Query 032006
Match_columns 149
No_of_seqs 111 out of 1058
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 08:20:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032006.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032006hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03189 Protease specific for 100.0 2.8E-33 6.1E-38 225.0 13.5 124 12-147 366-489 (490)
2 KOG0778 Protease, Ulp1 family 100.0 1E-33 2.3E-38 229.0 7.6 126 11-148 386-511 (511)
3 PF02902 Peptidase_C48: Ulp1 p 99.9 4.7E-27 1E-31 174.2 12.8 126 11-144 79-210 (216)
4 COG5160 ULP1 Protease, Ulp1 fa 99.9 6.5E-26 1.4E-30 182.3 5.8 121 11-147 449-569 (578)
5 KOG3246 Sentrin-specific cyste 99.8 1.4E-18 3.1E-23 126.8 11.8 112 11-142 84-211 (223)
6 PF00770 Peptidase_C5: Adenovi 98.0 7.4E-05 1.6E-09 53.5 8.7 94 15-120 17-116 (183)
7 PRK14848 deubiquitinase SseL; 98.0 5E-05 1.1E-09 57.5 7.8 86 16-121 189-276 (317)
8 KOG0779 Protease, Ulp1 family 97.7 4E-05 8.7E-10 65.2 4.7 120 11-140 434-582 (595)
9 PRK11836 deubiquitinase; Provi 97.7 0.00024 5.2E-09 55.0 7.5 101 15-122 219-328 (403)
10 PF03290 Peptidase_C57: Vaccin 97.6 0.00042 9.1E-09 55.3 8.0 37 13-50 229-265 (423)
11 PF03421 YopJ: YopJ Serine/Thr 94.6 0.44 9.6E-06 34.7 8.7 88 17-121 73-163 (177)
12 PRK15371 effector protein YopJ 88.3 5 0.00011 31.4 8.5 26 95-121 161-186 (287)
13 PF12252 SidE: Dot/Icm substra 85.1 2.6 5.6E-05 38.6 5.9 35 18-55 48-88 (1439)
14 KOG4110 NADH:ubiquinone oxidor 75.0 3.3 7.2E-05 27.6 2.5 32 86-118 16-47 (120)
15 PF09907 DUF2136: Uncharacteri 62.5 20 0.00044 22.3 4.1 37 7-43 23-63 (76)
16 cd02549 Peptidase_C39A A sub-f 55.8 40 0.00086 22.4 5.1 39 10-49 72-116 (141)
17 PF03412 Peptidase_C39: Peptid 50.3 11 0.00024 25.0 1.6 23 99-123 6-28 (131)
18 COG2260 Predicted Zn-ribbon RN 48.1 9.5 0.00021 22.6 0.8 39 105-144 9-54 (59)
19 PRK13130 H/ACA RNA-protein com 47.3 7.4 0.00016 22.8 0.3 39 104-143 8-53 (56)
20 cd02418 Peptidase_C39B A sub-f 42.7 63 0.0014 21.3 4.5 23 24-47 87-109 (136)
21 cd02424 Peptidase_C39E A sub-f 39.2 25 0.00053 23.4 2.0 23 99-122 5-27 (129)
22 cd02425 Peptidase_C39F A sub-f 36.8 76 0.0016 20.5 4.1 24 25-49 83-106 (126)
23 KOG3315 Transport protein part 29.4 55 0.0012 23.8 2.4 28 95-123 131-158 (191)
24 PRK13193 pyrrolidone-carboxyla 28.1 34 0.00074 25.5 1.3 17 104-120 134-150 (209)
25 PF15644 Tox-PL: Papain fold t 27.4 75 0.0016 20.8 2.8 31 17-49 77-108 (111)
26 PF10087 DUF2325: Uncharacteri 27.3 64 0.0014 20.5 2.3 20 8-28 42-61 (97)
27 PF13280 WYL: WYL domain 26.0 96 0.0021 21.0 3.3 24 16-39 29-54 (172)
28 cd02421 Peptidase_C39_likeD A 25.2 77 0.0017 20.6 2.5 32 15-47 65-98 (124)
29 PRK13194 pyrrolidone-carboxyla 24.9 40 0.00087 25.1 1.2 16 104-119 134-149 (208)
30 cd02419 Peptidase_C39C A sub-f 24.7 1.2E+02 0.0025 19.7 3.4 24 25-49 82-105 (127)
31 PF11814 DUF3335: Peptidase_C3 22.8 2.8E+02 0.0061 20.8 5.3 42 7-49 121-168 (207)
32 PF05412 Peptidase_C33: Equine 22.6 1.1E+02 0.0023 20.5 2.7 18 105-122 8-25 (108)
33 PF02099 Josephin: Josephin; 22.5 1.4E+02 0.0031 21.1 3.6 29 19-50 101-129 (157)
34 PF05393 Hum_adeno_E3A: Human 21.5 67 0.0015 20.7 1.5 14 105-118 39-52 (94)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=2.8e-33 Score=224.98 Aligned_cols=124 Identities=29% Similarity=0.564 Sum_probs=112.5
Q ss_pred ccccCEEEEeeecCCCeEEEEEEEcCCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCCCCCCCCceE
Q 032006 12 FTDVDMIFIPVNLGGDHWVLALADLRARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKV 91 (149)
Q Consensus 12 ~~~~d~I~iPin~~~~HW~l~vvd~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~w~~ 91 (149)
+.++|+||||||. +.||+|+|||+++++|.|||||++ .+....+.+ ..|+..+...+.+.++ +.+.|+.
T Consensus 366 Lfs~D~IFIPIh~-n~HWsLaVId~k~k~I~yyDSLgg--~~~~vL~~L-------~rYL~~E~kdK~g~d~-D~s~W~~ 434 (490)
T PLN03189 366 LIDCDKIFVPIHQ-EIHWTLAVINKKDQKFQYLDSLKG--RDPKILDAL-------AKYYVDEVKDKSEKDI-DVSSWEQ 434 (490)
T ss_pred cccCceEEeeeec-CCeeEEEEEEcCCCeEEEEeCCCC--CCHHHHHHH-------HHHHHHHHhhhcCCCc-chhccee
Confidence 4578999999999 899999999999999999999998 766666665 8899988888877788 8889988
Q ss_pred EeccCCCcCCCCCCCchHHHHHHHHHHhcCCCceeccccHHHHHHHHHHHHhcCCc
Q 032006 92 RIVKDVPQQEPGSGDCGVFMLMFTMYLMFGLKLDFDSSHGHYFRKKIAVDIFPGDI 147 (149)
Q Consensus 92 ~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~~~~~~~~~~~~~~~R~~~~~~l~~~~l 147 (149)
..+.++|||.|| +|||||||+||++++.|.+++|+|+||+.+|++|+.||++.++
T Consensus 435 ~~~~~vPQQ~NG-~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrRma~EIl~~r~ 489 (490)
T PLN03189 435 EFVEDLPEQKNG-YDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLRTAKEILRLKA 489 (490)
T ss_pred ccCCCCCCCCCC-CCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHHHHHHHHHhhc
Confidence 666799999999 9999999999999999999999999999999999999998764
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-33 Score=229.00 Aligned_cols=126 Identities=33% Similarity=0.644 Sum_probs=116.6
Q ss_pred hccccCEEEEeeecCCCeEEEEEEEcCCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCCCCCCCCce
Q 032006 11 LFTDVDMIFIPVNLGGDHWVLALADLRARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWK 90 (149)
Q Consensus 11 ~~~~~d~I~iPin~~~~HW~l~vvd~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~w~ 90 (149)
++.+.|+||+|||. +.||+|+|||+++++|.|||||++. ++..+ +++ ++|+++|+..+.+.++ +.+.|+
T Consensus 386 ~if~~d~i~vPIH~-~vHW~l~vid~r~k~i~y~DS~~~~-~nr~~-~aL-------~~Yl~~E~~~k~~~~~-d~s~w~ 454 (511)
T KOG0778|consen 386 DIFDKDIIFVPIHL-GVHWCLAVIDLREKTIEYYDSLGGG-PNRIC-DAL-------AKYLQDESRDKSKKDF-DVSGWT 454 (511)
T ss_pred CccccceeEeeeec-CceEEEEEEEcccceEEEeeccCCC-CcchH-HHH-------HHHHHHHHhhhhcCCC-Cccchh
Confidence 46788999999999 9999999999999999999999961 34444 676 9999999999988888 999999
Q ss_pred EEeccCCCcCCCCCCCchHHHHHHHHHHhcCCCceeccccHHHHHHHHHHHHhcCCcC
Q 032006 91 VRIVKDVPQQEPGSGDCGVFMLMFTMYLMFGLKLDFDSSHGHYFRKKIAVDIFPGDIA 148 (149)
Q Consensus 91 ~~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~~~~~~~~~~~~~~~R~~~~~~l~~~~l~ 148 (149)
.....++|||.|| +|||+|+|+|++|++.+.|++|++.||++||++||+||+..+|+
T Consensus 455 ~~~~~~iP~Q~Ng-~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR~~m~~eI~~~~l~ 511 (511)
T KOG0778|consen 455 IEFVQNIPQQRNG-SDCGMFVCKYADYISRDVPLTFTQQDMPYFRKKMAKEILHLKLL 511 (511)
T ss_pred hhhhhccccccCC-CccceEEeeechhhccCCCcccChhhhHHHHHHHHHHHHhhhcC
Confidence 9888999999999 99999999999999999999999999999999999999999875
No 3
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=99.95 E-value=4.7e-27 Score=174.21 Aligned_cols=126 Identities=35% Similarity=0.605 Sum_probs=93.5
Q ss_pred hccccCEEEEeeecCCCeEEEEEEEcCCCeEEEEcCCCCCCCCH--HHHhhhcchHHHHHHHHHHHhcccCCCCCCCCCC
Q 032006 11 LFTDVDMIFIPVNLGGDHWVLALADLRARRMRIYDSLVTFREDK--TYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADP 88 (149)
Q Consensus 11 ~~~~~d~I~iPin~~~~HW~l~vvd~~~~~i~~~DSl~~~~~~~--~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~ 88 (149)
++.++++|++|+|.+++||+|++|+++.++|.+|||+++ ... .....+.. +..++...+....+... +..+
T Consensus 79 ~l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~--~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~-~~~~ 151 (216)
T PF02902_consen 79 NLFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGS--SNNDKRYKRVIEN----IIPFLKREYKKKEGRDP-DKSP 151 (216)
T ss_dssp TGGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTST--SSH-HHHHHHHHH----HHHHHHHHHHHHHSSCT--TTT
T ss_pred cccccCEEEEEEechhhccceeEEcccccEEEEEecccc--ccccccchhhhhh----hhhhhhhcccccccccc-ccce
Confidence 889999999999999999999999999999999999999 544 22222211 23444333322222222 4567
Q ss_pred ceEEeccCCCcCCCCCCCchHHHHHHHHHHhcCCCce----eccccHHHHHHHHHHHHhc
Q 032006 89 WKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMFGLKLD----FDSSHGHYFRKKIAVDIFP 144 (149)
Q Consensus 89 w~~~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~~~~~~----~~~~~~~~~R~~~~~~l~~ 144 (149)
|+......+|||.|+ +|||+|||+||++++.+.+.+ ++++++..+|.+++.++..
T Consensus 152 ~~~~~~~~~pqQ~n~-~dCGv~vl~~~~~~~~~~~~~~~~~l~~~~i~~~r~~~a~~~~e 210 (216)
T PF02902_consen 152 FKIVRPPNVPQQPNG-YDCGVYVLKFMECLLEGPSFDFSQELTEEDIKNFRKKLAVDLYE 210 (216)
T ss_dssp CEEEEECTS-SSSSS-SCHHHHHHHHHHHHHCTHHSTGCCSBTGHHHHHHHHHHHH----
T ss_pred eeecccccccCCCCC-CCcHHHHHHHHHHHHhCCCCcccccCCHHHHHHHHHHHHhhccc
Confidence 887776799999999 999999999999999998764 7899999999999988754
No 4
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=6.5e-26 Score=182.32 Aligned_cols=121 Identities=31% Similarity=0.429 Sum_probs=105.6
Q ss_pred hccccCEEEEeeecCCCeEEEEEEEcCCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCCCCCCCCce
Q 032006 11 LFTDVDMIFIPVNLGGDHWVLALADLRARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWK 90 (149)
Q Consensus 11 ~~~~~d~I~iPin~~~~HW~l~vvd~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~w~ 90 (149)
++.+.++||+|||. ..||.|.+||.++..|.+||||.+ ....+.+.+ ..|+.+|++...+. ++|.
T Consensus 449 dif~~k~I~iPIni-~~HW~l~II~~~~~~i~~~DSLan--~~~~v~~~L-------~~Y~ldE~k~~~~k-----~~~~ 513 (578)
T COG5160 449 DIFSKKYIFIPINI-SYHWFLAIIDNPKKNILYFDSLAN--THDPVLEFL-------RSYLLDEYKIQHDK-----DPQI 513 (578)
T ss_pred CccccceEEEEecc-cceEEEEEeecCcceeEEeccccc--CcHHHHHHH-------HHHHHHHHhcccCC-----chhh
Confidence 45677899999999 999999999999999999999999 667777776 89999997655443 3354
Q ss_pred EEeccCCCcCCCCCCCchHHHHHHHHHHhcCCCceeccccHHHHHHHHHHHHhcCCc
Q 032006 91 VRIVKDVPQQEPGSGDCGVFMLMFTMYLMFGLKLDFDSSHGHYFRKKIAVDIFPGDI 147 (149)
Q Consensus 91 ~~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~~~~~~~~~~~~~~~R~~~~~~l~~~~l 147 (149)
.....++|||.|| +|||||||+++++++++.+..|+..|++.+|+.|+++|+..++
T Consensus 514 ~~~~~~vPqQ~Ng-~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~~qi 569 (578)
T COG5160 514 KMKHCKVPQQRNG-SDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKDLQI 569 (578)
T ss_pred hhhcCCCCCCCCC-CccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHHHHH
Confidence 4445899999999 9999999999999999999999999999999999999987665
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.79 E-value=1.4e-18 Score=126.78 Aligned_cols=112 Identities=25% Similarity=0.304 Sum_probs=75.2
Q ss_pred hccccCEEEEeeec--------CCCeEEEEEEEcCCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCC
Q 032006 11 LFTDVDMIFIPVNL--------GGDHWVLALADLRARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPE 82 (149)
Q Consensus 11 ~~~~~d~I~iPin~--------~~~HW~l~vvd~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~ 82 (149)
++.++++||+|||. ||+||+|+|+..++++.++|||+.+ .+....+.+ .+.+..+++....
T Consensus 84 ~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n--~nt~~a~~l---~~kl~~ll~~~~~------ 152 (223)
T KOG3246|consen 84 DLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSN--GNTKDAKSL---MKKLRALLKKKFA------ 152 (223)
T ss_pred hcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccC--CCcHHHHHH---HHHHHHHHhhhhh------
Confidence 77899999999999 3579999999999999999999999 553333222 1112444433210
Q ss_pred CCCCCCceEEeccCCCcCCCCCCCchHHHHHHHHHHhcC----CCce----eccccHHHHHHHHHHHH
Q 032006 83 LQSADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMFG----LKLD----FDSSHGHYFRKKIAVDI 142 (149)
Q Consensus 83 ~~~~~~w~~~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~~----~~~~----~~~~~~~~~R~~~~~~l 142 (149)
+ .....+|||.|| +|||++||.+.+.++.. .-.+ ...+-+..+|.++..-|
T Consensus 153 -------~-~~~~~~~qQqNg-yDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~l~~LI 211 (223)
T KOG3246|consen 153 -------K-RVECKCLQQQNG-YDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREELLDLI 211 (223)
T ss_pred -------h-cccccChhhhcC-CchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHH
Confidence 1 113678899999 99999999988766543 2222 22234456666655443
No 6
>PF00770 Peptidase_C5: Adenovirus endoprotease; InterPro: IPR000855 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine aminopeptidases belong to the peptidase family C5 (adenain family, clan CE). Several adenovirus proteins are synthesised as precursors, requiring processing by a protease before the virion is assembled [, ]. Until recently, the adenovirus endopeptidase was classified as a serine protease, having been reported to be inhibited by serine protease inhibitors [, ]. However, it has since been shown to be inhibited by cysteine protease inhibitors, and the catalytic residues are believed to be His-54 and Cys-104 [, ].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1NLN_A 1AVP_A.
Probab=97.99 E-value=7.4e-05 Score=53.46 Aligned_cols=94 Identities=20% Similarity=0.335 Sum_probs=45.9
Q ss_pred cCEEEEeeec-----CCCeEEEEEEEcCCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcc-cCCCCCCCCCC
Q 032006 15 VDMIFIPVNL-----GGDHWVLALADLRARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFY-NIRPELQSADP 88 (149)
Q Consensus 15 ~d~I~iPin~-----~~~HW~l~vvd~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~~ 88 (149)
...--..||. ||.||..++.|+..++++.|||.+- .+++..+.- .+. ...+++..+.. ....-+
T Consensus 17 ~k~acAIVNT~~retGGvHWlA~Aw~P~s~t~YmFDPfGf--sd~~L~qiY-~Fe--Ye~llrRSAL~~~~dRCv----- 86 (183)
T PF00770_consen 17 HKPACAIVNTGGRETGGVHWLAFAWDPRSRTFYMFDPFGF--SDQKLKQIY-QFE--YEGLLRRSALSSTPDRCV----- 86 (183)
T ss_dssp TS-EEEEEESS-TTT--S-EEEEEEETTTTEEEEE-TT-----HHHHHHHH-------HHHHHHHHHHH-TTSEE-----
T ss_pred CCcceEEEecCCcccCceeEEEEEecCCcceEEEeCCCCC--CHHHHHHHH-hhh--HHHHHHHHhhcCCCCceE-----
Confidence 3444667777 5899999999999999999999988 655443211 111 01222222111 111111
Q ss_pred ceEEeccCCCcCCCCCCCchHHHHHHHHHHhc
Q 032006 89 WKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMF 120 (149)
Q Consensus 89 w~~~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~ 120 (149)
+++. ..-..|-..|..||.|+|.|+.++..
T Consensus 87 -~Lvk-stqtVQ~p~SaaCGLFC~lFL~aF~~ 116 (183)
T PF00770_consen 87 -TLVK-STQTVQCPCSAACGLFCCLFLHAFVH 116 (183)
T ss_dssp -EEEE-E-EE-S-TT---HHHHHHHHHHHHHH
T ss_pred -EEEe-ccceeeccCchhHHHHHHHHHHHHHh
Confidence 2222 22224554459999999999998854
No 7
>PRK14848 deubiquitinase SseL; Provisional
Probab=97.95 E-value=5e-05 Score=57.48 Aligned_cols=86 Identities=15% Similarity=0.208 Sum_probs=49.7
Q ss_pred CEEEEeeecCCCeEEEEEEEc--CCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCCCCCCCCceEEe
Q 032006 16 DMIFIPVNLGGDHWVLALADL--RARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRI 93 (149)
Q Consensus 16 d~I~iPin~~~~HW~l~vvd~--~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~w~~~~ 93 (149)
+.=+||||. ++||+|+++.. ++.+..+|.|++. -+....+.+ +.. +.. .+.. ...+-.+
T Consensus 189 ~nevF~INt-g~HWil~~~~Ki~~kiKC~iFNs~~~--l~eNs~~~i------i~~---ak~---ag~~--~e~di~f-- 249 (317)
T PRK14848 189 HNEVFLINT-GDHWLLCLFYKLAEKIKCLIFNTYYD--LNENTKQEI------IEA---AKI---AGIS--ENEDVNF-- 249 (317)
T ss_pred cceEEEecC-CCcEEEEEhHHhhhhceEEEeecHhh--hhhhHHHHH------HHH---HHh---hCcc--cCCceEE--
Confidence 344599998 99999998753 3456678999877 332222222 111 000 0000 1111222
Q ss_pred ccCCCcCCCCCCCchHHHHHHHHHHhcC
Q 032006 94 VKDVPQQEPGSGDCGVFMLMFTMYLMFG 121 (149)
Q Consensus 94 ~~~~p~Q~n~s~dCGvfvl~~~~~~~~~ 121 (149)
...-.|.+-+..||.|||.+++.+..+
T Consensus 250 -Ie~nLQqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 250 -IETNLQNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred -eehhhhhhCCCcchHHHHHHHHHHHhc
Confidence 223345555599999999999977654
No 8
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=4e-05 Score=65.21 Aligned_cols=120 Identities=20% Similarity=0.194 Sum_probs=65.7
Q ss_pred hccccCEEEEeeecCCCeEEEEEEEcCCCeE------EEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCCC-
Q 032006 11 LFTDVDMIFIPVNLGGDHWVLALADLRARRM------RIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPEL- 83 (149)
Q Consensus 11 ~~~~~d~I~iPin~~~~HW~l~vvd~~~~~i------~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~- 83 (149)
.+.+.++|++|+|. ..||.+.++....... ...++....... ..+..+...++.+........+
T Consensus 434 d~~~k~yi~~P~~E-~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~ 504 (595)
T KOG0779|consen 434 DLFNKDYVFVPTHE-RFHWKLAIICNPDLETETPRPRLELLILKLSADF--------PIVENILDFMKVASIYNNELIVT 504 (595)
T ss_pred ccccceeEEecCch-HhhhhccccccCccccCccccchhhhhhcccccc--------chhhhhhhhhhhcccccCccccc
Confidence 34567799999999 9999999986553321 122222110000 1111123333333221111100
Q ss_pred -CCCCCceEEe--------ccCCCcCCCCCCCchHHHHHHHHHHhcCCCc-------------eeccccHHHHHHHHHH
Q 032006 84 -QSADPWKVRI--------VKDVPQQEPGSGDCGVFMLMFTMYLMFGLKL-------------DFDSSHGHYFRKKIAV 140 (149)
Q Consensus 84 -~~~~~w~~~~--------~~~~p~Q~n~s~dCGvfvl~~~~~~~~~~~~-------------~~~~~~~~~~R~~~~~ 140 (149)
.....|.+.. ....|||.|. .|||+|++.|++.+..+++. +|.+.++..+|..+-.
T Consensus 505 ~~~~~~~~~~~~~~~~~s~~v~~p~q~n~-~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~ 582 (595)
T KOG0779|consen 505 EDLELEEELPRRLPRGKSETVREPQQNND-VDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRN 582 (595)
T ss_pred ccccccccccccCcccccccccccCccCc-ccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhc
Confidence 0111222110 0122899999 99999999999999877642 2667777777776543
No 9
>PRK11836 deubiquitinase; Provisional
Probab=97.66 E-value=0.00024 Score=54.97 Aligned_cols=101 Identities=23% Similarity=0.323 Sum_probs=53.8
Q ss_pred cCEEEEeeecCCCeEEEEEEE--------cCCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHH-hcccCCCCCCC
Q 032006 15 VDMIFIPVNLGGDHWVLALAD--------LRARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDV-GFYNIRPELQS 85 (149)
Q Consensus 15 ~d~I~iPin~~~~HW~l~vvd--------~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~-~~~~~~~~~~~ 85 (149)
++.=+||||. ++||+|+++. .++.+..+|.|+..-..+++ +..+.+...+..-+..+ ...+..... .
T Consensus 219 k~~elFpINt-g~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~--~t~q~ii~a~~~~~~~~~~~~~ik~~~-~ 294 (403)
T PRK11836 219 KEVQLFPINT-GGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKE--NSLKRVINSFNSELMGEMSNNNIKVHL-T 294 (403)
T ss_pred ccceEEEecC-CCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchh--hHHHHHHHhhhhhhhhhcchhhhcccc-c
Confidence 5667899998 9999999873 23456778898877332221 11111122212112222 111222222 2
Q ss_pred CCCceEEeccCCCcCCCCCCCchHHHHHHHHHHhcCC
Q 032006 86 ADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMFGL 122 (149)
Q Consensus 86 ~~~w~~~~~~~~p~Q~n~s~dCGvfvl~~~~~~~~~~ 122 (149)
...-.+ ...-.|++-+..||.||++.++-++.+.
T Consensus 295 e~ei~f---ie~dLQq~vpngCGlFv~~a~Qe~i~q~ 328 (403)
T PRK11836 295 EPEIIF---LHADLQQYLSQSCGAFVCMAAQEVIEQR 328 (403)
T ss_pred CCceEE---EechhhhcCCCccceehHHHHHHHHHHh
Confidence 222222 2233444555999999998887555443
No 10
>PF03290 Peptidase_C57: Vaccinia virus I7 processing peptidase; InterPro: IPR004970 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This is a group of cysteine peptidases which constitute MEROPS peptidase family C57 (clan CE). The type example is vaccinia virus I7 processing peptidase (vaccinia virus); protein I7 is expressed in the late phase of infection [].
Probab=97.58 E-value=0.00042 Score=55.32 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=33.7
Q ss_pred cccCEEEEeeecCCCeEEEEEEEcCCCeEEEEcCCCCC
Q 032006 13 TDVDMIFIPVNLGGDHWVLALADLRARRMRIYDSLVTF 50 (149)
Q Consensus 13 ~~~d~I~iPin~~~~HW~l~vvd~~~~~i~~~DSl~~~ 50 (149)
.+..++.+|++- .+||.++++|.+++-+.+|||-+..
T Consensus 229 ~~~RyvmFgfcY-~~Hwkc~IfDk~~~~v~FydSgG~~ 265 (423)
T PF03290_consen 229 SKKRYVMFGFCY-MSHWKCCIFDKEKKIVYFYDSGGNI 265 (423)
T ss_pred ccccEEEeeeee-hhcceEEEEeccccEEEEEcCCCCC
Confidence 356789999999 9999999999999999999999883
No 11
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=94.58 E-value=0.44 Score=34.66 Aligned_cols=88 Identities=14% Similarity=0.202 Sum_probs=50.0
Q ss_pred EEEEeeecCCCeEEEEEEE-c--CCCeEEEEcCCCCCCCCHHHHhhhcchHHHHHHHHHHHhcccCCCCCCCCCCceEEe
Q 032006 17 MIFIPVNLGGDHWVLALAD-L--RARRMRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRI 93 (149)
Q Consensus 17 ~I~iPin~~~~HW~l~vvd-~--~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~w~~~~ 93 (149)
..++|...++.|-+.+-|- . .+.+|.+++|-........ .... .+...+. ..+.+ .++++.
T Consensus 73 R~Iv~~~~~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~~~~~~-l~~~-------~~~~~~~-~~~~~------~~~~~~- 136 (177)
T PF03421_consen 73 RAIVNLGGDGIHHVALDVRHTPNGKPSLIVFEPASFYGMKPA-LAGY-------TKLAEEA-RQKLL------PNAKFA- 136 (177)
T ss_pred EEEEeCCCCCCcEEEEEEeecCCCCceEEEEccccccCCcch-hhhH-------HHHHHHH-HhccC------CCcEEE-
Confidence 3566654445666655554 2 2568999999976222222 1111 1111111 11111 233443
Q ss_pred ccCCCcCCCCCCCchHHHHHHHHHHhcC
Q 032006 94 VKDVPQQEPGSGDCGVFMLMFTMYLMFG 121 (149)
Q Consensus 94 ~~~~p~Q~n~s~dCGvfvl~~~~~~~~~ 121 (149)
+....-|... +|||+|.+.++.....+
T Consensus 137 ~ie~diQkS~-~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 137 VIEMDIQKSP-SDCGIFSLSLAKKMYKE 163 (177)
T ss_pred EEecccccCc-CcchhhHHHHHHHHhhc
Confidence 3677899999 99999999999887643
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=88.34 E-value=5 Score=31.45 Aligned_cols=26 Identities=23% Similarity=0.529 Sum_probs=20.8
Q ss_pred cCCCcCCCCCCCchHHHHHHHHHHhcC
Q 032006 95 KDVPQQEPGSGDCGVFMLMFTMYLMFG 121 (149)
Q Consensus 95 ~~~p~Q~n~s~dCGvfvl~~~~~~~~~ 121 (149)
...--|... +|||+|.+.++......
T Consensus 161 ie~d~QkS~-~dC~mFSL~~AkK~~~e 186 (287)
T PRK15371 161 VEMDIQRSS-SECGIFSLALAKKLYLE 186 (287)
T ss_pred EecccccCc-ccchhhhHHHHHHHhhh
Confidence 455578888 99999999999777544
No 13
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=85.09 E-value=2.6 Score=38.60 Aligned_cols=35 Identities=23% Similarity=0.547 Sum_probs=26.2
Q ss_pred EEEeeecC------CCeEEEEEEEcCCCeEEEEcCCCCCCCCHH
Q 032006 18 IFIPVNLG------GDHWVLALADLRARRMRIYDSLVTFREDKT 55 (149)
Q Consensus 18 I~iPin~~------~~HW~l~vvd~~~~~i~~~DSl~~~~~~~~ 55 (149)
=|+||-.| ..||+.++ --.....+.||||+. ...+
T Consensus 48 gfmpvltgv~p~~~sghwimli-kg~gn~y~lfdplg~--~sg~ 88 (1439)
T PF12252_consen 48 GFMPVLTGVSPRQDSGHWIMLI-KGQGNQYYLFDPLGK--TSGE 88 (1439)
T ss_pred CCceeecCcCCCCcCceeEEEE-EcCCCceEEeccccc--cccc
Confidence 37787773 57999987 455667899999999 5443
No 14
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=74.96 E-value=3.3 Score=27.64 Aligned_cols=32 Identities=25% Similarity=0.495 Sum_probs=25.6
Q ss_pred CCCceEEeccCCCcCCCCCCCchHHHHHHHHHH
Q 032006 86 ADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYL 118 (149)
Q Consensus 86 ~~~w~~~~~~~~p~Q~n~s~dCGvfvl~~~~~~ 118 (149)
...|.+.-....|....+ .|||.|-..+++|.
T Consensus 16 ~~r~p~tds~~~p~~~q~-r~cg~FE~e~~eC~ 47 (120)
T KOG4110|consen 16 IDRWPTTDSTEQPYKHQG-RDCGKFEKEWMECA 47 (120)
T ss_pred hhhccccccccCcccccc-ccccHHHHHHHHHH
Confidence 456665555677877788 99999999999998
No 15
>PF09907 DUF2136: Uncharacterized protein conserved in bacteria (DUF2136); InterPro: IPR018669 HigB (YgjN) is the toxin of the HigB-HigA toxin-antitoxin system, acting as a translation-dependent mRNA interferase. HigB inhibits protein synthesis by cleaving translated mRNAs within the coding region []. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=62.47 E-value=20 Score=22.30 Aligned_cols=37 Identities=22% Similarity=0.465 Sum_probs=25.8
Q ss_pred hhhhhccccCEE---EEeeecCCCeEEEEE-EEcCCCeEEE
Q 032006 7 LMSKLFTDVDMI---FIPVNLGGDHWVLAL-ADLRARRMRI 43 (149)
Q Consensus 7 ~~~~~~~~~d~I---~iPin~~~~HW~l~v-vd~~~~~i~~ 43 (149)
=+|+.+.+.|.+ ++-.|.+|++.-|++ |+.+.+.+++
T Consensus 23 elk~~f~~ad~v~~~~~vFnI~GN~yRlI~~I~f~~~~v~I 63 (76)
T PF09907_consen 23 ELKQQFPSADIVKNNRVVFNIGGNKYRLIAKIDFERQIVYI 63 (76)
T ss_pred HHHHHCcchhhhcCCEEEEEcCCCcEEEEEEEEeCceEEEE
Confidence 355667777776 666777777666665 7888777665
No 16
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=55.77 E-value=40 Score=22.44 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=25.0
Q ss_pred hhccccCEEEEeee-----cCCCeEEEEE-EEcCCCeEEEEcCCCC
Q 032006 10 KLFTDVDMIFIPVN-----LGGDHWVLAL-ADLRARRMRIYDSLVT 49 (149)
Q Consensus 10 ~~~~~~d~I~iPin-----~~~~HW~l~v-vd~~~~~i~~~DSl~~ 49 (149)
+.+....-+++-+. ..+.||++++ +| .+..+.+.||..+
T Consensus 72 ~~l~~~~Pvi~~~~~~~~~~~~gH~vVv~g~~-~~~~~~i~DP~~~ 116 (141)
T cd02549 72 RQLAAGHPVIVSVNLGVSITPSGHAMVVIGYD-RKGNVYVNDPGGG 116 (141)
T ss_pred HHHHCCCeEEEEEecCcccCCCCeEEEEEEEc-CCCCEEEECCCCC
Confidence 44444444555443 2377999887 44 3677999999765
No 17
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=50.27 E-value=11 Score=25.00 Aligned_cols=23 Identities=26% Similarity=0.639 Sum_probs=15.1
Q ss_pred cCCCCCCCchHHHHHHHHHHhcCCC
Q 032006 99 QQEPGSGDCGVFMLMFTMYLMFGLK 123 (149)
Q Consensus 99 ~Q~n~s~dCGvfvl~~~~~~~~~~~ 123 (149)
.|.+. .|||+-++.++-.. .|.+
T Consensus 6 ~Q~~~-~dcg~acl~~l~~~-~g~~ 28 (131)
T PF03412_consen 6 KQSDS-NDCGLACLAMLLKY-YGIP 28 (131)
T ss_dssp --SST-T-HHHHHHHHHHHH-TT--
T ss_pred EeCCC-CCHHHHHHHHHHHH-hCCC
Confidence 78888 99999999988766 3544
No 18
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=48.06 E-value=9.5 Score=22.56 Aligned_cols=39 Identities=15% Similarity=0.266 Sum_probs=25.7
Q ss_pred CCchHHHHHHHHHHhcCC------CceeccccH-HHHHHHHHHHHhc
Q 032006 105 GDCGVFMLMFTMYLMFGL------KLDFDSSHG-HYFRKKIAVDIFP 144 (149)
Q Consensus 105 ~dCGvfvl~~~~~~~~~~------~~~~~~~~~-~~~R~~~~~~l~~ 144 (149)
-.||+|+++ =.|=-.|. |..|+.+|- .++|.++-..+..
T Consensus 9 ~~cg~YTLk-e~Cp~CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~~ 54 (59)
T COG2260 9 PKCGRYTLK-EKCPVCGGDTKVPHPPRFSPEDKYGKYRRELKKRLGL 54 (59)
T ss_pred cCCCceeec-ccCCCCCCccccCCCCCCCccchHHHHHHHHHHHhcc
Confidence 569999988 32333332 236888776 7888888776654
No 19
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=47.34 E-value=7.4 Score=22.84 Aligned_cols=39 Identities=21% Similarity=0.340 Sum_probs=24.6
Q ss_pred CCCchHHHHHHHHHHhcCCC------ceeccccH-HHHHHHHHHHHh
Q 032006 104 SGDCGVFMLMFTMYLMFGLK------LDFDSSHG-HYFRKKIAVDIF 143 (149)
Q Consensus 104 s~dCGvfvl~~~~~~~~~~~------~~~~~~~~-~~~R~~~~~~l~ 143 (149)
+.+||+|++ -..|=..|.+ ..|+.+|- .++|..+-.++.
T Consensus 8 C~~CgvYTL-k~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 8 CPKCGVYTL-KEICPVCGGKTKNPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred CCCCCCEEc-cccCcCCCCCCCCCCCCCCCCCCccHHHHHHHHHHhh
Confidence 368999999 3333333433 35888766 678877766554
No 20
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=42.68 E-value=63 Score=21.27 Aligned_cols=23 Identities=17% Similarity=0.413 Sum_probs=17.2
Q ss_pred cCCCeEEEEEEEcCCCeEEEEcCC
Q 032006 24 LGGDHWVLALADLRARRMRIYDSL 47 (149)
Q Consensus 24 ~~~~HW~l~vvd~~~~~i~~~DSl 47 (149)
.++.||+++. ...+..+.++||.
T Consensus 87 ~~~~~~~Vl~-~~~~~~~~i~dp~ 109 (136)
T cd02418 87 WKLNHYVVVY-KIKKKKILIADPA 109 (136)
T ss_pred CCCCeEEEEE-EEcCCEEEEECCC
Confidence 4467998775 4557789999993
No 21
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=39.17 E-value=25 Score=23.44 Aligned_cols=23 Identities=17% Similarity=0.362 Sum_probs=17.2
Q ss_pred cCCCCCCCchHHHHHHHHHHhcCC
Q 032006 99 QQEPGSGDCGVFMLMFTMYLMFGL 122 (149)
Q Consensus 99 ~Q~n~s~dCGvfvl~~~~~~~~~~ 122 (149)
.|.+. .|||+.++..+-.+..|.
T Consensus 5 ~q~~~-~dcgla~l~~i~~~~~g~ 27 (129)
T cd02424 5 KQTDL-NDCGIAVIQMLYNHYYKK 27 (129)
T ss_pred EecCc-cchHHHHHHHHHHHhcCC
Confidence 57777 899999998886653343
No 22
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=36.81 E-value=76 Score=20.53 Aligned_cols=24 Identities=17% Similarity=0.454 Sum_probs=18.2
Q ss_pred CCCeEEEEEEEcCCCeEEEEcCCCC
Q 032006 25 GGDHWVLALADLRARRMRIYDSLVT 49 (149)
Q Consensus 25 ~~~HW~l~vvd~~~~~i~~~DSl~~ 49 (149)
.++||+++. ...+..+.++||..+
T Consensus 83 ~~~~~~Vl~-~~~~~~~~i~dp~~~ 106 (126)
T cd02425 83 NNNHFVVLE-KIKKNKVTIVDPAIG 106 (126)
T ss_pred cCCcEEEEE-EEECCEEEEEcCCCC
Confidence 367998876 456778899999665
No 23
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.37 E-value=55 Score=23.82 Aligned_cols=28 Identities=14% Similarity=0.228 Sum_probs=24.4
Q ss_pred cCCCcCCCCCCCchHHHHHHHHHHhcCCC
Q 032006 95 KDVPQQEPGSGDCGVFMLMFTMYLMFGLK 123 (149)
Q Consensus 95 ~~~p~Q~n~s~dCGvfvl~~~~~~~~~~~ 123 (149)
..+|.-.++ .+|+-|++-.++.++.+..
T Consensus 131 ISVPke~~~-lnc~~fvaGIiea~L~~ag 158 (191)
T KOG3315|consen 131 ISVPKENGT-LNCAAFVAGIIEAVLDNAG 158 (191)
T ss_pred eecccccCc-ccHHHHHHHHHHHHHHhCC
Confidence 567999999 9999999999999987654
No 24
>PRK13193 pyrrolidone-carboxylate peptidase; Provisional
Probab=28.13 E-value=34 Score=25.50 Aligned_cols=17 Identities=24% Similarity=0.481 Sum_probs=13.9
Q ss_pred CCCchHHHHHHHHHHhc
Q 032006 104 SGDCGVFMLMFTMYLMF 120 (149)
Q Consensus 104 s~dCGvfvl~~~~~~~~ 120 (149)
|+|.|-|+|.++.+.+.
T Consensus 134 S~~AG~yvCN~vyY~sl 150 (209)
T PRK13193 134 SLSAGSYLCNNAMYIII 150 (209)
T ss_pred ecCCccchhHHHHHHHH
Confidence 59999999988877643
No 25
>PF15644 Tox-PL: Papain fold toxin 1; PDB: 3B21_A.
Probab=27.42 E-value=75 Score=20.83 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=18.8
Q ss_pred EEEEeeecCC-CeEEEEEEEcCCCeEEEEcCCCC
Q 032006 17 MIFIPVNLGG-DHWVLALADLRARRMRIYDSLVT 49 (149)
Q Consensus 17 ~I~iPin~~~-~HW~l~vvd~~~~~i~~~DSl~~ 49 (149)
.|.+..--++ .|++.++ +. ++.|.++|+-.+
T Consensus 77 ~v~~~~~gg~~gHa~nvv-~~-~G~i~~~D~Q~G 108 (111)
T PF15644_consen 77 IVSVSWKGGGPGHAFNVV-NQ-NGKIVFLDPQSG 108 (111)
T ss_dssp EEEETT-----TTEEEEE-EE--SSEEEEBTTTT
T ss_pred EEEEEEeccccceEEEEE-eC-CCeEEEEeCCCC
Confidence 4455554444 8988888 44 455999999765
No 26
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.25 E-value=64 Score=20.52 Aligned_cols=20 Identities=10% Similarity=0.321 Sum_probs=11.8
Q ss_pred hhhhccccCEEEEeeecCCCe
Q 032006 8 MSKLFTDVDMIFIPVNLGGDH 28 (149)
Q Consensus 8 ~~~~~~~~d~I~iPin~~~~H 28 (149)
+...+.+.|.|+++.+. -+|
T Consensus 42 l~~~i~~aD~VIv~t~~-vsH 61 (97)
T PF10087_consen 42 LPSKIKKADLVIVFTDY-VSH 61 (97)
T ss_pred HHHhcCCCCEEEEEeCC-cCh
Confidence 45556666666666666 443
No 27
>PF13280 WYL: WYL domain
Probab=26.00 E-value=96 Score=21.05 Aligned_cols=24 Identities=21% Similarity=0.257 Sum_probs=18.7
Q ss_pred CEEEEeeec--CCCeEEEEEEEcCCC
Q 032006 16 DMIFIPVNL--GGDHWVLALADLRAR 39 (149)
Q Consensus 16 d~I~iPin~--~~~HW~l~vvd~~~~ 39 (149)
...+.|+.. .+++|+|++.+...+
T Consensus 29 ~~~v~P~~l~~~~~~~Yl~~~~~~~~ 54 (172)
T PF13280_consen 29 ERRVDPYRLYYYNGRWYLIAYDRERE 54 (172)
T ss_pred EEEEEEEEEEEECCEEEEEEEecccc
Confidence 567778777 388999999987654
No 28
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=25.22 E-value=77 Score=20.56 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=22.0
Q ss_pred cCEEEEeeec--CCCeEEEEEEEcCCCeEEEEcCC
Q 032006 15 VDMIFIPVNL--GGDHWVLALADLRARRMRIYDSL 47 (149)
Q Consensus 15 ~d~I~iPin~--~~~HW~l~vvd~~~~~i~~~DSl 47 (149)
-+.+-+|+-. .+.||+++. ...+..+.++|+.
T Consensus 65 l~~~~lP~i~~~~~g~~~Vl~-~~~~~~~~i~dp~ 98 (124)
T cd02421 65 IPTLLLPAILLLKNGRACVLL-GVDDGHARILDPE 98 (124)
T ss_pred CCcccCCEEEEEcCCCEEEEE-EecCCeEEEEccC
Confidence 3445566665 467887776 4556779999997
No 29
>PRK13194 pyrrolidone-carboxylate peptidase; Provisional
Probab=24.90 E-value=40 Score=25.11 Aligned_cols=16 Identities=31% Similarity=0.638 Sum_probs=13.4
Q ss_pred CCCchHHHHHHHHHHh
Q 032006 104 SGDCGVFMLMFTMYLM 119 (149)
Q Consensus 104 s~dCGvfvl~~~~~~~ 119 (149)
|+|.|=|+|.|+.+.+
T Consensus 134 S~dAG~ylCN~iyY~s 149 (208)
T PRK13194 134 SYSAGTYLCNYVMYLT 149 (208)
T ss_pred eCCCccchhHHHHHHH
Confidence 6999999998887654
No 30
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=24.66 E-value=1.2e+02 Score=19.73 Aligned_cols=24 Identities=25% Similarity=0.391 Sum_probs=18.4
Q ss_pred CCCeEEEEEEEcCCCeEEEEcCCCC
Q 032006 25 GGDHWVLALADLRARRMRIYDSLVT 49 (149)
Q Consensus 25 ~~~HW~l~vvd~~~~~i~~~DSl~~ 49 (149)
+.+||+++. ...+..+.++||-.+
T Consensus 82 ~~g~~~Vl~-~~~~~~~~i~dp~~~ 105 (127)
T cd02419 82 DMNHFVVLK-KVSRRRIVIHDPALG 105 (127)
T ss_pred CCCEEEEEE-EEcCCEEEEECCccC
Confidence 467998876 457788999999543
No 31
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=22.84 E-value=2.8e+02 Score=20.77 Aligned_cols=42 Identities=14% Similarity=0.238 Sum_probs=29.8
Q ss_pred hhhhhccccCEEEEeeec------CCCeEEEEEEEcCCCeEEEEcCCCC
Q 032006 7 LMSKLFTDVDMIFIPVNL------GGDHWVLALADLRARRMRIYDSLVT 49 (149)
Q Consensus 7 ~~~~~~~~~d~I~iPin~------~~~HW~l~vvd~~~~~i~~~DSl~~ 49 (149)
.+++.+..-..+++=|.. ..-||+++. ......|++=||--.
T Consensus 121 ~l~~~l~~G~~~lvLIS~y~~~g~k~PHWV~v~-g~d~~~vyihDP~~d 168 (207)
T PF11814_consen 121 DLRAALAAGAIVLVLISTYRMDGKKVPHWVVVT-GVDDDFVYIHDPDVD 168 (207)
T ss_pred HHHHHHHCCCEEEEEEeecccCCCCCCeEEEEE-EecCCEEEEeCCCCC
Confidence 455666666665555533 256999987 667799999999877
No 32
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=22.64 E-value=1.1e+02 Score=20.48 Aligned_cols=18 Identities=33% Similarity=0.554 Sum_probs=14.6
Q ss_pred CCchHHHHHHHHHHhcCC
Q 032006 105 GDCGVFMLMFTMYLMFGL 122 (149)
Q Consensus 105 ~dCGvfvl~~~~~~~~~~ 122 (149)
..||+.++.++...+.|.
T Consensus 8 G~CG~H~i~aI~n~m~~~ 25 (108)
T PF05412_consen 8 GSCGWHCIAAIMNHMMGG 25 (108)
T ss_pred CchHHHHHHHHHHHhhcc
Confidence 789999999987766553
No 33
>PF02099 Josephin: Josephin; InterPro: IPR006155 Human genes containing triplet repeats can markedly expand in length, leading to neuropsychiatric disease. Expansion of triplet repeats explains the phenomenon of anticipation, i.e. the increasing severity or earlier age of onset in successive generations in a pedigree []. A novel gene containing CAG repeats has been identified and mapped to chromosome 14q32.1, the genetic locus for Machado-Joseph disease (MJD). Normally, the gene contains 13-36 CAG repeats, but most clinically diagnosed patients and all affected members of a family with the clinical and pathological diagnosis of MJD show expansion of the repeat number, from 68-79 []. Similar abnormalities in related genes may give rise to diseases similar to MJD. MJD is a neurodegenerative disorder characterised by cerebellar ataxia, pyramidal and extra-pyramidal signs, peripheral nerve palsy, external ophtalmoplegia, facial and lingual fasciculation and bulging. The disease is autosomal dominant, with late onset of symptoms, generally after the fourth decade.; GO: 0008242 omega peptidase activity; PDB: 3O65_G 1YZB_A 2JRI_A 2DOS_A 2AGA_A.
Probab=22.49 E-value=1.4e+02 Score=21.11 Aligned_cols=29 Identities=21% Similarity=0.127 Sum_probs=22.1
Q ss_pred EEeeecCCCeEEEEEEEcCCCeEEEEcCCCCC
Q 032006 19 FIPVNLGGDHWVLALADLRARRMRIYDSLVTF 50 (149)
Q Consensus 19 ~iPin~~~~HW~l~vvd~~~~~i~~~DSl~~~ 50 (149)
=+-+|. ..||+.+- .-.+..+-+||+-..
T Consensus 101 gfI~N~-~~HWf~iR--ki~~~wyNLDS~l~~ 129 (157)
T PF02099_consen 101 GFICNL-SRHWFAIR--KIGGQWYNLDSKLKE 129 (157)
T ss_dssp EEEEEC-TTEEEEEE--EETTEEEEECTTTSS
T ss_pred EEEecc-CcceEEEE--eeCCeeEeccCCCCC
Confidence 345666 99999874 237899999999883
No 34
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=21.50 E-value=67 Score=20.69 Aligned_cols=14 Identities=29% Similarity=0.923 Sum_probs=10.7
Q ss_pred CCchHHHHHHHHHH
Q 032006 105 GDCGVFMLMFTMYL 118 (149)
Q Consensus 105 ~dCGvfvl~~~~~~ 118 (149)
.=||+|+|..+.++
T Consensus 39 vI~~iFil~Vilwf 52 (94)
T PF05393_consen 39 VICGIFILLVILWF 52 (94)
T ss_pred HHHHHHHHHHHHHH
Confidence 67999998766555
Done!