Query 008833
Match_columns 552
No_of_seqs 194 out of 870
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 17:09:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008833.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008833hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0778 Protease, Ulp1 family 100.0 2.3E-44 5E-49 385.2 19.3 215 281-531 284-509 (511)
2 PLN03189 Protease specific for 100.0 2.4E-41 5.3E-46 359.4 18.4 223 283-531 254-488 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 8.1E-39 1.7E-43 338.1 18.6 197 306-532 372-569 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.9 2.2E-25 4.9E-30 215.9 16.0 194 330-532 1-213 (216)
5 KOG0779 Protease, Ulp1 family 99.9 3.5E-26 7.5E-31 254.3 8.7 490 8-536 10-593 (595)
6 KOG3246 Sentrin-specific cyste 99.9 1.3E-23 2.7E-28 202.9 11.9 184 313-530 14-214 (223)
7 PF03290 Peptidase_C57: Vaccin 94.7 0.059 1.3E-06 57.4 6.0 39 396-440 228-266 (423)
8 PRK11836 deubiquitinase; Provi 92.3 0.22 4.9E-06 51.4 5.3 44 394-437 214-259 (403)
9 PF15328 GCOM2: Putative GRINL 90.2 0.25 5.4E-06 49.6 3.3 37 73-109 3-41 (223)
10 PRK14848 deubiquitinase SseL; 85.7 0.69 1.5E-05 47.1 3.2 33 401-437 190-222 (317)
11 PLN03189 Protease specific for 70.7 1.7 3.6E-05 48.3 0.7 21 490-510 436-456 (490)
12 COG5160 ULP1 Protease, Ulp1 fa 68.9 2 4.3E-05 47.9 0.8 73 443-532 486-565 (578)
13 KOG4439 RNA polymerase II tran 61.9 8.4 0.00018 44.8 4.0 32 81-112 209-240 (901)
14 PF02902 Peptidase_C48: Ulp1 p 61.7 1.5 3.3E-05 42.2 -1.6 20 491-510 157-176 (216)
15 KOG0778 Protease, Ulp1 family 49.0 6.5 0.00014 44.1 0.5 48 443-495 431-478 (511)
16 KOG3246 Sentrin-specific cyste 39.2 11 0.00024 37.8 0.3 43 492-535 158-215 (223)
17 PF15463 ECM11: Extracellular 30.1 75 0.0016 29.5 4.3 52 59-110 65-116 (139)
18 PRK00306 50S ribosomal protein 25.8 1.3E+02 0.0028 24.4 4.4 52 59-110 5-63 (66)
19 PF00770 Peptidase_C5: Adenovi 22.6 1.1E+02 0.0024 29.9 4.0 27 409-441 33-59 (183)
20 PHA02130 hypothetical protein 22.4 44 0.00095 27.6 1.0 35 383-417 15-50 (81)
21 PF03421 YopJ: YopJ Serine/Thr 22.0 3.6E+02 0.0078 26.2 7.5 35 402-440 74-110 (177)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.3e-44 Score=385.23 Aligned_cols=215 Identities=26% Similarity=0.441 Sum_probs=177.0
Q ss_pred ccCCCCccchHHHHHHHHhhccceeecCCCCCCCCeEEecchhcccCCCCCcCHHHHHHHHHHHHHhcCCCCcCCCcEEE
Q 008833 281 SEGSLHIETTEQADEFAECMIDAKIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHF 360 (552)
Q Consensus 281 ~~~~~~~~~~e~~~~~~~~~~~~~i~yp~~~~~~~i~Lt~~DL~~L~p~~WLND~IInFYl~~L~~~~~~~~~~~~~v~~ 360 (552)
.+..+++++.+...++..++.... .--.--...+|.||.+||.||.+++||||+||||||++|.+....+.. .++||+
T Consensus 284 ~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~-yp~~h~ 361 (511)
T KOG0778|consen 284 KEDSFPPLTEEREAQVQRAFSSRN-STEILVTHFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSK-YPKVHA 361 (511)
T ss_pred CccccccccHHHHHHHHHHhccCC-cccceehhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCC-CceEEE
Confidence 455677777666677776665311 111111245699999999999999999999999999999999876543 789999
Q ss_pred EchhhHHHHHHhhhcCCCCchhhhHHHhhhhccccccccceEEEeeecCcceEEEEEEcCCCCCCCCCeEEEEcCCCCCC
Q 008833 361 FNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHC 440 (552)
Q Consensus 361 fnTfFy~kL~~~~~~kg~d~~~~y~~VkrWtk~~dLfekd~IfIPIn~~~HWsLvVI~~p~k~~e~~p~I~~~DSL~~~~ 440 (552)
||||||++|... +|+.|+|||+++|||++|+||||||.++||+|+||+...+ +|.|||||++..
T Consensus 362 FnTFFy~kL~~~----------gy~~VkRWTk~v~if~~d~i~vPIH~~vHW~l~vid~r~k------~i~y~DS~~~~~ 425 (511)
T KOG0778|consen 362 FNTFFYTKLVGR----------GYAGVKRWTKKVDIFDKDIIFVPIHLGVHWCLAVIDLREK------TIEYYDSLGGGP 425 (511)
T ss_pred Eechhhhhhhhc----------chHHHHhHhhccCccccceeEeeeecCceEEEEEEEcccc------eEEEeeccCCCC
Confidence 999999999863 6999999999999999999999999999999999999998 999999999765
Q ss_pred ChhHHHHHHHHHHHHHHhhhccCCCCCccccccccccCCCccCCCchhhhhhcccccccCCCCCccccc-----------
Q 008833 441 SLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPRFMEEAPERLKKKDLAMFGKR----------- 509 (552)
Q Consensus 441 ~~~i~~~l~~yL~~E~~~k~~~~~~~d~pi~~~~w~~vP~Q~N~~Dcg~Fi~~~PqQ~n~~DCGvF~~~----------- 509 (552)
++ ++..|+.||++|+..+.+. ++.+ ..|.. .|+.++|+|.||+|||||+|+
T Consensus 426 nr-~~~aL~~Yl~~E~~~k~~~----~~d~--s~w~~-----------~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~ 487 (511)
T KOG0778|consen 426 NR-ICDALAKYLQDESRDKSKK----DFDV--SGWTI-----------EFVQNIPQQRNGSDCGMFVCKYADYISRDVPL 487 (511)
T ss_pred cc-hHHHHHHHHHHHHhhhhcC----CCCc--cchhh-----------hhhhccccccCCCccceEEeeechhhccCCCc
Confidence 53 6699999999999887543 2211 24663 467789999999999999874
Q ss_pred ccCHHHHHHHHHHHHHHHHHHH
Q 008833 510 WFRPEEASGLRIKIRNLLKKQF 531 (552)
Q Consensus 510 wF~~edi~~lR~~I~~LIl~L~ 531 (552)
||++.||+.+|++|+.+|+.+.
T Consensus 488 ~ftq~dmp~fR~~m~~eI~~~~ 509 (511)
T KOG0778|consen 488 TFTQQDMPYFRKKMAKEILHLK 509 (511)
T ss_pred ccChhhhHHHHHHHHHHHHhhh
Confidence 6999999999999999999763
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=2.4e-41 Score=359.38 Aligned_cols=223 Identities=22% Similarity=0.415 Sum_probs=172.4
Q ss_pred CCCCccchHHHHHHHHhhccc---eeecCCCCCCCCeEEecchhcccCCCCCcCHHHHHHHHHHHHHhcCCCCcCCCcEE
Q 008833 283 GSLHIETTEQADEFAECMIDA---KIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCH 359 (552)
Q Consensus 283 ~~~~~~~~e~~~~~~~~~~~~---~i~yp~~~~~~~i~Lt~~DL~~L~p~~WLND~IInFYl~~L~~~~~~~~~~~~~v~ 359 (552)
..+.|+++|+..+|.++|... .+.... .+.+|+||..||.||.|++||||+||||||+||.+....+.....++|
T Consensus 254 ~~~~pLT~e~~~~V~~al~~~~~~~vlvs~--~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h 331 (490)
T PLN03189 254 EPFIPLTREEETEVKRAFSANNRRKVLVTH--ENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCH 331 (490)
T ss_pred ccCcCCCHHHHHHHHHHhcCCCccceeeec--CCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceE
Confidence 457889999999999998642 122211 257899999999999999999999999999999876543333356899
Q ss_pred EEchhhHHHHHHhhhcCCCCchhhhHHHhhhhcc----ccccccceEEEeeecCcceEEEEEEcCCCCCCCCCeEEEEcC
Q 008833 360 FFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG----VNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDS 435 (552)
Q Consensus 360 ~fnTfFy~kL~~~~~~kg~d~~~~y~~VkrWtk~----~dLfekd~IfIPIn~~~HWsLvVI~~p~k~~e~~p~I~~~DS 435 (552)
+||||||++|.... ...+|..|+||+++ ++||++++||||||.+.||+|+||+++.+ +|+||||
T Consensus 332 ~FNTFFytkL~~~~------~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k------~I~yyDS 399 (490)
T PLN03189 332 FFNTFFYKKLVSGK------SGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQ------KFQYLDS 399 (490)
T ss_pred EEehHHHHHHhhcC------CcCChHHHHHHhhhcccccccccCceEEeeeecCCeeEEEEEEcCCC------eEEEEeC
Confidence 99999999998741 12469999999974 57999999999999999999999999988 9999999
Q ss_pred CCCCCChhHHHHHHHHHHHHHHhhhccCCCCCccccccccc-----cCCCccCCCchhhhhhcccccccCCCCCcccccc
Q 008833 436 LKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQ-----HLPRRIDDRIIPRFMEEAPERLKKKDLAMFGKRW 510 (552)
Q Consensus 436 L~~~~~~~i~~~l~~yL~~E~~~k~~~~~~~d~pi~~~~w~-----~vP~Q~N~~Dcg~Fi~~~PqQ~n~~DCGvF~~~w 510 (552)
|++.+. .+++.|++||..|++.+.+. ++. ...|. .+|+|.|++|||+|+..+.+.... +. ...
T Consensus 400 Lgg~~~-~vL~~L~rYL~~E~kdK~g~----d~D--~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~Sr-G~----~Lt 467 (490)
T PLN03189 400 LKGRDP-KILDALAKYYVDEVKDKSEK----DID--VSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYSR-GL----GLC 467 (490)
T ss_pred CCCCCH-HHHHHHHHHHHHHHhhhcCC----Ccc--hhcceeccCCCCCCCCCCCCHHHHHHHHHHHHcC-CC----CCC
Confidence 998764 58999999999999876432 221 12353 455666666666665554433321 11 125
Q ss_pred cCHHHHHHHHHHHHHHHHHHH
Q 008833 511 FRPEEASGLRIKIRNLLKKQF 531 (552)
Q Consensus 511 F~~edi~~lR~~I~~LIl~L~ 531 (552)
|+|++|+.+|++|...|+.+.
T Consensus 468 FSQeDMp~fRrRma~EIl~~r 488 (490)
T PLN03189 468 FGQEHMPYFRLRTAKEILRLK 488 (490)
T ss_pred cChhhhHHHHHHHHHHHHHhh
Confidence 999999999999999999875
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.1e-39 Score=338.11 Aligned_cols=197 Identities=26% Similarity=0.430 Sum_probs=154.8
Q ss_pred ecCCCCCCCCeEEecchhcccCCCCCcCHHHHHHHHHHHHHhcCCCCcCCCcEEEEchhhHHHHHHhhhcCCCCchhhhH
Q 008833 306 YYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFI 385 (552)
Q Consensus 306 ~yp~~~~~~~i~Lt~~DL~~L~p~~WLND~IInFYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~~~~y~ 385 (552)
.||+-+ +.+|+||..||.||.+++||||+||||||+||...... ...+++||+||||||++|.+. +|.
T Consensus 372 ~~~~~~-~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~-~s~~~~vh~FnTFFYT~Lsrr----------Gy~ 439 (578)
T COG5160 372 CYPFND-RSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKN-TSKREQVHLFNTFFYTKLSRR----------GYS 439 (578)
T ss_pred cccccC-cCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccC-cccccceEEeehhhHHHHHHH----------HhH
Confidence 788865 79999999999999999999999999999999555433 235789999999999999874 799
Q ss_pred HHhhhhccccccccceEEEeeecCcceEEEEEEcCCCCCCCCCeEEEEcCCCCCCChhHHHHHHHHHHHHHHhhhccCCC
Q 008833 386 KFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSP 465 (552)
Q Consensus 386 ~VkrWtk~~dLfekd~IfIPIn~~~HWsLvVI~~p~k~~e~~p~I~~~DSL~~~~~~~i~~~l~~yL~~E~~~k~~~~~~ 465 (552)
+|+||++++|||+++|||||||...||+|+|||.+.+ .|+|||||++.+ ..+++.|+.|+.+||+....+.
T Consensus 440 gVrrW~kk~dif~~k~I~iPIni~~HW~l~II~~~~~------~i~~~DSLan~~-~~v~~~L~~Y~ldE~k~~~~k~-- 510 (578)
T COG5160 440 GVRRWTKKTDIFSKKYIFIPINISYHWFLAIIDNPKK------NILYFDSLANTH-DPVLEFLRSYLLDEYKIQHDKD-- 510 (578)
T ss_pred HHHHHHhccCccccceEEEEecccceEEEEEeecCcc------eeEEecccccCc-HHHHHHHHHHHHHHHhcccCCc--
Confidence 9999999999999999999999999999999999887 999999999876 5799999999999998643321
Q ss_pred CCccccccccccCCCccCCCchhhhhhcccccccCCCCCcc-cccccCHHHHHHHHHHHHHHHHHHHh
Q 008833 466 SDLPIAERIWQHLPRRIDDRIIPRFMEEAPERLKKKDLAMF-GKRWFRPEEASGLRIKIRNLLKKQFQ 532 (552)
Q Consensus 466 ~d~pi~~~~w~~vP~Q~N~~Dcg~Fi~~~PqQ~n~~DCGvF-~~~wF~~edi~~lR~~I~~LIl~L~~ 532 (552)
..+. ..-..+|+|.|++|||+|+....+ |+.- .+.||...|++.+|+.|+..|+.+.-
T Consensus 511 ~~~~---~~~~~vPqQ~Ng~DCGV~vc~~~~------~~~~~~p~~f~~nd~~r~Rk~m~h~i~~~qi 569 (578)
T COG5160 511 PQIK---MKHCKVPQQRNGSDCGVFVCMFIR------YFLENPPEQFSKNDRPRARKNMAHTIKDLQI 569 (578)
T ss_pred hhhh---hhcCCCCCCCCCCccceEEEEeee------ecccCChhhcCccchHHHHHHHHHHHHHHHH
Confidence 0111 112334444444444444322111 1110 13589999999999999999988753
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=99.93 E-value=2.2e-25 Score=215.91 Aligned_cols=194 Identities=26% Similarity=0.452 Sum_probs=128.0
Q ss_pred CCcCHHHHHHHHHHHHHhcCCCCcCCCcEEEEchhhHHHHHHhhhcCCCC----------chhhhHHHhhhhccc---cc
Q 008833 330 AYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD----------KDSFFIKFRRWWKGV---NI 396 (552)
Q Consensus 330 ~WLND~IInFYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d----------~~~~y~~VkrWtk~~---dL 396 (552)
+||||.|||||++||......+.....++++|+||||..|......-+.+ ....+..+.+|++.. ++
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 69999999999999986643333457899999999999998332100000 023577899999887 99
Q ss_pred cccceEEEeeec-CcceEEEEEEcCCCCCCCCCeEEEEcCCCCCCC----hhHHHHHHHHHHHHHHhhhccCC-CCCccc
Q 008833 397 FQKSYVLIPIHE-DVHWSLVIICIPDKEDESGPIILHLDSLKLHCS----LSIFSNIRSFLKEEWNYLKQEVS-PSDLPI 470 (552)
Q Consensus 397 fekd~IfIPIn~-~~HWsLvVI~~p~k~~e~~p~I~~~DSL~~~~~----~~i~~~l~~yL~~E~~~k~~~~~-~~d~pi 470 (552)
+++++||||||. +.||+|+||+.+.+ +|++||||++... ..++..+..||..++........ ...+.
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~~------~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~- 153 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPKK------RIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDPDKSPFK- 153 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTTT------EEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTCE-
T ss_pred cccCEEEEEEechhhccceeEEccccc------EEEEEeccccccccccchhhhhhhhhhhhhccccccccccccceee-
Confidence 999999999999 99999999999998 9999999998765 35778888999888765433211 11121
Q ss_pred cccccccCCCccCCCchhhhhhcccccccCCCCCcccccccCHHHHHHHHHHHHHHHHHHHh
Q 008833 471 AERIWQHLPRRIDDRIIPRFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQ 532 (552)
Q Consensus 471 ~~~~w~~vP~Q~N~~Dcg~Fi~~~PqQ~n~~DCGvF~~~wF~~edi~~lR~~I~~LIl~L~~ 532 (552)
......+|+|.|++|||.|+...-+.+....- ......|+++++..+|.+|+..|.+...
T Consensus 154 -~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~-~~~~~~l~~~~i~~~r~~~a~~~~e~~~ 213 (216)
T PF02902_consen 154 -IVRPPNVPQQPNGYDCGVYVLKFMECLLEGPS-FDFSQELTEEDIKNFRKKLAVDLYEELG 213 (216)
T ss_dssp -EEEECTS-SSSSSSCHHHHHHHHHHHHHCTHH-STGCCSBTGHHHHHHHHHHHH-------
T ss_pred -ecccccccCCCCCCCcHHHHHHHHHHHHhCCC-CcccccCCHHHHHHHHHHHHhhcccccc
Confidence 11223667788888888777654443321100 0000118899999999999988877654
No 5
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=3.5e-26 Score=254.32 Aligned_cols=490 Identities=20% Similarity=0.215 Sum_probs=322.7
Q ss_pred ccCCCcccccccccCCCCCCCCceeeeccCCCCCCCCCCCCCCCCCCCchhhcCCCCchHHHHHHHHhhhhhcccccCCC
Q 008833 8 RNKRKLNIDWEEVLPGRNDDVPAELIVKKSGPPTPAQKSVPMSDDPGSGEELDRQIPDQELGVRIARMKDTYSKVRHCLP 87 (552)
Q Consensus 8 ~~~~~~~id~~~~~~~~~~~~~~~~iv~~~~~~~~~~~~~~~~~~~~d~~~~~~~~tD~~L~e~i~r~~~~l~~~~~rLp 87 (552)
..++...|+|.-++- +..-.+.+++|-++++. .|+...|...+.. ..+.|..|.+.-.|..+.+..++.+.+
T Consensus 10 ~~~~~~~~~~~~~~~-~~~~~~~~~~v~~~~~~----~~~~~~~i~~~~~---l~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (595)
T KOG0779|consen 10 SEVKSSSIMVESADV-KELLIRRLEFVVLIKKS----RPNYLNDIIIDLV---LLKDDNTLNDEYTRELSILFILAVKKG 81 (595)
T ss_pred cccccceeEeccCCC-ccceeeccccccccccC----Ccccccccccchh---eeccccCCCccccceeeecccCCcccc
Confidence 357889999999884 65667778887776655 4555677777777 889999999999999999889999999
Q ss_pred cchHhHHHHHHHHHHHHHHHhhhCC------------C--CccccccccccCCCCC------CC---ccccccC------
Q 008833 88 DKGKKILATVTRLEKECERRRLAGA------------V--PVCLDIDGCDKLTQSP------SS---DCFTQRT------ 138 (552)
Q Consensus 88 D~G~K~r~~i~~~~~E~~rR~~~~~------------~--~~~~d~~~~~~~~qs~------ss---~~~~~~~------ 138 (552)
+.|.+-+..|..++.+.-+|+..+. - ..-.|.. +++...-. .+ +.|+...
T Consensus 82 ~~~~~~~~ki~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (595)
T KOG0779|consen 82 LTSLTEPLKIAVLEEQKPHAVVPKKIISVSELRNTNLTEGTFYSDYL-NRIKNIFESVRKFFNQVSYPKFMPNVTSFMPS 160 (595)
T ss_pred ccccccccccccccccCCccccccccccchhccccCCcccceecccc-cccccccchhcchhhhcccccccchhhcccCC
Confidence 9999999999999999888877654 0 0001111 22111111 00 1111110
Q ss_pred -----------CCCcccccCcchhhhhhccccccccchhhhhhHHhhhhhcccccccccCCccccccccccccCCCCcc-
Q 008833 139 -----------PSPQIQSKSSFTSVFREKMEENRDCREANAFDKELSILAHCDRRKMRSDGDLSQRGRQNVRSSSRKWP- 206 (552)
Q Consensus 139 -----------~ss~~~~~s~f~~~f~~~~e~~~~~~~~~af~kel~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 206 (552)
+..=......|-.+|... ..++..-..++..++.... ++...-+ .++..+..-+..+.
T Consensus 161 ~~~~~q~~~~~~~~i~i~~~~~~~~fi~~--~~~~~~~~~~~~~~~~~~l-~~~~~~~-------~~~~~~~~~~~~k~~ 230 (595)
T KOG0779|consen 161 PLEKCQLQRVFTWTINITRKLFKKLFIKI--FKNEPFHFKAVKFLLPSAL-TKSDVCD-------IADLEVIFLNSRKDS 230 (595)
T ss_pred cccccccccccceeeeeeecchhhhcccC--cccCchhhhhhhcccchhc-cchhhhh-------hhcccccchhcccch
Confidence 011112344455555543 2344455555566666655 3332211 12222222222222
Q ss_pred -cc-------cCCCCCCC--CCCccccccccCCCC-CCCCCCCcc-------------------CCCcccccccccCCCc
Q 008833 207 -FH-------KGDKSFNS--NGSQKDRASLTCPSH-QSGENSSSC-------------------LPKKKESFEVLPSKNP 256 (552)
Q Consensus 207 -~~-------~~~~~~~~--n~~q~~~~s~~~~~~-~~~~~~~~~-------------------~~~~~~~~~~~~~~~~ 256 (552)
.+ ...+.+.+ -..+-.+.+|...++ +++...++. .....|.....+..+.
T Consensus 231 ~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~ 310 (595)
T KOG0779|consen 231 HSLVISSINSPNIKTFFSKEVKSRPTPASYFIFSSFLPGLDPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSE 310 (595)
T ss_pred hhhhhcccccccchhhhccccccCCCcccccccccccCCCCccccccccchhhhhhhcccccccccchhhhhhcCcccch
Confidence 11 00111110 111222222322221 222222222 4556677777777776
Q ss_pred ccccc--cCeeecCCCCCCCcCCcccccCCCCccchHHHHHHHHhhccceeecCCC-CCCCCeEEecchhcccCCCCCcC
Q 008833 257 RLRKE--QNLVLLDEDESPVEDASEESEGSLHIETTEQADEFAECMIDAKIYYPSR-VDPESVEICYTDINHLAPAAYLT 333 (552)
Q Consensus 257 ~~~~~--~~~v~ld~~~~~~e~~~~~~~~~~~~~~~e~~~~~~~~~~~~~i~yp~~-~~~~~i~Lt~~DL~~L~p~~WLN 333 (552)
.++.. .++..+++.+-. +.. .+...++. .-.|++. .. ..+.++..||.||.++++||
T Consensus 311 s~~~~~~~~~~~~~~~~~~------------~~l------~~~~~~el-~~~~~p~~~~-~~~~v~~~Dl~cl~~~e~L~ 370 (595)
T KOG0779|consen 311 SRSRDSLDNWFPVKEADKQ------------RTL------IVKLAIEL-LEVRVPQICN-QSHQVNNNDLVCLEEGEFLN 370 (595)
T ss_pred hcccccccccccccccccc------------cch------HHHhhccc-cccCCccccc-cccceeccchhhccccchhh
Confidence 66665 344444432211 111 12223332 2233332 22 36789999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCcCCCcEEEEchhhHHHHHHhhhcCCCC--chhhhHHHhhhhccccccccceEEEeeecCcc
Q 008833 334 SPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD--KDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVH 411 (552)
Q Consensus 334 D~IInFYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d--~~~~y~~VkrWtk~~dLfekd~IfIPIn~~~H 411 (552)
|.||+||++|+..+..........+|+|++|||..+.+....++.+ ....+..+++|++.+++|.++||++|+|+..|
T Consensus 371 d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~~~d~~~k~yi~~P~~E~~h 450 (595)
T KOG0779|consen 371 DTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTRHFDLFNKDYVFVPTHERFH 450 (595)
T ss_pred hhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeeeccccccceeEEecCchHhh
Confidence 9999999999999887644567899999999999999987666555 34567899999999999999999999999999
Q ss_pred eEEEEEEcCCCCCCCCCeEEEEcCCCCCCChhHHHHHHHHHHHHHHhhhccCCCCCccccccccccC----------CCc
Q 008833 412 WSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHL----------PRR 481 (552)
Q Consensus 412 WsLvVI~~p~k~~e~~p~I~~~DSL~~~~~~~i~~~l~~yL~~E~~~k~~~~~~~d~pi~~~~w~~v----------P~Q 481 (552)
|.|+|||+++.+.+......+++++..+....+...+..+|..+|.+.+......+.++....|..+ |+|
T Consensus 451 w~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~p~q 530 (595)
T KOG0779|consen 451 WKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELEEELPRRLPRGKSETVREPQQ 530 (595)
T ss_pred hhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCcccccccccccccccccCcccccccccccCc
Confidence 9999999999887777789999999888777788889999999998876553444454444455444 478
Q ss_pred cCCCchhhhhh--------cccccccCCCCCcccccccCHHHHHHHHHHHHHHHHHHHhhhcc
Q 008833 482 IDDRIIPRFME--------EAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQISSA 536 (552)
Q Consensus 482 ~N~~Dcg~Fi~--------~~PqQ~n~~DCGvF~~~wF~~edi~~lR~~I~~LIl~L~~~~~~ 536 (552)
.|..|||.|+. ++|+..+..|-++....||.+.++.++|..++++|..|+.....
T Consensus 531 ~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~~~~l~~~~~~ 593 (595)
T KOG0779|consen 531 NNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRNLGRKLFTSQSS 593 (595)
T ss_pred cCcccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhccccccccccCC
Confidence 88889888776 35666666677766556999999999999999999999876544
No 6
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.90 E-value=1.3e-23 Score=202.95 Aligned_cols=184 Identities=20% Similarity=0.308 Sum_probs=125.4
Q ss_pred CCCeEEecchhcccCCCCCcCHHHHHHHHHHHHHhcCCCCcCCCcEEEEchhhHHHHHHhhhcCCCCchhhhHHHhhhhc
Q 008833 313 PESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWK 392 (552)
Q Consensus 313 ~~~i~Lt~~DL~~L~p~~WLND~IInFYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~~~~y~~VkrWtk 392 (552)
...|.|+.+|+..|.+..||||.+|+||++||.+..... ..+.|++++-....|... + .-..+.....
T Consensus 14 y~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s---~~~~~ll~P~~t~~l~~~----~-----~~~e~~~~~~ 81 (223)
T KOG3246|consen 14 YFDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRS---EPDLHLLRPSLTFFLRHA----P-----NPEEIAMVLD 81 (223)
T ss_pred eeehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhccc---CcchhccCHHHHHHHHhC----C-----CcHHHHHhcC
Confidence 477999999999999999999999999999999987653 234678776444444432 1 1235666777
Q ss_pred cccccccceEEEeeec---------CcceEEEEEEcCCCCCCCCCeEEEEcCCCCCCCh---hHHHHHHHHHHHHHHhhh
Q 008833 393 GVNIFQKSYVLIPIHE---------DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSL---SIFSNIRSFLKEEWNYLK 460 (552)
Q Consensus 393 ~~dLfekd~IfIPIn~---------~~HWsLvVI~~p~k~~e~~p~I~~~DSL~~~~~~---~i~~~l~~yL~~E~~~k~ 460 (552)
..++++|+|||+|||+ |+||+|+|+..+.+ .++||||+.+++.. .+.+.++.+|......+.
T Consensus 82 pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~------~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~~~ 155 (223)
T KOG3246|consen 82 PLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDG------KFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAKRV 155 (223)
T ss_pred hhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCC------cEEEeecccCCCcHHHHHHHHHHHHHHhhhhhhcc
Confidence 8899999999999997 36999999999998 99999999988753 466667666654332210
Q ss_pred ccCCCCCccccccccccCCCccCCCchhhhhhcc----cccccCCCCCccc-ccccCHHHHHHHHHHHHHHHHHH
Q 008833 461 QEVSPSDLPIAERIWQHLPRRIDDRIIPRFMEEA----PERLKKKDLAMFG-KRWFRPEEASGLRIKIRNLLKKQ 530 (552)
Q Consensus 461 ~~~~~~d~pi~~~~w~~vP~Q~N~~Dcg~Fi~~~----PqQ~n~~DCGvF~-~~wF~~edi~~lR~~I~~LIl~L 530 (552)
-...|+|.|+||||.||... .+++. -||+=. -.-..+..|.++|..|..||..|
T Consensus 156 --------------~~~~~qQqNgyDCG~hV~~~t~~l~~~~~--~~~~~~~~~~~~~~~i~~lr~~l~~LI~sl 214 (223)
T KOG3246|consen 156 --------------ECKCLQQQNGYDCGLHVCCNTRVLAERLL--RCPYATSSQLLVVDLIKALREELLDLIQSL 214 (223)
T ss_pred --------------cccChhhhcCCchhHHHHHHHHHHHHHHh--ccccccccchhhHHHHHHHHHHHHHHHHHh
Confidence 02235566777777776542 22222 123211 01123445566666666666555
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=94.68 E-value=0.059 Score=57.43 Aligned_cols=39 Identities=26% Similarity=0.233 Sum_probs=33.2
Q ss_pred ccccceEEEeeecCcceEEEEEEcCCCCCCCCCeEEEEcCCCCCC
Q 008833 396 IFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHC 440 (552)
Q Consensus 396 Lfekd~IfIPIn~~~HWsLvVI~~p~k~~e~~p~I~~~DSL~~~~ 440 (552)
=-++.|+.+|++...||..+|++...+ .+.+|||-|...
T Consensus 228 ~~~~RyvmFgfcY~~Hwkc~IfDk~~~------~v~FydSgG~~P 266 (423)
T PF03290_consen 228 NSKKRYVMFGFCYMSHWKCCIFDKEKK------IVYFYDSGGNIP 266 (423)
T ss_pred hccccEEEeeeeehhcceEEEEecccc------EEEEEcCCCCCH
Confidence 346789999999999999999998776 888999987653
No 8
>PRK11836 deubiquitinase; Provisional
Probab=92.26 E-value=0.22 Score=51.43 Aligned_cols=44 Identities=25% Similarity=0.311 Sum_probs=29.7
Q ss_pred ccccccceEEEeeecCcceEEEEEEcCCCCC--CCCCeEEEEcCCC
Q 008833 394 VNIFQKSYVLIPIHEDVHWSLVIICIPDKED--ESGPIILHLDSLK 437 (552)
Q Consensus 394 ~dLfekd~IfIPIn~~~HWsLvVI~~p~k~~--e~~p~I~~~DSL~ 437 (552)
..++-+++=+||||.+.||.|+++..-..+. ..+..-++|.|+.
T Consensus 214 ~~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~ 259 (403)
T PRK11836 214 DPSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLR 259 (403)
T ss_pred CCCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHh
Confidence 4566678889999999999999886432110 0123456677775
No 9
>PF15328 GCOM2: Putative GRINL1B complex locus protein 2
Probab=90.19 E-value=0.25 Score=49.64 Aligned_cols=37 Identities=35% Similarity=0.406 Sum_probs=31.2
Q ss_pred HHhhhhhc--ccccCCCcchHhHHHHHHHHHHHHHHHhh
Q 008833 73 ARMKDTYS--KVRHCLPDKGKKILATVTRLEKECERRRL 109 (552)
Q Consensus 73 ~r~~~~l~--~~~~rLpD~G~K~r~~i~~~~~E~~rR~~ 109 (552)
+|+...|. ++-.+|||||+||+..+..|..++.+|.-
T Consensus 3 ~rq~klL~nkkfi~kLpDKGkKI~~~~~kL~~ai~~r~e 41 (223)
T PF15328_consen 3 RRQEKLLRNKKFICKLPDKGKKIQDFVEKLKAAIAEREE 41 (223)
T ss_pred hHHHHHhcchhhhhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 46666663 77799999999999999999999999844
No 10
>PRK14848 deubiquitinase SseL; Provisional
Probab=85.69 E-value=0.69 Score=47.11 Aligned_cols=33 Identities=15% Similarity=0.203 Sum_probs=22.7
Q ss_pred eEEEeeecCcceEEEEEEcCCCCCCCCCeEEEEcCCC
Q 008833 401 YVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLK 437 (552)
Q Consensus 401 ~IfIPIn~~~HWsLvVI~~p~k~~e~~p~I~~~DSL~ 437 (552)
.=+||||.+.||.|+++..-.. +..-++|.|+.
T Consensus 190 nevF~INtg~HWil~~~~Ki~~----kiKC~iFNs~~ 222 (317)
T PRK14848 190 NEVFLINTGDHWLLCLFYKLAE----KIKCLIFNTYY 222 (317)
T ss_pred ceEEEecCCCcEEEEEhHHhhh----hceEEEeecHh
Confidence 3458999999999998764321 13455667775
No 11
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=70.71 E-value=1.7 Score=48.32 Aligned_cols=21 Identities=33% Similarity=0.605 Sum_probs=18.0
Q ss_pred hhhcccccccCCCCCcccccc
Q 008833 490 FMEEAPERLKKKDLAMFGKRW 510 (552)
Q Consensus 490 Fi~~~PqQ~n~~DCGvF~~~w 510 (552)
|+..+|+|.|++|||||+|.+
T Consensus 436 ~~~~vPQQ~NG~DCGVFVL~y 456 (490)
T PLN03189 436 FVEDLPEQKNGYDCGMFMIKY 456 (490)
T ss_pred cCCCCCCCCCCCCHHHHHHHH
Confidence 346789999999999999864
No 12
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=68.88 E-value=2 Score=47.88 Aligned_cols=73 Identities=16% Similarity=0.204 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHHHHhhhccCCCCCccccccccccCCCccCCCchhhhhhcccccccCCCCCcccccc---cC---HHH-
Q 008833 443 SIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPRFMEEAPERLKKKDLAMFGKRW---FR---PEE- 515 (552)
Q Consensus 443 ~i~~~l~~yL~~E~~~k~~~~~~~d~pi~~~~w~~vP~Q~N~~Dcg~Fi~~~PqQ~n~~DCGvF~~~w---F~---~ed- 515 (552)
..-..|.+||...+....+. - ...-| | +.++-..+|||.|++|||||+|+. |. |++
T Consensus 486 n~~~~v~~~L~~Y~ldE~k~--~---------~~k~~-~-----~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f 548 (578)
T COG5160 486 NTHDPVLEFLRSYLLDEYKI--Q---------HDKDP-Q-----IKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQF 548 (578)
T ss_pred cCcHHHHHHHHHHHHHHHhc--c---------cCCch-h-----hhhhcCCCCCCCCCCccceEEEEeeeecccCChhhc
Confidence 45678888988765543221 0 11112 2 233445789999999999999963 42 444
Q ss_pred HHHHHHHHHHHHHHHHh
Q 008833 516 ASGLRIKIRNLLKKQFQ 532 (552)
Q Consensus 516 i~~lR~~I~~LIl~L~~ 532 (552)
...-|-+++..+...+.
T Consensus 549 ~~nd~~r~Rk~m~h~i~ 565 (578)
T COG5160 549 SKNDRPRARKNMAHTIK 565 (578)
T ss_pred CccchHHHHHHHHHHHH
Confidence 35567777776665543
No 13
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=61.89 E-value=8.4 Score=44.81 Aligned_cols=32 Identities=38% Similarity=0.617 Sum_probs=28.4
Q ss_pred ccccCCCcchHhHHHHHHHHHHHHHHHhhhCC
Q 008833 81 KVRHCLPDKGKKILATVTRLEKECERRRLAGA 112 (552)
Q Consensus 81 ~~~~rLpD~G~K~r~~i~~~~~E~~rR~~~~~ 112 (552)
.+...|||+|.++..+|+.+.+|++||..-+.
T Consensus 209 ~~~~~Lpd~g~~~~kr~~el~~~~~~~~~~~~ 240 (901)
T KOG4439|consen 209 KAIDDLPDKGARLIKRLQELDRELERRMQFGE 240 (901)
T ss_pred hhhhhCCccHHHHHHHHHHHHHHHHHHHhhhh
Confidence 44569999999999999999999999998653
No 14
>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=61.66 E-value=1.5 Score=42.20 Aligned_cols=20 Identities=10% Similarity=0.260 Sum_probs=15.6
Q ss_pred hhcccccccCCCCCcccccc
Q 008833 491 MEEAPERLKKKDLAMFGKRW 510 (552)
Q Consensus 491 i~~~PqQ~n~~DCGvF~~~w 510 (552)
...+|+|.|++|||+|++.+
T Consensus 157 ~~~~pqQ~n~~dCGv~vl~~ 176 (216)
T PF02902_consen 157 PPNVPQQPNGYDCGVYVLKF 176 (216)
T ss_dssp ECTS-SSSSSSCHHHHHHHH
T ss_pred cccccCCCCCCCcHHHHHHH
Confidence 34679999999999998753
No 15
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=48.99 E-value=6.5 Score=44.10 Aligned_cols=48 Identities=13% Similarity=0.113 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHHHhhhccCCCCCccccccccccCCCccCCCchhhhhhccc
Q 008833 443 SIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPRFMEEAP 495 (552)
Q Consensus 443 ~i~~~l~~yL~~E~~~k~~~~~~~d~pi~~~~w~~vP~Q~N~~Dcg~Fi~~~P 495 (552)
.+.+.|...-...-+..-. . .+|.+. .-.++|+|.||+|||+|+....
T Consensus 431 aL~~Yl~~E~~~k~~~~~d-~--s~w~~~--~~~~iP~Q~Ng~DCG~f~c~~~ 478 (511)
T KOG0778|consen 431 ALAKYLQDESRDKSKKDFD-V--SGWTIE--FVQNIPQQRNGSDCGMFVCKYA 478 (511)
T ss_pred HHHHHHHHHHhhhhcCCCC-c--cchhhh--hhhccccccCCCccceEEeeec
Confidence 5777777777666554322 1 123321 1258999999999999987543
No 16
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=39.21 E-value=11 Score=37.84 Aligned_cols=43 Identities=12% Similarity=-0.016 Sum_probs=34.3
Q ss_pred hcccccccCCCCCcccc-------ccc--------CHHHHHHHHHHHHHHHHHHHhhhc
Q 008833 492 EEAPERLKKKDLAMFGK-------RWF--------RPEEASGLRIKIRNLLKKQFQISS 535 (552)
Q Consensus 492 ~~~PqQ~n~~DCGvF~~-------~wF--------~~edi~~lR~~I~~LIl~L~~~~~ 535 (552)
...+|| |++|||+|+| .|| .+.++..+|+.++..|.+|+..-.
T Consensus 158 ~~~qQq-NgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~l~~LI~slg 215 (223)
T KOG3246|consen 158 KCLQQQ-NGYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREELLDLIQSLG 215 (223)
T ss_pred cChhhh-cCCchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHhC
Confidence 357777 9999999985 344 356778899999999999997643
No 17
>PF15463 ECM11: Extracellular mutant protein 11
Probab=30.07 E-value=75 Score=29.54 Aligned_cols=52 Identities=17% Similarity=0.178 Sum_probs=41.6
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccccCCCcchHhHHHHHHHHHHHHHHHhhh
Q 008833 59 LDRQIPDQELGVRIARMKDTYSKVRHCLPDKGKKILATVTRLEKECERRRLA 110 (552)
Q Consensus 59 ~~~~~tD~~L~e~i~r~~~~l~~~~~rLpD~G~K~r~~i~~~~~E~~rR~~~ 110 (552)
.|+.+|..+-.+.=..+-.....|..+|-+.=.++|.++..++.|+.+|-.+
T Consensus 65 ~fs~ls~~eWe~~Gd~~l~qf~~l~~kl~~~R~~~r~~~~~fe~eI~~R~ea 116 (139)
T PF15463_consen 65 FFSNLSFDEWEEAGDWFLEQFSELMQKLKEARRKLRKKFAVFEDEINRRAEA 116 (139)
T ss_pred HHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7788888877766655555555666888888999999999999999998664
No 18
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=25.83 E-value=1.3e+02 Score=24.41 Aligned_cols=52 Identities=17% Similarity=0.296 Sum_probs=38.3
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccc-----cCC--CcchHhHHHHHHHHHHHHHHHhhh
Q 008833 59 LDRQIPDQELGVRIARMKDTYSKVR-----HCL--PDKGKKILATVTRLEKECERRRLA 110 (552)
Q Consensus 59 ~~~~~tD~~L~e~i~r~~~~l~~~~-----~rL--pD~G~K~r~~i~~~~~E~~rR~~~ 110 (552)
+++.+|+.||++.|...+..|-.+. ..+ |-.-..+|+.|.|+.=.+..|..+
T Consensus 5 elr~ls~~eL~~~l~~lkkeL~~lR~~~~~~~~~n~~~i~~~rk~IARi~Tvl~er~~~ 63 (66)
T PRK00306 5 ELRELSVEELNEKLLELKKELFNLRFQKATGQLENTHRLREVRRDIARIKTVLRERELG 63 (66)
T ss_pred HHhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3589999999999999988873221 223 334467788999998888877765
No 19
>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=22.61 E-value=1.1e+02 Score=29.87 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=18.2
Q ss_pred CcceEEEEEEcCCCCCCCCCeEEEEcCCCCCCC
Q 008833 409 DVHWSLVIICIPDKEDESGPIILHLDSLKLHCS 441 (552)
Q Consensus 409 ~~HWsLvVI~~p~k~~e~~p~I~~~DSL~~~~~ 441 (552)
+.||.-+..+.... +++.||.+|-.+.
T Consensus 33 GvHWlA~Aw~P~s~------t~YmFDPfGfsd~ 59 (183)
T PF00770_consen 33 GVHWLAFAWDPRSR------TFYMFDPFGFSDQ 59 (183)
T ss_dssp -S-EEEEEEETTTT------EEEEE-TT---HH
T ss_pred ceeEEEEEecCCcc------eEEEeCCCCCCHH
Confidence 69999999888776 9999999998753
No 20
>PHA02130 hypothetical protein
Probab=22.43 E-value=44 Score=27.57 Aligned_cols=35 Identities=20% Similarity=0.508 Sum_probs=29.9
Q ss_pred hhHHHhhhhc-cccccccceEEEeeecCcceEEEEE
Q 008833 383 FFIKFRRWWK-GVNIFQKSYVLIPIHEDVHWSLVII 417 (552)
Q Consensus 383 ~y~~VkrWtk-~~dLfekd~IfIPIn~~~HWsLvVI 417 (552)
..+.++.|.. +.+-++-|++=||.-...||-|+-.
T Consensus 15 s~~sl~~wl~~~~dswdddil~ipfkstv~w~lcp~ 50 (81)
T PHA02130 15 SWESLREWLDERFDSWDDDILSIPFKSTVYWDLCPY 50 (81)
T ss_pred HHHHHHHHHHhcccccccchhcccccceeeeccCcc
Confidence 3568899984 6799999999999999999999754
No 21
>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=22.03 E-value=3.6e+02 Score=26.24 Aligned_cols=35 Identities=9% Similarity=0.292 Sum_probs=21.0
Q ss_pred EEEeeec-CcceEEEEEE-cCCCCCCCCCeEEEEcCCCCCC
Q 008833 402 VLIPIHE-DVHWSLVIIC-IPDKEDESGPIILHLDSLKLHC 440 (552)
Q Consensus 402 IfIPIn~-~~HWsLvVI~-~p~k~~e~~p~I~~~DSL~~~~ 440 (552)
.+|++.. +.|-..+=|- .++ .++.|++|+|-....
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~----~k~SlI~~Epa~~~~ 110 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN----GKPSLIVFEPASFYG 110 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC----CCceEEEEccccccC
Confidence 4556443 4565554443 222 467999999997554
Done!