NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1802776413|ref|NP_001365062|]
View 

alkylated DNA repair protein alkB homolog 8 isoform 3 [Homo sapiens]

Protein Classification

alkylated DNA repair protein alkB homolog 8( domain architecture ID 10557103)

alkylated DNA repair protein alkB homolog 8 (ALKBH8) catalyzes tRNA methylation to generate 5-methylcarboxymethyl uridine (mcm(5)U) at the wobble position of certain tRNAs, a critical anticodon loop modification linked to DNA damage survival

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 1.13e-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: 125.77  E-value: 1.13e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413  42 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEvVDDLGQKITLYLNFVE 121
Cdd:cd12431     1 TQHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKE-LELPQQNVPLYLSFVE 79


                  .
gi 1802776413 122 K 122
Cdd:cd12431    80 K 80
2OG-FeII_Oxy super family cl21496
2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and ...
 152-334 9.40e-17

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: 78.90  E-value: 9.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 152 LLESVDWTEDTDNQNSQKSLKHRRVKHFGYEF---HYENNNVDKDKPLsgGLPDICESFLEKW----LRKGYIKHKPDQM 224
Cdd:pfam13532  21 LLEEGPFRQPTTQGGRPMSVRMTNCGQLGWVTdgpGYRYSGVDPVTGE--PWPPFPEALLQLAerlaAEAGYPGWSPNAC 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 225 TINQYEPGQGIPAHID-THSAFEDEIVSLSLGSEIVMDFKHPDG----IAVPvmLPRRSLLVMTGESRYLWtHGITCRKF 299
Cdd:pfam13532  99 LVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATFRFGGKSRsdptISLR--LESGDVLVMGGESRLAY-HGVPPIRR 175

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1802776413 300 DTvqaSESLksgiitsdvgdltlskRGLRTSFTFR 334
Cdd:pfam13532 176 GT---HPLL----------------GGGRINLTFR 191
ALKBH8_N pfam09004
Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain ...
 1-37 4.98e-11

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: 57.53  E-value: 4.98e-11
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1802776413   1 MDSNHQSNYKLSKTEKKFLRKQIKAKH-TLLRHEGIET 37
Cdd:pfam09004   1 WTTNTTSLLKKAQQRLYFLRKLKKANHpTLFYHEGIES 38
UbiE super family cl43651
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 379-455 1.57e-03

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


The actual alignment was detected with superfamily member COG2226:

Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 39.21  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 379 YEEIAGHFSSTRHtpwphIVEFLKALPsGSIVADIGCGNGKYL------------------------------GINKEL- 427
Cdd:COG2226     1 FDRVAARYDGREA-----LLAALGLRP-GARVLDLGCGTGRLAlalaergarvtgvdispemlelareraaeaGLNVEFv 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1802776413 428 ------------------------YMERRVAALQEIVRLLRPGGKALIYVWA 455
Cdd:COG2226    75 vgdaedlpfpdgsfdlvissfvlhHLPDPERALAEIARVLKPGGRLVVVDFS 126
 
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 1.13e-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: 125.77  E-value: 1.13e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413  42 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEvVDDLGQKITLYLNFVE 121
Cdd:cd12431     1 TQHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKE-LELPQQNVPLYLSFVE 79


                  .
gi 1802776413 122 K 122
Cdd:cd12431    80 K 80
2OG-FeII_Oxy_2 pfam13532
2OG-Fe(II) oxygenase superfamily;
152-334 9.40e-17

2OG-Fe(II) oxygenase superfamily;


Pssm-ID: 433285  Cd Length: 191  Bit Score: 78.90  E-value: 9.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 152 LLESVDWTEDTDNQNSQKSLKHRRVKHFGYEF---HYENNNVDKDKPLsgGLPDICESFLEKW----LRKGYIKHKPDQM 224
Cdd:pfam13532  21 LLEEGPFRQPTTQGGRPMSVRMTNCGQLGWVTdgpGYRYSGVDPVTGE--PWPPFPEALLQLAerlaAEAGYPGWSPNAC 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 225 TINQYEPGQGIPAHID-THSAFEDEIVSLSLGSEIVMDFKHPDG----IAVPvmLPRRSLLVMTGESRYLWtHGITCRKF 299
Cdd:pfam13532  99 LVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATFRFGGKSRsdptISLR--LESGDVLVMGGESRLAY-HGVPPIRR 175

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1802776413 300 DTvqaSESLksgiitsdvgdltlskRGLRTSFTFR 334
Cdd:pfam13532 176 GT---HPLL----------------GGGRINLTFR 191
ALKBH8_N pfam09004
Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain ...
 1-37 4.98e-11

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: 57.53  E-value: 4.98e-11
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1802776413   1 MDSNHQSNYKLSKTEKKFLRKQIKAKH-TLLRHEGIET 37
Cdd:pfam09004   1 WTTNTTSLLKKAQQRLYFLRKLKKANHpTLFYHEGIES 38
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
226-294 1.79e-08

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


Pssm-ID: 442379  Cd Length: 200  Bit Score: 54.78  E-value: 1.79e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1802776413 226 INQYEPGQgipAHIDTHS------AFEDEIVSLSLGSEIVMDFKHPD--GIAVPVMLPRRSLLVMTGESRYLWTHGI 294
Cdd:COG3145   107 LNLYRDGQ---DRMGWHQddeeelGFNPPIASVSLGATRRFRFGHKErkDPTRSLPLEHGDLLVMGGPTQLAWQHGV 180
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 50-105 9.18e-04

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: 37.98  E-value: 9.18e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1802776413  50 GGLGNGVSRNQLLPVLEKCGLV-DALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEV 105
Cdd:pfam00076   4 GNLPPDTTEEDLKDLFSKFGPIkSIRLVRDEtgrsKGFAFVEFEDEEDAEKAIEALNGKEL 64
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 379-455 1.57e-03

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: 39.21  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 379 YEEIAGHFSSTRHtpwphIVEFLKALPsGSIVADIGCGNGKYL------------------------------GINKEL- 427
Cdd:COG2226     1 FDRVAARYDGREA-----LLAALGLRP-GARVLDLGCGTGRLAlalaergarvtgvdispemlelareraaeaGLNVEFv 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1802776413 428 ------------------------YMERRVAALQEIVRLLRPGGKALIYVWA 455
Cdd:COG2226    75 vgdaedlpfpdgsfdlvissfvlhHLPDPERALAEIARVLKPGGRLVVVDFS 126
 
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 1.13e-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: 125.77  E-value: 1.13e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413  42 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEvVDDLGQKITLYLNFVE 121
Cdd:cd12431     1 TQHLVVANGGLGNGVSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKE-LELPQQNVPLYLSFVE 79


                  .
gi 1802776413 122 K 122
Cdd:cd12431    80 K 80
2OG-FeII_Oxy_2 pfam13532
2OG-Fe(II) oxygenase superfamily;
152-334 9.40e-17

2OG-Fe(II) oxygenase superfamily;


Pssm-ID: 433285  Cd Length: 191  Bit Score: 78.90  E-value: 9.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 152 LLESVDWTEDTDNQNSQKSLKHRRVKHFGYEF---HYENNNVDKDKPLsgGLPDICESFLEKW----LRKGYIKHKPDQM 224
Cdd:pfam13532  21 LLEEGPFRQPTTQGGRPMSVRMTNCGQLGWVTdgpGYRYSGVDPVTGE--PWPPFPEALLQLAerlaAEAGYPGWSPNAC 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 225 TINQYEPGQGIPAHID-THSAFEDEIVSLSLGSEIVMDFKHPDG----IAVPvmLPRRSLLVMTGESRYLWtHGITCRKF 299
Cdd:pfam13532  99 LVNFYRDGARMGLHQDrDESGPGAPIVSLSLGASATFRFGGKSRsdptISLR--LESGDVLVMGGESRLAY-HGVPPIRR 175

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1802776413 300 DTvqaSESLksgiitsdvgdltlskRGLRTSFTFR 334
Cdd:pfam13532 176 GT---HPLL----------------GGGRINLTFR 191
ALKBH8_N pfam09004
Alkylated DNA repair protein alkB homolog 8, N-terminal; This domain is the N-terminal domain ...
 1-37 4.98e-11

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: 57.53  E-value: 4.98e-11
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1802776413   1 MDSNHQSNYKLSKTEKKFLRKQIKAKH-TLLRHEGIET 37
Cdd:pfam09004   1 WTTNTTSLLKKAQQRLYFLRKLKKANHpTLFYHEGIES 38
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
226-294 1.79e-08

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


Pssm-ID: 442379  Cd Length: 200  Bit Score: 54.78  E-value: 1.79e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1802776413 226 INQYEPGQgipAHIDTHS------AFEDEIVSLSLGSEIVMDFKHPD--GIAVPVMLPRRSLLVMTGESRYLWTHGI 294
Cdd:COG3145   107 LNLYRDGQ---DRMGWHQddeeelGFNPPIASVSLGATRRFRFGHKErkDPTRSLPLEHGDLLVMGGPTQLAWQHGV 180
RRM1_hnRNPR_like cd12249
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 50-105 4.10e-04

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: 39.11  E-value: 4.10e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1802776413  50 GGLGNGVSRNQLLPVLEKCGLVDA--LLMPP---NKPYSFARYRTTEESKRAYVTLNGKEV 105
Cdd:cd12249     7 GKIPRDVFEDELVPLFEKCGKIYElrLMMDFsglNRGYAFVTYTNKEAAQRAVKTLNNYEI 67
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 50-105 9.18e-04

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: 37.98  E-value: 9.18e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1802776413  50 GGLGNGVSRNQLLPVLEKCGLV-DALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEV 105
Cdd:pfam00076   4 GNLPPDTTEEDLKDLFSKFGPIkSIRLVRDEtgrsKGFAFVEFEDEEDAEKAIEALNGKEL 64
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 379-455 1.57e-03

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: 39.21  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802776413 379 YEEIAGHFSSTRHtpwphIVEFLKALPsGSIVADIGCGNGKYL------------------------------GINKEL- 427
Cdd:COG2226     1 FDRVAARYDGREA-----LLAALGLRP-GARVLDLGCGTGRLAlalaergarvtgvdispemlelareraaeaGLNVEFv 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1802776413 428 ------------------------YMERRVAALQEIVRLLRPGGKALIYVWA 455
Cdd:COG2226    75 vgdaedlpfpdgsfdlvissfvlhHLPDPERALAEIARVLKPGGRLVVVDFS 126
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 50-113 6.53e-03

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: 36.12  E-value: 6.53e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1802776413  50 GGLGNGVSRNQLLPVLEKCGLVDALLMPPNK---------PYSFARYRTTEESKRAYVTLNGKEVvddLGQKI 113
Cdd:cd12355     5 GNLDPRLTEYHLLKLLSKYGKIKKFDFLFHKtgplkgqprGYCFVTFETKEEAEKAIECLNGKLA---LGKKL 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH