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Conserved domains on  [gi|494613928|ref|WP_007372173|]
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MULTISPECIES: DUF4942 domain-containing protein [Enterobacterales]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF4942 super family cl16358
Domain of unknown function (DUF4942); The function of this family is not known.
 103-291 4.38e-18

Domain of unknown function (DUF4942); The function of this family is not known.


The actual alignment was detected with superfamily member pfam13708:

Pssm-ID: 433419  Cd Length: 184  Bit Score: 82.37  E-value: 4.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  103 ALDEKYWQKLLDLTGVKPFMPTERYDDWneglrawrkssESNFEKLKPVPFNEESIFSTAFALNEEKKDYFAQMVHGVFE 182
Cdd:pfam13708   1 SLDDRAWRSLMDLSGLRSLLSAAARKEF-----------DNQLSEGAVPEFTVENIYATFEGLIANRDEIFERGVIDVFD 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  183 KLSALHKTNRAQGFSNKLIIASCLP--SRDNRRSYDYLNYFNDLRKVIGLMYGRSGAEDVNSAAVKEYMMSNPGEWVSID 260
Cdd:pfam13708  70 GLSRGYKSNEKFKIGKRIILSGFLScyGWWNELSYNRADKLDDLDRILALLDGKPIPDHILRRVADAARVSRYRGGQVVE 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 494613928  261 NDSLKVKGFINGNVHILIEE-ETCDNLNLVLS 291
Cdd:pfam13708 150 TRYFDVRWFKNGTLHLFFKRpDLVDKLNRIVA 181
RsmC super family cl34491
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 439-520 1.30e-07

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


The actual alignment was detected with superfamily member COG2813:

Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 52.11  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 439 IGLgALLKGLPEGvDVTGFDIHPAAVAITglRWNVTLNDFLLVK--------PENTGLFERILMNPPFSDSRW----IAH 506
Cdd:COG2813   63 IGL-ALAKRNPEA-RVTLVDVNARAVELA--RANAAANGLENVEvlwsdglsGVPDGSFDLILSNPPFHAGRAvdkeVAH 138

                         90
                 ....*....|....*.
gi 494613928 507 --FQHAMRFLKPGGRL 520
Cdd:COG2813  139 alIADAARHLRPGGEL 154
 
Name Accession Description Interval E-value
DUF4942 pfam13708
Domain of unknown function (DUF4942); The function of this family is not known.
 103-291 4.38e-18

Domain of unknown function (DUF4942); The function of this family is not known.


Pssm-ID: 433419  Cd Length: 184  Bit Score: 82.37  E-value: 4.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  103 ALDEKYWQKLLDLTGVKPFMPTERYDDWneglrawrkssESNFEKLKPVPFNEESIFSTAFALNEEKKDYFAQMVHGVFE 182
Cdd:pfam13708   1 SLDDRAWRSLMDLSGLRSLLSAAARKEF-----------DNQLSEGAVPEFTVENIYATFEGLIANRDEIFERGVIDVFD 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  183 KLSALHKTNRAQGFSNKLIIASCLP--SRDNRRSYDYLNYFNDLRKVIGLMYGRSGAEDVNSAAVKEYMMSNPGEWVSID 260
Cdd:pfam13708  70 GLSRGYKSNEKFKIGKRIILSGFLScyGWWNELSYNRADKLDDLDRILALLDGKPIPDHILRRVADAARVSRYRGGQVVE 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 494613928  261 NDSLKVKGFINGNVHILIEE-ETCDNLNLVLS 291
Cdd:pfam13708 150 TRYFDVRWFKNGTLHLFFKRpDLVDKLNRIVA 181
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 439-520 1.30e-07

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: 52.11  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 439 IGLgALLKGLPEGvDVTGFDIHPAAVAITglRWNVTLNDFLLVK--------PENTGLFERILMNPPFSDSRW----IAH 506
Cdd:COG2813   63 IGL-ALAKRNPEA-RVTLVDVNARAVELA--RANAAANGLENVEvlwsdglsGVPDGSFDLILSNPPFHAGRAvdkeVAH 138

                         90
                 ....*....|....*.
gi 494613928 507 --FQHAMRFLKPGGRL 520
Cdd:COG2813  139 alIADAARHLRPGGEL 154
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 440-518 6.53e-04

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 39.08  E-value: 6.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  440 GLGALLKGLPE--GVDVTGFDIHPAAVAIT-------GLRWNVTLNDFL-LVKPENTglFERILMNPPF---SDSRWIAH 506
Cdd:pfam13649   7 GTGRLTLALARrgGARVTGVDLSPEMLERAreraaeaGLNVEFVQGDAEdLPFPDGS--FDLVVSSGVLhhlPDPDLEAA 84

                          90
                  ....*....|..
gi 494613928  507 FQHAMRFLKPGG 518
Cdd:pfam13649  85 LREIARVLKPGG 96
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 433-524 8.67e-03

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: 36.25  E-value: 8.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 433 RLLEPNIGLGALLKGL--PEGVDVTGFDIHPAAVAITGLRW------NVTLN--DFLLVKPENTGLFERILMNPPFSDS- 501
Cdd:cd02440    1 RVLDLGCGTGALALALasGPGARVTGVDISPVALELARKAAaalladNVEVLkgDAEELPPEADESFDVIISDPPLHHLv 80

                         90       100
                 ....*....|....*....|....
gi 494613928 502 -RWIAHFQHAMRFLKPGGRLIAIL 524
Cdd:cd02440   81 eDLARFLEEARRLLKPGGVLVLTL 104
 
Name Accession Description Interval E-value
DUF4942 pfam13708
Domain of unknown function (DUF4942); The function of this family is not known.
 103-291 4.38e-18

Domain of unknown function (DUF4942); The function of this family is not known.


Pssm-ID: 433419  Cd Length: 184  Bit Score: 82.37  E-value: 4.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  103 ALDEKYWQKLLDLTGVKPFMPTERYDDWneglrawrkssESNFEKLKPVPFNEESIFSTAFALNEEKKDYFAQMVHGVFE 182
Cdd:pfam13708   1 SLDDRAWRSLMDLSGLRSLLSAAARKEF-----------DNQLSEGAVPEFTVENIYATFEGLIANRDEIFERGVIDVFD 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  183 KLSALHKTNRAQGFSNKLIIASCLP--SRDNRRSYDYLNYFNDLRKVIGLMYGRSGAEDVNSAAVKEYMMSNPGEWVSID 260
Cdd:pfam13708  70 GLSRGYKSNEKFKIGKRIILSGFLScyGWWNELSYNRADKLDDLDRILALLDGKPIPDHILRRVADAARVSRYRGGQVVE 149

                         170       180       190
                  ....*....|....*....|....*....|..
gi 494613928  261 NDSLKVKGFINGNVHILIEE-ETCDNLNLVLS 291
Cdd:pfam13708 150 TRYFDVRWFKNGTLHLFFKRpDLVDKLNRIVA 181
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 439-520 1.30e-07

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: 52.11  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 439 IGLgALLKGLPEGvDVTGFDIHPAAVAITglRWNVTLNDFLLVK--------PENTGLFERILMNPPFSDSRW----IAH 506
Cdd:COG2813   63 IGL-ALAKRNPEA-RVTLVDVNARAVELA--RANAAANGLENVEvlwsdglsGVPDGSFDLILSNPPFHAGRAvdkeVAH 138

                         90
                 ....*....|....*.
gi 494613928 507 --FQHAMRFLKPGGRL 520
Cdd:COG2813  139 alIADAARHLRPGGEL 154
HsdM COG0286
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
441-538 1.95e-07

Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];


Pssm-ID: 440055 [Multi-domain]  Cd Length: 243  Bit Score: 52.50  E-value: 1.95e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 441 LGALLKGLPEGVDVTGFDIHPAAVAITGLRW--------NVTLNDFLLVKPENTGLFERILMNPPFSDS----------- 501
Cdd:COG0286   65 LKEHGGDERKKLSLYGQEINPTTYRLAKMNLllhgigdpNIELGDTLSNDGDELEKFDVVLANPPFGGKwkkeelkddll 144

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 494613928 502 -RWIAH-----------FQHAMRFLKPGGRLIAILPGSAkehlLTREAG 538
Cdd:COG0286  145 gRFGYGlppksnadllfLQHILSLLKPGGRAAVVLPDGV----LFRGAE 189
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 413-521 9.65e-07

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


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 48.77  E-value: 9.65e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 413 ATVGELQKRAIDE----CMVASGMRLLEPNIGLGALLKGLPE--GVDVTGFDIHPAAVAI-------TGLRWNVT--LND 477
Cdd:COG2230   30 DTLEEAQEAKLDLilrkLGLKPGMRVLDIGCGWGGLALYLARryGVRVTGVTLSPEQLEYareraaeAGLADRVEvrLAD 109

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 494613928 478 FLLVKPENTglFERIL---MNPPFSDSRWIAHFQHAMRFLKPGGRLI 521
Cdd:COG2230  110 YRDLPADGQ--FDAIVsigMFEHVGPENYPAYFAKVARLLKPGGRLL 154
YtxK COG0827
Adenine-specific DNA N6-methylase [Replication, recombination and repair];
409-539 3.59e-05

Adenine-specific DNA N6-methylase [Replication, recombination and repair];


Pssm-ID: 440589 [Multi-domain]  Cd Length: 327  Bit Score: 46.10  E-value: 3.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 409 HQFY-ATVGELQKRAIDECMVASGMRLLEPNIG----LGALLKGLPEGVDVTGFDIHPAAVAIT-------GLRWNVTLN 476
Cdd:COG0827   93 HQMTpDAIGLLIGYLVEKFTKKEGLRILDPAVGtgnlLTTVLNQLKKKVNAYGVEVDDLLIRLAavlanlqGHPVELFHQ 172

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 477 DFLlvKPENTGLFERILMNPP----------------FSDSRWIAH---FQHAMRFLKPGGRLIAILPgsakEHLLTREA 537
Cdd:COG0827  173 DAL--QPLLIDPVDVVISDLPvgyypnderakrfklkADEGHSYAHhlfIEQSLNYLKPGGYLFFLVP----SNLFESDQ 246


                 ..
gi 494613928 538 GP 539
Cdd:COG0827  247 AA 248
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 428-525 7.06e-05

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 44.37  E-value: 7.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 428 VASGMRLLEpnIG-----LGALLKGLPEGVDVTGFDIHPAAVAItgLRWNVTLN-----------DFLLVKPEN-TGLFE 490
Cdd:COG4123   35 VKKGGRVLD--LGtgtgvIALMLAQRSPGARITGVEIQPEAAEL--ARRNVALNgledritvihgDLKEFAAELpPGSFD 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 494613928 491 RILMNPPF----------SDSRWIAHFQHAM----------RFLKPGGRLIAILP 525
Cdd:COG4123  111 LVVSNPPYfkagsgrkspDEARAIARHEDALtledliraaaRLLKPGGRFALIHP 165
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 427-525 1.40e-04

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: 41.93  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 427 MVASGMRLLEPNIGLGALLKGL-PEGVDVTGFDIHPAAVAITGLRWNVTLNDFL------LVKPENTglFERILMN---P 496
Cdd:COG2227   21 LLPAGGRVLDVGCGTGRLALALaRRGADVTGVDISPEALEIARERAAELNVDFVqgdledLPLEDGS--FDLVICSevlE 98

                         90       100
                 ....*....|....*....|....*....
gi 494613928 497 PFSDsrWIAHFQHAMRFLKPGGRLIAILP 525
Cdd:COG2227   99 HLPD--PAALLRELARLLKPGGLLLLSTP 125
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 440-518 6.53e-04

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 39.08  E-value: 6.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  440 GLGALLKGLPE--GVDVTGFDIHPAAVAIT-------GLRWNVTLNDFL-LVKPENTglFERILMNPPF---SDSRWIAH 506
Cdd:pfam13649   7 GTGRLTLALARrgGARVTGVDLSPEMLERAreraaeaGLNVEFVQGDAEdLPFPDGS--FDLVVSSGVLhhlPDPDLEAA 84

                          90
                  ....*....|..
gi 494613928  507 FQHAMRFLKPGG 518
Cdd:pfam13649  85 LREIARVLKPGG 96
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 412-523 8.50e-04

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: 39.98  E-value: 8.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 412 YATVGELQKRAIDECMVASGMRLLEPNIGLGALLKGLPE-GVDVTGFDIHPAAVAI-------TGLRWNVTLNDFllvkp 483
Cdd:COG2226    4 VAARYDGREALLAALGLRPGARVLDLGCGTGRLALALAErGARVTGVDISPEMLELareraaeAGLNVEFVVGDA----- 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 494613928 484 entglferilMNPPFSD-------SRWIAHF--------QHAMRFLKPGGRLIAI 523
Cdd:COG2226   79 ----------EDLPFPDgsfdlviSSFVLHHlpdperalAEIARVLKPGGRLVVV 123
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
439-499 1.92e-03

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 39.89  E-value: 1.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 494613928 439 IGLGALLKGlpeGVDVTGFDIHPAAVAIT-------GLRWNVTLNDFLlvKPENTGLFERILMNPPFS 499
Cdd:COG2263   59 LAIGAALLG---AKKVVGVDIDPEALEIArenaerlGVRVDFIRADVT--RIPLGGSVDTVVMNPPFG 121
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 439-521 4.09e-03

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 38.34  E-value: 4.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928  439 IGLgALLKGLPEgVDVTGFDIHPAAVAITglRWNVTLNDFLLVK--------PENTGLFERILMNPPFSDSR----WIAH 506
Cdd:pfam05175  45 LGA-ALAKESPD-AELTMVDINARALESA--RENLAANGLENGEvvasdvysGVEDGKFDLIISNPPFHAGLattyNVAQ 120

                          90
                  ....*....|....*..
gi 494613928  507 --FQHAMRFLKPGGRLI 521
Cdd:pfam05175 121 rfIADAKRHLRPGGELW 137
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 433-524 8.67e-03

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: 36.25  E-value: 8.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494613928 433 RLLEPNIGLGALLKGL--PEGVDVTGFDIHPAAVAITGLRW------NVTLN--DFLLVKPENTGLFERILMNPPFSDS- 501
Cdd:cd02440    1 RVLDLGCGTGALALALasGPGARVTGVDISPVALELARKAAaalladNVEVLkgDAEELPPEADESFDVIISDPPLHHLv 80

                         90       100
                 ....*....|....*....|....
gi 494613928 502 -RWIAHFQHAMRFLKPGGRLIAIL 524
Cdd:cd02440   81 eDLARFLEEARRLLKPGGVLVLTL 104
 
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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