basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins; ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 109287753  97 KACREKVRRDKLNERFLELGAVLEPGKTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEKIKELKAEKNELR 172
Cdd:cd11446    1 KACREKLRRDKLNERFMELSNVLEPGRPPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQEESKELKAEKNELR 76

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins; ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 109287753  97 KACREKVRRDKLNERFLELGAVLEPGKTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEKIKELKAEKNELR 172
Cdd:cd11446    1 KACREKLRRDKLNERFMELSNVLEPGRPPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQEESKELKAEKNELR 76

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 109287753   100 REKVRRDKLNERFLELGAVLEPG-KTPKMDKSSILNDAIRVMAELRSEAQK 149
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTLpKNKKLSKAEILRLAIEYIKSLQEELQK 53

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 109287753   93 RPSSKACREKVRRDKLNERFLELGAVLePGKTP--KMDKSSILNDAIRVMAELR 144
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELL-PTLPPdkKLSKAEILRLAIEYIKHLQ 53

N-terminal domain of unknown function (DUF4140); This family is often found at the N-terminus of its member proteins, with DUF4139, pfam13598, at the C-terminus.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 109287753  158 QEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFL 192
Cdd:pfam13600  65 DPELKALRAELEELEDELARLEDELAALEARLAFL 99

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins; ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 109287753  97 KACREKVRRDKLNERFLELGAVLEPGKTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEKIKELKAEKNELR 172
Cdd:cd11446    1 KACREKLRRDKLNERFMELSNVLEPGRPPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQEESKELKAEKNELR 76

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein ABA-INDUCIBLE bHLH-TYPE (AIB) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AIB and MYC proteins (MYC2, MYC3 and MYC4). AIB, also termed AtbHLH17, or EN 35, is a transcription activator that regulates positively abscisic acid (ABA) response. MYC2, also termed protein jasmonate insensitive 1, or R-homologous Arabidopsis protein 1 (RAP-1), or AtbHLH6, or EN 38, or Z-box binding factor 1 protein, is a transcriptional activator involved in abscisic acid (ABA), jasmonic acid (JA), and light signaling pathways. MYC3, also termed protein altered tryptophan regulation 2, or AtbHLH5, or transcription factor ATR2, or EN 36, is a transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. MYC4, also termed AtbHLH4, or EN 37, is a transcription factor involved in jasmonic acid (JA) gene regulation. MYC2, together with MYC3 and MYC4, controls additively subsets of JA-dependent responses.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 109287753 101 EKVRRDKLNERFLELGAVLEpgKTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEKIKELKAE 167
Cdd:cd11449   13 ERQRREKLNQRFYALRAVVP--NVSKMDKASLLGDAISYINELKSKVQDMETEKKEMKRQESEKKTE 77

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein NAI1 and similar proteins; NAI1, also termed AtbHLH20, or EN 27, is a bHLH transcription activator that regulates the expression of at least NAI2, PYK10 and PBP1. It is required for and mediates the formation of endoplasmic reticulum bodies (ER bodies). It plays a role in the symbiotic interactions with the endophytes of the Sebacinaceae fungus family, such as Piriformospora indica and Sebacina.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109287753 101 EKVRRDKLNERFLELGAVLePGkTPKMDKSSILNDAIRVMaelrseaqklkesnESLQEKIKELKAEKNELRDEKQKLKA 180
Cdd:cd11452   10 ERKRREKLSQRFIALSALV-PG-LKKMDKASVLGDAIKHI--------------KQLQERVKELEEEKKEKRLMSVVIVK 73

                 ..
gi 109287753 181 EK 182
Cdd:cd11452   74 KS 75

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 109287753   100 REKVRRDKLNERFLELGAVLEPG-KTPKMDKSSILNDAIRVMAELRSEAQK 149
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTLpKNKKLSKAEILRLAIEYIKSLQEELQK 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 (TT8) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as TT8, EGL1, and GL3. TT8, also termed AtbHLH42, or EN 32, is involved in the control of flavonoid pigmentation and plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). EGL1, also termed AtbHLH2, or EN 30, or AtMYC146, or protein enhancer of GLABRA 3, is involved in epidermal cell fate specification and regulates negatively stomata formation but promotes trichome formation. GL3, also termed AtbHLH1, or AtMYC6, or protein shapeshifter, or EN 31, is involved in epidermal cell fate specification. It regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 109287753  96 SKACREKVRRDKLNERFLELGAVLePGKTpKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEKIK 162
Cdd:cd11451    5 SHAMAERRRREKLNERFITLRSMV-PFVT-KMDKVSILGDAIEYLKQLQRRVEELESRRKSSDTETR 69

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins; CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109287753 101 EKVRRDKLNERFLELGAVLePGKTPKMDKSSILNDAIRVMaelrseaQKLKESNESLQEKIKELKAEKNELRDEKQKLKA 180
Cdd:cd11398   15 ERRRRENINEGINELAALV-PGNAREKNKGAILARAVEYI-------QELQETEAKNIEKWTLEKLLTDQAIAELAALNE 86

                 .
gi 109287753 181 E 181
Cdd:cd11398   87 K 87

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 109287753 133 LNDAIRvmaELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNARP 196
Cdd:COG1340   48 LNAQVK---ELREEAQELREKRDELNEKVKELKEERDELNEKLNELREELDELRKELAELNKAG 108

Helix-loop-helix DNA-binding domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 109287753   93 RPSSKACREKVRRDKLNERFLELGAVLePGKTP--KMDKSSILNDAIRVMAELR 144
Cdd:pfam00010   1 RREAHNERERRRRDRINDAFDELRELL-PTLPPdkKLSKAEILRLAIEYIKHLQ 53

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 109287753 141 AELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNAR 195
Cdd:COG3883   26 SELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAE 80

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 109287753 138 RVMAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNARPSfvPHPPVIPASAFTAPQGqa 217
Cdd:COG4942  178 ALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEELEALIARLEAEAA--AAAERTPAAGFAALKG-- 253

                         90
                 ....*....|.
gi 109287753 218 agqKLMMPVIG 228
Cdd:COG4942  254 ---KLPWPVSG 261

TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 109287753  141 AELRSEAQKLKESNESLQEKIKELKAE----KNELRDEKQKLKAEKESLEQQIKFLNAR 195
Cdd:pfam07926  53 AEDIKALQALREELNELKAEIAELKAEaesaKAELEESEESWEEQKKELEKELSELEKR 111

N-terminal domain of unknown function (DUF4140); This family is often found at the N-terminus of its member proteins, with DUF4139, pfam13598, at the C-terminus.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 109287753  158 QEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFL 192
Cdd:pfam13600  65 DPELKALRAELEELEDELARLEDELAALEARLAFL 99

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109287753  102 KVRRDKLNERFLELGAVLEpgktpkMDKSSI-LNDAIRVMAELRSEAQKLKESN---ESLQEKIKELKAEKNELRDEKQK 177
Cdd:COG4913   637 EAELDALQERREALQRLAE------YSWDEIdVASAEREIAELEAELERLDASSddlAALEEQLEELEAELEELEEELDE 710

                          90
                  ....*....|....*...
gi 109287753  178 LKAEKESLEQQIKFLNAR 195
Cdd:COG4913   711 LKGEIGRLEKELEQAEEE 728

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 109287753 100 REKVRRDKLNERfleLGAVLEPGKTPKMD---KSSILNDAIRVMAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQ 176
Cdd:COG4942   98 ELEAQKEELAEL---LRALYRLGRQPPLAlllSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERA 174

                         90
                 ....*....|....*...
gi 109287753 177 KLKAEKESLEQQIKFLNA 194
Cdd:COG4942  175 ELEALLAELEEERAALEA 192

Cell division protein ZapB; ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 109287753  139 VMAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQ 188
Cdd:pfam06005   5 LLEQLETKIQAAVDTIALLQMENEELKEENEELKEEANELEEENQQLKQE 54

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 109287753 140 MAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNAR 195
Cdd:COG4372  103 LESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQ 158

Uncharacterized protein, contains DUF3084 domain [Function unknown];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 109287753 140 MAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNA 194
Cdd:COG4372  117 LEELQKERQDLEQQRKQLEAQIAELQSEIAEREEELKELEEQLESLQEELAALEQ 171

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family; The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 109287753 101 EKVRRDKLNERFLELgAVLEPGKTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQE 159
Cdd:cd11394   14 EKRYRSSINDRIIEL-KDLVVGPDAKMNKSAVLRKAIDYIRYLQKVNQKLKQENMALKK 71

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins; The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body.

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 109287753 101 EKVRRDKLNERFLELGAVLePGKTPKMDKSSILNDAI 137
Cdd:cd11441    8 EKKRRDQFNVLINELASML-PGRGRKMDKSTVLKKTI 43

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 109287753  141 AELRSEAQKLKESnesLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNARPSFVPHP 202
Cdd:COG4913   383 AALRAEAAALLEA---LEEELEALEEALAEAEAALRDLRRELRELEAEIASLERRKSNIPAR 441

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
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 109287753   141 AELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNAR 195
Cdd:TIGR02168  270 EELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQ 324

DNA double-strand break repair ATPase Rad50;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109287753  96 SKACREKVRRDKLNERFLELGAVLEPGKTpkmdKSSILNDAIRVMAELRSEAQKLK-ESNESLQEKIKELKAEKNELRDE 174
Cdd:PRK03918 331 KELEEKEERLEELKKKLKELEKRLEELEE----RHELYEEAKAKKEELERLKKRLTgLTPEKLEKELEELEKAKEEIEEE 406

                         90       100
                 ....*....|....*....|
gi 109287753 175 KQKLKAEKESLEQQIKFLNA 194
Cdd:PRK03918 407 ISKITARIGELKKEIKELKK 426

Afadin- and alpha -actinin-Binding; This family is found in mammals where it is localized at cell-cell adherens junctions, and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins localized at Cell-Cell Adherens Junctions.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 109287753  133 LNDAIRV----MAELRSEAQKLKESNESLQEKI-----KELKAEKNeLRDEKQKLKAEKESLE------QQIK 190
Cdd:pfam11559  57 LNETIRTleaeIERLQSKIERLKTQLEDLERELallqaKERQLEKK-LKTLEQKLKNEKEELQrlknalQQIK 128

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family; Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 109287753 100 REKVRRDKLNERFLELGAVLePG-KTPKMDKSSILNDAIRVMaelrseaQKLKESNESLQEKIKELKA 166
Cdd:cd11404    9 SEKKRRELIKKGYDELCALV-PGlDPQKRTKADILQKAADWI-------QELKEENEKLEEQLDELKE 68

Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 109287753 133 LNDAIRVMAELRSEAQKLKESNESLQEKIKELKAEKN-------ELRDEKQKLKAEKESLEQQIK 190
Cdd:COG1340   10 LEELEEKIEELREEIEELKEKRDELNEELKELAEKRDelnaqvkELREEAQELREKRDELNEKVK 74

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar proteins; AIG1, also termed AtbHLH32, or EN 54, or protein target of MOOPTEROS 5, is a transcription factor required for MONOPTEROS-dependent root initiation in embryo.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 109287753  87 RSESGTRPSSKAcrEKVRRDKLNERFLELGAVLePGKTpKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEK 160
Cdd:cd11455    3 KALAASKSHSEA--ERRRRERINSHLATLRTLL-PNLS-KTDKASLLAEVVQHVKELKRQAAEITTPPDVPTED 72

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family; The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 109287753 101 EKVRRDKLNERFLELGAVLEPGKTPKM--DKSSILNDAIRVMAELRSEAQKLKESNE 155
Cdd:cd11397   13 ERRRRFNINDRIKELGTLLPKSNDPDMrwNKGTILKASVDYIRKLQKEQERLRQLEE 69

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109287753  97 KACREKVRRDKLNERFLELGAVLEpGKTPKMDKSSILNDAIRVMAELRSEAQKLKESNE---SLQEKIKELKAEKNELRD 173
Cdd:COG4717  389 AALEQAEEYQELKEELEELEEQLE-ELLGELEELLEALDEEELEEELEELEEELEELEEeleELREELAELEAELEQLEE 467

                         90
                 ....*....|....*....
gi 109287753 174 EK--QKLKAEKESLEQQIK 190
Cdd:COG4717  468 DGelAELLQELEELKAELR 486

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 2 (SREBP2) and similar proteins; SREBP2, also termed Class D basic helix-loop-helix protein 2 (bHLHd2), or sterol regulatory element-binding transcription factor 2 (SREBF2), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcription activator of cholesterol biosynthesis.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 109287753  91 GTRPSSKACREKVRRDKLNERFLELGAVLEpGKTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQ 158
Cdd:cd18922    4 GERRTTHNIIEKRYRSSINDKIIELKDLVM-GTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMALK 70

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 109287753 131 SILNDAIR-VMAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIK 190
Cdd:COG1579  106 SDLEDEILeLMERIEELEEELAELEAELAELEAELEEKKAELDEELAELEAELEELEAERE 166

Domain of unknown function (DUF5082); This entry contains proteins that are uncharacterized.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 109287753  140 MAELRSEAQklkesneSLQEKIKELKAEKNELRDEKQKLKAEKESLEQQI 189
Cdd:pfam16888  12 IAQLRSEIA-------ALEEKIERLKEAKTKLDAEKESLHDKKTKLQGPL 54

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.

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                 ....*....|....*....|....*....|....*....|....*....|.
gi 109287753 140 MAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIK 190
Cdd:cd22887   13 LAELEAELASLEEEIKDLEEELKEKNKANEILNDELIALQIENNLLEEKLR 63

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 109287753  142 ELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLN 193
Cdd:TIGR04523 423 LLEKEIERLKETIIKNNSEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLS 474

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 109287753 105 RDKLNERFLELGavlepgkTPKMDKSSILNDAIRVMAELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKES 184
Cdd:COG4717   48 LERLEKEADELF-------KPQGRKPELNLKELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEK 120

                 ....*...
gi 109287753 185 LEQQIKFL 192
Cdd:COG4717  121 LEKLLQLL 128

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 109287753  142 ELRSEAQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQIKFLNA 194
Cdd:TIGR04523 572 ELKQTQKSLKKKQEEKQELIDQKEKEKKDLIKEIEEKEKKISSLEKELEKAKK 624

recombination and DNA strand exchange inhibitor protein; Reviewed

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 109287753 133 LNDAIRVMAELRseaQKLKESNESLQEKIKELKAEKNELRDEKQKLKAEKESLEQQ 188
Cdd:PRK00409 518 LNELIASLEELE---RELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEE 570