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Conserved domains on  [gi|446084841|ref|WP_000162696|]
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MULTISPECIES: RinA family phage transcriptional activator [Bacteria]

Protein Classification

RinA family phage transcriptional activator( domain architecture ID 10019420)

RinA family phage transcriptional activator is a DUF722 domain-containing protein; similar to Staphylococcus virus 11 transcriptional activator RinA, which activates int gene expression, probably by direct DNA-binding

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
phage_rinA TIGR01636
phage transcriptional activator, RinA family; This model represents a family of phage proteins, ...
 8-139 2.38e-61

phage transcriptional activator, RinA family; This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions]


:

Pssm-ID: 130697  Cd Length: 134  Bit Score: 184.72  E-value: 2.38e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446084841    8 LKLSTVRKLEDELCDYPNYHKQLEDLRSEIMTPWIPTDTNIGGEFVPSNTSKTEMAVTNYLCSIRRGKILEFKSAIERII 87
Cdd:TIGR01636   1 LRTSTFNYIEDELADYYKTEKYLRQREEELRHPYQEADLNAGGRGQGLHSVVTERMVITIAMDRRLWNLERNRDAIENCL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446084841   88 NTSSRKEREFIQEYYFNKK--ELVKVCDDIHISDRTAHRIKRKIISRLAEELGE 139
Cdd:TIGR01636  81 NEADEQTRVIIQELYMKKRplTLVGLAQQLFISKSTAYRLRNHIIEAVAEELGM 134
 
Name Accession Description Interval E-value
phage_rinA TIGR01636
phage transcriptional activator, RinA family; This model represents a family of phage proteins, ...
 8-139 2.38e-61

phage transcriptional activator, RinA family; This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions]


Pssm-ID: 130697  Cd Length: 134  Bit Score: 184.72  E-value: 2.38e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446084841    8 LKLSTVRKLEDELCDYPNYHKQLEDLRSEIMTPWIPTDTNIGGEFVPSNTSKTEMAVTNYLCSIRRGKILEFKSAIERII 87
Cdd:TIGR01636   1 LRTSTFNYIEDELADYYKTEKYLRQREEELRHPYQEADLNAGGRGQGLHSVVTERMVITIAMDRRLWNLERNRDAIENCL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446084841   88 NTSSRKEREFIQEYYFNKK--ELVKVCDDIHISDRTAHRIKRKIISRLAEELGE 139
Cdd:TIGR01636  81 NEADEQTRVIIQELYMKKRplTLVGLAQQLFISKSTAYRLRNHIIEAVAEELGM 134
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 78-139 9.79e-03

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 34.80  E-value: 9.79e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446084841  78 EFKSAIERIINTSSRKEREFIQEYYFNK---KELVKVcddIHISDRTAHRIKRKIISRLAEELGE 139
Cdd:COG1191  175 ELREALAEAIEQLPERERLVLSLYYFEEltlKEIAEV---LGVSESRVSRLHKKALARLREYLKE 236
DUF1492 pfam07374
Protein of unknown function (DUF1492); This family consists of several hypothetical, highly ...
 75-133 9.84e-03

Protein of unknown function (DUF1492); This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281.


Pssm-ID: 311366  Cd Length: 100  Bit Score: 33.66  E-value: 9.84e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446084841   75 KILEFKSAIERIINTSSRKereFIQEYYFNKKELVKVCDDIHISDRTAHRIKRKIISRL 133
Cdd:pfam07374  44 RKLELGRMINNLENPDSRS---VLRMVYIDKMTIWQVCDKLNISRTTYYRLLRVATKEL 99
 
Name Accession Description Interval E-value
phage_rinA TIGR01636
phage transcriptional activator, RinA family; This model represents a family of phage proteins, ...
 8-139 2.38e-61

phage transcriptional activator, RinA family; This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions]


Pssm-ID: 130697  Cd Length: 134  Bit Score: 184.72  E-value: 2.38e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446084841    8 LKLSTVRKLEDELCDYPNYHKQLEDLRSEIMTPWIPTDTNIGGEFVPSNTSKTEMAVTNYLCSIRRGKILEFKSAIERII 87
Cdd:TIGR01636   1 LRTSTFNYIEDELADYYKTEKYLRQREEELRHPYQEADLNAGGRGQGLHSVVTERMVITIAMDRRLWNLERNRDAIENCL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 446084841   88 NTSSRKEREFIQEYYFNKK--ELVKVCDDIHISDRTAHRIKRKIISRLAEELGE 139
Cdd:TIGR01636  81 NEADEQTRVIIQELYMKKRplTLVGLAQQLFISKSTAYRLRNHIIEAVAEELGM 134
phage_arpU TIGR01637
phage transcriptional regulator, ArpU family; This model represents a family of phage proteins, ...
 12-140 3.32e-04

phage transcriptional regulator, ArpU family; This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions]


Pssm-ID: 273725  Cd Length: 132  Bit Score: 38.15  E-value: 3.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446084841   12 TVRKLEDELCDYPNYHKQLEDLRSEIMTPwipTDTNIGGEFVPSNTSKTEMAVTNylcsiRRGKILEFKSAIERIINTSS 91
Cdd:TIGR01637  10 TRANVKRFLEDYRRLRRIAGRSLTPKLSP---SLSLEPPSFTNEFHSKTEEAAIH-----NLDAEQEARAIVNAIVNQLD 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446084841   92 RKEREFIQEYYF--NKKELVKVCDDIHISDRTAHRIKRKIISRLAEELGEE 140
Cdd:TIGR01637  82 EISRQILYDKYLepDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYGIG 132
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 78-137 2.31e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.17  E-value: 2.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446084841   78 EFKSAIERIINTSSRKEREFIQEYYFNKKELVKVCDDIHISDRTAHRIKRKIISRLAEEL 137
Cdd:TIGR02937  99 EEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 78-139 9.79e-03

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 34.80  E-value: 9.79e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446084841  78 EFKSAIERIINTSSRKEREFIQEYYFNK---KELVKVcddIHISDRTAHRIKRKIISRLAEELGE 139
Cdd:COG1191  175 ELREALAEAIEQLPERERLVLSLYYFEEltlKEIAEV---LGVSESRVSRLHKKALARLREYLKE 236
DUF1492 pfam07374
Protein of unknown function (DUF1492); This family consists of several hypothetical, highly ...
 75-133 9.84e-03

Protein of unknown function (DUF1492); This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281.


Pssm-ID: 311366  Cd Length: 100  Bit Score: 33.66  E-value: 9.84e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446084841   75 KILEFKSAIERIINTSSRKereFIQEYYFNKKELVKVCDDIHISDRTAHRIKRKIISRL 133
Cdd:pfam07374  44 RKLELGRMINNLENPDSRS---VLRMVYIDKMTIWQVCDKLNISRTTYYRLLRVATKEL 99
 
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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