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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 174 NDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQPQPQPCFLPNPQTLSQAQ 253
Cdd:COG3883  132 ADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAELEAQQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAA 211

                 ..
gi 334183217 254 AP 255
Cdd:COG3883  212 AA 213

helix loop helix domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 334183217   140 REKQRRDRLNDKFTELSSVLEPGRTP-KTDKVAIINDAIRMVNQARDEAQK 189
Cdd:smart00353   3 RERRRRRKINEAFDELRSLLPTLPKNkKLSKAEILRLAIEYIKSLQEELQK 53

LRRFIP family; LRRFIP1 is a transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'- AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. LRRFIP2 may function as activator of the canonical Wnt signalling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217  136 SKAC-REKQRRDRLNDKFTELSS--------------VLEPGRTPKTDKVAIINDAIR-MVNQarDEAQKLKDL-NSSLQ 198
Cdd:pfam09738 148 NKELeRLKRNLRRLQFQLAELKEqlkqrdeliekhglVIVPDENTNGEEENSPADAKRaLVSV--EAAEVLESAgEGSLD 225

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334183217  199 EKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQPQPQPCFLPNPQTLSQAQAPGSKLV 260
Cdd:pfam09738 226 VRLKKLADEKEELLDEVRKLKLQLEEEKSKRNSTRSSQSPDGFGLENGSHVIEVQREANKQI 287

chromosome segregation protein SMC, primarily archaeal 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. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217   100 IAKGSVEVDGFLCDADVIKEPSSRKRIKTESCTGsnskacREKQRRDRLNDKFTELSSVlepgrtpktDKvaiindairm 179
Cdd:TIGR02169  324 LAKLEAEIDKLLAEIEELEREIEEERKRRDKLTE------EYAELKEELEDLRAELEEV---------DK---------- 378

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 334183217   180 vnqardEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:TIGR02169  379 ------EFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAA 428

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 334183217  198 QEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAI 232
Cdd:pfam13600  65 DPELKALRAELEELEDELARLEDELAALEARLAFL 99

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 334183217 141 EKQRRDRLNDKFTELSSVLePGrTPKTDKVAIINDAIRMVNQardeaqklkdlnssLQEKIKELKDEKNELRDEKQKLKV 220
Cdd:cd11452   10 ERKRREKLSQRFIALSALV-PG-LKKMDKASVLGDAIKHIKQ--------------LQERVKELEEEKKEKRLMSVVIVK 73

                 ..
gi 334183217 221 EK 222
Cdd:cd11452   74 KS 75

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family; The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334183217 140 REKQRRDRLNDKFTELSSVLEPGRTPKTDKVAIINDAIRMVNQardeaqklkdlnssLQEKIKELKDEKNELR 212
Cdd:cd19682    7 RERERRSELRELFDKLKQLLGLDSDEKASKLAVLTEAIEEIQQ--------------LKREEDELQKEKARLT 65

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 142 KQRRDRLNDkftELSSVlepgrtpktdkVAIINDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVE 221
Cdd:COG1340   28 KEKRDELNE---ELKEL-----------AEKRDELNAQVKELREEAQELREKRDELNEKVKELKEERDELNEKLNELREE 93

                         90
                 ....*....|....*..
gi 334183217 222 KERIDQQLKAIKTQPQP 238
Cdd:COG1340   94 LDELRKELAELNKAGGS 110

basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins; MYC1, also termed AtbHLH12, or EN 58, acts as a transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334183217 141 EKQRRDRLNDKFTELSSVLePGRTpKTDKVAIINDAIRMVNQardeaqklkdlnssLQEKIKELK 205
Cdd:cd18918    5 ERERREKLNEKFSDLRNLI-PNPT-KNDRASILSDAIKYINE--------------LQRTVEELK 53

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins; The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 141 EKQRRDRLNDKFTELSSVLEpgRTPKTDKVAIINDAIRMVNQARDEAQKlkdlnssLQEKIKELKDEKNE 210
Cdd:cd11443    7 ERRRRKKLNDRLYMLRSVVP--KITKMDRASILGDAIDYVKELLQEINE-------LQDELEGLPESESG 67

Cell division protein ZapB, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 334183217 173 INDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKA 231
Cdd:COG3074   13 VQQAVDTIELLQMEVEELKEKNEELEQENEELQSENEELQSENEQLKTENAEWQERIRS 71

basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. Members of the bHLH superfamily have two highly conserved and functionally distinct regions. The basic part is at the amino end of the bHLH that may bind DNA to a consensus hexanucleotide sequence known as the E box (CANNTG). Different families of bHLH proteins recognize different E-box consensus sequences. At the carboxyl-terminal end of the region is the HLH region that interacts with other proteins to form homo- and heterodimers. bHLH proteins function as a diverse set of regulatory factors because they recognize different DNA sequences and dimerize with different proteins. The bHLH proteins can be divided to cell-type specific and widely expressed proteins. The cell-type specific members of bHLH superfamily are involved in cell-fate determination and act in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 334183217 141 EKQRRDRLNDKFTELSSVLEPGRT-PKTDKVAIINDAIRMVNQARD 185
Cdd:cd00083    1 ERRRRDKINDAFEELKRLLPELPDsKKLSKASILQKAVEYIRELQS 46

reticulocyte binding protein 2-like protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217  121 SSRKRIKTESCTGSNSKAcREKQRRDRLNDKFTELSsvlEPGRTPKTDKVAIINDAIRMVNQARDEAQKLKDLNSSLQEK 200
Cdd:PTZ00440 2482 SHNEKIKSELLIINDALR-RVKEKKDEMNKLFNSLT---ENNNNNNNSAKNIVDNSTYIINELESHVSKLNELLSYIDNE 2557

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334183217  201 IKELKDEKNEL---------RDEKQKLKVEKERIDQQLKAIKTQPQPQPCFLPNPQTLSQAQAP 255
Cdd:PTZ00440 2558 IKELENEKLKLlekakieesRKERERIESETQEDNTDEEQINRQQQERLQKEEEQKAYSQERLN 2621

chromosome segregation protein SMC, primarily archaeal 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. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217   100 IAKGSVEVDGFLCDADVIKEPSSRKRIKTESCTGsnskacREKQRRDRLNDKFTELSSVlepgrtpktDKvaiindairm 179
Cdd:TIGR02169  324 LAKLEAEIDKLLAEIEELEREIEEERKRRDKLTE------EYAELKEELEDLRAELEEV---------DK---------- 378

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 334183217   180 vnqardEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:TIGR02169  379 ------EFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAA 428

basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins; The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 334183217 141 EKQRRDRLNDKFTELSSVLePGRTpKTDKVAIINDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDE 207
Cdd:cd11450   11 ERNRRQKLNQRLFALRSVV-PNIT-KMDKASIIKDAISYIQELQYQEKKLEAEIRELESRPPSTLSF 75

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 334183217  185 DEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKT 234
Cdd:TIGR04523 496 KELKKLNEEKKELEEKVKDLTKKISSLKEKIEKLESEKKEKESKISDLED 545

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
                  ....*....|....*....|....*....|....*....|....*.
gi 334183217  188 QKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIK 233
Cdd:pfam06005  14 QAAVDTIALLQMENEELKEENEELKEEANELEEENQQLKQERNQWQ 59

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217  142 KQRRDRLNDKFTELSSVLEPGRTPktDKVAiinDAIRMVNQARDEAQKLKDLNS---SLQEKIKELKDEKNELRDEKQKL 218
Cdd:COG4913   637 EAELDALQERREALQRLAEYSWDE--IDVA---SAEREIAELEAELERLDASSDdlaALEEQLEELEAELEELEEELDEL 711

                          90
                  ....*....|....*..
gi 334183217  219 KVEKERIDQQLKAIKTQ 235
Cdd:COG4913   712 KGEIGRLEKELEQAEEE 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334183217 173 INDAIR-MVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:COG4942  144 LAPARReQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKE 207

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 334183217 140 REKQRRDRLNDKFTELSSVLePG-RTPKTDKVAIINDAIrmvnqarDEAQKLKDLNSSLQEKIKELK 205
Cdd:cd11404    9 SEKKRRELIKKGYDELCALV-PGlDPQKRTKADILQKAA-------DWIQELKEENEKLEEQLDELK 67

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 334183217 141 EKQRRDRLNDKFTELSSVLePGRTPKTDKVAIIndairmvNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLkV 220
Cdd:cd11398   15 ERRRRENINEGINELAALV-PGNAREKNKGAIL-------ARAVEYIQELQETEAKNIEKWTLEKLLTDQAIAELAAL-N 85

                 ....
gi 334183217 221 EKER 224
Cdd:cd11398   86 EKLR 89

basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family; bHLH-PAS domain has been found in a large group of bHLH transcription regulators that are involved in gene expression responding to environmental change and controlling aspects of neural development, including proteins from aryl hydrocarbon receptor nuclear translocator (ARNT) family, hypoxia-inducible factor (HIF) family, aryl hydrocarbon receptor (AhR) family, neuronal PAS domain-containing protein (NPAS) family, Circadian locomotor output cycles protein kaput (CLOCK)-like family, and single-minded (SIM) family. bHLH-PAS transcriptional regulatory factors have a bHLH DNA-binding domain followed by two PAS domains and a C-terminal activation or repression domain. bHLH-PAS family members can be divided into class I and class II based on their dimerization partner. bHLH-PAS class I factors include AhR, HIF and SIM. The best characterized bHLH-PAS Class II protein is the ubiquitous ARNT. Some members of bHLH-PAS family act as transcriptional coactivators (such as NCoA) that lack the ability to dimerize and bind DNA.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 334183217 141 EKQRRDRLNDKFTELSSVL--EPGRTPKTDKVAII 173
Cdd:cd11391    8 AKKRRDKENAEISELASLLplPPAVGSKLDKLSVL 42

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334183217 173 INDAIRMvnqardeAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:COG4942  131 FLDAVRR-------LQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEE 186

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 334183217  181 NQARDEAQKLKDLN---SSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLK 230
Cdd:TIGR04523 503 EEKKELEEKVKDLTkkiSSLKEKIEKLESEKKEKESKISDLEDELNKDDFELK 555

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
                  ....*....|....*....|....*....|....*....|....*...
gi 334183217  188 QKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:TIGR04523 207 KKKIQKNKSLESQISELKKQNNQLKDNIEKKQQEINEKTTEISNTQTQ 254

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the Myc family; The Myc family is a member of the bHLHzip family of transcription factors that play important roles in the control of normal cell proliferation, growth, survival and differentiation. All Myc isoforms contain two independently functioning polypeptide chain regions: N-terminal transactivating residues and a C-terminal bHLHzip segment. The bHLHzip family of bHLH transcription factors are characterized by a highly conserved N-terminal basic region that may bind DNA at a consensus hexanucleotide sequence known as the E-box (CANNTG) followed by HLH and leucine zipper motifs that may interact with other proteins to form homo- and heterodimers. Myc heterodimerizes with Max enabling specific binding to E-box DNA sequences in the promoters of target genes. The Myc proto-oncoprotein family includes at least five different functional members: c-, N-, L-, S- and B-Myc (which is lacking the bHLH domain).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 141 EKQRRDRLNDKFTEL-SSVLEPGRTPKTDKVAIINDAIrmvnqardeaqklkdlnsslqEKIKELKDEKNELRDEKQKLK 219
Cdd:cd11400    9 ERQRRNDLKNSFEKLrDLVPELADNEKASKVVILKKAT---------------------EYIKQLQQEEKKLEKEKDKLK 67

                         90
                 ....*....|.
gi 334183217 220 VEKERIDQQLK 230
Cdd:cd11400   68 ARNEQLRKKLE 78

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 1 (SREBP1) and similar proteins; SREBP1, also termed Class D basic helix-loop-helix protein 1 (bHLHd1), or sterol regulatory element-binding transcription factor 1 (SREBF1), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcriptional activator required for lipid homeostasis. It may control transcription of the low-density lipoprotein receptor gene as well as the fatty acid. SREBP1 has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3').

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334183217 141 EKQRRDRLNDKFTELSSvLEPGRTPKTDKVAIINDAIRMVNQARDEAQKLKDLNSSLQEKIKE 203
Cdd:cd18921   14 EKRYRSSINDKIIELKD-LVVGTEAKLNKSAVLRKAIDYIRFLQQSNQKLKQENMALKMAVQK 75

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 145 RDRLNDKFTELSSVLepGRTPKtdkvaIINDAIRMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKER 224
Cdd:COG4717   48 LERLEKEADELFKPQ--GRKPE-----LNLKELKELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEK 120

                 ....*..
gi 334183217 225 IDQQLKA 231
Cdd:COG4717  121 LEKLLQL 127

Tektin family; Tektins are cytoskeletal proteins. They have been demonstrated in such cellular sites as centrioles, basal bodies, and along ciliary and flagellar doublet microtubules. Tektins form unique protofilaments, organized as longitudinal polymers of tektin heterodimers with axial periodicity matching tubulin. Tektin polypeptides consist of several alpha-helical regions that are predicted to form coiled coils. Indeed, tektins share considerable structural similarities with intermediate filament proteins. Possible functional roles for tektins are: stabilization of tubulin protofilaments; attachment of A and B-tubules in ciliary/flagellar microtubule doublets and C-tubules in centrioles; binding of axonemal components.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 334183217  178 RMVNQARDEAQKLKDL-NSSLQEKIKELKDEKNELrdEKQKLKVEKErIDQQLKAIKT 234
Cdd:pfam03148 229 SILEQTANDLRAQADAvNFALRKRIEETEDAKNKL--EWQLKKTLQE-IAELEKNIEA 283

Gas vesicle protein YhaH [General function prediction only];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334183217 178 RMVNQARDEAQKLKDLNSSLQEKIKELKDEKNELRDE-----KQKLKVEKERIDQQLKAIKTQ 235
Cdd:COG4980   35 KLKDKADDLKDKAEDLKDELKEKASELSEEAKEKLDElieeiKEKIEELKEEVEPKIEELKEE 97

endonuclease subunit; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 112 CDADVIKEPSSRKRIKTE--SCTGSNSKAcreKQRRDRLN---DKFTELSSVLepgRTPKTDKVAIINDAIRMVNQARD- 185
Cdd:PHA02562 290 CTQQISEGPDRITKIKDKlkELQHSLEKL---DTAIDELEeimDEFNEQSKKL---LELKNKISTNKQSLITLVDKAKKv 363

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 334183217 186 --EAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKER---IDQQLK--AIKTQ 235
Cdd:PHA02562 364 kaAIEELQAEFVDNAEELAKLQDELDKIVKTKSELVKEKYHrgiVTDLLKdsGIKAS 420

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
                  ....*....|....*....|....*....|....*....|....*...
gi 334183217  188 QKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:TIGR04523 401 QNQEKLNQQKDEQIKKLQQEKELLEKEIERLKETIIKNNSEIKDLTNQ 448

Leucine zipper; This family includes Leucine zipper transcription factor-like protein 1 (LZTFL1) and Leucine zipper protein 2 (LUZP2).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217  156 SSVLEPGRTPKTDKVAIIND--AIRMVNQardEAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIK 233
Cdd:pfam15294 105 SSNKKPNFELNKPKLEPLNEggGSALLHM---EIERLKEENEKLKERLKTLESQATQALDEKSKLEKALKDLQKEQGAKK 181

                  ....
gi 334183217  234 TQPQ 237
Cdd:pfam15294 182 DVKS 185

Cgr1 family; Members of this family are coiled-coil proteins that are involved in pre-rRNA processing.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 334183217  188 QKLKDLNSSLQEKIKELKDEKNELRD-------EKQKLKVEKER 224
Cdd:pfam03879  36 QEKRLELKAIKAKEKELKDEKEAERQrriqaikERREAKEEKER 79

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183217 140 REKQRRDRLNDKFTELSSVLEPGRtpktDKVAIINDAIrmvNQARDEAQKLKDLNSSL--------------QEKIKELK 205
Cdd:COG1340  150 EKAKKALEKNEKLKELRAELKELR----KEAEEIHKKI---KELAEEAQELHEEMIELykeadelrkeadelHKEIVEAQ 222

                         90       100
                 ....*....|....*....|....*...
gi 334183217 206 DEKNELRDEKQKLKVEKERIDQQLKAIK 233
Cdd:COG1340  223 EKADELHEEIIELQKELRELRKELKKLR 250

Prefoldin alpha subunit; Alpha subunits of prefoldin, a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 334183217 197 LQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKT 234
Cdd:cd00584    1 LAEQLQELREQIEALQEEIEQLEEEQAEIDEAKEALEE 38

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), MLX-interacting protein-like (MLXIPL) and similar proteins; The family includes MLXIP and MLXIPL. MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 334183217 141 EKQRRDRLNDKFTELSSVLEPGRTPKTDKVAiinDAIrMVNQARDEAQKLKDLNSSLQEKIKELKDE 207
Cdd:cd11405   11 EQKRRFNIKSGFDTLQSLIPSLGQNPNQKVS---KAA-MLQKAAEYIKSLKRERQQMQEEAEQLRQE 73

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 334183217 182 QARD-EAQKLKDLNSSLQEKIKELKDEKNELRDEKQKLKVEKERIDQQLKAIKTQ 235
Cdd:COG1579   13 QELDsELDRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELE 67

F-type ATP synthase, membrane subunit b; Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334183217 173 INDAIRMVNQARDEAQKLKDLNsslQEKIKELKDEKNELRDE--KQKLKVEKERIDQ---QLKAIKTQ 235
Cdd:cd06503   35 IAESLEEAEKAKEEAEELLAEY---EEKLAEARAEAQEIIEEarKEAEKIKEEILAEakeEAERILEQ 99