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Conserved domains on  [gi|1174747265|gb|OQV15575|]
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putative Meiosis arrest female protein 1 [Hypsibius exemplaris]

Protein Classification

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 ...
 161-283 7.69e-31

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: 118.10  E-value: 7.69e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  161 VAWFWDIENCRVPLNRSASQVVQCLRSKFEHLG--RERDFIVVCDTNKEMKKTIDELNVEQVTVVHVPCISKNAADDKLK 238
Cdd:cd10910      2 TGVFWDIENCPVPDGYDARRVGPNIRRALRKLGysGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKKIL 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1174747265  239 TLMHKYAVTHSPGDWLVLISGD-FNFTTELNVARHeCKLNIVIIHP 283
Cdd:cd10910     82 VDMLLWALDNPPPANIMLISGDvRDFAYALSRLRS-RGYNVLLAYP 126
LabA_like_C super family cl14879
C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved ...
 876-932 7.26e-09

C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains).


The actual alignment was detected with superfamily member cd09978:

Pssm-ID: 472713  Cd Length: 71  Bit Score: 53.45  E-value: 7.26e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1174747265  876 LSRFGGHVVDLLQKHGGSMPLNSFVVCYDQNFEKLK--EDADNGSFLEHLLLSIPGVTI 932
Cdd:cd09978      1 LKTFAPQVHSLLQTHEGTVPLLSFPDCYAAEFSALEvvQEGQGGVPLEHLITCIPGVNI 59
LabA_like_C super family cl14879
C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved ...
 1131-1197 1.61e-07

C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains).


The actual alignment was detected with superfamily member cd09981:

Pssm-ID: 472713  Cd Length: 71  Bit Score: 49.73  E-value: 1.61e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1174747265 1131 AQETFEVLVASPDYRIGFIPYPASYRKLFGRELRNRDYGCDKLMDVCALIEDVIKVEVVGKERFVVL 1197
Cdd:cd09981      5 SKEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVLECGEEKYLQL 71
PRK12323 super family cl46901
DNA polymerase III subunit gamma/tau;
422-536 1.21e-05

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK12323:

Pssm-ID: 481241 [Multi-domain]  Cd Length: 700  Bit Score: 49.87  E-value: 1.21e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  422 PLPTSHSASHFPIVAAQQPFISPPLHHSASGPLSMLTAGVPRAVIRQtfaSPPIQPGSASGPRPysisntAGPSLSEPRC 501
Cdd:PRK12323   392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQ---ASARGPGGAPAPAP------APAAAPAAAA 462

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1174747265  502 QVPMAGPIRPPNGKAHMPDVSPMAPVARAAPFAPP 536
Cdd:PRK12323   463 RPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP 497
LabA_like_C super family cl14879
C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved ...
 971-1035 7.41e-05

C-terminal domain of LabA_like proteins; This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains).


The actual alignment was detected with superfamily member cd09979:

Pssm-ID: 472713  Cd Length: 72  Bit Score: 42.07  E-value: 7.41e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174747265  971 VKDFLALRPRSAVTITDFPATFHRHCGATCDVRGWDRSRLVRVLRTVSKDVEVIGVEAEQVVTLT 1035
Cdd:cd09979      8 VIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 679-752 1.06e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


:

Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 38.80  E-value: 1.06e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174747265  679 VYFLNLPSDMDQTELYgeliMLLDQITSVDEMSLYDGASNTSR-YAHVKVTQPNLALILVKHFNGATFAGRTLEV 752
Cdd:cd00590      1 LFVGNLPPDTTEEDLR----ELFSKFGEVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
 
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 ...
 161-283 7.69e-31

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: 118.10  E-value: 7.69e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  161 VAWFWDIENCRVPLNRSASQVVQCLRSKFEHLG--RERDFIVVCDTNKEMKKTIDELNVEQVTVVHVPCISKNAADDKLK 238
Cdd:cd10910      2 TGVFWDIENCPVPDGYDARRVGPNIRRALRKLGysGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKKIL 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1174747265  239 TLMHKYAVTHSPGDWLVLISGD-FNFTTELNVARHeCKLNIVIIHP 283
Cdd:cd10910     82 VDMLLWALDNPPPANIMLISGDvRDFAYALSRLRS-RGYNVLLAYP 126
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 161-298 1.90e-13

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: 68.85  E-value: 1.90e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  161 VAWFWDIENCRVPLNRSASQVVQCLRSKfehlGRERDFIVVCD-TNKEMKKTIDELNVEQVTVVHVPCI-SKNAADDKLK 238
Cdd:pfam01936    2 VAVFIDGENCPLPDGVDYRKVLEEIRSG----GEVVRARAYGNwGDPDLRKFPDALSSTGIPVQHKPLTkGKNAVDVGLA 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174747265  239 TLMHKYAVTHSPgDWLVLISGDFNFTTELNVARHE-CKLNIVIIHPENINPGLLSTAKEHY 298
Cdd:pfam01936   78 VDALELAYDNNP-DTFVLVSGDGDFAPLLERLRERgKRVEVLGAEEPSTSDALINAADRFI 137
LOTUS_2_Limkain_b1 cd09978
The second LOTUS domain on Limkain b1(LKAP); The second LOTUS domain on Limkain b1(LKAP): ...
 876-932 7.26e-09

The second LOTUS domain on Limkain b1(LKAP); The second LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization


Pssm-ID: 193592  Cd Length: 71  Bit Score: 53.45  E-value: 7.26e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1174747265  876 LSRFGGHVVDLLQKHGGSMPLNSFVVCYDQNFEKLK--EDADNGSFLEHLLLSIPGVTI 932
Cdd:cd09978      1 LKTFAPQVHSLLQTHEGTVPLLSFPDCYAAEFSALEvvQEGQGGVPLEHLITCIPGVNI 59
LOTUS_5_Limkain_b1 cd09981
The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): ...
 1131-1197 1.61e-07

The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193595  Cd Length: 71  Bit Score: 49.73  E-value: 1.61e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1174747265 1131 AQETFEVLVASPDYRIGFIPYPASYRKLFGRELRNRDYGCDKLMDVCALIEDVIKVEVVGKERFVVL 1197
Cdd:cd09981      5 SKEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVLECGEEKYLQL 71
MARF1_LOTUS pfam19687
MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis ...
 872-932 1.03e-05

MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity).


Pssm-ID: 437519 [Multi-domain]  Cd Length: 211  Bit Score: 48.14  E-value: 1.03e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174747265  872 FRVL-LSRFGGHVVDLLQKHGGSMPLNSFVVCYDQNFEKL--KEDADNGSFLEHLLLSIPGVTI 932
Cdd:pfam19687  122 FVILsLKTFAPQVHSLLQTHEGTVPLLSFPECYAAKFSPLqlGSETMEGVPLEHLITCVPSITI 185
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
422-536 1.21e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 49.87  E-value: 1.21e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  422 PLPTSHSASHFPIVAAQQPFISPPLHHSASGPLSMLTAGVPRAVIRQtfaSPPIQPGSASGPRPysisntAGPSLSEPRC 501
Cdd:PRK12323   392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQ---ASARGPGGAPAPAP------APAAAPAAAA 462

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1174747265  502 QVPMAGPIRPPNGKAHMPDVSPMAPVARAAPFAPP 536
Cdd:PRK12323   463 RPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP 497
LOTUS_3_Limkain_b1 cd09979
The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): ...
 971-1035 7.41e-05

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193593  Cd Length: 72  Bit Score: 42.07  E-value: 7.41e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174747265  971 VKDFLALRPRSAVTITDFPATFHRHCGATCDVRGWDRSRLVRVLRTVSKDVEVIGVEAEQVVTLT 1035
Cdd:cd09979      8 VIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72
OST-HTH pfam12872
OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ...
 1136-1196 1.79e-04

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.


Pssm-ID: 463735  Cd Length: 64  Bit Score: 41.00  E-value: 1.79e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174747265 1136 EVLVASPDYRIGFIPYPASYRKLFGRELRNRDYGCDKLMDvcaLIE---DVIKVEVVGKERFVV 1196
Cdd:pfam12872    4 SLLRSDPDGWASLSELGSEYRKLFGEDFDPRNYGFSKLSD---LLKaipDVFEIEKRGGGGLVV 64
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 679-752 1.06e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 38.80  E-value: 1.06e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174747265  679 VYFLNLPSDMDQTELYgeliMLLDQITSVDEMSLYDGASNTSR-YAHVKVTQPNLALILVKHFNGATFAGRTLEV 752
Cdd:cd00590      1 LFVGNLPPDTTEEDLR----ELFSKFGEVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
 
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 ...
 161-283 7.69e-31

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: 118.10  E-value: 7.69e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  161 VAWFWDIENCRVPLNRSASQVVQCLRSKFEHLG--RERDFIVVCDTNKEMKKTIDELNVEQVTVVHVPCISKNAADDKLK 238
Cdd:cd10910      2 TGVFWDIENCPVPDGYDARRVGPNIRRALRKLGysGPVSITAYGDLSKVPKDVLSELSSSGVSLVHVPHGGKKAADKKIL 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1174747265  239 TLMHKYAVTHSPGDWLVLISGD-FNFTTELNVARHeCKLNIVIIHP 283
Cdd:cd10910     82 VDMLLWALDNPPPANIMLISGDvRDFAYALSRLRS-RGYNVLLAYP 126
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 161-298 1.90e-13

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: 68.85  E-value: 1.90e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  161 VAWFWDIENCRVPLNRSASQVVQCLRSKfehlGRERDFIVVCD-TNKEMKKTIDELNVEQVTVVHVPCI-SKNAADDKLK 238
Cdd:pfam01936    2 VAVFIDGENCPLPDGVDYRKVLEEIRSG----GEVVRARAYGNwGDPDLRKFPDALSSTGIPVQHKPLTkGKNAVDVGLA 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174747265  239 TLMHKYAVTHSPgDWLVLISGDFNFTTELNVARHE-CKLNIVIIHPENINPGLLSTAKEHY 298
Cdd:pfam01936   78 VDALELAYDNNP-DTFVLVSGDGDFAPLLERLRERgKRVEVLGAEEPSTSDALINAADRFI 137
LOTUS_2_Limkain_b1 cd09978
The second LOTUS domain on Limkain b1(LKAP); The second LOTUS domain on Limkain b1(LKAP): ...
 876-932 7.26e-09

The second LOTUS domain on Limkain b1(LKAP); The second LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization


Pssm-ID: 193592  Cd Length: 71  Bit Score: 53.45  E-value: 7.26e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1174747265  876 LSRFGGHVVDLLQKHGGSMPLNSFVVCYDQNFEKLK--EDADNGSFLEHLLLSIPGVTI 932
Cdd:cd09978      1 LKTFAPQVHSLLQTHEGTVPLLSFPDCYAAEFSALEvvQEGQGGVPLEHLITCIPGVNI 59
LOTUS_5_Limkain_b1 cd09981
The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): ...
 1131-1197 1.61e-07

The fifth LOTUS domain on Limkain b1(LKAP); The fifth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193595  Cd Length: 71  Bit Score: 49.73  E-value: 1.61e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1174747265 1131 AQETFEVLVASPDYRIGFIPYPASYRKLFGRELRNRDYGCDKLMDVCALIEDVIKVEVVGKERFVVL 1197
Cdd:cd09981      5 SKEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVLECGEEKYLQL 71
MARF1_LOTUS pfam19687
MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis ...
 872-932 1.03e-05

MARF1 LOTUS domain; This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity).


Pssm-ID: 437519 [Multi-domain]  Cd Length: 211  Bit Score: 48.14  E-value: 1.03e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174747265  872 FRVL-LSRFGGHVVDLLQKHGGSMPLNSFVVCYDQNFEKL--KEDADNGSFLEHLLLSIPGVTI 932
Cdd:pfam19687  122 FVILsLKTFAPQVHSLLQTHEGTVPLLSFPECYAAKFSPLqlGSETMEGVPLEHLITCVPSITI 185
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
422-536 1.21e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 49.87  E-value: 1.21e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  422 PLPTSHSASHFPIVAAQQPFISPPLHHSASGPLSMLTAGVPRAVIRQtfaSPPIQPGSASGPRPysisntAGPSLSEPRC 501
Cdd:PRK12323   392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQ---ASARGPGGAPAPAP------APAAAPAAAA 462

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1174747265  502 QVPMAGPIRPPNGKAHMPDVSPMAPVARAAPFAPP 536
Cdd:PRK12323   463 RPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP 497
PIN_LabA-like cd06167
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 164-283 2.12e-05

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: 45.10  E-value: 2.12e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  164 FWDIENCRVPLNrsasqvVQCLRSkFEHLGRERDFIVVCDTNKEMKKTIdELNVEQVTVVHVPCISKNAADDKLKtlMHK 243
Cdd:cd06167      3 LVDADNCSNGFG------ALILRR-YAGLFLQMGFEKYANINAQPLLVP-PSNNRGFTVIRVAAKRKDAADVALV--RQA 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1174747265  244 YAVTHSPG-DWLVLISGDFNFTTELNVARHECKLNIVIIHP 283
Cdd:cd06167     73 GRLAYTGApDTVVLVSGDKLDFSDLIEKAKEAGLNVIVVGP 113
LOTUS_3_Limkain_b1 cd09979
The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): ...
 971-1035 7.41e-05

The third LOTUS domain on Limkain b1(LKAP); The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193593  Cd Length: 72  Bit Score: 42.07  E-value: 7.41e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174747265  971 VKDFLALRPRSAVTITDFPATFHRHCGATCDVRGWDRSRLVRVLRTVSKDVEVIGVEAEQVVTLT 1035
Cdd:cd09979      8 VIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQILGMGSKRLLTLS 72
LOTUS cd08824
LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ...
 876-944 8.38e-05

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel 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. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193585 [Multi-domain]  Cd Length: 70  Bit Score: 41.84  E-value: 8.38e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174747265  876 LSRFGGHVVDLLQKHGGSMPLNSFVVCYDQNF-EKLKEDADNGSFLEHLLLSIPGVTIRVEPDEPRMLTL 944
Cdd:cd08824      1 LKQLAKQLRSLLQSYPGGLPLSKLPQLYKKKFgKPLDLSEYGFSKLSDLLEALPGVVIVLSQGGERIVSL 70
OST-HTH pfam12872
OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate ...
 1136-1196 1.79e-04

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.


Pssm-ID: 463735  Cd Length: 64  Bit Score: 41.00  E-value: 1.79e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174747265 1136 EVLVASPDYRIGFIPYPASYRKLFGRELRNRDYGCDKLMDvcaLIE---DVIKVEVVGKERFVV 1196
Cdd:pfam12872    4 SLLRSDPDGWASLSELGSEYRKLFGEDFDPRNYGFSKLSD---LLKaipDVFEIEKRGGGGLVV 64
LOTUS cd08824
LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and ...
 1127-1197 9.47e-04

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel 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. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193585 [Multi-domain]  Cd Length: 70  Bit Score: 39.14  E-value: 9.47e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1174747265 1127 VQRLAQETFEVLVASPdYRIGFIPYPASYRKLFGRELRNRDYGCDKLMDVCALIEDVIKVEVVGKERFVVL 1197
Cdd:cd08824      1 LKQLAKQLRSLLQSYP-GGLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIVLSQGGERIVSL 70
LOTUS_8_Limkain_b1 cd09984
The eighth LOTUS domain on Limkain b1(LKAP); The eighth LOTUS domain on Limkain b1(LKAP): ...
 1151-1202 9.80e-04

The eighth LOTUS domain on Limkain b1(LKAP); The eighth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel 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. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.


Pssm-ID: 193598  Cd Length: 76  Bit Score: 39.12  E-value: 9.80e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1174747265 1151 YPASYRKLFGRELRNRDYGCDKLMDVCALIEDVIKVEVVGKERFVVLRNDKR 1202
Cdd:cd09984     25 FSSAYSKYVGETLQPKNYGYNSLEELLGAIPQVVWIKGHGHKRIVVLKNDMK 76
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 679-752 1.06e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 38.80  E-value: 1.06e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174747265  679 VYFLNLPSDMDQTELYgeliMLLDQITSVDEMSLYDGASNTSR-YAHVKVTQPNLALILVKHFNGATFAGRTLEV 752
Cdd:cd00590      1 LFVGNLPPDTTEEDLR----ELFSKFGEVVSVRIVRDRDGKSKgFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
 676-753 4.71e-03

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 37.30  E-value: 4.71e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174747265  676 CLDVYflNLPSDMDQTELYgELIMLLDQITSVDEMslYDGASNTSR-YAHVKVTQPNLALILVKHFNGATFAGRTLEVT 753
Cdd:cd12377      1 CIFVY--NLAPDADESLLW-QLFGPFGAVQNVKII--RDFTTNKCKgYGFVTMTNYDEAAVAIASLNGYRLGGRVLQVS 74
 
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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