Query 039663
Match_columns 102
No_of_seqs 107 out of 260
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 11:56:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039663.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039663hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08284 RVP_2: Retroviral asp 99.9 4.2E-23 9.1E-28 144.4 7.8 69 2-72 64-132 (135)
2 cd05479 RP_DDI RP_DDI; retrope 99.7 2.7E-16 5.9E-21 107.8 8.3 67 2-69 58-124 (124)
3 cd05484 retropepsin_like_LTR_2 99.2 8.7E-11 1.9E-15 75.9 6.1 50 2-53 42-91 (91)
4 PF02160 Peptidase_A3: Caulifl 98.6 4.2E-07 9E-12 68.0 9.0 73 2-77 50-124 (201)
5 cd00303 retropepsin_like Retro 98.5 4.9E-07 1.1E-11 53.2 6.3 52 2-53 41-92 (92)
6 TIGR03698 clan_AA_DTGF clan AA 98.4 2.2E-06 4.8E-11 57.6 7.0 62 2-67 46-107 (107)
7 PF09668 Asp_protease: Asparty 98.0 3.1E-05 6.7E-10 53.9 6.8 50 11-61 75-124 (124)
8 PF00077 RVP: Retroviral aspar 97.9 4.4E-05 9.4E-10 49.3 6.6 52 3-57 46-97 (100)
9 cd05483 retropepsin_like_bacte 97.8 5.9E-05 1.3E-09 47.4 5.4 50 2-53 44-96 (96)
10 PF13650 Asp_protease_2: Aspar 97.8 0.00013 2.7E-09 45.4 6.6 48 2-51 41-90 (90)
11 TIGR02281 clan_AA_DTGA clan AA 97.6 0.00057 1.2E-08 46.7 8.3 64 2-67 54-119 (121)
12 cd06094 RP_Saci_like RP_Saci_l 97.0 0.004 8.6E-08 41.3 6.4 53 1-56 35-88 (89)
13 cd06095 RP_RTVL_H_like Retrope 96.9 0.0028 6E-08 40.5 5.3 50 2-53 37-86 (86)
14 cd05480 NRIP_C NRIP_C; putativ 96.9 0.0048 1E-07 41.9 6.6 54 9-63 49-102 (103)
15 COG5550 Predicted aspartyl pro 96.0 0.026 5.7E-07 39.5 5.8 62 3-68 57-118 (125)
16 cd05481 retropepsin_like_LTR_1 95.1 0.11 2.4E-06 33.8 6.2 47 1-49 43-89 (93)
17 KOG0012 DNA damage inducible p 93.1 0.2 4.3E-06 40.8 5.0 62 12-74 287-348 (380)
18 PF12384 Peptidase_A2B: Ty3 tr 91.7 0.83 1.8E-05 33.7 6.3 46 11-57 86-131 (177)
19 COG2383 Uncharacterized conser 86.2 0.21 4.5E-06 34.0 -0.1 20 46-65 51-70 (109)
20 COG3577 Predicted aspartyl pro 81.7 2.8 6.2E-05 31.8 4.3 54 2-57 148-203 (215)
21 PF04930 FUN14: FUN14 family; 65.2 2 4.3E-05 28.3 -0.1 22 46-67 31-52 (100)
22 PF00026 Asp: Eukaryotic aspar 60.7 46 0.00099 24.6 6.6 58 12-70 235-315 (317)
23 COG4615 PvdE ABC-type sideroph 47.7 25 0.00055 29.8 3.6 47 55-101 339-405 (546)
24 KOG1542 Cysteine proteinase Ca 47.6 5.7 0.00012 32.5 -0.2 42 29-73 261-302 (372)
25 cd05477 gastricsin Gastricsins 46.4 1.3E+02 0.0027 22.8 7.1 59 12-71 238-317 (318)
26 PF04746 DUF575: Protein of un 46.0 10 0.00022 25.5 0.9 12 44-55 28-39 (101)
27 PF01684 ET: ET module; Inter 44.0 42 0.00091 21.6 3.5 23 7-29 12-35 (82)
28 KOG4584 Uncharacterized conser 39.6 18 0.00039 29.3 1.5 23 28-50 196-218 (348)
29 KOG1370 S-adenosylhomocysteine 37.0 35 0.00076 28.1 2.8 92 10-102 270-377 (434)
30 PF10771 DUF2582: Protein of u 32.8 28 0.00062 21.5 1.3 33 38-70 32-64 (65)
31 PF00622 SPRY: SPRY domain; I 31.4 77 0.0017 20.0 3.3 21 57-77 71-91 (124)
32 PF07833 Cu_amine_oxidN1: Copp 31.1 1.2E+02 0.0027 18.2 4.5 28 52-79 13-41 (93)
33 cd05485 Cathepsin_D_like Cathe 30.6 2.3E+02 0.005 21.7 6.4 58 12-70 247-328 (329)
34 PHA01782 hypothetical protein 29.4 33 0.00072 25.3 1.4 34 49-82 73-110 (177)
35 cd05474 SAP_like SAPs, pepsin- 29.0 2.4E+02 0.0051 20.8 7.0 58 13-71 217-294 (295)
36 PHA02088 hypothetical protein 28.9 66 0.0014 22.1 2.7 28 50-78 39-73 (125)
37 cd06097 Aspergillopepsin_like 28.7 80 0.0017 23.4 3.4 41 12-70 237-277 (278)
38 cd06396 PB1_NBR1 The PB1 domai 28.2 1.6E+02 0.0035 18.9 4.3 35 66-100 2-36 (81)
39 cd05488 Proteinase_A_fungi Fun 27.4 2.8E+02 0.006 21.1 6.6 57 13-70 243-319 (320)
40 cd05476 pepsin_A_like_plant Ch 27.2 2.5E+02 0.0054 20.6 5.9 29 43-72 235-263 (265)
41 KOG3217 Protein tyrosine phosp 26.3 25 0.00054 25.6 0.3 13 39-51 82-94 (159)
42 cd05471 pepsin_like Pepsin-lik 26.1 1.1E+02 0.0023 22.1 3.6 26 44-70 257-282 (283)
43 PRK09502 iscA iron-sulfur clus 26.1 1.5E+02 0.0032 19.3 4.0 55 3-64 26-81 (107)
44 cd05482 HIV_retropepsin_like R 25.8 1.7E+02 0.0036 18.8 4.1 44 8-52 43-86 (87)
45 PF12385 Peptidase_C70: Papain 25.7 96 0.0021 22.8 3.2 15 49-63 102-116 (166)
46 PF03633 Glyco_hydro_65C: Glyc 25.6 1.2E+02 0.0027 17.1 3.2 12 60-71 14-25 (54)
47 PF14645 Chibby: Chibby family 25.1 1.6E+02 0.0034 20.1 4.0 38 35-77 24-61 (116)
48 cd07977 TFIIE_beta_winged_heli 25.0 62 0.0013 20.3 1.9 23 49-71 45-70 (75)
49 TIGR02011 IscA iron-sulfur clu 24.7 1.8E+02 0.0038 18.9 4.2 29 36-64 51-79 (105)
50 PRK12442 translation initiatio 24.3 2.1E+02 0.0046 18.8 4.4 40 2-45 21-62 (87)
51 PF11604 CusF_Ec: Copper bindi 24.3 33 0.00072 21.0 0.5 19 54-72 16-35 (70)
52 PF09292 Neil1-DNA_bind: Endon 24.2 63 0.0014 18.2 1.6 28 50-84 7-36 (39)
53 PRK10126 tyrosine phosphatase; 22.1 90 0.002 21.4 2.5 29 38-69 71-104 (147)
No 1
>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=99.89 E-value=4.2e-23 Score=144.41 Aligned_cols=69 Identities=35% Similarity=0.611 Sum_probs=64.2
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeC
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYR 72 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~ 72 (102)
|+.|. ++|+.+.|.+.|++|+|++||++|.+||++|||++||||||||||++|+| .+||++++++|+..
T Consensus 64 ~~~V~-~~g~~~~~~~~~~~~~~~i~g~~~~~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~v~f~~p 132 (135)
T PF08284_consen 64 PIVVS-APGGSINCEGVCPDVPLSIQGHEFVVDLLVLDLGGYDVILGMDWLKKHNP-VIDWATKTVTFNSP 132 (135)
T ss_pred eeEEe-cccccccccceeeeEEEEECCeEEEeeeEEecccceeeEeccchHHhCCC-EEEccCCEEEEeCC
Confidence 56666 56888999999999999999999999999999999999999999999998 79999999999864
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=99.67 E-value=2.7e-16 Score=107.76 Aligned_cols=67 Identities=12% Similarity=0.127 Sum_probs=61.6
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEE
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEF 69 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f 69 (102)
++.+++++++...+.+.|+.++++++|.+|..+|.|+|+.++|+|||||||++++ +.+||++++|+|
T Consensus 58 ~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~Vl~~~~~d~ILG~d~L~~~~-~~ID~~~~~i~~ 124 (124)
T cd05479 58 RFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQ-CVIDLKENVLRI 124 (124)
T ss_pred ceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEEECCCCcCEEecHHHHHhCC-eEEECCCCEEEC
Confidence 3567788767789999999999999999999999999999999999999999999 689999999975
No 3
>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=99.16 E-value=8.7e-11 Score=75.92 Aligned_cols=50 Identities=14% Similarity=0.229 Sum_probs=47.7
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHh
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE 53 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~ 53 (102)
..+|+.|||+.+.+.+.| .+++++||.+|..+++|++.+ +|.+||+|||+
T Consensus 42 ~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~-~~~lLG~~wl~ 91 (91)
T cd05484 42 KKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE-GLNLLGRDWLD 91 (91)
T ss_pred cEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC-CCCccChhhcC
Confidence 468999999999999999 899999999999999999999 99999999985
No 4
>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=98.59 E-value=4.2e-07 Score=67.95 Aligned_cols=73 Identities=16% Similarity=0.215 Sum_probs=64.5
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeE-eecCCCcceeechhHHhhhCceEEeccceEEEEEeCC-eEEE
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFH-ILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRR-QPIK 77 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~-vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g-~~v~ 77 (102)
|+.|+.|||+....+.+|+++.+.|.|+.|...++ ..+ .|.|+|||+.+++.+.|. +.|. .++.|+..+ ..+.
T Consensus 50 ~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq~~-~g~d~IlG~NF~r~y~Pf-iq~~-~~I~f~~~~~~~~~ 124 (201)
T PF02160_consen 50 PIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQQE-SGIDIILGNNFLRLYEPF-IQTE-DRIQFHKKGLQKVE 124 (201)
T ss_pred cEEEEEecCCceEEEEEecCceEEEccEEEeccEEEEec-CCCCEEecchHHHhcCCc-EEEc-cEEEEEeCCcceee
Confidence 68999999999999999999999999999999655 666 689999999999999996 8886 479999887 4443
No 5
>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=98.51 E-value=4.9e-07 Score=53.23 Aligned_cols=52 Identities=31% Similarity=0.505 Sum_probs=47.0
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHh
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE 53 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~ 53 (102)
+..+..++|......+.+..+.+.+++..+...+++.+..++|+|||++||.
T Consensus 41 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~ilG~~~l~ 92 (92)
T cd00303 41 PLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92 (92)
T ss_pred ceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCCcCEEecccccC
Confidence 4567788888888888888999999999999999999999999999999984
No 6
>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=98.35 E-value=2.2e-06 Score=57.57 Aligned_cols=62 Identities=23% Similarity=0.349 Sum_probs=50.0
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEE
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTM 67 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm 67 (102)
+..|..|||......- .-..+.++|++..+...+.+... ++.|||.||++++ +.+||+++++
T Consensus 46 ~~~~~tA~G~~~~~~v--~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~L~~l~-l~id~~~~~~ 107 (107)
T TIGR03698 46 QRRVYLADGREVLTDV--AKASIIINGLEIDAFVESLGYVD-EPLLGTELLEGLG-IVIDYRNQGL 107 (107)
T ss_pred CcEEEecCCcEEEEEE--EEEEEEECCEEEEEEEEecCCCC-ccEecHHHHhhCC-EEEehhhCcC
Confidence 3578999998777664 47889999999866666666666 9999999999998 5799998764
No 7
>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=97.98 E-value=3.1e-05 Score=53.92 Aligned_cols=50 Identities=18% Similarity=0.293 Sum_probs=42.8
Q ss_pred CeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEe
Q 039663 11 ERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTD 61 (102)
Q Consensus 11 ~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D 61 (102)
+.-+.-|+...+++++++..|+..|.|+|=...|++||.|||.+|.- .+|
T Consensus 75 G~~~i~G~Ih~~~l~ig~~~~~~s~~Vle~~~~d~llGld~L~~~~c-~ID 124 (124)
T PF09668_consen 75 GTQKILGRIHSVQLKIGGLFFPCSFTVLEDQDVDLLLGLDMLKRHKC-CID 124 (124)
T ss_dssp ---EEEEEEEEEEEEETTEEEEEEEEEETTSSSSEEEEHHHHHHTT--EEE
T ss_pred CcCceeEEEEEEEEEECCEEEEEEEEEeCCCCcceeeeHHHHHHhCc-ccC
Confidence 56678889999999999999999999999889999999999999974 455
No 8
>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=97.94 E-value=4.4e-05 Score=49.33 Aligned_cols=52 Identities=25% Similarity=0.316 Sum_probs=45.0
Q ss_pred eEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCc
Q 039663 3 FLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGK 57 (102)
Q Consensus 3 ~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~ 57 (102)
..|.-++|.. ...+.+ .+++++.+..|...+++.|-..+| |||+|||++++.
T Consensus 46 ~~v~~~~g~~-~~~~~~-~~~v~~~~~~~~~~~~v~~~~~~~-ILG~D~L~~~~~ 97 (100)
T PF00077_consen 46 ITVRGAGGSS-SILGST-TVEVKIGGKEFNHTFLVVPDLPMN-ILGRDFLKKLNA 97 (100)
T ss_dssp EEEEETTEEE-EEEEEE-EEEEEETTEEEEEEEEESSTCSSE-EEEHHHHTTTTC
T ss_pred ceeccCCCcc-eeeeEE-EEEEEEECccceEEEEecCCCCCC-EeChhHHHHcCC
Confidence 4677787877 776665 799999999999999999987788 999999999985
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=97.82 E-value=5.9e-05 Score=47.37 Aligned_cols=50 Identities=16% Similarity=0.232 Sum_probs=42.6
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEE-eeeEeecCCC--cceeechhHHh
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFE-VDFHILDFSG--ANAGLAVQWLE 53 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~-~dl~vL~L~~--~DvILGmdWL~ 53 (102)
+.+++.++|........ --++++++..|. ..+.++|... .|.|||+|||+
T Consensus 44 ~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~~~v~d~~~~~~~gIlG~d~l~ 96 (96)
T cd05483 44 KVTVQTANGRVRAARVR--LDSLQIGGITLRNVPAVVLPGDALGVDGLLGMDFLR 96 (96)
T ss_pred cEEEEecCCCccceEEE--cceEEECCcEEeccEEEEeCCcccCCceEeChHHhC
Confidence 45788899998887776 457799999998 5899999998 99999999984
No 10
>PF13650 Asp_protease_2: Aspartyl protease
Probab=97.80 E-value=0.00013 Score=45.42 Aligned_cols=48 Identities=17% Similarity=0.302 Sum_probs=38.9
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEE-EeeeEeec-CCCcceeechhH
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEF-EVDFHILD-FSGANAGLAVQW 51 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F-~~dl~vL~-L~~~DvILGmdW 51 (102)
+..++.++|.........+ ++++++..+ ..++.+.+ -..+|.||||||
T Consensus 41 ~~~~~~~~g~~~~~~~~~~--~i~ig~~~~~~~~~~v~~~~~~~~~iLG~df 90 (90)
T PF13650_consen 41 PISVSGAGGSVTVYRGRVD--SITIGGITLKNVPFLVVDLGDPIDGILGMDF 90 (90)
T ss_pred eEEEEeCCCCEEEEEEEEE--EEEECCEEEEeEEEEEECCCCCCEEEeCCcC
Confidence 3677889999555445544 899999999 67899999 668999999998
No 11
>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=97.62 E-value=0.00057 Score=46.71 Aligned_cols=64 Identities=16% Similarity=0.285 Sum_probs=49.5
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEE-eeeEeecCCC-cceeechhHHhhhCceEEeccceEE
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFE-VDFHILDFSG-ANAGLAVQWLEKLGKIVTDHKALTM 67 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~-~dl~vL~L~~-~DvILGmdWL~~~g~i~~D~~~~tm 67 (102)
+..+..|||.... ....--++++++.++. .++.|+|.+. -|.+||||.|+++.++.+|-.+.++
T Consensus 54 ~~~~~ta~G~~~~--~~~~l~~l~iG~~~~~nv~~~v~~~~~~~~~LLGm~fL~~~~~~~~~~~~l~l 119 (121)
T TIGR02281 54 TVTVSTANGQIKA--ARVTLDRVAIGGIVVNDVDAMVAEGGALSESLLGMSFLNRLSRFTVRGGKLIL 119 (121)
T ss_pred eEEEEeCCCcEEE--EEEEeCEEEECCEEEeCcEEEEeCCCcCCceEcCHHHHhccccEEEECCEEEE
Confidence 3578899997543 3345667999999998 7899999874 5899999999999877666655443
No 12
>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=96.97 E-value=0.004 Score=41.27 Aligned_cols=53 Identities=19% Similarity=0.379 Sum_probs=46.9
Q ss_pred CceEEEecCCCeEEecceeeceEEEEcCE-EEEeeeEeecCCCcceeechhHHhhhC
Q 039663 1 MSFLVDVGNGERIRSEGHCSKVKFEMQGV-EFEVDFHILDFSGANAGLAVQWLEKLG 56 (102)
Q Consensus 1 ~~~~V~va~G~~l~~~~~~~~v~~~iqg~-~F~~dl~vL~L~~~DvILGmdWL~~~g 56 (102)
+++.+..|||..|..-|. ..+.+.++.. .|.-+|.|=|.. .-|||+|.|++||
T Consensus 35 ~~~~l~AANgt~I~tyG~-~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~~~~ 88 (89)
T cd06094 35 SPLTLQAANGTPIATYGT-RSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQHYG 88 (89)
T ss_pred CceEEEeCCCCeEeeeee-EEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHHHcC
Confidence 467899999999999995 6899999885 999999998886 4799999999986
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=96.94 E-value=0.0028 Score=40.50 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=36.8
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHh
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLE 53 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~ 53 (102)
+..+.-++|..-..-....+ .+.++++++..++.+.|- ..|.|||||+|.
T Consensus 37 ~~~v~gagG~~~~~v~~~~~-~v~vg~~~~~~~~~v~~~-~~~~lLG~dfL~ 86 (86)
T cd06095 37 SVLIRGVSGQSQQPVTTYRT-LVDLGGHTVSHSFLVVPN-CPDPLLGRDLLS 86 (86)
T ss_pred cEEEEeCCCcccccEEEeee-EEEECCEEEEEEEEEEcC-CCCcEechhhcC
Confidence 46788888886212222222 699999999999988873 479999999984
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=96.93 E-value=0.0048 Score=41.87 Aligned_cols=54 Identities=17% Similarity=0.237 Sum_probs=47.4
Q ss_pred CCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEecc
Q 039663 9 NGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHK 63 (102)
Q Consensus 9 ~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~ 63 (102)
-|...+-.|....++++|++..++-.|-|||-...|++||.|=|.+|.. .+|.+
T Consensus 49 vgt~~kiiGrih~~~ikig~~~~~CSftVld~~~~d~llGLdmLkrhqc-~IdL~ 102 (103)
T cd05480 49 LPTSVKVIGQIERLVLQLGQLTVECSAQVVDDNEKNFSLGLQTLKSLKC-VINLE 102 (103)
T ss_pred CCcceeEeeEEEEEEEEeCCEEeeEEEEEEcCCCcceEeeHHHHhhcce-eeecc
Confidence 3445677889999999999999999999999889999999999999975 57765
No 15
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=95.98 E-value=0.026 Score=39.52 Aligned_cols=62 Identities=19% Similarity=0.200 Sum_probs=50.4
Q ss_pred eEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEE
Q 039663 3 FLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTME 68 (102)
Q Consensus 3 ~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~ 68 (102)
.++..|+|+.+.+.- .-..+++.|.+..+-..+.|....+ ++|++||+.+|- .+|.+...++
T Consensus 57 ~~~~~a~~~~v~t~V--~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~~lk~l~~-~vn~~~g~LE 118 (125)
T COG5550 57 IRIVLADGGVVKTSV--ALATIKIDGVEKVAFVLASDNLPEP-LIGVNLLKLLGL-VVNPKTGKLE 118 (125)
T ss_pred hhhhhhcCCEEEEEE--EEEEEEECCEEEEEEEEccCCCccc-chhhhhhhhccE-EEcCCcceEe
Confidence 356678888877654 4689999999999988888888888 999999999984 7898665554
No 16
>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=95.11 E-value=0.11 Score=33.82 Aligned_cols=47 Identities=19% Similarity=0.317 Sum_probs=40.1
Q ss_pred CceEEEecCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeech
Q 039663 1 MSFLVDVGNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAV 49 (102)
Q Consensus 1 ~~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGm 49 (102)
++++++.+||..+...|. ..+++.+++..+..+|+|++-.+-. |||.
T Consensus 43 t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~~~~~-lLG~ 89 (93)
T cd05481 43 SPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKEEGPP-LLGA 89 (93)
T ss_pred CCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECCCCCc-eEcc
Confidence 367899999999999999 5899999999999999999986443 4554
No 17
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=93.14 E-value=0.2 Score=40.76 Aligned_cols=62 Identities=13% Similarity=0.198 Sum_probs=56.1
Q ss_pred eEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeCCe
Q 039663 12 RIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQ 74 (102)
Q Consensus 12 ~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g~ 74 (102)
..+-.|....++++|+...++-.|-|++=...|+-||.|=|++|+. .||.++..+.|...+.
T Consensus 287 ~~ki~g~Ih~~~lki~~~~l~c~ftV~d~~~~d~llGLd~Lrr~~c-cIdL~~~~L~ig~~~t 348 (380)
T KOG0012|consen 287 TEKILGRIHQAQLKIEDLYLPCSFTVLDRRDMDLLLGLDMLRRHQC-CIDLKTNVLRIGNTET 348 (380)
T ss_pred cccccceeEEEEEEeccEeeccceEEecCCCcchhhhHHHHHhccc-eeecccCeEEecCCCc
Confidence 5566788899999999999999999999999999999999999997 6999999999866555
No 18
>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=91.72 E-value=0.83 Score=33.71 Aligned_cols=46 Identities=9% Similarity=0.106 Sum_probs=39.2
Q ss_pred CeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCc
Q 039663 11 ERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGK 57 (102)
Q Consensus 11 ~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~ 57 (102)
+...|... ..+++.+.+..|...+||+|--.+|+|+|..-|.+|..
T Consensus 86 ~~~~tsEA-v~ld~~i~n~~i~i~aYV~d~m~~dlIIGnPiL~ryp~ 131 (177)
T PF12384_consen 86 ESATTSEA-VTLDFYIDNKLIDIAAYVTDNMDHDLIIGNPILDRYPT 131 (177)
T ss_pred CceEEEEe-EEEEEEECCeEEEEEEEEeccCCcceEeccHHHhhhHH
Confidence 33445444 47999999999999999999999999999999999853
No 19
>COG2383 Uncharacterized conserved protein [Function unknown]
Probab=86.20 E-value=0.21 Score=34.04 Aligned_cols=20 Identities=35% Similarity=0.614 Sum_probs=17.9
Q ss_pred eechhHHhhhCceEEeccce
Q 039663 46 GLAVQWLEKLGKIVTDHKAL 65 (102)
Q Consensus 46 ILGmdWL~~~g~i~~D~~~~ 65 (102)
||+..||+++|.|++||.+.
T Consensus 51 ilsl~~La~~GVItin~~al 70 (109)
T COG2383 51 ILSLFWLAQYGVITINWEAL 70 (109)
T ss_pred HHHHHHHHHcCeEEEcHHHH
Confidence 68899999999999999763
No 20
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=81.69 E-value=2.8 Score=31.84 Aligned_cols=54 Identities=15% Similarity=0.269 Sum_probs=41.7
Q ss_pred ceEEEecCCCeEEecceeeceEEEEcCEEEEe-eeEeecCCCc-ceeechhHHhhhCc
Q 039663 2 SFLVDVGNGERIRSEGHCSKVKFEMQGVEFEV-DFHILDFSGA-NAGLAVQWLEKLGK 57 (102)
Q Consensus 2 ~~~V~va~G~~l~~~~~~~~v~~~iqg~~F~~-dl~vL~L~~~-DvILGmdWL~~~g~ 57 (102)
++.|+.|||+.-...-... ++.|++.++.. +-+|++-+.. ..-|||.+|.+++-
T Consensus 148 ~~~v~TANG~~~AA~V~Ld--~v~IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~ 203 (215)
T COG3577 148 TITVSTANGRARAAPVTLD--RVQIGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSG 203 (215)
T ss_pred ceEEEccCCccccceEEee--eEEEccEEEcCchhheecCCccchhhhhHHHHhhccc
Confidence 6789999999776665553 45677777764 8889988854 46789999999985
No 21
>PF04930 FUN14: FUN14 family; InterPro: IPR007014 This is a family of short proteins found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices.
Probab=65.16 E-value=2 Score=28.26 Aligned_cols=22 Identities=27% Similarity=0.289 Sum_probs=18.9
Q ss_pred eechhHHhhhCceEEeccceEE
Q 039663 46 GLAVQWLEKLGKIVTDHKALTM 67 (102)
Q Consensus 46 ILGmdWL~~~g~i~~D~~~~tm 67 (102)
++.++||+..|-|.+||++.+-
T Consensus 31 ~l~lq~l~~~G~i~Vnw~kl~~ 52 (100)
T PF04930_consen 31 FLLLQYLASKGYIKVNWDKLEK 52 (100)
T ss_pred HHHHHHHHHCCeEEECHHHHHH
Confidence 5779999999999999998543
No 22
>PF00026 Asp: Eukaryotic aspartyl protease The Prosite entry also includes Pfam:PF00077.; InterPro: IPR001461 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 MEROPS peptidase family A1 (pepsin family, clan AA). The type example is pepsin A from Homo sapiens (Human) . More than 70 aspartic peptidases, from all from eukaryotic organisms, have been identified. These include pepsins, cathepsins, and renins. The enzymes are synthesised with signal peptides, and the proenzymes are secreted or passed into the lysosomal/endosomal system, where acidification leads to autocatalytic activation. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residues in both the P1 and P1' positions []. Crystallography has shown the active site to form a groove across the junction of the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors within the active site []. Specificity is determined by several hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. Cysteine residues are well conserved within the pepsin family, pepsin itself containing three disulphide loops. The first loop is found in all but the fungal enzymes, and is usually around five residues in length, but is longer in barrierpepsin and candidapepsin; the second loop is also small and found only in the animal enzymes; and the third loop is the largest, found in all members of the family, except for the cysteine-free polyporopepsin. The loops are spread unequally throughout the two lobes, suggesting that they formed after the initial gene duplication and fusion event []. This family does not include the retroviral nor retrotransposon aspartic proteases which are much smaller and appear to be homologous to the single domain aspartic proteases.; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 1CZI_E 3CMS_A 1CMS_A 4CMS_A 1YG9_A 2NR6_A 3LIZ_A 1FLH_A 3UTL_A 1QRP_E ....
Probab=60.66 E-value=46 Score=24.64 Aligned_cols=58 Identities=17% Similarity=0.241 Sum_probs=41.0
Q ss_pred eEEecce--eeceEEEEcCEEEEeee-----------------Eeec----CCCcceeechhHHhhhCceEEeccceEEE
Q 039663 12 RIRSEGH--CSKVKFEMQGVEFEVDF-----------------HILD----FSGANAGLAVQWLEKLGKIVTDHKALTME 68 (102)
Q Consensus 12 ~l~~~~~--~~~v~~~iqg~~F~~dl-----------------~vL~----L~~~DvILGmdWL~~~g~i~~D~~~~tm~ 68 (102)
.+.|+.. -|.+.+.++|.+|.... .+.+ -.....|||+.+|+.+ -+..|+.++++-
T Consensus 235 ~~~c~~~~~~p~l~f~~~~~~~~i~~~~~~~~~~~~~~~~C~~~i~~~~~~~~~~~~iLG~~fl~~~-y~vfD~~~~~ig 313 (317)
T PF00026_consen 235 SVPCNSTDSLPDLTFTFGGVTFTIPPSDYIFKIEDGNGGYCYLGIQPMDSSDDSDDWILGSPFLRNY-YVVFDYENNRIG 313 (317)
T ss_dssp EEETTGGGGSEEEEEEETTEEEEEEHHHHEEEESSTTSSEEEESEEEESSTTSSSEEEEEHHHHTTE-EEEEETTTTEEE
T ss_pred EEecccccccceEEEeeCCEEEEecchHhcccccccccceeEeeeecccccccCCceEecHHHhhce-EEEEeCCCCEEE
Confidence 4566655 67777777777765421 1122 3467899999999988 468999999998
Q ss_pred EE
Q 039663 69 FT 70 (102)
Q Consensus 69 f~ 70 (102)
|.
T Consensus 314 ~A 315 (317)
T PF00026_consen 314 FA 315 (317)
T ss_dssp EE
T ss_pred Ee
Confidence 75
No 23
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=47.70 E-value=25 Score=29.84 Aligned_cols=47 Identities=21% Similarity=0.153 Sum_probs=37.6
Q ss_pred hCceEEeccceEEEEEeCC--------------------eEEEEEecCCCCCCchhHHHHHhccccC
Q 039663 55 LGKIVTDHKALTMEFTYRR--------------------QPIKLVGAQNILPKPTQSIHLQSRIFTS 101 (102)
Q Consensus 55 ~g~i~~D~~~~tm~f~~~g--------------------~~v~l~g~~~~~~~~~q~~~l~~~~~~~ 101 (102)
.|||++--++..+.|--++ .+|.|.|.+-+..+..+||+|-|.+|+.
T Consensus 339 vgPiNl~ikrGelvFliG~NGsGKST~~~LLtGL~~PqsG~I~ldg~pV~~e~ledYR~LfSavFsD 405 (546)
T COG4615 339 VGPINLTIKRGELVFLIGGNGSGKSTLAMLLTGLYQPQSGEILLDGKPVSAEQLEDYRKLFSAVFSD 405 (546)
T ss_pred ecceeeEEecCcEEEEECCCCCcHHHHHHHHhcccCCCCCceeECCccCCCCCHHHHHHHHHHHhhh
Confidence 4788888888888875432 3588888888888999999999999974
No 24
>KOG1542 consensus Cysteine proteinase Cathepsin F [Posttranslational modification, protein turnover, chaperones]
Probab=47.58 E-value=5.7 Score=32.47 Aligned_cols=42 Identities=24% Similarity=0.334 Sum_probs=34.0
Q ss_pred EEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEEeCC
Q 039663 29 VEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRR 73 (102)
Q Consensus 29 ~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g 73 (102)
..+..||..|+...-+| ..||.++||+.+=-..+.|+|..+|
T Consensus 261 ~v~I~~f~~l~~nE~~i---a~wLv~~GPi~vgiNa~~mQ~YrgG 302 (372)
T KOG1542|consen 261 VVSIKDFSMLSNNEDQI---AAWLVTFGPLSVGINAKPMQFYRGG 302 (372)
T ss_pred eEEEeccEecCCCHHHH---HHHHHhcCCeEEEEchHHHHHhccc
Confidence 45667888999866555 4999999999888889999987766
No 25
>cd05477 gastricsin Gastricsins, asparate proteases produced in gastric mucosa. Gastricsin is also called pepsinogen C. Gastricsins are produced in gastric mucosa of mammals. It is synthesized by the chief cells in the stomach as an inactive zymogen. It is self-converted to a mature enzyme under acidic conditions. Human gastricsin is distributed throughout all parts of the stomach. Gastricsin is synthesized as an inactive progastricsin that has an approximately 40 residue prosequence. It is self-converting to a mature enzyme being triggered by a drop in pH from neutrality to acidic conditions. Like other aspartic proteases, gastricsin are characterized by two catalytic aspartic residues at the active site, and display optimal activity at acidic pH. Mature enzyme has a pseudo-2-fold symmetry that passes through the active site between the catalytic aspartate residues. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic aspartate residue, with an exten
Probab=46.39 E-value=1.3e+02 Score=22.82 Aligned_cols=59 Identities=15% Similarity=0.165 Sum_probs=41.5
Q ss_pred eEEecc--eeeceEEEEcCEEEEeee----------EeecC---------CCcceeechhHHhhhCceEEeccceEEEEE
Q 039663 12 RIRSEG--HCSKVKFEMQGVEFEVDF----------HILDF---------SGANAGLAVQWLEKLGKIVTDHKALTMEFT 70 (102)
Q Consensus 12 ~l~~~~--~~~~v~~~iqg~~F~~dl----------~vL~L---------~~~DvILGmdWL~~~g~i~~D~~~~tm~f~ 70 (102)
.+.|.. ..|.+.+.++|.+|.... -.+.+ +.-..|||...|+.+= +..|+.++++.|.
T Consensus 238 ~~~C~~~~~~p~l~~~f~g~~~~v~~~~y~~~~~~~C~~~i~~~~~~~~~~~~~~ilG~~fl~~~y-~vfD~~~~~ig~a 316 (318)
T cd05477 238 VVNCNNIQNLPTLTFTINGVSFPLPPSAYILQNNGYCTVGIEPTYLPSQNGQPLWILGDVFLRQYY-SVYDLGNNQVGFA 316 (318)
T ss_pred EEeCCccccCCcEEEEECCEEEEECHHHeEecCCCeEEEEEEecccCCCCCCceEEEcHHHhhheE-EEEeCCCCEEeee
Confidence 456764 257888999998887542 11211 2235899999999985 4799999999885
Q ss_pred e
Q 039663 71 Y 71 (102)
Q Consensus 71 ~ 71 (102)
.
T Consensus 317 ~ 317 (318)
T cd05477 317 T 317 (318)
T ss_pred e
Confidence 3
No 26
>PF04746 DUF575: Protein of unknown function (DUF575); InterPro: IPR006835 This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Probab=45.97 E-value=10 Score=25.51 Aligned_cols=12 Identities=17% Similarity=0.540 Sum_probs=10.0
Q ss_pred ceeechhHHhhh
Q 039663 44 NAGLAVQWLEKL 55 (102)
Q Consensus 44 DvILGmdWL~~~ 55 (102)
-++.||+||-+.
T Consensus 28 hiv~GieWLvS~ 39 (101)
T PF04746_consen 28 HIVMGIEWLVSR 39 (101)
T ss_pred eEEeehHHHHHH
Confidence 378999999876
No 27
>PF01684 ET: ET module; InterPro: IPR002603 The proteins in this entry have no known function, and are found in Caenorhabditis elegans and in Caenorhabditis briggsae. Each repeat contains 8-10 conserved cysteines that probably form 4-5 disulphide bridges. By inspection of the conservation of cysteines it looks like cysteines 1, 2, 3, 4, 9 and 10 are always present and that sometimes the pair 5 and 8 or the pair 6 and 7 are missing. This suggests that cysteines 5/8 and 6/7 make disulphide bridges.
Probab=44.03 E-value=42 Score=21.65 Aligned_cols=23 Identities=22% Similarity=0.657 Sum_probs=20.8
Q ss_pred ecCCCeEEecceeeceEE-EEcCE
Q 039663 7 VGNGERIRSEGHCSKVKF-EMQGV 29 (102)
Q Consensus 7 va~G~~l~~~~~~~~v~~-~iqg~ 29 (102)
+..|+...|+|.|..+++ .++|.
T Consensus 12 ~~~g~~~~C~G~CaSvs~~~~ng~ 35 (82)
T PF01684_consen 12 ISTGAEVACQGQCASVSITTYNGH 35 (82)
T ss_pred ccCCeeEEeCCEEEEEEEEeECCc
Confidence 567999999999999999 99993
No 28
>KOG4584 consensus Uncharacterized conserved protein [General function prediction only]
Probab=39.64 E-value=18 Score=29.28 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=18.9
Q ss_pred CEEEEeeeEeecCCCcceeechh
Q 039663 28 GVEFEVDFHILDFSGANAGLAVQ 50 (102)
Q Consensus 28 g~~F~~dl~vL~L~~~DvILGmd 50 (102)
|.++..-++.-|=+|+|+||||=
T Consensus 196 ~~p~K~~lif~DNSG~DvILGil 218 (348)
T KOG4584|consen 196 GKPHKCALIFVDNSGFDVILGIL 218 (348)
T ss_pred CCCcceEEEEecCCCcceeeeec
Confidence 55667778888899999999984
No 29
>KOG1370 consensus S-adenosylhomocysteine hydrolase [Coenzyme transport and metabolism]
Probab=37.04 E-value=35 Score=28.05 Aligned_cols=92 Identities=12% Similarity=0.137 Sum_probs=50.1
Q ss_pred CCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEE-EeCCeEEEEEecC------
Q 039663 10 GERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEF-TYRRQPIKLVGAQ------ 82 (102)
Q Consensus 10 G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f-~~~g~~v~l~g~~------ 82 (102)
|+.+-+..-|.++-..--=...+.|.+|-++|-+|+=.-+.||.+-..-..+-+-+.=.. .++|+.|.|-...
T Consensus 270 ~difVTtTGc~dii~~~H~~~mk~d~IvCN~Ghfd~EiDv~~L~~~~~~~~~vk~QvD~~~~~~gr~iIlLAeGRLvNL~ 349 (434)
T KOG1370|consen 270 VDIFVTTTGCKDIITGEHFDQMKNDAIVCNIGHFDTEIDVKWLNTPALTWENVKPQVDRYILPNGKHIILLAEGRLVNLG 349 (434)
T ss_pred CCEEEEccCCcchhhHHHHHhCcCCcEEeccccccceeehhhccCCcceeeecccccceeeccCCcEEEEEecCceeecc
Confidence 344444444444422222234578999999999999999999998543222222222222 2355555544322
Q ss_pred ---------CCCCCchhHHHHHhccccCC
Q 039663 83 ---------NILPKPTQSIHLQSRIFTSP 102 (102)
Q Consensus 83 ---------~~~~~~~q~~~l~~~~~~~~ 102 (102)
-+..+.+|.-++.+ +||.|
T Consensus 350 CatghpSFvmS~sftnQvlAqIe-Lwt~p 377 (434)
T KOG1370|consen 350 CATGHPSFVMSNSFTNQVLAQIE-LWTAP 377 (434)
T ss_pred cccCCCceEEecchHHHHHHHHH-HhcCC
Confidence 11245667777765 45543
No 30
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=32.79 E-value=28 Score=21.50 Aligned_cols=33 Identities=24% Similarity=0.335 Sum_probs=25.8
Q ss_pred ecCCCcceeechhHHhhhCceEEeccceEEEEE
Q 039663 38 LDFSGANAGLAVQWLEKLGKIVTDHKALTMEFT 70 (102)
Q Consensus 38 L~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~ 70 (102)
..+..-|+-+++=||++-+.|.++-++..+.|.
T Consensus 32 ~~l~~~~~~~AiGWLarE~KI~~~~~~~~~~v~ 64 (65)
T PF10771_consen 32 TGLSDKEVYLAIGWLARENKIEFEEKNGELYVS 64 (65)
T ss_dssp CT-SCHHHHHHHHHHHCTTSEEEEEETTEEEEE
T ss_pred hCcCHHHHHHHHHHHhccCceeEEeeCCEEEEE
Confidence 455677889999999999999888777776653
No 31
>PF00622 SPRY: SPRY domain; InterPro: IPR003877 The SPRY domain is of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin []. Ca2+-release from the sarcoplasmic or endoplasmic reticulum, the intracellular Ca2+ store, is mediated by the ryanodine receptor (RyR) and/or the inositol trisphosphate receptor (IP3R).; GO: 0005515 protein binding; PDB: 2V24_A 3EK9_A 2AFJ_A 2IWG_E 3EMW_A 2WL1_A 3TOJ_B 2VOK_A 2VOL_B 2FNJ_A ....
Probab=31.41 E-value=77 Score=20.01 Aligned_cols=21 Identities=10% Similarity=-0.054 Sum_probs=18.2
Q ss_pred ceEEeccceEEEEEeCCeEEE
Q 039663 57 KIVTDHKALTMEFTYRRQPIK 77 (102)
Q Consensus 57 ~i~~D~~~~tm~f~~~g~~v~ 77 (102)
-+.+|+.++++.|+.+|+.+.
T Consensus 71 G~~lD~~~g~l~F~~ng~~~~ 91 (124)
T PF00622_consen 71 GCGLDLDNGELSFYKNGKFLG 91 (124)
T ss_dssp EEEEETTTTEEEEEETTEEEE
T ss_pred EEEEeecccEEEEEECCccce
Confidence 468999999999999998744
No 32
>PF07833 Cu_amine_oxidN1: Copper amine oxidase N-terminal domain; InterPro: IPR012854 Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor []: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen [, ]. In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling []. The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other [, ]. This entry represents a domain found at the N-terminal of certain copper amine oxidases, as well as in related proteins such as cell wall hydrolase and N-acetylmuramoyl-L-alanine amidase. This domain consists of a five-stranded antiparallel beta-sheet twisted around an alpha helix [, ]. ; PDB: 1SPU_A 2WGQ_A 2WO0_A 1JRQ_A 1QAF_B 1D6U_B 1QAL_A 2WOF_A 1OAC_B 1QAK_A ....
Probab=31.09 E-value=1.2e+02 Score=18.20 Aligned_cols=28 Identities=39% Similarity=0.483 Sum_probs=19.6
Q ss_pred HhhhC-ceEEeccceEEEEEeCCeEEEEE
Q 039663 52 LEKLG-KIVTDHKALTMEFTYRRQPIKLV 79 (102)
Q Consensus 52 L~~~g-~i~~D~~~~tm~f~~~g~~v~l~ 79 (102)
.+.+| .+.||=+++++.+..++..+.+.
T Consensus 13 ~~~lg~~v~~d~~~~~v~i~~~~~~i~~~ 41 (93)
T PF07833_consen 13 AEALGAKVSWDNKTKTVTITKGKKSIKLK 41 (93)
T ss_dssp HHHHT-EEEEETTTTEEEEEETTEEEEE-
T ss_pred HHHcCCEEEEEcCCcEEEEEeeeceeeec
Confidence 44555 45666678889998888887776
No 33
>cd05485 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets an
Probab=30.58 E-value=2.3e+02 Score=21.68 Aligned_cols=58 Identities=14% Similarity=0.173 Sum_probs=39.6
Q ss_pred eEEecc--eeeceEEEEcCEEEEee---eEe-----------ec--------CCCcceeechhHHhhhCceEEeccceEE
Q 039663 12 RIRSEG--HCSKVKFEMQGVEFEVD---FHI-----------LD--------FSGANAGLAVQWLEKLGKIVTDHKALTM 67 (102)
Q Consensus 12 ~l~~~~--~~~~v~~~iqg~~F~~d---l~v-----------L~--------L~~~DvILGmdWL~~~g~i~~D~~~~tm 67 (102)
.+.|.. ..|.+.+.++|.+|... +++ +. -.+-..|||...|+.+= +..|++++++
T Consensus 247 ~~~C~~~~~~p~i~f~fgg~~~~i~~~~yi~~~~~~~~~~C~~~~~~~~~~~~~~~~~IlG~~fl~~~y-~vFD~~~~~i 325 (329)
T cd05485 247 MVNCSAIPSLPDITFVLGGKSFSLTGKDYVLKVTQMGQTICLSGFMGIDIPPPAGPLWILGDVFIGKYY-TEFDLGNNRV 325 (329)
T ss_pred EEeccccccCCcEEEEECCEEeEEChHHeEEEecCCCCCEEeeeEEECcCCCCCCCeEEEchHHhccce-EEEeCCCCEE
Confidence 457765 35788888888887743 211 10 11224799999999884 4699999999
Q ss_pred EEE
Q 039663 68 EFT 70 (102)
Q Consensus 68 ~f~ 70 (102)
.|.
T Consensus 326 g~a 328 (329)
T cd05485 326 GFA 328 (329)
T ss_pred eec
Confidence 874
No 34
>PHA01782 hypothetical protein
Probab=29.41 E-value=33 Score=25.31 Aligned_cols=34 Identities=29% Similarity=0.574 Sum_probs=21.9
Q ss_pred hhHHhhhCceEEeccceE---EEEEeC-CeEEEEEecC
Q 039663 49 VQWLEKLGKIVTDHKALT---MEFTYR-RQPIKLVGAQ 82 (102)
Q Consensus 49 mdWL~~~g~i~~D~~~~t---m~f~~~-g~~v~l~g~~ 82 (102)
.+||.+||+|.++-..++ ..|-++ +..-.|.|..
T Consensus 73 ~~wlv~~Gkv~vntDkk~aKefpf~~nK~~~tdLegA~ 110 (177)
T PHA01782 73 AEWLVKFGKVQVNTDKKSAKEFPFVYNKFGKTDLEGAT 110 (177)
T ss_pred HHHHHHhCCccccccccccccCceeeccccchhhHhhh
Confidence 489999999988887774 445442 2333344433
No 35
>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=29.01 E-value=2.4e+02 Score=20.78 Aligned_cols=58 Identities=14% Similarity=0.197 Sum_probs=39.3
Q ss_pred EEeccee-eceEEEEcCEEEEeee---E-------------eecCCC---cceeechhHHhhhCceEEeccceEEEEEe
Q 039663 13 IRSEGHC-SKVKFEMQGVEFEVDF---H-------------ILDFSG---ANAGLAVQWLEKLGKIVTDHKALTMEFTY 71 (102)
Q Consensus 13 l~~~~~~-~~v~~~iqg~~F~~dl---~-------------vL~L~~---~DvILGmdWL~~~g~i~~D~~~~tm~f~~ 71 (102)
+.|...- |.+.+.++|.+|.... + .+.+.. -..|||.-+|+.+- +..|..++++.|.+
T Consensus 217 ~~C~~~~~p~i~f~f~g~~~~i~~~~~~~~~~~~~~~~~~C~~~i~~~~~~~~iLG~~fl~~~y-~vfD~~~~~ig~a~ 294 (295)
T cd05474 217 VDCDAKDDGSLTFNFGGATISVPLSDLVLPASTDDGGDGACYLGIQPSTSDYNILGDTFLRSAY-VVYDLDNNEISLAQ 294 (295)
T ss_pred EeCCCCCCCEEEEEECCeEEEEEHHHhEeccccCCCCCCCeEEEEEeCCCCcEEeChHHhhcEE-EEEECCCCEEEeec
Confidence 4555433 6788888887776431 1 122222 24899999999885 57999999998854
No 36
>PHA02088 hypothetical protein
Probab=28.87 E-value=66 Score=22.08 Aligned_cols=28 Identities=25% Similarity=0.348 Sum_probs=18.2
Q ss_pred hHHhhhCceEEeccce-------EEEEEeCCeEEEE
Q 039663 50 QWLEKLGKIVTDHKAL-------TMEFTYRRQPIKL 78 (102)
Q Consensus 50 dWL~~~g~i~~D~~~~-------tm~f~~~g~~v~l 78 (102)
.||+++| |+.++++. ++-|.++|..+.+
T Consensus 39 ~wl~ky~-~sm~~k~~~ig~f~k~vf~~~~g~n~~f 73 (125)
T PHA02088 39 TWLAKYG-ISMNFKNGVVGAFEKVVFFMPGGDNAIF 73 (125)
T ss_pred HHHHHhc-eEEeccCCcccchheEEEEecCCCccch
Confidence 5999998 67788763 3334555554443
No 37
>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=28.69 E-value=80 Score=23.43 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=31.2
Q ss_pred eEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHHhhhCceEEeccceEEEEE
Q 039663 12 RIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFT 70 (102)
Q Consensus 12 ~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~ 70 (102)
.+.|+...|.+.+.+ ..|||-..|+++= ...|+.++++-|.
T Consensus 237 ~~~C~~~~P~i~f~~-----------------~~ilGd~fl~~~y-~vfD~~~~~ig~A 277 (278)
T cd06097 237 VFPCDTTLPDLSFAV-----------------FSILGDVFLKAQY-VVFDVGGPKLGFA 277 (278)
T ss_pred EEECCCCCCCEEEEE-----------------EEEEcchhhCcee-EEEcCCCceeeec
Confidence 467776555555555 5799999999985 4799999998874
No 38
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=28.21 E-value=1.6e+02 Score=18.94 Aligned_cols=35 Identities=9% Similarity=0.071 Sum_probs=27.9
Q ss_pred EEEEEeCCeEEEEEecCCCCCCchhHHHHHhcccc
Q 039663 66 TMEFTYRRQPIKLVGAQNILPKPTQSIHLQSRIFT 100 (102)
Q Consensus 66 tm~f~~~g~~v~l~g~~~~~~~~~q~~~l~~~~~~ 100 (102)
+++.+++|+.+.+.=.++...+..++++...+.|.
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~ 36 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFG 36 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhC
Confidence 57778999998888777666678888888887774
No 39
>cd05488 Proteinase_A_fungi Fungal Proteinase A , aspartic proteinase superfamily. Fungal Proteinase A, a proteolytic enzyme distributed among a variety of organisms, is a member of the aspartic proteinase superfamily. In Saccharomyces cerevisiae, targeted to the vacuole as a zymogen, activation of proteinases A at acidic pH can occur by two different pathways: a one-step process to release mature proteinase A, involving the intervention of proteinase B, or a step-wise pathway via the auto-activation product known as pseudo-proteinase A. Once active, S. cerevisiae proteinase A is essential to the activities of other yeast vacuolar hydrolases, including proteinase B and carboxypeptidase Y. The mature enzyme is bilobal, with each lobe providing one of the two catalytically essential aspartic acid residues in the active site. The crystal structure of free proteinase A shows that flap loop is atypically pointing directly into the S(1) pocket of the enzyme. Proteinase A preferentially hydro
Probab=27.42 E-value=2.8e+02 Score=21.05 Aligned_cols=57 Identities=18% Similarity=0.215 Sum_probs=39.9
Q ss_pred EEecce--eeceEEEEcCEEEEeee--EeecC----------------CCcceeechhHHhhhCceEEeccceEEEEE
Q 039663 13 IRSEGH--CSKVKFEMQGVEFEVDF--HILDF----------------SGANAGLAVQWLEKLGKIVTDHKALTMEFT 70 (102)
Q Consensus 13 l~~~~~--~~~v~~~iqg~~F~~dl--~vL~L----------------~~~DvILGmdWL~~~g~i~~D~~~~tm~f~ 70 (102)
+.|... .|.+.+.++|.+|.... ++++. .+-..|||...|+.+- +..|+.+++|-|.
T Consensus 243 ~~C~~~~~~P~i~f~f~g~~~~i~~~~y~~~~~g~C~~~~~~~~~~~~~~~~~ilG~~fl~~~y-~vfD~~~~~iG~a 319 (320)
T cd05488 243 VDCSKVDSLPDLTFNFDGYNFTLGPFDYTLEVSGSCISAFTGMDFPEPVGPLAIVGDAFLRKYY-SVYDLGNNAVGLA 319 (320)
T ss_pred eeccccccCCCEEEEECCEEEEECHHHheecCCCeEEEEEEECcCCCCCCCeEEEchHHhhheE-EEEeCCCCEEeec
Confidence 567643 57899999998887541 11111 1235899999998875 5799999998874
No 40
>cd05476 pepsin_A_like_plant Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants. This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, 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. 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. The enzymes specifically cleave bonds in peptides which
Probab=27.21 E-value=2.5e+02 Score=20.63 Aligned_cols=29 Identities=10% Similarity=-0.024 Sum_probs=24.0
Q ss_pred cceeechhHHhhhCceEEeccceEEEEEeC
Q 039663 43 ANAGLAVQWLEKLGKIVTDHKALTMEFTYR 72 (102)
Q Consensus 43 ~DvILGmdWL~~~g~i~~D~~~~tm~f~~~ 72 (102)
--.|||-.+|+.+- +..|..++++-|...
T Consensus 235 ~~~ilG~~fl~~~~-~vFD~~~~~iGfa~~ 263 (265)
T cd05476 235 GVSILGNIQQQNFL-VEYDLENSRLGFAPA 263 (265)
T ss_pred CcEEEChhhcccEE-EEEECCCCEEeeecC
Confidence 34799999999985 468999999988654
No 41
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=26.28 E-value=25 Score=25.59 Aligned_cols=13 Identities=31% Similarity=0.220 Sum_probs=10.6
Q ss_pred cCCCcceeechhH
Q 039663 39 DFSGANAGLAVQW 51 (102)
Q Consensus 39 ~L~~~DvILGmdW 51 (102)
|...||-|||||=
T Consensus 82 DF~~FDYI~~MDe 94 (159)
T KOG3217|consen 82 DFREFDYILAMDE 94 (159)
T ss_pred HhhhcceeEEecH
Confidence 5568999999983
No 42
>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=26.12 E-value=1.1e+02 Score=22.12 Aligned_cols=26 Identities=19% Similarity=0.047 Sum_probs=22.7
Q ss_pred ceeechhHHhhhCceEEeccceEEEEE
Q 039663 44 NAGLAVQWLEKLGKIVTDHKALTMEFT 70 (102)
Q Consensus 44 DvILGmdWL~~~g~i~~D~~~~tm~f~ 70 (102)
..|||.-+|+.+- +..|..++++.|.
T Consensus 257 ~~ilG~~fl~~~y-~vfD~~~~~igfa 282 (283)
T cd05471 257 LWILGDVFLRNYY-TVFDLDNNRIGFA 282 (283)
T ss_pred EEEccHhhhhheE-EEEeCCCCEEeec
Confidence 8999999999996 4789999988874
No 43
>PRK09502 iscA iron-sulfur cluster assembly protein; Provisional
Probab=26.07 E-value=1.5e+02 Score=19.34 Aligned_cols=55 Identities=15% Similarity=0.135 Sum_probs=33.7
Q ss_pred eEEEecCCCeEEecceeeceEEEEc-CEEEEeeeEeecCCCcceeechhHHhhhCceEEeccc
Q 039663 3 FLVDVGNGERIRSEGHCSKVKFEMQ-GVEFEVDFHILDFSGANAGLAVQWLEKLGKIVTDHKA 64 (102)
Q Consensus 3 ~~V~va~G~~l~~~~~~~~v~~~iq-g~~F~~dl~vL~L~~~DvILGmdWL~~~g~i~~D~~~ 64 (102)
+||.|..|+ |.++.+.+. -.+...+=.+++..++.++.=-.=+..+....+||.+
T Consensus 26 LRi~v~~~G-------CsG~~Y~l~~~~~~~~~D~~~~~~g~~v~id~~s~~~l~g~~IDy~~ 81 (107)
T PRK09502 26 LRLGVRTSG-------CSGMAYVLEFVDEPTPEDIVFEDKGVKVVVDGKSLQFLDGTQLDFVK 81 (107)
T ss_pred EEEEEECCC-------cCCeeeEeeecCCCCCCCEEEEcCCeEEEEeHHHHhHhCCCEEEEee
Confidence 566666555 334444443 1223334456788888888777666666666888875
No 44
>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=25.79 E-value=1.7e+02 Score=18.82 Aligned_cols=44 Identities=16% Similarity=0.081 Sum_probs=30.9
Q ss_pred cCCCeEEecceeeceEEEEcCEEEEeeeEeecCCCcceeechhHH
Q 039663 8 GNGERIRSEGHCSKVKFEMQGVEFEVDFHILDFSGANAGLAVQWL 52 (102)
Q Consensus 8 a~G~~l~~~~~~~~v~~~iqg~~F~~dl~vL~L~~~DvILGmdWL 52 (102)
+-|+.++..... ++++++.++.....+.+.+.....-|+|=|-|
T Consensus 43 GIGG~~~~~~~~-~v~i~i~~~~~~g~vlv~~~~~P~nllGRd~L 86 (87)
T cd05482 43 GIGGAITPSQSS-VLLLEIDGEGHLGTILVYVLSLPVNLWGRDIL 86 (87)
T ss_pred eccceEEEEEEe-eEEEEEcCCeEEEEEEEccCCCcccEEccccC
Confidence 445666655554 79999999999999998886444456665543
No 45
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=25.72 E-value=96 Score=22.76 Aligned_cols=15 Identities=13% Similarity=0.268 Sum_probs=11.0
Q ss_pred hhHHhhhCceEEecc
Q 039663 49 VQWLEKLGKIVTDHK 63 (102)
Q Consensus 49 mdWL~~~g~i~~D~~ 63 (102)
-+||++|||+.+-|+
T Consensus 102 ~~LL~~yGPLwv~~~ 116 (166)
T PF12385_consen 102 ANLLREYGPLWVAWE 116 (166)
T ss_pred HHHHHHcCCeEEEec
Confidence 368999999855543
No 46
>PF03633 Glyco_hydro_65C: Glycosyl hydrolase family 65, C-terminal domain ; InterPro: IPR005194 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This family of glycosyl hydrolases (GH65 from CAZY) contains this domain and includes vacuolar acid trehalase and maltose phosphorylases. Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown [].; PDB: 1H54_A.
Probab=25.59 E-value=1.2e+02 Score=17.11 Aligned_cols=12 Identities=8% Similarity=-0.006 Sum_probs=5.4
Q ss_pred EeccceEEEEEe
Q 039663 60 TDHKALTMEFTY 71 (102)
Q Consensus 60 ~D~~~~tm~f~~ 71 (102)
+.|+...+.+.-
T Consensus 14 ~~~rg~~l~v~i 25 (54)
T PF03633_consen 14 LRYRGHWLEVEI 25 (54)
T ss_dssp EEETTEEEEEEE
T ss_pred EEECCEEEEEEE
Confidence 344444444443
No 47
>PF14645 Chibby: Chibby family
Probab=25.14 E-value=1.6e+02 Score=20.08 Aligned_cols=38 Identities=24% Similarity=0.122 Sum_probs=27.0
Q ss_pred eEeecCCCcceeechhHHhhhCceEEeccceEEEEEeCCeEEE
Q 039663 35 FHILDFSGANAGLAVQWLEKLGKIVTDHKALTMEFTYRRQPIK 77 (102)
Q Consensus 35 l~vL~L~~~DvILGmdWL~~~g~i~~D~~~~tm~f~~~g~~v~ 77 (102)
+..++-..-..=||+| +||+.++....++.| -+|+|+.
T Consensus 24 ~~~~d~~t~~~el~ld----~~p~~l~Lg~~~l~F-~dG~W~~ 61 (116)
T PF14645_consen 24 LYPLDRSTRQAELGLD----YGPPRLNLGDQTLVF-EDGQWTS 61 (116)
T ss_pred CCCCchhhhhcccccc----cCCceEeECCeEEEE-ECCEEec
Confidence 3333333333446666 589999999999999 8899994
No 48
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=24.97 E-value=62 Score=20.30 Aligned_cols=23 Identities=26% Similarity=0.382 Sum_probs=19.2
Q ss_pred hhHHhhhCce---EEeccceEEEEEe
Q 039663 49 VQWLEKLGKI---VTDHKALTMEFTY 71 (102)
Q Consensus 49 mdWL~~~g~i---~~D~~~~tm~f~~ 71 (102)
.+||+.+..+ .+|+++.+..|.+
T Consensus 45 ~~~L~~~~~~~n~~~~~~~~tf~fkP 70 (75)
T cd07977 45 KEWLKSEALVNNPKIDPKDGTFSFKP 70 (75)
T ss_pred HHHHHhhhhccCceeccCCCEEEecc
Confidence 3899998777 8999999888864
No 49
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=24.69 E-value=1.8e+02 Score=18.87 Aligned_cols=29 Identities=14% Similarity=0.091 Sum_probs=20.5
Q ss_pred EeecCCCcceeechhHHhhhCceEEeccc
Q 039663 36 HILDFSGANAGLAVQWLEKLGKIVTDHKA 64 (102)
Q Consensus 36 ~vL~L~~~DvILGmdWL~~~g~i~~D~~~ 64 (102)
.+++.+|+.++.==.=+..+....+||.+
T Consensus 51 ~v~~~~g~~v~id~~s~~~l~g~~IDy~~ 79 (105)
T TIGR02011 51 IVFEDKGVKIVIDGKSLQYLDGTQLDFVK 79 (105)
T ss_pred EEEEcCCEEEEEcHHHhHHhCCCEEEEec
Confidence 45677888888765555556566889876
No 50
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=24.27 E-value=2.1e+02 Score=18.76 Aligned_cols=40 Identities=23% Similarity=0.288 Sum_probs=26.4
Q ss_pred ceEEEecCCCeEEec--ceeeceEEEEcCEEEEeeeEeecCCCcce
Q 039663 2 SFLVDVGNGERIRSE--GHCSKVKFEMQGVEFEVDFHILDFSGANA 45 (102)
Q Consensus 2 ~~~V~va~G~~l~~~--~~~~~v~~~iqg~~F~~dl~vL~L~~~Dv 45 (102)
.++|++.||..+.|. |....-.++|- +-|-..+++..||.
T Consensus 21 ~frV~LenG~~vla~isGKmR~~rIrIl----~GD~V~VE~spYDl 62 (87)
T PRK12442 21 RFRVTLENGVEVGAYASGRMRKHRIRIL----AGDRVTLELSPYDL 62 (87)
T ss_pred EEEEEeCCCCEEEEEeccceeeeeEEec----CCCEEEEEECcccC
Confidence 478999999988763 44444444442 45667777777774
No 51
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=24.26 E-value=33 Score=21.02 Aligned_cols=19 Identities=26% Similarity=0.289 Sum_probs=11.6
Q ss_pred hhCce-EEeccceEEEEEeC
Q 039663 54 KLGKI-VTDHKALTMEFTYR 72 (102)
Q Consensus 54 ~~g~i-~~D~~~~tm~f~~~ 72 (102)
+|+|| .++|...||.|...
T Consensus 16 ~H~pIp~l~wpaMTM~F~v~ 35 (70)
T PF11604_consen 16 SHEPIPELGWPAMTMDFPVA 35 (70)
T ss_dssp EE--BCCCTB-SEEEEEE--
T ss_pred ecCccccCCCCCeEEEEEcC
Confidence 46777 57999999999854
No 52
>PF09292 Neil1-DNA_bind: Endonuclease VIII-like 1, DNA bind; InterPro: IPR015371 This domain is predominantly found in Endonuclease VIII-like 1 proteins and adopts a glucocorticoid receptor-like fold. Structural analysis reveals a zincless finger motif that is required for glycosylase activity []. ; PDB: 1TDH_A.
Probab=24.22 E-value=63 Score=18.18 Aligned_cols=28 Identities=14% Similarity=0.303 Sum_probs=14.5
Q ss_pred hHHhhhC--ceEEeccceEEEEEeCCeEEEEEecCCC
Q 039663 50 QWLEKLG--KIVTDHKALTMEFTYRRQPIKLVGAQNI 84 (102)
Q Consensus 50 dWL~~~g--~i~~D~~~~tm~f~~~g~~v~l~g~~~~ 84 (102)
.||+-|+ .| +++. -++|+.|=++|++++
T Consensus 7 ~WLqCY~v~gM------~sl~-D~~gRTiWFqGdPGp 36 (39)
T PF09292_consen 7 AWLQCYSVPGM------KSLR-DRNGRTIWFQGDPGP 36 (39)
T ss_dssp HH-SSTT-TT-------EEEE--TTS-EEEESS---T
T ss_pred HHHHHhccccc------cccc-ccCCCEEEeeCCCCC
Confidence 5777765 23 4444 568888989998866
No 53
>PRK10126 tyrosine phosphatase; Provisional
Probab=22.09 E-value=90 Score=21.38 Aligned_cols=29 Identities=14% Similarity=0.114 Sum_probs=19.9
Q ss_pred ecCCCcceeech-----hHHhhhCceEEeccceEEEE
Q 039663 38 LDFSGANAGLAV-----QWLEKLGKIVTDHKALTMEF 69 (102)
Q Consensus 38 L~L~~~DvILGm-----dWL~~~g~i~~D~~~~tm~f 69 (102)
-++..+|+|+.| +.|....| ++..+...+
T Consensus 71 ~~~~~~DlIl~Md~~~~~~l~~~~p---~~~~k~~~l 104 (147)
T PRK10126 71 RLCRNYDLILTMEKRHIERLCEMAP---EMRGKVMLF 104 (147)
T ss_pred HHhccCCEEEECCHHHHHHHHHhcC---cccCcEEeh
Confidence 467789999999 46777666 445554443
Done!