Query 047525
Match_columns 340
No_of_seqs 174 out of 927
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 11:55:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047525.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047525hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0778 Protease, Ulp1 family 100.0 3.6E-43 7.8E-48 352.0 8.7 177 144-338 323-508 (511)
2 PLN03189 Protease specific for 100.0 1.4E-38 3.1E-43 316.7 12.1 176 144-337 293-486 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 3.4E-37 7.5E-42 305.7 5.6 173 143-337 385-566 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.9 7.3E-28 1.6E-32 217.5 6.7 169 153-335 1-208 (216)
5 KOG3246 Sentrin-specific cyste 99.9 4.5E-24 9.6E-29 192.9 10.0 165 145-334 23-206 (223)
6 KOG0779 Protease, Ulp1 family 99.1 9.3E-11 2E-15 122.6 5.9 156 141-311 355-545 (595)
7 PF03290 Peptidase_C57: Vaccin 95.6 0.025 5.4E-07 56.2 6.1 33 212-246 233-265 (423)
8 PRK11836 deubiquitinase; Provi 94.8 0.047 1E-06 52.6 5.2 42 203-249 215-264 (403)
9 PRK14848 deubiquitinase SseL; 94.3 0.067 1.4E-06 50.6 4.8 79 213-311 191-271 (317)
10 PF00770 Peptidase_C5: Adenovi 93.4 0.059 1.3E-06 48.3 2.5 85 217-311 24-112 (183)
11 PF03421 YopJ: YopJ Serine/Thr 78.5 7.7 0.00017 35.0 6.9 80 213-311 74-158 (177)
12 PRK15371 effector protein YopJ 67.6 15 0.00032 35.8 6.3 70 225-311 108-181 (287)
13 PF12252 SidE: Dot/Icm substra 22.1 1.4E+02 0.0029 34.4 4.9 39 213-252 48-91 (1439)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.6e-43 Score=352.03 Aligned_cols=177 Identities=23% Similarity=0.380 Sum_probs=156.5
Q ss_pred hhcccCCCCCccccCchhHHHHHHHHHHcC----CCCCCcceeeccccchhccccccCcc---ccccCCcCCCCceEEEE
Q 047525 144 FAYRKLKENQIFHNVVKKIISCYAEYLTGK----ESLKQDYETRNWFLPTLFGQIVANVS---GVSTIDRSDIEISIYVP 216 (340)
Q Consensus 144 ~~~~sL~pg~wLNd~vD~IInfYl~~L~~~----~~~~kv~~fnsfF~~~L~~~g~~~vk---k~~dlf~kd~~~~IfIP 216 (340)
-++++|.|+.||| |+||||||+||.++ +.+|++|+||||||++|...||++|+ ++++||++|+ ||||
T Consensus 323 ~dl~tl~~~~WLN---DevINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~~~gy~~VkRWTk~v~if~~d~---i~vP 396 (511)
T KOG0778|consen 323 KDLQTLRPGNWLN---DEVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLVGRGYAGVKRWTKKVDIFDKDI---IFVP 396 (511)
T ss_pred HHHhhccCccchh---HHHHHHHHHHHHhhccccCCCceEEEEechhhhhhhhcchHHHHhHhhccCccccce---eEee
Confidence 3579999999999 99999999999976 23788999999999999999999998 7799999996 9999
Q ss_pred eecCCCCceEEEEEEeCCCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCccccceeeCCCCcCCC
Q 047525 217 LYDGLAKHWYLAIMNIKDKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDILYPNNVPIQ 296 (340)
Q Consensus 217 IN~~~~~HW~L~VId~~~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i~~p~~vPqQ 296 (340)
||. +.||+|+|||.++++|.|||||++....... +|.+||..+. +.+ ....++++.|++....++|||
T Consensus 397 IH~--~vHW~l~vid~r~k~i~y~DS~~~~~nr~~~---aL~~Yl~~E~-~~k------~~~~~d~s~w~~~~~~~iP~Q 464 (511)
T KOG0778|consen 397 IHL--GVHWCLAVIDLREKTIEYYDSLGGGPNRICD---ALAKYLQDES-RDK------SKKDFDVSGWTIEFVQNIPQQ 464 (511)
T ss_pred eec--CceEEEEEEEcccceEEEeeccCCCCcchHH---HHHHHHHHHH-hhh------hcCCCCccchhhhhhhccccc
Confidence 999 6999999999999999999999977666656 8889998876 222 356788899999888899999
Q ss_pred CCCCchHHHHHHHccccccccCCCCC--CCCcccHHHHHHHhhh
Q 047525 297 PNGNDCGLYVMKFMETPCELLFPTYK--SLPNVDWSILAVVEDR 338 (340)
Q Consensus 297 ~N~~DCGVFVl~fae~~~~~l~~~F~--dip~iR~~i~~~~~~~ 338 (340)
.||+|||||+|+|+++.....+.+|+ |||.||.+|+.++.+.
T Consensus 465 ~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR~~m~~eI~~~ 508 (511)
T KOG0778|consen 465 RNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFRKKMAKEILHL 508 (511)
T ss_pred cCCCccceEEeeechhhccCCCcccChhhhHHHHHHHHHHHHhh
Confidence 99999999999999976566677887 9999999999988653
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.4e-38 Score=316.72 Aligned_cols=176 Identities=20% Similarity=0.285 Sum_probs=144.8
Q ss_pred hhcccCCCCCccccCchhHHHHHHHHHHcC----C-CCCCcceeeccccchhccc----cccCcc-----cc--ccCCcC
Q 047525 144 FAYRKLKENQIFHNVVKKIISCYAEYLTGK----E-SLKQDYETRNWFLPTLFGQ----IVANVS-----GV--STIDRS 207 (340)
Q Consensus 144 ~~~~sL~pg~wLNd~vD~IInfYl~~L~~~----~-~~~kv~~fnsfF~~~L~~~----g~~~vk-----k~--~dlf~k 207 (340)
.++.+|.||+||| |+||||||+||.++ + ..+++|+||||||++|... +|.+|+ ++ +++|++
T Consensus 293 ~DL~~L~Pg~WLN---DeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~kKigv~Lfs~ 369 (490)
T PLN03189 293 EILRCLKPGAWLN---DEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQKKLGYHLIDC 369 (490)
T ss_pred HHhhccCCCCccC---HHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhhcccccccccC
Confidence 3578999999999 99999999999864 2 2468999999999999875 688886 22 478999
Q ss_pred CCCceEEEEeecCCCCceEEEEEEeCCCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCcccccee
Q 047525 208 DIEISIYVPLYDGLAKHWYLAIMNIKDKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDI 287 (340)
Q Consensus 208 d~~~~IfIPIN~~~~~HW~L~VId~~~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i 287 (340)
|+ ||||||. +.||+|+|||+++++|.|||||++.+..... .|++|+..+. .+ ..+..++.+.|..
T Consensus 370 D~---IFIPIh~--n~HWsLaVId~k~k~I~yyDSLgg~~~~vL~---~L~rYL~~E~---kd----K~g~d~D~s~W~~ 434 (490)
T PLN03189 370 DK---IFVPIHQ--EIHWTLAVINKKDQKFQYLDSLKGRDPKILD---ALAKYYVDEV---KD----KSEKDIDVSSWEQ 434 (490)
T ss_pred ce---EEeeeec--CCeeEEEEEEcCCCeEEEEeCCCCCCHHHHH---HHHHHHHHHH---hh----hcCCCcchhccee
Confidence 95 9999999 5999999999999999999999998766554 7888886554 11 1355677888987
Q ss_pred eCCCCcCCCCCCCchHHHHHHHccccccccCCCCC--CCCcccHHHHHHHhh
Q 047525 288 LYPNNVPIQPNGNDCGLYVMKFMETPCELLFPTYK--SLPNVDWSILAVVED 337 (340)
Q Consensus 288 ~~p~~vPqQ~N~~DCGVFVl~fae~~~~~l~~~F~--dip~iR~~i~~~~~~ 337 (340)
..+.++|||.||+|||||||+||+......+..|+ |||.+|.+|+..|-.
T Consensus 435 ~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrRma~EIl~ 486 (490)
T PLN03189 435 EFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLRTAKEILR 486 (490)
T ss_pred ccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHHHHHHHHH
Confidence 76677999999999999999999954333445687 999999999987753
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-37 Score=305.67 Aligned_cols=173 Identities=21% Similarity=0.286 Sum_probs=142.7
Q ss_pred hhhcccCCCCCccccCchhHHHHHHHHHHcCC----CCCCcceeeccccchhccccccCcc---ccccCCcCCCCceEEE
Q 047525 143 LFAYRKLKENQIFHNVVKKIISCYAEYLTGKE----SLKQDYETRNWFLPTLFGQIVANVS---GVSTIDRSDIEISIYV 215 (340)
Q Consensus 143 ~~~~~sL~pg~wLNd~vD~IInfYl~~L~~~~----~~~kv~~fnsfF~~~L~~~g~~~vk---k~~dlf~kd~~~~IfI 215 (340)
..|+++|.+|+||| |+||||||+||..+. ..++||+||||||++|.+.||++|+ ++++||++++ |||
T Consensus 385 ~~D~~~L~~~~wLN---DtIIdFy~k~ls~~sk~~s~~~~vh~FnTFFYT~LsrrGy~gVrrW~kk~dif~~k~---I~i 458 (578)
T COG5160 385 NQDFKRLRNGDWLN---DTIIDFYMKLLSKISKNTSKREQVHLFNTFFYTKLSRRGYSGVRRWTKKTDIFSKKY---IFI 458 (578)
T ss_pred hHhhhhhccccchh---hHHHHHHHHHHHHhccCcccccceEEeehhhHHHHHHHHhHHHHHHHhccCccccce---EEE
Confidence 45689999999999 999999999998652 2678999999999999999999998 7789999996 999
Q ss_pred EeecCCCCceEEEEEEeCCCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCccccceeeCCCCcCC
Q 047525 216 PLYDGLAKHWYLAIMNIKDKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDILYPNNVPI 295 (340)
Q Consensus 216 PIN~~~~~HW~L~VId~~~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i~~p~~vPq 295 (340)
|||. ..||+|+|||.+++.|.|||||++.+..+.. .|+.|+..+. +.. .+.+.|....-.++||
T Consensus 459 PIni--~~HW~l~II~~~~~~i~~~DSLan~~~~v~~---~L~~Y~ldE~----k~~-------~~k~~~~~~~~~~vPq 522 (578)
T COG5160 459 PINI--SYHWFLAIIDNPKKNILYFDSLANTHDPVLE---FLRSYLLDEY----KIQ-------HDKDPQIKMKHCKVPQ 522 (578)
T ss_pred Eecc--cceEEEEEeecCcceeEEecccccCcHHHHH---HHHHHHHHHH----hcc-------cCCchhhhhhcCCCCC
Confidence 9999 5999999999999999999999999877666 7777765442 211 1222232233456999
Q ss_pred CCCCCchHHHHHHHccccccccCCCCC--CCCcccHHHHHHHhh
Q 047525 296 QPNGNDCGLYVMKFMETPCELLFPTYK--SLPNVDWSILAVVED 337 (340)
Q Consensus 296 Q~N~~DCGVFVl~fae~~~~~l~~~F~--dip~iR~~i~~~~~~ 337 (340)
|.||+|||||||+|++...+-.+.+|+ |+|++|+.|++.+.+
T Consensus 523 Q~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~ 566 (578)
T COG5160 523 QRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKD 566 (578)
T ss_pred CCCCCccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHH
Confidence 999999999999999964444456777 999999999998764
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=7.3e-28 Score=217.54 Aligned_cols=169 Identities=27% Similarity=0.369 Sum_probs=113.4
Q ss_pred CccccCchhHHHHHHHHHHcC-----CCCCCcceeeccccchhc--------------------cccccCcc---ccc--
Q 047525 153 QIFHNVVKKIISCYAEYLTGK-----ESLKQDYETRNWFLPTLF--------------------GQIVANVS---GVS-- 202 (340)
Q Consensus 153 ~wLNd~vD~IInfYl~~L~~~-----~~~~kv~~fnsfF~~~L~--------------------~~g~~~vk---k~~-- 202 (340)
+||| |+|||||+++|..+ ...+++++++|+|++.+. ...+.++. +..
T Consensus 1 ~wLn---d~iId~y~~~l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (216)
T PF02902_consen 1 EWLN---DSIIDFYLEYLRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNK 77 (216)
T ss_dssp --EE---HHHHHHHHHHHHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCT
T ss_pred CcCC---HHHHHHHHHHHHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhcccc
Confidence 5899 99999999999722 225689999999999998 22222222 333
Q ss_pred -cCCcCCCCceEEEEeecCCCCceEEEEEEeCCCceEEecCCCCCCC--CcccHHHHHHHHHHHHHHHhhhhcccCCCCC
Q 047525 203 -TIDRSDIEISIYVPLYDGLAKHWYLAIMNIKDKTADIWDSLPNSEI--EPNHRQEIVKQNLHALDLVLFRDIAFNFPSD 279 (340)
Q Consensus 203 -dlf~kd~~~~IfIPIN~~~~~HW~L~VId~~~~~I~~~DSL~~~~~--~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~ 279 (340)
+++++++ ||+|||.+ +.||+|+||+++.++|.+||||++... ........+..+|.... . .. ....
T Consensus 78 ~~l~~~~~---i~iPin~~-~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~-~-~~-----~~~~ 146 (216)
T PF02902_consen 78 KNLFDKDY---IFIPININ-NNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREY-K-KK-----EGRD 146 (216)
T ss_dssp STGGGSSE---EEEEEEET-TTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHH-H-HH-----HSSC
T ss_pred ccccccCE---EEEEEech-hhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhcc-c-cc-----cccc
Confidence 8899995 99999996 799999999999999999999999876 01111113333332211 1 11 1223
Q ss_pred CccccceeeCCCCcCCCCCCCchHHHHHHHccccccccCCC----CC--CCCcccHHHHHHH
Q 047525 280 WYFADFDILYPNNVPIQPNGNDCGLYVMKFMETPCELLFPT----YK--SLPNVDWSILAVV 335 (340)
Q Consensus 280 ~~~~~~~i~~p~~vPqQ~N~~DCGVFVl~fae~~~~~l~~~----F~--dip~iR~~i~~~~ 335 (340)
++.+.|....+..+|||.|++|||||||+||+......... +. ++..+|.+++..+
T Consensus 147 ~~~~~~~~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~~i~~~r~~~a~~~ 208 (216)
T PF02902_consen 147 PDKSPFKIVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQELTEEDIKNFRKKLAVDL 208 (216)
T ss_dssp T-TTTCEEEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCSBTGHHHHHHHHHHHH--
T ss_pred cccceeeecccccccCCCCCCCcHHHHHHHHHHHHhCCCCcccccCCHHHHHHHHHHHHhhc
Confidence 35567877777779999999999999999999322111111 44 8999999998654
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.90 E-value=4.5e-24 Score=192.91 Aligned_cols=165 Identities=20% Similarity=0.247 Sum_probs=106.9
Q ss_pred hcccCCCCCccccCchhHHHHHHHHHHcCC--CCCCcceee---ccccchhcc-ccccCccccccCCcCCCCceEEEEee
Q 047525 145 AYRKLKENQIFHNVVKKIISCYAEYLTGKE--SLKQDYETR---NWFLPTLFG-QIVANVSGVSTIDRSDIEISIYVPLY 218 (340)
Q Consensus 145 ~~~sL~pg~wLNd~vD~IInfYl~~L~~~~--~~~kv~~fn---sfF~~~L~~-~g~~~vkk~~dlf~kd~~~~IfIPIN 218 (340)
|.+.|+|+.||| |.+|+||.+||..+. +.+..++++ +||...... +....+....++.+|++ ||+|||
T Consensus 23 DVdlL~~p~wln---D~~I~F~~e~l~~~~~~s~~~~~ll~P~~t~~l~~~~~~~e~~~~~~pl~l~~k~~---iflpiN 96 (223)
T KOG3246|consen 23 DVDLLQPPEWLN---DRLIDFYYEYLEHRRSRSEPDLHLLRPSLTFFLRHAPNPEEIAMVLDPLDLNDKDF---IFLPIN 96 (223)
T ss_pred hhhhcCCCchhh---hhHHHHHHHHHHHhhcccCcchhccCHHHHHHHHhCCCcHHHHHhcChhhcCCCce---EEEEec
Confidence 357799999999 889999999999652 233332222 122221111 11222224558999997 999999
Q ss_pred cC-------CCCceEEEEEEeCCCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCccccceeeCCC
Q 047525 219 DG-------LAKHWYLAIMNIKDKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDILYPN 291 (340)
Q Consensus 219 ~~-------~~~HW~L~VId~~~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i~~p~ 291 (340)
++ ||+||+|+|+..++.+.+||||+.+.+..... .++++.=.. + .++ +. ...+.
T Consensus 97 Dn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~--~l~~kl~~l---l-~~~--------~~-----~~~~~ 157 (223)
T KOG3246|consen 97 DNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAK--SLMKKLRAL---L-KKK--------FA-----KRVEC 157 (223)
T ss_pred CCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHH--HHHHHHHHH---H-hhh--------hh-----hcccc
Confidence 97 56899999999999999999999998876554 233322111 1 111 11 01155
Q ss_pred CcCCCCCCCchHHHHHHHccc-----cccccCCCCC-CCCcccHHHHHH
Q 047525 292 NVPIQPNGNDCGLYVMKFMET-----PCELLFPTYK-SLPNVDWSILAV 334 (340)
Q Consensus 292 ~vPqQ~N~~DCGVFVl~fae~-----~~~~l~~~F~-dip~iR~~i~~~ 334 (340)
.+|||.||||||+|||.+++. .++.....+. +-|.++..+..+
T Consensus 158 ~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~ 206 (223)
T KOG3246|consen 158 KCLQQQNGYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREE 206 (223)
T ss_pred cChhhhcCCchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHH
Confidence 699999999999999999983 2233334444 444444444433
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.09 E-value=9.3e-11 Score=122.63 Aligned_cols=156 Identities=21% Similarity=0.169 Sum_probs=96.5
Q ss_pred hhhhhcccCCCCCccccCchhHHHHHHHHHHcC--C---CCCCcceeeccccchhccc---cccC---------cc---c
Q 047525 141 KNLFAYRKLKENQIFHNVVKKIISCYAEYLTGK--E---SLKQDYETRNWFLPTLFGQ---IVAN---------VS---G 200 (340)
Q Consensus 141 ~~~~~~~sL~pg~wLNd~vD~IInfYl~~L~~~--~---~~~kv~~fnsfF~~~L~~~---g~~~---------vk---k 200 (340)
.+.-|+.+|++|.+|+ |.|++||++|+... + ..+..|+|++|||..+.+. +... ++ +
T Consensus 355 v~~~Dl~cl~~~e~L~---d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~ 431 (595)
T KOG0779|consen 355 VNNNDLVCLEEGEFLN---DTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTR 431 (595)
T ss_pred eeccchhhccccchhh---hhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeee
Confidence 3455678999999999 77799999999854 1 1456899999999988652 1111 11 5
Q ss_pred cccCCcCCCCceEEEEeecCCCCceEEEEEEeCCC------ceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhc-c
Q 047525 201 VSTIDRSDIEISIYVPLYDGLAKHWYLAIMNIKDK------TADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDI-A 273 (340)
Q Consensus 201 ~~dlf~kd~~~~IfIPIN~~~~~HW~L~VId~~~~------~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~-~ 273 (340)
..|+|.+++ |++|+|. ..||.|++++.+.. .....+++......... ..+...+... +... +
T Consensus 432 ~~d~~~k~y---i~~P~~E--~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~----~~~~~~ 500 (595)
T KOG0779|consen 432 HFDLFNKDY---VFVPTHE--RFHWKLAIICNPDLETETPRPRLELLILKLSADFPIV--ENILDFMKVA----SIYNNE 500 (595)
T ss_pred cccccccee---EEecCch--HhhhhccccccCccccCccccchhhhhhccccccchh--hhhhhhhhhc----ccccCc
Confidence 679999996 9999999 49999999998753 33344444444332222 1222222111 1110 0
Q ss_pred cCCCCCCc--ccccee------eCCCCcCCCCCCCchHHHHHHHcc
Q 047525 274 FNFPSDWY--FADFDI------LYPNNVPIQPNGNDCGLYVMKFME 311 (340)
Q Consensus 274 ~~~~~~~~--~~~~~i------~~p~~vPqQ~N~~DCGVFVl~fae 311 (340)
.....+.. ..-++. .... .|||.|..|||+|++.|++
T Consensus 501 ~~~~~~~~~~~~~~~~~~~~~s~~v~-~p~q~n~~dcG~~~~~~v~ 545 (595)
T KOG0779|consen 501 LIVTEDLELEEELPRRLPRGKSETVR-EPQQNNDVDCGSFVLEFVE 545 (595)
T ss_pred ccccccccccccccccCccccccccc-ccCccCcccchhhHHHHHH
Confidence 00000000 000110 0112 3899999999999999998
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=95.61 E-value=0.025 Score=56.21 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=30.3
Q ss_pred eEEEEeecCCCCceEEEEEEeCCCceEEecCCCCC
Q 047525 212 SIYVPLYDGLAKHWYLAIMNIKDKTADIWDSLPNS 246 (340)
Q Consensus 212 ~IfIPIN~~~~~HW~L~VId~~~~~I~~~DSL~~~ 246 (340)
++.+|.+. ..||.++|+|-+++-+.+|||-|..
T Consensus 233 yvmFgfcY--~~Hwkc~IfDk~~~~v~FydSgG~~ 265 (423)
T PF03290_consen 233 YVMFGFCY--MSHWKCCIFDKEKKIVYFYDSGGNI 265 (423)
T ss_pred EEEeeeee--hhcceEEEEeccccEEEEEcCCCCC
Confidence 59999999 5999999999999999999998864
No 8
>PRK11836 deubiquitinase; Provisional
Probab=94.82 E-value=0.047 Score=52.64 Aligned_cols=42 Identities=17% Similarity=0.317 Sum_probs=30.6
Q ss_pred cCCcCCCCceEEEEeecCCCCceEEEEEE--------eCCCceEEecCCCCCCCC
Q 047525 203 TIDRSDIEISIYVPLYDGLAKHWYLAIMN--------IKDKTADIWDSLPNSEIE 249 (340)
Q Consensus 203 dlf~kd~~~~IfIPIN~~~~~HW~L~VId--------~~~~~I~~~DSL~~~~~~ 249 (340)
.+|-++. =+||||. |.||.|+++. .++.+.++|.|+..-+..
T Consensus 215 ~~~~k~~---elFpINt--g~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d 264 (403)
T PRK11836 215 PSWPKEV---QLFPINT--GGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHD 264 (403)
T ss_pred CCCcccc---eEEEecC--CCcEEEEEeHHhhhcccccceeEEEEEecHhhhccc
Confidence 6677775 8999997 7999999873 234455678888765443
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=94.27 E-value=0.067 Score=50.64 Aligned_cols=79 Identities=15% Similarity=0.238 Sum_probs=42.7
Q ss_pred EEEEeecCCCCceEEEEEEe--CCCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCccccceeeCC
Q 047525 213 IYVPLYDGLAKHWYLAIMNI--KDKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDILYP 290 (340)
Q Consensus 213 IfIPIN~~~~~HW~L~VId~--~~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i~~p 290 (340)
=+||||. |.||.|++..- .+.+.++|.|++.-+.. .+++.+... + .+ + .. .+-.+...
T Consensus 191 evF~INt--g~HWil~~~~Ki~~kiKC~iFNs~~~l~eN------s~~~ii~~a----k--~a---g--~~-~e~di~fI 250 (317)
T PRK14848 191 EVFLINT--GDHWLLCLFYKLAEKIKCLIFNTYYDLNEN------TKQEIIEAA----K--IA---G--IS-ENEDVNFI 250 (317)
T ss_pred eEEEecC--CCcEEEEEhHHhhhhceEEEeecHhhhhhh------HHHHHHHHH----H--hh---C--cc-cCCceEEe
Confidence 3599998 79999998732 23344678888765422 222222211 1 10 1 00 01111222
Q ss_pred CCcCCCCCCCchHHHHHHHcc
Q 047525 291 NNVPIQPNGNDCGLYVMKFME 311 (340)
Q Consensus 291 ~~vPqQ~N~~DCGVFVl~fae 311 (340)
..--||.=..-||.|||.+++
T Consensus 251 e~nLQqnVpngCGlFv~~aIq 271 (317)
T PRK14848 251 ETNLQNNVPNGCGLFCYHTIQ 271 (317)
T ss_pred ehhhhhhCCCcchHHHHHHHH
Confidence 212344447889999999987
No 10
>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=93.35 E-value=0.059 Score=48.25 Aligned_cols=85 Identities=16% Similarity=0.289 Sum_probs=39.7
Q ss_pred eecC----CCCceEEEEEEeCCCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCccccceeeCCCC
Q 047525 217 LYDG----LAKHWYLAIMNIKDKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDILYPNN 292 (340)
Q Consensus 217 IN~~----~~~HW~L~VId~~~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i~~p~~ 292 (340)
||.. ||.||.-...|++..+++.+|.+|-+..+ +.+-|-..-+-+.+++. -....+- -.+++....
T Consensus 24 VNT~~retGGvHWlA~Aw~P~s~t~YmFDPfGfsd~~------L~qiY~FeYe~llrRSA-L~~~~dR---Cv~Lvkstq 93 (183)
T PF00770_consen 24 VNTGGRETGGVHWLAFAWDPRSRTFYMFDPFGFSDQK------LKQIYQFEYEGLLRRSA-LSSTPDR---CVTLVKSTQ 93 (183)
T ss_dssp EESS-TTT--S-EEEEEEETTTTEEEEE-TT---HHH------HHHHH----HHHHHHHH-HHH-TTS---EEEEEEE-E
T ss_pred EecCCcccCceeEEEEEecCCcceEEEeCCCCCCHHH------HHHHHhhhHHHHHHHHh-hcCCCCc---eEEEEeccc
Confidence 5654 68999999999999999999999987432 22222111111112211 0000111 123344444
Q ss_pred cCCCCCCCchHHHHHHHcc
Q 047525 293 VPIQPNGNDCGLYVMKFME 311 (340)
Q Consensus 293 vPqQ~N~~DCGVFVl~fae 311 (340)
.-|=+++--||+|.|.|..
T Consensus 94 tVQ~p~SaaCGLFC~lFL~ 112 (183)
T PF00770_consen 94 TVQCPCSAACGLFCCLFLH 112 (183)
T ss_dssp E-S-TT---HHHHHHHHHH
T ss_pred eeeccCchhHHHHHHHHHH
Confidence 5556689999999999886
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=78.52 E-value=7.7 Score=34.96 Aligned_cols=80 Identities=10% Similarity=0.208 Sum_probs=46.5
Q ss_pred EEEEeecCCCCceEEEEEEeC-----CCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCcccccee
Q 047525 213 IYVPLYDGLAKHWYLAIMNIK-----DKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDI 287 (340)
Q Consensus 213 IfIPIN~~~~~HW~L~VId~~-----~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i 287 (340)
.++|... .++.-+++|.+ +..|++++|-.-...... +..+....... ..+ .. ..+.+
T Consensus 74 ~Iv~~~~---~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~~~~~~-----l~~~~~~~~~~-~~~----~~-----~~~~~ 135 (177)
T PF03421_consen 74 AIVNLGG---DGIHHVALDVRHTPNGKPSLIVFEPASFYGMKPA-----LAGYTKLAEEA-RQK----LL-----PNAKF 135 (177)
T ss_pred EEEeCCC---CCCcEEEEEEeecCCCCceEEEEccccccCCcch-----hhhHHHHHHHH-Hhc----cC-----CCcEE
Confidence 6777554 45556677766 468999999876543321 11111111100 000 01 23333
Q ss_pred eCCCCcCCCCCCCchHHHHHHHcc
Q 047525 288 LYPNNVPIQPNGNDCGLYVMKFME 311 (340)
Q Consensus 288 ~~p~~vPqQ~N~~DCGVFVl~fae 311 (340)
... ++..|.-.+|||+|-|.+|.
T Consensus 136 ~~i-e~diQkS~~dC~IFsLs~Ak 158 (177)
T PF03421_consen 136 AVI-EMDIQKSPSDCGIFSLSLAK 158 (177)
T ss_pred EEE-ecccccCcCcchhhHHHHHH
Confidence 333 38999999999999999987
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=67.64 E-value=15 Score=35.77 Aligned_cols=70 Identities=11% Similarity=0.342 Sum_probs=38.8
Q ss_pred eEEEEEEeC----CCceEEecCCCCCCCCcccHHHHHHHHHHHHHHHhhhhcccCCCCCCccccceeeCCCCcCCCCCCC
Q 047525 225 WYLAIMNIK----DKTADIWDSLPNSEIEPNHRQEIVKQNLHALDLVLFRDIAFNFPSDWYFADFDILYPNNVPIQPNGN 300 (340)
Q Consensus 225 W~L~VId~~----~~~I~~~DSL~~~~~~~~~~~~~lk~~L~~~~~l~~~~~~~~~~~~~~~~~~~i~~p~~vPqQ~N~~ 300 (340)
+..+++|.+ +..|++++|-........ ++...+ ...+ ... ...-..|.++ .+-.|.-.+
T Consensus 108 ~H~vavDvr~~~Gk~SIIvlEPa~~~~~~~a----~l~~rl--~~~l-e~~-------~l~~~~~avi---e~d~QkS~~ 170 (287)
T PRK15371 108 IHFSVIDYKHIDGKTSLILFEPANFNSMGPA----MLAIRT--KTAL-ERE-------QLPDCHFSMV---EMDIQRSSS 170 (287)
T ss_pred ceEEEEEEeccCCCeEEEEECCccccccchH----HHHHHH--HHHH-Hhc-------cCCCceEEEE---ecccccCcc
Confidence 566666654 468999999876532211 221111 1111 110 0111223322 267899999
Q ss_pred chHHHHHHHcc
Q 047525 301 DCGLYVMKFME 311 (340)
Q Consensus 301 DCGVFVl~fae 311 (340)
|||+|-|.+|.
T Consensus 171 dC~mFSL~~Ak 181 (287)
T PRK15371 171 ECGIFSLALAK 181 (287)
T ss_pred cchhhhHHHHH
Confidence 99999999986
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=22.10 E-value=1.4e+02 Score=34.40 Aligned_cols=39 Identities=21% Similarity=0.382 Sum_probs=26.9
Q ss_pred EEEEeecC-----CCCceEEEEEEeCCCceEEecCCCCCCCCccc
Q 047525 213 IYVPLYDG-----LAKHWYLAIMNIKDKTADIWDSLPNSEIEPNH 252 (340)
Q Consensus 213 IfIPIN~~-----~~~HW~L~VId~~~~~I~~~DSL~~~~~~~~~ 252 (340)
=|.||-.. ...||..++= -+....++||.||..+.+...
T Consensus 48 gfmpvltgv~p~~~sghwimlik-g~gn~y~lfdplg~~sg~~y~ 91 (1439)
T PF12252_consen 48 GFMPVLTGVSPRQDSGHWIMLIK-GQGNQYYLFDPLGKTSGEGYQ 91 (1439)
T ss_pred CCceeecCcCCCCcCceeEEEEE-cCCCceEEeccccccccccHH
Confidence 45665542 2579987654 566778999999987766543
Done!