Query 013302
Match_columns 446
No_of_seqs 222 out of 813
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:28:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013302hhsearch_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 2E-113 4E-118 887.5 28.8 406 1-446 1-414 (490)
2 KOG0778 Protease, Ulp1 family 100.0 1.2E-49 2.6E-54 415.5 20.9 349 41-446 74-435 (511)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 3.1E-29 6.8E-34 260.9 12.5 122 316-446 377-498 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.8 2.5E-20 5.5E-25 171.0 9.3 103 334-437 1-120 (216)
5 KOG3246 Sentrin-specific cyste 99.7 6.5E-17 1.4E-21 154.5 9.1 120 311-443 11-139 (223)
6 KOG0779 Protease, Ulp1 family 99.0 1.1E-10 2.5E-15 126.5 2.6 101 320-424 353-461 (595)
7 PF03290 Peptidase_C57: Vaccin 93.2 0.11 2.3E-06 54.8 4.5 37 400-436 230-266 (423)
8 PF00770 Peptidase_C5: Adenovi 67.6 7.1 0.00015 37.6 4.0 31 411-441 33-63 (183)
9 PRK14848 deubiquitinase SseL; 63.9 5.7 0.00012 40.4 2.8 34 217-250 19-54 (317)
10 PRK11836 deubiquitinase; Provi 59.0 8.1 0.00017 40.1 2.9 39 397-435 215-261 (403)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=2e-113 Score=887.46 Aligned_cols=406 Identities=59% Similarity=0.951 Sum_probs=367.6
Q ss_pred CCcccccCCCCCccc-ccCCCCCCccccCCCCccccccccCc-ccCCccccccccccCCCCCCcccccccCCcccccccc
Q 013302 1 MGALTSNRKRGDEYL-NYQIPYQNLHISKRPRFNYTQQNQNQ-TLISSNSTVSRMSRYPEAKPPLKREVHAPCRTLKFGF 78 (446)
Q Consensus 1 m~~~~~~~~~~~~~~-~~~~~~~~~~~~k~~~~~~~~~~~~~-~~~~~~~~~~~~~~yp~~~~~~~r~~hap~~~~~~~~ 78 (446)
|||||||+||+++|+ |+++++|+|||||||||| |+|++.. ..+||||||||||||||+|+||||||||||||+|||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 78 (490)
T PLN03189 1 MGALTSNHKRSDECFNNPLSNSPDFHISKKPRFS-MAQTPDSGNQHSSNSTASRISRYPEVKSPLRREVHAPCRILKFG- 78 (490)
T ss_pred CCcccccccccccccccccccCCccccccCCCcc-ccccccccCCccccccccchhcCCCccchhhhhhcCchhhhhcc-
Confidence 999999999999999 569999999999999999 5676622 128999999999999999999999999999999999
Q ss_pred cccccccccccccCCCCccc-cccchhhhHHHHHHHHHHHhHhhhccceecCceeeecCccccceeeeccCCchhhhhhh
Q 013302 79 ADKSNQAFGSKKANGYGENQ-NLGIRMGNVLRYHLEKAKKSAFGAFRYFSKDKEVIDADNEQEKVEVISDDSSVEEIDAI 157 (446)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 157 (446)
+.|+++++++. ++|++|||||++||++||+|||+|+||++|||||||||||.|++++|||||||||||||
T Consensus 79 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (490)
T PLN03189 79 ---------RDKSTDSSEKKQGLGNVMGNFLSRKYDMAKRSALDALRYYRKDKEVVDVGDELGKVEMISDDSSIEEVEAV 149 (490)
T ss_pred ---------cccccchhhhhcchhhhHHHHhhhhhHHHHHHHHHHHHHHhcCCeeeecccccccceeccCccchhhhhee
Confidence 99999999987 79999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCcccccCCCCCCCCCCCCCccccccccccccccccccCCCCCCCccccccCCcccHHHhhhccccCC----CcCH
Q 013302 158 EDGREGRSLVFDPRPRGSDENEKPVVDIGEIDGKSAEERNYHTNLQPSSSSVLTDTNNGDVSKMIDLLSLNG----EMTV 233 (446)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~----~~~~ 233 (446)
|.+..+ +++.++.+.. ..+++..+ +.+|++ +|.++++||+||+|++ ++++
T Consensus 150 ~~~~~~-----~~~~~~~~~~-----~~~~~~~~-----~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~ 203 (490)
T PLN03189 150 EMDVDE-----VEEKAEMGNG-----LSSDVKIV-----TKNGNL-----------RVEDTSKMLDSLVLNRPETDVLSV 203 (490)
T ss_pred ecccch-----hhhccccCcc-----ccccceEe-----ecCCcc-----------cccchhhhhhceeecCcccccccc
Confidence 944311 2222221111 22445544 789999 9999999999999998 8999
Q ss_pred HHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhhhcCCCCCCchhhhhcCCCCCCCCCCHHHHHHHHHHHcc-CCCceE
Q 013302 234 DVYKKLLQSVQKRGSKLKEIEFEIELNEKRWASLKQLWPLKKPEEEQVEELPREPFIPLTKEEEAAVERAFSA-NWRAVL 312 (446)
Q Consensus 234 ~~y~~~l~~~~~R~~~L~~~~~~~~l~Ekrr~~~~~~rp~k~p~~e~~e~vp~~~f~pLS~E~e~~V~~al~~-~~~~VL 312 (446)
++|+++++++++|+.+|++|+++++++|++++.+++.+|..+ |.+|++++++|+|||+||+++|++||++ +.++||
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~pLT~e~~~~V~~al~~~~~~~vl 280 (490)
T PLN03189 204 EAYRKLLQSAERRNSKLKDLGFEIELNEKRLSSLRQSRPKPK---EPVEEVPREPFIPLTREEETEVKRAFSANNRRKVL 280 (490)
T ss_pred HHHHHHHHHHHhhcchhhhccceeehhhhHHHHHhhhccCcc---ccccccccccCcCCCHHHHHHHHHHhcCCCcccee
Confidence 999999999999999999999999999999999998888632 3458899999999999999999999998 447899
Q ss_pred eeccCCceEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechHHHHhhhcCCCCCChhhhHHhhhcc
Q 013302 313 VSHTETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAK 392 (446)
Q Consensus 313 v~~~~~gI~It~~DL~~Lkp~~WLNDeIINFYL~lL~er~~~~p~~~~kvh~FNTFFytkL~~~k~g~gy~~VkRWtkrk 392 (446)
+++++++++||++||.||.|++||||+||||||+||.++...+|...++||+||||||++|...+.+++|.+|+|||+++
T Consensus 281 vs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~k 360 (490)
T PLN03189 281 VTHENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQK 360 (490)
T ss_pred eecCCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhhc
Confidence 99988999999999999999999999999999999999877777777899999999999999876778999999999988
Q ss_pred ccCCCccccceEEEeeccCCceEEEEEecCCCeEEEEcCCCCCCHHHHHhhhcC
Q 013302 393 KLGYGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLVFF 446 (446)
Q Consensus 393 KVg~nLfskD~IfIPIN~gsHWsLaVId~k~k~I~yyDSLgg~n~~vlk~L~~y 446 (446)
+++++||++|+||||||.+.||+|+||+++.++|+|||||++.+..+++.|++|
T Consensus 361 Kigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~~~vL~~L~rY 414 (490)
T PLN03189 361 KLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRDPKILDALAKY 414 (490)
T ss_pred ccccccccCceEEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHH
Confidence 888899999999999999999999999999999999999999999999999876
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-49 Score=415.50 Aligned_cols=349 Identities=34% Similarity=0.530 Sum_probs=273.0
Q ss_pred cccCCccccccccccCCCCCCcccccccCCcc-cccccccccccccccccccCCCCccccccchhhhHHHHHHHHHHHhH
Q 013302 41 QTLISSNSTVSRMSRYPEAKPPLKREVHAPCR-TLKFGFADKSNQAFGSKKANGYGENQNLGIRMGNVLRYHLEKAKKSA 119 (446)
Q Consensus 41 ~~~~~~~~~~~~~~~yp~~~~~~~r~~hap~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 119 (446)
.-..++.+..+.|.+||++....+|+.|++-| .+..+ +.+++.+++.. .+++++...+..++..|
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 55666666655 35559999999999999
Q ss_pred hhhccceecCceeeecCccccceeeeccCCchhhhhhh--h--ccccCcccccCCCCCCCCCCCCCcccccccccccccc
Q 013302 120 FGAFRYFSKDKEVIDADNEQEKVEVISDDSSVEEIDAI--E--DGREGRSLVFDPRPRGSDENEKPVVDIGEIDGKSAEE 195 (446)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~--~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (446)
...-.++.+++.+++.+.+.+..++++.|.+...++.. | ++.++.. ..+... +. .
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 99999999999999999999999999999996665532 2 1111110 000000 00 0
Q ss_pred ccccCCCCCCCccccc-cCCcccHHHh-hhccccCC-----CcCHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHHHHhhh
Q 013302 196 RNYHTNLQPSSSSVLT-DTNNGDVSKM-IDLLSLNG-----EMTVDVYKKLLQSVQKRGSKLKEIEFEIELNEKRWASLK 268 (446)
Q Consensus 196 ~~~~~~~~~~~~~~~~-~~~~~~~~~~-l~~l~~~~-----~~~~~~y~~~l~~~~~R~~~L~~~~~~~~l~Ekrr~~~~ 268 (446)
.+..+.. ....++.+++ .+++..+. ..+.++|+...++++++...++.+.+++...+.....+.
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 778899999888899999999999888877665554444
Q ss_pred hcCCCCCCchhhhhcCCCCCCCCCCHHHHHHHHHHHcc-CCCceEeeccCCceEEccccccccCCCCcccHHHHHHHHHH
Q 013302 269 QLWPLKKPEEEQVEELPREPFIPLTKEEEAAVERAFSA-NWRAVLVSHTETGIDITGKILQCLRPGAWLNDEVINVYLGL 347 (446)
Q Consensus 269 ~~rp~k~p~~e~~e~vp~~~f~pLS~E~e~~V~~al~~-~~~~VLv~~~~~gI~It~~DL~~Lkp~~WLNDeIINFYL~l 347 (446)
.+..+.+. ..++..+.+.|+||+++.+++++++++. +..++++++ ++|+||.+||+||.+++||||+||||||+|
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 1225566789999999999999999996 888999987 469999999999999999999999999999
Q ss_pred HHHhhhcCCccccceEEechHHHHhhhcCCCCCChhhhHHhhhccccCCCccccceEEEeeccCCceEEEEEecCCCeEE
Q 013302 348 LKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQ 427 (446)
Q Consensus 348 L~er~~~~p~~~~kvh~FNTFFytkL~~~k~g~gy~~VkRWtkrkKVg~nLfskD~IfIPIN~gsHWsLaVId~k~k~I~ 427 (446)
|+++....++ +|+||+||||||++|... ||++|+|||++ ++||++|+||||||.+.||||+|||.++++|.
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 9999988775 999999999999999977 99999999984 68999999999999999999999999999999
Q ss_pred EEcCCCCCCHHHHHhhhcC
Q 013302 428 YLDSLKGRDKKVLGDLVFF 446 (446)
Q Consensus 428 yyDSLgg~n~~vlk~L~~y 446 (446)
|||||++..+.+++.|++|
T Consensus 417 y~DS~~~~~nr~~~aL~~Y 435 (511)
T KOG0778|consen 417 YYDSLGGGPNRICDALAKY 435 (511)
T ss_pred EeeccCCCCcchHHHHHHH
Confidence 9999998877777999887
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=3.1e-29 Score=260.93 Aligned_cols=122 Identities=39% Similarity=0.701 Sum_probs=112.9
Q ss_pred cCCceEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechHHHHhhhcCCCCCChhhhHHhhhccccC
Q 013302 316 TETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLG 395 (446)
Q Consensus 316 ~~~gI~It~~DL~~Lkp~~WLNDeIINFYL~lL~er~~~~p~~~~kvh~FNTFFytkL~~~k~g~gy~~VkRWtkrkKVg 395 (446)
+.++|+||.+||.||.+++||||+||||||+||....+ .+...+++|+||||||++|... ||++|+||+++
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 3445688999999999999988 99999999983
Q ss_pred CCccccceEEEeeccCCceEEEEEecCCCeEEEEcCCCCCCHHHHHhhhcC
Q 013302 396 YGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLVFF 446 (446)
Q Consensus 396 ~nLfskD~IfIPIN~gsHWsLaVId~k~k~I~yyDSLgg~n~~vlk~L~~y 446 (446)
++||++++||||||...||+|+|||.+.+.|.|||||++.+..+++.|+.|
T Consensus 448 ~dif~~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y 498 (578)
T COG5160 448 TDIFSKKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSY 498 (578)
T ss_pred cCccccceEEEEecccceEEEEEeecCcceeEEecccccCcHHHHHHHHHH
Confidence 589999999999999999999999999999999999999999999999887
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=99.82 E-value=2.5e-20 Score=170.96 Aligned_cols=103 Identities=37% Similarity=0.664 Sum_probs=81.1
Q ss_pred CcccHHHHHHHHHHHHHhhhcCCccccceEEechHHHHhhhcC-----CC-----------CCChhhhHHhhhccccCCC
Q 013302 334 AWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACG-----NK-----------GYDFRAVKRWTSAKKLGYG 397 (446)
Q Consensus 334 ~WLNDeIINFYL~lL~er~~~~p~~~~kvh~FNTFFytkL~~~-----k~-----------g~gy~~VkRWtkrkKVg~n 397 (446)
+||||+|||||+++|.++...++....++++|+|+|++.|... .. ...+..+.+|++.. ...+
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 5999999999999998654323335578999999999999821 00 12567889998753 2347
Q ss_pred ccccceEEEeecc-CCceEEEEEecCCCeEEEEcCCCCCCH
Q 013302 398 LIECDKIFVPIHK-QIHWCLAVIDRKDKKFQYLDSLKGRDK 437 (446)
Q Consensus 398 LfskD~IfIPIN~-gsHWsLaVId~k~k~I~yyDSLgg~n~ 437 (446)
++++|+||||||. +.||+|+||+++.++|.+||||++.+.
T Consensus 80 l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~ 120 (216)
T PF02902_consen 80 LFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNN 120 (216)
T ss_dssp GGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH
T ss_pred ccccCEEEEEEechhhccceeEEcccccEEEEEeccccccc
Confidence 9999999999999 999999999999999999999999987
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.69 E-value=6.5e-17 Score=154.48 Aligned_cols=120 Identities=28% Similarity=0.418 Sum_probs=92.6
Q ss_pred eEeeccCCceEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechHHHHhhhcCCCCCChhhhHHhhh
Q 013302 311 VLVSHTETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTS 390 (446)
Q Consensus 311 VLv~~~~~gI~It~~DL~~Lkp~~WLNDeIINFYL~lL~er~~~~p~~~~kvh~FNTFFytkL~~~k~g~gy~~VkRWtk 390 (446)
+|.+ +.+.++.+|+..|+++.||||.+|.||.+||.++.... .+..|++++-.-..|.... .-+.+.....
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 46889999999999999999999999999999876432 2346777653332344331 2345666554
Q ss_pred ccccCCCccccceEEEeecc---------CCceEEEEEecCCCeEEEEcCCCCCCHHHHHhh
Q 013302 391 AKKLGYGLIECDKIFVPIHK---------QIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDL 443 (446)
Q Consensus 391 rkKVg~nLfskD~IfIPIN~---------gsHWsLaVId~k~k~I~yyDSLgg~n~~vlk~L 443 (446)
. .++.++++||+|||+ |+||+|+|+..++++++||||+.+.|...++.+
T Consensus 82 p----l~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l 139 (223)
T KOG3246|consen 82 P----LDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSL 139 (223)
T ss_pred h----hhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHH
Confidence 3 378999999999997 479999999999999999999999987666654
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.01 E-value=1.1e-10 Score=126.49 Aligned_cols=101 Identities=30% Similarity=0.576 Sum_probs=86.0
Q ss_pred eEEccccccccCCCCcccHHHHHHHHHHHHHhhhcCCccccceEEechHHHHhhhcCC--------CCCChhhhHHhhhc
Q 013302 320 IDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGN--------KGYDFRAVKRWTSA 391 (446)
Q Consensus 320 I~It~~DL~~Lkp~~WLNDeIINFYL~lL~er~~~~p~~~~kvh~FNTFFytkL~~~k--------~g~gy~~VkRWtkr 391 (446)
+.++..|+.||.++.+|||-|++||++++........+....+|+|++|||..+.+.. ..-.+..+++|++
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 3688899999999999999999999999998875544556789999999999988651 1124677899997
Q ss_pred cccCCCccccceEEEeeccCCceEEEEEecCCC
Q 013302 392 KKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDK 424 (446)
Q Consensus 392 kKVg~nLfskD~IfIPIN~gsHWsLaVId~k~k 424 (446)
++++|.+++|++|+|...||.|++|+.+..
T Consensus 432 ---~~d~~~k~yi~~P~~E~~hw~laiic~p~~ 461 (595)
T KOG0779|consen 432 ---HFDLFNKDYVFVPTHERFHWKLAIICNPDL 461 (595)
T ss_pred ---ccccccceeEEecCchHhhhhccccccCcc
Confidence 379999999999999999999999999864
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=93.16 E-value=0.11 Score=54.78 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=34.3
Q ss_pred ccceEEEeeccCCceEEEEEecCCCeEEEEcCCCCCC
Q 013302 400 ECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRD 436 (446)
Q Consensus 400 skD~IfIPIN~gsHWsLaVId~k~k~I~yyDSLgg~n 436 (446)
++.++.+|+|...||.++|+|..++-+.+|||-|...
T Consensus 230 ~~RyvmFgfcY~~Hwkc~IfDk~~~~v~FydSgG~~P 266 (423)
T PF03290_consen 230 KKRYVMFGFCYMSHWKCCIFDKEKKIVYFYDSGGNIP 266 (423)
T ss_pred cccEEEeeeeehhcceEEEEeccccEEEEEcCCCCCH
Confidence 6889999999999999999999999999999987653
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=67.59 E-value=7.1 Score=37.57 Aligned_cols=31 Identities=23% Similarity=0.444 Sum_probs=22.8
Q ss_pred CCceEEEEEecCCCeEEEEcCCCCCCHHHHH
Q 013302 411 QIHWCLAVIDRKDKKFQYLDSLKGRDKKVLG 441 (446)
Q Consensus 411 gsHWsLaVId~k~k~I~yyDSLgg~n~~vlk 441 (446)
|.||.-...||..++++.||-+|-++.+..+
T Consensus 33 GvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~q 63 (183)
T PF00770_consen 33 GVHWLAFAWDPRSRTFYMFDPFGFSDQKLKQ 63 (183)
T ss_dssp -S-EEEEEEETTTTEEEEE-TT---HHHHHH
T ss_pred ceeEEEEEecCCcceEEEeCCCCCCHHHHHH
Confidence 7999999999999999999999998877654
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=63.90 E-value=5.7 Score=40.40 Aligned_cols=34 Identities=21% Similarity=0.260 Sum_probs=24.6
Q ss_pred cHHHhhhccccCC-CcCHHHHHHHHHHHH-hhhhhh
Q 013302 217 DVSKMIDLLSLNG-EMTVDVYKKLLQSVQ-KRGSKL 250 (446)
Q Consensus 217 ~~~~~l~~l~~~~-~~~~~~y~~~l~~~~-~R~~~L 250 (446)
+++..|-+|.|+. -.|..+.+-+++-.. +|++.+
T Consensus 19 n~IdLL~NiALr~D~~G~~~E~iLfdlfsgk~~~~~ 54 (317)
T PRK14848 19 NCIDLLCNLALRNDDLGHKVEKLLFDLFSGKRSGSP 54 (317)
T ss_pred hHHHHHHHHhhccccccchHHHHHHHHHcCCccCCc
Confidence 6777788888887 778888877777764 555443
No 10
>PRK11836 deubiquitinase; Provisional
Probab=59.02 E-value=8.1 Score=40.10 Aligned_cols=39 Identities=21% Similarity=0.315 Sum_probs=28.2
Q ss_pred CccccceEEEeeccCCceEEEEEecC--------CCeEEEEcCCCCC
Q 013302 397 GLIECDKIFVPIHKQIHWCLAVIDRK--------DKKFQYLDSLKGR 435 (446)
Q Consensus 397 nLfskD~IfIPIN~gsHWsLaVId~k--------~k~I~yyDSLgg~ 435 (446)
.+|-++.=+||||.|.||.|+++..- +-+-.+|.|+..-
T Consensus 215 ~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l 261 (403)
T PRK11836 215 PSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRAL 261 (403)
T ss_pred CCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhhh
Confidence 35668888999999999999987542 2334566666643
Done!