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Conserved domains on  [gi|1333100485|ref|XP_023524031|]
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uncharacterized protein LOC111788088 [Cucurbita pepo subsp. pepo]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 288-368 1.37e-34

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


:

Pssm-ID: 462184  Cd Length: 112  Bit Score: 127.71  E-value: 1.37e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  288 QSPESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKELSEWRMAKAE 367
Cdd:pfam07500   27 EDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPEKLVTMSPEEMASEELKKEREKIEK 106


                   .
gi 1333100485  368 E 368
Cdd:pfam07500  107 E 107
SPOC_TFIIS cd21538
SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II ...
 603-744 1.28e-25

SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family; The transcription factor S-II (TFIIS) family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


:

Pssm-ID: 439201  Cd Length: 146  Bit Score: 103.50  E-value: 1.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  603 LWDGILQYNISTMTPVVGTYISGERTSAKDW----PSTLEIKGRVRLDAFEKFLQELPLSRSRAVMVLHLDLKKGcpESD 678
Cdd:cd21538      1 VWSGKLTMPGVASFPASARQVGGPDLSSTWWtdllPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDS--SSD 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  679 RANLQEVAESYVADERVGIAEPGS--GVEFYFC--SPHGRILEMVgrILLKENNELLNAIENGLIGVVVW 744
Cdd:cd21538     79 KAAFDELFDYFVSRDRYGVVGPKGlaVKDLYLVplPAGDPLPPFL--LLLDDGPGPEPRDEDLLLGVIVL 146
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 288-368 1.37e-34

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 127.71  E-value: 1.37e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  288 QSPESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKELSEWRMAKAE 367
Cdd:pfam07500   27 EDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPEKLVTMSPEEMASEELKKEREKIEK 106


                   .
gi 1333100485  368 E 368
Cdd:pfam07500  107 E 107
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
290-362 3.02e-32

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 120.88  E-value: 3.02e-32
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1333100485   290 PESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKELSEWR 362
Cdd:smart00510   28 PTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPEKLATMTAEELASAELKEKR 100
SPOC_TFIIS cd21538
SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II ...
 603-744 1.28e-25

SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family; The transcription factor S-II (TFIIS) family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439201  Cd Length: 146  Bit Score: 103.50  E-value: 1.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  603 LWDGILQYNISTMTPVVGTYISGERTSAKDW----PSTLEIKGRVRLDAFEKFLQELPLSRSRAVMVLHLDLKKGcpESD 678
Cdd:cd21538      1 VWSGKLTMPGVASFPASARQVGGPDLSSTWWtdllPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDS--SSD 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  679 RANLQEVAESYVADERVGIAEPGS--GVEFYFC--SPHGRILEMVgrILLKENNELLNAIENGLIGVVVW 744
Cdd:cd21538     79 KAAFDELFDYFVSRDRYGVVGPKGlaVKDLYLVplPAGDPLPPFL--LLLDDGPGPEPRDEDLLLGVIVL 146
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
 600-745 5.56e-25

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 101.66  E-value: 5.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  600 LEYLWDGILQYNISTMTPVVGTYISGERTSAKdwPSTLEIKGRVRLDAFEKFLQELPLSRSRAVMVLHLdlkkgCP--ES 677
Cdd:pfam07744    5 LEVIWQGTLAMKGVAEFSVRAHLVSGDIDSLL--PSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRF-----FPssES 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  678 DRANLQEVAESYVADERVGI--AEPGSGVEFYFCsPHGRILEMvgriLLKENNELLNAIENGLIGVVVWR 745
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVihAKSADVKDLYLF-PPCEFLEL----LLPVGLSLEVSEPNLLLGVVVRK 142
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 280-368 9.03e-19

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 87.97  E-value: 9.03e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  280 QNQGSKPVQS--PESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKE 357
Cdd:TIGR01385  151 AKDSDHPPQSidPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAE 230

                           90
                   ....*....|.
gi 1333100485  358 LSEWRMAKAEE 368
Cdd:TIGR01385  231 LKQEREEITKE 241
 
Name Accession Description Interval E-value
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 288-368 1.37e-34

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 127.71  E-value: 1.37e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  288 QSPESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKELSEWRMAKAE 367
Cdd:pfam07500   27 EDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEISPEKLVTMSPEEMASEELKKEREKIEK 106


                   .
gi 1333100485  368 E 368
Cdd:pfam07500  107 E 107
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
290-362 3.02e-32

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 120.88  E-value: 3.02e-32
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1333100485   290 PESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKELSEWR 362
Cdd:smart00510   28 PTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPEKLATMTAEELASAELKEKR 100
SPOC_TFIIS cd21538
SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II ...
 603-744 1.28e-25

SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family; The transcription factor S-II (TFIIS) family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module.


Pssm-ID: 439201  Cd Length: 146  Bit Score: 103.50  E-value: 1.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  603 LWDGILQYNISTMTPVVGTYISGERTSAKDW----PSTLEIKGRVRLDAFEKFLQELPLSRSRAVMVLHLDLKKGcpESD 678
Cdd:cd21538      1 VWSGKLTMPGVASFPASARQVGGPDLSSTWWtdllPSTLEIKGRIPLDKAEKYLCELRFSSSRDVVVVSLEPPDS--SSD 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  679 RANLQEVAESYVADERVGIAEPGS--GVEFYFC--SPHGRILEMVgrILLKENNELLNAIENGLIGVVVW 744
Cdd:cd21538     79 KAAFDELFDYFVSRDRYGVVGPKGlaVKDLYLVplPAGDPLPPFL--LLLDDGPGPEPRDEDLLLGVIVL 146
SPOC pfam07744
SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in ...
 600-745 5.56e-25

SPOC domain; The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.


Pssm-ID: 400205  Cd Length: 142  Bit Score: 101.66  E-value: 5.56e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  600 LEYLWDGILQYNISTMTPVVGTYISGERTSAKdwPSTLEIKGRVRLDAFEKFLQELPLSRSRAVMVLHLdlkkgCP--ES 677
Cdd:pfam07744    5 LEVIWQGTLAMKGVAEFSVRAHLVSGDIDSLL--PSLLRITGRIRLDAVWKYLDEVRRSITRDVLVVRF-----FPssES 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  678 DRANLQEVAESYVADERVGI--AEPGSGVEFYFCsPHGRILEMvgriLLKENNELLNAIENGLIGVVVWR 745
Cdd:pfam07744   78 DESAFDELIDYLQSKQRAGVihAKSADVKDLYLF-PPCEFLEL----LLPVGLSLEVSEPNLLLGVVVRK 142
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 280-368 9.03e-19

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 87.97  E-value: 9.03e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1333100485  280 QNQGSKPVQS--PESLAFKMEEELFKLFSGVNKKYKEKGRSLLFNLKDRNNPELRERVMNGEITPERLCSMTAEELASKE 357
Cdd:TIGR01385  151 AKDSDHPPQSidPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAE 230

                           90
                   ....*....|.
gi 1333100485  358 LSEWRMAKAEE 368
Cdd:TIGR01385  231 LKQEREEITKE 241
 
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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