Query 024972
Match_columns 259
No_of_seqs 136 out of 706
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 08:57:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024972.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024972hhsearch_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 2E-40 4.3E-45 319.7 4.1 156 84-240 312-501 (511)
2 PLN03189 Protease specific for 100.0 1.3E-38 2.9E-43 305.1 9.6 204 37-240 200-480 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 3.3E-36 7.1E-41 288.1 1.6 158 82-239 373-559 (578)
4 KOG3246 Sentrin-specific cyste 99.9 2.3E-23 5.1E-28 181.6 8.2 160 89-257 16-210 (223)
5 PF02902 Peptidase_C48: Ulp1 p 99.9 3E-23 6.5E-28 179.0 6.8 142 104-255 1-205 (216)
6 KOG0779 Protease, Ulp1 family 99.7 1.2E-17 2.5E-22 166.8 5.4 168 90-258 353-584 (595)
7 PRK14848 deubiquitinase SseL; 69.5 3.8 8.3E-05 37.7 2.6 22 202-223 255-276 (317)
8 PRK11836 deubiquitinase; Provi 67.3 8.8 0.00019 36.1 4.5 23 202-224 306-328 (403)
9 PF03421 YopJ: YopJ Serine/Thr 58.7 4.9 0.00011 34.7 1.2 33 192-224 132-164 (177)
10 PF03290 Peptidase_C57: Vaccin 45.3 14 0.0003 35.9 1.9 29 201-229 323-351 (423)
11 KOG3315 Transport protein part 33.5 41 0.00088 29.3 2.8 31 197-227 130-160 (191)
12 PRK15371 effector protein YopJ 33.0 27 0.00058 32.7 1.8 31 194-224 157-187 (287)
13 PF03412 Peptidase_C39: Peptid 27.6 42 0.0009 26.1 1.8 28 199-227 3-30 (131)
14 cd02424 Peptidase_C39E A sub-f 20.9 90 0.0019 24.4 2.6 20 201-220 4-23 (129)
15 PF08095 Toxin_25: Hefutoxin f 20.1 47 0.001 19.0 0.5 6 30-35 6-11 (22)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-40 Score=319.71 Aligned_cols=156 Identities=29% Similarity=0.469 Sum_probs=130.6
Q ss_pred cCCCCccceeccccccccCCCCCCHHHHHHHHHHHHhhhcccccCCeeeeeccccccccCCcchHHHHHHhhhcCCcccc
Q 024972 84 IKGKNSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSEDKKAGFTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKK 163 (259)
Q Consensus 84 ~~~k~~~si~~~Dl~~L~~~~WLND~IInfYle~L~~~~~~~~~~~~~~~~s~FF~~~l~~~~~~~V~rw~k~~~Lf~kd 163 (259)
....+.+.||.+||.||.+++||||+||||||++|.+....+.+.+.+|++|+|||+.|...||++|+|||++++||++|
T Consensus 312 ~~~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~~~gy~~VkRWTk~v~if~~d 391 (511)
T KOG0778|consen 312 LVTHFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLVGRGYAGVKRWTKKVDIFDKD 391 (511)
T ss_pred eehhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEEEechhhhhhhhcchHHHHhHhhccCccccc
Confidence 33444599999999999999999999999999999765554444778999999999999999999999999999999999
Q ss_pred eEEEee---eccc--hhh-------ccccCC--------------chHHHhhhcCCCC--------CCCCCCCCcCCCch
Q 024972 164 YVLVPI---VCWF--VMD-------IYKAED--------------RPETKELISRIPL--------LVPKVPQQRNGEEC 209 (259)
Q Consensus 164 ~IfIPI---~HW~--vlD-------sl~s~~--------------~~e~k~~i~~i~~--------~~~~~PqQ~Ng~DC 209 (259)
+||||| +||. +|| +|||++ ..|+.++ ++..+ .+.++|||.||+||
T Consensus 392 ~i~vPIH~~vHW~l~vid~r~k~i~y~DS~~~~~nr~~~aL~~Yl~~E~~~k-~~~~~d~s~w~~~~~~~iP~Q~Ng~DC 470 (511)
T KOG0778|consen 392 IIFVPIHLGVHWCLAVIDLREKTIEYYDSLGGGPNRICDALAKYLQDESRDK-SKKDFDVSGWTIEFVQNIPQQRNGSDC 470 (511)
T ss_pred eeEeeeecCceEEEEEEEcccceEEEeeccCCCCcchHHHHHHHHHHHHhhh-hcCCCCccchhhhhhhccccccCCCcc
Confidence 999999 9994 333 556654 2333332 22232 15789999999999
Q ss_pred hHHHHHHHHHHhcCCCCccCCCCCcchhhcC
Q 024972 210 GNFVLYFINLFVEGAPENFNLEDYPYFMEKN 240 (259)
Q Consensus 210 GvfVL~~a~~l~~~~p~~f~~~dmp~fr~~~ 240 (259)
|||+|+||++++.+.|++|+|+|||+||++|
T Consensus 471 G~f~c~~~~~~s~~~p~~ftq~dmp~fR~~m 501 (511)
T KOG0778|consen 471 GMFVCKYADYISRDVPLTFTQQDMPYFRKKM 501 (511)
T ss_pred ceEEeeechhhccCCCcccChhhhHHHHHHH
Confidence 9999999999999999999999999999874
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.3e-38 Score=305.09 Aligned_cols=204 Identities=20% Similarity=0.282 Sum_probs=153.9
Q ss_pred HHHHHHhhhhhhhhhhhcccccCCcccccccccccccc--------------------------------ccccccc--c
Q 024972 37 VAFLHARKMKISKQKIRNFELTAPCFLGTFSCRRRSKR--------------------------------RVKCKNT--S 82 (259)
Q Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~sk~--------------------------------~~~~~~~--~ 82 (259)
|.++++|+|+++.++.|+.+|.+-.|...+.+++++-- +....+. .
T Consensus 200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pLT~e~~~~V~~al~~~~~~~v 279 (490)
T PLN03189 200 VLSVEAYRKLLQSAERRNSKLKDLGFEIELNEKRLSSLRQSRPKPKEPVEEVPREPFIPLTREEETEVKRAFSANNRRKV 279 (490)
T ss_pred ccccHHHHHHHHHHHhhcchhhhccceeehhhhHHHHHhhhccCccccccccccccCcCCCHHHHHHHHHHhcCCCccce
Confidence 77899999999999999999999999999998887710 0111110 1
Q ss_pred ccC-CCCccceeccccccccCCCCCCHHHHHHHHHHHHhhhcc-cccCCeeeeeccccccccCCc----chHHHHHHhhh
Q 024972 83 LIK-GKNSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSE-DKKAGFTYLDSLWFDLYRKPS----SKAKVLTWIKR 156 (259)
Q Consensus 83 ~~~-~k~~~si~~~Dl~~L~~~~WLND~IInfYle~L~~~~~~-~~~~~~~~~~s~FF~~~l~~~----~~~~V~rw~k~ 156 (259)
+.. ++..++||..|+.+|.|++||||+||||||++|.+.... ......+|++++||++.|... +|+.|++|+++
T Consensus 280 lvs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~ 359 (490)
T PLN03189 280 LVTHENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQ 359 (490)
T ss_pred eeecCCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhh
Confidence 121 344678999999999999999999999999999753221 222345778888888777554 79999999975
Q ss_pred ----cCCcccceEEEee---eccch---------hhccccCCchH--------------HHhhh------cCCCCC-CCC
Q 024972 157 ----KHIFSKKYVLVPI---VCWFV---------MDIYKAEDRPE--------------TKELI------SRIPLL-VPK 199 (259)
Q Consensus 157 ----~~Lf~kd~IfIPI---~HW~v---------lDsl~s~~~~e--------------~k~~i------~~i~~~-~~~ 199 (259)
++||++|+||||| +||++ |-+|||++... +++.. ..+... ..+
T Consensus 360 kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~~~vL~~L~rYL~~E~kdK~g~d~D~s~W~~~~~~~ 439 (490)
T PLN03189 360 KKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRDPKILDALAKYYVDEVKDKSEKDIDVSSWEQEFVED 439 (490)
T ss_pred cccccccccCceEEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHhhhcCCCcchhcceeccCCC
Confidence 4689999999999 89942 12344443322 11110 112222 468
Q ss_pred CCCCcCCCchhHHHHHHHHHHhcCCCCccCCCCCcchhhcC
Q 024972 200 VPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEKN 240 (259)
Q Consensus 200 ~PqQ~Ng~DCGvfVL~~a~~l~~~~p~~f~~~dmp~fr~~~ 240 (259)
+|||.||+|||||||+||++++.+.+++|+|+|||+||+++
T Consensus 440 vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrRm 480 (490)
T PLN03189 440 LPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLRT 480 (490)
T ss_pred CCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHHH
Confidence 99999999999999999999999999999999999999874
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.3e-36 Score=288.05 Aligned_cols=158 Identities=29% Similarity=0.435 Sum_probs=130.8
Q ss_pred cccCCCCccceeccccccccCCCCCCHHHHHHHHHHHHhhhcccccCCeeeeeccccccccCCcchHHHHHHhhhcCCcc
Q 024972 82 SLIKGKNSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSEDKKAGFTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFS 161 (259)
Q Consensus 82 ~~~~~k~~~si~~~Dl~~L~~~~WLND~IInfYle~L~~~~~~~~~~~~~~~~s~FF~~~l~~~~~~~V~rw~k~~~Lf~ 161 (259)
+|..++.++.||-.|+.+|.+++||||.||||||+||.......-...-+|++++|||+.|...||++|+||+++++||+
T Consensus 373 ~~~~~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~~s~~~~vh~FnTFFYT~LsrrGy~gVrrW~kk~dif~ 452 (578)
T COG5160 373 YPFNDRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKNTSKREQVHLFNTFFYTKLSRRGYSGVRRWTKKTDIFS 452 (578)
T ss_pred ccccCcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccCcccccceEEeehhhHHHHHHHHhHHHHHHHhccCccc
Confidence 57889999999999999999999999999999999994332222234557899999999999899999999999999999
Q ss_pred cceEEEee---eccc------------hhhccc-----------cCCchHHHhhhc---CCCCCCCCCCCCcCCCchhHH
Q 024972 162 KKYVLVPI---VCWF------------VMDIYK-----------AEDRPETKELIS---RIPLLVPKVPQQRNGEECGNF 212 (259)
Q Consensus 162 kd~IfIPI---~HW~------------vlDsl~-----------s~~~~e~k~~i~---~i~~~~~~~PqQ~Ng~DCGvf 212 (259)
++|||||| .||+ ++|++. +|+..|++..+. .+.+...++|||.||+|||||
T Consensus 453 ~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y~ldE~k~~~~k~~~~~~~~~~vPqQ~Ng~DCGV~ 532 (578)
T COG5160 453 KKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSYLLDEYKIQHDKDPQIKMKHCKVPQQRNGSDCGVF 532 (578)
T ss_pred cceEEEEecccceEEEEEeecCcceeEEecccccCcHHHHHHHHHHHHHHHhcccCCchhhhhhcCCCCCCCCCCccceE
Confidence 99999999 8994 223332 233344443322 233457899999999999999
Q ss_pred HHHHHHHHhcCCCCccCCCCCcchhhc
Q 024972 213 VLYFINLFVEGAPENFNLEDYPYFMEK 239 (259)
Q Consensus 213 VL~~a~~l~~~~p~~f~~~dmp~fr~~ 239 (259)
||++++++++++|+.|.+.|+|.+|+.
T Consensus 533 vc~~~~~~~~~~p~~f~~nd~~r~Rk~ 559 (578)
T COG5160 533 VCMFIRYFLENPPEQFSKNDRPRARKN 559 (578)
T ss_pred EEEeeeecccCChhhcCccchHHHHHH
Confidence 999999999999999999999999975
No 4
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.89 E-value=2.3e-23 Score=181.61 Aligned_cols=160 Identities=16% Similarity=0.211 Sum_probs=107.9
Q ss_pred ccceeccccccccCCCCCCHHHHHHHHHHHHhhhcccccCCeeeeec--cccccccCCcchHHHHHHhhhcCCcccceEE
Q 024972 89 SSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSEDKKAGFTYLDS--LWFDLYRKPSSKAKVLTWIKRKHIFSKKYVL 166 (259)
Q Consensus 89 ~~si~~~Dl~~L~~~~WLND~IInfYle~L~~~~~~~~~~~~~~~~s--~FF~~~l~~~~~~~V~rw~k~~~Lf~kd~If 166 (259)
.+.++.+|++.|+++.||||.+|+||.|||.+........ ..++.+ +||.. .+...+.+.......++.+|++||
T Consensus 16 dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s~~~-~~ll~P~~t~~l~--~~~~~~e~~~~~~pl~l~~k~~if 92 (223)
T KOG3246|consen 16 DVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSEPD-LHLLRPSLTFFLR--HAPNPEEIAMVLDPLDLNDKDFIF 92 (223)
T ss_pred ehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccCcc-hhccCHHHHHHHH--hCCCcHHHHHhcChhhcCCCceEE
Confidence 4578999999999999999999999999997754332222 122222 23321 244567888899999999999999
Q ss_pred Eee------------eccc------------hhhccccCCchHHHhhh-------cCC-CCC-CCCCCCCcCCCchhHHH
Q 024972 167 VPI------------VCWF------------VMDIYKAEDRPETKELI-------SRI-PLL-VPKVPQQRNGEECGNFV 213 (259)
Q Consensus 167 IPI------------~HW~------------vlDsl~s~~~~e~k~~i-------~~i-~~~-~~~~PqQ~Ng~DCGvfV 213 (259)
+|| +||+ +.||+........+.++ ++. ... ...+|||+||||||+||
T Consensus 93 lpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~~~~~~~~qQqNgyDCG~hV 172 (223)
T KOG3246|consen 93 LPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAKRVECKCLQQQNGYDCGLHV 172 (223)
T ss_pred EEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHHHHHHHHHHhhhhhhcccccChhhhcCCchhHHH
Confidence 999 6995 44555555544444432 111 112 67889999999999999
Q ss_pred HHHHHHHhcCCCCccCCCCCcchhhcCCcChHhHHHHHHHhhhc
Q 024972 214 LYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNSS 257 (259)
Q Consensus 214 L~~a~~l~~~~p~~f~~~dmp~fr~~~wF~~e~~~~~r~~l~~~ 257 (259)
|++++.++... .+..|+... .-..+.-++++|+.|..|
T Consensus 173 ~~~t~~l~~~~----~~~~~~~~~--~~~~~~~i~~lr~~l~~L 210 (223)
T KOG3246|consen 173 CCNTRVLAERL----LRCPYATSS--QLLVVDLIKALREELLDL 210 (223)
T ss_pred HHHHHHHHHHH----hcccccccc--chhhHHHHHHHHHHHHHH
Confidence 99999988653 122222210 112345677788777654
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=99.88 E-value=3e-23 Score=178.97 Aligned_cols=142 Identities=29% Similarity=0.543 Sum_probs=92.2
Q ss_pred CCCCHHHHHHHHHHHHhhhc-ccccCCeeeeeccccccccC--------------------CcchHHHHHHhhhc---CC
Q 024972 104 NKLDSGKFEHLLDNLWRSFS-EDKKAGFTYLDSLWFDLYRK--------------------PSSKAKVLTWIKRK---HI 159 (259)
Q Consensus 104 ~WLND~IInfYle~L~~~~~-~~~~~~~~~~~s~FF~~~l~--------------------~~~~~~V~rw~k~~---~L 159 (259)
+||||+|||||+++|..... +......+++.+++|+..+. ...+..+.+|.+.. ++
T Consensus 1 ~wLnd~iId~y~~~l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 80 (216)
T PF02902_consen 1 EWLNDSIIDFYLEYLRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKKNL 80 (216)
T ss_dssp --EEHHHHHHHHHHHHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTSTG
T ss_pred CcCCHHHHHHHHHHHHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhccccccc
Confidence 69999999999999974332 22223334555555544443 12356778899887 99
Q ss_pred cccceEEEee----eccc------------hhhccccCCc-hHHH----hh---h---------cCC---CCC---CCCC
Q 024972 160 FSKKYVLVPI----VCWF------------VMDIYKAEDR-PETK----EL---I---------SRI---PLL---VPKV 200 (259)
Q Consensus 160 f~kd~IfIPI----~HW~------------vlDsl~s~~~-~e~k----~~---i---------~~i---~~~---~~~~ 200 (259)
+++++||+|| .||+ ++||+.+... .... .. + ... ++. ..++
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDPDKSPFKIVRPPNV 160 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTCEEEEECTS
T ss_pred cccCEEEEEEechhhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhccccccccccccceeeecccccc
Confidence 9999999999 7994 3455544433 0000 00 0 011 221 4689
Q ss_pred CCCcCCCchhHHHHHHHHHHhcCCCCccCCCCCcchhhcCCcChHhHHHHHHHhh
Q 024972 201 PQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLN 255 (259)
Q Consensus 201 PqQ~Ng~DCGvfVL~~a~~l~~~~p~~f~~~dmp~fr~~~wF~~e~~~~~r~~l~ 255 (259)
|||.||+|||+|||+||++++.+.+....+. |+.+++..+|+++.
T Consensus 161 pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~----------l~~~~i~~~r~~~a 205 (216)
T PF02902_consen 161 PQQPNGYDCGVYVLKFMECLLEGPSFDFSQE----------LTEEDIKNFRKKLA 205 (216)
T ss_dssp -SSSSSSCHHHHHHHHHHHHHCTHHSTGCCS----------BTGHHHHHHHHHHH
T ss_pred cCCCCCCCcHHHHHHHHHHHHhCCCCccccc----------CCHHHHHHHHHHHH
Confidence 9999999999999999999999986664432 56677777777765
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.69 E-value=1.2e-17 Score=166.80 Aligned_cols=168 Identities=25% Similarity=0.428 Sum_probs=126.1
Q ss_pred cceeccccccccCCCCCCHHHHHHHHHHHHhhhcc-cccCCeeeeeccccccccCCc------------chHHHHHHhhh
Q 024972 90 SSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSE-DKKAGFTYLDSLWFDLYRKPS------------SKAKVLTWIKR 156 (259)
Q Consensus 90 ~si~~~Dl~~L~~~~WLND~IInfYle~L~~~~~~-~~~~~~~~~~s~FF~~~l~~~------------~~~~V~rw~k~ 156 (259)
.+++..|+..|.++++|||-|++||++++...... .......+++++||+..+... ...++++|++.
T Consensus 353 ~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~~ 432 (595)
T KOG0779|consen 353 HQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTRH 432 (595)
T ss_pred cceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeeec
Confidence 38999999999999999999999999999875433 333566788888888865421 24568899999
Q ss_pred cCCcccceEEEee---eccchhh------------------ccccCCchHH----Hh-----------h--h--------
Q 024972 157 KHIFSKKYVLVPI---VCWFVMD------------------IYKAEDRPET----KE-----------L--I-------- 190 (259)
Q Consensus 157 ~~Lf~kd~IfIPI---~HW~vlD------------------sl~s~~~~e~----k~-----------~--i-------- 190 (259)
+++|.++||++|+ .||..-. +...-..... .. . .
T Consensus 433 ~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 (595)
T KOG0779|consen 433 FDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELEEE 512 (595)
T ss_pred cccccceeEEecCchHhhhhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCccccccccccccc
Confidence 9999999999999 8993211 1000000000 00 0 0
Q ss_pred --cCCC---CCCCCCCCCcCCCchhHHHHHHHHHHhcCCCCccCCCCCcchhhcCCcChHhHHHHHHHhhhcc
Q 024972 191 --SRIP---LLVPKVPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNSSE 258 (259)
Q Consensus 191 --~~i~---~~~~~~PqQ~Ng~DCGvfVL~~a~~l~~~~p~~f~~~dmp~fr~~~wF~~e~~~~~r~~l~~~~ 258 (259)
.+.+ -.....|||.|..|||+|++.|++.+..++|..++..+...+.+. ||.|.++.+||+.+|.+.
T Consensus 513 ~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~-~~~~~~~~~~r~~~r~~~ 584 (595)
T KOG0779|consen 513 LPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLE-WFPPKEILKFRDEIRNLG 584 (595)
T ss_pred ccccCcccccccccccCccCcccchhhHHHHHHHhhhChhhhcccccccccccc-cCCchHHhhhhhhhhccc
Confidence 0111 011223999999999999999999999999999998888888877 999999999999999874
No 7
>PRK14848 deubiquitinase SseL; Provisional
Probab=69.53 E-value=3.8 Score=37.68 Aligned_cols=22 Identities=27% Similarity=0.437 Sum_probs=17.6
Q ss_pred CCcCCCchhHHHHHHHHHHhcC
Q 024972 202 QQRNGEECGNFVLYFINLFVEG 223 (259)
Q Consensus 202 qQ~Ng~DCGvfVL~~a~~l~~~ 223 (259)
||.-..-||.|||.+++.+..+
T Consensus 255 QqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 255 QNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred hhhCCCcchHHHHHHHHHHHhc
Confidence 4445778999999999977755
No 8
>PRK11836 deubiquitinase; Provisional
Probab=67.26 E-value=8.8 Score=36.11 Aligned_cols=23 Identities=30% Similarity=0.427 Sum_probs=18.0
Q ss_pred CCcCCCchhHHHHHHHHHHhcCC
Q 024972 202 QQRNGEECGNFVLYFINLFVEGA 224 (259)
Q Consensus 202 qQ~Ng~DCGvfVL~~a~~l~~~~ 224 (259)
||.-..-||.|||+.+.-++.+.
T Consensus 306 Qq~vpngCGlFv~~a~Qe~i~q~ 328 (403)
T PRK11836 306 QQYLSQSCGAFVCMAAQEVIEQR 328 (403)
T ss_pred hhcCCCccceehHHHHHHHHHHh
Confidence 45457889999999998776655
No 9
>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=58.68 E-value=4.9 Score=34.72 Aligned_cols=33 Identities=18% Similarity=0.327 Sum_probs=27.6
Q ss_pred CCCCCCCCCCCCcCCCchhHHHHHHHHHHhcCC
Q 024972 192 RIPLLVPKVPQQRNGEECGNFVLYFINLFVEGA 224 (259)
Q Consensus 192 ~i~~~~~~~PqQ~Ng~DCGvfVL~~a~~l~~~~ 224 (259)
...+.+..+..|...+|||||-|.+|.....+.
T Consensus 132 ~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~~ 164 (177)
T PF03421_consen 132 NAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKED 164 (177)
T ss_pred CcEEEEEecccccCcCcchhhHHHHHHHHhhcc
Confidence 344557889999999999999999999987654
No 10
>PF03290 Peptidase_C57: Vaccinia virus I7 processing peptidase; InterPro: IPR004970 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This is a group of cysteine peptidases which constitute MEROPS peptidase family C57 (clan CE). The type example is vaccinia virus I7 processing peptidase (vaccinia virus); protein I7 is expressed in the late phase of infection [].
Probab=45.29 E-value=14 Score=35.93 Aligned_cols=29 Identities=31% Similarity=0.528 Sum_probs=25.0
Q ss_pred CCCcCCCchhHHHHHHHHHHhcCCCCccC
Q 024972 201 PQQRNGEECGNFVLYFINLFVEGAPENFN 229 (259)
Q Consensus 201 PqQ~Ng~DCGvfVL~~a~~l~~~~p~~f~ 229 (259)
-.|--.+|||||.+-|+-..+..+|..|.
T Consensus 323 vnQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 323 VNQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred hhhhcccccchHHHHHHHHHHccCchhHH
Confidence 46778999999999999998898888764
No 11
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.50 E-value=41 Score=29.31 Aligned_cols=31 Identities=23% Similarity=0.347 Sum_probs=27.6
Q ss_pred CCCCCCCcCCCchhHHHHHHHHHHhcCCCCc
Q 024972 197 VPKVPQQRNGEECGNFVLYFINLFVEGAPEN 227 (259)
Q Consensus 197 ~~~~PqQ~Ng~DCGvfVL~~a~~l~~~~p~~ 227 (259)
...+|.-.|+-.|+-||+-.++.++.++.+.
T Consensus 130 fISVPke~~~lnc~~fvaGIiea~L~~agfp 160 (191)
T KOG3315|consen 130 FISVPKENGTLNCAAFVAGIIEAVLDNAGFP 160 (191)
T ss_pred ceecccccCcccHHHHHHHHHHHHHHhCCCC
Confidence 5788999999999999999999999887554
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=33.01 E-value=27 Score=32.68 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=26.1
Q ss_pred CCCCCCCCCCcCCCchhHHHHHHHHHHhcCC
Q 024972 194 PLLVPKVPQQRNGEECGNFVLYFINLFVEGA 224 (259)
Q Consensus 194 ~~~~~~~PqQ~Ng~DCGvfVL~~a~~l~~~~ 224 (259)
.|.+...-.|.-.+|||||-|.+|.+.....
T Consensus 157 ~~avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 157 HFSMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred eEEEEecccccCcccchhhhHHHHHHHhhhh
Confidence 3446777889999999999999999988765
No 13
>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=27.55 E-value=42 Score=26.10 Aligned_cols=28 Identities=25% Similarity=0.476 Sum_probs=14.7
Q ss_pred CCCCCcCCCchhHHHHHHHHHHhcCCCCc
Q 024972 199 KVPQQRNGEECGNFVLYFINLFVEGAPEN 227 (259)
Q Consensus 199 ~~PqQ~Ng~DCGvfVL~~a~~l~~~~p~~ 227 (259)
++-+|....|||+-.|+++-.. .+.+.+
T Consensus 3 ~~v~Q~~~~dcg~acl~~l~~~-~g~~~s 30 (131)
T PF03412_consen 3 PVVKQSDSNDCGLACLAMLLKY-YGIPVS 30 (131)
T ss_dssp -----SSTT-HHHHHHHHHHHH-TT----
T ss_pred CeEEeCCCCCHHHHHHHHHHHH-hCCCch
Confidence 3457889999999999777666 444443
No 14
>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=20.94 E-value=90 Score=24.41 Aligned_cols=20 Identities=20% Similarity=0.338 Sum_probs=15.5
Q ss_pred CCCcCCCchhHHHHHHHHHH
Q 024972 201 PQQRNGEECGNFVLYFINLF 220 (259)
Q Consensus 201 PqQ~Ng~DCGvfVL~~a~~l 220 (259)
-+|....|||+..|..+-..
T Consensus 4 ~~q~~~~dcgla~l~~i~~~ 23 (129)
T cd02424 4 IKQTDLNDCGIAVIQMLYNH 23 (129)
T ss_pred EEecCccchHHHHHHHHHHH
Confidence 35778889999988776655
No 15
>PF08095 Toxin_25: Hefutoxin family; InterPro: IPR012630 This family consists of the hefutoxins that are found in the venom of the scorpion Heterometrus fulvipes (Indian black scorpion). These toxins, kappa-hefutoxin1 and kappa-hefutoxin2, exhibit no homology to any known toxins. The hefutoxins are potassium channel toxins [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1HP9_A.
Probab=20.07 E-value=47 Score=18.95 Aligned_cols=6 Identities=50% Similarity=1.608 Sum_probs=5.0
Q ss_pred chhHHH
Q 024972 30 RTCWLH 35 (259)
Q Consensus 30 ~~~~~~ 35 (259)
|+||+.
T Consensus 6 rscwk~ 11 (22)
T PF08095_consen 6 RSCWKA 11 (22)
T ss_dssp THHHHH
T ss_pred HHHHHc
Confidence 899984
Done!