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 94421475 365 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsgpVVHETHDLIVDLGDHREVLSFDVTQSPFFPVVL 444
Cdd:cd00303  10 VRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVK---TLGVILPVTIGIGGKTFTVDFYVLDLLSYDVIL 86

                ....*
gi 94421475 445 GVRWL 449
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 94421475    77 ECPEDLPEKFDGNPDMLAPFMAQCQIFMEKSTRDFSVDRVRVCFVTSMMTGRAARWASAKLERSHYLMHNYPAFMMEMKH 156
Cdd:pfam16297  22 SNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQ 101

                  ..
gi 94421475   157 VF 158
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 94421475 365 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsgpVVHETHDLIVDLGDHREVLSFDVTQSPFFPVVL 444
Cdd:cd00303  10 VRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVK---TLGVILPVTIGIGGKTFTVDFYVLDLLSYDVIL 86

                ....*
gi 94421475 445 GVRWL 449
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 94421475    77 ECPEDLPEKFDGNPDMLAPFMAQCQIFMEKSTRDFSVDRVRVCFVTSMMTGRAARWASAKLERSHYLMHNYPAFMMEMKH 156
Cdd:pfam16297  22 SNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQ 101

                  ..
gi 94421475   157 VF 158
Cdd:pfam16297 102 YF 103

basic region leucin zipper;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 94421475      3 ERRRdelsEEINNLREKVMKQSEENNNLQSQVQKLTEENTTLREQVE 49
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 94421475     3 ERRRDELSEEINNL---REKVMKQSEENNNLQSQVQKLTE-ENTTLR------EQVEptpEDEDDDIELR 62
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 94421475 365 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsgpVVHETHDLIVDLGDHREVLSFDVTQSPFFPVVL 444
Cdd:cd00303  10 VRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVK---TLGVILPVTIGIGGKTFTVDFYVLDLLSYDVIL 86

                ....*
gi 94421475 445 GVRWL 449
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 94421475    77 ECPEDLPEKFDGNPDMLAPFMAQCQIFMEKSTRDFSVDRVRVCFVTSMMTGRAARWASAKLERSHYLMHNYPAFMMEMKH 156
Cdd:pfam16297  22 SNPIPFPERFSGESGRLPEFIVQTMSYMLVDEKTFCNDAMKVAFLITRLSGRALEWVMPYIQSDSPILNNYRAFLNEMKQ 101

                  ..
gi 94421475   157 VF 158
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 94421475   368 MIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIA------SGPVVHETHDLIVDLgdhrevLSFDVTQspfFP 441
Cdd:pfam08284  34 LFDSGATHSFISHAFVGKLKLPVESLSNPLCIETPTGGSVTtnlicpSCPIEIQGISFLADL------ILLDMKD---LD 104

                          90       100
                  ....*....|....*....|....
gi 94421475   442 VVLGVRWLSTHDPNITWSTRSIVF 465
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 94421475   365 VRAMIDSGASGNFIDHEYVAQNGIPLRIKDWPILVEAIDGRPIAsGPVVHEThdliVDLGDHR-EVLSFDVTQSPFFPVV 443
Cdd:pfam13975  10 VRFLVDTGASVTVISEALAERLGLDRLVDAYPVTVRTANGTVRA-ARVRLDS----VKIGGIElRNVPAVVLPGDLDDVL 84

                  ....*..
gi 94421475   444 LGVRWLS 450
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 94421475  11 EEINNLREKVMKQSEENNNLQSQVQKLTEENTTLREQV 48
Cdd:cd14687  22 QWVQQLEEKVRKLESENKALKAEVDKLREEVLDLKNLL 59

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

                        10        20        30
                ....*....|....*....|....*....|..
gi 94421475   7 DELSEEINNLREKVMKQSEENNNLQSQVQKLT 38
Cdd:COG4839  65 YELNREIQSLESKISEQQKENEDLEQEVSELS 96