Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058 399 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsgpVVHETHDLIVDLGDHREVLSFDVTQSPFFPVVL 478
Cdd:cd00303   10 VRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVK---TLGVILPVTIGIGGKTFTVDFYVLDLLSYDVIL 86

                 ....*
gi 296785058 479 GVRWL 483
Cdd:cd00303   87 GRPWL 91

Retrotransposon gag protein; Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058  111 ECPEDLPEKFDGNPDMLAPFMAQCQIFMEKSTRDFSVDRVRVCFVTSMMTGRAARWASAKLERSHYLMHNYPAFMMEMKH 190
Cdd:pfam16297  22 SNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQ 101

                  ..
gi 296785058  191 VF 192
Cdd:pfam16297 102 YF 103

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058 399 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsgpVVHETHDLIVDLGDHREVLSFDVTQSPFFPVVL 478
Cdd:cd00303   10 VRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVK---TLGVILPVTIGIGGKTFTVDFYVLDLLSYDVIL 86

                 ....*
gi 296785058 479 GVRWL 483
Cdd:cd00303   87 GRPWL 91

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058  111 ECPEDLPEKFDGNPDMLAPFMAQCQIFMEKSTRDFSVDRVRVCFVTSMMTGRAARWASAKLERSHYLMHNYPAFMMEMKH 190
Cdd:pfam16297  22 SNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQ 101

                  ..
gi 296785058  191 VF 192
Cdd:pfam16297 102 YF 103

basic region leucin zipper;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 296785058    37 ERRRdelsEEINNLREKVMKQSEENNNLQSQVQKLTEENTTLREQVE 83
Cdd:smart00338  22 ERKK----AEIEELERKVEQLEAENERLKKEIERLRRELEKLKSELE 64

TATA element modulatory factor 1 TATA binding; This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organization in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058   37 ERRRDELSEEINNL---REKVMKQSEENNNLQSQVQKLTE-ENTTLR------EQVEptpEDEDDDIELR 96
Cdd:pfam12325  39 EAQRDEARQEIVKLmkeNEELKELKKELEELEKELKELEQrYETTLEllgeksEEVE---ELKADVEDLK 105

Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058 399 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsgpVVHETHDLIVDLGDHREVLSFDVTQSPFFPVVL 478
Cdd:cd00303   10 VRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVK---TLGVILPVTIGIGGKTFTVDFYVLDLLSYDVIL 86

                 ....*
gi 296785058 479 GVRWL 483
Cdd:cd00303   87 GRPWL 91

Domain of unknown function (DUF4939); This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058  111 ECPEDLPEKFDGNPDMLAPFMAQCQIFMEKSTRDFSVDRVRVCFVTSMMTGRAARWASAKLERSHYLMHNYPAFMMEMKH 190
Cdd:pfam16297  22 SNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQ 101

                  ..
gi 296785058  191 VF 192
Cdd:pfam16297 102 YF 103

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058  402 MIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIA------SGPVVHETHDLIVDLgdhrevLSFDVTQspfFP 475
Cdd:pfam08284  34 LFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTtnlicpSCPIEIQGISFLADL------ILLDMKD---LD 104

                          90       100
                  ....*....|....*....|....
gi 296785058  476 VVLGVRWLSTHDPNITWSTRSIVF 499
Cdd:pfam08284 105 VILGMDWLSKNKANIDCARRTVTL 128

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296785058  399 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsGPVVHEThdliVDLGDHR-EVLSFDVTQSPFFPVV 477
Cdd:pfam13975  10 VRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVRA-ARVRLDS----VKIGGIElRNVPAVVLPGDLDDVL 84

                  ....*..
gi 296785058  478 LGVRWLS 484
Cdd:pfam13975  85 LGMDFLK 91

Basic leucine zipper (bZIP) domain of Activating Transcription Factor-2 (ATF-2) and similar proteins: a DNA-binding and dimerization domain; ATF-2 is a sequence-specific DNA-binding protein that belongs to the Basic leucine zipper (bZIP) family of transcription factors. In response to stress, it activates a variety of genes including cyclin A, cyclin D, and c-Jun. ATF-2 also plays a role in the DNA damage response that is independent of its transcriptional activity. 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
                 ....*....|....*....|....*....|....*...
gi 296785058  45 EEINNLREKVMKQSEENNNLQSQVQKLTEENTTLREQV 82
Cdd:cd14687   22 QWVQQLEEKVRKLESENKALKAEVDKLREEVLDLKNLL 59

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

                         10        20        30
                 ....*....|....*....|....*....|..
gi 296785058  41 DELSEEINNLREKVMKQSEENNNLQSQVQKLT 72
Cdd:COG4839   65 YELNREIQSLESKISEQQKENEDLEQEVSELS 96