G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localization signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374  49 MASSEMEKSAKdkESKTPPPTSQEQSSTTSAgtnNPDWSSFQAY--SPMPPHGF----LASSPQAHPYMWGVQHIMPPYG 122
Cdd:pfam07777   1 MGSSEEETPSK--SSKPSSPAQSDQTATHPV---YPDWSAMQAYygPGVPPPPFfnspVASSPQPHPYMWGPQPMMPPYG 75

                          90       100
                  ....*....|....*....|.
gi 1806008374 123 TPPhPYVAMYPHGGIYAHPSM 143
Cdd:pfam07777  76 TPP-PYAAMYPPGGVYAHPSM 95

G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localization signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374  49 MASSEMEKSAKdkESKTPPPTSQEQSSTTSAgtnNPDWSSFQAY--SPMPPHGF----LASSPQAHPYMWGVQHIMPPYG 122
Cdd:pfam07777   1 MGSSEEETPSK--SSKPSSPAQSDQTATHPV---YPDWSAMQAYygPGVPPPPFfnspVASSPQPHPYMWGPQPMMPPYG 75

                          90       100
                  ....*....|....*....|.
gi 1806008374 123 TPPhPYVAMYPHGGIYAHPSM 143
Cdd:pfam07777  76 TPP-PYAAMYPPGGVYAHPSM 95

bZIP transcription factor; The Pfam entry includes the basic region and the leucine zipper region.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1806008374 357 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSEN 415
Cdd:pfam00170   1 KREKRKQSNREAARRSRQRKQAYIEELERRVKALEGENKTLRSELEELKKEVEKLKSKN 59

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1806008374 356 LKRQRRKQSNRESaRRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERL 422
Cdd:COG4026   121 LKSLQNIPEYNEL-REELLELKEKIDEIAKEKEKLTKENEELESELEELREEYKKLREENSILEEEF 186

chromosome segregation protein SMC, primarily archaeal 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. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374  333 GGMVTTGSRDSVQSQLW-LQDERELKRQRRKQsnrESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:TIGR02169  652 SGAMTGGSRAPRGGILFsRSEPAELQRLRERL---EGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQL 728

                           90
                   ....*....|...
gi 1806008374  412 LSENAALKERLEE 424
Cdd:TIGR02169  729 EQEEEKLKERLEE 741

G-box binding protein MFMR; This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localization signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374  49 MASSEMEKSAKdkESKTPPPTSQEQSSTTSAgtnNPDWSSFQAY--SPMPPHGF----LASSPQAHPYMWGVQHIMPPYG 122
Cdd:pfam07777   1 MGSSEEETPSK--SSKPSSPAQSDQTATHPV---YPDWSAMQAYygPGVPPPPFfnspVASSPQPHPYMWGPQPMMPPYG 75

                          90       100
                  ....*....|....*....|.
gi 1806008374 123 TPPhPYVAMYPHGGIYAHPSM 143
Cdd:pfam07777  76 TPP-PYAAMYPPGGVYAHPSM 95

bZIP transcription factor; The Pfam entry includes the basic region and the leucine zipper region.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1806008374 357 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSEN 415
Cdd:pfam00170   1 KREKRKQSNREAARRSRQRKQAYIEELERRVKALEGENKTLRSELEELKKEVEKLKSKN 59

Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1806008374 358 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSE 407
Cdd:cd14686     1 KERRRERNREAARRSRERKKERIEELEEEVEELEEENEELKAELEELRAE 50

Basic leucine zipper (bZIP) domain of X-box binding protein 1 (XBP1) and similar proteins: a DNA-binding and dimerization domain; XBP1, a member of the Basic leucine zipper (bZIP) family, is the key transcription factor that orchestrates the unfolded protein response (UPR). It is the most conserved component of the UPR and is critical for cell fate determination in response to ER stress. The inositol-requiring enzyme 1 (IRE1)-XBP1 pathway is one of the three major sensors at the ER membrane that initiates the UPR upon activation. IRE1, a type I transmembrane protein kinase and endoribonuclease, oligomerizes upon ER stress leading to its increased activity. It splices the XBP1 mRNA, producing a variant that translocates to the nucleus and activates its target genes, which are involved in protein folding, degradation, and trafficking. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1806008374 355 ELKRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLL 412
Cdd:cd14691     1 EEKDLRRKLKNRVAAQTARDRKKARMDELEERVRELEEENQKLRAENESLRARNEDLL 58

Basic leucine zipper (bZIP) domain of General control protein GCN4: a DNA-binding and dimerization domain; GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain. In amino acid-deprived cells, GCN4 is up-regulated leading to transcriptional activation of genes encoding amino acid biosynthetic enzymes. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1806008374 352 DERELKRQRrkqsNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYE 409
Cdd:cd12193     1 DPVAAKRAR----NTLAARRSRARKLEEMEELEKRVEELEAENEELKTRAEVLEAEAR 54

Basic leucine zipper (bZIP) domain of uncharaterized Plant BZIP transcription factors: a DNA-binding and dimerization domain; This subfamily is composed of uncharacterized plant bZIP transciption factors with similarity to Glycine max BZIP46, which may be a drought-responsive gene. Plant bZIPs are involved in developmental and physiological processes in response to stimuli/stresses such as light, hormones, and temperature changes. 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        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1806008374 357 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLR 398
Cdd:cd14707     1 RRQRRMIKNRESAARSRARKQAYTNELELEVAHLKEENARLK 42

Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains; AUREO is a BL-activated transcription factor specific to phototrophic stramenopiles. It has a bZIP and a BL-sensing light-oxygen voltage (LOV) domain. It has been shown to mediate BL-induced branching and regulate the development of the sex organ in Vaucheria frigida. 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. This subgroup also includes the Epstein-Barr virus (EBV) immediate-early transcription factor ZEBRA (BZLF1, Zta, Z, EB1). ZEBRA exhibits a variant of the bZIP fold, it has a unique dimer interface and a substantial hydrophobic pocket; it has a C-terminal moiety which stabilizes the coiled coil involved in dimer formation. ZEBRA functions to trigger the switch of EBV's biphasic infection cycle from latent to lytic infection. It activates the promoters of EBV lytic genes by binding ZEBRA response elements (ZREs) and inducing a cascade of expression of over 50 viral genes. It also down regulates latency-associated promoters, is an essential replication factor, induces host cell cycle arrest, and alters cellular immune responses and transcription factor activity.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1806008374 358 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYE 409
Cdd:cd14809     1 AERRRERNREHARKTRLRKKAYLESLKEQVAALQAENQRLRQQIRQAAPASA 52

Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily; Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. 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        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1806008374 358 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSR 403
Cdd:cd14812     1 KEARLIRNRAAAQLSRQRKKEEVEELEARVKELEAENRRLRQLLAQ 46

Basic leucine zipper (bZIP) domain of Activating Transcription Factor-4 (ATF-4) and similar proteins: a DNA-binding and dimerization domain; ATF-4 was also isolated and characterized as the cAMP-response element binding protein 2 (CREB2). It is a Basic leucine zipper (bZIP) transcription factor that has been reported to act as both an activator or repressor. It is a critical component in both the unfolded protein response (UPR) and amino acid response (AAR) pathways. Under certain stress conditions, ATF-4 transcription is increased; accumulation of ATF-4 induces the expression of genes involved in amino acid metabolism and transport, mitochondrial function, redox chemistry, and others that ensure protein synthesis and recovery from stress. 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        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1806008374 357 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSE---YEKLLSE 414
Cdd:cd14692     2 KKERKREQNKNAATRYRQKKREEKEELLSEEEELEDRNRELKDEVEELQREinyLKDLLRE 62

Basic leucine zipper (bZIP) domain of Plant RF2-like transcription factors: a DNA-binding and dimerization domain; This subfamily is composed of plant bZIP transciption factors with similarity to Oryza sativa RF2a and RF2b, which are important for plant development. They interact with, as homodimers or heterodimers with each other, and activate transcription from the RTBV (rice tungro bacilliform virus) promoter, which is regulated by sequence-specific DNA-binding proteins that bind to the essential cis element BoxII. RF2a and RF2b show differences in binding affinities to BoxII, expression patterns in different rice organs, and subcellular localization. Transgenic rice with increased RF2a and RF2b display increased resistance to rice tungro disease (RTD) with no impact on plant development. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1806008374 358 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSE 407
Cdd:cd14703     1 RAKRILANRQSAQRSRERKLQYISELERKVQTLQTEVATLSAQLALLEQE 50

Basic leucine zipper (bZIP) domain of Activating Transcription Factor-6 (ATF-6) and similar proteins: a DNA-binding and dimerization domain; ATF-6 is a type I membrane-bound Basic leucine zipper (bZIP) transcription factor that binds to the consensus ER stress response element (ERSE) and enhances the transcription of genes encoding glucose-regulated proteins Grp78, Grp94, and calreticulum. ATF-6 is one of three sensors of the unfolded protein response (UPR) in metazoans; the others being the kinases Ire1 and PERK. It contains an ER-lumenal domain that detects unfolded proteins. In response to ER stress, ATF-6 translocates from the ER to the Golgi with simultaneous cleavage in a process called regulated intramembrane proteolysis (Rip) to its transcriptionally competent form, which enters the nucleus and upregulates target UPR genes. The three UPR sensor branches cross-communicate to form a signaling network. 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        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1806008374 358 RQRRKQSNRESARRSRLRKqaecdelaqraealKEENASLRSEVSRIRSEYEKLLSENAALKERLE 423
Cdd:cd14700     1 RQQRMIKNRESACLSRKKK--------------KEYVQSLETKLEQLKQENQKLKSENETLRERLS 52

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1806008374 356 LKRQRRKQSNRESaRRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERL 422
Cdd:COG4026   121 LKSLQNIPEYNEL-REELLELKEKIDEIAKEKEKLTKENEELESELEELREEYKKLREENSILEEEF 186

Cell division protein ZapB, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning];

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1806008374 377 QAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEE 424
Cdd:COG3074    24 QMEVEELKEKNEELEQENEELQSENEELQSENEQLKTENAEWQERIRS 71

Basic leucine zipper (bZIP) domain of 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, NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, and 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. The small Mafs (MafF, MafK, MafG) do not contain a transactivation domain. They form dimers with cap'n'collar (CNC) proteins that harbor transactivation domains, and they act either as activators or repressors depending on their dimerization partner. They play roles in stress response and detoxification pathways. They have been implicated in various diseases such as diabetes, neurological diseases, thrombocytopenia and cancer. 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        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1806008374 354 RELKRQRRKQSNRESARRSRLRKQAEcdelaqrAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEEHG 426
Cdd:cd14697     5 IQLKQKRRTLKNRGYAQSCRAKRVQQ-------KEQLENEKAELRSQIEELKEENSELQQELDYYKQKFEALA 70

Basic leucine zipper (bZIP) domain of small 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 small Mafs (MafF, MafK, and MafG) do not contain a transactivation domain but do harbor the anxillary DNA-binding domain and a C-terminal bZIP domain. They form dimers with cap'n'collar (CNC) proteins that harbor transactivation domains, and they act either as activators or repressors depending on their dimerization partner. CNC transcription factors include NFE2 (nuclear factor, erythroid-derived 2) and similar proteins NFE2L1 (NFE2-like 1), NFE2L2, and NFE2L3, as well as BACH1 and BACH2. Small Mafs play roles in stress response and detoxification pathways. They also regulate the expression of betaA-globin and other genes activated during erythropoiesis. They have been implicated in various diseases such as diabetes, neurological diseases, thrombocytopenia and cancer. Triple deletion of the three small Mafs is embryonically lethal. 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        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1806008374 356 LKRQRRKQSNR---ESARRSRLRKQAECD----ELAQRAEALKEENASLRSEVSRIRSEYEKLL 412
Cdd:cd14717     7 LKQRRRTLKNRgyaASCRIKRVTQKEELEkqkaELQQEVEKLARENASMRLELDALRSKYEALQ 70

Basic leucine zipper (bZIP) domain of the oncogene Fos (Fos): a DNA-binding and dimerization domain; Fos proteins are members of the activator protein-1 (AP-1) complex, which is mainly composed of Basic leucine zipper (bZIP) dimers of the Jun and Fos families, and to a lesser extent, the activating transcription factor (ATF) and musculoaponeurotic fibrosarcoma (Maf) families. The broad combinatorial possibilities for various dimers determine binding specificity, affinity, and the spectrum of regulated genes. The AP-1 complex is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. There are four Fos proteins: c-Fos, FosB, Fos-related antigen 1 (Fra-1), and Fra-2. In addition, FosB also exists as smaller splice variants FosB2 and deltaFosB2. They all contain an N-terminal region and a bZIP domain. c-Fos and FosB also contain a C-terminal transactivation domain which is absent in Fra-1/2 and the smaller FosB variants. Fos proteins can only heterodimerize with Jun and other AP-1 proteins, but cannot homodimerize. Fos:Jun heterodimers are more stable and can bind DNA with more affinity that Jun:Jun homodimers. Fos proteins can enhance the trans-activating and transforming properties of Jun proteins. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1806008374 357 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:cd14721     1 KRRVRRERNKLAAAKCRQRRVDLTNTLQAETEQLEDEKSSLQNEIANLQKQKEQL 55

Basic leucine zipper (bZIP) domain of uncharaterized BZIP transcription factors with similarity to Triticum aestivum HBP-1b: a DNA-binding and dimerization domain; This subfamily is composed primarily of uncharacterized bZIP transciption factors from flowering plants, mosses, clubmosses, and algae. Included in this subfamily is wheat HBP-1b, which contains a C-terminal DOG1 domain, which is a specific plant regulator for seed dormancy. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1806008374 357 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRS 406
Cdd:cd14708     1 KVLRRLAQNREAARKSRLRKKAYVQQLEESVEKLKQLEQELQRARQQGRE 50

Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein gamma (CEBPG): a DNA-binding and dimerization domain; CEBPG is an important regulator of cellular senescence; mouse embryonic fibroblasts deficient of CEBPG proliferated poorly, entered senescence prematurely, and expressed elevated levels of proinflammatory genes. It is also the primary transcription factor that regulates antioxidant and DNA repair transcripts in normal bronchial epithelial cells. In a subset of AML patients with CEBPA hypermethylation, CEBPG is significantly overexpressed. CEBPG is the shortest CEBP protein and it lacks a transactivation domain. It acts as a regulator and buffering reservoir against the transcriptional activities of other CEBP proteins. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate many cellular processes. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. 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        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1806008374 351 QDERELKRQRrkqsNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:cd14713     3 SDEYRKRRER----NNLAVKKSREKSKQKAQETLQRVNQLKEENERLEAKIKLLSKELSVL 59

Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1806008374 351 QDERELKRQRRKQSNRESARRSRlrkQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERL 422
Cdd:pfam08614  96 EDERRLAALEAERAQLEEKLKDR---EEELREKRKLNQDLQDELVALQLQLNMAEEKLRKLEKENRELVERW 164

Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1806008374 350 LQDERELKRQRRKQSN-RESARRSRLRKQA---ECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEE 424
Cdd:COG4026   124 LQNIPEYNELREELLElKEKIDEIAKEKEKltkENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKSRFEE 202

Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein (CEBP) and similar proteins: a DNA-binding and dimerization domain; CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate the cell cycle, differentiation, growth, survival, energy metabolism, innate and adaptive immunity, and inflammation, among others. They are also associated with cancer and viral disease. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. Each possesses unique properties to regulate cell type-specific growth and differentiation. The sixth isoform, CEBPZ (zeta), lacks an intact DNA-binding domain and is excluded from this subfamily. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1806008374 358 RQRRKQSNrESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:cd14693     6 RQKRERNN-IAVRKSREKAKQRQLETQQKVQELRKENERLQKRVELLTKELSVL 58

Basic leucine zipper (bZIP) domain of CREBZF/Zhangfei transcription factor and similar proteins: a DNA-binding and dimerization domain; CREBZF (also called Zhangfei, ZF, LAZip, or SMILE) is a neuronal bZIP transcription factor that is involved in the infection cycle of herpes simplex virus (HSV) and related cellular processes. It suppresses the ability of the HSV transactivator VP16 to initiate the viral replicative cycle. CREBZF has also been implicated in the regulation of the human nerve growth factor receptor trkA and the tumor suppressor p53. 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        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1806008374 365 NRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:cd14706     8 NAIAARENRLKKKEYVENLEKSVDKLKSENKELKKANKKLQKLVEEL 54

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        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806008374 356 LKRQRRKQSNRESARRSRLRKqaecdeLAQRaEALKEENASLRSEVSRIRSEYEKLLSENAALKERLE 423
Cdd:cd14718     7 LKQKRRTLKNRGYAQSCRSKR------VQQR-HVLESEKCQLQQQVEQLKQEVSRLARERDAYKEKYE 67

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374  63 SKTPPPTSQEQSSTTSAGTNNPdwsSFQAYSPMPPHGFLASSPQAHPYMWGVQH--IMPPYGTPPHPYVAMYPHGGIYAH 140
Cdd:pfam03154 196 TAGPTPSAPSVPPQGSPATSQP---PNQTQSTAAPHTLIQQTPTLHPQRLPSPHppLQPMTQPPPPSQVSPQPLPQPSLH 272

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1806008374 141 PSMHPGSYPFS--PFAMPSNGIVEASGNTPGSMEADVVKPPE 180
Cdd:pfam03154 273 GQMPPMPHSLQtgPSHMQHPVPPQPFPLTPQSSQSQVPPGPS 314

DNA double-strand break repair Rad50 ATPase;

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806008374 350 LQDER----ELKRQRRKQSNRESARRSRLRKQAecDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLE 423
Cdd:PRK02224  514 LEERRedleELIAERRETIEEKRERAEELRERA--AELEAEAEEKREAAAEAEEEAEEAREEVAELNSKLAELKERIE 589

chromosome segregation protein SMC, primarily archaeal 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. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374  333 GGMVTTGSRDSVQSQLW-LQDERELKRQRRKQsnrESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:TIGR02169  652 SGAMTGGSRAPRGGILFsRSEPAELQRLRERL---EGLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIEKEIEQL 728

                           90
                   ....*....|...
gi 1806008374  412 LSENAALKERLEE 424
Cdd:TIGR02169  729 EQEEEKLKERLEE 741

Basic leucine zipper (bZIP) domain of BTB and CNC homolog (BACH) proteins: a DNA-binding and dimerization domain; BACH proteins are Cap'n'Collar (CNC) Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid region (called the CNC domain) located N-terminal to the bZIP DNA-binding domain. In addition, they contain a BTB domain (Broad complex-Tramtrack-Bric-a-brac domain, also known as the POZ [poxvirus and zinc finger] domain) that is absent in other CNC proteins. Veterbrates contain two members, BACH1 and BACH2. BACH1 forms heterodimers with small Mafs such as MafK to function as a repressor of heme oxygenase-1 (HO-1) gene (Hmox-1) enhancers. It has also been implicated as the master regulator of breast cancer bone metastasis. The BACH1 bZIP transcription factor should not be confused with the protein originally named as BRCA1-Associated C-terminal Helicase1 (BACH1), which has been renamed BRIP1 (BRCA1 Interacting Protein C-terminal Helicase1) and also called FANCJ. BACH2 is a B-cell specific transcription factor that plays a critical role in oxidative stress-mediated apoptosis. It plays an important role in class switching and somatic hypermutation of immunoglobulin genes. 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        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1806008374 360 RRKQSNRESARRSRLRKqAECDElaqraealkeenaSLRSEVSRIRSEYEKLLSENAALKERLEE 424
Cdd:cd14719    12 RRRSKNRIAAQRCRKRK-LDCIQ-------------NLECEIKKLVCEKEKLLGERNQLKASMGE 62

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374 350 LQDERELKRQRRKQSNRESARRSRLRKQAEcdELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEEHGNDD 429
Cdd:COG4372    89 LQAAQAELAQAQEELESLQEEAEELQEELE--ELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEEL 166

                          90
                  ....*....|...
gi 1806008374 430 PRSGRNDQQVDND 442
Cdd:COG4372   167 AALEQELQALSEA 179

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1806008374 350 LQDERELKRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEEHGND 428
Cdd:COG1196   218 LKEELKELEAELLLLKLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAE 296

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1806008374 349 WLQDERELKRQRRKQsnRESARRSRlRKQAECDELAQRAEALKEEnaSLRSEVSRIRSEYEKLLSENAA-LKERLEEHGN 427
Cdd:pfam13868 219 ERQKEREEAEKKARQ--RQELQQAR-EEQIELKERRLAEEAEREE--EEFERMLRKQAEDEEIEQEEAEkRRMKRLEHRR 293

                  .
gi 1806008374 428 D 428
Cdd:pfam13868 294 E 294

Cell division protein ZapB; ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1806008374 377 QAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEE 424
Cdd:pfam06005  24 QMENEELKEENEELKEEANELEEENQQLKQERNQWQERIRGLLGKLDE 71

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806008374 355 ELKRQRRKQSNRESARRSRLRKQAECDELAQRA---EALKEENASLRSEVSRIRSEYEKLLSENAALKERLEEHGNDD 429
Cdd:COG4717   392 EQAEEYQELKEELEELEEQLEELLGELEELLEAldeEELEEELEELEEELEELEEELEELREELAELEAELEQLEEDG 469

Basic leucine zipper (bZIP) domain of Cap'n'Collar (CNC) transcription factors: a DNA-binding and dimerization domain; CNC proteins form a subfamily of Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid region (called the CNC domain) located N-terminal to the bZIP DNA-binding domain. This subfamily includes Drosophila Cnc and four vertebrate counterparts, NFE2 (nuclear factor, erythroid-derived 2), NFE2-like 1 or NFE2-related factor 1 (NFE2L1 or Nrf1), NFE2L2 (or Nrf2), and NFE2L3 (or Nrf3). It also includes BACH1 and BACH2, which contain an additional BTB domain (Broad complex###Tramtrack###Bric-a-brac domain, also known as the POZ [poxvirus and zinc finger] domain). CNC proteins function during development and/or contribute in maintaining homeostasis during stress responses. In flies, Cnc functions both in development and in stress responses. In vertebrates, several CNC proteins encoded by distinct genes show varying functions and expression patterns. NFE2 is required for the proper development of platelets while the three Nrfs function in stress responses. Nrf2, the most extensively studied member of this subfamily, acts as a xenobiotic-activated receptor that regulates the adaptive response to oxidants and electrophiles. BACH1 forms heterodimers with small Mafs such as MafK to function as a repressor of heme oxygenase-1 (HO-1) gene (Hmox-1) enhancers. BACH2 is a B-cell specific transcription factor that plays a critical role in oxidative stress-mediated apoptosis. 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        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1806008374 360 RRKQSNRESARRSRLRK-------QAECDELAQRAEALKEENASLRSEVSRIRSEYEKL 411
Cdd:cd14698     9 RRRGKNKVAAQNCRKRKldqistlEDEVDELKEEKEKLLKERDELEAETREMKDKYSQL 67

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1806008374 349 WLQDERELKRQRRK--QSNRESARRSRLRKQAECDELAQRAEALKEENASLRSEVSRIRSEYEKLLSENAALKERLEE 424
Cdd:COG1196   236 ELEAELEELEAELEelEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRRE 313