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Conserved domains on  [gi|334188539|ref|NP_200927|]
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putative endonuclease or glycosyl hydrolase with C2H2-type zinc finger domain-containing protein [Arabidopsis thaliana]

Protein Classification

C2H2-type zinc finger protein( domain architecture ID 11587160)

Cys2His2 (C2H2)-type zinc finger protein may be involved in transcriptional regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_limkain_b1_N_like cd10910
N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ...
 12-136 1.92e-60

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


:

Pssm-ID: 350234  Cd Length: 126  Bit Score: 201.69  E-value: 1.92e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539  12 KTSVWWDIENCEVPRGWDAHVIALNVSSSLLKMNYCGPVSISAYGDTNLIPLHHQQALSSTGVALNHIPAGVKDASDKKI 91
Cdd:cd10910    1 KTGVFWDIENCPVPDGYDARRVGPNIRRALRKLGYSGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKKI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 334188539  92 LVDMLLWAIDNPAPANLLLISGD-RDFSNALHQLRMRRYNILLAQP 136
Cdd:cd10910   81 LVDMLLWALDNPPPANIMLISGDvRDFAYALSRLRSRGYNVLLAYP 126
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 294-328 2.92e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


:

Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 44.55  E-value: 2.92e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 334188539   294 VEPLLCKVCQISFTNNDTYKNHTYGKKHRNNLELQ 328
Cdd:smart00451   1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 701-724 7.78e-06

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


:

Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 43.25  E-value: 7.78e-06
                          10        20
                  ....*....|....*....|....
gi 334188539  701 WCQVCQISCNSKVAFASHTYGKKH 724
Cdd:pfam12874   2 YCELCNVTFNSESQLKSHLQGKKH 25
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 368-392 8.09e-06

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


:

Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 43.25  E-value: 8.09e-06
                          10        20
                  ....*....|....*....|....*
gi 334188539  368 FVCLMCNVVCQSQIVFNSHLRGKKH 392
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 468-499 3.70e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


:

Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.77  E-value: 3.70e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 334188539   468 KYICRMCNVGCHSPIVFETHLRGQKHAANLNQ 499
Cdd:smart00451   3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34
PRP11 super family cl25587
Splicing factor 3a, subunit 2 [RNA processing and modification];
412-578 3.90e-04

Splicing factor 3a, subunit 2 [RNA processing and modification];


The actual alignment was detected with superfamily member COG5246:

Pssm-ID: 227571 [Multi-domain]  Cd Length: 222  Bit Score: 43.12  E-value: 3.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539 412 GVGEKEQPSETVAELQLQSQKAQEKQvlvdskKLPEKGDEVKGQPKEMtalRNASAKYICRMCNVGCHSPIVFETHLRGQ 491
Cdd:COG5246    6 RGGSKTGGGGTASEIKKNKKRRSRQL------LLEAYGQDLMDDPYLS---KNHTGKYVCLLCKTKHLTEMSYVKHREGK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539 492 KHAANLnqSKDQALiDSKKLQEKGFGEKEQPRETIVE----------PQLQSQNAQENSKCFEKHVVMVNQSEVLINA-- 559
Cdd:COG5246   77 KHKENS--SRRSEE-KSSLGRENQTTHDFRQQQKIIEakqslkrsgiPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEmp 153

                        170       180       190
                 ....*....|....*....|....*....|...
gi 334188539 560 -----SKLEEKD-AQEK--------AQPIESIA 578
Cdd:COG5246  154 qyrivSSLEQNVeEYDEsfrylvfaCEPYENIA 186
 
Name Accession Description Interval E-value
PIN_limkain_b1_N_like cd10910
N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ...
 12-136 1.92e-60

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350234  Cd Length: 126  Bit Score: 201.69  E-value: 1.92e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539  12 KTSVWWDIENCEVPRGWDAHVIALNVSSSLLKMNYCGPVSISAYGDTNLIPLHHQQALSSTGVALNHIPAGVKDASDKKI 91
Cdd:cd10910    1 KTGVFWDIENCPVPDGYDARRVGPNIRRALRKLGYSGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKKI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 334188539  92 LVDMLLWAIDNPAPANLLLISGD-RDFSNALHQLRMRRYNILLAQP 136
Cdd:cd10910   81 LVDMLLWALDNPPPANIMLISGDvRDFAYALSRLRSRGYNVLLAYP 126
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 12-147 1.49e-28

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 111.61  E-value: 1.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539   12 KTSVWWDIENCEVPRGWDAHVIALNVSSsllkmnYCGPVSISAYGDTNLIPLHH-QQALSSTGVALNHIPAGV-KDASDK 89
Cdd:pfam01936   1 RVAVFIDGENCPLPDGVDYRKVLEEIRS------GGEVVRARAYGNWGDPDLRKfPDALSSTGIPVQHKPLTKgKNAVDV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539   90 KILVDMLLWAIDNPaPANLLLISGDRDFSNALHQLRMR--RYNILLAQPPRASVPLVAAA 147
Cdd:pfam01936  75 GLAVDALELAYDNN-PDTFVLVSGDGDFAPLLERLRERgkRVEVLGAEEPSTSDALINAA 133
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 294-328 2.92e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 44.55  E-value: 2.92e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 334188539   294 VEPLLCKVCQISFTNNDTYKNHTYGKKHRNNLELQ 328
Cdd:smart00451   1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 701-724 7.78e-06

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 43.25  E-value: 7.78e-06
                          10        20
                  ....*....|....*....|....
gi 334188539  701 WCQVCQISCNSKVAFASHTYGKKH 724
Cdd:pfam12874   2 YCELCNVTFNSESQLKSHLQGKKH 25
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 368-392 8.09e-06

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 43.25  E-value: 8.09e-06
                          10        20
                  ....*....|....*....|....*
gi 334188539  368 FVCLMCNVVCQSQIVFNSHLRGKKH 392
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 701-731 8.43e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 43.40  E-value: 8.43e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 334188539   701 WCQVCQISCNSKVAFASHTYGKKHRQNLESQ 731
Cdd:smart00451   5 YCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 299-321 3.35e-05

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 41.33  E-value: 3.35e-05
                          10        20
                  ....*....|....*....|...
gi 334188539  299 CKVCQISFTNNDTYKNHTYGKKH 321
Cdd:pfam12874   3 CELCNVTFNSESQLKSHLQGKKH 25
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 468-499 3.70e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.77  E-value: 3.70e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 334188539   468 KYICRMCNVGCHSPIVFETHLRGQKHAANLNQ 499
Cdd:smart00451   3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34
PRP11 COG5246
Splicing factor 3a, subunit 2 [RNA processing and modification];
412-578 3.90e-04

Splicing factor 3a, subunit 2 [RNA processing and modification];


Pssm-ID: 227571 [Multi-domain]  Cd Length: 222  Bit Score: 43.12  E-value: 3.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539 412 GVGEKEQPSETVAELQLQSQKAQEKQvlvdskKLPEKGDEVKGQPKEMtalRNASAKYICRMCNVGCHSPIVFETHLRGQ 491
Cdd:COG5246    6 RGGSKTGGGGTASEIKKNKKRRSRQL------LLEAYGQDLMDDPYLS---KNHTGKYVCLLCKTKHLTEMSYVKHREGK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539 492 KHAANLnqSKDQALiDSKKLQEKGFGEKEQPRETIVE----------PQLQSQNAQENSKCFEKHVVMVNQSEVLINA-- 559
Cdd:COG5246   77 KHKENS--SRRSEE-KSSLGRENQTTHDFRQQQKIIEakqslkrsgiPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEmp 153

                        170       180       190
                 ....*....|....*....|....*....|...
gi 334188539 560 -----SKLEEKD-AQEK--------AQPIESIA 578
Cdd:COG5246  154 qyrivSSLEQNVeEYDEsfrylvfaCEPYENIA 186
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 368-398 6.81e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.00  E-value: 6.81e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 334188539   368 FVCLMCNVVCQSQIVFNSHLRGKKHANMLSQ 398
Cdd:smart00451   4 FYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 469-493 2.43e-03

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 36.32  E-value: 2.43e-03
                          10        20
                  ....*....|....*....|....*
gi 334188539  469 YICRMCNVGCHSPIVFETHLRGQKH 493
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25
 
Name Accession Description Interval E-value
PIN_limkain_b1_N_like cd10910
N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human ...
 12-136 1.92e-60

N-terminal LabA-like PIN domain of limkain b1 and similar proteins; Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350234  Cd Length: 126  Bit Score: 201.69  E-value: 1.92e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539  12 KTSVWWDIENCEVPRGWDAHVIALNVSSSLLKMNYCGPVSISAYGDTNLIPLHHQQALSSTGVALNHIPAGVKDASDKKI 91
Cdd:cd10910    1 KTGVFWDIENCPVPDGYDARRVGPNIRRALRKLGYSGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKKI 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 334188539  92 LVDMLLWAIDNPAPANLLLISGD-RDFSNALHQLRMRRYNILLAQP 136
Cdd:cd10910   81 LVDMLLWALDNPPPANIMLISGDvRDFAYALSRLRSRGYNVLLAYP 126
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 12-147 1.49e-28

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 111.61  E-value: 1.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539   12 KTSVWWDIENCEVPRGWDAHVIALNVSSsllkmnYCGPVSISAYGDTNLIPLHH-QQALSSTGVALNHIPAGV-KDASDK 89
Cdd:pfam01936   1 RVAVFIDGENCPLPDGVDYRKVLEEIRS------GGEVVRARAYGNWGDPDLRKfPDALSSTGIPVQHKPLTKgKNAVDV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539   90 KILVDMLLWAIDNPaPANLLLISGDRDFSNALHQLRMR--RYNILLAQPPRASVPLVAAA 147
Cdd:pfam01936  75 GLAVDALELAYDNN-PDTFVLVSGDGDFAPLLERLRERgkRVEVLGAEEPSTSDALINAA 133
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 294-328 2.92e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 44.55  E-value: 2.92e-06
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 334188539   294 VEPLLCKVCQISFTNNDTYKNHTYGKKHRNNLELQ 328
Cdd:smart00451   1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 701-724 7.78e-06

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 43.25  E-value: 7.78e-06
                          10        20
                  ....*....|....*....|....
gi 334188539  701 WCQVCQISCNSKVAFASHTYGKKH 724
Cdd:pfam12874   2 YCELCNVTFNSESQLKSHLQGKKH 25
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 368-392 8.09e-06

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 43.25  E-value: 8.09e-06
                          10        20
                  ....*....|....*....|....*
gi 334188539  368 FVCLMCNVVCQSQIVFNSHLRGKKH 392
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 701-731 8.43e-06

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 43.40  E-value: 8.43e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 334188539   701 WCQVCQISCNSKVAFASHTYGKKHRQNLESQ 731
Cdd:smart00451   5 YCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 299-321 3.35e-05

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 41.33  E-value: 3.35e-05
                          10        20
                  ....*....|....*....|...
gi 334188539  299 CKVCQISFTNNDTYKNHTYGKKH 321
Cdd:pfam12874   3 CELCNVTFNSESQLKSHLQGKKH 25
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 468-499 3.70e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.77  E-value: 3.70e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 334188539   468 KYICRMCNVGCHSPIVFETHLRGQKHAANLNQ 499
Cdd:smart00451   3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34
PRP11 COG5246
Splicing factor 3a, subunit 2 [RNA processing and modification];
412-578 3.90e-04

Splicing factor 3a, subunit 2 [RNA processing and modification];


Pssm-ID: 227571 [Multi-domain]  Cd Length: 222  Bit Score: 43.12  E-value: 3.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539 412 GVGEKEQPSETVAELQLQSQKAQEKQvlvdskKLPEKGDEVKGQPKEMtalRNASAKYICRMCNVGCHSPIVFETHLRGQ 491
Cdd:COG5246    6 RGGSKTGGGGTASEIKKNKKRRSRQL------LLEAYGQDLMDDPYLS---KNHTGKYVCLLCKTKHLTEMSYVKHREGK 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539 492 KHAANLnqSKDQALiDSKKLQEKGFGEKEQPRETIVE----------PQLQSQNAQENSKCFEKHVVMVNQSEVLINA-- 559
Cdd:COG5246   77 KHKENS--SRRSEE-KSSLGRENQTTHDFRQQQKIIEakqslkrsgiPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEmp 153

                        170       180       190
                 ....*....|....*....|....*....|...
gi 334188539 560 -----SKLEEKD-AQEK--------AQPIESIA 578
Cdd:COG5246  154 qyrivSSLEQNVeEYDEsfrylvfaCEPYENIA 186
PIN_LabA-like cd06167
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 15-133 4.95e-04

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. This family also includes the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family.


Pssm-ID: 350201  Cd Length: 113  Bit Score: 40.86  E-value: 4.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334188539  15 VWWDIENCEVPRGwdahvialNVSSSLLKMNYCGPVSIsAYGDTNLIPLhHQQALSSTGVALNHIPAGVKDASDKKILVD 94
Cdd:cd06167    2 VLVDADNCSNGFG--------ALILRRYAGLFLQMGFE-KYANINAQPL-LVPPSNNRGFTVIRVAAKRKDAADVALVRQ 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 334188539  95 mLLWAIDNPAPANLLLISGD-RDFSNALHQLRMRRYNILL 133
Cdd:cd06167   72 -AGRLAYTGAPDTVVLVSGDkLDFSDLIEKAKEAGLNVIV 110
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 368-398 6.81e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 38.00  E-value: 6.81e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 334188539   368 FVCLMCNVVCQSQIVFNSHLRGKKHANMLSQ 398
Cdd:smart00451   4 FYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34
zf-met pfam12874
Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found ...
 469-493 2.43e-03

Zinc-finger of C2H2 type; This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding.


Pssm-ID: 463736 [Multi-domain]  Cd Length: 25  Bit Score: 36.32  E-value: 2.43e-03
                          10        20
                  ....*....|....*....|....*
gi 334188539  469 YICRMCNVGCHSPIVFETHLRGQKH 493
Cdd:pfam12874   1 FYCELCNVTFNSESQLKSHLQGKKH 25
zf-C2H2_jaz pfam12171
Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, ...
 367-392 9.98e-03

Zinc-finger double-stranded RNA-binding; This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization.


Pssm-ID: 432381 [Multi-domain]  Cd Length: 27  Bit Score: 34.45  E-value: 9.98e-03
                          10        20
                  ....*....|....*....|....*.
gi 334188539  367 EFVCLMCNVVCQSQIVFNSHLRGKKH 392
Cdd:pfam12171   1 QFYCVLCDKYFKSENALQNHLKSKKH 26
 
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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