Query psy12908
Match_columns 148
No_of_seqs 176 out of 1191
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 22:50:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12908hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0778|consensus 100.0 1.4E-41 3.1E-46 282.8 5.2 124 19-147 359-511 (511)
2 PLN03189 Protease specific for 100.0 3.8E-37 8.3E-42 254.7 9.2 127 17-146 329-489 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 8.9E-36 1.9E-40 246.3 1.7 122 20-146 423-569 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.9 8.2E-28 1.8E-32 182.0 5.8 129 12-141 23-208 (216)
5 KOG3246|consensus 99.8 5.8E-20 1.3E-24 138.4 8.4 96 46-141 81-207 (223)
6 KOG0779|consensus 98.9 4.1E-10 9E-15 97.6 0.7 126 12-139 389-582 (595)
7 PF03290 Peptidase_C57: Vaccin 98.0 1.4E-05 3E-10 65.5 6.1 69 52-121 230-347 (423)
8 PF00770 Peptidase_C5: Adenovi 97.2 0.00036 7.8E-09 51.6 3.2 62 58-119 22-117 (183)
9 PRK14848 deubiquitinase SseL; 96.8 0.0035 7.5E-08 49.2 6.1 67 53-120 188-277 (317)
10 PRK11836 deubiquitinase; Provi 96.6 0.0077 1.7E-07 48.3 6.8 68 51-119 217-327 (403)
11 KOG0778|consensus 96.1 0.0041 8.9E-08 53.2 2.9 38 1-39 385-422 (511)
12 PF03421 YopJ: YopJ Serine/Thr 91.1 0.95 2E-05 33.8 6.3 67 54-120 72-164 (177)
13 COG5160 ULP1 Protease, Ulp1 fa 86.1 0.63 1.4E-05 40.2 2.7 41 1-42 448-488 (578)
14 PLN03189 Protease specific for 84.8 0.77 1.7E-05 39.4 2.6 40 1-41 364-403 (490)
15 PRK15371 effector protein YopJ 68.5 16 0.00035 29.4 5.6 63 58-120 101-187 (287)
16 PF02902 Peptidase_C48: Ulp1 p 68.1 5.9 0.00013 29.3 3.0 37 2-38 79-115 (216)
17 PF12252 SidE: Dot/Icm substra 58.5 16 0.00035 34.6 4.4 56 56-112 48-125 (1439)
18 cd02424 Peptidase_C39E A sub-f 54.1 23 0.00049 24.2 3.7 24 98-121 5-28 (129)
19 PF03412 Peptidase_C39: Peptid 45.6 20 0.00042 24.3 2.3 26 96-122 4-29 (131)
20 KOG4110|consensus 44.7 21 0.00046 24.7 2.2 22 95-116 26-47 (120)
21 COG2260 Predicted Zn-ribbon RN 39.2 13 0.00028 22.8 0.5 38 103-142 9-53 (59)
22 cd02423 Peptidase_C39G A sub-f 32.1 98 0.0021 20.5 4.1 22 97-118 4-25 (129)
23 KOG3315|consensus 31.7 48 0.001 24.9 2.5 28 95-122 132-159 (191)
24 PRK13130 H/ACA RNA-protein com 26.3 35 0.00076 20.6 0.9 38 103-142 9-53 (56)
25 PF15644 Tox-PL: Papain fold t 24.5 75 0.0016 21.4 2.4 32 55-88 77-109 (111)
26 PHA02130 hypothetical protein 23.9 5.1 0.00011 25.1 -3.1 37 36-73 14-51 (81)
27 cd02549 Peptidase_C39A A sub-f 22.7 1.4E+02 0.003 20.1 3.6 23 64-87 93-116 (141)
28 PF09907 DUF2136: Uncharacteri 21.3 78 0.0017 20.2 1.8 44 36-81 19-63 (76)
29 cd04198 eIF-2B_gamma_N The N-t 20.8 17 0.00036 27.3 -1.6 44 68-111 158-210 (214)
No 1
>KOG0778|consensus
Probab=100.00 E-value=1.4e-41 Score=282.84 Aligned_cols=124 Identities=45% Similarity=0.835 Sum_probs=115.4
Q ss_pred EEEEEeeeecchhhhccCCCCCCCCCccccCccCCCEEEEeEEecCceEEEEEEcccCCeeEEecCCCCCCccccc----
Q psy12908 19 HWCLTTIDFRKKCLTYYDSMAGPDRGCLNVDLFSYDILLVPIHVQKIHWCLATIDFRKKCLTYYDSMAGPDRGCLN---- 94 (148)
Q Consensus 19 ~~~~~tff~~~L~~~~~~~~~~~~~w~~~~~l~~~~~i~iPin~~~~HW~l~~v~~~~~~i~~~DSl~~~~~~~~~---- 94 (148)
.++||||||++|.. .||++|+|||++++||++|+|++|||. +.||+|+|||.++++|.|||||++......+
T Consensus 359 ~h~FnTFFy~kL~~---~gy~~VkRWTk~v~if~~d~i~vPIH~-~vHW~l~vid~r~k~i~y~DS~~~~~nr~~~aL~~ 434 (511)
T KOG0778|consen 359 VHAFNTFFYTKLVG---RGYAGVKRWTKKVDIFDKDIIFVPIHL-GVHWCLAVIDLREKTIEYYDSLGGGPNRICDALAK 434 (511)
T ss_pred EEEEechhhhhhhh---cchHHHHhHhhccCccccceeEeeeec-CceEEEEEEEcccceEEEeeccCCCCcchHHHHHH
Confidence 34699999999998 899999999999999999999999999 9999999999999999999999965332111
Q ss_pred -------------------------cCCCCCCCCCchHHHHHHHHHHhcCCCCCCCCCCChHHHHHHHHHHHHhCCcC
Q psy12908 95 -------------------------DVPQQQNSSDCGVFTSTFAEYLSRNADIFKIKQKDMPYYRKKMMAEILSKKLL 147 (148)
Q Consensus 95 -------------------------~~p~Q~n~~DCGvfv~~~~~~~~~~~~~~~~~~~~~~~~R~~i~~~ll~~~l~ 147 (148)
++|||.||+|||+|+|+|+++++.|.|+ +|+|.||++||++|++||++++|+
T Consensus 435 Yl~~E~~~k~~~~~d~s~w~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~-~ftq~dmp~fR~~m~~eI~~~~l~ 511 (511)
T KOG0778|consen 435 YLQDESRDKSKKDFDVSGWTIEFVQNIPQQRNGSDCGMFVCKYADYISRDVPL-TFTQQDMPYFRKKMAKEILHLKLL 511 (511)
T ss_pred HHHHHHhhhhcCCCCccchhhhhhhccccccCCCccceEEeeechhhccCCCc-ccChhhhHHHHHHHHHHHHhhhcC
Confidence 8999999999999999999999999999 999999999999999999999985
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=3.8e-37 Score=254.73 Aligned_cols=127 Identities=33% Similarity=0.567 Sum_probs=113.5
Q ss_pred ceEEEEEeeeecchhhhc-cCCCCCCCCCccc----cCccCCCEEEEeEEecCceEEEEEEcccCCeeEEecCCCCCCcc
Q psy12908 17 KIHWCLTTIDFRKKCLTY-YDSMAGPDRGCLN----VDLFSYDILLVPIHVQKIHWCLATIDFRKKCLTYYDSMAGPDRG 91 (148)
Q Consensus 17 ~~~~~~~tff~~~L~~~~-~~~~~~~~~w~~~----~~l~~~~~i~iPin~~~~HW~l~~v~~~~~~i~~~DSl~~~~~~ 91 (148)
+.| +||||||++|...+ ..+|++|+||+++ .+++++++||||||. +.||+|+|||+++++|.|||||++.+..
T Consensus 329 k~h-~FNTFFytkL~~~~~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~-n~HWsLaVId~k~k~I~yyDSLgg~~~~ 406 (490)
T PLN03189 329 KCH-FFNTFFYKKLVSGKSGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQ-EIHWTLAVINKKDQKFQYLDSLKGRDPK 406 (490)
T ss_pred ceE-EEehHHHHHHhhcCCcCChHHHHHHhhhcccccccccCceEEeeeec-CCeeEEEEEEcCCCeEEEEeCCCCCCHH
Confidence 455 59999999999852 3479999999974 468999999999999 8999999999999999999999987653
Q ss_pred cc-----------------------------ccCCCCCCCCCchHHHHHHHHHHhcCCCCCCCCCCChHHHHHHHHHHHH
Q psy12908 92 CL-----------------------------NDVPQQQNSSDCGVFTSTFAEYLSRNADIFKIKQKDMPYYRKKMMAEIL 142 (148)
Q Consensus 92 ~~-----------------------------~~~p~Q~n~~DCGvfv~~~~~~~~~~~~~~~~~~~~~~~~R~~i~~~ll 142 (148)
.+ .++|||.||+|||||||+||++++.|.++ +|+|+||+.+|++|++||+
T Consensus 407 vL~~L~rYL~~E~kdK~g~d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~L-tFSQeDMp~fRrRma~EIl 485 (490)
T PLN03189 407 ILDALAKYYVDEVKDKSEKDIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGL-CFGQEHMPYFRLRTAKEIL 485 (490)
T ss_pred HHHHHHHHHHHHHhhhcCCCcchhcceeccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCC-CcChhhhHHHHHHHHHHHH
Confidence 21 17899999999999999999999999999 8999999999999999999
Q ss_pred hCCc
Q psy12908 143 SKKL 146 (148)
Q Consensus 143 ~~~l 146 (148)
..++
T Consensus 486 ~~r~ 489 (490)
T PLN03189 486 RLKA 489 (490)
T ss_pred Hhhc
Confidence 9875
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.9e-36 Score=246.28 Aligned_cols=122 Identities=34% Similarity=0.575 Sum_probs=115.2
Q ss_pred EEEEeeeecchhhhccCCCCCCCCCccccCccCCCEEEEeEEecCceEEEEEEcccCCeeEEecCCCCCCccccc-----
Q psy12908 20 WCLTTIDFRKKCLTYYDSMAGPDRGCLNVDLFSYDILLVPIHVQKIHWCLATIDFRKKCLTYYDSMAGPDRGCLN----- 94 (148)
Q Consensus 20 ~~~~tff~~~L~~~~~~~~~~~~~w~~~~~l~~~~~i~iPin~~~~HW~l~~v~~~~~~i~~~DSl~~~~~~~~~----- 94 (148)
++||||||++|.. .||++|+||+++++||++++|++|||. ..||+|++||.+.+.|.|||||++.+..+++
T Consensus 423 h~FnTFFYT~Lsr---rGy~gVrrW~kk~dif~~k~I~iPIni-~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y 498 (578)
T COG5160 423 HLFNTFFYTKLSR---RGYSGVRRWTKKTDIFSKKYIFIPINI-SYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSY 498 (578)
T ss_pred EEeehhhHHHHHH---HHhHHHHHHHhccCccccceEEEEecc-cceEEEEEeecCcceeEEecccccCcHHHHHHHHHH
Confidence 4699999999998 889999999999999999999999999 9999999999999999999999998765432
Q ss_pred --------------------cCCCCCCCCCchHHHHHHHHHHhcCCCCCCCCCCChHHHHHHHHHHHHhCCc
Q psy12908 95 --------------------DVPQQQNSSDCGVFTSTFAEYLSRNADIFKIKQKDMPYYRKKMMAEILSKKL 146 (148)
Q Consensus 95 --------------------~~p~Q~n~~DCGvfv~~~~~~~~~~~~~~~~~~~~~~~~R~~i~~~ll~~~l 146 (148)
++|||+||+|||||||+++++++.+.|. .|++.|++++|++|+++|+..++
T Consensus 499 ~ldE~k~~~~k~~~~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~-~f~~nd~~r~Rk~m~h~i~~~qi 569 (578)
T COG5160 499 LLDEYKIQHDKDPQIKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPE-QFSKNDRPRARKNMAHTIKDLQI 569 (578)
T ss_pred HHHHHhcccCCchhhhhhcCCCCCCCCCCccceEEEEeeeecccCChh-hcCccchHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999 99999999999999999998775
No 4
>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=99.94 E-value=8.2e-28 Score=181.97 Aligned_cols=129 Identities=27% Similarity=0.513 Sum_probs=103.0
Q ss_pred ccccCceEEEEEeeeecchhhhc-----------------cCCCCCCCCCcccc---CccCCCEEEEeEEecCceEEEEE
Q psy12908 12 PIHVQKIHWCLTTIDFRKKCLTY-----------------YDSMAGPDRGCLNV---DLFSYDILLVPIHVQKIHWCLAT 71 (148)
Q Consensus 12 p~~~~~~~~~~~tff~~~L~~~~-----------------~~~~~~~~~w~~~~---~l~~~~~i~iPin~~~~HW~l~~ 71 (148)
+...+. ..+++|+|+.++.... .+.+.++.+|.+.. ++++++++++|+|.+++||+|++
T Consensus 23 ~~~~~~-~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~i~iPin~~~~HW~l~v 101 (216)
T PF02902_consen 23 NKNSKR-VHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKKNLFDKDYIFIPININNNHWVLLV 101 (216)
T ss_dssp HHTSTT-EEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTSTGGGSSEEEEEEEETTTEEEEEE
T ss_pred ccCCCc-EEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhccccccccccCEEEEEEechhhccceeE
Confidence 334444 4569999999999210 13457888999876 89999999999999999999999
Q ss_pred EcccCCeeEEecCCCCCCc-----ccc-----------------------------ccCCCCCCCCCchHHHHHHHHHHh
Q psy12908 72 IDFRKKCLTYYDSMAGPDR-----GCL-----------------------------NDVPQQQNSSDCGVFTSTFAEYLS 117 (148)
Q Consensus 72 v~~~~~~i~~~DSl~~~~~-----~~~-----------------------------~~~p~Q~n~~DCGvfv~~~~~~~~ 117 (148)
|+++.+++.+|||+++... ..+ .++|||+|++|||+|||+|+++++
T Consensus 102 i~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~pqQ~n~~dCGv~vl~~~~~~~ 181 (216)
T PF02902_consen 102 IDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDPDKSPFKIVRPPNVPQQPNGYDCGVYVLKFMECLL 181 (216)
T ss_dssp EETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTCEEEEECTS-SSSSSSCHHHHHHHHHHHHH
T ss_pred EcccccEEEEEeccccccccccchhhhhhhhhhhhhccccccccccccceeeecccccccCCCCCCCcHHHHHHHHHHHH
Confidence 9999999999999999877 100 078999999999999999999999
Q ss_pred cCCCCCC---CCCCChHHHHHHHHHHH
Q psy12908 118 RNADIFK---IKQKDMPYYRKKMMAEI 141 (148)
Q Consensus 118 ~~~~~~~---~~~~~~~~~R~~i~~~l 141 (148)
.|.+... ++++++..+|++++.++
T Consensus 182 ~~~~~~~~~~l~~~~i~~~r~~~a~~~ 208 (216)
T PF02902_consen 182 EGPSFDFSQELTEEDIKNFRKKLAVDL 208 (216)
T ss_dssp CTHHSTGCCSBTGHHHHHHHHHHHH--
T ss_pred hCCCCcccccCCHHHHHHHHHHHHhhc
Confidence 9987732 79999999999999654
No 5
>KOG3246|consensus
Probab=99.81 E-value=5.8e-20 Score=138.36 Aligned_cols=96 Identities=23% Similarity=0.282 Sum_probs=71.8
Q ss_pred cccCccCCCEEEEeEEec--------CceEEEEEEcccCCeeEEecCCCCCCccccc--------------------cCC
Q psy12908 46 LNVDLFSYDILLVPIHVQ--------KIHWCLATIDFRKKCLTYYDSMAGPDRGCLN--------------------DVP 97 (148)
Q Consensus 46 ~~~~l~~~~~i~iPin~~--------~~HW~l~~v~~~~~~i~~~DSl~~~~~~~~~--------------------~~p 97 (148)
...++.++++|++|||.+ ++||+|+|+..++++.++|||+.+.+....+ .+|
T Consensus 81 ~pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~~~~~~~~ 160 (223)
T KOG3246|consen 81 DPLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAKRVECKCL 160 (223)
T ss_pred ChhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHHHHHHHHHHhhhhhhcccccCh
Confidence 445889999999999983 5799999999999999999999998765321 789
Q ss_pred CCCCCCCchHHHHHHHHHHhcCC---CCCCCCCCChHHHHHHHHHHH
Q psy12908 98 QQQNSSDCGVFTSTFAEYLSRNA---DIFKIKQKDMPYYRKKMMAEI 141 (148)
Q Consensus 98 ~Q~n~~DCGvfv~~~~~~~~~~~---~~~~~~~~~~~~~R~~i~~~l 141 (148)
||.||||||+|||.+.+.++... +..+-.+.+...+|+++-.+|
T Consensus 161 qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~l 207 (223)
T KOG3246|consen 161 QQQNGYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREEL 207 (223)
T ss_pred hhhcCCchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHHH
Confidence 99999999999999877665432 221334445544444444333
No 6
>KOG0779|consensus
Probab=98.88 E-value=4.1e-10 Score=97.62 Aligned_cols=126 Identities=25% Similarity=0.324 Sum_probs=88.8
Q ss_pred ccccCceEEEEEeeeecchhhhc----cC-----CCCCCCCCccccCccCCCEEEEeEEecCceEEEEEEcccCCe----
Q psy12908 12 PIHVQKIHWCLTTIDFRKKCLTY----YD-----SMAGPDRGCLNVDLFSYDILLVPIHVQKIHWCLATIDFRKKC---- 78 (148)
Q Consensus 12 p~~~~~~~~~~~tff~~~L~~~~----~~-----~~~~~~~w~~~~~l~~~~~i~iPin~~~~HW~l~~v~~~~~~---- 78 (148)
.......|+ +++|||..+..+- .+ ....+++|++..|++.++++++|+|. ..||.+++++.....
T Consensus 389 ~~~s~~~h~-f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~~~d~~~k~yi~~P~~E-~~hw~laiic~p~~e~es~ 466 (595)
T KOG0779|consen 389 KELSNDRHI-FSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTRHFDLFNKDYVFVPTHE-RFHWKLAIICNPDLETETP 466 (595)
T ss_pred cccCcchhh-hhhHHHhhhhhhhhhhhhhhhhccccCceeeeeeccccccceeEEecCch-HhhhhccccccCccccCcc
Confidence 344444554 9999999988752 11 35678899999999999999999999 999999988765321
Q ss_pred --eE----------------EecCCCCCCcc--cc---c--------------------cCCCCCCCCCchHHHHHHHHH
Q psy12908 79 --LT----------------YYDSMAGPDRG--CL---N--------------------DVPQQQNSSDCGVFTSTFAEY 115 (148)
Q Consensus 79 --i~----------------~~DSl~~~~~~--~~---~--------------------~~p~Q~n~~DCGvfv~~~~~~ 115 (148)
.. +.|+|...... .. . ..|||.|..|||+|++.|++.
T Consensus 467 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~ 546 (595)
T KOG0779|consen 467 RPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVER 546 (595)
T ss_pred ccchhhhhhccccccchhhhhhhhhhhcccccCcccccccccccccccccCcccccccccccCccCcccchhhHHHHHHH
Confidence 11 12222221110 00 0 348999999999999999999
Q ss_pred HhcCCCC------------CCCCCCChHHHHHHHHH
Q psy12908 116 LSRNADI------------FKIKQKDMPYYRKKMMA 139 (148)
Q Consensus 116 ~~~~~~~------------~~~~~~~~~~~R~~i~~ 139 (148)
+..+.+- .+|.+.++..+|..+-.
T Consensus 547 f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~ 582 (595)
T KOG0779|consen 547 FIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRN 582 (595)
T ss_pred hhhChhhhcccccccccccccCCchHHhhhhhhhhc
Confidence 9877543 24677777788876653
No 7
>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=98.01 E-value=1.4e-05 Score=65.49 Aligned_cols=69 Identities=22% Similarity=0.281 Sum_probs=55.9
Q ss_pred CCCEEEEeEEecCceEEEEEEcccCCeeEEecCCCCCCccccc-------------------------------------
Q psy12908 52 SYDILLVPIHVQKIHWCLATIDFRKKCLTYYDSMAGPDRGCLN------------------------------------- 94 (148)
Q Consensus 52 ~~~~i~iPin~~~~HW~l~~v~~~~~~i~~~DSl~~~~~~~~~------------------------------------- 94 (148)
++.++.+|.+- .+||.++++|.+++-+..|||.|....+.-.
T Consensus 230 ~~RyvmFgfcY-~~Hwkc~IfDk~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dIDVLfrfF 308 (423)
T PF03290_consen 230 KKRYVMFGFCY-MSHWKCCIFDKEKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDIDVLFRFF 308 (423)
T ss_pred cccEEEeeeee-hhcceEEEEeccccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchHHHHHHH
Confidence 57899999999 9999999999999999999999876432100
Q ss_pred ------------cCCCCCCCCCchHHHHHHHHHHhcCCC
Q psy12908 95 ------------DVPQQQNSSDCGVFTSTFAEYLSRNAD 121 (148)
Q Consensus 95 ------------~~p~Q~n~~DCGvfv~~~~~~~~~~~~ 121 (148)
----|-...+||+|++.||-.....+|
T Consensus 309 ~d~f~~~~gciNvevnQl~eseCGMF~~iFm~~c~~~pp 347 (423)
T PF03290_consen 309 EDSFGVKYGCINVEVNQLLESECGMFISIFMILCTLTPP 347 (423)
T ss_pred HhhcccceeEEEhhhhhhcccccchHHHHHHHHHHccCc
Confidence 223577889999999999987776655
No 8
>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=97.19 E-value=0.00036 Score=51.58 Aligned_cols=62 Identities=19% Similarity=0.346 Sum_probs=38.2
Q ss_pred EeEEe-----cCceEEEEEEcccCCeeEEecCCCCCCccccc-----------------------------cCCCCCCCC
Q psy12908 58 VPIHV-----QKIHWCLATIDFRKKCLTYYDSMAGPDRGCLN-----------------------------DVPQQQNSS 103 (148)
Q Consensus 58 iPin~-----~~~HW~l~~v~~~~~~i~~~DSl~~~~~~~~~-----------------------------~~p~Q~n~~ 103 (148)
..||. |+.||.....|+..++++.+|+.+=++.+-.+ +.-|=+++-
T Consensus 22 AIVNT~~retGGvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~qiY~FeYe~llrRSAL~~~~dRCv~LvkstqtVQ~p~Sa 101 (183)
T PF00770_consen 22 AIVNTGGRETGGVHWLAFAWDPRSRTFYMFDPFGFSDQKLKQIYQFEYEGLLRRSALSSTPDRCVTLVKSTQTVQCPCSA 101 (183)
T ss_dssp EEEESS-TTT--S-EEEEEEETTTTEEEEE-TT---HHHHHHHH----HHHHHHHHHHH-TTSEEEEEEE-EE-S-TT--
T ss_pred EEEecCCcccCceeEEEEEecCCcceEEEeCCCCCCHHHHHHHHhhhHHHHHHHHhhcCCCCceEEEEeccceeeccCch
Confidence 34566 68999999999999999999999976543111 233335788
Q ss_pred CchHHHHHHHHHHhcC
Q psy12908 104 DCGVFTSTFAEYLSRN 119 (148)
Q Consensus 104 DCGvfv~~~~~~~~~~ 119 (148)
-||.|.|.|..++..-
T Consensus 102 aCGLFC~lFL~aF~~~ 117 (183)
T PF00770_consen 102 ACGLFCCLFLHAFVHY 117 (183)
T ss_dssp -HHHHHHHHHHHHHH-
T ss_pred hHHHHHHHHHHHHHhC
Confidence 9999999999988754
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=96.84 E-value=0.0035 Score=49.21 Aligned_cols=67 Identities=18% Similarity=0.230 Sum_probs=42.2
Q ss_pred CCEEEEeEEecCceEEEEEEccc--CCeeEEecCCCCCCccccc--------------------cCCCCCC-CCCchHHH
Q psy12908 53 YDILLVPIHVQKIHWCLATIDFR--KKCLTYYDSMAGPDRGCLN--------------------DVPQQQN-SSDCGVFT 109 (148)
Q Consensus 53 ~~~i~iPin~~~~HW~l~~v~~~--~~~i~~~DSl~~~~~~~~~--------------------~~p~Q~n-~~DCGvfv 109 (148)
+..-++|||. ++||.|+++-.- +.+-.+|.|++.-.....+ ..-.|.| ...||.||
T Consensus 188 ~~nevF~INt-g~HWil~~~~Ki~~kiKC~iFNs~~~l~eNs~~~ii~~ak~ag~~~e~di~fIe~nLQqnVpngCGlFv 266 (317)
T PRK14848 188 SHNEVFLINT-GDHWLLCLFYKLAEKIKCLIFNTYYDLNENTKQEIIEAAKIAGISENEDVNFIETNLQNNVPNGCGLFC 266 (317)
T ss_pred CcceEEEecC-CCcEEEEEhHHhhhhceEEEeecHhhhhhhHHHHHHHHHHhhCcccCCceEEeehhhhhhCCCcchHHH
Confidence 3445599998 999999875321 2334556666543221100 3334444 56799999
Q ss_pred HHHHHHHhcCC
Q psy12908 110 STFAEYLSRNA 120 (148)
Q Consensus 110 ~~~~~~~~~~~ 120 (148)
|.+++.+..+.
T Consensus 267 ~~aIq~l~~~~ 277 (317)
T PRK14848 267 YHTIQLLSNAG 277 (317)
T ss_pred HHHHHHHHhcc
Confidence 99999887653
No 10
>PRK11836 deubiquitinase; Provisional
Probab=96.65 E-value=0.0077 Score=48.27 Aligned_cols=68 Identities=21% Similarity=0.399 Sum_probs=41.9
Q ss_pred cCCCEEEEeEEecCceEEEEEEcc--------cCCeeEEecCCCCCCcc---c--------------------cc-----
Q psy12908 51 FSYDILLVPIHVQKIHWCLATIDF--------RKKCLTYYDSMAGPDRG---C--------------------LN----- 94 (148)
Q Consensus 51 ~~~~~i~iPin~~~~HW~l~~v~~--------~~~~i~~~DSl~~~~~~---~--------------------~~----- 94 (148)
+-++.-++|||. ++||.|+++-. ++.+-.+|.|+..-... . .+
T Consensus 217 ~~k~~elFpINt-g~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~~~~~ik~~~~e 295 (403)
T PRK11836 217 WPKEVQLFPINT-GGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSLKRVINSFNSELMGEMSNNNIKVHLTE 295 (403)
T ss_pred CcccceEEEecC-CCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHHHHHHHhhhhhhhhhcchhhhcccccC
Confidence 346788899998 99999987521 22344556666543221 0 00
Q ss_pred ------cCCCCC-CCCCchHHHHHHHHHHhcC
Q psy12908 95 ------DVPQQQ-NSSDCGVFTSTFAEYLSRN 119 (148)
Q Consensus 95 ------~~p~Q~-n~~DCGvfv~~~~~~~~~~ 119 (148)
....|. =...||.|||+.+..++..
T Consensus 296 ~ei~fie~dLQq~vpngCGlFv~~a~Qe~i~q 327 (403)
T PRK11836 296 PEIIFLHADLQQYLSQSCGAFVCMAAQEVIEQ 327 (403)
T ss_pred CceEEEechhhhcCCCccceehHHHHHHHHHH
Confidence 333343 4678999999888754433
No 11
>KOG0778|consensus
Probab=96.15 E-value=0.0041 Score=53.22 Aligned_cols=38 Identities=55% Similarity=1.215 Sum_probs=34.2
Q ss_pred CCeeeeceEeeccccCceEEEEEeeeecchhhhccCCCC
Q psy12908 1 VDLFSYDILLVPIHVQKIHWCLTTIDFRKKCLTYYDSMA 39 (148)
Q Consensus 1 ~~~~~~d~~l~p~~~~~~~~~~~tff~~~L~~~~~~~~~ 39 (148)
||||++|+|++|+|. ++||++..+...+-...++++..
T Consensus 385 v~if~~d~i~vPIH~-~vHW~l~vid~r~k~i~y~DS~~ 422 (511)
T KOG0778|consen 385 VDIFDKDIIFVPIHL-GVHWCLAVIDLREKTIEYYDSLG 422 (511)
T ss_pred cCccccceeEeeeec-CceEEEEEEEcccceEEEeeccC
Confidence 799999999999999 79999999999888887777665
No 12
>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=91.05 E-value=0.95 Score=33.81 Aligned_cols=67 Identities=19% Similarity=0.263 Sum_probs=45.5
Q ss_pred CEEEEeEEecCceEEEEEEc-cc--CCeeEEecCCCCCCccc-c----------------------ccCCCCCCCCCchH
Q psy12908 54 DILLVPIHVQKIHWCLATID-FR--KKCLTYYDSMAGPDRGC-L----------------------NDVPQQQNSSDCGV 107 (148)
Q Consensus 54 ~~i~iPin~~~~HW~l~~v~-~~--~~~i~~~DSl~~~~~~~-~----------------------~~~p~Q~n~~DCGv 107 (148)
-..++|...++.|-+.+-|- .. +..+..++|-.-..... + -.+..|+..+|||+
T Consensus 72 ~R~Iv~~~~~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ie~diQkS~~dC~I 151 (177)
T PF03421_consen 72 WRAIVNLGGDGIHHVALDVRHTPNGKPSLIVFEPASFYGMKPALAGYTKLAEEARQKLLPNAKFAVIEMDIQKSPSDCGI 151 (177)
T ss_pred eEEEEeCCCCCCcEEEEEEeecCCCCceEEEEccccccCCcchhhhHHHHHHHHHhccCCCcEEEEEecccccCcCcchh
Confidence 35567766667777766554 22 34688888874322110 1 08899999999999
Q ss_pred HHHHHHHHHhcCC
Q psy12908 108 FTSTFAEYLSRNA 120 (148)
Q Consensus 108 fv~~~~~~~~~~~ 120 (148)
|.+.+|.......
T Consensus 152 FsLs~AkK~~~~~ 164 (177)
T PF03421_consen 152 FSLSLAKKMYKED 164 (177)
T ss_pred hHHHHHHHHhhcc
Confidence 9999998887543
No 13
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=86.13 E-value=0.63 Score=40.19 Aligned_cols=41 Identities=39% Similarity=0.794 Sum_probs=31.1
Q ss_pred CCeeeeceEeeccccCceEEEEEeeeecchhhhccCCCCCCC
Q psy12908 1 VDLFSYDILLVPIHVQKIHWCLTTIDFRKKCLTYYDSMAGPD 42 (148)
Q Consensus 1 ~~~~~~d~~l~p~~~~~~~~~~~tff~~~L~~~~~~~~~~~~ 42 (148)
||||+.|+|.+|+|. ..||++.-+.-++....++++.+.+.
T Consensus 448 ~dif~~k~I~iPIni-~~HW~l~II~~~~~~i~~~DSLan~~ 488 (578)
T COG5160 448 TDIFSKKYIFIPINI-SYHWFLAIIDNPKKNILYFDSLANTH 488 (578)
T ss_pred cCccccceEEEEecc-cceEEEEEeecCcceeEEecccccCc
Confidence 699999999999998 68998887776655555555544444
No 14
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=84.84 E-value=0.77 Score=39.42 Aligned_cols=40 Identities=38% Similarity=0.752 Sum_probs=30.0
Q ss_pred CCeeeeceEeeccccCceEEEEEeeeecchhhhccCCCCCC
Q psy12908 1 VDLFSYDILLVPIHVQKIHWCLTTIDFRKKCLTYYDSMAGP 41 (148)
Q Consensus 1 ~~~~~~d~~l~p~~~~~~~~~~~tff~~~L~~~~~~~~~~~ 41 (148)
+|+|++|+|++|+|. ..||++..+....-...++++..+.
T Consensus 364 v~Lfs~D~IFIPIh~-n~HWsLaVId~k~k~I~yyDSLgg~ 403 (490)
T PLN03189 364 YHLIDCDKIFVPIHQ-EIHWTLAVINKKDQKFQYLDSLKGR 403 (490)
T ss_pred cccccCceEEeeeec-CCeeEEEEEEcCCCeEEEEeCCCCC
Confidence 478999999999997 5899999887765555445554433
No 15
>PRK15371 effector protein YopJ; Provisional
Probab=68.50 E-value=16 Score=29.41 Aligned_cols=63 Identities=24% Similarity=0.392 Sum_probs=40.1
Q ss_pred EeEEecCceEEEEEEccc--CCeeEEecCCCCCCcc----------cc------------ccCCCCCCCCCchHHHHHHH
Q psy12908 58 VPIHVQKIHWCLATIDFR--KKCLTYYDSMAGPDRG----------CL------------NDVPQQQNSSDCGVFTSTFA 113 (148)
Q Consensus 58 iPin~~~~HW~l~~v~~~--~~~i~~~DSl~~~~~~----------~~------------~~~p~Q~n~~DCGvfv~~~~ 113 (148)
++...++.|-+.+-|-.. +.+|..++|-...... .+ -.+-.|+..+|||+|.+.+|
T Consensus 101 Vn~g~~~~H~vavDvr~~~Gk~SIIvlEPa~~~~~~~a~l~~rl~~~le~~~l~~~~~avie~d~QkS~~dC~mFSL~~A 180 (287)
T PRK15371 101 VNMGSGGIHFSVIDYKHIDGKTSLILFEPANFNSMGPAMLAIRTKTALEREQLPDCHFSMVEMDIQRSSSECGIFSLALA 180 (287)
T ss_pred EeCCCCcceEEEEEEeccCCCeEEEEECCccccccchHHHHHHHHHHHHhccCCCceEEEEecccccCcccchhhhHHHH
Confidence 333333456655544333 3468888887643111 01 16778999999999999999
Q ss_pred HHHhcCC
Q psy12908 114 EYLSRNA 120 (148)
Q Consensus 114 ~~~~~~~ 120 (148)
.......
T Consensus 181 kK~~~e~ 187 (287)
T PRK15371 181 KKLYLER 187 (287)
T ss_pred HHHhhhh
Confidence 8877654
No 16
>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=68.12 E-value=5.9 Score=29.28 Aligned_cols=37 Identities=41% Similarity=0.831 Sum_probs=27.2
Q ss_pred CeeeeceEeeccccCceEEEEEeeeecchhhhccCCC
Q psy12908 2 DLFSYDILLVPIHVQKIHWCLTTIDFRKKCLTYYDSM 38 (148)
Q Consensus 2 ~~~~~d~~l~p~~~~~~~~~~~tff~~~L~~~~~~~~ 38 (148)
++++.|.|++|.+.++.||++-....+.-....+++.
T Consensus 79 ~l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl 115 (216)
T PF02902_consen 79 NLFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSL 115 (216)
T ss_dssp TGGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TT
T ss_pred cccccCEEEEEEechhhccceeEEcccccEEEEEecc
Confidence 6789999999999867899888766665544334443
No 17
>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=58.54 E-value=16 Score=34.63 Aligned_cols=56 Identities=14% Similarity=0.315 Sum_probs=35.0
Q ss_pred EEEeEEec------CceEEEEEEcccCCeeEEecCCCCCCccccc-----cCC---------CC--CCCCCchHHHHHH
Q psy12908 56 LLVPIHVQ------KIHWCLATIDFRKKCLTYYDSMAGPDRGCLN-----DVP---------QQ--QNSSDCGVFTSTF 112 (148)
Q Consensus 56 i~iPin~~------~~HW~l~~v~~~~~~i~~~DSl~~~~~~~~~-----~~p---------~Q--~n~~DCGvfv~~~ 112 (148)
=|+||-.| ..||+.++- -.....+.||+|+...-...+ ..| -- -|.-=||.||-..
T Consensus 48 gfmpvltgv~p~~~sghwimlik-g~gn~y~lfdplg~~sg~~y~nil~~~lp~~~~lsvipn~~~ln~glcgywvas~ 125 (1439)
T PF12252_consen 48 GFMPVLTGVSPRQDSGHWIMLIK-GQGNQYYLFDPLGKTSGEGYQNILARQLPQGSTLSVIPNGPGLNMGLCGYWVASV 125 (1439)
T ss_pred CCceeecCcCCCCcCceeEEEEE-cCCCceEEeccccccccccHHHHHHHhCCCCCeeeeCCCCCCcCccchhhhhhhh
Confidence 35677542 689998874 456678999999976443211 222 21 1334699998753
No 18
>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=54.10 E-value=23 Score=24.16 Aligned_cols=24 Identities=17% Similarity=0.260 Sum_probs=17.3
Q ss_pred CCCCCCCchHHHHHHHHHHhcCCC
Q psy12908 98 QQQNSSDCGVFTSTFAEYLSRNAD 121 (148)
Q Consensus 98 ~Q~n~~DCGvfv~~~~~~~~~~~~ 121 (148)
.|.+..|||..++..+-....|.+
T Consensus 5 ~q~~~~dcgla~l~~i~~~~~g~~ 28 (129)
T cd02424 5 KQTDLNDCGIAVIQMLYNHYYKKK 28 (129)
T ss_pred EecCccchHHHHHHHHHHHhcCCC
Confidence 567778999999887766544443
No 19
>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=45.65 E-value=20 Score=24.29 Aligned_cols=26 Identities=23% Similarity=0.351 Sum_probs=14.9
Q ss_pred CCCCCCCCCchHHHHHHHHHHhcCCCC
Q psy12908 96 VPQQQNSSDCGVFTSTFAEYLSRNADI 122 (148)
Q Consensus 96 ~p~Q~n~~DCGvfv~~~~~~~~~~~~~ 122 (148)
+=.|.+..|||+-+++++... .|.+.
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~-~g~~~ 29 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKY-YGIPV 29 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHH-TT---
T ss_pred eEEeCCCCCHHHHHHHHHHHH-hCCCc
Confidence 346999999999999887666 45443
No 20
>KOG4110|consensus
Probab=44.71 E-value=21 Score=24.65 Aligned_cols=22 Identities=27% Similarity=0.659 Sum_probs=18.8
Q ss_pred cCCCCCCCCCchHHHHHHHHHH
Q psy12908 95 DVPQQQNSSDCGVFTSTFAEYL 116 (148)
Q Consensus 95 ~~p~Q~n~~DCGvfv~~~~~~~ 116 (148)
.+|.-..|+|||.|-..+++|.
T Consensus 26 ~~p~~~q~r~cg~FE~e~~eC~ 47 (120)
T KOG4110|consen 26 EQPYKHQGRDCGKFEKEWMECA 47 (120)
T ss_pred cCccccccccccHHHHHHHHHH
Confidence 5777778999999999988876
No 21
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.24 E-value=13 Score=22.75 Aligned_cols=38 Identities=16% Similarity=0.306 Sum_probs=24.1
Q ss_pred CCchHHHHHHHHHHhcC------CCCCCCCCCCh-HHHHHHHHHHHH
Q psy12908 103 SDCGVFTSTFAEYLSRN------ADIFKIKQKDM-PYYRKKMMAEIL 142 (148)
Q Consensus 103 ~DCGvfv~~~~~~~~~~------~~~~~~~~~~~-~~~R~~i~~~ll 142 (148)
-+||+|++. -.|=..| .|. .|+++|- .++|+.+..++.
T Consensus 9 ~~cg~YTLk-e~Cp~CG~~t~~~~Pp-rFSPeD~y~kYR~~lkk~~~ 53 (59)
T COG2260 9 PKCGRYTLK-EKCPVCGGDTKVPHPP-RFSPEDKYGKYRRELKKRLG 53 (59)
T ss_pred cCCCceeec-ccCCCCCCccccCCCC-CCCccchHHHHHHHHHHHhc
Confidence 359999998 2222223 244 7888775 678887776654
No 22
>cd02423 Peptidase_C39G 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=32.07 E-value=98 Score=20.50 Aligned_cols=22 Identities=14% Similarity=0.027 Sum_probs=16.0
Q ss_pred CCCCCCCCchHHHHHHHHHHhc
Q psy12908 97 PQQQNSSDCGVFTSTFAEYLSR 118 (148)
Q Consensus 97 p~Q~n~~DCGvfv~~~~~~~~~ 118 (148)
-.|.+..|||+..+.++.....
T Consensus 4 ~~q~~~~~~~l~~l~~~~~~~g 25 (129)
T cd02423 4 VRQSYDFSCGPAALATLLRYYG 25 (129)
T ss_pred eecCCCCChHHHHHHHHHHhcC
Confidence 3566777999998877655554
No 23
>KOG3315|consensus
Probab=31.73 E-value=48 Score=24.85 Aligned_cols=28 Identities=25% Similarity=0.534 Sum_probs=24.2
Q ss_pred cCCCCCCCCCchHHHHHHHHHHhcCCCC
Q psy12908 95 DVPQQQNSSDCGVFTSTFAEYLSRNADI 122 (148)
Q Consensus 95 ~~p~Q~n~~DCGvfv~~~~~~~~~~~~~ 122 (148)
.+|.-.|+.+|+.|+|-..+.++.+..+
T Consensus 132 SVPke~~~lnc~~fvaGIiea~L~~agf 159 (191)
T KOG3315|consen 132 SVPKENGTLNCAAFVAGIIEAVLDNAGF 159 (191)
T ss_pred ecccccCcccHHHHHHHHHHHHHHhCCC
Confidence 6899999999999999999988866543
No 24
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=26.27 E-value=35 Score=20.62 Aligned_cols=38 Identities=18% Similarity=0.291 Sum_probs=23.0
Q ss_pred CCchHHHHHHHHHHhcCC------CCCCCCCCCh-HHHHHHHHHHHH
Q psy12908 103 SDCGVFTSTFAEYLSRNA------DIFKIKQKDM-PYYRKKMMAEIL 142 (148)
Q Consensus 103 ~DCGvfv~~~~~~~~~~~------~~~~~~~~~~-~~~R~~i~~~ll 142 (148)
.+||+|++. ..+=.-|. |. .|+++|- .++|..+-.++.
T Consensus 9 ~~CgvYTLk-~~CP~CG~~t~~~~P~-rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 9 PKCGVYTLK-EICPVCGGKTKNPHPP-RFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred CCCCCEEcc-ccCcCCCCCCCCCCCC-CCCCCCccHHHHHHHHHHhh
Confidence 489999992 22222233 33 6887665 677877766553
No 25
>PF15644 Tox-PL: Papain fold toxin 1; PDB: 3B21_A.
Probab=24.47 E-value=75 Score=21.36 Aligned_cols=32 Identities=16% Similarity=0.101 Sum_probs=19.3
Q ss_pred EEEEeEEecC-ceEEEEEEcccCCeeEEecCCCCC
Q psy12908 55 ILLVPIHVQK-IHWCLATIDFRKKCLTYYDSMAGP 88 (148)
Q Consensus 55 ~i~iPin~~~-~HW~l~~v~~~~~~i~~~DSl~~~ 88 (148)
.|.++...++ .|++-++ ..+..|.++|+..+.
T Consensus 77 ~v~~~~~gg~~gHa~nvv--~~~G~i~~~D~Q~G~ 109 (111)
T PF15644_consen 77 IVSVSWKGGGPGHAFNVV--NQNGKIVFLDPQSGK 109 (111)
T ss_dssp EEEETT-----TTEEEEE--EE-SSEEEEBTTTTB
T ss_pred EEEEEEeccccceEEEEE--eCCCeEEEEeCCCCC
Confidence 3333333333 8999888 456669999998765
No 26
>PHA02130 hypothetical protein
Probab=23.89 E-value=5.1 Score=25.14 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=29.1
Q ss_pred CCCCCCCCCcc-ccCccCCCEEEEeEEecCceEEEEEEc
Q psy12908 36 DSMAGPDRGCL-NVDLFSYDILLVPIHVQKIHWCLATID 73 (148)
Q Consensus 36 ~~~~~~~~w~~-~~~l~~~~~i~iPin~~~~HW~l~~v~ 73 (148)
.++++++.|.. +.+-++.+++=||... ..||-|+-.+
T Consensus 14 ks~~sl~~wl~~~~dswdddil~ipfks-tv~w~lcp~~ 51 (81)
T PHA02130 14 KSWESLREWLDERFDSWDDDILSIPFKS-TVYWDLCPYA 51 (81)
T ss_pred HHHHHHHHHHHhcccccccchhcccccc-eeeeccCcch
Confidence 45677888875 5677788999999998 8999887543
No 27
>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=22.68 E-value=1.4e+02 Score=20.10 Aligned_cols=23 Identities=26% Similarity=0.198 Sum_probs=17.0
Q ss_pred CceEEEEE-EcccCCeeEEecCCCC
Q psy12908 64 KIHWCLAT-IDFRKKCLTYYDSMAG 87 (148)
Q Consensus 64 ~~HW~l~~-v~~~~~~i~~~DSl~~ 87 (148)
..||.+++ ++ .+..+.+.||..+
T Consensus 93 ~gH~vVv~g~~-~~~~~~i~DP~~~ 116 (141)
T cd02549 93 SGHAMVVIGYD-RKGNVYVNDPGGG 116 (141)
T ss_pred CCeEEEEEEEc-CCCCEEEECCCCC
Confidence 67998665 56 3667999999654
No 28
>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=21.31 E-value=78 Score=20.22 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=27.6
Q ss_pred CCCCCCCCCccccCccCCCEEEEeEEecCceEEE-EEEcccCCeeEE
Q psy12908 36 DSMAGPDRGCLNVDLFSYDILLVPIHVQKIHWCL-ATIDFRKKCLTY 81 (148)
Q Consensus 36 ~~~~~~~~w~~~~~l~~~~~i~iPin~~~~HW~l-~~v~~~~~~i~~ 81 (148)
.+.+.++.-..+.+.+..+.++|-|. +++..| +.|+.+.+.+++
T Consensus 19 ~~~~elk~~f~~ad~v~~~~~vFnI~--GN~yRlI~~I~f~~~~v~I 63 (76)
T PF09907_consen 19 KNPAELKQQFPSADIVKNNRVVFNIG--GNKYRLIAKIDFERQIVYI 63 (76)
T ss_pred CCHHHHHHHCcchhhhcCCEEEEEcC--CCcEEEEEEEEeCceEEEE
Confidence 33444555556667776677777554 566655 468988887665
No 29
>cd04198 eIF-2B_gamma_N The N-terminal domain of gamma subunit of the eIF-2B is a subfamily of glycosyltransferase 2. N-terminal domain of gamma subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta and epsilon. Subunit gamma shares sequence similarity with epsilon subunit, and with a family of bifunctional nucleotide-binding enzymes such as ADP-glucose pyrophosphorylase, suggesting that epsilon subunit may play roles in nucleotide binding activity. In yeast, eIF2B gamma enhances the activity of eIF2B-epsilon leading to the idea that these subunits form the catalytic subcomplex.
Probab=20.81 E-value=17 Score=27.25 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=28.2
Q ss_pred EEEEEcccCCeeEEecCCCCCCcc-ccc--------cCCCCCCCCCchHHHHH
Q psy12908 68 CLATIDFRKKCLTYYDSMAGPDRG-CLN--------DVPQQQNSSDCGVFTST 111 (148)
Q Consensus 68 ~l~~v~~~~~~i~~~DSl~~~~~~-~~~--------~~p~Q~n~~DCGvfv~~ 111 (148)
.++++|....++.+|+|..+.... .++ ++-.-+|-.||++|+|.
T Consensus 158 ~~~~~d~~~~~ll~~~~~~~~~~~~~~~~~~l~~~~~~~i~~~l~D~hiyi~~ 210 (214)
T cd04198 158 DVIGLDEKTQRLLFITSEEDLDEDLELRKSLLKRHPRVTITTKLLDAHVYIFK 210 (214)
T ss_pred ceEEEcCCCCEEEEECCHHHhhhhhhHHHHHHHhCCCEEEEcCcccceEEEEE
Confidence 466777777888888886432211 111 34456788999999874
Done!