NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1039739953|ref|XP_017170483|]
View 

poly(A) polymerase alpha isoform X7 [Mus musculus]

Protein Classification

NT_PAP_TUTase and PAP_RNA-bind domain-containing protein( domain architecture ID 13705838)

protein containing domains NT_PAP_TUTase, PAP_RNA-bind, and motB

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
21-363 0e+00

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


:

Pssm-ID: 428202 [Multi-domain]  Cd Length: 344  Bit Score: 657.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  21 GITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTF 100
Cdd:pfam04928   1 GVTPPISTAGPTEADLKLTDELIEELKAQGLFESEEETQKREEVLGKLNKLVKEFVKRVSKEKGLPESVAKEAGGKIFTF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 101 GSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPE 180
Cdd:pfam04928  81 GSYRLGVHGPGSDIDTLCVVPKHVTREDFFTSFLEMLKERPEVTELRAVPDAFVPVIKFKFSGISIDLLFARLALPSVPD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 181 DLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLY 260
Cdd:pfam04928 161 DLDLSDDSLLRNLDEKCVRSLNGCRVTDEILRLVPNVETFRTALRAIKLWAKRRGIYSNVLGFLGGVAWAMLVARICQLY 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 261 PNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEE 340
Cdd:pfam04928 241 PNAAPSTLVSKFFLIFSQWKWPQPVLLKPIEEGPLQLRVWNPRINPSDRFHLMPIITPAYPSMNSTHNVSRSTLEVIQEE 320
                         330       340
                  ....*....|....*....|...
gi 1039739953 341 FKQGLAITDEILLSKAEWSKLFE 363
Cdd:pfam04928 321 FKRGLEITDEIMLGKAPWKDLFE 343
PAP_RNA-bind pfam04926
Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the ...
367-495 3.51e-31

Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.


:

Pssm-ID: 428200 [Multi-domain]  Cd Length: 177  Bit Score: 120.09  E-value: 3.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 367 FFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKESPDREE-------------- 432
Cdd:pfam04926   2 FFHKYKYYLQVVASSKTKEAHLKWSGLVESKLRLLVQKLERVPGIALAHPFPKGFERVHVCKTEEEveevqqgslkyqvk 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 433 ---------------------------FRTMWVIGLVFKKtENSENLSVDLTYDIQSFTDTVYRqaiNSKMFELDMKIAA 485
Cdd:pfam04926  82 grktitnatkvtdenkedegdegstkvYTTTFYIGLELDP-KAKGSKKLDISYPVQEFKNLCKS---WEKYDEETMSITV 157
                         170
                  ....*....|
gi 1039739953 486 MHVKRKQLHQ 495
Cdd:pfam04926 158 RHVKNYDLPD 167
motB super family cl32828
flagellar motor protein MotB; Reviewed
501-646 5.36e-04

flagellar motor protein MotB; Reviewed


The actual alignment was detected with superfamily member PRK12799:

Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 43.17  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 501 VLQKRKKHSTEGvklTALNDSSLDL-------SMDSDNSMSVPSPTSAMKTSPLNSSGSSQGNSPAPAVTAASVTSIQAS 573
Cdd:PRK12799  263 VLNKQSQHDIEH---ENLDNRALDIekatglkQIDTHGTVPVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSAT 339
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039739953 574 EVSVPQANSSESPGGPSSESIPQTATQPAISP-----PPKPTVSRVVSSTRLVNPSPRPSGNTATKVPNPIVGVKRTS 646
Cdd:PRK12799  340 TTQASAVALSSAGVLPSDVTLPGTVALPAAEPvnmqpQPMSTTETQQSSTGNITSTANGPTTSLPAAPASNIPVSPTS 417
 
Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
21-363 0e+00

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


Pssm-ID: 428202 [Multi-domain]  Cd Length: 344  Bit Score: 657.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  21 GITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTF 100
Cdd:pfam04928   1 GVTPPISTAGPTEADLKLTDELIEELKAQGLFESEEETQKREEVLGKLNKLVKEFVKRVSKEKGLPESVAKEAGGKIFTF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 101 GSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPE 180
Cdd:pfam04928  81 GSYRLGVHGPGSDIDTLCVVPKHVTREDFFTSFLEMLKERPEVTELRAVPDAFVPVIKFKFSGISIDLLFARLALPSVPD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 181 DLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLY 260
Cdd:pfam04928 161 DLDLSDDSLLRNLDEKCVRSLNGCRVTDEILRLVPNVETFRTALRAIKLWAKRRGIYSNVLGFLGGVAWAMLVARICQLY 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 261 PNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEE 340
Cdd:pfam04928 241 PNAAPSTLVSKFFLIFSQWKWPQPVLLKPIEEGPLQLRVWNPRINPSDRFHLMPIITPAYPSMNSTHNVSRSTLEVIQEE 320
                         330       340
                  ....*....|....*....|...
gi 1039739953 341 FKQGLAITDEILLSKAEWSKLFE 363
Cdd:pfam04928 321 FKRGLEITDEIMLGKAPWKDLFE 343
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
9-540 0e+00

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 540.16  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953   9 GSQQTQPPQRHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQS 88
Cdd:PTZ00418   41 YLSYSIECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEE 120
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDI 168
Cdd:PTZ00418  121 EASQISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDL 200
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 169 LFARLALQTIPEDLDLRD-DSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGV 247
Cdd:PTZ00418  201 LFANLPLPTIPDCLNSLDdDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGV 280
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 248 SWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECN-----LNLPVWDPRVNPSDRYHLMPIITPAYPQ 322
Cdd:PTZ00418  281 SWAILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPnipglMNFKVWDPRVNPQDRAHLMPIITPAFPS 360
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 323 QNSTYNVSVSTRMVMVEEFKQGLAITDEI-LLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRIL 401
Cdd:PTZ00418  361 MNSTHNVTYTTKRVITEEFKRAHEIIKYIeKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFL 440
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 402 VGSLEknefiTLAHVNPQSFP-APKESPDREEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKmFELD 480
Cdd:PTZ00418  441 IKKLE-----TLNNLKIRPYPkFFKYQDDGWDYASSFFIGLVFFSKNVYNNSTFDLRYAIRDFVDIINNWPEMEK-YPDQ 514
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 481 MKIAAMHVKRKQlhqlLPSHVLQKRKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTS 540
Cdd:PTZ00418  515 IDINIKYLKKSQ----LPAFVLSQTPEEPVKTKANTKTNTSSATTSGQSGSSGSTSNSNS 570
PAP1 COG5186
Poly(A) polymerase Pap1 [RNA processing and modification];
17-451 2.20e-163

Poly(A) polymerase Pap1 [RNA processing and modification];


Pssm-ID: 227513 [Multi-domain]  Cd Length: 552  Bit Score: 482.13  E-value: 2.20e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  17 QRHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGK 96
Cdd:COG5186     4 KKKYGITGPLSTREATEEENRLNGELIKELKERGFFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGK 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  97 IFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQ 176
Cdd:COG5186    84 IFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSIP 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 177 TIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVART 256
Cdd:COG5186   164 VVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARI 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 257 CQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMV 336
Cdd:COG5186   244 CQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQHV 323
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 337 MVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHV 416
Cdd:COG5186   324 ILMEFVRAHKILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVDDILYAHP 403
                         410       420       430
                  ....*....|....*....|....*....|....*
gi 1039739953 417 NPQSFPAPKESPDREEFRtMWVIGLVFKKTENSEN 451
Cdd:COG5186   404 FPKAFRKVYNCVAEESIE-KIGSGVTLEVAYESTD 437
PAP_RNA-bind pfam04926
Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the ...
367-495 3.51e-31

Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.


Pssm-ID: 428200 [Multi-domain]  Cd Length: 177  Bit Score: 120.09  E-value: 3.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 367 FFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKESPDREE-------------- 432
Cdd:pfam04926   2 FFHKYKYYLQVVASSKTKEAHLKWSGLVESKLRLLVQKLERVPGIALAHPFPKGFERVHVCKTEEEveevqqgslkyqvk 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 433 ---------------------------FRTMWVIGLVFKKtENSENLSVDLTYDIQSFTDTVYRqaiNSKMFELDMKIAA 485
Cdd:pfam04926  82 grktitnatkvtdenkedegdegstkvYTTTFYIGLELDP-KAKGSKKLDISYPVQEFKNLCKS---WEKYDEETMSITV 157
                         170
                  ....*....|
gi 1039739953 486 MHVKRKQLHQ 495
Cdd:pfam04926 158 RHVKNYDLPD 167
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
60-214 2.66e-28

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 109.57  E-value: 2.66e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  60 RRILILGKLNNLVKEWireisesknlpqsvieNVGGKIFTFGSYRLGVHTKGADIDALCVAPRH-VDRSDFFTSFYDKLK 138
Cdd:cd05402     1 KREEVLDRLQELIKEW----------------FPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHrVDREDFLRKLAKLLK 64
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039739953 139 LQEEVKDLRAVEEAFVPVIKLCFD--GIEIDILFARlalqtipedldlrddsllknldircirsLNGCRVTDEILHLV 214
Cdd:cd05402    65 KSGEVVEVEPIINARVPIIKFVDKptGIEVDISFNN----------------------------LNGIRNTKLLRAYV 114
motB PRK12799
flagellar motor protein MotB; Reviewed
501-646 5.36e-04

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 43.17  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 501 VLQKRKKHSTEGvklTALNDSSLDL-------SMDSDNSMSVPSPTSAMKTSPLNSSGSSQGNSPAPAVTAASVTSIQAS 573
Cdd:PRK12799  263 VLNKQSQHDIEH---ENLDNRALDIekatglkQIDTHGTVPVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSAT 339
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039739953 574 EVSVPQANSSESPGGPSSESIPQTATQPAISP-----PPKPTVSRVVSSTRLVNPSPRPSGNTATKVPNPIVGVKRTS 646
Cdd:PRK12799  340 TTQASAVALSSAGVLPSDVTLPGTVALPAAEPvnmqpQPMSTTETQQSSTGNITSTANGPTTSLPAAPASNIPVSPTS 417
M14_CPM cd03866
Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase M subgroup; Peptidase M14 ...
609-682 8.69e-03

Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase M subgroup; Peptidase M14 Carboxypeptidase (CP) M (CPM) belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPM is an extracellular glycoprotein, bound to cell membranes via a glycosyl-phosphatidylinositol on the C-terminus of the protein. It specifically removes C-terminal basic residues such as lysine and arginine from peptides and proteins. The highest levels of CPM have been found in human lung and placenta, but significant amounts are present in kidney, blood vessels, intestine, brain, and peripheral nerves. CPM has also been found in soluble form in various body fluids, including amniotic fluid, seminal plasma and urine. Due to its wide distribution in a variety of tissues, it is believed that it plays an important role in the control of peptide hormones and growth factor activity on the cell surface and in the membrane-localized degradation of extracellular proteins, for example it hydrolyses the C-terminal arginine of epidermal growth factor (EGF) resulting in des-Arg-EGF which binds to the EGF receptor (EGFR) with an equal or greater affinity than native EGF. CPM is a required processing enzyme that generates specific agonists for the B1 receptor.


Pssm-ID: 349438  Cd Length: 289  Bit Score: 38.62  E-value: 8.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 609 PTVSRVVSSTRL-VNPSPRPSGNTATKVPNPIVGVKRTSSpNKEE----SPKKTKTEEEQVDLETSAV----QSETVPAS 679
Cdd:cd03866    87 PVITRLINSTRIhIMPSMNPDGFEATKKPDCYYTKGRYNK-NGYDlnrnFPDAFEENNVQRQPETRAVmdwiKNETFVLS 165

                  ...
gi 1039739953 680 ASL 682
Cdd:cd03866   166 ANL 168
 
Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
21-363 0e+00

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


Pssm-ID: 428202 [Multi-domain]  Cd Length: 344  Bit Score: 657.28  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  21 GITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGKIFTF 100
Cdd:pfam04928   1 GVTPPISTAGPTEADLKLTDELIEELKAQGLFESEEETQKREEVLGKLNKLVKEFVKRVSKEKGLPESVAKEAGGKIFTF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 101 GSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPE 180
Cdd:pfam04928  81 GSYRLGVHGPGSDIDTLCVVPKHVTREDFFTSFLEMLKERPEVTELRAVPDAFVPVIKFKFSGISIDLLFARLALPSVPD 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 181 DLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLY 260
Cdd:pfam04928 161 DLDLSDDSLLRNLDEKCVRSLNGCRVTDEILRLVPNVETFRTALRAIKLWAKRRGIYSNVLGFLGGVAWAMLVARICQLY 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 261 PNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEE 340
Cdd:pfam04928 241 PNAAPSTLVSKFFLIFSQWKWPQPVLLKPIEEGPLQLRVWNPRINPSDRFHLMPIITPAYPSMNSTHNVSRSTLEVIQEE 320
                         330       340
                  ....*....|....*....|...
gi 1039739953 341 FKQGLAITDEILLSKAEWSKLFE 363
Cdd:pfam04928 321 FKRGLEITDEIMLGKAPWKDLFE 343
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
9-540 0e+00

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 540.16  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953   9 GSQQTQPPQRHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQS 88
Cdd:PTZ00418   41 YLSYSIECALSYGVTDPISLNGPTEEDLKLSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEE 120
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  89 VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDI 168
Cdd:PTZ00418  121 EASQISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVYDGIDIDL 200
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 169 LFARLALQTIPEDLDLRD-DSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGV 247
Cdd:PTZ00418  201 LFANLPLPTIPDCLNSLDdDYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGV 280
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 248 SWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECN-----LNLPVWDPRVNPSDRYHLMPIITPAYPQ 322
Cdd:PTZ00418  281 SWAILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPnipglMNFKVWDPRVNPQDRAHLMPIITPAFPS 360
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 323 QNSTYNVSVSTRMVMVEEFKQGLAITDEI-LLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRIL 401
Cdd:PTZ00418  361 MNSTHNVTYTTKRVITEEFKRAHEIIKYIeKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFL 440
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 402 VGSLEknefiTLAHVNPQSFP-APKESPDREEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKmFELD 480
Cdd:PTZ00418  441 IKKLE-----TLNNLKIRPYPkFFKYQDDGWDYASSFFIGLVFFSKNVYNNSTFDLRYAIRDFVDIINNWPEMEK-YPDQ 514
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 481 MKIAAMHVKRKQlhqlLPSHVLQKRKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTS 540
Cdd:PTZ00418  515 IDINIKYLKKSQ----LPAFVLSQTPEEPVKTKANTKTNTSSATTSGQSGSSGSTSNSNS 570
PAP1 COG5186
Poly(A) polymerase Pap1 [RNA processing and modification];
17-451 2.20e-163

Poly(A) polymerase Pap1 [RNA processing and modification];


Pssm-ID: 227513 [Multi-domain]  Cd Length: 552  Bit Score: 482.13  E-value: 2.20e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  17 QRHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVKEWIREISESKNLPQSVIENVGGK 96
Cdd:COG5186     4 KKKYGITGPLSTREATEEENRLNGELIKELKERGFFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGK 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  97 IFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQ 176
Cdd:COG5186    84 IFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSIP 163
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 177 TIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVART 256
Cdd:COG5186   164 VVPDGLNLSDDNLLKSMDEKCILSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARI 243
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 257 CQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMV 336
Cdd:COG5186   244 CQLYPNASSFVIVCKFFEILSSWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQHV 323
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 337 MVEEFKQGLAITDEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHV 416
Cdd:COG5186   324 ILMEFVRAHKILSDIERNALDWRRLFEKSDFFSRYKLYLEITAMSSCEEDFLKWEGLVESKIRILVSKLEAVDDILYAHP 403
                         410       420       430
                  ....*....|....*....|....*....|....*
gi 1039739953 417 NPQSFPAPKESPDREEFRtMWVIGLVFKKTENSEN 451
Cdd:COG5186   404 FPKAFRKVYNCVAEESIE-KIGSGVTLEVAYESTD 437
PAP_RNA-bind pfam04926
Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the ...
367-495 3.51e-31

Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.


Pssm-ID: 428200 [Multi-domain]  Cd Length: 177  Bit Score: 120.09  E-value: 3.51e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 367 FFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPAPKESPDREE-------------- 432
Cdd:pfam04926   2 FFHKYKYYLQVVASSKTKEAHLKWSGLVESKLRLLVQKLERVPGIALAHPFPKGFERVHVCKTEEEveevqqgslkyqvk 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 433 ---------------------------FRTMWVIGLVFKKtENSENLSVDLTYDIQSFTDTVYRqaiNSKMFELDMKIAA 485
Cdd:pfam04926  82 grktitnatkvtdenkedegdegstkvYTTTFYIGLELDP-KAKGSKKLDISYPVQEFKNLCKS---WEKYDEETMSITV 157
                         170
                  ....*....|
gi 1039739953 486 MHVKRKQLHQ 495
Cdd:pfam04926 158 RHVKNYDLPD 167
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
60-214 2.66e-28

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 109.57  E-value: 2.66e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  60 RRILILGKLNNLVKEWireisesknlpqsvieNVGGKIFTFGSYRLGVHTKGADIDALCVAPRH-VDRSDFFTSFYDKLK 138
Cdd:cd05402     1 KREEVLDRLQELIKEW----------------FPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHrVDREDFLRKLAKLLK 64
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039739953 139 LQEEVKDLRAVEEAFVPVIKLCFD--GIEIDILFARlalqtipedldlrddsllknldircirsLNGCRVTDEILHLV 214
Cdd:cd05402    65 KSGEVVEVEPIINARVPIIKFVDKptGIEVDISFNN----------------------------LNGIRNTKLLRAYV 114
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
83-175 6.08e-14

Nucleotidyltransferase domain; Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalyzing the addition of a nucleotidyl group onto the drug.


Pssm-ID: 396474  Cd Length: 91  Bit Score: 67.83  E-value: 6.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  83 KNLPQSVIENVGG-KIFTFGSYRLGVHTKGADIDALCVAPRHVDrsdfFTSFYDKLKLQEEVKDLRAVEEAFVPVIKLCF 161
Cdd:pfam01909   2 RKLREILKELFPVaEVVLFGSYARGTALPGSDIDLLVVFPEPVE----EERLLKLAKIIKELEELLGLEVDLVTREKIEF 77
                          90
                  ....*....|....
gi 1039739953 162 DGIEIDILFARLAL 175
Cdd:pfam01909  78 PLVKIDILEERILL 91
motB PRK12799
flagellar motor protein MotB; Reviewed
501-646 5.36e-04

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 43.17  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 501 VLQKRKKHSTEGvklTALNDSSLDL-------SMDSDNSMSVPSPTSAMKTSPLNSSGSSQGNSPAPAVTAASVTSIQAS 573
Cdd:PRK12799  263 VLNKQSQHDIEH---ENLDNRALDIekatglkQIDTHGTVPVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSAT 339
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039739953 574 EVSVPQANSSESPGGPSSESIPQTATQPAISP-----PPKPTVSRVVSSTRLVNPSPRPSGNTATKVPNPIVGVKRTS 646
Cdd:PRK12799  340 TTQASAVALSSAGVLPSDVTLPGTVALPAAEPvnmqpQPMSTTETQQSSTGNITSTANGPTTSLPAAPASNIPVSPTS 417
TRF4 COG5260
DNA polymerase sigma [Replication, recombination and repair];
56-172 6.31e-04

DNA polymerase sigma [Replication, recombination and repair];


Pssm-ID: 227585 [Multi-domain]  Cd Length: 482  Bit Score: 42.84  E-value: 6.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953  56 EELQRRILILGKLNNLVKewiREISESknlpqsvienvggKIFTFGSYRLGVHTKGADIDaLCV-APRHVDRSDF-FTSF 133
Cdd:COG5260    73 EELKRRKALLEKLRTLLK---KEFPDA-------------DLKVFGSTETGLALPKSDID-LCIiSDPRGYKETRnAGSL 135
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1039739953 134 YDKLKLQEEVKDLRAVEEAFVPVIKLcFD---GIEIDILFAR 172
Cdd:COG5260   136 ASHLFKKNLAKEVVVVSTARVPIIKL-VDpqsGLHCDISFNN 176
M14_CPM cd03866
Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase M subgroup; Peptidase M14 ...
609-682 8.69e-03

Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase M subgroup; Peptidase M14 Carboxypeptidase (CP) M (CPM) belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPM is an extracellular glycoprotein, bound to cell membranes via a glycosyl-phosphatidylinositol on the C-terminus of the protein. It specifically removes C-terminal basic residues such as lysine and arginine from peptides and proteins. The highest levels of CPM have been found in human lung and placenta, but significant amounts are present in kidney, blood vessels, intestine, brain, and peripheral nerves. CPM has also been found in soluble form in various body fluids, including amniotic fluid, seminal plasma and urine. Due to its wide distribution in a variety of tissues, it is believed that it plays an important role in the control of peptide hormones and growth factor activity on the cell surface and in the membrane-localized degradation of extracellular proteins, for example it hydrolyses the C-terminal arginine of epidermal growth factor (EGF) resulting in des-Arg-EGF which binds to the EGF receptor (EGFR) with an equal or greater affinity than native EGF. CPM is a required processing enzyme that generates specific agonists for the B1 receptor.


Pssm-ID: 349438  Cd Length: 289  Bit Score: 38.62  E-value: 8.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039739953 609 PTVSRVVSSTRL-VNPSPRPSGNTATKVPNPIVGVKRTSSpNKEE----SPKKTKTEEEQVDLETSAV----QSETVPAS 679
Cdd:cd03866    87 PVITRLINSTRIhIMPSMNPDGFEATKKPDCYYTKGRYNK-NGYDlnrnFPDAFEENNVQRQPETRAVmdwiKNETFVLS 165

                  ...
gi 1039739953 680 ASL 682
Cdd:cd03866   166 ANL 168
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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