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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253  278 KKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIE 337
Cdd:pfam00170   1 KREKRKQSNREAARRSRQRKQAYIEELERRVKALEGENKTLRSELEELKKEVEKLKSKNK 60

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253 265 VSLTAKVKTEKLDKKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIEEVRKARG 344
Cdd:COG3883   10 TPAFADPQIQAKQKELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREELG 89

                 .
gi 341940253 345 K 345
Cdd:COG3883   90 E 90

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253   276 LDKKLKKMEQNKTAATRYRQKKRAEQEA----LTGECKELEKKNEALKEKA-------DSLAKEIQYLKDLIEEVRKARG 344
Cdd:TIGR02168  198 LERQLKSLERQAEKAERYKELKAELRELelalLVLRLEELREELEELQEELkeaeeelEELTAELQELEEKLEELRLEVS 277

                   ...
gi 341940253   345 KKR 347
Cdd:TIGR02168  278 ELE 280

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253  278 KKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIE 337
Cdd:pfam00170   1 KREKRKQSNREAARRSRQRKQAYIEELERRVKALEGENKTLRSELEELKKEVEKLKSKNK 60

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 341940253 279 KLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQ 330
Cdd:cd14686    1 KERRRERNREAARRSRERKKERIEELEEEVEELEEENEELKAELEELRAEVE 52

Basic leucine zipper (bZIP) domain of Fungal Zip1-like transcription factors: a DNA-binding and dimerization domain; This subfamily is composed of fungal bZIP transcription factors including Schizosaccharomyces pombe Zip1, Saccharomyces cerevisiae Methionine-requiring protein 28 (Met28p), and Neurospora crassa cys-3, among others. Zip1 is required for the production of key proteins involved in sulfur metabolism and also plays a role in cadmium response. Met28p acts as a cofactor of Met4p, a transcriptional activator of the sulfur metabolic network; it stabilizes DNA:Met4 complexes. 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 341940253 282 KMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLK 333
Cdd:cd14705    4 KRRRNTAASARFRAKKKQREQELEEKLKELEERIKELERRLDELESENKFLK 55

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 341940253 277 DKKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLK 333
Cdd:cd14701    2 QKKVRRREKNRDAAQRSRQKQTEKADKLHEESESLERANAALRKEIKDLTEELKYLT 58

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253 278 KKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIE 337
Cdd:cd14721    1 KRRVRRERNKLAAAKCRQRRVDLTNTLQAETEQLEDEKSSLQNEIANLQKQKEQLEFLLA 60

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 341940253 279 KLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKE 320
Cdd:cd14812    1 KEARLIRNRAAAQLSRQRKKEEVEELEARVKELEAENRRLRQ 42

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 341940253 278 KKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLI 336
Cdd:cd14722    1 RRRRRRERNKVAAAKCRNKKKERTDCLQKESEKLETQNAELKRQIEELKNEKQHLIDML 59

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 341940253 279 KLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKE 328
Cdd:cd14702    1 RRRRKQSNRESARRSRMRKQAHLEELEAQVEQLRAENSTLRAELNALSQE 50

Basic leucine zipper (bZIP) domain of Hepatic leukemia factor (HLF) and similar proteins: a DNA-binding and dimerization domain; HLF, also called vitellogenin gene-binding protein (VBP) in birds, is a circadian clock-controlled Basic leucine zipper (bZIP) transcription factor which is a direct transcriptional target of CLOCK/BMAL1. It is implicated, together with bZIPs DBP and TEF, in the regulation of genes involved in the metabolism of endobiotic and xenobiotic agents. Triple knockout mice display signs of early aging and suffer premature death, likely due to impaired defense against xenobiotic stress. A leukemogenic translocation results in the chimeric fusion protein E2A-HLF that results in a rare form of pro-B-cell acute lymphoblastic leukemia (ALL). 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 341940253 275 KLDKKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKD 334
Cdd:cd14695    1 KDDKYWERRRKNNLAAKRSRDARRLKENQIAIRAAFLEKENAALRAEIAKLKKELEDLRK 60

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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 341940253 278 KKLKKMEQNKTAATRYRQKKrAEQEA-LTGECKELEKKNEALKEKADSLAKEIQYLKDLIEE 338
Cdd:cd14696    1 KLERKRARNRIAASKCRKRK-LERIArLEDKVKELKNQNSELTSTASLLREQVCQLKQKVME 61

MAEBL; Provisional

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 341940253  269 AKVKTEKLDKKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIEEVRKARGKKR 347
Cdd:PTZ00121 1320 AKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKK 1398

Basic leucine zipper (bZIP) domain of Fungal HAC1-like transcription factors: a DNA-binding and dimerization domain; HAC1 (also called Hac1p or HacA) is a bZIP transcription factor that plays a critical role in the unfolded protein response (UPR). The UPR is initiated by the ER-resident protein kinase and endonuclease IRE1, which promotes non-conventional splicing of the HAC1 mRNA, facilitating its translation. HAC1 binds to and activates promoters of genes that encode chaperones and other targets of the UPR. 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 341940253 286 NKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEI 329
Cdd:cd14710    9 NRRAAHQSRERKRLHVEFLEKKCDLLEALLQRLQDLLAQLEEKL 52

Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein 1 (CREB1) and similar proteins: a DNA-binding and dimerization domain; CREB1 is a Basic leucine zipper (bZIP) transcription factor that plays a role in propagating signals initiated by receptor activation through the induction of cAMP-responsive genes. Because it responds to many signal transduction pathways, CREB1 is implicated to function in many processes including learning, memory, circadian rhythm, immune response, and reproduction, among others. 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 341940253 278 KKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEkadslakEIQYLKDLI 336
Cdd:cd14690    1 KRQLRLEKNREAARECRRKKKEYVKCLENRVAVLENENKELRE-------ELKILKELL 52

MAEBL; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253  270 KVKTEKLDKKLKKMEQNKTAATRYRQKKRAEQEALTGECK----ELEKKNEALKEKADSLAKEIQYlKDLIEEVRKARGK 345
Cdd:PTZ00121 1443 AKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAkkadEAKKKAEEAKKKADEAKKAAEA-KKKADEAKKAEEA 1521

                  ..
gi 341940253  346 KR 347
Cdd:PTZ00121 1522 KK 1523

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253   276 LDKKLKKMEQNKTAATRYRQKKRAEQEA----LTGECKELEKKNEALKEKA-------DSLAKEIQYLKDLIEEVRKARG 344
Cdd:TIGR02168  198 LERQLKSLERQAEKAERYKELKAELRELelalLVLRLEELREELEELQEELkeaeeelEELTAELQELEEKLEELRLEVS 277

                   ...
gi 341940253   345 KKR 347
Cdd:TIGR02168  278 ELE 280

DNA double-strand break repair ATPase Rad50;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 341940253 268 TAKVKTEKLDKkLKKMEQNKTAatryrQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIEEVRKARGK 345
Cdd:PRK03918 366 EAKAKKEELER-LKKRLTGLTP-----EKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGK 437

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 341940253 274 EKLDKKLKKMEQNKTAATRYRQKKRAEQEALTGECKELEKKNEALKEKADSLAKEIQYLKDLIEEVRKARGKK 346
Cdd:COG4372   76 EQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAER 148

Cell division protein FtsB [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 341940253 309 KELEKKNEALKEKADSLAKEIQYLK---DLIEEvrKAR 343
Cdd:COG2919   39 AELEAENAKLKARNAELEAEVADLKdgpDYIEE--RAR 74

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341940253 270 KVKTEKLDKKLKKMEQNKTAATRYRQKKRAEQEALTGECKE-------LEKKNEALKEKADSLAKEIQYLKDLIEEVRKA 342
Cdd:COG4942  156 RADLAELAALRAELEAERAELEALLAELEEERAALEALKAErqkllarLEKELAELAAELAELQQEAEELEALIARLEAE 235

                 ....*
gi 341940253 343 RGKKR 347
Cdd:COG4942  236 AAAAA 240