Query 034898
Match_columns 79
No_of_seqs 29 out of 31
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 07:29:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02902 Peptidase_C48: Ulp1 p 98.7 5.3E-08 1.1E-12 65.3 5.2 39 22-60 148-187 (216)
2 PLN03189 Protease specific for 97.3 0.00018 3.9E-09 59.9 3.3 48 7-54 407-461 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 96.5 0.00059 1.3E-08 58.0 -0.1 51 6-56 490-543 (578)
4 KOG3246 Sentrin-specific cyste 96.2 0.0053 1.2E-07 47.2 3.4 45 3-53 135-179 (223)
5 KOG0778 Protease, Ulp1 family 92.1 0.056 1.2E-06 45.5 0.6 52 5-56 426-484 (511)
6 PRK01242 rpl39e 50S ribosomal 45.0 21 0.00045 22.0 2.1 24 10-33 7-30 (50)
7 KOG0779 Protease, Ulp1 family 41.8 19 0.00041 30.6 2.0 37 34-70 528-570 (595)
8 PF13197 DUF4013: Protein of u 35.0 30 0.00066 23.4 1.8 27 45-71 21-47 (169)
9 PF11334 DUF3136: Protein of u 27.7 56 0.0012 21.2 2.1 23 47-69 14-38 (64)
10 PF05002 SGS: SGS domain ; In 24.8 66 0.0014 21.2 2.0 20 46-65 26-45 (82)
11 smart00413 ETS erythroblast tr 21.1 40 0.00086 22.6 0.5 20 48-69 6-25 (87)
12 COG4018 Uncharacterized protei 20.3 85 0.0018 26.9 2.3 28 31-58 306-346 (505)
No 1
>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=98.66 E-value=5.3e-08 Score=65.34 Aligned_cols=39 Identities=31% Similarity=0.651 Sum_probs=32.4
Q ss_pred CCCCceeEEe-cCCCCCCcccchhHHHHHHHHHHhcCccc
Q 034898 22 DRKSFVWKKV-KCPQQTTNVECGYYVIRFMKEIIESQDDS 60 (79)
Q Consensus 22 ~k~~~~Wi~~-kCprQ~gg~ECGYYVMr~M~~II~~~~~~ 60 (79)
+...++++.+ .||+|+++++||+|||+||..++.+....
T Consensus 148 ~~~~~~~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~ 187 (216)
T PF02902_consen 148 DKSPFKIVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFD 187 (216)
T ss_dssp -TTTCEEEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHST
T ss_pred ccceeeecccccccCCCCCCCcHHHHHHHHHHHHhCCCCc
Confidence 3567778887 99999999999999999999998887665
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=97.33 E-value=0.00018 Score=59.90 Aligned_cols=48 Identities=19% Similarity=0.450 Sum_probs=34.3
Q ss_pred HHHHhhHHHhhcCCCCC----CCceeE---EecCCCCCCcccchhHHHHHHHHHH
Q 034898 7 ILSAFKIFVAKMGNADR----KSFVWK---KVKCPQQTTNVECGYYVIRFMKEII 54 (79)
Q Consensus 7 i~salKi~v~~~~~~~k----~~~~Wi---~~kCprQ~gg~ECGYYVMr~M~~II 54 (79)
++..|+.|...+...+. ..-.|- ...+|+|.||+|||.||+.||..+.
T Consensus 407 vL~~L~rYL~~E~kdK~g~d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~S 461 (490)
T PLN03189 407 ILDALAKYYVDEVKDKSEKDIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYS 461 (490)
T ss_pred HHHHHHHHHHHHHhhhcCCCcchhcceeccCCCCCCCCCCCCHHHHHHHHHHHHc
Confidence 56677777766543221 223563 3589999999999999999998653
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=96.53 E-value=0.00059 Score=58.00 Aligned_cols=51 Identities=24% Similarity=0.460 Sum_probs=37.3
Q ss_pred HHHHHhhHHHhhcCCCC-CC--CceeEEecCCCCCCcccchhHHHHHHHHHHhc
Q 034898 6 YILSAFKIFVAKMGNAD-RK--SFVWKKVKCPQQTTNVECGYYVIRFMKEIIES 56 (79)
Q Consensus 6 ~i~salKi~v~~~~~~~-k~--~~~Wi~~kCprQ~gg~ECGYYVMr~M~~II~~ 56 (79)
.|+.-|+.|.-++.+.. .+ .+.-++.+||+|+||.|||-||+++......+
T Consensus 490 ~v~~~L~~Y~ldE~k~~~~k~~~~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~ 543 (578)
T COG5160 490 PVLEFLRSYLLDEYKIQHDKDPQIKMKHCKVPQQRNGSDCGVFVCMFIRYFLEN 543 (578)
T ss_pred HHHHHHHHHHHHHHhcccCCchhhhhhcCCCCCCCCCCccceEEEEeeeecccC
Confidence 45666777766665433 33 35667899999999999999999877665555
No 4
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=96.20 E-value=0.0053 Score=47.20 Aligned_cols=45 Identities=18% Similarity=0.298 Sum_probs=32.3
Q ss_pred hhHHHHHHhhHHHhhcCCCCCCCceeEEecCCCCCCcccchhHHHHHHHHH
Q 034898 3 ISNYILSAFKIFVAKMGNADRKSFVWKKVKCPQQTTNVECGYYVIRFMKEI 53 (79)
Q Consensus 3 isn~i~salKi~v~~~~~~~k~~~~Wi~~kCprQ~gg~ECGYYVMr~M~~I 53 (79)
.++.++.+++.|..+...+. .+-+|++|.||+|||-+||-+-..|
T Consensus 135 ~a~~l~~kl~~ll~~~~~~~------~~~~~~qQqNgyDCG~hV~~~t~~l 179 (223)
T KOG3246|consen 135 DAKSLMKKLRALLKKKFAKR------VECKCLQQQNGYDCGLHVCCNTRVL 179 (223)
T ss_pred HHHHHHHHHHHHHhhhhhhc------ccccChhhhcCCchhHHHHHHHHHH
Confidence 35667777777776543322 2678999999999999999765544
No 5
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=92.07 E-value=0.056 Score=45.52 Aligned_cols=52 Identities=27% Similarity=0.551 Sum_probs=35.5
Q ss_pred HHHHHHhhHHHhhcCC-CCCCCc---eeE--EecC-CCCCCcccchhHHHHHHHHHHhc
Q 034898 5 NYILSAFKIFVAKMGN-ADRKSF---VWK--KVKC-PQQTTNVECGYYVIRFMKEIIES 56 (79)
Q Consensus 5 n~i~salKi~v~~~~~-~~k~~~---~Wi--~~kC-prQ~gg~ECGYYVMr~M~~II~~ 56 (79)
|-|..||..|--.+.. ++++.+ -|. .++| |+|.||++||-||+.|-..|-.+
T Consensus 426 nr~~~aL~~Yl~~E~~~k~~~~~d~s~w~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~ 484 (511)
T KOG0778|consen 426 NRICDALAKYLQDESRDKSKKDFDVSGWTIEFVQNIPQQRNGSDCGMFVCKYADYISRD 484 (511)
T ss_pred cchHHHHHHHHHHHHhhhhcCCCCccchhhhhhhccccccCCCccceEEeeechhhccC
Confidence 4555666666555553 445555 563 3455 99999999999999888776543
No 6
>PRK01242 rpl39e 50S ribosomal protein L39e; Validated
Probab=44.99 E-value=21 Score=22.00 Aligned_cols=24 Identities=29% Similarity=0.339 Sum_probs=20.7
Q ss_pred HhhHHHhhcCCCCCCCceeEEecC
Q 034898 10 AFKIFVAKMGNADRKSFVWKKVKC 33 (79)
Q Consensus 10 alKi~v~~~~~~~k~~~~Wi~~kC 33 (79)
+.|++.+....+++..|+||..+-
T Consensus 7 ~~K~rLaK~~kQNrpvP~Wv~~KT 30 (50)
T PRK01242 7 GKKLRLAKALKQNRRVPAWVIVKT 30 (50)
T ss_pred HHHHHHHHHHhccCCCCeEEEEEc
Confidence 567888899999999999998764
No 7
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=41.77 E-value=19 Score=30.55 Aligned_cols=37 Identities=30% Similarity=0.657 Sum_probs=30.5
Q ss_pred CCCCCcccchhHHHHHHHHHHhcCcc------chhhhhhhhhh
Q 034898 34 PQQTTNVECGYYVIRFMKEIIESQDD------SIKKCVCWTRQ 70 (79)
Q Consensus 34 prQ~gg~ECGYYVMr~M~~II~~~~~------~i~~~~~~~~~ 70 (79)
|.|.|.++||-|+-.|...-+.+.+. +-+++++|-.+
T Consensus 528 p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~ 570 (595)
T KOG0779|consen 528 PQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPP 570 (595)
T ss_pred cCccCcccchhhHHHHHHHhhhChhhhcccccccccccccCCc
Confidence 99999999999999999998888775 45667776544
No 8
>PF13197 DUF4013: Protein of unknown function (DUF4013)
Probab=34.99 E-value=30 Score=23.39 Aligned_cols=27 Identities=15% Similarity=0.432 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhcCccchhhhhhhhhhh
Q 034898 45 YVIRFMKEIIESQDDSIKKCVCWTRQL 71 (79)
Q Consensus 45 YVMr~M~~II~~~~~~i~~~~~~~~~~ 71 (79)
|.+|.++....++++..||.=.|.+.+
T Consensus 21 Y~~~v~~~~~~g~~~~lP~~~~~~~l~ 47 (169)
T PF13197_consen 21 YLVRVIRSTAIGGSDPLPEFNDWGELF 47 (169)
T ss_pred HHHHHHHHhhccCCCCCCCchHHHHHH
Confidence 457889998888889999966777654
No 9
>PF11334 DUF3136: Protein of unknown function (DUF3136); InterPro: IPR021483 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=27.72 E-value=56 Score=21.15 Aligned_cols=23 Identities=22% Similarity=0.810 Sum_probs=18.6
Q ss_pred HHHHHHHHhcCc--cchhhhhhhhh
Q 034898 47 IRFMKEIIESQD--DSIKKCVCWTR 69 (79)
Q Consensus 47 Mr~M~~II~~~~--~~i~~~~~~~~ 69 (79)
++-|+-.|.++. +.|-+.|||.|
T Consensus 14 ckALr~Lv~~G~~~~~i~rTvCW~r 38 (64)
T PF11334_consen 14 CKALRRLVADGRSEEEIRRTVCWDR 38 (64)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 466788888775 57999999987
No 10
>PF05002 SGS: SGS domain ; InterPro: IPR007699 This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins. Sgt1p is a highly conserved eukaryotic protein that is required for both SCF (Skp1p/Cdc53p-Cullin-F-box)-mediated ubiquitination and kinetochore function in yeast and also plays a role in the cAMP pathway. Calcyclin (S100A6) is a member of the S100A family of calcium binding proteins and appears to play a role in cell proliferation [].; PDB: 1X5M_A 2JTT_D.
Probab=24.84 E-value=66 Score=21.17 Aligned_cols=20 Identities=25% Similarity=0.644 Sum_probs=16.6
Q ss_pred HHHHHHHHHhcCccchhhhh
Q 034898 46 VIRFMKEIIESQDDSIKKCV 65 (79)
Q Consensus 46 VMr~M~~II~~~~~~i~~~~ 65 (79)
+|.+|+.|+.++++.-.+.+
T Consensus 26 lm~lfkkiY~~gDDe~KRam 45 (82)
T PF05002_consen 26 LMNLFKKIYDNGDDEMKRAM 45 (82)
T ss_dssp HHHHHHHHHTTS-SCHHHHH
T ss_pred HHHHHHHHHccCCHHHHHHH
Confidence 89999999999999876654
No 11
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=21.12 E-value=40 Score=22.58 Aligned_cols=20 Identities=15% Similarity=0.592 Sum_probs=16.1
Q ss_pred HHHHHHHhcCccchhhhhhhhh
Q 034898 48 RFMKEIIESQDDSIKKCVCWTR 69 (79)
Q Consensus 48 r~M~~II~~~~~~i~~~~~~~~ 69 (79)
.|..+++.+... +.+|+||-
T Consensus 6 ~FL~~LL~d~~~--~~~I~W~~ 25 (87)
T smart00413 6 QFLLDLLLDPEN--GDIIRWTD 25 (87)
T ss_pred HHHHHHHcCccC--CCeEEeeC
Confidence 477888888764 99999996
No 12
>COG4018 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.27 E-value=85 Score=26.89 Aligned_cols=28 Identities=29% Similarity=0.516 Sum_probs=22.9
Q ss_pred ecCCCCCCcccchh-------------HHHHHHHHHHhcCc
Q 034898 31 VKCPQQTTNVECGY-------------YVIRFMKEIIESQD 58 (79)
Q Consensus 31 ~kCprQ~gg~ECGY-------------YVMr~M~~II~~~~ 58 (79)
.-=|..--||.||| =||+-|++-+.++.
T Consensus 306 tGFPkNHHGYMcGY~PgTArRGkFGLprVm~Imree~~sg~ 346 (505)
T COG4018 306 TGFPKNHHGYMCGYEPGTARRGKFGLPRVMAIMREELGSGY 346 (505)
T ss_pred cCCCccccceeecCCCCcccccccCcHHHHHHHHHHHhcCC
Confidence 34467778999999 49999999998874
Done!