Query 009157
Match_columns 542
No_of_seqs 215 out of 1120
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 21:06:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009157.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009157hhsearch_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 1E-49 2.2E-54 424.6 16.8 222 282-537 285-509 (511)
2 PLN03189 Protease specific for 100.0 3.2E-46 6.9E-51 394.8 24.4 227 283-537 254-488 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 7.6E-43 1.6E-47 366.7 15.2 195 306-535 372-566 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 2.6E-31 5.6E-36 257.7 16.6 186 330-533 1-208 (216)
5 KOG3246 Sentrin-specific cyste 99.9 1.8E-25 3.9E-30 214.3 15.4 182 313-537 14-215 (223)
6 KOG0779 Protease, Ulp1 family 99.9 4.6E-26 1E-30 252.6 10.1 485 8-532 10-583 (595)
7 PF03290 Peptidase_C57: Vaccin 97.1 0.001 2.3E-08 69.8 6.4 93 397-518 229-351 (423)
8 PRK14848 deubiquitinase SseL; 95.9 0.029 6.3E-07 56.3 8.2 36 400-439 189-224 (317)
9 PRK11836 deubiquitinase; Provi 95.7 0.029 6.3E-07 57.3 7.4 46 393-438 213-260 (403)
10 PF00770 Peptidase_C5: Adenovi 93.2 0.28 6E-06 46.9 6.9 78 409-512 33-117 (183)
11 PRK15371 effector protein YopJ 90.9 4.8 0.00011 41.8 13.4 28 486-513 160-187 (287)
12 PF15328 GCOM2: Putative GRINL 90.4 0.24 5.1E-06 49.6 3.3 37 73-109 3-41 (223)
13 PF03421 YopJ: YopJ Serine/Thr 87.8 4.1 8.9E-05 39.4 9.7 88 402-512 74-163 (177)
14 KOG4439 RNA polymerase II tran 63.8 7.4 0.00016 45.0 3.9 32 81-112 209-240 (901)
15 PF15463 ECM11: Extracellular 32.7 64 0.0014 29.8 4.2 52 59-110 65-116 (139)
16 PF12252 SidE: Dot/Icm substra 32.4 81 0.0018 38.4 5.8 38 403-447 49-93 (1439)
17 PRK00306 50S ribosomal protein 28.3 1.1E+02 0.0024 24.6 4.4 52 59-110 5-63 (66)
18 PHA02130 hypothetical protein 24.3 39 0.00084 27.5 1.1 37 383-419 15-52 (81)
19 KOG1924 RhoA GTPase effector D 20.8 1.1E+02 0.0023 36.3 4.0 28 313-344 764-791 (1102)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1e-49 Score=424.56 Aligned_cols=222 Identities=26% Similarity=0.484 Sum_probs=189.2
Q ss_pred cCCCCccchHHHHHHHHhhcC---CeeecCCCCCCCceEEecccccccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCce
Q 009157 282 EGSLHIETTEQADEFAECMID---AKIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDC 358 (542)
Q Consensus 282 ~~~~~~~~~e~~~e~~~~~~~---~~i~yP~~~~~~~i~Lt~~DL~~L~~~~WLND~IInfyl~~L~~~~~~~~~~~~~v 358 (542)
+..+++++.+...++.+.+.+ ..+.. ..+++.||.+||.||.+++||||+||||||++|.++.....+ .+++
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 445677776666666665542 22221 246799999999999999999999999999999999877655 8899
Q ss_pred EEEchhhHHHHHHhhhcCCCCchhhhHHHHhhhccccCCCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCC
Q 009157 359 HFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKL 438 (542)
Q Consensus 359 ~~fnTfFy~kL~~~~~~kg~d~~~~f~~vkrWtk~vdIf~kd~IfIPIn~~~HWsLvVId~~~k~~~~~~~I~~yDSL~~ 438 (542)
|+||||||++|.. .+|.+|+|||+++|||++|+||||||.+.||+|+||++.++ +|.|||||++
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 HAFNTFFYTKLVG----------RGYAGVKRWTKKVDIFDKDIIFVPIHLGVHWCLAVIDLREK------TIEYYDSLGG 423 (511)
T ss_pred EEEechhhhhhhh----------cchHHHHhHhhccCccccceeEeeeecCceEEEEEEEcccc------eEEEeeccCC
Confidence 9999999999986 25899999999999999999999999999999999999998 9999999997
Q ss_pred CCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChHHHHHHHHHHHhhhCCCCCC
Q 009157 439 HCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLK 518 (542)
Q Consensus 439 ~~~k~v~~~L~~~L~~e~~~~~~~~~~~Dl~~~~~~Wk~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~~p~~ft 518 (542)
..++ ++.+|..||.+|+..+.+. ++ +-..|... ...++|||.||+|||+|+|+|++|++++.|..||
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----DF--DVSGWTIE------FVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFT 490 (511)
T ss_pred CCcc-hHHHHHHHHHHHHhhhhcC----CC--Cccchhhh------hhhccccccCCCccceEEeeechhhccCCCcccC
Confidence 7654 4499999999999775432 32 23578752 3458999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHHHHhcC
Q 009157 519 KKDLAMVLPAITNRTCYVS 537 (542)
Q Consensus 519 q~dm~~fR~~i~~~ll~~~ 537 (542)
|+||+.||++|+++||+.-
T Consensus 491 q~dmp~fR~~m~~eI~~~~ 509 (511)
T KOG0778|consen 491 QQDMPYFRKKMAKEILHLK 509 (511)
T ss_pred hhhhHHHHHHHHHHHHhhh
Confidence 9999999999999999864
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=3.2e-46 Score=394.82 Aligned_cols=227 Identities=22% Similarity=0.441 Sum_probs=189.8
Q ss_pred CCCCccchHHHHHHHHhhcCC----eeecCCCCCCCceEEecccccccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCce
Q 009157 283 GSLHIETTEQADEFAECMIDA----KIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDC 358 (542)
Q Consensus 283 ~~~~~~~~e~~~e~~~~~~~~----~i~yP~~~~~~~i~Lt~~DL~~L~~~~WLND~IInfyl~~L~~~~~~~~~~~~~v 358 (542)
..+.|++.|+..+|.++|... .++.. .+++++||.+||.||.|++||||+||||||.||.++.........++
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 347889999999999988632 23322 35789999999999999999999999999999988654433345689
Q ss_pred EEEchhhHHHHHHhhhcCCCCchhhhHHHHhhhcc----ccCCCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEc
Q 009157 359 HFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG----VNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLD 434 (542)
Q Consensus 359 ~~fnTfFy~kL~~~~~~kg~d~~~~f~~vkrWtk~----vdIf~kd~IfIPIn~~~HWsLvVId~~~k~~~~~~~I~~yD 434 (542)
|+||||||++|.... ....|.+|+||++. +++|++++||||||.+.||+|+||+++.+ +|+|||
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 12358999999963 57999999999999999999999999988 999999
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChHHHHHHHHHHHhhhCC
Q 009157 435 SLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAP 514 (542)
Q Consensus 435 SL~~~~~k~v~~~L~~~L~~e~~~~~~~~~~~Dl~~~~~~Wk~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~~p 514 (542)
||++.+ ..+++.|+.||..+++.+. +.++ ..+.|... ...++|||.||||||||||+||++|+.+.+
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-PKILDALAKYYVDEVKDKS----EKDI--DVSSWEQE------FVEDLPEQKNGYDCGMFMIKYIDFYSRGLG 465 (490)
T ss_pred CCCCCC-HHHHHHHHHHHHHHHhhhc----CCCc--chhcceec------cCCCCCCCCCCCCHHHHHHHHHHHHcCCCC
Confidence 999876 4588999999999987643 2233 33568631 245899999999999999999999999999
Q ss_pred CCCCHHhHHHHHHHHHHHHHhcC
Q 009157 515 ERLKKKDLAMVLPAITNRTCYVS 537 (542)
Q Consensus 515 ~~ftq~dm~~fR~~i~~~ll~~~ 537 (542)
+.|+|+||+.||++|+++|+...
T Consensus 466 LtFSQeDMp~fRrRma~EIl~~r 488 (490)
T PLN03189 466 LCFGQEHMPYFRLRTAKEILRLK 488 (490)
T ss_pred CCcChhhhHHHHHHHHHHHHHhh
Confidence 99999999999999999999864
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.6e-43 Score=366.66 Aligned_cols=195 Identities=33% Similarity=0.585 Sum_probs=172.5
Q ss_pred ecCCCCCCCceEEecccccccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCCchhhhH
Q 009157 306 YYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFI 385 (542)
Q Consensus 306 ~yP~~~~~~~i~Lt~~DL~~L~~~~WLND~IInfyl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~~~~f~ 385 (542)
+||+- +.++|+||..|+.||.+++||||+||||||+||...... .....+||+||||||++|.+. +|.
T Consensus 372 ~~~~~-~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~-~s~~~~vh~FnTFFYT~Lsrr----------Gy~ 439 (578)
T COG5160 372 CYPFN-DRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKN-TSKREQVHLFNTFFYTKLSRR----------GYS 439 (578)
T ss_pred ccccc-CcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccC-cccccceEEeehhhHHHHHHH----------HhH
Confidence 78876 478999999999999999999999999999999665443 345789999999999999863 589
Q ss_pred HHHhhhccccCCCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCC
Q 009157 386 KFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSP 465 (542)
Q Consensus 386 ~vkrWtk~vdIf~kd~IfIPIn~~~HWsLvVId~~~k~~~~~~~I~~yDSL~~~~~k~v~~~L~~~L~~e~~~~~~~~~~ 465 (542)
+|+||++++|||+++|||||||...||+|+|||.+.+ .|.|||||++.+ ..+++.|..|+.+||+....+
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 999999999887 679999999999998753211
Q ss_pred CCCcccccccccCCccccccCCCcCCCCCCCChHHHHHHHHHHHhhhCCCCCCHHhHHHHHHHHHHHHHh
Q 009157 466 SDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMVLPAITNRTCY 535 (542)
Q Consensus 466 ~Dl~~~~~~Wk~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~~p~~ftq~dm~~fR~~i~~~ll~ 535 (542)
+.|. .....+||||.||+|||||||+|++|+++++|..|++.|++.+|+.|+..|+.
T Consensus 510 -------~~~~------~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~ 566 (578)
T COG5160 510 -------DPQI------KMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKD 566 (578)
T ss_pred -------chhh------hhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHH
Confidence 1232 34578999999999999999999999999999999999999999999987754
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=2.6e-31 Score=257.73 Aligned_cols=186 Identities=33% Similarity=0.627 Sum_probs=138.7
Q ss_pred CccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCC----------chhhhHHHHhhhccc---cC
Q 009157 330 AYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD----------KDSFFIKFRRWWKGV---NI 396 (542)
Q Consensus 330 ~WLND~IInfyl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d----------~~~~f~~vkrWtk~v---dI 396 (542)
+||||+|||||++||......+.....++++|+|+|+..|......-+.+ ....+..+.+|++.. ++
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 69999999999999996654333456899999999999998432110001 024567889999887 99
Q ss_pred CCCCEEEEEeec-CCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCc----HHHHHHHHHHHHHHHHHhhccCCCCCCccc
Q 009157 397 FQKSYVLIPIHE-DVHWSLVIICIPDKEDESGPIILHLDSLKLHCS----LSIFSNIRSFLKEEWNYLKQEVSPSDLPIA 471 (542)
Q Consensus 397 f~kd~IfIPIn~-~~HWsLvVId~~~k~~~~~~~I~~yDSL~~~~~----k~v~~~L~~~L~~e~~~~~~~~~~~Dl~~~ 471 (542)
+++++||||||. +.||+|+||+++.+ +|++||||++... ..++..+..+|...+....... .+
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~~------~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~---- 148 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPKK------RIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRD--PD---- 148 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTTT------EEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSC--T-----
T ss_pred cccCEEEEEEechhhccceeEEccccc------EEEEEeccccccccccchhhhhhhhhhhhhccccccccc--cc----
Confidence 999999999999 99999999999998 9999999998875 4567788888887765432221 11
Q ss_pred ccccccCCccccccCCCcCCCCCCCChHHHHHHHHHHHhhhCCCC----CCHHhHHHHHHHHHHHH
Q 009157 472 ERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPER----LKKKDLAMVLPAITNRT 533 (542)
Q Consensus 472 ~~~Wk~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~~p~~----ftq~dm~~fR~~i~~~l 533 (542)
...|.. ....++|||.|++|||+|||+||++++.+.+.. |++++|..+|++++..+
T Consensus 149 ~~~~~~------~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~~i~~~r~~~a~~~ 208 (216)
T PF02902_consen 149 KSPFKI------VRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQELTEEDIKNFRKKLAVDL 208 (216)
T ss_dssp TTTCEE------EEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCSBTGHHHHHHHHHHHH--
T ss_pred cceeee------cccccccCCCCCCCcHHHHHHHHHHHHhCCCCcccccCCHHHHHHHHHHHHhhc
Confidence 122321 235689999999999999999999999986554 89999999999999543
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.93 E-value=1.8e-25 Score=214.29 Aligned_cols=182 Identities=23% Similarity=0.394 Sum_probs=133.7
Q ss_pred CCceEEecccccccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCCchhhhHHHHhhhc
Q 009157 313 PESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWK 392 (542)
Q Consensus 313 ~~~i~Lt~~DL~~L~~~~WLND~IInfyl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d~~~~f~~vkrWtk 392 (542)
.+.+.|+.+|+..|.++.||||.+|+||.+||........ .+.|++++-.-..|.. .+.. .-+.....
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 YFDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSE---PDLHLLRPSLTFFLRH----APNP-----EEIAMVLD 81 (223)
T ss_pred eeehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccC---cchhccCHHHHHHHHh----CCCc-----HHHHHhcC
Confidence 4679999999999999999999999999999999876543 3467777633222322 2221 12334445
Q ss_pred cccCCCCCEEEEEeecC---------CceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcH---HHHHHHHHHHHHHHHHhh
Q 009157 393 GVNIFQKSYVLIPIHED---------VHWSLVIICIPDKEDESGPIILHLDSLKLHCSL---SIFSNIRSFLKEEWNYLK 460 (542)
Q Consensus 393 ~vdIf~kd~IfIPIn~~---------~HWsLvVId~~~k~~~~~~~I~~yDSL~~~~~k---~v~~~L~~~L~~e~~~~~ 460 (542)
..++++|++||+|||++ +||+|+|+..+++ +++||||+.+.+.+ .+.+.++.+|......
T Consensus 82 pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~------~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~-- 153 (223)
T KOG3246|consen 82 PLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDG------KFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAK-- 153 (223)
T ss_pred hhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCC------cEEEeecccCCCcHHHHHHHHHHHHHHhhhhhh--
Confidence 67999999999999973 6999999999998 99999999988753 4555565566542110
Q ss_pred ccCCCCCCcccccccccCCccccccCCCcCCCCCCCChHHHHHHHHHHHhhh----CCCC----CCHHhHHHHHHHHHHH
Q 009157 461 QEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEE----APER----LKKKDLAMVLPAITNR 532 (542)
Q Consensus 461 ~~~~~~Dl~~~~~~Wk~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~----~p~~----ftq~dm~~fR~~i~~~ 532 (542)
.....+|||.||||||+|||.+++.++.. .-.. +..+-+.++|..|..-
T Consensus 154 -----------------------~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~l~~L 210 (223)
T KOG3246|consen 154 -----------------------RVECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREELLDL 210 (223)
T ss_pred -----------------------cccccChhhhcCCchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHH
Confidence 11567999999999999999998877663 2122 4456778888888876
Q ss_pred HHhcC
Q 009157 533 TCYVS 537 (542)
Q Consensus 533 ll~~~ 537 (542)
|...|
T Consensus 211 I~slg 215 (223)
T KOG3246|consen 211 IQSLG 215 (223)
T ss_pred HHHhC
Confidence 65544
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=4.6e-26 Score=252.65 Aligned_cols=485 Identities=22% Similarity=0.252 Sum_probs=327.0
Q ss_pred ccCCCcccccccccCCCCCCCCceeeeccCCCCCCCCCCCCCCCCCCCchhhcCCCCchHHHHHHHHhhhhhcccccCCC
Q 009157 8 RNKRKLNIDWEEVLPGRNDDVPAELIVKKSGPPTPAQKSVPMSDDPGSGEELDRQIPDQELGVRIARMKDTYSKVRHCLP 87 (542)
Q Consensus 8 ~~~~~~~id~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~D~~L~e~i~r~~~~l~~~~~~lp 87 (542)
..++...|+|.-++- +..-.+.+++|-++++. .|+...|...+.. ..+.|..|.+.-.|..+.+..++.+.+
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 65667788887777655 4555677777777 889999999999999999889999999
Q ss_pred cchHhHHHHHHHHHHHHHHHhhhCC------------C--CccccccccccCCCCC------CC---ccccccC------
Q 009157 88 DKGKKILATVTRLEKECERRRLAGA------------V--PVCLDIDGCDKLTQSP------SS---DCFTQRT------ 138 (542)
Q Consensus 88 D~G~K~~~~i~~~~~E~~rR~~~~~------------~--~~~~d~~~~~~~~qs~------~s---~~~~~~~------ 138 (542)
+.|.+-+..|...+.+..+|+..+. - ..-.|.. +++...-. .+ +.|....
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 009157 139 -----------PSPQIQSKSSFTSVFREKMEENRDCREANAFDKELSILAHCDRRKMRSDGDLSQRGRQNVRSSSRKWP- 206 (542)
Q Consensus 139 -----------~ss~~~~~s~f~~~f~~~~e~~~~~~~~~af~kel~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 206 (542)
+..=......|-.+|... ..++..-..+...++.... ++...-+ .++..+..-+..+.
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 2344455556566666655 3332221 12223333333332
Q ss_pred -cc-------cCCCCCCC--CCCccccccccCCCC-CCCCCCccc-------------------CCCCCCccccccCCCc
Q 009157 207 -FH-------KGDKSFNS--NGSQKDRASLTCPSH-QSGENSSSC-------------------LPKKKESFEVLPSKNP 256 (542)
Q Consensus 207 -~~-------~~~~~~~~--n~~q~~~~s~~~~~~-~~~~~~~~~-------------------~~~~~~~~~~~~~~~~ 256 (542)
.+ ...+.+.+ -..+-.+.+|...++ .++...+++ .....|....+|.++.
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 4567777788888888
Q ss_pred ccccc--cceeecCCCCCCCcCCcccccCCCCccchHHHHHHHHhhcCCeeecCCC-CCCCceEEecccccccCCCCccC
Q 009157 257 RLRKE--QNLVLLDEDESPVEDASEESEGSLHIETTEQADEFAECMIDAKIYYPSR-VDPESVEICYTDINHLAPAAYLT 333 (542)
Q Consensus 257 ~~~~~--~~~v~ld~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~i~yP~~-~~~~~i~Lt~~DL~~L~~~~WLN 333 (542)
.++.. .++..+++.+.. .....+..-++.. .+++. .. ..+.++.+|+.||..+.+||
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 466655554432 1122222222222 23332 22 36789999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCC--chhhhHHHHhhhccccCCCCCEEEEEeecCCc
Q 009157 334 SPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD--KDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVH 411 (542)
Q Consensus 334 D~IInfyl~~L~~~~~~~~~~~~~v~~fnTfFy~kL~~~~~~kg~d--~~~~f~~vkrWtk~vdIf~kd~IfIPIn~~~H 411 (542)
|.||+||+.|+.............+|+|++|||..+.+.+..++.+ ....+..+++|++++++|.++||++|+|...|
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 9999999999999887755577899999999999999988776666 45677889999999999999999999999999
Q ss_pred eEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCC
Q 009157 412 WSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQ 491 (542)
Q Consensus 412 WsLvVId~~~k~~~~~~~I~~yDSL~~~~~k~v~~~L~~~L~~e~~~~~~~~~~~Dl~~~~~~Wk~lp~~i~~~~~~vPq 491 (542)
|.|++||++..+.+......+++++..+......+.+..+|..++.+.+......+.++....|..+++.++.-++. ||
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 99999999998887777889999998887666778889999998877665545566777777888888766655555 99
Q ss_pred CCCCCChHHHHHHHHHHHhhhCCCC-------------CCHHhHHHHHHHHHHH
Q 009157 492 QKNDYDCGLFVLFFMERFMEEAPER-------------LKKKDLAMVLPAITNR 532 (542)
Q Consensus 492 Q~Ng~DCGVFVL~yae~~~~~~p~~-------------ftq~dm~~fR~~i~~~ 532 (542)
|.|..|||+|++.|++.|+.+++.+ |.+.++..||..+-+.
T Consensus 530 q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~ 583 (595)
T KOG0779|consen 530 QNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRNL 583 (595)
T ss_pred ccCcccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhcc
Confidence 9999999999999999999987775 5667777888776653
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=97.06 E-value=0.001 Score=69.81 Aligned_cols=93 Identities=22% Similarity=0.279 Sum_probs=65.1
Q ss_pred CCCCEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCc------------------------------HHHHH
Q 009157 397 FQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCS------------------------------LSIFS 446 (542)
Q Consensus 397 f~kd~IfIPIn~~~HWsLvVId~~~k~~~~~~~I~~yDSL~~~~~------------------------------k~v~~ 446 (542)
-++.|+.+|++...||.++|+|...+ .+.+|||-|..+. ..-++
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 8889999876421 01245
Q ss_pred HHHHHHHHHHHHhhccCCCCCCcccccccccCCccccccCCCcCCCCCCCChHHHHHHHHHHHhhhCCCCCC
Q 009157 447 NIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLK 518 (542)
Q Consensus 447 ~L~~~L~~e~~~~~~~~~~~Dl~~~~~~Wk~lp~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~~p~~ft 518 (542)
.|.+|+...+.... +.|.+ ---|-..++||+|++.||-.....+|..|-
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 55555555331100 01111 125788899999999999988888886654
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=95.94 E-value=0.029 Score=56.27 Aligned_cols=36 Identities=14% Similarity=0.130 Sum_probs=24.9
Q ss_pred CEEEEEeecCCceEEEEEEcCCCCCCCCCeEEEEcCCCCC
Q 009157 400 SYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLH 439 (542)
Q Consensus 400 d~IfIPIn~~~HWsLvVId~~~k~~~~~~~I~~yDSL~~~ 439 (542)
+.=+||||.+.||.|+++..-.. ....++|.|+..-
T Consensus 189 ~nevF~INtg~HWil~~~~Ki~~----kiKC~iFNs~~~l 224 (317)
T PRK14848 189 HNEVFLINTGDHWLLCLFYKLAE----KIKCLIFNTYYDL 224 (317)
T ss_pred cceEEEecCCCcEEEEEhHHhhh----hceEEEeecHhhh
Confidence 33459999999999998754221 2366778887543
No 9
>PRK11836 deubiquitinase; Provisional
Probab=95.74 E-value=0.029 Score=57.28 Aligned_cols=46 Identities=24% Similarity=0.304 Sum_probs=31.6
Q ss_pred cccCCCCCEEEEEeecCCceEEEEEEcCCCC--CCCCCeEEEEcCCCC
Q 009157 393 GVNIFQKSYVLIPIHEDVHWSLVIICIPDKE--DESGPIILHLDSLKL 438 (542)
Q Consensus 393 ~vdIf~kd~IfIPIn~~~HWsLvVId~~~k~--~~~~~~I~~yDSL~~ 438 (542)
...+|-++.-+||||.+.||.|+++..-..+ .......++|.|+..
T Consensus 213 ~~~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~ 260 (403)
T PRK11836 213 SDPSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRA 260 (403)
T ss_pred cCCCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhh
Confidence 3456778888999999999999987543211 112346677888753
No 10
>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=93.17 E-value=0.28 Score=46.89 Aligned_cols=78 Identities=19% Similarity=0.344 Sum_probs=39.0
Q ss_pred CCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHH------hhccCCCCCCcccccccccCCccc
Q 009157 409 DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNY------LKQEVSPSDLPIAERIWQHLPRRI 482 (542)
Q Consensus 409 ~~HWsLvVId~~~k~~~~~~~I~~yDSL~~~~~k~v~~~L~~~L~~e~~~------~~~~~~~~Dl~~~~~~Wk~lp~~i 482 (542)
+.||.....+.... +++.||.+|.+.. ++ +++..=++.. +.. ..| +.|
T Consensus 33 GvHWlA~Aw~P~s~------t~YmFDPfGfsd~-~L----~qiY~FeYe~llrRSAL~~---~~d------------RCv 86 (183)
T PF00770_consen 33 GVHWLAFAWDPRSR------TFYMFDPFGFSDQ-KL----KQIYQFEYEGLLRRSALSS---TPD------------RCV 86 (183)
T ss_dssp -S-EEEEEEETTTT------EEEEE-TT---HH-HH----HHHH----HHHHHHHHHHH----TT------------SEE
T ss_pred ceeEEEEEecCCcc------eEEEeCCCCCCHH-HH----HHHHhhhHHHHHHHHhhcC---CCC------------ceE
Confidence 69999999999877 9999999998853 21 2211111111 110 011 223
Q ss_pred cc-cCCCcCCCCCCCChHHHHHHHHHHHhhh
Q 009157 483 DD-RIIPVPQQKNDYDCGLFVLFFMERFMEE 512 (542)
Q Consensus 483 ~~-~~~~vPqQ~Ng~DCGVFVL~yae~~~~~ 512 (542)
+. +..+.-|=.++--||+|.|+|+.+|..-
T Consensus 87 ~LvkstqtVQ~p~SaaCGLFC~lFL~aF~~~ 117 (183)
T PF00770_consen 87 TLVKSTQTVQCPCSAACGLFCCLFLHAFVHY 117 (183)
T ss_dssp EEEEE-EE-S-TT---HHHHHHHHHHHHHH-
T ss_pred EEEeccceeeccCchhHHHHHHHHHHHHHhC
Confidence 32 2234445557889999999999999873
No 11
>PRK15371 effector protein YopJ; Provisional
Probab=90.93 E-value=4.8 Score=41.79 Aligned_cols=28 Identities=21% Similarity=0.566 Sum_probs=23.9
Q ss_pred CCCcCCCCCCCChHHHHHHHHHHHhhhC
Q 009157 486 IIPVPQQKNDYDCGLFVLFFMERFMEEA 513 (542)
Q Consensus 486 ~~~vPqQ~Ng~DCGVFVL~yae~~~~~~ 513 (542)
....-.|+-.+|||+|-|.+|.+.....
T Consensus 160 vie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 160 MVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred EEecccccCcccchhhhHHHHHHHhhhh
Confidence 4466789999999999999999988763
No 12
>PF15328 GCOM2: Putative GRINL1B complex locus protein 2
Probab=90.38 E-value=0.24 Score=49.61 Aligned_cols=37 Identities=35% Similarity=0.406 Sum_probs=31.2
Q ss_pred HHhhhhhc--ccccCCCcchHhHHHHHHHHHHHHHHHhh
Q 009157 73 ARMKDTYS--KVRHCLPDKGKKILATVTRLEKECERRRL 109 (542)
Q Consensus 73 ~r~~~~l~--~~~~~lpD~G~K~~~~i~~~~~E~~rR~~ 109 (542)
+|+...|. ++-.+|||||+||+..+..|..++.+|.-
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 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=87.83 E-value=4.1 Score=39.38 Aligned_cols=88 Identities=15% Similarity=0.285 Sum_probs=50.6
Q ss_pred EEEEeec-CCceEEEEEE-cCCCCCCCCCeEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCCcccccccccCC
Q 009157 402 VLIPIHE-DVHWSLVIIC-IPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLP 479 (542)
Q Consensus 402 IfIPIn~-~~HWsLvVId-~~~k~~~~~~~I~~yDSL~~~~~k~v~~~L~~~L~~e~~~~~~~~~~~Dl~~~~~~Wk~lp 479 (542)
.+++... +.|-+.+=|- .++ ..+.|++|+|-........ |..+.........+. ..+
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~----~k~SlI~~Epa~~~~~~~~---l~~~~~~~~~~~~~~--~~~------------ 132 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN----GKPSLIVFEPASFYGMKPA---LAGYTKLAEEARQKL--LPN------------ 132 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC----CCceEEEEccccccCCcch---hhhHHHHHHHHHhcc--CCC------------
Confidence 4555442 4565555444 332 3579999999865432111 222222211111100 111
Q ss_pred ccccccCCCcCCCCCCCChHHHHHHHHHHHhhh
Q 009157 480 RRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEE 512 (542)
Q Consensus 480 ~~i~~~~~~vPqQ~Ng~DCGVFVL~yae~~~~~ 512 (542)
..+...++..|+..+|||+|-|.+|..+..+
T Consensus 133 --~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 133 --AKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred --cEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 1234568899999999999999999998775
No 14
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=63.77 E-value=7.4 Score=44.97 Aligned_cols=32 Identities=38% Similarity=0.617 Sum_probs=28.4
Q ss_pred ccccCCCcchHhHHHHHHHHHHHHHHHhhhCC
Q 009157 81 KVRHCLPDKGKKILATVTRLEKECERRRLAGA 112 (542)
Q Consensus 81 ~~~~~lpD~G~K~~~~i~~~~~E~~rR~~~~~ 112 (542)
.+...|||+|.++..+|+.+.+|++||..-+.
T Consensus 209 ~~~~~Lpd~g~~~~kr~~el~~~~~~~~~~~~ 240 (901)
T KOG4439|consen 209 KAIDDLPDKGARLIKRLQELDRELERRMQFGE 240 (901)
T ss_pred hhhhhCCccHHHHHHHHHHHHHHHHHHHhhhh
Confidence 44569999999999999999999999998653
No 15
>PF15463 ECM11: Extracellular mutant protein 11
Probab=32.65 E-value=64 Score=29.83 Aligned_cols=52 Identities=17% Similarity=0.178 Sum_probs=41.7
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccccCCCcchHhHHHHHHHHHHHHHHHhhh
Q 009157 59 LDRQIPDQELGVRIARMKDTYSKVRHCLPDKGKKILATVTRLEKECERRRLA 110 (542)
Q Consensus 59 ~~~~~~D~~L~e~i~r~~~~l~~~~~~lpD~G~K~~~~i~~~~~E~~rR~~~ 110 (542)
.|+++|..+-.+.=..+-.....|..+|-+.=.++|.++..++.|+.+|-.+
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 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=32.35 E-value=81 Score=38.36 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=26.2
Q ss_pred EEEeec-------CCceEEEEEEcCCCCCCCCCeEEEEcCCCCCCcHHHHHH
Q 009157 403 LIPIHE-------DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSN 447 (542)
Q Consensus 403 fIPIn~-------~~HWsLvVId~~~k~~~~~~~I~~yDSL~~~~~k~v~~~ 447 (542)
|+||-. ..||.++|=-. +...++||.||..+.....+.
T Consensus 49 fmpvltgv~p~~~sghwimlikg~-------gn~y~lfdplg~~sg~~y~ni 93 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLIKGQ-------GNQYYLFDPLGKTSGEGYQNI 93 (1439)
T ss_pred CceeecCcCCCCcCceeEEEEEcC-------CCceEEeccccccccccHHHH
Confidence 667764 58999988543 238999999997764433333
No 17
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=28.33 E-value=1.1e+02 Score=24.62 Aligned_cols=52 Identities=17% Similarity=0.296 Sum_probs=38.4
Q ss_pred hcCCCCchHHHHHHHHhhhhhcccc-----cCC--CcchHhHHHHHHHHHHHHHHHhhh
Q 009157 59 LDRQIPDQELGVRIARMKDTYSKVR-----HCL--PDKGKKILATVTRLEKECERRRLA 110 (542)
Q Consensus 59 ~~~~~~D~~L~e~i~r~~~~l~~~~-----~~l--pD~G~K~~~~i~~~~~E~~rR~~~ 110 (542)
+++.+|+.||++.|...+..|-.+. ..+ |-.-..+|+.|.|+.=.+..|..+
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 3489999999999999988873221 223 334467788999998888877765
No 18
>PHA02130 hypothetical protein
Probab=24.34 E-value=39 Score=27.53 Aligned_cols=37 Identities=19% Similarity=0.469 Sum_probs=30.5
Q ss_pred hhHHHHhhhc-cccCCCCCEEEEEeecCCceEEEEEEc
Q 009157 383 FFIKFRRWWK-GVNIFQKSYVLIPIHEDVHWSLVIICI 419 (542)
Q Consensus 383 ~f~~vkrWtk-~vdIf~kd~IfIPIn~~~HWsLvVId~ 419 (542)
..+.++.|.. +.+-++-|++-||.-...||-|+-++-
T Consensus 15 s~~sl~~wl~~~~dswdddil~ipfkstv~w~lcp~~q 52 (81)
T PHA02130 15 SWESLREWLDERFDSWDDDILSIPFKSTVYWDLCPYAQ 52 (81)
T ss_pred HHHHHHHHHHhcccccccchhcccccceeeeccCcchh
Confidence 3567888974 678889999999999999999987653
No 19
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.80 E-value=1.1e+02 Score=36.28 Aligned_cols=28 Identities=18% Similarity=0.456 Sum_probs=16.6
Q ss_pred CCceEEecccccccCCCCccCHHHHHHHHHHH
Q 009157 313 PESVEICYTDINHLAPAAYLTSPIMNFYIRYL 344 (542)
Q Consensus 313 ~~~i~Lt~~DL~~L~~~~WLND~IInfyl~~L 344 (542)
++.+.+....++.|.+.- ..|.|=|.|-
T Consensus 764 ~EQF~vvm~~vkrL~pRL----~~ilFKl~fs 791 (1102)
T KOG1924|consen 764 PEQFVVVMSQVKRLRPRL----SAILFKLTFS 791 (1102)
T ss_pred HHHHhHHHhhccccChhH----HHHHHHhhHH
Confidence 456666677788887752 2355555443
Done!