Query 044180
Match_columns 130
No_of_seqs 109 out of 268
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 12:12:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044180hhsearch_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 99.8 5.9E-21 1.3E-25 139.9 6.2 70 29-100 63-132 (135)
2 cd05479 RP_DDI RP_DDI; retrope 99.5 2.1E-14 4.5E-19 103.1 7.0 68 29-97 57-124 (124)
3 cd05484 retropepsin_like_LTR_2 98.9 2.4E-09 5.3E-14 72.4 5.7 53 27-81 39-91 (91)
4 PF02160 Peptidase_A3: Caulifl 98.2 1E-05 2.2E-10 63.4 8.7 76 27-105 47-124 (201)
5 cd00303 retropepsin_like Retro 98.2 8.2E-06 1.8E-10 50.3 6.2 54 28-81 39-92 (92)
6 TIGR03698 clan_AA_DTGF clan AA 97.8 4.4E-05 9.6E-10 53.6 5.6 63 29-95 45-107 (107)
7 PF09668 Asp_protease: Asparty 97.6 0.00014 3E-09 53.0 5.1 50 39-89 75-124 (124)
8 PF00077 RVP: Retroviral aspar 97.4 0.00028 6E-09 47.8 4.4 55 28-85 43-97 (100)
9 cd05483 retropepsin_like_bacte 97.3 0.00059 1.3E-08 44.8 4.9 53 27-81 41-96 (96)
10 PF13650 Asp_protease_2: Aspar 97.3 0.0011 2.4E-08 43.1 6.1 48 30-79 41-90 (90)
11 TIGR02281 clan_AA_DTGA clan AA 97.0 0.0035 7.5E-08 44.8 6.7 64 30-95 54-119 (121)
12 cd05480 NRIP_C NRIP_C; putativ 96.3 0.0098 2.1E-07 42.1 5.0 54 38-92 50-103 (103)
13 cd06094 RP_Saci_like RP_Saci_l 96.0 0.017 3.7E-07 39.9 5.0 55 27-84 33-88 (89)
14 cd06095 RP_RTVL_H_like Retrope 95.4 0.043 9.3E-07 36.6 5.0 52 28-81 35-86 (86)
15 COG5550 Predicted aspartyl pro 94.5 0.077 1.7E-06 38.8 4.6 63 30-96 56-118 (125)
16 cd05481 retropepsin_like_LTR_1 91.9 0.6 1.3E-05 31.8 5.5 49 27-77 41-89 (93)
17 KOG0012 DNA damage inducible p 91.1 0.29 6.2E-06 41.7 3.9 62 40-102 287-348 (380)
18 PF12384 Peptidase_A2B: Ty3 tr 89.1 1.2 2.5E-05 34.4 5.4 58 27-85 73-131 (177)
19 COG2383 Uncharacterized conser 71.6 0.72 1.6E-05 32.8 -1.2 20 74-93 51-70 (109)
20 COG3577 Predicted aspartyl pro 67.4 6.1 0.00013 31.4 3.0 58 29-88 147-206 (215)
21 PF00098 zf-CCHC: Zinc knuckle 58.0 3.2 6.9E-05 20.2 -0.1 8 13-20 2-9 (18)
22 cd06396 PB1_NBR1 The PB1 domai 55.2 37 0.00081 22.9 4.8 35 94-128 2-36 (81)
23 PF00026 Asp: Eukaryotic aspar 51.1 37 0.00081 26.5 5.0 31 68-99 286-316 (317)
24 PRK12442 translation initiatio 50.7 40 0.00086 23.2 4.4 53 27-91 18-72 (87)
25 KOG2872 Uroporphyrinogen decar 44.6 6.9 0.00015 33.0 -0.2 33 69-112 271-303 (359)
26 PF05515 Viral_NABP: Viral nuc 43.4 11 0.00023 27.7 0.7 21 6-26 55-77 (124)
27 cd06398 PB1_Joka2 The PB1 doma 41.6 88 0.0019 21.3 5.0 36 94-129 2-40 (91)
28 PF13913 zf-C2HC_2: zinc-finge 40.9 6.8 0.00015 20.5 -0.5 13 12-24 3-15 (25)
29 PF04930 FUN14: FUN14 family; 38.5 6.4 0.00014 27.0 -1.1 24 74-97 31-54 (100)
30 PF14645 Chibby: Chibby family 38.3 54 0.0012 23.4 3.7 31 73-108 34-64 (116)
31 PRK13908 putative recombinatio 37.6 16 0.00035 28.8 0.9 15 12-26 139-163 (204)
32 PF09040 H-K_ATPase_N: Gastric 34.8 16 0.00034 21.5 0.4 12 1-12 21-32 (41)
33 PF14787 zf-CCHC_5: GAG-polypr 34.8 14 0.0003 21.4 0.1 21 11-31 2-22 (36)
34 CHL00008 petG cytochrome b6/f 34.4 20 0.00044 20.8 0.8 12 2-13 24-35 (37)
35 KOG1542 Cysteine proteinase Ca 34.2 9.5 0.00021 32.6 -0.9 42 57-101 261-302 (372)
36 PF09538 FYDLN_acid: Protein o 33.1 15 0.00033 26.0 0.1 17 10-26 8-24 (108)
37 PRK00665 petG cytochrome b6-f 32.3 22 0.00048 20.6 0.7 11 2-12 24-34 (37)
38 COG2081 Predicted flavoprotein 31.3 73 0.0016 27.7 4.0 35 50-84 144-185 (408)
39 KOG4584 Uncharacterized conser 30.1 28 0.00061 29.4 1.2 23 56-78 196-218 (348)
40 PF00622 SPRY: SPRY domain; I 29.8 93 0.002 20.6 3.7 21 85-105 71-91 (124)
41 PF11148 DUF2922: Protein of u 28.0 1.2E+02 0.0026 19.2 3.7 38 91-128 1-40 (69)
42 PF00670 AdoHcyase_NAD: S-aden 27.7 1.3E+02 0.0028 22.8 4.4 51 60-110 101-152 (162)
43 TIGR00008 infA translation ini 27.7 1.3E+02 0.0029 19.6 3.9 43 27-73 16-60 (68)
44 cd05477 gastricsin Gastricsins 27.5 2.2E+02 0.0049 22.6 6.1 28 71-99 290-317 (318)
45 PRK14891 50S ribosomal protein 27.5 42 0.00091 24.8 1.6 34 11-48 4-38 (131)
46 PF04746 DUF575: Protein of un 27.0 22 0.00048 24.9 0.1 11 73-83 29-39 (101)
47 PF08844 DUF1815: Domain of un 26.4 1.1E+02 0.0025 21.5 3.6 28 11-42 32-60 (105)
48 KOG3217 Protein tyrosine phosp 25.6 25 0.00055 26.7 0.2 12 67-78 82-93 (159)
49 cd06097 Aspergillopepsin_like 24.6 95 0.0021 24.2 3.4 26 72-98 252-277 (278)
50 TIGR02300 FYDLN_acid conserved 24.0 29 0.00063 25.5 0.3 18 9-26 7-24 (129)
51 PF13975 gag-asp_proteas: gag- 23.6 64 0.0014 20.4 1.8 20 30-49 51-70 (72)
52 smart00647 IBR In Between Ring 23.4 34 0.00073 20.5 0.5 14 11-24 48-61 (64)
53 PF11164 DUF2948: Protein of u 23.4 97 0.0021 23.0 2.9 36 21-56 92-127 (138)
54 cd05476 pepsin_A_like_plant Ch 21.6 2.2E+02 0.0048 22.0 4.9 53 48-101 196-264 (265)
55 PF01684 ET: ET module; Inter 21.6 1.3E+02 0.0028 20.3 3.0 22 35-56 12-34 (82)
56 PF09706 Cas_CXXC_CXXC: CRISPR 21.5 28 0.00061 22.5 -0.2 17 9-25 3-19 (69)
57 cd07429 Cby_like Chibby, a nuc 21.3 1.3E+02 0.0029 21.4 3.2 43 62-109 23-65 (108)
58 TIGR03318 YdfZ_fam putative se 21.3 48 0.001 21.6 0.8 20 6-25 40-60 (65)
59 PF02529 PetG: Cytochrome B6-F 21.3 35 0.00077 19.8 0.2 11 2-12 24-34 (37)
60 PHA01782 hypothetical protein 21.1 39 0.00084 26.0 0.5 33 78-111 74-111 (177)
61 KOG1370 S-adenosylhomocysteine 20.9 1.1E+02 0.0023 26.4 3.0 73 38-110 270-343 (434)
62 PF14452 Multi_ubiq: Multiubiq 20.7 2.3E+02 0.005 17.8 4.2 27 93-122 1-27 (72)
63 COG3880 Modulator of heat shoc 20.5 63 0.0014 25.0 1.5 33 13-53 2-35 (176)
64 PF02989 DUF228: Lyme disease 20.2 71 0.0015 24.8 1.7 82 10-109 67-149 (184)
65 smart00507 HNHc HNH nucleases. 20.1 53 0.0012 18.2 0.8 16 7-23 7-22 (52)
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=99.83 E-value=5.9e-21 Score=139.86 Aligned_cols=70 Identities=33% Similarity=0.593 Sum_probs=64.2
Q ss_pred CceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeC
Q 044180 29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYR 100 (130)
Q Consensus 29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~ 100 (130)
.++.|. ++|+.+.|.+.|++++|.+||++|..||++|++++||||||||||++|+| .|||.+++++|+..
T Consensus 63 ~~~~V~-~~g~~~~~~~~~~~~~~~i~g~~~~~dl~vl~l~~~DvILGm~WL~~~~~-~IDw~~k~v~f~~p 132 (135)
T PF08284_consen 63 RPIVVS-APGGSINCEGVCPDVPLSIQGHEFVVDLLVLDLGGYDVILGMDWLKKHNP-VIDWATKTVTFNSP 132 (135)
T ss_pred CeeEEe-cccccccccceeeeEEEEECCeEEEeeeEEecccceeeEeccchHHhCCC-EEEccCCEEEEeCC
Confidence 345555 67888999999999999999999999999999999999999999999999 89999999999843
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=99.53 E-value=2.1e-14 Score=103.15 Aligned_cols=68 Identities=12% Similarity=0.133 Sum_probs=61.9
Q ss_pred CceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEE
Q 044180 29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEF 97 (130)
Q Consensus 29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f 97 (130)
.++.+++++++...+.+.|..++++++|.+|..+|.++|+.++|+|||||||++++ +.|||++++|+|
T Consensus 57 ~~~~~~~~g~g~~~~~g~~~~~~l~i~~~~~~~~~~Vl~~~~~d~ILG~d~L~~~~-~~ID~~~~~i~~ 124 (124)
T cd05479 57 KRFQGIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQ-CVIDLKENVLRI 124 (124)
T ss_pred cceEEEEecCCCcEEEeEEEEEEEEECCEEeeeEEEEECCCCcCEEecHHHHHhCC-eEEECCCCEEEC
Confidence 35677888766688899999999999999999999999999999999999999999 599999999975
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=98.93 E-value=2.4e-09 Score=72.42 Aligned_cols=53 Identities=15% Similarity=0.207 Sum_probs=49.5
Q ss_pred ccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchh
Q 044180 27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE 81 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~ 81 (130)
+....+|..|||+.+.+.+.| .+++.++|.+|..+++|++.. +|.|||+|||+
T Consensus 39 ~~~~~~v~~a~G~~~~~~G~~-~~~v~~~~~~~~~~~~v~~~~-~~~lLG~~wl~ 91 (91)
T cd05484 39 KPTKKRLRTATGTKLSVLGQI-LVTVKYGGKTKVLTLYVVKNE-GLNLLGRDWLD 91 (91)
T ss_pred ccccEEEEecCCCEeeEeEEE-EEEEEECCEEEEEEEEEEECC-CCCccChhhcC
Confidence 345689999999999999999 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=98.20 E-value=1e-05 Score=63.36 Aligned_cols=76 Identities=16% Similarity=0.240 Sum_probs=65.5
Q ss_pred ccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeE-EeecCCcceeecccchhccCceEEeccccEEEEEeCC-eEE
Q 044180 27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFH-ILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRG-QPI 104 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~-vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g-~~I 104 (130)
...++.|+.|||+......+|++..++|.|+.|...++ ..+ .|.|+|||+.+|+.+.|. +.|.. +++|+..+ ..+
T Consensus 47 ~~~~i~v~~an~~~~~i~~~~~~~~i~I~~~~F~IP~iYq~~-~g~d~IlG~NF~r~y~Pf-iq~~~-~I~f~~~~~~~~ 123 (201)
T PF02160_consen 47 SKKPIKVKGANGSIIQINKKAKNGKIQIADKIFRIPTIYQQE-SGIDIILGNNFLRLYEPF-IQTED-RIQFHKKGLQKV 123 (201)
T ss_pred CCCcEEEEEecCCceEEEEEecCceEEEccEEEeccEEEEec-CCCCEEecchHHHhcCCc-EEEcc-EEEEEeCCccee
Confidence 34468999999999999999999999999999998776 566 689999999999999994 88864 79999877 444
Q ss_pred E
Q 044180 105 K 105 (130)
Q Consensus 105 ~ 105 (130)
.
T Consensus 124 ~ 124 (201)
T PF02160_consen 124 E 124 (201)
T ss_pred e
Confidence 3
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=98.16 E-value=8.2e-06 Score=50.33 Aligned_cols=54 Identities=28% Similarity=0.525 Sum_probs=47.5
Q ss_pred cCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchh
Q 044180 28 IMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE 81 (130)
Q Consensus 28 ~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~ 81 (130)
..+..+..++|......+.+..+.+.+++..+...+++.+..++|+|||++||.
T Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~ilG~~~l~ 92 (92)
T cd00303 39 PTPLKVKGANGSSVKTLGVILPVTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92 (92)
T ss_pred CCceEEEecCCCEeccCcEEEEEEEEeCCEEEEEEEEEEcCCCcCEEecccccC
Confidence 345677888888888888888999999999999999999999999999999984
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=97.84 E-value=4.4e-05 Score=53.65 Aligned_cols=63 Identities=24% Similarity=0.388 Sum_probs=47.8
Q ss_pred CceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEE
Q 044180 29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTM 95 (130)
Q Consensus 29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl 95 (130)
...+|..|||....... .-..+.++|.+....+.+.+... ++.|||.||++++ +.+||++..|
T Consensus 45 ~~~~~~tA~G~~~~~~v--~~~~v~igg~~~~~~v~~~~~~~-~~LLG~~~L~~l~-l~id~~~~~~ 107 (107)
T TIGR03698 45 DQRRVYLADGREVLTDV--AKASIIINGLEIDAFVESLGYVD-EPLLGTELLEGLG-IVIDYRNQGL 107 (107)
T ss_pred cCcEEEecCCcEEEEEE--EEEEEEECCEEEEEEEEecCCCC-ccEecHHHHhhCC-EEEehhhCcC
Confidence 35689999998766553 46677889998855544445545 8999999999997 5899998754
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=97.59 E-value=0.00014 Score=52.96 Aligned_cols=50 Identities=18% Similarity=0.320 Sum_probs=42.5
Q ss_pred CeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEe
Q 044180 39 EQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTD 89 (130)
Q Consensus 39 ~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD 89 (130)
+.-...|....+++++++..|+..|.|+|-...|++||.|||.+|.. .||
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 55567778999999999999999999999889999999999999976 565
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=97.40 E-value=0.00028 Score=47.76 Aligned_cols=55 Identities=25% Similarity=0.392 Sum_probs=45.3
Q ss_pred cCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCc
Q 044180 28 IMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGK 85 (130)
Q Consensus 28 ~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~ 85 (130)
.....|.-++|.. ...+. ..+.+.+.+..|...+++.+-..+| |||.|||.+++.
T Consensus 43 ~~~~~v~~~~g~~-~~~~~-~~~~v~~~~~~~~~~~~v~~~~~~~-ILG~D~L~~~~~ 97 (100)
T PF00077_consen 43 KTSITVRGAGGSS-SILGS-TTVEVKIGGKEFNHTFLVVPDLPMN-ILGRDFLKKLNA 97 (100)
T ss_dssp EEEEEEEETTEEE-EEEEE-EEEEEEETTEEEEEEEEESSTCSSE-EEEHHHHTTTTC
T ss_pred cCCceeccCCCcc-eeeeE-EEEEEEEECccceEEEEecCCCCCC-EeChhHHHHcCC
Confidence 3445666677776 66665 5889999999999999999988888 999999999986
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=97.29 E-value=0.00059 Score=44.83 Aligned_cols=53 Identities=13% Similarity=0.150 Sum_probs=43.5
Q ss_pred ccCceeEEeeCCCeEeecceeeccEEeecCEEEE-ceeEEeecCC--cceeecccchh
Q 044180 27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFE-ADFHILDFFG--ANAVLAVQWLE 81 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~-~dl~vL~l~g--~DvILGmdWL~ 81 (130)
.....++..++|........ -.++++++..|. ..+.++|... .|.|||+|||.
T Consensus 41 ~~~~~~~~~~~G~~~~~~~~--~~~i~ig~~~~~~~~~~v~d~~~~~~~gIlG~d~l~ 96 (96)
T cd05483 41 LGGKVTVQTANGRVRAARVR--LDSLQIGGITLRNVPAVVLPGDALGVDGLLGMDFLR 96 (96)
T ss_pred CCCcEEEEecCCCccceEEE--cceEEECCcEEeccEEEEeCCcccCCceEeChHHhC
Confidence 34567888899998877666 446789999998 5899999997 99999999984
No 10
>PF13650 Asp_protease_2: Aspartyl protease
Probab=97.28 E-value=0.0011 Score=43.11 Aligned_cols=48 Identities=15% Similarity=0.305 Sum_probs=38.5
Q ss_pred ceeEEeeCCCeEeecceeeccEEeecCEEE-EceeEEee-cCCcceeecccc
Q 044180 30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEF-EADFHILD-FFGANAVLAVQW 79 (130)
Q Consensus 30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f-~~dl~vL~-l~g~DvILGmdW 79 (130)
+..+..++|.........+ ++++++..+ ..++.+.+ -..+|.||||||
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 4778889998555444544 788999998 67888999 678999999998
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=96.97 E-value=0.0035 Score=44.84 Aligned_cols=64 Identities=14% Similarity=0.280 Sum_probs=48.3
Q ss_pred ceeEEeeCCCeEeecceeeccEEeecCEEEE-ceeEEeecCC-cceeecccchhccCceEEeccccEE
Q 044180 30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFE-ADFHILDFFG-ANAVLAVQWLEKLGKIVTDHKALTM 95 (130)
Q Consensus 30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~-~dl~vL~l~g-~DvILGmdWL~~~g~i~iD~~~~tl 95 (130)
+..+..|||..... ...--++++.+..+. .++.++|.+. .|.+||||+|.++.++.+|-.+.+|
T Consensus 54 ~~~~~ta~G~~~~~--~~~l~~l~iG~~~~~nv~~~v~~~~~~~~~LLGm~fL~~~~~~~~~~~~l~l 119 (121)
T TIGR02281 54 TVTVSTANGQIKAA--RVTLDRVAIGGIVVNDVDAMVAEGGALSESLLGMSFLNRLSRFTVRGGKLIL 119 (121)
T ss_pred eEEEEeCCCcEEEE--EEEeCEEEECCEEEeCcEEEEeCCCcCCceEcCHHHHhccccEEEECCEEEE
Confidence 56788899976432 335556789999988 7888999874 5899999999999877777655444
No 12
>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=96.32 E-value=0.0098 Score=42.11 Aligned_cols=54 Identities=17% Similarity=0.225 Sum_probs=47.4
Q ss_pred CCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccc
Q 044180 38 GEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKA 92 (130)
Q Consensus 38 G~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~ 92 (130)
|....-.|....++++|++..++-.|.|||-...|++||.|=|.+|.. .||.++
T Consensus 50 gt~~kiiGrih~~~ikig~~~~~CSftVld~~~~d~llGLdmLkrhqc-~IdL~k 103 (103)
T cd05480 50 PTSVKVIGQIERLVLQLGQLTVECSAQVVDDNEKNFSLGLQTLKSLKC-VINLEK 103 (103)
T ss_pred CcceeEeeEEEEEEEEeCCEEeeEEEEEEcCCCcceEeeHHHHhhcce-eeeccC
Confidence 444567788899999999999999999999999999999999999977 788653
No 13
>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=96.03 E-value=0.017 Score=39.93 Aligned_cols=55 Identities=20% Similarity=0.391 Sum_probs=47.6
Q ss_pred ccCceeEEeeCCCeEeecceeeccEEeecCE-EEEceeEEeecCCcceeecccchhccC
Q 044180 27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGV-EFEADFHILDFFGANAVLAVQWLEKLG 84 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~-~f~~dl~vL~l~g~DvILGmdWL~~~g 84 (130)
+..++.++.|||..|..-|. ..+.+.++.. .|.-+|.|=|+. .-|||+|.|..|+
T Consensus 33 ~~~~~~l~AANgt~I~tyG~-~~l~ldlGlrr~~~w~FvvAdv~--~pIlGaDfL~~~~ 88 (89)
T cd06094 33 KPSPLTLQAANGTPIATYGT-RSLTLDLGLRRPFAWNFVVADVP--HPILGADFLQHYG 88 (89)
T ss_pred cCCceEEEeCCCCeEeeeee-EEEEEEcCCCcEEeEEEEEcCCC--cceecHHHHHHcC
Confidence 45678999999999999995 8888888875 999999998886 4799999999886
No 14
>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=95.43 E-value=0.043 Score=36.57 Aligned_cols=52 Identities=13% Similarity=0.206 Sum_probs=36.5
Q ss_pred cCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchh
Q 044180 28 IMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLE 81 (130)
Q Consensus 28 ~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~ 81 (130)
..+..|.-++|..-.......+ .+.+.+.++..++.+.+- ..|.|||||+|.
T Consensus 35 ~~~~~v~gagG~~~~~v~~~~~-~v~vg~~~~~~~~~v~~~-~~~~lLG~dfL~ 86 (86)
T cd06095 35 TTSVLIRGVSGQSQQPVTTYRT-LVDLGGHTVSHSFLVVPN-CPDPLLGRDLLS 86 (86)
T ss_pred CCcEEEEeCCCcccccEEEeee-EEEECCEEEEEEEEEEcC-CCCcEechhhcC
Confidence 3467788888886111111222 688999999998888773 469999999984
No 15
>COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]
Probab=94.51 E-value=0.077 Score=38.79 Aligned_cols=63 Identities=21% Similarity=0.295 Sum_probs=49.9
Q ss_pred ceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEE
Q 044180 30 SFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTME 96 (130)
Q Consensus 30 ~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~ 96 (130)
..++..++|+.+.+. .....++++|.+..+-....+....+ ++|++||+.+|- .+|.+.-.++
T Consensus 56 ~~~~~~a~~~~v~t~--V~~~~iki~g~e~~~~Vl~s~~~~~~-liG~~~lk~l~~-~vn~~~g~LE 118 (125)
T COG5550 56 TIRIVLADGGVVKTS--VALATIKIDGVEKVAFVLASDNLPEP-LIGVNLLKLLGL-VVNPKTGKLE 118 (125)
T ss_pred ChhhhhhcCCEEEEE--EEEEEEEECCEEEEEEEEccCCCccc-chhhhhhhhccE-EEcCCcceEe
Confidence 456778888876654 34667789999998888888888888 999999999976 8998665554
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=91.90 E-value=0.6 Score=31.78 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=41.6
Q ss_pred ccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecc
Q 044180 27 KIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAV 77 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGm 77 (130)
+.+++.++.+||..+...|. ..+++.+++..+..+|+|+|..+-. |||.
T Consensus 41 ~~t~~~L~~~~g~~~~~~G~-~~~~v~~~~~~~~~~f~Vvd~~~~~-lLG~ 89 (93)
T cd05481 41 RPSPVRLTAYGGSTIPVEGG-VKLKCRYRNPKYNLTFQVVKEEGPP-LLGA 89 (93)
T ss_pred ccCCeEEEeeCCCEeeeeEE-EEEEEEECCcEEEEEEEEECCCCCc-eEcc
Confidence 45678999999999999999 6899999999999999999986544 4454
No 17
>KOG0012 consensus DNA damage inducible protein [Replication, recombination and repair]
Probab=91.13 E-value=0.29 Score=41.69 Aligned_cols=62 Identities=13% Similarity=0.212 Sum_probs=56.3
Q ss_pred eEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeCCe
Q 044180 40 QIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQ 102 (130)
Q Consensus 40 ~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g~ 102 (130)
...-.|.+..++++|+...++-.|-|++-...|+-||.|=|.+|+. -||.++..|.|...+.
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 4555778899999999999999999999999999999999999998 7999999999876655
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=89.07 E-value=1.2 Score=34.37 Aligned_cols=58 Identities=10% Similarity=0.129 Sum_probs=45.5
Q ss_pred ccCceeEEeeC-CCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCc
Q 044180 27 KIMSFLVDVSN-GEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGK 85 (130)
Q Consensus 27 ~~~~~~V~van-G~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~ 85 (130)
.+++++++-+- ++...|... ..+++.+++..|...++|+|--++|+|+|..-|.++..
T Consensus 73 ~app~~fRG~vs~~~~~tsEA-v~ld~~i~n~~i~i~aYV~d~m~~dlIIGnPiL~ryp~ 131 (177)
T PF12384_consen 73 DAPPFRFRGFVSGESATTSEA-VTLDFYIDNKLIDIAAYVTDNMDHDLIIGNPILDRYPT 131 (177)
T ss_pred cCCCEEEeeeccCCceEEEEe-EEEEEEECCeEEEEEEEEeccCCcceEeccHHHhhhHH
Confidence 46777777333 333444443 67899999999999999999999999999999988763
No 19
>COG2383 Uncharacterized conserved protein [Function unknown]
Probab=71.57 E-value=0.72 Score=32.76 Aligned_cols=20 Identities=35% Similarity=0.740 Sum_probs=17.7
Q ss_pred eecccchhccCceEEecccc
Q 044180 74 VLAVQWLEKLGKIVTDHKAL 93 (130)
Q Consensus 74 ILGmdWL~~~g~i~iD~~~~ 93 (130)
||+..||+++|-|++||.+.
T Consensus 51 ilsl~~La~~GVItin~~al 70 (109)
T COG2383 51 ILSLFWLAQYGVITINWEAL 70 (109)
T ss_pred HHHHHHHHHcCeEEEcHHHH
Confidence 57889999999999999764
No 20
>COG3577 Predicted aspartyl protease [General function prediction only]
Probab=67.37 E-value=6.1 Score=31.40 Aligned_cols=58 Identities=16% Similarity=0.295 Sum_probs=41.3
Q ss_pred CceeEEeeCCCeEeecceeeccEEeecCEEEE-ceeEEeecCCcc-eeecccchhccCceEE
Q 044180 29 MSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFE-ADFHILDFFGAN-AVLAVQWLEKLGKIVT 88 (130)
Q Consensus 29 ~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~-~dl~vL~l~g~D-vILGmdWL~~~g~i~i 88 (130)
-++.|+.|||..-...-....+ .|.+.++. .+-+|++-+..| .-|||.+|.+++...+
T Consensus 147 y~~~v~TANG~~~AA~V~Ld~v--~IG~I~~~nV~A~V~~~g~L~~sLLGMSfL~rL~~fq~ 206 (215)
T COG3577 147 YTITVSTANGRARAAPVTLDRV--QIGGIRVKNVDAMVAEDGALDESLLGMSFLNRLSGFQV 206 (215)
T ss_pred CceEEEccCCccccceEEeeeE--EEccEEEcCchhheecCCccchhhhhHHHHhhccceEe
Confidence 3667888999875555444443 57777776 377888888665 4579999999987433
No 21
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=58.04 E-value=3.2 Score=20.20 Aligned_cols=8 Identities=63% Similarity=1.219 Sum_probs=6.9
Q ss_pred ceEecCCC
Q 044180 13 LRFNCDEP 20 (130)
Q Consensus 13 lcf~cde~ 20 (130)
.||+|++.
T Consensus 2 ~C~~C~~~ 9 (18)
T PF00098_consen 2 KCFNCGEP 9 (18)
T ss_dssp BCTTTSCS
T ss_pred cCcCCCCc
Confidence 69999995
No 22
>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=55.20 E-value=37 Score=22.92 Aligned_cols=35 Identities=11% Similarity=0.186 Sum_probs=30.0
Q ss_pred EEEEEeCCeEEEEEeccCCCCChhhHHHHHhcccC
Q 044180 94 TMEFTYRGQPIKLVGAQNIRPKPTQSIHLQSRIFD 128 (130)
Q Consensus 94 tl~f~~~g~~I~l~G~~~~~is~~Q~~~l~~~~~~ 128 (130)
+++.+++|..+++.=.++...+-.++..++.+.|.
T Consensus 2 ~vKaty~~d~~rf~~~~~~~~~~~~L~~ev~~rf~ 36 (81)
T cd06396 2 NLKVTYNGESQSFLVSDSENTTWASVEAMVKVSFG 36 (81)
T ss_pred EEEEEECCeEEEEEecCCCCCCHHHHHHHHHHHhC
Confidence 57778999999998888777888999999999886
No 23
>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=51.08 E-value=37 Score=26.45 Aligned_cols=31 Identities=16% Similarity=0.090 Sum_probs=25.9
Q ss_pred cCCcceeecccchhccCceEEeccccEEEEEe
Q 044180 68 FFGANAVLAVQWLEKLGKIVTDHKALTMEFTY 99 (130)
Q Consensus 68 l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~ 99 (130)
-.....|||+.+|+.+=- ..|+.++++.|..
T Consensus 286 ~~~~~~iLG~~fl~~~y~-vfD~~~~~ig~A~ 316 (317)
T PF00026_consen 286 DDSDDWILGSPFLRNYYV-VFDYENNRIGFAQ 316 (317)
T ss_dssp TSSSEEEEEHHHHTTEEE-EEETTTTEEEEEE
T ss_pred ccCCceEecHHHhhceEE-EEeCCCCEEEEec
Confidence 346688999999999854 8999999999864
No 24
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=50.73 E-value=40 Score=23.20 Aligned_cols=53 Identities=23% Similarity=0.328 Sum_probs=35.9
Q ss_pred ccCceeEEeeCCCeEee--cceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEecc
Q 044180 27 KIMSFLVDVSNGEQIRS--EGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHK 91 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~--~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~ 91 (130)
+...|+|.+.||..+.| +|....-.++| ..-|-+.+++..||.- -|.|.+-++
T Consensus 18 p~~~frV~LenG~~vla~isGKmR~~rIrI----l~GD~V~VE~spYDlt--------kGRIiyR~~ 72 (87)
T PRK12442 18 PDSRFRVTLENGVEVGAYASGRMRKHRIRI----LAGDRVTLELSPYDLT--------KGRINFRHK 72 (87)
T ss_pred CCCEEEEEeCCCCEEEEEeccceeeeeEEe----cCCCEEEEEECcccCC--------ceeEEEEec
Confidence 45679999999999776 45555444444 3557788888888853 456555443
No 25
>KOG2872 consensus Uroporphyrinogen decarboxylase [Coenzyme transport and metabolism]
Probab=44.55 E-value=6.9 Score=32.96 Aligned_cols=33 Identities=21% Similarity=0.400 Sum_probs=22.3
Q ss_pred CCcceeecccchhccCceEEeccccEEEEEeCCeEEEEEeccCC
Q 044180 69 FGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGAQNI 112 (130)
Q Consensus 69 ~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g~~I~l~G~~~~ 112 (130)
.||||| |.|| ++|=++-. ...|+.|++||+-+-
T Consensus 271 tG~DVv-gLDW-------Tvdp~ear---~~~g~~VtlQGNlDP 303 (359)
T KOG2872|consen 271 TGYDVV-GLDW-------TVDPAEAR---RRVGNRVTLQGNLDP 303 (359)
T ss_pred cCCcEE-eecc-------cccHHHHH---HhhCCceEEecCCCh
Confidence 489987 8899 55543321 346778999998743
No 26
>PF05515 Viral_NABP: Viral nucleic acid binding ; InterPro: IPR008891 This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP).
Probab=43.40 E-value=11 Score=27.67 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=14.3
Q ss_pred hHHHhc--cceEecCCCCCcccc
Q 044180 6 QICRAQ--GLRFNCDEPFNPAIE 26 (130)
Q Consensus 6 ~~rr~~--Glcf~cde~f~p~h~ 26 (130)
+.|||+ |.||.|+.--.-+|.
T Consensus 55 ~KRRAkR~~~C~~CG~~l~~~~~ 77 (124)
T PF05515_consen 55 AKRRAKRYNRCFKCGRYLHNNGN 77 (124)
T ss_pred HHHHHHHhCccccccceeecCCc
Confidence 457777 899999983333443
No 27
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. 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. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=41.59 E-value=88 Score=21.27 Aligned_cols=36 Identities=8% Similarity=0.080 Sum_probs=28.2
Q ss_pred EEEEEeCCeEEEEEeccC---CCCChhhHHHHHhcccCC
Q 044180 94 TMEFTYRGQPIKLVGAQN---IRPKPTQSIHLQSRIFDS 129 (130)
Q Consensus 94 tl~f~~~g~~I~l~G~~~---~~is~~Q~~~l~~~~~~~ 129 (130)
+++.+++|..+++.-... ..++..+|+..+.+.|.-
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l 40 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSL 40 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCC
Confidence 567788998877776653 468999999999988853
No 28
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=40.91 E-value=6.8 Score=20.45 Aligned_cols=13 Identities=31% Similarity=0.388 Sum_probs=10.7
Q ss_pred cceEecCCCCCcc
Q 044180 12 GLRFNCDEPFNPA 24 (130)
Q Consensus 12 Glcf~cde~f~p~ 24 (130)
-.|..|+.+|.|+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 3589999999875
No 29
>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=38.48 E-value=6.4 Score=27.05 Aligned_cols=24 Identities=25% Similarity=0.378 Sum_probs=19.6
Q ss_pred eecccchhccCceEEeccccEEEE
Q 044180 74 VLAVQWLEKLGKIVTDHKALTMEF 97 (130)
Q Consensus 74 ILGmdWL~~~g~i~iD~~~~tl~f 97 (130)
++.++||+..|=|.+||.+.+-..
T Consensus 31 ~l~lq~l~~~G~i~Vnw~kl~~~~ 54 (100)
T PF04930_consen 31 FLLLQYLASKGYIKVNWDKLEKDV 54 (100)
T ss_pred HHHHHHHHHCCeEEECHHHHHHHH
Confidence 456799999999999999865443
No 30
>PF14645 Chibby: Chibby family
Probab=38.29 E-value=54 Score=23.39 Aligned_cols=31 Identities=26% Similarity=0.251 Sum_probs=24.9
Q ss_pred eeecccchhccCceEEeccccEEEEEeCCeEEEEEe
Q 044180 73 AVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVG 108 (130)
Q Consensus 73 vILGmdWL~~~g~i~iD~~~~tl~f~~~g~~I~l~G 108 (130)
.=||+|+ ||+.++....++.| .+|+|+.-.|
T Consensus 34 ~el~ld~----~p~~l~Lg~~~l~F-~dG~W~~e~~ 64 (116)
T PF14645_consen 34 AELGLDY----GPPRLNLGDQTLVF-EDGQWTSESG 64 (116)
T ss_pred ccccccc----CCceEeECCeEEEE-ECCEEeccCC
Confidence 3467774 89999999999999 8999994444
No 31
>PRK13908 putative recombination protein RecO; Provisional
Probab=37.61 E-value=16 Score=28.82 Aligned_cols=15 Identities=47% Similarity=0.665 Sum_probs=12.9
Q ss_pred cceEecCCC----------CCcccc
Q 044180 12 GLRFNCDEP----------FNPAIE 26 (130)
Q Consensus 12 Glcf~cde~----------f~p~h~ 26 (130)
..||-|||+ |-|+|.
T Consensus 139 ~~Cf~Ce~~i~~~iaL~RaflpaH~ 163 (204)
T PRK13908 139 FICFLCDEKIENEIALARAFLPAHP 163 (204)
T ss_pred CeEEecCCccccchHHHHhhcccCh
Confidence 579999998 888886
No 32
>PF09040 H-K_ATPase_N: Gastric H+/K+-ATPase, N terminal domain; InterPro: IPR015127 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the N-terminal domain found in gastric H+/K+-transporter ATPases. This domain adopts an alpha-helical conformation under hydrophobic conditions. The domain contains tyrosine residues, phosphorylation of which regulates the function of the ATPase. Additionally, the domain also interacts with various structural proteins, including the spectrin-binding domain of ankyrin III []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0008900 hydrogen:potassium-exchanging ATPase activity, 0015991 ATP hydrolysis coupled proton transport, 0016020 membrane; PDB: 1IWF_A 1IWC_A.
Probab=34.85 E-value=16 Score=21.47 Aligned_cols=12 Identities=50% Similarity=0.573 Sum_probs=8.7
Q ss_pred ChhhhhHHHhcc
Q 044180 1 MAAEMQICRAQG 12 (130)
Q Consensus 1 ~~a~~~~rr~~G 12 (130)
|+|.||.+++.|
T Consensus 21 m~AK~~kkk~~~ 32 (41)
T PF09040_consen 21 MAAKMSKKKAGG 32 (41)
T ss_dssp SSHCCHHHT-S-
T ss_pred HHHHHhhhhccC
Confidence 789999888775
No 33
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=34.82 E-value=14 Score=21.43 Aligned_cols=21 Identities=29% Similarity=0.233 Sum_probs=10.8
Q ss_pred ccceEecCCCCCccccccCce
Q 044180 11 QGLRFNCDEPFNPAIEKIMSF 31 (130)
Q Consensus 11 ~Glcf~cde~f~p~h~~~~~~ 31 (130)
.++|++|+.-|.=+.++....
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp --C-TTTSSSCS-TTT---TC
T ss_pred CccCcccCCCcchhhhhhhhh
Confidence 589999999877666644433
No 34
>CHL00008 petG cytochrome b6/f complex subunit V
Probab=34.39 E-value=20 Score=20.80 Aligned_cols=12 Identities=33% Similarity=0.335 Sum_probs=9.7
Q ss_pred hhhhhHHHhccc
Q 044180 2 AAEMQICRAQGL 13 (130)
Q Consensus 2 ~a~~~~rr~~Gl 13 (130)
+|.+||||..-+
T Consensus 24 aAylQYrRg~~l 35 (37)
T CHL00008 24 TAYLQYRRGDQL 35 (37)
T ss_pred HHHHHHhhcccc
Confidence 799999997643
No 35
>KOG1542 consensus Cysteine proteinase Cathepsin F [Posttranslational modification, protein turnover, chaperones]
Probab=34.15 E-value=9.5 Score=32.61 Aligned_cols=42 Identities=26% Similarity=0.373 Sum_probs=32.8
Q ss_pred EEEEceeEEeecCCcceeecccchhccCceEEeccccEEEEEeCC
Q 044180 57 VEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRG 101 (130)
Q Consensus 57 ~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g 101 (130)
..+..||..|+..--+|+ .||.++||+++=-....|.|..+|
T Consensus 261 ~v~I~~f~~l~~nE~~ia---~wLv~~GPi~vgiNa~~mQ~YrgG 302 (372)
T KOG1542|consen 261 VVSIKDFSMLSNNEDQIA---AWLVTFGPLSVGINAKPMQFYRGG 302 (372)
T ss_pred eEEEeccEecCCCHHHHH---HHHHhcCCeEEEEchHHHHHhccc
Confidence 455667888888655665 999999999887778888877666
No 36
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=33.11 E-value=15 Score=25.98 Aligned_cols=17 Identities=12% Similarity=0.155 Sum_probs=13.6
Q ss_pred hccceEecCCCCCcccc
Q 044180 10 AQGLRFNCDEPFNPAIE 26 (130)
Q Consensus 10 ~~Glcf~cde~f~p~h~ 26 (130)
.|.+|..|+.+|--..+
T Consensus 8 tKR~Cp~CG~kFYDLnk 24 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNK 24 (108)
T ss_pred CcccCCCCcchhccCCC
Confidence 47899999999966554
No 37
>PRK00665 petG cytochrome b6-f complex subunit PetG; Reviewed
Probab=32.34 E-value=22 Score=20.64 Aligned_cols=11 Identities=36% Similarity=0.075 Sum_probs=9.1
Q ss_pred hhhhhHHHhcc
Q 044180 2 AAEMQICRAQG 12 (130)
Q Consensus 2 ~a~~~~rr~~G 12 (130)
+|.+||||..-
T Consensus 24 aAylQYrRg~~ 34 (37)
T PRK00665 24 AAWNQYKRGNQ 34 (37)
T ss_pred HHHHHHhcccc
Confidence 79999999654
No 38
>COG2081 Predicted flavoproteins [General function prediction only]
Probab=31.26 E-value=73 Score=27.75 Aligned_cols=35 Identities=14% Similarity=0.160 Sum_probs=24.7
Q ss_pred cEEeecCE-EEEceeEEeecCCccee------ecccchhccC
Q 044180 50 VKFEMQGV-EFEADFHILDFFGANAV------LAVQWLEKLG 84 (130)
Q Consensus 50 ~~~~iqg~-~f~~dl~vL~l~g~DvI------LGmdWL~~~g 84 (130)
..+...+- ++..|-.||-+||.-+= +|++|++++|
T Consensus 144 f~l~t~~g~~i~~d~lilAtGG~S~P~lGstg~gy~iA~~~G 185 (408)
T COG2081 144 FRLDTSSGETVKCDSLILATGGKSWPKLGSTGFGYPIARQFG 185 (408)
T ss_pred EEEEcCCCCEEEccEEEEecCCcCCCCCCCCchhhHHHHHcC
Confidence 44444444 56777778888877665 7889998888
No 39
>KOG4584 consensus Uncharacterized conserved protein [General function prediction only]
Probab=30.10 E-value=28 Score=29.40 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=17.6
Q ss_pred CEEEEceeEEeecCCcceeeccc
Q 044180 56 GVEFEADFHILDFFGANAVLAVQ 78 (130)
Q Consensus 56 g~~f~~dl~vL~l~g~DvILGmd 78 (130)
|.++..-++..|=+|+|+||||=
T Consensus 196 ~~p~K~~lif~DNSG~DvILGil 218 (348)
T KOG4584|consen 196 GKPHKCALIFVDNSGFDVILGIL 218 (348)
T ss_pred CCCcceEEEEecCCCcceeeeec
Confidence 44555566778889999999983
No 40
>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=29.82 E-value=93 Score=20.62 Aligned_cols=21 Identities=14% Similarity=0.066 Sum_probs=18.5
Q ss_pred ceEEeccccEEEEEeCCeEEE
Q 044180 85 KIVTDHKALTMEFTYRGQPIK 105 (130)
Q Consensus 85 ~i~iD~~~~tl~f~~~g~~I~ 105 (130)
.+.+|+.+.+|.|+.+|+.+.
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 669999999999999998744
No 41
>PF11148 DUF2922: Protein of unknown function (DUF2922); InterPro: IPR021321 This bacterial family of proteins has no known function.
Probab=27.99 E-value=1.2e+02 Score=19.21 Aligned_cols=38 Identities=13% Similarity=0.132 Sum_probs=26.4
Q ss_pred cccEEEEE-eCCeEEEEEeccCC-CCChhhHHHHHhcccC
Q 044180 91 KALTMEFT-YRGQPIKLVGAQNI-RPKPTQSIHLQSRIFD 128 (130)
Q Consensus 91 ~~~tl~f~-~~g~~I~l~G~~~~-~is~~Q~~~l~~~~~~ 128 (130)
+.+.|+|. -.|+..++.=..-- .++..+++..+..|-+
T Consensus 1 KtL~l~F~~~~gk~~ti~i~~pk~~lt~~~V~~~m~~ii~ 40 (69)
T PF11148_consen 1 KTLELVFKTEDGKTFTISIPNPKEDLTEAEVKAAMQAIIA 40 (69)
T ss_pred CEEEEEEEcCCCCEEEEEcCCCCCCCCHHHHHHHHHHHHH
Confidence 35678886 56777666544433 3899999998887754
No 42
>PF00670 AdoHcyase_NAD: S-adenosyl-L-homocysteine hydrolase, NAD binding domain; InterPro: IPR015878 S-adenosyl-L-homocysteine hydrolase (3.3.1.1 from EC) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. AdoHcyase is an ubiquitous enzyme which binds and requires NAD+ as a cofactor. AdoHcyase is a highly conserved protein [] of about 430 to 470 amino acids. This entry represents the glycine-rich region in the central part of AdoHcyase, which is thought to be involved in NAD-binding.; GO: 0004013 adenosylhomocysteinase activity; PDB: 2ZJ1_C 3DHY_B 2ZIZ_C 2ZJ0_D 3CE6_B 3GLQ_B 3D64_A 3G1U_C 1A7A_A 3NJ4_C ....
Probab=27.70 E-value=1.3e+02 Score=22.81 Aligned_cols=51 Identities=14% Similarity=0.061 Sum_probs=39.5
Q ss_pred EceeEEeecCCcceeecccchhccCceEEeccccEEEEE-eCCeEEEEEecc
Q 044180 60 EADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFT-YRGQPIKLVGAQ 110 (130)
Q Consensus 60 ~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~-~~g~~I~l~G~~ 110 (130)
..+.++-+.+.+|.=+-++||+.++--...-+.....++ ++|+.|.|-+..
T Consensus 101 kdgail~n~Gh~d~Eid~~~L~~~~~~~~~v~~~v~~y~l~~G~~i~lLa~G 152 (162)
T PF00670_consen 101 KDGAILANAGHFDVEIDVDALEANAVEREEVRPQVDRYTLPDGRRIILLAEG 152 (162)
T ss_dssp -TTEEEEESSSSTTSBTHHHHHTCTSEEEEEETTEEEEEETTSEEEEEEGGG
T ss_pred cCCeEEeccCcCceeEeeccccccCcEEEEcCCCeeEEEeCCCCEEEEEECC
Confidence 456788899999999999999999654555556677777 468888887765
No 43
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=27.69 E-value=1.3e+02 Score=19.56 Aligned_cols=43 Identities=14% Similarity=0.208 Sum_probs=27.0
Q ss_pred ccCceeEEeeCCCeEee--cceeeccEEeecCEEEEceeEEeecCCcce
Q 044180 27 KIMSFLVDVSNGEQIRS--EGHCSKVKFEMQGVEFEADFHILDFFGANA 73 (130)
Q Consensus 27 ~~~~~~V~vanG~~l~~--~~~c~~~~~~iqg~~f~~dl~vL~l~g~Dv 73 (130)
+...|+|++.||..+.| +|.-..-.++| ..-|-+.+++..||.
T Consensus 16 ~~~~f~V~l~ng~~vla~i~GKmr~~rI~I----~~GD~V~Ve~spyd~ 60 (68)
T TIGR00008 16 PNAMFRVELENGHEVLAHISGKIRMHYIRI----LPGDKVKVELSPYDL 60 (68)
T ss_pred CCCEEEEEECCCCEEEEEecCcchhccEEE----CCCCEEEEEECcccC
Confidence 45678999999998776 44444333333 234566666776663
No 44
>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=27.53 E-value=2.2e+02 Score=22.56 Aligned_cols=28 Identities=18% Similarity=0.108 Sum_probs=23.7
Q ss_pred cceeecccchhccCceEEeccccEEEEEe
Q 044180 71 ANAVLAVQWLEKLGKIVTDHKALTMEFTY 99 (130)
Q Consensus 71 ~DvILGmdWL~~~g~i~iD~~~~tl~f~~ 99 (130)
-..|||...|+.+-. ..|+.+.++.|..
T Consensus 290 ~~~ilG~~fl~~~y~-vfD~~~~~ig~a~ 317 (318)
T cd05477 290 PLWILGDVFLRQYYS-VYDLGNNQVGFAT 317 (318)
T ss_pred ceEEEcHHHhhheEE-EEeCCCCEEeeee
Confidence 358999999999855 7999999999864
No 45
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=27.50 E-value=42 Score=24.78 Aligned_cols=34 Identities=15% Similarity=0.251 Sum_probs=22.8
Q ss_pred ccceEecCCCCCccccccCceeEEeeCCCe-Eeecceee
Q 044180 11 QGLRFNCDEPFNPAIEKIMSFLVDVSNGEQ-IRSEGHCS 48 (130)
Q Consensus 11 ~Glcf~cde~f~p~h~~~~~~~V~vanG~~-l~~~~~c~ 48 (130)
..+|.+|+-+--|+|. ..-|+ .+|.+ ..|+.+|.
T Consensus 4 ~e~CsFcG~kIyPG~G---~~fVR-~DGkvf~FcssKC~ 38 (131)
T PRK14891 4 TRTCDYTGEEIEPGTG---TMFVR-KDGTVLHFVDSKCE 38 (131)
T ss_pred eeeecCcCCcccCCCC---cEEEe-cCCCEEEEecHHHH
Confidence 3589999999999996 22222 22333 45888875
No 46
>PF04746 DUF575: Protein of unknown function (DUF575); InterPro: IPR006835 This represents a conserved region found in a number of Chlamydophila pneumoniae proteins.
Probab=26.97 E-value=22 Score=24.90 Aligned_cols=11 Identities=27% Similarity=0.755 Sum_probs=9.2
Q ss_pred eeecccchhcc
Q 044180 73 AVLAVQWLEKL 83 (130)
Q Consensus 73 vILGmdWL~~~ 83 (130)
+|.|||||-+.
T Consensus 29 iv~GieWLvS~ 39 (101)
T PF04746_consen 29 IVMGIEWLVSR 39 (101)
T ss_pred EEeehHHHHHH
Confidence 67899999875
No 47
>PF08844 DUF1815: Domain of unknown function (DUF1815); InterPro: IPR014943 This entry is about 100 amino acids in length and is functionally uncharacterised.
Probab=26.42 E-value=1.1e+02 Score=21.49 Aligned_cols=28 Identities=21% Similarity=0.498 Sum_probs=17.0
Q ss_pred ccceEecCCCCCcccc-ccCceeEEeeCCCeEe
Q 044180 11 QGLRFNCDEPFNPAIE-KIMSFLVDVSNGEQIR 42 (130)
Q Consensus 11 ~Glcf~cde~f~p~h~-~~~~~~V~vanG~~l~ 42 (130)
.--||-||+ ++. ..-.|-|.++++..|.
T Consensus 32 ~AsCYtC~d----G~~~~~ASFmv~lg~~HliR 60 (105)
T PF08844_consen 32 LASCYTCGD----GRDMNSASFMVSLGDNHLIR 60 (105)
T ss_pred eeEEEecCC----CCCCCceeEEEEcCCCcEEE
Confidence 457999975 222 2345677777766554
No 48
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=25.56 E-value=25 Score=26.65 Aligned_cols=12 Identities=33% Similarity=0.484 Sum_probs=10.1
Q ss_pred ecCCcceeeccc
Q 044180 67 DFFGANAVLAVQ 78 (130)
Q Consensus 67 ~l~g~DvILGmd 78 (130)
|...||.|||||
T Consensus 82 DF~~FDYI~~MD 93 (159)
T KOG3217|consen 82 DFREFDYILAMD 93 (159)
T ss_pred HhhhcceeEEec
Confidence 556799999997
No 49
>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=24.59 E-value=95 Score=24.21 Aligned_cols=26 Identities=19% Similarity=0.169 Sum_probs=22.4
Q ss_pred ceeecccchhccCceEEeccccEEEEE
Q 044180 72 NAVLAVQWLEKLGKIVTDHKALTMEFT 98 (130)
Q Consensus 72 DvILGmdWL~~~g~i~iD~~~~tl~f~ 98 (130)
..|||-..|+.+-. ..|+.++++.|.
T Consensus 252 ~~ilGd~fl~~~y~-vfD~~~~~ig~A 277 (278)
T cd06097 252 FSILGDVFLKAQYV-VFDVGGPKLGFA 277 (278)
T ss_pred EEEEcchhhCceeE-EEcCCCceeeec
Confidence 56999999999866 899999999875
No 50
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=24.01 E-value=29 Score=25.53 Aligned_cols=18 Identities=11% Similarity=0.025 Sum_probs=13.8
Q ss_pred HhccceEecCCCCCcccc
Q 044180 9 RAQGLRFNCDEPFNPAIE 26 (130)
Q Consensus 9 r~~Glcf~cde~f~p~h~ 26 (130)
-.|.+|.+|+.+|--..+
T Consensus 7 GtKr~Cp~cg~kFYDLnk 24 (129)
T TIGR02300 7 GTKRICPNTGSKFYDLNR 24 (129)
T ss_pred CccccCCCcCccccccCC
Confidence 357899999999875554
No 51
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=23.62 E-value=64 Score=20.41 Aligned_cols=20 Identities=25% Similarity=0.405 Sum_probs=17.1
Q ss_pred ceeEEeeCCCeEeecceeec
Q 044180 30 SFLVDVSNGEQIRSEGHCSK 49 (130)
Q Consensus 30 ~~~V~vanG~~l~~~~~c~~ 49 (130)
+.+|++|||....+.+...+
T Consensus 51 ~~~v~~a~g~~~~~~g~~~~ 70 (72)
T PF13975_consen 51 PIRVKLANGSVIEIRGVAEN 70 (72)
T ss_pred CEEEEECCCCccccceEEEe
Confidence 68999999999998887654
No 52
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=23.45 E-value=34 Score=20.51 Aligned_cols=14 Identities=21% Similarity=0.669 Sum_probs=10.3
Q ss_pred ccceEecCCCCCcc
Q 044180 11 QGLRFNCDEPFNPA 24 (130)
Q Consensus 11 ~Glcf~cde~f~p~ 24 (130)
..-||+|+++|.+.
T Consensus 48 ~~fC~~C~~~~H~~ 61 (64)
T smart00647 48 FSFCFRCKVPWHSP 61 (64)
T ss_pred CeECCCCCCcCCCC
Confidence 35689999988543
No 53
>PF11164 DUF2948: Protein of unknown function (DUF2948); InterPro: IPR021335 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=23.44 E-value=97 Score=23.00 Aligned_cols=36 Identities=28% Similarity=0.453 Sum_probs=21.7
Q ss_pred CCccccccCceeEEeeCCCeEeecceeeccEEeecC
Q 044180 21 FNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQG 56 (130)
Q Consensus 21 f~p~h~~~~~~~V~vanG~~l~~~~~c~~~~~~iqg 56 (130)
|.|+..+...+..+.|+|+.|.-+-.|-++.+.--|
T Consensus 92 fe~~e~p~G~v~L~fAGgg~IrL~VE~ie~~L~D~~ 127 (138)
T PF11164_consen 92 FEPGEAPAGHVLLTFAGGGAIRLEVECIEVQLRDLG 127 (138)
T ss_pred EEeCCCCCcEEEEEECCCcEEEEEEEEEEEEEeecC
Confidence 444444455566666777777777777666655543
No 54
>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=21.64 E-value=2.2e+02 Score=21.98 Aligned_cols=53 Identities=11% Similarity=0.126 Sum_probs=36.2
Q ss_pred eccEEeec-CEEEEcee--EEe------------ec-CCcceeecccchhccCceEEeccccEEEEEeCC
Q 044180 48 SKVKFEMQ-GVEFEADF--HIL------------DF-FGANAVLAVQWLEKLGKIVTDHKALTMEFTYRG 101 (130)
Q Consensus 48 ~~~~~~iq-g~~f~~dl--~vL------------~l-~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g 101 (130)
|.+.+.+. |..|.... +++ .. ..--.|||..+|+.+-- ..|..++++.|...+
T Consensus 196 P~i~~~f~~~~~~~i~~~~y~~~~~~~~~C~~~~~~~~~~~~ilG~~fl~~~~~-vFD~~~~~iGfa~~~ 264 (265)
T cd05476 196 PDLTLHFDGGADLELPPENYFVDVGEGVVCLAILSSSSGGVSILGNIQQQNFLV-EYDLENSRLGFAPAD 264 (265)
T ss_pred CCEEEEECCCCEEEeCcccEEEECCCCCEEEEEecCCCCCcEEEChhhcccEEE-EEECCCCEEeeecCC
Confidence 77888887 66555332 111 11 23347999999999855 789999999987643
No 55
>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=21.61 E-value=1.3e+02 Score=20.26 Aligned_cols=22 Identities=27% Similarity=0.764 Sum_probs=19.9
Q ss_pred eeCCCeEeecceeeccEE-eecC
Q 044180 35 VSNGEQIRSEGHCSKVKF-EMQG 56 (130)
Q Consensus 35 vanG~~l~~~~~c~~~~~-~iqg 56 (130)
+..|+...|+|.|..+++ .++|
T Consensus 12 ~~~g~~~~C~G~CaSvs~~~~ng 34 (82)
T PF01684_consen 12 ISTGAEVACQGQCASVSITTYNG 34 (82)
T ss_pred ccCCeeEEeCCEEEEEEEEeECC
Confidence 557889999999999999 9999
No 56
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=21.49 E-value=28 Score=22.48 Aligned_cols=17 Identities=12% Similarity=0.018 Sum_probs=12.1
Q ss_pred HhccceEecCCCCCccc
Q 044180 9 RAQGLRFNCDEPFNPAI 25 (130)
Q Consensus 9 r~~Glcf~cde~f~p~h 25 (130)
..+++|+.|+|.=...+
T Consensus 3 k~~~~C~~Cg~r~~~~~ 19 (69)
T PF09706_consen 3 KKKYNCIFCGERPSKKK 19 (69)
T ss_pred CCCCcCcCCCCcccccc
Confidence 46799999998544333
No 57
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=21.34 E-value=1.3e+02 Score=21.36 Aligned_cols=43 Identities=23% Similarity=0.328 Sum_probs=30.1
Q ss_pred eeEEeecCCcceeecccchhccCceEEeccccEEEEEeCCeEEEEEec
Q 044180 62 DFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEFTYRGQPIKLVGA 109 (130)
Q Consensus 62 dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f~~~g~~I~l~G~ 109 (130)
++..++-..-+.=||.++ ||+.+....+.+.|. +|+||.=.|-
T Consensus 23 ~~~~~d~~t~~~El~l~y----g~i~l~Lg~~~l~F~-dG~W~~e~~~ 65 (108)
T cd07429 23 NLRLLDRSTRQAELGLDY----GPIRLKLGGQELVFE-DGRWISESGG 65 (108)
T ss_pred cccccCCCcccccccccc----CCceeeeCCceEEee-CCEEecCCCC
Confidence 444445444444566664 899999999999976 8888775554
No 58
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=21.29 E-value=48 Score=21.60 Aligned_cols=20 Identities=30% Similarity=0.340 Sum_probs=13.5
Q ss_pred hHHHhc-cceEecCCCCCccc
Q 044180 6 QICRAQ-GLRFNCDEPFNPAI 25 (130)
Q Consensus 6 ~~rr~~-Glcf~cde~f~p~h 25 (130)
|.||++ =+-=.|+|+|.|-.
T Consensus 40 Q~rR~k~Vel~g~e~~f~P~e 60 (65)
T TIGR03318 40 QARREKCVELEGCEERFAPLD 60 (65)
T ss_pred HhhhccEEEEecccceecchh
Confidence 566665 22368999999854
No 59
>PF02529 PetG: Cytochrome B6-F complex subunit 5; InterPro: IPR003683 This family consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].; GO: 0009512 cytochrome b6f complex; PDB: 1Q90_G 2ZT9_G 1VF5_G 2D2C_G 2E74_G 2E75_G 2E76_G.
Probab=21.27 E-value=35 Score=19.83 Aligned_cols=11 Identities=36% Similarity=0.292 Sum_probs=7.7
Q ss_pred hhhhhHHHhcc
Q 044180 2 AAEMQICRAQG 12 (130)
Q Consensus 2 ~a~~~~rr~~G 12 (130)
+|+.||||.+-
T Consensus 24 ~Ay~QY~Rg~q 34 (37)
T PF02529_consen 24 AAYLQYRRGNQ 34 (37)
T ss_dssp HHHHHHCS--T
T ss_pred HHHHHHhcccc
Confidence 68999999763
No 60
>PHA01782 hypothetical protein
Probab=21.11 E-value=39 Score=26.03 Aligned_cols=33 Identities=30% Similarity=0.582 Sum_probs=22.4
Q ss_pred cchhccCceEEeccccE---EEEE--eCCeEEEEEeccC
Q 044180 78 QWLEKLGKIVTDHKALT---MEFT--YRGQPIKLVGAQN 111 (130)
Q Consensus 78 dWL~~~g~i~iD~~~~t---l~f~--~~g~~I~l~G~~~ 111 (130)
+||.++|+|.++-.+++ ..|- ..++ -.|.|..+
T Consensus 74 ~wlv~~Gkv~vntDkk~aKefpf~~nK~~~-tdLegA~~ 111 (177)
T PHA01782 74 EWLVKFGKVQVNTDKKSAKEFPFVYNKFGK-TDLEGATA 111 (177)
T ss_pred HHHHHhCCccccccccccccCceeeccccc-hhhHhhhc
Confidence 89999999999988885 3343 3333 34555543
No 61
>KOG1370 consensus S-adenosylhomocysteine hydrolase [Coenzyme transport and metabolism]
Probab=20.90 E-value=1.1e+02 Score=26.44 Aligned_cols=73 Identities=12% Similarity=0.148 Sum_probs=43.1
Q ss_pred CCeEeecceeeccEEeecCEEEEceeEEeecCCcceeecccchhccCceEEeccccEEEE-EeCCeEEEEEecc
Q 044180 38 GEQIRSEGHCSKVKFEMQGVEFEADFHILDFFGANAVLAVQWLEKLGKIVTDHKALTMEF-TYRGQPIKLVGAQ 110 (130)
Q Consensus 38 G~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~g~DvILGmdWL~~~g~i~iD~~~~tl~f-~~~g~~I~l~G~~ 110 (130)
+..+.+..-|.++-..-.=.....|.+|-++|.+|+=..+.||.+..--..+-+-+.=.+ .++|+.|.|-...
T Consensus 270 ~difVTtTGc~dii~~~H~~~mk~d~IvCN~Ghfd~EiDv~~L~~~~~~~~~vk~QvD~~~~~~gr~iIlLAeG 343 (434)
T KOG1370|consen 270 VDIFVTTTGCKDIITGEHFDQMKNDAIVCNIGHFDTEIDVKWLNTPALTWENVKPQVDRYILPNGKHIILLAEG 343 (434)
T ss_pred CCEEEEccCCcchhhHHHHHhCcCCcEEeccccccceeehhhccCCcceeeecccccceeeccCCcEEEEEecC
Confidence 444444444555433222234567899999999999999999999543222222122222 2577777776654
No 62
>PF14452 Multi_ubiq: Multiubiquitin
Probab=20.72 E-value=2.3e+02 Score=17.76 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=16.5
Q ss_pred cEEEEEeCCeEEEEEeccCCCCChhhHHHH
Q 044180 93 LTMEFTYRGQPIKLVGAQNIRPKPTQSIHL 122 (130)
Q Consensus 93 ~tl~f~~~g~~I~l~G~~~~~is~~Q~~~l 122 (130)
|+.+|.-+|+.+.| ..-.||..|+..|
T Consensus 1 r~~~i~vn~~~~~~---~~~~iTg~qi~~l 27 (72)
T PF14452_consen 1 RTFRIIVNGRPYEW---PDPTITGRQILAL 27 (72)
T ss_pred CeEEEEECCeEEEE---CCCCcCHHHHHHH
Confidence 34566667776665 3344777777665
No 63
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=20.53 E-value=63 Score=24.99 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=25.4
Q ss_pred ceEecCCCCCccccccCceeE-EeeCCCeEeecceeeccEEe
Q 044180 13 LRFNCDEPFNPAIEKIMSFLV-DVSNGEQIRSEGHCSKVKFE 53 (130)
Q Consensus 13 lcf~cde~f~p~h~~~~~~~V-~vanG~~l~~~~~c~~~~~~ 53 (130)
+|++|.+ +.-++.+ +|-||+.+. ..+|..|+-.
T Consensus 2 iCq~Cqq-------npAti~~tkI~~~~k~e-~~vCe~Ca~~ 35 (176)
T COG3880 2 ICQNCQQ-------NPATIHFTKIINGEKIE-LYVCETCAKP 35 (176)
T ss_pred cchhhcC-------CcceEEEEEeecCCeeE-eehhhcCCCc
Confidence 6899987 2235677 689999999 8899888744
No 64
>PF02989 DUF228: Lyme disease proteins of unknown function; InterPro: IPR004239 This group comprises proteins of unknown function from Borrelia burgdorferi, the causitive organism of Lyme disease.
Probab=20.20 E-value=71 Score=24.85 Aligned_cols=82 Identities=15% Similarity=0.264 Sum_probs=47.1
Q ss_pred hccceEecCCCCCccccccCceeEEeeCCCeEeecceeeccEEeecCEEEEceeEEeecC-CcceeecccchhccCceEE
Q 044180 10 AQGLRFNCDEPFNPAIEKIMSFLVDVSNGEQIRSEGHCSKVKFEMQGVEFEADFHILDFF-GANAVLAVQWLEKLGKIVT 88 (130)
Q Consensus 10 ~~Glcf~cde~f~p~h~~~~~~~V~vanG~~l~~~~~c~~~~~~iqg~~f~~dl~vL~l~-g~DvILGmdWL~~~g~i~i 88 (130)
.+|-||+|+-|.++. ...+.|..+.|..+- |.|.++. +|+....|+|+- +|.- ||-.-.+ +|
T Consensus 67 ~kgfPYKrGVKLv~~---~~~~~Ve~Ggg~DLY--GICvDiD------efs~tAtVvPITnnFeg-----yLvak~~-~i 129 (184)
T PF02989_consen 67 FKGFPYKRGVKLVDK---ENEIYVEAGGGSDLY--GICVDID------EFSKTATVVPITNNFEG-----YLVAKDS-TI 129 (184)
T ss_pred ccCCCccceeEecCC---CceEEEEeCCCCccE--EEEEehh------hccceEEEEeccCCeEE-----EEEECCC-CC
Confidence 579999999999943 335677766666654 5666553 455555566654 2333 2222221 22
Q ss_pred eccccEEEEEeCCeEEEEEec
Q 044180 89 DHKALTMEFTYRGQPIKLVGA 109 (130)
Q Consensus 89 D~~~~tl~f~~~g~~I~l~G~ 109 (130)
.. .-.|.|...|......|.
T Consensus 130 k~-gdkL~fN~~G~leK~~g~ 149 (184)
T PF02989_consen 130 KA-GDKLIFNKDGELEKATGN 149 (184)
T ss_pred Cc-CcEEEecCCCeEEEccCC
Confidence 21 134566666766666665
No 65
>smart00507 HNHc HNH nucleases.
Probab=20.11 E-value=53 Score=18.17 Aligned_cols=16 Identities=25% Similarity=0.561 Sum_probs=12.4
Q ss_pred HHHhccceEecCCCCCc
Q 044180 7 ICRAQGLRFNCDEPFNP 23 (130)
Q Consensus 7 ~rr~~Glcf~cde~f~p 23 (130)
..|. +.|..|++++.+
T Consensus 7 ~~r~-~~C~~C~~~~~~ 22 (52)
T smart00507 7 LHRD-GVCAYCGKPASE 22 (52)
T ss_pred HHHC-CCCcCCcCCCCC
Confidence 3466 899999998754
Done!