Query 038478
Match_columns 228
No_of_seqs 105 out of 141
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 11:28:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038478.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038478hhsearch_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 8E-35 1.7E-39 279.7 6.2 137 16-171 343-496 (511)
2 PLN03189 Protease specific for 100.0 1.9E-32 4.2E-37 261.9 13.9 147 15-179 312-483 (490)
3 KOG3246 Sentrin-specific cyste 100.0 1.7E-28 3.7E-33 215.1 11.5 126 46-197 84-217 (223)
4 PF02902 Peptidase_C48: Ulp1 p 99.9 2.9E-23 6.2E-28 171.8 13.4 105 45-153 78-182 (216)
5 COG5160 ULP1 Protease, Ulp1 fa 99.9 2.4E-23 5.2E-28 200.6 5.6 107 30-153 419-542 (578)
6 KOG0779 Protease, Ulp1 family 98.1 1.8E-06 3.9E-11 85.9 3.1 143 46-201 434-594 (595)
7 PF00770 Peptidase_C5: Adenovi 96.5 0.0092 2E-07 52.1 7.2 90 59-158 31-121 (183)
8 PF03290 Peptidase_C57: Vaccin 96.1 0.012 2.5E-07 56.8 5.8 95 50-158 231-347 (423)
9 PRK11836 deubiquitinase; Provi 95.6 0.053 1.1E-06 51.2 8.0 104 46-153 215-327 (403)
10 PRK14848 deubiquitinase SseL; 94.5 0.11 2.4E-06 48.2 6.6 83 53-153 191-275 (317)
11 PF03421 YopJ: YopJ Serine/Thr 82.5 4.8 0.0001 34.7 6.6 83 52-151 73-160 (177)
12 PF08072 BDHCT: BDHCT (NUC031) 48.8 13 0.00027 25.6 1.6 19 8-26 20-38 (41)
13 PF14738 PaaSYMP: Solute carri 45.0 82 0.0018 26.8 6.4 53 167-219 102-154 (154)
14 PRK15371 effector protein YopJ 34.3 1.6E+02 0.0036 27.6 7.1 41 130-176 162-202 (287)
15 PF05878 Phyto_Pns9_10: Phytor 31.9 2.1E+02 0.0045 27.3 7.3 64 150-215 174-238 (312)
16 PHA03074 late transcription fa 30.1 2.4E+02 0.0051 25.8 7.1 59 157-217 40-98 (225)
17 PHA01748 hypothetical protein 28.9 1.5E+02 0.0034 21.1 4.8 34 185-219 11-45 (60)
18 PRK13988 cell division topolog 22.6 79 0.0017 25.1 2.5 35 162-196 18-57 (97)
19 PF03412 Peptidase_C39: Peptid 22.6 63 0.0014 24.6 1.9 21 131-151 4-24 (131)
20 KOG4110 NADH:ubiquinone oxidor 22.3 80 0.0017 26.2 2.5 30 120-149 16-45 (120)
21 KOG3315 Transport protein part 21.9 56 0.0012 29.0 1.6 37 130-169 132-168 (191)
22 PRK13991 cell division topolog 20.2 1.3E+02 0.0029 23.4 3.3 35 162-196 16-55 (87)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8e-35 Score=279.68 Aligned_cols=137 Identities=20% Similarity=0.313 Sum_probs=122.9
Q ss_pred hHhhhHHHhhccccccchhhhhhhhhhhcc-----------------cccccceEEEeeeCCCcceeeeEeeeCCCeEEE
Q 038478 16 VEKLQERVLRNACDIDTLHEDVVMRDFYMK-----------------DVGKCAKIFVPVNHGFCHWYLLIIFIPEMRAEI 78 (228)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-----------------DLfscdkIFVPVN~ggsHWsL~VId~keK~f~y 78 (228)
.++|.||.=+.|- +.+|| +||+||+. |||+||+||||||. ++||||+|||+++|+|+|
T Consensus 343 m~ll~ers~~~~~-yp~~h---~FnTFFy~kL~~~gy~~VkRWTk~v~if~~d~i~vPIH~-~vHW~l~vid~r~k~i~y 417 (511)
T KOG0778|consen 343 MELLKERSKKDSK-YPKVH---AFNTFFYTKLVGRGYAGVKRWTKKVDIFDKDIIFVPIHL-GVHWCLAVIDLREKTIEY 417 (511)
T ss_pred HHHHHhhccccCC-CceEE---EEechhhhhhhhcchHHHHhHhhccCccccceeEeeeec-CceEEEEEEEcccceEEE
Confidence 6899999999888 99999 99999998 99999999999998 699999999999999999
Q ss_pred EcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcCCcccceeeccCCcCCCCCCCCchHHHHHHHHHHhccccCCC
Q 038478 79 WDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAGTKFEHFTVLQVTEFAVIPESYNYGVLILLMMQRGGKWLQNP 158 (228)
Q Consensus 79 yDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~~d~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae~~~~w~~~p 158 (228)
|||+++.++. +..+|.+|+.+|+.++....+|+++|.++.+.++|||.||||||||||+|++.+.. +.|
T Consensus 418 ~DS~~~~~nr---------~~~aL~~Yl~~E~~~k~~~~~d~s~w~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~--~~p 486 (511)
T KOG0778|consen 418 YDSLGGGPNR---------ICDALAKYLQDESRDKSKKDFDVSGWTIEFVQNIPQQRNGSDCGMFVCKYADYISR--DVP 486 (511)
T ss_pred eeccCCCCcc---------hHHHHHHHHHHHHhhhhcCCCCccchhhhhhhccccccCCCccceEEeeechhhcc--CCC
Confidence 9999976543 34677889999999999999999999999999999999999999999999999987 565
Q ss_pred CcccCcchhHHHH
Q 038478 159 TFQCDFDTERSQL 171 (228)
Q Consensus 159 ~f~~~~~~~~~~~ 171 (228)
..|+|..|=-
T Consensus 487 ---~~ftq~dmp~ 496 (511)
T KOG0778|consen 487 ---LTFTQQDMPY 496 (511)
T ss_pred ---cccChhhhHH
Confidence 6777766543
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=99.98 E-value=1.9e-32 Score=261.94 Aligned_cols=147 Identities=19% Similarity=0.271 Sum_probs=126.6
Q ss_pred hhHhhhHHHhhccccccchhhhhhhhhhhcc-------------------------cccccceEEEeeeCCCcceeeeEe
Q 038478 15 GVEKLQERVLRNACDIDTLHEDVVMRDFYMK-------------------------DVGKCAKIFVPVNHGFCHWYLLII 69 (228)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-------------------------DLfscdkIFVPVN~ggsHWsL~VI 69 (228)
-+++|+||..++|.++.+|| +|+++|+. +|+++|+||||||. ++||||+||
T Consensus 312 Ym~LL~er~~~~p~~~~k~h---~FNTFFytkL~~~~~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~-n~HWsLaVI 387 (490)
T PLN03189 312 YLELLKEREAREPKKFLKCH---FFNTFFYKKLVSGKSGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQ-EIHWTLAVI 387 (490)
T ss_pred HHHHHHHhhhcCcccccceE---EEehHHHHHHhhcCCcCChHHHHHHhhhcccccccccCceEEeeeec-CCeeEEEEE
Confidence 46789999999999999999 99999942 58899999999996 499999999
Q ss_pred eeCCCeEEEEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcCCcccceeeccCCcCCCCCCCCchHHHHHHHHH
Q 038478 70 FIPEMRAEIWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAGTKFEHFTVLQVTEFAVIPESYNYGVLILLMMQ 149 (228)
Q Consensus 70 d~keK~f~yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~~d~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae 149 (228)
|+++++|+|||||++.+. .++..|..|+.++.+.+.+..++++.|....++++|||+||||||||||+||+
T Consensus 388 d~k~k~I~yyDSLgg~~~---------~vL~~L~rYL~~E~kdK~g~d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE 458 (490)
T PLN03189 388 NKKDQKFQYLDSLKGRDP---------KILDALAKYYVDEVKDKSEKDIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYID 458 (490)
T ss_pred EcCCCeEEEEeCCCCCCH---------HHHHHHHHHHHHHHhhhcCCCcchhcceeccCCCCCCCCCCCCHHHHHHHHHH
Confidence 999999999999998643 35778888999998888877888899987777899999999999999999999
Q ss_pred HhccccCCCCcccCcchhHHHHHHHHHHHH
Q 038478 150 RGGKWLQNPTFQCDFDTERSQLVLQLLTSI 179 (228)
Q Consensus 150 ~~~~w~~~p~f~~~~~~~~~~~v~~~v~~~ 179 (228)
.++. +.| ..|+|+.|..-+......
T Consensus 459 ~~Sr--G~~---LtFSQeDMp~fRrRma~E 483 (490)
T PLN03189 459 FYSR--GLG---LCFGQEHMPYFRLRTAKE 483 (490)
T ss_pred HHcC--CCC---CCcChhhhHHHHHHHHHH
Confidence 9866 333 468999988877766443
No 3
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.95 E-value=1.7e-28 Score=215.09 Aligned_cols=126 Identities=18% Similarity=0.305 Sum_probs=103.7
Q ss_pred cccccceEEEeee--------CCCcceeeeEeeeCCCeEEEEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcC
Q 038478 46 DVGKCAKIFVPVN--------HGFCHWYLLIIFIPEMRAEIWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAG 117 (228)
Q Consensus 46 DLfscdkIFVPVN--------~ggsHWsL~VId~keK~f~yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~ 117 (228)
++.+|+.||+||| .||+||||+|+++++++|+||||++++|+.. ++.+++.+..+++.+..+
T Consensus 84 ~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~-----a~~l~~kl~~ll~~~~~~----- 153 (223)
T KOG3246|consen 84 DLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKD-----AKSLMKKLRALLKKKFAK----- 153 (223)
T ss_pred hcCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHH-----HHHHHHHHHHHHhhhhhh-----
Confidence 6899999999999 6889999999999999999999999999865 788888888888642111
Q ss_pred CcccceeeccCCcCCCCCCCCchHHHHHHHHHHhccccCCCCcccCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038478 118 TKFEHFTVLQVTEFAVIPESYNYGVLILLMMQRGGKWLQNPTFQCDFDTERSQLVLQLLTSIVNSIKEKVMEKSRDYNMA 197 (228)
Q Consensus 118 ~d~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae~~~~w~~~p~f~~~~~~~~~~~v~~~v~~~V~~mr~evl~~i~~l~~~ 197 (228)
.....+|||+||||||+|||++++.+++|........ .+..+++..++.+|+|++++|..|...
T Consensus 154 --------~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~--------~~~~~~~~~i~~lr~~l~~LI~slg~~ 217 (223)
T KOG3246|consen 154 --------RVECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYAT--------SSQLLVVDLIKALREELLDLIQSLGSI 217 (223)
T ss_pred --------cccccChhhhcCCchhHHHHHHHHHHHHHHhcccccc--------ccchhhHHHHHHHHHHHHHHHHHhCcc
Confidence 1134679999999999999999999999877532211 344456999999999999999988644
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=99.90 E-value=2.9e-23 Score=171.82 Aligned_cols=105 Identities=23% Similarity=0.389 Sum_probs=81.5
Q ss_pred ccccccceEEEeeeCCCcceeeeEeeeCCCeEEEEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcCCccccee
Q 038478 45 KDVGKCAKIFVPVNHGFCHWYLLIIFIPEMRAEIWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAGTKFEHFT 124 (228)
Q Consensus 45 ~DLfscdkIFVPVN~ggsHWsL~VId~keK~f~yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~~d~~~f~ 124 (228)
++++++|.||+|||.++.||+|+|||.+++++.||||+++.+. .......+..+..++.....+......+.+.|.
T Consensus 78 ~~l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~----~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 153 (216)
T PF02902_consen 78 KNLFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNN----DKRYKRVIENIIPFLKREYKKKEGRDPDKSPFK 153 (216)
T ss_dssp STGGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-----HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTCE
T ss_pred ccccccCEEEEEEechhhccceeEEcccccEEEEEeccccccc----cccchhhhhhhhhhhhhccccccccccccceee
Confidence 4889999999999987899999999999999999999999765 122344555556666655545444455667777
Q ss_pred eccCCcCCCCCCCCchHHHHHHHHHHhcc
Q 038478 125 VLQVTEFAVIPESYNYGVLILLMMQRGGK 153 (228)
Q Consensus 125 v~~~~~iPqQ~NGyDCGVFVlk~ae~~~~ 153 (228)
.....++|||+||+|||||||+||+.+..
T Consensus 154 ~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~ 182 (216)
T PF02902_consen 154 IVRPPNVPQQPNGYDCGVYVLKFMECLLE 182 (216)
T ss_dssp EEEECTS-SSSSSSCHHHHHHHHHHHHHC
T ss_pred ecccccccCCCCCCCcHHHHHHHHHHHHh
Confidence 77777999999999999999999998855
No 5
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=2.4e-23 Score=200.57 Aligned_cols=107 Identities=19% Similarity=0.305 Sum_probs=86.9
Q ss_pred ccchhhhhhhhhhhcc-----------------cccccceEEEeeeCCCcceeeeEeeeCCCeEEEEcCCCCCCCCccch
Q 038478 30 IDTLHEDVVMRDFYMK-----------------DVGKCAKIFVPVNHGFCHWYLLIIFIPEMRAEIWDPNPSTLTSKMFN 92 (228)
Q Consensus 30 ~~~~~~~~~~~~~~l~-----------------DLfscdkIFVPVN~ggsHWsL~VId~keK~f~yyDSL~~~n~~~~~~ 92 (228)
-...| .|++||+- |||+.++||||||. ..||+|+|||.+++.|.|||||++...
T Consensus 419 ~~~vh---~FnTFFYT~LsrrGy~gVrrW~kk~dif~~k~I~iPIni-~~HW~l~II~~~~~~i~~~DSLan~~~----- 489 (578)
T COG5160 419 REQVH---LFNTFFYTKLSRRGYSGVRRWTKKTDIFSKKYIFIPINI-SYHWFLAIIDNPKKNILYFDSLANTHD----- 489 (578)
T ss_pred ccceE---EeehhhHHHHHHHHhHHHHHHHhccCccccceEEEEecc-cceEEEEEeecCcceeEEecccccCcH-----
Confidence 34457 89999997 99999999999997 589999999999999999999999753
Q ss_pred hHHHHHHHHHHHHHhhhhhhhhhcCCcccceeeccCCcCCCCCCCCchHHHHHHHHHHhcc
Q 038478 93 SEAKTILRSLDKILNGDARKVLAAGTKFEHFTVLQVTEFAVIPESYNYGVLILLMMQRGGK 153 (228)
Q Consensus 93 ~~a~~vl~~L~~yl~de~kkk~~~~~d~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae~~~~ 153 (228)
.+++.|..|+-+|.+...++.. |..-...++|||+||+|||||||++++...+
T Consensus 490 ----~v~~~L~~Y~ldE~k~~~~k~~----~~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~ 542 (578)
T COG5160 490 ----PVLEFLRSYLLDEYKIQHDKDP----QIKMKHCKVPQQRNGSDCGVFVCMFIRYFLE 542 (578)
T ss_pred ----HHHHHHHHHHHHHHhcccCCch----hhhhhcCCCCCCCCCCccceEEEEeeeeccc
Confidence 3678888888887555443332 2222345899999999999999999987744
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=98.09 E-value=1.8e-06 Score=85.85 Aligned_cols=143 Identities=15% Similarity=0.136 Sum_probs=82.7
Q ss_pred cccccceEEEeeeCCCcceeeeEeeeCCCeEE------EEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhh----
Q 038478 46 DVGKCAKIFVPVNHGFCHWYLLIIFIPEMRAE------IWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLA---- 115 (228)
Q Consensus 46 DLfscdkIFVPVN~ggsHWsL~VId~keK~f~------yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~---- 115 (228)
|++..++||+|+|+ ..||.|+++..+....+ +++++.......+ +-.+.. .+..+......
T Consensus 434 d~~~k~yi~~P~~E-~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~----~~~~~~----~~~~~~~~~~~~~~~ 504 (595)
T KOG0779|consen 434 DLFNKDYVFVPTHE-RFHWKLAIICNPDLETETPRPRLELLILKLSADFPI----VENILD----FMKVASIYNNELIVT 504 (595)
T ss_pred ccccceeEEecCch-HhhhhccccccCccccCccccchhhhhhccccccch----hhhhhh----hhhhcccccCccccc
Confidence 99999999999995 49999999999866544 5666655444331 112222 22221111110
Q ss_pred --cCCcccceee------ccCCcCCCCCCCCchHHHHHHHHHHhccccCCCCcccCcchhHHHHHHHHHHHHHHHHHHHH
Q 038478 116 --AGTKFEHFTV------LQVTEFAVIPESYNYGVLILLMMQRGGKWLQNPTFQCDFDTERSQLVLQLLTSIVNSIKEKV 187 (228)
Q Consensus 116 --~~~d~~~f~v------~~~~~iPqQ~NGyDCGVFVlk~ae~~~~w~~~p~f~~~~~~~~~~~v~~~v~~~V~~mr~ev 187 (228)
.+.+..-+.. ..+.. |||.|..|||+|++.|+++.= .+|.....--+.-..-+....+..-..+|.++
T Consensus 505 ~~~~~~~~~~~~~~~~~s~~v~~-p~q~n~~dcG~~~~~~v~~f~---e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~ 580 (595)
T KOG0779|consen 505 EDLELEEELPRRLPRGKSETVRE-PQQNNDVDCGSFVLEFVERFI---EDAPERFNIEDEGTINLEWFPPKEILKFRDEI 580 (595)
T ss_pred ccccccccccccCcccccccccc-cCccCcccchhhHHHHHHHhh---hChhhhcccccccccccccCCchHHhhhhhhh
Confidence 0111111110 11223 899999999999999999873 34332221111111111222377788899999
Q ss_pred HHHHHHHHHhcccc
Q 038478 188 MEKSRDYNMANKIT 201 (228)
Q Consensus 188 l~~i~~l~~~~~~~ 201 (228)
=.+++.+......+
T Consensus 581 r~~~~~l~~~~~~~ 594 (595)
T KOG0779|consen 581 RNLGRKLFTSQSSE 594 (595)
T ss_pred hccccccccccCCC
Confidence 88888877665543
No 7
>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=96.53 E-value=0.0092 Score=52.06 Aligned_cols=90 Identities=19% Similarity=0.247 Sum_probs=49.0
Q ss_pred CCCcceeeeEeeeCCCeEEEEcCCCCCCCCccchhHHHHHHH-HHHHHHhhhhhhhhhcCCcccceeeccCCcCCCCCCC
Q 038478 59 HGFCHWYLLIIFIPEMRAEIWDPNPSTLTSKMFNSEAKTILR-SLDKILNGDARKVLAAGTKFEHFTVLQVTEFAVIPES 137 (228)
Q Consensus 59 ~ggsHWsL~VId~keK~f~yyDSL~~~n~~~~~~~~a~~vl~-~L~~yl~de~kkk~~~~~d~~~f~v~~~~~iPqQ~NG 137 (228)
.||+||--.+.|-+.++++.+|.+|=+ +.+++++-. ..+.++....-. ...|- =.+........|=+++
T Consensus 31 tGGvHWlA~Aw~P~s~t~YmFDPfGfs------d~~L~qiY~FeYe~llrRSAL~---~~~dR-Cv~LvkstqtVQ~p~S 100 (183)
T PF00770_consen 31 TGGVHWLAFAWDPRSRTFYMFDPFGFS------DQKLKQIYQFEYEGLLRRSALS---STPDR-CVTLVKSTQTVQCPCS 100 (183)
T ss_dssp T--S-EEEEEEETTTTEEEEE-TT---------HHHHHHHH----HHHHHHHHHH---H-TTS-EEEEEEE-EE-S-TT-
T ss_pred cCceeEEEEEecCCcceEEEeCCCCCC------HHHHHHHHhhhHHHHHHHHhhc---CCCCc-eEEEEeccceeeccCc
Confidence 799999999999999999999999986 556666654 223333222111 01110 0112233455677799
Q ss_pred CchHHHHHHHHHHhccccCCC
Q 038478 138 YNYGVLILLMMQRGGKWLQNP 158 (228)
Q Consensus 138 yDCGVFVlk~ae~~~~w~~~p 158 (228)
--||.|-|+|.-..-.|-.+|
T Consensus 101 aaCGLFC~lFL~aF~~~p~~p 121 (183)
T PF00770_consen 101 AACGLFCCLFLHAFVHYPDNP 121 (183)
T ss_dssp --HHHHHHHHHHHHHH-TTS-
T ss_pred hhHHHHHHHHHHHHHhCCCCc
Confidence 999999999999999998887
No 8
>PF03290 Peptidase_C57: Vaccinia virus I7 processing peptidase; InterPro: IPR004970 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This is a group of cysteine peptidases which constitute MEROPS peptidase family C57 (clan CE). The type example is vaccinia virus I7 processing peptidase (vaccinia virus); protein I7 is expressed in the late phase of infection [].
Probab=96.07 E-value=0.012 Score=56.79 Aligned_cols=95 Identities=12% Similarity=0.050 Sum_probs=59.0
Q ss_pred cceEEEeeeCCCcceeeeEeeeCCCeEEEEcCCCCCCCCc------c-------c---hhH---H---HHHHHHHHHHHh
Q 038478 50 CAKIFVPVNHGFCHWYLLIIFIPEMRAEIWDPNPSTLTSK------M-------F---NSE---A---KTILRSLDKILN 107 (228)
Q Consensus 50 cdkIFVPVN~ggsHWsL~VId~keK~f~yyDSL~~~n~~~------~-------~---~~~---a---~~vl~~L~~yl~ 107 (228)
+..+.+|.. =.+||.++|+|.+++-+..|||-|..+... + + +.. + .-=+..|-+++.
T Consensus 231 ~RyvmFgfc-Y~~Hwkc~IfDk~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dIDVLfrfF~ 309 (423)
T PF03290_consen 231 KRYVMFGFC-YMSHWKCCIFDKEKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDIDVLFRFFE 309 (423)
T ss_pred ccEEEeeee-ehhcceEEEEeccccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchHHHHHHHH
Confidence 344899997 458999999999999999999988754320 0 0 000 0 000123444554
Q ss_pred hhhhhhhhcCCcccceeeccCCcCCCCCCCCchHHHHHHHHHHhccccCCC
Q 038478 108 GDARKVLAAGTKFEHFTVLQVTEFAVIPESYNYGVLILLMMQRGGKWLQNP 158 (228)
Q Consensus 108 de~kkk~~~~~d~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae~~~~w~~~p 158 (228)
+.... .-..+ ..-.-|--..|||||.+-||-.+.. ..|
T Consensus 310 d~f~~--------~~gci---NvevnQl~eseCGMF~~iFm~~c~~--~pp 347 (423)
T PF03290_consen 310 DSFGV--------KYGCI---NVEVNQLLESECGMFISIFMILCTL--TPP 347 (423)
T ss_pred hhccc--------ceeEE---EhhhhhhcccccchHHHHHHHHHHc--cCc
Confidence 43211 11111 1124588899999999999999876 555
No 9
>PRK11836 deubiquitinase; Provisional
Probab=95.60 E-value=0.053 Score=51.23 Aligned_cols=104 Identities=13% Similarity=0.133 Sum_probs=62.1
Q ss_pred cccccceEEEeeeCCCcceeeeEeee--------CCCeEEEEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcC
Q 038478 46 DVGKCAKIFVPVNHGFCHWYLLIIFI--------PEMRAEIWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAG 117 (228)
Q Consensus 46 DLfscdkIFVPVN~ggsHWsL~VId~--------keK~f~yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~ 117 (228)
.+.-.+.=+||||- |.||-|+++.. .+-+..+|.|+..-++.. ....+++.+.....+..+.....-++
T Consensus 215 ~~~~k~~elFpINt-g~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~--~~t~q~ii~a~~~~~~~~~~~~~ik~ 291 (403)
T PRK11836 215 PSWPKEVQLFPINT-GGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDK--ENSLKRVINSFNSELMGEMSNNNIKV 291 (403)
T ss_pred CCCcccceEEEecC-CCcEEEEEeHHhhhcccccceeEEEEEecHhhhccch--hhHHHHHHHhhhhhhhhhcchhhhcc
Confidence 44457778999995 58999998753 234566888887776653 23356676665444443332211111
Q ss_pred CcccceeeccCCcCCCCCCCCchHHHHHHHHH-Hhcc
Q 038478 118 TKFEHFTVLQVTEFAVIPESYNYGVLILLMMQ-RGGK 153 (228)
Q Consensus 118 ~d~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae-~~~~ 153 (228)
. .+.=+|.+.+-=-||.=..-||.|||+.++ .++.
T Consensus 292 ~-~~e~ei~fie~dLQq~vpngCGlFv~~a~Qe~i~q 327 (403)
T PRK11836 292 H-LTEPEIIFLHADLQQYLSQSCGAFVCMAAQEVIEQ 327 (403)
T ss_pred c-ccCCceEEEechhhhcCCCccceehHHHHHHHHHH
Confidence 1 111112333422566667789999999999 6665
No 10
>PRK14848 deubiquitinase SseL; Provisional
Probab=94.49 E-value=0.11 Score=48.21 Aligned_cols=83 Identities=12% Similarity=0.158 Sum_probs=49.9
Q ss_pred EEEeeeCCCcceeeeEeeeC--CCeEEEEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcCCcccceeeccCCc
Q 038478 53 IFVPVNHGFCHWYLLIIFIP--EMRAEIWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAGTKFEHFTVLQVTE 130 (228)
Q Consensus 53 IFVPVN~ggsHWsL~VId~k--eK~f~yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~~d~~~f~v~~~~~ 130 (228)
=.||||- |.||-|+.+..- +-+..+|.|+..-+... .+++.+. .+..+ .....|+ .+.+-
T Consensus 191 evF~INt-g~HWil~~~~Ki~~kiKC~iFNs~~~l~eNs-----~~~ii~~-ak~ag------~~~e~di-----~fIe~ 252 (317)
T PRK14848 191 EVFLINT-GDHWLLCLFYKLAEKIKCLIFNTYYDLNENT-----KQEIIEA-AKIAG------ISENEDV-----NFIET 252 (317)
T ss_pred eEEEecC-CCcEEEEEhHHhhhhceEEEeecHhhhhhhH-----HHHHHHH-HHhhC------cccCCce-----EEeeh
Confidence 3499995 589999988633 23456888887765543 3444432 11111 0112222 23332
Q ss_pred CCCCCCCCchHHHHHHHHHHhcc
Q 038478 131 FAVIPESYNYGVLILLMMQRGGK 153 (228)
Q Consensus 131 iPqQ~NGyDCGVFVlk~ae~~~~ 153 (228)
=-||.=..-||.|||.+++.+.+
T Consensus 253 nLQqnVpngCGlFv~~aIq~l~~ 275 (317)
T PRK14848 253 NLQNNVPNGCGLFCYHTIQLLSN 275 (317)
T ss_pred hhhhhCCCcchHHHHHHHHHHHh
Confidence 25666667799999999998865
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=82.50 E-value=4.8 Score=34.67 Aligned_cols=83 Identities=16% Similarity=0.212 Sum_probs=47.8
Q ss_pred eEEEeeeCCCcceeeeEeeeC-----CCeEEEEcCCCCCCCCccchhHHHHHHHHHHHHHhhhhhhhhhcCCcccceeec
Q 038478 52 KIFVPVNHGFCHWYLLIIFIP-----EMRAEIWDPNPSTLTSKMFNSEAKTILRSLDKILNGDARKVLAAGTKFEHFTVL 126 (228)
Q Consensus 52 kIFVPVN~ggsHWsL~VId~k-----eK~f~yyDSL~~~n~~~~~~~~a~~vl~~L~~yl~de~kkk~~~~~d~~~f~v~ 126 (228)
+.+||+ ++.++.-+++|.+ +-.+..++|-.-.+... . +........+. .++......+ .
T Consensus 73 R~Iv~~--~~~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~~~~~----~----l~~~~~~~~~~-~~~~~~~~~~---~-- 136 (177)
T PF03421_consen 73 RAIVNL--GGDGIHHVALDVRHTPNGKPSLIVFEPASFYGMKP----A----LAGYTKLAEEA-RQKLLPNAKF---A-- 136 (177)
T ss_pred EEEEeC--CCCCCcEEEEEEeecCCCCceEEEEccccccCCcc----h----hhhHHHHHHHH-HhccCCCcEE---E--
Confidence 477885 4466667777776 44566799876544321 1 11111112121 1112223332 2
Q ss_pred cCCcCCCCCCCCchHHHHHHHHHHh
Q 038478 127 QVTEFAVIPESYNYGVLILLMMQRG 151 (228)
Q Consensus 127 ~~~~iPqQ~NGyDCGVFVlk~ae~~ 151 (228)
+-++..|...+|||+|.+-+|.-.
T Consensus 137 -~ie~diQkS~~dC~IFsLs~AkK~ 160 (177)
T PF03421_consen 137 -VIEMDIQKSPSDCGIFSLSLAKKM 160 (177)
T ss_pred -EEecccccCcCcchhhHHHHHHHH
Confidence 335689999999999999998765
No 12
>PF08072 BDHCT: BDHCT (NUC031) domain; InterPro: IPR012532 This is a C-terminal domain in Bloom's syndrome DEAD helicase subfamily []. The helicase articipates in DNA replication and repair, exhibiting a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.; GO: 0003677 DNA binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006260 DNA replication, 0005634 nucleus
Probab=48.76 E-value=13 Score=25.63 Aligned_cols=19 Identities=47% Similarity=0.672 Sum_probs=15.9
Q ss_pred HHHHHhhhhHhhhHHHhhc
Q 038478 8 NLLATVCGVEKLQERVLRN 26 (228)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~ 26 (228)
.|-|--||-|+||.|..|.
T Consensus 20 eL~aL~CG~eLlqqR~~Rr 38 (41)
T PF08072_consen 20 ELKALSCGNELLQQRDIRR 38 (41)
T ss_pred HHHHcchHHHHHHHHHHHH
Confidence 3557789999999999984
No 13
>PF14738 PaaSYMP: Solute carrier (proton/amino acid symporter), TRAMD3 or PAT1
Probab=45.02 E-value=82 Score=26.83 Aligned_cols=53 Identities=17% Similarity=0.203 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHhHHHHhHHh
Q 038478 167 ERSQLVLQLLTSIVNSIKEKVMEKSRDYNMANKITSELMCAAVENKYLKNLRK 219 (228)
Q Consensus 167 ~~~~~v~~~v~~~V~~mr~evl~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (228)
.|++++.+.+..-...+.+..-..+++.+++..-.-+-.-+.++.+|.+.|||
T Consensus 102 ~RLell~~~l~~RE~~~~~~~~~Rle~~~~~~~~~k~~~i~ki~~~~~r~lRK 154 (154)
T PF14738_consen 102 RRLELLKKMLQEREKEQEEANEQRLERLWQKKQKEKERKIEKIEKERIRALRK 154 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34444444444444444444444445555555555555566677777777775
No 14
>PRK15371 effector protein YopJ; Provisional
Probab=34.32 E-value=1.6e+02 Score=27.63 Aligned_cols=41 Identities=12% Similarity=0.168 Sum_probs=27.8
Q ss_pred cCCCCCCCCchHHHHHHHHHHhccccCCCCcccCcchhHHHHHHHHH
Q 038478 130 EFAVIPESYNYGVLILLMMQRGGKWLQNPTFQCDFDTERSQLVLQLL 176 (228)
Q Consensus 130 ~iPqQ~NGyDCGVFVlk~ae~~~~w~~~p~f~~~~~~~~~~~v~~~v 176 (228)
.+-.|.-.+|||||.+-+|... +..++ .|++.+-..+...+
T Consensus 162 e~d~QkS~~dC~mFSL~~AkK~---~~e~d---~fd~lH~~~~~~~l 202 (287)
T PRK15371 162 EMDIQRSSSECGIFSLALAKKL---YLERD---KLLKLHEDNIKGIL 202 (287)
T ss_pred ecccccCcccchhhhHHHHHHH---hhhhH---HHHHHHHHHhhCcc
Confidence 3467999999999999998765 33322 35555555555444
No 15
>PF05878 Phyto_Pns9_10: Phytoreovirus nonstructural protein Pns9/Pns10; InterPro: IPR008776 This family consists of the Phytoreovirus nonstructural proteins Pns9 and Pns10. The function of this family is unknown.
Probab=31.88 E-value=2.1e+02 Score=27.34 Aligned_cols=64 Identities=16% Similarity=0.220 Sum_probs=43.7
Q ss_pred HhccccCCCCcccCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc-hHHHHHHHHhHHHH
Q 038478 150 RGGKWLQNPTFQCDFDTERSQLVLQLLTSIVNSIKEKVMEKSRDYNMANKIT-SELMCAAVENKYLK 215 (228)
Q Consensus 150 ~~~~w~~~p~f~~~~~~~~~~~v~~~v~~~V~~mr~evl~~i~~l~~~~~~~-~~~~~~~~~~~~~~ 215 (228)
-+.+|..+++- .+.+..--+--+.|+...+.-.|++|+.+|+.|..-+.-. +|-.|+ +-++|-.
T Consensus 174 Dv~~wleKl~~-a~~g~~~~QKsk~qM~~~i~~~Rn~I~n~I~~fVn~n~nS~~eh~Re-~a~~y~q 238 (312)
T PF05878_consen 174 DVVEWLEKLPS-AKGGILSNQKSKAQMRPEIQRIRNEILNKIQQFVNLNENSQNEHFRE-VANSYKQ 238 (312)
T ss_pred hHHHHHhCCcc-ccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccHHHHH-HHHHHHH
Confidence 34567766533 3444445566778889999999999999999998876544 444444 4456643
No 16
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=30.14 E-value=2.4e+02 Score=25.80 Aligned_cols=59 Identities=19% Similarity=0.202 Sum_probs=50.4
Q ss_pred CCCcccCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHhHHHHhH
Q 038478 157 NPTFQCDFDTERSQLVLQLLTSIVNSIKEKVMEKSRDYNMANKITSELMCAAVENKYLKNL 217 (228)
Q Consensus 157 ~p~f~~~~~~~~~~~v~~~v~~~V~~mr~evl~~i~~l~~~~~~~~~~~~~~~~~~~~~~~ 217 (228)
.+.|..+--..++.-|++++-+ +.|-.++.+..+.+|..+-+..+++-|+.-..|||.=
T Consensus 40 ks~fhvsNKlIHlrNVLrrlls--~qcs~~ii~ell~lm~kn~i~~~didan~vs~fLK~~ 98 (225)
T PHA03074 40 KSNFHVSNKLIHLRNVLRRLLS--NQCSGEIISELLELMNKNQISTKDVDANFVSSFLKAK 98 (225)
T ss_pred hcccccccceeeHHHHHHHHHH--hHhhHHHHHHHHHHHHHccCChhhhhHHHHHHHHHHH
Confidence 3345566777899999999855 8899999999999999999999999999999999863
No 17
>PHA01748 hypothetical protein
Probab=28.92 E-value=1.5e+02 Score=21.10 Aligned_cols=34 Identities=29% Similarity=0.418 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhcccc-hHHHHHHHHhHHHHhHHh
Q 038478 185 EKVMEKSRDYNMANKIT-SELMCAAVENKYLKNLRK 219 (228)
Q Consensus 185 ~evl~~i~~l~~~~~~~-~~~~~~~~~~~~~~~~~~ 219 (228)
.++++.+..|..+...+ |+.+|.|++ .|++.-..
T Consensus 11 ~el~~eld~~a~~~g~~RSE~Ir~Ai~-~~~~~~~~ 45 (60)
T PHA01748 11 EDLLELLDRYAIKHGLNRSEAIRKAIE-KMVKDELK 45 (60)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHH-HHHHHHHH
Confidence 46777888887666554 789999998 66665443
No 18
>PRK13988 cell division topological specificity factor MinE; Provisional
Probab=22.64 E-value=79 Score=25.14 Aligned_cols=35 Identities=26% Similarity=0.407 Sum_probs=29.4
Q ss_pred cCcchhHHHHHH--H--HH-HHHHHHHHHHHHHHHHHHHH
Q 038478 162 CDFDTERSQLVL--Q--LL-TSIVNSIKEKVMEKSRDYNM 196 (228)
Q Consensus 162 ~~~~~~~~~~v~--~--~v-~~~V~~mr~evl~~i~~l~~ 196 (228)
.+.-.+|+++++ + .+ |+....||++|++-|..|+.
T Consensus 18 a~~AK~RLk~iL~~dR~~~sp~~l~~mk~dIl~VIskYv~ 57 (97)
T PRK13988 18 ASTARERLQLVLAHDRADLSPELLEQMRKEILEVVARYVE 57 (97)
T ss_pred HHHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHee
Confidence 466788999888 2 24 89999999999999999986
No 19
>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=22.56 E-value=63 Score=24.59 Aligned_cols=21 Identities=19% Similarity=0.245 Sum_probs=13.5
Q ss_pred CCCCCCCCchHHHHHHHHHHh
Q 038478 131 FAVIPESYNYGVLILLMMQRG 151 (228)
Q Consensus 131 iPqQ~NGyDCGVFVlk~ae~~ 151 (228)
+-.|....|||+-.+.++-..
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~ 24 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKY 24 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHH
T ss_pred eEEeCCCCCHHHHHHHHHHHH
Confidence 356889999999999887654
No 20
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=22.28 E-value=80 Score=26.15 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=22.5
Q ss_pred ccceeeccCCcCCCCCCCCchHHHHHHHHH
Q 038478 120 FEHFTVLQVTEFAVIPESYNYGVLILLMMQ 149 (228)
Q Consensus 120 ~~~f~v~~~~~iPqQ~NGyDCGVFVlk~ae 149 (228)
+..|-......+|--.-|+|||-|--.+++
T Consensus 16 ~~r~p~tds~~~p~~~q~r~cg~FE~e~~e 45 (120)
T KOG4110|consen 16 IDRWPTTDSTEQPYKHQGRDCGKFEKEWME 45 (120)
T ss_pred hhhccccccccCccccccccccHHHHHHHH
Confidence 344544445577888899999999888877
No 21
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.88 E-value=56 Score=29.03 Aligned_cols=37 Identities=14% Similarity=0.256 Sum_probs=30.0
Q ss_pred cCCCCCCCCchHHHHHHHHHHhccccCCCCcccCcchhHH
Q 038478 130 EFAVIPESYNYGVLILLMMQRGGKWLQNPTFQCDFDTERS 169 (228)
Q Consensus 130 ~iPqQ~NGyDCGVFVlk~ae~~~~w~~~p~f~~~~~~~~~ 169 (228)
++|.-.|+-.|+-|||-+++.. ..++.|.|..++-|.
T Consensus 132 SVPke~~~lnc~~fvaGIiea~---L~~agfpckVTAh~~ 168 (191)
T KOG3315|consen 132 SVPKENGTLNCAAFVAGIIEAV---LDNAGFPCKVTAHWH 168 (191)
T ss_pred ecccccCcccHHHHHHHHHHHH---HHhCCCCCceeeeec
Confidence 6799999999999999999987 445567677776665
No 22
>PRK13991 cell division topological specificity factor MinE; Provisional
Probab=20.23 E-value=1.3e+02 Score=23.37 Aligned_cols=35 Identities=20% Similarity=0.332 Sum_probs=28.6
Q ss_pred cCcchhHHHHHH--H--HH-HHHHHHHHHHHHHHHHHHHH
Q 038478 162 CDFDTERSQLVL--Q--LL-TSIVNSIKEKVMEKSRDYNM 196 (228)
Q Consensus 162 ~~~~~~~~~~v~--~--~v-~~~V~~mr~evl~~i~~l~~ 196 (228)
.+.-.+|+++++ + .+ |+-...||.||++-|..|+.
T Consensus 16 a~~AKeRLqliLahdR~~~~p~~l~~lk~eil~VIsKYv~ 55 (87)
T PRK13991 16 SELAKQRLLTVLVHDRVKLTPEMMEQMKADLAEVIKRYVP 55 (87)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 455678888887 2 23 88999999999999999986
Done!