Query psy11442
Match_columns 1362
No_of_seqs 801 out of 1642
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 18:35:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11442.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11442hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05380 Peptidase_A17: Pao re 100.0 2.3E-39 5E-44 340.3 8.2 155 157-334 1-159 (159)
2 PF03564 DUF1759: Protein of u 100.0 6.5E-29 1.4E-33 257.4 14.2 144 1168-1312 1-144 (145)
3 PF03564 DUF1759: Protein of u 99.8 1.6E-20 3.5E-25 194.7 4.8 102 812-913 1-102 (145)
4 PF05585 DUF1758: Putative pep 98.7 1.2E-08 2.5E-13 108.5 5.3 65 7-71 1-65 (164)
5 cd01644 RT_pepA17 RT_pepA17: R 98.1 1.9E-06 4.1E-11 95.5 3.4 59 70-130 155-213 (213)
6 PF00336 DNA_pol_viral_C: DNA 97.7 6.3E-05 1.4E-09 79.7 6.4 101 246-389 96-196 (245)
7 cd05480 NRIP_C NRIP_C; putativ 97.4 5.4E-05 1.2E-09 72.4 1.6 40 17-56 8-51 (103)
8 cd06222 RnaseH RNase H (RNase 97.2 0.0011 2.3E-08 65.2 7.6 81 298-385 39-127 (130)
9 PF09668 Asp_protease: Asparty 97.1 0.00022 4.7E-09 72.1 1.9 48 17-67 34-84 (124)
10 PF00075 RNase_H: RNase H; In 96.3 0.0074 1.6E-07 61.2 6.5 72 298-379 38-116 (132)
11 cd05479 RP_DDI RP_DDI; retrope 96.3 0.004 8.6E-08 63.3 4.3 52 4-56 14-68 (124)
12 PF13650 Asp_protease_2: Aspar 96.0 0.0044 9.5E-08 58.3 2.5 49 17-66 8-58 (90)
13 PF13975 gag-asp_proteas: gag- 95.9 0.014 3E-07 53.6 5.4 51 17-68 18-70 (72)
14 cd05484 retropepsin_like_LTR_2 95.8 0.0056 1.2E-07 58.6 2.5 55 17-72 10-65 (91)
15 KOG0012|consensus 95.4 0.0088 1.9E-07 69.2 2.6 41 15-55 243-286 (380)
16 PF13456 RVT_3: Reverse transc 94.6 0.072 1.6E-06 49.6 6.0 69 303-379 4-75 (87)
17 PRK00203 rnhA ribonuclease H; 93.9 0.25 5.4E-06 51.9 8.9 72 298-378 41-125 (150)
18 PF14223 UBN2: gag-polypeptide 93.7 0.31 6.8E-06 48.9 8.9 100 1224-1327 4-109 (119)
19 PF14227 UBN2_2: gag-polypepti 93.1 0.85 1.8E-05 45.8 11.0 97 1224-1328 5-108 (119)
20 cd05483 retropepsin_like_bacte 93.1 0.075 1.6E-06 50.5 3.1 45 17-61 12-57 (96)
21 COG0328 RnhA Ribonuclease HI [ 93.1 0.52 1.1E-05 49.8 9.4 74 298-378 41-128 (154)
22 cd06095 RP_RTVL_H_like Retrope 93.0 0.072 1.6E-06 50.6 2.8 46 17-64 8-53 (86)
23 PF00077 RVP: Retroviral aspar 92.6 0.024 5.2E-07 55.0 -1.0 50 18-70 16-65 (100)
24 PRK07708 hypothetical protein; 92.5 0.81 1.8E-05 51.3 10.7 168 167-383 23-201 (219)
25 PRK13907 rnhA ribonuclease H; 92.1 1.1 2.5E-05 45.4 10.5 80 298-385 39-122 (128)
26 PF08284 RVP_2: Retroviral asp 91.7 0.15 3.3E-06 52.7 3.5 41 17-57 31-73 (135)
27 cd05481 retropepsin_like_LTR_1 91.7 0.12 2.6E-06 50.0 2.6 53 17-70 9-65 (93)
28 PRK06548 ribonuclease H; Provi 91.1 1.2 2.7E-05 47.4 9.6 72 298-377 40-124 (161)
29 PF14893 PNMA: PNMA 91.0 0.66 1.4E-05 54.9 8.2 134 1163-1300 164-308 (331)
30 TIGR02281 clan_AA_DTGA clan AA 90.9 0.21 4.6E-06 50.6 3.6 39 18-56 22-62 (121)
31 PRK08719 ribonuclease H; Revie 90.5 1.4 3E-05 46.3 9.3 69 298-377 48-129 (147)
32 PF12384 Peptidase_A2B: Ty3 tr 89.2 0.22 4.8E-06 52.3 2.0 60 16-75 43-103 (177)
33 PRK07238 bifunctional RNase H/ 87.2 3.2 6.9E-05 50.3 10.6 81 298-386 43-128 (372)
34 TIGR03698 clan_AA_DTGF clan AA 86.5 1 2.2E-05 44.7 4.8 43 4-46 1-45 (107)
35 PF14893 PNMA: PNMA 85.7 1.2 2.5E-05 52.8 5.6 85 807-891 164-256 (331)
36 PF05380 Peptidase_A17: Pao re 79.5 1 2.2E-05 47.9 1.8 20 164-183 125-144 (159)
37 cd00303 retropepsin_like Retro 77.0 2.3 5.1E-05 37.8 3.2 41 17-57 8-50 (92)
38 cd05482 HIV_retropepsin_like R 56.0 7.3 0.00016 37.4 2.0 37 16-57 7-47 (87)
39 KOG3752|consensus 53.6 88 0.0019 37.7 10.5 72 298-376 254-346 (371)
40 cd06094 RP_Saci_like RP_Saci_l 52.1 5.7 0.00012 38.2 0.5 56 8-70 2-57 (89)
41 PF03732 Retrotrans_gag: Retro 51.6 24 0.00053 33.1 4.8 88 1202-1298 4-95 (96)
42 PF12382 Peptidase_A2E: Retrot 41.8 13 0.00029 35.9 1.2 43 19-61 48-90 (137)
43 PF00665 rve: Integrase core d 32.8 28 0.00061 34.2 2.0 58 625-690 43-119 (120)
44 COG3577 Predicted aspartyl pro 32.2 60 0.0013 36.0 4.5 44 6-49 96-147 (215)
No 1
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=100.00 E-value=2.3e-39 Score=340.27 Aligned_cols=155 Identities=27% Similarity=0.365 Sum_probs=146.2
Q ss_pred CCcccccchhhHHHHHHHHHhhccccccchhhccccccceeccccccccccccCCCChhhHHHHHHHHHhhccccccccc
Q psy11442 157 APTKQLLSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINNDITFLLR 236 (1362)
Q Consensus 157 ~tkR~~lS~p~~el~~a~~~a~~~Dpl~G~l~p~~~~~k~~~q~~~~~~l~Wd~~l~~~~~~~w~~~~~~l~~~~~~~ip 236 (1362)
||||+++|+ +|++|||| |+++|+++++|+++|++|+.+++||+++|+++...|.+|++++..+.++.||
T Consensus 1 pTKR~ils~----------ia~~yDPl-Gl~~p~~i~~K~llq~lw~~~l~WD~~lp~el~~~w~~~~~~l~~~~~i~iP 69 (159)
T PF05380_consen 1 PTKRQILSF----------IASIYDPL-GLLAPIIIRAKLLLQKLWQSKLDWDDPLPDELRKEWKKWLKELESLSPIRIP 69 (159)
T ss_pred CChHHHHHH----------HHHHcCcc-hhhHHHHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHhhcccccCC
Confidence 699999999 99999999 9999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeecce----eeecccccccceEEEEEeccccccccccCCCceeeeeeeeeeccccccCcccccchhhHHHHHHHHH
Q psy11442 237 KILVIVLRV----IYFPSNLFLIRYGGMVLSFSPLLIGQSYPSGFKFCNRGLIKAKSKVAPTKQLLSIPRLELCAALLLS 312 (1362)
Q Consensus 237 R~~~~~~~~----~~F~~DAS~~ayga~~Ylr~~~~~g~~~~~~~~~~~~~li~aKsrv~P~k~~~tIPRlEL~a~~l~~ 312 (1362)
|++...... |+|| |||+.|||||+|+| . +.+|.. + ++|++|||||+|+|. .||||||||||++|+
T Consensus 70 R~i~~~~~~~~~L~~F~-DAS~~aygavvYlr------~-~~~~~~-~-~~ll~aKsrv~P~k~-~tIPRlEL~a~~l~~ 138 (159)
T PF05380_consen 70 RCIPISDYRSVELHVFC-DASESAYGAVVYLR------S-YSDGSV-Q-VRLLFAKSRVAPLKT-VTIPRLELLAALLGV 138 (159)
T ss_pred cccccccccceeeeEee-cccccceeeEeEee------e-ccCCce-e-eeeeeecccccCCCC-CcHHHHHHHHHHHHH
Confidence 977533221 9999 99999999999999 6 677776 6 899999999999999 799999999999999
Q ss_pred HHHHHHHHHhccCCcccEEEee
Q psy11442 313 RLYNSLHNYLTKLNVKNVTFFS 334 (1362)
Q Consensus 313 ~l~~~~~~~l~~~~i~~~~~~t 334 (1362)
+|+..+.++|+ +++.+++|||
T Consensus 139 ~l~~~~~~~l~-~~~~~~~~wt 159 (159)
T PF05380_consen 139 RLANTVKKELD-IEISQVVFWT 159 (159)
T ss_pred HHHHHHHHHcC-CCcceeEEeC
Confidence 99999999999 9999999997
No 2
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=99.96 E-value=6.5e-29 Score=257.38 Aligned_cols=144 Identities=33% Similarity=0.546 Sum_probs=139.5
Q ss_pred cccccccchHHHHHHHHHhhcCCCCChhhHHHHhhhccchhhhhhhcCCCCCcccHHHHHHHHHHHhhhhhhHHHHHHHH
Q psy11442 1168 FSGEFSEFNVFYESFKSLIHDNKELDNTQKVQYLVSKLSGKALTVCAGVPATVDNYSIIFNNLVEKYQCKRSQAKAYLSN 1247 (1362)
Q Consensus 1168 FdGd~~ew~~F~~~F~~~Ih~~~~ls~~~K~~~Lrs~L~GeA~~~I~~l~ls~~nY~~A~~~L~~rYg~~~~ii~~~l~~ 1247 (1362)
||||+.+|+.|+++|+++||+|++++|++|++||++||+|+|+++|++++++++||+.||+.|+++||||+.++++|+++
T Consensus 1 F~G~~~~~~~F~~~F~~~v~~n~~~~d~~K~~~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~~~~~ 80 (145)
T PF03564_consen 1 FDGDPSEWPEFIDQFDSLVHENPDLSDIEKLNYLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRIIQALLEE 80 (145)
T ss_pred CCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCcCCCCChhHHHHHHHHHHHHHHHHHhCCCCCCchhHHHHHHHhcCCHHHHHHHHHhcCCC
Q psy11442 1248 ILNFKQIKGESPDQLNSLIDELCASVLALKKVDLDSLSDFMLAHITLSKIDSETARLFEMSLKSG 1312 (1362)
Q Consensus 1248 L~~lp~i~~~~~~~Lr~l~d~v~~~i~aL~~Lg~~~~~~~~l~~ii~~KLP~~~~~~W~~~~~~~ 1312 (1362)
|+++|++..++..+|+.++++++.++.+|+++|++. .+.+++++|++|||..++.+|.++..+.
T Consensus 81 l~~l~~~~~~d~~~L~~~~~~v~~~i~~L~~lg~~~-~~~~l~~~i~~KLp~~~~~~w~~~~~~~ 144 (145)
T PF03564_consen 81 LRNLPPISNDDPEALRSLVDKVNNCIRALKALGVNV-DDPLLISIILSKLPPEIREKWEEHVKKK 144 (145)
T ss_pred HhccccccchhHHHHHHHHHHHHHHHHHHHHcCCCC-CCHHHHHHHHHHCCHHHHHHHHHHhhcc
Confidence 999999999999999999999999999999999976 4889999999999999999999987643
No 3
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=99.80 E-value=1.6e-20 Score=194.69 Aligned_cols=102 Identities=31% Similarity=0.547 Sum_probs=97.6
Q ss_pred ccccccchhhHHHHHHHHhhcCCCCChHHHHHHHHHhcchhHHHhhccCCCCCCcHHHHHHHHHHhhhchHHHHHHHHHH
Q psy11442 812 FSGEFSEFNVFYESFKSLIHDNKELDNTQKVQYLVSKLSGKALTVCAGVPATADNYSIIFNNLVEKYQCKRSQAKAYLSN 891 (1362)
Q Consensus 812 F~Gd~~~w~~F~d~F~~~i~~~~~ls~~~Kf~yL~s~L~G~A~~~I~~l~lt~~nY~~A~~~L~~ry~~~~~i~~~~l~~ 891 (1362)
||||+.+|+.|+++|+++||+|+++++++||+||++||+|+|+++|++++++++||+.||++|++||||++.++++|+++
T Consensus 1 F~G~~~~~~~F~~~F~~~v~~n~~~~d~~K~~~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~~~~~ 80 (145)
T PF03564_consen 1 FDGDPSEWPEFIDQFDSLVHENPDLSDIEKLNYLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRIIQALLEE 80 (145)
T ss_pred CCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccccccCCcCCCccccccce
Q psy11442 892 ILNFKQIKGQNVNEVPELKKSV 913 (1362)
Q Consensus 892 L~~lp~i~~esv~~lpElkk~~ 913 (1362)
|+++|++.+++..++..+...+
T Consensus 81 l~~l~~~~~~d~~~L~~~~~~v 102 (145)
T PF03564_consen 81 LRNLPPISNDDPEALRSLVDKV 102 (145)
T ss_pred HhccccccchhHHHHHHHHHHH
Confidence 9999999988888887775543
No 4
>PF05585 DUF1758: Putative peptidase (DUF1758); InterPro: IPR008737 This is a family of nematode proteins of unknown function []. However, it seems likely that these proteins act as aspartic peptidases.
Probab=98.71 E-value=1.2e-08 Score=108.51 Aligned_cols=65 Identities=26% Similarity=0.357 Sum_probs=58.6
Q ss_pred EEEecCCCCeEEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCcccCCCccchhhH
Q psy11442 7 AFILNASGQLSSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPDNKGAVSCTLA 71 (1362)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 (1362)
|.|+|..|.++++|||||||||.|+||++||++|||+..+..+.++|++|...+..++.+.+.+.
T Consensus 1 v~V~n~~g~~~~~~~LlDsGSq~SfIt~~la~~L~L~~~~~~~~~~~~~g~~~~~~~~~~~~~i~ 65 (164)
T PF05585_consen 1 VNVFNPNGNQVEARALLDSGSQRSFITESLANKLNLPGTGEKILVIGTFGSSSPKSKKCVRVKIS 65 (164)
T ss_pred CEEECCCCCEEEEEEEEecCCchhHHhHHHHHHhCCCCCCceEEEEeccCccCccceeEEEEEEE
Confidence 68999999999999999999999999999999999999999999999999887777765555444
No 5
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=98.08 E-value=1.9e-06 Score=95.55 Aligned_cols=59 Identities=34% Similarity=0.513 Sum_probs=50.3
Q ss_pred hHhHHHHHHHHHhcCCceeEEeechHHHhccCCCCCcccCCcCCCCCCceEEeeeeecCCc
Q psy11442 70 LATSNKVIFSENKGCFELRKWASNSQQLLNTVPHEHCEVPLRQNEESTFKILSVFIGNQQL 130 (1362)
Q Consensus 70 ~~~~~~~~~~~~~~~f~lrk~~sN~~~~~~~i~~~~~~~~~~~~~~~~~K~LG~~w~~~~D 130 (1362)
....++|.++|+++||+||||+||++++++.+|++.. ......+.+.|+||+.|++.+|
T Consensus 155 ~~~~~~v~~~L~~~Gf~l~kw~sn~~~~l~~~~~~~~--~~~~~~~~~~k~LGl~W~~~~D 213 (213)
T cd01644 155 VNVAKRLIALLKKGGFNLRKWASNSQEVLDDLPEERV--LLDRDSDVTEKTLGLRWNPKTD 213 (213)
T ss_pred HHHHHHHHHHHHhCCccchhcccCchhhhhccccccc--ccccccccchhcccceeeccCC
Confidence 4467899999999999999999999999999998732 2234566789999999999887
No 6
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=97.69 E-value=6.3e-05 Score=79.72 Aligned_cols=101 Identities=25% Similarity=0.230 Sum_probs=65.9
Q ss_pred eeecccccccceEEEEEeccccccccccCCCceeeeeeeeeeccccccCcccccchhhHHHHHHHHHHHHHHHHHHhccC
Q psy11442 246 IYFPSNLFLIRYGGMVLSFSPLLIGQSYPSGFKFCNRGLIKAKSKVAPTKQLLSIPRLELCAALLLSRLYNSLHNYLTKL 325 (1362)
Q Consensus 246 ~~F~~DAS~~ayga~~Ylr~~~~~g~~~~~~~~~~~~~li~aKsrv~P~k~~~tIPRlEL~a~~l~~~l~~~~~~~l~~~ 325 (1362)
-+|+ ||+-.++|.++ - . |. ...-++| +.|+. =.||+||.+|- .
T Consensus 96 ~Vfa-DATpTgwgi~i--~------~----~~----~~~Tfs~--~l~Ih------taELlaaClAr------------~ 138 (245)
T PF00336_consen 96 QVFA-DATPTGWGISI--T------G----QR----MRGTFSK--PLPIH------TAELLAACLAR------------L 138 (245)
T ss_pred ceec-cCCCCcceeee--c------C----ce----eeeeecc--cccch------HHHHHHHHHHH------------h
Confidence 7899 99999999873 1 1 11 2222333 44444 37998887654 2
Q ss_pred CcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhCCCCceEeecCCCCCCCCCCCCCCc
Q psy11442 326 NVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLADGCKWYHVPTSENPCDCASRGLLP 389 (1362)
Q Consensus 326 ~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~~~~~w~hvpt~~NPAD~~SRG~s~ 389 (1362)
-+..-.+-|||++||+ +++..|=-+=--.-..++...++-||||+-||||..|||.-.
T Consensus 139 ~~~~r~l~tDnt~Vls------rkyts~PW~lac~A~wiLrgts~~yVPS~~NPAD~PsR~~~~ 196 (245)
T PF00336_consen 139 MSGARCLGTDNTVVLS------RKYTSFPWLLACAANWILRGTSFYYVPSKYNPADDPSRGKLG 196 (245)
T ss_pred ccCCcEEeecCcEEEe------cccccCcHHHHHHHHHhhcCceEEEeccccCcCCCCCCCccc
Confidence 2334458899999986 344443222111223456688999999999999999999854
No 7
>cd05480 NRIP_C NRIP_C; putative nuclear receptor interacting protein. Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.
Probab=97.43 E-value=5.4e-05 Score=72.39 Aligned_cols=40 Identities=33% Similarity=0.571 Sum_probs=34.1
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCccee----eeceeeeecCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRY----KCGISISGIGD 56 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~ 56 (1362)
+||+|++|||.|.++|+..||+|+||.|. ++..+-.|+|.
T Consensus 8 ~~vkAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gvgt 51 (103)
T cd05480 8 KELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPT 51 (103)
T ss_pred EEEEEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCCCc
Confidence 79999999999999999999999999965 55455566665
No 8
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=97.17 E-value=0.0011 Score=65.18 Aligned_cols=81 Identities=20% Similarity=0.144 Sum_probs=60.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhC---CCCceEeec
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLA---DGCKWYHVP 374 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~---~~~~w~hvp 374 (1362)
.|.-..|+.|++.|.+.+. . ..+..+.++|||..++..+++.......-....+..|++.. ....++|||
T Consensus 39 ~s~~~aEl~al~~al~~~~------~-~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~ 111 (130)
T cd06222 39 TTNNRAELLALIEALELAL------E-LGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVP 111 (130)
T ss_pred CcHHHHHHHHHHHHHHHHH------h-CCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcC
Confidence 7788999999999987766 3 57899999999999999999865422233444455565554 467889999
Q ss_pred C-----CCCCCCCCCC
Q psy11442 375 T-----SENPCDCASR 385 (1362)
Q Consensus 375 t-----~~NPAD~~SR 385 (1362)
+ ..+.||..+|
T Consensus 112 ~h~~~~~n~~ad~la~ 127 (130)
T cd06222 112 GHSGIEGNERADALAK 127 (130)
T ss_pred CCCCCcchHHHHHHHH
Confidence 9 4446886554
No 9
>PF09668 Asp_protease: Aspartyl protease; InterPro: IPR019103 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 3S8I_A 2I1A_B.
Probab=97.10 E-value=0.00022 Score=72.10 Aligned_cols=48 Identities=25% Similarity=0.534 Sum_probs=30.7
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCccee---eeceeeeecCCCCcccCCCccc
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRY---KCGISISGIGDNGVPDNKGAVS 67 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ 67 (1362)
+|++|++|||.|.|+|+..||+|+||.+. +......|+ +....-|+++
T Consensus 34 ~~vkA~VDtGAQ~tims~~~a~r~gL~~lid~r~~g~a~Gv---G~~~i~G~Ih 84 (124)
T PF09668_consen 34 VPVKAFVDTGAQSTIMSKSCAERCGLMRLIDKRFAGVAKGV---GTQKILGRIH 84 (124)
T ss_dssp EEEEEEEETT-SS-EEEHHHHHHTTGGGGEEGGG-EE----------EEEEEEE
T ss_pred EEEEEEEeCCCCccccCHHHHHHcCChhhccccccccccCC---CcCceeEEEE
Confidence 58999999999999999999999999742 333445555 4445666665
No 10
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=96.33 E-value=0.0074 Score=61.22 Aligned_cols=72 Identities=22% Similarity=0.179 Sum_probs=50.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhc-----CCCc--cchhHHHHHHHHHhhCCCCce
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRT-----APHL--LQTYVANRVVEINKLADGCKW 370 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~-----~~~~--~~~fv~NRv~~I~~~~~~~~w 370 (1362)
.|.=+.||+|+..|.+.+ . -..++++|||+.++.+|.. ..+. ...-+.+++.+....-....+
T Consensus 38 ~s~~~aEl~Ai~~AL~~~-------~---~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~ 107 (132)
T PF00075_consen 38 QSNNRAELQAIIEALKAL-------E---HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRF 107 (132)
T ss_dssp ECHHHHHHHHHHHHHHTH-------S---TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEE
T ss_pred cchhhhheehHHHHHHHh-------h---cccccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEee
Confidence 788899999999888732 1 1578999999999998876 2211 110244466666555557899
Q ss_pred EeecCCCCC
Q psy11442 371 YHVPTSENP 379 (1362)
Q Consensus 371 ~hvpt~~NP 379 (1362)
+|||+..|-
T Consensus 108 ~~V~~H~~~ 116 (132)
T PF00075_consen 108 RWVPGHSGV 116 (132)
T ss_dssp EESSSSSSS
T ss_pred eeccCcCCC
Confidence 999998764
No 11
>cd05479 RP_DDI RP_DDI; retropepsin-like domain of DNA damage inducible protein. The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI.
Probab=96.30 E-value=0.004 Score=63.33 Aligned_cols=52 Identities=21% Similarity=0.416 Sum_probs=37.5
Q ss_pred ceEEEEecCCCCeEEEEEeecCCCcchhhHHHHHHHhCcceeee---ceeeeecCC
Q psy11442 4 TARAFILNASGQLSSIRVIVDPGSQVSCITNDCVQRLGLKRYKC---GISISGIGD 56 (1362)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~ 56 (1362)
|..++|.-.-+.. |+++|||||++.|+|+.+||+||||..... .+.+.|.|+
T Consensus 14 ~~~~~v~~~Ing~-~~~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~ 68 (124)
T cd05479 14 VPMLYINVEINGV-PVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGT 68 (124)
T ss_pred eeEEEEEEEECCE-EEEEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCC
Confidence 3344444333333 899999999999999999999999976432 346677665
No 12
>PF13650 Asp_protease_2: Aspartyl protease
Probab=95.96 E-value=0.0044 Score=58.29 Aligned_cols=49 Identities=35% Similarity=0.611 Sum_probs=40.9
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeec--eeeeecCCCCcccCCCcc
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCG--ISISGIGDNGVPDNKGAV 66 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 66 (1362)
+|+++|||+|++.++|+.+.|++||++..... ..+.|.+|. .....+.+
T Consensus 8 ~~~~~liDTGa~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~g~-~~~~~~~~ 58 (90)
T PF13650_consen 8 KPVRFLIDTGASISVISRSLAKKLGLKPRPKSVPISVSGAGGS-VTVYRGRV 58 (90)
T ss_pred EEEEEEEcCCCCcEEECHHHHHHcCCCCcCCceeEEEEeCCCC-EEEEEEEE
Confidence 49999999999999999999999999988764 678888887 55554543
No 13
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=95.91 E-value=0.014 Score=53.65 Aligned_cols=51 Identities=24% Similarity=0.414 Sum_probs=41.6
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeec--eeeeecCCCCcccCCCccch
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCG--ISISGIGDNGVPDNKGAVSC 68 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 68 (1362)
+++.+|+|+||..|+|..+.|+||||+..+-. ..|. +.+-.+....|+++|
T Consensus 18 ~~~~alvDtGat~~fis~~~a~rLgl~~~~~~~~~~v~-~a~g~~~~~~g~~~~ 70 (72)
T PF13975_consen 18 VQVKALVDTGATHNFISESLAKRLGLPLEKPPSPIRVK-LANGSVIEIRGVAEN 70 (72)
T ss_pred EEEEEEEeCCCcceecCHHHHHHhCCCcccCCCCEEEE-ECCCCccccceEEEe
Confidence 78889999999999999999999999999888 5666 455555556666655
No 14
>cd05484 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classif
Probab=95.81 E-value=0.0056 Score=58.61 Aligned_cols=55 Identities=15% Similarity=0.205 Sum_probs=45.8
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcc-eeeeceeeeecCCCCcccCCCccchhhHh
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLK-RYKCGISISGIGDNGVPDNKGAVSCTLAT 72 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (1362)
+|+++|||+||.+++|+.+.+.++|++ -.+....+.|.+|.. ..+.|.+.|.+..
T Consensus 10 ~~i~~lvDTGA~~svis~~~~~~lg~~~~~~~~~~v~~a~G~~-~~~~G~~~~~v~~ 65 (91)
T cd05484 10 KPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTK-LSVLGQILVTVKY 65 (91)
T ss_pred EEEEEEEcCCcceEEeCHHHHHHhCCCccccccEEEEecCCCE-eeEeEEEEEEEEE
Confidence 489999999999999999999999988 556678999999965 6677776665543
No 15
>KOG0012|consensus
Probab=95.39 E-value=0.0088 Score=69.19 Aligned_cols=41 Identities=27% Similarity=0.568 Sum_probs=35.0
Q ss_pred CeEEEEEeecCCCcchhhHHHHHHHhCccee---eeceeeeecC
Q psy11442 15 QLSSIRVIVDPGSQVSCITNDCVQRLGLKRY---KCGISISGIG 55 (1362)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~ 55 (1362)
+-+||+|.||||-|-++|+.+||+|+||+|. ++-.+--|+|
T Consensus 243 ng~~VKAfVDsGaq~timS~~Caer~gL~rlid~r~~g~a~gvg 286 (380)
T KOG0012|consen 243 NGVPVKAFVDSGAQTTIMSAACAERCGLNRLIDKRFQGEARGVG 286 (380)
T ss_pred CCEEEEEEEcccchhhhhhHHHHHHhChHHHhhhhhhccccCCC
Confidence 3489999999999999999999999999974 5555666666
No 16
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=94.60 E-value=0.072 Score=49.64 Aligned_cols=69 Identities=22% Similarity=0.237 Sum_probs=49.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhCC---CCceEeecCCCCC
Q psy11442 303 LELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLAD---GCKWYHVPTSENP 379 (1362)
Q Consensus 303 lEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~~---~~~w~hvpt~~NP 379 (1362)
.|+.|+..|.+++. . +.+.++.+.|||..+...|++...... .....+.+|+.+.. ...|+|||-+.|=
T Consensus 4 aE~~al~~al~~a~------~-~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~ 75 (87)
T PF13456_consen 4 AEALALLEALQLAW------E-LGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFWNVSVSHIPREQNK 75 (87)
T ss_dssp HHHHHHHHHHHHHH------C-CT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCSCEEEEE--GGGSH
T ss_pred HHHHHHHHHHHHHH------H-CCCCEEEEEecCccccccccccccccc-cccccchhhhhhhccccceEEEEEChHHhH
Confidence 47888887776553 3 678999999999999999998754434 66777777777765 5889999999884
No 17
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=93.88 E-value=0.25 Score=51.93 Aligned_cols=72 Identities=22% Similarity=0.264 Sum_probs=47.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHH----HHhcC-CCccc----hhHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLA----WLRTA-PHLLQ----TYVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~----wi~~~-~~~~~----~fv~NR--v~~I~~~~~ 366 (1362)
.|--|.||+|++.|.+.+. ....+.++|||+.++. |+.+= .+.|+ .-|+|+ .++|.++..
T Consensus 41 ~TN~~aEL~Ai~~AL~~~~---------~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~ 111 (150)
T PRK00203 41 TTNNRMELMAAIEALEALK---------EPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK 111 (150)
T ss_pred CcHHHHHHHHHHHHHHHcC---------CCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc
Confidence 7888999999998876431 1246899999987764 44320 11122 245665 566666554
Q ss_pred --CCceEeecCCCC
Q psy11442 367 --GCKWYHVPTSEN 378 (1362)
Q Consensus 367 --~~~w~hvpt~~N 378 (1362)
...|.|||+..+
T Consensus 112 ~~~v~~~wV~~H~~ 125 (150)
T PRK00203 112 RHQIKWHWVKGHAG 125 (150)
T ss_pred cCceEEEEecCCCC
Confidence 578999997664
No 18
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=93.73 E-value=0.31 Score=48.89 Aligned_cols=100 Identities=17% Similarity=0.228 Sum_probs=74.4
Q ss_pred HHHHHHHHHHhhhhhhH----HHHHHHHhhccCcCCCCChhHHHHHHHHHHHHHHHHHhCCCCCCchhHHHHHHHhcCCH
Q psy11442 1224 SIIFNNLVEKYQCKRSQ----AKAYLSNILNFKQIKGESPDQLNSLIDELCASVLALKKVDLDSLSDFMLAHITLSKIDS 1299 (1362)
Q Consensus 1224 ~~A~~~L~~rYg~~~~i----i~~~l~~L~~lp~i~~~~~~~Lr~l~d~v~~~i~aL~~Lg~~~~~~~~l~~ii~~KLP~ 1299 (1362)
.++|+.|+++|.....+ ...+..++.++ +-.+...+..++..+...+..|.++|.+ +.+..++..+++.||+
T Consensus 4 ~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~---k~~~~~sv~~y~~~~~~i~~~L~~~g~~-i~d~~~v~~iL~~Lp~ 79 (119)
T PF14223_consen 4 KEAWDALKKRYEGQSKVKQARVQQLKSQLENL---KMKDGESVDEYISRLKEIVDELRAIGKP-ISDEDLVSKILRSLPP 79 (119)
T ss_pred HHHHHHHHHHHcCCchHHHHHHHHHHHHHHHH---HhcccccHHHHHHHHHHhhhhhhhcCCc-ccchhHHHHHHhcCCc
Confidence 46899999999988763 33444444444 4346678899999999999999999986 3677899999999997
Q ss_pred HHHHHHHHhcCCCCCC--CHHHHHHHHHHH
Q psy11442 1300 ETARLFEMSLKSGEIP--TFSKVHNFLKDQ 1327 (1362)
Q Consensus 1300 ~~~~~W~~~~~~~~~p--t~~~ll~FL~~r 1327 (1362)
.-......-......+ |++++..-|...
T Consensus 80 ~y~~~~~~i~~~~~~~~~t~~el~~~L~~~ 109 (119)
T PF14223_consen 80 SYDTFVTAIRNSKDLPKMTLEELISRLLAE 109 (119)
T ss_pred hhHHHHHHHHhcCCCCcCCHHHHHHHHHHH
Confidence 6555544433444555 899999888643
No 19
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=93.14 E-value=0.85 Score=45.76 Aligned_cols=97 Identities=20% Similarity=0.239 Sum_probs=74.0
Q ss_pred HHHHHHHHHHhhhhhhHHH-HHHHHhhccCcCCCCChhHHHHHHHHHHHHHHHHHhCCCCCCchhHHHHHHHhcCCHHHH
Q psy11442 1224 SIIFNNLVEKYQCKRSQAK-AYLSNILNFKQIKGESPDQLNSLIDELCASVLALKKVDLDSLSDFMLAHITLSKIDSETA 1302 (1362)
Q Consensus 1224 ~~A~~~L~~rYg~~~~ii~-~~l~~L~~lp~i~~~~~~~Lr~l~d~v~~~i~aL~~Lg~~~~~~~~l~~ii~~KLP~~~~ 1302 (1362)
..+|+.|+..|+....... ..+++|.++ +-.+...++..++.++..+..|+++|.+. .+..++.+|+.+||+.
T Consensus 5 ~~~W~~L~~~y~~~~~~~~~~l~~kl~~~---k~~~~~~v~~hi~~~~~l~~~L~~~g~~i-~d~~~~~~lL~sLP~s-- 78 (119)
T PF14227_consen 5 KEMWDKLKKKYEKKSFANKIYLLRKLYSL---KMDEGGSVRDHINEFRSLVNQLKSLGVPI-DDEDKVIILLSSLPPS-- 78 (119)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHh---HhccchhHHHHHHHHHHHHHhhccccccc-hHHHHHHHHHHcCCHh--
Confidence 4689999999999877553 445666665 33445668899999999999999999874 6667889999999977
Q ss_pred HHHHHhcC------CCCCCCHHHHHHHHHHHH
Q psy11442 1303 RLFEMSLK------SGEIPTFSKVHNFLKDQV 1328 (1362)
Q Consensus 1303 ~~W~~~~~------~~~~pt~~~ll~FL~~r~ 1328 (1362)
|+..+. ....+|++++..-|.++-
T Consensus 79 --y~~~~~~l~~~~~~~~~tl~~v~~~L~~ee 108 (119)
T PF14227_consen 79 --YDSFVTALLYSKPEDELTLEEVKSKLLQEE 108 (119)
T ss_pred --HHHHHHHHHccCCCCCcCHHHHHHHHHHHH
Confidence 555432 236789998888877633
No 20
>cd05483 retropepsin_like_bacteria Bacterial aspartate proteases, retropepsin-like protease family. This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.
Probab=93.06 E-value=0.075 Score=50.46 Aligned_cols=45 Identities=18% Similarity=0.379 Sum_probs=35.5
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCc-ceeeeceeeeecCCCCccc
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGL-KRYKCGISISGIGDNGVPD 61 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 61 (1362)
+|+++|||+||+.++|+..+|..||+ ........+.+.+|.....
T Consensus 12 ~~~~~llDTGa~~s~i~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~ 57 (96)
T cd05483 12 QPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAA 57 (96)
T ss_pred EEEEEEEECCCCcEEcCHHHHHHcCCCccCCCcEEEEecCCCccce
Confidence 79999999999999999999999998 2333455677777665543
No 21
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=93.06 E-value=0.52 Score=49.76 Aligned_cols=74 Identities=24% Similarity=0.289 Sum_probs=51.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHH----HHhcC-CCccch----hHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLA----WLRTA-PHLLQT----YVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~----wi~~~-~~~~~~----fv~NR--v~~I~~~~~ 366 (1362)
.|=-|+||+|++.|.+.+.. .....+.++|||+.|.. |+.+. ...|++ .|.|+ ..++.++..
T Consensus 41 tTNNraEl~A~i~AL~~l~~-------~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~ 113 (154)
T COG0328 41 TTNNRAELRALIEALEALKE-------LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLK 113 (154)
T ss_pred ccChHHHHHHHHHHHHHHHh-------cCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHh
Confidence 67789999999988875544 45788999999997753 64433 223553 44443 555555554
Q ss_pred ---CCceEeecCCCC
Q psy11442 367 ---GCKWYHVPTSEN 378 (1362)
Q Consensus 367 ---~~~w~hvpt~~N 378 (1362)
.+.|++|++..+
T Consensus 114 ~~~~v~~~WVkgH~g 128 (154)
T COG0328 114 RHELVFWEWVKGHAG 128 (154)
T ss_pred hCCeEEEEEeeCCCC
Confidence 569999998765
No 22
>cd06095 RP_RTVL_H_like Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements. This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where
Probab=93.01 E-value=0.072 Score=50.56 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=38.4
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCcccCCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPDNKG 64 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (1362)
+|++.|||.|++.++|+...|+++.+ ..+.+.+.|+||.....+++
T Consensus 8 ~~~~fLvDTGA~~tii~~~~a~~~~~--~~~~~~v~gagG~~~~~v~~ 53 (86)
T cd06095 8 VPIVFLVDTGATHSVLKSDLGPKQEL--STTSVLIRGVSGQSQQPVTT 53 (86)
T ss_pred EEEEEEEECCCCeEEECHHHhhhccC--CCCcEEEEeCCCcccccEEE
Confidence 48999999999999999999999944 45889999999997334433
No 23
>PF00077 RVP: Retroviral aspartyl protease The Prosite entry also includes Pfam:PF00026; InterPro: IPR018061 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to the MEROPS peptidase family A2 (retropepsin family, clan AA), subfamily A2A. The family includes the single domain aspartic proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). Retroviral aspartyl protease is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins.; PDB: 3D3T_B 3SQF_A 1NSO_A 2HB3_A 2HS2_A 2HS1_B 3K4V_A 3GGV_C 1HTG_B 2FDE_A ....
Probab=92.65 E-value=0.024 Score=54.96 Aligned_cols=50 Identities=26% Similarity=0.475 Sum_probs=44.1
Q ss_pred EEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCcccCCCccchhh
Q psy11442 18 SIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPDNKGAVSCTL 70 (1362)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 (1362)
+++||||+||-+|+|..++...++.. .+....+.|+||.. ..+|.+.+.+
T Consensus 16 ~i~~LlDTGA~vsiI~~~~~~~~~~~-~~~~~~v~~~~g~~--~~~~~~~~~v 65 (100)
T PF00077_consen 16 KIKALLDTGADVSIISEKDWKKLGPP-PKTSITVRGAGGSS--SILGSTTVEV 65 (100)
T ss_dssp EEEEEEETTBSSEEESSGGSSSTSSE-EEEEEEEEETTEEE--EEEEEEEEEE
T ss_pred EEEEEEecCCCcceeccccccccccc-ccCCceeccCCCcc--eeeeEEEEEE
Confidence 99999999999999999999999888 88888999999988 7777665544
No 24
>PRK07708 hypothetical protein; Validated
Probab=92.53 E-value=0.81 Score=51.29 Aligned_cols=168 Identities=14% Similarity=0.131 Sum_probs=89.8
Q ss_pred hHHHHHHHHHhhccccccchhhccccccceeccccccccccccCCCChhhHHHHHHHHHhhccccccccceeeeeeccee
Q psy11442 167 RLELCAALLLSRLYNSLHNYLTKLNVKNVTTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINNDITFLLRKILVIVLRVI 246 (1362)
Q Consensus 167 ~~el~~a~~~a~~~Dpl~G~l~p~~~~~k~~~q~~~~~~l~Wd~~l~~~~~~~w~~~~~~l~~~~~~~ipR~~~~~~~~~ 246 (1362)
-|++--|+.+|.-|.-- |-+..+.+.= ..+..|- .+...++..++.. =|. ..+
T Consensus 23 ~~~~~~~~~~~~~~~~~-~~~~~~~~~d--------~~~~~~~-------~k~~~~~~~~~~~-----ep~------~~~ 75 (219)
T PRK07708 23 WMNIEEALQLAEDFEKT-GRVKELEFYD--------EMDTEWS-------LKELKKLSKEVEE-----EPH------EIL 75 (219)
T ss_pred cccHHHHHHHHHHHhhc-CCceeEEEec--------CCCCEee-------HHHHhhhhhhhcc-----CCC------cEE
Confidence 45666777888888777 6554443211 1233332 2334444444443 111 126
Q ss_pred eecccccc------cceEEEEEeccccccccccCCCceeeeeeeeeeccccccCcccccchhhHHHHHHHHHHHHHHHHH
Q psy11442 247 YFPSNLFL------IRYGGMVLSFSPLLIGQSYPSGFKFCNRGLIKAKSKVAPTKQLLSIPRLELCAALLLSRLYNSLHN 320 (1362)
Q Consensus 247 ~F~~DAS~------~ayga~~Ylr~~~~~g~~~~~~~~~~~~~li~aKsrv~P~k~~~tIPRlEL~a~~l~~~l~~~~~~ 320 (1362)
+|+ |+|- .|+|+|+|.. +|.. . ..+.....+.+. .|=-..|+.|++.|.+++...
T Consensus 76 vY~-DGs~~~n~g~aG~GvVI~~~----------~g~~-~--~~~~~~~~l~~~---~TNN~AEy~Ali~aL~~A~e~-- 136 (219)
T PRK07708 76 VYF-DGGFDKETKLAGLGIVIYYK----------QGNK-R--YRIRRNAYIEGI---YDNNEAEYAALYYAMQELEEL-- 136 (219)
T ss_pred EEE-eeccCCCCCCcEEEEEEEEC----------CCCE-E--EEEEeecccccc---ccCcHHHHHHHHHHHHHHHHc--
Confidence 777 8865 3455555443 3332 1 112222233321 355677999999887765332
Q ss_pred HhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhC---C-CCceEeecCCCCC-CCCC
Q psy11442 321 YLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLA---D-GCKWYHVPTSENP-CDCA 383 (1362)
Q Consensus 321 ~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~---~-~~~w~hvpt~~NP-AD~~ 383 (1362)
. +.-..+.+++||+.+..|+.+.-+....-...-+.+|+++. . ...+.|||-++|= ||.+
T Consensus 137 --g-~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~L 201 (219)
T PRK07708 137 --G-VKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQL 201 (219)
T ss_pred --C-CCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHH
Confidence 2 22234889999999999999763322222112223333332 2 3567899998885 5543
No 25
>PRK13907 rnhA ribonuclease H; Provisional
Probab=92.12 E-value=1.1 Score=45.42 Aligned_cols=80 Identities=23% Similarity=0.138 Sum_probs=54.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhC---CCCceEeec
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLA---DGCKWYHVP 374 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~---~~~~w~hvp 374 (1362)
.|=-+.|+.|++.|.+++.. ..+..+.++|||+.+..++++...+- .-...-+++++.+. +...+.|||
T Consensus 39 ~tn~~AE~~All~aL~~a~~-------~g~~~v~i~sDS~~vi~~~~~~~~~~-~~~~~l~~~~~~l~~~f~~~~~~~v~ 110 (128)
T PRK13907 39 MSNHEAEYHALLAALKYCTE-------HNYNIVSFRTDSQLVERAVEKEYAKN-KMFAPLLEEALQYIKSFDLFFIKWIP 110 (128)
T ss_pred cCCcHHHHHHHHHHHHHHHh-------CCCCEEEEEechHHHHHHHhHHHhcC-hhHHHHHHHHHHHHhcCCceEEEEcC
Confidence 56678999999988876532 45668999999999999999754321 11223344554443 345668999
Q ss_pred CCCCC-CCCCCC
Q psy11442 375 TSENP-CDCASR 385 (1362)
Q Consensus 375 t~~NP-AD~~SR 385 (1362)
...|= ||.+.|
T Consensus 111 r~~N~~Ad~LA~ 122 (128)
T PRK13907 111 SSQNKVADELAR 122 (128)
T ss_pred chhchhHHHHHH
Confidence 98885 665433
No 26
>PF08284 RVP_2: Retroviral aspartyl protease; InterPro: IPR013242 This region defines single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases.
Probab=91.71 E-value=0.15 Score=52.74 Aligned_cols=41 Identities=27% Similarity=0.391 Sum_probs=34.3
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceee--eceeeeecCCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYK--CGISISGIGDN 57 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ 57 (1362)
+|+.||||||+--|+|...||.++||.-.+ ..+.|.+-|+.
T Consensus 31 ~~~~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~~V~~~g~~ 73 (135)
T PF08284_consen 31 IPASVLIDSGATHSFISSSFAKKLGLPLEPLPRPIVVSAPGGS 73 (135)
T ss_pred EEEEEEEecCCCcEEccHHHHHhcCCEEEEccCeeEEeccccc
Confidence 799999999999999999999999998876 44566655443
No 27
>cd05481 retropepsin_like_LTR_1 Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identifi
Probab=91.70 E-value=0.12 Score=49.97 Aligned_cols=53 Identities=15% Similarity=0.315 Sum_probs=43.7
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhC----cceeeeceeeeecCCCCcccCCCccchhh
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLG----LKRYKCGISISGIGDNGVPDNKGAVSCTL 70 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 (1362)
+++|++||+|+++|+|......+|| =.-+++++.+++-++...+ ++|.+.|.+
T Consensus 9 ~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~-~~G~~~~~v 65 (93)
T cd05481 9 QSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIP-VEGGVKLKC 65 (93)
T ss_pred eeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEee-eeEEEEEEE
Confidence 9999999999999999999999998 3556778889999888765 456455544
No 28
>PRK06548 ribonuclease H; Provisional
Probab=91.07 E-value=1.2 Score=47.44 Aligned_cols=72 Identities=21% Similarity=0.105 Sum_probs=45.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHh--------cCCCc-cchhHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLR--------TAPHL-LQTYVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~--------~~~~~-~~~fv~NR--v~~I~~~~~ 366 (1362)
.|==|+||+|++.|.+ .+. .....+.++|||+.|+.=|. +.-++ -+.-|.|+ +++|.++..
T Consensus 40 ~TNnraEl~Aii~aL~-------~~~-~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~ 111 (161)
T PRK06548 40 ATNNIAELTAVRELLI-------ATR-HTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME 111 (161)
T ss_pred CCHHHHHHHHHHHHHH-------hhh-cCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh
Confidence 5667999999987653 222 23346899999999874333 22211 23457777 445544442
Q ss_pred --CCceEeecCCC
Q psy11442 367 --GCKWYHVPTSE 377 (1362)
Q Consensus 367 --~~~w~hvpt~~ 377 (1362)
...|.||++..
T Consensus 112 ~~~v~~~wVkgHs 124 (161)
T PRK06548 112 NRNIRMSWVNAHT 124 (161)
T ss_pred cCceEEEEEecCC
Confidence 57899998754
No 29
>PF14893 PNMA: PNMA
Probab=91.01 E-value=0.66 Score=54.90 Aligned_cols=134 Identities=16% Similarity=0.221 Sum_probs=99.5
Q ss_pred CCCCCccccc------ccchHHHHHHHHHhhcCCCCChhhHHHHhhhccchhhhhhhcCCCC--CcccHHHHHHHHHHHh
Q psy11442 1163 LELPSFSGEF------SEFNVFYESFKSLIHDNKELDNTQKVQYLVSKLSGKALTVCAGVPA--TVDNYSIIFNNLVEKY 1234 (1362)
Q Consensus 1163 i~Lp~FdGd~------~ew~~F~~~F~~~Ih~~~~ls~~~K~~~Lrs~L~GeA~~~I~~l~l--s~~nY~~A~~~L~~rY 1234 (1362)
.+|+.|+|.. ..|.+|.+.++.++..-.++++.+|-..|..+|.|.|.+.++.+.. .......-++.|+..|
T Consensus 164 ~~L~iFSG~~~~~~gee~fe~Wl~~a~~~v~~W~~~~e~ekrrrlle~L~GpA~~~~r~l~~~nP~~t~~~~l~aL~~~F 243 (331)
T PF14893_consen 164 RDLRIFSGREEPAPGEESFESWLEHANEMVKKWNDVSEEEKRRRLLESLRGPALDSRRKLQKKNPKQTAQDCLKALGQVF 243 (331)
T ss_pred hhhhhhcCCCCCCCCcccHHHHHHHHHHHHHhccCCchhhchhhhHHhcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhc
Confidence 5788999975 7799999999999999877999999999999999999999998854 3556788899999999
Q ss_pred hhhhhHHHHHHHHhhccCcCCCCChhHHHHHHHHHHHHHHHHHhCC-CC--CCchhHHHHHHHhcCCHH
Q psy11442 1235 QCKRSQAKAYLSNILNFKQIKGESPDQLNSLIDELCASVLALKKVD-LD--SLSDFMLAHITLSKIDSE 1300 (1362)
Q Consensus 1235 g~~~~ii~~~l~~L~~lp~i~~~~~~~Lr~l~d~v~~~i~aL~~Lg-~~--~~~~~~l~~ii~~KLP~~ 1300 (1362)
|++.-..+.+.+-+.... .....+..++..++..+...-.-| .. ..+..-+-+.+..-.+.+
T Consensus 244 g~~es~~~~~~kf~~~~Q----~~~E~ls~yv~RlE~lLqkav~k~a~~p~~adq~rl~q~l~~a~~~e 308 (331)
T PF14893_consen 244 GSSESRETLEAKFLNTFQ----EPGEKLSAYVKRLESLLQKAVEKGAIKPSEADQVRLRQVLSGAVLSE 308 (331)
T ss_pred CCcccHHHHHHHHHHhhc----cCCCCHHHHHHHHHHHHHHHHHhcCCCccccCHHHHHHHHccCCCCH
Confidence 999998888777654432 233455667777777666643333 22 223334555554444443
No 30
>TIGR02281 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family. This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria).
Probab=90.88 E-value=0.21 Score=50.65 Aligned_cols=39 Identities=26% Similarity=0.491 Sum_probs=31.6
Q ss_pred EEEEeecCCCcchhhHHHHHHHhCcceeee--ceeeeecCC
Q psy11442 18 SIRVIVDPGSQVSCITNDCVQRLGLKRYKC--GISISGIGD 56 (1362)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 56 (1362)
|+++|||+|++.++|+.+.|++|||+...- .+.+.+.+|
T Consensus 22 ~~~flVDTGAs~t~is~~~A~~Lgl~~~~~~~~~~~~ta~G 62 (121)
T TIGR02281 22 NVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANG 62 (121)
T ss_pred EEEEEEECCCCcEEcCHHHHHHcCCCcccCCceEEEEeCCC
Confidence 999999999999999999999999987542 334444444
No 31
>PRK08719 ribonuclease H; Reviewed
Probab=90.45 E-value=1.4 Score=46.34 Aligned_cols=69 Identities=19% Similarity=0.124 Sum_probs=41.9
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHH--------hcCCCc-cchhHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWL--------RTAPHL-LQTYVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi--------~~~~~~-~~~fv~NR--v~~I~~~~~ 366 (1362)
.|-=|.||.|++.|.+.+. . ...++|||+.|+.=| ++.=++ -..-|.|+ .++|.++..
T Consensus 48 ~Tnn~aEl~A~~~aL~~~~------~-----~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~ 116 (147)
T PRK08719 48 TDNAELELLALIEALEYAR------D-----GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA 116 (147)
T ss_pred ccHHHHHHHHHHHHHHHcC------C-----CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC
Confidence 5788999999988876432 1 237999998887443 222111 11245553 233433332
Q ss_pred --CCceEeecCCC
Q psy11442 367 --GCKWYHVPTSE 377 (1362)
Q Consensus 367 --~~~w~hvpt~~ 377 (1362)
...|.|||+..
T Consensus 117 ~~~i~~~~VkgH~ 129 (147)
T PRK08719 117 RKYVEVEKVTAHS 129 (147)
T ss_pred CCcEEEEEecCCC
Confidence 47799999854
No 32
>PF12384 Peptidase_A2B: Ty3 transposon peptidase; InterPro: IPR024650 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species [].
Probab=89.18 E-value=0.22 Score=52.33 Aligned_cols=60 Identities=27% Similarity=0.331 Sum_probs=45.5
Q ss_pred eEEEEEeecCCCcchhhHHHHHHHhCcceeeece-eeeecCCCCcccCCCccchhhHhHHH
Q psy11442 16 LSSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGI-SISGIGDNGVPDNKGAVSCTLATSNK 75 (1362)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (1362)
-.|+++|+|+||-.|+|-.+.++.|+|+...-.. .+-|.+...-..-..+|..+|+.-+.
T Consensus 43 ~t~i~vLfDSGSPTSfIr~di~~kL~L~~~~app~~fRG~vs~~~~~tsEAv~ld~~i~n~ 103 (177)
T PF12384_consen 43 GTPIKVLFDSGSPTSFIRSDIVEKLELPTHDAPPFRFRGFVSGESATTSEAVTLDFYIDNK 103 (177)
T ss_pred CcEEEEEEeCCCccceeehhhHHhhCCccccCCCEEEeeeccCCceEEEEeEEEEEEECCe
Confidence 3589999999999999999999999999876554 56666655555556666666655443
No 33
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=87.24 E-value=3.2 Score=50.28 Aligned_cols=81 Identities=14% Similarity=0.099 Sum_probs=55.9
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCC----ccchhHHHHHHHHHhhCCCCceEee
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPH----LLQTYVANRVVEINKLADGCKWYHV 373 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~----~~~~fv~NRv~~I~~~~~~~~w~hv 373 (1362)
.|--..|+.|++.|.+++.. ..+..+.+++||..+..-+.+.-+ .+..+ ...+.++........|.||
T Consensus 43 ~tnn~AE~~All~gL~~a~~-------~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~-~~~i~~l~~~f~~~~i~~v 114 (372)
T PRK07238 43 ATNNVAEYRGLIAGLEAAAE-------LGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPL-AAQARELASQFGRVTYTWI 114 (372)
T ss_pred CCchHHHHHHHHHHHHHHHh-------CCCCeEEEEeCcHHHHHHhCCCCccCChHHHHH-HHHHHHHHhcCCceEEEEC
Confidence 55568999999988876643 346689999999999999986432 12222 1334444444567889999
Q ss_pred cCCCCC-CCCCCCC
Q psy11442 374 PTSENP-CDCASRG 386 (1362)
Q Consensus 374 pt~~NP-AD~~SRG 386 (1362)
|..+|= ||...+.
T Consensus 115 ~r~~N~~AD~LA~~ 128 (372)
T PRK07238 115 PRARNAHADRLANE 128 (372)
T ss_pred CchhhhHHHHHHHH
Confidence 987775 7765553
No 34
>TIGR03698 clan_AA_DTGF clan AA aspartic protease, AF_0612 family. Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria.
Probab=86.46 E-value=1 Score=44.73 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=36.2
Q ss_pred ceEEEEecC-CCCeEEEEEeecCCCcchh-hHHHHHHHhCcceee
Q psy11442 4 TARAFILNA-SGQLSSIRVIVDPGSQVSC-ITNDCVQRLGLKRYK 46 (1362)
Q Consensus 4 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 46 (1362)
|+-|.|+|. .....+|++|+|+|.--.+ |+.+-|++|||....
T Consensus 1 ~~~v~~~~p~~~~~~~v~~LVDTGat~~~~l~~~~a~~lgl~~~~ 45 (107)
T TIGR03698 1 TLDVELSNPKNPEFMEVRALVDTGFSGFLLVPPDIVNKLGLPELD 45 (107)
T ss_pred CEEEEEeCCCCCCceEEEEEEECCCCeEEecCHHHHHHcCCCccc
Confidence 467888887 5556799999999998776 999999999998754
No 35
>PF14893 PNMA: PNMA
Probab=85.73 E-value=1.2 Score=52.84 Aligned_cols=85 Identities=16% Similarity=0.222 Sum_probs=72.8
Q ss_pred CCCCcccccc------cchhhHHHHHHHHhhcCCCCChHHHHHHHHHhcchhHHHhhccCCC--CCCcHHHHHHHHHHhh
Q psy11442 807 LELPSFSGEF------SEFNVFYESFKSLIHDNKELDNTQKVQYLVSKLSGKALTVCAGVPA--TADNYSIIFNNLVEKY 878 (1362)
Q Consensus 807 ~~lp~F~Gd~------~~w~~F~d~F~~~i~~~~~ls~~~Kf~yL~s~L~G~A~~~I~~l~l--t~~nY~~A~~~L~~ry 878 (1362)
.+|+.|+|.. ..|..|.+.++.++..-.++++.+|-..|..+|.|.|++++..+.. -........+.|..-|
T Consensus 164 ~~L~iFSG~~~~~~gee~fe~Wl~~a~~~v~~W~~~~e~ekrrrlle~L~GpA~~~~r~l~~~nP~~t~~~~l~aL~~~F 243 (331)
T PF14893_consen 164 RDLRIFSGREEPAPGEESFESWLEHANEMVKKWNDVSEEEKRRRLLESLRGPALDSRRKLQKKNPKQTAQDCLKALGQVF 243 (331)
T ss_pred hhhhhhcCCCCCCCCcccHHHHHHHHHHHHHhccCCchhhchhhhHHhcccHHHHHHHHHHhcCCCCCHHHHHHHHHHhc
Confidence 5678999965 7799999999999999988999999999999999999999998855 3567889999999999
Q ss_pred hchHHHHHHHHHH
Q psy11442 879 QCKRSQAKAYLSN 891 (1362)
Q Consensus 879 ~~~~~i~~~~l~~ 891 (1362)
|++......+.+-
T Consensus 244 g~~es~~~~~~kf 256 (331)
T PF14893_consen 244 GSSESRETLEAKF 256 (331)
T ss_pred CCcccHHHHHHHH
Confidence 9887666555443
No 36
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=79.49 E-value=1 Score=47.94 Aligned_cols=20 Identities=65% Similarity=0.815 Sum_probs=18.9
Q ss_pred chhhHHHHHHHHHhhccccc
Q psy11442 164 SIPRLELCAALLLSRLYNSL 183 (1362)
Q Consensus 164 S~p~~el~~a~~~a~~~Dpl 183 (1362)
|+||||||||++.+++.+-+
T Consensus 125 tIPRlEL~a~~l~~~l~~~~ 144 (159)
T PF05380_consen 125 TIPRLELLAALLGVRLANTV 144 (159)
T ss_pred cHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998876
No 37
>cd00303 retropepsin_like Retropepsins; pepsin-like aspartate proteases. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples
Probab=77.02 E-value=2.3 Score=37.77 Aligned_cols=41 Identities=24% Similarity=0.532 Sum_probs=31.2
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCc--ceeeeceeeeecCCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGL--KRYKCGISISGIGDN 57 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ 57 (1362)
.++++|+|.||.+++|...++.++++ ...+....+.+..+.
T Consensus 8 ~~~~~liDtgs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (92)
T cd00303 8 VPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGS 50 (92)
T ss_pred EEEEEEEcCCCcccccCHHHHHHcCCCcccCCCceEEEecCCC
Confidence 79999999999999999999999987 223333444555443
No 38
>cd05482 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases. This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This gro
Probab=56.05 E-value=7.3 Score=37.39 Aligned_cols=37 Identities=22% Similarity=0.295 Sum_probs=27.2
Q ss_pred eEEEEEeecCCCcchhhHHHHHHHhCcceee----eceeeeecCCC
Q psy11442 16 LSSIRVIVDPGSQVSCITNDCVQRLGLKRYK----CGISISGIGDN 57 (1362)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~ 57 (1362)
-+++++|||+|+.+++|....- ..+. -...|.||||.
T Consensus 7 g~~~~~llDTGAd~Tvi~~~~~-----p~~w~~~~~~~~i~GIGG~ 47 (87)
T cd05482 7 GKLFEGLLDTGADVSIIAENDW-----PKNWPIQPAPSNLTGIGGA 47 (87)
T ss_pred CEEEEEEEccCCCCeEEccccc-----CCCCccCCCCeEEEeccce
Confidence 3789999999999999997332 2221 33588999975
No 39
>KOG3752|consensus
Probab=53.64 E-value=88 Score=37.68 Aligned_cols=72 Identities=21% Similarity=0.152 Sum_probs=47.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHh----cCC----------CccchhHHH-----HH
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLR----TAP----------HLLQTYVAN-----RV 358 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~----~~~----------~~~~~fv~N-----Rv 358 (1362)
.|--|-||.|+..|. +++++ .++.++++-|||.-+..|+. +-. .+.+.+|.| .+
T Consensus 254 qtNnrAEl~Av~~AL------kka~~-~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~ 326 (371)
T KOG3752|consen 254 QTNNRAELIAAIEAL------KKARS-KNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNEL 326 (371)
T ss_pred ccccHHHHHHHHHHH------HHHHh-cCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHH
Confidence 688899999997554 56666 67779999999998887653 211 112222322 22
Q ss_pred HH-HHhh-CCCCceEeecCC
Q psy11442 359 VE-INKL-ADGCKWYHVPTS 376 (1362)
Q Consensus 359 ~~-I~~~-~~~~~w~hvpt~ 376 (1362)
.+ +++. -...+|.||++.
T Consensus 327 ~~l~q~~~~~~vq~~~V~Gh 346 (371)
T KOG3752|consen 327 DELEQEISNKKVQQEYVGGH 346 (371)
T ss_pred HHHHhhhccCceEEEEecCc
Confidence 22 3332 246899999987
No 40
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=52.11 E-value=5.7 Score=38.19 Aligned_cols=56 Identities=20% Similarity=0.355 Sum_probs=39.8
Q ss_pred EEecCCCCeEEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCcccCCCccchhh
Q psy11442 8 FILNASGQLSSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPDNKGAVSCTL 70 (1362)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 (1362)
+|+|+. .-+|-|||+|++||+|-..-.++ +.+++...+.+..|+.+.. -|...+++
T Consensus 2 ~v~D~~---s~~~fLVDTGA~vSviP~~~~~~---~~~~~~~~l~AANgt~I~t-yG~~~l~l 57 (89)
T cd06094 2 HVRDRT---SGLRFLVDTGAAVSVLPASSTKK---SLKPSPLTLQAANGTPIAT-YGTRSLTL 57 (89)
T ss_pred eeEECC---CCcEEEEeCCCceEeeccccccc---cccCCceEEEeCCCCeEee-eeeEEEEE
Confidence 466654 34799999999999998665554 3677888888888887654 34454443
No 41
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=51.57 E-value=24 Score=33.08 Aligned_cols=88 Identities=8% Similarity=0.092 Sum_probs=58.8
Q ss_pred hhccchhhhhhhcCCCCCc----ccHHHHHHHHHHHhhhhhhHHHHHHHHhhccCcCCCCChhHHHHHHHHHHHHHHHHH
Q psy11442 1202 VSKLSGKALTVCAGVPATV----DNYSIIFNNLVEKYQCKRSQAKAYLSNILNFKQIKGESPDQLNSLIDELCASVLALK 1277 (1362)
Q Consensus 1202 rs~L~GeA~~~I~~l~ls~----~nY~~A~~~L~~rYg~~~~ii~~~l~~L~~lp~i~~~~~~~Lr~l~d~v~~~i~aL~ 1277 (1362)
-.+|+|+|+.....+.... .+|+...+.|.++|+.+.... ...++|.++.+ .. ..+..++..++.....+.
T Consensus 4 ~~~L~g~A~~w~~~~~~~~~~~~~~W~~~~~~~~~~f~~~~~~~-~~~~~l~~l~Q-~~---esv~~y~~rf~~l~~~~~ 78 (96)
T PF03732_consen 4 PSFLKGPARQWYRNLRPNEIRDFITWEEFKDAFRKRFFPPDRKE-QARQELNSLRQ-GN---ESVREYVNRFRELARRAP 78 (96)
T ss_pred hHhccCHHHHHHHHhHhcCCCCCCCHHHHHHHHHHHHhhhhccc-cchhhhhhhhc-cC---CcHHHHHHHHHHHHHHCC
Confidence 4689999999988774433 379999999999999875443 44566666655 33 456667777766666554
Q ss_pred hCCCCCCchhHHHHHHHhcCC
Q psy11442 1278 KVDLDSLSDFMLAHITLSKID 1298 (1362)
Q Consensus 1278 ~Lg~~~~~~~~l~~ii~~KLP 1298 (1362)
. .+.+..++..+++-|.
T Consensus 79 ~----~~~e~~~v~~f~~GL~ 95 (96)
T PF03732_consen 79 P----PMDEEMLVERFIRGLR 95 (96)
T ss_pred C----CcCHHHHHHHHHHCCC
Confidence 3 2344566666666553
No 42
>PF12382 Peptidase_A2E: Retrotransposon peptidase; InterPro: IPR024648 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This entry represents a small family of fungal retroviral aspartyl peptidases.
Probab=41.85 E-value=13 Score=35.85 Aligned_cols=43 Identities=26% Similarity=0.201 Sum_probs=33.9
Q ss_pred EEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCccc
Q psy11442 19 IRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPD 61 (1362)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (1362)
+-.|||.|.|+++||++-+..-.|.-+.|.-.|.-=|.-|-..
T Consensus 48 ipclidtgaq~niiteetvrahklptrpw~~sviyggvyp~ki 90 (137)
T PF12382_consen 48 IPCLIDTGAQVNIITEETVRAHKLPTRPWSQSVIYGGVYPNKI 90 (137)
T ss_pred ceeEEccCceeeeeehhhhhhccCCCCcchhheEecccccccc
Confidence 4569999999999999999999999999987665434444333
No 43
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=32.80 E-value=28 Score=34.16 Aligned_cols=58 Identities=17% Similarity=0.135 Sum_probs=35.9
Q ss_pred cCCC-chhhHHHHhhhhhhcccc-----ee-cCCccccccchhhhhhHhhhHhhh-h---------hccccccc--hhhh
Q psy11442 625 NPSN-LGNSYLGAERRFYSLERK-----LH-ANPSLLFSGVAWSKFKCKACRVLI-S---------IIHALHGL--AYIK 685 (1362)
Q Consensus 625 v~~l-st~sfl~al~rf~~rrG~-----fv-a~~~~~~~~~~~~~~~~~~~~~l~-~---------~i~W~GGl--r~Vk 685 (1362)
+.+- +++.++++|.+.+..+|. ++ ++..++.+.. +... +. . ..+|..|. |..+
T Consensus 43 ~~~~~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~~~----~~~~----~~~~~i~~~~~~~~~p~~ng~vEr~~~ 114 (120)
T PF00665_consen 43 VSSKETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTSHA----FEAW----CKHLGIKHVFTPPYTPQQNGFVERFNR 114 (120)
T ss_dssp ESSSSHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHSHH----HHHH----HHHHT-EEEESSTSSTHHHHHHHHHHH
T ss_pred eecccccccccccccccccccccccceecccccccccccch----hhhH----HHHcCceEeeCCCCChhhccHHHHHHH
Confidence 5566 889999999999998887 33 4444333321 2222 22 3 33566666 8888
Q ss_pred HHHHH
Q psy11442 686 SAKHH 690 (1362)
Q Consensus 686 svK~~ 690 (1362)
.+|+-
T Consensus 115 ~l~~~ 119 (120)
T PF00665_consen 115 TLKRR 119 (120)
T ss_dssp HHHHH
T ss_pred HHHHh
Confidence 88764
No 44
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=32.19 E-value=60 Score=36.02 Aligned_cols=44 Identities=16% Similarity=0.360 Sum_probs=36.7
Q ss_pred EEEEecCCCCe--------EEEEEeecCCCcchhhHHHHHHHhCcceeeece
Q psy11442 6 RAFILNASGQL--------SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGI 49 (1362)
Q Consensus 6 ~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (1362)
++--++.+|+| ++|+.|+|.|--.-++|++-|.|||+...+-+.
T Consensus 96 v~Lak~~~GHF~a~~~VNGk~v~fLVDTGATsVal~~~dA~RlGid~~~l~y 147 (215)
T COG3577 96 VSLAKSRDGHFEANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDY 147 (215)
T ss_pred EEEEecCCCcEEEEEEECCEEEEEEEecCcceeecCHHHHHHhCCCccccCC
Confidence 33457788877 689999999999999999999999999885544
Done!