Query 004112
Match_columns 773
No_of_seqs 262 out of 1104
Neff 5.1
Searched_HMMs 46136
Date Thu Mar 28 17:45:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004112hhsearch_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 2.8E-41 6E-46 375.5 13.7 181 366-578 317-498 (511)
2 COG5160 ULP1 Protease, Ulp1 fa 100.0 2E-40 4.3E-45 363.6 13.7 183 358-576 372-555 (578)
3 PLN03189 Protease specific for 100.0 4.4E-39 9.5E-44 355.5 21.3 186 364-577 285-476 (490)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 3.6E-28 7.9E-33 243.7 18.1 196 381-609 1-215 (216)
5 KOG3246 Sentrin-specific cyste 99.9 4.2E-26 9.1E-31 229.3 14.7 189 366-608 16-217 (223)
6 KOG0779 Protease, Ulp1 family 99.8 1.9E-21 4.2E-26 224.8 6.2 232 366-611 352-593 (595)
7 KOG0779 Protease, Ulp1 family 97.7 4.4E-06 9.6E-11 98.1 -2.1 449 233-751 7-474 (595)
8 PF03290 Peptidase_C57: Vaccin 96.2 0.011 2.4E-07 65.5 7.2 92 448-570 229-351 (423)
9 PRK14848 deubiquitinase SseL; 94.0 0.097 2.1E-06 55.5 5.8 88 451-564 189-276 (317)
10 PRK11836 deubiquitinase; Provi 93.9 0.14 2.9E-06 55.4 6.9 107 444-564 213-327 (403)
11 PF03421 YopJ: YopJ Serine/Thr 78.2 12 0.00026 38.3 8.9 86 453-564 74-163 (177)
12 PF00770 Peptidase_C5: Adenovi 64.0 1.1E+02 0.0023 31.6 11.7 127 460-609 33-162 (183)
13 PRK15371 effector protein YopJ 54.5 45 0.00097 36.8 7.8 31 535-565 157-187 (287)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.8e-41 Score=375.51 Aligned_cols=181 Identities=32% Similarity=0.670 Sum_probs=157.8
Q ss_pred ceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhccc-ccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHHhhhcc
Q 004112 366 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAE-EKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRK 444 (773)
Q Consensus 366 ~VsLt~~DL~~L~pg~WLND~IIdFYL~yL~~~~~~~-~~~rv~~FnSfFy~kL~~~~k~pssls~~~~~y~~VkrWtk~ 444 (773)
++.||..||.||.+++||||+||||||++|.++.... ..+++|+||||||++|.. .+|+.|+|||++
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 5899999999999999999999999999999986543 277899999999999985 579999999999
Q ss_pred cCCCCCCeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCc
Q 004112 445 VDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTS 524 (773)
Q Consensus 445 vdLFeKD~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~E~k~k~~~~~ 524 (773)
+|||++|+||||||.+.||+|+||+.. .++|.|||||++...+++.+|..||++|++.|.+...
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 999999999999999999999999864 3699999999987666669999999999998876543
Q ss_pred ccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhc
Q 004112 525 EDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLS 578 (773)
Q Consensus 525 ~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~~r 578 (773)
|++ .|.. . ...++|||.||+|||+|+|+|++++..+.|+.|+|.+|+.||
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 322 3432 1 234899999999999999999999999999999998887653
No 2
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-40 Score=363.62 Aligned_cols=183 Identities=37% Similarity=0.745 Sum_probs=159.4
Q ss_pred eccCCCCCceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhc-ccccCcEEEechHHHHHhhccCCCCCCcchhhHHHH
Q 004112 358 VYPEGDSDAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQ-AEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFL 436 (773)
Q Consensus 358 vYp~~d~~~VsLt~~DL~~L~pg~WLND~IIdFYL~yL~~~~~-~~~~~rv~~FnSfFy~kL~~~~k~pssls~~~~~y~ 436 (773)
+||..+..++.||..|+.||.+++||||+||||||+||...-+ ...+.+||+||||||++|.. .+|+
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 23467899999999999974 6899
Q ss_pred HHHhhhcccCCCCCCeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHHHH
Q 004112 437 RVRKWTRKVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEW 516 (773)
Q Consensus 437 ~VkrWtk~vdLFeKD~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~E~ 516 (773)
+|+||+++++||+++|||||||...||+|+|||.+. +.|+|||||++.+..+.+.|+.|+.+||
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 HHhccCCcccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhh
Q 004112 517 KERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKK 576 (773)
Q Consensus 517 k~k~~~~~~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~ 576 (773)
+..+.... | ++....+||||.||+|||||||+++++|+.++|..|.+.++++
T Consensus 504 k~~~~k~~------~--~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r 555 (578)
T COG5160 504 KIQHDKDP------Q--IKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPR 555 (578)
T ss_pred hcccCCch------h--hhhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchHH
Confidence 87665431 2 2345679999999999999999999999999876655554443
No 3
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=4.4e-39 Score=355.46 Aligned_cols=186 Identities=27% Similarity=0.604 Sum_probs=155.1
Q ss_pred CCceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhcc--cccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHHhh
Q 004112 364 SDAVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQA--EEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKW 441 (773)
Q Consensus 364 ~~~VsLt~~DL~~L~pg~WLND~IIdFYL~yL~~~~~~--~~~~rv~~FnSfFy~kL~~~~k~pssls~~~~~y~~VkrW 441 (773)
+.++.||.+||.||.|++||||.|||||+++|.++... ....++|+||||||++|.... +..+|.+|+||
T Consensus 285 ~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~--------~~ygY~~VrRW 356 (490)
T PLN03189 285 NSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGK--------SGYDYKAVRRW 356 (490)
T ss_pred CCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcC--------CcCChHHHHHH
Confidence 45899999999999999999999999999999876432 234689999999999998631 12469999999
Q ss_pred hcc----cCCCCCCeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHH
Q 004112 442 TRK----VDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWK 517 (773)
Q Consensus 442 tk~----vdLFeKD~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~E~k 517 (773)
|++ ++||++|+||||||.+.||+|+||+++. ++|+|||||++.+..+.+.|+.||..|++
T Consensus 357 Tk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~----------------k~I~yyDSLgg~~~~vL~~L~rYL~~E~k 420 (490)
T PLN03189 357 TTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKD----------------QKFQYLDSLKGRDPKILDALAKYYVDEVK 420 (490)
T ss_pred hhhcccccccccCceEEeeeecCCeeEEEEEEcCC----------------CeEEEEeCCCCCCHHHHHHHHHHHHHHHh
Confidence 964 5799999999999999999999999764 58999999999988889999999999998
Q ss_pred HhccCCcccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhh
Q 004112 518 ERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKL 577 (773)
Q Consensus 518 ~k~~~~~~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~~ 577 (773)
.+.+... +++ .|.. ....++|||.||+|||||||+||++|..+.++.|+|.+|+.|
T Consensus 421 dK~g~d~-D~s-~W~~--~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~f 476 (490)
T PLN03189 421 DKSEKDI-DVS-SWEQ--EFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYF 476 (490)
T ss_pred hhcCCCc-chh-ccee--ccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHH
Confidence 8765432 332 2321 123689999999999999999999999998888887777654
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=3.6e-28 Score=243.73 Aligned_cols=196 Identities=34% Similarity=0.645 Sum_probs=135.2
Q ss_pred CCcCHHHHHHHHHHHHHhh--cccccCcEEEechHHHHHhhccC----CCCCC---cch-hhHHHHHHHhhhccc---CC
Q 004112 381 TFVNDTIIDFYIKYLKNQI--QAEEKHRFHFFNSFFFRKLADLD----KDPSS---ISD-GKAAFLRVRKWTRKV---DI 447 (773)
Q Consensus 381 ~WLND~IIdFYL~yL~~~~--~~~~~~rv~~FnSfFy~kL~~~~----k~pss---ls~-~~~~y~~VkrWtk~v---dL 447 (773)
+||||.|||||++||..++ ......++++|+|+|+.+|.... +.+.. ... ....+..+.+|++.. ++
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 6999999999999998654 33456799999999999998311 11100 000 134578899999887 99
Q ss_pred CCCCeEEEEeec-cCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcch-----hHHHHHHHHHHHHHHHhcc
Q 004112 448 FGKDYIFIPVNF-NLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHA-----GLKNLVQSYLCEEWKERHK 521 (773)
Q Consensus 448 FeKD~IfIPIN~-nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~-----~v~~~Lr~YL~~E~k~k~~ 521 (773)
+++++||||||. +.||+|+||+.+. .+|++||||++.+. .+...+..+|..++.....
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 CCcccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhHHHHHHHHHH
Q 004112 522 DTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKRSLIQKL 601 (773)
Q Consensus 522 ~~~~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis~kR~~I~~L 601 (773)
... +. ..|. ...+.++|||.|++|||+|||+||++++.+.+..+. ..|...++...|..+...
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 233568999999999999999999999988543321 115677888999999998
Q ss_pred HHHHHHhc
Q 004112 602 ISELLRNR 609 (773)
Q Consensus 602 I~eL~e~~ 609 (773)
|.+....+
T Consensus 208 ~~e~~~~~ 215 (216)
T PF02902_consen 208 LYEELGSR 215 (216)
T ss_dssp --------
T ss_pred cccccccC
Confidence 88766543
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.94 E-value=4.2e-26 Score=229.28 Aligned_cols=189 Identities=25% Similarity=0.406 Sum_probs=136.4
Q ss_pred ceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhcccccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHHhhhccc
Q 004112 366 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQAEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRKV 445 (773)
Q Consensus 366 ~VsLt~~DL~~L~pg~WLND~IIdFYL~yL~~~~~~~~~~rv~~FnSfFy~kL~~~~k~pssls~~~~~y~~VkrWtk~v 445 (773)
.|.|+++|+..|+++.||||.+|+||.+||.+........ .|+++|-.-..|.... .-+.++......
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 7899875544444321 113455566778
Q ss_pred CCCCCCeEEEEeecc---------CceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhH----HHHHHHHH
Q 004112 446 DIFGKDYIFIPVNFN---------LHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGL----KNLVQSYL 512 (773)
Q Consensus 446 dLFeKD~IfIPIN~n---------sHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v----~~~Lr~YL 512 (773)
++++|+|||+|||++ +||+|+|+..|. ..++||||+.+.|... .+.++.+|
T Consensus 84 ~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~----------------~~f~hyDS~~n~nt~~a~~l~~kl~~ll 147 (223)
T KOG3246|consen 84 DLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPD----------------GKFYHYDSLSNGNTKDAKSLMKKLRALL 147 (223)
T ss_pred hcCCCceEEEEecCCCcccccCCCcceEEEEEEeeC----------------CcEEEeecccCCCcHHHHHHHHHHHHHH
Confidence 999999999999995 599999999875 3799999999988653 44444444
Q ss_pred HHHHHHhccCCcccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhH
Q 004112 513 CEEWKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEAS 592 (773)
Q Consensus 513 ~~E~k~k~~~~~~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis 592 (773)
..... ...+..+|||.|+||||+|||+|++.++... .+..+.. ...-..+.-+.
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 1125679999999999999999998887651 1111111 11122455678
Q ss_pred HHHHHHHHHHHHHHHh
Q 004112 593 LKRSLIQKLISELLRN 608 (773)
Q Consensus 593 ~kR~~I~~LI~eL~e~ 608 (773)
.+|+.|..||..|.-.
T Consensus 202 ~lr~~l~~LI~slg~~ 217 (223)
T KOG3246|consen 202 ALREELLDLIQSLGSI 217 (223)
T ss_pred HHHHHHHHHHHHhCcc
Confidence 8999999999888643
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.83 E-value=1.9e-21 Score=224.83 Aligned_cols=232 Identities=28% Similarity=0.519 Sum_probs=163.5
Q ss_pred ceEEehhhhhccCCCCCcCHHHHHHHHHHHHHhhc--ccccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHHhhhc
Q 004112 366 AVSISKRDIDLLQPDTFVNDTIIDFYIKYLKNQIQ--AEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTR 443 (773)
Q Consensus 366 ~VsLt~~DL~~L~pg~WLND~IIdFYL~yL~~~~~--~~~~~rv~~FnSfFy~kL~~~~k~pssls~~~~~y~~VkrWtk 443 (773)
.+.++..|+.||.++.+|||.|++||++|+..... ++....+|+|++|||.++.+.......-.-....+.++++|++
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 55789999999999999999999999999987643 4557789999999999998743211110002235778999999
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcch-hHHHHHHHHHHHHHHHhccC
Q 004112 444 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHA-GLKNLVQSYLCEEWKERHKD 522 (773)
Q Consensus 444 ~vdLFeKD~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~-~v~~~Lr~YL~~E~k~k~~~ 522 (773)
.+++|.++||++|+|...||.|++||+|+.... ......+++++..... .....+..++..+|......
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 1123444455444322 23444556666555433221
Q ss_pred -Cccccccccc---c---eeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhHHHH
Q 004112 523 -TSEDVSSKFL---N---FRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKR 595 (773)
Q Consensus 523 -~~~D~ss~~~---n---~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis~kR 595 (773)
...+....|. + .....+..|||.|..|||+|+++|++.|+.++|..++-.+. ...+..||.+.++..+|
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 1112211111 0 00111234999999999999999999999998887652211 11234599999999999
Q ss_pred HHHHHHHHHHHHhccc
Q 004112 596 SLIQKLISELLRNRSR 611 (773)
Q Consensus 596 ~~I~~LI~eL~e~~s~ 611 (773)
..++++|+.|+..++.
T Consensus 578 ~~~r~~~~~l~~~~~~ 593 (595)
T KOG0779|consen 578 DEIRNLGRKLFTSQSS 593 (595)
T ss_pred hhhhccccccccccCC
Confidence 9999999999987754
No 7
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.70 E-value=4.4e-06 Score=98.12 Aligned_cols=449 Identities=18% Similarity=0.072 Sum_probs=232.7
Q ss_pred eccCceEEeccCccccccceeeccccchhhhhhhhhccccccEEEEEEeecccccccCCCC---------------CCCC
Q 004112 233 FSCTGIKIKDSNACGVQESFTFEKGIDDIVDIKFQWLQRFGSVEVKLHVILNDVAQDDNAC---------------GTSG 297 (773)
Q Consensus 233 fS~~~iki~~st~~~~~~~f~~Ew~iddIvsI~~~~~q~~gt~~I~l~~~~~~~~~~~~~~---------------~~~g 297 (773)
+.+++.+...-........+.+.-..+.|+.++.- -..+..-++...++++..+...-.. -.+-
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~-~~~~~~~i~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (595)
T KOG0779|consen 7 QLRSEVKSSSIMVESADVKELLIRRLEFVVLIKKS-RPNYLNDIIIDLVLLKDDNTLNDEYTRELSILFILAVKKGLTSL 85 (595)
T ss_pred ccccccccceeEeccCCCccceeeccccccccccC-CcccccccccchheeccccCCCccccceeeecccCCcccccccc
Confidence 44455555555555556666666666666666533 2234445555556665554322211 0233
Q ss_pred cceeeeeeccCchhhhHHHHhhhcccchhhhhcccCCCCCCCC--CCcccccCCCCCCCceeeccCCCCCceEEehhhhh
Q 004112 298 IEELKFSFSDCNWSEQLEKITSLNAKYLALWSVDHDNPVDMDG--VGQRRYFPNFDEPFEDVVYPEGDSDAVSISKRDID 375 (773)
Q Consensus 298 ~~~~~~~~~~~~~s~~~~~i~s~~~~y~~~~~~~~~~d~e~~~--~~~~~~~p~~~e~~~~vvYp~~d~~~VsLt~~DL~ 375 (773)
.+.+++++...+|..++.... +..++++|.+-........+ ......++.....|..+.||...+..+......+.
T Consensus 86 ~~~~ki~~~~~~~~~~~~~~~--~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (595)
T KOG0779|consen 86 TEPLKIAVLEEQKPHAVVPKK--IISVSELRNTNLTEGTFYSDYLNRIKNIFESVRKFFNQVSYPKFMPNVTSFMPSPLE 163 (595)
T ss_pred ccccccccccccCCccccccc--cccchhccccCCcccceecccccccccccchhcchhhhcccccccchhhcccCCccc
Confidence 445566666666665544444 66777777766555544443 33334444344445556676666555555555555
Q ss_pred ccCCCCCcCHHHHHHHHHHHHHhhcccccCcEEEechHHHHHhhccCCCCCCcchhhHHHHHHHhhhcccCCCCCCeEEE
Q 004112 376 LLQPDTFVNDTIIDFYIKYLKNQIQAEEKHRFHFFNSFFFRKLADLDKDPSSISDGKAAFLRVRKWTRKVDIFGKDYIFI 455 (773)
Q Consensus 376 ~L~pg~WLND~IIdFYL~yL~~~~~~~~~~rv~~FnSfFy~kL~~~~k~pssls~~~~~y~~VkrWtk~vdLFeKD~IfI 455 (773)
.++...--|..|.-.+..+....+.......+|++-..++-... ..|+...++-.+.++++
T Consensus 164 ~~q~~~~~~~~i~i~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~-------------------l~~~~~~~~~~~~~~~~ 224 (595)
T KOG0779|consen 164 KCQLQRVFTWTINITRKLFKKLFIKIFKNEPFHFKAVKFLLPSA-------------------LTKSDVCDIADLEVIFL 224 (595)
T ss_pred ccccccccceeeeeeecchhhhcccCcccCchhhhhhhcccchh-------------------ccchhhhhhhcccccch
Confidence 44433332222222222222221111112233333332221111 11111112223344555
Q ss_pred EeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccccccee
Q 004112 456 PVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSKFLNFR 535 (773)
Q Consensus 456 PIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~E~k~k~~~~~~D~ss~~~n~~ 535 (773)
+.....||.-...-++ ..+..++..+|+.+.......+...+.+..
T Consensus 225 ~~~k~~~~~~~~~~~~----------------------------------~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~ 270 (595)
T KOG0779|consen 225 NSRKDSHSLVISSINS----------------------------------PNIKTFFSKEVKSRPTPASYFIFSSFLPGL 270 (595)
T ss_pred hcccchhhhhhccccc----------------------------------ccchhhhccccccCCCcccccccccccCCC
Confidence 5555544222111111 111223333333222221112222233333
Q ss_pred eccCCCCCCCCCCChHHHHHHHHHHHHccCCCccChhhhhhhcccccCCCCCchhhHHHHHHHHHHHHHHHHhcccc-cc
Q 004112 536 FIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPLKLKKLSSFLNVDWFPPGEASLKRSLIQKLISELLRNRSRV-CL 614 (773)
Q Consensus 536 ~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~dI~~~r~~l~~~WF~p~eis~kR~~I~~LI~eL~e~~s~~-~~ 614 (773)
..+.+.+++.+..|||+.+.++-.-........+.+.....-+.....+||+..+....|+.+.++..+|...+... |.
T Consensus 271 ~~~~~~~~~dd~~~~~~~~~~~~~~~~~~~~~~~s~~q~~s~~~~~~~~~~~~~~~~~~~~l~~~~~~el~~~~~p~~~~ 350 (595)
T KOG0779|consen 271 DPPAELHQNDDIDDIGIILNESPLDKPFEWLLANSPNQSESRSRDSLDNWFPVKEADKQRTLIVKLAIELLEVRVPQICN 350 (595)
T ss_pred CccccccccchhhhhhhcccccccccchhhhhhcCcccchhcccccccccccccccccccchHHHhhccccccCCccccc
Confidence 44668889999999997765544332222222233333333344556799999999999999999999999877432 22
Q ss_pred CccccchhhccccccccccchhhhccccccccCCCCCCCCCCceEEEeccCCCCCccccccCCchhHhhhcCCCcccccc
Q 004112 615 DEHQSSRFLENSVNEMRLEFLSEKCSAATAQHGNLSNSQAGQGVEITLLGATSGRNLQCANDSSLVLKELLEPGVTAGSL 694 (773)
Q Consensus 615 d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 694 (773)
+ . ...+.+.. ..+ +++.-...+..+-.-..-.+.+++. ...+..++-.+....+++.+.+.+.+..
T Consensus 351 --~-~---~~v~~~Dl--~cl-~~~e~L~d~i~dfyl~~i~~~~l~~-~~~s~~~h~f~tffyk~l~~~~~~~~~d---- 416 (595)
T KOG0779|consen 351 --Q-S---HQVNNNDL--VCL-EEGEFLNDTIKDFYLEYIRQYLLSQ-KELSNDRHIFSTFFYKRLCRKLRQKSND---- 416 (595)
T ss_pred --c-c---cceeccch--hhc-cccchhhhhhhhhhhHHHHHhhhcc-cccCcchhhhhhHHHhhhhhhhhhhhhh----
Confidence 1 1 11111111 111 1111111223333333333555555 5566667777778888888888887766
Q ss_pred ccccCCCCCCCceeccCccc-cccccccccceeEEeccCCCCceeeeccCCCcccccc
Q 004112 695 LAYQSFGEPSSYYHLNGAAS-AREHDVETAEEYGYLAAGSNGFQQITELTPQVGSISF 751 (773)
Q Consensus 695 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 751 (773)
..|+++..+.+.+...-.+| .....+.++|+++...+..-+.+..++.+-+....-+
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=96.18 E-value=0.011 Score=65.47 Aligned_cols=92 Identities=16% Similarity=0.313 Sum_probs=62.0
Q ss_pred CCCCeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcc---------------------hh---
Q 004112 448 FGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTH---------------------AG--- 503 (773)
Q Consensus 448 FeKD~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~---------------------~~--- 503 (773)
-.+.|+.+|.+...||..+|++... .-+.+|||-|... ..
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk~~----------------~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s 292 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDKEK----------------KIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTS 292 (423)
T ss_pred ccccEEEeeeeehhcceEEEEeccc----------------cEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCccc
Confidence 4578999999999999999998543 3455556554421 00
Q ss_pred -------HHHHHHHHHHHHHHHhccCCcccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHccCCCccC
Q 004112 504 -------LKNLVQSYLCEEWKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAEAPVSFS 570 (773)
Q Consensus 504 -------v~~~Lr~YL~~E~k~k~~~~~~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ft 570 (773)
-+..|.+|+...+..+.+ ..|. .| -|--..+||+|.+.||-.....+|..|.
T Consensus 293 ~l~n~n~dIDVLfrfF~d~f~~~~g---------ciNv-----ev-nQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 293 NLDNENCDIDVLFRFFEDSFGVKYG---------CINV-----EV-NQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred ccccccCchHHHHHHHHhhccccee---------EEEh-----hh-hhhcccccchHHHHHHHHHHccCchhHH
Confidence 135666666655533221 1121 11 5778899999999999999988888763
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=94.00 E-value=0.097 Score=55.52 Aligned_cols=88 Identities=23% Similarity=0.358 Sum_probs=48.3
Q ss_pred CeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccc
Q 004112 451 DYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSK 530 (773)
Q Consensus 451 D~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~E~k~k~~~~~~D~ss~ 530 (773)
+.=+||||.+.||.|+++..- ..|.+|+ +|.|+..-+... +++.+.. .+ +.+.. +.
T Consensus 189 ~nevF~INtg~HWil~~~~Ki-------------~~kiKC~-iFNs~~~l~eNs---~~~ii~~-ak-~ag~~-~e---- 244 (317)
T PRK14848 189 HNEVFLINTGDHWLLCLFYKL-------------AEKIKCL-IFNTYYDLNENT---KQEIIEA-AK-IAGIS-EN---- 244 (317)
T ss_pred cceEEEecCCCcEEEEEhHHh-------------hhhceEE-EeecHhhhhhhH---HHHHHHH-HH-hhCcc-cC----
Confidence 444599999999999988421 1244564 578876654322 2222221 11 11111 00
Q ss_pred ccceeeccCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004112 531 FLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 564 (773)
Q Consensus 531 ~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~ 564 (773)
..+.|+..++ ||.=..-||+||+++++.+...
T Consensus 245 -~di~fIe~nL-QqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 245 -EDVNFIETNL-QNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred -CceEEeehhh-hhhCCCcchHHHHHHHHHHHhc
Confidence 1122333333 4444568999999999976654
No 10
>PRK11836 deubiquitinase; Provisional
Probab=93.94 E-value=0.14 Score=55.36 Aligned_cols=107 Identities=21% Similarity=0.366 Sum_probs=56.6
Q ss_pred ccCCCCCCeEEEEeeccCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchh----HHHHHHHH---HHHH-
Q 004112 444 KVDIFGKDYIFIPVNFNLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAG----LKNLVQSY---LCEE- 515 (773)
Q Consensus 444 ~vdLFeKD~IfIPIN~nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~----v~~~Lr~Y---L~~E- 515 (773)
.-.++-++.=+||||.+.||.|+++..- ++ +.....+.+|+ +|.|+..-+.. ....+..| |..|
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 4456678888999999999999988421 11 11122345564 57887665322 12222221 1111
Q ss_pred HHHhccCCcccccccccceeeccCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004112 516 WKERHKDTSEDVSSKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 564 (773)
Q Consensus 516 ~k~k~~~~~~D~ss~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~ 564 (773)
...+.+... . -..+.|+..++ ||.=..-||+||++.+..++..
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 01223333333 4444578999999999866654
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=78.19 E-value=12 Score=38.25 Aligned_cols=86 Identities=17% Similarity=0.280 Sum_probs=51.2
Q ss_pred EEEEeec-cCceEEEEEe-cCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHH--HHHHhccCCccccc
Q 004112 453 IFIPVNF-NLHWSLIVIC-HPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCE--EWKERHKDTSEDVS 528 (773)
Q Consensus 453 IfIPIN~-nsHWsLlVIc-~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~--E~k~k~~~~~~D~s 528 (773)
.++|+.. ..|-..+=|- .++ .++.|++|+|-.-.+.... |..+... +...+..
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 4555443 4666666553 322 3578999999754332111 2222221 1111111
Q ss_pred ccccceeeccCCCCCCCCCCChHHHHHHHHHHHHcc
Q 004112 529 SKFLNFRFIPLELPQQENSFDCGLFLLHYLELFLAE 564 (773)
Q Consensus 529 s~~~n~~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~ 564 (773)
.+.++..+++..|+..+|||+|-|.+|......
T Consensus 131 ---~~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 131 ---PNAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred ---CCcEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 134455678999999999999999999988765
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=64.01 E-value=1.1e+02 Score=31.59 Aligned_cols=127 Identities=16% Similarity=0.189 Sum_probs=52.7
Q ss_pred cCceEEEEEecCCCccccchhhccccCCCCeEEEEcCCCCcchhHHHHHHHHHHHHHHHhccCCccccccccc-ceee-c
Q 004112 460 NLHWSLIVICHPGDVASFKVEDLKRSEKVPCILHMDSIKGTHAGLKNLVQSYLCEEWKERHKDTSEDVSSKFL-NFRF-I 537 (773)
Q Consensus 460 nsHWsLlVIc~P~~~~~~~d~d~~~s~k~p~Il~fDSL~g~~~~v~~~Lr~YL~~E~k~k~~~~~~D~ss~~~-n~~~-v 537 (773)
+.||.-+..+ | +..+++.||.+|-+..++.+. -.-+|....+.. -+.+.-. =+++ .
T Consensus 33 GvHWlA~Aw~-P---------------~s~t~YmFDPfGfsd~~L~qi----Y~FeYe~llrRS--AL~~~~dRCv~Lvk 90 (183)
T PF00770_consen 33 GVHWLAFAWD-P---------------RSRTFYMFDPFGFSDQKLKQI----YQFEYEGLLRRS--ALSSTPDRCVTLVK 90 (183)
T ss_dssp -S-EEEEEEE-T---------------TTTEEEEE-TT---HHHHHHH----H----HHHHHHH--HHHH-TTSEEEEEE
T ss_pred ceeEEEEEec-C---------------CcceEEEeCCCCCCHHHHHHH----HhhhHHHHHHHH--hhcCCCCceEEEEe
Confidence 4899888775 3 236899999999887654432 122222211100 0000000 0111 1
Q ss_pred cCCCCCCCCCCChHHHHHHHHHHHHccCCCccChh-hhhhhcccccCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 004112 538 PLELPQQENSFDCGLFLLHYLELFLAEAPVSFSPL-KLKKLSSFLNVDWFPPGEASLKRSLIQKLISELLRNR 609 (773)
Q Consensus 538 ~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~P~~Ftq~-dI~~~r~~l~~~WF~p~eis~kR~~I~~LI~eL~e~~ 609 (773)
..+.-|=.++--||+|-+.|+.+|..-+.--+... .|.......+.....|..+..+|..= +.+...+..+
T Consensus 91 stqtVQ~p~SaaCGLFC~lFL~aF~~~p~~pm~~np~mdl~~gvp~~~l~~P~~~~~l~~NQ-e~LY~fl~~~ 162 (183)
T PF00770_consen 91 STQTVQCPCSAACGLFCCLFLHAFVHYPDNPMDNNPTMDLVTGVPNSMLQSPQVQPILHRNQ-EKLYRFLNSH 162 (183)
T ss_dssp E-EE-S-TT---HHHHHHHHHHHHHH-TTS-SSSSTTGGGS--EEGGGTT-CCCHHHHHHHH-HHHHHHHHHH
T ss_pred ccceeeccCchhHHHHHHHHHHHHHhCCCCcCCCCCeecccCCccCcccCCchhhHHHHHhH-HHHHHHHHHc
Confidence 12333555889999999999999987532222211 12222233334455665555555543 3334444444
No 13
>PRK15371 effector protein YopJ; Provisional
Probab=54.48 E-value=45 Score=36.78 Aligned_cols=31 Identities=29% Similarity=0.493 Sum_probs=25.8
Q ss_pred eeccCCCCCCCCCCChHHHHHHHHHHHHccC
Q 004112 535 RFIPLELPQQENSFDCGLFLLHYLELFLAEA 565 (773)
Q Consensus 535 ~~v~~~VPQQ~Ng~DCGVFVL~YaE~fl~~~ 565 (773)
.+..+.+-.|+-.+|||+|-|.+|....+..
T Consensus 157 ~~avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 157 HFSMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred eEEEEecccccCcccchhhhHHHHHHHhhhh
Confidence 4445678899999999999999999888763
Done!