N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
221-585
3.20e-30
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
The actual alignment was detected with superfamily member COG5139:
Pssm-ID: 469629 Cd Length: 397 Bit Score: 122.89 E-value: 3.20e-30
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
3-321
1.88e-07
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
The actual alignment was detected with superfamily member NF033609:
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 54.53 E-value: 1.88e-07
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
429-482
2.29e-11
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.
Pssm-ID: 462573 [Multi-domain] Cd Length: 52 Bit Score: 59.07 E-value: 2.29e-11
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
3-321
1.88e-07
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 54.53 E-value: 1.88e-07
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
2-271
3.42e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 50.29 E-value: 3.42e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
2-310
3.89e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 49.91 E-value: 3.89e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
46-321
3.03e-05
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 47.21 E-value: 3.03e-05
Extracellular matrix protein 1 (ECM1); This family consists of several eukaryotic ...
1-105
1.83e-03
Extracellular matrix protein 1 (ECM1); This family consists of several eukaryotic extracellular matrix protein 1 (ECM1) sequences. ECM1 has been shown to regulate endochondral bone formation, stimulate the proliferation of endothelial cells and induce angiogenesis. Mutations in the ECM1 gene can cause lipoid proteinosis, a disorder which causes generalized thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness.
Pssm-ID: 461739 Cd Length: 518 Bit Score: 41.36 E-value: 1.83e-03
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
429-482
2.29e-11
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.
Pssm-ID: 462573 [Multi-domain] Cd Length: 52 Bit Score: 59.07 E-value: 2.29e-11
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
3-321
1.88e-07
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 54.53 E-value: 1.88e-07
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
2-271
3.42e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 50.29 E-value: 3.42e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
2-310
3.89e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 49.91 E-value: 3.89e-06
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
46-321
3.03e-05
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.
Pssm-ID: 468110 [Multi-domain] Cd Length: 934 Bit Score: 47.21 E-value: 3.03e-05
Extracellular matrix protein 1 (ECM1); This family consists of several eukaryotic ...
1-105
1.83e-03
Extracellular matrix protein 1 (ECM1); This family consists of several eukaryotic extracellular matrix protein 1 (ECM1) sequences. ECM1 has been shown to regulate endochondral bone formation, stimulate the proliferation of endothelial cells and induce angiogenesis. Mutations in the ECM1 gene can cause lipoid proteinosis, a disorder which causes generalized thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness.
Pssm-ID: 461739 Cd Length: 518 Bit Score: 41.36 E-value: 1.83e-03
Ebola nucleoprotein; This family consists of Ebola and Marburg virus nucleoproteins. These ...
5-86
9.13e-03
Ebola nucleoprotein; This family consists of Ebola and Marburg virus nucleoproteins. These proteins are responsible for encapsidation of genomic RNA. It has been found that nucleoprotein DNA vaccines can offer protection from the virus.
Pssm-ID: 398905 Cd Length: 717 Bit Score: 38.95 E-value: 9.13e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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