PANDIT+

KeywordFamilyClanGene   

Entry: LacI (PF00356) * this family does not contain any human sequence in the seed alignment although some of the annotation data are human specific [read more]

Display a clan
Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).
Display a clan
Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary

Description

Bacterial regulatory proteins, lacI family

 
Literature
 
Clan

CL0123 (HTH)

The clan contains the following members: PF04218(CENP-B_N); PF01381(HTH_3); PF02954(HTH_8); PF04760(IF2_N); PF00249(Myb_DNA-binding); PF01399(PCI); PF03399(SAC3_GANP); PF04542(Sigma70_r2); PF04545(Sigma70_r4); PF00440(TetR_N); PF00486(Trans_reg_C); PF01316(Arg_repressor); PF04182(B-block_TFIIIC); PF00325(Crp); PF01978(TrmB); PF02001(DUF134); PF02650(DUF199); PF01638(DUF24); PF03444(DUF293); PF04079(DUF387); PF02319(E2F_TDP); PF03789(ELK); PF00178(Ets); PF04703(FaeA); PF02742(Fe_dep_repr_C); PF01325(Fe_dep_repress); PF01475(FUR); PF00196(GerE); PF00392(GntR); PF00046(Homeobox); PF00447(HSF_DNA-bind); PF00126(HTH_1); PF04967(HTH_10); PF01022(HTH_5); PF01418(HTH_6); PF02796(HTH_7); PF00165(HTH_AraC); PF03811(Ins_element1); PF00356(LacI); PF01726(LexA_DNA_bind); PF01047(MarR); PF00376(MerR); PF05043(Mga); PF03962(Mnd1); PF02316(Mu_DNA_bind); PF03551(PadR); PF00292(PAX); PF03965(Pencillinase_R); PF00157(Pou); PF03288(Pox_D5); PF01051(Rep_3); PF04796(RepA_C); PF02257(RFX_DNA_binding); PF05158(RNA_pol_Rpc34); PF03428(RP-C); PF02334(RTP); PF04963(Sigma54_CBD); PF04552(Sigma54_DBD); PF04539(Sigma70_r3); PF02002(TFIIE_alpha); PF01710(Transposase_14); PF01498(Transposase_5); PF01527(Transposase_8); PF03221(Transposase_Tc5); PF01371(Trp_repressor); PF02082(Rrf2); PF04297(UPF0122); PF02295(z-alpha); PF05225(HTH_psq); PF05269(Phage_CII); PF05331(DUF742); PF05339(DUF739); PF05584(Sulfolobus_pRN); PF05732(RepL); PF05920(Coprinus_mating); PF05930(Phage_AlpA); PF06056(Terminase_5); PF06163(DUF977); PF06504(RepC); PF06530(Phage_antitermQ); PF06576(DUF1133); PF06627(DUF1153); PF06970(RepA_N); PF06971(Put_DNA-bind_N); PF07022(Phage_CI_repr); PF07037(DUF1323); PF07042(TrfA); PF07106(TBPIP); PF07278(DUF1441); PF07374(DUF1492); PF07381(DUF1495); PF07453(NUMOD1); PF07544(CSE2); PF07638(Sigma70_ECF); PF07750(GcrA); PF07825(Exc); PF07848(PaaX); PF07900(DUF1670); PF08100(Dimerisation);
 
InterPro entry IPR000843
 

Alignment
New Hampshire tree

The seed alignment for this family in the PANDIT database contains 27 aligned sequences:

  ASCG_ECOLI/1-27   CCPA_BACME/2-28   CCPB_BACSU/1-27   CSCR_SHIFL/1-27   CYTR_ECOLI/9-35   DEGA_BACSU/2-28   EBGR_ECOLI/1-27   ENDR_PAEPO/2-28   FRUR_ECOLI/1-26   GALR_ECOLI/1-27   GALR_HAEIN/1-27   GALS_ECOLI/1-27   GNTR_ECOLI/5-31   IDNR_ECOLI/5-31   LACI_ECOLI/3-29   LACI_KLEPN/5-31   MALI_ECOLI/6-32   MALR_STRPN/1-27   PURR_ECOLI/1-26   RAFR_ECOLI/1-25   RBSR_BACSU/1-27   RBSR_ECOLI/1-26   RBTR_KLEAE/3-29   SCRR_KLEPN/5-31   SCRR_PEDPE/2-28   SCRR_VIBAL/1-27   TRER_ECOLI/4-30  

The full alignment for this family in the Pfam database contains 9366 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Escherichia coli K12 (13);   Bacillus subtilis (3);   Klebsiella pneumoniae (2);   Vibrio alginolyticus (1);   Klebsiella aerogenes (1);   Streptococcus pneumoniae (1);   Haemophilus influenzae (1);   Shigella flexneri (1);   Bacillus megaterium (1);   Pediococcus pentosaceus (1);   Escherichia coli (1);   Paenibacillus polymyxa (1);  

The full alignment covers 625 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-1741.90-1706.551624-1704.092041-1687.318996-1687.299736

Tree Length  

55.0155.0078655.0078655.0078655.00786

κ  

0.991.1782211.1749521.1669951.169206

ω-ratio  

ω=0.1318p0=0.515038 ~ ω0=0.125863
p1=0.484962 ~ ω1=1		p0=0.675196 ~ ω0=0.140505
p1=0.324543 ~ ω1=1
p2=0.000261 ~ ω2=999		ω~Β(1.029968,4.976778)p0=0.999967 ~ ω~Β(1.018637,4.766258)
p1=3.3e-05 ~ ω=523.851711

P-value for testing  
positive selection  

M1 vs M2: P-value=0.085471
domain classification: conserved		M7 vs M8: P-value=0.980924
domain classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

 -1765.90075-1764.12355

Mean ω-ratio  

ω = 0.19125ω = 0.24387

Coeff. of variation  
of ω-ratio  

 CVω = 0.77927CVω = 1.0501
 

Annotations

InteractionsThis domain has 0 known interactions:
StructuresThis domain has 54 structures:
Notation: PDB_ID (PDB chain, PDB residues)
More...
Gene Ontologies
Cellular component
 intracellular[GO:0005622]
Biological Process
 regulation of transcription, DNA-dependent[GO:0006355]
Molecular Function
 transcription factor activity[GO:0003700]
KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Citrate cycle (TCA cycle) [KEGG]
Pentose phosphate pathway [KEGG]
Pyruvate metabolism [KEGG]
Propanoate metabolism [KEGG]
Butanoate metabolism [KEGG]
Energy Metabolism
Oxidative phosphorylation [KEGG]
Carbon fixation in photosynthetic organisms [KEGG]
Nitrogen metabolism [KEGG]
Sulfur metabolism [KEGG]
Lipid Metabolism
Fatty acid metabolism [KEGG]
Synthesis and degradation of ketone bodies [KEGG]
Glycerolipid metabolism [KEGG]
Nucleotide Metabolism
Purine metabolism [KEGG]
Pyrimidine metabolism [KEGG]
Amino Acid Metabolism
Alanine and aspartate metabolism [KEGG]
Glycine, serine and threonine metabolism [KEGG]
Methionine metabolism [KEGG]
Cysteine metabolism [KEGG]
Valine, leucine and isoleucine degradation [KEGG]
Lysine degradation [KEGG]
Tryptophan metabolism [KEGG]
Metabolism of Other Amino Acids
Taurine and hypotaurine metabolism [KEGG]
Selenoamino acid metabolism [KEGG]
D-Alanine metabolism [KEGG]
Glutathione metabolism [KEGG]
Metabolism of Cofactors and Vitamins
One carbon pool by folate [KEGG]
Thiamine metabolism [KEGG]
Nicotinate and nicotinamide metabolism [KEGG]
Lipoic acid metabolism [KEGG]
Xenobiotics Biodegradation and Metabolism
Benzoate degradation via CoA ligation [KEGG]
Atrazine degradation [KEGG]
Drug metabolism - other enzymes [KEGG]
Genetic Information Processing
Transcription
RNA polymerase [KEGG]
Folding, Sorting and Degradation
Type IV secretion system [KEGG]
Replication and Repair
Nucleotide excision repair [KEGG]
Mismatch repair [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Phosphotransferase system (PTS) [KEGG]
Signal Transduction
Two-component system [KEGG]
Cellular Processes
Cell Motility
Flagellar assembly [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

none

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data
 
Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment
 
Associated diseases and disorders
Links to OMIM - for human genes coding for sequences from full alignment