-------------------------------------------------------------------------------- Domain name : PF01569.13_PAP2 Domain size : 70 Domain Description : PAP2 superfamily Domain gathering score : 16.0 Domain trusted cutoff : 16.0 Domain architecture : non-TM/SP [1 199], TM [200 261] -------------------------------------------------------------------------------- Example 1 gi|33086600|gb|AAP92612.1| Ab2-371 [Rattus norvegicus] 1640 (length) 1267 1336 .. (wrt seq) 43 195 .. (wrt HMM) No.of residues in non-TM/SP region : 112 [56%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- Cu_amine_oxid Copper amine oxidase, enzyme domain 707.5 1.1e-209 2 PA28_beta Proteasome activator pa28 beta subuni 392.4 7.8e-115 1 Cu_amine_oxidN2 Copper amine oxidase, N2 domain 186.4 7.8e-53 2 Cu_amine_oxidN3 Copper amine oxidase, N3 domain 131.2 3.8e-39 1 PA28_alpha Proteasome activator pa28 alpha subun 52.9 1.4e-13 2 PAP2 PAP2 superfamily 36.7 1.2e-09 1 Inhibitor_I29 Cathepsin propeptide inhibitor domain 11.7 0.0089 2 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- PA28_alpha 1/2 7 15 .. 1 9 [. 2.7 7 PA28_alpha 2/2 48 72 .. 40 64 .] 50.2 8e-13 PA28_beta 1/1 107 256 .. 1 150 [] 392.4 7.8e-115 Inhibitor_I29 1/2 268 276 .. 53 61 .] 5.9 0.51 Cu_amine_oxidN2 1/2 274 347 .. 1 78 [. 76.7 1.2e-20 Cu_amine_oxid 1/2 364 389 .. 27 52 .. 1.8 1.5 Inhibitor_I29 2/2 427 435 .. 53 61 .] 5.9 0.51 Cu_amine_oxidN2 2/2 433 519 .. 1 91 [] 109.8 7.1e-30 Cu_amine_oxidN3 1/1 536 636 .. 1 111 [] 131.2 3.8e-39 Cu_amine_oxid 2/2 675 1091 .. 1 449 [] 705.7 3.9e-209 PAP2 1/1 1266 1323 .. 24 115 .. 36.7 1.2e-09 Alignments of top-scoring domains: PA28_alpha: domain 1 of 2, from 7 to 15: score 2.7, E = 7 CS --HHHHHHH *->varEakkKV<-* v++E+k+KV gi|3308660 7 VDQEVKLKV 15 PA28_alpha: domain 2 of 2, from 48 to 72: score 50.2, E = 8e-13 CS HSGGG--S-GGGS------XXXXXX *->KEdkLNkaDLsalhadldIPVPDPp<-* +E++LN++DL+++h+d+++PVPDP+ gi|3308660 48 QEPILNIHDLTQIHSDMNLPVPDPI 72 PA28_beta: domain 1 of 1, from 107 to 256: score 392.4, E = 7.8e-115 CS XXXXB---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----SS- *->pcGslksNeklVallekVKPeIwdLiEkcnlVktWiQlLIPRIEDGN p+G+lksN++lV+++ekVKPeI++LiEkcn+Vk+W+QlLIPRIEDGN gi|3308660 107 PNGMLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGN 153 CS -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTBTH nFGVaIQEkvleelraVetkaeaFldqISkYFseRGdaVaKaAKyPHVeD nFGV+IQE++++elr+Ve++a+++ldqIS+Y+++R+++V+K+AKyPHVeD gi|3308660 154 NFGVSIQEETVAELRTVESEAASYLDQISRYYITRAKLVSKIAKYPHVED 203 CS HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH-S--XXXX YRrlVhElDEaeYvsLRLmvlELRnaYAtLyDiIlkNlEKIkrPRgenke YRr+V+E+DE+eY+sLRL+++ELRn+Y+tL+D+IlkN+EKIkrPR++n+e gi|3308660 204 YRRTVTEIDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRSSNAE 253 CS XXX smY<-* ++ gi|3308660 254 TLI 256 Inhibitor_I29: domain 1 of 2, from 268 to 276: score 5.9, E = 0.51 *->FaDLTneEF<-* FaDL++eE gi|3308660 268 FADLSPEEL 276 Cu_amine_oxidN2: domain 1 of 2, from 274 to 347: score 76.7, E = 1.2e-20 CS CTTSHHHHHHHHHHHHHHHHCT.TTTTTEEEEEEEEE--HHHHHHHH *->HPLdpLtaeEinkvrtILkssallagkstrfhsveLlEPdKkaVlqw ++L+++++++i+ ++L ++a++++++++++sveL++P+K+a+l++ gi|3308660 274 EELTAVMSFLIKHLGPGLVDAAQARPSDNCVFSVELQLPAKAAALAH 320 CS HHSCSSSSSS-EEEEEEEEETTSSSEEEEEE lekggplvappRkArVvaldgaqtRshElvV<-* l++gg + p R A +++++g+q+ +++v+ gi|3308660 321 LDRGGLP--PVRAALAIIFFGGQP--KPNVI 347 Cu_amine_oxid: domain 1 of 2, from 364 to 389: score 1.8, E = 1.5 CS TTEEEEEEEETTTEEEEEEEEEEETT *->anWsFhvGfdpReGlvIsdVrfnDeg<-* ++W+F++G++++ l+I+d+rf++ g gi|3308660 364 SLWTFTFGHGVFGDLRIFDIRFKGSG 389 Inhibitor_I29: domain 2 of 2, from 427 to 435: score 5.9, E = 0.51 *->FaDLTneEF<-* FaDL++eE gi|3308660 427 FADLSPEEL 435 Cu_amine_oxidN2: domain 2 of 2, from 433 to 519: score 109.8, E = 7.1e-30 CS CTTSHHHHHHHHHHHHHHHHCT.TTTTTEEEEEEEEE--HHHHHHHH *->HPLdpLtaeEinkvrtILkssallagkstrfhsveLlEPdKkaVlqw ++L+++++++i+ ++L ++a++++++++++sveL++P+K+a+l++ gi|3308660 433 EELTAVMSFLIKHLGPGLVDAAQARPSDNCVFSVELQLPAKAAALAH 479 CS HHSCSSSSSS-EEEEEEEEETTSSSEEEEEEETTTTEEEEEEEE lekggplvappRkArVvaldgaqtRshElvVDLttGkvvswril<-* l++ggp+ p R+A +++++g+q+ +++v +L +G++++++++ gi|3308660 480 LDRGGPP--PVREALAIIFFGGQP--KPNVSELVVGPLPHPSYM 519 Cu_amine_oxidN3: domain 1 of 1, from 536 to 636: score 131.2, E = 3.8e-39 CS S---HHHHHHHHHHHHHTTGHHHHHHHHHTT.TCCGGGGEEEEEEE- *->PpvtleEfasaeevplrrtdPefiealkkRGflvnglsdvvciPwtv +pv+++E+++++e++++r++P++ + l++++f++ ++ ++ +t gi|3308660 536 RPVLTREYQDIQEMIFHRELPQASGLLHHCCFYKR--QGHNLLKMTT 580 CS SSSSTST.GTTS-EEEEEEEE-SSTT...S-GGGSEECTEEEEEETTTTE GwfGeasleeGrRllkalcfyrdgtvsPmdnyyahPieGLeilvDldakk +++G +s G+R+++++++y+ +++ ++y hPi+ Le+lvD++a++ gi|3308660 581 APRGLQS---GDRATWFGIYYNLSGA----GFYPHPIG-LELLVDHKALD 622 CS EEEEEEECCEETTE VieitDrgvripvp<-* ++ +t+++v+++++ gi|3308660 623 PALWTIQKVFYQGR 636 Cu_amine_oxid: domain 2 of 2, from 675 to 1091: score 705.7, E = 3.9e-209 CS S- --EEEEE-TT-SSEEEETTTEEEETTEEEEEEEETTTEEEEEEE *->pd.lkPLqitQPeGPsFrvtGgnlVeWanWsFhvGfdpReGlvIsdV p +++PLq++ PeGP+F+v+G + V +++W F++G ++++G++I+d+ gi|3308660 675 PGrAPPLQFH-PEGPRFSVQG-SQVRSSLWAFSFGLGAFSGPRIFDI 719 CS EEEETTEEEEEEEEEEEEEEEEEB-SSSTTTTTEEEEHHHHCTTTTTBB- rfnDegtkRpVmYrgSlsEmvVPYGDpspawyrKnYfDsGEyGlGkmanp rf++e +V+Y++S++E++++YG++spa + + Y+D ++G+Gk+++p gi|3308660 720 RFQGE----RVAYEISVQEAIALYGGNSPASMSTCYMDG-SFGIGKYSTP 764 CS STTTTSSTTSEEEEEE.EEESTTS-EEEEEEEEEEEEEEEEEEEEE EES LspGcDCpgnatYlDaFhfadadGnPitipNAICvFEedaGlilwK.Hsd L++G+DCp+ atY+D+ hf+ ++++P+t+++A+CvFE+++Gl+l+++Hsd gi|3308660 765 LTRGVDCPYLATYVDW-HFLLESQTPKTLRDAFCVFEQNQGLPLRRhHSD 813 CS TTCTT.ECEEEEEEEEEEEEEEEEETTEEEEEEEEEETTSEEEEEEEEEE lrqnneginevrrsrkLVVrfisTVgNYDYifdWiFytdGaIeaevkATG +++ +++++ +++LVVr+++T+ NYDY++d +F+ +GaIe++++ATG gi|3308660 814 FYS---HYFGGVVETVLVVRSVATLLNYDYVWDMVFHSNGAIEVKFHATG 860 CS --EEEEESTTSTSTTHCCCTTTEEEEETTEEEEEEEEEEEEEEEETTTSS ILnvkglkygnkDeigeeeeryGtlvsenvigpvHqHlfhfRlDldiDGl ++ ++ +++ +e++G++v+e+++g+vH+H hf++Dld++Gl gi|3308660 861 YITSAFFFGA--------GEKFGNRVAEHTLGTVHTHNAHFKVDLDVAGL 902 CS EEEEEEEEEEEEEEECCTTTSTTSEEEEEEEEEEEEEBBHHHHEETTSGG kNsvvavdlKkvrvpmGapgnprgnalkalQlkrkllktEkdAafkldsa kN+ +a+dl +vpm++p+ p+ ++++lQ++rkll+tE++Aaf l+ a gi|3308660 903 KNWAWAEDL--AFVPMNVPWQPEF-QMQRLQVTRKLLETEEEAAFPLGNA 949 CS GTEEEEEEEEEEETTTS-CEEEEEEEEESBBSS-STTTSHHHHTHHHHHC tpRtwlivNpnkkNrvGgnPvGYkLipgstatllldpdssparDWiYHRa tpR +l++++n++N++G + +GY+++++s+a +l+++s++++ ++ gi|3308660 950 TPR-YLYLASNHSNKWG-HRRGYRIQILSFAGKPLPQESPIEK-----AF 992 CS GGGGSSEEEEE-TTT--STTTSS-TTTTSSSSS.SSSSHHHHHTT-CBSS aFarnqLwVTpYkeeElyagGdYvnQsqgDgpWaPTdgLadwikrnrsIe ++ r++L+VT++keeE+ ++++Y +q+D pW+PT+++ d+i+ n++I gi|3308660 993 TWGRYHLAVTQRKEEEPSSSSIY---NQND-PWTPTVDFTDFIS-NETIA 1037 CS SEEEEEEEEEEEEE--GGGGSSB.SEEEEEEEEEEEECSSSSSGTTTTCC ntDiVvWhTfGftHvPraEDwPNTiMPvesvgFlLrPhNFFdenPsLdvp ++D+V+W+T+Gf+H+P+aED+PNT+++++ vgF+LrP+NFFde+Ps+++p gi|3308660 1038 GEDLVAWVTAGFLHIPHAEDIPNTVTVGNGVGFFLRPYNFFDEDPSFYSP 1087 CS SSEE psve<-* +s++ gi|3308660 1088 DSIY 1091 PAP2: domain 1 of 1, from 1266 to 1323: score 36.7, E = 1.2e-09 CS CC-B--..HHHHHHHHHHHTT-GGGHHHHHHCHHCHCCCHHCCHH H *->lfgrpRApPhflavcqpdwgdstcsdlwyeellgyefycmagspg.l lfg+ R P +++ l gi|3308660 1266 LFGQ-R--P---------------------------------YWWvL 1276 CS HT-- SS-B--TTCSSTTBS-SS-SSS-HHHHHHHHHHHHHHHHCTT drid.lfgsvlltsafalvseagpSFPSGHaafaaafalflalylpr<-* d+++ ++ sv+l +f++++e+gp+ PSGHa+++a ++++++ + gi|3308660 1277 DTDYySNSSVPLIKQFPVTCETGPGSPSGHAMGTAGVYYVMVTSTLA 1323 Example 2 gi|118103025|ref|XP_418136.2| PREDICTED: similar to Aoc2 protein [Gallus gallus] 1153 (length) 945 1000 .. (wrt seq) 195 261 .] (wrt HMM) No.of residues in non-TM/SP region : 5 [3%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- Cu_amine_oxid Copper amine oxidase, enzyme domain 563.0 3.5e-166 1 PAP2 PAP2 superfamily 67.4 4e-18 2 Cu_amine_oxidN2 Copper amine oxidase, N2 domain 62.5 1.1e-16 1 Cu_amine_oxidN3 Copper amine oxidase, N3 domain 51.0 7.1e-15 1 DUF1965 Domain of unknown function (DUF1965) 8.6 0.052 1 Complex1_24kDa Respiratory-chain NADH dehydrogenase 8.1 0.079 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- Complex1_24kDa 1/1 52 68 .. 145 161 .] 8.1 0.079 Cu_amine_oxidN2 1/1 75 144 .. 18 91 .] 62.5 1.1e-16 Cu_amine_oxidN3 1/1 161 258 .. 1 111 [] 51.0 7.1e-15 DUF1965 1/1 244 270 .. 21 47 .. 8.6 0.052 Cu_amine_oxid 1/1 301 714 .. 1 449 [] 563.0 3.5e-166 PAP2 1/2 859 916 .. 1 93 [. 31.8 2.8e-08 PAP2 2/2 945 1000 .. 122 177 .] 35.6 2.5e-09 Alignments of top-scoring domains: Complex1_24kDa: domain 1 of 1, from 52 to 68: score 8.1, E = 0.079 *->yEdLTpekieeLLdrlk<-* ++dLTpe+++++ l+ gi|1181030 52 FADLTPEELAQVVQYLR 68 Cu_amine_oxidN2: domain 1 of 1, from 75 to 144: score 62.5, E = 1.1e-16 CS HHHCT.TTTTTEEEEEEEEE--HHHHHHHHHHSCSSSSSS-EEEEEE *->LkssallagkstrfhsveLlEPdKkaVlqwlekggplvappRkArVv L ++a +++++++++sv++++P+K++Vl++l+ gg ppR+A +v gi|1181030 75 LADAARAKPSDNCIASVDVQLPAKAEVLRFLDAGGAR--PPREALAV 119 CS EEETTSSSEEEEEEETTTTEEEEEEEE aldgaqtRshElvVDLttGkvvswril<-* +++gaq+ ++v++ +G+++ + ++ gi|1181030 120 LYFGAQA--EPNVTEYVVGPLPAPTYH 144 Cu_amine_oxidN3: domain 1 of 1, from 161 to 258: score 51.0, E = 7.1e-15 CS S---HHHHHHHHHHHHHTTGHHHHHHHHHTT.TCCGGGGEEEEEEE- *->PpvtleEfasaeevplrrtdPefiealkkRGflvnglsdvvciPwtv + vt +E+a + e++ +++ + ++l++++ + ++ ++++t gi|1181030 161 RAVTGAEYAAINELIQ-KELRKAPRFLAACC--AS--DGTDLATITT 202 CS SSSSTST.GTTS-EEEEEEEE-SSTT...S-GGGSEECTEEEEEETTTTE GwfGeasleeGrRllkalcfyrdgtvsPmdnyyahPieGLeilvDldakk +++G +s G+R++++++f+ + ++ +y++ P++ Le+lv + ++ gi|1181030 203 APRGLKS---GDRTTWFVLFHGIAGS----GYFVLPVG-LEVLVEHGPLD 244 CS EEEEEEECCEETTE VieitDrgvripvp<-* V + +v+++++ gi|1181030 245 VSQWYLCQVFYNGR 258 DUF1965: domain 1 of 1, from 244 to 270: score 8.6, E = 0.052 CS -GGG-EEEEEEETTEEESSHHHHHHHH *->DpSkWkLlGwLYNdkfYtttEEFReAy<-* D+S+W L YN+ ++ + E+ A+ gi|1181030 244 DVSQWYLCQVFYNGRYFPSIAELENAF 270 Cu_amine_oxid: domain 1 of 1, from 301 to 714: score 563.0, E = 3.5e-166 CS S---EEEEE-TT-SSEEEETTTEEEETTEEEEEEEETTTEEEEEEEE *->pdlkPLqitQPeGPsFrvtGgnlVeWanWsFhvGfdpReGlvIsdVr p PLq++ P+GP+++v++ n+V++++Ws +G++p G++++d+r gi|1181030 301 P--GPLQFE-PQGPRYSVRD-NRVTYQGWSIAFGMNPNTGPRLFDIR 343 CS EEETTEEEEEEEEEEEEEEEEEB-SSSTTTTTEEEEHHHHCTTTTTBB-S fnDegtkRpVmYrgSlsEmvVPYGDpspawyrKnYfDsGEyGlGkmanpL f++e +++Y++Sl+E+ ++YG++ p+ + ++Y+D ++G+G+ a +L gi|1181030 344 FRGE----RIIYELSLQEALALYGSNCPGGMSTRYLDG-SFGIGRFAYEL 388 CS TTTTSSTTSEEEEEE.EEESTTS-EEEEEEEEEEEEEEEEEEEEE EEST spGcDCpgnatYlDaFhfadadGnPitipNAICvFEedaGlilwK.Hsdl ++G+DCp+ atY+D h+++++ +Pit N +C+FE d++l+l+++ sd gi|1181030 389 VRGVDCPYLATYVDR-HYLSESDVPITNQNSLCIFEHDTSLPLRRhFSDA 437 CS TCTT.ECEEEEEEEEEEEEEEEEETTEEEEEEEEEETTSEEEEEEEEEE- rqnneginevrrsrkLVVrfisTVgNYDYifdWiFytdGaIeaevkATGI + +++++r+ +LV+r +sT+ NYDY++d+ Fy +Ga e++v+ATG+ gi|1181030 438 HS---LYYGGLRKNTLVIRAVSTLINYDYVWDFMFYSNGAVEVRVHATGY 484 CS -EEEEESTTSTSTTHCCCTTTEEEEETTEEEEEEEEEEEEEEEETTTSSE LnvkglkygnkDeigeeeeryGtlvsenvigpvHqHlfhfRlDldiDGlk ++ +l ++ ++ yG+ v ++++g+ H H +h+++DldiDG gi|1181030 485 ISSSFLHDQ--------GTNYGNKVGPHTLGTMHLHHIHYKVDLDIDGQL 526 CS EEEEEEEEEEEEEECCTTTSTTSEEEEEEEEEEEEEBBHHHHEETTSGGG NsvvavdlKkvrvpmGapgnprgnalkalQlkrkllktEkdAafkldsat Ns++ d+ ++m +p++p++ al+++ l r+ l++E +Aaf l+ ++ gi|1181030 527 NSLESHDM--GYQTMRVPWSPEN-ALQQPYLRRERLERENEAAFPLNASL 573 CS TEEEEEEEEEEETTTS-CEEEEEEEEESBBSS-STTTSHHHHTHHHHHCG pRtwlivNpnkkNrvGgnPvGYkLipgstatllldpdssparDWiYHRaa pR +l ++ +k Nr+G + ++Y+ + s++ + l+ s++++ +++ gi|1181030 574 PR-YLSFTGPKPNRWG-HLRSYRVQVVSFPGEHLPTSSPMEK-----AIS 616 CS GGGSSEEEEE-TTT--STTTSS-TTTTSSSSS.SSSSHHHHHTT-CBSSS FarnqLwVTpYkeeElyagGdYvnQsqgDgpWaPTdgLadwikrnrsIen + r+ L+VT++keeE+ ++++Y +q+D pW+PT+++ad+i+ +++I n gi|1181030 617 WGRYKLAVTRRKEEEPTSTSVY---NQND-PWTPTVTFADFIN-DETIAN 661 CS EEEEEEEEEEEEE--GGGGSSB.SEEEEEEEEEEEECSSSSSGTTTTCCS tDiVvWhTfGftHvPraEDwPNTiMPvesvgFlLrPhNFFdenPsLdvpp +D+V+W +Gf+HvP+aED+PNT+++++ vgF+LrP+N Fde+PsL++p+ gi|1181030 662 EDLVAWISVGFLHVPHAEDIPNTVTVGNGVGFFLRPYNYFDEDPSLYSPD 711 CS SEE sve<-* ++ gi|1181030 712 GIY 714 PAP2: domain 1 of 2, from 859 to 916: score 31.8, E = 2.8e-08 CS CCHHHHHHHHHHHHHHHHHHHHH CC-B--..HHHHHHHHHHHTT-G *->aalalllalvaslllnglaylKl.lfgrpRApPhflavcqpdwgdst ++ l++++v++ +ln + +K+ lfg+ R P gi|1181030 859 VGIRLIWVAVIGDWLNLV--FKWiLFGE-R--P-------------- 886 CS GGHHHHHHCHHCHCCCHHCCHH HHT-- SS-B--TTCSSTTBS-SS-S csdlwyeellgyefycmagspg.ldrid.lfgsvlltsafalvseagpS< +++ +++++ +++s + ++f+l++e+gp+ gi|1181030 887 -------------------YWWvHETDYySNASAPAIQQFPLTCETGPG 916 CS -* gi|1181030 - - PAP2: domain 2 of 2, from 945 to 1000: score 35.6, E = 2.5e-09 CS CGS-EECHHHHCCHHHHHHHHHHHCTSS-HHHHCHHHCHCHCCCCHC *->rllrlllgllllllallvglSRvylgvHypsDVlaGallGaliaalv r l+ +l+ ++++ ++v+lSR++ +H+p++V+aG++ G+++a+ + gi|1181030 945 RILWAMLWTGFWAVQVCVCLSRIFIAAHFPHQVIAGVISGMAVAETF 991 CS HCHCCCGB- llfvrrlld<-* ++++ + + gi|1181030 992 QHIHSIYHA 1000