Query 020018
Match_columns 332
No_of_seqs 188 out of 1204
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 06:22:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020018.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020018hhsearch_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 5.8E-46 1.3E-50 361.9 13.4 257 43-316 241-508 (511)
2 PLN03189 Protease specific for 100.0 1.2E-43 2.6E-48 343.1 20.0 213 94-317 267-488 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 1.5E-37 3.2E-42 298.9 12.0 194 105-319 375-570 (578)
4 KOG3246 Sentrin-specific cyste 100.0 1.8E-30 3.9E-35 226.2 15.4 195 104-332 10-214 (223)
5 PF02902 Peptidase_C48: Ulp1 p 100.0 5.6E-30 1.2E-34 229.5 15.5 186 125-316 1-211 (216)
6 KOG0779 Protease, Ulp1 family 99.2 3.9E-12 8.4E-17 130.0 4.4 207 110-332 352-587 (595)
7 PF03290 Peptidase_C57: Vaccin 97.4 0.00012 2.6E-09 69.8 3.9 102 186-298 227-350 (423)
8 PRK11836 deubiquitinase; Provi 97.2 0.0039 8.4E-08 57.7 10.7 157 123-296 162-330 (403)
9 PRK14848 deubiquitinase SseL; 96.8 0.0071 1.5E-07 55.0 8.6 138 123-293 133-276 (317)
10 PF00770 Peptidase_C5: Adenovi 96.6 0.0046 9.9E-08 53.1 5.6 90 199-298 32-122 (183)
11 PF03421 YopJ: YopJ Serine/Thr 73.4 12 0.00027 32.7 6.6 83 193-290 74-160 (177)
12 PRK15371 effector protein YopJ 72.0 18 0.00038 34.2 7.6 23 268-290 161-183 (287)
13 PF12252 SidE: Dot/Icm substra 54.1 17 0.00038 39.9 4.5 34 194-228 49-89 (1439)
14 KOG4110 NADH:ubiquinone oxidor 38.3 61 0.0013 26.0 4.2 31 260-290 17-47 (120)
15 PF03412 Peptidase_C39: Peptid 24.8 48 0.001 26.4 1.7 21 270-290 4-24 (131)
16 PF13280 WYL: WYL domain 24.0 69 0.0015 26.4 2.7 23 191-213 29-54 (172)
17 COG4508 Dimeric dUTPase [Carbo 22.6 51 0.0011 27.6 1.4 15 4-18 60-74 (161)
18 TIGR00667 aat leucyl/phenylala 22.5 97 0.0021 27.4 3.3 16 123-138 77-92 (185)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.8e-46 Score=361.89 Aligned_cols=257 Identities=23% Similarity=0.308 Sum_probs=208.7
Q ss_pred CCCCHHHHHhhhhhhhcccccccceeeecc-cccccccc---cchhhhhhhhhhc---ccccc--cCCcceEEeeCCeee
Q 020018 43 SPISEDAKQLILYLFDDKLNTMYDLIYTNC-FYDNCICK---VCSNIIILLLFVE---ITPFF--HGKREIVVDIGDNSI 113 (332)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~---~~~~~~~~~~~~~---~~~~~--~~~~~vlv~~~~~~L 113 (332)
.+.=||+......+-.....+.+.++++.- .-....++ .-..-++++...+ ++... ..+.++++..+++.|
T Consensus 241 ~~~~ee~~s~~~~~~~e~~~~~~~~i~l~~~~~k~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~I 320 (511)
T KOG0778|consen 241 EKSLEELVSDLKSLRFEIFQKRGELIPLRSVQEKLEKPKVEVKKEDSFPPLTEEREAQVQRAFSSRNSTEILVTHFNIDI 320 (511)
T ss_pred hhhHHHHHHHHHHhhhhhcccccccchhhhhhcccccccccccCccccccccHHHHHHHHHHhccCCcccceehhccccc
Confidence 455566666666666666677777776542 11111110 0011223333332 22222 346788889999999
Q ss_pred ehhhhhccCCCCCcCHHHHHHHHhhhhHHhhhhcC-CCCcEEEECchhHHHhhhccccchhHhhhhhhhhccCCcCCCCe
Q 020018 114 TRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKDV-TSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRYMSRLDTCEK 192 (332)
Q Consensus 114 ~~~Dl~~L~~~~WLND~IIn~y~~~lnl~~~~~~~-~~~~~~~~~s~f~~~l~~~~~~~~~~~v~rw~~~~~~~l~~~~~ 192 (332)
|.+||+||.+++||||+|||||+++ |+++..+. ..+++|+||||||++|.. .+|+.|+|||+ +++++++++
T Consensus 321 t~~dl~tl~~~~WLNDevINfYm~l--l~ers~~~~~yp~~h~FnTFFy~kL~~----~gy~~VkRWTk--~v~if~~d~ 392 (511)
T KOG0778|consen 321 TGKDLQTLRPGNWLNDEVINFYMEL--LKERSKKDSKYPKVHAFNTFFYTKLVG----RGYAGVKRWTK--KVDIFDKDI 392 (511)
T ss_pred cHHHHhhccCccchhHHHHHHHHHH--HHhhccccCCCceEEEEechhhhhhhh----cchHHHHhHhh--ccCccccce
Confidence 9999999999999999999999999 98887653 378999999999999997 78999999999 899999999
Q ss_pred eEEeEcCCCceeEEEEEecCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhhcCccccccceeecCCCCCC
Q 020018 193 IYVPINSDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQICRQAGLPQ 272 (332)
Q Consensus 193 I~iPIn~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~~~~~~~~~w~~~~~~~vPq 272 (332)
||||||-+.||+|+|||.++++|.|||||++..... +..|++||.+|+.++.+.++|.+.|.+....++||
T Consensus 393 i~vPIH~~vHW~l~vid~r~k~i~y~DS~~~~~nr~---------~~aL~~Yl~~E~~~k~~~~~d~s~w~~~~~~~iP~ 463 (511)
T KOG0778|consen 393 IFVPIHLGVHWCLAVIDLREKTIEYYDSLGGGPNRI---------CDALAKYLQDESRDKSKKDFDVSGWTIEFVQNIPQ 463 (511)
T ss_pred eEeeeecCceEEEEEEEcccceEEEeeccCCCCcch---------HHHHHHHHHHHHhhhhcCCCCccchhhhhhhcccc
Confidence 999999999999999999999999999999765443 46799999999999999999999999988899999
Q ss_pred CCCCCChHHHHHHHhHhhccccCCCCC-CCChHHHHHHHHHHhhc
Q 020018 273 QPNGFDCGYYVMKYMDSPCIVVHDSYQ-HDSDHARLLLALYLVQS 316 (332)
Q Consensus 273 Q~Ng~DCGvfvl~~~e~l~~~~~~~~~-~d~~~~R~~la~~L~~~ 316 (332)
|.||+|||+|+|+|++|++.+.+..|+ .|||++|.+||.+|+..
T Consensus 464 Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR~~m~~eI~~~ 508 (511)
T KOG0778|consen 464 QRNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFRKKMAKEILHL 508 (511)
T ss_pred ccCCCccceEEeeechhhccCCCcccChhhhHHHHHHHHHHHHhh
Confidence 999999999999999999988888885 67899999999988754
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.2e-43 Score=343.08 Aligned_cols=213 Identities=23% Similarity=0.437 Sum_probs=181.3
Q ss_pred ccccccCC--cceEEee--CCeeeehhhhhccCCCCCcCHHHHHHHHhhhhHHhhhhc--CCCCcEEEECchhHHHhhhc
Q 020018 94 ITPFFHGK--REIVVDI--GDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKD--VTSPRCWFLPTYYSQAALAD 167 (332)
Q Consensus 94 ~~~~~~~~--~~vlv~~--~~~~L~~~Dl~~L~~~~WLND~IIn~y~~~lnl~~~~~~--~~~~~~~~~~s~f~~~l~~~ 167 (332)
+...+..+ +++++.. +++.+|.+|+.||.|++||||+|||||+++ |.+.... ...+++++|+|||+++|...
T Consensus 267 V~~al~~~~~~~vlvs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~L--L~er~~~~p~~~~k~h~FNTFFytkL~~~ 344 (490)
T PLN03189 267 VKRAFSANNRRKVLVTHENSNIDITGEILRCLKPGAWLNDEVINLYLEL--LKEREAREPKKFLKCHFFNTFFYKKLVSG 344 (490)
T ss_pred HHHHhcCCCccceeeecCCCceEEEHHHhhccCCCCccCHHHHHHHHHH--HHHhhhcCcccccceEEEehHHHHHHhhc
Confidence 44444433 5788854 588999999999999999999999999999 7654332 23478999999999999986
Q ss_pred cccchhHhhhhhhhh--ccCCcCCCCeeEEeEcCCCceeEEEEEecCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHH
Q 020018 168 WSSLNFAQAAGFRDR--YMSRLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVL 245 (332)
Q Consensus 168 ~~~~~~~~v~rw~~~--~~~~l~~~~~I~iPIn~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l 245 (332)
....+|.+++||+++ .+.+++++++||||||.+.||+|+|||++.++|.|||||++.+... ++.|..|+
T Consensus 345 ~~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~~~v---------L~~L~rYL 415 (490)
T PLN03189 345 KSGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRDPKI---------LDALAKYY 415 (490)
T ss_pred CCcCChHHHHHHhhhcccccccccCceEEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCCHHH---------HHHHHHHH
Confidence 555689999999973 3457899999999999999999999999999999999999876543 67799999
Q ss_pred HHHHHhhhcCccccccceeecCCCCCCCCCCCChHHHHHHHhHhhccccCCCCC-CCChHHHHHHHHHHhhch
Q 020018 246 RQEARALFCNQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSYQ-HDSDHARLLLALYLVQSP 317 (332)
Q Consensus 246 ~~e~~~~~~~~~~~~~w~~~~~~~vPqQ~Ng~DCGvfvl~~~e~l~~~~~~~~~-~d~~~~R~~la~~L~~~~ 317 (332)
..++.++.+.+++.+.|......++|||.||+|||||||+||++|+.+.+..|+ .||+.+|++|+.+|+...
T Consensus 416 ~~E~kdK~g~d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrRma~EIl~~r 488 (490)
T PLN03189 416 VDEVKDKSEKDIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLRTAKEILRLK 488 (490)
T ss_pred HHHHhhhcCCCcchhcceeccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHHHHHHHHHhh
Confidence 999888888888999998766689999999999999999999999988888885 669999999999988643
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-37 Score=298.90 Aligned_cols=194 Identities=20% Similarity=0.343 Sum_probs=167.1
Q ss_pred EEeeCCeeeehhhhhccCCCCCcCHHHHHHHHhhhhHHhhhhc-CCCCcEEEECchhHHHhhhccccchhHhhhhhhhhc
Q 020018 105 VVDIGDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKD-VTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRY 183 (332)
Q Consensus 105 lv~~~~~~L~~~Dl~~L~~~~WLND~IIn~y~~~lnl~~~~~~-~~~~~~~~~~s~f~~~l~~~~~~~~~~~v~rw~~~~ 183 (332)
.+...+++||..|+.+|.+++||||+|||||+++ +....+. -..+++|+|+||||++|.+ .+|++|+||++
T Consensus 375 ~~~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~--ls~~sk~~s~~~~vh~FnTFFYT~Lsr----rGy~gVrrW~k-- 446 (578)
T COG5160 375 FNDRSSIEITNQDFKRLRNGDWLNDTIIDFYMKL--LSKISKNTSKREQVHLFNTFFYTKLSR----RGYSGVRRWTK-- 446 (578)
T ss_pred ccCcCcceeehHhhhhhccccchhhHHHHHHHHH--HHHhccCcccccceEEeehhhHHHHHH----HHhHHHHHHHh--
Confidence 4467889999999999999999999999999999 7555433 2357899999999999997 78999999999
Q ss_pred cCCcCCCCeeEEeEcCCCceeEEEEEecCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhhcCccccccce
Q 020018 184 MSRLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQ 263 (332)
Q Consensus 184 ~~~l~~~~~I~iPIn~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~~~~~~~~~w~ 263 (332)
+++++++++||||||-.+||+|+|||.+...|.+||||++..... ++.|+.|+.+|.+...+ .+.|.
T Consensus 447 k~dif~~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v---------~~~L~~Y~ldE~k~~~~----k~~~~ 513 (578)
T COG5160 447 KTDIFSKKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPV---------LEFLRSYLLDEYKIQHD----KDPQI 513 (578)
T ss_pred ccCccccceEEEEecccceEEEEEeecCcceeEEecccccCcHHH---------HHHHHHHHHHHHhcccC----Cchhh
Confidence 999999999999999999999999999999999999999987443 67899999988664433 33354
Q ss_pred eecCCCCCCCCCCCChHHHHHHHhHhhccccCCCCC-CCChHHHHHHHHHHhhchhH
Q 020018 264 ICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSYQ-HDSDHARLLLALYLVQSPLN 319 (332)
Q Consensus 264 ~~~~~~vPqQ~Ng~DCGvfvl~~~e~l~~~~~~~~~-~d~~~~R~~la~~L~~~~~n 319 (332)
.....+||||.||+|||||||+++++...+.+..|. .|++.+|+.|+..+....++
T Consensus 514 ~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~~qi~ 570 (578)
T COG5160 514 KMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKDLQIN 570 (578)
T ss_pred hhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999999999877666775 56899999999998866554
No 4
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.97 E-value=1.8e-30 Score=226.17 Aligned_cols=195 Identities=23% Similarity=0.351 Sum_probs=150.2
Q ss_pred eEEeeCCeeeehhhhhccCCCCCcCHHHHHHHHhhhhHHhhhhcCCCCcEEEECchhHHHhhhccccchhHhhhhhhhhc
Q 020018 104 IVVDIGDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRY 183 (332)
Q Consensus 104 vlv~~~~~~L~~~Dl~~L~~~~WLND~IIn~y~~~lnl~~~~~~~~~~~~~~~~s~f~~~l~~~~~~~~~~~v~rw~~~~ 183 (332)
++.+++++.|+.+|++.|.++.|+||.+|+||.++ +...... ..+..++++|.....+.+.. .-+.++....
T Consensus 10 v~Lsy~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~--l~~~~~~-s~~~~~ll~P~~t~~l~~~~---~~~e~~~~~~-- 81 (223)
T KOG3246|consen 10 VVLSYFDVSLRQSDVDLLQPPEWLNDRLIDFYYEY--LEHRRSR-SEPDLHLLRPSLTFFLRHAP---NPEEIAMVLD-- 81 (223)
T ss_pred eEEEeeehhhhhhhhhhcCCCchhhhhHHHHHHHH--HHHhhcc-cCcchhccCHHHHHHHHhCC---CcHHHHHhcC--
Confidence 88899999999999999999999999999999999 7655332 23447899987766665532 2233444444
Q ss_pred cCCcCCCCeeEEeEc---------CCCceeEEEEEecCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhhc
Q 020018 184 MSRLDTCEKIYVPIN---------SDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFC 254 (332)
Q Consensus 184 ~~~l~~~~~I~iPIn---------~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~~ 254 (332)
..++.++++||+||| +|+||+|+|++.+.++++||||+.+.++.. |..+++.++.++..+..
T Consensus 82 pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~-----a~~l~~kl~~ll~~~~~---- 152 (223)
T KOG3246|consen 82 PLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKD-----AKSLMKKLRALLKKKFA---- 152 (223)
T ss_pred hhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHH-----HHHHHHHHHHHHhhhhh----
Confidence 458999999999999 467999999999999999999999999887 55667888888765321
Q ss_pred CccccccceeecCCCCCCCCCCCChHHHHHHHhHhhccccCC-CCCCCChHHHHHHHHHHhhchhHHHHHHHHHHHHhC
Q 020018 255 NQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHD-SYQHDSDHARLLLALYLVQSPLNKIRCRLIQEARKL 332 (332)
Q Consensus 255 ~~~~~~~w~~~~~~~vPqQ~Ng~DCGvfvl~~~e~l~~~~~~-~~~~d~~~~R~~la~~L~~~~~n~~R~~ll~~i~~l 332 (332)
...+..+|||.||||||+|||.+.+.++.+... .+.. ....+...-++++|.+++++|..|
T Consensus 153 ---------~~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~--------~~~~~~~~~i~~lr~~l~~LI~sl 214 (223)
T KOG3246|consen 153 ---------KRVECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYAT--------SSQLLVVDLIKALREELLDLIQSL 214 (223)
T ss_pred ---------hcccccChhhhcCCchhHHHHHHHHHHHHHHhcccccc--------ccchhhHHHHHHHHHHHHHHHHHh
Confidence 112678999999999999999999998776543 2221 112234556788999999999865
No 5
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=99.97 E-value=5.6e-30 Score=229.49 Aligned_cols=186 Identities=25% Similarity=0.460 Sum_probs=132.7
Q ss_pred CCcCHHHHHHHHhhhhHHhhh--hcCCCCcEEEECchhHHHhhhccc----------------cchhHhhhhhhhh-ccC
Q 020018 125 EWIDGDIITMYADYKNMKEAE--KDVTSPRCWFLPTYYSQAALADWS----------------SLNFAQAAGFRDR-YMS 185 (332)
Q Consensus 125 ~WLND~IIn~y~~~lnl~~~~--~~~~~~~~~~~~s~f~~~l~~~~~----------------~~~~~~v~rw~~~-~~~ 185 (332)
+||||+|||+|+++ +.+.. .....+++++++|+|++.+..... ...+..+.+|.+. ...
T Consensus 1 ~wLnd~iId~y~~~--l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (216)
T PF02902_consen 1 EWLNDSIIDFYLEY--LRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKK 78 (216)
T ss_dssp --EEHHHHHHHHHH--HHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTS
T ss_pred CcCCHHHHHHHHHH--HHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhccccc
Confidence 69999999999999 65332 123468999999999998881100 1235667788873 234
Q ss_pred CcCCCCeeEEeEcC-CCceeEEEEEecCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhhcCcccccccee
Q 020018 186 RLDTCEKIYVPINS-DGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQI 264 (332)
Q Consensus 186 ~l~~~~~I~iPIn~-~~HW~L~vVd~~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~~~~~~~~~w~~ 264 (332)
+++++++|++|||. ++||+|+|||++.++|++|||+++..... . ....+..+..++........+...+.+.|..
T Consensus 79 ~l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~-~---~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 154 (216)
T PF02902_consen 79 NLFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNNDK-R---YKRVIENIIPFLKREYKKKEGRDPDKSPFKI 154 (216)
T ss_dssp TGGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-H-H---HHHHHHHHHHHHHHHHHHHHSSCT-TTTCEE
T ss_pred cccccCEEEEEEechhhccceeEEcccccEEEEEeccccccccc-c---chhhhhhhhhhhhhccccccccccccceeee
Confidence 89999999999996 99999999999999999999999987711 1 1223566777777665554455556677887
Q ss_pred ecCCCCCCCCCCCChHHHHHHHhHhhccccCCC----CC-CCChHHHHHHHHHHhhc
Q 020018 265 CRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDS----YQ-HDSDHARLLLALYLVQS 316 (332)
Q Consensus 265 ~~~~~vPqQ~Ng~DCGvfvl~~~e~l~~~~~~~----~~-~d~~~~R~~la~~L~~~ 316 (332)
....++|||.|++|||+|||+||+++..+.... +. .++..+|.+++..+...
T Consensus 155 ~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~~i~~~r~~~a~~~~e~ 211 (216)
T PF02902_consen 155 VRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQELTEEDIKNFRKKLAVDLYEE 211 (216)
T ss_dssp EEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCSBTGHHHHHHHHHHHH-----
T ss_pred cccccccCCCCCCCcHHHHHHHHHHHHhCCCCcccccCCHHHHHHHHHHHHhhcccc
Confidence 777899999999999999999999998776554 32 45777888888776544
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.25 E-value=3.9e-12 Score=129.99 Aligned_cols=207 Identities=14% Similarity=0.203 Sum_probs=132.6
Q ss_pred CeeeehhhhhccCCCCCcCHHHHHHHHhhhhHHhhhh--cCCCCcEEEECchhHHHhhhccccc--------hhHhhhhh
Q 020018 110 DNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEK--DVTSPRCWFLPTYYSQAALADWSSL--------NFAQAAGF 179 (332)
Q Consensus 110 ~~~L~~~Dl~~L~~~~WLND~IIn~y~~~lnl~~~~~--~~~~~~~~~~~s~f~~~l~~~~~~~--------~~~~v~rw 179 (332)
.+.++..|+.||.++..|||.+++||+++ +..... ....+.+++++++|+..+.+..... ....+++|
T Consensus 352 ~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~--i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~ 429 (595)
T KOG0779|consen 352 SHQVNNNDLVCLEEGEFLNDTIKDFYLEY--IRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTW 429 (595)
T ss_pred ccceeccchhhccccchhhhhhhhhhhHH--HHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeee
Confidence 45899999999999999999999999999 544322 2456899999999998776653211 12245668
Q ss_pred hhhccCCcCCCCeeEEeEcCCCceeEEEEEecCcc------eeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhh
Q 020018 180 RDRYMSRLDTCEKIYVPINSDGHWYMLVVDISHAT------ATIWDSLESPSRREKMINESLAILASLDFVLRQEARALF 253 (332)
Q Consensus 180 ~~~~~~~l~~~~~I~iPIn~~~HW~L~vVd~~~~~------I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~ 253 (332)
++ ..+++.+++|++|+|...||.++++..+... ....+++.-..... +...+..++..+.....
T Consensus 430 ~~--~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~ 499 (595)
T KOG0779|consen 430 TR--HFDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLILKLSADFP--------IVENILDFMKVASIYNN 499 (595)
T ss_pred ee--ccccccceeEEecCchHhhhhccccccCccccCccccchhhhhhccccccc--------hhhhhhhhhhhcccccC
Confidence 77 8999999999999999999999999876542 23334333332221 12223344433322110
Q ss_pred c------Ccccccccee------ecCCCCCCCCCCCChHHHHHHHhHhhccccCCCCC-CCChHHHHHHHHHHhhchhHH
Q 020018 254 C------NQFTFLNFQI------CRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSYQ-HDSDHARLLLALYLVQSPLNK 320 (332)
Q Consensus 254 ~------~~~~~~~w~~------~~~~~vPqQ~Ng~DCGvfvl~~~e~l~~~~~~~~~-~d~~~~R~~la~~L~~~~~n~ 320 (332)
. .+.+..-|+. ...+ .|||.|..|||+|++.|++.+.......++ .|. .=..+. .+...+..+
T Consensus 500 ~~~~~~~~~~~~~~~~~~~~~~s~~v~-~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~--~~~~l~-~~~~~~~~~ 575 (595)
T KOG0779|consen 500 ELIVTEDLELEEELPRRLPRGKSETVR-EPQQNNDVDCGSFVLEFVERFIEDAPERFNIEDE--GTINLE-WFPPKEILK 575 (595)
T ss_pred cccccccccccccccccCccccccccc-ccCccCcccchhhHHHHHHHhhhChhhhcccccc--cccccc-cCCchHHhh
Confidence 0 0111111111 0112 289999999999999999988665444322 010 001122 345788888
Q ss_pred HHHHHHHHHHhC
Q 020018 321 IRCRLIQEARKL 332 (332)
Q Consensus 321 ~R~~ll~~i~~l 332 (332)
+|..+..++++|
T Consensus 576 ~r~~~r~~~~~l 587 (595)
T KOG0779|consen 576 FRDEIRNLGRKL 587 (595)
T ss_pred hhhhhhcccccc
Confidence 888888888775
No 7
>PF03290 Peptidase_C57: Vaccinia virus I7 processing peptidase; InterPro: IPR004970 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This is a group of cysteine peptidases which constitute MEROPS peptidase family C57 (clan CE). The type example is vaccinia virus I7 processing peptidase (vaccinia virus); protein I7 is expressed in the late phase of infection [].
Probab=97.44 E-value=0.00012 Score=69.83 Aligned_cols=102 Identities=10% Similarity=0.070 Sum_probs=68.4
Q ss_pred CcCCCCeeEEeEcCCCceeEEEEEecCcceeeecCCCCCChhh----------------------HhhHHHHHHHHHHHH
Q 020018 186 RLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESPSRRE----------------------KMINESLAILASLDF 243 (332)
Q Consensus 186 ~l~~~~~I~iPIn~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~----------------------~rl~~~~~i~~~L~~ 243 (332)
.-.++.++.+|.+..+||.++|+|.+++-+.+|||-|.....- ..+..+..=++.|.+
T Consensus 227 k~~~~RyvmFgfcY~~Hwkc~IfDk~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dIDVLfr 306 (423)
T PF03290_consen 227 KNSKKRYVMFGFCYMSHWKCCIFDKEKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDIDVLFR 306 (423)
T ss_pred hhccccEEEeeeeehhcceEEEEeccccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchHHHHH
Confidence 3456789999999999999999999999999999998542110 001111111455777
Q ss_pred HHHHHHHhhhcCccccccceeecCCCCCCCCCCCChHHHHHHHhHhhccccCCCC
Q 020018 244 VLRQEARALFCNQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSY 298 (332)
Q Consensus 244 ~l~~e~~~~~~~~~~~~~w~~~~~~~vPqQ~Ng~DCGvfvl~~~e~l~~~~~~~~ 298 (332)
++.+....+. . ...---.|-..++||+|++.||-..+...+..|
T Consensus 307 fF~d~f~~~~--------g---ciNvevnQl~eseCGMF~~iFm~~c~~~ppk~f 350 (423)
T PF03290_consen 307 FFEDSFGVKY--------G---CINVEVNQLLESECGMFISIFMILCTLTPPKGF 350 (423)
T ss_pred HHHhhcccce--------e---EEEhhhhhhcccccchHHHHHHHHHHccCchhH
Confidence 7765432111 1 111124688999999999999998776555544
No 8
>PRK11836 deubiquitinase; Provisional
Probab=97.19 E-value=0.0039 Score=57.72 Aligned_cols=157 Identities=18% Similarity=0.206 Sum_probs=76.3
Q ss_pred CCCCcCHHHHHHHHhhhhHHhhhhc--CCCCcEEEECchhHHHhhhccccchhHhhhhhhhhccCCcCCCCeeEEeEcCC
Q 020018 123 PGEWIDGDIITMYADYKNMKEAEKD--VTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRYMSRLDTCEKIYVPINSD 200 (332)
Q Consensus 123 ~~~WLND~IIn~y~~~lnl~~~~~~--~~~~~~~~~~s~f~~~l~~~~~~~~~~~v~rw~~~~~~~l~~~~~I~iPIn~~ 200 (332)
+...|+.+-|+.|..- +...... ..+| +.+..|+--...+.. .-.+.++ ....|-++.=+||||.|
T Consensus 162 ~nRmltsDEia~~~q~--~~~~~~n~~VNyP-iGLi~P~t~~~~L~~---~L~E~i~------~~~~~~k~~elFpINtg 229 (403)
T PRK11836 162 KNRQLTTDEIACYLQK--IAANAKNTQVNYP-TGLYVPYSTRTHLED---ALNENIK------SDPSWPKEVQLFPINTG 229 (403)
T ss_pred ccccccHHHHHHHhcc--cccCCccceecCC-ceeeecCcccchhHH---HHHHhhh------cCCCCcccceEEEecCC
Confidence 4566787888888776 5554321 1123 333333322211111 1111221 34566778889999999
Q ss_pred CceeEEEEEe--------cCcceeeecCCCCCChhh-HhhHHHHHHHHHHHHHHHHHH-HhhhcCccccccceeecCCCC
Q 020018 201 GHWYMLVVDI--------SHATATIWDSLESPSRRE-KMINESLAILASLDFVLRQEA-RALFCNQFTFLNFQICRQAGL 270 (332)
Q Consensus 201 ~HW~L~vVd~--------~~~~I~~yDSL~~~~~~~-~rl~~~~~i~~~L~~~l~~e~-~~~~~~~~~~~~w~~~~~~~v 270 (332)
+||.|+++.. .+.+..+|.|+..-+... .-+++ +++....-+-.+. ..+.... ..+=.+....--
T Consensus 230 ~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~q~---ii~a~~~~~~~~~~~~~ik~~--~~e~ei~fie~d 304 (403)
T PRK11836 230 GHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSLKR---VINSFNSELMGEMSNNNIKVH--LTEPEIIFLHAD 304 (403)
T ss_pred CcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHHHH---HHHhhhhhhhhhcchhhhccc--ccCCceEEEech
Confidence 9999998742 234567888887653331 11111 1222111111111 1111111 111111111222
Q ss_pred CCCCCCCChHHHHHHHhHhhccccCC
Q 020018 271 PQQPNGFDCGYYVMKYMDSPCIVVHD 296 (332)
Q Consensus 271 PqQ~Ng~DCGvfvl~~~e~l~~~~~~ 296 (332)
-||.=...||.||+..+..+......
T Consensus 305 LQq~vpngCGlFv~~a~Qe~i~q~~~ 330 (403)
T PRK11836 305 LQQYLSQSCGAFVCMAAQEVIEQRES 330 (403)
T ss_pred hhhcCCCccceehHHHHHHHHHHhhh
Confidence 34545678999999988855444433
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=96.80 E-value=0.0071 Score=54.96 Aligned_cols=138 Identities=9% Similarity=0.054 Sum_probs=70.1
Q ss_pred CCCCcCHHHHHHHHhhhhHHhhhhc--CCCCcEEEECchhHHHhhhccccchhHhhhhhhhhccCCcCCCCeeEEeEcCC
Q 020018 123 PGEWIDGDIITMYADYKNMKEAEKD--VTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRYMSRLDTCEKIYVPINSD 200 (332)
Q Consensus 123 ~~~WLND~IIn~y~~~lnl~~~~~~--~~~~~~~~~~s~f~~~l~~~~~~~~~~~v~rw~~~~~~~l~~~~~I~iPIn~~ 200 (332)
+...|+.+-|+.|..- +.+.... ..+|- .+..|+-....+.. .-.++++. -+.+..=+||||.|
T Consensus 133 ~~Rmlt~DEi~~~~q~--~~~~~~~~~VNyP~-GL~~P~s~~~~L~~---~L~E~i~~--------s~~~~nevF~INtg 198 (317)
T PRK14848 133 GARMLSSDELAAATQG--LVQESPLLSVNYPI-GLIHPTTKENILST---QLLEKIAQ--------SGLSHNEVFLINTG 198 (317)
T ss_pred ccccccHHHHHHHhhc--cccCCccceecCCc-eeeecCccchhHHH---HHHhhhhh--------cCCCcceEEEecCC
Confidence 5677888888888776 6554321 12233 33333322211111 11112211 11223345999999
Q ss_pred CceeEEEEEe--cCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhhcC--ccccccceeecCCCCCCCCCC
Q 020018 201 GHWYMLVVDI--SHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCN--QFTFLNFQICRQAGLPQQPNG 276 (332)
Q Consensus 201 ~HW~L~vVd~--~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~~~--~~~~~~w~~~~~~~vPqQ~Ng 276 (332)
+||.|+++.. .+-+..+|.|++.-+... + +.+.. . ..+.+. .-+. .....--||.=.
T Consensus 199 ~HWil~~~~Ki~~kiKC~iFNs~~~l~eNs--~-------~~ii~---~--ak~ag~~~e~di-----~fIe~nLQqnVp 259 (317)
T PRK14848 199 DHWLLCLFYKLAEKIKCLIFNTYYDLNENT--K-------QEIIE---A--AKIAGISENEDV-----NFIETNLQNNVP 259 (317)
T ss_pred CcEEEEEhHHhhhhceEEEeecHhhhhhhH--H-------HHHHH---H--HHhhCcccCCce-----EEeehhhhhhCC
Confidence 9999998743 234567888887765322 1 11111 0 111111 1111 112222345556
Q ss_pred CChHHHHHHHhHhhccc
Q 020018 277 FDCGYYVMKYMDSPCIV 293 (332)
Q Consensus 277 ~DCGvfvl~~~e~l~~~ 293 (332)
..||.||+.+++.+...
T Consensus 260 ngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 260 NGCGLFCYHTIQLLSNA 276 (317)
T ss_pred CcchHHHHHHHHHHHhc
Confidence 78999999999977544
No 10
>PF00770 Peptidase_C5: Adenovirus endoprotease; InterPro: IPR000855 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine aminopeptidases belong to the peptidase family C5 (adenain family, clan CE). Several adenovirus proteins are synthesised as precursors, requiring processing by a protease before the virion is assembled [, ]. Until recently, the adenovirus endopeptidase was classified as a serine protease, having been reported to be inhibited by serine protease inhibitors [, ]. However, it has since been shown to be inhibited by cysteine protease inhibitors, and the catalytic residues are believed to be His-54 and Cys-104 [, ].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1NLN_A 1AVP_A.
Probab=96.59 E-value=0.0046 Score=53.12 Aligned_cols=90 Identities=16% Similarity=0.230 Sum_probs=42.5
Q ss_pred CCCceeEEEEEecCcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHh-hhcCccccccceeecCCCCCCCCCCC
Q 020018 199 SDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARA-LFCNQFTFLNFQICRQAGLPQQPNGF 277 (332)
Q Consensus 199 ~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~-~~~~~~~~~~w~~~~~~~vPqQ~Ng~ 277 (332)
+|.||..+..|+..++++.||++|=.+.+-.++-.- .-...|+...-. ..+.-+ +.+...+.-|=+++-
T Consensus 32 GGvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~qiY~F-----eYe~llrRSAL~~~~dRCv-----~LvkstqtVQ~p~Sa 101 (183)
T PF00770_consen 32 GGVHWLAFAWDPRSRTFYMFDPFGFSDQKLKQIYQF-----EYEGLLRRSALSSTPDRCV-----TLVKSTQTVQCPCSA 101 (183)
T ss_dssp --S-EEEEEEETTTTEEEEE-TT---HHHHHHHH---------HHHHHHHHHHH-TTSEE-----EEEEE-EE-S-TT--
T ss_pred CceeEEEEEecCCcceEEEeCCCCCCHHHHHHHHhh-----hHHHHHHHHhhcCCCCceE-----EEEeccceeeccCch
Confidence 788999999999999999999998766543111100 011112211111 001111 111223334445777
Q ss_pred ChHHHHHHHhHhhccccCCCC
Q 020018 278 DCGYYVMKYMDSPCIVVHDSY 298 (332)
Q Consensus 278 DCGvfvl~~~e~l~~~~~~~~ 298 (332)
.||+|.+.|+.++..+...++
T Consensus 102 aCGLFC~lFL~aF~~~p~~pm 122 (183)
T PF00770_consen 102 ACGLFCCLFLHAFVHYPDNPM 122 (183)
T ss_dssp -HHHHHHHHHHHHHH-TTS-S
T ss_pred hHHHHHHHHHHHHHhCCCCcC
Confidence 999999999999877766555
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=73.42 E-value=12 Score=32.68 Aligned_cols=83 Identities=12% Similarity=0.148 Sum_probs=46.2
Q ss_pred eEEeEc-CCCceeEEEEE-ec--CcceeeecCCCCCChhhHhhHHHHHHHHHHHHHHHHHHHhhhcCccccccceeecCC
Q 020018 193 IYVPIN-SDGHWYMLVVD-IS--HATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQICRQA 268 (332)
Q Consensus 193 I~iPIn-~~~HW~L~vVd-~~--~~~I~~yDSL~~~~~~~~rl~~~~~i~~~L~~~l~~e~~~~~~~~~~~~~w~~~~~~ 268 (332)
.++|+. .+.|...+=|- .. +..+.++||-.-.+.... +... .+. +.+. ..+.+. .+.+ ...
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~~~~~~-l~~~---~~~----~~~~-~~~~~~-----~~~~-~~i 138 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPNGKPSLIVFEPASFYGMKPA-LAGY---TKL----AEEA-RQKLLP-----NAKF-AVI 138 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCCCCceEEEEccccccCCcch-hhhH---HHH----HHHH-HhccCC-----CcEE-EEE
Confidence 455644 55566555444 22 346899999876543321 1100 111 1111 111111 2333 246
Q ss_pred CCCCCCCCCChHHHHHHHhHhh
Q 020018 269 GLPQQPNGFDCGYYVMKYMDSP 290 (332)
Q Consensus 269 ~vPqQ~Ng~DCGvfvl~~~e~l 290 (332)
.+..|+..+|||+|.|.+|...
T Consensus 139 e~diQkS~~dC~IFsLs~AkK~ 160 (177)
T PF03421_consen 139 EMDIQKSPSDCGIFSLSLAKKM 160 (177)
T ss_pred ecccccCcCcchhhHHHHHHHH
Confidence 7899999999999999999865
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=71.99 E-value=18 Score=34.17 Aligned_cols=23 Identities=13% Similarity=0.349 Sum_probs=20.2
Q ss_pred CCCCCCCCCCChHHHHHHHhHhh
Q 020018 268 AGLPQQPNGFDCGYYVMKYMDSP 290 (332)
Q Consensus 268 ~~vPqQ~Ng~DCGvfvl~~~e~l 290 (332)
...-.|+..+|||+|.|.+|...
T Consensus 161 ie~d~QkS~~dC~mFSL~~AkK~ 183 (287)
T PRK15371 161 VEMDIQRSSSECGIFSLALAKKL 183 (287)
T ss_pred EecccccCcccchhhhHHHHHHH
Confidence 56788999999999999999865
No 13
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=54.14 E-value=17 Score=39.90 Aligned_cols=34 Identities=26% Similarity=0.579 Sum_probs=27.1
Q ss_pred EEeEc-------CCCceeEEEEEecCcceeeecCCCCCChhh
Q 020018 194 YVPIN-------SDGHWYMLVVDISHATATIWDSLESPSRRE 228 (332)
Q Consensus 194 ~iPIn-------~~~HW~L~vVd~~~~~I~~yDSL~~~~~~~ 228 (332)
|+||- ..+||..++ --+.+..+.||+||..+...
T Consensus 49 fmpvltgv~p~~~sghwimli-kg~gn~y~lfdplg~~sg~~ 89 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLI-KGQGNQYYLFDPLGKTSGEG 89 (1439)
T ss_pred CceeecCcCCCCcCceeEEEE-EcCCCceEEecccccccccc
Confidence 77777 789999876 45678899999999986654
No 14
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=38.26 E-value=61 Score=26.00 Aligned_cols=31 Identities=19% Similarity=0.456 Sum_probs=25.8
Q ss_pred ccceeecCCCCCCCCCCCChHHHHHHHhHhh
Q 020018 260 LNFQICRQAGLPQQPNGFDCGYYVMKYMDSP 290 (332)
Q Consensus 260 ~~w~~~~~~~vPqQ~Ng~DCGvfvl~~~e~l 290 (332)
..|.+.-...+|.-..|.|||.|=..++++.
T Consensus 17 ~r~p~tds~~~p~~~q~r~cg~FE~e~~eC~ 47 (120)
T KOG4110|consen 17 DRWPTTDSTEQPYKHQGRDCGKFEKEWMECA 47 (120)
T ss_pred hhccccccccCccccccccccHHHHHHHHHH
Confidence 4576666778888888999999999999986
No 15
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 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 sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=24.79 E-value=48 Score=26.44 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=13.9
Q ss_pred CCCCCCCCChHHHHHHHhHhh
Q 020018 270 LPQQPNGFDCGYYVMKYMDSP 290 (332)
Q Consensus 270 vPqQ~Ng~DCGvfvl~~~e~l 290 (332)
+=+|.+..|||+-+++++-..
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~ 24 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKY 24 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHH
T ss_pred eEEeCCCCCHHHHHHHHHHHH
Confidence 457889999999999987654
No 16
>PF13280 WYL: WYL domain
Probab=23.96 E-value=69 Score=26.40 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=19.1
Q ss_pred CeeEEeEc---CCCceeEEEEEecCc
Q 020018 191 EKIYVPIN---SDGHWYMLVVDISHA 213 (332)
Q Consensus 191 ~~I~iPIn---~~~HW~L~vVd~~~~ 213 (332)
...+.|+. .+++|+|++.|...+
T Consensus 29 ~~~v~P~~l~~~~~~~Yl~~~~~~~~ 54 (172)
T PF13280_consen 29 ERRVDPYRLYYYNGRWYLIAYDRERE 54 (172)
T ss_pred EEEEEEEEEEEECCEEEEEEEecccc
Confidence 66788988 899999999987654
No 17
>COG4508 Dimeric dUTPase [Carbohydrate transport and metabolism]
Probab=22.59 E-value=51 Score=27.61 Aligned_cols=15 Identities=40% Similarity=0.525 Sum_probs=13.1
Q ss_pred hhHHHHHHHhhhhhh
Q 020018 4 QTTKAMEEYMDGHIQ 18 (332)
Q Consensus 4 ~~~~~~~~~~~~~~~ 18 (332)
.++++.|||+||.|-
T Consensus 60 ~~~~ilEEY~dglHF 74 (161)
T COG4508 60 DLAKILEEYSDGLHF 74 (161)
T ss_pred cHHHHHHHHhhhHHH
Confidence 578999999999875
No 18
>TIGR00667 aat leucyl/phenylalanyl-tRNA--protein transferase. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway. This enzyme transfers a Leu or Phe to the amino end of certain proteins to enable degradation.
Probab=22.45 E-value=97 Score=27.36 Aligned_cols=16 Identities=25% Similarity=0.819 Sum_probs=13.8
Q ss_pred CCCCcCHHHHHHHHhh
Q 020018 123 PGEWIDGDIITMYADY 138 (332)
Q Consensus 123 ~~~WLND~IIn~y~~~ 138 (332)
++.|+++++|++|.++
T Consensus 77 ~gTWI~~e~~~aY~~L 92 (185)
T TIGR00667 77 EGTWISDELVEAYHRL 92 (185)
T ss_pred CCCCCCHHHHHHHHHH
Confidence 4689999999999887
Done!