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Conserved domains on  [gi|2453130692|ref|NP_001404728|]
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protein IRON-RELATED TRANSCRIPTION FACTOR 3 [Oryza sativa Japonica Group]

Protein Classification

basic helix-loop-helix domain-containing protein( domain architecture ID 385)

basic helix-loop-helix (bHLH) domain-containing protein is a DNA-binding protein that may act as a transcription factor

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
bHLH_SF super family cl00081
basic Helix Loop Helix (bHLH) domain superfamily; bHLH proteins are transcriptional regulators ...
 41-114 6.88e-27

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.


The actual alignment was detected with superfamily member cd11446:

Pssm-ID: 469605 [Multi-domain]  Cd Length: 76  Bit Score: 98.94  E-value: 6.88e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2453130692  41 KSEREKLKRGHLNDLFGELGNMLEADR-QSNGKACILTDTTRILRDLLSQVKSLRQENSTLQNESNYVTMERNEL 114
Cdd:cd11446     1 KACREKLRRDKLNERFMELSNVLEPGRpPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQEESKELKAEKNEL 75
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 133-241 9.96e-04

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 40.31  E-value: 9.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2453130692  133 RMRATGSPGWGHGATGSPLPvPPSPGTVFPSQQPMQPSPMTTSTVFPLQQPLPQPTVIEPSARQPLELKLFLEAPPAEDP 212
Cdd:PHA03247  2882 PVRRLARPAVSRSTESFALP-PDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960

                           90       100
                   ....*....|....*....|....*....
gi 2453130692  213 EPSEDQEAPNNVARPQPRYPTEASSWPIS 241
Cdd:PHA03247  2961 QPWLGALVPGRVAVPRFRVPQPAPSREAP 2989
 
Name Accession Description Interval E-value
bHLH_AtILR3_like cd11446
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine ...
 41-114 6.88e-27

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.


Pssm-ID: 381452 [Multi-domain]  Cd Length: 76  Bit Score: 98.94  E-value: 6.88e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2453130692  41 KSEREKLKRGHLNDLFGELGNMLEADR-QSNGKACILTDTTRILRDLLSQVKSLRQENSTLQNESNYVTMERNEL 114
Cdd:cd11446     1 KACREKLRRDKLNERFMELSNVLEPGRpPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQEESKELKAEKNEL 75
PHA03247 PHA03247
large tegument protein UL36; Provisional
 133-241 9.96e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 40.31  E-value: 9.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2453130692  133 RMRATGSPGWGHGATGSPLPvPPSPGTVFPSQQPMQPSPMTTSTVFPLQQPLPQPTVIEPSARQPLELKLFLEAPPAEDP 212
Cdd:PHA03247  2882 PVRRLARPAVSRSTESFALP-PDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960

                           90       100
                   ....*....|....*....|....*....
gi 2453130692  213 EPSEDQEAPNNVARPQPRYPTEASSWPIS 241
Cdd:PHA03247  2961 QPWLGALVPGRVAVPRFRVPQPAPSREAP 2989
ZapB COG3074
Cell division protein ZapB, interacts with FtsZ [Cell cycle control, cell division, chromosome ...
 58-133 1.15e-03

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


Pssm-ID: 442308 [Multi-domain]  Cd Length: 79  Bit Score: 36.87  E-value: 1.15e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2453130692  58 ELGNMLEADRQSngkaciLTDTTRILRdllSQVKSLRQENSTLQNESNYVTMERNELQDENGALRSEISDLQNELR 133
Cdd:COG3074     4 ELLEELEAKVQQ------AVDTIELLQ---MEVEELKEKNEELEQENEELQSENEELQSENEQLKTENAEWQERIR 70
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 129-245 4.54e-03

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.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 37.86  E-value: 4.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2453130692 129 QNELRMRATGSPGWGHGATGSPLPVPPSPGTVFPSQQPMQP-SPMTTSTVFPLQQPLPQptviepsarqplelklFLEAP 207
Cdd:TIGR01628 377 QLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPrMSMMPTPMGPGGPLRPN----------------GLAPM 440

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2453130692 208 PAEDPEPSEDQEAPNNVARPQPRYPTEASSWPISLGLP 245
Cdd:TIGR01628 441 NAVRAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLP 478
 
Name Accession Description Interval E-value
bHLH_AtILR3_like cd11446
basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine ...
 41-114 6.88e-27

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.


Pssm-ID: 381452 [Multi-domain]  Cd Length: 76  Bit Score: 98.94  E-value: 6.88e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2453130692  41 KSEREKLKRGHLNDLFGELGNMLEADR-QSNGKACILTDTTRILRDLLSQVKSLRQENSTLQNESNYVTMERNEL 114
Cdd:cd11446     1 KACREKLRRDKLNERFMELSNVLEPGRpPKTDKATILGDAIRMLKQLRGEVQKLKEENSSLQEESKELKAEKNEL 75
bHLHzip_MGA_like cd19682
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) ...
 37-103 1.23e-04

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.


Pssm-ID: 381525 [Multi-domain]  Cd Length: 65  Bit Score: 39.18  E-value: 1.23e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2453130692  37 RKVHKSeREKLKRGHLNDLFGELGNMLEADRQSNG-KACILTDTtrilrdlLSQVKSLRQENSTLQNE 103
Cdd:cd19682     1 RLRHKK-RERERRSELRELFDKLKQLLGLDSDEKAsKLAVLTEA-------IEEIQQLKREEDELQKE 60
PHA03247 PHA03247
large tegument protein UL36; Provisional
 133-241 9.96e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 40.31  E-value: 9.96e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2453130692  133 RMRATGSPGWGHGATGSPLPvPPSPGTVFPSQQPMQPSPMTTSTVFPLQQPLPQPTVIEPSARQPLELKLFLEAPPAEDP 212
Cdd:PHA03247  2882 PVRRLARPAVSRSTESFALP-PDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960

                           90       100
                   ....*....|....*....|....*....
gi 2453130692  213 EPSEDQEAPNNVARPQPRYPTEASSWPIS 241
Cdd:PHA03247  2961 QPWLGALVPGRVAVPRFRVPQPAPSREAP 2989
ZapB COG3074
Cell division protein ZapB, interacts with FtsZ [Cell cycle control, cell division, chromosome ...
 58-133 1.15e-03

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


Pssm-ID: 442308 [Multi-domain]  Cd Length: 79  Bit Score: 36.87  E-value: 1.15e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2453130692  58 ELGNMLEADRQSngkaciLTDTTRILRdllSQVKSLRQENSTLQNESNYVTMERNELQDENGALRSEISDLQNELR 133
Cdd:COG3074     4 ELLEELEAKVQQ------AVDTIELLQ---MEVEELKEKNEELEQENEELQSENEELQSENEQLKTENAEWQERIR 70
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 149-234 1.95e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 39.30  E-value: 1.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2453130692  149 SPLPVPPSPGTVFPSQQPMQPSPMTTSTVFPLQQPLPQPTVIEPSARQPlelkLFLEAPPAEDPEPSEDQEAPnnvARPQ 228
Cdd:PRK10263   433 YYAPAPEQPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQP----QPVEQQPVVEPEPVVEETKP---ARPP 505


                   ....*.
gi 2453130692  229 PRYPTE 234
Cdd:PRK10263   506 LYYFEE 511
bZIP_ATF2 cd14687
Basic leucine zipper (bZIP) domain of Activating Transcription Factor-2 (ATF-2) and similar ...
 94-134 3.78e-03

Basic leucine zipper (bZIP) domain of Activating Transcription Factor-2 (ATF-2) and similar proteins: a DNA-binding and dimerization domain; ATF-2 is a sequence-specific DNA-binding protein that belongs to the Basic leucine zipper (bZIP) family of transcription factors. In response to stress, it activates a variety of genes including cyclin A, cyclin D, and c-Jun. ATF-2 also plays a role in the DNA damage response that is independent of its transcriptional activity. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription.


Pssm-ID: 269835 [Multi-domain]  Cd Length: 61  Bit Score: 34.81  E-value: 3.78e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 2453130692  94 RQENSTLQNESNYVTMERNELQDENGALRSEISDLQNELRM 134
Cdd:cd14687    21 KQWVQQLEEKVRKLESENKALKAEVDKLREEVLDLKNLLLA 61
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 129-245 4.54e-03

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.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 37.86  E-value: 4.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2453130692 129 QNELRMRATGSPGWGHGATGSPLPVPPSPGTVFPSQQPMQP-SPMTTSTVFPLQQPLPQptviepsarqplelklFLEAP 207
Cdd:TIGR01628 377 QLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQQFNGQPLGWPrMSMMPTPMGPGGPLRPN----------------GLAPM 440

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2453130692 208 PAEDPEPSEDQEAPNNVARPQPRYPTEASSWPISLGLP 245
Cdd:TIGR01628 441 NAVRAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLP 478
bHLHzip_scHMS1_like cd11399
basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription ...
 26-102 5.76e-03

basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription factor HMS1 and similar proteins; HMS1, also termed high-copy MEP suppressor protein 1, is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation.


Pssm-ID: 381405 [Multi-domain]  Cd Length: 96  Bit Score: 35.14  E-value: 5.76e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2453130692  26 ISDKKC--RKKVPrkvhkSEREKLKRGHLNDLFGELGNMLEADRQSNgKACILTDTTRILRDLLSQVKSLRQENSTLQN 102
Cdd:cd11399    18 INDRIAelRDSVP-----ALREAYKSARGEDEDEEDLGGLTPATKLN-KATILSKATEYIRHLEKKNKRLSRENASLRE 90
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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