5JJ4,2RPZ


Conserved Protein Domain Family
APOBEC_N

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pfam08210: APOBEC_N 
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APOBEC-like N-terminal domain
A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum.
Statistics
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PSSM-Id: 336956
View PSSM: pfam08210
Aligned: 27 rows
Threshold Bit Score: 102.776
Threshold Setting Gi: 255074389
Created: 28-Mar-2017
Updated: 23-May-2017
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JJ4_C        377 FTSNFNN---GIGRHKTy--LCYEVERLDSATsf-----slD--FGY----------------------------LRNK- 415
gi 74751569    47 efCQIFGfpyGTTFPQTkhlTFYELKTSSGSLv--------Q--KGHassct---------------------------- 88
gi 17566846   157 VPKHVQNc-fLEHKHESsglIVTLIGEDYVYRgd-----fyHesKGE----------------------------P---- 198
gi 156350041   49 hkkiakagdkVLGNKKEfcgAFYHVPRSKSGCldkqscaiaK--RGHdatpltavalvkyeqqessewaiksvrrYTNC- 125
gi 255074389   53 aFFHCSPtpeLSSHPDE---LCLRVACDPAGRkc------eT--KGVvvv-----------------------aaLRDRa 98
gi 803129030   51 efyqifGfpyGPTYPPTkhlTFYELKTSSGSLv--------Q--KGHassct---------------------------- 92
gi 1033366091  51 EFHQAFGfpyGPTHHQNkhlLFYEVRHFSGKLm--------Q--KGHatnct---------------------------- 92
gi 562838969   52 FKFQFRNveySSGRNKTf--LCYVVEAQAKGGqv-----qaT--RGY----------------------------LEDE- 93
gi 992220930    6 FRFQFKNveyCSGRNKTl--LCYLVDQSSGADg-------lL--RGF----------------------------LEDE- 45
2RPZ_A         14 FKFQFRNveySSGRNKTf--LCYVVEVQSKGGqa-----qaT--QGY----------------------------LEDE- 55
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JJ4_C        416 ----------Ng---cHVELLFLRYis---------------dwD-LD---P------------GRCYRVTWFTSWSPCY 451
gi 74751569    89 ------------gnyiHPESMLFE---------------------------Mngylds-aiynnDSIRHIILYSNNSPCN 128
gi 17566846   199 ----------------HVEEQLVAAiy---------------dlIsKY---T------------VDLHEIQIFVSKSPCF 232
gi 156350041  126 ----------Sdk-mkHAEEFFLMDid---------------cqL-EA---RhkgeegfldfwnKKKWQITMYLTMQPCH 175
gi 255074389   99 gdlrflsrysNcplssHAEEYVVRDeelvravmemapeddarssT-KT---P------------GSAGTLTLYQRLQPCH 162
gi 803129030   93 ------------gndtHPESMLFE---------------------------Mngyfds-avhsnDGMRHIILYSSNSPCN 132
gi 1033366091  93 ------------endiHPESMLFE---------------------------Tggylds-ivrnwENVMYIILYSNYSPCN 132
gi 562838969   94 ----------Haa--aHAEEAFFNT-------------------I-LPafdP------------ALRYNVTWYVSSSPCA 129
gi 992220930   46 ----------Hag--lHAELAFFQL-------------------I-LPqydP------------SVNYTVTWYVSSSPCA 81
2RPZ_A         56 ----------Hag--aHAEEAFFNTil----------------pA-FD---P------------ALKYNVTWYVSSSPCA 91
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JJ4_C        452 D------------------CARHVADFLRGN----PNLSLRIFTARL-----Y---F----------------CEDR-K- 483
gi 74751569   129 Ean--------------hcCISKMYNFLITY----PGITLSIYFSQL-----Y---Htemdf--------------pasa 168
gi 17566846   233 HqdcepkcevvdecksnkaCAKLLGLLLSKVrkeiKKVDVKMTVKFL-----Y---P----------------HLNRgDl 288
gi 156350041  176 Lstdtggt-----kedqscCEVMIKAKEKLG----DNVEIVIKPTHLcqvgwYkgkP----------------REKP-Kn 229
gi 255074389  163 Gssdnr--------gplwsCSDALVAGLHREllgpRGVSLRVAVSYT-----Y---RahwdvrgfesererrwWGPK-Ve 225
gi 803129030  133 Ean--------------hcCISKMYTFLAKY----PDITLSIYFSQL-----Y---Hteaef--------------pasp 172
gi 1033366091 133 Eae--------------qcCISKIYHFLMKY----PGITLCIYFSQL-----Y---Hteedl--------------pisp 172
gi 562838969  130 A------------------CADRIIKTLSKT----KNLRLLILVGRL-----F---M----------------WEEP-Ei 162
gi 992220930   82 H------------------CCSKLLEILQER----KTLRLNIFSARLle----------------------aeEEEG-Qe 116
2RPZ_A         92 A------------------CADRILKTLSKT----KNLRLLILVSRL-----F---M----------------WEEP-Ev 124
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JJ4_C        484 AEPegLRRLHRA---GVQIAIMTFKDyf--ycWNTF---VEN---H----E---RTF-----------------KAWEGL 528
gi 74751569   169 wNReaLRSLASLw-pRVVLSPISGGIwh--svLHSF---I---------------------------------------- 202
gi 17566846   289 YTKqgILCMLQA---GIKVEPLLMKDwcsimdWSPH---VDH---K----G---DYL-----------------QLWNNH 335
gi 156350041  230 AEKgvRKLFKTT---GIELECMKEGDwk--ylLQYAqpeVEN---KlpdyD---TSR-----------------RKTEDE 281
gi 255074389  226 AARegIRVFAAAakdGVTLEALNAED------WAFL---VSL---C----D---EDVardyaaafgeggegfgsKGCGVF 286
gi 803129030  173 wNReaLRSLASLs-pRVTLSPISGGMwy--slLSNF---V---------------------------------------- 206
gi 1033366091 173 wNCeaLQSLASLw-pQVTLNPLCGGLwh--svLHSF---V---------------------------------------- 206
gi 562838969  163 QAA--LRKMREA---GCKLRIMKPQDfe--yiWQNF---VEqeegE----S---KAF-----------------EPWEDI 208
gi 992220930  117 DNRagMKALAGA---GCKLRVMKPLDfs--ysWDTF---VEH---E----D---ERF-----------------TPWEDC 161
2RPZ_A        125 QAA--LKKLKEA---GCKLRIMKPQDfe--yiWQNF---VEQ---E----EgesKAF-----------------EPWEDI 170
                         330
                  ....*....|...
5JJ4_C        529 HENSVRLSRQLRR 541
gi 74751569   203 --SGVSGSHVFQP 213
gi 17566846   336 HLDKAVAQSQLFI 348
gi 156350041  282 KIGEELHNQQLEQ 294
gi 255074389  287 TAPAVAHRRAMDE 299
gi 803129030  207 --SGVQGATVFQP 217
gi 1033366091 207 --TSVPQAGCYHP 217
gi 562838969  209 QENFLYYEEKLAD 221
gi 992220930  162 QENYEYHHEKLAQ 174
2RPZ_A        171 QENFLYYEEKLAD 183
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