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Conserved domains on  [gi|544940217|ref|WP_021348548|]
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MULTISPECIES: four helix bundle protein [Elizabethkingia]

Protein Classification

four helix bundle protein( domain architecture ID 11611522)

uncharacterized four helix bundle protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
23S_rRNA_IVP_like cd16377
23S rRNA-intervening sequence protein and similar proteins; A family of functionally ...
 9-115 2.15e-50

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: 155.24  E-value: 2.15e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   9 EVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYDQN 88
Cdd:cd16377    1 IVWQKAHELVLEIYKLTKKFPKEERYGLTSQIRRAAVSIPSNIAEGFGRRSKKEFLRFLYIARGSLAELETQLILAKDLG 80

                         90       100
                 ....*....|....*....|....*..
gi 544940217  89 YISEDELTVVLGKTLICKKLLNGFINY 115
Cdd:cd16377   81 YISEEEFEELLELLEEIGKMLNGLIKS 107
 
Name Accession Description Interval E-value
23S_rRNA_IVP_like cd16377
23S rRNA-intervening sequence protein and similar proteins; A family of functionally ...
 9-115 2.15e-50

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: 155.24  E-value: 2.15e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   9 EVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYDQN 88
Cdd:cd16377    1 IVWQKAHELVLEIYKLTKKFPKEERYGLTSQIRRAAVSIPSNIAEGFGRRSKKEFLRFLYIARGSLAELETQLILAKDLG 80

                         90       100
                 ....*....|....*....|....*..
gi 544940217  89 YISEDELTVVLGKTLICKKLLNGFINY 115
Cdd:cd16377   81 YISEEEFEELLELLEEIGKMLNGLIKS 107
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 7-111 4.85e-44

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: 139.13  E-value: 4.85e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217    7 ELEVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYD 86
Cdd:pfam05635   2 DLEVWQKAMELALEIYKLTKKFPKEEKYGLTSQIRRAAVSIPANIAEGYGRRSKKDFIRFLSIARGSLAELETQLELAKD 81

                          90       100
                  ....*....|....*....|....*
gi 544940217   87 QNYISEDELTVVLGKTLICKKLLNG 111
Cdd:pfam05635  82 LGYISEEEYEELLKEIEEISKMLNG 106
TIGR02436 TIGR02436
four helix bundle protein; This family describes a protein of unknown function whose structure ...
 10-117 7.16e-44

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: 138.76  E-value: 7.16e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   10 VWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYDQNY 89
Cdd:TIGR02436   1 VWQKAMDLALEIYKLTKTFPKEELYGLTSQIRRAATSIPANIAEGYGRRSKKDFIRFLSIALGSLAETETQLELAKDLGY 80

                          90       100
                  ....*....|....*....|....*...
gi 544940217   90 ISEDELTVVLGKTLICKKLLNGFINYYK 117
Cdd:TIGR02436  81 IDEEQYEELLEELEEIIKMLNGLIKSLK 108
PRK12275 PRK12275
hypothetical protein; Reviewed
 5-117 4.76e-40

hypothetical protein; Reviewed


Pssm-ID: 183395  Cd Length: 116  Bit Score: 129.21  E-value: 4.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   5 YTELEVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYIS 84
Cdd:PRK12275   4 FEDLDVWKRSMKLAIEIYKLTKLFPDEERYGLTSQLRRAAVSIPSNIAEGYGRESKKDFIRFLYIALGSLAELETQLYIA 83

                         90       100       110
                 ....*....|....*....|....*....|...
gi 544940217  85 YDQNYISEDELTVVLGKTLICKKLLNGFINYYK 117
Cdd:PRK12275  84 KELGYITKEQYESILQEYDEIAKMLNGLIKKLK 116
 
Name Accession Description Interval E-value
23S_rRNA_IVP_like cd16377
23S rRNA-intervening sequence protein and similar proteins; A family of functionally ...
 9-115 2.15e-50

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: 155.24  E-value: 2.15e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   9 EVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYDQN 88
Cdd:cd16377    1 IVWQKAHELVLEIYKLTKKFPKEERYGLTSQIRRAAVSIPSNIAEGFGRRSKKEFLRFLYIARGSLAELETQLILAKDLG 80

                         90       100
                 ....*....|....*....|....*..
gi 544940217  89 YISEDELTVVLGKTLICKKLLNGFINY 115
Cdd:cd16377   81 YISEEEFEELLELLEEIGKMLNGLIKS 107
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 7-111 4.85e-44

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: 139.13  E-value: 4.85e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217    7 ELEVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYD 86
Cdd:pfam05635   2 DLEVWQKAMELALEIYKLTKKFPKEEKYGLTSQIRRAAVSIPANIAEGYGRRSKKDFIRFLSIARGSLAELETQLELAKD 81

                          90       100
                  ....*....|....*....|....*
gi 544940217   87 QNYISEDELTVVLGKTLICKKLLNG 111
Cdd:pfam05635  82 LGYISEEEYEELLKEIEEISKMLNG 106
TIGR02436 TIGR02436
four helix bundle protein; This family describes a protein of unknown function whose structure ...
 10-117 7.16e-44

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: 138.76  E-value: 7.16e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   10 VWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYISYDQNY 89
Cdd:TIGR02436   1 VWQKAMDLALEIYKLTKTFPKEELYGLTSQIRRAATSIPANIAEGYGRRSKKDFIRFLSIALGSLAETETQLELAKDLGY 80

                          90       100
                  ....*....|....*....|....*...
gi 544940217   90 ISEDELTVVLGKTLICKKLLNGFINYYK 117
Cdd:TIGR02436  81 IDEEQYEELLEELEEIIKMLNGLIKSLK 108
PRK12275 PRK12275
hypothetical protein; Reviewed
 5-117 4.76e-40

hypothetical protein; Reviewed


Pssm-ID: 183395  Cd Length: 116  Bit Score: 129.21  E-value: 4.76e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217   5 YTELEVWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRTANDTIQFLHIARGSLYELETQFYIS 84
Cdd:PRK12275   4 FEDLDVWKRSMKLAIEIYKLTKLFPDEERYGLTSQLRRAAVSIPSNIAEGYGRESKKDFIRFLYIALGSLAELETQLYIA 83

                         90       100       110
                 ....*....|....*....|....*....|...
gi 544940217  85 YDQNYISEDELTVVLGKTLICKKLLNGFINYYK 117
Cdd:PRK12275  84 KELGYITKEQYESILQEYDEIAKMLNGLIKKLK 116
Avd_IVP_like cd16375
proteins similar to the diversity-generating retroelement protein bAvd; A superfamily of ...
 10-89 2.34e-09

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: 50.75  E-value: 2.34e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217  10 VWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEGCGRRtandTIQFLHIARGSLYELETQFYISYDQNY 89
Cdd:cd16375    1 AVEDSEELIEMLYPITESFPDQEHGGAREQFLKALLGQPELFAEGAARN----QSRFLSAADAGLAELDFQLQFAAGIGA 76
Avd_like cd16376
diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory ...
 10-115 8.39e-06

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: 41.37  E-value: 8.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544940217  10 VWQESRKLTNIAYELVQKYPKDELFGITSQIRRSAVSVPANIAEgCGRRTANDTIQFLHIARGSLYELETQFYISYDQNY 89
Cdd:cd16376    1 IYKKTYDLLKYLYPILKKFPKSERYTLGQRIENLALDLLELIIE-ANKSPKREKLPLLREADVKLELLKFLLRLAYELKL 79

                         90       100
                 ....*....|....*....|....*.
gi 544940217  90 ISEDELTVVLGKTLICKKLLNGFINY 115
Cdd:cd16376   80 ISNKKYEVLSEKLDEIGKMLGGWIKS 105
 
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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