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Conserved domains on  [gi|61675696|ref|NP_080579|]
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alkylated DNA repair protein alkB homolog 8 isoform 2 [Mus musculus]

Protein Classification

DUF1891 and RRM_ALKBH8 domain-containing protein( domain architecture ID 11181630)

protein containing domains DUF1891, RRM_ALKBH8, 2OG-FeII_Oxy, and AdoMet_MTases

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 42-122 1.98e-34

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


:

Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 125.38  E-value: 1.98e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  42 TQSLVIANGGLGNGVSRKQLLLTLEKCGPVEALLMPPNKPYAFVIFQTIEESKKAYFTLNGKEiIDDLGQKIFLYLNFVE 121
Cdd:cd12431   1 TQHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKE-LELPQQNVPLYLSFVE 79


                .
gi 61675696 122 K 122
Cdd:cd12431  80 K 80
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 379-505 7.23e-21

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


:

Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 89.28  E-value: 7.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 379 YNEIASHFSSTRhspwpRIVEFLKALPsGSIVADIGCGNGKYLGI--NKDLYMIGCDRSQNLVDICRER------QFQAL 450
Cdd:COG2226   1 FDRVAARYDGRE-----ALLAALGLRP-GARVLDLGCGTGRLALAlaERGARVTGVDISPEMLELARERaaeaglNVEFV 74

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 61675696 451 VCDALAVPVRSGSCDACISIAVIHHFataERRVEALQELARLLRPGGQALIYVWA 505
Cdd:COG2226  75 VGDAEDLPFPDGSFDLVISSFVLHHL---PDPERALAEIARVLKPGGRLVVVDFS 126
2OG-FeII_Oxy super family cl21496
2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and ...
 184-334 9.52e-18

2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.


The actual alignment was detected with superfamily member pfam13532:

Pssm-ID: 473886  Cd Length: 191  Bit Score: 81.59  E-value: 9.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   184 HYESNTVDKDKPLPG-GLPEVCSSILEKLLKE-GYIKHKPDQLTINQYEPGHGIPAHID-THSAFEDEIISLSLGSAIVM 260
Cdd:pfam13532  56 GYRYSGVDPVTGEPWpPFPEALLQLAERLAAEaGYPGWSPNACLVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATF 135

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 61675696   261 DFKHPEGV--TVQVMLPRRSLLVMTGESRYLWtHGITPRKFDTVQaseqfkggiitsdigdltlSKRGMRTSFTFR 334
Cdd:pfam13532 136 RFGGKSRSdpTISLRLESGDVLVMGGESRLAY-HGVPPIRRGTHP-------------------LLGGGRINLTFR 191
ALKBH8_N pfam09004
Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain ...
 1-37 1.02e-10

Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain of Alkylated DNA repair protein alkB homolog 8 (ALKBH8) and its homologs. This domain corresponds to the basic alpha-helix located at the N-terminal of the RRM domain, which enhances its RNA binding affinity.


:

Pssm-ID: 117570  Cd Length: 38  Bit Score: 56.76  E-value: 1.02e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 61675696     1 MNINHKGVLKLTKMEKKFLRKQSKARH-VLLKHEGIQA 37
Cdd:pfam09004   1 WTTNTTSLLKKAQQRLYFLRKLKKANHpTLFYHEGIES 38
 
Name Accession Description Interval E-value
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 42-122 1.98e-34

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 125.38  E-value: 1.98e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  42 TQSLVIANGGLGNGVSRKQLLLTLEKCGPVEALLMPPNKPYAFVIFQTIEESKKAYFTLNGKEiIDDLGQKIFLYLNFVE 121
Cdd:cd12431   1 TQHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKE-LELPQQNVPLYLSFVE 79


                .
gi 61675696 122 K 122
Cdd:cd12431  80 K 80
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 379-505 7.23e-21

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 89.28  E-value: 7.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 379 YNEIASHFSSTRhspwpRIVEFLKALPsGSIVADIGCGNGKYLGI--NKDLYMIGCDRSQNLVDICRER------QFQAL 450
Cdd:COG2226   1 FDRVAARYDGRE-----ALLAALGLRP-GARVLDLGCGTGRLALAlaERGARVTGVDISPEMLELARERaaeaglNVEFV 74

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 61675696 451 VCDALAVPVRSGSCDACISIAVIHHFataERRVEALQELARLLRPGGQALIYVWA 505
Cdd:COG2226  75 VGDAEDLPFPDGSFDLVISSFVLHHL---PDPERALAEIARVLKPGGRLVVVDFS 126
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 410-497 3.04e-19

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 83.00  E-value: 3.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   410 VADIGCGNGKYLGINKDLY---MIGCDRSQNLVDICRER------QFQALVCDALAVPVRSGSCDACISIAVIHHFATAE 480
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGgarVTGVDLSPEMLERARERaaeaglNVEFVQGDAEDLPFPDGSFDLVVSSGVLHHLPDPD 80

                          90
                  ....*....|....*..
gi 61675696   481 RRvEALQELARLLRPGG 497
Cdd:pfam13649  81 LE-AALREIARVLKPGG 96
2OG-FeII_Oxy_2 pfam13532
2OG-Fe(II) oxygenase superfamily;
184-334 9.52e-18

2OG-Fe(II) oxygenase superfamily;


Pssm-ID: 433285  Cd Length: 191  Bit Score: 81.59  E-value: 9.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   184 HYESNTVDKDKPLPG-GLPEVCSSILEKLLKE-GYIKHKPDQLTINQYEPGHGIPAHID-THSAFEDEIISLSLGSAIVM 260
Cdd:pfam13532  56 GYRYSGVDPVTGEPWpPFPEALLQLAERLAAEaGYPGWSPNACLVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATF 135

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 61675696   261 DFKHPEGV--TVQVMLPRRSLLVMTGESRYLWtHGITPRKFDTVQaseqfkggiitsdigdltlSKRGMRTSFTFR 334
Cdd:pfam13532 136 RFGGKSRSdpTISLRLESGDVLVMGGESRLAY-HGVPPIRRGTHP-------------------LLGGGRINLTFR 191
PRK08317 PRK08317
hypothetical protein; Provisional
 396-501 3.64e-14

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 72.66  E-value: 3.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  396 RIVEFLkALPSGSIVADIGCGNG---KYLG--INKDLYMIGCDRSQNLVDICRER------QFQALVCDALAVPVRSGSC 464
Cdd:PRK08317  10 RTFELL-AVQPGDRVLDVGCGPGndaRELArrVGPEGRVVGIDRSEAMLALAKERaaglgpNVEFVRGDADGLPFPDGSF 88

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 61675696  465 DACISIAVIHHFATAERrveALQELARLLRPGGQALI 501
Cdd:PRK08317  89 DAVRSDRVLQHLEDPAR---ALAEIARVLRPGGRVVV 122
ALKBH8_N pfam09004
Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain ...
 1-37 1.02e-10

Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain of Alkylated DNA repair protein alkB homolog 8 (ALKBH8) and its homologs. This domain corresponds to the basic alpha-helix located at the N-terminal of the RRM domain, which enhances its RNA binding affinity.


Pssm-ID: 117570  Cd Length: 38  Bit Score: 56.76  E-value: 1.02e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 61675696     1 MNINHKGVLKLTKMEKKFLRKQSKARH-VLLKHEGIQA 37
Cdd:pfam09004   1 WTTNTTSLLKKAQQRLYFLRKLKKANHpTLFYHEGIES 38
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
171-338 8.78e-10

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


Pssm-ID: 442379  Cd Length: 200  Bit Score: 58.63  E-value: 8.78e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 171 LKHRRVKHFGYEF----------------HYeSNTVDKDKPLPGGLPEVCSSIlekllkEGYIKHKPDQLTINQYEPGHg 234
Cdd:COG3145  43 WRQPVIPIFGKTMsvprlnawygwvgagyRY-SGTDPEPPPWPPALLALKRRV------EAAAGFPFNSCLLNLYRDGQ- 114

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 235 ipAHIDTHS------AFEDEIISLSLGSAIVMDFKHPE--GVTVQVMLPRRSLLVMTGESRYLWTHGITPRKFDTvqase 306
Cdd:COG3145 115 --DRMGWHQddeeelGFNPPIASVSLGATRRFRFGHKErkDPTRSLPLEHGDLLVMGGPTQLAWQHGVPKTKKGT----- 187

                       170       180       190
                ....*....|....*....|....*....|..
gi 61675696 307 qfkggiitsdigdltlskrGMRTSFTFRKVRR 338
Cdd:COG3145 188 -------------------GPRINLTFRRIGP 200
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 410-501 1.29e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 55.90  E-value: 1.29e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 410 VADIGCGNGKY---LGINKDLYMIGCDRSQNLVDICRERQFQA-------LVCDALAVP-VRSGSCDACISIAVIHHFAt 478
Cdd:cd02440   2 VLDLGCGTGALalaLASGPGARVTGVDISPVALELARKAAAALladnvevLKGDAEELPpEADESFDVIISDPPLHHLV- 80

                        90       100
                ....*....|....*....|...
gi 61675696 479 aERRVEALQELARLLRPGGQALI 501
Cdd:cd02440  81 -EDLARFLEEARRLLKPGGVLVL 102
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 50-105 5.65e-08

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.92  E-value: 5.65e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 61675696    50 GGLGNGVSRKQLLLTLEKCGPVEALLMPP-----NKPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:pfam00076   4 GNLPPDTTEEDLKDLFSKFGPIKSIRLVRdetgrSKGFAFVEFEDEEDAEKAIEALNGKEL 64
RRM smart00360
RNA recognition motif;
50-105 5.62e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.20  E-value: 5.62e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 61675696     50 GGLGNGVSRKQLLLTLEKCGPVEALLMPPN------KPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:smart00360   5 GNLPPDTTEEELRELFSKFGKVESVRLVRDketgksKGFAFVEFESEEDAEKALEALNGKEL 66
 
Name Accession Description Interval E-value
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 42-122 1.98e-34

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 125.38  E-value: 1.98e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  42 TQSLVIANGGLGNGVSRKQLLLTLEKCGPVEALLMPPNKPYAFVIFQTIEESKKAYFTLNGKEiIDDLGQKIFLYLNFVE 121
Cdd:cd12431   1 TQHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKE-LELPQQNVPLYLSFVE 79


                .
gi 61675696 122 K 122
Cdd:cd12431  80 K 80
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 379-505 7.23e-21

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 89.28  E-value: 7.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 379 YNEIASHFSSTRhspwpRIVEFLKALPsGSIVADIGCGNGKYLGI--NKDLYMIGCDRSQNLVDICRER------QFQAL 450
Cdd:COG2226   1 FDRVAARYDGRE-----ALLAALGLRP-GARVLDLGCGTGRLALAlaERGARVTGVDISPEMLELARERaaeaglNVEFV 74

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 61675696 451 VCDALAVPVRSGSCDACISIAVIHHFataERRVEALQELARLLRPGGQALIYVWA 505
Cdd:COG2226  75 VGDAEDLPFPDGSFDLVISSFVLHHL---PDPERALAEIARVLKPGGRLVVVDFS 126
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 410-497 3.04e-19

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 83.00  E-value: 3.04e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   410 VADIGCGNGKYLGINKDLY---MIGCDRSQNLVDICRER------QFQALVCDALAVPVRSGSCDACISIAVIHHFATAE 480
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGgarVTGVDLSPEMLERARERaaeaglNVEFVQGDAEDLPFPDGSFDLVVSSGVLHHLPDPD 80

                          90
                  ....*....|....*..
gi 61675696   481 RRvEALQELARLLRPGG 497
Cdd:pfam13649  81 LE-AALREIARVLKPGG 96
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 412-501 3.13e-19

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 82.71  E-value: 3.13e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   412 DIGCGNGKYLGINKDLYM--IGCDRSQNLVDICRER----QFQALVCDALAVPVRSGSCDACISIAVIHHFataERRVEA 485
Cdd:pfam08241   2 DVGCGTGLLTELLARLGArvTGVDISPEMLELAREKapreGLTFVVGDAEDLPFPDNSFDLVLSSEVLHHV---EDPERA 78

                          90
                  ....*....|....*.
gi 61675696   486 LQELARLLRPGGQALI 501
Cdd:pfam08241  79 LREIARVLKPGGILII 94
2OG-FeII_Oxy_2 pfam13532
2OG-Fe(II) oxygenase superfamily;
184-334 9.52e-18

2OG-Fe(II) oxygenase superfamily;


Pssm-ID: 433285  Cd Length: 191  Bit Score: 81.59  E-value: 9.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   184 HYESNTVDKDKPLPG-GLPEVCSSILEKLLKE-GYIKHKPDQLTINQYEPGHGIPAHID-THSAFEDEIISLSLGSAIVM 260
Cdd:pfam13532  56 GYRYSGVDPVTGEPWpPFPEALLQLAERLAAEaGYPGWSPNACLVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATF 135

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 61675696   261 DFKHPEGV--TVQVMLPRRSLLVMTGESRYLWtHGITPRKFDTVQaseqfkggiitsdigdltlSKRGMRTSFTFR 334
Cdd:pfam13532 136 RFGGKSRSdpTISLRLESGDVLVMGGESRLAY-HGVPPIRRGTHP-------------------LLGGGRINLTFR 191
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 387-501 2.09e-16

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 75.82  E-value: 2.09e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 387 SSTRHSPW-PRIVEFL-KALPSGSIVADIGCGNGKYL------GINkdlyMIGCDRSQNLVDICRER----QFQALVCDA 454
Cdd:COG2227   3 DPDARDFWdRRLAALLaRLLPAGGRVLDVGCGTGRLAlalarrGAD----VTGVDISPEALEIARERaaelNVDFVQGDL 78

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 61675696 455 LAVPVRSGSCDACISIAVIHHFATAErrvEALQELARLLRPGGQALI 501
Cdd:COG2227  79 EDLPLEDGSFDLVICSEVLEHLPDPA---ALLRELARLLKPGGLLLL 122
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 384-509 1.50e-14

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 72.64  E-value: 1.50e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 384 SHFSSTRHSP-WPRIVEFLKALPSGSIVADIGCGNGKYLGINKDLY---MIGCDRSQNLVDICRERQFQA-------LVC 452
Cdd:COG0500   3 DSYYSDELLPgLAALLALLERLPKGGRVLDLGCGTGRNLLALAARFggrVIGIDLSPEAIALARARAAKAglgnvefLVA 82

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 61675696 453 DALA-VPVRSGSCDACISIAVIHHFAtAERRVEALQELARLLRPGGQALIYVWAMEQE 509
Cdd:COG0500  83 DLAElDPLPAESFDLVVAFGVLHHLP-PEEREALLRELARALKPGGVLLLSASDAAAA 139
PRK08317 PRK08317
hypothetical protein; Provisional
 396-501 3.64e-14

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 72.66  E-value: 3.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  396 RIVEFLkALPSGSIVADIGCGNG---KYLG--INKDLYMIGCDRSQNLVDICRER------QFQALVCDALAVPVRSGSC 464
Cdd:PRK08317  10 RTFELL-AVQPGDRVLDVGCGPGndaRELArrVGPEGRVVGIDRSEAMLALAKERaaglgpNVEFVRGDADGLPFPDGSF 88

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 61675696  465 DACISIAVIHHFATAERrveALQELARLLRPGGQALI 501
Cdd:PRK08317  89 DAVRSDRVLQHLEDPAR---ALAEIARVLRPGGRVVV 122
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 396-503 1.59e-13

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 68.80  E-value: 1.59e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 396 RIVEFLkALPSGSIVADIGCGNG---KYLGINKDLYMIGCDRSQNLVDICRER--------QFQALVCDALAVPvRSGSC 464
Cdd:COG2230  42 LILRKL-GLKPGMRVLDIGCGWGglaLYLARRYGVRVTGVTLSPEQLEYARERaaeagladRVEVRLADYRDLP-ADGQF 119

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 61675696 465 DACISIAVIHHFATAERRvEALQELARLLRPGGQALIYV 503
Cdd:COG2230 120 DAIVSIGMFEHVGPENYP-AYFAKVARLLKPGGRLLLHT 157
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
372-497 9.43e-12

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 64.25  E-value: 9.43e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 372 QKHVHQVYNEIA----SHFSSTRHSPWPRIV--EFLKALPSGSI--VADIGCGNGkYLGI---NKDLYMIGCDRSQNLVD 440
Cdd:COG4976   4 DAYVEALFDQYAdsydAALVEDLGYEAPALLaeELLARLPPGPFgrVLDLGCGTG-LLGEalrPRGYRLTGVDLSEEMLA 82

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 61675696 441 ICRERQFQA--LVCDALAVPVRSGSCDACISIAVIHHFATAERrveALQELARLLRPGG 497
Cdd:COG4976  83 KAREKGVYDrlLVADLADLAEPDGRFDLIVAADVLTYLGDLAA---VFAGVARALKPGG 138
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
410-503 9.62e-12

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 61.76  E-value: 9.62e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 410 VADIGCGNGKY----LGINKDLYMIGCDRSQNLVDICRER--QFQALVCDALAVPVRsGSCDACISIAVIHHFataERRV 483
Cdd:COG4106   5 VLDLGCGTGRLtallAERFPGARVTGVDLSPEMLARARARlpNVRFVVADLRDLDPP-EPFDLVVSNAALHWL---PDHA 80

                        90       100
                ....*....|....*....|
gi 61675696 484 EALQELARLLRPGGQALIYV 503
Cdd:COG4106  81 ALLARLAAALAPGGVLAVQV 100
ALKBH8_N pfam09004
Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain ...
 1-37 1.02e-10

Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain of Alkylated DNA repair protein alkB homolog 8 (ALKBH8) and its homologs. This domain corresponds to the basic alpha-helix located at the N-terminal of the RRM domain, which enhances its RNA binding affinity.


Pssm-ID: 117570  Cd Length: 38  Bit Score: 56.76  E-value: 1.02e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 61675696     1 MNINHKGVLKLTKMEKKFLRKQSKARH-VLLKHEGIQA 37
Cdd:pfam09004   1 WTTNTTSLLKKAQQRLYFLRKLKKANHpTLFYHEGIES 38
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 364-501 2.76e-10

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 60.94  E-value: 2.76e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  364 SKEALELEQKHVHQVYNEIASHF-------SSTRHSPWPRivEFLKAL--PSGSIVADIGCGNG-------KYLGINKdl 427
Cdd:PRK00216   2 MTVAEEEKQEKVAEMFDSIAPKYdlmndllSFGLHRVWRR--KTIKWLgvRPGDKVLDLACGTGdlaialaKAVGKTG-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  428 YMIGCDRSQNLVDICRER--------QFQALVCDALAVPVRSGSCDaCISIA-----VIHhfataerRVEALQELARLLR 494
Cdd:PRK00216  78 EVVGLDFSEGMLAVGREKlrdlglsgNVEFVQGDAEALPFPDNSFD-AVTIAfglrnVPD-------IDKALREMYRVLK 149


                 ....*..
gi 61675696  495 PGGQALI 501
Cdd:PRK00216 150 PGGRLVI 156
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
171-338 8.78e-10

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


Pssm-ID: 442379  Cd Length: 200  Bit Score: 58.63  E-value: 8.78e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 171 LKHRRVKHFGYEF----------------HYeSNTVDKDKPLPGGLPEVCSSIlekllkEGYIKHKPDQLTINQYEPGHg 234
Cdd:COG3145  43 WRQPVIPIFGKTMsvprlnawygwvgagyRY-SGTDPEPPPWPPALLALKRRV------EAAAGFPFNSCLLNLYRDGQ- 114

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 235 ipAHIDTHS------AFEDEIISLSLGSAIVMDFKHPE--GVTVQVMLPRRSLLVMTGESRYLWTHGITPRKFDTvqase 306
Cdd:COG3145 115 --DRMGWHQddeeelGFNPPIASVSLGATRRFRFGHKErkDPTRSLPLEHGDLLVMGGPTQLAWQHGVPKTKKGT----- 187

                       170       180       190
                ....*....|....*....|....*....|..
gi 61675696 307 qfkggiitsdigdltlskrGMRTSFTFRKVRR 338
Cdd:COG3145 188 -------------------GPRINLTFRRIGP 200
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 410-501 1.29e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 55.90  E-value: 1.29e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 410 VADIGCGNGKY---LGINKDLYMIGCDRSQNLVDICRERQFQA-------LVCDALAVP-VRSGSCDACISIAVIHHFAt 478
Cdd:cd02440   2 VLDLGCGTGALalaLASGPGARVTGVDISPVALELARKAAAALladnvevLKGDAEELPpEADESFDVIISDPPLHHLV- 80

                        90       100
                ....*....|....*....|...
gi 61675696 479 aERRVEALQELARLLRPGGQALI 501
Cdd:cd02440  81 -EDLARFLEEARRLLKPGGVLVL 102
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 50-105 5.65e-08

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.92  E-value: 5.65e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 61675696    50 GGLGNGVSRKQLLLTLEKCGPVEALLMPP-----NKPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:pfam00076   4 GNLPPDTTEEDLKDLFSKFGPIKSIRLVRdetgrSKGFAFVEFEDEEDAEKAIEALNGKEL 64
Methyltransf_12 pfam08242
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 412-497 8.18e-08

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 400515 [Multi-domain]  Cd Length: 98  Bit Score: 50.44  E-value: 8.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   412 DIGCGNG----KYLGINKDLYMIGCDRSQNLVDICRER--QFQALVCDALAVPVR------SGSCDACISIAVIHHFATa 479
Cdd:pfam08242   2 EIGCGTGtllrALLEALPGLEYTGLDISPAALEAARERlaALGLLNAVRVELFQLdlgeldPGSFDVVVASNVLHHLAD- 80

                          90
                  ....*....|....*...
gi 61675696   480 erRVEALQELARLLRPGG 497
Cdd:pfam08242  81 --PRAVLRNIRRLLKPGG 96
RRM smart00360
RNA recognition motif;
50-105 5.62e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.20  E-value: 5.62e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 61675696     50 GGLGNGVSRKQLLLTLEKCGPVEALLMPPN------KPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:smart00360   5 GNLPPDTTEEELRELFSKFGKVESVRLVRDketgksKGFAFVEFESEEDAEKALEALNGKEL 66
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 50-105 1.02e-06

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: 46.51  E-value: 1.02e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 61675696  50 GGLGNGVSRKQLLLTLEKCGPVEALLMPPN-----KPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:cd00590   4 GNLPPDTTEEDLRELFSKFGEVVSVRIVRDrdgksKGFAFVEFESPEDAEKALEALNGTEL 64
Ubie_methyltran pfam01209
ubiE/COQ5 methyltransferase family;
371-498 3.63e-05

ubiE/COQ5 methyltransferase family;


Pssm-ID: 395966 [Multi-domain]  Cd Length: 228  Bit Score: 45.51  E-value: 3.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   371 EQKhVHQVYNEIASHF-------SSTRHSPWPRIVEFLKALPSGSIVADIGCGNGKYL-----GINKDLYMIGCDRSQNL 438
Cdd:pfam01209   1 EQR-VGDVFSSVASKYdlmndviSFGIHRLWKDFTMKCMGVKRGNKFLDVAGGTGDWTfglsdSAGSSGKVVGLDINENM 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 61675696   439 VDICRER-------QFQALVCDALAVPVRSGSCDaCISIAV-IHHFATaerRVEALQELARLLRPGGQ 498
Cdd:pfam01209  80 LKEGEKKakeegkyNIEFLQGNAEELPFEDDSFD-IVTISFgLRNFPD---YLKVLKEAFRVLKPGGR 143
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 406-531 4.19e-05

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 43.94  E-value: 4.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   406 SGSIVADIGCGNGKYL-----GINKDLYMIGCDRSQNLVDICRER-------QFQALVCDALAVP--VRSGSCDACISIA 471
Cdd:pfam13847   3 KGMRVLDLGCGTGHLSfelaeELGPNAEVVGIDISEEAIEKARENaqklgfdNVEFEQGDIEELPelLEDDKFDVVISNC 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61675696   472 VIHHFAtaeRRVEALQELARLLRPGGQALI-YVWAMEQEYKN--QKSKYLRGKRISQGDKDEL 531
Cdd:pfam13847  83 VLNHIP---DPDKVLQEILRVLKPGGRLIIsDPDSLAELPAHvkEDSTYYAGCVGGAILKKKL 142
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 50-114 1.50e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 40.75  E-value: 1.50e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 61675696  50 GGLGNGVSRKQLLLTLEKCGPVEALLM-----PPNK----PYAFVIFQTIEESKKAYFTLNGKEIiddLGQKIF 114
Cdd:cd12355   5 GNLDPRLTEYHLLKLLSKYGKIKKFDFlfhktGPLKgqprGYCFVTFETKEEAEKAIECLNGKLA---LGKKLV 75
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 400-501 1.63e-04

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 43.25  E-value: 1.63e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696 400 FLKALP--SGSIVADIGCGNGkYLGI-----NKDLYMIGCDRSQNLVDICRE-------RQFQALVCDALAvPVRSGSCD 465
Cdd:COG2813  41 LLEHLPepLGGRVLDLGCGYG-VIGLalakrNPEARVTLVDVNARAVELARAnaaanglENVEVLWSDGLS-GVPDGSFD 118

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 61675696 466 ACISIAVIHhfATAERRVEALQEL----ARLLRPGGQALI 501
Cdd:COG2813 119 LILSNPPFH--AGRAVDKEVAHALiadaARHLRPGGELWL 156
PRK15068 PRK15068
tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB;
394-498 2.30e-04

tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB;


Pssm-ID: 237898  Cd Length: 322  Bit Score: 43.69  E-value: 2.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696  394 WPRIVEFLKALpSGSIVADIGCGNGKY----LGINKDLyMIGCDRSQNLVdiCrerQFQA---LVCDALAV---PVR--- 460
Cdd:PRK15068 111 WDRVLPHLSPL-KGRTVLDVGCGNGYHmwrmLGAGAKL-VVGIDPSQLFL--C---QFEAvrkLLGNDQRAhllPLGieq 183

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 61675696  461 ---SGSCDACISIAVIHHfataeRR--VEALQELARLLRPGGQ 498
Cdd:PRK15068 184 lpaLKAFDTVFSMGVLYH-----RRspLDHLKQLKDQLVPGGE 221
Methyltransf_23 pfam13489
Methyltransferase domain; This family appears to be a methyltransferase domain.
 390-505 2.38e-04

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 404385 [Multi-domain]  Cd Length: 162  Bit Score: 42.03  E-value: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61675696   390 RHSPWPRIVEFL-KALPSGSIVADIGCGNGKYLGINKDLY--MIGCDRSQNLVDICRERQFQALVCDALAvPVRSGSCDA 466
Cdd:pfam13489   5 RERLLADLLLRLlPKLPSPGRVLDFGCGTGIFLRLLRAQGfsVTGVDPSPIAIERALLNVRFDQFDEQEA-AVPAGKFDV 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 61675696   467 CISIAVIHHFATAERrveALQELARLLRPGGQALIYVWA 505
Cdd:pfam13489  84 IVAREVLEHVPDPPA---LLRQIAALLKPGGLLLLSTPL 119
RRM_Srp1p_like cd12467
RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and ...
 51-108 3.34e-04

RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins; This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain.


Pssm-ID: 240913 [Multi-domain]  Cd Length: 78  Bit Score: 39.79  E-value: 3.34e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61675696  51 GLGNGVSRKQLLLTLEKCGPVEALLMPP-----NKPYAFVIFQTIEESKKAYFTLNGKEIIDD 108
Cdd:cd12467   6 GFGAETRARDLAYEFERYGRLVRCDIPPprtfqSRPFAFVEYESHRDAEDAYEEMHGRRFPDT 68
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 50-105 2.25e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.


Pssm-ID: 409695 [Multi-domain]  Cd Length: 78  Bit Score: 37.18  E-value: 2.25e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 61675696  50 GGLGNGVSRKQLLLTLEKCGPVEA--LLMPP---NKPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:cd12249   7 GKIPRDVFEDELVPLFEKCGKIYElrLMMDFsglNRGYAFVTYTNKEAAQRAVKTLNNYEI 67
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 66-107 2.46e-03

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 37.04  E-value: 2.46e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 61675696  66 EKCGPVEALLMPpnKPYAFVIFQTIEESKKAYFTLNGKEIID 107
Cdd:cd12233  22 EPFGPLVRCDIR--KTFAFVEFEDSEDATKALEALHGSRIDG 61
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 66-107 6.18e-03

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 36.08  E-value: 6.18e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 61675696  66 EKCGPVEALLMPP---------NKPYAFVIFQTIEESKKAyFTLNGKEIID 107
Cdd:cd12298  22 EKFGEIESINIPKkqknrkgrhNNGFAFVTFEDADSAESA-LQLNGTLLDN 71
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 50-105 6.71e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 35.72  E-value: 6.71e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 61675696  50 GGLGNGVSRKQLLLTLEKCGPVEALLMPPNKPYAFVIFQTIEESKKAYFTLNGKEI 105
Cdd:cd12354   6 GNITKGLTEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAIVSVNGTII 61
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 50-103 9.27e-03

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 35.45  E-value: 9.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 61675696  50 GGLGNGVSRKQLLLTLEKCGPVEALLMPPNKPYAFVIFQTIEESKKAYFTLNGK 103
Cdd:cd12262   9 GNLDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIK 62
 
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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