Query 041329
Match_columns 384
No_of_seqs 223 out of 413
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 06:01:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041329.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041329hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09331 DUF1985: Domain of un 100.0 6.1E-45 1.3E-49 321.0 8.8 137 75-217 1-142 (142)
2 KOG0778 Protease, Ulp1 family 100.0 3.2E-32 7E-37 278.1 10.3 178 193-383 321-511 (511)
3 PLN03189 Protease specific for 99.9 9.8E-28 2.1E-32 243.6 7.0 95 286-382 395-489 (490)
4 COG5160 ULP1 Protease, Ulp1 fa 99.8 5.9E-21 1.3E-25 193.6 0.9 173 193-383 384-570 (578)
5 PF02902 Peptidase_C48: Ulp1 p 99.6 4.9E-15 1.1E-19 136.4 6.7 89 287-377 111-208 (216)
6 KOG3246 Sentrin-specific cyste 98.7 4.3E-08 9.4E-13 91.1 7.0 82 286-378 123-208 (223)
7 PF10536 PMD: Plant mobile dom 98.6 6.6E-08 1.4E-12 97.3 5.7 182 56-262 2-194 (363)
8 KOG0778 Protease, Ulp1 family 85.9 0.28 6E-06 51.9 0.5 86 197-310 359-444 (511)
9 KOG0779 Protease, Ulp1 family 81.4 1.1 2.4E-05 48.6 2.9 40 333-373 528-580 (595)
10 PRK14848 deubiquitinase SseL; 39.8 42 0.00092 32.8 4.3 27 329-356 250-276 (317)
11 PF03421 YopJ: YopJ Serine/Thr 35.3 27 0.00059 32.0 2.2 26 331-357 139-164 (177)
12 KOG4110 NADH:ubiquinone oxidor 33.7 36 0.00079 29.0 2.5 61 321-382 16-95 (120)
13 PF03290 Peptidase_C57: Vaccin 26.0 44 0.00095 34.5 2.0 49 299-360 301-349 (423)
14 KOG1769 Ubiquitin-like protein 23.0 98 0.0021 26.0 3.2 41 57-102 30-72 (99)
No 1
>PF09331 DUF1985: Domain of unknown function (DUF1985); InterPro: IPR015410 This domain is functionally uncharacterised; it is found in a set of Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.
Probab=100.00 E-value=6.1e-45 Score=320.98 Aligned_cols=137 Identities=36% Similarity=0.575 Sum_probs=127.1
Q ss_pred HHHHhhhcccccCCcceeEEEcceeeeeehhhhhhhhccccCCCCccchh--hh---HHHhhhhhcCCcccccchHHHHH
Q 041329 75 LLLRQVAHEEDSREDQLWFQIGEHLIRLSIVEWCLVTGLSFGVDTKRKID--EM---EERLRNTYFGGVHRKINVNEFDA 149 (384)
Q Consensus 75 lL~Rql~~~~~~K~~E~W~v~~G~PIRfsl~Ef~lvTGL~C~~~p~~~~~--~~---~~~~~~~lFg~~~~~~tv~~v~~ 149 (384)
||+||+ +|+|++|+||+|||+||||||+|||+||||||+++|+.+.. .+ +.++|+++|| .+++||++||++
T Consensus 1 lL~rql---~~~k~~e~W~~~~g~piRfsl~Ef~lvTGL~C~~~p~~~~~~~~~~~~~~~fw~~Lf~-~~~~vtv~dv~~ 76 (142)
T PF09331_consen 1 LLLRQL---VTEKKYEIWFVFNGVPIRFSLREFALVTGLNCGPYPKEKKVDKKGKKEKGSFWNKLFG-REEDVTVEDVIA 76 (142)
T ss_pred CCceee---eccCCceEEEEECCEeeEecHHHHHhhcCCcCCCCCcccchhhccccchhhhhhhhcc-ccccCcHHHHHH
Confidence 689999 99999999999999999999999999999999999985432 22 2289999999 578999999999
Q ss_pred HHHhhhccccCchhhhHHHHHhhhhheeecCCCCCCCChhhhhhhhchhhhhcCCchhHHHHHHHHHH
Q 041329 150 VFKELKFEEMDDMDALKIALFYFADIVLNARNNHCQINFDWLDEVDDIEYFRKCPWGLLSWKMIYESL 217 (384)
Q Consensus 150 ~L~~~~~~~~~~~~rlrla~L~~v~gvll~~~~~~~i~~~~~~~v~Dle~f~~yPWGr~aF~~lm~~I 217 (384)
+|++++ .+++++|+|+|+|+|++|||+|++++++|+.++++||+|+|+|++|||||+||+.||++|
T Consensus 77 ~L~~~~--~~~~~~Rlrla~L~~v~gvl~~~~~~~~i~~~~~~~v~Dl~~f~~yPWGr~sF~~~~~sI 142 (142)
T PF09331_consen 77 KLKKMK--KWDSEDRLRLALLLFVDGVLIATSKTTKIPKEHLKMVDDLEKFLNYPWGRYSFDMLMKSI 142 (142)
T ss_pred HHhhcc--cCChhhHHHHHHHHhhheeeeccCCCCCCCHHHHHHHhhHHHHhcCCcHHHHHHHHHhcC
Confidence 999986 689999999999999999999999999999999999999999999999999999999976
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=3.2e-32 Score=278.09 Aligned_cols=178 Identities=19% Similarity=0.195 Sum_probs=141.2
Q ss_pred hhhchhhhhcCCchhHHHHHHHHHHhhhhhcchhhhhhccccCCCCCccceecccchhh--h--hhhhhccccCCCCCCC
Q 041329 193 EVDDIEYFRKCPWGLLSWKMIYESLDNALFEKDEKFKRTRLKNPDHNIEKYNLYGFTSG--V--QVFLNQLWNNGDCAVD 268 (384)
Q Consensus 193 ~v~Dle~f~~yPWGr~aF~~lm~~Ik~~~~~~~~~y~~~kl~~~~~~~~~y~l~GF~~~--L--ql~a~e~~p~~~~~v~ 268 (384)
..+|+..+..+-|=.. ..++-....+. .+.++.++-+..|+++.|.++ . .+-++++|++++++++
T Consensus 321 t~~dl~tl~~~~WLND---evINfYm~ll~--------ers~~~~~yp~~h~FnTFFy~kL~~~gy~~VkRWTk~v~if~ 389 (511)
T KOG0778|consen 321 TGKDLQTLRPGNWLND---EVINFYMELLK--------ERSKKDSKYPKVHAFNTFFYTKLVGRGYAGVKRWTKKVDIFD 389 (511)
T ss_pred cHHHHhhccCccchhH---HHHHHHHHHHH--------hhccccCCCceEEEEechhhhhhhhcchHHHHhHhhccCccc
Confidence 4589999999999776 45554444442 111121223345666666553 2 4456899999887776
Q ss_pred cc---cccccceeeeeccce------eeccCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCcccccccCCCCCCCCC
Q 041329 269 SL---VFDDRLNSYLCGRQH------TMSKSMTDVDMPLEVIFPRWLEYVGFYNIRPELRSADPWKVIAVKSAPQQEPGT 339 (384)
Q Consensus 269 n~---~f~er~I~y~~~~i~------~~~DS~g~~~~~~~~~l~~yL~~E~~~~k~~~~~~~~~W~~~~~~~~P~Q~N~g 339 (384)
.. +..+..|||.-..|+ .||||||+.....+++|++||++|+ .+|++.++|.++|.++..+++|||.| |
T Consensus 390 ~d~i~vPIH~~vHW~l~vid~r~k~i~y~DS~~~~~nr~~~aL~~Yl~~E~-~~k~~~~~d~s~w~~~~~~~iP~Q~N-g 467 (511)
T KOG0778|consen 390 KDIIFVPIHLGVHWCLAVIDLREKTIEYYDSLGGGPNRICDALAKYLQDES-RDKSKKDFDVSGWTIEFVQNIPQQRN-G 467 (511)
T ss_pred cceeEeeeecCceEEEEEEEcccceEEEeeccCCCCcchHHHHHHHHHHHH-hhhhcCCCCccchhhhhhhccccccC-C
Confidence 42 456677888644444 7899999665555599999999999 99999999999999999999999999 9
Q ss_pred CCchhHHHHHHHHHhcCCCcccCccchHHHHHHHHHHHHcCccc
Q 041329 340 GDCGVFVLMVTMYLMFGLRLEFNASHVEYFRKKIAVDIFNDDIV 383 (384)
Q Consensus 340 ~DCGVF~c~~a~~ls~~~~~~Fsq~dmp~~R~~m~~Ei~~~~l~ 383 (384)
+|||||+||||+|+++|.|++|||+|||+||++||+||++++|.
T Consensus 468 ~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR~~m~~eI~~~~l~ 511 (511)
T KOG0778|consen 468 SDCGMFVCKYADYISRDVPLTFTQQDMPYFRKKMAKEILHLKLL 511 (511)
T ss_pred CccceEEeeechhhccCCCcccChhhhHHHHHHHHHHHHhhhcC
Confidence 99999999999999999999999999999999999999999874
No 3
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=99.94 E-value=9.8e-28 Score=243.61 Aligned_cols=95 Identities=21% Similarity=0.326 Sum_probs=90.8
Q ss_pred eeccCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCcccccccCCCCCCCCCCCchhHHHHHHHHHhcCCCcccCccc
Q 041329 286 TMSKSMTDVDMPLEVIFPRWLEYVGFYNIRPELRSADPWKVIAVKSAPQQEPGTGDCGVFVLMVTMYLMFGLRLEFNASH 365 (384)
Q Consensus 286 ~~~DS~g~~~~~~~~~l~~yL~~E~~~~k~~~~~~~~~W~~~~~~~~P~Q~N~g~DCGVF~c~~a~~ls~~~~~~Fsq~d 365 (384)
.+|||||+.+..+++.|++||.+|+ ++|++.+++.++|+.....++|||.| |+|||||+|+||+|+++|.+++|+|+|
T Consensus 395 ~yyDSLgg~~~~vL~~L~rYL~~E~-kdK~g~d~D~s~W~~~~~~~vPQQ~N-G~DCGVFVL~yAE~~SrG~~LtFSQeD 472 (490)
T PLN03189 395 QYLDSLKGRDPKILDALAKYYVDEV-KDKSEKDIDVSSWEQEFVEDLPEQKN-GYDCGMFMIKYIDFYSRGLGLCFGQEH 472 (490)
T ss_pred EEEeCCCCCCHHHHHHHHHHHHHHH-hhhcCCCcchhcceeccCCCCCCCCC-CCCHHHHHHHHHHHHcCCCCCCcChhh
Confidence 4669999999999999999999999 99999999999999887789999999 999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHcCcc
Q 041329 366 VEYFRKKIAVDIFNDDI 382 (384)
Q Consensus 366 mp~~R~~m~~Ei~~~~l 382 (384)
||++|+||++||++.++
T Consensus 473 Mp~fRrRma~EIl~~r~ 489 (490)
T PLN03189 473 MPYFRLRTAKEILRLKA 489 (490)
T ss_pred hHHHHHHHHHHHHHhhc
Confidence 99999999999998875
No 4
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.80 E-value=5.9e-21 Score=193.64 Aligned_cols=173 Identities=17% Similarity=0.153 Sum_probs=123.4
Q ss_pred hhhchhhhhcCCchhHH-HHHHHHHHhhhhhcchhhhhhccccCCCCCccceecccchhh-h---hhhhhccccCCCCCC
Q 041329 193 EVDDIEYFRKCPWGLLS-WKMIYESLDNALFEKDEKFKRTRLKNPDHNIEKYNLYGFTSG-V---QVFLNQLWNNGDCAV 267 (384)
Q Consensus 193 ~v~Dle~f~~yPWGr~a-F~~lm~~Ik~~~~~~~~~y~~~kl~~~~~~~~~y~l~GF~~~-L---ql~a~e~~p~~~~~v 267 (384)
...|+..+.+=.|=... -+--|+-|+... +..-+..+.+.++.|.+- | .+-.+++|+++++.+
T Consensus 384 T~~D~~~L~~~~wLNDtIIdFy~k~ls~~s------------k~~s~~~~vh~FnTFFYT~LsrrGy~gVrrW~kk~dif 451 (578)
T COG5160 384 TNQDFKRLRNGDWLNDTIIDFYMKLLSKIS------------KNTSKREQVHLFNTFFYTKLSRRGYSGVRRWTKKTDIF 451 (578)
T ss_pred ehHhhhhhccccchhhHHHHHHHHHHHHhc------------cCcccccceEEeehhhHHHHHHHHhHHHHHHHhccCcc
Confidence 35788888888886541 112222222221 111223355677777552 3 333477899887776
Q ss_pred Ccc-c--ccccceeeeeccce------eeccCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCcccccccCCCCCCCC
Q 041329 268 DSL-V--FDDRLNSYLCGRQH------TMSKSMTDVDMPLEVIFPRWLEYVGFYNIRPELRSADPWKVIAVKSAPQQEPG 338 (384)
Q Consensus 268 ~n~-~--f~er~I~y~~~~i~------~~~DS~g~~~~~~~~~l~~yL~~E~~~~k~~~~~~~~~W~~~~~~~~P~Q~N~ 338 (384)
++. + ...-..||+..-|. .|||||++....+++.|+.|+.+|. +. ..+.++|......++|||.|
T Consensus 452 ~~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y~ldE~-k~----~~~k~~~~~~~~~~vPqQ~N- 525 (578)
T COG5160 452 SKKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSYLLDEY-KI----QHDKDPQIKMKHCKVPQQRN- 525 (578)
T ss_pred ccceEEEEecccceEEEEEeecCcceeEEecccccCcHHHHHHHHHHHHHHH-hc----ccCCchhhhhhcCCCCCCCC-
Confidence 542 1 22224455522111 6889999999999999999999998 43 44556687777789999999
Q ss_pred CCCchhHHHHHHHHHhcCCCcccCccchHHHHHHHHHHHHcCccc
Q 041329 339 TGDCGVFVLMVTMYLMFGLRLEFNASHVEYFRKKIAVDIFNDDIV 383 (384)
Q Consensus 339 g~DCGVF~c~~a~~ls~~~~~~Fsq~dmp~~R~~m~~Ei~~~~l~ 383 (384)
|+|||||+||+++|.+.+.|..|++.|||.+|++|+++|++.+|.
T Consensus 526 g~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~~qi~ 570 (578)
T COG5160 526 GSDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKDLQIN 570 (578)
T ss_pred CCccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999987763
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=99.55 E-value=4.9e-15 Score=136.39 Aligned_cols=89 Identities=25% Similarity=0.370 Sum_probs=75.0
Q ss_pred eccCCCCCCc-----hHHHHHHHHHHHhcccccCCCCCCCCCcccccccCCCCCCCCCCCchhHHHHHHHHHhcCCCcc-
Q 041329 287 MSKSMTDVDM-----PLEVIFPRWLEYVGFYNIRPELRSADPWKVIAVKSAPQQEPGTGDCGVFVLMVTMYLMFGLRLE- 360 (384)
Q Consensus 287 ~~DS~g~~~~-----~~~~~l~~yL~~E~~~~k~~~~~~~~~W~~~~~~~~P~Q~N~g~DCGVF~c~~a~~ls~~~~~~- 360 (384)
+||||++... .++..+..||..+. .++.+...+.++|......++|||.| ++|||||+|+|+++++.+.+.+
T Consensus 111 ~~DSl~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~pqQ~n-~~dCGv~vl~~~~~~~~~~~~~~ 188 (216)
T PF02902_consen 111 VYDSLGSSNNDKRYKRVIENIIPFLKREY-KKKEGRDPDKSPFKIVRPPNVPQQPN-GYDCGVYVLKFMECLLEGPSFDF 188 (216)
T ss_dssp EE-TTSTSSH-HHHHHHHHHHHHHHHHHH-HHHHSSCT-TTTCEEEEECTS-SSSS-SSCHHHHHHHHHHHHHCTHHSTG
T ss_pred EEeccccccccccchhhhhhhhhhhhhcc-ccccccccccceeeecccccccCCCC-CCCcHHHHHHHHHHHHhCCCCcc
Confidence 4499999999 78899999999887 66666666778998887889999999 9999999999999999998877
Q ss_pred ---cCccchHHHHHHHHHHH
Q 041329 361 ---FNASHVEYFRKKIAVDI 377 (384)
Q Consensus 361 ---Fsq~dmp~~R~~m~~Ei 377 (384)
|+|+||+.+|++|+.+|
T Consensus 189 ~~~l~~~~i~~~r~~~a~~~ 208 (216)
T PF02902_consen 189 SQELTEEDIKNFRKKLAVDL 208 (216)
T ss_dssp CCSBTGHHHHHHHHHHHH--
T ss_pred cccCCHHHHHHHHHHHHhhc
Confidence 79999999999999654
No 6
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=98.67 E-value=4.3e-08 Score=91.07 Aligned_cols=82 Identities=15% Similarity=0.015 Sum_probs=60.1
Q ss_pred eeccCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCcccccccCCCCCCCCCCCchhHHHHHHHHH----hcCCCccc
Q 041329 286 TMSKSMTDVDMPLEVIFPRWLEYVGFYNIRPELRSADPWKVIAVKSAPQQEPGTGDCGVFVLMVTMYL----MFGLRLEF 361 (384)
Q Consensus 286 ~~~DS~g~~~~~~~~~l~~yL~~E~~~~k~~~~~~~~~W~~~~~~~~P~Q~N~g~DCGVF~c~~a~~l----s~~~~~~F 361 (384)
.+|||+++.|....+.+.+=+.+-- .++.. ......+|||+| |||||+++|.+++.| +++.--+=
T Consensus 123 ~hyDS~~n~nt~~a~~l~~kl~~ll--~~~~~--------~~~~~~~~qQqN-gyDCG~hV~~~t~~l~~~~~~~~~~~~ 191 (223)
T KOG3246|consen 123 YHYDSLSNGNTKDAKSLMKKLRALL--KKKFA--------KRVECKCLQQQN-GYDCGLHVCCNTRVLAERLLRCPYATS 191 (223)
T ss_pred EEeecccCCCcHHHHHHHHHHHHHH--hhhhh--------hcccccChhhhc-CCchhHHHHHHHHHHHHHHhccccccc
Confidence 5799999999988877776666553 22111 111557899999 999999999886654 55554557
Q ss_pred CccchHHHHHHHHHHHH
Q 041329 362 NASHVEYFRKKIAVDIF 378 (384)
Q Consensus 362 sq~dmp~~R~~m~~Ei~ 378 (384)
+|.+.+.+|+++..||.
T Consensus 192 ~~~~~~~~i~~lr~~l~ 208 (223)
T KOG3246|consen 192 SQLLVVDLIKALREELL 208 (223)
T ss_pred cchhhHHHHHHHHHHHH
Confidence 78888889988887765
No 7
>PF10536 PMD: Plant mobile domain; InterPro: IPR019557 This entry represents a domain found in a variety of transposases [].
Probab=98.57 E-value=6.6e-08 Score=97.28 Aligned_cols=182 Identities=14% Similarity=0.172 Sum_probs=125.5
Q ss_pred cccceecc--ccccchHHHHHHHHHhhhcccccCCcceeEEEcceeeeeehhhhhhhhccccCCCCccc-hhhhHHHhhh
Q 041329 56 FGHFLECQ--SFSFSRVILHNLLLRQVAHEEDSREDQLWFQIGEHLIRLSIVEWCLVTGLSFGVDTKRK-IDEMEERLRN 132 (384)
Q Consensus 56 Fg~ll~~~--~~~~s~k~~h~lL~Rql~~~~~~K~~E~W~v~~G~PIRfsl~Ef~lvTGL~C~~~p~~~-~~~~~~~~~~ 132 (384)
||-+..+. .......++-.|.-|== ...+- |++.+-.+..+|+++++++|||+.+.|-.. ...+...+..
T Consensus 2 ~g~~~~i~~s~~~~~~~li~al~erW~-----~et~t--F~~~~gEmtiTL~DV~~llGLpi~G~pv~~~~~~~~~~~~~ 74 (363)
T PF10536_consen 2 FGILDAIMASRITIDRSLISALVERWD-----PETNT--FHFPWGEMTITLEDVAMLLGLPIDGRPVTGPLPPDWRDLCE 74 (363)
T ss_pred chhHhhhhhhcCCCCHHHHHHHHHHhC-----cccCe--eecccccccchhhhhhhccccccccccccCccccchhhHHH
Confidence 56666665 55666667766544443 22345 999999999999999999999998776421 1111233333
Q ss_pred hhcCC-------cccccchHHHHHHHHhhhccccCchhhhHHHHHhhhhheeecCCCCC-CCChhhhhhhhchhhhhcCC
Q 041329 133 TYFGG-------VHRKINVNEFDAVFKELKFEEMDDMDALKIALFYFADIVLNARNNHC-QINFDWLDEVDDIEYFRKCP 204 (384)
Q Consensus 133 ~lFg~-------~~~~~tv~~v~~~L~~~~~~~~~~~~rlrla~L~~v~gvll~~~~~~-~i~~~~~~~v~Dle~f~~yP 204 (384)
.|.|. ....++...+.+.+.+.. .++++...-|+|+...|.++.+++.. .|+..++.++.|++...+|.
T Consensus 75 ~ll~~~~~~~~~~~~~~~~~wl~~~~~~~~---~~d~~~~~rAFll~~lg~~lfp~~~~~~v~~~~l~~~~~l~~~~~~~ 151 (363)
T PF10536_consen 75 ELLGVSPQIKSKKGSSIRLSWLEEFFSNRP---EDDEEQYHRAFLLYWLGSFLFPDKSGDYVSPRYLPLAVDLARIKRYA 151 (363)
T ss_pred HHhcccccccccccccchhhheeccccccc---cchHHHHHHHHHHHhhhceeccCCCcceeeeeEEeeeeccccccccc
Confidence 44332 112244444445442221 11223566888888888888877766 89999999999999999999
Q ss_pred chhHHHHHHHHHHhhhhhcchhhhhhccccCCCCCccceecccchhhhhhhhhccccC
Q 041329 205 WGLLSWKMIYESLDNALFEKDEKFKRTRLKNPDHNIEKYNLYGFTSGVQVFLNQLWNN 262 (384)
Q Consensus 205 WGr~aF~~lm~~Ik~~~~~~~~~y~~~kl~~~~~~~~~y~l~GF~~~Lql~a~e~~p~ 262 (384)
||..+...+.+++.++.. +.. ....+.|....||+|+.|++|.
T Consensus 152 wg~a~La~ly~~L~~~~~---------~~~------~~~~~~g~~~llq~W~werf~~ 194 (363)
T PF10536_consen 152 WGSAVLAYLYRDLCKASR---------KSA------SQSNIGGPLWLLQLWAWERFPV 194 (363)
T ss_pred cHHHHHHHHHHHHHHHhh---------hcc------cccccccceeeeccchhheeec
Confidence 999999999998886531 110 2357899999999999999885
No 8
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=85.86 E-value=0.28 Score=51.85 Aligned_cols=86 Identities=8% Similarity=0.064 Sum_probs=70.1
Q ss_pred hhhhhcCCchhHHHHHHHHHHhhhhhcchhhhhhccccCCCCCccceecccchhhhhhhhhccccCCCCCCCcccccccc
Q 041329 197 IEYFRKCPWGLLSWKMIYESLDNALFEKDEKFKRTRLKNPDHNIEKYNLYGFTSGVQVFLNQLWNNGDCAVDSLVFDDRL 276 (384)
Q Consensus 197 le~f~~yPWGr~aF~~lm~~Ik~~~~~~~~~y~~~kl~~~~~~~~~y~l~GF~~~Lql~a~e~~p~~~~~v~n~~f~er~ 276 (384)
+++|.+| .|..|.. ++++-+++|+++++.+.+.-.+.|+++.+ ||+ .+|.+ ..++.
T Consensus 359 ~h~FnTF-----Fy~kL~~------------~gy~~VkRWTk~v~if~~d~i~vPIH~~v--HW~---l~vid--~r~k~ 414 (511)
T KOG0778|consen 359 VHAFNTF-----FYTKLVG------------RGYAGVKRWTKKVDIFDKDIIFVPIHLGV--HWC---LAVID--LREKT 414 (511)
T ss_pred EEEEech-----hhhhhhh------------cchHHHHhHhhccCccccceeEeeeecCc--eEE---EEEEE--cccce
Confidence 4677776 7777743 44567789999999999999999999844 999 77665 79999
Q ss_pred eeeeeccceeeccCCCCCCchHHHHHHHHHHHhc
Q 041329 277 NSYLCGRQHTMSKSMTDVDMPLEVIFPRWLEYVG 310 (384)
Q Consensus 277 I~y~~~~i~~~~DS~g~~~~~~~~~l~~yL~~E~ 310 (384)
|.||+ ++++.-+.....+++.|.+.-.+.+
T Consensus 415 i~y~D----S~~~~~nr~~~aL~~Yl~~E~~~k~ 444 (511)
T KOG0778|consen 415 IEYYD----SLGGGPNRICDALAKYLQDESRDKS 444 (511)
T ss_pred EEEee----ccCCCCcchHHHHHHHHHHHHhhhh
Confidence 99994 5778888999889999999987776
No 9
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=81.35 E-value=1.1 Score=48.56 Aligned_cols=40 Identities=33% Similarity=0.492 Sum_probs=32.6
Q ss_pred CCCCCCCCCchhHHHHHHHHHhcCCCcc-------------cCccchHHHHHHH
Q 041329 333 PQQEPGTGDCGVFVLMVTMYLMFGLRLE-------------FNASHVEYFRKKI 373 (384)
Q Consensus 333 P~Q~N~g~DCGVF~c~~a~~ls~~~~~~-------------Fsq~dmp~~R~~m 373 (384)
|||.| .+|||+|+..|++....+.+-. |.+.++-.+|..+
T Consensus 528 p~q~n-~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~ 580 (595)
T KOG0779|consen 528 PQQNN-DVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEI 580 (595)
T ss_pred cCccC-cccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhh
Confidence 89999 9999999999999887775543 7777777777654
No 10
>PRK14848 deubiquitinase SseL; Provisional
Probab=39.80 E-value=42 Score=32.79 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=20.6
Q ss_pred ccCCCCCCCCCCCchhHHHHHHHHHhcC
Q 041329 329 VKSAPQQEPGTGDCGVFVLMVTMYLMFG 356 (384)
Q Consensus 329 ~~~~P~Q~N~g~DCGVF~c~~a~~ls~~ 356 (384)
.+.--||.- ..-||.|+|++++-|+..
T Consensus 250 Ie~nLQqnV-pngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 250 IETNLQNNV-PNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred eehhhhhhC-CCcchHHHHHHHHHHHhc
Confidence 333345555 889999999999988766
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=35.30 E-value=27 Score=32.04 Aligned_cols=26 Identities=23% Similarity=0.381 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCchhHHHHHHHHHhcCC
Q 041329 331 SAPQQEPGTGDCGVFVLMVTMYLMFGL 357 (384)
Q Consensus 331 ~~P~Q~N~g~DCGVF~c~~a~~ls~~~ 357 (384)
++.-|.. .+|||+|..-+|..+....
T Consensus 139 e~diQkS-~~dC~IFsLs~AkK~~~~~ 164 (177)
T PF03421_consen 139 EMDIQKS-PSDCGIFSLSLAKKMYKED 164 (177)
T ss_pred ecccccC-cCcchhhHHHHHHHHhhcc
Confidence 6788999 9999999999999987654
No 12
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=33.68 E-value=36 Score=29.00 Aligned_cols=61 Identities=20% Similarity=0.302 Sum_probs=42.1
Q ss_pred CCCcccccccCCCCCCCCCCCchhHHHHHHHHH-----hcCCC---c---cc-----CccchH---HHHHHHHHHHHcCc
Q 041329 321 ADPWKVIAVKSAPQQEPGTGDCGVFVLMVTMYL-----MFGLR---L---EF-----NASHVE---YFRKKIAVDIFNDD 381 (384)
Q Consensus 321 ~~~W~~~~~~~~P~Q~N~g~DCGVF~c~~a~~l-----s~~~~---~---~F-----sq~dmp---~~R~~m~~Ei~~~~ 381 (384)
...|.+......|.-.- |.|||-|--++.||. .+|.. + +| -|+.|. .+|++-...|+.|+
T Consensus 16 ~~r~p~tds~~~p~~~q-~r~cg~FE~e~~eC~eayG~~~g~keC~ie~~dFqECv~~qKqmrra~aiR~qr~Kl~leGk 94 (120)
T KOG4110|consen 16 IDRWPTTDSTEQPYKHQ-GRDCGKFEKEWMECAEAYGLERGEKECAIEYDDFQECVLMQKQMRRAHAIRKQRYKLILEGK 94 (120)
T ss_pred hhhccccccccCccccc-cccccHHHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 35788876778898888 999999988888875 33422 1 12 344443 46777777788876
Q ss_pred c
Q 041329 382 I 382 (384)
Q Consensus 382 l 382 (384)
.
T Consensus 95 ~ 95 (120)
T KOG4110|consen 95 Y 95 (120)
T ss_pred c
Confidence 4
No 13
>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=26.02 E-value=44 Score=34.47 Aligned_cols=49 Identities=12% Similarity=0.116 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhcccccCCCCCCCCCcccccccCCCCCCCCCCCchhHHHHHHHHHhcCCCcc
Q 041329 299 EVIFPRWLEYVGFYNIRPELRSADPWKVIAVKSAPQQEPGTGDCGVFVLMVTMYLMFGLRLE 360 (384)
Q Consensus 299 ~~~l~~yL~~E~~~~k~~~~~~~~~W~~~~~~~~P~Q~N~g~DCGVF~c~~a~~ls~~~~~~ 360 (384)
.+.|.+++.++- ..+.| ...-=--|-- .+|||+|+|-|+-.....-|=.
T Consensus 301 IDVLfrfF~d~f-~~~~g-----------ciNvevnQl~-eseCGMF~~iFm~~c~~~ppk~ 349 (423)
T PF03290_consen 301 IDVLFRFFEDSF-GVKYG-----------CINVEVNQLL-ESECGMFISIFMILCTLTPPKG 349 (423)
T ss_pred hHHHHHHHHhhc-cccee-----------EEEhhhhhhc-ccccchHHHHHHHHHHccCchh
Confidence 467888888774 32222 1111134777 9999999999998888776633
No 14
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=22.97 E-value=98 Score=25.97 Aligned_cols=41 Identities=12% Similarity=0.160 Sum_probs=27.9
Q ss_pred ccceec--cccccchHHHHHHHHHhhhcccccCCcceeEEEcceeeee
Q 041329 57 GHFLEC--QSFSFSRVILHNLLLRQVAHEEDSREDQLWFQIGEHLIRL 102 (384)
Q Consensus 57 g~ll~~--~~~~~s~k~~h~lL~Rql~~~~~~K~~E~W~v~~G~PIRf 102 (384)
|..++| .....-.|+|-. .|+.. -..-+++-|+|+|++|+=
T Consensus 30 ~~~~~Fkikr~t~LkKLM~a-Yc~r~----Gl~~~s~RFlFdG~rI~~ 72 (99)
T KOG1769|consen 30 GSVVVFKIKRHTPLKKLMKA-YCERQ----GLSMNSLRFLFDGQRIRE 72 (99)
T ss_pred CCEEEEEeecCChHHHHHHH-HHHHc----CCccceEEEEECCcCcCC
Confidence 444444 345666778866 56665 445589999999999874
Done!