Query 022637
Match_columns 294
No_of_seqs 194 out of 1243
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 05:02:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022637.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022637hhsearch_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 2E-55 4.4E-60 408.5 17.5 222 42-280 288-510 (511)
2 PLN03189 Protease specific for 100.0 1.3E-52 2.8E-57 386.7 22.8 227 42-279 256-488 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 8.3E-43 1.8E-47 319.7 12.8 199 64-282 372-571 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 2.8E-32 6.1E-37 235.4 14.8 188 87-279 1-212 (216)
5 KOG3246 Sentrin-specific cyste 100.0 6.4E-32 1.4E-36 223.8 14.1 193 64-294 8-214 (223)
6 KOG0779 Protease, Ulp1 family 99.4 1.4E-13 3E-18 134.5 3.8 175 72-257 352-552 (595)
7 PF03290 Peptidase_C57: Vaccin 97.8 2.9E-05 6.3E-10 70.5 5.8 102 148-260 227-350 (423)
8 PRK11836 deubiquitinase; Provi 97.1 0.0019 4.1E-08 56.9 7.7 102 147-253 214-325 (403)
9 PRK14848 deubiquitinase SseL; 97.0 0.0016 3.4E-08 56.3 5.6 83 155-254 191-275 (317)
10 PF00770 Peptidase_C5: Adenovi 96.7 0.0042 9E-08 50.8 5.9 90 161-260 32-122 (183)
11 PRK15371 effector protein YopJ 90.7 5.1 0.00011 36.0 11.6 136 83-252 39-183 (287)
12 PF03421 YopJ: YopJ Serine/Thr 81.3 12 0.00025 31.4 8.3 81 155-252 74-160 (177)
13 PF12252 SidE: Dot/Icm substra 43.0 58 0.0013 34.6 6.0 34 156-190 49-89 (1439)
14 KOG4110 NADH:ubiquinone oxidor 34.9 28 0.00061 26.4 1.8 30 223-252 18-47 (120)
15 PF07797 DUF1639: Protein of u 25.3 36 0.00078 22.1 0.8 46 45-93 1-46 (50)
16 PF03412 Peptidase_C39: Peptid 24.8 44 0.00096 25.5 1.5 21 232-252 4-24 (131)
17 COG3242 Uncharacterized protei 24.4 99 0.0021 21.0 2.8 24 263-286 22-45 (62)
18 PF13280 WYL: WYL domain 21.3 77 0.0017 25.1 2.3 23 153-175 29-54 (172)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-55 Score=408.50 Aligned_cols=222 Identities=26% Similarity=0.432 Sum_probs=205.9
Q ss_pred CCCCCHHHHHHHHHHhccCCCCcceeeecCCeEEehhhhcccCCCCcccHHHHHHHHHHHhhhhhhhccCCCceEEccch
Q 022637 42 PSPISEDAKQLILYLFDDKLNTMEIVVDIGDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKDVTSPRCWFLPTY 121 (294)
Q Consensus 42 ~~~ls~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~~dl~~L~~~~wLnD~vI~~~~~~ll~~~~~~~~~~~~~~~~~t~ 121 (294)
+.+|++++...++.++... +.+++++..+++.||.+||.||.+++||||+||||||++ |.+++......++||+||||
T Consensus 288 ~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~i~It~~dl~tl~~~~WLNDevINfYm~l-l~ers~~~~~yp~~h~FnTF 365 (511)
T KOG0778|consen 288 FPPLTEEREAQVQRAFSSR-NSTEILVTHFNIDITGKDLQTLRPGNWLNDEVINFYMEL-LKERSKKDSKYPKVHAFNTF 365 (511)
T ss_pred cccccHHHHHHHHHHhccC-CcccceehhccccccHHHHhhccCccchhHHHHHHHHHH-HHhhccccCCCceEEEEech
Confidence 4699999999999999764 889999999999999999999999999999999999999 99998876669999999999
Q ss_pred HHHHhhccccccchhhhhhhhhhcccCCCCCCeeEeeecCCCceeEEEEeecCceEEEecCCCCCCchhhhhHHHHHHHH
Q 022637 122 YSQAALADWSSLNFAQAAGFRDRYMSRLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILA 201 (294)
Q Consensus 122 f~~~l~~~~~~~~~~~v~r~~~~~~~~l~~~d~IfiPIn~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~l~~~~~i~~ 201 (294)
||++|.. +||++|+|||+ ++++|++|+||||||-+.||+|+|||.++++|.|||||++..... +.
T Consensus 366 Fy~kL~~----~gy~~VkRWTk--~v~if~~d~i~vPIH~~vHW~l~vid~r~k~i~y~DS~~~~~nr~---------~~ 430 (511)
T KOG0778|consen 366 FYTKLVG----RGYAGVKRWTK--KVDIFDKDIIFVPIHLGVHWCLAVIDLREKTIEYYDSLGGGPNRI---------CD 430 (511)
T ss_pred hhhhhhh----cchHHHHhHhh--ccCccccceeEeeeecCceEEEEEEEcccceEEEeeccCCCCcch---------HH
Confidence 9999998 89999999999 899999999999999999999999999999999999999775554 57
Q ss_pred HHHHHHHHHHHHhhCCCCCCCcceeccCCccCCCCCCCCcHHHHHHhhHhhccccCCCC-CCCcHHHHHHHHHHHHcCCc
Q 022637 202 SLDFVLRQEARALFCNQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSY-QHDSDHARLLLALYLVQSPL 280 (294)
Q Consensus 202 ~l~~~l~~e~~~k~~~~~~~~~w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~~~~-~~d~~~~R~~l~~~l~~~~~ 280 (294)
.|.+||.+|+.+|.+.++|++.|.+....++|||.||+|||+|+|+|++|++.+.+..| |.|||.+|.+||.||++..+
T Consensus 431 aL~~Yl~~E~~~k~~~~~d~s~w~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR~~m~~eI~~~~l 510 (511)
T KOG0778|consen 431 ALAKYLQDESRDKSKKDFDVSGWTIEFVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFRKKMAKEILHLKL 510 (511)
T ss_pred HHHHHHHHHHhhhhcCCCCccchhhhhhhccccccCCCccceEEeeechhhccCCCcccChhhhHHHHHHHHHHHHhhhc
Confidence 89999999999999999999999998888999999999999999999999987777666 46799999999999998754
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.3e-52 Score=386.66 Aligned_cols=227 Identities=21% Similarity=0.406 Sum_probs=199.5
Q ss_pred CCCCCHHHHHHHHHHhccCCCCcceeeec--CCeEEehhhhcccCCCCcccHHHHHHHHHHHhhhhhhhc-cCCCceEEc
Q 022637 42 PSPISEDAKQLILYLFDDKLNTMEIVVDI--GDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKD-VTSPRCWFL 118 (294)
Q Consensus 42 ~~~ls~~~~~~~~~~l~~~~~~~~~l~~~--~~~~l~~~dl~~L~~~~wLnD~vI~~~~~~ll~~~~~~~-~~~~~~~~~ 118 (294)
+.|||++++..+..+|... +.++++++. +++.||++|+.||.+++||||+|||||+++ |.++.... ...+++|+|
T Consensus 256 ~~pLT~e~~~~V~~al~~~-~~~~vlvs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~L-L~er~~~~p~~~~k~h~F 333 (490)
T PLN03189 256 FIPLTREEETEVKRAFSAN-NRRKVLVTHENSNIDITGEILRCLKPGAWLNDEVINLYLEL-LKEREAREPKKFLKCHFF 333 (490)
T ss_pred CcCCCHHHHHHHHHHhcCC-CccceeeecCCCceEEEHHHhhccCCCCccCHHHHHHHHHH-HHHhhhcCcccccceEEE
Confidence 3699999999999999874 557888865 578999999999999999999999999999 87765432 245789999
Q ss_pred cchHHHHhhccccccchhhhhhhhhh--cccCCCCCCeeEeeecCCCceeEEEEeecCceEEEecCCCCCCchhhhhHHH
Q 022637 119 PTYYSQAALADWSSLNFAQAAGFRDR--YMSRLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESPSRREKMINES 196 (294)
Q Consensus 119 ~t~f~~~l~~~~~~~~~~~v~r~~~~--~~~~l~~~d~IfiPIn~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~l~~~ 196 (294)
||||+++|....++.+|.+|+||+++ .+.+++++|+||||||.+.||+|+|||+++++|.|||||++.+...
T Consensus 334 NTFFytkL~~~~~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~~~v------ 407 (490)
T PLN03189 334 NTFFYKKLVSGKSGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRDPKI------ 407 (490)
T ss_pred ehHHHHHHhhcCCcCChHHHHHHhhhcccccccccCceEEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCCHHH------
Confidence 99999999987666789999999983 3467999999999999999999999999999999999999876554
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCCCcceeccCCccCCCCCCCCcHHHHHHhhHhhccccCCCC-CCCcHHHHHHHHHHH
Q 022637 197 LAILASLDFVLRQEARALFCNQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSY-QHDSDHARLLLALYL 275 (294)
Q Consensus 197 ~~i~~~l~~~l~~e~~~k~~~~~~~~~w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~~~~-~~d~~~~R~~l~~~l 275 (294)
++.|..|+..|+.++.+.+++.+.|......++|||.||+|||||||+||++|+.+.+..| |.||+.+|++|++||
T Consensus 408 ---L~~L~rYL~~E~kdK~g~d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrRma~EI 484 (490)
T PLN03189 408 ---LDALAKYYVDEVKDKSEKDIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLRTAKEI 484 (490)
T ss_pred ---HHHHHHHHHHHHhhhcCCCcchhcceeccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHHHHHHH
Confidence 7889999999999998889999999886668999999999999999999999987766666 467999999999999
Q ss_pred HcCC
Q 022637 276 VQSP 279 (294)
Q Consensus 276 ~~~~ 279 (294)
+...
T Consensus 485 l~~r 488 (490)
T PLN03189 485 LRLK 488 (490)
T ss_pred HHhh
Confidence 8654
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.3e-43 Score=319.66 Aligned_cols=199 Identities=20% Similarity=0.311 Sum_probs=174.3
Q ss_pred cceeeecCCeEEehhhhcccCCCCcccHHHHHHHHHHHhhhhhhhccCCCceEEccchHHHHhhccccccchhhhhhhhh
Q 022637 64 MEIVVDIGDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRD 143 (294)
Q Consensus 64 ~~~l~~~~~~~l~~~dl~~L~~~~wLnD~vI~~~~~~ll~~~~~~~~~~~~~~~~~t~f~~~l~~~~~~~~~~~v~r~~~ 143 (294)
...++..+++.||.+|+.+|.+++||||+|||||+++ +.++.......+++|+|+||||++|.+ .||++|+||++
T Consensus 372 ~~~~~~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~-ls~~sk~~s~~~~vh~FnTFFYT~Lsr----rGy~gVrrW~k 446 (578)
T COG5160 372 CYPFNDRSSIEITNQDFKRLRNGDWLNDTIIDFYMKL-LSKISKNTSKREQVHLFNTFFYTKLSR----RGYSGVRRWTK 446 (578)
T ss_pred cccccCcCcceeehHhhhhhccccchhhHHHHHHHHH-HHHhccCcccccceEEeehhhHHHHHH----HHhHHHHHHHh
Confidence 3556778899999999999999999999999999999 766655555688999999999999998 89999999999
Q ss_pred hcccCCCCCCeeEeeecCCCceeEEEEeecCceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHhhCCCCCCCc
Q 022637 144 RYMSRLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLN 223 (294)
Q Consensus 144 ~~~~~l~~~d~IfiPIn~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k~~~~~~~~~ 223 (294)
+.++|+.++||||||-..||+|+|||.+++.|.|||||++..... ++.|+.|+.+|++...++ +.
T Consensus 447 --k~dif~~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v---------~~~L~~Y~ldE~k~~~~k----~~ 511 (578)
T COG5160 447 --KTDIFSKKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPV---------LEFLRSYLLDEYKIQHDK----DP 511 (578)
T ss_pred --ccCccccceEEEEecccceEEEEEeecCcceeEEecccccCcHHH---------HHHHHHHHHHHHhcccCC----ch
Confidence 999999999999999999999999999999999999999987554 889999999997755433 33
Q ss_pred ceeccCCccCCCCCCCCcHHHHHHhhHhhccccCCCCC-CCcHHHHHHHHHHHHcCCcHH
Q 022637 224 FQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSYQ-HDSDHARLLLALYLVQSPLNK 282 (294)
Q Consensus 224 w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~~~~~-~d~~~~R~~l~~~l~~~~~n~ 282 (294)
|......+||||.||+|||||||+++++...+.+..|. .|++.+|++|+..|+...+|.
T Consensus 512 ~~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~~qi~y 571 (578)
T COG5160 512 QIKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKDLQINY 571 (578)
T ss_pred hhhhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHHHHHHH
Confidence 54446789999999999999999999998766555553 568999999999999887764
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=100.00 E-value=2.8e-32 Score=235.41 Aligned_cols=188 Identities=26% Similarity=0.451 Sum_probs=137.1
Q ss_pred CcccHHHHHHHHHHHhhhhhh-hccCCCceEEccchHHHHhhccc----------------cccchhhhhhhhhh-cccC
Q 022637 87 EWIDGDIITMYADYKNMKEAE-KDVTSPRCWFLPTYYSQAALADW----------------SSLNFAQAAGFRDR-YMSR 148 (294)
Q Consensus 87 ~wLnD~vI~~~~~~ll~~~~~-~~~~~~~~~~~~t~f~~~l~~~~----------------~~~~~~~v~r~~~~-~~~~ 148 (294)
+||||+|||+|+++ +.++.. .....+++++++|+|++.+...- ....+.++.+|++. ...+
T Consensus 1 ~wLnd~iId~y~~~-l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (216)
T PF02902_consen 1 EWLNDSIIDFYLEY-LRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKKN 79 (216)
T ss_dssp --EEHHHHHHHHHH-HHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTST
T ss_pred CcCCHHHHHHHHHH-HHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhcccccc
Confidence 69999999999999 664321 23468999999999999988210 01345678888873 2348
Q ss_pred CCCCCeeEeeecC-CCceeEEEEeecCceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHhhCCCCCCCcceec
Q 022637 149 LDTCEKIYVPINS-DGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQIC 227 (294)
Q Consensus 149 l~~~d~IfiPIn~-~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k~~~~~~~~~w~~~ 227 (294)
++++++||+|||. ++||+|+|||++.++|++||||++..... . ....+..+..+|...+........+.++|...
T Consensus 80 l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~-~---~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 155 (216)
T PF02902_consen 80 LFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNNDK-R---YKRVIENIIPFLKREYKKKEGRDPDKSPFKIV 155 (216)
T ss_dssp GGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-H-H---HHHHHHHHHHHHHHHHHHHHSSCT-TTTCEEE
T ss_pred ccccCEEEEEEechhhccceeEEcccccEEEEEeccccccccc-c---chhhhhhhhhhhhhccccccccccccceeeec
Confidence 9999999999996 99999999999999999999999997711 1 22336777888877776666555567788876
Q ss_pred cCCccCCCCCCCCcHHHHHHhhHhhccccCCC----C-CCCcHHHHHHHHHHHHcCC
Q 022637 228 RQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDS----Y-QHDSDHARLLLALYLVQSP 279 (294)
Q Consensus 228 ~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~~~----~-~~d~~~~R~~l~~~l~~~~ 279 (294)
...++|||.|++|||+|||+||+++..+.... + +.++..+|.+++.++....
T Consensus 156 ~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~~i~~~r~~~a~~~~e~~ 212 (216)
T PF02902_consen 156 RPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQELTEEDIKNFRKKLAVDLYEEL 212 (216)
T ss_dssp EECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCSBTGHHHHHHHHHHHH------
T ss_pred ccccccCCCCCCCcHHHHHHHHHHHHhCCCCcccccCCHHHHHHHHHHHHhhccccc
Confidence 67799999999999999999999997554433 2 2468899999998776443
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.98 E-value=6.4e-32 Score=223.78 Aligned_cols=193 Identities=22% Similarity=0.310 Sum_probs=146.2
Q ss_pred cceeeecCCeEEehhhhcccCCCCcccHHHHHHHHHHHhhhhhhhccCCCceEEccchHHHHhhccccccchhhhhhhhh
Q 022637 64 MEIVVDIGDNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEKDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRD 143 (294)
Q Consensus 64 ~~~l~~~~~~~l~~~dl~~L~~~~wLnD~vI~~~~~~ll~~~~~~~~~~~~~~~~~t~f~~~l~~~~~~~~~~~v~r~~~ 143 (294)
+.++.++.++.++.+|+..|.++.|+||.+|+||.+| +..+... ..+..++++|.....+.... ..+.++.+..
T Consensus 8 ~pv~Lsy~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~-l~~~~~~--s~~~~~ll~P~~t~~l~~~~---~~~e~~~~~~ 81 (223)
T KOG3246|consen 8 DPVVLSYFDVSLRQSDVDLLQPPEWLNDRLIDFYYEY-LEHRRSR--SEPDLHLLRPSLTFFLRHAP---NPEEIAMVLD 81 (223)
T ss_pred CceEEEeeehhhhhhhhhhcCCCchhhhhHHHHHHHH-HHHhhcc--cCcchhccCHHHHHHHHhCC---CcHHHHHhcC
Confidence 4478899999999999999999999999999999999 5544322 23347999998777666632 3355666655
Q ss_pred hcccCCCCCCeeEeeec---------CCCceeEEEEeecCceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHh
Q 022637 144 RYMSRLDTCEKIYVPIN---------SDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARAL 214 (294)
Q Consensus 144 ~~~~~l~~~d~IfiPIn---------~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k 214 (294)
..++.++++||+||| +|+||+|+|++.++++++||||+.+.|... +..++++++.+++.....
T Consensus 82 --pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~-----a~~l~~kl~~ll~~~~~~- 153 (223)
T KOG3246|consen 82 --PLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKD-----AKSLMKKLRALLKKKFAK- 153 (223)
T ss_pred --hhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHH-----HHHHHHHHHHHHhhhhhh-
Confidence 668999999999999 457999999999999999999999998877 455578888877654211
Q ss_pred hCCCCCCCcceeccCCccCCCCCCCCcHHHHHHhhHhhccccCC-----CCCCCcHHHHHHHHHHHHcCCcHHHHHHHHH
Q 022637 215 FCNQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHD-----SYQHDSDHARLLLALYLVQSPLNKIRCRLIQ 289 (294)
Q Consensus 215 ~~~~~~~~~w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~~-----~~~~d~~~~R~~l~~~l~~~~~n~~R~~~~~ 289 (294)
. ....+|||.||||||+|||.+.+.++..... .++.+.+. .++.+|.++..
T Consensus 154 ---------~---~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~------------~i~~lr~~l~~ 209 (223)
T KOG3246|consen 154 ---------R---VECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVD------------LIKALREELLD 209 (223)
T ss_pred ---------c---ccccChhhhcCCchhHHHHHHHHHHHHHHhccccccccchhhHH------------HHHHHHHHHHH
Confidence 1 1578999999999999999999988753221 12222233 34556777777
Q ss_pred HHHhC
Q 022637 290 EARKL 294 (294)
Q Consensus 290 ~i~~~ 294 (294)
+|..|
T Consensus 210 LI~sl 214 (223)
T KOG3246|consen 210 LIQSL 214 (223)
T ss_pred HHHHh
Confidence 66543
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.40 E-value=1.4e-13 Score=134.49 Aligned_cols=175 Identities=14% Similarity=0.158 Sum_probs=120.9
Q ss_pred CeEEehhhhcccCCCCcccHHHHHHHHHHHhhhhhhh-ccCCCceEEccchHHHHhhcccc--c------cchhhhhhhh
Q 022637 72 DNSITRSSMRTLLPGEWIDGDIITMYADYKNMKEAEK-DVTSPRCWFLPTYYSQAALADWS--S------LNFAQAAGFR 142 (294)
Q Consensus 72 ~~~l~~~dl~~L~~~~wLnD~vI~~~~~~ll~~~~~~-~~~~~~~~~~~t~f~~~l~~~~~--~------~~~~~v~r~~ 142 (294)
.+.++..|+.||.++..|||.+++||+++ +...... +...+.+++|+++|+..+.+... + .....+++|+
T Consensus 352 ~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~-i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~ 430 (595)
T KOG0779|consen 352 SHQVNNNDLVCLEEGEFLNDTIKDFYLEY-IRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWT 430 (595)
T ss_pred ccceeccchhhccccchhhhhhhhhhhHH-HHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeee
Confidence 44789999999999999999999999999 5443322 56789999999999998877532 1 1345677788
Q ss_pred hhcccCCCCCCeeEeeecCCCceeEEEEeecCc------eEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHhhC
Q 022637 143 DRYMSRLDTCEKIYVPINSDGHWYMLVVDISHA------TATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFC 216 (294)
Q Consensus 143 ~~~~~~l~~~d~IfiPIn~~~HW~L~vv~~~~~------~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k~~ 216 (294)
+ ..+++.+++|++|+|...||.+++++.+.. ....++++....... +.+.+...+..++.....
T Consensus 431 ~--~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~ 500 (595)
T KOG0779|consen 431 R--HFDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLILKLSADFP--------IVENILDFMKVASIYNNE 500 (595)
T ss_pred e--ccccccceeEEecCchHhhhhccccccCccccCccccchhhhhhccccccc--------hhhhhhhhhhhcccccCc
Confidence 8 999999999999999999999999987754 344445444443332 133344455544333211
Q ss_pred C------CCCCCcceec-----cCCccCCCCCCCCcHHHHHHhhHhhccccC
Q 022637 217 N------QFTFLNFQIC-----RQAGLPQQPNGFDCGYYVMKYMDSPCIVVH 257 (294)
Q Consensus 217 ~------~~~~~~w~~~-----~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~ 257 (294)
. +++..-|... .....|||.|..|||+|++.|++......+
T Consensus 501 ~~~~~~~~~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~ 552 (595)
T KOG0779|consen 501 LIVTEDLELEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAP 552 (595)
T ss_pred ccccccccccccccccCcccccccccccCccCcccchhhHHHHHHHhhhChh
Confidence 1 1111111110 112238999999999999999998754333
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=97.84 E-value=2.9e-05 Score=70.51 Aligned_cols=102 Identities=11% Similarity=0.111 Sum_probs=68.4
Q ss_pred CCCCCCeeEeeecCCCceeEEEEeecCceEEEecCCCCC---------------------Cchh-hhhHHHHHHHHHHHH
Q 022637 148 RLDTCEKIYVPINSDGHWYMLVVDISHATATIWDSLESP---------------------SRRE-KMINESLAILASLDF 205 (294)
Q Consensus 148 ~l~~~d~IfiPIn~~~HW~L~vv~~~~~~i~~~DSl~~~---------------------~~~~-~~l~~~~~i~~~l~~ 205 (294)
.--+..++.+|++..+||.++|+|.+++-+.+|||-|.. +... ..+.++-.-++.|.+
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 345678999999999999999999999999999999862 1100 111111112466777
Q ss_pred HHHHHHHHhhCCCCCCCcceeccCCccCCCCCCCCcHHHHHHhhHhhccccCCCC
Q 022637 206 VLRQEARALFCNQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPCIVVHDSY 260 (294)
Q Consensus 206 ~l~~e~~~k~~~~~~~~~w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~~~~~~~~~ 260 (294)
++.+....+. .-+ .---.|-..++||+|++-||-..+...+..+
T Consensus 307 fF~d~f~~~~--------gci---NvevnQl~eseCGMF~~iFm~~c~~~ppk~f 350 (423)
T PF03290_consen 307 FFEDSFGVKY--------GCI---NVEVNQLLESECGMFISIFMILCTLTPPKGF 350 (423)
T ss_pred HHHhhcccce--------eEE---EhhhhhhcccccchHHHHHHHHHHccCchhH
Confidence 7766542221 111 1123588899999999999998776555544
No 8
>PRK11836 deubiquitinase; Provisional
Probab=97.13 E-value=0.0019 Score=56.94 Aligned_cols=102 Identities=17% Similarity=0.226 Sum_probs=56.5
Q ss_pred cCCCCCCeeEeeecCCCceeEEEEe--------ecCceEEEecCCCCCCchh-hhhHHHHHHHHHHHH-HHHHHHHHhhC
Q 022637 147 SRLDTCEKIYVPINSDGHWYMLVVD--------ISHATATIWDSLESPSRRE-KMINESLAILASLDF-VLRQEARALFC 216 (294)
Q Consensus 147 ~~l~~~d~IfiPIn~~~HW~L~vv~--------~~~~~i~~~DSl~~~~~~~-~~l~~~~~i~~~l~~-~l~~e~~~k~~ 216 (294)
...+-++.=+||||.++||.|+++. .++.+..+|.|+..-+... ..+ +.|++.... .+.+....+..
T Consensus 214 ~~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~---q~ii~a~~~~~~~~~~~~~ik 290 (403)
T PRK11836 214 DPSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSL---KRVINSFNSELMGEMSNNNIK 290 (403)
T ss_pred CCCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHH---HHHHHhhhhhhhhhcchhhhc
Confidence 3455678889999999999999863 2355788899988764442 111 112222222 22222222211
Q ss_pred CCCCCCcceeccCCccCCCCCCCCcHHHHHHhhHhhc
Q 022637 217 NQFTFLNFQICRQAGLPQQPNGFDCGYYVMKYMDSPC 253 (294)
Q Consensus 217 ~~~~~~~w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~~ 253 (294)
. ...+=++.+...--||.=...||.|+|+.++.+.
T Consensus 291 ~--~~~e~ei~fie~dLQq~vpngCGlFv~~a~Qe~i 325 (403)
T PRK11836 291 V--HLTEPEIIFLHADLQQYLSQSCGAFVCMAAQEVI 325 (403)
T ss_pred c--cccCCceEEEechhhhcCCCccceehHHHHHHHH
Confidence 1 1112222222223355556689999999988443
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=96.97 E-value=0.0016 Score=56.29 Aligned_cols=83 Identities=11% Similarity=0.089 Sum_probs=47.2
Q ss_pred eEeeecCCCceeEEEEee--cCceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHhhCCCCCCCcceeccCCcc
Q 022637 155 IYVPINSDGHWYMLVVDI--SHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQICRQAGL 232 (294)
Q Consensus 155 IfiPIn~~~HW~L~vv~~--~~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k~~~~~~~~~w~~~~~~~~ 232 (294)
=+||||.++||.|+++.. .+.+..+|.|+..-+... ++.+.. . ..+.+.. + +=++.+...-
T Consensus 191 evF~INtg~HWil~~~~Ki~~kiKC~iFNs~~~l~eNs---------~~~ii~---~--ak~ag~~-~--e~di~fIe~n 253 (317)
T PRK14848 191 EVFLINTGDHWLLCLFYKLAEKIKCLIFNTYYDLNENT---------KQEIIE---A--AKIAGIS-E--NEDVNFIETN 253 (317)
T ss_pred eEEEecCCCcEEEEEhHHhhhhceEEEeecHhhhhhhH---------HHHHHH---H--HHhhCcc-c--CCceEEeehh
Confidence 349999999999998642 245677888888765332 111111 0 1111110 0 1111122223
Q ss_pred CCCCCCCCcHHHHHHhhHhhcc
Q 022637 233 PQQPNGFDCGYYVMKYMDSPCI 254 (294)
Q Consensus 233 PqQ~Ng~DCGvfvl~~~e~~~~ 254 (294)
-||.=...||.|+|.+++.+..
T Consensus 254 LQqnVpngCGlFv~~aIq~l~~ 275 (317)
T PRK14848 254 LQNNVPNGCGLFCYHTIQLLSN 275 (317)
T ss_pred hhhhCCCcchHHHHHHHHHHHh
Confidence 3455556899999999997754
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=96.71 E-value=0.0042 Score=50.76 Aligned_cols=90 Identities=16% Similarity=0.232 Sum_probs=42.4
Q ss_pred CCCceeEEEEeecCceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHH-hhCCCCCCCcceeccCCccCCCCCCC
Q 022637 161 SDGHWYMLVVDISHATATIWDSLESPSRREKMINESLAILASLDFVLRQEARA-LFCNQFTFLNFQICRQAGLPQQPNGF 239 (294)
Q Consensus 161 ~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~-k~~~~~~~~~w~~~~~~~~PqQ~Ng~ 239 (294)
+|.||.-+..|++.++++.+|..|-++.+-+.+..- + -...|+...-. ..+. -.+++...+.-|=.++-
T Consensus 32 GGvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~qiY~F-e----Ye~llrRSAL~~~~dR-----Cv~LvkstqtVQ~p~Sa 101 (183)
T PF00770_consen 32 GGVHWLAFAWDPRSRTFYMFDPFGFSDQKLKQIYQF-E----YEGLLRRSALSSTPDR-----CVTLVKSTQTVQCPCSA 101 (183)
T ss_dssp --S-EEEEEEETTTTEEEEE-TT---HHHHHHHH---------HHHHHHHHHHH-TTS-----EEEEEEE-EE-S-TT--
T ss_pred CceeEEEEEecCCcceEEEeCCCCCCHHHHHHHHhh-h----HHHHHHHHhhcCCCCc-----eEEEEeccceeeccCch
Confidence 788999999999999999999999886553221110 0 11111111100 0011 12223334455666788
Q ss_pred CcHHHHHHhhHhhccccCCCC
Q 022637 240 DCGYYVMKYMDSPCIVVHDSY 260 (294)
Q Consensus 240 DCGvfvl~~~e~~~~~~~~~~ 260 (294)
.||+|.|.|+..+......++
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 999999999988754444333
No 11
>PRK15371 effector protein YopJ; Provisional
Probab=90.70 E-value=5.1 Score=36.01 Aligned_cols=136 Identities=13% Similarity=0.160 Sum_probs=67.0
Q ss_pred cCCCCcccHH--HHHHHHHHHhhhhhhhccCCCceEEccc--hHHHHhhccccccchhhhhhhhhhcccCCCCCCeeEee
Q 022637 83 LLPGEWIDGD--IITMYADYKNMKEAEKDVTSPRCWFLPT--YYSQAALADWSSLNFAQAAGFRDRYMSRLDTCEKIYVP 158 (294)
Q Consensus 83 L~~~~wLnD~--vI~~~~~~ll~~~~~~~~~~~~~~~~~t--~f~~~l~~~~~~~~~~~v~r~~~~~~~~l~~~d~IfiP 158 (294)
|..|.|++.. .+|...--+|.+..+.+...-+..+|++ -|+..+.... -.++..|. .+
T Consensus 39 ~~~G~~~~~~~~~~Di~~lp~lv~~~N~r~P~LNL~~f~s~~~f~~aik~~~----~~g~~~~R--------------~I 100 (287)
T PRK15371 39 IADGSWIHKNYARTDLEVMPALVAQANNKYPEMNLKLVTSPLDLSIEIKETI----ENGVESSR--------------FI 100 (287)
T ss_pred HHcCCCCCchhHHhhHHhhHHHHHHHhccCCCCCeeecCCHHHHHHHHHHHh----hcccccce--------------eE
Confidence 5577888743 3343322214443333323445666664 4444444311 01222222 23
Q ss_pred ecCCCc-eeEEEEeec----CceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHhhCCCCCCCcceeccCCccC
Q 022637 159 INSDGH-WYMLVVDIS----HATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQICRQAGLP 233 (294)
Q Consensus 159 In~~~H-W~L~vv~~~----~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k~~~~~~~~~w~~~~~~~~P 233 (294)
||.+.| +-.+++|.+ +.+|..++|-...+... +.. .-.+...|..+ .+.-..|.+ ...-
T Consensus 101 Vn~g~~~~H~vavDvr~~~Gk~SIIvlEPa~~~~~~~-----a~l-~~rl~~~le~~-------~l~~~~~av---ie~d 164 (287)
T PRK15371 101 VNMGSGGIHFSVIDYKHIDGKTSLILFEPANFNSMGP-----AML-AIRTKTALERE-------QLPDCHFSM---VEMD 164 (287)
T ss_pred EeCCCCcceEEEEEEeccCCCeEEEEECCccccccch-----HHH-HHHHHHHHHhc-------cCCCceEEE---Eecc
Confidence 442333 444455543 34799999977653322 100 01122222211 022233433 5567
Q ss_pred CCCCCCCcHHHHHHhhHhh
Q 022637 234 QQPNGFDCGYYVMKYMDSP 252 (294)
Q Consensus 234 qQ~Ng~DCGvfvl~~~e~~ 252 (294)
-|+-.+|||+|.+.++...
T Consensus 165 ~QkS~~dC~mFSL~~AkK~ 183 (287)
T PRK15371 165 IQRSSSECGIFSLALAKKL 183 (287)
T ss_pred cccCcccchhhhHHHHHHH
Confidence 7999999999999999876
No 12
>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=81.28 E-value=12 Score=31.37 Aligned_cols=81 Identities=14% Similarity=0.217 Sum_probs=46.3
Q ss_pred eEeeec-CCCceeEEEEeec-----CceEEEecCCCCCCchhhhhHHHHHHHHHHHHHHHHHHHHhhCCCCCCCcceecc
Q 022637 155 IYVPIN-SDGHWYMLVVDIS-----HATATIWDSLESPSRREKMINESLAILASLDFVLRQEARALFCNQFTFLNFQICR 228 (294)
Q Consensus 155 IfiPIn-~~~HW~L~vv~~~-----~~~i~~~DSl~~~~~~~~~l~~~~~i~~~l~~~l~~e~~~k~~~~~~~~~w~~~~ 228 (294)
.++|+. .+.|... +|.+ +..+.+++|-.-.+.... + ....+.+.+ ...+... .+.+ .
T Consensus 74 ~Iv~~~~~~~H~~a--~Dvr~~~~~k~SlI~~Epa~~~~~~~~-l-------~~~~~~~~~-~~~~~~~-----~~~~-~ 136 (177)
T PF03421_consen 74 AIVNLGGDGIHHVA--LDVRHTPNGKPSLIVFEPASFYGMKPA-L-------AGYTKLAEE-ARQKLLP-----NAKF-A 136 (177)
T ss_pred EEEeCCCCCCcEEE--EEEeecCCCCceEEEEccccccCCcch-h-------hhHHHHHHH-HHhccCC-----CcEE-E
Confidence 355544 4556554 4544 457999999876654431 1 111111111 1111111 2333 2
Q ss_pred CCccCCCCCCCCcHHHHHHhhHhh
Q 022637 229 QAGLPQQPNGFDCGYYVMKYMDSP 252 (294)
Q Consensus 229 ~~~~PqQ~Ng~DCGvfvl~~~e~~ 252 (294)
.....-|+..+|||+|.+.++...
T Consensus 137 ~ie~diQkS~~dC~IFsLs~AkK~ 160 (177)
T PF03421_consen 137 VIEMDIQKSPSDCGIFSLSLAKKM 160 (177)
T ss_pred EEecccccCcCcchhhHHHHHHHH
Confidence 477889999999999999999876
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=42.98 E-value=58 Score=34.62 Aligned_cols=34 Identities=26% Similarity=0.579 Sum_probs=27.4
Q ss_pred Eeeec-------CCCceeEEEEeecCceEEEecCCCCCCchh
Q 022637 156 YVPIN-------SDGHWYMLVVDISHATATIWDSLESPSRRE 190 (294)
Q Consensus 156 fiPIn-------~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~ 190 (294)
|+||. ..+||..+ |--+.+..+.||.||..++..
T Consensus 49 fmpvltgv~p~~~sghwiml-ikg~gn~y~lfdplg~~sg~~ 89 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIML-IKGQGNQYYLFDPLGKTSGEG 89 (1439)
T ss_pred CceeecCcCCCCcCceeEEE-EEcCCCceEEecccccccccc
Confidence 67776 67899876 456788999999999987665
No 14
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=34.92 E-value=28 Score=26.43 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=24.0
Q ss_pred cceeccCCccCCCCCCCCcHHHHHHhhHhh
Q 022637 223 NFQICRQAGLPQQPNGFDCGYYVMKYMDSP 252 (294)
Q Consensus 223 ~w~~~~~~~~PqQ~Ng~DCGvfvl~~~e~~ 252 (294)
.|.+.-...+|--..|.|||.|-..++++.
T Consensus 18 r~p~tds~~~p~~~q~r~cg~FE~e~~eC~ 47 (120)
T KOG4110|consen 18 RWPTTDSTEQPYKHQGRDCGKFEKEWMECA 47 (120)
T ss_pred hccccccccCccccccccccHHHHHHHHHH
Confidence 566555567787777899999999999976
No 15
>PF07797 DUF1639: Protein of unknown function (DUF1639); InterPro: IPR012438 This approximately 50-residue region is found in a number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre.
Probab=25.28 E-value=36 Score=22.10 Aligned_cols=46 Identities=11% Similarity=0.176 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHhccCCCCcceeeecCCeEEehhhhcccCCCCcccHHH
Q 022637 45 ISEDAKQLILYLFDDKLNTMEIVVDIGDNSITRSSMRTLLPGEWIDGDI 93 (294)
Q Consensus 45 ls~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~~dl~~L~~~~wLnD~v 93 (294)
||.+|+..--.++..+.++... ...-..-...+.+|.||.||.+--
T Consensus 1 Lsr~EieeDf~am~G~kpprRP---kKRpk~Vqk~ld~lfPG~wL~~vt 46 (50)
T PF07797_consen 1 LSRKEIEEDFLAMTGSKPPRRP---KKRPKNVQKQLDSLFPGLWLSEVT 46 (50)
T ss_pred CCHHHHHHHHHHHhCCCCCCCC---CcccHHHHHHHhhcCcchhhhhcC
Confidence 5667776655665444333222 112222345677889999997743
No 16
>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=44 Score=25.51 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=13.8
Q ss_pred cCCCCCCCCcHHHHHHhhHhh
Q 022637 232 LPQQPNGFDCGYYVMKYMDSP 252 (294)
Q Consensus 232 ~PqQ~Ng~DCGvfvl~~~e~~ 252 (294)
+-.|.+..|||+-++.++-..
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 446889999999999987654
No 17
>COG3242 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.37 E-value=99 Score=21.01 Aligned_cols=24 Identities=25% Similarity=0.165 Sum_probs=21.5
Q ss_pred CcHHHHHHHHHHHHcCCcHHHHHH
Q 022637 263 DSDHARLLLALYLVQSPLNKIRCR 286 (294)
Q Consensus 263 d~~~~R~~l~~~l~~~~~n~~R~~ 286 (294)
--|..++||+.++..-+.|.+|..
T Consensus 22 l~P~~wkk~~~~l~~lpd~~LR~~ 45 (62)
T COG3242 22 LAPRAWKKMATALLELPDNQLRRF 45 (62)
T ss_pred cChHHHHHHHHHHHHCCHHHHHHH
Confidence 458999999999999999999975
No 18
>PF13280 WYL: WYL domain
Probab=21.26 E-value=77 Score=25.07 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=19.0
Q ss_pred CeeEeeec---CCCceeEEEEeecCc
Q 022637 153 EKIYVPIN---SDGHWYMLVVDISHA 175 (294)
Q Consensus 153 d~IfiPIn---~~~HW~L~vv~~~~~ 175 (294)
...+.|+. .+++|+|+..|...+
T Consensus 29 ~~~v~P~~l~~~~~~~Yl~~~~~~~~ 54 (172)
T PF13280_consen 29 ERRVDPYRLYYYNGRWYLIAYDRERE 54 (172)
T ss_pred EEEEEEEEEEEECCEEEEEEEecccc
Confidence 66788888 888999999987654
Done!