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Conserved domains on  [gi|136255554|ref|NP_001077046|]
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RNA polymerase-associated protein RTF1 homolog [Danio rerio]

Protein Classification

RNA polymerase-associated RTF1 family protein( domain architecture ID 13428836)

RNA polymerase-associated RTF1 family protein such as yeast RNA polymerase-associated protein RTF1, a component of the multifunctional complex PAF1, which is involved in transcription, elongation, and transcription-coupled histone modification.

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Plus-3 pfam03126
Plus-3 domain; This domain is about 90 residues in length and is often found associated with ...
325-425 2.95e-47

Plus-3 domain; This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor.


:

Pssm-ID: 460817  Cd Length: 103  Bit Score: 161.96  E-value: 2.95e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554  325 LNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSN--KPVYRVAEIIDVVETAKIYQLGSTRTNKGLQLRHGNDTRV 402
Cdd:pfam03126   1 INRIRLSRSLLEKWCFYPFFEDAVVGCFVRVNIGPDREtgQPVYRLAQIVGVKESGKPYKLGKKTTNKYLVVRHGKAERV 80
                          90       100
                  ....*....|....*....|...
gi 136255554  403 FRLEFVSNQEFTESEFMKWKEAM 425
Cdd:pfam03126  81 FPMDFVSNSPFTEEEFERWRQTL 103
COG5296 super family cl34975
Transcription factor involved in TATA site selection and in elongation by RNA polymerase II ...
152-589 1.09e-35

Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription];


The actual alignment was detected with superfamily member COG5296:

Pssm-ID: 227615 [Multi-domain]  Cd Length: 521  Bit Score: 141.72  E-value: 1.09e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 152 DEEDRARLEQMTEKEREQELFNRIEKREVLKRRFEIKQKLKTAKKKekeekkkkqeeeqekrkqSQVPDTqvvmshnkeR 231
Cdd:COG5296   77 DEADRAKIMAMTEIERESILFEREEEISKLMERRELAIRMEQQHRS------------------SGCTDT---------R 129
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 232 RIKRDEKLDKKSQAMEELKAEREKRKNRTAELLAKRqplkTSEVYSDDEEEEEDDDDKSSVKSDRSSRSSSFDEEEEKEE 311
Cdd:COG5296  130 RSTRYEPLTSAAEEKKKKLLELKKTREREERLYSER----HIELQRFKDYKELEESEQGLQEEYTPSYAEEAVEDISRTD 205
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 312 APPKSQpvslpdELNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSNKPVYRVAEIIDVVETAKIYQLGSTRTNKG 391
Cdd:COG5296  206 DFAELY------DFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKGSTYSKPYGRKEVKTNRY 279
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 392 LQLRHGNDTRVFRLEFVSNQEFTESEFMKWKEAMMIAGMQLPTLDEINKKEQSIKEAVNYKFNDKDIEDIVKEKDRFRKA 471
Cdd:COG5296  280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPK 359
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 472 PPNYAMKKTQLLKEKAMAEESGDGDKAKTLQDQLNELEERAEALDRQRTKNISAISYINQRNRSWNIVESEKAlvaegQN 551
Cdd:COG5296  360 RSNVIHEKTELRQKRQRAIELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLA-----EQ 434
                        410       420       430
                 ....*....|....*....|....*....|....*...
gi 136255554 552 SKNQQMDPFTRRQcKPTMVSNARDPSVHAAILAHLNQK 589
Cdd:COG5296  435 RMNEEAATATPMS-APTSVLTQPSPSLSTSIMPKLNPS 471
 
Name Accession Description Interval E-value
Plus-3 pfam03126
Plus-3 domain; This domain is about 90 residues in length and is often found associated with ...
325-425 2.95e-47

Plus-3 domain; This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor.


Pssm-ID: 460817  Cd Length: 103  Bit Score: 161.96  E-value: 2.95e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554  325 LNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSN--KPVYRVAEIIDVVETAKIYQLGSTRTNKGLQLRHGNDTRV 402
Cdd:pfam03126   1 INRIRLSRSLLEKWCFYPFFEDAVVGCFVRVNIGPDREtgQPVYRLAQIVGVKESGKPYKLGKKTTNKYLVVRHGKAERV 80
                          90       100
                  ....*....|....*....|...
gi 136255554  403 FRLEFVSNQEFTESEFMKWKEAM 425
Cdd:pfam03126  81 FPMDFVSNSPFTEEEFERWRQTL 103
Plus3 smart00719
Short conserved domain in transcriptional regulators; Plus3 domains occur in the Saccharomyces ...
319-426 1.17e-40

Short conserved domain in transcriptional regulators; Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.


Pssm-ID: 197843  Cd Length: 109  Bit Score: 143.98  E-value: 1.17e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554   319 VSLPDELNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSNK-PVYRVAEIIDVVETAKIYQLGSTRTNKGLQLRHG 397
Cdd:smart00719   1 AIVFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKqPIYRLVQVTGVKEADKPYSLGGKTTNVLLEVLNG 80
                           90       100
                   ....*....|....*....|....*....
gi 136255554   398 NDTRVFRLEFVSNQEFTESEFMKWKEAMM 426
Cdd:smart00719  81 DSEKVVQINFISNQDFTEEEFQRWKQAIK 109
COG5296 COG5296
Transcription factor involved in TATA site selection and in elongation by RNA polymerase II ...
152-589 1.09e-35

Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription];


Pssm-ID: 227615 [Multi-domain]  Cd Length: 521  Bit Score: 141.72  E-value: 1.09e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 152 DEEDRARLEQMTEKEREQELFNRIEKREVLKRRFEIKQKLKTAKKKekeekkkkqeeeqekrkqSQVPDTqvvmshnkeR 231
Cdd:COG5296   77 DEADRAKIMAMTEIERESILFEREEEISKLMERRELAIRMEQQHRS------------------SGCTDT---------R 129
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 232 RIKRDEKLDKKSQAMEELKAEREKRKNRTAELLAKRqplkTSEVYSDDEEEEEDDDDKSSVKSDRSSRSSSFDEEEEKEE 311
Cdd:COG5296  130 RSTRYEPLTSAAEEKKKKLLELKKTREREERLYSER----HIELQRFKDYKELEESEQGLQEEYTPSYAEEAVEDISRTD 205
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 312 APPKSQpvslpdELNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSNKPVYRVAEIIDVVETAKIYQLGSTRTNKG 391
Cdd:COG5296  206 DFAELY------DFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKGSTYSKPYGRKEVKTNRY 279
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 392 LQLRHGNDTRVFRLEFVSNQEFTESEFMKWKEAMMIAGMQLPTLDEINKKEQSIKEAVNYKFNDKDIEDIVKEKDRFRKA 471
Cdd:COG5296  280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPK 359
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 472 PPNYAMKKTQLLKEKAMAEESGDGDKAKTLQDQLNELEERAEALDRQRTKNISAISYINQRNRSWNIVESEKAlvaegQN 551
Cdd:COG5296  360 RSNVIHEKTELRQKRQRAIELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLA-----EQ 434
                        410       420       430
                 ....*....|....*....|....*....|....*...
gi 136255554 552 SKNQQMDPFTRRQcKPTMVSNARDPSVHAAILAHLNQK 589
Cdd:COG5296  435 RMNEEAATATPMS-APTSVLTQPSPSLSTSIMPKLNPS 471
 
Name Accession Description Interval E-value
Plus-3 pfam03126
Plus-3 domain; This domain is about 90 residues in length and is often found associated with ...
325-425 2.95e-47

Plus-3 domain; This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor.


Pssm-ID: 460817  Cd Length: 103  Bit Score: 161.96  E-value: 2.95e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554  325 LNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSN--KPVYRVAEIIDVVETAKIYQLGSTRTNKGLQLRHGNDTRV 402
Cdd:pfam03126   1 INRIRLSRSLLEKWCFYPFFEDAVVGCFVRVNIGPDREtgQPVYRLAQIVGVKESGKPYKLGKKTTNKYLVVRHGKAERV 80
                          90       100
                  ....*....|....*....|...
gi 136255554  403 FRLEFVSNQEFTESEFMKWKEAM 425
Cdd:pfam03126  81 FPMDFVSNSPFTEEEFERWRQTL 103
Plus3 smart00719
Short conserved domain in transcriptional regulators; Plus3 domains occur in the Saccharomyces ...
319-426 1.17e-40

Short conserved domain in transcriptional regulators; Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.


Pssm-ID: 197843  Cd Length: 109  Bit Score: 143.98  E-value: 1.17e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554   319 VSLPDELNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSNK-PVYRVAEIIDVVETAKIYQLGSTRTNKGLQLRHG 397
Cdd:smart00719   1 AIVFDNLNLLRLRRSLVEELLKPPTFESKVVGCFVRVKIGPNDQKqPIYRLVQVTGVKEADKPYSLGGKTTNVLLEVLNG 80
                           90       100
                   ....*....|....*....|....*....
gi 136255554   398 NDTRVFRLEFVSNQEFTESEFMKWKEAMM 426
Cdd:smart00719  81 DSEKVVQINFISNQDFTEEEFQRWKQAIK 109
COG5296 COG5296
Transcription factor involved in TATA site selection and in elongation by RNA polymerase II ...
152-589 1.09e-35

Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription];


Pssm-ID: 227615 [Multi-domain]  Cd Length: 521  Bit Score: 141.72  E-value: 1.09e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 152 DEEDRARLEQMTEKEREQELFNRIEKREVLKRRFEIKQKLKTAKKKekeekkkkqeeeqekrkqSQVPDTqvvmshnkeR 231
Cdd:COG5296   77 DEADRAKIMAMTEIERESILFEREEEISKLMERRELAIRMEQQHRS------------------SGCTDT---------R 129
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 232 RIKRDEKLDKKSQAMEELKAEREKRKNRTAELLAKRqplkTSEVYSDDEEEEEDDDDKSSVKSDRSSRSSSFDEEEEKEE 311
Cdd:COG5296  130 RSTRYEPLTSAAEEKKKKLLELKKTREREERLYSER----HIELQRFKDYKELEESEQGLQEEYTPSYAEEAVEDISRTD 205
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 312 APPKSQpvslpdELNRIRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNSSNKPVYRVAEIIDVVETAKIYQLGSTRTNKG 391
Cdd:COG5296  206 DFAELY------DFNQCRVGRDMVARNVFKPIFEDEVIGCFTRVRIGERGGYLVYRIVGVGKGSTYSKPYGRKEVKTNRY 279
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 392 LQLRHGNDTRVFRLEFVSNQEFTESEFMKWKEAMMIAGMQLPTLDEINKKEQSIKEAVNYKFNDKDIEDIVKEKDRFRKA 471
Cdd:COG5296  280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEISKMVACKDEVHPK 359
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 136255554 472 PPNYAMKKTQLLKEKAMAEESGDGDKAKTLQDQLNELEERAEALDRQRTKNISAISYINQRNRSWNIVESEKAlvaegQN 551
Cdd:COG5296  360 RSNVIHEKTELRQKRQRAIELKNKKAAMEYQRQLEEIEDNEGARVHNVNSGRPLLAKVNERNRRRNHTEIRLA-----EQ 434
                        410       420       430
                 ....*....|....*....|....*....|....*...
gi 136255554 552 SKNQQMDPFTRRQcKPTMVSNARDPSVHAAILAHLNQK 589
Cdd:COG5296  435 RMNEEAATATPMS-APTSVLTQPSPSLSTSIMPKLNPS 471
 
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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