Query 041134
Match_columns 267
No_of_seqs 191 out of 593
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 04:05:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041134.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041134hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd05484 retropepsin_like_LTR_2 99.4 2.1E-12 4.5E-17 98.1 8.1 79 128-211 2-91 (91)
2 cd05479 RP_DDI RP_DDI; retrope 98.9 3.5E-09 7.6E-14 85.1 8.3 95 124-222 14-120 (124)
3 cd05481 retropepsin_like_LTR_1 98.9 2.7E-09 5.8E-14 81.8 6.9 76 131-208 3-90 (93)
4 PF09668 Asp_protease: Asparty 98.7 4.3E-08 9.4E-13 78.9 6.5 89 124-216 22-122 (124)
5 PF00077 RVP: Retroviral aspar 98.6 1.7E-08 3.7E-13 77.3 2.8 84 125-216 4-98 (100)
6 cd00303 retropepsin_like Retro 98.6 2.5E-07 5.4E-12 65.7 8.3 79 130-211 2-92 (92)
7 PF08284 RVP_2: Retroviral asp 98.6 3.3E-07 7.1E-12 74.9 8.6 104 124-231 19-134 (135)
8 PF13650 Asp_protease_2: Aspar 98.5 3.8E-07 8.3E-12 67.6 7.7 79 129-209 1-90 (90)
9 cd05483 retropepsin_like_bacte 97.9 5.6E-05 1.2E-09 56.4 7.7 82 127-211 3-96 (96)
10 TIGR02281 clan_AA_DTGA clan AA 97.9 5.6E-05 1.2E-09 60.5 7.9 90 123-214 8-108 (121)
11 cd06094 RP_Saci_like RP_Saci_l 97.7 5.1E-05 1.1E-09 57.5 4.1 67 139-214 10-88 (89)
12 PF13975 gag-asp_proteas: gag- 97.4 0.00075 1.6E-08 48.9 6.8 63 123-187 5-67 (72)
13 cd06095 RP_RTVL_H_like Retrope 97.3 0.00098 2.1E-08 49.9 6.5 73 130-210 2-85 (86)
14 cd05480 NRIP_C NRIP_C; putativ 96.7 0.0053 1.2E-07 47.5 6.1 84 130-216 2-98 (103)
15 KOG0012 DNA damage inducible p 96.3 0.0038 8.3E-08 58.2 4.0 97 108-218 222-335 (380)
16 TIGR03698 clan_AA_DTGF clan AA 96.1 0.016 3.4E-07 45.3 6.0 73 140-217 18-100 (107)
17 PF12384 Peptidase_A2B: Ty3 tr 95.8 0.038 8.1E-07 46.5 6.9 92 124-219 32-135 (177)
18 COG3577 Predicted aspartyl pro 93.9 0.16 3.5E-06 44.2 6.0 89 124-214 103-202 (215)
19 COG5550 Predicted aspartyl pro 92.2 0.6 1.3E-05 37.5 6.6 82 132-215 21-108 (125)
20 PF05585 DUF1758: Putative pep 85.2 2.2 4.7E-05 35.4 5.5 43 135-180 9-51 (164)
21 cd05482 HIV_retropepsin_like R 82.5 6.3 0.00014 29.7 6.5 74 130-210 2-86 (87)
22 PF02160 Peptidase_A3: Caulifl 78.8 6.3 0.00014 34.4 6.1 82 131-217 11-107 (201)
23 cd05471 pepsin_like Pepsin-lik 64.0 14 0.0003 32.4 5.1 71 137-216 201-271 (283)
24 cd05474 SAP_like SAPs, pepsin- 31.1 1.3E+02 0.0028 26.6 6.0 70 128-206 4-77 (295)
25 PF12382 Peptidase_A2E: Retrot 28.3 1.2E+02 0.0026 23.6 4.3 24 141-164 50-73 (137)
26 KOG2209 Oxysterol-binding prot 27.6 54 0.0012 30.9 2.7 79 153-231 149-242 (445)
27 COG4067 Uncharacterized protei 25.9 73 0.0016 26.7 3.0 34 183-216 114-150 (162)
28 PF10622 Ehbp: Energy-converti 23.1 80 0.0017 23.1 2.3 26 181-211 5-31 (78)
29 cd05472 cnd41_like Chloroplast 21.1 1.8E+02 0.0038 26.0 4.9 21 140-160 173-193 (299)
30 cd06097 Aspergillopepsin_like 21.0 2.4E+02 0.0051 24.9 5.6 22 139-160 199-220 (278)
31 KOG4353 RNA export factor NXT1 20.8 50 0.0011 26.9 1.0 22 201-222 48-70 (139)
No 1
>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=99.37 E-value=2.1e-12 Score=98.07 Aligned_cols=79 Identities=22% Similarity=0.425 Sum_probs=72.7
Q ss_pred EEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-----------eEEEEEee
Q 041134 128 VISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVK 196 (267)
Q Consensus 128 vi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~Vvd 196 (267)
++++.|+|..+ ++|||+||++|+|+.+.+.++|.++ ++++...+.+|+|.....+|.+ .++|.|++
T Consensus 2 ~~~~~Ing~~i-~~lvDTGA~~svis~~~~~~lg~~~--~~~~~~~v~~a~G~~~~~~G~~~~~v~~~~~~~~~~~~v~~ 78 (91)
T cd05484 2 TVTLLVNGKPL-KFQLDTGSAITVISEKTWRKLGSPP--LKPTKKRLRTATGTKLSVLGQILVTVKYGGKTKVLTLYVVK 78 (91)
T ss_pred EEEEEECCEEE-EEEEcCCcceEEeCHHHHHHhCCCc--cccccEEEEecCCCEeeEeEEEEEEEEECCEEEEEEEEEEE
Confidence 57889999988 8999999999999999999999987 9999999999999999899886 77899998
Q ss_pred eCCccceeecchhhh
Q 041134 197 ATSPYNAILGRQWIH 211 (267)
Q Consensus 197 ~~~~yn~iLGrpwLh 211 (267)
.. |+.||||.||.
T Consensus 79 ~~--~~~lLG~~wl~ 91 (91)
T cd05484 79 NE--GLNLLGRDWLD 91 (91)
T ss_pred CC--CCCccChhhcC
Confidence 87 99999999983
No 2
>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=98.94 E-value=3.5e-09 Score=85.09 Aligned_cols=95 Identities=20% Similarity=0.278 Sum_probs=70.6
Q ss_pred CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEE
Q 041134 124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTD 191 (267)
Q Consensus 124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~ 191 (267)
...+++.+.|++..+ +.|||+||+.|++..+..+++|+....-.+......|.++ ....|.+ .++
T Consensus 14 ~~~~~v~~~Ing~~~-~~LvDTGAs~s~Is~~~a~~lgl~~~~~~~~~~~~~g~g~--~~~~g~~~~~~l~i~~~~~~~~ 90 (124)
T cd05479 14 VPMLYINVEINGVPV-KAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGT--QKILGRIHLAQVKIGNLFLPCS 90 (124)
T ss_pred eeEEEEEEEECCEEE-EEEEeCCCceEEeCHHHHHHcCCccccCcceEEEEecCCC--cEEEeEEEEEEEEECCEEeeeE
Confidence 346899999999986 8999999999999999999999975431122223333332 3344544 678
Q ss_pred EEEeeeCCccceeecchhhhhccccccccee
Q 041134 192 FLVVKATSPYNAILGRQWIHKMRVVPSTYHQ 222 (267)
Q Consensus 192 F~Vvd~~~~yn~iLGrpwLh~~~aipst~hq 222 (267)
|.|++.. .++.|||.+||..++++...-.+
T Consensus 91 ~~Vl~~~-~~d~ILG~d~L~~~~~~ID~~~~ 120 (124)
T cd05479 91 FTVLEDD-DVDFLIGLDMLKRHQCVIDLKEN 120 (124)
T ss_pred EEEECCC-CcCEEecHHHHHhCCeEEECCCC
Confidence 8888776 88999999999999987654443
No 3
>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=98.93 E-value=2.7e-09 Score=81.76 Aligned_cols=76 Identities=21% Similarity=0.370 Sum_probs=63.3
Q ss_pred eeeCCeeeeEEeecCCCccccchHHHHHhhcc-CcCCCCCCCccEEeeeCCeeeeccee-----------eEEEEEeeeC
Q 041134 131 IKIGNCLVRRILIDNGSSVNILDDATVEKMRL-EQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVKAT 198 (267)
Q Consensus 131 ~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~-~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~Vvd~~ 198 (267)
+.|++..--|.+||+||++|+||.+++++||- ....|+++...|++|+|+...+.|.+ ++.|.|+|..
T Consensus 3 ~~i~g~~~v~~~vDtGA~vnllp~~~~~~l~~~~~~~L~~t~~~L~~~~g~~~~~~G~~~~~v~~~~~~~~~~f~Vvd~~ 82 (93)
T cd05481 3 MKINGKQSVKFQLDTGATCNVLPLRWLKSLTPDKDPELRPSPVRLTAYGGSTIPVEGGVKLKCRYRNPKYNLTFQVVKEE 82 (93)
T ss_pred eEeCCceeEEEEEecCCEEEeccHHHHhhhccCCCCcCccCCeEEEeeCCCEeeeeEEEEEEEEECCcEEEEEEEEECCC
Confidence 45666345578999999999999999999983 34679999999999999999999976 8889999875
Q ss_pred Cccceeecch
Q 041134 199 SPYNAILGRQ 208 (267)
Q Consensus 199 ~~yn~iLGrp 208 (267)
. ..|||+.
T Consensus 83 ~--~~lLG~~ 90 (93)
T cd05481 83 G--PPLLGAK 90 (93)
T ss_pred C--CceEccc
Confidence 3 3588875
No 4
>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=98.68 E-value=4.3e-08 Score=78.85 Aligned_cols=89 Identities=17% Similarity=0.229 Sum_probs=61.3
Q ss_pred CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEE
Q 041134 124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTD 191 (267)
Q Consensus 124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~ 191 (267)
...|+|.+.|+|..| +.+||+|+..|||+.+.++++|+.. +-.....-...+-.+..++|.| .+.
T Consensus 22 v~mLyI~~~ing~~v-kA~VDtGAQ~tims~~~a~r~gL~~--lid~r~~g~a~GvG~~~i~G~Ih~~~l~ig~~~~~~s 98 (124)
T PF09668_consen 22 VSMLYINCKINGVPV-KAFVDTGAQSTIMSKSCAERCGLMR--LIDKRFAGVAKGVGTQKILGRIHSVQLKIGGLFFPCS 98 (124)
T ss_dssp ----EEEEEETTEEE-EEEEETT-SS-EEEHHHHHHTTGGG--GEEGGG-EE-------EEEEEEEEEEEEETTEEEEEE
T ss_pred cceEEEEEEECCEEE-EEEEeCCCCccccCHHHHHHcCChh--hccccccccccCCCcCceeEEEEEEEEEECCEEEEEE
Confidence 347999999999999 9999999999999999999999843 4433322222222455688888 788
Q ss_pred EEEeeeCCccceeecchhhhhcccc
Q 041134 192 FLVVKATSPYNAILGRQWIHKMRVV 216 (267)
Q Consensus 192 F~Vvd~~~~yn~iLGrpwLh~~~ai 216 (267)
|.|+++ .+...|||..||.+.+++
T Consensus 99 ~~Vle~-~~~d~llGld~L~~~~c~ 122 (124)
T PF09668_consen 99 FTVLED-QDVDLLLGLDMLKRHKCC 122 (124)
T ss_dssp EEEETT-SSSSEEEEHHHHHHTT-E
T ss_pred EEEeCC-CCcceeeeHHHHHHhCcc
Confidence 999984 455899999999987765
No 5
>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=98.64 E-value=1.7e-08 Score=77.34 Aligned_cols=84 Identities=30% Similarity=0.446 Sum_probs=67.0
Q ss_pred CceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-----------eEEEE
Q 041134 125 DALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFL 193 (267)
Q Consensus 125 ~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~ 193 (267)
..-++++.|++..+ +.|||+||++++++.+.++..+.. ......+.|++|.. ...|.. ...|.
T Consensus 4 ~rp~i~v~i~g~~i-~~LlDTGA~vsiI~~~~~~~~~~~----~~~~~~v~~~~g~~-~~~~~~~~~v~~~~~~~~~~~~ 77 (100)
T PF00077_consen 4 NRPYITVKINGKKI-KALLDTGADVSIISEKDWKKLGPP----PKTSITVRGAGGSS-SILGSTTVEVKIGGKEFNHTFL 77 (100)
T ss_dssp SSSEEEEEETTEEE-EEEEETTBSSEEESSGGSSSTSSE----EEEEEEEEETTEEE-EEEEEEEEEEEETTEEEEEEEE
T ss_pred CCceEEEeECCEEE-EEEEecCCCcceeccccccccccc----ccCCceeccCCCcc-eeeeEEEEEEEEECccceEEEE
Confidence 34468899999866 689999999999999887666543 45566788888877 666666 55788
Q ss_pred EeeeCCccceeecchhhhhcccc
Q 041134 194 VVKATSPYNAILGRQWIHKMRVV 216 (267)
Q Consensus 194 Vvd~~~~yn~iLGrpwLh~~~ai 216 (267)
|+++ .++| ||||.||.++++.
T Consensus 78 v~~~-~~~~-ILG~D~L~~~~~~ 98 (100)
T PF00077_consen 78 VVPD-LPMN-ILGRDFLKKLNAV 98 (100)
T ss_dssp ESST-CSSE-EEEHHHHTTTTCE
T ss_pred ecCC-CCCC-EeChhHHHHcCCE
Confidence 8887 8888 9999999999875
No 6
>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=98.61 E-value=2.5e-07 Score=65.74 Aligned_cols=79 Identities=30% Similarity=0.552 Sum_probs=61.3
Q ss_pred EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEEEEEeee
Q 041134 130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTDFLVVKA 197 (267)
Q Consensus 130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~F~Vvd~ 197 (267)
++.+++ ...+.|+|+||+++++..+.+.+++. ..........+.++++......+.. ...|.|++.
T Consensus 2 ~~~~~~-~~~~~liDtgs~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ 79 (92)
T cd00303 2 KGKING-VPVRALVDSGASVNFISESLAKKLGL-PPRLLPTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDL 79 (92)
T ss_pred EEEECC-EEEEEEEcCCCcccccCHHHHHHcCC-CcccCCCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcC
Confidence 456677 66689999999999999999999987 2334456677888888765555541 556777776
Q ss_pred CCccceeecchhhh
Q 041134 198 TSPYNAILGRQWIH 211 (267)
Q Consensus 198 ~~~yn~iLGrpwLh 211 (267)
. .|+.|||++||+
T Consensus 80 ~-~~~~ilG~~~l~ 92 (92)
T cd00303 80 L-SYDVILGRPWLE 92 (92)
T ss_pred C-CcCEEecccccC
Confidence 6 899999999984
No 7
>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=98.56 E-value=3.3e-07 Score=74.89 Aligned_cols=104 Identities=20% Similarity=0.349 Sum_probs=79.2
Q ss_pred CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEE
Q 041134 124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTD 191 (267)
Q Consensus 124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~ 191 (267)
.+.+...+.|++..+ .+|||.||+-|.+..+...+++++...+..+- .+.+.++. ....+.. .++
T Consensus 19 ~~vi~g~~~I~~~~~-~vLiDSGAThsFIs~~~a~~~~l~~~~l~~~~-~V~~~g~~-~~~~~~~~~~~~~i~g~~~~~d 95 (135)
T PF08284_consen 19 PDVITGTFLINSIPA-SVLIDSGATHSFISSSFAKKLGLPLEPLPRPI-VVSAPGGS-INCEGVCPDVPLSIQGHEFVVD 95 (135)
T ss_pred CCeEEEEEEeccEEE-EEEEecCCCcEEccHHHHHhcCCEEEEccCee-EEeccccc-ccccceeeeEEEEECCeEEEee
Confidence 455666677777665 68999999999999999999999988886543 33343332 2222221 667
Q ss_pred EEEeeeCCccceeecchhhhhcccccccceeeeeeecCCc
Q 041134 192 FLVVKATSPYNAILGRQWIHKMRVVPSTYHQVLCYQTIYG 231 (267)
Q Consensus 192 F~Vvd~~~~yn~iLGrpwLh~~~aipst~hq~vk~~~~~G 231 (267)
|.|++. ..|.+|||.+||.+..+......-.|.|-.|+|
T Consensus 96 l~vl~l-~~~DvILGm~WL~~~~~~IDw~~k~v~f~~p~~ 134 (135)
T PF08284_consen 96 LLVLDL-GGYDVILGMDWLKKHNPVIDWATKTVTFNSPSG 134 (135)
T ss_pred eEEecc-cceeeEeccchHHhCCCEEEccCCEEEEeCCCC
Confidence 888776 569999999999999998888888888888887
No 8
>PF13650 Asp_protease_2: Aspartyl protease
Probab=98.54 E-value=3.8e-07 Score=67.64 Aligned_cols=79 Identities=29% Similarity=0.488 Sum_probs=63.0
Q ss_pred EEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee-----------eEEEEEeee
Q 041134 129 ISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL-----------LTDFLVVKA 197 (267)
Q Consensus 129 i~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i-----------~v~F~Vvd~ 197 (267)
|.+.|++..+ +.|+|+||+.+++..+.++++|+....... ...+.|++|......+.+ ++.|.|++.
T Consensus 1 V~v~vng~~~-~~liDTGa~~~~i~~~~~~~l~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~i~ig~~~~~~~~~~v~~~ 78 (90)
T PF13650_consen 1 VPVKVNGKPV-RFLIDTGASISVISRSLAKKLGLKPRPKSV-PISVSGAGGSVTVYRGRVDSITIGGITLKNVPFLVVDL 78 (90)
T ss_pred CEEEECCEEE-EEEEcCCCCcEEECHHHHHHcCCCCcCCce-eEEEEeCCCCEEEEEEEEEEEEECCEEEEeEEEEEECC
Confidence 4567888855 899999999999999999999997654432 356688888755554444 678888887
Q ss_pred CCccceeecchh
Q 041134 198 TSPYNAILGRQW 209 (267)
Q Consensus 198 ~~~yn~iLGrpw 209 (267)
...+..|||.+|
T Consensus 79 ~~~~~~iLG~df 90 (90)
T PF13650_consen 79 GDPIDGILGMDF 90 (90)
T ss_pred CCCCEEEeCCcC
Confidence 889999999987
No 9
>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=97.91 E-value=5.6e-05 Score=56.42 Aligned_cols=82 Identities=20% Similarity=0.334 Sum_probs=59.2
Q ss_pred eEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeee--------eccee---eEEEEEe
Q 041134 127 LVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTY--------SDGSL---LTDFLVV 195 (267)
Q Consensus 127 Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~--------~lG~i---~v~F~Vv 195 (267)
+++.+.|++..+ +.|+|+||+..+++.+..++++.. ..........+.+|.... .+|.. ++.+.|+
T Consensus 3 ~~v~v~i~~~~~-~~llDTGa~~s~i~~~~~~~l~~~--~~~~~~~~~~~~~G~~~~~~~~~~~i~ig~~~~~~~~~~v~ 79 (96)
T cd05483 3 FVVPVTINGQPV-RFLLDTGASTTVISEELAERLGLP--LTLGGKVTVQTANGRVRAARVRLDSLQIGGITLRNVPAVVL 79 (96)
T ss_pred EEEEEEECCEEE-EEEEECCCCcEEcCHHHHHHcCCC--ccCCCcEEEEecCCCccceEEEcceEEECCcEEeccEEEEe
Confidence 578889998665 899999999999999999999872 233344456666665332 23332 5678888
Q ss_pred eeCC-ccceeecchhhh
Q 041134 196 KATS-PYNAILGRQWIH 211 (267)
Q Consensus 196 d~~~-~yn~iLGrpwLh 211 (267)
|... +...|||..||.
T Consensus 80 d~~~~~~~gIlG~d~l~ 96 (96)
T cd05483 80 PGDALGVDGLLGMDFLR 96 (96)
T ss_pred CCcccCCceEeChHHhC
Confidence 7765 578899999873
No 10
>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=97.90 E-value=5.6e-05 Score=60.51 Aligned_cols=90 Identities=16% Similarity=0.362 Sum_probs=68.3
Q ss_pred CCCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeee--------ccee---eEE
Q 041134 123 HDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYS--------DGSL---LTD 191 (267)
Q Consensus 123 h~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~--------lG~i---~v~ 191 (267)
....+++.+.|+|..+ +.|||+|++..+++....+++|+.+..+. ....+.+.+|...-. +|.+ ++.
T Consensus 8 ~~g~~~v~~~InG~~~-~flVDTGAs~t~is~~~A~~Lgl~~~~~~-~~~~~~ta~G~~~~~~~~l~~l~iG~~~~~nv~ 85 (121)
T TIGR02281 8 GDGHFYATGRVNGRNV-RFLVDTGATSVALNEEDAQRLGLDLNRLG-YTVTVSTANGQIKAARVTLDRVAIGGIVVNDVD 85 (121)
T ss_pred CCCeEEEEEEECCEEE-EEEEECCCCcEEcCHHHHHHcCCCcccCC-ceEEEEeCCCcEEEEEEEeCEEEECCEEEeCcE
Confidence 4456899999999855 89999999999999999999999876543 345566777753322 2332 678
Q ss_pred EEEeeeCCccceeecchhhhhcc
Q 041134 192 FLVVKATSPYNAILGRQWIHKMR 214 (267)
Q Consensus 192 F~Vvd~~~~yn~iLGrpwLh~~~ 214 (267)
+.|++.......|||-.+|.+++
T Consensus 86 ~~v~~~~~~~~~LLGm~fL~~~~ 108 (121)
T TIGR02281 86 AMVAEGGALSESLLGMSFLNRLS 108 (121)
T ss_pred EEEeCCCcCCceEcCHHHHhccc
Confidence 88887654457899999998875
No 11
>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=97.68 E-value=5.1e-05 Score=57.45 Aligned_cols=67 Identities=25% Similarity=0.444 Sum_probs=54.1
Q ss_pred eEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee------------eEEEEEeeeCCccceeec
Q 041134 139 RRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL------------LTDFLVVKATSPYNAILG 206 (267)
Q Consensus 139 ~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i------------~v~F~Vvd~~~~yn~iLG 206 (267)
.+.|||+||.++++|.+..+.. ++++...|.+.||+...+.|.. ...|.|.|... +|||
T Consensus 10 ~~fLVDTGA~vSviP~~~~~~~------~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~~---pIlG 80 (89)
T cd06094 10 LRFLVDTGAAVSVLPASSTKKS------LKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVPH---PILG 80 (89)
T ss_pred cEEEEeCCCceEeecccccccc------ccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCCc---ceec
Confidence 3679999999999998876542 5677778999999988888876 56788888765 5999
Q ss_pred chhhhhcc
Q 041134 207 RQWIHKMR 214 (267)
Q Consensus 207 rpwLh~~~ 214 (267)
..+|.+++
T Consensus 81 aDfL~~~~ 88 (89)
T cd06094 81 ADFLQHYG 88 (89)
T ss_pred HHHHHHcC
Confidence 99998754
No 12
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=97.38 E-value=0.00075 Score=48.95 Aligned_cols=63 Identities=19% Similarity=0.311 Sum_probs=49.5
Q ss_pred CCCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeecce
Q 041134 123 HDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGS 187 (267)
Q Consensus 123 h~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~ 187 (267)
....+++.+.|++..+. .|||+||+.|+|+.++.++||++..... ....+.-.||+.....|.
T Consensus 5 ~~g~~~v~~~I~g~~~~-alvDtGat~~fis~~~a~rLgl~~~~~~-~~~~v~~a~g~~~~~~g~ 67 (72)
T PF13975_consen 5 DPGLMYVPVSIGGVQVK-ALVDTGATHNFISESLAKRLGLPLEKPP-SPIRVKLANGSVIEIRGV 67 (72)
T ss_pred cCCEEEEEEEECCEEEE-EEEeCCCcceecCHHHHHHhCCCcccCC-CCEEEEECCCCccccceE
Confidence 34568899999998888 9999999999999999999998754332 246667777776665554
No 13
>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=97.27 E-value=0.00098 Score=49.88 Aligned_cols=73 Identities=23% Similarity=0.389 Sum_probs=53.1
Q ss_pred EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeecc----ee-------eEEEEEeeeC
Q 041134 130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDG----SL-------LTDFLVVKAT 198 (267)
Q Consensus 130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG----~i-------~v~F~Vvd~~ 198 (267)
++.|+|..+ +.|||+|++..+++...++++ .+......+.|.+|....+.. .+ ...|.|++..
T Consensus 2 ~v~InG~~~-~fLvDTGA~~tii~~~~a~~~-----~~~~~~~~v~gagG~~~~~v~~~~~~v~vg~~~~~~~~~v~~~~ 75 (86)
T cd06095 2 TITVEGVPI-VFLVDTGATHSVLKSDLGPKQ-----ELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVPNC 75 (86)
T ss_pred EEEECCEEE-EEEEECCCCeEEECHHHhhhc-----cCCCCcEEEEeCCCcccccEEEeeeEEEECCEEEEEEEEEEcCC
Confidence 567888864 679999999999999999887 345577889999997522221 12 4456666532
Q ss_pred Cccceeecchhh
Q 041134 199 SPYNAILGRQWI 210 (267)
Q Consensus 199 ~~yn~iLGrpwL 210 (267)
+ ..|||+.||
T Consensus 76 -~-~~lLG~dfL 85 (86)
T cd06095 76 -P-DPLLGRDLL 85 (86)
T ss_pred -C-CcEechhhc
Confidence 3 779999987
No 14
>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=96.70 E-value=0.0053 Score=47.46 Aligned_cols=84 Identities=21% Similarity=0.281 Sum_probs=57.9
Q ss_pred EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCC-CCCccEEeeeCCeeeeccee------------eEEEEEee
Q 041134 130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIK-PFEQPLIGFSGIVTYSDGSL------------LTDFLVVK 196 (267)
Q Consensus 130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~-~~~~~l~gf~g~~~~~lG~i------------~v~F~Vvd 196 (267)
...|+|+.| +.+||.|+..|||++...+++|+..--.. ...-.-.|. |++...+|.| ...|.|+|
T Consensus 2 nCk~nG~~v-kAfVDsGaQ~timS~~caercgL~r~v~~~r~~g~A~gv-gt~~kiiGrih~~~ikig~~~~~CSftVld 79 (103)
T cd05480 2 SCQCAGKEL-RALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSL-PTSVKVIGQIERLVLQLGQLTVECSAQVVD 79 (103)
T ss_pred ceeECCEEE-EEEEecCCchhhcCHHHHHHcChHhhhhhccccccccCC-CcceeEeeEEEEEEEEeCCEEeeEEEEEEc
Confidence 456888887 68999999999999999999998532111 111111111 1223556666 77899998
Q ss_pred eCCccceeecchhhhhcccc
Q 041134 197 ATSPYNAILGRQWIHKMRVV 216 (267)
Q Consensus 197 ~~~~yn~iLGrpwLh~~~ai 216 (267)
. .+.+.+||-.-|.+.++.
T Consensus 80 ~-~~~d~llGLdmLkrhqc~ 98 (103)
T cd05480 80 D-NEKNFSLGLQTLKSLKCV 98 (103)
T ss_pred C-CCcceEeeHHHHhhccee
Confidence 4 567899999888776654
No 15
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=96.34 E-value=0.0038 Score=58.20 Aligned_cols=97 Identities=20% Similarity=0.330 Sum_probs=71.2
Q ss_pred eeEeCCCCCccccCCCCCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC-----ee
Q 041134 108 EVSFLPQDLKLIQSPHDDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI-----VT 182 (267)
Q Consensus 108 ~I~F~~~d~~~v~~ph~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~-----~~ 182 (267)
.|+..|++... -..|+|.+.|+|+.| +++||.|+..|||++...+++|++.- +-..|.|. +.
T Consensus 222 ai~~~pe~f~~-----v~ML~iN~~ing~~V-KAfVDsGaq~timS~~Caer~gL~rl-------id~r~~g~a~gvg~~ 288 (380)
T KOG0012|consen 222 AIEYHPEDFTQ-----VTMLYINCEINGVPV-KAFVDSGAQTTIMSAACAERCGLNRL-------IDKRFQGEARGVGTE 288 (380)
T ss_pred hhhcCcccccc-----ceEEEEEEEECCEEE-EEEEcccchhhhhhHHHHHHhChHHH-------hhhhhhccccCCCcc
Confidence 45555555432 357999999999999 58999999999999999999998653 33344442 33
Q ss_pred eeccee------------eEEEEEeeeCCccceeecchhhhhcccccc
Q 041134 183 YSDGSL------------LTDFLVVKATSPYNAILGRQWIHKMRVVPS 218 (267)
Q Consensus 183 ~~lG~i------------~v~F~Vvd~~~~yn~iLGrpwLh~~~aips 218 (267)
..+|.| ...|.|+|... -+.+||-.-|.+.+|...
T Consensus 289 ki~g~Ih~~~lki~~~~l~c~ftV~d~~~-~d~llGLd~Lrr~~ccId 335 (380)
T KOG0012|consen 289 KILGRIHQAQLKIEDLYLPCSFTVLDRRD-MDLLLGLDMLRRHQCCID 335 (380)
T ss_pred cccceeEEEEEEeccEeeccceEEecCCC-cchhhhHHHHHhccceee
Confidence 446666 55788887653 478899999988776653
No 16
>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=96.15 E-value=0.016 Score=45.34 Aligned_cols=73 Identities=21% Similarity=0.225 Sum_probs=48.4
Q ss_pred EEeecCCCcccc-chHHHHHhhccCcCCCCCCCccEEeeeCCe-eeec-------ceeeEEEEEeee-CCccceeecchh
Q 041134 140 RILIDNGSSVNI-LDDATVEKMRLEQDKIKPFEQPLIGFSGIV-TYSD-------GSLLTDFLVVKA-TSPYNAILGRQW 209 (267)
Q Consensus 140 riLvD~GSs~ni-l~~~~~~~mg~~~~~L~~~~~~l~gf~g~~-~~~l-------G~i~v~F~Vvd~-~~~yn~iLGrpw 209 (267)
+.|||+|++-.+ ++.+.+++||+++.. .....-.+|.. .... |.+.....|+.. ..+ ..+||..|
T Consensus 18 ~~LVDTGat~~~~l~~~~a~~lgl~~~~----~~~~~tA~G~~~~~~v~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~ 92 (107)
T TIGR03698 18 RALVDTGFSGFLLVPPDIVNKLGLPELD----QRRVYLADGREVLTDVAKASIIINGLEIDAFVESLGYVD-EPLLGTEL 92 (107)
T ss_pred EEEEECCCCeEEecCHHHHHHcCCCccc----CcEEEecCCcEEEEEEEEEEEEECCEEEEEEEEecCCCC-ccEecHHH
Confidence 689999999997 999999999998743 34666667742 1111 111223333322 223 67999999
Q ss_pred hhhccccc
Q 041134 210 IHKMRVVP 217 (267)
Q Consensus 210 Lh~~~aip 217 (267)
|.++..+.
T Consensus 93 L~~l~l~i 100 (107)
T TIGR03698 93 LEGLGIVI 100 (107)
T ss_pred HhhCCEEE
Confidence 99887654
No 17
>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=95.76 E-value=0.038 Score=46.55 Aligned_cols=92 Identities=14% Similarity=0.244 Sum_probs=63.4
Q ss_pred CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC-eeeeccee-----------eEE
Q 041134 124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI-VTYSDGSL-----------LTD 191 (267)
Q Consensus 124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~-~~~~lG~i-----------~v~ 191 (267)
++.+.+.+.|.+-.+ ++|+|.||-..++......+|+++.. .-+..-+.||.+. ....--.+ .+.
T Consensus 32 g~T~~v~l~~~~t~i-~vLfDSGSPTSfIr~di~~kL~L~~~--~app~~fRG~vs~~~~~tsEAv~ld~~i~n~~i~i~ 108 (177)
T PF12384_consen 32 GKTAIVQLNCKGTPI-KVLFDSGSPTSFIRSDIVEKLELPTH--DAPPFRFRGFVSGESATTSEAVTLDFYIDNKLIDIA 108 (177)
T ss_pred CcEEEEEEeecCcEE-EEEEeCCCccceeehhhHHhhCCccc--cCCCEEEeeeccCCceEEEEeEEEEEEECCeEEEEE
Confidence 467888899998887 58999999999999999999987652 3334456666543 11111111 445
Q ss_pred EEEeeeCCccceeecchhhhhccccccc
Q 041134 192 FLVVKATSPYNAILGRQWIHKMRVVPST 219 (267)
Q Consensus 192 F~Vvd~~~~yn~iLGrpwLh~~~aipst 219 (267)
++|.|. -.+.+|+|-|.|.+..-+-++
T Consensus 109 aYV~d~-m~~dlIIGnPiL~ryp~l~~~ 135 (177)
T PF12384_consen 109 AYVTDN-MDHDLIIGNPILDRYPTLLYS 135 (177)
T ss_pred EEEecc-CCcceEeccHHHhhhHHHHHH
Confidence 555544 478999999999876655443
No 18
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=93.86 E-value=0.16 Score=44.24 Aligned_cols=89 Identities=13% Similarity=0.318 Sum_probs=72.2
Q ss_pred CCceEEEeeeCCeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCee--------eeccee---eEEE
Q 041134 124 DDALVISIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVT--------YSDGSL---LTDF 192 (267)
Q Consensus 124 ~~~Lvi~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~--------~~lG~i---~v~F 192 (267)
+-.+.+...|++..|+ -|||+|++.=.+......++|+....|. .+.++..-||..+ ..+|.| +|+-
T Consensus 103 ~GHF~a~~~VNGk~v~-fLVDTGATsVal~~~dA~RlGid~~~l~-y~~~v~TANG~~~AA~V~Ld~v~IG~I~~~nV~A 180 (215)
T COG3577 103 DGHFEANGRVNGKKVD-FLVDTGATSVALNEEDARRLGIDLNSLD-YTITVSTANGRARAAPVTLDRVQIGGIRVKNVDA 180 (215)
T ss_pred CCcEEEEEEECCEEEE-EEEecCcceeecCHHHHHHhCCCccccC-CceEEEccCCccccceEEeeeEEEccEEEcCchh
Confidence 3457888999999985 7899999999999999999999988876 5567777787533 335655 7888
Q ss_pred EEeeeCCccceeecchhhhhcc
Q 041134 193 LVVKATSPYNAILGRQWIHKMR 214 (267)
Q Consensus 193 ~Vvd~~~~yn~iLGrpwLh~~~ 214 (267)
.|++....-+.+||..||.+..
T Consensus 181 ~V~~~g~L~~sLLGMSfL~rL~ 202 (215)
T COG3577 181 MVAEDGALDESLLGMSFLNRLS 202 (215)
T ss_pred heecCCccchhhhhHHHHhhcc
Confidence 8998888889999999997754
No 19
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=92.20 E-value=0.6 Score=37.52 Aligned_cols=82 Identities=17% Similarity=0.171 Sum_probs=50.3
Q ss_pred eeCCeeeeEEeecCCCc-cccchHHHHHhhccCcCCCC-----CCCccEEeeeCCeeeecceeeEEEEEeeeCCccceee
Q 041134 132 KIGNCLVRRILIDNGSS-VNILDDATVEKMRLEQDKIK-----PFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAIL 205 (267)
Q Consensus 132 ~I~~~~V~riLvD~GSs-~nil~~~~~~~mg~~~~~L~-----~~~~~l~gf~g~~~~~lG~i~v~F~Vvd~~~~yn~iL 205 (267)
+.+++.-.+ |||+|.+ -=++|..++++||.++.+-- .-+.......-....-.|.-.+.|..+-+..+-+ ++
T Consensus 21 ~~Gd~~~~~-LiDTGFtg~lvlp~~vaek~~~~~~~~~~~~~a~~~~v~t~V~~~~iki~g~e~~~~Vl~s~~~~~~-li 98 (125)
T COG5550 21 GQGDFVYDE-LIDTGFTGYLVLPPQVAEKLGLPLFSTIRIVLADGGVVKTSVALATIKIDGVEKVAFVLASDNLPEP-LI 98 (125)
T ss_pred CCCcEEeee-EEecCCceeEEeCHHHHHhcCCCccCChhhhhhcCCEEEEEEEEEEEEECCEEEEEEEEccCCCccc-ch
Confidence 345555555 9999987 78899999999999874211 1111111111112222222255666666667777 99
Q ss_pred cchhhhhccc
Q 041134 206 GRQWIHKMRV 215 (267)
Q Consensus 206 GrpwLh~~~a 215 (267)
|+-||+....
T Consensus 99 G~~~lk~l~~ 108 (125)
T COG5550 99 GVNLLKLLGL 108 (125)
T ss_pred hhhhhhhccE
Confidence 9999987544
No 20
>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=85.17 E-value=2.2 Score=35.41 Aligned_cols=43 Identities=26% Similarity=0.348 Sum_probs=33.2
Q ss_pred CeeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCC
Q 041134 135 NCLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGI 180 (267)
Q Consensus 135 ~~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~ 180 (267)
+....|+|+|.||..+++..+.+++|+++.. +......|..|+
T Consensus 9 ~~~~~~~LlDsGSq~SfIt~~la~~L~L~~~---~~~~~~~~~~g~ 51 (164)
T PF05585_consen 9 NQVEARALLDSGSQRSFITESLANKLNLPGT---GEKILVIGTFGS 51 (164)
T ss_pred CEEEEEEEEecCCchhHHhHHHHHHhCCCCC---CceEEEEeccCc
Confidence 3566789999999999999999999998753 233455566554
No 21
>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=82.53 E-value=6.3 Score=29.68 Aligned_cols=74 Identities=30% Similarity=0.462 Sum_probs=42.2
Q ss_pred EeeeCCeeeeEEeecCCCccccchHHHHHhhccCcC-CCCCCCccEEeeeCCeeeecc-ee---------eEEEEEeeeC
Q 041134 130 SIKIGNCLVRRILIDNGSSVNILDDATVEKMRLEQD-KIKPFEQPLIGFSGIVTYSDG-SL---------LTDFLVVKAT 198 (267)
Q Consensus 130 ~~~I~~~~V~riLvD~GSs~nil~~~~~~~mg~~~~-~L~~~~~~l~gf~g~~~~~lG-~i---------~v~F~Vvd~~ 198 (267)
++.|++.. .+.|+|+||-.-++...-+ +.. .+......+.|..|......- .+ .-.|.|....
T Consensus 2 ~~~i~g~~-~~~llDTGAd~Tvi~~~~~-----p~~w~~~~~~~~i~GIGG~~~~~~~~~v~i~i~~~~~~g~vlv~~~~ 75 (87)
T cd05482 2 TLYINGKL-FEGLLDTGADVSIIAENDW-----PKNWPIQPAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVLS 75 (87)
T ss_pred EEEECCEE-EEEEEccCCCCeEEccccc-----CCCCccCCCCeEEEeccceEEEEEEeeEEEEEcCCeEEEEEEEccCC
Confidence 45566554 4679999999998876433 211 144456678888775222111 12 2234444433
Q ss_pred Cccceeecchhh
Q 041134 199 SPYNAILGRQWI 210 (267)
Q Consensus 199 ~~yn~iLGrpwL 210 (267)
.|.| |+||..|
T Consensus 76 ~P~n-llGRd~L 86 (87)
T cd05482 76 LPVN-LWGRDIL 86 (87)
T ss_pred Cccc-EEccccC
Confidence 5555 7888765
No 22
>PF02160 Peptidase_A3: Cauliflower mosaic virus peptidase (A3); InterPro: IPR000588 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 sequences contain an aspartic peptidase signature that belongs to MEROPS peptidase family A3, subfamily A3A (cauliflower mosaic virus-type endopeptidase, clan AA). Cauliflower mosaic virus belongs to the Retro-transcribing viruses, which have a double-stranded DNA genome. The genome includes an open reading frame (ORF V) that shows similarities to the pol gene of retroviruses. This ORF codes for a polyprotein that includes a reverse transcriptase, which, on the basis of a DTG triplet near the N terminus, was suggested to include an aspartic protease. The presence of an aspartic protease has been confirmed by mutational studies, implicating Asp-45 in catalysis. The protease releases itself from the polyprotein and is involved in reactions required to process the ORF IV polyprotein, which includes the viral coat protein []. The viral aspartic peptidase signature has also been found associated with a polyprotein encoded by integrated pararetrovirus-like sequences in the genome of Nicotiana tabacum (Common tobacco) []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis
Probab=78.85 E-value=6.3 Score=34.38 Aligned_cols=82 Identities=13% Similarity=0.220 Sum_probs=47.7
Q ss_pred eeeCCeee--eEEeecCCCccccchHHHHHhhccCcCCCCCCC--ccEEeeeCCeee-----eccee---eEEEE---Ee
Q 041134 131 IKIGNCLV--RRILIDNGSSVNILDDATVEKMRLEQDKIKPFE--QPLIGFSGIVTY-----SDGSL---LTDFL---VV 195 (267)
Q Consensus 131 ~~I~~~~V--~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~--~~l~gf~g~~~~-----~lG~i---~v~F~---Vv 195 (267)
+.+.|+.- -..+||+|++++++....+ |....+.+. ..+.|+|++... ..|.| ...|. |.
T Consensus 11 i~~~gy~~~~~~~~vDTGAt~C~~~~~ii-----P~e~we~~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iY 85 (201)
T PF02160_consen 11 ISFPGYKKFNYHCYVDTGATICCASKKII-----PEEYWEKSKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIY 85 (201)
T ss_pred EEEcCceeEEEEEEEeCCCceEEecCCcC-----CHHHHHhCCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEE
Confidence 44445432 2358999999988755543 222223332 478899876332 23333 12221 22
Q ss_pred eeCCccceeecchhhhhccccc
Q 041134 196 KATSPYNAILGRQWIHKMRVVP 217 (267)
Q Consensus 196 d~~~~yn~iLGrpwLh~~~aip 217 (267)
...+-...|||.+||..+.-..
T Consensus 86 q~~~g~d~IlG~NF~r~y~Pfi 107 (201)
T PF02160_consen 86 QQESGIDIILGNNFLRLYEPFI 107 (201)
T ss_pred EecCCCCEEecchHHHhcCCcE
Confidence 3446678999999998777654
No 23
>cd05471 pepsin_like Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH. Pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, renin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (renin, cathepsin D and E, pepsin) or commercially (chymosin) important. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residu
Probab=64.04 E-value=14 Score=32.43 Aligned_cols=71 Identities=14% Similarity=0.086 Sum_probs=40.3
Q ss_pred eeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeecceeeEEEEEeeeCCccceeecchhhhhcccc
Q 041134 137 LVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSLLTDFLVVKATSPYNAILGRQWIHKMRVV 216 (267)
Q Consensus 137 ~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i~v~F~Vvd~~~~yn~iLGrpwLh~~~ai 216 (267)
.-..++||.|++.-.+|.++++++--....-.........+.......+-.|.+.| ..|||-++|...-++
T Consensus 201 ~~~~~iiDsGt~~~~lp~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~p~i~f~f---------~~ilG~~fl~~~y~v 271 (283)
T cd05471 201 GGGGAIVDSGTSLIYLPSSVYDAILKALGAAVSSSDGGYGVDCSPCDTLPDITFTF---------LWILGDVFLRNYYTV 271 (283)
T ss_pred CCcEEEEecCCCCEeCCHHHHHHHHHHhCCcccccCCcEEEeCcccCcCCCEEEEE---------EEEccHhhhhheEEE
Confidence 44579999999999999999998743221111110111111112222223333344 679999998765444
No 24
>cd05474 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins. SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode preproenzymes, approximately 60 amino acid longer than the mature enzyme, which are processed when transported via the secretory pathway. The mature enzymes contain sequence motifs typical for all aspartyl proteinases, including the two conserved aspartate residues other active site and conserved cysteine residues implicated in the maintenance of the three-dimensional structure. Most Sap proteins contain putative N-glycosylation sites, but it remains to be determined which Sap proteins are glycosylated. This family of aspartate proteases
Probab=31.11 E-value=1.3e+02 Score=26.61 Aligned_cols=70 Identities=24% Similarity=0.227 Sum_probs=41.9
Q ss_pred EEEeeeCC-eeeeEEeecCCCccccchHHHHHhhccCcCCCCCCCccEEeeeCCeeeeccee---eEEEEEeeeCCccce
Q 041134 128 VISIKIGN-CLVRRILIDNGSSVNILDDATVEKMRLEQDKIKPFEQPLIGFSGIVTYSDGSL---LTDFLVVKATSPYNA 203 (267)
Q Consensus 128 vi~~~I~~-~~V~riLvD~GSs~nil~~~~~~~mg~~~~~L~~~~~~l~gf~g~~~~~lG~i---~v~F~Vvd~~~~yn~ 203 (267)
++.+.|+. -.--.+++|+||+.-+++ .+ .+.+ ..+.-..|+-..-+..+|.. ++.|.++.......-
T Consensus 4 ~~~i~iGtp~q~~~v~~DTgS~~~wv~--~~-~~~Y------~~g~~~~G~~~~D~v~~g~~~~~~~~fg~~~~~~~~~G 74 (295)
T cd05474 4 SAELSVGTPPQKVTVLLDTGSSDLWVP--DF-SISY------GDGTSASGTWGTDTVSIGGATVKNLQFAVANSTSSDVG 74 (295)
T ss_pred EEEEEECCCCcEEEEEEeCCCCcceee--ee-EEEe------ccCCcEEEEEEEEEEEECCeEecceEEEEEecCCCCcc
Confidence 44555654 234568999999999998 11 1111 11234566666666666655 567888776555666
Q ss_pred eec
Q 041134 204 ILG 206 (267)
Q Consensus 204 iLG 206 (267)
|||
T Consensus 75 ilG 77 (295)
T cd05474 75 VLG 77 (295)
T ss_pred eee
Confidence 654
No 25
>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=28.27 E-value=1.2e+02 Score=23.64 Aligned_cols=24 Identities=42% Similarity=0.660 Sum_probs=20.6
Q ss_pred EeecCCCccccchHHHHHhhccCc
Q 041134 141 ILIDNGSSVNILDDATVEKMRLEQ 164 (267)
Q Consensus 141 iLvD~GSs~nil~~~~~~~mg~~~ 164 (267)
.|||+|+.+|++-..+..+-.++.
T Consensus 50 clidtgaq~niiteetvrahklpt 73 (137)
T PF12382_consen 50 CLIDTGAQVNIITEETVRAHKLPT 73 (137)
T ss_pred eEEccCceeeeeehhhhhhccCCC
Confidence 589999999999999988866654
No 26
>KOG2209 consensus Oxysterol-binding protein [Signal transduction mechanisms]
Probab=27.64 E-value=54 Score=30.88 Aligned_cols=79 Identities=18% Similarity=0.281 Sum_probs=43.1
Q ss_pred hHHHHHhhccCcCC-CCCCCccEEeeeCCe--eeecceeeEEEEEeee--------CCccceeecchhhhh---cccccc
Q 041134 153 DDATVEKMRLEQDK-IKPFEQPLIGFSGIV--TYSDGSLLTDFLVVKA--------TSPYNAILGRQWIHK---MRVVPS 218 (267)
Q Consensus 153 ~~~~~~~mg~~~~~-L~~~~~~l~gf~g~~--~~~lG~i~v~F~Vvd~--------~~~yn~iLGrpwLh~---~~aips 218 (267)
|.|+|-+-|++-.= +..+-.|-.+|=|.+ ..|.|+|.+.|.=-.- =.-||+|+|+-|+.. |+.+.+
T Consensus 149 PiSAfhaEgl~~dF~fhGsi~PklkFWgksvea~Pkgtitle~~k~nEaYtWtnp~CcvhNiIvGklwieqyg~~eI~nh 228 (445)
T KOG2209|consen 149 PISAFHAEGLNNDFIFHGSIYPKLKFWGKSVEAEPKGTITLELLKHNEAYTWTNPTCCVHNIIVGKLWIEQYGNVEIINH 228 (445)
T ss_pred ChhHhhhcccCcceEEeeeecccceeccceeecCCCceEEEEecccCcceeccCCcceeeeehhhhhhHhhcCcEEEEec
Confidence 55777777664321 122333444555543 3677887555532111 123799999999974 555555
Q ss_pred cc-eeeeeeecCCc
Q 041134 219 TY-HQVLCYQTIYG 231 (267)
Q Consensus 219 t~-hq~vk~~~~~G 231 (267)
.. |-+|--..+.|
T Consensus 229 ~Tg~~~vl~Fk~~G 242 (445)
T KOG2209|consen 229 KTGHKCVLNFKPCG 242 (445)
T ss_pred CccceeEEeccccc
Confidence 33 66654334433
No 27
>COG4067 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]
Probab=25.85 E-value=73 Score=26.74 Aligned_cols=34 Identities=21% Similarity=0.368 Sum_probs=24.9
Q ss_pred eeccee--eEEEEEeee-CCccceeecchhhhhcccc
Q 041134 183 YSDGSL--LTDFLVVKA-TSPYNAILGRQWIHKMRVV 216 (267)
Q Consensus 183 ~~lG~i--~v~F~Vvd~-~~~yn~iLGrpwLh~~~ai 216 (267)
..+|.. .++|...|- .-.|.+||||.+|+.+.++
T Consensus 114 l~lG~~~~~~E~tLtDR~~m~Yp~LlGrk~l~~~~~~ 150 (162)
T COG4067 114 LCLGGRILPIEFTLTDRSNMRYPVLLGRKALRHFGAV 150 (162)
T ss_pred EeeCCeeeeEEEEeecccccccceEecHHHHhhCCeE
Confidence 445555 778887764 3479999999999985543
No 28
>PF10622 Ehbp: Energy-converting hydrogenase B subunit P (EhbP); InterPro: IPR019597 Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane. This entry contains subunit P of Ehb.
Probab=23.05 E-value=80 Score=23.07 Aligned_cols=26 Identities=31% Similarity=0.394 Sum_probs=18.3
Q ss_pred eeeecceeeEEEEEeeeCCcc-ceeecchhhh
Q 041134 181 VTYSDGSLLTDFLVVKATSPY-NAILGRQWIH 211 (267)
Q Consensus 181 ~~~~lG~i~v~F~Vvd~~~~y-n~iLGrpwLh 211 (267)
.+.+||- ++++...|| |+|.|.|.=.
T Consensus 5 ~~mslGG-----YI~Et~FPyRNvIV~Npt~E 31 (78)
T PF10622_consen 5 HTMSLGG-----YIRETPFPYRNVIVGNPTDE 31 (78)
T ss_pred eEEeecc-----EEEeccCCcccEEEeCCCCC
Confidence 3455665 677788888 8888887543
No 29
>cd05472 cnd41_like Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This fami
Probab=21.15 E-value=1.8e+02 Score=26.04 Aligned_cols=21 Identities=19% Similarity=0.452 Sum_probs=19.0
Q ss_pred EEeecCCCccccchHHHHHhh
Q 041134 140 RILIDNGSSVNILDDATVEKM 160 (267)
Q Consensus 140 riLvD~GSs~nil~~~~~~~m 160 (267)
.++||.|+++-.+|.++++++
T Consensus 173 ~~ivDSGTt~~~lp~~~~~~l 193 (299)
T cd05472 173 GVIIDSGTVITRLPPSAYAAL 193 (299)
T ss_pred CeEEeCCCcceecCHHHHHHH
Confidence 489999999999999998875
No 30
>cd06097 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin. The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive aspergillosis owing to its elastolytic activity and Aspergillopepsins from the mold A. saitoi are used in fermentation industry. Aspartic proteinases are a group of proteolytic enzymes in which the scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in a DT(S)G motif at the active site. They have a similar fold composed of two beta-barrel domains. Between the N-terminal and C-terminal domains, each of which contributes one catalytic aspartic residue, there is an extended active-
Probab=21.01 E-value=2.4e+02 Score=24.94 Aligned_cols=22 Identities=32% Similarity=0.465 Sum_probs=19.1
Q ss_pred eEEeecCCCccccchHHHHHhh
Q 041134 139 RRILIDNGSSVNILDDATVEKM 160 (267)
Q Consensus 139 ~riLvD~GSs~nil~~~~~~~m 160 (267)
..++||.|++.-.+|.++++++
T Consensus 199 ~~~iiDSGTs~~~lP~~~~~~l 220 (278)
T cd06097 199 FSAIADTGTTLILLPDAIVEAY 220 (278)
T ss_pred ceEEeecCCchhcCCHHHHHHH
Confidence 4579999999999998888766
No 31
>KOG4353 consensus RNA export factor NXT1 [RNA processing and modification]
Probab=20.76 E-value=50 Score=26.86 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=18.4
Q ss_pred cceeecchhhh-hccccccccee
Q 041134 201 YNAILGRQWIH-KMRVVPSTYHQ 222 (267)
Q Consensus 201 yn~iLGrpwLh-~~~aipst~hq 222 (267)
-|++.|+..|. .|++.||+-||
T Consensus 48 Gn~v~g~esls~ff~~LPsS~~q 70 (139)
T KOG4353|consen 48 GNPVSGTESLSEFFNMLPSSEFQ 70 (139)
T ss_pred CCcchhHHHHHHHHHhCCCcccc
Confidence 37788999996 67789999998
Done!