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 1216930678   1 MGSSEMDKPAKEkeakalASASAQELTSTTSTGTVNPDWTGFQAY--SPIPPHGF----LASSPQAHPYMWGVQHIMPPY 74
Cdd:pfam07777   1 MGSSEEETPSKS------SKPSSPAQSDQTATHPVYPDWSAMQAYygPGVPPPPFfnspVASSPQPHPYMWGPQPMMPPY 74

                          90       100
                  ....*....|....*....|...
gi 1216930678  75 GTPPhPYVAMYPHGGIYAHPSIP 97
Cdd:pfam07777  75 GTPP-PYAAMYPPGGVYAHPSMP 96

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 1216930678   1 MGSSEMDKPAKEkeakalASASAQELTSTTSTGTVNPDWTGFQAY--SPIPPHGF----LASSPQAHPYMWGVQHIMPPY 74
Cdd:pfam07777   1 MGSSEEETPSKS------SKPSSPAQSDQTATHPVYPDWSAMQAYygPGVPPPPFfnspVASSPQPHPYMWGPQPMMPPY 74

                          90       100
                  ....*....|....*....|...
gi 1216930678  75 GTPPhPYVAMYPHGGIYAHPSIP 97
Cdd:pfam07777  75 GTPP-PYAAMYPPGGVYAHPSMP 96

Basic leucine zipper (bZIP) domain of Plant G-box binding factor 1 (GBF1)-like transcription factors: a DNA-binding and dimerization domain; This subfamily is composed of plant bZIP transciption factors including Arabidopsis thaliana G-box binding factor 1 (GBF1), Zea mays Opaque-2 and Ocs element-binding factor 1 (OCSBF-1), Triticum aestivum Histone-specific transcription factor HBP1 (or HBP-1a), Petroselinum crispum Light-inducible protein CPRF3 and CPRF6, and Nicotiana tabacum BZI-3, among many others. bZIP G-box binding factors (GBFs) contain an N-terminal proline-rich domain in addition to the bZIP domain. GBFs are involved in developmental and physiological processes in response to stimuli such as light or hormones. Opaque-2 plays a role in affecting lysine content and carbohydrate metabolism, acting indirectly on starch/amino acid ratio. 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 1216930678 311 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEY 361
Cdd:cd14702     1 RRRRKQSNRESARRSRMRKQAHLEELEAQVEQLRAENSTLRAELNALSQEY 51

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1216930678 306 ERELKRQRRKQSNRE---SARRSRLRK-QAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERL 375
Cdd:COG4372    65 EEELEQARSELEQLEeelEELNEQLQAaQAELAQAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQI 138

rod shape-determining protein MreC; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1216930678 335 ELAQRAEALKEENSNLRSEVNRikgeYEQLLAENASLKERLG 376
Cdd:PRK13922   73 DLREENEELKKELLELESRLQE----LEQLEAENARLRELLN 110

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 1216930678   1 MGSSEMDKPAKEkeakalASASAQELTSTTSTGTVNPDWTGFQAY--SPIPPHGF----LASSPQAHPYMWGVQHIMPPY 74
Cdd:pfam07777   1 MGSSEEETPSKS------SKPSSPAQSDQTATHPVYPDWSAMQAYygPGVPPPPFfnspVASSPQPHPYMWGPQPMMPPY 74

                          90       100
                  ....*....|....*....|...
gi 1216930678  75 GTPPhPYVAMYPHGGIYAHPSIP 97
Cdd:pfam07777  75 GTPP-PYAAMYPPGGVYAHPSMP 96

Basic leucine zipper (bZIP) domain of Plant G-box binding factor 1 (GBF1)-like transcription factors: a DNA-binding and dimerization domain; This subfamily is composed of plant bZIP transciption factors including Arabidopsis thaliana G-box binding factor 1 (GBF1), Zea mays Opaque-2 and Ocs element-binding factor 1 (OCSBF-1), Triticum aestivum Histone-specific transcription factor HBP1 (or HBP-1a), Petroselinum crispum Light-inducible protein CPRF3 and CPRF6, and Nicotiana tabacum BZI-3, among many others. bZIP G-box binding factors (GBFs) contain an N-terminal proline-rich domain in addition to the bZIP domain. GBFs are involved in developmental and physiological processes in response to stimuli such as light or hormones. Opaque-2 plays a role in affecting lysine content and carbohydrate metabolism, acting indirectly on starch/amino acid ratio. 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 1216930678 311 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEY 361
Cdd:cd14702     1 RRRRKQSNRESARRSRMRKQAHLEELEAQVEQLRAENSTLRAELNALSQEY 51

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 1216930678 311 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGE 360
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 1216930678 308 ELKRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLL 365
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 1216930678 305 DERELKRQRrkqsNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYE 362
Cdd:cd12193     1 DPVAAKRAR----NTLAARRSRARKLEEMEELEKRVEELEAENEELKTRAEVLEAEAR 54

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1216930678 310 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQL 364
Cdd:cd14692     2 KKERKREQNKNAATRYRQKKREEKEELLSEEEELEDRNRELKDEVEELQREINYL 56

Basic region leucine zipper;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1216930678 310 KRQRRKQsNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVnrikgeyEQLLAE 367
Cdd:pfam07716   2 YRDRRRK-NNEAAKRSREKKKQKEEELEERVKELERENAQLRQKV-------EQLEKE 51

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 1216930678 311 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLR 351
Cdd:cd14812     1 KEARLIRNRAAAQLSRQRKKEEVEELEARVKELEAENRRLR 41

Basic leucine zipper (bZIP) domain of BATF proteins: a DNA-binding and dimerization domain; Basic leucine zipper (bZIP) transcription factor ATF-like (BATF or SFA2), BATF2 (or SARI) and BATF3 form heterodimers with Jun proteins. They function as inhibitors of AP-1-driven transcription. Unlike most bZIP transcription factors that contain additional domains, BATF and BATF3 contain only the the bZIP DNA-binding and dimerization domain. BATF2 contains an additional C-terminal domain of unknown function. BATF:Jun hetrodimers preferentially bind to TPA response elements (TREs) with the consensus sequence TGA(C/G)TCA, and can also bind to a TGACGTCA cyclic AMP response element (CRE). In addition to negative regulation, BATF proteins also show positive transcriptional activities in the development of classical dendritic cells and T helper cell subsets, and in antibody production. 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 1216930678 308 ELKRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGE 360
Cdd:cd14701     1 DQKKVRRREKNRDAAQRSRQKQTEKADKLHEESESLERANAALRKEIKDLTEE 53

Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain; ATF-3 is a Basic leucine zipper (bZIP) transcription factor that is induced by various stress signals such as cytokines, genetoxic agents, or physiological stresses. It is implicated in cancer and host defense against pathogens. It negatively regulates the transcription of pro-inflammatory cytokines and is critical in preventing acute inflammatory syndromes. Mice deficient with ATF3 display increased susceptibility to endotoxic shock induced death. ATF3 dimerizes with Jun and other ATF proteins; the heterodimers function either as activators or repressors depending on the promoter context. 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 1216930678 310 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLL 365
Cdd:cd14722     1 RRRRRRERNKVAAAKCRNKKKERTDCLQKESEKLETQNAELKRQIEELKNEKQHLI 56

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 1216930678 311 RQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSevnrikgeyeqllaENASLKERL 375
Cdd:cd14700     1 RQQRMIKNRESACLSRKKKKEYVQSLETKLEQLKQENQKLKS--------------ENETLRERL 51

Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein 3 (CREB3) and similar proteins: a DNA-binding and dimerization domain; This subfamily is composed of CREB3 (also called LZIP or Luman), and the CREB3-like proteins CREB3L1 (or OASIS), CREB3L2, CREB3L3 (or CREBH), and CREB3L4 (or AIbZIP). They are type II membrane-associated members of the Basic leucine zipper (bZIP) family of transcription factors, with their N-termini facing the cytoplasm and their C-termini penetrating through the ER membrane. They contain an N-terminal transcriptional activation domain followed bZIP and transmembrane domains, and a C-terminal tail. They play important roles in ER stress and the unfolded protein response (UPR), as well as in many other biological processes such as cell secretion, bone and cartilage formation, and carcinogenesis. 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 1216930678 309 LKRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVnrikgeyEQLLAENASLKERL 375
Cdd:cd14689     1 LKKVRRKIRNKISAQESRRRKKEYIDGLESRVAACTAENQELKKKV-------EELEKQNRSLLSQL 60

Basic leucine zipper (bZIP) domain of Yeast Activator Protein (YAP) and similar proteins: a DNA-binding and dimerization domain; This subfamily is composed predominantly of AP-1-like transcription factors including Saccharomyces cerevisiae YAPs, Schizosaccharomyces pombe PAP1, and similar proteins. Members of this subfamily belong to the Basic leucine zipper (bZIP) family of transcription factors. The YAP subfamily is composed of eight members (YAP1-8) which may all be involved in stress responses. YAP1 is the major oxidative stress regulator and is also involved in iron metabolism (like YAP5) and detoxification of arsenic (like YAP8). YAP2 is involved in cadmium stress responses while YAP4 and YAP6 play roles in osmotic 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 1216930678 310 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASL 371
Cdd:cd14688     2 PKERRRAQNREAQRAFRERKKERIKELEQRVAELEEELAELEEELQELRAELRELESELQSL 63

Basic leucine zipper (bZIP) domain of Jun proteins and similar proteins: a DNA-binding and dimerization domain; Jun is a member 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 three Jun proteins: c-Jun, JunB, and JunD. c-Jun is the most potent transcriptional activator of the AP-1 proteins. Both c-Jun and JunB are essential during development; deletion of either results in embryonic lethality in mice. c-Jun is essential in hepatogenesis and liver erythropoiesis, while JunB is required in vasculogenesis and angiogenesis in extraembryonic tissues. While JunD is dispensable in embryonic development, it is involved in transcription regulation of target genes that help cells to cope with environmental signals. 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 1216930678 310 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQL 364
Cdd:cd14696     1 KLERKRARNRIAASKCRKRKLERIARLEDKVKELKNQNSELTSTASLLREQVCQL 55

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1216930678 309 LKRQRRKQSNRESaRRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERL 375
Cdd:COG4026   121 LKSLQNIPEYNEL-REELLELKEKIDEIAKEKEKLTKENEELESELEELREEYKKLREENSILEEEF 186

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 1216930678 304 QDERELKRQRrkqsNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQL 364
Cdd:cd14713     3 SDEYRKRRER----NNLAVKKSREKSKQKAQETLQRVNQLKEENERLEAKIKLLSKELSVL 59

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 1216930678 310 KRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQL 364
Cdd:cd14721     1 KRRVRRERNKLAAAKCRQRRVDLTNTLQAETEQLEDEKSSLQNEIANLQKQKEQL 55

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 1216930678 309 LKRQRRKQSNR---ESARRSRLRKQAECD----ELAQRAEALKEENSNLRSEVNRIKGEYEQLL 365
Cdd:cd14717     7 LKQRRRTLKNRgyaASCRIKRVTQKEELEkqkaELQQEVEKLARENASMRLELDALRSKYEALQ 70

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1216930678 330 QAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERL 375
Cdd:COG3074    24 QMEVEELKEKNEELEQENEELQSENEELQSENEQLKTENAEWQERI 69

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1216930678 303 LQDERELKRQRRKQSNRESARRSRLRK-----QAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERL 375
Cdd:COG4372    89 LQAAQAELAQAQEELESLQEEAEELQEeleelQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEEL 166

Coiled-coil region of CCDC155 or KASH; This coiled-coil region is found in the central part of KASH or Klarsicht/ANC-1/Syne/homology proteins. KASH are a meiosis-specific proteins that localize at telomeres and interact with SUN1, thus being implicated in meiotic chromosome dynamics and homolog pairing.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1216930678 305 DERELKRQRRKQSNRESARRSRL--RKQAECDE--LAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERLGEF 378
Cdd:pfam14662  65 LEEELEDLKLIVNSLEEARRSLLaqNKQLEKENqsLLQEIESLQEENKKNQAERDKLQKKKKELLKSKACLKEQLHSC 142

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1216930678 294 RDTVQSQIwlqdeRELKRQRRKQSNRESARRSRL-RKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLK 372
Cdd:COG4372    75 LEQLEEEL-----EELNEQLQAAQAELAQAQEELeSLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAERE 149

                  ...
gi 1216930678 373 ERL 375
Cdd:COG4372   150 EEL 152

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1216930678 303 LQD-ERELKRQRRKqsnRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERLGEFPGH 381
Cdd:COG1579    12 LQElDSELDRLEHR---LKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGNVRNN 88

                  ....*
gi 1216930678 382 EEFRA 386
Cdd:COG1579    89 KEYEA 93

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1216930678 303 LQDERELKRQRRKQSN-RESARRSRLRKQA---ECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERLGE 377
Cdd:COG4026   124 LQNIPEYNELREELLElKEKIDEIAKEKEKltkENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKSRFEE 202

Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1216930678 304 QDERELKRQRRKQSNRESARRSRlrkQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKERL 375
Cdd:cd22887     8 ELEKRLAELEAELASLEEEIKDL---EEELKEKNKANEILNDELIALQIENNLLEEKLRKLQEENDELVERW 76

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 1216930678 313 RRKQSNRESARRSRLRKqAECDElaqraealkeensNLRSEVNRIKGEYEQLLAENASLKERLGE 377
Cdd:cd14719    12 RRRSKNRIAAQRCRKRK-LDCIQ-------------NLECEIKKLVCEKEKLLGERNQLKASMGE 62

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1216930678 320 ESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAENASLKER 374
Cdd:COG4026   152 EKLTKENEELESELEELREEYKKLREENSILEEEFDNIKSEYSDLKSRFEELLKK 206

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 1216930678 313 RRKQSNRESARRSRLRK-------QAECDELAQRAEALKEENSNLRSEVNRIKGEYEQL 364
Cdd:cd14698     9 RRRGKNKVAAQNCRKRKldqistlEDEVDELKEEKEKLLKERDELEAETREMKDKYSQL 67

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1216930678 303 LQDERELKRQR--RKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSevNRikgEYEQLLAENASLKERLGE 377
Cdd:COG1579    36 LEDELAALEARleAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGNVRN--NK---EYEALQKEIESLKRRISD 107

leucine zipper domain found in c-Myc-binding protein and similar proteins; MycBP, also called associate of Myc 1 (AMY-1), is a novel c-Myc binding protein that may control the transcriptional activity of Myc. It stimulates the activation of E box-dependent transcription by Myc. This model corresponds to the conserved region that shows high sequence similarity with the leucine zipper (ZIP) domain located at the C-terminus of TGF-beta-stimulated clone-22 domain (TSC22D) family transcription factors. The first helix of ZIP is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1216930678 340 AEALKEENSNLRSEvnrikgeYEQLLAENASLKERL 375
Cdd:cd21937    21 VEALRLENEELKQK-------NEELEEENKELKAKL 49

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1216930678 295 DTVQSqiwLQDERELKRQRRKQSnresarrsrlrkQAECDELAQRAEALKEENSNLRSEVNRIKGEYEQLLAEN 368
Cdd:COG3074    18 DTIEL---LQMEVEELKEKNEEL------------EQENEELQSENEELQSENEQLKTENAEWQERIRSLLGKI 76

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1216930678 307 RELKRQRRKQSNRESARRSRLRKQAECDELAQRAEALKEENSNLRSEVNRIKG--EYEQLLAENASLKERLGEFP 379
Cdd:COG4717    71 KELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKllQLLPLYQELEALEAELAELP 145

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 1216930678   9 PAKEKEAKALASASAQELTSTTSTGTVNPDwtgFQAYSPIPPHGFLASSPQAHPYMWGVQH--IMPPYGTPPHPYVAMYP 86
Cdd:pfam03154 189 PGTTQAATAGPTPSAPSVPPQGSPATSQPP---NQTQSTAAPHTLIQQTPTLHPQRLPSPHppLQPMTQPPPPSQVSPQP 265

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1216930678  87 HGGIYAHPSIPPGSYPFS--PFAMPSPnGIAEASGYTPGSTEADGKPS 132
Cdd:pfam03154 266 LPQPSLHGQMPPMPHSLQtgPSHMQHP-VPPQPFPLTPQSSQSQVPPG 312