Query 016505
Match_columns 388
No_of_seqs 235 out of 1123
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 07:27:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016505hhsearch_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 6.6E-48 1.4E-52 388.0 16.1 211 99-343 285-498 (511)
2 PLN03189 Protease specific for 100.0 2.4E-45 5.2E-50 366.7 23.2 217 100-343 254-477 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 3.2E-44 6.9E-49 356.2 15.6 196 123-366 372-567 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 3.3E-31 7.2E-36 244.6 17.2 196 147-369 1-214 (216)
5 KOG3246 Sentrin-specific cyste 100.0 1.5E-29 3.2E-34 228.0 16.4 189 131-367 15-215 (223)
6 KOG0779 Protease, Ulp1 family 99.9 6E-28 1.3E-32 253.2 7.5 242 131-373 351-594 (595)
7 PF03290 Peptidase_C57: Vaccin 97.4 0.00029 6.4E-09 69.5 6.4 91 214-334 229-350 (423)
8 PRK14848 deubiquitinase SseL; 95.8 0.017 3.8E-07 54.3 5.7 35 218-256 190-224 (317)
9 PRK11836 deubiquitinase; Provi 95.8 0.02 4.3E-07 55.0 6.0 46 210-255 213-260 (403)
10 PF00770 Peptidase_C5: Adenovi 93.2 0.23 5E-06 44.4 6.0 83 226-331 33-119 (183)
11 PF03421 YopJ: YopJ Serine/Thr 89.3 2.3 5E-05 38.6 8.6 88 219-329 74-163 (177)
12 PRK15371 effector protein YopJ 83.8 5.4 0.00012 38.9 8.2 29 302-330 159-187 (287)
13 PHA02130 hypothetical protein 28.0 34 0.00073 25.8 1.2 36 200-235 15-51 (81)
14 PF12252 SidE: Dot/Icm substra 26.9 1.2E+02 0.0026 34.9 5.7 33 220-259 49-88 (1439)
15 KOG3315 Transport protein part 20.8 91 0.002 28.2 2.8 27 303-329 130-156 (191)
16 PF03412 Peptidase_C39: Peptid 20.5 80 0.0017 26.0 2.4 22 306-327 4-25 (131)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.6e-48 Score=388.00 Aligned_cols=211 Identities=28% Similarity=0.518 Sum_probs=175.1
Q ss_pred cCCCCccchhhhHHHHHhhcc---ceeecCCCCCCCCeEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCce
Q 016505 99 EGSLHIETTEQADEFAECMID---AKIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDC 175 (388)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~~~~---~~i~yp~~~~~~~i~l~~~Dl~~L~~~~wLND~IInfyl~~L~~~~~~~~~~~~~~ 175 (388)
+..+.+++.+...++..++.. ..+.. ...++.||.+||+||.+++||||+||||||++|.+....... ++++
T Consensus 285 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~-yp~~ 359 (511)
T KOG0778|consen 285 EDSFPPLTEEREAQVQRAFSSRNSTEILV----THFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSK-YPKV 359 (511)
T ss_pred ccccccccHHHHHHHHHHhccCCccccee----hhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCC-CceE
Confidence 344455565556666666542 12211 235699999999999999999999999999999999876554 8899
Q ss_pred EEEchhhHHHHHHhhhcCCCCchhHHHHHHHhhhcccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCEEEEEcCCCC
Q 016505 176 HFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKL 255 (388)
Q Consensus 176 ~ifnsfF~~~L~~~~~~kg~d~~~~~~~vkrwtk~~~if~kd~I~IPIn~~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~ 255 (388)
|+||||||++|.+. +|.+|+|||++++||++|+||||||.+.||+|+||++.++ +|.|||||++
T Consensus 360 h~FnTFFy~kL~~~----------gy~~VkRWTk~v~if~~d~i~vPIH~~vHW~l~vid~r~k------~i~y~DS~~~ 423 (511)
T KOG0778|consen 360 HAFNTFFYTKLVGR----------GYAGVKRWTKKVDIFDKDIIFVPIHLGVHWCLAVIDLREK------TIEYYDSLGG 423 (511)
T ss_pred EEEechhhhhhhhc----------chHHHHhHhhccCccccceeEeeeecCceEEEEEEEcccc------eEEEeeccCC
Confidence 99999999999863 4899999999999999999999999999999999999998 9999999997
Q ss_pred CCcHHHHHHHHHHHHHHHHHhhccCCCCCcccchhhhccCCccccccCCCcCCCCCCCChHHHHHHHHHHHHhhCCcccc
Q 016505 256 HCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLK 335 (388)
Q Consensus 256 ~~~~~i~~~l~~~L~~e~~~~~~~~~~~d~~~~~~~w~~lp~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p~~~~ 335 (388)
..++ ++..|.+||.+|+..+.+. + ++.+.|+.. ...++|||.||+|||||+|+|+++++++.|..|+
T Consensus 424 ~~nr-~~~aL~~Yl~~E~~~k~~~----~--~d~s~w~~~------~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ft 490 (511)
T KOG0778|consen 424 GPNR-ICDALAKYLQDESRDKSKK----D--FDVSGWTIE------FVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFT 490 (511)
T ss_pred CCcc-hHHHHHHHHHHHHhhhhcC----C--CCccchhhh------hhhccccccCCCccceEEeeechhhccCCCcccC
Confidence 7654 5599999999999875432 2 334578742 3458999999999999999999999999999999
Q ss_pred chhhhhhh
Q 016505 336 KKDLAMFG 343 (388)
Q Consensus 336 q~d~~~f~ 343 (388)
|+|||.||
T Consensus 491 q~dmp~fR 498 (511)
T KOG0778|consen 491 QQDMPYFR 498 (511)
T ss_pred hhhhHHHH
Confidence 99998643
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=2.4e-45 Score=366.67 Aligned_cols=217 Identities=24% Similarity=0.501 Sum_probs=176.6
Q ss_pred CCCCccchhhhHHHHHhhccc---eeecCCCCCCCCeEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCceE
Q 016505 100 GSLHIETTEQADEFAECMIDA---KIYYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCH 176 (388)
Q Consensus 100 ~~~~~~~~~~~~~~~~~~~~~---~i~yp~~~~~~~i~l~~~Dl~~L~~~~wLND~IInfyl~~L~~~~~~~~~~~~~~~ 176 (388)
..+.|++.+++.+|..+|... .+.... .+.+++||.+||.||.+++||||+|||||+++|............++|
T Consensus 254 ~~~~pLT~e~~~~V~~al~~~~~~~vlvs~--~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h 331 (490)
T PLN03189 254 EPFIPLTREEETEVKRAFSANNRRKVLVTH--ENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCH 331 (490)
T ss_pred ccCcCCCHHHHHHHHHHhcCCCccceeeec--CCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceE
Confidence 567889999999999998752 222211 246899999999999999999999999999999876544333456899
Q ss_pred EEchhhHHHHHHhhhcCCCCchhHHHHHHHhhhc----ccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCEEEEEcC
Q 016505 177 FFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG----VNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDS 252 (388)
Q Consensus 177 ifnsfF~~~L~~~~~~kg~d~~~~~~~vkrwtk~----~~if~kd~I~IPIn~~~HW~L~VV~~~~~~~~~~~~I~~~DS 252 (388)
+||||||++|.... ....|.+|+|||+. ++||++++||||||.+.||+|+||+++.+ +|.||||
T Consensus 332 ~FNTFFytkL~~~~------~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k------~I~yyDS 399 (490)
T PLN03189 332 FFNTFFYKKLVSGK------SGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQ------KFQYLDS 399 (490)
T ss_pred EEehHHHHHHhhcC------CcCChHHHHHHhhhcccccccccCceEEeeeecCCeeEEEEEEcCCC------eEEEEeC
Confidence 99999999998741 11258999999974 57999999999999999999999999998 9999999
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCcccchhhhccCCccccccCCCcCCCCCCCChHHHHHHHHHHHHhhCCc
Q 016505 253 LKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPE 332 (388)
Q Consensus 253 L~~~~~~~i~~~l~~~L~~e~~~~~~~~~~~d~~~~~~~w~~lp~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p~ 332 (388)
|++.+. .+++.|+.||..|++.+.+ .+ +..+.|... ...++|||.||+|||||||+||++++.+.+.
T Consensus 400 Lgg~~~-~vL~~L~rYL~~E~kdK~g----~d--~D~s~W~~~------~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~L 466 (490)
T PLN03189 400 LKGRDP-KILDALAKYYVDEVKDKSE----KD--IDVSSWEQE------FVEDLPEQKNGYDCGMFMIKYIDFYSRGLGL 466 (490)
T ss_pred CCCCCH-HHHHHHHHHHHHHHhhhcC----CC--cchhcceec------cCCCCCCCCCCCCHHHHHHHHHHHHcCCCCC
Confidence 998764 5889999999999876432 22 333567531 2468999999999999999999999999888
Q ss_pred cccchhhhhhh
Q 016505 333 RLKKKDLAMFG 343 (388)
Q Consensus 333 ~~~q~d~~~f~ 343 (388)
.|+|+||+.||
T Consensus 467 tFSQeDMp~fR 477 (490)
T PLN03189 467 CFGQEHMPYFR 477 (490)
T ss_pred CcChhhhHHHH
Confidence 88888886544
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.2e-44 Score=356.22 Aligned_cols=196 Identities=34% Similarity=0.604 Sum_probs=165.6
Q ss_pred ecCCCCCCCCeEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCCchhHHH
Q 016505 123 YYPSRVDPESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFI 202 (388)
Q Consensus 123 ~yp~~~~~~~i~l~~~Dl~~L~~~~wLND~IInfyl~~L~~~~~~~~~~~~~~~ifnsfF~~~L~~~~~~kg~d~~~~~~ 202 (388)
.||+-+ +.+|+||.+||.||.+++||||+||||||+||...... ....+++|+||||||++|.+. +|.
T Consensus 372 ~~~~~~-~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~-~s~~~~vh~FnTFFYT~Lsrr----------Gy~ 439 (578)
T COG5160 372 CYPFND-RSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKN-TSKREQVHLFNTFFYTKLSRR----------GYS 439 (578)
T ss_pred cccccC-cCcceeehHhhhhhccccchhhHHHHHHHHHHHHhccC-cccccceEEeehhhHHHHHHH----------HhH
Confidence 688764 58999999999999999999999999999999555432 335679999999999999863 589
Q ss_pred HHHHhhhcccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCEEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCC
Q 016505 203 KFRRWWKGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSP 282 (388)
Q Consensus 203 ~vkrwtk~~~if~kd~I~IPIn~~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~~~i~~~l~~~L~~e~~~~~~~~~~ 282 (388)
.|+||+++++||++++||||||...||+|+|||.+.+ .|.|||||++.+ ..+++.|+.|+.+||+....
T Consensus 440 gVrrW~kk~dif~~k~I~iPIni~~HW~l~II~~~~~------~i~~~DSLan~~-~~v~~~L~~Y~ldE~k~~~~---- 508 (578)
T COG5160 440 GVRRWTKKTDIFSKKYIFIPINISYHWFLAIIDNPKK------NILYFDSLANTH-DPVLEFLRSYLLDEYKIQHD---- 508 (578)
T ss_pred HHHHHHhccCccccceEEEEecccceEEEEEeecCcc------eeEEecccccCc-HHHHHHHHHHHHHHHhcccC----
Confidence 9999999999999999999999999999999999987 999999999887 57899999999999865321
Q ss_pred CCcccchhhhccCCccccccCCCcCCCCCCCChHHHHHHHHHHHHhhCCccccchhhhhhhccCCCHHHHHHHHHHHHHH
Q 016505 283 SDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNL 362 (388)
Q Consensus 283 ~d~~~~~~~w~~lp~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p~~~~q~d~~~f~~~~f~~~~i~~~R~~i~~l 362 (388)
...| +.....+||||.||+|||||||+|++++++++|..|.++|++ .+|+.|+..
T Consensus 509 ------k~~~------~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~-------------r~Rk~m~h~ 563 (578)
T COG5160 509 ------KDPQ------IKMKHCKVPQQRNGSDCGVFVCMFIRYFLENPPEQFSKNDRP-------------RARKNMAHT 563 (578)
T ss_pred ------Cchh------hhhhcCCCCCCCCCCccceEEEEeeeecccCChhhcCccchH-------------HHHHHHHHH
Confidence 1112 234678999999999999999999999999988877776665 466666666
Q ss_pred HHHH
Q 016505 363 LKKQ 366 (388)
Q Consensus 363 Il~l 366 (388)
|+.+
T Consensus 564 i~~~ 567 (578)
T COG5160 564 IKDL 567 (578)
T ss_pred HHHH
Confidence 5544
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=3.3e-31 Score=244.64 Aligned_cols=196 Identities=32% Similarity=0.594 Sum_probs=136.6
Q ss_pred CccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCC----------chhHHHHHHHhhhcc---cC
Q 016505 147 AYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD----------KDSFFIKFRRWWKGV---NI 213 (388)
Q Consensus 147 ~wLND~IInfyl~~L~~~~~~~~~~~~~~~ifnsfF~~~L~~~~~~kg~d----------~~~~~~~vkrwtk~~---~i 213 (388)
+||||.|||||++||..+...+.....++++|+|+|++.|......-+.+ ....+..+.+|++.. ++
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 59999999999999986654333456799999999999998432110001 123467888999887 99
Q ss_pred CCCcEEEEEeec-CCceEEEEEEcCCCCCCCCCEEEEEcCCCCCCc----HHHHHHHHHHHHHHHHHhhccCCCCCcccc
Q 016505 214 FQKSYVLIPIHE-DVHWSLVIICIPDKEDESGPIILHLDSLKLHCS----LSIFSNIRSFLKEEWNYLKQEVSPSDLPIA 288 (388)
Q Consensus 214 f~kd~I~IPIn~-~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~----~~i~~~l~~~L~~e~~~~~~~~~~~d~~~~ 288 (388)
+++++||||||. +.||+|+||+.+.+ +|++||||+.... ..++..+..+|...+....... . .
T Consensus 81 ~~~~~i~iPin~~~~HW~l~vi~~~~~------~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~----~--~ 148 (216)
T PF02902_consen 81 FDKDYIFIPININNNHWVLLVIDLPKK------RIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRD----P--D 148 (216)
T ss_dssp GGSSEEEEEEEETTTEEEEEEEETTTT------EEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSC----T---
T ss_pred cccCEEEEEEechhhccceeEEccccc------EEEEEeccccccccccchhhhhhhhhhhhhccccccccc----c--c
Confidence 999999999999 99999999999998 9999999998765 3567788888887765433211 1 1
Q ss_pred hhhhccCCccccccCCCcCCCCCCCChHHHHHHHHHHHHhhCCccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHhh
Q 016505 289 ERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQ 368 (388)
Q Consensus 289 ~~~w~~lp~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p~~~~q~d~~~f~~~~f~~~~i~~~R~~i~~lIl~l~~ 368 (388)
...|.. ....++|||.|++|||+|||+||++++.+.+....+ .|+.+++..+|.++...|.+...
T Consensus 149 ~~~~~~------~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~---------~l~~~~i~~~r~~~a~~~~e~~~ 213 (216)
T PF02902_consen 149 KSPFKI------VRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQ---------ELTEEDIKNFRKKLAVDLYEELG 213 (216)
T ss_dssp TTTCEE------EEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCC---------SBTGHHHHHHHHHHHH-------
T ss_pred cceeee------cccccccCCCCCCCcHHHHHHHHHHHHhCCCCcccc---------cCCHHHHHHHHHHHHhhcccccc
Confidence 112321 345689999999999999999999999985443211 15677888899999888877654
Q ss_pred h
Q 016505 369 I 369 (388)
Q Consensus 369 ~ 369 (388)
.
T Consensus 214 ~ 214 (216)
T PF02902_consen 214 S 214 (216)
T ss_dssp -
T ss_pred c
Confidence 3
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.97 E-value=1.5e-29 Score=228.04 Aligned_cols=189 Identities=24% Similarity=0.422 Sum_probs=142.5
Q ss_pred CCeEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCCchhHHHHHHHhhhc
Q 016505 131 ESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGDKDSFFIKFRRWWKG 210 (388)
Q Consensus 131 ~~i~l~~~Dl~~L~~~~wLND~IInfyl~~L~~~~~~~~~~~~~~~ifnsfF~~~L~~~~~~kg~d~~~~~~~vkrwtk~ 210 (388)
..+.++.+|+..|+++.||||.+|+||.+||........ ...|++++ .++..+++.+.. +.++.....
T Consensus 15 ~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s~---~~~~ll~P----~~t~~l~~~~~~-----~e~~~~~~p 82 (223)
T KOG3246|consen 15 FDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSE---PDLHLLRP----SLTFFLRHAPNP-----EEIAMVLDP 82 (223)
T ss_pred eehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccC---cchhccCH----HHHHHHHhCCCc-----HHHHHhcCh
Confidence 679999999999999999999999999999999877543 23455543 344433333322 235566677
Q ss_pred ccCCCCcEEEEEeecC---------CceEEEEEEcCCCCCCCCCEEEEEcCCCCCCc---HHHHHHHHHHHHHHHHHhhc
Q 016505 211 VNIFQKSYVLIPIHED---------VHWSLVIICIPDKEDESGPIILHLDSLKLHCS---LSIFSNIRSFLKEEWNYLKQ 278 (388)
Q Consensus 211 ~~if~kd~I~IPIn~~---------~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~---~~i~~~l~~~L~~e~~~~~~ 278 (388)
.++.+|++||+|||++ +||+|+|+..+++ +++||||+.+.+. +.+.++++.+|+.....
T Consensus 83 l~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~------~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~--- 153 (223)
T KOG3246|consen 83 LDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDG------KFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAK--- 153 (223)
T ss_pred hhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCC------cEEEeecccCCCcHHHHHHHHHHHHHHhhhhhh---
Confidence 8999999999999984 5999999999998 9999999988764 45666777666642110
Q ss_pred cCCCCCcccchhhhccCCccccccCCCcCCCCCCCChHHHHHHHHHHHHhhCCccccchhhhhhhccCCCHHHHHHHHHH
Q 016505 279 EVSPSDLPIAERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIK 358 (388)
Q Consensus 279 ~~~~~d~~~~~~~w~~lp~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p~~~~q~d~~~f~~~~f~~~~i~~~R~~ 358 (388)
..+..+|||.||||||+|||.+++.++... .+..|+. ......++.|+++|+.
T Consensus 154 ----------------------~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~----~~~~~~~-~~~~~~~~~i~~lr~~ 206 (223)
T KOG3246|consen 154 ----------------------RVECKCLQQQNGYDCGLHVCCNTRVLAERL----LRCPYAT-SSQLLVVDLIKALREE 206 (223)
T ss_pred ----------------------cccccChhhhcCCchhHHHHHHHHHHHHHH----hcccccc-ccchhhHHHHHHHHHH
Confidence 125679999999999999999999998762 2222221 1223556788999999
Q ss_pred HHHHHHHHh
Q 016505 359 IRNLLKKQF 367 (388)
Q Consensus 359 i~~lIl~l~ 367 (388)
|+.||..|.
T Consensus 207 l~~LI~slg 215 (223)
T KOG3246|consen 207 LLDLIQSLG 215 (223)
T ss_pred HHHHHHHhC
Confidence 999999886
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=6e-28 Score=253.21 Aligned_cols=242 Identities=36% Similarity=0.649 Sum_probs=205.8
Q ss_pred CCeEEecchhcccCCCCccCHHHHHHHHHHHHHhcCCCCcCCCceEEEchhhHHHHHHhhhcCCCC--chhHHHHHHHhh
Q 016505 131 ESVEICYTDINHLAPAAYLTSPIMNFYIRYLQLQASPTNRAIRDCHFFNTYFYSKLKEAVSHKGGD--KDSFFIKFRRWW 208 (388)
Q Consensus 131 ~~i~l~~~Dl~~L~~~~wLND~IInfyl~~L~~~~~~~~~~~~~~~ifnsfF~~~L~~~~~~kg~d--~~~~~~~vkrwt 208 (388)
..+.++..|+.||.++++|||.||+||++|+..+..........+|+|++|||..+.+.+..++.+ ....+..+++|+
T Consensus 351 ~~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~ 430 (595)
T KOG0779|consen 351 QSHQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWT 430 (595)
T ss_pred cccceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeee
Confidence 367999999999999999999999999999999987755578899999999999999988776666 455677899999
Q ss_pred hcccCCCCcEEEEEeecCCceEEEEEEcCCCCCCCCCEEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCcccc
Q 016505 209 KGVNIFQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIA 288 (388)
Q Consensus 209 k~~~if~kd~I~IPIn~~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~~~i~~~l~~~L~~e~~~~~~~~~~~d~~~~ 288 (388)
+.+++|.++||++|+|+..||.|+++|+++.+.+......+++++..+....+++.+..+|+.++...+......+.++.
T Consensus 431 ~~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 510 (595)
T KOG0779|consen 431 RHFDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELE 510 (595)
T ss_pred eccccccceeEEecCchHhhhhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCccccccccccc
Confidence 99999999999999999999999999999988777778888888887766667788999999888765544345566666
Q ss_pred hhhhccCCccccccCCCcCCCCCCCChHHHHHHHHHHHHhhCCccccchhhhhhhccCCCHHHHHHHHHHHHHHHHHHhh
Q 016505 289 ERIWQHLPRRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEEAPERLKKKDLAMFGKRWFRPEEASGLRIKIRNLLKKQFQ 368 (388)
Q Consensus 289 ~~~w~~lp~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p~~~~q~d~~~f~~~~f~~~~i~~~R~~i~~lIl~l~~ 368 (388)
...|..+++.+...++. |||.|..|||+|++.|++.++.+++.+++..+...+...||.+.++.++|..++++++.|+.
T Consensus 511 ~~~~~~~~~~~s~~v~~-p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~~~~l~~ 589 (595)
T KOG0779|consen 511 EELPRRLPRGKSETVRE-PQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRNLGRKLFT 589 (595)
T ss_pred ccccccCcccccccccc-cCccCcccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhcccccccc
Confidence 67788777665444444 99999999999999999999999988877666666666699999999999999999999998
Q ss_pred hhccC
Q 016505 369 ISSAE 373 (388)
Q Consensus 369 ~~~~~ 373 (388)
...++
T Consensus 590 ~~~~~ 594 (595)
T KOG0779|consen 590 SQSSE 594 (595)
T ss_pred ccCCC
Confidence 76654
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=97.41 E-value=0.00029 Score=69.49 Aligned_cols=91 Identities=22% Similarity=0.296 Sum_probs=65.1
Q ss_pred CCCcEEEEEeecCCceEEEEEEcCCCCCCCCCEEEEEcCCCCCCc------------------------------HHHHH
Q 016505 214 FQKSYVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLHCS------------------------------LSIFS 263 (388)
Q Consensus 214 f~kd~I~IPIn~~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~------------------------------~~i~~ 263 (388)
-+++|+.+|.+...||..+|++...+ -+.+|||-|..+. ..-++
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk~~~------~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dID 302 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDKEKK------IVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDID 302 (423)
T ss_pred ccccEEEeeeeehhcceEEEEecccc------EEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchH
Confidence 45799999999999999999998877 8888999876421 01234
Q ss_pred HHHHHHHHHHHHhhccCCCCCcccchhhhccCCccccccCCCc-CCCCCCCChHHHHHHHHHHHHhhCCccc
Q 016505 264 NIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLPRRIDDRIIPV-PQQKNDYDCGLFVLFFMERFMEEAPERL 334 (388)
Q Consensus 264 ~l~~~L~~e~~~~~~~~~~~d~~~~~~~w~~lp~~i~~~~~~v-PqQ~N~~DCGvFvl~~ae~~~~~~p~~~ 334 (388)
.|.+|+...+.... -..+| --|--..+||+|++.||......+|..|
T Consensus 303 VLfrfF~d~f~~~~------------------------gciNvevnQl~eseCGMF~~iFm~~c~~~ppk~f 350 (423)
T PF03290_consen 303 VLFRFFEDSFGVKY------------------------GCINVEVNQLLESECGMFISIFMILCTLTPPKGF 350 (423)
T ss_pred HHHHHHHhhcccce------------------------eEEEhhhhhhcccccchHHHHHHHHHHccCchhH
Confidence 56666655432110 01111 2688889999999999998888888765
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=95.82 E-value=0.017 Score=54.32 Aligned_cols=35 Identities=14% Similarity=0.135 Sum_probs=24.1
Q ss_pred EEEEEeecCCceEEEEEEcCCCCCCCCCEEEEEcCCCCC
Q 016505 218 YVLIPIHEDVHWSLVIICIPDKEDESGPIILHLDSLKLH 256 (388)
Q Consensus 218 ~I~IPIn~~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~ 256 (388)
.=+||||.+.||.|+++..-.. +..-++|.|+..-
T Consensus 190 nevF~INtg~HWil~~~~Ki~~----kiKC~iFNs~~~l 224 (317)
T PRK14848 190 NEVFLINTGDHWLLCLFYKLAE----KIKCLIFNTYYDL 224 (317)
T ss_pred ceEEEecCCCcEEEEEhHHhhh----hceEEEeecHhhh
Confidence 3459999999999998864322 1245677777543
No 9
>PRK11836 deubiquitinase; Provisional
Probab=95.79 E-value=0.02 Score=54.98 Aligned_cols=46 Identities=24% Similarity=0.291 Sum_probs=31.0
Q ss_pred cccCCCCcEEEEEeecCCceEEEEEEcCCCCC--CCCCEEEEEcCCCC
Q 016505 210 GVNIFQKSYVLIPIHEDVHWSLVIICIPDKED--ESGPIILHLDSLKL 255 (388)
Q Consensus 210 ~~~if~kd~I~IPIn~~~HW~L~VV~~~~~~~--~~~~~I~~~DSL~~ 255 (388)
...+|-++.=+||||.+.||.|+++..-..+. .....-++|.|+..
T Consensus 213 ~~~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~ 260 (403)
T PRK11836 213 SDPSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRA 260 (403)
T ss_pred cCCCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhh
Confidence 34566678889999999999999986543211 11234567777753
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=93.19 E-value=0.23 Score=44.38 Aligned_cols=83 Identities=18% Similarity=0.307 Sum_probs=40.2
Q ss_pred CCceEEEEEEcCCCCCCCCCEEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhcc-CC--CCCcccchhhhccCCcccc-c
Q 016505 226 DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQE-VS--PSDLPIAERIWQHLPRRID-D 301 (388)
Q Consensus 226 ~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~~~i~~~l~~~L~~e~~~~~~~-~~--~~d~~~~~~~w~~lp~~i~-~ 301 (388)
+.||.-+..+.... +++.||.+|-+..+ |+++-.-+++.+-+. .- ..| +.++ +
T Consensus 33 GvHWlA~Aw~P~s~------t~YmFDPfGfsd~~-----L~qiY~FeYe~llrRSAL~~~~d------------RCv~Lv 89 (183)
T PF00770_consen 33 GVHWLAFAWDPRSR------TFYMFDPFGFSDQK-----LKQIYQFEYEGLLRRSALSSTPD------------RCVTLV 89 (183)
T ss_dssp -S-EEEEEEETTTT------EEEEE-TT---HHH-----HHHHH----HHHHHHHHHHH-TT------------SEEEEE
T ss_pred ceeEEEEEecCCcc------eEEEeCCCCCCHHH-----HHHHHhhhHHHHHHHHhhcCCCC------------ceEEEE
Confidence 48999999998887 99999999987532 222222222221100 00 011 1222 1
Q ss_pred cCCCcCCCCCCCChHHHHHHHHHHHHhhCC
Q 016505 302 RIIPVPQQKNDYDCGLFVLFFMERFMEEAP 331 (388)
Q Consensus 302 ~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~p 331 (388)
+..+.-|=.++--||+|.|.|..+|...+.
T Consensus 90 kstqtVQ~p~SaaCGLFC~lFL~aF~~~p~ 119 (183)
T PF00770_consen 90 KSTQTVQCPCSAACGLFCCLFLHAFVHYPD 119 (183)
T ss_dssp EE-EE-S-TT---HHHHHHHHHHHHHH-TT
T ss_pred eccceeeccCchhHHHHHHHHHHHHHhCCC
Confidence 223344667888999999999999998753
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=89.35 E-value=2.3 Score=38.56 Aligned_cols=88 Identities=17% Similarity=0.332 Sum_probs=50.8
Q ss_pred EEEEeec-CCceEEEEEE-cCCCCCCCCCEEEEEcCCCCCCcHHHHHHHHHHHHHHHHHhhccCCCCCcccchhhhccCC
Q 016505 219 VLIPIHE-DVHWSLVIIC-IPDKEDESGPIILHLDSLKLHCSLSIFSNIRSFLKEEWNYLKQEVSPSDLPIAERIWQHLP 296 (388)
Q Consensus 219 I~IPIn~-~~HW~L~VV~-~~~~~~~~~~~I~~~DSL~~~~~~~i~~~l~~~L~~e~~~~~~~~~~~d~~~~~~~w~~lp 296 (388)
.+|+... ..|-..+=|- .++ .++.|++++|-........ +..+.........+ .+|
T Consensus 74 ~Iv~~~~~~~H~~a~Dvr~~~~----~k~SlI~~Epa~~~~~~~~---l~~~~~~~~~~~~~---------------~~~ 131 (177)
T PF03421_consen 74 AIVNLGGDGIHHVALDVRHTPN----GKPSLIVFEPASFYGMKPA---LAGYTKLAEEARQK---------------LLP 131 (177)
T ss_pred EEEeCCCCCCcEEEEEEeecCC----CCceEEEEccccccCCcch---hhhHHHHHHHHHhc---------------cCC
Confidence 3555443 5666655554 332 3579999999864432111 22222221111110 001
Q ss_pred ccccccCCCcCCCCCCCChHHHHHHHHHHHHhh
Q 016505 297 RRIDDRIIPVPQQKNDYDCGLFVLFFMERFMEE 329 (388)
Q Consensus 297 ~~i~~~~~~vPqQ~N~~DCGvFvl~~ae~~~~~ 329 (388)
...+...++..|+..+|||+|.|.+|..+...
T Consensus 132 -~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 132 -NAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred -CcEEEEEecccccCcCcchhhHHHHHHHHhhc
Confidence 12245678899999999999999999998765
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=83.85 E-value=5.4 Score=38.90 Aligned_cols=29 Identities=21% Similarity=0.544 Sum_probs=24.4
Q ss_pred cCCCcCCCCCCCChHHHHHHHHHHHHhhC
Q 016505 302 RIIPVPQQKNDYDCGLFVLFFMERFMEEA 330 (388)
Q Consensus 302 ~~~~vPqQ~N~~DCGvFvl~~ae~~~~~~ 330 (388)
....+-.|+-.+|||+|.|.+|.+.....
T Consensus 159 avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 159 SMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred EEEecccccCcccchhhhHHHHHHHhhhh
Confidence 34566789999999999999999988764
No 13
>PHA02130 hypothetical protein
Probab=28.01 E-value=34 Score=25.82 Aligned_cols=36 Identities=19% Similarity=0.499 Sum_probs=30.0
Q ss_pred HHHHHHHhhh-cccCCCCcEEEEEeecCCceEEEEEE
Q 016505 200 FFIKFRRWWK-GVNIFQKSYVLIPIHEDVHWSLVIIC 235 (388)
Q Consensus 200 ~~~~vkrwtk-~~~if~kd~I~IPIn~~~HW~L~VV~ 235 (388)
.++.++.|+. +.+-++-+++=||.-...||-|+-++
T Consensus 15 s~~sl~~wl~~~~dswdddil~ipfkstv~w~lcp~~ 51 (81)
T PHA02130 15 SWESLREWLDERFDSWDDDILSIPFKSTVYWDLCPYA 51 (81)
T ss_pred HHHHHHHHHHhcccccccchhcccccceeeeccCcch
Confidence 3567888985 57889999999999999999998654
No 14
>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=26.93 E-value=1.2e+02 Score=34.88 Aligned_cols=33 Identities=18% Similarity=0.328 Sum_probs=23.8
Q ss_pred EEEeec-------CCceEEEEEEcCCCCCCCCCEEEEEcCCCCCCcH
Q 016505 220 LIPIHE-------DVHWSLVIICIPDKEDESGPIILHLDSLKLHCSL 259 (388)
Q Consensus 220 ~IPIn~-------~~HW~L~VV~~~~~~~~~~~~I~~~DSL~~~~~~ 259 (388)
|+||-. ..||..+|= -+++ ..++||.||....+
T Consensus 49 fmpvltgv~p~~~sghwimlik-g~gn------~y~lfdplg~~sg~ 88 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLIK-GQGN------QYYLFDPLGKTSGE 88 (1439)
T ss_pred CceeecCcCCCCcCceeEEEEE-cCCC------ceEEeccccccccc
Confidence 667664 589987764 4455 89999999976543
No 15
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.82 E-value=91 Score=28.16 Aligned_cols=27 Identities=26% Similarity=0.627 Sum_probs=24.4
Q ss_pred CCCcCCCCCCCChHHHHHHHHHHHHhh
Q 016505 303 IIPVPQQKNDYDCGLFVLFFMERFMEE 329 (388)
Q Consensus 303 ~~~vPqQ~N~~DCGvFvl~~ae~~~~~ 329 (388)
...||.-.|+..|+.||+-.++.++.+
T Consensus 130 fISVPke~~~lnc~~fvaGIiea~L~~ 156 (191)
T KOG3315|consen 130 FISVPKENGTLNCAAFVAGIIEAVLDN 156 (191)
T ss_pred ceecccccCcccHHHHHHHHHHHHHHh
Confidence 356899999999999999999999876
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=20.54 E-value=80 Score=25.96 Aligned_cols=22 Identities=32% Similarity=0.646 Sum_probs=14.9
Q ss_pred cCCCCCCCChHHHHHHHHHHHH
Q 016505 306 VPQQKNDYDCGLFVLFFMERFM 327 (388)
Q Consensus 306 vPqQ~N~~DCGvFvl~~ae~~~ 327 (388)
+=+|....|||+-+++++-...
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~~ 25 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKYY 25 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHHT
T ss_pred eEEeCCCCCHHHHHHHHHHHHh
Confidence 4478888999999999888774
Done!