Query 036268
Match_columns 249
No_of_seqs 126 out of 263
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 11:01:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036268.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036268hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0778 Protease, Ulp1 family 99.9 1.3E-28 2.7E-33 238.1 6.4 132 93-226 282-438 (511)
2 PLN03189 Protease specific for 99.8 1.7E-20 3.6E-25 181.2 6.9 142 63-227 266-418 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 99.8 1.9E-19 4E-24 175.5 3.5 114 74-214 375-490 (578)
4 PF02902 Peptidase_C48: Ulp1 p 99.5 2.1E-13 4.5E-18 111.1 8.6 56 158-213 62-120 (216)
5 KOG3246 Sentrin-specific cyste 98.2 2.3E-06 5.1E-11 77.0 6.3 48 170-217 82-137 (223)
6 KOG0779 Protease, Ulp1 family 97.3 4.7E-05 1E-09 76.0 -0.3 70 129-201 391-462 (595)
7 KOG0778 Protease, Ulp1 family 82.7 0.34 7.5E-06 48.7 -0.4 81 43-145 290-374 (511)
8 PF03290 Peptidase_C57: Vaccin 80.4 2.2 4.7E-05 42.2 4.1 40 171-211 226-265 (423)
9 PF00770 Peptidase_C5: Adenovi 33.9 52 0.0011 29.7 3.6 29 185-213 31-59 (183)
10 PRK11836 deubiquitinase; Provi 32.6 1E+02 0.0023 30.3 5.6 65 175-243 218-292 (403)
11 PF00154 RecA: recA bacterial 22.8 52 0.0011 31.3 1.8 62 12-83 2-64 (322)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=1.3e-28 Score=238.09 Aligned_cols=132 Identities=20% Similarity=0.263 Sum_probs=107.1
Q ss_pred hccCcccchhhhhhcccCcc-----------ccccceeeeecCCCCCCc-hhhHHHhhhhhhc------CCC-----ccc
Q 036268 93 FFNDESRIGDVLQTLEPNSK-----------ESSKKYWLTVKDYMPSIP-DWVHKVFLNQLWN------NGD-----CAV 149 (249)
Q Consensus 93 ~f~~~~r~~~v~q~Lq~~~k-----------~~~kr~~lT~~d~~~~~p-~wv~~~F~nq~~~------~g~-----c~~ 149 (249)
..+.++.+..+.+..+++++ +.++++.||.+|+.++.| +|||+-..|.|+. ..+ ||.
T Consensus 282 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~ 361 (511)
T KOG0778|consen 282 VKKEDSFPPLTEEREAQVQRAFSSRNSTEILVTHFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHA 361 (511)
T ss_pred ccCccccccccHHHHHHHHHHhccCCcccceehhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEE
Confidence 34455555555555555444 447889999999999988 8999777777764 344 899
Q ss_pred cceeccccc--cccccccccccccCceeecEEEEeeeCCCCeEEEEEEEcCCCeEEEEeCCCCCCchhHHHHHHHHHHH
Q 036268 150 DSLVFEDHL--NNYLCGRQHTMSKSMTDVDMLLIPVNLDGAHWVVARVDFRKNKVWIYDSLLTFCDDKRYKLKFKLLEV 226 (249)
Q Consensus 150 ~~l~~~d~l--~GY~~VkRWTkkVDIFskDlILIPInv~n~HW~LaVId~r~K~I~YYDSLgg~n~~~~~~li~~yLak 226 (249)
|+.+|+..+ +||++|||||++||||++|+||||||++ +||||||||+++|+|+||||||+.....| ..+.+||..
T Consensus 362 FnTFFy~kL~~~gy~~VkRWTk~v~if~~d~i~vPIH~~-vHW~l~vid~r~k~i~y~DS~~~~~nr~~-~aL~~Yl~~ 438 (511)
T KOG0778|consen 362 FNTFFYTKLVGRGYAGVKRWTKKVDIFDKDIIFVPIHLG-VHWCLAVIDLREKTIEYYDSLGGGPNRIC-DALAKYLQD 438 (511)
T ss_pred EechhhhhhhhcchHHHHhHhhccCccccceeEeeeecC-ceEEEEEEEcccceEEEeeccCCCCcchH-HHHHHHHHH
Confidence 999998775 6999999999999999999999999995 99999999999999999999997755555 666666655
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=99.81 E-value=1.7e-20 Score=181.24 Aligned_cols=142 Identities=19% Similarity=0.235 Sum_probs=104.2
Q ss_pred hhhhcccccc--ce-ee--ecccccceeeeeeeh--hhccCcccchhhhhhcccCccccccceeeeecCCCCCCchhhHH
Q 036268 63 CVVKTKNKIP--RI-VQ--WKPMASSRINFAEVY--SFFNDESRIGDVLQTLEPNSKESSKKYWLTVKDYMPSIPDWVHK 135 (249)
Q Consensus 63 ~~~~~~n~~~--ri-v~--~~~~~~~~~n~~~~~--~~f~~~~r~~~v~q~Lq~~~k~~~kr~~lT~~d~~~~~p~wv~~ 135 (249)
=|.+|+...+ .| |. -+++.+.+=.++||. +|.||+. |++++.+|++..+...+.+ +. -+++|+
T Consensus 266 ~V~~al~~~~~~~vlvs~~~~~i~IT~~DL~~L~Pg~WLNDeV-INfYm~LL~er~~~~p~~~--------~k-~h~FNT 335 (490)
T PLN03189 266 EVKRAFSANNRRKVLVTHENSNIDITGEILRCLKPGAWLNDEV-INLYLELLKEREAREPKKF--------LK-CHFFNT 335 (490)
T ss_pred HHHHHhcCCCccceeeecCCCceEEEHHHhhccCCCCccCHHH-HHHHHHHHHHhhhcCcccc--------cc-eEEEeh
Confidence 3555665554 23 32 245666666888888 8999999 9999999986542221110 01 146677
Q ss_pred HhhhhhhcCCCccccceeccccccccccccccccc----cCceeecEEEEeeeCCCCeEEEEEEEcCCCeEEEEeCCCCC
Q 036268 136 VFLNQLWNNGDCAVDSLVFEDHLNNYLCGRQHTMS----KSMTDVDMLLIPVNLDGAHWVVARVDFRKNKVWIYDSLLTF 211 (249)
Q Consensus 136 ~F~nq~~~~g~c~~~~l~~~d~l~GY~~VkRWTkk----VDIFskDlILIPInv~n~HW~LaVId~r~K~I~YYDSLgg~ 211 (249)
||+++|...+. ..||.+|+|||++ +++|++|+||||||.+ +||||+|||+++++|.||||||+.
T Consensus 336 FFytkL~~~~~-----------~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n-~HWsLaVId~k~k~I~yyDSLgg~ 403 (490)
T PLN03189 336 FFYKKLVSGKS-----------GYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQE-IHWTLAVINKKDQKFQYLDSLKGR 403 (490)
T ss_pred HHHHHHhhcCC-----------cCChHHHHHHhhhcccccccccCceEEeeeecC-CeeEEEEEEcCCCeEEEEeCCCCC
Confidence 77777766542 2599999999974 5799999999999986 999999999999999999999998
Q ss_pred CchhHHHHHHHHHHHH
Q 036268 212 CDDKRYKLKFKLLEVI 227 (249)
Q Consensus 212 n~~~~~~li~~yLak~ 227 (249)
+. ..++.+.+||...
T Consensus 404 ~~-~vL~~L~rYL~~E 418 (490)
T PLN03189 404 DP-KILDALAKYYVDE 418 (490)
T ss_pred CH-HHHHHHHHHHHHH
Confidence 65 4566666776553
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=1.9e-19 Score=175.51 Aligned_cols=114 Identities=24% Similarity=0.394 Sum_probs=82.9
Q ss_pred eeeecccccceeeeeeeh--hhccCcccchhhhhhcccCccccccceeeeecCCCCCCchhhHHHhhhhhhcCCCccccc
Q 036268 74 IVQWKPMASSRINFAEVY--SFFNDESRIGDVLQTLEPNSKESSKKYWLTVKDYMPSIPDWVHKVFLNQLWNNGDCAVDS 151 (249)
Q Consensus 74 iv~~~~~~~~~~n~~~~~--~~f~~~~r~~~v~q~Lq~~~k~~~kr~~lT~~d~~~~~p~wv~~~F~nq~~~~g~c~~~~ 151 (249)
++.+.++++--=.|+++. +|.||.- +.+++..|++.++-+.++ |+ || -||+||+...
T Consensus 375 ~~~~~~i~IT~~D~~~L~~~~wLNDtI-IdFy~k~ls~~sk~~s~~------------~~-vh--~FnTFFYT~L----- 433 (578)
T COG5160 375 FNDRSSIEITNQDFKRLRNGDWLNDTI-IDFYMKLLSKISKNTSKR------------EQ-VH--LFNTFFYTKL----- 433 (578)
T ss_pred ccCcCcceeehHhhhhhccccchhhHH-HHHHHHHHHHhccCcccc------------cc-eE--EeehhhHHHH-----
Confidence 455566666666666666 6777776 777777776665433211 11 11 2333333331
Q ss_pred eeccccccccccccccccccCceeecEEEEeeeCCCCeEEEEEEEcCCCeEEEEeCCCCCCch
Q 036268 152 LVFEDHLNNYLCGRQHTMSKSMTDVDMLLIPVNLDGAHWVVARVDFRKNKVWIYDSLLTFCDD 214 (249)
Q Consensus 152 l~~~d~l~GY~~VkRWTkkVDIFskDlILIPInv~n~HW~LaVId~r~K~I~YYDSLgg~n~~ 214 (249)
...||++|||||+++|||++|+|+||||+. .||||||||.+++.|.|||||++...+
T Consensus 434 -----srrGy~gVrrW~kk~dif~~k~I~iPIni~-~HW~l~II~~~~~~i~~~DSLan~~~~ 490 (578)
T COG5160 434 -----SRRGYSGVRRWTKKTDIFSKKYIFIPINIS-YHWFLAIIDNPKKNILYFDSLANTHDP 490 (578)
T ss_pred -----HHHHhHHHHHHHhccCccccceEEEEeccc-ceEEEEEeecCcceeEEecccccCcHH
Confidence 146999999999999999999999999997 999999999999999999999998744
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=99.46 E-value=2.1e-13 Score=111.07 Aligned_cols=56 Identities=29% Similarity=0.578 Sum_probs=51.7
Q ss_pred cccccccccccccc---CceeecEEEEeeeCCCCeEEEEEEEcCCCeEEEEeCCCCCCc
Q 036268 158 LNNYLCGRQHTMSK---SMTDVDMLLIPVNLDGAHWVVARVDFRKNKVWIYDSLLTFCD 213 (249)
Q Consensus 158 l~GY~~VkRWTkkV---DIFskDlILIPInv~n~HW~LaVId~r~K~I~YYDSLgg~n~ 213 (249)
...+.++.+|++.. +++++|+|++|||.++.||+|++||++.++|.+||||++...
T Consensus 62 ~~~~~~~~~~~~~~~~~~l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~ 120 (216)
T PF02902_consen 62 KDFYNGVQRWFRKKNKKNLFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNN 120 (216)
T ss_dssp HHCHHHCGGGGTTCCTSTGGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH
T ss_pred hHhhhhhhhhhhccccccccccCEEEEEEechhhccceeEEcccccEEEEEeccccccc
Confidence 45789999999988 999999999999997799999999999999999999999887
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=98.22 E-value=2.3e-06 Score=77.03 Aligned_cols=48 Identities=23% Similarity=0.432 Sum_probs=43.4
Q ss_pred ccCceeecEEEEeeeCCC--------CeEEEEEEEcCCCeEEEEeCCCCCCchhHH
Q 036268 170 SKSMTDVDMLLIPVNLDG--------AHWVVARVDFRKNKVWIYDSLLTFCDDKRY 217 (249)
Q Consensus 170 kVDIFskDlILIPInv~n--------~HW~LaVId~r~K~I~YYDSLgg~n~~~~~ 217 (249)
..+++++|+|++|||-++ +||+|-|+..++.++.||||+++.|...+-
T Consensus 82 pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~ 137 (223)
T KOG3246|consen 82 PLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAK 137 (223)
T ss_pred hhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHH
Confidence 568999999999999875 599999999999999999999999987643
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.32 E-value=4.7e-05 Score=75.96 Aligned_cols=70 Identities=16% Similarity=0.190 Sum_probs=53.2
Q ss_pred CchhhHHHhhhhhhcCCCccccceeccc--cccccccccccccccCceeecEEEEeeeCCCCeEEEEEEEcCCCe
Q 036268 129 IPDWVHKVFLNQLWNNGDCAVDSLVFED--HLNNYLCGRQHTMSKSMTDVDMLLIPVNLDGAHWVVARVDFRKNK 201 (249)
Q Consensus 129 ~p~wv~~~F~nq~~~~g~c~~~~l~~~d--~l~GY~~VkRWTkkVDIFskDlILIPInv~n~HW~LaVId~r~K~ 201 (249)
+-++.| ||+.||+...|..-.=--++ .......+++|++.+|+|.+|.|++|+|.. .||.||+|+.+.+.
T Consensus 391 ~s~~~h--~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~~~d~~~k~yi~~P~~E~-~hw~laiic~p~~e 462 (595)
T KOG0779|consen 391 LSNDRH--IFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTRHFDLFNKDYVFVPTHER-FHWKLAIICNPDLE 462 (595)
T ss_pred cCcchh--hhhhHHHhhhhhhhhhhhhhhhhccccCceeeeeeccccccceeEEecCchH-hhhhccccccCccc
Confidence 335666 77777777777532111122 224788999999999999999999999998 99999999998753
No 7
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=82.69 E-value=0.34 Score=48.69 Aligned_cols=81 Identities=21% Similarity=0.276 Sum_probs=56.0
Q ss_pred ccchhhHHHHHHHhcCCCchhhhhccccccceeeecccccceeeeeeeh--hhccCcccchhhhhhcccCccccccceee
Q 036268 43 GFTSGVQAWIYEAIGGLPSTCVVKTKNKIPRIVQWKPMASSRINFAEVY--SFFNDESRIGDVLQTLEPNSKESSKKYWL 120 (249)
Q Consensus 43 ~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~riv~~~~~~~~~~n~~~~~--~~f~~~~r~~~v~q~Lq~~~k~~~kr~~l 120 (249)
+.|---++=+.+|.++- |...-+|..+.+.+.+=.+.+|. +|+|||. |++++++|.+-++...
T Consensus 290 ~l~~~~~~~~~~~~~~~---------~~~~~~~~~~~i~It~~dl~tl~~~~WLNDev-INfYm~ll~ers~~~~----- 354 (511)
T KOG0778|consen 290 PLTEEREAQVQRAFSSR---------NSTEILVTHFNIDITGKDLQTLRPGNWLNDEV-INFYMELLKERSKKDS----- 354 (511)
T ss_pred cccHHHHHHHHHHhccC---------CcccceehhccccccHHHHhhccCccchhHHH-HHHHHHHHHhhccccC-----
Confidence 34445556666666643 33455677777888888999998 9999999 9999999999874331
Q ss_pred eecCCCCCCc--hhhHHHhhhhhhcCC
Q 036268 121 TVKDYMPSIP--DWVHKVFLNQLWNNG 145 (249)
Q Consensus 121 T~~d~~~~~p--~wv~~~F~nq~~~~g 145 (249)
..| +.+|+|||..+-..|
T Consensus 355 -------~yp~~h~FnTFFy~kL~~~g 374 (511)
T KOG0778|consen 355 -------KYPKVHAFNTFFYTKLVGRG 374 (511)
T ss_pred -------CCceEEEEechhhhhhhhcc
Confidence 133 455667776665443
No 8
>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=80.43 E-value=2.2 Score=42.25 Aligned_cols=40 Identities=20% Similarity=0.271 Sum_probs=34.4
Q ss_pred cCceeecEEEEeeeCCCCeEEEEEEEcCCCeEEEEeCCCCC
Q 036268 171 KSMTDVDMLLIPVNLDGAHWVVARVDFRKNKVWIYDSLLTF 211 (249)
Q Consensus 171 VDIFskDlILIPInv~n~HW~LaVId~r~K~I~YYDSLgg~ 211 (249)
|.=-++..+.+|.==. .||-|+|+|-.++-+..|||-|..
T Consensus 226 ik~~~~RyvmFgfcY~-~Hwkc~IfDk~~~~v~FydSgG~~ 265 (423)
T PF03290_consen 226 IKNSKKRYVMFGFCYM-SHWKCCIFDKEKKIVYFYDSGGNI 265 (423)
T ss_pred HhhccccEEEeeeeeh-hcceEEEEeccccEEEEEcCCCCC
Confidence 3345677889998876 999999999999999999998875
No 9
>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=33.91 E-value=52 Score=29.73 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=19.9
Q ss_pred CCCCeEEEEEEEcCCCeEEEEeCCCCCCc
Q 036268 185 LDGAHWVVARVDFRKNKVWIYDSLLTFCD 213 (249)
Q Consensus 185 v~n~HW~LaVId~r~K~I~YYDSLgg~n~ 213 (249)
.+++||.--+-|.+.+++..+|.+|=+++
T Consensus 31 tGGvHWlA~Aw~P~s~t~YmFDPfGfsd~ 59 (183)
T PF00770_consen 31 TGGVHWLAFAWDPRSRTFYMFDPFGFSDQ 59 (183)
T ss_dssp T--S-EEEEEEETTTTEEEEE-TT---HH
T ss_pred cCceeEEEEEecCCcceEEEeCCCCCCHH
Confidence 35699999999999999999999998643
No 10
>PRK11836 deubiquitinase; Provisional
Probab=32.62 E-value=1e+02 Score=30.30 Aligned_cols=65 Identities=18% Similarity=0.319 Sum_probs=39.3
Q ss_pred eecEEEEeeeCCCCeEEEEEEEc--------CCCeEEEEeCCCCC--CchhHHHHHHHHHHHHhhhhhccceeeecCCC
Q 036268 175 DVDMLLIPVNLDGAHWVVARVDF--------RKNKVWIYDSLLTF--CDDKRYKLKFKLLEVIFPRWLEYVGFYNIRPE 243 (249)
Q Consensus 175 skDlILIPInv~n~HW~LaVId~--------r~K~I~YYDSLgg~--n~~~~~~li~~yLak~l~~il~~~s~Y~i~~~ 243 (249)
-++.=++|||-+ .||.|++.-- .+.+--.|.|...- +..+..+.++.++-+.|-+. .|-=+|++.
T Consensus 218 ~k~~elFpINtg-~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~---~~~~~ik~~ 292 (403)
T PRK11836 218 PKEVQLFPINTG-GHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSLKRVINSFNSELMGE---MSNNNIKVH 292 (403)
T ss_pred cccceEEEecCC-CcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHHHHHHHhhhhhhhhh---cchhhhccc
Confidence 366778899975 9999997632 12222234444332 35678888888877766554 333344443
No 11
>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []. In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....
Probab=22.80 E-value=52 Score=31.31 Aligned_cols=62 Identities=35% Similarity=0.453 Sum_probs=36.0
Q ss_pred hhhhHHhhhccccccccccccccccccceecccchhhHHHHHHH-hcCCCchhhhhccccccceeeecccccc
Q 036268 12 SLDDALFEKNEKFKTTRLKNLDHNIEKYNLYGFTSGVQAWIYEA-IGGLPSTCVVKTKNKIPRIVQWKPMASS 83 (249)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~n~~~riv~~~~~~~~ 83 (249)
.|+.|+=+-+.+|....+--|..+-+.-+.--+.+|+.+.=+.. +||+|. +||||.+|-++|
T Consensus 2 ~l~~~~~~i~k~~g~~~i~~lg~~~~~~~~~~i~TG~~~LD~aLg~GG~p~----------G~ivEi~G~~ss 64 (322)
T PF00154_consen 2 ALEKALKQIEKKFGKGSIMRLGDNAESQNIEVISTGSPALDYALGIGGLPR----------GRIVEIYGPESS 64 (322)
T ss_dssp HHHHHHHHHHHHHTTTSSEETTS-C-GCSS-EE--S-HHHHHHTSSSSEET----------TSEEEEEESTTS
T ss_pred hHHHHHHHHHHHhCCCceeecCCcccccccceEecCCcccchhhccCcccc----------CceEEEeCCCCC
Confidence 46777777778887766555544433334455788888765543 379984 677777765543
Done!