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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIAGDHHEKATVYKVQ 91
Cdd:cd17999     1 LRPYQQEGINWLAFLNKYNLHGILCDDMGLGKTLQTLCILASDHHKRANSFNSE 54

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIAGDHHEKATVYKVQ 91
Cdd:cd17999     1 LRPYQQEGINWLAFLNKYNLHGILCDDMGLGKTLQTLCILASDHHKRANSFNSE 54

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1524850981  41 YQQDGVNWLAFL-NRYKLHGILCDDMGLGKTLQSICIIAGDHHEK 84
Cdd:pfam00176   1 YQIEGVNWMLSLeNNLGRGGILADEMGLGKTLQTISLLLYLKHVD 45

DEAD-like helicases superfamily;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1524850981   37 ELRKYQQDGVNWLAFLNRyklHGILCDDMGLGKTLQSICIIA 78
Cdd:smart00487   8 PLRPYQKEAIEALLSGLR---DVILAAPTGSGKTLAALLPAL 46

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIAGDHHEKATVYKVQ 91
Cdd:cd17999     1 LRPYQQEGINWLAFLNKYNLHGILCDDMGLGKTLQTLCILASDHHKRANSFNSE 54

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1524850981  30 IPVPIKAELRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:COG0553   234 LPAGLKATLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLL 282

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:cd18003     1 LREYQHIGLDWLATLYEKNLNGILADEMGLGKTIQTIALLA 41

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1524850981  37 ELRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:cd17993     1 ELRDYQLTGLNWLAHSWCKGNNGILADEMGLGKTVQTISFLS 42

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1524850981  38 LRKYQQDGVNWLaflnrYKLHGILCDDMGLGKTLQSICIIAGDHHEKATVYK 89
Cdd:cd18008     1 LLPYQKQGLAWM-----LPRGGILADEMGLGKTIQALALILATRPQDPKIPE 47

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1524850981  35 KAELRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:cd17997     1 GGTMRDYQIRGLNWLISLFENGINGILADEMGLGKTLQTISLLG 44

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1524850981  38 LRKYQQDGVNWLaflnrYKLH-----GILCDDMGLGKTLQSICIIAGDHHEKA 85
Cdd:cd18001     1 LYPHQREGVAWL-----WSLHdggkgGILADDMGLGKTVQICAFLSGMFDSGL 48

Probable chromatin-remodeling complex ATPase chain; Provisional

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1524850981   31 PVPIKAELRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:PLN03142   163 PSCIKGKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLG 210

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:cd18002     1 LKEYQLKGLNWLANLYEQGINGILADEMGLGKTVQSIAVLA 41

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1524850981  38 LRKYQQDGVNWLAFLNryklhGILCDDMGLGKTLQSICIIA 78
Cdd:cd18070     1 LLPYQRRAVNWMLVPG-----GILADEMGLGKTVEVLALIL 36

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIA 78
Cdd:cd18060     1 LREYQLEGVNWLLFNWYNRQNCILADEMGLGKTIQSIAFLQ 41

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; 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. CHD2 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1524850981  37 ELRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIAGDHHE 83
Cdd:cd18054    20 ELRDYQLEGLNWLAHSWCKNNSVILADEMGLGKTIQTISFLSYLFHQ 66

DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1524850981  34 IKAELRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICII 77
Cdd:cd18062    20 VNGVLKQYQIKGLEWLVSLYNNNLNGILADEMGLGKTIQTIALI 63

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1524850981  38 LRKYQQDGVNWLAfLNRYKLHG-ILCDDMGLGKTLQSICIIA 78
Cdd:cd18006     1 LRPYQLEGVNWLL-QCRAEQHGcILGDEMGLGKTCQTISLLW 41

DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1524850981  38 LRKYQQDGVNW-LAFLNRyklhGILCDDMGLGKTLQSICIIA 78
Cdd:cd18010     1 LLPFQREGVCFaLRRGGR----VLIADEMGLGKTVQAIAIAA 38

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1524850981  38 LRKYQQDGVNWL----AFLNRYKLHG-ILCDDMGLGKTLQSICII 77
Cdd:cd18004     1 LRPHQREGVQFLydclTGRRGYGGGGaILADEMGLGKTLQAIALV 45

DEAD-like helicases superfamily;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1524850981   37 ELRKYQQDGVNWLAFLNRyklHGILCDDMGLGKTLQSICIIA 78
Cdd:smart00487   8 PLRPYQKEAIEALLSGLR---DVILAAPTGSGKTLAALLPAL 46

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHG-ILCDDMGLGKTLQSICII 77
Cdd:cd18072     1 LLLHQKQALAWLLWRERQKPRGgILADDMGLGKTLTMIALI 41

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQSICIIAGDHHE 83
Cdd:cd18057     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQTIVFLYSLYKE 46

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 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.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1524850981  38 LRKYQQDGVNWLAFLNRYKLHGILCDDMGLGKTLQS 73
Cdd:cd18056     1 LHPYQLEGLNWLRFSWAQGTDTILADEMGLGKTVQT 36

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.

                          10
                  ....*....|....*...
gi 1524850981  60 ILCDDMGLGKTLQSICII 77
Cdd:cd18007    30 ILAHTMGLGKTLQVITFL 47