Query 022034
Match_columns 303
No_of_seqs 153 out of 1046
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 07:30:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022034.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022034hhsearch_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 1.2E-45 2.5E-50 358.3 10.4 183 88-283 316-500 (511)
2 PLN03189 Protease specific for 100.0 4.9E-43 1.1E-47 337.5 17.4 186 86-283 284-479 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 2.4E-41 5.1E-46 324.3 9.4 181 86-282 377-558 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 5.1E-30 1.1E-34 226.9 13.0 175 104-299 1-205 (216)
5 KOG3246 Sentrin-specific cyste 100.0 1.5E-28 3.3E-33 214.0 13.2 184 88-301 15-210 (223)
6 KOG0779 Protease, Ulp1 family 99.8 1.3E-19 2.8E-24 183.1 7.0 210 89-302 352-584 (595)
7 PF03290 Peptidase_C57: Vaccin 97.2 0.00082 1.8E-08 64.1 7.0 94 160-274 229-352 (423)
8 PRK11836 deubiquitinase; Provi 97.0 0.0017 3.6E-08 60.1 6.1 159 102-268 162-328 (403)
9 PRK14848 deubiquitinase SseL; 96.7 0.0046 1E-07 56.1 6.8 88 163-268 189-277 (317)
10 PF00770 Peptidase_C5: Adenovi 92.6 0.18 3.9E-06 43.5 4.3 81 172-270 33-120 (183)
11 PF03421 YopJ: YopJ Serine/Thr 90.2 2.1 4.6E-05 37.3 8.8 89 165-268 74-164 (177)
12 PRK15371 effector protein YopJ 80.8 10 0.00022 35.6 8.6 67 193-268 121-187 (287)
13 PF12252 SidE: Dot/Icm substra 58.2 24 0.00052 38.7 6.3 31 171-211 61-91 (1439)
14 PF07797 DUF1639: Protein of u 44.1 6.2 0.00013 27.2 -0.4 15 98-112 34-48 (50)
15 KOG3315 Transport protein part 36.8 36 0.00077 29.6 3.0 30 241-270 130-159 (191)
16 PF03412 Peptidase_C39: Peptid 22.9 57 0.0012 25.7 1.9 23 243-265 3-25 (131)
17 PF08095 Toxin_25: Hefutoxin f 20.8 48 0.001 18.6 0.6 6 30-35 6-11 (22)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-45 Score=358.33 Aligned_cols=183 Identities=25% Similarity=0.399 Sum_probs=159.3
Q ss_pred CCeeeecccccccCCCCCCCHHHHHHHHHHHHhhhcccc-CCCeEEEechhhhhhcCCCchHHHHHHHhhccccccceEE
Q 022034 88 NSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSEDK-KAGFTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKKYVL 166 (303)
Q Consensus 88 ~~~~i~~~Dl~~L~~~~wLND~iI~~yl~~L~~~~~~~~-~~~~~~~~s~ff~~l~~~~~~~~v~~w~k~~~if~k~~I~ 166 (303)
++++||.+||.||.+++||||+||||||++|.+....+. -.++|+||+|||++|. ..||++|+|||+++|||++|.||
T Consensus 316 ~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~-~~gy~~VkRWTk~v~if~~d~i~ 394 (511)
T KOG0778|consen 316 FNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLV-GRGYAGVKRWTKKVDIFDKDIIF 394 (511)
T ss_pred ccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEEEechhhhhhh-hcchHHHHhHhhccCccccceeE
Confidence 569999999999999999999999999999987554332 2568999999999987 56899999999999999999999
Q ss_pred EeeecCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCCcccccCCceee-CCCCC
Q 022034 167 VPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLL-VPKVP 245 (303)
Q Consensus 167 iPIn~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~-~~~vP 245 (303)
||||.+.||+|+||+. ++++|.|||||++...+.. ..|.+||.+++..+.+. .+....|.+. ..++|
T Consensus 395 vPIH~~vHW~l~vid~---------r~k~i~y~DS~~~~~nr~~-~aL~~Yl~~E~~~k~~~--~~d~s~w~~~~~~~iP 462 (511)
T KOG0778|consen 395 VPIHLGVHWCLAVIDL---------REKTIEYYDSLGGGPNRIC-DALAKYLQDESRDKSKK--DFDVSGWTIEFVQNIP 462 (511)
T ss_pred eeeecCceEEEEEEEc---------ccceEEEeeccCCCCcchH-HHHHHHHHHHHhhhhcC--CCCccchhhhhhhccc
Confidence 9999999999999995 4589999999997765434 79999999988765432 2344678864 45899
Q ss_pred CCCCCCchHHHHHHHHHHHHcCCCCCcCCCCCcchhhc
Q 022034 246 QQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEK 283 (303)
Q Consensus 246 qQ~N~~DCGvfVl~f~~~~~~~~~~~f~~~d~p~fr~~ 283 (303)
||.||+|||||||+|++|+.++.|+.|+|.|||+||+.
T Consensus 463 ~Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR~~ 500 (511)
T KOG0778|consen 463 QQRNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFRKK 500 (511)
T ss_pred cccCCCccceEEeeechhhccCCCcccChhhhHHHHHH
Confidence 99999999999999999999999999999999999974
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=4.9e-43 Score=337.55 Aligned_cols=186 Identities=20% Similarity=0.336 Sum_probs=157.4
Q ss_pred CCCCeeeecccccccCCCCCCCHHHHHHHHHHHHhhhc--cccCCCeEEEechhhhhhcCC---CchHHHHHHHhh----
Q 022034 86 GKNSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFS--EDKKAGFTYLDSLWFDLYRKP---SSKAKVLTWIKR---- 156 (303)
Q Consensus 86 ~~~~~~i~~~Dl~~L~~~~wLND~iI~~yl~~L~~~~~--~~~~~~~~~~~s~ff~~l~~~---~~~~~v~~w~k~---- 156 (303)
+..+++||.+||.||.|++||||+||||||.+|..... +....++|+||||||.+|... .+|++|++|+++
T Consensus 284 ~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~kKig 363 (490)
T PLN03189 284 ENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQKKLG 363 (490)
T ss_pred CCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhhcccc
Confidence 55789999999999999999999999999999976432 122257999999999998764 279999999974
Q ss_pred ccccccceEEEeeecCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCCcccccCC
Q 022034 157 KHIFSKKYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISR 236 (303)
Q Consensus 157 ~~if~k~~I~iPIn~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~~~~~~~~ 236 (303)
.++|++++||||||.+.||+|+||+++. ++|.|||||++.+.. +.+.|+.||..+++.+... ....+.
T Consensus 364 v~Lfs~D~IFIPIh~n~HWsLaVId~k~---------k~I~yyDSLgg~~~~-vL~~L~rYL~~E~kdK~g~--d~D~s~ 431 (490)
T PLN03189 364 YHLIDCDKIFVPIHQEIHWTLAVINKKD---------QKFQYLDSLKGRDPK-ILDALAKYYVDEVKDKSEK--DIDVSS 431 (490)
T ss_pred cccccCceEEeeeecCCeeEEEEEEcCC---------CeEEEEeCCCCCCHH-HHHHHHHHHHHHHhhhcCC--Ccchhc
Confidence 4689999999999999999999999643 799999999998765 4568999999888754321 123467
Q ss_pred ceee-CCCCCCCCCCCchHHHHHHHHHHHHcCCCCCcCCCCCcchhhc
Q 022034 237 IPLL-VPKVPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEK 283 (303)
Q Consensus 237 ~~~~-~~~vPqQ~N~~DCGvfVl~f~~~~~~~~~~~f~~~d~p~fr~~ 283 (303)
|... ..++|||.||+|||||||+||++++++.+++|+|+|||+||++
T Consensus 432 W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrR 479 (490)
T PLN03189 432 WEQEFVEDLPEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLR 479 (490)
T ss_pred ceeccCCCCCCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHH
Confidence 7754 5689999999999999999999999999999999999999975
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-41 Score=324.31 Aligned_cols=181 Identities=29% Similarity=0.499 Sum_probs=156.6
Q ss_pred CCCCeeeecccccccCCCCCCCHHHHHHHHHHHHhhhc-cccCCCeEEEechhhhhhcCCCchHHHHHHHhhccccccce
Q 022034 86 GKNSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFS-EDKKAGFTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKKY 164 (303)
Q Consensus 86 ~~~~~~i~~~Dl~~L~~~~wLND~iI~~yl~~L~~~~~-~~~~~~~~~~~s~ff~~l~~~~~~~~v~~w~k~~~if~k~~ 164 (303)
+..+|+||..|+.+|.+++||||+||||||+||..... .-.+.++|.|++|||++|. ..||++|++|++++|||+++|
T Consensus 377 ~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~~s~~~~vh~FnTFFYT~Ls-rrGy~gVrrW~kk~dif~~k~ 455 (578)
T COG5160 377 DRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKNTSKREQVHLFNTFFYTKLS-RRGYSGVRRWTKKTDIFSKKY 455 (578)
T ss_pred CcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccCcccccceEEeehhhHHHHH-HHHhHHHHHHHhccCccccce
Confidence 77999999999999999999999999999999954322 1234679999999998876 568999999999999999999
Q ss_pred EEEeeecCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCCcccccCCceeeCCCC
Q 022034 165 VLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLVPKV 244 (303)
Q Consensus 165 I~iPIn~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~~v 244 (303)
||||||...||+|+|||.+. +.|+|||||++.+. .+...|+.|+.++++..+... ..+.+...+|
T Consensus 456 I~iPIni~~HW~l~II~~~~---------~~i~~~DSLan~~~-~v~~~L~~Y~ldE~k~~~~k~-----~~~~~~~~~v 520 (578)
T COG5160 456 IFIPINISYHWFLAIIDNPK---------KNILYFDSLANTHD-PVLEFLRSYLLDEYKIQHDKD-----PQIKMKHCKV 520 (578)
T ss_pred EEEEecccceEEEEEeecCc---------ceeEEecccccCcH-HHHHHHHHHHHHHHhcccCCc-----hhhhhhcCCC
Confidence 99999999999999999754 78999999999985 466689999999887543311 1234567899
Q ss_pred CCCCCCCchHHHHHHHHHHHHcCCCCCcCCCCCcchhh
Q 022034 245 PQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFME 282 (303)
Q Consensus 245 PqQ~N~~DCGvfVl~f~~~~~~~~~~~f~~~d~p~fr~ 282 (303)
|||.||+|||||||+|++|++.++|..|.+.|+|.+|+
T Consensus 521 PqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk 558 (578)
T COG5160 521 PQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRARK 558 (578)
T ss_pred CCCCCCCccceEEEEeeeecccCChhhcCccchHHHHH
Confidence 99999999999999999999999999999999998876
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=99.97 E-value=5.1e-30 Score=226.89 Aligned_cols=175 Identities=27% Similarity=0.496 Sum_probs=127.0
Q ss_pred CCCCHHHHHHHHHHHHhhh--ccccCCCeEEEechhhhhhcCC-------------------CchHHHHHHHhhc---cc
Q 022034 104 NKLDSGKFEHLLDNLWRSF--SEDKKAGFTYLDSLWFDLYRKP-------------------SSKAKVLTWIKRK---HI 159 (303)
Q Consensus 104 ~wLND~iI~~yl~~L~~~~--~~~~~~~~~~~~s~ff~~l~~~-------------------~~~~~v~~w~k~~---~i 159 (303)
+||||+|||||+++|.... .+....++++++|+|+..+... ..+..+.+|++.. ++
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 6999999999999997443 2334468999999999887611 1246777888776 99
Q ss_pred cccceEEEeeec-CCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCC----cchHHHHHHHHHHHHHhcCCCCccccc
Q 022034 160 FSKKYVLVPIVC-WRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNP----WRFEPDIRKFVMDIYKAEDRPETKELI 234 (303)
Q Consensus 160 f~k~~I~iPIn~-~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~----~~l~~~i~~~L~~~~~~~~~~~~~~~~ 234 (303)
+++++|++|||. +.||+|+||+.+. .+|++||||+.... ..+...+..+|...+....... ...
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~---------~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~ 149 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPK---------KRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRD--PDK 149 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTT---------TEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSC--T-T
T ss_pred cccCEEEEEEechhhccceeEEcccc---------cEEEEEeccccccccccchhhhhhhhhhhhhccccccccc--ccc
Confidence 999999999999 9999999999654 79999999999886 2334567777776654322111 123
Q ss_pred CCcee-eCCCCCCCCCCCchHHHHHHHHHHHHcCCCCCcCCCCCcchhhcCCCCHHHHHHHHHHHh
Q 022034 235 SRIPL-LVPKVPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLN 299 (303)
Q Consensus 235 ~~~~~-~~~~vPqQ~N~~DCGvfVl~f~~~~~~~~~~~f~~~d~p~fr~~~Wf~~~~i~~~R~~l~ 299 (303)
..|.. ....+|||.|++|||+|||+||++++.+.+....+. |+.+++..+|+++.
T Consensus 150 ~~~~~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~----------l~~~~i~~~r~~~a 205 (216)
T PF02902_consen 150 SPFKIVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQE----------LTEEDIKNFRKKLA 205 (216)
T ss_dssp TTCEEEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCS----------BTGHHHHHHHHHHH
T ss_pred ceeeecccccccCCCCCCCcHHHHHHHHHHHHhCCCCccccc----------CCHHHHHHHHHHHH
Confidence 45554 456999999999999999999999999875543221 56667777777765
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.96 E-value=1.5e-28 Score=213.98 Aligned_cols=184 Identities=17% Similarity=0.192 Sum_probs=133.3
Q ss_pred CCeeeecccccccCCCCCCCHHHHHHHHHHHHhhhccccCCCeEEEechhhhhhcCCCchHHHHHHHhhccccccceEEE
Q 022034 88 NSSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSFSEDKKAGFTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKKYVLV 167 (303)
Q Consensus 88 ~~~~i~~~Dl~~L~~~~wLND~iI~~yl~~L~~~~~~~~~~~~~~~~s~ff~~l~~~~~~~~v~~w~k~~~if~k~~I~i 167 (303)
.++.++.+|+..|.++.||||.+|+||.+||...-..... ..+++.+-.-..+......+.+.......++++|++||+
T Consensus 15 ~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s~~-~~~ll~P~~t~~l~~~~~~~e~~~~~~pl~l~~k~~ifl 93 (223)
T KOG3246|consen 15 FDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSEP-DLHLLRPSLTFFLRHAPNPEEIAMVLDPLDLNDKDFIFL 93 (223)
T ss_pred eehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccCc-chhccCHHHHHHHHhCCCcHHHHHhcChhhcCCCceEEE
Confidence 5788999999999999999999999999999764433222 246676643333334455678888888889999999999
Q ss_pred eeecC---------CceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcc---hHHHHHHHHHHHHHhcCCCCcccccC
Q 022034 168 PIVCW---------RHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWR---FEPDIRKFVMDIYKAEDRPETKELIS 235 (303)
Q Consensus 168 PIn~~---------~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~---l~~~i~~~L~~~~~~~~~~~~~~~~~ 235 (303)
|||++ +||+|+|+..|. ..++||||+.+.+... +.++++.+|.. +..
T Consensus 94 piNDn~~~~~~~GGsHWSLLV~sr~~---------~~f~hyDS~~n~nt~~a~~l~~kl~~ll~~----~~~-------- 152 (223)
T KOG3246|consen 94 PINDNSNVTRASGGSHWSLLVFSRPD---------GKFYHYDSLSNGNTKDAKSLMKKLRALLKK----KFA-------- 152 (223)
T ss_pred EecCCCcccccCCCcceEEEEEEeeC---------CcEEEeecccCCCcHHHHHHHHHHHHHHhh----hhh--------
Confidence 99983 699999999765 6899999999998743 33344444433 211
Q ss_pred CceeeCCCCCCCCCCCchHHHHHHHHHHHHcCCCCCcCCCCCcchhhcCCCCHHHHHHHHHHHhcC
Q 022034 236 RIPLLVPKVPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNSS 301 (303)
Q Consensus 236 ~~~~~~~~vPqQ~N~~DCGvfVl~f~~~~~~~~~~~f~~~d~p~fr~~~Wf~~~~i~~~R~~l~~~ 301 (303)
......+|||.||+|||+|||.+++.++... ....|+.- .--..+..+.++|++|.+|
T Consensus 153 --~~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~----~~~~~~~~--~~~~~~~~i~~lr~~l~~L 210 (223)
T KOG3246|consen 153 --KRVECKCLQQQNGYDCGLHVCCNTRVLAERL----LRCPYATS--SQLLVVDLIKALREELLDL 210 (223)
T ss_pred --hcccccChhhhcCCchhHHHHHHHHHHHHHH----hccccccc--cchhhHHHHHHHHHHHHHH
Confidence 0115688999999999999999998888652 11112210 1123566799999998765
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.78 E-value=1.3e-19 Score=183.13 Aligned_cols=210 Identities=26% Similarity=0.430 Sum_probs=153.9
Q ss_pred CeeeecccccccCCCCCCCHHHHHHHHHHHHhhh-c-cccCCCeEEEechhhhhhcCCC-----------chHHHHHHHh
Q 022034 89 SSSVKCKDMITKRKKNKLDSGKFEHLLDNLWRSF-S-EDKKAGFTYLDSLWFDLYRKPS-----------SKAKVLTWIK 155 (303)
Q Consensus 89 ~~~i~~~Dl~~L~~~~wLND~iI~~yl~~L~~~~-~-~~~~~~~~~~~s~ff~~l~~~~-----------~~~~v~~w~k 155 (303)
.+.++..|+.+|.+++.|||.+++||++++.... + .+.....++++++|+..+.+.. ....+.+|++
T Consensus 352 ~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~ 431 (595)
T KOG0779|consen 352 SHQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTR 431 (595)
T ss_pred ccceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeee
Confidence 5699999999999999999999999999987643 2 3333678899999888766421 2457788999
Q ss_pred hccccccceEEEeeecCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCC-cc---
Q 022034 156 RKHIFSKKYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPE-TK--- 231 (303)
Q Consensus 156 ~~~if~k~~I~iPIn~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~-~~--- 231 (303)
..++|.++||++|+|...||.|+++|+|+..-+++ ......+++.......+...+..++..++....... ..
T Consensus 432 ~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 (595)
T KOG0779|consen 432 HFDLFNKDYVFVPTHERFHWKLAIICNPDLETETP---RPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLE 508 (595)
T ss_pred ccccccceeEEecCchHhhhhccccccCccccCcc---ccchhhhhhccccccchhhhhhhhhhhcccccCccccccccc
Confidence 99999999999999999999999999997654443 224455555555544445566666665443211100 00
Q ss_pred ---cccCCce---eeCCCCCCCCCCCchHHHHHHHHHHHHcCCCCCcCCCCCcchhhcCCCCHHHHHHHHHHHhcCc
Q 022034 232 ---ELISRIP---LLVPKVPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNSSE 302 (303)
Q Consensus 232 ---~~~~~~~---~~~~~vPqQ~N~~DCGvfVl~f~~~~~~~~~~~f~~~d~p~fr~~~Wf~~~~i~~~R~~l~~~~ 302 (303)
..+...+ -.....|||.|.+|||+|++.|++.++.+++..++..+...+-.. ||.|.++.++|.++.++.
T Consensus 509 ~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~-~~~~~~~~~~r~~~r~~~ 584 (595)
T KOG0779|consen 509 LEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLE-WFPPKEILKFRDEIRNLG 584 (595)
T ss_pred ccccccccCcccccccccccCccCcccchhhHHHHHHHhhhChhhhcccccccccccc-cCCchHHhhhhhhhhccc
Confidence 0011111 112233999999999999999999999999988777666655555 999999999999998874
No 7
>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=97.23 E-value=0.00082 Score=64.11 Aligned_cols=94 Identities=20% Similarity=0.247 Sum_probs=63.0
Q ss_pred cccceEEEeeecCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCc------------------------------c
Q 022034 160 FSKKYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPW------------------------------R 209 (303)
Q Consensus 160 f~k~~I~iPIn~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~------------------------------~ 209 (303)
-+++||.+|++...||..+|+|.. +.-+.+|||-|..... .
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk~---------~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~ 299 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDKE---------KKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENC 299 (423)
T ss_pred ccccEEEeeeeehhcceEEEEecc---------ccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccC
Confidence 468999999999999999999842 2446777776654310 1
Q ss_pred hHHHHHHHHHHHHHhcCCCCcccccCCceeeCCCCCCCCCCCchHHHHHHHHHHHHcCCCCCcCC
Q 022034 210 FEPDIRKFVMDIYKAEDRPETKELISRIPLLVPKVPQQRNGEECGNFVLYFINLFVEGAPENFNL 274 (303)
Q Consensus 210 l~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~~vPqQ~N~~DCGvfVl~f~~~~~~~~~~~f~~ 274 (303)
-.+.|.+|....++.+ ....... -.|--.+|||+|++.||-..+..+|..|..
T Consensus 300 dIDVLfrfF~d~f~~~-----------~gciNve-vnQl~eseCGMF~~iFm~~c~~~ppk~fk~ 352 (423)
T PF03290_consen 300 DIDVLFRFFEDSFGVK-----------YGCINVE-VNQLLESECGMFISIFMILCTLTPPKGFKS 352 (423)
T ss_pred chHHHHHHHHhhcccc-----------eeEEEhh-hhhhcccccchHHHHHHHHHHccCchhHHH
Confidence 1234555665544321 1112222 347788999999999999999998876553
No 8
>PRK11836 deubiquitinase; Provisional
Probab=96.96 E-value=0.0017 Score=60.08 Aligned_cols=159 Identities=18% Similarity=0.226 Sum_probs=75.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhhccccCCCeEEEechhhhhhcCCCc-hHHHHHHHhhccccccceEEEeeecCCceeEEEE
Q 022034 102 KKNKLDSGKFEHLLDNLWRSFSEDKKAGFTYLDSLWFDLYRKPSS-KAKVLTWIKRKHIFSKKYVLVPIVCWRHWNLLIL 180 (303)
Q Consensus 102 ~~~wLND~iI~~yl~~L~~~~~~~~~~~~~~~~s~ff~~l~~~~~-~~~v~~w~k~~~if~k~~I~iPIn~~~HW~L~Vi 180 (303)
+.+.|...-|..|..-+....+. . .+-.+.-.+..+..... -..+..-++...++-++.=+||||.++||.|+++
T Consensus 162 ~nRmltsDEia~~~q~~~~~~~n-~---~VNyPiGLi~P~t~~~~L~~~L~E~i~~~~~~~k~~elFpINtg~HWil~~l 237 (403)
T PRK11836 162 KNRQLTTDEIACYLQKIAANAKN-T---QVNYPTGLYVPYSTRTHLEDALNENIKSDPSWPKEVQLFPINTGGHWILVSL 237 (403)
T ss_pred ccccccHHHHHHHhcccccCCcc-c---eecCCceeeecCcccchhHHHHHHhhhcCCCCcccceEEEecCCCcEEEEEe
Confidence 45567777777777655332110 0 01111111111111110 1233333444566778899999999999999998
Q ss_pred ecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCC-----cc--cccCCceeeCCCCCCCCCCCch
Q 022034 181 CNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPE-----TK--ELISRIPLLVPKVPQQRNGEEC 253 (303)
Q Consensus 181 ~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~-----~~--~~~~~~~~~~~~vPqQ~N~~DC 253 (303)
.--.....-+.+.+ .++|.|+..-+... ....++.+. .+..+-.++ .+ .....+-+...+ -||.=..-|
T Consensus 238 ~Ki~~~~~~~ekiK-C~IFNs~~~l~~d~-~~t~q~ii~-a~~~~~~~~~~~~~ik~~~~e~ei~fie~d-LQq~vpngC 313 (403)
T PRK11836 238 QKIVNEKNNTQQIK-CVIFNSLRALGHDK-ENSLKRVIN-SFNSELMGEMSNNNIKVHLTEPEIIFLHAD-LQQYLSQSC 313 (403)
T ss_pred HHhhhcccccceeE-EEEEecHhhhccch-hhHHHHHHH-hhhhhhhhhcchhhhcccccCCceEEEech-hhhcCCCcc
Confidence 64221101111233 45777777654321 111222221 111111100 00 011222233333 233345789
Q ss_pred HHHHHHHHHHHHcCC
Q 022034 254 GNFVLYFINLFVEGA 268 (303)
Q Consensus 254 GvfVl~f~~~~~~~~ 268 (303)
|+||++-+.-++...
T Consensus 314 GlFv~~a~Qe~i~q~ 328 (403)
T PRK11836 314 GAFVCMAAQEVIEQR 328 (403)
T ss_pred ceehHHHHHHHHHHh
Confidence 999999998666543
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=96.72 E-value=0.0046 Score=56.13 Aligned_cols=88 Identities=17% Similarity=0.244 Sum_probs=50.2
Q ss_pred ceEEEeeecCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCCcccccCCceeeCC
Q 022034 163 KYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLVP 242 (303)
Q Consensus 163 ~~I~iPIn~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~ 242 (303)
+.=+||||.++||.|+++.--.+ +.+ .++|.|+..-+.. .+++.+.. .+.-+..+ -..+-+..
T Consensus 189 ~nevF~INtg~HWil~~~~Ki~~------kiK-C~iFNs~~~l~eN----s~~~ii~~-ak~ag~~~----e~di~fIe- 251 (317)
T PRK14848 189 HNEVFLINTGDHWLLCLFYKLAE------KIK-CLIFNTYYDLNEN----TKQEIIEA-AKIAGISE----NEDVNFIE- 251 (317)
T ss_pred cceEEEecCCCcEEEEEhHHhhh------hce-EEEeecHhhhhhh----HHHHHHHH-HHhhCccc----CCceEEee-
Confidence 44469999999999999864332 234 4577787776532 22333322 11111110 01222232
Q ss_pred CCCCCCC-CCchHHHHHHHHHHHHcCC
Q 022034 243 KVPQQRN-GEECGNFVLYFINLFVEGA 268 (303)
Q Consensus 243 ~vPqQ~N-~~DCGvfVl~f~~~~~~~~ 268 (303)
.-.|+| ..-||+|||++++.+....
T Consensus 252 -~nLQqnVpngCGlFv~~aIq~l~~~~ 277 (317)
T PRK14848 252 -TNLQNNVPNGCGLFCYHTIQLLSNAG 277 (317)
T ss_pred -hhhhhhCCCcchHHHHHHHHHHHhcc
Confidence 233434 5689999999999777653
No 10
>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=92.59 E-value=0.18 Score=43.50 Aligned_cols=81 Identities=17% Similarity=0.320 Sum_probs=40.1
Q ss_pred CCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHH-----HHHH-HHHhcCCCCcccccCCceee-CCCC
Q 022034 172 WRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRK-----FVMD-IYKAEDRPETKELISRIPLL-VPKV 244 (303)
Q Consensus 172 ~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~-----~L~~-~~~~~~~~~~~~~~~~~~~~-~~~v 244 (303)
+.||.-+..+ |. ...++.||+++-++. ++.+ |-+ .|.. .+.+. + ...++++ ....
T Consensus 33 GvHWlA~Aw~-P~--------s~t~YmFDPfGfsd~-~L~q-iY~FeYe~llrRSAL~~~--~-----dRCv~Lvkstqt 94 (183)
T PF00770_consen 33 GVHWLAFAWD-PR--------SRTFYMFDPFGFSDQ-KLKQ-IYQFEYEGLLRRSALSST--P-----DRCVTLVKSTQT 94 (183)
T ss_dssp -S-EEEEEEE-TT--------TTEEEEE-TT---HH-HHHH-HH----HHHHHHHHHHH---T-----TSEEEEEEE-EE
T ss_pred ceeEEEEEec-CC--------cceEEEeCCCCCCHH-HHHH-HHhhhHHHHHHHHhhcCC--C-----CceEEEEeccce
Confidence 5899988887 64 378999999999875 2321 111 1111 11100 1 1233333 3344
Q ss_pred CCCCCCCchHHHHHHHHHHHHcCCCC
Q 022034 245 PQQRNGEECGNFVLYFINLFVEGAPE 270 (303)
Q Consensus 245 PqQ~N~~DCGvfVl~f~~~~~~~~~~ 270 (303)
-|=.++--||+|.|+|..+|...+..
T Consensus 95 VQ~p~SaaCGLFC~lFL~aF~~~p~~ 120 (183)
T PF00770_consen 95 VQCPCSAACGLFCCLFLHAFVHYPDN 120 (183)
T ss_dssp -S-TT---HHHHHHHHHHHHHH-TTS
T ss_pred eeccCchhHHHHHHHHHHHHHhCCCC
Confidence 44558889999999999999987643
No 11
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=90.21 E-value=2.1 Score=37.25 Aligned_cols=89 Identities=13% Similarity=0.179 Sum_probs=54.8
Q ss_pred EEEeeec-CCceeEEEEe-cCCCCCCCCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCCcccccCCceeeCC
Q 022034 165 VLVPIVC-WRHWNLLILC-NFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLVP 242 (303)
Q Consensus 165 I~iPIn~-~~HW~L~Vi~-~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~ 242 (303)
.+||+.. +.|-+.+=+- .++ .+..+++++|......... +..++........ .....+.+...
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~-------~k~SlI~~Epa~~~~~~~~---l~~~~~~~~~~~~-----~~~~~~~~~~i 138 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN-------GKPSLIVFEPASFYGMKPA---LAGYTKLAEEARQ-----KLLPNAKFAVI 138 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC-------CCceEEEEccccccCCcch---hhhHHHHHHHHHh-----ccCCCcEEEEE
Confidence 4556443 4666655444 333 3577999999977654221 2223222111110 11235567788
Q ss_pred CCCCCCCCCchHHHHHHHHHHHHcCC
Q 022034 243 KVPQQRNGEECGNFVLYFINLFVEGA 268 (303)
Q Consensus 243 ~vPqQ~N~~DCGvfVl~f~~~~~~~~ 268 (303)
.+.-|+..+|||+|-|.+|.+.....
T Consensus 139 e~diQkS~~dC~IFsLs~AkK~~~~~ 164 (177)
T PF03421_consen 139 EMDIQKSPSDCGIFSLSLAKKMYKED 164 (177)
T ss_pred ecccccCcCcchhhHHHHHHHHhhcc
Confidence 99999999999999999999987653
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=80.81 E-value=10 Score=35.63 Aligned_cols=67 Identities=16% Similarity=0.242 Sum_probs=41.2
Q ss_pred CCeEEEeeCCCCCCCcchHHHHHHHHHHHHHhcCCCCcccccCCceeeCCCCCCCCCCCchHHHHHHHHHHHHcCC
Q 022034 193 TPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLVPKVPQQRNGEECGNFVLYFINLFVEGA 268 (303)
Q Consensus 193 ~~~i~~~DSl~~~~~~~l~~~i~~~L~~~~~~~~~~~~~~~~~~~~~~~~~vPqQ~N~~DCGvfVl~f~~~~~~~~ 268 (303)
++.|++++|........-.-.++ +...++... .....+.....--|+-.+|||+|-|.+|.+.....
T Consensus 121 k~SIIvlEPa~~~~~~~a~l~~r--l~~~le~~~-------l~~~~~avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 121 KTSLILFEPANFNSMGPAMLAIR--TKTALEREQ-------LPDCHFSMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred CeEEEEECCccccccchHHHHHH--HHHHHHhcc-------CCCceEEEEecccccCcccchhhhHHHHHHHhhhh
Confidence 56799999987653211000111 222222111 11234556677889999999999999999988764
No 13
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=58.24 E-value=24 Score=38.71 Aligned_cols=31 Identities=26% Similarity=0.349 Sum_probs=24.3
Q ss_pred cCCceeEEEEecCCCCCCCCCCCCeEEEeeCCCCCCCcchH
Q 022034 171 CWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFE 211 (303)
Q Consensus 171 ~~~HW~L~Vi~~p~~~~~s~~~~~~i~~~DSl~~~~~~~l~ 211 (303)
+++||..++-- ++ ...++||+|+....+...
T Consensus 61 ~sghwimlikg-~g---------n~y~lfdplg~~sg~~y~ 91 (1439)
T PF12252_consen 61 DSGHWIMLIKG-QG---------NQYYLFDPLGKTSGEGYQ 91 (1439)
T ss_pred cCceeEEEEEc-CC---------CceEEeccccccccccHH
Confidence 46999988774 55 689999999998765554
No 14
>PF07797 DUF1639: Protein of unknown function (DUF1639); InterPro: IPR012438 This approximately 50-residue region is found in a number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre.
Probab=44.13 E-value=6.2 Score=27.16 Aligned_cols=15 Identities=7% Similarity=-0.338 Sum_probs=11.3
Q ss_pred cccCCCCCCCHHHHH
Q 022034 98 ITKRKKNKLDSGKFE 112 (303)
Q Consensus 98 ~~L~~~~wLND~iI~ 112 (303)
..|.||.||.|-.-+
T Consensus 34 d~lfPG~wL~~vt~d 48 (50)
T PF07797_consen 34 DSLFPGLWLSEVTPD 48 (50)
T ss_pred hhcCcchhhhhcCcc
Confidence 578899999875443
No 15
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.81 E-value=36 Score=29.60 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=26.6
Q ss_pred CCCCCCCCCCCchHHHHHHHHHHHHcCCCC
Q 022034 241 VPKVPQQRNGEECGNFVLYFINLFVEGAPE 270 (303)
Q Consensus 241 ~~~vPqQ~N~~DCGvfVl~f~~~~~~~~~~ 270 (303)
...||.-.|+-.|+.||+-.++.++.+..+
T Consensus 130 fISVPke~~~lnc~~fvaGIiea~L~~agf 159 (191)
T KOG3315|consen 130 FISVPKENGTLNCAAFVAGIIEAVLDNAGF 159 (191)
T ss_pred ceecccccCcccHHHHHHHHHHHHHHhCCC
Confidence 568899999999999999999999997643
No 16
>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=22.91 E-value=57 Score=25.72 Aligned_cols=23 Identities=22% Similarity=0.423 Sum_probs=15.2
Q ss_pred CCCCCCCCCchHHHHHHHHHHHH
Q 022034 243 KVPQQRNGEECGNFVLYFINLFV 265 (303)
Q Consensus 243 ~vPqQ~N~~DCGvfVl~f~~~~~ 265 (303)
++-+|.+..|||+-.+.++-...
T Consensus 3 ~~v~Q~~~~dcg~acl~~l~~~~ 25 (131)
T PF03412_consen 3 PVVKQSDSNDCGLACLAMLLKYY 25 (131)
T ss_dssp -----SSTT-HHHHHHHHHHHHT
T ss_pred CeEEeCCCCCHHHHHHHHHHHHh
Confidence 34578899999999999888884
No 17
>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=20.85 E-value=48 Score=18.58 Aligned_cols=6 Identities=50% Similarity=1.608 Sum_probs=5.0
Q ss_pred chhhHH
Q 022034 30 RTCWLH 35 (303)
Q Consensus 30 ~~~~~~ 35 (303)
|+||+.
T Consensus 6 rscwk~ 11 (22)
T PF08095_consen 6 RSCWKA 11 (22)
T ss_dssp THHHHH
T ss_pred HHHHHc
Confidence 899975
Done!