Morc6 ribosomal protein S5 domain 2-like; This domain is found in MORC6 proteins in eukaryotes. Arabidopsis microrchidia (MORC) ATPase family proteins are conserved among plants and animals and are involved in transcriptional silencing. In Arabidopsis, MORC6/DMS11 was reported to function in the condensation of pericentromeric heterochromatin, thereby facilitating transcriptional silencing. Further studies demonstrate that MORC6 and its homologs MORC1 and MORC2 form a complex which associates with SUVH9, required for Pol V occupancy in the RdDM (RNA-directed DNA methylation) pathway.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213 249 YSLRAYCSILYLK--PRMQIIIRGQKVKTQLVSKSLAYIERDVYRPKFLT---KTVRITFGF--NCRNKDHYGIMMYHKN 321
Cdd:pfam17942   1 YSLRAYASILYLRlpPNFQIILRGKKVEHHNIADDLKYPEKITYKPQVGGgkeVVVITTIGFlkEAPHINVHGFNVYHKN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2071063213 322 RLIKAYEKVGCQlkANNMGVGVVGVIECNFLKPTHNKQDFDYTNEYRLTILALGEKLNDYW 382
Cdd:pfam17942  81 RLIKPFWRVGNQ--AGSKGRGVIGVLEANFIEPTHDKQDFERTSLYQRLEARLKQMLKEYW 139

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2071063213 409 TWVQCDACLKWRKLPDGID--QLPEKWYCSNNPDPQFRNC 446
Cdd:pfam07496   1 YWVQCDSCLKWRRLPTEIDpyELPEPWYCSMNPDPKYNSC 40

Morc6 ribosomal protein S5 domain 2-like; This domain is found in MORC6 proteins in eukaryotes. Arabidopsis microrchidia (MORC) ATPase family proteins are conserved among plants and animals and are involved in transcriptional silencing. In Arabidopsis, MORC6/DMS11 was reported to function in the condensation of pericentromeric heterochromatin, thereby facilitating transcriptional silencing. Further studies demonstrate that MORC6 and its homologs MORC1 and MORC2 form a complex which associates with SUVH9, required for Pol V occupancy in the RdDM (RNA-directed DNA methylation) pathway.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213 249 YSLRAYCSILYLK--PRMQIIIRGQKVKTQLVSKSLAYIERDVYRPKFLT---KTVRITFGF--NCRNKDHYGIMMYHKN 321
Cdd:pfam17942   1 YSLRAYASILYLRlpPNFQIILRGKKVEHHNIADDLKYPEKITYKPQVGGgkeVVVITTIGFlkEAPHINVHGFNVYHKN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2071063213 322 RLIKAYEKVGCQlkANNMGVGVVGVIECNFLKPTHNKQDFDYTNEYRLTILALGEKLNDYW 382
Cdd:pfam17942  81 RLIKPFWRVGNQ--AGSKGRGVIGVLEANFIEPTHDKQDFERTSLYQRLEARLKQMLKEYW 139

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2071063213 409 TWVQCDACLKWRKLPDGID--QLPEKWYCSNNPDPQFRNC 446
Cdd:pfam07496   1 YWVQCDSCLKWRRLPTEIDpyELPEPWYCSMNPDPKYNSC 40

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2071063213   32 AVAELIDNAYDPDVNAKQIWIDKTVISDHICLTFTDNGNGMTADKLHKMLSFGFS--DKVTVNGHVPVGLY 100
Cdd:smart00387   9 VLSNLLDNAIKYTPEGGRITVTLERDGDHVEITVEDNGPGIPPEDLEKIFEPFFRtdKRSRKIGGTGLGLS 79

Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain; Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The large Mafs (c-Maf, MafA, MafB, and neural retina leucine zipper or NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, a C-terminal bZIP domain. They function as critical regulators of terminal differentiation in the blood and in many tissues such as bone, brain, kidney, pancreas, and retina. MafA and MafB also play crucial roles in islet beta cells; they regulate genes essential for glucose sensing and insulin secretion cooperatively and sequentially. Large Mafs are also implicated in oncogenesis; MafB and c-Maf chromosomal translocations result in multiple myelomas. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription.

                          10        20
                  ....*....|....*....|....*..
gi 2071063213 697 QLQELRSELLLVTQERDDYKRKCQVFA 723
Cdd:cd14718    44 QVEQLKQEVSRLARERDAYKEKYEKLA 70

AT-hook-containing transcription factor; This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2071063213 842 LEMEKSHMHSRCEELKTEVEQLKSTSQQAGADVSTSSS 879
Cdd:pfam12443  44 LEAEIYQLGQRLQELKDQTDQLKQKVEEFSKDIAQDSP 81

Morc6 ribosomal protein S5 domain 2-like; This domain is found in MORC6 proteins in eukaryotes. Arabidopsis microrchidia (MORC) ATPase family proteins are conserved among plants and animals and are involved in transcriptional silencing. In Arabidopsis, MORC6/DMS11 was reported to function in the condensation of pericentromeric heterochromatin, thereby facilitating transcriptional silencing. Further studies demonstrate that MORC6 and its homologs MORC1 and MORC2 form a complex which associates with SUVH9, required for Pol V occupancy in the RdDM (RNA-directed DNA methylation) pathway.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213 249 YSLRAYCSILYLK--PRMQIIIRGQKVKTQLVSKSLAYIERDVYRPKFLT---KTVRITFGF--NCRNKDHYGIMMYHKN 321
Cdd:pfam17942   1 YSLRAYASILYLRlpPNFQIILRGKKVEHHNIADDLKYPEKITYKPQVGGgkeVVVITTIGFlkEAPHINVHGFNVYHKN 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2071063213 322 RLIKAYEKVGCQlkANNMGVGVVGVIECNFLKPTHNKQDFDYTNEYRLTILALGEKLNDYW 382
Cdd:pfam17942  81 RLIKPFWRVGNQ--AGSKGRGVIGVLEANFIEPTHDKQDFERTSLYQRLEARLKQMLKEYW 139

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 2071063213 409 TWVQCDACLKWRKLPDGID--QLPEKWYCSNNPDPQFRNC 446
Cdd:pfam07496   1 YWVQCDSCLKWRRLPTEIDpyELPEPWYCSMNPDPKYNSC 40

Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2071063213  30 FSAVAELIDNAYDPDVNAKQIWIDKTVISDHICLTFTDNGNGMTADKLHKML-SFGFSDKVTVNGHVPVGLY 100
Cdd:cd00075     2 EQVLSNLLDNALKYSPPGGTIEISLRQEGDGVVLEVEDNGPGIPEEDLERIFeRFYRGDKSREGGGTGLGLA 73

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213  697 QLQELRSELLLVTQERDDYKRKCQVFADQIQVLQRRLLEMND--QCVKKEMCHQSTEMDA-VFLLGSVNGQSESPG---- 769
Cdd:TIGR00606  710 KLKSTESELKKKEKRRDEMLGLAPGRQSIIDLKEKEIPELRNklQKVNRDIQRLKNDIEEqETLLGTIMPEEESAKvclt 789

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213  770 --HVGSQYQQALEEIER-LKKQCSALQHVKGECSQSSCTESKSEMDEmavqlddvfrQLDKCTIERDQYRSEVQLLEMEK 846
Cdd:TIGR00606  790 dvTIMERFQMELKDVERkIAQQAAKLQGSDLDRTVQQVNQEKQEKQH----------ELDTVVSKIELNRKLIQDQQEQI 859

                          170       180
                   ....*....|....*....|....*.
gi 2071063213  847 SHMHSRCEELKTEVEQLKSTSQQAGA 872
Cdd:TIGR00606  860 QHLKSKTNELKSEKLQIGTNLQRRQQ 885

Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain; Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The large Mafs (c-Maf, MafA, MafB, and neural retina leucine zipper or NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, a C-terminal bZIP domain. They function as critical regulators of terminal differentiation in the blood and in many tissues such as bone, brain, kidney, pancreas, and retina. MafA and MafB also play crucial roles in islet beta cells; they regulate genes essential for glucose sensing and insulin secretion cooperatively and sequentially. Large Mafs are also implicated in oncogenesis; MafB and c-Maf chromosomal translocations result in multiple myelomas. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription.

                          10        20
                  ....*....|....*....|....*..
gi 2071063213 697 QLQELRSELLLVTQERDDYKRKCQVFA 723
Cdd:cd14718    44 QVEQLKQEVSRLARERDAYKEKYEKLA 70

AT-hook-containing transcription factor; This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2071063213 842 LEMEKSHMHSRCEELKTEVEQLKSTSQQAGADVSTSSS 879
Cdd:pfam12443  44 LEAEIYQLGQRLQELKDQTDQLKQKVEEFSKDIAQDSP 81

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213  685 ETSAESADAAGHQLQELRSELLLVTQERDDYKRKCQVFADQIQVLQRRLLEMNDQCVKKEMCHQSTEMDAVFLLGSVNGQ 764
Cdd:TIGR02168  242 EELQEELKEAEEELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEEL 321

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213  765 SESPGHVGSQYQQALEEIERLKKQcsaLQHVKGECsqsscTESKSEMDEMAVQLDDVFRQLDKCTIERDQYRSEVQLLEM 844
Cdd:TIGR02168  322 EAQLEELESKLDELAEELAELEEK---LEELKEEL-----ESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLEL 393

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2071063213  845 EKSHMHSRCEELKTEVEQLKSTSQQAGADVST 876
Cdd:TIGR02168  394 QIASLNNEIERLEARLERLEDRRERLQQEIEE 425

HOOK protein coiled-coil region; This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organizms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas this central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head. This entry includes the central coiled-coiled domain and the divergent C-terminal domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213 696 HQLQELRSELLLVTQERDDYKRKCQVFADQIQVLQRRLLEMndQCVKKEMCHQSTEMDAvfLLGSVNGQSESPGHVGSqY 775
Cdd:pfam05622  66 KQLEQLQEENFRLETARDDYRIKCEELEKEVLELQHRNEEL--TSLAEEAQALKDEMDI--LRESSDKVKKLEATVET-Y 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2071063213 776 QQALEEIERLKKQCSALQHVKGECSQSSCT---ES-------------KSEMDEMAVQLDDVFRQLDKCTIERDQYRSEV 839
Cdd:pfam05622 141 KKKLEDLGDLRRQVKLLEERNAEYMQRTLQleeELkkanalrgqletyKRQVQELHGKLSEESKKADKLEFEYKKLEEKL 220

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 2071063213 840 QLLEMEKSHMHSRCEELKTEVEQLKSTSQQAGADVSTSSSAEEAVSYVD 888
Cdd:pfam05622 221 EALQKEKERLIIERDTLRETNEELRCAQLQQAELSQADALLSPSSDPGD 269