Query 004028
Match_columns 778
No_of_seqs 258 out of 1099
Neff 5.1
Searched_HMMs 46136
Date Thu Mar 28 16:17:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004028.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004028hhsearch_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 3.3E-41 7.2E-46 375.1 13.6 181 371-583 317-498 (511)
2 COG5160 ULP1 Protease, Ulp1 fa 100.0 4.2E-40 9.1E-45 361.4 13.5 184 363-582 372-556 (578)
3 PLN03189 Protease specific for 100.0 5.4E-39 1.2E-43 355.0 21.2 187 368-582 284-476 (490)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 3.9E-28 8.4E-33 243.6 18.3 196 386-614 1-215 (216)
5 KOG3246 Sentrin-specific cyste 99.9 2.7E-26 5.8E-31 230.9 14.8 190 371-614 16-218 (223)
6 KOG0779 Protease, Ulp1 family 99.8 3.8E-21 8.3E-26 222.5 6.3 232 371-616 352-593 (595)
7 KOG0779 Protease, Ulp1 family 97.8 3E-06 6.6E-11 99.5 -2.1 449 238-756 7-474 (595)
8 PF03290 Peptidase_C57: Vaccin 96.2 0.011 2.3E-07 65.7 7.1 92 453-575 229-351 (423)
9 PRK14848 deubiquitinase SseL; 93.9 0.098 2.1E-06 55.5 5.6 88 456-569 189-276 (317)
10 PRK11836 deubiquitinase; Provi 93.6 0.16 3.5E-06 54.9 6.7 107 449-569 213-327 (403)
11 PF03421 YopJ: YopJ Serine/Thr 80.3 9.8 0.00021 38.9 9.0 86 458-569 74-163 (177)
12 PF00770 Peptidase_C5: Adenovi 76.2 42 0.00092 34.5 11.8 125 465-611 33-160 (183)
13 PRK15371 effector protein YopJ 54.3 49 0.0011 36.5 8.1 31 540-570 157-187 (287)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.3e-41 Score=375.07 Aligned_cols=181 Identities=32% Similarity=0.670 Sum_probs=157.9
Q ss_pred ceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhccc-ccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhcc
Q 004028 371 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAE-EKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRK 449 (778)
Q Consensus 371 ~vsLt~~DL~~L~p~~WLND~IIdFYL~yL~~~~~~~-~~~rv~~FnSfFy~kL~~~~k~Pssl~d~~~~y~~VkrWtkk 449 (778)
++.||..||.||.+++||||+||||||++|.++.... ..+++|+||||||++|.. .+|+.|+|||++
T Consensus 317 ~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~~------------~gy~~VkRWTk~ 384 (511)
T KOG0778|consen 317 NIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLVG------------RGYAGVKRWTKK 384 (511)
T ss_pred cccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEEEechhhhhhhh------------cchHHHHhHhhc
Confidence 5899999999999999999999999999999986553 278899999999999985 589999999999
Q ss_pred cCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCc
Q 004028 450 VDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTS 529 (778)
Q Consensus 450 vdLFeKD~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~E~k~k~k~~~ 529 (778)
+|||++|+||||||.+.||+|+||+.. .++|.|||||++...+++.+|..||.+|++.|.+...
T Consensus 385 v~if~~d~i~vPIH~~vHW~l~vid~r----------------~k~i~y~DS~~~~~nr~~~aL~~Yl~~E~~~k~~~~~ 448 (511)
T KOG0778|consen 385 VDIFDKDIIFVPIHLGVHWCLAVIDLR----------------EKTIEYYDSLGGGPNRICDALAKYLQDESRDKSKKDF 448 (511)
T ss_pred cCccccceeEeeeecCceEEEEEEEcc----------------cceEEEeeccCCCCcchHHHHHHHHHHHHhhhhcCCC
Confidence 999999999999999999999999863 3699999999977666669999999999998876543
Q ss_pred ccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhc
Q 004028 530 EDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLS 583 (778)
Q Consensus 530 ~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~r 583 (778)
|++ .|.. . ...++|||.||+|||+|+|+|++++..+.|+.|+|.+|+.||
T Consensus 449 -d~s-~w~~-~-~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR 498 (511)
T KOG0778|consen 449 -DVS-GWTI-E-FVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFR 498 (511)
T ss_pred -Ccc-chhh-h-hhhccccccCCCccceEEeeechhhccCCCcccChhhhHHHH
Confidence 333 3432 1 234899999999999999999999999999999999887653
No 2
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.2e-40 Score=361.35 Aligned_cols=184 Identities=37% Similarity=0.738 Sum_probs=160.2
Q ss_pred eccCCCCCceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhc-ccccCcEEEechHHHHHhhccCCCCCCcchhhHHHH
Q 004028 363 VYPEGDSDAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQ-AEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFL 441 (778)
Q Consensus 363 vYp~~d~~~vsLt~~DL~~L~p~~WLND~IIdFYL~yL~~~~~-~~~~~rv~~FnSfFy~kL~~~~k~Pssl~d~~~~y~ 441 (778)
+||.-+..+++||..|+.||.+++||||+|||||++||...-+ ....++||+||||||++|.. .+|+
T Consensus 372 ~~~~~~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~~s~~~~vh~FnTFFYT~Lsr------------rGy~ 439 (578)
T COG5160 372 CYPFNDRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKNTSKREQVHLFNTFFYTKLSR------------RGYS 439 (578)
T ss_pred cccccCcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccCcccccceEEeehhhHHHHHH------------HHhH
Confidence 5888888999999999999999999999999999999965432 23567899999999999974 6899
Q ss_pred HHhhhhcccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHH
Q 004028 442 RVRKWTRKVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEW 521 (778)
Q Consensus 442 ~VkrWtkkvdLFeKD~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~E~ 521 (778)
+|+||+++++||+++|||||||...||+|+|||.+. +.|+|||||++.+..+.+.|+.|+.+||
T Consensus 440 gVrrW~kk~dif~~k~I~iPIni~~HW~l~II~~~~----------------~~i~~~DSLan~~~~v~~~L~~Y~ldE~ 503 (578)
T COG5160 440 GVRRWTKKTDIFSKKYIFIPINISYHWFLAIIDNPK----------------KNILYFDSLANTHDPVLEFLRSYLLDEY 503 (578)
T ss_pred HHHHHHhccCccccceEEEEecccceEEEEEeecCc----------------ceeEEecccccCcHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999764 5899999999999999999999999999
Q ss_pred HHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhh
Q 004028 522 KERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKL 582 (778)
Q Consensus 522 k~k~k~~~~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~ 582 (778)
+..+++.. | .+....+||||.||+|||||||+++++|+.++|..|.+.+++++
T Consensus 504 k~~~~k~~------~--~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~ 556 (578)
T COG5160 504 KIQHDKDP------Q--IKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRA 556 (578)
T ss_pred hcccCCch------h--hhhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchHHH
Confidence 87665431 2 23456799999999999999999999999998776655555443
No 3
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=5.4e-39 Score=354.97 Aligned_cols=187 Identities=27% Similarity=0.606 Sum_probs=155.8
Q ss_pred CCCceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhcc--cccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhh
Q 004028 368 DSDAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQA--EEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRK 445 (778)
Q Consensus 368 d~~~vsLt~~DL~~L~p~~WLND~IIdFYL~yL~~~~~~--~~~~rv~~FnSfFy~kL~~~~k~Pssl~d~~~~y~~Vkr 445 (778)
++.++.||.+||.||.|++||||.|||||+++|.++... ....++|+||||||++|.... +..+|.+|+|
T Consensus 284 ~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~--------~~ygY~~VrR 355 (490)
T PLN03189 284 ENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGK--------SGYDYKAVRR 355 (490)
T ss_pred CCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcC--------CcCChHHHHH
Confidence 345799999999999999999999999999999876432 234689999999999998621 1246999999
Q ss_pred hhcc----cCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHH
Q 004028 446 WTRK----VDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEW 521 (778)
Q Consensus 446 Wtkk----vdLFeKD~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~E~ 521 (778)
||++ ++||++|+||||||.+.||+|+||+++. ++|+|||||++.+..+.+.|+.||..|+
T Consensus 356 WTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~----------------k~I~yyDSLgg~~~~vL~~L~rYL~~E~ 419 (490)
T PLN03189 356 WTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKD----------------QKFQYLDSLKGRDPKILDALAKYYVDEV 419 (490)
T ss_pred HhhhcccccccccCceEEeeeecCCeeEEEEEEcCC----------------CeEEEEeCCCCCCHHHHHHHHHHHHHHH
Confidence 9964 5799999999999999999999999764 5899999999998888999999999999
Q ss_pred HHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhh
Q 004028 522 KERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKL 582 (778)
Q Consensus 522 k~k~k~~~~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~ 582 (778)
+.+.+... +++ .|.. ....++|||.||+|||||||+||+++..+.++.|+|.+|+.|
T Consensus 420 kdK~g~d~-D~s-~W~~--~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~f 476 (490)
T PLN03189 420 KDKSEKDI-DVS-SWEQ--EFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYF 476 (490)
T ss_pred hhhcCCCc-chh-ccee--ccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHH
Confidence 88765432 332 2321 123589999999999999999999999999888888877654
No 4
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=99.96 E-value=3.9e-28 Score=243.56 Aligned_cols=196 Identities=34% Similarity=0.645 Sum_probs=135.6
Q ss_pred CCcCHHHHHHHHHHHHHhh--cccccCcEEEechHHHHHhhccC----CCCCC---cch-hhHHHHHHhhhhccc---CC
Q 004028 386 TFVNDTIIDFYIKYLKNQI--QAEEKHRFHFFNSFFFRKLADLD----KDPSS---ISD-GKAAFLRVRKWTRKV---DI 452 (778)
Q Consensus 386 ~WLND~IIdFYL~yL~~~~--~~~~~~rv~~FnSfFy~kL~~~~----k~Pss---l~d-~~~~y~~VkrWtkkv---dL 452 (778)
+||||.|||||++||..+. ......++++|+|+|+.+|.... +.+.. ... ....+..+.+|++.. ++
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 5999999999999998654 34457899999999999998311 11100 000 134578899999887 99
Q ss_pred CCCCeEEEEeec-cCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcch-----hHHHHHHHHHHHHHHHhcc
Q 004028 453 FGKDYIFIPVNF-NLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHA-----GLKNLVQSYLCEEWKERHK 526 (778)
Q Consensus 453 FeKD~IfIPIN~-nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~-----~l~~~L~~YL~~E~k~k~k 526 (778)
+++++||||||. +.||+|+||+.+. .+|++||||++.+. .+...+..+|..++.....
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~----------------~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 144 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPK----------------KRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEG 144 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTT----------------TEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHS
T ss_pred cccCEEEEEEechhhccceeEEcccc----------------cEEEEEeccccccccccchhhhhhhhhhhhhccccccc
Confidence 999999999999 9999999999865 48999999999876 4667788888888765443
Q ss_pred CCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhHHHHHHHHHH
Q 004028 527 DTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKRSLIQKL 606 (778)
Q Consensus 527 ~~~~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis~kR~~I~~L 606 (778)
... +. ..|. ...+.++|||.|++|||+|||+||++++.+.+..+. ..+...++...|..+...
T Consensus 145 ~~~-~~-~~~~--~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~-------------~~l~~~~i~~~r~~~a~~ 207 (216)
T PF02902_consen 145 RDP-DK-SPFK--IVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFS-------------QELTEEDIKNFRKKLAVD 207 (216)
T ss_dssp SCT--T-TTCE--EEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGC-------------CSBTGHHHHHHHHHHHH-
T ss_pred ccc-cc-ceee--ecccccccCCCCCCCcHHHHHHHHHHHHhCCCCccc-------------ccCCHHHHHHHHHHHHhh
Confidence 221 11 1121 234568999999999999999999999988543321 115778888999999999
Q ss_pred HHHHHHhc
Q 004028 607 ISELLRNR 614 (778)
Q Consensus 607 I~eL~~~~ 614 (778)
|.+...++
T Consensus 208 ~~e~~~~~ 215 (216)
T PF02902_consen 208 LYEELGSR 215 (216)
T ss_dssp --------
T ss_pred cccccccC
Confidence 88776544
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.94 E-value=2.7e-26 Score=230.88 Aligned_cols=190 Identities=25% Similarity=0.403 Sum_probs=136.5
Q ss_pred ceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhcccccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhccc
Q 004028 371 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRKV 450 (778)
Q Consensus 371 ~vsLt~~DL~~L~p~~WLND~IIdFYL~yL~~~~~~~~~~rv~~FnSfFy~kL~~~~k~Pssl~d~~~~y~~VkrWtkkv 450 (778)
.|.|+++|+..|+++.||||.+|+||.+||.+........ .|+++|-.-..|.... .-+.+.......
T Consensus 16 dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s~~~-~~ll~P~~t~~l~~~~-----------~~~e~~~~~~pl 83 (223)
T KOG3246|consen 16 DVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSEPD-LHLLRPSLTFFLRHAP-----------NPEEIAMVLDPL 83 (223)
T ss_pred ehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccCcc-hhccCHHHHHHHHhCC-----------CcHHHHHhcChh
Confidence 4789999999999999999999999999999875543333 6888875444444321 112445556677
Q ss_pred CCCCCCeEEEEeecc---------CceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhH----HHHHHHHH
Q 004028 451 DIFGKDYIFIPVNFN---------LHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGL----KNLVQSYL 517 (778)
Q Consensus 451 dLFeKD~IfIPIN~n---------sHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l----~~~L~~YL 517 (778)
++++|+|||+|||++ +||+|+|+..|.. .++||||+.+.|... .+.++.+|
T Consensus 84 ~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~----------------~f~hyDS~~n~nt~~a~~l~~kl~~ll 147 (223)
T KOG3246|consen 84 DLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDG----------------KFYHYDSLSNGNTKDAKSLMKKLRALL 147 (223)
T ss_pred hcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCC----------------cEEEeecccCCCcHHHHHHHHHHHHHH
Confidence 999999999999995 5999999998753 799999999988653 34444444
Q ss_pred HHHHHHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhH
Q 004028 518 CEEWKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEAS 597 (778)
Q Consensus 518 ~~E~k~k~k~~~~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis 597 (778)
..... ...+..+|||.||||||+|||++++.++... .+..+.. ...-..+.-+.
T Consensus 148 ~~~~~-----------------~~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~----~~~~~~~-----~~~~~~~~~i~ 201 (223)
T KOG3246|consen 148 KKKFA-----------------KRVECKCLQQQNGYDCGLHVCCNTRVLAERL----LRCPYAT-----SSQLLVVDLIK 201 (223)
T ss_pred hhhhh-----------------hcccccChhhhcCCchhHHHHHHHHHHHHHH----hcccccc-----ccchhhHHHHH
Confidence 32110 1125689999999999999999998877641 1111111 11123455688
Q ss_pred HHHHHHHHHHHHHHHhc
Q 004028 598 LKRSLIQKLISELLRNR 614 (778)
Q Consensus 598 ~kR~~I~~LI~eL~~~~ 614 (778)
.+|+.|..||..|.-..
T Consensus 202 ~lr~~l~~LI~slg~~~ 218 (223)
T KOG3246|consen 202 ALREELLDLIQSLGSIV 218 (223)
T ss_pred HHHHHHHHHHHHhCccC
Confidence 89999999999887443
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.83 E-value=3.8e-21 Score=222.51 Aligned_cols=232 Identities=28% Similarity=0.519 Sum_probs=162.8
Q ss_pred ceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhc--ccccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhc
Q 004028 371 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQ--AEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTR 448 (778)
Q Consensus 371 ~vsLt~~DL~~L~p~~WLND~IIdFYL~yL~~~~~--~~~~~rv~~FnSfFy~kL~~~~k~Pssl~d~~~~y~~VkrWtk 448 (778)
.+.++..|+.||.++.+|||.|++||++|+..... ++....+|+|++|||.++.+.......-.-....+.++++|++
T Consensus 352 ~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~ 431 (595)
T KOG0779|consen 352 SHQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTR 431 (595)
T ss_pred ccceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeee
Confidence 45789999999999999999999999999987643 4567889999999999998743211100001235778999999
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcch-hHHHHHHHHHHHHHHHhccC
Q 004028 449 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHA-GLKNLVQSYLCEEWKERHKD 527 (778)
Q Consensus 449 kvdLFeKD~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~-~l~~~L~~YL~~E~k~k~k~ 527 (778)
.+++|.++||++|+|...||.|++||+|+.... ......+++++..... .....+..++..+|......
T Consensus 432 ~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~e----------s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 501 (595)
T KOG0779|consen 432 HFDLFNKDYVFVPTHERFHWKLAIICNPDLETE----------TPRPRLELLILKLSADFPIVENILDFMKVASIYNNEL 501 (595)
T ss_pred ccccccceeEEecCchHhhhhccccccCccccC----------ccccchhhhhhccccccchhhhhhhhhhhcccccCcc
Confidence 999999999999999999999999999975211 1123444455443322 23344556666555433221
Q ss_pred -Cccccccccccee------eecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhHHHH
Q 004028 528 -TSEDVSSKFLNFR------FIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKR 600 (778)
Q Consensus 528 -~~~D~s~~f~n~~------~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis~kR 600 (778)
...+....|.-.+ ...+..|||.|..|||+|+++|++.|+.++|..++-.+. ...+..||++.++..+|
T Consensus 502 ~~~~~~~~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~----~~~~l~~~~~~~~~~~r 577 (595)
T KOG0779|consen 502 IVTEDLELEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAPERFNIEDE----GTINLEWFPPKEILKFR 577 (595)
T ss_pred cccccccccccccccCcccccccccccCccCcccchhhHHHHHHHhhhChhhhcccccc----cccccccCCchHHhhhh
Confidence 1112211111000 111223999999999999999999999998887652221 11234599999999999
Q ss_pred HHHHHHHHHHHHhccc
Q 004028 601 SLIQKLISELLRNRSR 616 (778)
Q Consensus 601 ~~I~~LI~eL~~~~s~ 616 (778)
..++++|+.|+...+.
T Consensus 578 ~~~r~~~~~l~~~~~~ 593 (595)
T KOG0779|consen 578 DEIRNLGRKLFTSQSS 593 (595)
T ss_pred hhhhccccccccccCC
Confidence 9999999999977653
No 7
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.77 E-value=3e-06 Score=99.52 Aligned_cols=449 Identities=18% Similarity=0.067 Sum_probs=234.2
Q ss_pred eccCceEEeccCCcccccceeeccccchhhhhhhhhhcccccEEEEEEeecccccccCCCC---------------CCCC
Q 004028 238 FSCTGIKIKDSNACGVQESFTFEKGIDDIVDIKFQWLQRFGSVEVKLHVILNDVAQDDNAC---------------GTSG 302 (778)
Q Consensus 238 fS~~~iki~~st~~~~~~~f~~Ew~iddIvsI~~~~~q~~gt~~Ikl~~~~~~~~~~~~~~---------------~~~g 302 (778)
+.+++.+...-........+.+.-..+.|+.++.- -..+..-++...++++..+...-.. -.+-
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~-~~~~~~~i~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (595)
T KOG0779|consen 7 QLRSEVKSSSIMVESADVKELLIRRLEFVVLIKKS-RPNYLNDIIIDLVLLKDDNTLNDEYTRELSILFILAVKKGLTSL 85 (595)
T ss_pred ccccccccceeEeccCCCccceeeccccccccccC-CcccccccccchheeccccCCCccccceeeecccCCcccccccc
Confidence 34445555555555555566566666666666532 2234444555555555544322211 0233
Q ss_pred cceeeeeeccCchhhhHHHHhhhcccchhchhcccCCCCCCCC--CCcccccCCCCCCCceeeccCCCCCceEEehhhhh
Q 004028 303 IEELKFSFSDCNWSEQLEKITSLNAKYLALWSVDHDNPVDMDG--VGQRRYFPNFDEPFEDVVYPEGDSDAVSISKRDID 380 (778)
Q Consensus 303 ~~~~~~~~~~~~~s~~~~~i~s~~~~y~~~~~~~~~~d~e~~~--~~~~~~~p~~~e~~~~vvYp~~d~~~vsLt~~DL~ 380 (778)
.+.+++++...+|..++.... +..++++|.+-......+.+ ......++.....|..+.||...+.........+.
T Consensus 86 ~~~~ki~~~~~~~~~~~~~~~--~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (595)
T KOG0779|consen 86 TEPLKIAVLEEQKPHAVVPKK--IISVSELRNTNLTEGTFYSDYLNRIKNIFESVRKFFNQVSYPKFMPNVTSFMPSPLE 163 (595)
T ss_pred ccccccccccccCCccccccc--cccchhccccCCcccceecccccccccccchhcchhhhcccccccchhhcccCCccc
Confidence 445566666666665544444 66777877766655554443 33334444334445556676666555555555555
Q ss_pred ccCCCCCcCHHHHHHHHHHHHHhhcccccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhcccCCCCCCeEEE
Q 004028 381 LLQPDTFVNDTIIDFYIKYLKNQIQAEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRKVDIFGKDYIFI 460 (778)
Q Consensus 381 ~L~p~~WLND~IIdFYL~yL~~~~~~~~~~rv~~FnSfFy~kL~~~~k~Pssl~d~~~~y~~VkrWtkkvdLFeKD~IfI 460 (778)
.++...--+..|.-.+..+....+.......+|++-..++.... .+|+...++-.+.++++
T Consensus 164 ~~q~~~~~~~~i~i~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~-------------------l~~~~~~~~~~~~~~~~ 224 (595)
T KOG0779|consen 164 KCQLQRVFTWTINITRKLFKKLFIKIFKNEPFHFKAVKFLLPSA-------------------LTKSDVCDIADLEVIFL 224 (595)
T ss_pred ccccccccceeeeeeecchhhhcccCcccCchhhhhhhcccchh-------------------ccchhhhhhhcccccch
Confidence 44433332222222222222222111112233333333221111 11111112223344555
Q ss_pred EeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccccccee
Q 004028 461 PVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSKFLNFR 540 (778)
Q Consensus 461 PIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~E~k~k~k~~~~D~s~~f~n~~ 540 (778)
+.....||.-...-++ ..+..++..+|+.+.......+...+.+..
T Consensus 225 ~~~k~~~~~~~~~~~~----------------------------------~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~ 270 (595)
T KOG0779|consen 225 NSRKDSHSLVISSINS----------------------------------PNIKTFFSKEVKSRPTPASYFIFSSFLPGL 270 (595)
T ss_pred hcccchhhhhhccccc----------------------------------ccchhhhccccccCCCcccccccccccCCC
Confidence 5555544222111111 111233333333322222222222233334
Q ss_pred eecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhHHHHHHHHHHHHHHHHhcccc-cc
Q 004028 541 FIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKRSLIQKLISELLRNRSRV-CL 619 (778)
Q Consensus 541 ~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis~kR~~I~~LI~eL~~~~s~~-~~ 619 (778)
..+.+.+++.+..|||+.+..+-.-........+.+.....-+.....+||+..+....|+.+.++..+|...+... |.
T Consensus 271 ~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~s~~~~~~~~~~~~~~~~~~~~l~~~~~~el~~~~~p~~~~ 350 (595)
T KOG0779|consen 271 DPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSESRSRDSLDNWFPVKEADKQRTLIVKLAIELLEVRVPQICN 350 (595)
T ss_pred CccccccccchhhhhhhcccccccccchhhhhhcCcccchhcccccccccccccccccccchHHHhhccccccCCccccc
Confidence 45668889999999997766554332222222233333333344556789999999999999999999998877422 32
Q ss_pred CccccchhhcccccccccchhhhhccccccccCCCCCCCCCCceEEEeccCCCCCccccccCCchhHhhhcCCCcccccc
Q 004028 620 DEHQSSRFLENSVNEMRLEFLSEKCSAATAQHGNLSNSQAGQGVEITLLGATSGRNLQCANDSSLVLKELLEPGVTAGSL 699 (778)
Q Consensus 620 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 699 (778)
+ . ...+.+.. .. .+++.-...+..+-.-..-.+.++++ ...+..++-.+....+++.+.+.+.+..
T Consensus 351 --~-~---~~v~~~Dl--~c-l~~~e~L~d~i~dfyl~~i~~~~l~~-~~~s~~~h~f~tffyk~l~~~~~~~~~d---- 416 (595)
T KOG0779|consen 351 --Q-S---HQVNNNDL--VC-LEEGEFLNDTIKDFYLEYIRQYLLSQ-KELSNDRHIFSTFFYKRLCRKLRQKSND---- 416 (595)
T ss_pred --c-c---cceeccch--hh-ccccchhhhhhhhhhhHHHHHhhhcc-cccCcchhhhhhHHHhhhhhhhhhhhhh----
Confidence 1 1 11111111 11 11111111223333333333555555 5566667777778888888888887766
Q ss_pred ccccCCCCCCCceeccCccc-cccccccccceeEEeccCCCCceeeeccCCCcccccc
Q 004028 700 LAYQSFGEPSSYYHLNGAAS-AREHDVETAEEYGYLAAGSNGFQQITELTPQVGSISF 756 (778)
Q Consensus 700 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 756 (778)
..|+++..+.+.+...-.+| .....+.++|+++...+..-+.+..++.+-+....-+
T Consensus 417 ~~~~~~~~~~~~~~~~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~ 474 (595)
T KOG0779|consen 417 QIQDNRAVRLRTWTRHFDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLI 474 (595)
T ss_pred hhhccccCceeeeeeccccccceeEEecCchHhhhhccccccCccccCccccchhhhh
Confidence 33488888888888887777 6777889999999999988888887776655544433
No 8
>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=96.19 E-value=0.011 Score=65.67 Aligned_cols=92 Identities=16% Similarity=0.332 Sum_probs=62.1
Q ss_pred CCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCc-------------------c--hh---
Q 004028 453 FGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGT-------------------H--AG--- 508 (778)
Q Consensus 453 FeKD~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~-------------------~--~~--- 508 (778)
-++.|+.+|++...||..+|++...+ -+.+|||-|.. + ..
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk~~~----------------~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s 292 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDKEKK----------------IVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTS 292 (423)
T ss_pred ccccEEEeeeeehhcceEEEEecccc----------------EEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCccc
Confidence 45789999999999999999975433 34555554432 1 00
Q ss_pred -------HHHHHHHHHHHHHHHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccC
Q 004028 509 -------LKNLVQSYLCEEWKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFS 575 (778)
Q Consensus 509 -------l~~~L~~YL~~E~k~k~k~~~~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ft 575 (778)
-+..|.+|+...+..+.+ ..| +.| -|--..+||+|.+-||-.....+|..|.
T Consensus 293 ~l~n~n~dIDVLfrfF~d~f~~~~g---------ciN-----vev-nQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 293 NLDNENCDIDVLFRFFEDSFGVKYG---------CIN-----VEV-NQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred ccccccCchHHHHHHHHhhccccee---------EEE-----hhh-hhhcccccchHHHHHHHHHHccCchhHH
Confidence 135666777665543221 122 112 5778899999999999999988888763
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=93.89 E-value=0.098 Score=55.54 Aligned_cols=88 Identities=25% Similarity=0.386 Sum_probs=48.4
Q ss_pred CeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccc
Q 004028 456 DYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSK 535 (778)
Q Consensus 456 D~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~E~k~k~k~~~~D~s~~ 535 (778)
+.=+||||.+.||.|+++..- ..|.+|+ +|.|+..-+. +.+++.+.. .+ +.+ ..++
T Consensus 189 ~nevF~INtg~HWil~~~~Ki-------------~~kiKC~-iFNs~~~l~e---Ns~~~ii~~-ak-~ag-~~~e---- 244 (317)
T PRK14848 189 HNEVFLINTGDHWLLCLFYKL-------------AEKIKCL-IFNTYYDLNE---NTKQEIIEA-AK-IAG-ISEN---- 244 (317)
T ss_pred cceEEEecCCCcEEEEEhHHh-------------hhhceEE-EeecHhhhhh---hHHHHHHHH-HH-hhC-cccC----
Confidence 445699999999999988421 1244565 5788766542 222222221 11 111 1100
Q ss_pred ccceeeecCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004028 536 FLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 569 (778)
Q Consensus 536 f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~ 569 (778)
..+.|+..++ ||.=..-||+|++++++.+-..
T Consensus 245 -~di~fIe~nL-QqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 245 -EDVNFIETNL-QNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred -CceEEeehhh-hhhCCCcchHHHHHHHHHHHhc
Confidence 1123333333 3334568999999999966654
No 10
>PRK11836 deubiquitinase; Provisional
Probab=93.57 E-value=0.16 Score=54.88 Aligned_cols=107 Identities=21% Similarity=0.400 Sum_probs=56.8
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchh----HHHHHHHH---HHHH-
Q 004028 449 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAG----LKNLVQSY---LCEE- 520 (778)
Q Consensus 449 kvdLFeKD~IfIPIN~nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~----l~~~L~~Y---L~~E- 520 (778)
.-.++-++.=+||||.+.||.|+++.. +++ +.....+.+|+ +|.|+...+.. ....+..| |..|
T Consensus 213 ~~~~~~k~~elFpINtg~HWil~~l~K---i~~----~~~~~ekiKC~-IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~ 284 (403)
T PRK11836 213 SDPSWPKEVQLFPINTGGHWILVSLQK---IVN----EKNNTQQIKCV-IFNSLRALGHDKENSLKRVINSFNSELMGEM 284 (403)
T ss_pred cCCCCcccceEEEecCCCcEEEEEeHH---hhh----cccccceeEEE-EEecHhhhccchhhHHHHHHHhhhhhhhhhc
Confidence 445677889999999999999998842 111 11122345565 57887665332 12222111 1111
Q ss_pred HHHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004028 521 WKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 569 (778)
Q Consensus 521 ~k~k~k~~~~D~s~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~ 569 (778)
...+.+..... ..+.|+..++ ||.=..-||+||++-+..++..
T Consensus 285 ~~~~ik~~~~e-----~ei~fie~dL-Qq~vpngCGlFv~~a~Qe~i~q 327 (403)
T PRK11836 285 SNNNIKVHLTE-----PEIIFLHADL-QQYLSQSCGAFVCMAAQEVIEQ 327 (403)
T ss_pred chhhhcccccC-----CceEEEechh-hhcCCCccceehHHHHHHHHHH
Confidence 11122211100 1123444443 3334568999999998866654
No 11
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=80.29 E-value=9.8 Score=38.91 Aligned_cols=86 Identities=17% Similarity=0.280 Sum_probs=51.4
Q ss_pred EEEEeec-cCceEEEEEe-cCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHH--HHHHhccCCccccc
Q 004028 458 IFIPVNF-NLHWSLIVIC-HPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCE--EWKERHKDTSEDVS 533 (778)
Q Consensus 458 IfIPIN~-nsHWsLlVIc-~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~--E~k~k~k~~~~D~s 533 (778)
.++|+.. ..|-..+=|- .++ .++.|++|+|-.-.+.... |..+... +...+..
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~--------------~k~SlI~~Epa~~~~~~~~--l~~~~~~~~~~~~~~~------- 130 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN--------------GKPSLIVFEPASFYGMKPA--LAGYTKLAEEARQKLL------- 130 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC--------------CCceEEEEccccccCCcch--hhhHHHHHHHHHhccC-------
Confidence 4455443 4676666553 332 3578999999754332111 2222221 1111111
Q ss_pred ccccceeeecCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004028 534 SKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 569 (778)
Q Consensus 534 ~~f~n~~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~ 569 (778)
.++++..+++..|+..+|||+|-|.+|..+.+.
T Consensus 131 ---~~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 131 ---PNAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred ---CCcEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 123555678999999999999999999988765
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=76.18 E-value=42 Score=34.47 Aligned_cols=125 Identities=18% Similarity=0.200 Sum_probs=53.1
Q ss_pred cCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccccc-ceeee-
Q 004028 465 NLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSKFL-NFRFI- 542 (778)
Q Consensus 465 nsHWsLlVIc~P~~v~~~~d~d~~~s~k~p~Il~fDSL~~~~~~l~~~L~~YL~~E~k~k~k~~~~D~s~~f~-n~~~v- 542 (778)
+.||.-+..+ | +..++++||.++-+..++.+. -.-||....+... +.+.-. =++.+
T Consensus 33 GvHWlA~Aw~-P---------------~s~t~YmFDPfGfsd~~L~qi----Y~FeYe~llrRSA--L~~~~dRCv~Lvk 90 (183)
T PF00770_consen 33 GVHWLAFAWD-P---------------RSRTFYMFDPFGFSDQKLKQI----YQFEYEGLLRRSA--LSSTPDRCVTLVK 90 (183)
T ss_dssp -S-EEEEEEE-T---------------TTTEEEEE-TT---HHHHHHH----H----HHHHHHHH--HHH-TTSEEEEEE
T ss_pred ceeEEEEEec-C---------------CcceEEEeCCCCCCHHHHHHH----HhhhHHHHHHHHh--hcCCCCceEEEEe
Confidence 4899888775 4 236899999999887654432 2223322111000 000000 01111
Q ss_pred cCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhh-hhhhcccccCCCCCchhhHHHHHHHHHHHHHHH
Q 004028 543 PLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLK-LKKLSSFLNVDWFPPGEASLKRSLIQKLISELL 611 (778)
Q Consensus 543 ~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~P~~Ftq~d-I~~~r~~l~~~WF~p~eis~kR~~I~~LI~eL~ 611 (778)
..+.-|=.++--||+|-+.|+.+|..-+---+.... |.-.....+.....|..+...|..-.+|-.=|.
T Consensus 91 stqtVQ~p~SaaCGLFC~lFL~aF~~~p~~pm~~np~mdl~~gvp~~~l~~P~~~~~l~~NQe~LY~fl~ 160 (183)
T PF00770_consen 91 STQTVQCPCSAACGLFCCLFLHAFVHYPDNPMDNNPTMDLVTGVPNSMLQSPQVQPILHRNQEKLYRFLN 160 (183)
T ss_dssp E-EE-S-TT---HHHHHHHHHHHHHH-TTS-SSSSTTGGGS--EEGGGTT-CCCHHHHHHHHHHHHHHHH
T ss_pred ccceeeccCchhHHHHHHHHHHHHHhCCCCcCCCCCeecccCCccCcccCCchhhHHHHHhHHHHHHHHH
Confidence 122334458899999999999999975322222111 122222333445567666666666555444443
No 13
>PRK15371 effector protein YopJ; Provisional
Probab=54.26 E-value=49 Score=36.53 Aligned_cols=31 Identities=29% Similarity=0.493 Sum_probs=25.9
Q ss_pred eeecCCCCCCCCCCChHHHHHHHHHHHHccC
Q 004028 540 RFIPLELPQQENSFDCGLFLLHYLELFLAEA 570 (778)
Q Consensus 540 ~~v~~~VPQQ~Ng~DCGVFVL~yaE~fl~~~ 570 (778)
.+.....-.|+-.+|||+|-|.+|.+..+..
T Consensus 157 ~~avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 157 HFSMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred eEEEEecccccCcccchhhhHHHHHHHhhhh
Confidence 4445678899999999999999999988763
Done!