhvRSSSLRVLVYQGVKKHG--FLQPHMLAEQDVVITTYDVLRTELNYVdiphsNSEDGRRF 811
Cdd:cd18001     52 VLVVMPTSLIPHWVKEFAK--WTPGLRVKVFHGTSKKEreRNLERIQRGGGVLLTTYGMVLSNTEQL-----SADDHDEF 124

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  812 RnqkrymaipsplvaveWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd18001    125 K----------------WDYVILDEGHKIKNSKTKSAKSLREIPAKNRIILTGTPIQNNLKELWALFDFA 178
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 103-395 2.09e-07

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 55.62  E-value: 2.09e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  103 IVVLPYHADGSWKVLLGELAFYLPSEQIVSEEFHERGFTLMRGDSDNHLLVCVHKGSEEEYSDGRKECLGAYGQIILVEP 182
Cdd:COG0553     36 ARELLLLLLAADALLLLALLLLLELLLLLAALLLLALLLLALSALALLLLRLLLALLLLALLLLLAGLLALALLLLALLG 115

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  183 TLGGEILEGLRWLQNKKIIGLYQRPGEGRALKVGIYLLEAGLSKPEFLSDGGGRPKKANQLIQKLMEKFYSFIIPDVLEE 262
Cdd:COG0553    116 LLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALLLGRLLLLALLLLALEALLLLGLLLALALLALLELALL 195

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  263 DEEESDMELERQNIEELYDFVRHTHQQDIQLLREDVQHP--ALIPILRPYQSEAVNWMLHRenftstpgggkytenalhf 340
Cdd:COG0553    196 AAEAELLLLLELLLELELLAEAAVDAFRLRRLREALESLpaGLKATLRPYQLEGAAWLLFL------------------- 256

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1201872072  341 lwrevvtldgvkiyynpftgciiREYPFagpqwpGGILADEMGLGKTVEVLALIL 395
Cdd:COG0553    257 -----------------------RRLGL------GGLLADDMGLGKTIQALALLL 282
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
 732-933 3.15e-07

DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 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: 350822 [Multi-domain]  Cd Length: 244  Bit Score: 53.13  E-value: 3.15e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKHGFLQPHML-AEQDVVITTYDVLRTElnyvdiphsnsedgrr 810
Cdd:cd18064     66 GPHMVLVPKSTLHNWMAEFKRWVPTLRAVCLIGDKDQRAAFVRDVLLpGEWDVCVTSYEMLIKE---------------- 129

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  811 frnqkrymaiPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFLGIDPYWVKH 890
Cdd:cd18064    130 ----------KSVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAE 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1201872072  891 WWDQLLYRPYC---RKNSQPLYSLIAKIMWRSAKKDVldQIQIPPQ 933
Cdd:cd18064    200 DFDSWFDTNNClgdQKLVERLHMVLRPFLLRRIKADV--EKSLPPK 243
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
 732-881 5.01e-07

DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 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: 350823 [Multi-domain]  Cd Length: 233  Bit Score: 52.33  E-value: 5.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHVrsSSLRVLVYQGVK--KHGFLQPHML-AEQDVVITTYDVLRTElnyvdiphsnsedg 808
Cdd:cd18065     66 GPHMVLVPKSTLHNWMNEFKRWV--PSLRAVCLIGDKdaRAAFIRDVMMpGEWDVCVTSYEMVIKE-------------- 129

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1201872072  809 rrfrnqkrymaiPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd18065    130 ------------KSVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFL 190
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 726-877 1.01e-06

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: 51.61  E-value: 1.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  726 MKPVST--GATLIISPSSICHQWVDEINRHvrsSSLRVLVYQGVKKHGFLQPHMLAEQ-DVVITTYDVLRtelnyvdiph 802
Cdd:cd18005     63 KPPASSakKPVLIVAPLSVLYNWKDELDTW---GHFEVGVYHGSRKDDELEGRLKAGRlEVVVTTYDTLR---------- 129

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1201872072  803 snsedgrrfrnqkryMAIPSpLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGL 877
Cdd:cd18005    130 ---------------RCIDS-LNSINWSAVIADEAHRIKNPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCL 188
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 677-722 3.04e-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: 45.39  E-value: 3.04e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1201872072  677 CICGELglVDYKARVQCLKCHLWQHAECVNYKEENLKIKpFYCPHC 722
Cdd:cd15550      2 CICGFE--HDDGFMICCDKCSVWQHGDCMGIDRENIPDS-YLCEQC 44
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 729-880 5.44e-06

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: 48.47  E-value: 5.44e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  729 VSTGATLIISPSSICHQWVDEINR----------HVRSSSLRVLVYQGVKKHGF-LQPHMLAEQDVVITTYDVLRTelny 797
Cdd:cd18000     48 LGLGPSLIVCPATVLKQWVKEFHRwwppfrvvvlHSSGSGTGSEEKLGSIERKSqLIRKVVGDGGILITTYEGFRK---- 123

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  798 vdiphsnsedgrrfrNQKrymaipsPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGL 877
Cdd:cd18000    124 ---------------HKD-------LLLNHNWQYVILDEGHKIRNPDAEITLACKQLRTPHRLILSGTPIQNNLKELWSL 181


                   ...
gi 1201872072  878 VLF 880
Cdd:cd18000    182 FDF 184
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 691-722 1.71e-05

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: 43.31  E-value: 1.71e-05
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1201872072  691 VQCLKCHLWQHAECVNYKEENLK-IKPFYCPHC 722
Cdd:cd15517     17 VQCDGCDKWFHQFCLGLSNERYAdEDKFKCPNC 49
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 677-722 1.76e-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: 43.46  E-value: 1.76e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1201872072  677 CICGELGLVDyKARVQCLKCHLWQHAECVN-YKEENLKIKPFYCPHC 722
Cdd:cd15489      3 IVCGKGGDLG-GELLQCDGCGKWFHADCLGpPLSSFVPNGKWICPVC 48
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 360-394 2.27e-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: 47.38  E-value: 2.27e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1201872072  360 GCIIREYPFAGPQW--------PGGILADEMGLGKTVEVLALI 394
Cdd:cd18009      1 GGVMRPYQLEGMEWlrmlwengINGILADEMGLGKTIQTIALL 43
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 677-722 2.29e-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: 42.97  E-value: 2.29e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 1201872072   677 CICGELGlvDYKARVQCLKCHLWQHAECVNYK-EENLKIKPFYCPHC 722
Cdd:smart00249    3 SVCGKPD--DGGELLQCDGCDRWYHQTCLGPPlLEEEPDGKWYCPKC 47
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
 363-394 3.70e-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: 46.59  E-value: 3.70e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1201872072  363 IREYPFAGPQWP--------GGILADEMGLGKTVEVLALI 394
Cdd:cd17996      4 LKEYQLKGLQWMvslynnnlNGILADEMGLGKTIQTISLI 43
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 691-725 7.64e-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: 41.71  E-value: 7.64e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1201872072  691 VQCLKCHLWQHAECVNYKEENLKIKP--FYCPHCLVA 725
Cdd:pfam00628   15 VQCDGCDDWFHLACLGPPLDPAEIPSgeWLCPECKPK 51
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
 732-885 1.08e-04

DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L 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: 350764 [Multi-domain]  Cd Length: 216  Bit Score: 45.12  E-value: 1.08e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVK-KHGFLQPHMLAEQ--DVVITTYDVLRTElnyvdiphsnsedg 808
Cdd:cd18006     51 GPFLVLCPLSVLDNWKEELNRF--APDLSVITYMGDKeKRLDLQQDIKSTNrfHVLLTTYEICLKD-------------- 114

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1201872072  809 rrfrnqkrymaiPSPLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFlgIDP 885
Cdd:cd18006    115 ------------ASFLKSFPWASLVVDEAHRLKNQNSLLHKTLSEFSVDFRLLLTGTPIQNSLQELYALLSF--IEP 177
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 375-403 1.35e-04

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: 45.06  E-value: 1.35e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1201872072  375 GGILADEMGLGKTVEVLALIL-----THTRQDIK 403
Cdd:cd18005     21 GGILGDDMGLGKTVQVIAFLAavlgkTGTRRDRE 54
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
 693-722 1.57e-04

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: 40.44  E-value: 1.57e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1201872072  693 CLKCHLWQHAECVNYKEENLK-IKPFYCPHC 722
Cdd:cd15553     16 CDNCEEWYHGDCINITEKEAKaIKEWYCQQC 46
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
 307-400 1.86e-04

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: 44.55  E-value: 1.86e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  307 LRPYQSEAVNWMLhrenftstpgggkytenalhFLWRevvtldgvkiyynpftgciireypfagpQWPGGILADEMGLGK 386
Cdd:cd17995      1 LRDYQLEGVNWLL--------------------FNWY----------------------------NRRNCILADEMGLGK 32

                           90
                   ....*....|....
gi 1201872072  387 TVEVLALiLTHTRQ 400
Cdd:cd17995     33 TIQSIAF-LEHLYQ 45
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 735-896 1.98e-04

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: 44.20  E-value: 1.98e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  735 LIISPSSICHQWVDEINRHVrSSSLRVLVYQGVKKHGFLQPHMLAEQDVVITTYDVLRtelnyvdiphsnSEDGRRfrnq 814
Cdd:cd18011     51 LILCPASLVEQWQDELQDKF-GLPFLILDRETAAQLRRLIGNPFEEFPIVIVSLDLLK------------RSEERR---- 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  815 krymaipSPLVAVEWWRICLDEAQMV----ECTTAKAAEMALRLSGINRWCV--SGTPVQRGLEDLYGLVLFLgiDPYwV 888
Cdd:cd18011    114 -------GLLLSEEWDLVVVDEAHKLrnsgGGKETKRYKLGRLLAKRARHVLllTATPHNGKEEDFRALLSLL--DPG-R 183


                   ....*...
gi 1201872072  889 KHWWDQLL 896
Cdd:cd18011    184 FAVLGRFL 191
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 691-722 2.08e-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: 39.96  E-value: 2.08e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1201872072  691 VQCLKCHLWQHAECVNYKEENLKIKPFYCPHC 722
Cdd:cd15522     15 IGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 363-397 2.81e-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: 43.88  E-value: 2.81e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1201872072  363 IREYPFAGPQW--------PGGILADEMGLGKTVEVLALiLTH 397
Cdd:cd18003      1 LREYQHIGLDWlatlyeknLNGILADEMGLGKTIQTIAL-LAH 42
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 375-394 3.86e-04

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: 43.08  E-value: 3.86e-04
                           10        20
                   ....*....|....*....|
gi 1201872072  375 GGILADEMGLGKTVEVLALI 394
Cdd:cd18000     21 GGILGDEMGLGKTIQIIAFL 40
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 732-881 4.96e-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: 43.11  E-value: 4.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  732 GATLIISPSSICHQWVDEINRHVrsSSLRVLVYQG------VKKHGFLQPHMLaeqDVVITTYD-VLRtelnyvdiphsn 804
Cdd:cd18003     51 GPHLIVVPTSVMLNWEMEFKRWC--PGFKILTYYGsakerkLKRQGWMKPNSF---HVCITSYQlVVQ------------ 113

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1201872072  805 seDGRRFRNQKrymaipsplvaveWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDLYGLVLFL 881
Cdd:cd18003    114 --DHQVFKRKK-------------WKYLILDEAHNIKNFKSQRWQTLLNFNTQRRLLLTGTPLQNSLMELWSLMHFL 175
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
 363-400 6.22e-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: 6.22e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1201872072  363 IREYPFAGPQW--------PGGILADEMGLGKTVEVLALI--LTHTRQ 400
Cdd:cd17993      2 LRDYQLTGLNWlahswckgNNGILADEMGLGKTVQTISFLsyLFHSQQ 49
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 375-400 1.03e-03

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: 42.27  E-value: 1.03e-03
                           10        20
                   ....*....|....*....|....*.
gi 1201872072  375 GGILADEMGLGKTVEVLALILTHTRQ 400
Cdd:cd18004     26 GAILADEMGLGKTLQAIALVWTLLKQ 51
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
 349-400 1.54e-03

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: 41.69  E-value: 1.54e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1201872072  349 DGVKIYYNPFTGCIIREYPfagpqwpGGILADEMGLGKTVEVLALILTHTRQ 400
Cdd:cd18067      7 EGVKFLYRCVTGRRIRGSH-------GCIMADEMGLGKTLQCITLMWTLLRQ 51
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 375-396 1.68e-03

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: 41.70  E-value: 1.68e-03
                           10        20
                   ....*....|....*....|..
gi 1201872072  375 GGILADEMGLGKTVEVLALILT 396
Cdd:cd18072     22 GGILADDMGLGKTLTMIALILA 43
PHD_HAC_like cd15614
PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar ...
 691-722 1.80e-03

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: 38.49  E-value: 1.80e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1201872072  691 VQCLKCHLWQHAECVNYKEENLKIK--PFYCPHC 722
Cdd:cd15614     40 VQCDKCERWQHQICGLYNGRRNADEtaEYVCPLC 73
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
 677-722 3.27e-03

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: 37.05  E-value: 3.27e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1201872072  677 CICG---ELGLVdykarVQCLKCHLWQHAECVNYKEENLKIKP-----FYCPHC 722
Cdd:cd15570      2 CPCGssmEDGSM-----IQCEGCKTWQHMDCVLIPDKPADGLPelpskFYCELC 50
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 722-881 3.69e-03

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: 40.45  E-value: 3.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  722 CLVAMKpvSTGATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKH-----GFLQPHMLAEQD--VVITTYDVLRTE 794
Cdd:cd18009     45 HLRERG--VWGPFLVIAPLSTLPNWVNEFARF--TPSVPVLLYHGTKEErerlrKKIMKREGTLQDfpVVVTSYEIAMRD 120

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1201872072  795 LNYvdiphsnsedgrrfrnqkrymaipspLVAVEWWRICLDEAQMVECTTAKAAEMALRLSGINRWCVSGTPVQRGLEDL 874
Cdd:cd18009    121 RKA--------------------------LQHYAWKYLIVDEGHRLKNLNCRLIQELKTFNSDNRLLLTGTPLQNNLSEL 174


                   ....*..
gi 1201872072  875 YGLVLFL 881
Cdd:cd18009    175 WSLLNFL 181
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
 691-722 3.70e-03

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), 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 interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), 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. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.


Pssm-ID: 277083 [Multi-domain]  Cd Length: 50  Bit Score: 36.92  E-value: 3.70e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1201872072  691 VQCLKCHLWQHAECVNYKEENLKIKP-FYCPHC 722
Cdd:cd15610     18 VQCDGCEEWFHLLCVGLSPEEVAEDEdYICPSC 50
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 361-394 4.72e-03

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 41.32  E-value: 4.72e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1201872072  361 CI---IREYPFAGPQWP--------GGILADEMGLGKTVEVLALI 394
Cdd:PLN03142   165 CIkgkMRDYQLAGLNWLirlyengiNGILADEMGLGKTLQTISLL 209
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 375-392 5.64e-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: 5.64e-03
                           10
                   ....*....|....*...
gi 1201872072  375 GGILADEMGLGKTVEVLA 392
Cdd:cd18001     21 GGILADDMGLGKTVQICA 38
PHD_PHF2_like cd15554
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ...
 677-722 7.26e-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: 35.82  E-value: 7.26e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1201872072  677 CICGElglvDYKAR---VQCLKCHLWQHAECVNYKEENLK-IKPFYCPHC 722
Cdd:cd15554      2 CICRQ----PYDVTrfmIECDVCKDWFHGSCVGVEEHQANdIERYHCPNC 47
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
 363-394 8.50e-03

DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 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: 350760 [Multi-domain]  Cd Length: 229  Bit Score: 39.41  E-value: 8.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1201872072  363 IREYPFAGPQWPG--------GILADEMGLGKTVEVLALI 394
Cdd:cd18002      1 LKEYQLKGLNWLAnlyeqginGILADEMGLGKTVQSIAVL 40
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 363-400 8.95e-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: 39.23  E-value: 8.95e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1201872072  363 IREYPFAGPQWP--------GGILADEMGLGKTVEVLALI--LTHTRQ 400
Cdd:cd17997      4 MRDYQIRGLNWLislfengiNGILADEMGLGKTLQTISLLgyLKHYKN 51
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 376-400 9.18e-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: 38.91  E-value: 9.18e-03
                           10        20
                   ....*....|....*....|....*
gi 1201872072  376 GILADEMGLGKTVEVLALiLTHTRQ 400
Cdd:cd17998     22 GILADEMGLGKTIQVIAF-LAYLKE 45
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 337-404 9.26e-03

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: 39.58  E-value: 9.26e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1201872072  337 ALHFLWREVVtldGVKIYYNPFTGCIireypfagpqwpggiLADEMGLGKTVEVLALILTHTRQDIKQ 404
Cdd:cd18007      8 GVRFLWSNLV---GTDVGSDEGGGCI---------------LAHTMGLGKTLQVITFLHTYLAAAPRR 57
 
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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