NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|293079|gb|AAA75526|]
View 

unknown [Leptospira weilii serovar Sarmin]

Protein Classification

four helix bundle protein( domain architecture ID 10528985)

uncharacterized four helix bundle protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 8-115 3.17e-32

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: 109.47  E-value: 3.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079       8 EDFDVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRY 87
Cdd:pfam05635   1 EDLEVWQKAMELALEIYKLTKKFPKEEKYGLTSQIRRAAVSIPANIAEGYGRR--SKKDFIRFLSIARGSLAELETQLEL 78

                          90       100
                  ....*....|....*....|....*...
gi 293079      88 SKDLGYITEDQYSEWSDECLQIAKILSK 115
Cdd:pfam05635  79 AKDLGYISEEEYEELLKEIEEISKMLNG 106
 
Name Accession Description Interval E-value
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 8-115 3.17e-32

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: 109.47  E-value: 3.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079       8 EDFDVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRY 87
Cdd:pfam05635   1 EDLEVWQKAMELALEIYKLTKKFPKEEKYGLTSQIRRAAVSIPANIAEGYGRR--SKKDFIRFLSIARGSLAELETQLEL 78

                          90       100
                  ....*....|....*....|....*...
gi 293079      88 SKDLGYITEDQYSEWSDECLQIAKILSK 115
Cdd:pfam05635  79 AKDLGYISEEEYEELLKEIEEISKMLNG 106
23S_rRNA_IVP_like cd16377
23S rRNA-intervening sequence protein and similar proteins; A family of functionally ...
 11-116 4.80e-32

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: 109.02  E-value: 4.80e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079    11 DVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRYSKD 90
Cdd:cd16377   1 IVWQKAHELVLEIYKLTKKFPKEERYGLTSQIRRAAVSIPSNIAEGFGRR--SKKEFLRFLYIARGSLAELETQLILAKD 78

                        90       100
                ....*....|....*....|....*.
gi 293079    91 LGYITEDQYSEWSDECLQIAKILSKL 116
Cdd:cd16377  79 LGYISEEEFEELLELLEEIGKMLNGL 104
PRK12275 PRK12275
hypothetical protein; Reviewed
 5-116 5.27e-32

hypothetical protein; Reviewed


Pssm-ID: 183395  Cd Length: 116  Bit Score: 109.18  E-value: 5.27e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079      5 KRIEDFDVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALW 84
Cdd:PRK12275   2 MDFEDLDVWKRSMKLAIEIYKLTKLFPDEERYGLTSQLRRAAVSIPSNIAEGYGRE--SKKDFIRFLYIALGSLAELETQ 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 293079     85 LRYSKDLGYITEDQYSEWSDECLQIAKILSKL 116
Cdd:PRK12275  80 LYIAKELGYITKEQYESILQEYDEIAKMLNGL 111
TIGR02436 TIGR02436
four helix bundle protein; This family describes a protein of unknown function whose structure ...
 12-116 9.62e-31

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: 105.64  E-value: 9.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079      12 VFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRYSKDL 91
Cdd:TIGR02436   1 VWQKAMDLALEIYKLTKTFPKEELYGLTSQIRRAATSIPANIAEGYGRR--SKKDFIRFLSIALGSLAETETQLELAKDL 78

                          90       100
                  ....*....|....*....|....*
gi 293079      92 GYITEDQYSEWSDECLQIAKILSKL 116
Cdd:TIGR02436  79 GYIDEEQYEELLEELEEIIKMLNGL 103
 
Name Accession Description Interval E-value
23S_rRNA_IVP pfam05635
23S rRNA-intervening sequence protein; This family consists of bacterial proteins encoded ...
 8-115 3.17e-32

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: 109.47  E-value: 3.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079       8 EDFDVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRY 87
Cdd:pfam05635   1 EDLEVWQKAMELALEIYKLTKKFPKEEKYGLTSQIRRAAVSIPANIAEGYGRR--SKKDFIRFLSIARGSLAELETQLEL 78

                          90       100
                  ....*....|....*....|....*...
gi 293079      88 SKDLGYITEDQYSEWSDECLQIAKILSK 115
Cdd:pfam05635  79 AKDLGYISEEEYEELLKEIEEISKMLNG 106
23S_rRNA_IVP_like cd16377
23S rRNA-intervening sequence protein and similar proteins; A family of functionally ...
 11-116 4.80e-32

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: 109.02  E-value: 4.80e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079    11 DVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRYSKD 90
Cdd:cd16377   1 IVWQKAHELVLEIYKLTKKFPKEERYGLTSQIRRAAVSIPSNIAEGFGRR--SKKEFLRFLYIARGSLAELETQLILAKD 78

                        90       100
                ....*....|....*....|....*.
gi 293079    91 LGYITEDQYSEWSDECLQIAKILSKL 116
Cdd:cd16377  79 LGYISEEEFEELLELLEEIGKMLNGL 104
PRK12275 PRK12275
hypothetical protein; Reviewed
 5-116 5.27e-32

hypothetical protein; Reviewed


Pssm-ID: 183395  Cd Length: 116  Bit Score: 109.18  E-value: 5.27e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079      5 KRIEDFDVFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALW 84
Cdd:PRK12275   2 MDFEDLDVWKRSMKLAIEIYKLTKLFPDEERYGLTSQLRRAAVSIPSNIAEGYGRE--SKKDFIRFLYIALGSLAELETQ 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 293079     85 LRYSKDLGYITEDQYSEWSDECLQIAKILSKL 116
Cdd:PRK12275  80 LYIAKELGYITKEQYESILQEYDEIAKMLNGL 111
TIGR02436 TIGR02436
four helix bundle protein; This family describes a protein of unknown function whose structure ...
 12-116 9.62e-31

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: 105.64  E-value: 9.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079      12 VFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGFAKQnfSKREFKKYLIIAIGSANESALWLRYSKDL 91
Cdd:TIGR02436   1 VWQKAMDLALEIYKLTKTFPKEELYGLTSQIRRAATSIPANIAEGYGRR--SKKDFIRFLSIALGSLAETETQLELAKDL 78

                          90       100
                  ....*....|....*....|....*
gi 293079      92 GYITEDQYSEWSDECLQIAKILSKL 116
Cdd:TIGR02436  79 GYIDEEQYEELLEELEEIIKMLNGL 103
Avd_like cd16376
diversity-generating retroelement protein bAvd and similar proteins; The bacterial accessory ...
 12-113 1.79e-05

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: 40.60  E-value: 1.79e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079    12 VFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGfakqNFSKREFKK-YLIIAIGSANESALWLRYSKD 90
Cdd:cd16376   1 IYKKTYDLLKYLYPILKKFPKSERYTLGQRIENLALDLLELIIEA----NKSPKREKLpLLREADVKLELLKFLLRLAYE 76

                        90       100
                ....*....|....*....|...
gi 293079    91 LGYITEDQYSEWSDECLQIAKIL 113
Cdd:cd16376  77 LKLISNKKYEVLSEKLDEIGKML 99
Avd_IVP_like cd16375
proteins similar to the diversity-generating retroelement protein bAvd; A superfamily of ...
 12-113 7.04e-05

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: 39.20  E-value: 7.04e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 293079    12 VFNRAYALSLKIDKISLEMPKFEQLDLANQLRRSSKSICSNFAEGfakqnfSKREFKKYLIIAIGSANESALWLRYSKDL 91
Cdd:cd16375   1 AVEDSEELIEMLYPITESFPDQEHGGAREQFLKALLGQPELFAEG------AARNQSRFLSAADAGLAELDFQLQFAAGI 74

                        90       100
                ....*....|....*....|....*
gi 293079    92 GYIT---EDQYSEWSDECLQIAKIL 113
Cdd:cd16375  75 GASTpedDESAQRLIAEVFAILGAL 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH