Query 012548
Match_columns 461
No_of_seqs 232 out of 846
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 03:47:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012548hhsearch_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 1E-115 2E-120 907.6 31.7 420 1-461 1-429 (490)
2 KOG0778 Protease, Ulp1 family 100.0 1.8E-53 4E-58 445.7 23.6 364 41-461 74-450 (511)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 3.4E-31 7.3E-36 276.5 14.8 134 316-458 377-510 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.9 2E-21 4.2E-26 179.1 12.4 125 334-459 1-147 (216)
5 KOG3246 Sentrin-specific cyste 99.7 1.8E-16 3.8E-21 152.1 11.7 127 311-450 11-150 (223)
6 KOG0779 Protease, Ulp1 family 99.1 3.1E-11 6.6E-16 131.4 2.6 131 320-454 353-498 (595)
7 PF03290 Peptidase_C57: Vaccin 91.1 0.25 5.4E-06 52.3 4.3 36 400-435 230-265 (423)
8 PRK14848 deubiquitinase SseL; 63.8 6.7 0.00015 40.1 3.3 34 217-250 19-54 (317)
9 PF00770 Peptidase_C5: Adenovi 62.3 9.8 0.00021 36.8 3.9 30 411-440 33-62 (183)
10 PRK11836 deubiquitinase; Provi 57.4 8.4 0.00018 40.1 2.7 39 397-435 215-261 (403)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.1e-115 Score=907.60 Aligned_cols=420 Identities=60% Similarity=0.968 Sum_probs=382.4
Q ss_pred CCcccccCCCCCccc-ccCCCCCCccccCCCCccccccccCc-ccCCccccccccccCCCCCCcccccccCCcccccccc
Q 012548 1 MGALTSNRKRGDEYL-NYQIPYQNLHISKRPRFNYTQQNQNQ-TLISSNSTVSRMSRYPEAKPPLKREVHAPCRTLKFGF 78 (461)
Q Consensus 1 m~~~~~~~~~~~~~~-~~~~~~~~~~~~k~~~~~~~~~~~~~-~~~~~~~~~~~~~~yp~~~~~~~r~~hap~~~~~~~~ 78 (461)
|||||||+||+++|+ |+++++|+|||||||||| |+|++.. ..+||||||||||||||+|+||||||||||||+|||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 78 (490)
T PLN03189 1 MGALTSNHKRSDECFNNPLSNSPDFHISKKPRFS-MAQTPDSGNQHSSNSTASRISRYPEVKSPLRREVHAPCRILKFG- 78 (490)
T ss_pred CCcccccccccccccccccccCCccccccCCCcc-ccccccccCCccccccccchhcCCCccchhhhhhcCchhhhhcc-
Confidence 999999999999999 569999999999999999 5666622 128999999999999999999999999999999999
Q ss_pred cccccccccccccCCCCccc-cccchhhhHHHHHHHHHHHhHhhhccccccCceeeecCccccceeeeccCCchhhhhhh
Q 012548 79 ADKSNQAFGSKKANGYGENQ-NLGIRMGNVLRYHLEKAKKSAFGAFRYFSKDKEVIDADNEQEKVEVISDDSSVEEIDAI 157 (461)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 157 (461)
+.|+++++++. ++|++|||||++||++||+|||+|+||++|||||||||||.|++++|||||||||||||
T Consensus 79 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (490)
T PLN03189 79 ---------RDKSTDSSEKKQGLGNVMGNFLSRKYDMAKRSALDALRYYRKDKEVVDVGDELGKVEMISDDSSIEEVEAV 149 (490)
T ss_pred ---------cccccchhhhhcchhhhHHHHhhhhhHHHHHHHHHHHHHHhcCCeeeecccccccceeccCccchhhhhee
Confidence 99999999987 79999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCcccccCCCCCC-CCCCCCCccccccccccccccccccCCCCCCCccccccCCcccHHHhhhhcccCC----CcC
Q 012548 158 EDGREGRSLVFDPRPRG-SDENEKPVVDIGEIDGKSAEERNYHTNLQPSSSSVLTDTNNGDVSKMIDLLSLNG----EMT 232 (461)
Q Consensus 158 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~----~~~ 232 (461)
|.+..+ +.+.++ +.+ ..+++..+ +.+|++ +|.++++||+||.|++ +++
T Consensus 150 ~~~~~~-----~~~~~~~~~~------~~~~~~~~-----~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~ 202 (490)
T PLN03189 150 EMDVDE-----VEEKAEMGNG------LSSDVKIV-----TKNGNL-----------RVEDTSKMLDSLVLNRPETDVLS 202 (490)
T ss_pred ecccch-----hhhccccCcc------ccccceEe-----ecCCcc-----------cccchhhhhhceeecCccccccc
Confidence 944311 222222 222 22444444 789999 9999999999999998 899
Q ss_pred hHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhcCCCCCCchhhhhcCCCCCCCCCCHHHHHHHHHHHcc-CCCce
Q 012548 233 VDVYKKLLQSVQKRGSKLKEIEFEIELNEKRWASLKQLWPLKKPEEEQVEELPREPFIPLTKEEEAAVERAFSA-NWRAV 311 (461)
Q Consensus 233 ~~~yk~~l~~~~~R~~~l~~~~~~~~l~Ekrr~~~~~~rp~k~p~~e~ve~v~~e~f~pLS~E~e~~V~~al~~-~~~~V 311 (461)
+++||++++++++|+.+|++|+++++++|++++++++.+|..+ |.+|++++++|+|||+||+.+|++||++ +..+|
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~pLT~e~~~~V~~al~~~~~~~v 279 (490)
T PLN03189 203 VEAYRKLLQSAERRNSKLKDLGFEIELNEKRLSSLRQSRPKPK---EPVEEVPREPFIPLTREEETEVKRAFSANNRRKV 279 (490)
T ss_pred cHHHHHHHHHHHhhcchhhhccceeehhhhHHHHHhhhccCcc---ccccccccccCcCCCHHHHHHHHHHhcCCCccce
Confidence 9999999999999999999999999999999999998888632 3458899999999999999999999998 44789
Q ss_pred EeeccCCceEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechhHHHhhhcCCCCCChhhHhhhhhc
Q 012548 312 LVSHTETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSA 391 (461)
Q Consensus 312 Lv~~~~~gI~It~~DL~~L~p~~WLNDeIINFYL~lL~er~~~ep~~~~kvh~FNSFFy~kL~~~k~g~~y~~VkRWTkr 391 (461)
|+++++++|+||++||.||.|++||||+||||||++|.++...+|...++||+||||||++|...+.+++|.+|+|||++
T Consensus 280 lvs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~ 359 (490)
T PLN03189 280 LVTHENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQ 359 (490)
T ss_pred eeecCCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhh
Confidence 99998899999999999999999999999999999999987777777789999999999999987677899999999998
Q ss_pred ccccCCccccceEEeeeccCCceeEEEeeeCCCeEEEEcCCCCCCHHHHHHHHHHHHHHHhhhhCCCCCC
Q 012548 392 KKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLARYFVEEVRDKCGKDIDV 461 (461)
Q Consensus 392 kKv~idLfekD~IfIPIN~gsHWsLaVI~~k~k~I~yyDSLgg~n~~vl~~L~~YL~~E~kdK~g~~~D~ 461 (461)
++++++||++|+||||||.+.||+|+||+++.++|+|||||++.+..+++.|++||.+|+++|++.+||+
T Consensus 360 kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~~~vL~~L~rYL~~E~kdK~g~d~D~ 429 (490)
T PLN03189 360 KKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRDPKILDALAKYYVDEVKDKSEKDIDV 429 (490)
T ss_pred cccccccccCceEEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHhhhcCCCcch
Confidence 8888899999999999999999999999999999999999999999999999999999999999988874
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.8e-53 Score=445.70 Aligned_cols=364 Identities=35% Similarity=0.549 Sum_probs=288.1
Q ss_pred cccCCccccccccccCCCCCCcccccccCCcc-cccccccccccccccccccCCCCccccccchhhhHHHHHHHHHHHhH
Q 012548 41 QTLISSNSTVSRMSRYPEAKPPLKREVHAPCR-TLKFGFADKSNQAFGSKKANGYGENQNLGIRMGNVLRYHLEKAKKSA 119 (461)
Q Consensus 41 ~~~~~~~~~~~~~~~yp~~~~~~~r~~hap~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 119 (461)
.-..++.+..+.|.+||++....+|+.|+|-| .+..+ +.+++.+++.. .+++++...+..++..|
T Consensus 74 ~~~s~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~----------r~~s~~~~s~~----~~~~~~~~~~~~~~~~~ 139 (511)
T KOG0778|consen 74 GRSSSSRPRDPPIPDRPEVSSDTRRKDFESYRWLLRNS----------RTKSNSVGSPY----TSPGLLRRQYDSSARNA 139 (511)
T ss_pred cccccccCCCCCCccchhhccccccccccccccccccc----------ccccccccCCc----cCcchhhhhcchhhhcc
Confidence 45567788889999999999999999999998 55555 56666666655 34559999999999999
Q ss_pred hhhccccccCceeeecCccccceeeeccCCchhhhhhh--h--ccccCcccccCCCCCCCCCCCCCcccccccccccccc
Q 012548 120 FGAFRYFSKDKEVIDADNEQEKVEVISDDSSVEEIDAI--E--DGREGRSLVFDPRPRGSDENEKPVVDIGEIDGKSAEE 195 (461)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~--~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (461)
...-.++.+++.+++.+.+.+..++++.|.+...++.. | ++.++.. ..+... +. .
T Consensus 140 ~~~s~~v~~~~~~~~~~~s~~~~~~~~~d~s~~~~s~~~~~~~~~~~~~~--------~~~s~~-~~---~--------- 198 (511)
T KOG0778|consen 140 LRVSPFVESGPKTVSRGSSVEWTEMVSDDPSELKVSNTLNEGDESQEKSE--------IKDSEK-ST---D--------- 198 (511)
T ss_pred cccccccCCCcchhcccccccceeecccCCcccccccccccccccccccc--------cccCcC-CC---c---------
Confidence 99999999999999999999999999999996655532 2 1111110 000000 00 0
Q ss_pred ccccCCCCCCCccccc-cCCcccHHHh-hhhcccCC-----CcChHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhh
Q 012548 196 RNYHTNLQPSSSSVLT-DTNNGDVSKM-IDLLSLNG-----EMTVDVYKKLLQSVQKRGSKLKEIEFEIELNEKRWASLK 268 (461)
Q Consensus 196 ~~~~~~~~~~~~~~~~-~~~~~~~~~~-l~~l~~~~-----~~~~~~yk~~l~~~~~R~~~l~~~~~~~~l~Ekrr~~~~ 268 (461)
.+..+.. ....++.+++ .+++..+. ..+.++|+...++++++...++.+.+++...+.....+.
T Consensus 199 ---------~~~~~~n~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~a~q~~~~~~ee~~s~~~~~~~e~~~~~~~~i~l~ 269 (511)
T KOG0778|consen 199 ---------EHARIKNGENIKTERAENNFDSLSLRREEESDHRGEKAYQNKEKSLEELVSDLKSLRFEIFQKRGELIPLR 269 (511)
T ss_pred ---------chhhhhcccchhhhhhhhhhhhhhhcCccchhhhhHHHHhhhhhhHHHHHHHHHHhhhhhcccccccchhh
Confidence 0000000 1112233333 55555554 788999999888999999999999888877665554444
Q ss_pred hcCCCCCCchhhhhcCCCCCCCCCCHHHHHHHHHHHcc-CCCceEeeccCCceEEccccccccCCCCcccHHHHHHHHHH
Q 012548 269 QLWPLKKPEEEQVEELPREPFIPLTKEEEAAVERAFSA-NWRAVLVSHTETGIDITGKILQCLRPGAWLNDEVINVYLGL 347 (461)
Q Consensus 269 ~~rp~k~p~~e~ve~v~~e~f~pLS~E~e~~V~~al~~-~~~~VLv~~~~~gI~It~~DL~~L~p~~WLNDeIINFYL~l 347 (461)
.+....+. ..++..+++.|+||+++++++++++++. +..++++++ ++|.||.+||+||.+++||||+||||||+|
T Consensus 270 ~~~~k~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~i~It~~dl~tl~~~~WLNDevINfYm~l 345 (511)
T KOG0778|consen 270 SVQEKLEK--PKVEVKKEDSFPPLTEEREAQVQRAFSSRNSTEILVTH--FNIDITGKDLQTLRPGNWLNDEVINFYMEL 345 (511)
T ss_pred hhhccccc--ccccccCccccccccHHHHHHHHHHhccCCcccceehh--ccccccHHHHhhccCccchhHHHHHHHHHH
Confidence 33332111 1235667789999999999999999995 888999987 469999999999999999999999999999
Q ss_pred HHHhhhcCCccccceEEechhHHHhhhcCCCCCChhhHhhhhhcccccCCccccceEEeeeccCCceeEEEeeeCCCeEE
Q 012548 348 LKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQ 427 (461)
Q Consensus 348 L~er~~~ep~~~~kvh~FNSFFy~kL~~~k~g~~y~~VkRWTkrkKv~idLfekD~IfIPIN~gsHWsLaVI~~k~k~I~ 427 (461)
|+++....++ +|+||+||||||++|... ||++|+|||++ ++||++|+||||||.++||||+||+.++++|.
T Consensus 346 l~ers~~~~~-yp~~h~FnTFFy~kL~~~----gy~~VkRWTk~----v~if~~d~i~vPIH~~vHW~l~vid~r~k~i~ 416 (511)
T KOG0778|consen 346 LKERSKKDSK-YPKVHAFNTFFYTKLVGR----GYAGVKRWTKK----VDIFDKDIIFVPIHLGVHWCLAVIDLREKTIE 416 (511)
T ss_pred HHhhccccCC-CceEEEEechhhhhhhhc----chHHHHhHhhc----cCccccceeEeeeecCceEEEEEEEcccceEE
Confidence 9999987776 999999999999999987 99999999984 68999999999999999999999999999999
Q ss_pred EEcCCCCCCHHHHHHHHHHHHHHHhhhhCCCCCC
Q 012548 428 YLDSLKGRDKKVLGDLARYFVEEVRDKCGKDIDV 461 (461)
Q Consensus 428 yyDSLgg~n~~vl~~L~~YL~~E~kdK~g~~~D~ 461 (461)
|||||++....+++.|++||++|+.+|.+++||+
T Consensus 417 y~DS~~~~~nr~~~aL~~Yl~~E~~~k~~~~~d~ 450 (511)
T KOG0778|consen 417 YYDSLGGGPNRICDALAKYLQDESRDKSKKDFDV 450 (511)
T ss_pred EeeccCCCCcchHHHHHHHHHHHHhhhhcCCCCc
Confidence 9999998766666999999999999999999985
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=3.4e-31 Score=276.55 Aligned_cols=134 Identities=38% Similarity=0.695 Sum_probs=124.4
Q ss_pred cCCceEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechhHHHhhhcCCCCCChhhHhhhhhccccc
Q 012548 316 TETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLG 395 (461)
Q Consensus 316 ~~~gI~It~~DL~~L~p~~WLNDeIINFYL~lL~er~~~ep~~~~kvh~FNSFFy~kL~~~k~g~~y~~VkRWTkrkKv~ 395 (461)
+.++|+||.+||.||.+++||||+||||||+||....+ .+...+++|+||||||++|... ||++|+|||++
T Consensus 377 ~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk-~~s~~~~vh~FnTFFYT~Lsrr----Gy~gVrrW~kk---- 447 (578)
T COG5160 377 DRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISK-NTSKREQVHLFNTFFYTKLSRR----GYSGVRRWTKK---- 447 (578)
T ss_pred CcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhcc-CcccccceEEeehhhHHHHHHH----HhHHHHHHHhc----
Confidence 46899999999999999999999999999999966553 3345678999999999999988 99999999983
Q ss_pred CCccccceEEeeeccCCceeEEEeeeCCCeEEEEcCCCCCCHHHHHHHHHHHHHHHhhhhCCC
Q 012548 396 YGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLARYFVEEVRDKCGKD 458 (461)
Q Consensus 396 idLfekD~IfIPIN~gsHWsLaVI~~k~k~I~yyDSLgg~n~~vl~~L~~YL~~E~kdK~g~~ 458 (461)
++||++++||||||...||+|+|||.+.+.|.|||||++.+..+++.|+.|+.+||+.-.+++
T Consensus 448 ~dif~~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y~ldE~k~~~~k~ 510 (578)
T COG5160 448 TDIFSKKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSYLLDEYKIQHDKD 510 (578)
T ss_pred cCccccceEEEEecccceEEEEEeecCcceeEEecccccCcHHHHHHHHHHHHHHHhcccCCc
Confidence 589999999999999999999999999999999999999999999999999999999998887
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=99.86 E-value=2e-21 Score=179.11 Aligned_cols=125 Identities=34% Similarity=0.639 Sum_probs=99.5
Q ss_pred CcccHHHHHHHHHHHHHhhhcCCccccceEEechhHHHhhhcC-----CC-----------CCChhhHhhhhhcccccCC
Q 012548 334 AWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACG-----NK-----------GYDFRAVKRWTSAKKLGYG 397 (461)
Q Consensus 334 ~WLNDeIINFYL~lL~er~~~ep~~~~kvh~FNSFFy~kL~~~-----k~-----------g~~y~~VkRWTkrkKv~id 397 (461)
+||||+|||||+++|.++...++....++++|+||||+.|... .. ...+..+.+|++.. ...+
T Consensus 1 ~wLnd~iId~y~~~l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 79 (216)
T PF02902_consen 1 EWLNDSIIDFYLEYLRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKK-NKKN 79 (216)
T ss_dssp --EEHHHHHHHHHHHHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTC-CTST
T ss_pred CcCCHHHHHHHHHHHHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhcc-cccc
Confidence 5999999999999998654323345678999999999999821 00 12568899998753 2347
Q ss_pred ccccceEEeeecc-CCceeEEEeeeCCCeEEEEcCCCCCCH-----HHHHHHHHHHHHHHhhhhCCCC
Q 012548 398 LIECDKIFVPIHK-QIHWCLAVIDRKDKKFQYLDSLKGRDK-----KVLGDLARYFVEEVRDKCGKDI 459 (461)
Q Consensus 398 LfekD~IfIPIN~-gsHWsLaVI~~k~k~I~yyDSLgg~n~-----~vl~~L~~YL~~E~kdK~g~~~ 459 (461)
++++|+||||||. +.||+|+||+++.++|.+||||++.+. .++..+..||..++..+.+..+
T Consensus 80 l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 147 (216)
T PF02902_consen 80 LFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDP 147 (216)
T ss_dssp GGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred ccccCEEEEEEechhhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhcccccccccc
Confidence 9999999999999 999999999999999999999999987 7889999999999988776554
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.68 E-value=1.8e-16 Score=152.08 Aligned_cols=127 Identities=26% Similarity=0.414 Sum_probs=95.6
Q ss_pred eEeeccCCceEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechhHHHhhhcCCCCCChhhHhhhhh
Q 012548 311 VLVSHTETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTS 390 (461)
Q Consensus 311 VLv~~~~~gI~It~~DL~~L~p~~WLNDeIINFYL~lL~er~~~ep~~~~kvh~FNSFFy~kL~~~k~g~~y~~VkRWTk 390 (461)
+|.+ +.+.++.+|+..|.++.||||.+|+||.+||.++.... .+..|++++-.-.-|.... .-+-++....
T Consensus 11 ~Lsy---~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s---~~~~~ll~P~~t~~l~~~~---~~~e~~~~~~ 81 (223)
T KOG3246|consen 11 VLSY---FDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRS---EPDLHLLRPSLTFFLRHAP---NPEEIAMVLD 81 (223)
T ss_pred EEEe---eehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhccc---CcchhccCHHHHHHHHhCC---CcHHHHHhcC
Confidence 4554 46889999999999999999999999999999875322 2346777753322233331 2344555544
Q ss_pred cccccCCccccceEEeeecc---------CCceeEEEeeeCCCeEEEEcCCCCCCH----HHHHHHHHHHHHH
Q 012548 391 AKKLGYGLIECDKIFVPIHK---------QIHWCLAVIDRKDKKFQYLDSLKGRDK----KVLGDLARYFVEE 450 (461)
Q Consensus 391 rkKv~idLfekD~IfIPIN~---------gsHWsLaVI~~k~k~I~yyDSLgg~n~----~vl~~L~~YL~~E 450 (461)
. .++.++++||+|||+ |+||+|+|+..++++++||||+.+.|+ .+.+.++.+|..+
T Consensus 82 p----l~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~ 150 (223)
T KOG3246|consen 82 P----LDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSLMKKLRALLKKK 150 (223)
T ss_pred h----hhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHHHHHHHHHHhhh
Confidence 2 378999999999998 479999999999999999999999986 4566666666653
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.09 E-value=3.1e-11 Score=131.45 Aligned_cols=131 Identities=25% Similarity=0.438 Sum_probs=104.0
Q ss_pred eEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechhHHHhhhcC--C------CCCChhhHhhhhhc
Q 012548 320 IDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACG--N------KGYDFRAVKRWTSA 391 (461)
Q Consensus 320 I~It~~DL~~L~p~~WLNDeIINFYL~lL~er~~~ep~~~~kvh~FNSFFy~kL~~~--k------~g~~y~~VkRWTkr 391 (461)
+.++..|+.||.++.+|||.|++||++++.............+|+|++|||..+.+. . .......+++|++
T Consensus 353 ~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~- 431 (595)
T KOG0779|consen 353 HQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTR- 431 (595)
T ss_pred cceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeee-
Confidence 368899999999999999999999999998876443445678999999999988765 1 1224667899997
Q ss_pred ccccCCccccceEEeeeccCCceeEEEeeeCCC------eEEEEcCCCCCC-HHHHHHHHHHHHHHHhhh
Q 012548 392 KKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDK------KFQYLDSLKGRD-KKVLGDLARYFVEEVRDK 454 (461)
Q Consensus 392 kKv~idLfekD~IfIPIN~gsHWsLaVI~~k~k------~I~yyDSLgg~n-~~vl~~L~~YL~~E~kdK 454 (461)
++++|.+++|++|+|...||.|++|+.+.. ....++++.... ......+..++..++...
T Consensus 432 ---~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 498 (595)
T KOG0779|consen 432 ---HFDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYN 498 (595)
T ss_pred ---ccccccceeEEecCchHhhhhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhccccc
Confidence 479999999999999999999999999863 456666666654 345666777777666544
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=91.13 E-value=0.25 Score=52.34 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=33.7
Q ss_pred ccceEEeeeccCCceeEEEeeeCCCeEEEEcCCCCC
Q 012548 400 ECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGR 435 (461)
Q Consensus 400 ekD~IfIPIN~gsHWsLaVI~~k~k~I~yyDSLgg~ 435 (461)
++.++.+|+|...||.++|++...+-+.+|||-|..
T Consensus 230 ~~RyvmFgfcY~~Hwkc~IfDk~~~~v~FydSgG~~ 265 (423)
T PF03290_consen 230 KKRYVMFGFCYMSHWKCCIFDKEKKIVYFYDSGGNI 265 (423)
T ss_pred cccEEEeeeeehhcceEEEEeccccEEEEEcCCCCC
Confidence 688999999999999999999999999999998863
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=63.85 E-value=6.7 Score=40.06 Aligned_cols=34 Identities=21% Similarity=0.260 Sum_probs=25.0
Q ss_pred cHHHhhhhcccCC-CcChHHHHHHHHHHH-hhhhhh
Q 012548 217 DVSKMIDLLSLNG-EMTVDVYKKLLQSVQ-KRGSKL 250 (461)
Q Consensus 217 ~~~~~l~~l~~~~-~~~~~~yk~~l~~~~-~R~~~l 250 (461)
+++..|-+|.|+. -.|..+.+-+++-.. +|+..+
T Consensus 19 n~IdLL~NiALr~D~~G~~~E~iLfdlfsgk~~~~~ 54 (317)
T PRK14848 19 NCIDLLCNLALRNDDLGHKVEKLLFDLFSGKRSGSP 54 (317)
T ss_pred hHHHHHHHHhhccccccchHHHHHHHHHcCCccCCc
Confidence 6777888888887 778888887887775 555443
No 9
>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=62.29 E-value=9.8 Score=36.78 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=21.8
Q ss_pred CCceeEEEeeeCCCeEEEEcCCCCCCHHHH
Q 012548 411 QIHWCLAVIDRKDKKFQYLDSLKGRDKKVL 440 (461)
Q Consensus 411 gsHWsLaVI~~k~k~I~yyDSLgg~n~~vl 440 (461)
|.||.-...++..++++++|.+|-++.++.
T Consensus 33 GvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~ 62 (183)
T PF00770_consen 33 GVHWLAFAWDPRSRTFYMFDPFGFSDQKLK 62 (183)
T ss_dssp -S-EEEEEEETTTTEEEEE-TT---HHHHH
T ss_pred ceeEEEEEecCCcceEEEeCCCCCCHHHHH
Confidence 799999999999999999999999987544
No 10
>PRK11836 deubiquitinase; Provisional
Probab=57.41 E-value=8.4 Score=40.11 Aligned_cols=39 Identities=21% Similarity=0.315 Sum_probs=28.2
Q ss_pred CccccceEEeeeccCCceeEEEeeeC--------CCeEEEEcCCCCC
Q 012548 397 GLIECDKIFVPIHKQIHWCLAVIDRK--------DKKFQYLDSLKGR 435 (461)
Q Consensus 397 dLfekD~IfIPIN~gsHWsLaVI~~k--------~k~I~yyDSLgg~ 435 (461)
.+|-++.=++|||.|.||.|+++..- +-+-.+|.|+..-
T Consensus 215 ~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l 261 (403)
T PRK11836 215 PSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRAL 261 (403)
T ss_pred CCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhhh
Confidence 46678888999999999999987541 2344566676543
Done!