Query 008283
Match_columns 571
No_of_seqs 226 out of 1131
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 21:50:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008283hhsearch_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 9.1E-47 2E-51 404.3 16.6 215 282-527 285-499 (511)
2 PLN03189 Protease specific for 100.0 2E-43 4.3E-48 375.8 24.0 225 284-549 255-487 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 6.9E-42 1.5E-46 361.4 16.0 197 306-550 372-568 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 6.9E-30 1.5E-34 249.7 17.1 195 330-551 1-213 (216)
5 KOG0779 Protease, Ulp1 family 100.0 1.1E-29 2.3E-34 283.4 9.1 510 8-556 10-594 (595)
6 KOG3246 Sentrin-specific cyste 100.0 4.4E-28 9.6E-33 233.4 15.5 190 314-551 15-216 (223)
7 PF03290 Peptidase_C57: Vaccin 97.1 0.00088 1.9E-08 70.8 6.4 93 397-518 229-351 (423)
8 PRK11836 deubiquitinase; Provi 95.5 0.08 1.7E-06 54.5 9.4 96 328-438 162-260 (403)
9 PRK14848 deubiquitinase SseL; 95.3 0.036 7.8E-07 56.0 6.3 35 401-439 190-224 (317)
10 PRK15371 effector protein YopJ 90.3 4.2 9.1E-05 42.5 12.4 28 485-512 159-186 (287)
11 PF15328 GCOM2: Putative GRINL 90.1 0.26 5.6E-06 49.7 3.3 37 73-109 3-41 (223)
12 PF00770 Peptidase_C5: Adenovi 90.0 0.65 1.4E-05 44.7 5.7 81 409-512 33-117 (183)
13 PF03421 YopJ: YopJ Serine/Thr 87.8 2.7 5.8E-05 41.0 8.5 88 402-512 74-163 (177)
14 KOG4439 RNA polymerase II tran 62.7 8 0.00017 45.0 4.0 32 81-112 209-240 (901)
15 PF12252 SidE: Dot/Icm substra 33.5 75 0.0016 38.8 5.8 39 403-448 49-94 (1439)
16 PF15463 ECM11: Extracellular 30.4 74 0.0016 29.6 4.3 52 59-110 65-116 (139)
17 PRK00306 50S ribosomal protein 27.4 1.2E+02 0.0025 24.6 4.4 52 59-110 5-63 (66)
18 PHA02130 hypothetical protein 26.4 35 0.00075 28.0 1.1 37 383-419 15-52 (81)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.1e-47 Score=404.32 Aligned_cols=215 Identities=28% Similarity=0.494 Sum_probs=177.2
Q ss_pred cCCCCccchHhHHHHHHhhccCeeecCCCCCCCceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCceEEE
Q 008283 282 EGSLHIETTEQADEFAECMIDAKIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFF 361 (571)
Q Consensus 282 ~~~~~~~~~e~~~e~~~~~~~~~i~yp~~~~~~~v~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~v~~f 361 (571)
+..+++++.+...++.+.+.+..-.-. ....+++.||.+||.||.+++||||+||||||++|+++...... ++++|+|
T Consensus 285 ~~~~~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~-yp~~h~F 362 (511)
T KOG0778|consen 285 EDSFPPLTEEREAQVQRAFSSRNSTEI-LVTHFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSK-YPKVHAF 362 (511)
T ss_pred ccccccccHHHHHHHHHHhccCCcccc-eehhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCC-CceEEEE
Confidence 445666666666666666542111000 01246799999999999999999999999999999999876655 8899999
Q ss_pred chhhHHHHHHhhhcCCCCchhHHHHHHhhhccccCCCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCc
Q 008283 362 NTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCS 441 (571)
Q Consensus 362 nTfFy~kL~~~~~~kg~d~~~~~~~vkrW~k~vnif~kd~IfIPIn~~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~ 441 (571)
|||||++|... +|++|+|||++++||++|+||||||.+.||+|+||++..+ +|.|||||++..+
T Consensus 363 nTFFy~kL~~~----------gy~~VkRWTk~v~if~~d~i~vPIH~~vHW~l~vid~r~k------~i~y~DS~~~~~n 426 (511)
T KOG0778|consen 363 NTFFYTKLVGR----------GYAGVKRWTKKVDIFDKDIIFVPIHLGVHWCLAVIDLREK------TIEYYDSLGGGPN 426 (511)
T ss_pred echhhhhhhhc----------chHHHHhHhhccCccccceeEeeeecCceEEEEEEEcccc------eEEEeeccCCCCc
Confidence 99999999962 5889999999999999999999999999999999999998 9999999997655
Q ss_pred HHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhhCCcccchhh
Q 008283 442 LSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKD 521 (571)
Q Consensus 442 k~i~~~L~~yL~~e~~~~~~~~~~~D~~~~~~~W~~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~~p~~ftq~d 521 (571)
+ ++..|..||.+|+..+.+. + ++-..|+.. ...++|||.||+|||||+|+|+++++++.|+.|+|+|
T Consensus 427 r-~~~aL~~Yl~~E~~~k~~~----~--~d~s~w~~~------~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~d 493 (511)
T KOG0778|consen 427 R-ICDALAKYLQDESRDKSKK----D--FDVSGWTIE------FVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFTQQD 493 (511)
T ss_pred c-hHHHHHHHHHHHHhhhhcC----C--CCccchhhh------hhhccccccCCCccceEEeeechhhccCCCcccChhh
Confidence 4 4599999999999875432 2 233568752 3458999999999999999999999999999999999
Q ss_pred hhcccc
Q 008283 522 LAMFGK 527 (571)
Q Consensus 522 m~~frr 527 (571)
||+||+
T Consensus 494 mp~fR~ 499 (511)
T KOG0778|consen 494 MPYFRK 499 (511)
T ss_pred hHHHHH
Confidence 986543
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=2e-43 Score=375.82 Aligned_cols=225 Identities=23% Similarity=0.471 Sum_probs=182.1
Q ss_pred CCCccchHhHHHHHHhhccC----eeecCCCCCCCceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCceE
Q 008283 284 SLHIETTEQADEFAECMIDA----KIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCH 359 (571)
Q Consensus 284 ~~~~~~~e~~~e~~~~~~~~----~i~yp~~~~~~~v~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~v~ 359 (571)
.+.|++.++..+|.++|... .++.. .+++++||.+||.||.+++||||+|||||++||.++.........++|
T Consensus 255 ~~~pLT~e~~~~V~~al~~~~~~~vlvs~---~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h 331 (490)
T PLN03189 255 PFIPLTREEETEVKRAFSANNRRKVLVTH---ENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCH 331 (490)
T ss_pred cCcCCCHHHHHHHHHHhcCCCccceeeec---CCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceE
Confidence 47888999999999988632 23322 246899999999999999999999999999999886544444457899
Q ss_pred EEchhhHHHHHHhhhcCCCCchhHHHHHHhhhcc----ccCCCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcC
Q 008283 360 FFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG----VNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDS 435 (571)
Q Consensus 360 ~fnTfFy~kL~~~~~~kg~d~~~~~~~vkrW~k~----vnif~kd~IfIPIn~~~HWsLlVI~~p~k~~~~~~~I~~yDS 435 (571)
+||||||++|.... ....|.+|+||+++ +++|++++||||||.+.||+|+||+++.+ +|+||||
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 99999999998731 12358999999964 57999999999999999999999999988 9999999
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhhCCc
Q 008283 436 LKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPE 515 (571)
Q Consensus 436 Lg~~~~k~i~~~L~~yL~~e~~~~~~~~~~~D~~~~~~~W~~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~~p~ 515 (571)
|++.+ ..+++.|..||..|++.+. +.++ ..+.|... ...++|||.||||||||||+||++|+.+.+.
T Consensus 400 Lgg~~-~~vL~~L~rYL~~E~kdK~----g~d~--D~s~W~~~------~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~L 466 (490)
T PLN03189 400 LKGRD-PKILDALAKYYVDEVKDKS----EKDI--DVSSWEQE------FVEDLPEQKNGYDCGMFMIKYIDFYSRGLGL 466 (490)
T ss_pred CCCCC-HHHHHHHHHHHHHHHhhhc----CCCc--chhcceec------cCCCCCCCCCCCCHHHHHHHHHHHHcCCCCC
Confidence 99875 4588999999999987643 2232 33567531 2458999999999999999999999999888
Q ss_pred ccchhhhhcccccCcCHHHHHHHHHHHHHHHHHH
Q 008283 516 RLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQ 549 (571)
Q Consensus 516 ~ftq~dm~~frr~~f~pe~i~~~R~~I~~lIl~L 549 (571)
.|+|+||++ +|.+|..-|+.+
T Consensus 467 tFSQeDMp~-------------fRrRma~EIl~~ 487 (490)
T PLN03189 467 CFGQEHMPY-------------FRLRTAKEILRL 487 (490)
T ss_pred CcChhhhHH-------------HHHHHHHHHHHh
Confidence 888877765 566666666554
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.9e-42 Score=361.41 Aligned_cols=197 Identities=34% Similarity=0.596 Sum_probs=167.5
Q ss_pred ecCCCCCCCceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCCchhHHH
Q 008283 306 YYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFI 385 (571)
Q Consensus 306 ~yp~~~~~~~v~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~~~~~~ 385 (571)
+||+-+ .++++||..|+.||.+++||||.||||||+||...... ....+++|+||||||++|.+. +|.
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 788875 68999999999999999999999999999999665443 345788999999999999963 589
Q ss_pred HHHhhhccccCCCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCC
Q 008283 386 KFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSP 465 (571)
Q Consensus 386 ~vkrW~k~vnif~kd~IfIPIn~~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~k~i~~~L~~yL~~e~~~~~~~~~~ 465 (571)
+|+||+++++||+++|||||||...||+|+|||.+.+ .|.|||||++.+ ..+++.|..|+.+||+....+
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 679999999999998763321
Q ss_pred CCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhhCCcccchhhhhcccccCcCHHHHHHHHHHHHHH
Q 008283 466 SDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNL 545 (571)
Q Consensus 466 ~D~~~~~~~W~~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~~p~~ftq~dm~~frr~~f~pe~i~~~R~~I~~l 545 (571)
+.| +.+...+||||.||+|||||||+|++++++++|..|.++|+ ..+|..|+..
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 123 23457799999999999999999999999998877666555 4566777766
Q ss_pred HHHHh
Q 008283 546 LKKQF 550 (571)
Q Consensus 546 Il~L~ 550 (571)
|+.+.
T Consensus 564 i~~~q 568 (578)
T COG5160 564 IKDLQ 568 (578)
T ss_pred HHHHH
Confidence 66543
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=6.9e-30 Score=249.68 Aligned_cols=195 Identities=32% Similarity=0.605 Sum_probs=137.2
Q ss_pred CccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCCc----------hhHHHHHHhhhccc---cC
Q 008283 330 AYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDK----------DSFFIKFRRWWKGV---NI 396 (571)
Q Consensus 330 ~WLND~IInfYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~----------~~~~~~vkrW~k~v---ni 396 (571)
+||||.|||||++||.++...+.....++++|+|+||+.|......-+.+. ...+..+.+|++.. ++
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 699999999999999976543334568899999999999984321100110 24567889999887 99
Q ss_pred CCCCEEEEEeec-CCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCc----HHHHHHHHHHHHHHHHHhhccCCCCCCccc
Q 008283 397 FQKSYVLIPIHE-DVHWSLVIICIPDKEDESGPIILHLDSLKLHCS----LSIFSNIRSFLKEEWNYLKQEVSPSDLPIA 471 (571)
Q Consensus 397 f~kd~IfIPIn~-~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~----k~i~~~L~~yL~~e~~~~~~~~~~~D~~~~ 471 (571)
+++++||||||. +.||+|+||+++.+ +|++||||++... ..++..+..+|...+....... . .
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 ccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhhCCcccchhhhhcccccCcCHHHHHHHHHHHHHHHHHHhh
Q 008283 472 ERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQ 551 (571)
Q Consensus 472 ~~~W~~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~~p~~ftq~dm~~frr~~f~pe~i~~~R~~I~~lIl~L~~ 551 (571)
...|.. ....++|||.|++|||+|||+||++++.+.+....+ .|+.+++..+|.++...|.+...
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 235589999999999999999999999985443221 15678888999999888877654
No 5
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=1.1e-29 Score=283.38 Aligned_cols=510 Identities=23% Similarity=0.279 Sum_probs=351.6
Q ss_pred ccCCCcccccccccCCCCCCCCceeeeccCCCCCCCCCCCCCCCCCCCchhhcCCCCchHHHHHHHHhhhhhcccccCCC
Q 008283 8 RNKRKLNIDWEEVLPGRNDDVPAELIVKKSGPPTPAQKSVPMSDDPGSGEELDRQIPDQELGVRIARMKDTYSKVRHCLP 87 (571)
Q Consensus 8 ~~~~~~~id~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~D~~L~e~i~r~~~~~~~~~~~lp 87 (571)
..++...|+|.-++- +..-.+.+++|-++++. .|+...|...+.. ..+.|..|.+.-.|..+.+..++.+.+
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 4455677777777 889999999999999999889999999
Q ss_pred cchHhHHHHHHHHHHHHHHHhhhCC------------C--CccccccccccCCCCC------CC---ccccccC------
Q 008283 88 DKGKKILATVTRLEKECERRRLAGA------------V--PVCLDIDGCDKLTQSP------SS---DCFTQRT------ 138 (571)
Q Consensus 88 D~G~K~~~~i~~~~~E~~rR~~~~~------------~--~~~~d~~~~~~~~qs~------~s---~~~~~~~------ 138 (571)
+.|.+-+..|...+++..+|+..+. - ..-.|.. +++...-. .+ +.|....
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 008283 139 -----------PSPQIQSKSSFTSVFREKMEENRDCREANAFDKELSILAHCDRRKMRSDGDLSQRGRQNVRSSSRKWP- 206 (571)
Q Consensus 139 -----------~ss~~~~~s~f~~~f~~~~e~~~~~~~~~af~kel~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 206 (571)
+..=......|-.+|... ..++..-..++..++.... ++...-+ .++..+..-+..+.
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 008283 207 -FH-------KGDKSFNS--NGSQKDRASLTCPSH-QSGENSSSC-------------------LPKKKESFEVLPSKNP 256 (571)
Q Consensus 207 -~~-------~~~~~~~~--n~~q~~~~s~~~~~~-~~~~~~~~~-------------------~~~~~~~~~~~~~~~~ 256 (571)
.+ ...+.+.+ -..+-.+.+|...++ +++...+++ .....|....+|.++.
T Consensus 231 ~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~ 310 (595)
T KOG0779|consen 231 HSLVISSINSPNIKTFFSKEVKSRPTPASYFIFSSFLPGLDPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSE 310 (595)
T ss_pred hhhhhcccccccchhhhccccccCCCcccccccccccCCCCccccccccchhhhhhhcccccccccchhhhhhcCcccch
Confidence 11 00111100 111222222222221 122222222 4567778888888888
Q ss_pred ccccc--cceeccCCCCCCCcCCcccccCCCCccchHhHHHHHHhhccCeeecCCCCCCCceEEecchhcccCCCCccCH
Q 008283 257 RLRKE--QNLVLLDEDESPVEDASEESEGSLHIETTEQADEFAECMIDAKIYYPSRVDPESVEICYTDINHLAPAAYLTS 334 (571)
Q Consensus 257 ~~~~~--~~~v~ld~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~i~yp~~~~~~~v~Lt~~DL~~L~~~~WLND 334 (571)
.++.. .++..+++.+-. .....+..-++..+ +-|.... ..+.++..|+.||.++++|||
T Consensus 311 s~~~~~~~~~~~~~~~~~~------------~~l~~~~~~el~~~------~~p~~~~-~~~~v~~~Dl~cl~~~e~L~d 371 (595)
T KOG0779|consen 311 SRSRDSLDNWFPVKEADKQ------------RTLIVKLAIELLEV------RVPQICN-QSHQVNNNDLVCLEEGEFLND 371 (595)
T ss_pred hcccccccccccccccccc------------cchHHHhhcccccc------CCccccc-cccceeccchhhccccchhhh
Confidence 87776 566666655432 12233333333332 1222122 367899999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCC--chhHHHHHHhhhccccCCCCCEEEEEeecCCce
Q 008283 335 PIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD--KDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVHW 412 (571)
Q Consensus 335 ~IInfYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d--~~~~~~~vkrW~k~vnif~kd~IfIPIn~~~HW 412 (571)
.||+||++|+..+..........+|+|++|||..+.+.+..++.+ ....+..+++|++.+++|.++||++|+|...||
T Consensus 372 ~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~~~d~~~k~yi~~P~~E~~hw 451 (595)
T KOG0779|consen 372 TIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTRHFDLFNKDYVFVPTHERFHW 451 (595)
T ss_pred hhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeeeccccccceeEEecCchHhhh
Confidence 999999999999887655577899999999999999988777766 556778899999999999999999999999999
Q ss_pred EEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCC
Q 008283 413 SLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQ 492 (571)
Q Consensus 413 sLlVI~~p~k~~~~~~~I~~yDSLg~~~~k~i~~~L~~yL~~e~~~~~~~~~~~D~~~~~~~W~~lp~~i~~~~~~vPqQ 492 (571)
.|++||++..+.+......+++++..+....+...+..+|..++.+.+......+.++....|..+++.+...++. |||
T Consensus 452 ~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~-p~q 530 (595)
T KOG0779|consen 452 KLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELEEELPRRLPRGKSETVRE-PQQ 530 (595)
T ss_pred hccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCcccccccccccccccccCcccccccccc-cCc
Confidence 9999999998777777888999988877666778889999998887666555667777777888877666544444 999
Q ss_pred CCCCChhHHHHHHHHHHHhhCCcccchhhhhcccccCcCHHHHHHHHHHHHHHHHHHhhhhccC
Q 008283 493 KNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQISSAE 556 (571)
Q Consensus 493 ~Ng~DCGVFVL~y~e~~~~~~p~~ftq~dm~~frr~~f~pe~i~~~R~~I~~lIl~L~~~~~~~ 556 (571)
.|..|||+|++.|++.++.+++.+++..+...+...||.|.++.++|..++++|+.|+....++
T Consensus 531 ~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~~~~l~~~~~~~ 594 (595)
T KOG0779|consen 531 NNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRNLGRKLFTSQSSE 594 (595)
T ss_pred cCcccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhccccccccccCCC
Confidence 9999999999999999999999888777777766679999999999999999999999876654
No 6
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.95 E-value=4.4e-28 Score=233.42 Aligned_cols=190 Identities=24% Similarity=0.417 Sum_probs=140.9
Q ss_pred CceEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHHHHHHhhhcCCCCchhHHHHHHhhhcc
Q 008283 314 ESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG 393 (571)
Q Consensus 314 ~~v~Lt~~DL~~L~~~~WLND~IInfYl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~~~~~~~vkrW~k~ 393 (571)
+.|.|+.+|+..|.++.||||.+|+||.+||.+...... .+.|++++- ++..+++.+.+ +.+......
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 123334466
Q ss_pred ccCCCCCEEEEEeecC---------CceEEEEEEcCCCCCCCCCeEEEEcCCCCCCc---HHHHHHHHHHHHHHHHHhhc
Q 008283 394 VNIFQKSYVLIPIHED---------VHWSLVIICIPDKEDESGPIILHLDSLKLHCS---LSIFSNIRSFLKEEWNYLKQ 461 (571)
Q Consensus 394 vnif~kd~IfIPIn~~---------~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~---k~i~~~L~~yL~~e~~~~~~ 461 (571)
.++++|++||+|||++ +||+|+|+..+.+ +++||||+.+.+. +.+.+.++.+|......
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 7999999999999983 6999999999998 9999999988875 35566666666542110
Q ss_pred cCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhhCCcccchhhhhcccccCcCHHHHHHHHHH
Q 008283 462 EVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIK 541 (571)
Q Consensus 462 ~~~~~D~~~~~~~W~~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~~p~~ftq~dm~~frr~~f~pe~i~~~R~~ 541 (571)
..+..+|||.||||||+|||.+++.++... .+..|.. .-.-..+..|+++|..
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 2222221 1122457789999999
Q ss_pred HHHHHHHHhh
Q 008283 542 IRNLLKKQFQ 551 (571)
Q Consensus 542 I~~lIl~L~~ 551 (571)
|+.||..|..
T Consensus 207 l~~LI~slg~ 216 (223)
T KOG3246|consen 207 LLDLIQSLGS 216 (223)
T ss_pred HHHHHHHhCc
Confidence 9999998763
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=97.11 E-value=0.00088 Score=70.77 Aligned_cols=93 Identities=22% Similarity=0.279 Sum_probs=64.6
Q ss_pred CCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCc------------------------------HHHHH
Q 008283 397 FQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCS------------------------------LSIFS 446 (571)
Q Consensus 397 f~kd~IfIPIn~~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~------------------------------k~i~~ 446 (571)
-++.|+.+|++...||..+|+|...+ .+++|||-|.... ..-++
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 45789999999999999999999877 8888999876421 01244
Q ss_pred HHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChhHHHHHHHHHHHhhCCcccc
Q 008283 447 NIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLK 518 (571)
Q Consensus 447 ~L~~yL~~e~~~~~~~~~~~D~~~~~~~W~~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~~p~~ft 518 (571)
.|.+|+...+.... ..|.+ ---|--.++||+|++.||-.....+|..|.
T Consensus 303 VLfrfF~d~f~~~~-------------------gciNv----evnQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 303 VLFRFFEDSFGVKY-------------------GCINV----EVNQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred HHHHHHHhhcccce-------------------eEEEh----hhhhhcccccchHHHHHHHHHHccCchhHH
Confidence 55555554321100 01111 125778899999999999988888887653
No 8
>PRK11836 deubiquitinase; Provisional
Probab=95.48 E-value=0.08 Score=54.49 Aligned_cols=96 Identities=20% Similarity=0.260 Sum_probs=51.3
Q ss_pred CCCccCHHHHHHHHHHHHHhcCCCCCCCCceEEEchhhHH-HHHHhhhcCCCCchhHHHHHHhhhccccCCCCCEEEEEe
Q 008283 328 PAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYS-KLKEAVSHKGGDKDSFFIKFRRWWKGVNIFQKSYVLIPI 406 (571)
Q Consensus 328 ~~~WLND~IInfYl~~L~~~~~~~~~~~~~v~~fnTfFy~-kL~~~~~~kg~d~~~~~~~vkrW~k~vnif~kd~IfIPI 406 (571)
+.+.|...=|..|.+-+..........+ .+.+..++--. -|.. ....++ +.-.+|-++.=+|||
T Consensus 162 ~nRmltsDEia~~~q~~~~~~~n~~VNy-PiGLi~P~t~~~~L~~----------~L~E~i----~~~~~~~k~~elFpI 226 (403)
T PRK11836 162 KNRQLTTDEIACYLQKIAANAKNTQVNY-PTGLYVPYSTRTHLED----------ALNENI----KSDPSWPKEVQLFPI 226 (403)
T ss_pred ccccccHHHHHHHhcccccCCccceecC-CceeeecCcccchhHH----------HHHHhh----hcCCCCcccceEEEe
Confidence 4567788888888877765442211111 12222221111 1111 111122 334566678889999
Q ss_pred ecCCceEEEEEEcCCCC--CCCCCeEEEEcCCCC
Q 008283 407 HEDVHWSLVIICIPDKE--DESGPIILHLDSLKL 438 (571)
Q Consensus 407 n~~~HWsLlVI~~p~k~--~~~~~~I~~yDSLg~ 438 (571)
|.+.||.|+++..-..+ ......-++|.|+..
T Consensus 227 Ntg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~ 260 (403)
T PRK11836 227 NTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRA 260 (403)
T ss_pred cCCCcEEEEEeHHhhhcccccceeEEEEEecHhh
Confidence 99999999987543211 112345667788753
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=95.34 E-value=0.036 Score=55.96 Aligned_cols=35 Identities=14% Similarity=0.135 Sum_probs=23.9
Q ss_pred EEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCC
Q 008283 401 YVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLH 439 (571)
Q Consensus 401 ~IfIPIn~~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~ 439 (571)
.=+||||.+.||.|+++..-.. ...-++|.|+..-
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 3359999999999998754321 1356677777543
No 10
>PRK15371 effector protein YopJ; Provisional
Probab=90.32 E-value=4.2 Score=42.51 Aligned_cols=28 Identities=21% Similarity=0.571 Sum_probs=24.1
Q ss_pred cCCCcCCCCCCCChhHHHHHHHHHHHhh
Q 008283 485 RIIPVPQQKNDYDCGLFVLFFMERFMEE 512 (571)
Q Consensus 485 ~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~ 512 (571)
..+.+-.|.-.+|||||-|.++.+....
T Consensus 159 avie~d~QkS~~dC~mFSL~~AkK~~~e 186 (287)
T PRK15371 159 SMVEMDIQRSSSECGIFSLALAKKLYLE 186 (287)
T ss_pred EEEecccccCcccchhhhHHHHHHHhhh
Confidence 3556778999999999999999988776
No 11
>PF15328 GCOM2: Putative GRINL1B complex locus protein 2
Probab=90.11 E-value=0.26 Score=49.69 Aligned_cols=37 Identities=35% Similarity=0.406 Sum_probs=31.3
Q ss_pred HHhhhhhc--ccccCCCcchHhHHHHHHHHHHHHHHHhh
Q 008283 73 ARMKDTYS--KVRHCLPDKGKKILATVTRLEKECERRRL 109 (571)
Q Consensus 73 ~r~~~~~~--~~~~~lpD~G~K~~~~i~~~~~E~~rR~~ 109 (571)
+|+...|. ++-.+|||||+||+..+..|..++.+|.-
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 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=89.99 E-value=0.65 Score=44.70 Aligned_cols=81 Identities=20% Similarity=0.315 Sum_probs=38.3
Q ss_pred CCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccC---CCCCCcccccccccCCcccccc
Q 008283 409 DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEV---SPSDLPIAERIWQHLPRRIDDR 485 (571)
Q Consensus 409 ~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~k~i~~~L~~yL~~e~~~~~~~~---~~~D~~~~~~~W~~lp~~i~~~ 485 (571)
+.||..+..+.... ++|.||.+|-++. ++ .++..-++..+-+.. ...| +.|..+
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 9999999998752 21 121221221111000 0011 222221
Q ss_pred -CCCcCCCCCCCChhHHHHHHHHHHHhh
Q 008283 486 -IIPVPQQKNDYDCGLFVLFFMERFMEE 512 (571)
Q Consensus 486 -~~~vPqQ~Ng~DCGVFVL~y~e~~~~~ 512 (571)
..+.-|=.++--||+|.|.|+.+|...
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 122333357789999999999999875
No 13
>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=87.85 E-value=2.7 Score=40.96 Aligned_cols=88 Identities=16% Similarity=0.305 Sum_probs=51.5
Q ss_pred EEEEeec-CCceEEEEEE-cCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCC
Q 008283 402 VLIPIHE-DVHWSLVIIC-IPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLP 479 (571)
Q Consensus 402 IfIPIn~-~~HWsLlVI~-~p~k~~~~~~~I~~yDSLg~~~~k~i~~~L~~yL~~e~~~~~~~~~~~D~~~~~~~W~~lp 479 (571)
.+++... ..|.+.+=|- .++ ..+.|++|+|-........ |..+.........+. . |
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~----~k~SlI~~Epa~~~~~~~~---l~~~~~~~~~~~~~~--~-------------~ 131 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN----GKPSLIVFEPASFYGMKPA---LAGYTKLAEEARQKL--L-------------P 131 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC----CCceEEEEccccccCCcch---hhhHHHHHHHHHhcc--C-------------C
Confidence 3555443 5676655444 333 3579999999865432111 233322211111000 1 1
Q ss_pred ccccccCCCcCCCCCCCChhHHHHHHHHHHHhh
Q 008283 480 RRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEE 512 (571)
Q Consensus 480 ~~i~~~~~~vPqQ~Ng~DCGVFVL~y~e~~~~~ 512 (571)
...+..+++..|...+|||||-|.++.++..+
T Consensus 132 -~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 132 -NAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred -CcEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 12245678999999999999999999988765
No 14
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=62.66 E-value=8 Score=44.97 Aligned_cols=32 Identities=38% Similarity=0.617 Sum_probs=28.4
Q ss_pred ccccCCCcchHhHHHHHHHHHHHHHHHhhhCC
Q 008283 81 KVRHCLPDKGKKILATVTRLEKECERRRLAGA 112 (571)
Q Consensus 81 ~~~~~lpD~G~K~~~~i~~~~~E~~rR~~~~~ 112 (571)
.+...|||+|.++..+|+.+.+|++||..-+.
T Consensus 209 ~~~~~Lpd~g~~~~kr~~el~~~~~~~~~~~~ 240 (901)
T KOG4439|consen 209 KAIDDLPDKGARLIKRLQELDRELERRMQFGE 240 (901)
T ss_pred hhhhhCCccHHHHHHHHHHHHHHHHHHHhhhh
Confidence 44569999999999999999999999998653
No 15
>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=33.48 E-value=75 Score=38.85 Aligned_cols=39 Identities=15% Similarity=0.282 Sum_probs=26.7
Q ss_pred EEEeec-------CCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHH
Q 008283 403 LIPIHE-------DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNI 448 (571)
Q Consensus 403 fIPIn~-------~~HWsLlVI~~p~k~~~~~~~I~~yDSLg~~~~k~i~~~L 448 (571)
|+||-. ..||.++|-- +++ ..|.||.||..+.....+.|
T Consensus 49 fmpvltgv~p~~~sghwimlikg-~gn------~y~lfdplg~~sg~~y~nil 94 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLIKG-QGN------QYYLFDPLGKTSGEGYQNIL 94 (1439)
T ss_pred CceeecCcCCCCcCceeEEEEEc-CCC------ceEEeccccccccccHHHHH
Confidence 566654 5899988754 333 89999999987654444443
No 16
>PF15463 ECM11: Extracellular mutant protein 11
Probab=30.39 E-value=74 Score=29.63 Aligned_cols=52 Identities=17% Similarity=0.178 Sum_probs=41.7
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccccCCCcchHhHHHHHHHHHHHHHHHhhh
Q 008283 59 LDRQIPDQELGVRIARMKDTYSKVRHCLPDKGKKILATVTRLEKECERRRLA 110 (571)
Q Consensus 59 ~~~~~~D~~L~e~i~r~~~~~~~~~~~lpD~G~K~~~~i~~~~~E~~rR~~~ 110 (571)
.|+.+|..+-.+.=..+-.....|..+|-+.=.++|.++..++.|+.+|-.+
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 17
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=27.36 E-value=1.2e+02 Score=24.63 Aligned_cols=52 Identities=17% Similarity=0.296 Sum_probs=38.4
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccc-----cCC--CcchHhHHHHHHHHHHHHHHHhhh
Q 008283 59 LDRQIPDQELGVRIARMKDTYSKVR-----HCL--PDKGKKILATVTRLEKECERRRLA 110 (571)
Q Consensus 59 ~~~~~~D~~L~e~i~r~~~~~~~~~-----~~l--pD~G~K~~~~i~~~~~E~~rR~~~ 110 (571)
+++.+|+.||++.|...+..|-.+. ..+ |-.-..+|+.|.|+.=.+..|..+
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 18
>PHA02130 hypothetical protein
Probab=26.41 E-value=35 Score=27.97 Aligned_cols=37 Identities=19% Similarity=0.475 Sum_probs=30.3
Q ss_pred HHHHHHhhh-ccccCCCCCEEEEEeecCCceEEEEEEc
Q 008283 383 FFIKFRRWW-KGVNIFQKSYVLIPIHEDVHWSLVIICI 419 (571)
Q Consensus 383 ~~~~vkrW~-k~vnif~kd~IfIPIn~~~HWsLlVI~~ 419 (571)
..+.++.|. .+.+-++-+++-||.....||-|+-++.
T Consensus 15 s~~sl~~wl~~~~dswdddil~ipfkstv~w~lcp~~q 52 (81)
T PHA02130 15 SWESLREWLDERFDSWDDDILSIPFKSTVYWDLCPYAQ 52 (81)
T ss_pred HHHHHHHHHHhcccccccchhcccccceeeeccCcchh
Confidence 356788887 4678889999999999999999987643
Done!