Query 002578
Match_columns 906
No_of_seqs 256 out of 1104
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:49:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002578.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002578hhsearch_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 3.4E-40 7.3E-45 368.7 22.2 258 280-585 204-487 (490)
2 KOG0778 Protease, Ulp1 family 100.0 3.1E-40 6.7E-45 371.5 14.8 193 344-585 315-508 (511)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 2.7E-40 5.8E-45 367.5 13.8 199 337-588 371-570 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 1.1E-28 2.4E-33 248.0 18.5 196 361-589 1-215 (216)
5 KOG3246 Sentrin-specific cyste 99.9 4E-26 8.6E-31 233.4 15.7 188 345-586 15-215 (223)
6 KOG0779 Protease, Ulp1 family 99.8 6E-22 1.3E-26 231.1 6.8 232 346-591 352-593 (595)
7 KOG0779 Protease, Ulp1 family 96.0 0.0013 2.7E-08 78.8 -1.3 302 354-677 107-415 (595)
8 PRK14848 deubiquitinase SseL; 95.0 0.05 1.1E-06 58.8 6.4 88 431-544 189-276 (317)
9 PF03290 Peptidase_C57: Vaccin 95.0 0.052 1.1E-06 61.6 6.8 108 428-550 229-351 (423)
10 PRK11836 deubiquitinase; Provi 93.0 0.19 4.2E-06 55.4 6.2 107 425-545 214-328 (403)
11 PF03421 YopJ: YopJ Serine/Thr 73.0 18 0.0004 37.6 8.8 29 516-544 135-163 (177)
12 PF00770 Peptidase_C5: Adenovi 51.8 37 0.0008 35.7 6.3 81 440-545 33-118 (183)
13 PRK15371 effector protein YopJ 41.0 98 0.0021 35.0 7.9 27 519-545 161-187 (287)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=3.4e-40 Score=368.75 Aligned_cols=258 Identities=22% Similarity=0.458 Sum_probs=196.6
Q ss_pred cCchhhhhhhccccccccccccccccCcchhhhhhhccccC--------CCCCccccCCCcccccc----ccCC------
Q 002578 280 QHWPERLNKIISLDVRYKERWNTVDFDSKYEENSLLSQKSR--------LPSKCCSIEFDEPFEDV----VYPK------ 341 (906)
Q Consensus 280 ~~~~~~~e~i~s~~~R~~~~~~~v~~d~d~e~~~~~~~~~~--------~p~k~~~~~~de~~e~~----vYP~------ 341 (906)
|.|.+..+.....+.|++++.-.+.+.. ...+.+++... .+..++.| |.++|+.. ..+.
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~p-LT~e~~~~V~~al~~~~~~~vl 280 (490)
T PLN03189 204 EAYRKLLQSAERRNSKLKDLGFEIELNE--KRLSSLRQSRPKPKEPVEEVPREPFIP-LTREEETEVKRAFSANNRRKVL 280 (490)
T ss_pred HHHHHHHHHHHhhcchhhhccceeehhh--hHHHHHhhhccCccccccccccccCcC-CCHHHHHHHHHHhcCCCcccee
Confidence 4677777777788899988876665532 22334443332 22234444 44444432 2221
Q ss_pred --CCCCceEEehhhhcccCCCCccCHHHHHHHHHHHHhhcccC--CCCcEEEechHHHHHhhccCCCCCchhhhhhHHHH
Q 002578 342 --DDPDAVLISERDVKLLEPDTFINDTIIDFYIKYLNNKIQTD--RQQDFHFFNSFFFRKLADLDKDPSSACEGRAAFQR 417 (906)
Q Consensus 342 --~~~~~IsLt~sDL~~L~pgeWLND~IInFYLeyL~~~l~~e--~~~rvhfFNSFFysKL~~~~k~Pss~~~~~~~yqr 417 (906)
..+.+++||++||.||.|++||||+|||||+++|.++...+ ...++|+||||||++|.... ...+|++
T Consensus 281 vs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~--------~~ygY~~ 352 (490)
T PLN03189 281 VTHENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGK--------SGYDYKA 352 (490)
T ss_pred eecCCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcC--------CcCChHH
Confidence 23568999999999999999999999999999998764322 34689999999999998631 1247999
Q ss_pred HHhhhhc----ccccCCceEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchhhHHHHHHHHH
Q 002578 418 VRKWTRK----VNLFEKDYIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRGLKNLIQGYLS 493 (906)
Q Consensus 418 VkrWTKk----vDLFeKDyIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~l~~~Ir~YL~ 493 (906)
|+|||++ ++||++|+||||||.+.||+|+||+++. ++|.|||||++.+..+.+.|+.||.
T Consensus 353 VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~----------------k~I~yyDSLgg~~~~vL~~L~rYL~ 416 (490)
T PLN03189 353 VRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKD----------------QKFQYLDSLKGRDPKILDALAKYYV 416 (490)
T ss_pred HHHHhhhcccccccccCceEEeeeecCCeeEEEEEEcCC----------------CeEEEEeCCCCCCHHHHHHHHHHHH
Confidence 9999974 5799999999999999999999999874 4899999999998888999999999
Q ss_pred HHHHHhcCCCCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHhHH
Q 002578 494 EEWKERHSNTDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEVSM 573 (906)
Q Consensus 494 ~E~k~K~~~~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dIs~ 573 (906)
.|++.+++...+. +.|.. ....++|||.||+|||||||+||++|.++.++.| ++.++..
T Consensus 417 ~E~kdK~g~d~D~--s~W~~--~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtF-----------------SQeDMp~ 475 (490)
T PLN03189 417 DEVKDKSEKDIDV--SSWEQ--EFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCF-----------------GQEHMPY 475 (490)
T ss_pred HHHhhhcCCCcch--hccee--ccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCc-----------------ChhhhHH
Confidence 9999887654431 33431 1235899999999999999999999999876554 5567888
Q ss_pred HHHHHHHHHHHH
Q 002578 574 KRAQIKKLLYEI 585 (906)
Q Consensus 574 kR~~IrkLIleL 585 (906)
+|.+|..-|+++
T Consensus 476 fRrRma~EIl~~ 487 (490)
T PLN03189 476 FRLRTAKEILRL 487 (490)
T ss_pred HHHHHHHHHHHh
Confidence 999998888765
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.1e-40 Score=371.53 Aligned_cols=193 Identities=29% Similarity=0.619 Sum_probs=166.8
Q ss_pred CCceEEehhhhcccCCCCccCHHHHHHHHHHHHhhcccCC-CCcEEEechHHHHHhhccCCCCCchhhhhhHHHHHHhhh
Q 002578 344 PDAVLISERDVKLLEPDTFINDTIIDFYIKYLNNKIQTDR-QQDFHFFNSFFFRKLADLDKDPSSACEGRAAFQRVRKWT 422 (906)
Q Consensus 344 ~~~IsLt~sDL~~L~pgeWLND~IInFYLeyL~~~l~~e~-~~rvhfFNSFFysKL~~~~k~Pss~~~~~~~yqrVkrWT 422 (906)
..++.||..||.||.+++||||+||||||++|.++..... -+++|+||||||.+|.. ++|+.|+|||
T Consensus 315 ~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~~------------~gy~~VkRWT 382 (511)
T KOG0778|consen 315 HFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLVG------------RGYAGVKRWT 382 (511)
T ss_pred hccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEEEechhhhhhhh------------cchHHHHhHh
Confidence 4569999999999999999999999999999999876542 57899999999999986 6899999999
Q ss_pred hcccccCCceEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchhhHHHHHHHHHHHHHHhcCC
Q 002578 423 RKVNLFEKDYIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRGLKNLIQGYLSEEWKERHSN 502 (906)
Q Consensus 423 KkvDLFeKDyIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~l~~~Ir~YL~~E~k~K~~~ 502 (906)
+++|||++|.||||||.+.||+|+||+... ++|.|||||++...+++.+|..||..|+..|++.
T Consensus 383 k~v~if~~d~i~vPIH~~vHW~l~vid~r~----------------k~i~y~DS~~~~~nr~~~aL~~Yl~~E~~~k~~~ 446 (511)
T KOG0778|consen 383 KKVDIFDKDIIFVPIHLGVHWCLAVIDLRE----------------KTIEYYDSLGGGPNRICDALAKYLQDESRDKSKK 446 (511)
T ss_pred hccCccccceeEeeeecCceEEEEEEEccc----------------ceEEEeeccCCCCcchHHHHHHHHHHHHhhhhcC
Confidence 999999999999999999999999999653 5999999999765555599999999999998877
Q ss_pred CCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHhHHHHHHHHHHH
Q 002578 503 TDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEVSMKRAQIKKLL 582 (906)
Q Consensus 503 ~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dIs~kR~~IrkLI 582 (906)
..+- +.|.. .+ ..++|||.||+|||+|+|+|++++.++.|+.|+ ..++-.+|+.|...|
T Consensus 447 ~~d~--s~w~~-~~-~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ft-----------------q~dmp~fR~~m~~eI 505 (511)
T KOG0778|consen 447 DFDV--SGWTI-EF-VQNIPQQRNGSDCGMFVCKYADYISRDVPLTFT-----------------QQDMPYFRKKMAKEI 505 (511)
T ss_pred CCCc--cchhh-hh-hhccccccCCCccceEEeeechhhccCCCcccC-----------------hhhhHHHHHHHHHHH
Confidence 6642 23432 22 348999999999999999999999999987654 456777899999988
Q ss_pred HHH
Q 002578 583 YEI 585 (906)
Q Consensus 583 leL 585 (906)
+.+
T Consensus 506 ~~~ 508 (511)
T KOG0778|consen 506 LHL 508 (511)
T ss_pred Hhh
Confidence 864
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.7e-40 Score=367.55 Aligned_cols=199 Identities=33% Similarity=0.689 Sum_probs=174.4
Q ss_pred cccCCCCCCceEEehhhhcccCCCCccCHHHHHHHHHHHHhhccc-CCCCcEEEechHHHHHhhccCCCCCchhhhhhHH
Q 002578 337 VVYPKDDPDAVLISERDVKLLEPDTFINDTIIDFYIKYLNNKIQT-DRQQDFHFFNSFFFRKLADLDKDPSSACEGRAAF 415 (906)
Q Consensus 337 ~vYP~~~~~~IsLt~sDL~~L~pgeWLND~IInFYLeyL~~~l~~-e~~~rvhfFNSFFysKL~~~~k~Pss~~~~~~~y 415 (906)
.+||..+..+++||..|+.||+++.||||+|||||++||...-.. ..++++|+||||||++|.+ .+|
T Consensus 371 ~~~~~~~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~~s~~~~vh~FnTFFYT~Lsr------------rGy 438 (578)
T COG5160 371 SCYPFNDRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKNTSKREQVHLFNTFFYTKLSR------------RGY 438 (578)
T ss_pred ccccccCcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccCcccccceEEeehhhHHHHHH------------HHh
Confidence 469999999999999999999999999999999999999665443 3578999999999999985 689
Q ss_pred HHHHhhhhcccccCCceEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchhhHHHHHHHHHHH
Q 002578 416 QRVRKWTRKVNLFEKDYIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRGLKNLIQGYLSEE 495 (906)
Q Consensus 416 qrVkrWTKkvDLFeKDyIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~l~~~Ir~YL~~E 495 (906)
+.|+||++++|||+++|||||||...||+|+|||.+. +.|.|||||++.+..+.+.|+.|+.+|
T Consensus 439 ~gVrrW~kk~dif~~k~I~iPIni~~HW~l~II~~~~----------------~~i~~~DSLan~~~~v~~~L~~Y~ldE 502 (578)
T COG5160 439 SGVRRWTKKTDIFSKKYIFIPINISYHWFLAIIDNPK----------------KNILYFDSLANTHDPVLEFLRSYLLDE 502 (578)
T ss_pred HHHHHHHhccCccccceEEEEecccceEEEEEeecCc----------------ceeEEecccccCcHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999764 589999999999999999999999999
Q ss_pred HHHhcCCCCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHhHHHH
Q 002578 496 WKERHSNTDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEVSMKR 575 (906)
Q Consensus 496 ~k~K~~~~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dIs~kR 575 (906)
|+..+.... | +.....+||||.||+|||||||+|+++|+.++|. ||...++...|
T Consensus 503 ~k~~~~k~~------~--~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~-----------------~f~~nd~~r~R 557 (578)
T COG5160 503 YKIQHDKDP------Q--IKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPE-----------------QFSKNDRPRAR 557 (578)
T ss_pred HhcccCCch------h--hhhhcCCCCCCCCCCccceEEEEeeeecccCChh-----------------hcCccchHHHH
Confidence 987665321 2 2455679999999999999999999999999764 55566777889
Q ss_pred HHHHHHHHHHHHh
Q 002578 576 AQIKKLLYEISKD 588 (906)
Q Consensus 576 ~~IrkLIleL~ke 588 (906)
+.|+..|..+.-.
T Consensus 558 k~m~h~i~~~qi~ 570 (578)
T COG5160 558 KNMAHTIKDLQIN 570 (578)
T ss_pred HHHHHHHHHHHHH
Confidence 9999888876543
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=99.96 E-value=1.1e-28 Score=248.03 Aligned_cols=196 Identities=35% Similarity=0.670 Sum_probs=137.1
Q ss_pred CccCHHHHHHHHHHHHhhcc--cCCCCcEEEechHHHHHhhccC----CCCCc---h-hhhhhHHHHHHhhhhcc---cc
Q 002578 361 TFINDTIIDFYIKYLNNKIQ--TDRQQDFHFFNSFFFRKLADLD----KDPSS---A-CEGRAAFQRVRKWTRKV---NL 427 (906)
Q Consensus 361 eWLND~IInFYLeyL~~~l~--~e~~~rvhfFNSFFysKL~~~~----k~Pss---~-~~~~~~yqrVkrWTKkv---DL 427 (906)
+||||+|||||++||.++.. .....++++|+|+|+.+|.... +++.. . ......+..+++|++.. ++
T Consensus 1 ~wLnd~iId~y~~~l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 80 (216)
T PF02902_consen 1 EWLNDSIIDFYLEYLRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKKNL 80 (216)
T ss_dssp --EEHHHHHHHHHHHHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTSTG
T ss_pred CcCCHHHHHHHHHHHHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhccccccc
Confidence 59999999999999986542 3356899999999999998311 11100 0 00134567889999887 99
Q ss_pred cCCceEEEEeec-CCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCch-----hhHHHHHHHHHHHHHHhcC
Q 002578 428 FEKDYIFIPVNY-SLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHR-----GLKNLIQGYLSEEWKERHS 501 (906)
Q Consensus 428 FeKDyIFIPIN~-~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~-----~l~~~Ir~YL~~E~k~K~~ 501 (906)
+++++||||||. +.||+|+||+.+. .+|++||||++.+. .+...+..+|...+.....
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~----------------~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 144 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPK----------------KRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEG 144 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTT----------------TEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHS
T ss_pred cccCEEEEEEechhhccceeEEcccc----------------cEEEEEeccccccccccchhhhhhhhhhhhhccccccc
Confidence 999999999999 9999999999875 48999999998876 4667788888888766544
Q ss_pred CCCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHhHHHHHHHHHH
Q 002578 502 NTDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEVSMKRAQIKKL 581 (906)
Q Consensus 502 ~~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dIs~kR~~IrkL 581 (906)
...+ ..+|. ...+.++|||.|++|||+|||+||++++.+.+..+. ..|+..++...|.++...
T Consensus 145 ~~~~--~~~~~--~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~-------------~~l~~~~i~~~r~~~a~~ 207 (216)
T PF02902_consen 145 RDPD--KSPFK--IVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFS-------------QELTEEDIKNFRKKLAVD 207 (216)
T ss_dssp SCT---TTTCE--EEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGC-------------CSBTGHHHHHHHHHHHH-
T ss_pred cccc--cceee--ecccccccCCCCCCCcHHHHHHHHHHHHhCCCCccc-------------ccCCHHHHHHHHHHHHhh
Confidence 3221 12232 234568999999999999999999999998654421 116778999999999998
Q ss_pred HHHHHHhc
Q 002578 582 LYEISKDH 589 (906)
Q Consensus 582 IleL~ke~ 589 (906)
|.+....+
T Consensus 208 ~~e~~~~~ 215 (216)
T PF02902_consen 208 LYEELGSR 215 (216)
T ss_dssp --------
T ss_pred cccccccC
Confidence 88776543
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.94 E-value=4e-26 Score=233.35 Aligned_cols=188 Identities=25% Similarity=0.473 Sum_probs=136.1
Q ss_pred CceEEehhhhcccCCCCccCHHHHHHHHHHHHhhcccCCCCcEEEechHHHHHhhccCCCCCchhhhhhHHHHHHhhhhc
Q 002578 345 DAVLISERDVKLLEPDTFINDTIIDFYIKYLNNKIQTDRQQDFHFFNSFFFRKLADLDKDPSSACEGRAAFQRVRKWTRK 424 (906)
Q Consensus 345 ~~IsLt~sDL~~L~pgeWLND~IInFYLeyL~~~l~~e~~~rvhfFNSFFysKL~~~~k~Pss~~~~~~~yqrVkrWTKk 424 (906)
..+.|+++|++.|+++.||||.+|+||.+||.+........ .|+++|-.-..|... .+| +.++.....
T Consensus 15 ~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s~~~-~~ll~P~~t~~l~~~-~~~----------~e~~~~~~p 82 (223)
T KOG3246|consen 15 FDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSEPD-LHLLRPSLTFFLRHA-PNP----------EEIAMVLDP 82 (223)
T ss_pred eehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccCcc-hhccCHHHHHHHHhC-CCc----------HHHHHhcCh
Confidence 46889999999999999999999999999999876554333 689988544444442 111 456666777
Q ss_pred ccccCCceEEEEeecC---------CcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchh----hHHHHHHH
Q 002578 425 VNLFEKDYIFIPVNYS---------LHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRG----LKNLIQGY 491 (906)
Q Consensus 425 vDLFeKDyIFIPIN~~---------sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~----l~~~Ir~Y 491 (906)
.++++|+|||+|||++ +||+|+|+..|. ..++||||+.+.|.. +.+.++.+
T Consensus 83 l~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~----------------~~f~hyDS~~n~nt~~a~~l~~kl~~l 146 (223)
T KOG3246|consen 83 LDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPD----------------GKFYHYDSLSNGNTKDAKSLMKKLRAL 146 (223)
T ss_pred hhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeC----------------CcEEEeecccCCCcHHHHHHHHHHHHH
Confidence 8999999999999983 699999999875 379999999998865 44455555
Q ss_pred HHHHHHHhcCCCCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHh
Q 002578 492 LSEEWKERHSNTDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEV 571 (906)
Q Consensus 492 L~~E~k~K~~~~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dI 571 (906)
|.. + +. ...+..+|||.||||||+|||.+++.++...- ...+.. ...-..+..+
T Consensus 147 l~~----~-----------~~--~~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~----~~~~~~-----~~~~~~~~~i 200 (223)
T KOG3246|consen 147 LKK----K-----------FA--KRVECKCLQQQNGYDCGLHVCCNTRVLAERLL----RCPYAT-----SSQLLVVDLI 200 (223)
T ss_pred Hhh----h-----------hh--hcccccChhhhcCCchhHHHHHHHHHHHHHHh----cccccc-----ccchhhHHHH
Confidence 532 1 11 11266899999999999999999998776521 111111 0112234567
Q ss_pred HHHHHHHHHHHHHHH
Q 002578 572 SMKRAQIKKLLYEIS 586 (906)
Q Consensus 572 s~kR~~IrkLIleL~ 586 (906)
.++|+.|+.||..|.
T Consensus 201 ~~lr~~l~~LI~slg 215 (223)
T KOG3246|consen 201 KALREELLDLIQSLG 215 (223)
T ss_pred HHHHHHHHHHHHHhC
Confidence 888888888887775
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=6e-22 Score=231.12 Aligned_cols=232 Identities=28% Similarity=0.519 Sum_probs=166.4
Q ss_pred ceEEehhhhcccCCCCccCHHHHHHHHHHHHhhcc--cCCCCcEEEechHHHHHhhccCCCCCchhhhhhHHHHHHhhhh
Q 002578 346 AVLISERDVKLLEPDTFINDTIIDFYIKYLNNKIQ--TDRQQDFHFFNSFFFRKLADLDKDPSSACEGRAAFQRVRKWTR 423 (906)
Q Consensus 346 ~IsLt~sDL~~L~pgeWLND~IInFYLeyL~~~l~--~e~~~rvhfFNSFFysKL~~~~k~Pss~~~~~~~yqrVkrWTK 423 (906)
.+.++..|+.||.++++|||.||+||++|+..+.. +.....+|+|++|||+++.+.......-......+.++++|++
T Consensus 352 ~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~ 431 (595)
T KOG0779|consen 352 SHQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTR 431 (595)
T ss_pred ccceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeee
Confidence 56889999999999999999999999999997654 3467899999999999998743221111012345678999999
Q ss_pred cccccCCceEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCch-hhHHHHHHHHHHHHHHhcCC
Q 002578 424 KVNLFEKDYIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHR-GLKNLIQGYLSEEWKERHSN 502 (906)
Q Consensus 424 kvDLFeKDyIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~-~l~~~Ir~YL~~E~k~K~~~ 502 (906)
.+++|.++||++|+|+..||+|+++|+|+... .......+++++..... .....+..+|..+|......
T Consensus 432 ~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~----------es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 501 (595)
T KOG0779|consen 432 HFDLFNKDYVFVPTHERFHWKLAIICNPDLET----------ETPRPRLELLILKLSADFPIVENILDFMKVASIYNNEL 501 (595)
T ss_pred ccccccceeEEecCchHhhhhccccccCcccc----------CccccchhhhhhccccccchhhhhhhhhhhcccccCcc
Confidence 99999999999999999999999999997421 11223455666554433 34455667776666543322
Q ss_pred -CCCCCCcccceec------cccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHhHHHH
Q 002578 503 -TDDEVPSKFLRLQ------FAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEVSMKR 575 (906)
Q Consensus 503 -~~Dd~sskf~~lr------~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dIs~kR 575 (906)
...+.+..|...+ -.....|||.|.+|||+|++.|++.|+.++|..+. +.... ..+..||++.++.++|
T Consensus 502 ~~~~~~~~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~---~~~~~-~~~l~~~~~~~~~~~r 577 (595)
T KOG0779|consen 502 IVTEDLELEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAPERFN---IEDEG-TINLEWFPPKEILKFR 577 (595)
T ss_pred cccccccccccccccCcccccccccccCccCcccchhhHHHHHHHhhhChhhhcc---ccccc-ccccccCCchHHhhhh
Confidence 1111111111100 01112399999999999999999999999988754 11111 1224599999999999
Q ss_pred HHHHHHHHHHHHhccC
Q 002578 576 AQIKKLLYEISKDHSR 591 (906)
Q Consensus 576 ~~IrkLIleL~ke~~~ 591 (906)
..++++++.|+...+.
T Consensus 578 ~~~r~~~~~l~~~~~~ 593 (595)
T KOG0779|consen 578 DEIRNLGRKLFTSQSS 593 (595)
T ss_pred hhhhccccccccccCC
Confidence 9999999999887654
No 7
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=95.99 E-value=0.0013 Score=78.82 Aligned_cols=302 Identities=22% Similarity=0.150 Sum_probs=169.5
Q ss_pred hcccCCCCccCHHHHHHHHHHHHhhcccCCCCcEEEechHHHHHhhccCCCCCchhhhhhHHHHHHhhh--hcccccCCc
Q 002578 354 VKLLEPDTFINDTIIDFYIKYLNNKIQTDRQQDFHFFNSFFFRKLADLDKDPSSACEGRAAFQRVRKWT--RKVNLFEKD 431 (906)
Q Consensus 354 L~~L~pgeWLND~IInFYLeyL~~~l~~e~~~rvhfFNSFFysKL~~~~k~Pss~~~~~~~yqrVkrWT--KkvDLFeKD 431 (906)
.....+-.+.|++...+|..|+ ...........++|+..+|.++..........+......+++.+|+ ....+|.+.
T Consensus 107 ~~~~~~~~~t~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~i~i~~~~~~~~ 185 (595)
T KOG0779|consen 107 IISVSELRNTNLTEGTFYSDYL-NRIKNIFESVRKFFNQVSYPKFMPNVTSFMPSPLEKCQLQRVFTWTINITRKLFKKL 185 (595)
T ss_pred cccchhccccCCcccceecccc-cccccccchhcchhhhcccccccchhhcccCCcccccccccccceeeeeeecchhhh
Confidence 3344455678888888888888 5544444456788888888777653221111111222334554465 456788999
Q ss_pred eEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCch-----hhHHHHHHHHHHHHHHhcCCCCCC
Q 002578 432 YIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHR-----GLKNLIQGYLSEEWKERHSNTDDE 506 (906)
Q Consensus 432 yIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~-----~l~~~Ir~YL~~E~k~K~~~~~Dd 506 (906)
+|.++.+...||.+...+.|..+... .+ ......++..+.+-.+.|. .....+..++..+|+.+....-..
T Consensus 186 fi~~~~~~~~~~~~~~~~~~~~l~~~---~~-~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~ 261 (595)
T KOG0779|consen 186 FIKIFKNEPFHFKAVKFLLPSALTKS---DV-CDIADLEVIFLNSRKDSHSLVISSINSPNIKTFFSKEVKSRPTPASYF 261 (595)
T ss_pred cccCcccCchhhhhhhcccchhccch---hh-hhhhcccccchhcccchhhhhhcccccccchhhhccccccCCCccccc
Confidence 99999999999999999988643211 01 0122345666666555331 112233445555554433222222
Q ss_pred CCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCCccccccccccccCCCCChhHhHHHHHHHHHHHHHHH
Q 002578 507 VPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFNPLKKKQVSNFLNRNWFPPAEVSMKRAQIKKLLYEIS 586 (906)
Q Consensus 507 ~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fsp~~i~~~s~fL~~nWFpp~dIs~kR~~IrkLIleL~ 586 (906)
....+....-.+...+++.+..|||+.+...-..........+.+......+.....+||+..+....|..+.++..+|.
T Consensus 262 ~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~s~~~~~~~~~~~~~~~~~~~~l~~~~~~el~ 341 (595)
T KOG0779|consen 262 IFSSFLPGLDPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSESRSRDSLDNWFPVKEADKQRTLIVKLAIELL 341 (595)
T ss_pred ccccccCCCCccccccccchhhhhhhcccccccccchhhhhhcCcccchhcccccccccccccccccccchHHHhhcccc
Confidence 22222222234567889999999997766655433333333333333333345556799999999999999999999998
Q ss_pred HhccCCCCCCCCCCCCCCCCCCCCCcCccccccccccCccCCCCCCCCCCCCCCCcccceEEEecCCCCCCCCccCCCCC
Q 002578 587 KDHSRRKDPSADSVDEHPSSQPTNDKIGKETGAVILGQMWNPTLPGQQGFSSISDAEKGIQISISGASPQRDAQCTRDPE 666 (906)
Q Consensus 587 ke~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 666 (906)
..+...... . .+ +. +-.| ..++++. .- +.....+.-..+-.+.+.++ ...++.++-.+...-+
T Consensus 342 ~~~~p~~~~-~-----~~--~v----~~~D--l~cl~~~-e~-L~d~i~dfyl~~i~~~~l~~-~~~s~~~h~f~tffyk 404 (595)
T KOG0779|consen 342 EVRVPQICN-Q-----SH--QV----NNND--LVCLEEG-EF-LNDTIKDFYLEYIRQYLLSQ-KELSNDRHIFSTFFYK 404 (595)
T ss_pred ccCCccccc-c-----cc--ce----eccc--hhhcccc-ch-hhhhhhhhhhHHHHHhhhcc-cccCcchhhhhhHHHh
Confidence 887763211 1 01 11 1111 1222110 00 11123333334455666665 6777777777766666
Q ss_pred cchhhhhccCC
Q 002578 667 FSFKEQCKLGT 677 (906)
Q Consensus 667 ~~~~~~~~~~~ 677 (906)
.+.+.+...|-
T Consensus 405 ~l~~~~~~~~~ 415 (595)
T KOG0779|consen 405 RLCRKLRQKSN 415 (595)
T ss_pred hhhhhhhhhhh
Confidence 66666655544
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=94.97 E-value=0.05 Score=58.83 Aligned_cols=88 Identities=20% Similarity=0.393 Sum_probs=48.4
Q ss_pred ceEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchhhHHHHHHHHHHHHHHhcCCCCCCCCcc
Q 002578 431 DYIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRGLKNLIQGYLSEEWKERHSNTDDEVPSK 510 (906)
Q Consensus 431 DyIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~l~~~Ir~YL~~E~k~K~~~~~Dd~ssk 510 (906)
+.=+||||.+.||.|+++..- ..|.+| ++|.|++.-+....+.| +.. .+..+...+ +
T Consensus 189 ~nevF~INtg~HWil~~~~Ki-------------~~kiKC-~iFNs~~~l~eNs~~~i---i~~---ak~ag~~~e---~ 245 (317)
T PRK14848 189 HNEVFLINTGDHWLLCLFYKL-------------AEKIKC-LIFNTYYDLNENTKQEI---IEA---AKIAGISEN---E 245 (317)
T ss_pred cceEEEecCCCcEEEEEhHHh-------------hhhceE-EEeecHhhhhhhHHHHH---HHH---HHhhCcccC---C
Confidence 444599999999999987521 123445 56888776543222222 211 111111111 0
Q ss_pred cceeccccCCCCCcCCCCChHHHHHHHHHHHHcc
Q 002578 511 FLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKE 544 (906)
Q Consensus 511 f~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~ 544 (906)
.+.|+..++ ||.=..-||+|++++++.+...
T Consensus 246 --di~fIe~nL-QqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 246 --DVNFIETNL-QNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred --ceEEeehhh-hhhCCCcchHHHHHHHHHHHhc
Confidence 122333332 4444467999999999966554
No 9
>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=94.97 E-value=0.052 Score=61.56 Aligned_cols=108 Identities=16% Similarity=0.320 Sum_probs=64.4
Q ss_pred cCCceEEEEeecCCcEEEEEEecCCCCCccchhh---hhhccCCCeEEEEcCCCCCch------h------hHHHHHHHH
Q 002578 428 FEKDYIFIPVNYSLHWSLIVICHPGEVPYFRDDE---IEKSLKVPCILHMDSIKGSHR------G------LKNLIQGYL 492 (906)
Q Consensus 428 FeKDyIFIPIN~~sHWsLvVIc~P~~v~~~~D~e---i~~~~K~p~Il~LDSL~gs~~------~------l~~~Ir~YL 492 (906)
-++.|+.+|.+...||..+|++....+..|-|.. .++-.+-+.+++|+.-.|-++ . -.+.|.+|+
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dIDVLfrfF 308 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDKEKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDIDVLFRFF 308 (423)
T ss_pred ccccEEEeeeeehhcceEEEEeccccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchHHHHHHH
Confidence 4679999999999999999998654333222210 001112223344433222111 0 145567777
Q ss_pred HHHHHHhcCCCCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccCccCCC
Q 002578 493 SEEWKERHSNTDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEALSNFN 550 (906)
Q Consensus 493 ~~E~k~K~~~~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~Pi~Fs 550 (906)
...+..+.+ +.++. -.|--..+||+|.+.||-.....+|..|.
T Consensus 309 ~d~f~~~~g---------ciNve------vnQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 309 EDSFGVKYG---------CINVE------VNQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred Hhhccccee---------EEEhh------hhhhcccccchHHHHHHHHHHccCchhHH
Confidence 655433221 11111 26888999999999999999999888774
No 10
>PRK11836 deubiquitinase; Provisional
Probab=92.95 E-value=0.19 Score=55.37 Aligned_cols=107 Identities=21% Similarity=0.338 Sum_probs=56.7
Q ss_pred ccccCCceEEEEeecCCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchh----hHHHHHHHHH----HHH
Q 002578 425 VNLFEKDYIFIPVNYSLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRG----LKNLIQGYLS----EEW 496 (906)
Q Consensus 425 vDLFeKDyIFIPIN~~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~----l~~~Ir~YL~----~E~ 496 (906)
-.++-++.=+||||.+.||.|+++..-- . +.....+.+| ++|.|+..-+.. ....+..|-. +..
T Consensus 214 ~~~~~k~~elFpINtg~HWil~~l~Ki~---~----~~~~~ekiKC-~IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~~ 285 (403)
T PRK11836 214 DPSWPKEVQLFPINTGGHWILVSLQKIV---N----EKNNTQQIKC-VIFNSLRALGHDKENSLKRVINSFNSELMGEMS 285 (403)
T ss_pred CCCCcccceEEEecCCCcEEEEEeHHhh---h----cccccceeEE-EEEecHhhhccchhhHHHHHHHhhhhhhhhhcc
Confidence 4566788889999999999999885211 0 0001123444 567887654322 2233332211 111
Q ss_pred HHhcCCCCCCCCcccceeccccCCCCCcCCCCChHHHHHHHHHHHHccC
Q 002578 497 KERHSNTDDEVPSKFLRLQFAPLELPQQQNSFDCGLFLLHYVELFLKEA 545 (906)
Q Consensus 497 k~K~~~~~Dd~sskf~~lr~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~ 545 (906)
..+.+..... + .+.|+..++ ||.=..-||+|+++-+..++...
T Consensus 286 ~~~ik~~~~e---~--ei~fie~dL-Qq~vpngCGlFv~~a~Qe~i~q~ 328 (403)
T PRK11836 286 NNNIKVHLTE---P--EIIFLHADL-QQYLSQSCGAFVCMAAQEVIEQR 328 (403)
T ss_pred hhhhcccccC---C--ceEEEechh-hhcCCCccceehHHHHHHHHHHh
Confidence 1122111111 1 123444333 44445689999999998666553
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=73.03 E-value=18 Score=37.64 Aligned_cols=29 Identities=38% Similarity=0.676 Sum_probs=24.8
Q ss_pred cccCCCCCcCCCCChHHHHHHHHHHHHcc
Q 002578 516 FAPLELPQQQNSFDCGLFLLHYVELFLKE 544 (906)
Q Consensus 516 ~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~ 544 (906)
+..+++..|+..+|||+|-|.+|..+.++
T Consensus 135 ~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 135 FAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred EEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 34457889999999999999999988765
No 12
>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=51.84 E-value=37 Score=35.72 Aligned_cols=81 Identities=22% Similarity=0.356 Sum_probs=39.0
Q ss_pred CCcEEEEEEecCCCCCccchhhhhhccCCCeEEEEcCCCCCchhhHHHHH----HHHHHHHHHhcCCCCCCCCcccceec
Q 002578 440 SLHWSLIVICHPGEVPYFRDDEIEKSLKVPCILHMDSIKGSHRGLKNLIQ----GYLSEEWKERHSNTDDEVPSKFLRLQ 515 (906)
Q Consensus 440 ~sHWsLvVIc~P~~v~~~~D~ei~~~~K~p~Il~LDSL~gs~~~l~~~Ir----~YL~~E~k~K~~~~~Dd~sskf~~lr 515 (906)
+.||.-+..+ |. ..++++||.++-+..++.+.-+ ..|+.-.-... +.+ .+.
T Consensus 33 GvHWlA~Aw~-P~---------------s~t~YmFDPfGfsd~~L~qiY~FeYe~llrRSAL~~~-------~dR--Cv~ 87 (183)
T PF00770_consen 33 GVHWLAFAWD-PR---------------SRTFYMFDPFGFSDQKLKQIYQFEYEGLLRRSALSST-------PDR--CVT 87 (183)
T ss_dssp -S-EEEEEEE-TT---------------TTEEEEE-TT---HHHHHHHH----HHHHHHHHHHH--------TTS--EEE
T ss_pred ceeEEEEEec-CC---------------cceEEEeCCCCCCHHHHHHHHhhhHHHHHHHHhhcCC-------CCc--eEE
Confidence 5899888776 53 3589999999998876544321 11111111100 011 122
Q ss_pred c-ccCCCCCcCCCCChHHHHHHHHHHHHccC
Q 002578 516 F-APLELPQQQNSFDCGLFLLHYVELFLKEA 545 (906)
Q Consensus 516 ~-v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~ 545 (906)
+ ...+.-|=+++--||+|-+.|+.+|...+
T Consensus 88 LvkstqtVQ~p~SaaCGLFC~lFL~aF~~~p 118 (183)
T PF00770_consen 88 LVKSTQTVQCPCSAACGLFCCLFLHAFVHYP 118 (183)
T ss_dssp EEEE-EE-S-TT---HHHHHHHHHHHHHH-T
T ss_pred EEeccceeeccCchhHHHHHHHHHHHHHhCC
Confidence 1 12233355689999999999999998875
No 13
>PRK15371 effector protein YopJ; Provisional
Probab=41.00 E-value=98 Score=34.98 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=23.1
Q ss_pred CCCCCcCCCCChHHHHHHHHHHHHccC
Q 002578 519 LELPQQQNSFDCGLFLLHYVELFLKEA 545 (906)
Q Consensus 519 ~~VPQQ~Ng~DCGVFVL~YaE~fl~~~ 545 (906)
...=.|+-.+|||+|-|.+|.+..+..
T Consensus 161 ie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 161 VEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred EecccccCcccchhhhHHHHHHHhhhh
Confidence 456689999999999999999887653
Done!