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Conserved domains on  [gi|1276961812|gb|PIP76069|]
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hypothetical protein COW86_00120 [Candidatus Kuenenbacteria bacterium CG22_combo_CG10-13_8_21_14_all_39_9]

Protein Classification

four helix bundle protein( domain architecture ID 11611519)

four helix bundle protein similar to Bordetella bacteriophage diversity-generating retroelement (DGR) protein Avd (accessory variability determinant), which is involved in retrohoming processes together with a reverse transcriptase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Avd_like cd16376
diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory ...
 8-113 3.78e-36

diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory variability determinant (bAvd) protein, together with a reverse transcriptase, is involved in retrohoming processes as part of a diversity-generating retroelement (DGR), a type of system that is involved in generating sequence variation in bacterial proteins by inserting coding information from a template region into a variable region of a protein coding gene. bAvd forms homopentamers and interacts with the reverse transcriptase as well as with DNA and/or RNA.


:

Pssm-ID: 319868  Cd Length: 106  Bit Score: 118.79  E-value: 3.78e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812   8 IFKKTYELYKEFYGFRNTVSKQDRYTIWQRCEDLILEILEYILGASQLSKIEKLPILQKASTKLNLLRVFLRLCKDTKVL 87
Cdd:cd16376     1 IYKKTYDLLKYLYPILKKFPKSERYTLGQRIENLALDLLELIIEANKSPKREKLPLLREADVKLELLKFLLRLAYELKLI 80

                          90       100
                  ....*....|....*....|....*.
gi 1276961812  88 DSKKYIRLEQNVDEIGRMLGGWIKST 113
Cdd:cd16376    81 SNKKYEVLSEKLDEIGKMLGGWIKSL 106
 
Name Accession Description Interval E-value
Avd_like cd16376
diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory ...
 8-113 3.78e-36

diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory variability determinant (bAvd) protein, together with a reverse transcriptase, is involved in retrohoming processes as part of a diversity-generating retroelement (DGR), a type of system that is involved in generating sequence variation in bacterial proteins by inserting coding information from a template region into a variable region of a protein coding gene. bAvd forms homopentamers and interacts with the reverse transcriptase as well as with DNA and/or RNA.


Pssm-ID: 319868  Cd Length: 106  Bit Score: 118.79  E-value: 3.78e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812   8 IFKKTYELYKEFYGFRNTVSKQDRYTIWQRCEDLILEILEYILGASQLSKIEKLPILQKASTKLNLLRVFLRLCKDTKVL 87
Cdd:cd16376     1 IYKKTYDLLKYLYPILKKFPKSERYTLGQRIENLALDLLELIIEANKSPKREKLPLLREADVKLELLKFLLRLAYELKLI 80

                          90       100
                  ....*....|....*....|....*.
gi 1276961812  88 DSKKYIRLEQNVDEIGRMLGGWIKST 113
Cdd:cd16376    81 SNKKYEVLSEKLDEIGKMLGGWIKSL 106
DivGenRetAVD NF033474
diversity-generating retroelement protein Avd; Avd (accessory variability determinant) is part ...
 7-111 1.03e-17

diversity-generating retroelement protein Avd; Avd (accessory variability determinant) is part of diversity-generating retroelement (GDR) system through which a portion of a protein-coding gene can be rewritten, creating diversity that can affect host range. The founding member of this family, bAvd, from a Bordetella bacteriophage, belongs to a retrohoming element called BPP-1. Members of this family are four-helix bundle proteins, related to those of family TIGR02436, some of whose members are found in long intervening sequence (IVS) regions in 23S rRNA.


Pssm-ID: 468041  Cd Length: 104  Bit Score: 72.18  E-value: 1.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812   7 PIFKKTYELYKEFYGFRNTVSKQDRYTIWQRCEDLILEILEYILGASQLSkiEKLPILQKASTKLNLLRVFLRLCKDTKV 86
Cdd:NF033474    2 PIIQKTYDLIKYLYPILQRFPKSHKFVLADRILNALYDLLELLIEANKRS--NKKSKLYALDAELDVLRYLLRLAADLKL 79

                          90       100
                  ....*....|....*....|....*
gi 1276961812  87 LDSKKYIRLEQNVDEIGRMLGGWIK 111
Cdd:NF033474   80 LSPKRYEYASRLLNEIGRMLGGWIK 104
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 34-108 2.55e-05

23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes. It folds into an anti-parallel four-helix bundle and forms homopentamers.


Pssm-ID: 461698  Cd Length: 106  Bit Score: 40.14  E-value: 2.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812  34 IWQRCEDLILEILE----------YIL-----------------GASQLSKIEKLPILQKASTKLNLLRVFLRLCKDTKV 86
Cdd:pfam05635   5 VWQKAMELALEIYKltkkfpkeekYGLtsqirraavsipaniaeGYGRRSKKDFIRFLSIARGSLAELETQLELAKDLGY 84

                          90       100
                  ....*....|....*....|..
gi 1276961812  87 LDSKKYIRLEQNVDEIGRMLGG 108
Cdd:pfam05635  85 ISEEEYEELLKEIEEISKMLNG 106
TIGR02436 TIGR02436
four helix bundle protein; This family describes a protein of unknown function whose structure ...
 74-114 7.28e-04

four helix bundle protein; This family describes a protein of unknown function whose structure is a bundle of four long alpha helices. Some of the first members of this family were found encoded in the (atypically large) intervening sequence (IVS) of Leptospira 23S RNA, a region often present in the rRNA gene and removed during rRNA processing without re-ligation. However, this location is not conserved, and naming this protein as a 23S RNA protein is both confusing and inaccurate.


Pssm-ID: 274132  Cd Length: 108  Bit Score: 36.30  E-value: 7.28e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1276961812  74 LRVFLRLCKDTKVLDSKKYIRLEQNVDEIGRMLGGWIKSTR 114
Cdd:TIGR02436  68 TETQLELAKDLGYIDEEQYEELLEELEEIIKMLNGLIKSLK 108
 
Name Accession Description Interval E-value
Avd_like cd16376
diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory ...
 8-113 3.78e-36

diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory variability determinant (bAvd) protein, together with a reverse transcriptase, is involved in retrohoming processes as part of a diversity-generating retroelement (DGR), a type of system that is involved in generating sequence variation in bacterial proteins by inserting coding information from a template region into a variable region of a protein coding gene. bAvd forms homopentamers and interacts with the reverse transcriptase as well as with DNA and/or RNA.


Pssm-ID: 319868  Cd Length: 106  Bit Score: 118.79  E-value: 3.78e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812   8 IFKKTYELYKEFYGFRNTVSKQDRYTIWQRCEDLILEILEYILGASQLSKIEKLPILQKASTKLNLLRVFLRLCKDTKVL 87
Cdd:cd16376     1 IYKKTYDLLKYLYPILKKFPKSERYTLGQRIENLALDLLELIIEANKSPKREKLPLLREADVKLELLKFLLRLAYELKLI 80

                          90       100
                  ....*....|....*....|....*.
gi 1276961812  88 DSKKYIRLEQNVDEIGRMLGGWIKST 113
Cdd:cd16376    81 SNKKYEVLSEKLDEIGKMLGGWIKSL 106
DivGenRetAVD NF033474
diversity-generating retroelement protein Avd; Avd (accessory variability determinant) is part ...
 7-111 1.03e-17

diversity-generating retroelement protein Avd; Avd (accessory variability determinant) is part of diversity-generating retroelement (GDR) system through which a portion of a protein-coding gene can be rewritten, creating diversity that can affect host range. The founding member of this family, bAvd, from a Bordetella bacteriophage, belongs to a retrohoming element called BPP-1. Members of this family are four-helix bundle proteins, related to those of family TIGR02436, some of whose members are found in long intervening sequence (IVS) regions in 23S rRNA.


Pssm-ID: 468041  Cd Length: 104  Bit Score: 72.18  E-value: 1.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812   7 PIFKKTYELYKEFYGFRNTVSKQDRYTIWQRCEDLILEILEYILGASQLSkiEKLPILQKASTKLNLLRVFLRLCKDTKV 86
Cdd:NF033474    2 PIIQKTYDLIKYLYPILQRFPKSHKFVLADRILNALYDLLELLIEANKRS--NKKSKLYALDAELDVLRYLLRLAADLKL 79

                          90       100
                  ....*....|....*....|....*
gi 1276961812  87 LDSKKYIRLEQNVDEIGRMLGGWIK 111
Cdd:NF033474   80 LSPKRYEYASRLLNEIGRMLGGWIK 104
23S_rRNA_IVP_like cd16377
23S rRNA-intervening sequence protein and similar proteins; A family of functionally ...
 74-112 8.74e-06

23S rRNA-intervening sequence protein and similar proteins; A family of functionally uncharacterized bacterial proteins, some of which are encoded by an atypically large intervening sequence present within some 23S rRNA genes. The distantly related bAvd protein, which also forms a homopentamer of four-helix bundles, has been suggested to interact with nucleic acids and a reverse transcriptase.


Pssm-ID: 319869  Cd Length: 108  Bit Score: 41.22  E-value: 8.74e-06
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1276961812  74 LRVFLRLCKDTKVLDSKKYIRLEQNVDEIGRMLGGWIKS 112
Cdd:cd16377    69 LETQLILAKDLGYISEEEFEELLELLEEIGKMLNGLIKS 107
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 34-108 2.55e-05

23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes. It folds into an anti-parallel four-helix bundle and forms homopentamers.


Pssm-ID: 461698  Cd Length: 106  Bit Score: 40.14  E-value: 2.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812  34 IWQRCEDLILEILE----------YIL-----------------GASQLSKIEKLPILQKASTKLNLLRVFLRLCKDTKV 86
Cdd:pfam05635   5 VWQKAMELALEIYKltkkfpkeekYGLtsqirraavsipaniaeGYGRRSKKDFIRFLSIARGSLAELETQLELAKDLGY 84

                          90       100
                  ....*....|....*....|..
gi 1276961812  87 LDSKKYIRLEQNVDEIGRMLGG 108
Cdd:pfam05635  85 ISEEEYEELLKEIEEISKMLNG 106
TIGR02436 TIGR02436
four helix bundle protein; This family describes a protein of unknown function whose structure ...
 74-114 7.28e-04

four helix bundle protein; This family describes a protein of unknown function whose structure is a bundle of four long alpha helices. Some of the first members of this family were found encoded in the (atypically large) intervening sequence (IVS) of Leptospira 23S RNA, a region often present in the rRNA gene and removed during rRNA processing without re-ligation. However, this location is not conserved, and naming this protein as a 23S RNA protein is both confusing and inaccurate.


Pssm-ID: 274132  Cd Length: 108  Bit Score: 36.30  E-value: 7.28e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1276961812  74 LRVFLRLCKDTKVLDSKKYIRLEQNVDEIGRMLGGWIKSTR 114
Cdd:TIGR02436  68 TETQLELAKDLGYIDEEQYEELLEELEEIIKMLNGLIKSLK 108
Avd_IVP_like cd16375
proteins similar to the diversity-generating retroelement protein bAvd; A superfamily of ...
 8-110 4.43e-03

proteins similar to the diversity-generating retroelement protein bAvd; A superfamily of four-helix bundles that form homopentamers, including the bacterial accessory variability determinant (bAvd) protein and a family of functionally uncharacterized bacterial proteins, some of which are encoded by an atypically large intervening sequence present within some 23S rRNA genes.


Pssm-ID: 319867  Cd Length: 103  Bit Score: 34.19  E-value: 4.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1276961812   8 IFKKTYELYKEFYGFRNTVSKQDRYTIWQRCEDLILEILEYILGASQLSKIEKLPIlqkASTKLNLLRVFLRLCKDTKVL 87
Cdd:cd16375     1 AVEDSEELIEMLYPITESFPDQEHGGAREQFLKALLGQPELFAEGAARNQSRFLSA---ADAGLAELDFQLQFAAGIGAS 77

                          90       100
                  ....*....|....*....|...
gi 1276961812  88 DSKKYIRLEQNVDEIGRMLGGWI 110
Cdd:cd16375    78 TPEDDESAQRLIAEVFAILGALI 100
 
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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