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Conserved domains on  [gi|1958778105|ref|XP_038966540|]
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zinc finger CCHC domain-containing protein 17 isoform X1 [Rattus norvegicus]

Protein Classification

S1 domain-containing protein( domain architecture ID 237)

S1 domain-containing protein may bind RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1-62 1.55e-36

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05686:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 73  Bit Score: 122.59  E-value: 1.55e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   1 MVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 62
Cdd:cd05686    13 SVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
 
Name Accession Description Interval E-value
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1-62 1.55e-36

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 122.59  E-value: 1.55e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   1 MVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 62
Cdd:cd05686    13 SVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-64 3.77e-14

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 70.07  E-value: 3.77e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:COG0539   200 ITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 2-66 1.85e-13

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 68.54  E-value: 1.85e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958778105   2 VTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 66
Cdd:PRK11824  632 IVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-61 7.83e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 54.74  E-value: 7.83e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105   2 VTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 61
Cdd:TIGR00717 198 ITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
2-61 2.10e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.52  E-value: 2.10e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105    2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 61
Cdd:smart00316  13 ITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 2-63 4.76e-06

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 43.04  E-value: 4.76e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   2 VTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSM 63
Cdd:pfam00575  14 VTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL--KVDKDRRRIILSI 72
 
Name Accession Description Interval E-value
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1-62 1.55e-36

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 122.59  E-value: 1.55e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   1 MVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 62
Cdd:cd05686    13 SVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 2-71 2.88e-14

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 65.34  E-value: 2.88e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGC--RKQGLVHRTHMSS-CRVDKPSEIVDVGDKVWVKLIGreMKNDRIkvSLSMKVVNQGTG 71
Cdd:cd05684    11 IMDFGCFVQLEGLkgRKEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVIS--IQNGKI--SLSMKDVDQDTG 79
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-64 3.77e-14

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 70.07  E-value: 3.77e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:COG0539   200 ITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 2-66 1.85e-13

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 68.54  E-value: 1.85e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958778105   2 VTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 66
Cdd:PRK11824  632 IVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 2-63 1.59e-12

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 60.25  E-value: 1.59e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSM 63
Cdd:cd04472    11 IKDFGAFVEIlPG--KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIE---VDDRGRISLSR 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-64 2.52e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 65.19  E-value: 2.52e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 64
Cdd:PRK06299  212 ITDYGAFVDLGGV--DGLLHITDISWKRVNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-64 5.82e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 63.74  E-value: 5.82e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:PRK06676  203 LTDFGAFVDIGGV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERI--SLSLK 261
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 2-62 8.17e-12

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 58.41  E-value: 8.17e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLS 62
Cdd:cd05688    12 ITDFGAFVDLGGV--DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 2-64 1.20e-11

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 58.07  E-value: 1.20e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 64
Cdd:cd05692    11 LKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID---ARGRISLSIK 69
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-64 2.70e-11

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 61.60  E-value: 2.70e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958778105   2 VTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 64
Cdd:COG0539   285 LTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVL--DIDPEERRISLSIK 345
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 2-60 5.62e-11

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 56.47  E-value: 5.62e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958778105   2 VTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 60
Cdd:cd05685    11 VTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 2-60 1.00e-10

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 55.46  E-value: 1.00e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 60
Cdd:cd00164     8 ITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
2-72 1.70e-10

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 59.65  E-value: 1.70e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   2 VTDYGAFIKIpGCrKQ-GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMKVVNQGTGK 72
Cdd:COG2183   652 VTDFGAFVDI-GV-HQdGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRI--SLSMKLDDEAGAA 719
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-64 2.00e-09

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 56.49  E-value: 2.00e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIG--REMKndriKVSLSMK 64
Cdd:PRK00087  488 LTDFGAFVDIGGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDidKENK----KLSLSLK 546
rpsA PRK13806
30S ribosomal protein S1; Provisional
 5-64 2.03e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 56.66  E-value: 2.03e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   5 YGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKL--IGREMKNDRIKVSLSMK 64
Cdd:PRK13806  216 FGAFVELaPGV--EGMVHISELSWSRVQKADEAVSVGDTVRVKVlgIERAKKGKGLRISLSIK 276
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 2-106 2.68e-09

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 53.26  E-value: 2.68e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMkvvnqgtgKDLDPNNvii 81
Cdd:COG1098    16 ITPFGAFVELPE-GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID---EDGKISLSI--------KQAEEKP--- 80

                          90       100
                  ....*....|....*....|....*
gi 1958778105  82 EQEERRRRSFQDYTGQKiTLEAVLN 106
Cdd:COG1098    81 KRPPRPRRNSRPKAGFE-SFEDKLS 104
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-61 7.83e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 54.74  E-value: 7.83e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105   2 VTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 61
Cdd:TIGR00717 198 ITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 2-64 8.98e-09

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 50.79  E-value: 8.98e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 64
Cdd:cd05708    13 VEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVL--KIDAEKKRISLGLK 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
4-67 1.21e-08

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 54.18  E-value: 1.21e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958778105   4 DYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMKVVN 67
Cdd:PRK00087  575 PFGAFVELePGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKIL--EVDPEEKRIRLSIKEVE 635
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 3-94 1.39e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 53.73  E-value: 1.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105   3 TDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMkvvnqgtgKDLDPNNvii 81
Cdd:PRK06676  289 TDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRI--SLSI--------KALEEAP--- 353

                          90
                  ....*....|...
gi 1958778105  82 EQEERRRRSFQDY 94
Cdd:PRK06676  354 AEEEDRREEYRQY 366
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
2-61 2.10e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.52  E-value: 2.10e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105    2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 61
Cdd:smart00316  13 ITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 2-64 3.95e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 52.74  E-value: 3.95e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMK 64
Cdd:PRK07899  219 IVNFGAFVDLGGV--DGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM--DRERVSLSLK 277
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-64 6.39e-08

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 52.03  E-value: 6.39e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958778105   3 TDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLigREMKNDRIKVSLSMK 64
Cdd:PRK13806  304 APFGAFVEIlPGI--EGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKI--KDIDPAKRRISLSLR 363
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 5-76 5.06e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 49.27  E-value: 5.06e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958778105   5 YGAFIKIP-GCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMKVVNQG---TGKDLDP 76
Cdd:PRK07899  307 FGAFVRVEeGI--EGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDL--ERRRISLSLKQANEGvtpESEDFDP 378
PRK05807 PRK05807
RNA-binding protein S1;
2-93 2.55e-06

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 45.51  E-value: 2.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105   2 VTDYGAFIKIPGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMKVVNQgTGKDLDPNNVII 81
Cdd:PRK05807   16 ITNFGAFVEVEG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID---DNGKISLSIKQAMK-QKKSVKPAEIDW 89

                          90
                  ....*....|....
gi 1958778105  82 EQEERRRR--SFQD 93
Cdd:PRK05807   90 QKEKNKNNngNFED 103
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-64 3.95e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 46.70  E-value: 3.95e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958778105   2 VTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:PRK06299  297 ITDYGAFVELeEGI--EGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRI--SLGLK 357
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 2-63 4.76e-06

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 43.04  E-value: 4.76e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   2 VTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSM 63
Cdd:pfam00575  14 VTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL--KVDKDRRRIILSI 72
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 2-64 1.38e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 45.27  E-value: 1.38e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958778105   2 VTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMkNDRIKVSLSMK 64
Cdd:PLN00207  765 IAPYGAFVEIaPG--REGLCHISELSSNWLAKPEDAFKVGDRIDVKLI--EV-NDKGQLRLSRR 823
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-64 2.12e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.77  E-value: 2.12e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGCRKqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:PRK06299  471 VKDKGAFVELEDGVE-GLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRI--SLSIK 530
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-61 3.99e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 43.57  E-value: 3.99e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958778105   2 VTDYGAFIKIpGCRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 61
Cdd:TIGR00717 283 LTDYGVFVEI-EEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 5-85 4.84e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 43.25  E-value: 4.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958778105   5 YGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMKVVNQGTGKDL-DPNNVIIEQ 83
Cdd:PRK07400  210 YGAFIDIGGV--SGLLHISEISHEHIETPHSVFNVNDEMKVMII--DLDAERGRISLSTKQLEPEPGDMLkDPQKVFDKA 285


                  ..
gi 1958778105  84 EE 85
Cdd:PRK07400  286 EE 287
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-64 6.98e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 43.18  E-value: 6.98e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDriKVSLSMK 64
Cdd:TIGR00717 457 IKDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNR--KVSLSVK 516
PRK08059 PRK08059
general stress protein 13; Validated
 4-64 2.05e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 39.64  E-value: 2.05e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958778105   4 DYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:PRK08059   20 PYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKI--SLSIR 77
PRK08582 PRK08582
RNA-binding protein S1;
2-64 5.58e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 38.86  E-value: 5.58e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 64
Cdd:PRK08582   16 ITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE---DDGKIGLSIK 74
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 2-61 5.82e-04

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 37.09  E-value: 5.82e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 61
Cdd:cd05690    11 ITDFGIFVGLDG-GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVL--NIDVERERISL 68
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 2-61 8.07e-04

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 36.79  E-value: 8.07e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958778105   2 VTDYGAFIKI-PGCrkQGLVHRTHMSSCRVD-KPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 61
Cdd:cd05689    14 LTDYGCFVELeEGV--EGLVHVSEMDWTNKNiHPSKVVSLGDEVEVMVL--DIDEERRRISL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-64 1.08e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 39.38  E-value: 1.08e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958778105   2 VTDYGAFIKIPGCrKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 64
Cdd:PRK06299  384 ITDFGAFVGLEGG-IDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI--SLGIK 444
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-61 5.11e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 37.38  E-value: 5.11e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVD---VGDKVWVKLIGREMKNDRIKVSL 61
Cdd:PRK12269  763 VTDFGIFVRVPG-GVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNVKDRKVAFSV 824
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-67 5.30e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 37.38  E-value: 5.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCR-VDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVN 67
Cdd:PRK12269  589 IADFGAFIELAE-GIEGLAHISEFSWVKkTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN 654
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-51 5.91e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 37.16  E-value: 5.91e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958778105   2 VTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGRE 51
Cdd:PRK06676   28 VEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-60 9.70e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 36.46  E-value: 9.70e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958778105   2 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 60
Cdd:PRK00087  313 VNENEVFVDVGY-KSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLS 370
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 3-61 9.97e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 36.61  E-value: 9.97e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958778105   3 TDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 61
Cdd:PRK12269  505 TSFGAFIDLGGF--DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561
 
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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