Query 008203
Match_columns 574
No_of_seqs 259 out of 1124
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 20:48:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008203.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008203hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0778 Protease, Ulp1 family 100.0 3.4E-46 7.3E-51 400.3 16.7 212 285-530 285-499 (511)
2 PLN03189 Protease specific for 100.0 4E-43 8.7E-48 373.8 24.1 226 286-552 254-487 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 1.3E-41 2.9E-46 359.5 16.1 196 309-552 372-567 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 7.8E-30 1.7E-34 249.4 17.1 195 333-554 1-213 (216)
5 KOG0779 Protease, Ulp1 family 100.0 8.3E-30 1.8E-34 284.5 9.9 512 8-559 10-594 (595)
6 KOG3246 Sentrin-specific cyste 100.0 1.8E-28 3.9E-33 236.4 16.0 191 317-555 15-217 (223)
7 PF03290 Peptidase_C57: Vaccin 97.0 0.0013 2.8E-08 69.6 6.4 92 400-521 229-351 (423)
8 PRK14848 deubiquitinase SseL; 95.2 0.043 9.3E-07 55.5 6.3 35 404-442 190-224 (317)
9 PRK11836 deubiquitinase; Provi 94.6 0.16 3.4E-06 52.5 8.6 46 396-441 213-260 (403)
10 PF15328 GCOM2: Putative GRINL 90.2 0.26 5.6E-06 49.7 3.4 37 73-109 3-41 (223)
11 PRK15371 effector protein YopJ 90.2 4.2 9.2E-05 42.5 12.3 28 488-515 159-186 (287)
12 PF03421 YopJ: YopJ Serine/Thr 87.8 2.7 5.8E-05 41.0 8.4 88 405-515 74-163 (177)
13 PF00770 Peptidase_C5: Adenovi 87.6 1.1 2.3E-05 43.4 5.3 81 412-515 33-117 (183)
14 KOG4439 RNA polymerase II tran 66.5 6.2 0.00013 45.9 4.0 31 81-111 209-239 (901)
15 PF15463 ECM11: Extracellular 32.9 69 0.0015 29.9 4.5 52 59-110 65-116 (139)
16 PF12252 SidE: Dot/Icm substra 29.1 97 0.0021 38.0 5.7 38 406-450 49-93 (1439)
17 PRK00306 50S ribosomal protein 27.8 1.2E+02 0.0026 24.6 4.5 52 59-110 5-63 (66)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-46 Score=400.28 Aligned_cols=212 Identities=28% Similarity=0.521 Sum_probs=177.3
Q ss_pred cCCCCccchHhHHHHHHhhcc---CeeecCCCCCCCceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCce
Q 008203 285 EGSLHIETTEQADEFAECMID---AKIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDC 361 (574)
Q Consensus 285 ~~~~~~~~~e~~~e~~~~~~~---~~i~yP~~~~~~~i~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~~ 361 (574)
+..+++++.+...++.+.+.+ ..+-. ..+++.||.+||.||.+++||||+||||||++|.++...... ++++
T Consensus 285 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~-yp~~ 359 (511)
T KOG0778|consen 285 EDSFPPLTEEREAQVQRAFSSRNSTEILV----THFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSK-YPKV 359 (511)
T ss_pred ccccccccHHHHHHHHHHhccCCccccee----hhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCC-CceE
Confidence 445667776666777766542 11111 246799999999999999999999999999999999876544 7899
Q ss_pred EEEchhhHHHHHHhhhcCCCCchhhhHHHHhhhccccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEecCCCC
Q 008203 362 HFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKL 441 (574)
Q Consensus 362 ~~fnTfFy~kL~~~~~~kg~d~~~~~~~vkrWtk~~nifekd~IfIPIn~~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~ 441 (574)
|+||||||++|... +|.+|+|||+++|||++|+||||||.+.||+|+||++..+ +|.|||||++
T Consensus 360 h~FnTFFy~kL~~~----------gy~~VkRWTk~v~if~~d~i~vPIH~~vHW~l~vid~r~k------~i~y~DS~~~ 423 (511)
T KOG0778|consen 360 HAFNTFFYTKLVGR----------GYAGVKRWTKKVDIFDKDIIFVPIHLGVHWCLAVIDLREK------TIEYYDSLGG 423 (511)
T ss_pred EEEechhhhhhhhc----------chHHHHhHhhccCccccceeEeeeecCceEEEEEEEcccc------eEEEeeccCC
Confidence 99999999999862 5899999999999999999999999999999999999999 9999999997
Q ss_pred CCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhcCCcccc
Q 008203 442 HCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLK 521 (574)
Q Consensus 442 ~~~k~i~~~L~~yL~~e~~~~~~~~~~~d~~~~~~~W~~~p~~i~~~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~~p~~ft 521 (574)
..++ ++..|..||..|+..+.+. | |+...|+.. ...++|||.||+|||||+|+|++++.++.|..|+
T Consensus 424 ~~nr-~~~aL~~Yl~~E~~~k~~~----~--~d~s~w~~~------~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ft 490 (511)
T KOG0778|consen 424 GPNR-ICDALAKYLQDESRDKSKK----D--FDVSGWTIE------FVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFT 490 (511)
T ss_pred CCcc-hHHHHHHHHHHHHhhhhcC----C--CCccchhhh------hhhccccccCCCccceEEeeechhhccCCCcccC
Confidence 6544 5599999999999775432 2 233568753 2458999999999999999999999999999999
Q ss_pred hhhhhcccc
Q 008203 522 KKDLAMFGK 530 (574)
Q Consensus 522 q~dm~~f~~ 530 (574)
|+|||+||+
T Consensus 491 q~dmp~fR~ 499 (511)
T KOG0778|consen 491 QQDMPYFRK 499 (511)
T ss_pred hhhhHHHHH
Confidence 999987543
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=4e-43 Score=373.78 Aligned_cols=226 Identities=23% Similarity=0.471 Sum_probs=181.5
Q ss_pred CCCCccchHhHHHHHHhhccC----eeecCCCCCCCceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCce
Q 008203 286 GSLHIETTEQADEFAECMIDA----KIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDC 361 (574)
Q Consensus 286 ~~~~~~~~e~~~e~~~~~~~~----~i~yP~~~~~~~i~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~~ 361 (574)
..+.|++.|+..+|.++|... .++.. .+++++||.+||.||.+++||||+||||||.||.++...+.....++
T Consensus 254 ~~~~pLT~e~~~~V~~al~~~~~~~vlvs~---~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~ 330 (490)
T PLN03189 254 EPFIPLTREEETEVKRAFSANNRRKVLVTH---ENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKC 330 (490)
T ss_pred ccCcCCCHHHHHHHHHHhcCCCccceeeec---CCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccce
Confidence 347888999999999988632 23322 24689999999999999999999999999999987654433345689
Q ss_pred EEEchhhHHHHHHhhhcCCCCchhhhHHHHhhhcc----ccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEec
Q 008203 362 HFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG----VNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLD 437 (574)
Q Consensus 362 ~~fnTfFy~kL~~~~~~kg~d~~~~~~~vkrWtk~----~nifekd~IfIPIn~~~HWsLlVI~~~~k~~~~~p~I~~lD 437 (574)
|+||||||++|.... ....|.+|+||++. +++|++++||||||.+.||+|+||+++.+ +|+|||
T Consensus 331 h~FNTFFytkL~~~~------~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k------~I~yyD 398 (490)
T PLN03189 331 HFFNTFFYKKLVSGK------SGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQ------KFQYLD 398 (490)
T ss_pred EEEehHHHHHHhhcC------CcCChHHHHHHhhhcccccccccCceEEeeeecCCeeEEEEEEcCCC------eEEEEe
Confidence 999999999998731 12358999999974 57999999999999999999999999988 999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhcCC
Q 008203 438 SLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAP 517 (574)
Q Consensus 438 SL~~~~~k~i~~~L~~yL~~e~~~~~~~~~~~d~~~~~~~W~~~p~~i~~~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~~p 517 (574)
||++.+ ..+++.|..||..|++.+.+ .++ ....|... ...++|||.||||||||||+||++|..+.+
T Consensus 399 SLgg~~-~~vL~~L~rYL~~E~kdK~g----~d~--D~s~W~~~------~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~ 465 (490)
T PLN03189 399 SLKGRD-PKILDALAKYYVDEVKDKSE----KDI--DVSSWEQE------FVEDLPEQKNGYDCGMFMIKYIDFYSRGLG 465 (490)
T ss_pred CCCCCC-HHHHHHHHHHHHHHHhhhcC----CCc--chhcceec------cCCCCCCCCCCCCHHHHHHHHHHHHcCCCC
Confidence 999875 45889999999999876432 222 33567531 245899999999999999999999999988
Q ss_pred cccchhhhhcccccCCCHHHHHHHHHHHHHHHHHH
Q 008203 518 ERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQ 552 (574)
Q Consensus 518 ~~ftq~dm~~f~~~wf~p~~i~~~R~~I~~lIl~L 552 (574)
..|+|+||++ +|.+|..-|+.+
T Consensus 466 LtFSQeDMp~-------------fRrRma~EIl~~ 487 (490)
T PLN03189 466 LCFGQEHMPY-------------FRLRTAKEILRL 487 (490)
T ss_pred CCcChhhhHH-------------HHHHHHHHHHHh
Confidence 8888877765 555555555543
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-41 Score=359.52 Aligned_cols=196 Identities=34% Similarity=0.604 Sum_probs=166.0
Q ss_pred ecCCCCCCCceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCCchhhhH
Q 008203 309 YYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFI 388 (574)
Q Consensus 309 ~yP~~~~~~~i~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~~~~fnTfFy~kL~~~~~~kg~d~~~~~~ 388 (574)
+||.-+ .++|+||..|+.||.+++||||.||||||+||...... ....+++|+||||||++|... +|.
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 688774 68999999999999999999999999999999555433 345688999999999999863 589
Q ss_pred HHHhhhccccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEecCCCCCCcHHHHHHHHHHHHHHHHHhhccCCC
Q 008203 389 KFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSP 468 (574)
Q Consensus 389 ~vkrWtk~~nifekd~IfIPIn~~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~~~k~i~~~L~~yL~~e~~~~~~~~~~ 468 (574)
+|+||++++|||+++|||||||...||+|+|||.+.+ .|.|||||++.+ ..+++.|+.|+.+||+....+
T Consensus 440 gVrrW~kk~dif~~k~I~iPIni~~HW~l~II~~~~~------~i~~~DSLan~~-~~v~~~L~~Y~ldE~k~~~~k--- 509 (578)
T COG5160 440 GVRRWTKKTDIFSKKYIFIPINISYHWFLAIIDNPKK------NILYFDSLANTH-DPVLEFLRSYLLDEYKIQHDK--- 509 (578)
T ss_pred HHHHHHhccCccccceEEEEecccceEEEEEeecCcc------eeEEecccccCc-HHHHHHHHHHHHHHHhcccCC---
Confidence 9999999999999999999999999999999999987 999999999876 679999999999998764322
Q ss_pred CCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhcCCcccchhhhhcccccCCCHHHHHHHHHHHHHH
Q 008203 469 SDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNL 548 (574)
Q Consensus 469 ~d~~~~~~~W~~~p~~i~~~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~~p~~ftq~dm~~f~~~wf~p~~i~~~R~~I~~l 548 (574)
+.| +.+...+||||.||+|||||||+|++++++++|..|.++|+ ..+|+.|...
T Consensus 510 -------~~~------~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~-------------~r~Rk~m~h~ 563 (578)
T COG5160 510 -------DPQ------IKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDR-------------PRARKNMAHT 563 (578)
T ss_pred -------chh------hhhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccch-------------HHHHHHHHHH
Confidence 113 23457799999999999999999999999998876666555 4566666666
Q ss_pred HHHH
Q 008203 549 LKKQ 552 (574)
Q Consensus 549 Il~L 552 (574)
|+.+
T Consensus 564 i~~~ 567 (578)
T COG5160 564 IKDL 567 (578)
T ss_pred HHHH
Confidence 6554
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=99.97 E-value=7.8e-30 Score=249.43 Aligned_cols=195 Identities=32% Similarity=0.609 Sum_probs=137.3
Q ss_pred CccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCCc----------hhhhHHHHhhhccc---cC
Q 008203 333 AYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDK----------DSFFIKFRRWWKGV---NI 399 (574)
Q Consensus 333 ~WLND~IInfYl~~L~~~~~~~~~~~~~~~~fnTfFy~kL~~~~~~kg~d~----------~~~~~~vkrWtk~~---ni 399 (574)
+||||.|||||++||.+..........++++|+|+||+.|......-+.+. ...+..+.+|++.. ++
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 699999999999999976543334567899999999999984321100110 24567889999887 99
Q ss_pred CCCcEEEEEeec-CCceEEEEEEcCCCCCCCCCeEEEecCCCCCCc----HHHHHHHHHHHHHHHHHhhccCCCCCCccc
Q 008203 400 FQKSYVLIPIHE-DVHWSLVIICIPDKEDESGPIILHLDSLKLHCS----LSIFSNIRSFLKEEWNYLKQEVSPSDLPIA 474 (574)
Q Consensus 400 fekd~IfIPIn~-~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~~~----k~i~~~L~~yL~~e~~~~~~~~~~~d~~~~ 474 (574)
+++++||||||. +.||+|+||+++.+ +|++||||++... ..++..+..+|...+....... . .
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~~------~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~----~ 148 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPKK------RIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRD--P----D 148 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTTT------EEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSC--T-----
T ss_pred cccCEEEEEEechhhccceeEEccccc------EEEEEeccccccccccchhhhhhhhhhhhhccccccccc--c----c
Confidence 999999999999 99999999999998 9999999998875 4567888888887765433221 1 1
Q ss_pred ccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhcCCcccchhhhhcccccCCCHHHHHHHHHHHHHHHHHHhh
Q 008203 475 ERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQ 554 (574)
Q Consensus 475 ~~~W~~~p~~i~~~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~~p~~ftq~dm~~f~~~wf~p~~i~~~R~~I~~lIl~L~~ 554 (574)
...|.. ....++|||.|++|||+|||+||++++.+.+....+ .|..+++..+|.++...|.+...
T Consensus 149 ~~~~~~------~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~---------~l~~~~i~~~r~~~a~~~~e~~~ 213 (216)
T PF02902_consen 149 KSPFKI------VRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQ---------ELTEEDIKNFRKKLAVDLYEELG 213 (216)
T ss_dssp TTTCEE------EEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCC---------SBTGHHHHHHHHHHHH-------
T ss_pred cceeee------cccccccCCCCCCCcHHHHHHHHHHHHhCCCCcccc---------cCCHHHHHHHHHHHHhhcccccc
Confidence 122321 235589999999999999999999999885443211 15667888999999888777654
No 5
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=8.3e-30 Score=284.52 Aligned_cols=512 Identities=23% Similarity=0.269 Sum_probs=349.2
Q ss_pred ccCCCcccccccccCCCCCCCCceeeeccCCCCCCCCCCCCCCCCCCCchhhcCCCCchHHHHHHHHhhhhhcccccCCC
Q 008203 8 RNKRKLNIDWEEVLPGRNDDVPAELIVKKSGPPTPAQKSVPMSDDPGSGEELDRQIPDQELGVRIARMKDTYSKVRHCLP 87 (574)
Q Consensus 8 ~~~~~~~id~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~D~~L~e~i~r~~~~l~~~~~~lp 87 (574)
..++...|+|.-++- +..-.+.+++|-++++. .|+...|...+.. ..+.|..|.+.-.|..+.+..++.+.+
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-Cc-cccccccCcccCCCC------CCCCccccc--------
Q 008203 88 DKGKKILATVTRLEKECERRRLAGA------------V-PV-CLDIDGCDKLTQSPS------SDASDCFTQ-------- 139 (574)
Q Consensus 88 D~G~K~~~~i~~~~~E~~rR~~~~~------------~-~~-~~~~~~~~~~~q~~~------~~~s~~~~~-------- 139 (574)
+.|.+-+..|...+++..+|+..+. - .+ -.+.. +++.....+ ......++.
T Consensus 82 ~~~~~~~~ki~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (595)
T KOG0779|consen 82 LTSLTEPLKIAVLEEQKPHAVVPKKIISVSELRNTNLTEGTFYSDYL-NRIKNIFESVRKFFNQVSYPKFMPNVTSFMPS 160 (595)
T ss_pred ccccccccccccccccCCccccccccccchhccccCCcccceecccc-cccccccchhcchhhhcccccccchhhcccCC
Confidence 9999999999999999888887554 0 00 00111 222111111 000111110
Q ss_pred ---------cCCCCcccccCcchhhhhhccccccccchhhhhhHHhhhhhcccccccccCCccccccccccccCCCCcc-
Q 008203 140 ---------RTPSPQIQSKSSFTSVFREKMEENRDCREANAFDKELSILAHCDRRKMRSDGDLSQRGRQNVRSSSRKWP- 209 (574)
Q Consensus 140 ---------~~~ss~~~~~s~f~~~f~~~~e~~~~~~~~~af~kel~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 209 (574)
..+..=......|-.+|... ..++..-..++..++.... ++...-+ .++..+..-+..+.
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 00011112334444444442 2233444555555555555 3332211 12222222222222
Q ss_pred -cc-------cCCCCCCC--CCCccccccccCCCC-CCCCCCccc-------------------CCCCCCCcccccCCCc
Q 008203 210 -FH-------KGDKSFNS--NGSQKDRASLTCPSH-QSGENSSSC-------------------LPKKKESFEVLPSKNP 259 (574)
Q Consensus 210 -~~-------~~~~~~~~--n~~q~~~~s~~~~~~-~~~~~~~~~-------------------~~~~~~~~~~~~~~~~ 259 (574)
.+ ...+.+.+ -..+-.+.+|...++ +++...+++ .....|....+|.++.
T Consensus 231 ~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~ 310 (595)
T KOG0779|consen 231 HSLVISSINSPNIKTFFSKEVKSRPTPASYFIFSSFLPGLDPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSE 310 (595)
T ss_pred hhhhhcccccccchhhhccccccCCCcccccccccccCCCCccccccccchhhhhhhcccccccccchhhhhhcCcccch
Confidence 11 00111110 111222222222221 222222222 4567778888888888
Q ss_pred ccccc--cceeccCCCCCCCcCCcccccCCCCccchHhHHHHHHhhccCeeecCCC-CCCCceEEecchhcccCCCCccC
Q 008203 260 RLRKE--QNLVLLDEDESPVEDASEESEGSLHIETTEQADEFAECMIDAKIYYPSR-VDPESVEICYTDINHLAPAAYLT 336 (574)
Q Consensus 260 ~~~~~--~~~v~ld~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~i~yP~~-~~~~~i~Lt~~DL~~L~~~~WLN 336 (574)
.++.. .++..+++.+-. .....+..-++.. .+++. .. ..+.++..|+.||.++++||
T Consensus 311 s~~~~~~~~~~~~~~~~~~------------~~l~~~~~~el~~-------~~~p~~~~-~~~~v~~~Dl~cl~~~e~L~ 370 (595)
T KOG0779|consen 311 SRSRDSLDNWFPVKEADKQ------------RTLIVKLAIELLE-------VRVPQICN-QSHQVNNNDLVCLEEGEFLN 370 (595)
T ss_pred hcccccccccccccccccc------------cchHHHhhccccc-------cCCccccc-cccceeccchhhccccchhh
Confidence 87776 566666554432 1123333333332 23322 22 36789999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCC--chhhhHHHHhhhccccCCCCcEEEEEeecCCc
Q 008203 337 SPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD--KDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVH 414 (574)
Q Consensus 337 D~IInfYl~~L~~~~~~~~~~~~~~~~fnTfFy~kL~~~~~~kg~d--~~~~~~~vkrWtk~~nifekd~IfIPIn~~~H 414 (574)
|.||+||++|+..+..........+|+|++|||..+.+.+..++.+ ....+.++++|++.+++|.++||++|+|...|
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 9999999999999887755567899999999999999988777766 55677889999999999999999999999999
Q ss_pred eEEEEEEcCCCCCCCCCeEEEecCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCC
Q 008203 415 WSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQ 494 (574)
Q Consensus 415 WsLlVI~~~~k~~~~~p~I~~lDSL~~~~~k~i~~~L~~yL~~e~~~~~~~~~~~d~~~~~~~W~~~p~~i~~~~~~vPq 494 (574)
|.|++||+++.+.+......+++++..+....+...+..++..++.+.+......+.++....|..+++.+...++. ||
T Consensus 451 w~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~-p~ 529 (595)
T KOG0779|consen 451 WKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELEEELPRRLPRGKSETVRE-PQ 529 (595)
T ss_pred hhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCcccccccccccccccccCcccccccccc-cC
Confidence 99999999998777777888889888877666778889999998877666555667777777888877666544444 99
Q ss_pred CCCCCChhHHHHHHHHHHHhcCCcccchhhhhcccccCCCHHHHHHHHHHHHHHHHHHhhhhccC
Q 008203 495 QKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQISSAE 559 (574)
Q Consensus 495 Q~Ng~DCGVFVL~f~e~~~~~~p~~ftq~dm~~f~~~wf~p~~i~~~R~~I~~lIl~L~~~~~~~ 559 (574)
|.|.+|||+|++.|++.|+.+++.+++..+.......||.|.++.++|..|+++|+.|+....++
T Consensus 530 q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~~~~l~~~~~~~ 594 (595)
T KOG0779|consen 530 QNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRNLGRKLFTSQSSE 594 (595)
T ss_pred ccCcccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhccccccccccCCC
Confidence 99999999999999999999999888776766666669999999999999999999999876543
No 6
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.96 E-value=1.8e-28 Score=236.37 Aligned_cols=191 Identities=24% Similarity=0.421 Sum_probs=142.7
Q ss_pred CceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCCchhhhHHHHhhhcc
Q 008203 317 ESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG 396 (574)
Q Consensus 317 ~~i~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~~~~fnTfFy~kL~~~~~~kg~d~~~~~~~vkrWtk~ 396 (574)
+.+.|+.+|+..|.++.||||.+|+||.+||.+...... .+.|++++- ++..++..+.+ +.+......
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 FDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSE---PDLHLLRPS----LTFFLRHAPNP-----EEIAMVLDP 82 (223)
T ss_pred eehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccC---cchhccCHH----HHHHHHhCCCc-----HHHHHhcCh
Confidence 789999999999999999999999999999999876543 335777663 33333333322 124444567
Q ss_pred ccCCCCcEEEEEeecC---------CceEEEEEEcCCCCCCCCCeEEEecCCCCCCc---HHHHHHHHHHHHHHHHHhhc
Q 008203 397 VNIFQKSYVLIPIHED---------VHWSLVIICIPDKEDESGPIILHLDSLKLHCS---LSIFSNIRSFLKEEWNYLKQ 464 (574)
Q Consensus 397 ~nifekd~IfIPIn~~---------~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~~~---k~i~~~L~~yL~~e~~~~~~ 464 (574)
.++++|++||+|||++ +||+|+|+..+.+ +++||||+.+.+. +.+++.++.+|......
T Consensus 83 l~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~------~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~--- 153 (223)
T KOG3246|consen 83 LDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDG------KFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAK--- 153 (223)
T ss_pred hhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCC------cEEEeecccCCCcHHHHHHHHHHHHHHhhhhhh---
Confidence 7999999999999984 6999999999998 9999999988764 45667777676642110
Q ss_pred cCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhcCCcccchhhhhcccccCCCHHHHHHHHHH
Q 008203 465 EVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIK 544 (574)
Q Consensus 465 ~~~~~d~~~~~~~W~~~p~~i~~~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~~p~~ftq~dm~~f~~~wf~p~~i~~~R~~ 544 (574)
..+..+|||.||||||+|||.+.+.++... .+..+.. .-....+..|+++|+.
T Consensus 154 ----------------------~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~----~~~~~~~-~~~~~~~~~i~~lr~~ 206 (223)
T KOG3246|consen 154 ----------------------RVECKCLQQQNGYDCGLHVCCNTRVLAERL----LRCPYAT-SSQLLVVDLIKALREE 206 (223)
T ss_pred ----------------------cccccChhhhcCCchhHHHHHHHHHHHHHH----hcccccc-ccchhhHHHHHHHHHH
Confidence 125679999999999999999999888762 1212211 1122456788999999
Q ss_pred HHHHHHHHhhh
Q 008203 545 IRNLLKKQFQI 555 (574)
Q Consensus 545 I~~lIl~L~~~ 555 (574)
|+.||..|...
T Consensus 207 l~~LI~slg~~ 217 (223)
T KOG3246|consen 207 LLDLIQSLGSI 217 (223)
T ss_pred HHHHHHHhCcc
Confidence 99999988643
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=96.99 E-value=0.0013 Score=69.60 Aligned_cols=92 Identities=23% Similarity=0.302 Sum_probs=64.4
Q ss_pred CCCcEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEecCCCCCCc------------------------------HHHHH
Q 008203 400 FQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCS------------------------------LSIFS 449 (574)
Q Consensus 400 fekd~IfIPIn~~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~~~------------------------------k~i~~ 449 (574)
-.+.|+.||++...||..+|+|...+ -+++|||-|..+. ..-++
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk~~~------~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dID 302 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDKEKK------IVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDID 302 (423)
T ss_pred ccccEEEeeeeehhcceEEEEecccc------EEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchH
Confidence 45789999999999999999998877 8888888875421 01234
Q ss_pred HHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCc-CCCCCCCChhHHHHHHHHHHHhcCCcccc
Q 008203 450 NIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPV-PQQKNDYDCGLFVLFFMERFMEEAPERLK 521 (574)
Q Consensus 450 ~L~~yL~~e~~~~~~~~~~~d~~~~~~~W~~~p~~i~~~~~~v-PqQ~Ng~DCGVFVL~f~e~~~~~~p~~ft 521 (574)
.|.+|+...+... .-.++| --|--.++||+|++-||-.....+|..|.
T Consensus 303 VLfrfF~d~f~~~------------------------~gciNvevnQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 303 VLFRFFEDSFGVK------------------------YGCINVEVNQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred HHHHHHHhhcccc------------------------eeEEEhhhhhhcccccchHHHHHHHHHHccCchhHH
Confidence 5555555433110 011222 26788899999999999988888887653
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=95.19 E-value=0.043 Score=55.47 Aligned_cols=35 Identities=14% Similarity=0.135 Sum_probs=24.1
Q ss_pred EEEEEeecCCceEEEEEEcCCCCCCCCCeEEEecCCCCC
Q 008203 404 YVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLH 442 (574)
Q Consensus 404 ~IfIPIn~~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~ 442 (574)
.=+||||.+.||.|+++..-.. ....++|.|+..-
T Consensus 190 nevF~INtg~HWil~~~~Ki~~----kiKC~iFNs~~~l 224 (317)
T PRK14848 190 NEVFLINTGDHWLLCLFYKLAE----KIKCLIFNTYYDL 224 (317)
T ss_pred ceEEEecCCCcEEEEEhHHhhh----hceEEEeecHhhh
Confidence 3459999999999998754221 1356677887543
No 9
>PRK11836 deubiquitinase; Provisional
Probab=94.57 E-value=0.16 Score=52.46 Aligned_cols=46 Identities=24% Similarity=0.304 Sum_probs=30.9
Q ss_pred cccCCCCcEEEEEeecCCceEEEEEEcCCCC--CCCCCeEEEecCCCC
Q 008203 396 GVNIFQKSYVLIPIHEDVHWSLVIICIPDKE--DESGPIILHLDSLKL 441 (574)
Q Consensus 396 ~~nifekd~IfIPIn~~~HWsLlVI~~~~k~--~~~~p~I~~lDSL~~ 441 (574)
...++-++.=+||||.+.||.|+++..-..+ .......++|.|+..
T Consensus 213 ~~~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~ 260 (403)
T PRK11836 213 SDPSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRA 260 (403)
T ss_pred cCCCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhh
Confidence 3456667888999999999999987543211 112345677888753
No 10
>PF15328 GCOM2: Putative GRINL1B complex locus protein 2
Probab=90.19 E-value=0.26 Score=49.70 Aligned_cols=37 Identities=35% Similarity=0.406 Sum_probs=31.5
Q ss_pred HHhhhhhc--ccccCCCcchHhHHHHHHHHHHHHHHHhh
Q 008203 73 ARMKDTYS--KVRHCLPDKGKKILATVTRLEKECERRRL 109 (574)
Q Consensus 73 ~r~~~~l~--~~~~~lpD~G~K~~~~i~~~~~E~~rR~~ 109 (574)
+|+...|. ++-.+|||||+||+..+..|..++.+|.-
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 45666663 77799999999999999999999999955
No 11
>PRK15371 effector protein YopJ; Provisional
Probab=90.17 E-value=4.2 Score=42.53 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=23.9
Q ss_pred cCCCcCCCCCCCChhHHHHHHHHHHHhc
Q 008203 488 RIIPVPQQKNDYDCGLFVLFFMERFMEE 515 (574)
Q Consensus 488 ~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~ 515 (574)
..+.+-.|.-.+|||+|.|.||.+....
T Consensus 159 avie~d~QkS~~dC~mFSL~~AkK~~~e 186 (287)
T PRK15371 159 SMVEMDIQRSSSECGIFSLALAKKLYLE 186 (287)
T ss_pred EEEecccccCcccchhhhHHHHHHHhhh
Confidence 3456778999999999999999988776
No 12
>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=87.78 E-value=2.7 Score=41.02 Aligned_cols=88 Identities=15% Similarity=0.277 Sum_probs=51.2
Q ss_pred EEEEeec-CCceEEEEEE-cCCCCCCCCCeEEEecCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCC
Q 008203 405 VLIPIHE-DVHWSLVIIC-IPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLP 482 (574)
Q Consensus 405 IfIPIn~-~~HWsLlVI~-~~~k~~~~~p~I~~lDSL~~~~~k~i~~~L~~yL~~e~~~~~~~~~~~d~~~~~~~W~~~p 482 (574)
.++++.. ..|-..+=|- .++ ..+.|++|+|-........ |..+.........+. ..
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~----~k~SlI~~Epa~~~~~~~~---l~~~~~~~~~~~~~~--~~------------- 131 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN----GKPSLIVFEPASFYGMKPA---LAGYTKLAEEARQKL--LP------------- 131 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC----CCceEEEEccccccCCcch---hhhHHHHHHHHHhcc--CC-------------
Confidence 3555443 5676655444 333 3579999999865432111 333332211111100 11
Q ss_pred ccccccCCCcCCCCCCCChhHHHHHHHHHHHhc
Q 008203 483 RRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEE 515 (574)
Q Consensus 483 ~~i~~~~~~vPqQ~Ng~DCGVFVL~f~e~~~~~ 515 (574)
...+..+++..|...+|||+|.|.++......
T Consensus 132 -~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 132 -NAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred -CcEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 12234678899999999999999999988765
No 13
>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=87.61 E-value=1.1 Score=43.35 Aligned_cols=81 Identities=20% Similarity=0.315 Sum_probs=38.1
Q ss_pred CCceEEEEEEcCCCCCCCCCeEEEecCCCCCCcHHHHHHHHHHHHHHHHHhhcc---CCCCCCcccccccccCCcccccc
Q 008203 412 DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQE---VSPSDLPIAERIWQHLPRRIDDR 488 (574)
Q Consensus 412 ~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~~~k~i~~~L~~yL~~e~~~~~~~---~~~~d~~~~~~~W~~~p~~i~~~ 488 (574)
+.||.-+..+.+.. ++++||.+|-++. ++ .++-.-++..+-.. ....| +.+..+
T Consensus 33 GvHWlA~Aw~P~s~------t~YmFDPfGfsd~-~L----~qiY~FeYe~llrRSAL~~~~d------------RCv~Lv 89 (183)
T PF00770_consen 33 GVHWLAFAWDPRSR------TFYMFDPFGFSDQ-KL----KQIYQFEYEGLLRRSALSSTPD------------RCVTLV 89 (183)
T ss_dssp -S-EEEEEEETTTT------EEEEE-TT---HH-HH----HHHH----HHHHHHHHHHH-TT------------SEEEEE
T ss_pred ceeEEEEEecCCcc------eEEEeCCCCCCHH-HH----HHHHhhhHHHHHHHHhhcCCCC------------ceEEEE
Confidence 58999999999887 9999999998753 21 11111122111000 00011 122211
Q ss_pred -CCCcCCCCCCCChhHHHHHHHHHHHhc
Q 008203 489 -IIPVPQQKNDYDCGLFVLFFMERFMEE 515 (574)
Q Consensus 489 -~~~vPqQ~Ng~DCGVFVL~f~e~~~~~ 515 (574)
....-|=.++--||+|.|+|+.+|...
T Consensus 90 kstqtVQ~p~SaaCGLFC~lFL~aF~~~ 117 (183)
T PF00770_consen 90 KSTQTVQCPCSAACGLFCCLFLHAFVHY 117 (183)
T ss_dssp EE-EE-S-TT---HHHHHHHHHHHHHH-
T ss_pred eccceeeccCchhHHHHHHHHHHHHHhC
Confidence 122234457889999999999999876
No 14
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=66.54 E-value=6.2 Score=45.85 Aligned_cols=31 Identities=39% Similarity=0.637 Sum_probs=28.0
Q ss_pred ccccCCCcchHhHHHHHHHHHHHHHHHhhhC
Q 008203 81 KVRHCLPDKGKKILATVTRLEKECERRRLAG 111 (574)
Q Consensus 81 ~~~~~lpD~G~K~~~~i~~~~~E~~rR~~~~ 111 (574)
.+...|||+|.++..+|+.+.+|++||..-+
T Consensus 209 ~~~~~Lpd~g~~~~kr~~el~~~~~~~~~~~ 239 (901)
T KOG4439|consen 209 KAIDDLPDKGARLIKRLQELDRELERRMQFG 239 (901)
T ss_pred hhhhhCCccHHHHHHHHHHHHHHHHHHHhhh
Confidence 4456999999999999999999999999965
No 15
>PF15463 ECM11: Extracellular mutant protein 11
Probab=32.88 E-value=69 Score=29.86 Aligned_cols=52 Identities=17% Similarity=0.178 Sum_probs=42.1
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccccCCCcchHhHHHHHHHHHHHHHHHhhh
Q 008203 59 LDRQIPDQELGVRIARMKDTYSKVRHCLPDKGKKILATVTRLEKECERRRLA 110 (574)
Q Consensus 59 ~~~~~~D~~L~e~i~r~~~~l~~~~~~lpD~G~K~~~~i~~~~~E~~rR~~~ 110 (574)
.|+.+|..+-.+.=..+-.....|..+|-+.=.++|.++..++.|+.+|-.+
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 7788888877766655555555666888888999999999999999999874
No 16
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=29.08 E-value=97 Score=38.01 Aligned_cols=38 Identities=16% Similarity=0.265 Sum_probs=26.1
Q ss_pred EEEeec-------CCceEEEEEEcCCCCCCCCCeEEEecCCCCCCcHHHHHH
Q 008203 406 LIPIHE-------DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSN 450 (574)
Q Consensus 406 fIPIn~-------~~HWsLlVI~~~~k~~~~~p~I~~lDSL~~~~~k~i~~~ 450 (574)
|+||-. ..||.++|-- +++ ..+.||.||..+.....+.
T Consensus 49 fmpvltgv~p~~~sghwimlikg-~gn------~y~lfdplg~~sg~~y~ni 93 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLIKG-QGN------QYYLFDPLGKTSGEGYQNI 93 (1439)
T ss_pred CceeecCcCCCCcCceeEEEEEc-CCC------ceEEeccccccccccHHHH
Confidence 566654 5899988753 333 8999999998765444333
No 17
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=27.77 E-value=1.2e+02 Score=24.62 Aligned_cols=52 Identities=17% Similarity=0.296 Sum_probs=38.7
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccc-----cCC--CcchHhHHHHHHHHHHHHHHHhhh
Q 008203 59 LDRQIPDQELGVRIARMKDTYSKVR-----HCL--PDKGKKILATVTRLEKECERRRLA 110 (574)
Q Consensus 59 ~~~~~~D~~L~e~i~r~~~~l~~~~-----~~l--pD~G~K~~~~i~~~~~E~~rR~~~ 110 (574)
+++.+|+.||++.|...+..|-.+. ..+ |-.-..+|+.|.|+.=.+..|..+
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 334567889999999888888765
Done!