Query 033908
Match_columns 109
No_of_seqs 119 out of 658
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 07:39:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033908.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033908hhsearch_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 8.8E-31 1.9E-35 205.7 4.3 97 1-108 415-511 (511)
2 PLN03189 Protease specific for 100.0 3E-29 6.5E-34 195.9 9.6 96 1-107 394-489 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 99.8 1.8E-22 3.9E-27 158.3 1.7 93 1-108 478-570 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.8 5.3E-19 1.1E-23 125.0 8.6 97 1-103 109-209 (216)
5 KOG3246 Sentrin-specific cyste 99.3 1.1E-11 2.4E-16 88.8 7.0 81 2-102 123-207 (223)
6 KOG0779 Protease, Ulp1 family 96.9 0.00066 1.4E-08 55.8 3.0 41 58-99 528-581 (595)
7 PF03421 YopJ: YopJ Serine/Thr 86.7 0.81 1.8E-05 32.2 3.1 33 48-82 132-164 (177)
8 PRK14848 deubiquitinase SseL; 73.7 6.9 0.00015 29.5 4.2 23 59-81 254-276 (317)
9 PF03290 Peptidase_C57: Vaccin 72.7 2.8 6.1E-05 33.1 2.1 27 58-85 323-349 (423)
10 PRK15371 effector protein YopJ 71.4 2.8 6.1E-05 31.8 1.8 27 56-83 162-188 (287)
11 KOG4110 NADH:ubiquinone oxidor 69.0 5.5 0.00012 26.1 2.5 59 48-107 18-95 (120)
12 PRK11836 deubiquitinase; Provi 49.4 11 0.00024 29.1 1.6 20 58-78 305-324 (403)
13 COG2260 Predicted Zn-ribbon RN 44.9 9.3 0.0002 22.2 0.5 39 66-105 10-55 (59)
14 PF03412 Peptidase_C39: Peptid 44.7 22 0.00048 22.5 2.3 23 59-83 6-28 (131)
15 PF09778 Guanylate_cyc_2: Guan 42.2 9.9 0.00021 27.7 0.4 11 59-70 5-15 (212)
16 KOG3315 Transport protein part 40.1 30 0.00066 24.5 2.5 28 56-84 132-159 (191)
17 PF00770 Peptidase_C5: Adenovi 39.2 78 0.0017 22.5 4.4 21 59-80 96-116 (183)
18 PF05393 Hum_adeno_E3A: Human 33.2 35 0.00075 21.6 1.7 13 66-78 40-52 (94)
19 PRK13130 H/ACA RNA-protein com 32.7 18 0.00039 20.8 0.4 38 66-104 10-54 (56)
20 cd02424 Peptidase_C39E A sub-f 29.1 62 0.0013 20.6 2.6 19 59-78 5-23 (129)
21 cd02423 Peptidase_C39G A sub-f 28.6 75 0.0016 19.8 2.9 22 57-79 3-24 (129)
22 COG5418 Predicted secreted pro 27.3 38 0.00082 23.5 1.3 36 22-72 81-116 (164)
23 smart00273 ENTH Epsin N-termin 26.0 58 0.0012 21.0 2.0 19 61-80 97-115 (127)
24 PF07559 FlaE: Flagellar basal 25.9 29 0.00064 22.2 0.6 9 1-9 15-23 (130)
25 COG3863 Uncharacterized distan 21.7 1.2E+02 0.0026 22.1 3.0 32 31-62 192-223 (231)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=8.8e-31 Score=205.67 Aligned_cols=97 Identities=29% Similarity=0.562 Sum_probs=90.3
Q ss_pred CEEEeCCCCCCCChhHHhhcCchHHHHHHHHHHHhhhccCCCCCCCCCceeeecCCCCCCCCCCCcchHHHHHHHHHHhc
Q 033908 1 MRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMF 80 (109)
Q Consensus 1 I~~~DSl~~~~~~~~~~~~~~~~~~~l~~yl~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~ 80 (109)
|.|||||++. .+..+ + .|.+||++|+.+|.+..++.+ .|.+..+.++|||.||+ |||||+|+|++|++.
T Consensus 415 i~y~DS~~~~-~nr~~-~-------aL~~Yl~~E~~~k~~~~~d~s-~w~~~~~~~iP~Q~Ng~-DCG~f~c~~~~~~s~ 483 (511)
T KOG0778|consen 415 IEYYDSLGGG-PNRIC-D-------ALAKYLQDESRDKSKKDFDVS-GWTIEFVQNIPQQRNGS-DCGMFVCKYADYISR 483 (511)
T ss_pred EEEeeccCCC-CcchH-H-------HHHHHHHHHHhhhhcCCCCcc-chhhhhhhccccccCCC-ccceEEeeechhhcc
Confidence 6899999972 44455 8 999999999999999999999 99999889999999999 999999999999999
Q ss_pred CCCCccCcccHHHHHHHHHHHHhcCCCC
Q 033908 81 GLKLDFDSSHGHYFRKKIAVDIFPGDIA 108 (109)
Q Consensus 81 ~~~~~f~q~~~~~~R~~~~~el~~~~l~ 108 (109)
+.|++|+|.|||+||++||+||++++|+
T Consensus 484 ~~p~~ftq~dmp~fR~~m~~eI~~~~l~ 511 (511)
T KOG0778|consen 484 DVPLTFTQQDMPYFRKKMAKEILHLKLL 511 (511)
T ss_pred CCCcccChhhhHHHHHHHHHHHHhhhcC
Confidence 9999999999999999999999999885
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=99.96 E-value=3e-29 Score=195.91 Aligned_cols=96 Identities=28% Similarity=0.517 Sum_probs=89.1
Q ss_pred CEEEeCCCCCCCChhHHhhcCchHHHHHHHHHHHhhhccCCCCCCCCCceeeecCCCCCCCCCCCcchHHHHHHHHHHhc
Q 033908 1 MRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMF 80 (109)
Q Consensus 1 I~~~DSl~~~~~~~~~~~~~~~~~~~l~~yl~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~ 80 (109)
|.|||||++ .+..+++ .|++|+..|+.++.+..++.+ .|+...+.++|||.||+ |||||||+||+|++.
T Consensus 394 I~yyDSLgg--~~~~vL~-------~L~rYL~~E~kdK~g~d~D~s-~W~~~~~~~vPQQ~NG~-DCGVFVL~yAE~~Sr 462 (490)
T PLN03189 394 FQYLDSLKG--RDPKILD-------ALAKYYVDEVKDKSEKDIDVS-SWEQEFVEDLPEQKNGY-DCGMFMIKYIDFYSR 462 (490)
T ss_pred EEEEeCCCC--CCHHHHH-------HHHHHHHHHHhhhcCCCcchh-cceeccCCCCCCCCCCC-CHHHHHHHHHHHHcC
Confidence 689999999 6778888 999999999999888888887 99887667899999999 999999999999999
Q ss_pred CCCCccCcccHHHHHHHHHHHHhcCCC
Q 033908 81 GLKLDFDSSHGHYFRKKIAVDIFPGDI 107 (109)
Q Consensus 81 ~~~~~f~q~~~~~~R~~~~~el~~~~l 107 (109)
|.+++|+|+||++||++|++||++.++
T Consensus 463 G~~LtFSQeDMp~fRrRma~EIl~~r~ 489 (490)
T PLN03189 463 GLGLCFGQEHMPYFRLRTAKEILRLKA 489 (490)
T ss_pred CCCCCcChhhhHHHHHHHHHHHHHhhc
Confidence 999999999999999999999998875
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=1.8e-22 Score=158.27 Aligned_cols=93 Identities=29% Similarity=0.368 Sum_probs=80.7
Q ss_pred CEEEeCCCCCCCChhHHhhcCchHHHHHHHHHHHhhhccCCCCCCCCCceeeecCCCCCCCCCCCcchHHHHHHHHHHhc
Q 033908 1 MRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMF 80 (109)
Q Consensus 1 I~~~DSl~~~~~~~~~~~~~~~~~~~l~~yl~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~ 80 (109)
|.|||||++ ....+++ .|++|+.+|++...++. +|......++|||.||+ |||||||+|++|++.
T Consensus 478 i~~~DSLan--~~~~v~~-------~L~~Y~ldE~k~~~~k~-----~~~~~~~~~vPqQ~Ng~-DCGV~vc~~~~~~~~ 542 (578)
T COG5160 478 ILYFDSLAN--THDPVLE-------FLRSYLLDEYKIQHDKD-----PQIKMKHCKVPQQRNGS-DCGVFVCMFIRYFLE 542 (578)
T ss_pred eEEeccccc--CcHHHHH-------HHHHHHHHHHhcccCCc-----hhhhhhcCCCCCCCCCC-ccceEEEEeeeeccc
Confidence 689999999 5688888 99999999987554432 45544456899999999 999999999999999
Q ss_pred CCCCccCcccHHHHHHHHHHHHhcCCCC
Q 033908 81 GLKLDFDSSHGHYFRKKIAVDIFPGDIA 108 (109)
Q Consensus 81 ~~~~~f~q~~~~~~R~~~~~el~~~~l~ 108 (109)
+.|..|++.|++.+|+.|+++|++..|.
T Consensus 543 ~~p~~f~~nd~~r~Rk~m~h~i~~~qi~ 570 (578)
T COG5160 543 NPPEQFSKNDRPRARKNMAHTIKDLQIN 570 (578)
T ss_pred CChhhcCccchHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999987653
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=99.79 E-value=5.3e-19 Score=125.02 Aligned_cols=97 Identities=30% Similarity=0.501 Sum_probs=70.4
Q ss_pred CEEEeCCCCCCCChhHHhhcCchHHHHHHHHHHHhhhccCCCCCCCCCceeeecCCCCCCCCCCCcchHHHHHHHHHHhc
Q 033908 1 MRIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMF 80 (109)
Q Consensus 1 I~~~DSl~~~~~~~~~~~~~~~~~~~l~~yl~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~ 80 (109)
|.+||||++ ... .+........+..+|..++....+...+.. +|+...+.++|||.|++ |||||||+|+++++.
T Consensus 109 i~~~DSl~~--~~~--~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~~~~pqQ~n~~-dCGv~vl~~~~~~~~ 182 (216)
T PF02902_consen 109 IYVYDSLGS--SNN--DKRYKRVIENIIPFLKREYKKKEGRDPDKS-PFKIVRPPNVPQQPNGY-DCGVYVLKFMECLLE 182 (216)
T ss_dssp EEEE-TTST--SSH---HHHHHHHHHHHHHHHHHHHHHHSSCT-TT-TCEEEEECTS-SSSSSS-CHHHHHHHHHHHHHC
T ss_pred EEEEecccc--ccc--cccchhhhhhhhhhhhhccccccccccccc-eeeecccccccCCCCCC-CcHHHHHHHHHHHHh
Confidence 579999999 444 000111223888888877765544444555 88887777899999999 999999999999999
Q ss_pred CCCCc----cCcccHHHHHHHHHHHHh
Q 033908 81 GLKLD----FDSSHGHYFRKKIAVDIF 103 (109)
Q Consensus 81 ~~~~~----f~q~~~~~~R~~~~~el~ 103 (109)
+.+.. |++++++.+|++++.++-
T Consensus 183 ~~~~~~~~~l~~~~i~~~r~~~a~~~~ 209 (216)
T PF02902_consen 183 GPSFDFSQELTEEDIKNFRKKLAVDLY 209 (216)
T ss_dssp THHSTGCCSBTGHHHHHHHHHHHH---
T ss_pred CCCCcccccCCHHHHHHHHHHHHhhcc
Confidence 98766 799999999999997653
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.28 E-value=1.1e-11 Score=88.80 Aligned_cols=81 Identities=20% Similarity=0.122 Sum_probs=50.9
Q ss_pred EEEeCCCCCCCChhHHhhcCchHHHHHHHHHHHhhhccCCCCCCCCCceeeecCCCCCCCCCCCcchHHHHHHHHHHhcC
Q 033908 2 RIYDSLVTFREDKTYLRKFKPLQVVFPQWLQDVGFYNIRPELQSADPWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMFG 81 (109)
Q Consensus 2 ~~~DSl~~~~~~~~~~~~~~~~~~~l~~yl~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~~ 81 (109)
.||||+.+ .+...++ .++++++..+..+.. .+.+...|||+||+ |||+|||++++.++..
T Consensus 123 ~hyDS~~n--~nt~~a~---~l~~kl~~ll~~~~~--------------~~~~~~~~qQqNgy-DCG~hV~~~t~~l~~~ 182 (223)
T KOG3246|consen 123 YHYDSLSN--GNTKDAK---SLMKKLRALLKKKFA--------------KRVECKCLQQQNGY-DCGLHVCCNTRVLAER 182 (223)
T ss_pred EEeecccC--CCcHHHH---HHHHHHHHHHhhhhh--------------hcccccChhhhcCC-chhHHHHHHHHHHHHH
Confidence 58999999 5655555 234466666664321 11144678999999 9999999998877543
Q ss_pred ----CCCccCcccHHHHHHHHHHHH
Q 033908 82 ----LKLDFDSSHGHYFRKKIAVDI 102 (109)
Q Consensus 82 ----~~~~f~q~~~~~~R~~~~~el 102 (109)
.-.+-.|.+.+..|+.+-.||
T Consensus 183 ~~~~~~~~~~~~~~~~~i~~lr~~l 207 (223)
T KOG3246|consen 183 LLRCPYATSSQLLVVDLIKALREEL 207 (223)
T ss_pred HhccccccccchhhHHHHHHHHHHH
Confidence 223444555544555444443
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=96.94 E-value=0.00066 Score=55.78 Aligned_cols=41 Identities=32% Similarity=0.441 Sum_probs=34.6
Q ss_pred CCCCCCCCcchHHHHHHHHHHhcCCCC-------------ccCcccHHHHHHHHH
Q 033908 58 PQQEPGSGDCGVFMLMFTMYLMFGLKL-------------DFDSSHGHYFRKKIA 99 (109)
Q Consensus 58 PqQ~N~~~DCGvFvl~~~e~l~~~~~~-------------~f~q~~~~~~R~~~~ 99 (109)
|||.|.+ |||+|++.|++.+..+.+. .|.+.++-.+|..+-
T Consensus 528 p~q~n~~-dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r 581 (595)
T KOG0779|consen 528 PQQNNDV-DCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIR 581 (595)
T ss_pred cCccCcc-cchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhh
Confidence 8999999 9999999999999776654 388888888887664
No 7
>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=86.72 E-value=0.81 Score=32.21 Aligned_cols=33 Identities=24% Similarity=0.340 Sum_probs=25.9
Q ss_pred CceeeecCCCCCCCCCCCcchHHHHHHHHHHhcCC
Q 033908 48 PWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMFGL 82 (109)
Q Consensus 48 ~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~~~ 82 (109)
.+++.. ..+.-|+..+ |||+|-|.+|.....+.
T Consensus 132 ~~~~~~-ie~diQkS~~-dC~IFsLs~AkK~~~~~ 164 (177)
T PF03421_consen 132 NAKFAV-IEMDIQKSPS-DCGIFSLSLAKKMYKED 164 (177)
T ss_pred CcEEEE-EecccccCcC-cchhhHHHHHHHHhhcc
Confidence 444543 3689999999 99999999999886644
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=73.72 E-value=6.9 Score=29.50 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=17.4
Q ss_pred CCCCCCCcchHHHHHHHHHHhcC
Q 033908 59 QQEPGSGDCGVFMLMFTMYLMFG 81 (109)
Q Consensus 59 qQ~N~~~DCGvFvl~~~e~l~~~ 81 (109)
.|+|-.+-||.|||++++.+..+
T Consensus 254 LQqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 254 LQNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred hhhhCCCcchHHHHHHHHHHHhc
Confidence 34444449999999999988765
No 9
>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=72.71 E-value=2.8 Score=33.12 Aligned_cols=27 Identities=22% Similarity=0.408 Sum_probs=21.1
Q ss_pred CCCCCCCCcchHHHHHHHHHHhcCCCCc
Q 033908 58 PQQEPGSGDCGVFMLMFTMYLMFGLKLD 85 (109)
Q Consensus 58 PqQ~N~~~DCGvFvl~~~e~l~~~~~~~ 85 (109)
-.|--.+ |||+|++-|+-......|-.
T Consensus 323 vnQl~es-eCGMF~~iFm~~c~~~ppk~ 349 (423)
T PF03290_consen 323 VNQLLES-ECGMFISIFMILCTLTPPKG 349 (423)
T ss_pred hhhhccc-ccchHHHHHHHHHHccCchh
Confidence 3677889 99999999988776666544
No 10
>PRK15371 effector protein YopJ; Provisional
Probab=71.43 E-value=2.8 Score=31.83 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=22.4
Q ss_pred CCCCCCCCCCcchHHHHHHHHHHhcCCC
Q 033908 56 DVPQQEPGSGDCGVFMLMFTMYLMFGLK 83 (109)
Q Consensus 56 ~~PqQ~N~~~DCGvFvl~~~e~l~~~~~ 83 (109)
..--|+..+ |||+|-|.+|.....+..
T Consensus 162 e~d~QkS~~-dC~mFSL~~AkK~~~e~d 188 (287)
T PRK15371 162 EMDIQRSSS-ECGIFSLALAKKLYLERD 188 (287)
T ss_pred ecccccCcc-cchhhhHHHHHHHhhhhH
Confidence 457899999 999999999998766553
No 11
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=69.04 E-value=5.5 Score=26.12 Aligned_cols=59 Identities=27% Similarity=0.410 Sum_probs=39.8
Q ss_pred CceeeecCCCCCCCCCCCcchHHHHHHHHHHhc-C----CC---C---cc-----CcccH---HHHHHHHHHHHhcCCC
Q 033908 48 PWKVRIVKDVPQQEPGSGDCGVFMLMFTMYLMF-G----LK---L---DF-----DSSHG---HYFRKKIAVDIFPGDI 107 (109)
Q Consensus 48 ~w~~~~~~~~PqQ~N~~~DCGvFvl~~~e~l~~-~----~~---~---~f-----~q~~~---~~~R~~~~~el~~~~l 107 (109)
.|.+.-...+|.-..+. |||-|=..+.||.-. | .. + +| -|..| ..+|++=...++.|+.
T Consensus 18 r~p~tds~~~p~~~q~r-~cg~FE~e~~eC~eayG~~~g~keC~ie~~dFqECv~~qKqmrra~aiR~qr~Kl~leGk~ 95 (120)
T KOG4110|consen 18 RWPTTDSTEQPYKHQGR-DCGKFEKEWMECAEAYGLERGEKECAIEYDDFQECVLMQKQMRRAHAIRKQRYKLILEGKY 95 (120)
T ss_pred hccccccccCccccccc-cccHHHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCc
Confidence 67776556788888889 999999999998622 2 11 1 12 23333 5677777777787774
No 12
>PRK11836 deubiquitinase; Provisional
Probab=49.38 E-value=11 Score=29.05 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=14.5
Q ss_pred CCCCCCCCcchHHHHHHHHHH
Q 033908 58 PQQEPGSGDCGVFMLMFTMYL 78 (109)
Q Consensus 58 PqQ~N~~~DCGvFvl~~~e~l 78 (109)
-||.-.. .||.|||+-+.-+
T Consensus 305 LQq~vpn-gCGlFv~~a~Qe~ 324 (403)
T PRK11836 305 LQQYLSQ-SCGAFVCMAAQEV 324 (403)
T ss_pred hhhcCCC-ccceehHHHHHHH
Confidence 3444445 9999999988744
No 13
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=44.88 E-value=9.3 Score=22.22 Aligned_cols=39 Identities=13% Similarity=0.110 Sum_probs=25.3
Q ss_pred cchHHHHHHHHHH-hc-----CCCCccCccc-HHHHHHHHHHHHhcC
Q 033908 66 DCGVFMLMFTMYL-MF-----GLKLDFDSSH-GHYFRKKIAVDIFPG 105 (109)
Q Consensus 66 DCGvFvl~~~e~l-~~-----~~~~~f~q~~-~~~~R~~~~~el~~~ 105 (109)
+||+|+|. =.|= +- -.|-.||++| ....|..+..++...
T Consensus 10 ~cg~YTLk-e~Cp~CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~~~ 55 (59)
T COG2260 10 KCGRYTLK-EKCPVCGGDTKVPHPPRFSPEDKYGKYRRELKKRLGLL 55 (59)
T ss_pred CCCceeec-ccCCCCCCccccCCCCCCCccchHHHHHHHHHHHhccc
Confidence 69999988 1121 11 2356799887 577788777776543
No 14
>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=44.74 E-value=22 Score=22.55 Aligned_cols=23 Identities=26% Similarity=0.647 Sum_probs=13.5
Q ss_pred CCCCCCCcchHHHHHHHHHHhcCCC
Q 033908 59 QQEPGSGDCGVFMLMFTMYLMFGLK 83 (109)
Q Consensus 59 qQ~N~~~DCGvFvl~~~e~l~~~~~ 83 (109)
+|.... |||+-.+.++-.. .|.+
T Consensus 6 ~Q~~~~-dcg~acl~~l~~~-~g~~ 28 (131)
T PF03412_consen 6 KQSDSN-DCGLACLAMLLKY-YGIP 28 (131)
T ss_dssp --SSTT--HHHHHHHHHHHH-TT--
T ss_pred EeCCCC-CHHHHHHHHHHHH-hCCC
Confidence 677888 9999988876544 3443
No 15
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=42.20 E-value=9.9 Score=27.67 Aligned_cols=11 Identities=45% Similarity=0.670 Sum_probs=10.0
Q ss_pred CCCCCCCcchHH
Q 033908 59 QQEPGSGDCGVF 70 (109)
Q Consensus 59 qQ~N~~~DCGvF 70 (109)
+|...+ |||+=
T Consensus 5 ~Q~~~W-DCGlA 15 (212)
T PF09778_consen 5 QQRYNW-DCGLA 15 (212)
T ss_pred eeeccc-cccHH
Confidence 799999 99986
No 16
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.14 E-value=30 Score=24.55 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=24.4
Q ss_pred CCCCCCCCCCcchHHHHHHHHHHhcCCCC
Q 033908 56 DVPQQEPGSGDCGVFMLMFTMYLMFGLKL 84 (109)
Q Consensus 56 ~~PqQ~N~~~DCGvFvl~~~e~l~~~~~~ 84 (109)
.||.-.|+- .|+-|||-.++.+..+..+
T Consensus 132 SVPke~~~l-nc~~fvaGIiea~L~~agf 159 (191)
T KOG3315|consen 132 SVPKENGTL-NCAAFVAGIIEAVLDNAGF 159 (191)
T ss_pred ecccccCcc-cHHHHHHHHHHHHHHhCCC
Confidence 579999999 9999999999998776643
No 17
>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=39.22 E-value=78 Score=22.51 Aligned_cols=21 Identities=24% Similarity=0.491 Sum_probs=14.1
Q ss_pred CCCCCCCcchHHHHHHHHHHhc
Q 033908 59 QQEPGSGDCGVFMLMFTMYLMF 80 (109)
Q Consensus 59 qQ~N~~~DCGvFvl~~~e~l~~ 80 (109)
|=.++- -||+|.|+|..++..
T Consensus 96 Q~p~Sa-aCGLFC~lFL~aF~~ 116 (183)
T PF00770_consen 96 QCPCSA-ACGLFCCLFLHAFVH 116 (183)
T ss_dssp S-TT----HHHHHHHHHHHHHH
T ss_pred eccCch-hHHHHHHHHHHHHHh
Confidence 444666 999999999999864
No 18
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=33.22 E-value=35 Score=21.57 Aligned_cols=13 Identities=31% Similarity=1.078 Sum_probs=9.3
Q ss_pred cchHHHHHHHHHH
Q 033908 66 DCGVFMLMFTMYL 78 (109)
Q Consensus 66 DCGvFvl~~~e~l 78 (109)
=||+|+|..+-++
T Consensus 40 I~~iFil~Vilwf 52 (94)
T PF05393_consen 40 ICGIFILLVILWF 52 (94)
T ss_pred HHHHHHHHHHHHH
Confidence 6999977665544
No 19
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=32.72 E-value=18 Score=20.78 Aligned_cols=38 Identities=16% Similarity=0.203 Sum_probs=23.2
Q ss_pred cchHHHHHHHHHH------hcCCCCccCccc-HHHHHHHHHHHHhc
Q 033908 66 DCGVFMLMFTMYL------MFGLKLDFDSSH-GHYFRKKIAVDIFP 104 (109)
Q Consensus 66 DCGvFvl~~~e~l------~~~~~~~f~q~~-~~~~R~~~~~el~~ 104 (109)
+||+|+|. ..|= ..-.|-.|+++| ....|..+-.++..
T Consensus 10 ~CgvYTLk-~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~~ 54 (56)
T PRK13130 10 KCGVYTLK-EICPVCGGKTKNPHPPRFSPEDKYGKYRRALKKRRKL 54 (56)
T ss_pred CCCCEEcc-ccCcCCCCCCCCCCCCCCCCCCccHHHHHHHHHHhhc
Confidence 78999882 1121 112345699888 57777777666543
No 20
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=29.12 E-value=62 Score=20.59 Aligned_cols=19 Identities=21% Similarity=0.417 Sum_probs=13.7
Q ss_pred CCCCCCCcchHHHHHHHHHH
Q 033908 59 QQEPGSGDCGVFMLMFTMYL 78 (109)
Q Consensus 59 qQ~N~~~DCGvFvl~~~e~l 78 (109)
.|.... |||+..+..+-..
T Consensus 5 ~q~~~~-dcgla~l~~i~~~ 23 (129)
T cd02424 5 KQTDLN-DCGIAVIQMLYNH 23 (129)
T ss_pred EecCcc-chHHHHHHHHHHH
Confidence 566888 9999976655433
No 21
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=28.59 E-value=75 Score=19.79 Aligned_cols=22 Identities=23% Similarity=0.223 Sum_probs=15.2
Q ss_pred CCCCCCCCCcchHHHHHHHHHHh
Q 033908 57 VPQQEPGSGDCGVFMLMFTMYLM 79 (109)
Q Consensus 57 ~PqQ~N~~~DCGvFvl~~~e~l~ 79 (109)
+=.|.+.. |||+..+.++-...
T Consensus 3 ~~~q~~~~-~~~l~~l~~~~~~~ 24 (129)
T cd02423 3 VVRQSYDF-SCGPAALATLLRYY 24 (129)
T ss_pred ceecCCCC-ChHHHHHHHHHHhc
Confidence 34677888 99999766554443
No 22
>COG5418 Predicted secreted protein [Function unknown]
Probab=27.31 E-value=38 Score=23.48 Aligned_cols=36 Identities=17% Similarity=0.241 Sum_probs=20.8
Q ss_pred chHHHHHHHHHHHhhhccCCCCCCCCCceeeecCCCCCCCCCCCcchHHHH
Q 033908 22 PLQVVFPQWLQDVGFYNIRPELQSADPWKVRIVKDVPQQEPGSGDCGVFML 72 (109)
Q Consensus 22 ~~~~~l~~yl~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N~~~DCGvFvl 72 (109)
+++.-|.++|+++..+ ..+++.+ .|| |+- .||||.-
T Consensus 81 ki~~pi~~~l~e~k~d----------~~kii~I-GV~---~Sp-TCgVy~t 116 (164)
T COG5418 81 KIADPIGRVLEEEKPD----------GIKIIFI-GVK---GSP-TCGVYTT 116 (164)
T ss_pred HHHHHHHHHHHHhCcC----------CceEEEE-ecC---CCC-ccceEec
Confidence 4455666666655321 4556554 344 566 9999963
No 23
>smart00273 ENTH Epsin N-terminal homology (ENTH) domain.
Probab=25.99 E-value=58 Score=21.03 Aligned_cols=19 Identities=26% Similarity=0.468 Sum_probs=16.8
Q ss_pred CCCCCcchHHHHHHHHHHhc
Q 033908 61 EPGSGDCGVFMLMFTMYLMF 80 (109)
Q Consensus 61 ~N~~~DCGvFvl~~~e~l~~ 80 (109)
.+|. |+|++|=.|+++|..
T Consensus 97 ~~~~-d~g~~VR~ya~~L~~ 115 (127)
T smart00273 97 SRGK-DQGANIRTYAKYLLE 115 (127)
T ss_pred CCCe-eCcHHHHHHHHHHHH
Confidence 5889 999999999999864
No 24
>PF07559 FlaE: Flagellar basal body protein FlaE; InterPro: IPR011491 This domain is found in several bacterial FlaE flagellar proteins. These proteins are part of the flagellar basal body rod complex.; GO: 0030694 bacterial-type flagellum basal body, rod; PDB: 2BGY_A 1WLG_B 2BGZ_A 3A69_A.
Probab=25.95 E-value=29 Score=22.22 Aligned_cols=9 Identities=44% Similarity=0.789 Sum_probs=5.0
Q ss_pred CEEEeCCCC
Q 033908 1 MRIYDSLVT 9 (109)
Q Consensus 1 I~~~DSl~~ 9 (109)
|.+|||+|.
T Consensus 15 ~~vYDSlG~ 23 (130)
T PF07559_consen 15 ITVYDSLGN 23 (130)
T ss_dssp EEEE-TT--
T ss_pred EEEECCCCC
Confidence 468999999
No 25
>COG3863 Uncharacterized distant relative of cell wall-associated hydrolases [Function unknown]
Probab=21.65 E-value=1.2e+02 Score=22.08 Aligned_cols=32 Identities=25% Similarity=0.255 Sum_probs=22.8
Q ss_pred HHHHhhhccCCCCCCCCCceeeecCCCCCCCC
Q 033908 31 LQDVGFYNIRPELQSADPWKVRIVKDVPQQEP 62 (109)
Q Consensus 31 l~~e~~~k~~~~~~~~~~w~~~~~~~~PqQ~N 62 (109)
+-.-++++.|.+++....|..+++.++|.|+-
T Consensus 192 iWaAyk~~~G~DID~n~g~~~~yp~dv~~q~~ 223 (231)
T COG3863 192 IWAAYKANGGPDIDQNPGWSWRYPYDVAPQEL 223 (231)
T ss_pred HHHHHHHhcCCCcCCCCCcceecccCCCchhh
Confidence 44445566688887765687678889998863
Done!