DNA translocase FtsK; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194224  418 KQHLQAQRAPPPLQQ----MQATPPPPRLQQMQAP--PPLQAKPRQTLASAPPPLQIKILPAAPQSERRL--PIILGAGE 489
Cdd:PRK10263  776 PQYQQPQQPVAPQPQyqqpQQPVAPQPQYQQPQQPvaPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDTLlhPLLMRNGD 855

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 190194224  490 E---HSPAEAV----MDTPSPSAADDLAEDAME-----VE------------LNVSPAPESSRSD---APGV 534
Cdd:PRK10263  856 SrplHKPTTPLpsldLLTPPPSEVEPVDTFALEqmarlVEarladfrikadvVNYSPGPVITRFElnlAPGV 927

HMG (high mobility group) box;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190194224  257 PQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAY 324
Cdd:pfam00505   1 PKRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEKEKARYEKEHPEY 68

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194224 238 PVRKPAGGKKGRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEY 317
Cdd:COG5648   52 PRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERY 131

                 ....*....
gi 190194224 318 LKALAAYKA 326
Cdd:COG5648  132 QREKEEYNK 140

DNA translocase FtsK; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194224  418 KQHLQAQRAPPPLQQ----MQATPPPPRLQQMQAP--PPLQAKPRQTLASAPPPLQIKILPAAPQSERRL--PIILGAGE 489
Cdd:PRK10263  776 PQYQQPQQPVAPQPQyqqpQQPVAPQPQYQQPQQPvaPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDTLlhPLLMRNGD 855

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 190194224  490 E---HSPAEAV----MDTPSPSAADDLAEDAME-----VE------------LNVSPAPESSRSD---APGV 534
Cdd:PRK10263  856 SrplHKPTTPLpsldLLTPPPSEVEPVDTFALEqmarlVEarladfrikadvVNYSPGPVITRFElnlAPGV 927

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 190194224 259 KPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEY 317
Cdd:cd00084    1 RPLSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKEDKERY 59

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 190194224 257 PQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd21980    2 PKAPLTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEKDKERYVKELEAYQ 70

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190194224 258 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd22006    1 KKPKTAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEKYKEEKEKYLKVVGEEK 68

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 190194224 255 NEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd21979    1 NAPKRPPSAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAKLKEKYEKDIAAYR 71

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 190194224 259 KPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd21994    1 RPMSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEKAKERYDKAMKEYK 67

second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the second one.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190194224 257 PQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAY 324
Cdd:cd22007    1 PKRPQSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKKLKEAYLQEMEEY 68

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 190194224  254 PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEY 317
Cdd:pfam09011   1 PNKPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMAKEDKNRY 64

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 190194224 257 PQKPVSAYALFFRDTQAAIKGQN-PNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYKAE 327
Cdd:cd22011    1 PKRPSSAYFLFSQEIRKNLKSQGsPEEKVPELSKRAAEQWRSLTLAEKQPYYDEVEVLKKQYDVEKEEYEKE 72

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 190194224 253 DPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYKAEQ 328
Cdd:cd22013    5 DPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQVDKERYKKEMSGYKNGQ 80

high mobility group protein; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 190194224 253 DPNEPQKPVSAYALFFRDTQAAIKGQNPNAT--FGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAY 324
Cdd:PTZ00199  19 DPNAPKRALSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY 92

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 190194224 259 KPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEY 317
Cdd:cd22005    2 RPPTAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEKEKAEY 60

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 190194224 259 KPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTE 316
Cdd:cd01389    3 RPPNAFILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEEKEE 60

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194224 257 PQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRkaeaaktEYLKALAAYKA 326
Cdd:cd22012    2 PKRPASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQE-------EYEKALEEYEE 64

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) and similar proteins; NHP10, also called high mobility group protein 2, is probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 190194224 253 DPNEPQKPVSAYALFF---RDT-QAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAY 324
Cdd:cd22016    4 DPNAPKRPANAFFLFCqeqREKvREEYKEEHQEIDHHDLTKALAQAWRNLDAEDKKPYYELYEKDKERYEKEMEEY 79

high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 and similar proteins; Cmb1 binds to cytosines in base mismatches and opposite chemically altered guanines. It contains only one HMG-box domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 190194224 257 PQKPVSAYALFFRDTQaaiKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKAL 321
Cdd:cd22014    1 PKRPPSPFLLFMEEFR---RNEDNGKNLVELSRIAAEAWKNMSEDEKQPYIDRAKELLEEYKKQL 62

high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins; HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 190194224 258 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAE 311
Cdd:cd21982    2 KKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDKLVWKQKAQ 55

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 190194224 256 EPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTE 316
Cdd:cd21993    1 ENKKKKSGFQLWLEENRSSIEEENPELSEAEIIKLAMQRFRALPKEEKQKWNEKAKGDSDE 61

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 190194224 257 PQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKA 310
Cdd:cd21977    1 KKKWVNGFIMFCRLNRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPYCVRA 54

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 190194224 258 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKA 320
Cdd:cd21990    3 RRPMNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQVKEAHFKA 65

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 190194224 260 PVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd22004    5 PMNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEAERLREEHKKEYPDYK 70

high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors; This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190194224 258 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd22028    3 KRPMNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKRLRAQHMKEHPDYK 70

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and similar proteins; SOX-18 is a transcription factor involved in the development of cardiovascular and lymphatic vessels during embryonic development. It binds to the consensus sequence 5'-AACAAAG-3' and is able to trans-activate transcription via this site. SOX-18 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190194224 258 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAKTEYLKALAAYK 325
Cdd:cd22048    5 RRPMNAFMVWAKDERKRLAQQNPDLHNAVLSKMLGQSWKSLSAAEKRPFVEEAERLRVQHLQDHPNYK 72

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190194224  420 HLQAQRAPPPLQQ-------MQATPPPPRLQQMQAPPPLQAKPR------------QTLASAPPPLQIKILpaapqSERR 480
Cdd:TIGR01628 439 PMNAVRAPSRNAQnaaqkppMQPVMYPPNYQSLPLSQDLPQPQStasqggqnkklaQVLASATPQMQKQVL-----GERL 513

                          90
                  ....*....|....*.
gi 190194224  481 LPIIlgagEEHSPAEA 496
Cdd:TIGR01628 514 FPLV----EAIEPALA 525

second high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and similar proteins; TFA, also called TFAM, mitochondrial transcription factor 1 (TF1), transcription factor 6 (TCF-6), or transcription factor 6-like 2, binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. It is a component of the mitochondrial transcription initiation complex, composed of at least TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA. TFA is required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. It can unwind DNA. It bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. TFA is required for maintenance of normal levels of mitochondrial DNA and may play a role in organizing and compacting mitochondrial DNA. TFA contains two HMG-box domains. This model corresponds to the second one.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 190194224 257 PQKPVSAYALFFRDTQAAIKGQNPNATFgevsKIVASMWDSLGEEQKQVYKRKAEAAKTEY 317
Cdd:cd21987   21 PKRPRSAFNIFVSEHFQEAKGDSPQEKL----KTLKEEWKNLSSSQKQLYIQLAEDDKIRY 77

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and similar proteins; SOX-30 is a crucial transcription factor that controls the transition from a late meiotic to a post-meiotic gene expression program and subsequent round spermatid development. It specially prevents Wnt-signaling to suppress metastasis. SOX-30 binds to the DNA sequence 5'-ACAAT-3' and shows a preference for guanine residues surrounding this core motif. SOX-30 is the only member of the group H of SRY-related high-mobility group (HMG) box (Sox) transcription factors.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 190194224 258 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKAEAAK 314
Cdd:cd22033    3 KRPMNAFMVWARIHRPALAKANPNANNADISVQLGEEWNKLTEEQKKPYYDEAQKLK 59