Query 004981
Match_columns 721
No_of_seqs 255 out of 1101
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 16:06:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004981.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004981hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0778 Protease, Ulp1 family 100.0 3.4E-42 7.4E-47 380.1 13.5 182 365-578 316-498 (511)
2 COG5160 ULP1 Protease, Ulp1 fa 100.0 5E-41 1.1E-45 365.7 13.3 183 358-576 372-555 (578)
3 PLN03189 Protease specific for 100.0 1.2E-39 2.6E-44 357.3 21.3 187 363-577 284-476 (490)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 2E-28 4.3E-33 244.5 18.6 195 381-608 1-214 (216)
5 KOG3246 Sentrin-specific cyste 99.9 8.7E-27 1.9E-31 232.2 15.0 189 366-608 16-217 (223)
6 KOG0779 Protease, Ulp1 family 99.8 1.1E-21 2.3E-26 225.5 6.5 232 366-611 352-593 (595)
7 KOG0779 Protease, Ulp1 family 97.1 5.6E-05 1.2E-09 88.4 -2.1 418 232-719 6-441 (595)
8 PF03290 Peptidase_C57: Vaccin 96.0 0.015 3.2E-07 64.0 7.0 91 448-570 229-351 (423)
9 PRK14848 deubiquitinase SseL; 94.6 0.078 1.7E-06 55.6 6.7 88 451-564 189-276 (317)
10 PRK11836 deubiquitinase; Provi 94.1 0.12 2.6E-06 55.2 6.9 107 444-564 213-327 (403)
11 PF03421 YopJ: YopJ Serine/Thr 77.9 13 0.00028 37.6 9.0 31 534-564 133-163 (177)
12 PF00770 Peptidase_C5: Adenovi 70.7 73 0.0016 32.4 11.9 125 460-606 33-160 (183)
13 PRK15371 effector protein YopJ 54.3 50 0.0011 36.1 8.1 31 535-565 157-187 (287)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-42 Score=380.07 Aligned_cols=182 Identities=32% Similarity=0.658 Sum_probs=158.7
Q ss_pred CceEEehhhhhccCCCCcccHHHHHHHHHHHHHHhhhh-ccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhc
Q 004981 365 DAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAE-EKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTR 443 (721)
Q Consensus 365 ~~isLt~~DL~~L~~~~WLND~IIdFYl~yL~~~~~~~-~~~rv~~FnSfFy~kL~~~~k~pss~~~~~~~y~~VkrWtk 443 (721)
.++.||..||.||.+++||||+||||||++|.++.... ..+++|+||||||++|.. .+|++|+|||+
T Consensus 316 ~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~~------------~gy~~VkRWTk 383 (511)
T KOG0778|consen 316 FNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLVG------------RGYAGVKRWTK 383 (511)
T ss_pred ccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEEEechhhhhhhh------------cchHHHHhHhh
Confidence 35999999999999999999999999999999886543 267899999999999985 68999999999
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCC
Q 004981 444 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDT 523 (721)
Q Consensus 444 ~vdLFeKD~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v~~~Lr~yL~~E~k~k~~~~ 523 (721)
++|||++|+||||||.+.||+|+||+.. .++|.|||||++...+++.+|.+||++|+..|.+..
T Consensus 384 ~v~if~~d~i~vPIH~~vHW~l~vid~r----------------~k~i~y~DS~~~~~nr~~~aL~~Yl~~E~~~k~~~~ 447 (511)
T KOG0778|consen 384 KVDIFDKDIIFVPIHLGVHWCLAVIDLR----------------EKTIEYYDSLGGGPNRICDALAKYLQDESRDKSKKD 447 (511)
T ss_pred ccCccccceeEeeeecCceEEEEEEEcc----------------cceEEEeeccCCCCcchHHHHHHHHHHHHhhhhcCC
Confidence 9999999999999999999999999863 369999999998766666999999999999887654
Q ss_pred cccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhc
Q 004981 524 SEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLS 578 (721)
Q Consensus 524 ~~d~s~~~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~~~ 578 (721)
. |++ .|.. . ...++|||.||+|||+|+|+|+++++++.|+.|+|.+|+.||
T Consensus 448 ~-d~s-~w~~-~-~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR 498 (511)
T KOG0778|consen 448 F-DVS-GWTI-E-FVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFR 498 (511)
T ss_pred C-Ccc-chhh-h-hhhccccccCCCccceEEeeechhhccCCCcccChhhhHHHH
Confidence 3 333 3532 2 234899999999999999999999999999999998887643
No 2
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5e-41 Score=365.66 Aligned_cols=183 Identities=37% Similarity=0.748 Sum_probs=160.0
Q ss_pred eccCCCCCceEEehhhhhccCCCCcccHHHHHHHHHHHHHHhh-hhccCcEEEechHHHHHhhccCCCCCCcchhhHHHH
Q 004981 358 VYPEGDSDAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQ-AEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFL 436 (721)
Q Consensus 358 vYp~~d~~~isLt~~DL~~L~~~~WLND~IIdFYl~yL~~~~~-~~~~~rv~~FnSfFy~kL~~~~k~pss~~~~~~~y~ 436 (721)
+||..+.++|+||..|+.||.+++||||+||||||+||...-. ...++++|+||||||++|.+ .+|+
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 5888888999999999999999999999999999999955432 23467899999999999974 7899
Q ss_pred HHhhhhcccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHH
Q 004981 437 RVRKWTRKVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEW 516 (721)
Q Consensus 437 ~VkrWtk~vdLFeKD~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v~~~Lr~yL~~E~ 516 (721)
+|+||++++|||+++|||||||...||+|+|||.+. +.|+|||||++.+..+.+.|+.|+.+||
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 HHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhh
Q 004981 517 KERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKK 576 (721)
Q Consensus 517 k~k~~~~~~d~s~~~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~ 576 (721)
+..+++.. |. ++...+||||.||+|||||||+++++|+.++|..|.+.++++
T Consensus 504 k~~~~k~~------~~--~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r 555 (578)
T COG5160 504 KIQHDKDP------QI--KMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPR 555 (578)
T ss_pred hcccCCch------hh--hhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchHH
Confidence 87665431 22 345679999999999999999999999999876665555544
No 3
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.2e-39 Score=357.34 Aligned_cols=187 Identities=27% Similarity=0.610 Sum_probs=156.1
Q ss_pred CCCceEEehhhhhccCCCCcccHHHHHHHHHHHHHHhhhh--ccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhh
Q 004981 363 DSDAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAE--EKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRK 440 (721)
Q Consensus 363 d~~~isLt~~DL~~L~~~~WLND~IIdFYl~yL~~~~~~~--~~~rv~~FnSfFy~kL~~~~k~pss~~~~~~~y~~Vkr 440 (721)
++.+++||.+||.||.|++||||+|||||++||.++...+ ...++|+||||||++|.... +..+|.+|+|
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 3458999999999999999999999999999998764322 34689999999999998621 1247999999
Q ss_pred hhcc----cCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHH
Q 004981 441 WTRK----VDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEW 516 (721)
Q Consensus 441 Wtk~----vdLFeKD~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v~~~Lr~yL~~E~ 516 (721)
||++ ++||++++||||||.+.||+|+||+++. ++|+|||||++.+..+.+.|+.||..|+
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 9974 5799999999999999999999999864 4899999999998889999999999999
Q ss_pred HHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhh
Q 004981 517 KERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKL 577 (721)
Q Consensus 517 k~k~~~~~~d~s~~~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~~ 577 (721)
+.+++... +++ .|.. ....++|||.||+|||||||+||++++++.++.|+|.+|+.|
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 98765432 332 3421 123689999999999999999999999999888888777654
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=2e-28 Score=244.49 Aligned_cols=195 Identities=34% Similarity=0.646 Sum_probs=136.2
Q ss_pred CcccHHHHHHHHHHHHHHh--hhhccCcEEEechHHHHHhhccC----CCCCC--c-c-hhhHHHHHHhhhhccc---CC
Q 004981 381 TFVNDTIIDFYIKYLKNQI--QAEEKHRFHFFNSFFFRKLADLD----KDPSS--I-S-DGKAAFLRVRKWTRKV---DI 447 (721)
Q Consensus 381 ~WLND~IIdFYl~yL~~~~--~~~~~~rv~~FnSfFy~kL~~~~----k~pss--~-~-~~~~~y~~VkrWtk~v---dL 447 (721)
+||||+|||||++||...+ ......+++||+|+|+.+|.... +.+.. . . .....+..+.+|++.. ++
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 0 0 0134678899999887 99
Q ss_pred CCCCeEEEEeec-cCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcch-----hHHHHHHHHHHHHHHHhcc
Q 004981 448 FGKDYIFIPVNF-NLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHA-----GLKNLVQSYLCEEWKERHK 521 (721)
Q Consensus 448 FeKD~IfIPIN~-nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~-----~v~~~Lr~yL~~E~k~k~~ 521 (721)
+++++||||||. +.||+|+||+.+. .+|++||||++.+. .+...+..+|..++.....
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 9999999999875 48999999999877 4677888898888765443
Q ss_pred CCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCChhhhHHHHHHHHHH
Q 004981 522 DTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKRSLIQKL 601 (721)
Q Consensus 522 ~~~~d~s~~~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~~~~~~~~~WF~p~ei~~kR~~I~~L 601 (721)
... +. ..|. ...+.++|||.|++|||+|||+||++++.+.+..+. ..|...++...|..+...
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 1221 234558999999999999999999999998544321 115677888899999988
Q ss_pred HHHHHHh
Q 004981 602 ISELLRN 608 (721)
Q Consensus 602 I~eL~~~ 608 (721)
|.+....
T Consensus 208 ~~e~~~~ 214 (216)
T PF02902_consen 208 LYEELGS 214 (216)
T ss_dssp -------
T ss_pred ccccccc
Confidence 8776654
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.94 E-value=8.7e-27 Score=232.19 Aligned_cols=189 Identities=25% Similarity=0.409 Sum_probs=138.0
Q ss_pred ceEEehhhhhccCCCCcccHHHHHHHHHHHHHHhhhhccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhccc
Q 004981 366 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRKV 445 (721)
Q Consensus 366 ~isLt~~DL~~L~~~~WLND~IIdFYl~yL~~~~~~~~~~rv~~FnSfFy~kL~~~~k~pss~~~~~~~y~~VkrWtk~v 445 (721)
.+.|+++|+..|+++.||||.+|+||.+||.+........ .||+.|-.-..|.... .-+.+.......
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 4789999999999999999999999999999876543333 7899875544454321 113455566778
Q ss_pred CCCCCCeEEEEeecc---------CceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhH----HHHHHHHH
Q 004981 446 DIFGKDYIFIPVNFN---------LHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGL----KNLVQSYL 512 (721)
Q Consensus 446 dLFeKD~IfIPIN~n---------sHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v----~~~Lr~yL 512 (721)
++++|+|||+|||.+ +||+|+|+..|.+ .++||||+.+.|... .++++.+|
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 999999999999985 5999999998764 799999999988653 44444444
Q ss_pred HHHHHHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCChhhhH
Q 004981 513 CEEWKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEAS 592 (721)
Q Consensus 513 ~~E~k~k~~~~~~d~s~~~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~~~~~~~~~WF~p~ei~ 592 (721)
..... ...+..+|||.||||||+|||++++.++... .+..+.. ...-..+.-+.
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 33110 1125689999999999999999998887651 1111111 11223455688
Q ss_pred HHHHHHHHHHHHHHHh
Q 004981 593 LKRSLIQKLISELLRN 608 (721)
Q Consensus 593 ~kR~~I~~LI~eL~~~ 608 (721)
.+|+.|..||..|.-.
T Consensus 202 ~lr~~l~~LI~slg~~ 217 (223)
T KOG3246|consen 202 ALREELLDLIQSLGSI 217 (223)
T ss_pred HHHHHHHHHHHHhCcc
Confidence 9999999999988743
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.84 E-value=1.1e-21 Score=225.49 Aligned_cols=232 Identities=28% Similarity=0.529 Sum_probs=164.4
Q ss_pred ceEEehhhhhccCCCCcccHHHHHHHHHHHHHHhh--hhccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhc
Q 004981 366 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQ--AEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTR 443 (721)
Q Consensus 366 ~isLt~~DL~~L~~~~WLND~IIdFYl~yL~~~~~--~~~~~rv~~FnSfFy~kL~~~~k~pss~~~~~~~y~~VkrWtk 443 (721)
.+.++..|+.||.++.+|||.|++||++|+..... ++....+|+|++|||.++.+.......-.-....+.++++|++
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 56899999999999999999999999999987643 4567889999999999998743211110002346778999999
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcch-hHHHHHHHHHHHHHHHhccC
Q 004981 444 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHA-GLKNLVQSYLCEEWKERHKD 522 (721)
Q Consensus 444 ~vdLFeKD~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~-~v~~~Lr~yL~~E~k~k~~~ 522 (721)
.+|+|.++||++|+|+..||.|+++|+|+.... ......+++++..... .....+..++..+|......
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 999999999999999999999999999975321 1123444455444322 23444566666655443222
Q ss_pred -Cccccccccc---ce---eeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCChhhhHHHH
Q 004981 523 -TSEDVSSKFL---NF---RFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKR 595 (721)
Q Consensus 523 -~~~d~s~~~~---n~---~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~~~~~~~~~WF~p~ei~~kR 595 (721)
...++...|. +. .-..+..|||.|.+|||+|+++|++.|+.++|..++-.+. ...+..||++.++.++|
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 1112221121 10 0111223999999999999999999999999887651111 11234599999999999
Q ss_pred HHHHHHHHHHHHhccc
Q 004981 596 SLIQKLISELLRNRSR 611 (721)
Q Consensus 596 ~~I~~LI~eL~~~~s~ 611 (721)
..++++|..|...++.
T Consensus 578 ~~~r~~~~~l~~~~~~ 593 (595)
T KOG0779|consen 578 DEIRNLGRKLFTSQSS 593 (595)
T ss_pred hhhhccccccccccCC
Confidence 9999999999987753
No 7
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.15 E-value=5.6e-05 Score=88.41 Aligned_cols=418 Identities=18% Similarity=0.084 Sum_probs=216.1
Q ss_pred EeecCceEeeccCCcCCCceeeeeecchhhhhhHhhhhcccccEEEEEEeecccccccCCCCC---------------CC
Q 004981 232 VFSCTGIKIKDSNACGVQESFTFEKGIDDIVDIKFQWLQRFGSVEVKLHVILNDVAQDDNACG---------------TS 296 (721)
Q Consensus 232 tfS~~~~ki~~~t~~~~~~~f~~Ew~iddIv~I~~~~~~~~~~~~I~l~~~~~~~~~~~~~~~---------------~~ 296 (721)
-+.++..++...........+.+.-..+.|+.+..- -..++..++...++++..+...-... ..
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~-~~~~~~~i~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (595)
T KOG0779|consen 6 EQLRSEVKSSSIMVESADVKELLIRRLEFVVLIKKS-RPNYLNDIIIDLVLLKDDNTLNDEYTRELSILFILAVKKGLTS 84 (595)
T ss_pred cccccccccceeEeccCCCccceeeccccccccccC-CcccccccccchheeccccCCCccccceeeecccCCccccccc
Confidence 344555555555566666666677777777777533 23345556666666665543221110 33
Q ss_pred CcceeeeeeccCcchhhhHHhhhhcchhhhhhhcccCCCCCCCC--CCcccccCCCCCCCceeeccCCCCCceEEehhhh
Q 004981 297 GIEELKFSFSDCNWSEQLEKITSLNAKYLALWSVDHDNPVDMDG--VGQRRYFPNFDEPFEDVVYPEGDSDAVSISKRDI 374 (721)
Q Consensus 297 g~~~~~~~~~~~~~s~~~~~i~~~~~~y~~~~~~~~~~d~e~~~--~~~~~~~p~~~~~~~~vvYp~~d~~~isLt~~DL 374 (721)
-.+.+++++...+|..++...+ +..++++|.+-........+ +.....++.....|..+.||...+.........+
T Consensus 85 ~~~~~ki~~~~~~~~~~~~~~~--~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (595)
T KOG0779|consen 85 LTEPLKIAVLEEQKPHAVVPKK--IISVSELRNTNLTEGTFYSDYLNRIKNIFESVRKFFNQVSYPKFMPNVTSFMPSPL 162 (595)
T ss_pred cccccccccccccCCccccccc--cccchhccccCCcccceecccccccccccchhcchhhhcccccccchhhcccCCcc
Confidence 4556677777777776665555 77788888876666555443 3444444544555666777777666666666666
Q ss_pred hccCCCCcccHHHHHHHHHHHHHHhhhhccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHhhhhcccCCCCCCeEE
Q 004981 375 DLLQPDTFVNDTIIDFYIKYLKNQIQAEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRKVDIFGKDYIF 454 (721)
Q Consensus 375 ~~L~~~~WLND~IIdFYl~yL~~~~~~~~~~rv~~FnSfFy~kL~~~~k~pss~~~~~~~y~~VkrWtk~vdLFeKD~If 454 (721)
..++...--+..|.-.+..+....+.......+|++-..++-... .+|+...++-.+.+++
T Consensus 163 ~~~q~~~~~~~~i~i~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~-------------------l~~~~~~~~~~~~~~~ 223 (595)
T KOG0779|consen 163 EKCQLQRVFTWTINITRKLFKKLFIKIFKNEPFHFKAVKFLLPSA-------------------LTKSDVCDIADLEVIF 223 (595)
T ss_pred cccccccccceeeeeeecchhhhcccCcccCchhhhhhhcccchh-------------------ccchhhhhhhcccccc
Confidence 655544333333222222222222211112233333332221111 1111111222334445
Q ss_pred EEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCcccccccccce
Q 004981 455 IPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSKFLNF 534 (721)
Q Consensus 455 IPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v~~~Lr~yL~~E~k~k~~~~~~d~s~~~~n~ 534 (721)
++.....||.-...-++ ..+..++..+++.+.......+...+.+.
T Consensus 224 ~~~~k~~~~~~~~~~~~----------------------------------~~~~~~~s~~~~~~~~~~s~~~~~~~~~~ 269 (595)
T KOG0779|consen 224 LNSRKDSHSLVISSINS----------------------------------PNIKTFFSKEVKSRPTPASYFIFSSFLPG 269 (595)
T ss_pred hhcccchhhhhhccccc----------------------------------ccchhhhccccccCCCcccccccccccCC
Confidence 55554544222111111 11123333333322222212222223333
Q ss_pred eeecCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCChhhhHHHHHHHHHHHHHHHHhcccc-c
Q 004981 535 RFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKRSLIQKLISELLRNRSRV-C 613 (721)
Q Consensus 535 ~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~dI~~~~~~~~~~WF~p~ei~~kR~~I~~LI~eL~~~~s~~-~ 613 (721)
...+.+.+++.+..|||+.+-++-.-........+.+.....-+.....+||+..+....|+.+.++..+|...+... |
T Consensus 270 ~~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~s~~~~~~~~~~~~~~~~~~~~l~~~~~~el~~~~~p~~~ 349 (595)
T KOG0779|consen 270 LDPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSESRSRDSLDNWFPVKEADKQRTLIVKLAIELLEVRVPQIC 349 (595)
T ss_pred CCccccccccchhhhhhhcccccccccchhhhhhcCcccchhcccccccccccccccccccchHHHhhccccccCCcccc
Confidence 344668899999999997766554333222222333333333444556799999999999999999999998777422 2
Q ss_pred cCcccccccccccccccccchhcccccccccccCCCCCCCCCCCeEEEeeccCCCccccccCCCchhhhhhcCcCccccc
Q 004981 614 LDEHQSSRFLENSVNEMRLEFLSEKCSAATAQHGNLSNSQAGQGVEITLLGATSGRNLQCANDSSLVLKELLEPGVTAGS 693 (721)
Q Consensus 614 ~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 693 (721)
. + ....+.+.+ .+++. +---..+.+.-.-..-.+.+.+. -+.++.++..+....+++.+++..-+-.
T Consensus 350 ~--~----~~~v~~~Dl--~cl~~-~e~L~d~i~dfyl~~i~~~~l~~-~~~s~~~h~f~tffyk~l~~~~~~~~~d--- 416 (595)
T KOG0779|consen 350 N--Q----SHQVNNNDL--VCLEE-GEFLNDTIKDFYLEYIRQYLLSQ-KELSNDRHIFSTFFYKRLCRKLRQKSND--- 416 (595)
T ss_pred c--c----ccceeccch--hhccc-cchhhhhhhhhhhHHHHHhhhcc-cccCcchhhhhhHHHhhhhhhhhhhhhh---
Confidence 2 1 112222222 11111 11111234444444456667766 7888888888888888888887765544
Q ss_pred ccccccCCCCCcceeecCcccccccc
Q 004981 694 LLAYQSFGEPSSYYHLNGAASAREVF 719 (721)
Q Consensus 694 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 719 (721)
..++++-++.+.+...-.+|.++.|
T Consensus 417 -~~~~~~~~~~~~~~~~~d~~~k~yi 441 (595)
T KOG0779|consen 417 -QIQDNRAVRLRTWTRHFDLFNKDYV 441 (595)
T ss_pred -hhhccccCceeeeeeccccccceeE
Confidence 1235555666666555555555443
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=96.02 E-value=0.015 Score=64.02 Aligned_cols=91 Identities=14% Similarity=0.282 Sum_probs=62.2
Q ss_pred CCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcc---------------------hh---
Q 004981 448 FGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTH---------------------AG--- 503 (721)
Q Consensus 448 FeKD~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~---------------------~~--- 503 (721)
-.+.|+.+|.+...||..+|++.... -+.+|||-|... ..
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 35789999999999999999975432 455555554421 00
Q ss_pred -------HHHHHHHHHHHHHHHhccCCcccccccccceeeecCCC-CCCCCCCChHHHHHHHHHHHHccCCCccC
Q 004981 504 -------LKNLVQSYLCEEWKERHKDTSEDVSSKFLNFRFIPLEL-PQQENSFDCGLFLLHYLELFLAEAPVSFS 570 (721)
Q Consensus 504 -------v~~~Lr~yL~~E~k~k~~~~~~d~s~~~~n~~~v~~~v-PQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ft 570 (721)
-+..|..|+...+..+.+ ..++ --|--..+||+|.+.||-.....+|..|.
T Consensus 293 ~l~n~n~dIDVLfrfF~d~f~~~~g----------------ciNvevnQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 293 NLDNENCDIDVLFRFFEDSFGVKYG----------------CINVEVNQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred ccccccCchHHHHHHHHhhccccee----------------EEEhhhhhhcccccchHHHHHHHHHHccCchhHH
Confidence 145666666665533221 1122 35778899999999999999999888763
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=94.65 E-value=0.078 Score=55.65 Aligned_cols=88 Identities=22% Similarity=0.362 Sum_probs=48.4
Q ss_pred CeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccc
Q 004981 451 DYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSK 530 (721)
Q Consensus 451 D~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v~~~Lr~yL~~E~k~k~~~~~~d~s~~ 530 (721)
+.=+||||.+.||.|+++..- ..|.+|+ +|.|++.-+....+ +.+.. . .+.+.. +.
T Consensus 189 ~nevF~INtg~HWil~~~~Ki-------------~~kiKC~-iFNs~~~l~eNs~~---~ii~~-a-k~ag~~-~e---- 244 (317)
T PRK14848 189 HNEVFLINTGDHWLLCLFYKL-------------AEKIKCL-IFNTYYDLNENTKQ---EIIEA-A-KIAGIS-EN---- 244 (317)
T ss_pred cceEEEecCCCcEEEEEhHHh-------------hhhceEE-EeecHhhhhhhHHH---HHHHH-H-HhhCcc-cC----
Confidence 344599999999999988421 1245564 57887665432222 22211 1 111111 00
Q ss_pred ccceeeecCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004981 531 FLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 564 (721)
Q Consensus 531 ~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~ 564 (721)
..+.|+..++ ||.=..-||+||+++++.+-..
T Consensus 245 -~di~fIe~nL-QqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 245 -EDVNFIETNL-QNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred -CceEEeehhh-hhhCCCcchHHHHHHHHHHHhc
Confidence 0123444333 3334567999999999976654
No 10
>PRK11836 deubiquitinase; Provisional
Probab=94.14 E-value=0.12 Score=55.25 Aligned_cols=107 Identities=21% Similarity=0.366 Sum_probs=56.2
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchh----HHHHHHHH---HHHH-
Q 004981 444 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAG----LKNLVQSY---LCEE- 515 (721)
Q Consensus 444 ~vdLFeKD~IfIPIN~nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~----v~~~Lr~y---L~~E- 515 (721)
.-.++-++.=+||||.+.||.|+++..- ++ +.....+.+|+ +|.|+..-+.. ..+.+..| |..|
T Consensus 213 ~~~~~~k~~elFpINtg~HWil~~l~Ki---~~----~~~~~ekiKC~-IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~ 284 (403)
T PRK11836 213 SDPSWPKEVQLFPINTGGHWILVSLQKI---VN----EKNNTQQIKCV-IFNSLRALGHDKENSLKRVINSFNSELMGEM 284 (403)
T ss_pred cCCCCcccceEEEecCCCcEEEEEeHHh---hh----cccccceeEEE-EEecHhhhccchhhHHHHHHHhhhhhhhhhc
Confidence 3456667888999999999999988421 11 11122345564 57887655322 22222221 1111
Q ss_pred HHHhccCCcccccccccceeeecCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004981 516 WKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 564 (721)
Q Consensus 516 ~k~k~~~~~~d~s~~~~n~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~ 564 (721)
...+.+... . -..+.|+..++ ||.=..-||+||++-+.-++..
T Consensus 285 ~~~~ik~~~---~--e~ei~fie~dL-Qq~vpngCGlFv~~a~Qe~i~q 327 (403)
T PRK11836 285 SNNNIKVHL---T--EPEIIFLHADL-QQYLSQSCGAFVCMAAQEVIEQ 327 (403)
T ss_pred chhhhcccc---c--CCceEEEechh-hhcCCCccceehHHHHHHHHHH
Confidence 111111111 0 01233444443 3434568999999998866554
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=77.94 E-value=13 Score=37.64 Aligned_cols=31 Identities=29% Similarity=0.547 Sum_probs=26.6
Q ss_pred eeeecCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004981 534 FRFIPLELPQQENSFDCGLFLLHYLELFLAE 564 (721)
Q Consensus 534 ~~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~ 564 (721)
.++..+++..|+..+|||+|-|.+|..+...
T Consensus 133 ~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 133 AKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred cEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 3455678999999999999999999988765
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=70.69 E-value=73 Score=32.39 Aligned_cols=125 Identities=17% Similarity=0.185 Sum_probs=52.7
Q ss_pred cCceEEEEEecCCCcccccccccccCCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccc-ccccceeee-
Q 004981 460 NLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVS-SKFLNFRFI- 537 (721)
Q Consensus 460 nsHWsLlVI~~P~~~~~~~d~d~~~~~k~~~Il~fDSL~~~~~~v~~~Lr~yL~~E~k~k~~~~~~d~s-~~~~n~~~v- 537 (721)
+.||.-...+ |. ..+++.||.+|-+..++.+. -.-||..-.+.. .+. ..-.=++.+
T Consensus 33 GvHWlA~Aw~-P~---------------s~t~YmFDPfGfsd~~L~qi----Y~FeYe~llrRS--AL~~~~dRCv~Lvk 90 (183)
T PF00770_consen 33 GVHWLAFAWD-PR---------------SRTFYMFDPFGFSDQKLKQI----YQFEYEGLLRRS--ALSSTPDRCVTLVK 90 (183)
T ss_dssp -S-EEEEEEE-TT---------------TTEEEEE-TT---HHHHHHH----H----HHHHHHH--HHHH-TTSEEEEEE
T ss_pred ceeEEEEEec-CC---------------cceEEEeCCCCCCHHHHHHH----HhhhHHHHHHHH--hhcCCCCceEEEEe
Confidence 4899888775 42 35899999999887654332 222232211100 011 000001111
Q ss_pred cCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhh-hhhhcccccCCCCChhhhHHHHHHHHHHHHHHH
Q 004981 538 PLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLK-LKKLSSFLNVDWFPPGEASLKRSLIQKLISELL 606 (721)
Q Consensus 538 ~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~p~~Ftq~d-I~~~~~~~~~~WF~p~ei~~kR~~I~~LI~eL~ 606 (721)
..+.-|=.++--||+|-+.|+.+|..-+.--+.... |.-.....+.....|......|..-.+|-.=|.
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 123344558899999999999999975422222111 122222233445566666666666444443333
No 13
>PRK15371 effector protein YopJ; Provisional
Probab=54.31 E-value=50 Score=36.05 Aligned_cols=31 Identities=29% Similarity=0.493 Sum_probs=26.1
Q ss_pred eeecCCCCCCCCCCChHHHHHHHHHHHHccC
Q 004981 535 RFIPLELPQQENSFDCGLFLLHYLELFLAEA 565 (721)
Q Consensus 535 ~~v~~~vPQQ~Ng~DCGVFVL~yaE~fl~~~ 565 (721)
.+....+-.|.-.+|||+|-|.+|.+.....
T Consensus 157 ~~avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 157 HFSMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred eEEEEecccccCcccchhhhHHHHHHHhhhh
Confidence 4445678899999999999999999988764
Done!