Query 031417
Match_columns 160
No_of_seqs 114 out of 148
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 13:48:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031417.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031417hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03189 Protease specific for 99.9 2E-25 4.3E-30 203.3 7.4 131 10-145 349-488 (490)
2 KOG0778 Protease, Ulp1 family 99.9 3.5E-25 7.6E-30 202.7 3.4 122 18-144 384-508 (511)
3 KOG3246 Sentrin-specific cyste 99.8 2.9E-21 6.4E-26 161.6 5.8 135 9-160 71-214 (223)
4 PF02902 Peptidase_C48: Ulp1 p 99.7 1E-17 2.2E-22 130.5 7.1 125 18-156 77-207 (216)
5 COG5160 ULP1 Protease, Ulp1 fa 99.7 2.7E-18 5.8E-23 158.1 1.9 121 18-148 447-571 (578)
6 KOG0779 Protease, Ulp1 family 96.1 0.0039 8.5E-08 59.0 2.9 137 17-160 431-587 (595)
7 PRK11836 deubiquitinase; Provi 75.8 4.4 9.5E-05 36.9 4.4 25 98-122 304-328 (403)
8 PF03421 YopJ: YopJ Serine/Thr 72.5 4.4 9.6E-05 33.0 3.3 39 76-120 124-162 (177)
9 PRK14848 deubiquitinase SseL; 71.1 5.8 0.00013 35.3 3.9 23 98-120 253-275 (317)
10 PF03290 Peptidase_C57: Vaccin 34.9 22 0.00047 33.2 1.5 45 66-121 301-345 (423)
11 PRK15371 effector protein YopJ 26.0 45 0.00098 29.6 1.9 26 97-122 162-187 (287)
12 PHA01750 hypothetical protein 24.0 73 0.0016 23.1 2.3 24 133-156 31-54 (75)
13 cd00280 TRFH Telomeric Repeat 23.1 1.5E+02 0.0032 25.3 4.3 40 106-145 54-98 (200)
14 KOG4110 NADH:ubiquinone oxidor 22.2 2.2E+02 0.0048 22.4 4.8 28 90-117 19-46 (120)
15 smart00099 btg1 tob/btg1 famil 20.9 2.5E+02 0.0053 21.6 4.8 53 45-107 4-59 (108)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=99.92 E-value=2e-25 Score=203.31 Aligned_cols=131 Identities=21% Similarity=0.246 Sum_probs=107.6
Q ss_pred CchhHHhhc------cCCCCCceEEeecccccccchhhhhHHHHhHhhhhhhccCCCcchHHHHHHHHHHHHHHHhhcCC
Q 031417 10 DYKNMKEAE------KDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRYMGRLDTCEKLASLDFVLRQEARALFGN 83 (160)
Q Consensus 10 ~~~~~~~a~------~d~~~~~~~flpin~~~~~~~~~~~~~~~~~~~~~d~~~g~~d~~~~l~iL~~yl~~E~~~k~~~ 83 (160)
+|.++|+-. .++.+.+.||+|||.+ .||+.-++.+..+.+.|+||+.|....+ ++.|..|+.+|++++.+.
T Consensus 349 gY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n-~HWsLaVId~k~k~I~yyDSLgg~~~~v--L~~L~rYL~~E~kdK~g~ 425 (490)
T PLN03189 349 DYKAVRRWTTQKKLGYHLIDCDKIFVPIHQE-IHWTLAVINKKDQKFQYLDSLKGRDPKI--LDALAKYYVDEVKDKSEK 425 (490)
T ss_pred ChHHHHHHhhhcccccccccCceEEeeeecC-CeeEEEEEEcCCCeEEEEeCCCCCCHHH--HHHHHHHHHHHHhhhcCC
Confidence 456666433 3677889999999974 3555555566778899999999988876 789999999999999999
Q ss_pred CcccccceeeccCCCCCCCCCCCchHHHHHHHHHHhhhhcCCCccCchH---HHHHHHHHHhhcc
Q 031417 84 RFSFFNFQICCQAGVPQQPNGFDCGYYVMKYMDNLSIVVHDSYQHDSDH---ARLLLALYLVQSP 145 (160)
Q Consensus 84 ~~d~~~w~~~~~~~~PqQ~Ng~DCGVfV~~~~~~i~~~~~~~~~F~q~~---~R~~mv~eiv~~~ 145 (160)
++++++|......++|||.||+|||||||+||++++ ++.+++|+|.| +|++|++||++..
T Consensus 426 d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~S--rG~~LtFSQeDMp~fRrRma~EIl~~r 488 (490)
T PLN03189 426 DIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYS--RGLGLCFGQEHMPYFRLRTAKEILRLK 488 (490)
T ss_pred CcchhcceeccCCCCCCCCCCCCHHHHHHHHHHHHc--CCCCCCcChhhhHHHHHHHHHHHHHhh
Confidence 999999998767889999999999999999999885 56789999876 5777777777543
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=3.5e-25 Score=202.66 Aligned_cols=122 Identities=21% Similarity=0.246 Sum_probs=107.9
Q ss_pred ccCCCCCceEEeecccccccchhhhhHHHHhHhhhhhhccCCCcchHHHHHHHHHHHHHHHhhcCCCcccccceeeccCC
Q 031417 18 EKDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRYMGRLDTCEKLASLDFVLRQEARALFGNRFSFFNFQICCQAG 97 (160)
Q Consensus 18 ~~d~~~~~~~flpin~~~~~~~~~~~~~~~~~~~~~d~~~g~~d~~~~l~iL~~yl~~E~~~k~~~~~d~~~w~~~~~~~ 97 (160)
.+|.-+.+-||+||.. .-||+.-++.+-.+.+.|+||+.|..+.. ..+|..||.+|+.+|.+.++|+++|.++...+
T Consensus 384 ~v~if~~d~i~vPIH~-~vHW~l~vid~r~k~i~y~DS~~~~~nr~--~~aL~~Yl~~E~~~k~~~~~d~s~w~~~~~~~ 460 (511)
T KOG0778|consen 384 KVDIFDKDIIFVPIHL-GVHWCLAVIDLREKTIEYYDSLGGGPNRI--CDALAKYLQDESRDKSKKDFDVSGWTIEFVQN 460 (511)
T ss_pred ccCccccceeEeeeec-CceEEEEEEEcccceEEEeeccCCCCcch--HHHHHHHHHHHHhhhhcCCCCccchhhhhhhc
Confidence 3788888999999999 66899999999999999999999887775 58999999999999999999999999999899
Q ss_pred CCCCCCCCCchHHHHHHHHHHhhhhcCCCccCchH---HHHHHHHHHhhc
Q 031417 98 VPQQPNGFDCGYYVMKYMDNLSIVVHDSYQHDSDH---ARLLLALYLVQS 144 (160)
Q Consensus 98 ~PqQ~Ng~DCGVfV~~~~~~i~~~~~~~~~F~q~~---~R~~mv~eiv~~ 144 (160)
+|||.||+|||||||+|+++++ ++.|++|+|.+ ||++|++||+++
T Consensus 461 iP~Q~Ng~DCG~f~c~~~~~~s--~~~p~~ftq~dmp~fR~~m~~eI~~~ 508 (511)
T KOG0778|consen 461 IPQQRNGSDCGMFVCKYADYIS--RDVPLTFTQQDMPYFRKKMAKEILHL 508 (511)
T ss_pred cccccCCCccceEEeeechhhc--cCCCcccChhhhHHHHHHHHHHHHhh
Confidence 9999999999999999999885 78899999665 466666666644
No 3
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.83 E-value=2.9e-21 Score=161.64 Aligned_cols=135 Identities=22% Similarity=0.304 Sum_probs=92.6
Q ss_pred cCchhHHhhc-c-CCCCCceEEeecccccc-----cchhhhhHHHHhHhhhhhhc--cCCCcchHHHHHHHHHHHHHHHh
Q 031417 9 ADYKNMKEAE-K-DVTSPRCWFLPTYYSQA-----ALADWSSLNFAQAAGFRDRY--MGRLDTCEKLASLDFVLRQEARA 79 (160)
Q Consensus 9 ~~~~~~~~a~-~-d~~~~~~~flpin~~~~-----~~~~~~~~~~~~~~~~~d~~--~g~~d~~~~l~iL~~yl~~E~~~ 79 (160)
+|+..++.++ | |+.+-+.||+||||++. +|+|||||-+++.++=..|| .+.+++....+ +-+..++
T Consensus 71 ~~~~e~~~~~~pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~-----l~~kl~~ 145 (223)
T KOG3246|consen 71 PNPEEIAMVLDPLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKS-----LMKKLRA 145 (223)
T ss_pred CCcHHHHHhcChhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHH-----HHHHHHH
Confidence 5555555544 5 78999999999999974 48999999999988755555 33333332211 2233334
Q ss_pred hcCCCcccccceeeccCCCCCCCCCCCchHHHHHHHHHHhhhhcCCCccCchHHHHHHHHHHhhccHHHHHHHHHHHHHh
Q 031417 80 LFGNRFSFFNFQICCQAGVPQQPNGFDCGYYVMKYMDNLSIVVHDSYQHDSDHARLLLALYLVQSPLNKIRRRLIQEARK 159 (160)
Q Consensus 80 k~~~~~d~~~w~~~~~~~~PqQ~Ng~DCGVfV~~~~~~i~~~~~~~~~F~q~~~R~~mv~eiv~~~v~~mR~~~l~~i~~ 159 (160)
..++.+.. ..+..||||.||||||+|||++++.|+......-.-+ -++.++..-++++|+++..+|.+
T Consensus 146 ll~~~~~~-----~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~-------~~~~~~~~~i~~lr~~l~~LI~s 213 (223)
T KOG3246|consen 146 LLKKKFAK-----RVECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYAT-------SSQLLVVDLIKALREELLDLIQS 213 (223)
T ss_pred HHhhhhhh-----cccccChhhhcCCchhHHHHHHHHHHHHHHhcccccc-------ccchhhHHHHHHHHHHHHHHHHH
Confidence 44444431 1257899999999999999999999987642211100 23556678899999999999976
Q ss_pred C
Q 031417 160 L 160 (160)
Q Consensus 160 ~ 160 (160)
|
T Consensus 214 l 214 (223)
T KOG3246|consen 214 L 214 (223)
T ss_pred h
Confidence 4
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=99.72 E-value=1e-17 Score=130.55 Aligned_cols=125 Identities=23% Similarity=0.354 Sum_probs=87.3
Q ss_pred ccCCCCCceEEeecccccccchhhhhH---HHHhHhhhhhhccCCCc---chHHHHHHHHHHHHHHHhhcCCCcccccce
Q 031417 18 EKDVTSPRCWFLPTYYSQAALADWSSL---NFAQAAGFRDRYMGRLD---TCEKLASLDFVLRQEARALFGNRFSFFNFQ 91 (160)
Q Consensus 18 ~~d~~~~~~~flpin~~~~~~~~~~~~---~~~~~~~~~d~~~g~~d---~~~~l~iL~~yl~~E~~~k~~~~~d~~~w~ 91 (160)
..++...+.||+|||.+ +.||+++ +....+-++||+.+... ....+..+..++..+..+.....++...|.
T Consensus 77 ~~~l~~~~~i~iPin~~---~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 153 (216)
T PF02902_consen 77 KKNLFDKDYIFIPININ---NNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDPDKSPFK 153 (216)
T ss_dssp TSTGGGSSEEEEEEEET---TTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTCE
T ss_pred cccccccCEEEEEEech---hhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhccccccccccccceee
Confidence 34778889999999977 6677665 45667889999988777 112246777788888877777776777787
Q ss_pred eeccCCCCCCCCCCCchHHHHHHHHHHhhhhcCCCccCchHHHHHHHHHHhhccHHHHHHHHHHH
Q 031417 92 ICCQAGVPQQPNGFDCGYYVMKYMDNLSIVVHDSYQHDSDHARLLLALYLVQSPLNKIRRRLIQE 156 (160)
Q Consensus 92 ~~~~~~~PqQ~Ng~DCGVfV~~~~~~i~~~~~~~~~F~q~~~R~~mv~eiv~~~v~~mR~~~l~~ 156 (160)
.....++|||.||+|||||||+||+.++.+... .+.+. +.+..+..+|.++..+
T Consensus 154 ~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~--~~~~~---------l~~~~i~~~r~~~a~~ 207 (216)
T PF02902_consen 154 IVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSF--DFSQE---------LTEEDIKNFRKKLAVD 207 (216)
T ss_dssp EEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHS--TGCCS---------BTGHHHHHHHHHHHH-
T ss_pred ecccccccCCCCCCCcHHHHHHHHHHHHhCCCC--ccccc---------CCHHHHHHHHHHHHhh
Confidence 767789999999999999999999998765432 21110 2255566666666544
No 5
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.70 E-value=2.7e-18 Score=158.09 Aligned_cols=121 Identities=21% Similarity=0.196 Sum_probs=95.9
Q ss_pred ccCCCCCceEEeecccccccchhhhhHHHHhHhhhhhhccCCCcchHHHHHHHHHHHHHHHhhcC-CCcccccceeeccC
Q 031417 18 EKDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRYMGRLDTCEKLASLDFVLRQEARALFG-NRFSFFNFQICCQA 96 (160)
Q Consensus 18 ~~d~~~~~~~flpin~~~~~~~~~~~~~~~~~~~~~d~~~g~~d~~~~l~iL~~yl~~E~~~k~~-~~~d~~~w~~~~~~ 96 (160)
..|.-+.++||+|||. +.||..-.+.+-..++.|+||+.+..+.. +.-|+.|+.+|.+.-.+ ++| ....+.
T Consensus 447 k~dif~~k~I~iPIni-~~HW~l~II~~~~~~i~~~DSLan~~~~v--~~~L~~Y~ldE~k~~~~k~~~-----~~~~~~ 518 (578)
T COG5160 447 KTDIFSKKYIFIPINI-SYHWFLAIIDNPKKNILYFDSLANTHDPV--LEFLRSYLLDEYKIQHDKDPQ-----IKMKHC 518 (578)
T ss_pred ccCccccceEEEEecc-cceEEEEEeecCcceeEEecccccCcHHH--HHHHHHHHHHHHhcccCCchh-----hhhhcC
Confidence 5678888999999999 67999999999999999999999888775 78899999999886544 333 122468
Q ss_pred CCCCCCCCCCchHHHHHHHHHHhhhhcCCCccCchH---HHHHHHHHHhhccHHH
Q 031417 97 GVPQQPNGFDCGYYVMKYMDNLSIVVHDSYQHDSDH---ARLLLALYLVQSPLNK 148 (160)
Q Consensus 97 ~~PqQ~Ng~DCGVfV~~~~~~i~~~~~~~~~F~q~~---~R~~mv~eiv~~~v~~ 148 (160)
+||||.||+|||||||+++++.+ .+.|..|++++ +|+.|+-+|....+++
T Consensus 519 ~vPqQ~Ng~DCGV~vc~~~~~~~--~~~p~~f~~nd~~r~Rk~m~h~i~~~qi~y 571 (578)
T COG5160 519 KVPQQRNGSDCGVFVCMFIRYFL--ENPPEQFSKNDRPRARKNMAHTIKDLQINY 571 (578)
T ss_pred CCCCCCCCCccceEEEEeeeecc--cCChhhcCccchHHHHHHHHHHHHHHHHHH
Confidence 89999999999999998888664 56688888654 5666666666554443
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=96.12 E-value=0.0039 Score=59.00 Aligned_cols=137 Identities=13% Similarity=0.144 Sum_probs=67.3
Q ss_pred hccCCCCCceEEeecccccccchhhhhHHHHhHhhhhhhc--------cCCCcchHHHHHHHHHHHHHHHhhcCC----C
Q 031417 17 AEKDVTSPRCWFLPTYYSQAALADWSSLNFAQAAGFRDRY--------MGRLDTCEKLASLDFVLRQEARALFGN----R 84 (160)
Q Consensus 17 a~~d~~~~~~~flpin~~~~~~~~~~~~~~~~~~~~~d~~--------~g~~d~~~~l~iL~~yl~~E~~~k~~~----~ 84 (160)
+.+|...-.+||+|+|- .+||++--++....---++ .+-.+.+.........++.+....... +
T Consensus 431 ~~~d~~~k~yi~~P~~E----~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 506 (595)
T KOG0779|consen 431 RHFDLFNKDYVFVPTHE----RFHWKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTED 506 (595)
T ss_pred eccccccceeEEecCch----HhhhhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCccccccc
Confidence 56788999999999984 6788765443332222111 222222222222222233222221111 0
Q ss_pred cccccceee--------ccCCCCCCCCCCCchHHHHHHHHHHhhhhcCCCccCchHHHHHHHHHHhhccHHHHHHHHHHH
Q 031417 85 FSFFNFQIC--------CQAGVPQQPNGFDCGYYVMKYMDNLSIVVHDSYQHDSDHARLLLALYLVQSPLNKIRRRLIQE 156 (160)
Q Consensus 85 ~d~~~w~~~--------~~~~~PqQ~Ng~DCGVfV~~~~~~i~~~~~~~~~F~q~~~R~~mv~eiv~~~v~~mR~~~l~~ 156 (160)
.. ..|++. ...--|||.|.+|||+|+..|++......+ .++.-.+.=..-+..+.+....++|.++=.+
T Consensus 507 ~~-~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~--e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~ 583 (595)
T KOG0779|consen 507 LE-LEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAP--ERFNIEDEGTINLEWFPPKEILKFRDEIRNL 583 (595)
T ss_pred cc-ccccccccCcccccccccccCccCcccchhhHHHHHHHhhhChh--hhcccccccccccccCCchHHhhhhhhhhcc
Confidence 00 012221 011128999999999999999996654332 2211000000000023466677777777666
Q ss_pred HHhC
Q 031417 157 ARKL 160 (160)
Q Consensus 157 i~~~ 160 (160)
+|+|
T Consensus 584 ~~~l 587 (595)
T KOG0779|consen 584 GRKL 587 (595)
T ss_pred cccc
Confidence 6654
No 7
>PRK11836 deubiquitinase; Provisional
Probab=75.82 E-value=4.4 Score=36.88 Aligned_cols=25 Identities=20% Similarity=0.098 Sum_probs=18.9
Q ss_pred CCCCCCCCCchHHHHHHHHHHhhhh
Q 031417 98 VPQQPNGFDCGYYVMKYMDNLSIVV 122 (160)
Q Consensus 98 ~PqQ~Ng~DCGVfV~~~~~~i~~~~ 122 (160)
--||.=...||.|||+-+..+...+
T Consensus 304 dLQq~vpngCGlFv~~a~Qe~i~q~ 328 (403)
T PRK11836 304 DLQQYLSQSCGAFVCMAAQEVIEQR 328 (403)
T ss_pred hhhhcCCCccceehHHHHHHHHHHh
Confidence 3577777889999999888555444
No 8
>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=72.49 E-value=4.4 Score=32.96 Aligned_cols=39 Identities=21% Similarity=0.266 Sum_probs=27.8
Q ss_pred HHHhhcCCCcccccceeeccCCCCCCCCCCCchHHHHHHHHHHhh
Q 031417 76 EARALFGNRFSFFNFQICCQAGVPQQPNGFDCGYYVMKYMDNLSI 120 (160)
Q Consensus 76 E~~~k~~~~~d~~~w~~~~~~~~PqQ~Ng~DCGVfV~~~~~~i~~ 120 (160)
+...+.+..+.++ ..++.-|...+|||+|.+-+|...+.
T Consensus 124 ~~~~~~~~~~~~~------~ie~diQkS~~dC~IFsLs~AkK~~~ 162 (177)
T PF03421_consen 124 EARQKLLPNAKFA------VIEMDIQKSPSDCGIFSLSLAKKMYK 162 (177)
T ss_pred HHHhccCCCcEEE------EEecccccCcCcchhhHHHHHHHHhh
Confidence 3334334455543 25678999999999999998887764
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=71.06 E-value=5.8 Score=35.35 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=18.4
Q ss_pred CCCCCCCCCchHHHHHHHHHHhh
Q 031417 98 VPQQPNGFDCGYYVMKYMDNLSI 120 (160)
Q Consensus 98 ~PqQ~Ng~DCGVfV~~~~~~i~~ 120 (160)
--||.=...||.|||.+++.+..
T Consensus 253 nLQqnVpngCGlFv~~aIq~l~~ 275 (317)
T PRK14848 253 NLQNNVPNGCGLFCYHTIQLLSN 275 (317)
T ss_pred hhhhhCCCcchHHHHHHHHHHHh
Confidence 35777778899999999997654
No 10
>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=34.88 E-value=22 Score=33.22 Aligned_cols=45 Identities=13% Similarity=0.229 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhhcCCCcccccceeeccCCCCCCCCCCCchHHHHHHHHHHhhh
Q 031417 66 LASLDFVLRQEARALFGNRFSFFNFQICCQAGVPQQPNGFDCGYYVMKYMDNLSIV 121 (160)
Q Consensus 66 l~iL~~yl~~E~~~k~~~~~d~~~w~~~~~~~~PqQ~Ng~DCGVfV~~~~~~i~~~ 121 (160)
.++|..++.++...+. -+++ ++ --|--.+|||+|.+-||-.+.+.
T Consensus 301 IDVLfrfF~d~f~~~~----gciN----ve---vnQl~eseCGMF~~iFm~~c~~~ 345 (423)
T PF03290_consen 301 IDVLFRFFEDSFGVKY----GCIN----VE---VNQLLESECGMFISIFMILCTLT 345 (423)
T ss_pred hHHHHHHHHhhcccce----eEEE----hh---hhhhcccccchHHHHHHHHHHcc
Confidence 4677777766553321 1111 11 24888999999999999876544
No 11
>PRK15371 effector protein YopJ; Provisional
Probab=25.99 E-value=45 Score=29.63 Aligned_cols=26 Identities=15% Similarity=0.344 Sum_probs=21.6
Q ss_pred CCCCCCCCCCchHHHHHHHHHHhhhh
Q 031417 97 GVPQQPNGFDCGYYVMKYMDNLSIVV 122 (160)
Q Consensus 97 ~~PqQ~Ng~DCGVfV~~~~~~i~~~~ 122 (160)
.+--|.-.+|||+|.+-+|...+...
T Consensus 162 e~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 162 EMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred ecccccCcccchhhhHHHHHHHhhhh
Confidence 45679999999999999998776543
No 12
>PHA01750 hypothetical protein
Probab=23.96 E-value=73 Score=23.14 Aligned_cols=24 Identities=17% Similarity=0.120 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhccHHHHHHHHHHH
Q 031417 133 ARLLLALYLVQSPLNKIRRRLIQE 156 (160)
Q Consensus 133 ~R~~mv~eiv~~~v~~mR~~~l~~ 156 (160)
+-+..++|||++.+..+|.|+-..
T Consensus 31 ~lkdAvkeIV~~ELdNL~~ei~~~ 54 (75)
T PHA01750 31 ALKDAVKEIVNSELDNLKTEIEEL 54 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999997543
No 13
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=23.11 E-value=1.5e+02 Score=25.32 Aligned_cols=40 Identities=13% Similarity=0.183 Sum_probs=30.3
Q ss_pred CchHHHHHHHHHHhhhhcCCCccCchH-----HHHHHHHHHhhcc
Q 031417 106 DCGYYVMKYMDNLSIVVHDSYQHDSDH-----ARLLLALYLVQSP 145 (160)
Q Consensus 106 DCGVfV~~~~~~i~~~~~~~~~F~q~~-----~R~~mv~eiv~~~ 145 (160)
+|-+++|+|.-.|..|....-+|+.+. .=-.+++++....
T Consensus 54 ~k~l~i~QfLsRI~eG~~LD~~Fd~~~~~TPLESAl~v~~~I~~E 98 (200)
T cd00280 54 LKTLRIMQFLSRIAEGKNLDCQFENDEELTPLESALMVLESIEKE 98 (200)
T ss_pred hhHhHHHHHHHHHHcCCCCCCccCCCCCcChHHHHHHHHHHHHHh
Confidence 699999999999998888888899875 3444555555333
No 14
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=22.16 E-value=2.2e+02 Score=22.43 Aligned_cols=28 Identities=21% Similarity=0.489 Sum_probs=21.6
Q ss_pred ceeeccCCCCCCCCCCCchHHHHHHHHH
Q 031417 90 FQICCQAGVPQQPNGFDCGYYVMKYMDN 117 (160)
Q Consensus 90 w~~~~~~~~PqQ~Ng~DCGVfV~~~~~~ 117 (160)
|-+--...+|--.-|.|||-|-..++++
T Consensus 19 ~p~tds~~~p~~~q~r~cg~FE~e~~eC 46 (120)
T KOG4110|consen 19 WPTTDSTEQPYKHQGRDCGKFEKEWMEC 46 (120)
T ss_pred ccccccccCccccccccccHHHHHHHHH
Confidence 4433356789888999999999988874
No 15
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=20.89 E-value=2.5e+02 Score=21.62 Aligned_cols=53 Identities=19% Similarity=0.377 Sum_probs=37.0
Q ss_pred HHHhHhhhhhhcc---CCCcchHHHHHHHHHHHHHHHhhcCCCcccccceeeccCCCCCCCCCCCc
Q 031417 45 NFAQAAGFRDRYM---GRLDTCEKLASLDFVLRQEARALFGNRFSFFNFQICCQAGVPQQPNGFDC 107 (160)
Q Consensus 45 ~~~~~~~~~d~~~---g~~d~~~~l~iL~~yl~~E~~~k~~~~~d~~~w~~~~~~~~PqQ~Ng~DC 107 (160)
-++.|.+|..+|+ |..+.- .+++...-|.+...+++..-|. .+.|+--.||-|
T Consensus 4 EI~~av~Fl~~~l~~~~~l~~~-~v~~F~~~L~~~L~~~y~~HWy---------P~~P~kGqayRC 59 (108)
T smart00099 4 EIAAAVNFITSLLRKHNKLSKR-RVEIFAEKLTRLLKEKYKNHWY---------PEKPYKGSGFRC 59 (108)
T ss_pred HHHHHHHHHHHHHHHcCCCCHH-HHHHHHHHHHHHHHHHHhcCCC---------CCCCCCCcceEE
Confidence 4678999999997 433332 3456666666666677777775 567888888877
Done!