Query 029358
Match_columns 194
No_of_seqs 147 out of 1046
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 11:38:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029358.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029358hhsearch_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 5.2E-43 1.1E-47 307.8 8.8 158 4-174 337-500 (511)
2 PLN03189 Protease specific for 100.0 3.7E-39 7.9E-44 281.5 14.7 158 5-174 308-479 (490)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 1.7E-38 3.6E-43 276.5 6.0 154 5-174 401-559 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 6.4E-29 1.4E-33 199.5 11.9 156 14-190 22-205 (216)
5 KOG3246 Sentrin-specific cyste 99.8 1.1E-19 2.5E-24 143.9 11.8 146 21-192 56-210 (223)
6 KOG0779 Protease, Ulp1 family 99.7 1.6E-18 3.4E-23 158.3 6.6 174 15-192 389-583 (595)
7 PF03290 Peptidase_C57: Vaccin 97.4 0.00042 9.2E-09 59.9 6.0 92 51-164 229-351 (423)
8 PRK11836 deubiquitinase; Provi 97.3 0.00035 7.6E-09 58.6 5.1 110 47-158 213-327 (403)
9 PRK14848 deubiquitinase SseL; 97.1 0.0011 2.5E-08 54.4 6.0 90 53-159 188-277 (317)
10 PF03421 YopJ: YopJ Serine/Thr 93.1 0.8 1.7E-05 36.1 8.4 89 55-158 73-163 (177)
11 PF00770 Peptidase_C5: Adenovi 86.7 0.65 1.4E-05 36.4 2.8 81 63-159 33-118 (183)
12 PRK15371 effector protein YopJ 84.3 6 0.00013 33.6 7.7 65 84-159 121-187 (287)
13 PF04508 Pox_A_type_inc: Viral 50.6 6 0.00013 20.5 0.2 14 181-194 2-15 (23)
14 KOG0779 Protease, Ulp1 family 41.6 4.2 9.2E-05 38.0 -2.0 177 15-192 133-336 (595)
15 PF03412 Peptidase_C39: Peptid 40.5 19 0.0004 25.9 1.6 22 135-156 4-25 (131)
16 PF12252 SidE: Dot/Icm substra 40.4 75 0.0016 32.1 5.9 35 57-101 49-90 (1439)
17 KOG3315 Transport protein part 39.6 25 0.00055 27.6 2.3 28 132-159 130-157 (191)
18 PHA02130 hypothetical protein 35.9 16 0.00035 24.0 0.6 36 37-72 15-51 (81)
19 KOG4110 NADH:ubiquinone oxidor 31.1 49 0.0011 24.0 2.4 31 127-157 18-49 (120)
20 COG5019 CDC3 Septin family pro 22.4 74 0.0016 28.1 2.5 37 149-191 153-189 (373)
21 cd02424 Peptidase_C39E A sub-f 22.2 57 0.0012 23.4 1.5 19 137-155 5-23 (129)
22 KOG0271 Notchless-like WD40 re 20.6 1.4E+02 0.003 26.7 3.8 36 62-97 155-191 (480)
23 cd02423 Peptidase_C39G A sub-f 20.1 1.3E+02 0.0028 21.1 3.1 22 136-157 4-25 (129)
No 1
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.2e-43 Score=307.76 Aligned_cols=158 Identities=25% Similarity=0.447 Sum_probs=138.3
Q ss_pred HHHHHHHhhcCcCCCCc-----EEEeccchhhhccCCCCchhHHHhhhccCCCccceEEEeccCCCcceeEEEecCCCCc
Q 029358 4 QICSNLWRSFSEDKKAG-----FTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKKYVLVPIVCWRHWNLLILCNFGGSF 78 (194)
Q Consensus 4 ~~~~~~~~~l~~~~~~~-----~~~~nsfF~~~l~~~~~~~~v~rw~k~~~if~~d~i~iPin~~~HW~L~vi~~p~~~~ 78 (194)
+|++.+...|.+-.+.+ +|+||||||++|.. .||++|+|||+++|||++|+||||||.+.||+|+||+.
T Consensus 337 evINfYm~ll~ers~~~~~yp~~h~FnTFFy~kL~~-~gy~~VkRWTk~v~if~~d~i~vPIH~~vHW~l~vid~----- 410 (511)
T KOG0778|consen 337 EVINFYMELLKERSKKDSKYPKVHAFNTFFYTKLVG-RGYAGVKRWTKKVDIFDKDIIFVPIHLGVHWCLAVIDL----- 410 (511)
T ss_pred HHHHHHHHHHHhhccccCCCceEEEEechhhhhhhh-cchHHHHhHhhccCccccceeEeeeecCceEEEEEEEc-----
Confidence 57888888887755444 99999999999987 69999999999999999999999999999999999987
Q ss_pred CcCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHHhCCCCCcccCCCccc-cCCCCCCCCCCCCcHHHHHHHHHHHhc
Q 029358 79 ESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPL-LVPKVPQQRNGEECGNFVLYFINLFVE 157 (194)
Q Consensus 79 ~~~~~~~~i~~~DSl~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~P~Q~N~~DCGvfvl~~~e~~~~ 157 (194)
++++|.|||||++.....+ ..|.+||.+|+..+.+. .++.+.|.. ...++|||.||+|||+|+|+|+++++.
T Consensus 411 ----r~k~i~y~DS~~~~~nr~~-~aL~~Yl~~E~~~k~~~--~~d~s~w~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~ 483 (511)
T KOG0778|consen 411 ----REKTIEYYDSLGGGPNRIC-DALAKYLQDESRDKSKK--DFDVSGWTIEFVQNIPQQRNGSDCGMFVCKYADYISR 483 (511)
T ss_pred ----ccceEEEeeccCCCCcchH-HHHHHHHHHHHhhhhcC--CCCccchhhhhhhccccccCCCccceEEeeechhhcc
Confidence 5689999999997755444 79999999998766442 355567885 456899999999999999999999999
Q ss_pred CCCCCcCCCCCcchhhh
Q 029358 158 GAPENFNLEDYPYFMEK 174 (194)
Q Consensus 158 ~~~~~f~~~d~~~~r~~ 174 (194)
+.|++|+|.|||.||++
T Consensus 484 ~~p~~ftq~dmp~fR~~ 500 (511)
T KOG0778|consen 484 DVPLTFTQQDMPYFRKK 500 (511)
T ss_pred CCCcccChhhhHHHHHH
Confidence 99999999999999975
No 2
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=3.7e-39 Score=281.51 Aligned_cols=158 Identities=22% Similarity=0.417 Sum_probs=130.6
Q ss_pred HHHHHHhhcCc------CCCCcEEEeccchhhhccCCC---CchhHHHhhhc----cCCCccceEEEeccCCCcceeEEE
Q 029358 5 ICSNLWRSFSE------DKKAGFTYLDSLWFDLYRKPS---SKAKVLTWIKR----KHIFSKKYVLVPIVCWRHWNLLIL 71 (194)
Q Consensus 5 ~~~~~~~~l~~------~~~~~~~~~nsfF~~~l~~~~---~~~~v~rw~k~----~~if~~d~i~iPin~~~HW~L~vi 71 (194)
|+..+...|.+ ....++|+||||||++|.+.. +|++|+||+++ +++|++|+||||||.+.||+|+||
T Consensus 308 VINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~kKigv~Lfs~D~IFIPIh~n~HWsLaVI 387 (490)
T PLN03189 308 VINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQKKLGYHLIDCDKIFVPIHQEIHWTLAVI 387 (490)
T ss_pred HHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhhcccccccccCceEEeeeecCCeeEEEEE
Confidence 45555555532 234689999999999999742 79999999975 468999999999999999999999
Q ss_pred ecCCCCcCcCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHHhCCCCCcccCCCccc-cCCCCCCCCCCCCcHHHHHH
Q 029358 72 CNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPL-LVPKVPQQRNGEECGNFVLY 150 (194)
Q Consensus 72 ~~p~~~~~~~~~~~~i~~~DSl~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~P~Q~N~~DCGvfvl~ 150 (194)
+++ .++|.|||||++.+.. +.+.|++||..+++.+... ....+.|.. ....+|||.||+|||||||+
T Consensus 388 d~k---------~k~I~yyDSLgg~~~~-vL~~L~rYL~~E~kdK~g~--d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~ 455 (490)
T PLN03189 388 NKK---------DQKFQYLDSLKGRDPK-ILDALAKYYVDEVKDKSEK--DIDVSSWEQEFVEDLPEQKNGYDCGMFMIK 455 (490)
T ss_pred EcC---------CCeEEEEeCCCCCCHH-HHHHHHHHHHHHHhhhcCC--CcchhcceeccCCCCCCCCCCCCHHHHHHH
Confidence 985 4699999999998764 5568999999988765322 234467775 34689999999999999999
Q ss_pred HHHHHhcCCCCCcCCCCCcchhhh
Q 029358 151 FINLFVEGAPENFNLEDYPYFMEK 174 (194)
Q Consensus 151 ~~e~~~~~~~~~f~~~d~~~~r~~ 174 (194)
||++++.+.+++|+|+|||.+|++
T Consensus 456 yAE~~SrG~~LtFSQeDMp~fRrR 479 (490)
T PLN03189 456 YIDFYSRGLGLCFGQEHMPYFRLR 479 (490)
T ss_pred HHHHHcCCCCCCcChhhhHHHHHH
Confidence 999999999999999999999976
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-38 Score=276.50 Aligned_cols=154 Identities=32% Similarity=0.560 Sum_probs=129.5
Q ss_pred HHHHHHhhcCcC-----CCCcEEEeccchhhhccCCCCchhHHHhhhccCCCccceEEEeccCCCcceeEEEecCCCCcC
Q 029358 5 ICSNLWRSFSED-----KKAGFTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKKYVLVPIVCWRHWNLLILCNFGGSFE 79 (194)
Q Consensus 5 ~~~~~~~~l~~~-----~~~~~~~~nsfF~~~l~~~~~~~~v~rw~k~~~if~~d~i~iPin~~~HW~L~vi~~p~~~~~ 79 (194)
|+.++.+-++.- .++++|+||||||++|.+ .||++|+||+++++||++++||||||...||+|+|||.+
T Consensus 401 IIdFy~k~ls~~sk~~s~~~~vh~FnTFFYT~Lsr-rGy~gVrrW~kk~dif~~k~I~iPIni~~HW~l~II~~~----- 474 (578)
T COG5160 401 IIDFYMKLLSKISKNTSKREQVHLFNTFFYTKLSR-RGYSGVRRWTKKTDIFSKKYIFIPINISYHWFLAIIDNP----- 474 (578)
T ss_pred HHHHHHHHHHHhccCcccccceEEeehhhHHHHHH-HHhHHHHHHHhccCccccceEEEEecccceEEEEEeecC-----
Confidence 444444444332 356799999999999986 799999999999999999999999999999999999985
Q ss_pred cCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHHhCCCCCcccCCCccccCCCCCCCCCCCCcHHHHHHHHHHHhcCC
Q 029358 80 SKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLVPKVPQQRNGEECGNFVLYFINLFVEGA 159 (194)
Q Consensus 80 ~~~~~~~i~~~DSl~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~N~~DCGvfvl~~~e~~~~~~ 159 (194)
.+.|.++|||++.+. .+...++.|+.+|++..+.... .......++|||.||+|||||||+|++++++++
T Consensus 475 ----~~~i~~~DSLan~~~-~v~~~L~~Y~ldE~k~~~~k~~-----~~~~~~~~vPqQ~Ng~DCGV~vc~~~~~~~~~~ 544 (578)
T COG5160 475 ----KKNILYFDSLANTHD-PVLEFLRSYLLDEYKIQHDKDP-----QIKMKHCKVPQQRNGSDCGVFVCMFIRYFLENP 544 (578)
T ss_pred ----cceeEEecccccCcH-HHHHHHHHHHHHHHhcccCCch-----hhhhhcCCCCCCCCCCccceEEEEeeeecccCC
Confidence 468999999999986 4666899999999876543211 123466799999999999999999999999999
Q ss_pred CCCcCCCCCcchhhh
Q 029358 160 PENFNLEDYPYFMEK 174 (194)
Q Consensus 160 ~~~f~~~d~~~~r~~ 174 (194)
|..|.++|+|.+|+.
T Consensus 545 p~~f~~nd~~r~Rk~ 559 (578)
T COG5160 545 PEQFSKNDRPRARKN 559 (578)
T ss_pred hhhcCccchHHHHHH
Confidence 999999999988864
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=99.96 E-value=6.4e-29 Score=199.49 Aligned_cols=156 Identities=29% Similarity=0.522 Sum_probs=115.4
Q ss_pred CcCCCCcEEEeccchhhhccCC-------------------CCchhHHHhhhcc---CCCccceEEEeccC-CCcceeEE
Q 029358 14 SEDKKAGFTYLDSLWFDLYRKP-------------------SSKAKVLTWIKRK---HIFSKKYVLVPIVC-WRHWNLLI 70 (194)
Q Consensus 14 ~~~~~~~~~~~nsfF~~~l~~~-------------------~~~~~v~rw~k~~---~if~~d~i~iPin~-~~HW~L~v 70 (194)
.+...+++++|+|+|+++|.+. ..+.++.+|++.. +++++++|++|||. +.||+|+|
T Consensus 22 ~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~i~iPin~~~~HW~l~v 101 (216)
T PF02902_consen 22 ENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKKNLFDKDYIFIPININNNHWVLLV 101 (216)
T ss_dssp THHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTSTGGGSSEEEEEEEETTTEEEEEE
T ss_pred CccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhccccccccccCEEEEEEechhhccceeE
Confidence 4677899999999999999821 2457889999887 99999999999999 89999999
Q ss_pred EecCCCCcCcCCCCCeEEEeeCCCCCCC----cchHHHHHHHHHHHHHHhCCCCCcccCCCccc-cCCCCCCCCCCCCcH
Q 029358 71 LCNFGGSFESKTRTPCMLLLDSLEMSNP----WRFEPDIRKFVMDIYKAEDRPETKELISRIPL-LVPKVPQQRNGEECG 145 (194)
Q Consensus 71 i~~p~~~~~~~~~~~~i~~~DSl~~~~~----~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~P~Q~N~~DCG 145 (194)
|+.+. .+|.+||||++... ..+...+..+|...+....... .....|.. ....+|||.|++|||
T Consensus 102 i~~~~---------~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~~pqQ~n~~dCG 170 (216)
T PF02902_consen 102 IDLPK---------KRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRD--PDKSPFKIVRPPNVPQQPNGYDCG 170 (216)
T ss_dssp EETTT---------TEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSC--T-TTTCEEEEECTS-SSSSSSCHH
T ss_pred Ecccc---------cEEEEEeccccccccccchhhhhhhhhhhhhccccccccc--cccceeeecccccccCCCCCCCcH
Confidence 99854 69999999999876 2344567778877664432211 12234553 456899999999999
Q ss_pred HHHHHHHHHHhcCCCCCcCCCCCcchhhhCCCCHHHHHHHHHHhh
Q 029358 146 NFVLYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLN 190 (194)
Q Consensus 146 vfvl~~~e~~~~~~~~~f~~~d~~~~r~~~wf~~~~i~~~R~~i~ 190 (194)
+|||+||++++.+.+....+. |+.+++...|+++.
T Consensus 171 v~vl~~~~~~~~~~~~~~~~~----------l~~~~i~~~r~~~a 205 (216)
T PF02902_consen 171 VYVLKFMECLLEGPSFDFSQE----------LTEEDIKNFRKKLA 205 (216)
T ss_dssp HHHHHHHHHHHCTHHSTGCCS----------BTGHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCccccc----------CCHHHHHHHHHHHH
Confidence 999999999999975543221 45566666666654
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.82 E-value=1.1e-19 Score=143.86 Aligned_cols=146 Identities=18% Similarity=0.216 Sum_probs=97.6
Q ss_pred EEEeccchhhhccCCCCchhHHHhhhccCCCccceEEEeccCC---------CcceeEEEecCCCCcCcCCCCCeEEEee
Q 029358 21 FTYLDSLWFDLYRKPSSKAKVLTWIKRKHIFSKKYVLVPIVCW---------RHWNLLILCNFGGSFESKTRTPCMLLLD 91 (194)
Q Consensus 21 ~~~~nsfF~~~l~~~~~~~~v~rw~k~~~if~~d~i~iPin~~---------~HW~L~vi~~p~~~~~~~~~~~~i~~~D 91 (194)
.|++++=---.+....+-+.+.......++.+|++||+|||++ +||+|.|+..|. ...++||
T Consensus 56 ~~ll~P~~t~~l~~~~~~~e~~~~~~pl~l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~---------~~f~hyD 126 (223)
T KOG3246|consen 56 LHLLRPSLTFFLRHAPNPEEIAMVLDPLDLNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPD---------GKFYHYD 126 (223)
T ss_pred hhccCHHHHHHHHhCCCcHHHHHhcChhhcCCCceEEEEecCCCcccccCCCcceEEEEEEeeC---------CcEEEee
Confidence 4666653323344444567778877888999999999999983 599999999864 5899999
Q ss_pred CCCCCCCcchHHHHHHHHHHHHHHhCCCCCcccCCCccccCCCCCCCCCCCCcHHHHHHHHHHHhcCCCCCcCCCCCcch
Q 029358 92 SLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLVPKVPQQRNGEECGNFVLYFINLFVEGAPENFNLEDYPYF 171 (194)
Q Consensus 92 Sl~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~N~~DCGvfvl~~~e~~~~~~~~~f~~~d~~~~ 171 (194)
|+.+.+..... .+.+-+....+.+.. ...+..+|||.||||||+|||.+.+.+...- ....|+..
T Consensus 127 S~~n~nt~~a~-~l~~kl~~ll~~~~~----------~~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~----~~~~~~~~ 191 (223)
T KOG3246|consen 127 SLSNGNTKDAK-SLMKKLRALLKKKFA----------KRVECKCLQQQNGYDCGLHVCCNTRVLAERL----LRCPYATS 191 (223)
T ss_pred cccCCCcHHHH-HHHHHHHHHHhhhhh----------hcccccChhhhcCCchhHHHHHHHHHHHHHH----hccccccc
Confidence 99999874333 222223332222110 0125678999999999999999987776542 11112211
Q ss_pred hhhCCCCHHHHHHHHHHhhhc
Q 029358 172 MEKNWFTAEDLDCFCERLNSS 192 (194)
Q Consensus 172 r~~~wf~~~~i~~~R~~i~~~ 192 (194)
..-..+..|.++|++|+.|
T Consensus 192 --~~~~~~~~i~~lr~~l~~L 210 (223)
T KOG3246|consen 192 --SQLLVVDLIKALREELLDL 210 (223)
T ss_pred --cchhhHHHHHHHHHHHHHH
Confidence 1223456789999998875
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.74 E-value=1.6e-18 Score=158.34 Aligned_cols=174 Identities=27% Similarity=0.472 Sum_probs=123.8
Q ss_pred cCCCCcEEEeccchhhhccCCC-----------CchhHHHhhhccCCCccceEEEeccCCCcceeEEEecCCCCcCcCCC
Q 029358 15 EDKKAGFTYLDSLWFDLYRKPS-----------SKAKVLTWIKRKHIFSKKYVLVPIVCWRHWNLLILCNFGGSFESKTR 83 (194)
Q Consensus 15 ~~~~~~~~~~nsfF~~~l~~~~-----------~~~~v~rw~k~~~if~~d~i~iPin~~~HW~L~vi~~p~~~~~~~~~ 83 (194)
.+..+..|+|++|||.++.++. ...++++|++..|+|.++||++|+|+..||.++++|+|....++.
T Consensus 389 ~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~-- 466 (595)
T KOG0779|consen 389 KELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTRHFDLFNKDYVFVPTHERFHWKLAIICNPDLETETP-- 466 (595)
T ss_pred cccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeeeccccccceeEEecCchHhhhhccccccCccccCcc--
Confidence 6778889999999999998742 345789999999999999999999999999999999997654432
Q ss_pred CCeEEEeeCCCCCCCcchHHHHHHHHHHHHHHhCCCC-Cccc------CCCcc---ccCCCCCCCCCCCCcHHHHHHHHH
Q 029358 84 TPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPE-TKEL------ISRIP---LLVPKVPQQRNGEECGNFVLYFIN 153 (194)
Q Consensus 84 ~~~i~~~DSl~~~~~~~~~~~i~~~l~~~~~~~~~~~-~~~~------~~~~~---~~~~~~P~Q~N~~DCGvfvl~~~e 153 (194)
......+++......-+...+..++..++....... .... +...+ ......|||.|..|||+|++.|++
T Consensus 467 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~ 545 (595)
T KOG0779|consen 467 -RPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLELEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVE 545 (595)
T ss_pred -ccchhhhhhccccccchhhhhhhhhhhcccccCcccccccccccccccccCcccccccccccCccCcccchhhHHHHHH
Confidence 223444555444433333455555654432211100 0000 00111 111123999999999999999999
Q ss_pred HHhcCCCCCcCCCCCcchhhhCCCCHHHHHHHHHHhhhc
Q 029358 154 LFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNSS 192 (194)
Q Consensus 154 ~~~~~~~~~f~~~d~~~~r~~~wf~~~~i~~~R~~i~~~ 192 (194)
.+..+++..++..+....-.. ||.+.++.++|.++|.+
T Consensus 546 ~f~e~~~e~~~~~~~~~~~l~-~~~~~~~~~~r~~~r~~ 583 (595)
T KOG0779|consen 546 RFIEDAPERFNIEDEGTINLE-WFPPKEILKFRDEIRNL 583 (595)
T ss_pred HhhhChhhhcccccccccccc-cCCchHHhhhhhhhhcc
Confidence 999999988777666665545 99999999999999875
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=97.36 E-value=0.00042 Score=59.93 Aligned_cols=92 Identities=21% Similarity=0.260 Sum_probs=61.8
Q ss_pred CccceEEEeccCCCcceeEEEecCCCCcCcCCCCCeEEEeeCCCCCCCc------------------------------c
Q 029358 51 FSKKYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPW------------------------------R 100 (194)
Q Consensus 51 f~~d~i~iPin~~~HW~L~vi~~p~~~~~~~~~~~~i~~~DSl~~~~~~------------------------------~ 100 (194)
-++.++.+|.+...||.++|++. ++.-+.+|||.|....+ .
T Consensus 229 ~~~RyvmFgfcY~~Hwkc~IfDk---------~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~ 299 (423)
T PF03290_consen 229 SKKRYVMFGFCYMSHWKCCIFDK---------EKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENC 299 (423)
T ss_pred ccccEEEeeeeehhcceEEEEec---------cccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccC
Confidence 46789999999999999999986 23457788887764210 0
Q ss_pred hHHHHHHHHHHHHHHhCCCCCcccCCCccccCCC-CCCCCCCCCcHHHHHHHHHHHhcCCCCCcC
Q 029358 101 FEPDIRKFVMDIYKAEDRPETKELISRIPLLVPK-VPQQRNGEECGNFVLYFINLFVEGAPENFN 164 (194)
Q Consensus 101 ~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~P~Q~N~~DCGvfvl~~~e~~~~~~~~~f~ 164 (194)
-.+.+.+|+...+..+ .-..+ ---|--..|||+|.+-|+-.....||..|.
T Consensus 300 dIDVLfrfF~d~f~~~-------------~gciNvevnQl~eseCGMF~~iFm~~c~~~ppk~fk 351 (423)
T PF03290_consen 300 DIDVLFRFFEDSFGVK-------------YGCINVEVNQLLESECGMFISIFMILCTLTPPKGFK 351 (423)
T ss_pred chHHHHHHHHhhcccc-------------eeEEEhhhhhhcccccchHHHHHHHHHHccCchhHH
Confidence 0134455554433211 11111 145788999999999999988888887653
No 8
>PRK11836 deubiquitinase; Provisional
Probab=97.34 E-value=0.00035 Score=58.58 Aligned_cols=110 Identities=20% Similarity=0.211 Sum_probs=56.2
Q ss_pred ccCCCccceEEEeccCCCcceeEEEecCCCCcCcCCCCCeEEEeeCCCCCCCc--chHHHHHHHHHHHHHHhCCC-CCcc
Q 029358 47 RKHIFSKKYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPW--RFEPDIRKFVMDIYKAEDRP-ETKE 123 (194)
Q Consensus 47 ~~~if~~d~i~iPin~~~HW~L~vi~~p~~~~~~~~~~~~i~~~DSl~~~~~~--~~~~~i~~~l~~~~~~~~~~-~~~~ 123 (194)
...++-++.-+||||.+.||.|+++-........+.+-+| +++.|+..-+.. ...+.|+.-...+....... ..+.
T Consensus 213 ~~~~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC-~IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~~~~~ik~ 291 (403)
T PRK11836 213 SDPSWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKC-VIFNSLRALGHDKENSLKRVINSFNSELMGEMSNNNIKV 291 (403)
T ss_pred cCCCCcccceEEEecCCCcEEEEEeHHhhhcccccceeEE-EEEecHhhhccchhhHHHHHHHhhhhhhhhhcchhhhcc
Confidence 3456678999999999999999998432211011112334 577888765432 22223333222222110000 0000
Q ss_pred c--CCCccccCCCCCCCCCCCCcHHHHHHHHHHHhcC
Q 029358 124 L--ISRIPLLVPKVPQQRNGEECGNFVLYFINLFVEG 158 (194)
Q Consensus 124 ~--~~~~~~~~~~~P~Q~N~~DCGvfvl~~~e~~~~~ 158 (194)
. ...+.+...+ -||.-...||.||++-++-++..
T Consensus 292 ~~~e~ei~fie~d-LQq~vpngCGlFv~~a~Qe~i~q 327 (403)
T PRK11836 292 HLTEPEIIFLHAD-LQQYLSQSCGAFVCMAAQEVIEQ 327 (403)
T ss_pred cccCCceEEEech-hhhcCCCccceehHHHHHHHHHH
Confidence 0 0112222222 34445789999999988755443
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=97.13 E-value=0.0011 Score=54.45 Aligned_cols=90 Identities=18% Similarity=0.278 Sum_probs=51.5
Q ss_pred cceEEEeccCCCcceeEEEecCCCCcCcCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHHhCCCCCcccCCCccccC
Q 029358 53 KKYVLVPIVCWRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLV 132 (194)
Q Consensus 53 ~d~i~iPin~~~HW~L~vi~~p~~~~~~~~~~~~i~~~DSl~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~ 132 (194)
++.-+||||.++||.|++.-...+ +-+| ++|.|++.-+.... +.|+. . .+..+..+. ..+-+..
T Consensus 188 ~~nevF~INtg~HWil~~~~Ki~~------kiKC-~iFNs~~~l~eNs~-~~ii~---~-ak~ag~~~e----~di~fIe 251 (317)
T PRK14848 188 SHNEVFLINTGDHWLLCLFYKLAE------KIKC-LIFNTYYDLNENTK-QEIIE---A-AKIAGISEN----EDVNFIE 251 (317)
T ss_pred CcceEEEecCCCcEEEEEhHHhhh------hceE-EEeecHhhhhhhHH-HHHHH---H-HHhhCcccC----CceEEee
Confidence 455669999999999999854332 2345 57788876653222 22222 1 221121100 0112222
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHhcCC
Q 029358 133 PKVPQQRNGEECGNFVLYFINLFVEGA 159 (194)
Q Consensus 133 ~~~P~Q~N~~DCGvfvl~~~e~~~~~~ 159 (194)
.+ -||.=..-||.||+.+++.+..+.
T Consensus 252 ~n-LQqnVpngCGlFv~~aIq~l~~~~ 277 (317)
T PRK14848 252 TN-LQNNVPNGCGLFCYHTIQLLSNAG 277 (317)
T ss_pred hh-hhhhCCCcchHHHHHHHHHHHhcc
Confidence 22 344447899999999999887663
No 10
>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=93.12 E-value=0.8 Score=36.12 Aligned_cols=89 Identities=13% Similarity=0.179 Sum_probs=54.1
Q ss_pred eEEEeccC-CCcceeEEEe-cCCCCcCcCCCCCeEEEeeCCCCCCCcchHHHHHHHHHHHHHHhCCCCCcccCCCccccC
Q 029358 55 YVLVPIVC-WRHWNLLILC-NFGGSFESKTRTPCMLLLDSLEMSNPWRFEPDIRKFVMDIYKAEDRPETKELISRIPLLV 132 (194)
Q Consensus 55 ~i~iPin~-~~HW~L~vi~-~p~~~~~~~~~~~~i~~~DSl~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~ 132 (194)
-.++|... +.|-..+=|- .++ .+..+++++|-.-...... +..+.....+.... ....+.+..
T Consensus 73 R~Iv~~~~~~~H~~a~Dvr~~~~-------~k~SlI~~Epa~~~~~~~~---l~~~~~~~~~~~~~-----~~~~~~~~~ 137 (177)
T PF03421_consen 73 RAIVNLGGDGIHHVALDVRHTPN-------GKPSLIVFEPASFYGMKPA---LAGYTKLAEEARQK-----LLPNAKFAV 137 (177)
T ss_pred EEEEeCCCCCCcEEEEEEeecCC-------CCceEEEEccccccCCcch---hhhHHHHHHHHHhc-----cCCCcEEEE
Confidence 35666554 4677766664 333 3567999999976543210 22222221111100 011345566
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHhcC
Q 029358 133 PKVPQQRNGEECGNFVLYFINLFVEG 158 (194)
Q Consensus 133 ~~~P~Q~N~~DCGvfvl~~~e~~~~~ 158 (194)
..+..|....|||+|-|.+|......
T Consensus 138 ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 138 IEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred EecccccCcCcchhhHHHHHHHHhhc
Confidence 78899999999999999999888754
No 11
>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=86.67 E-value=0.65 Score=36.35 Aligned_cols=81 Identities=17% Similarity=0.311 Sum_probs=37.6
Q ss_pred CCcceeEEEecCCCCcCcCCCCCeEEEeeCCCCCCCcchHHH----HHHHHHHHHHHhCCCCCcccCCCcccc-CCCCCC
Q 029358 63 WRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRFEPD----IRKFVMDIYKAEDRPETKELISRIPLL-VPKVPQ 137 (194)
Q Consensus 63 ~~HW~L~vi~~p~~~~~~~~~~~~i~~~DSl~~~~~~~~~~~----i~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~P~ 137 (194)
+.||.-..-+ | +..+++.+|++|=++. ++.+. -...|...+... .+++ .++.+ ....-|
T Consensus 33 GvHWlA~Aw~-P--------~s~t~YmFDPfGfsd~-~L~qiY~FeYe~llrRSAL~~-~~dR-----Cv~LvkstqtVQ 96 (183)
T PF00770_consen 33 GVHWLAFAWD-P--------RSRTFYMFDPFGFSDQ-KLKQIYQFEYEGLLRRSALSS-TPDR-----CVTLVKSTQTVQ 96 (183)
T ss_dssp -S-EEEEEEE-T--------TTTEEEEE-TT---HH-HHHHHH----HHHHHHHHHHH--TTS-----EEEEEEE-EE-S
T ss_pred ceeEEEEEec-C--------CcceEEEeCCCCCCHH-HHHHHHhhhHHHHHHHHhhcC-CCCc-----eEEEEeccceee
Confidence 4899888875 3 3478999999997764 23211 011111111110 1111 22322 233444
Q ss_pred CCCCCCcHHHHHHHHHHHhcCC
Q 029358 138 QRNGEECGNFVLYFINLFVEGA 159 (194)
Q Consensus 138 Q~N~~DCGvfvl~~~e~~~~~~ 159 (194)
=.++--||+|.+.|..+|..-+
T Consensus 97 ~p~SaaCGLFC~lFL~aF~~~p 118 (183)
T PF00770_consen 97 CPCSAACGLFCCLFLHAFVHYP 118 (183)
T ss_dssp -TT---HHHHHHHHHHHHHH-T
T ss_pred ccCchhHHHHHHHHHHHHHhCC
Confidence 4589999999999999998775
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=84.32 E-value=6 Score=33.62 Aligned_cols=65 Identities=15% Similarity=0.248 Sum_probs=39.3
Q ss_pred CCeEEEeeCCCCCCC-cc-hHHHHHHHHHHHHHHhCCCCCcccCCCccccCCCCCCCCCCCCcHHHHHHHHHHHhcCC
Q 029358 84 TPCMLLLDSLEMSNP-WR-FEPDIRKFVMDIYKAEDRPETKELISRIPLLVPKVPQQRNGEECGNFVLYFINLFVEGA 159 (194)
Q Consensus 84 ~~~i~~~DSl~~~~~-~~-~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~N~~DCGvfvl~~~e~~~~~~ 159 (194)
+..|++++|-..... .. +.-.++..|.. ...+ ...+....+-.|.-.+|||+|-|.+|.+.....
T Consensus 121 k~SIIvlEPa~~~~~~~a~l~~rl~~~le~----~~l~-------~~~~avie~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 121 KTSLILFEPANFNSMGPAMLAIRTKTALER----EQLP-------DCHFSMVEMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred CeEEEEECCccccccchHHHHHHHHHHHHh----ccCC-------CceEEEEecccccCcccchhhhHHHHHHHhhhh
Confidence 467999999876431 11 11112222211 1111 223444667889999999999999998877654
No 13
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=50.59 E-value=6 Score=20.54 Aligned_cols=14 Identities=14% Similarity=0.404 Sum_probs=11.8
Q ss_pred HHHHHHHHhhhccC
Q 029358 181 DLDCFCERLNSSEN 194 (194)
Q Consensus 181 ~i~~~R~~i~~~~~ 194 (194)
++..+|..|+.||+
T Consensus 2 E~~rlr~rI~dLer 15 (23)
T PF04508_consen 2 EMNRLRNRISDLER 15 (23)
T ss_pred hHHHHHHHHHHHHH
Confidence 67889999998874
No 14
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=41.59 E-value=4.2 Score=38.04 Aligned_cols=177 Identities=14% Similarity=0.127 Sum_probs=92.9
Q ss_pred cCCCCcEEEeccchhhhccCCC-----------CchhHHHhh--hccCCCccceEEEeccCCCcceeEEEecCCCCcCc-
Q 029358 15 EDKKAGFTYLDSLWFDLYRKPS-----------SKAKVLTWI--KRKHIFSKKYVLVPIVCWRHWNLLILCNFGGSFES- 80 (194)
Q Consensus 15 ~~~~~~~~~~nsfF~~~l~~~~-----------~~~~v~rw~--k~~~if~~d~i~iPin~~~HW~L~vi~~p~~~~~~- 80 (194)
+.......+|+..+|.++..+. ...++.+|+ .....|.++++.++.+...||.+.....|.....+
T Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~i~i~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~l~~~~ 212 (595)
T KOG0779|consen 133 NIFESVRKFFNQVSYPKFMPNVTSFMPSPLEKCQLQRVFTWTINITRKLFKKLFIKIFKNEPFHFKAVKFLLPSALTKSD 212 (595)
T ss_pred cccchhcchhhhcccccccchhhcccCCcccccccccccceeeeeeecchhhhcccCcccCchhhhhhhcccchhccchh
Confidence 3445566788888888887541 334554455 44578899999999999999999999887542211
Q ss_pred --CCCCCeEEEeeCCCCCCC----cchHHHHHHHHHHHHHHhCCCCCcccC-CCccc--cCCCCCCCCCCCCcHHHHHHH
Q 029358 81 --KTRTPCMLLLDSLEMSNP----WRFEPDIRKFVMDIYKAEDRPETKELI-SRIPL--LVPKVPQQRNGEECGNFVLYF 151 (194)
Q Consensus 81 --~~~~~~i~~~DSl~~~~~----~~~~~~i~~~l~~~~~~~~~~~~~~~~-~~~~~--~~~~~P~Q~N~~DCGvfvl~~ 151 (194)
.....++..+++-.+.+. ......+..++..++...+.+...... ...+. .....+++.+..|||+.+-..
T Consensus 213 ~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~dd~~~~~~~~~~~ 292 (595)
T KOG0779|consen 213 VCDIADLEVIFLNSRKDSHSLVISSINSPNIKTFFSKEVKSRPTPASYFIFSSFLPGLDPPAELHQNDDIDDIGIILNES 292 (595)
T ss_pred hhhhhcccccchhcccchhhhhhcccccccchhhhccccccCCCcccccccccccCCCCccccccccchhhhhhhccccc
Confidence 112234555555444221 000112233343333322221111111 11121 334678888888898665543
Q ss_pred HH----HHhcCCCCCcCCCCCcchhhhCCCCHHHHHHHHHHhhhc
Q 029358 152 IN----LFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNSS 192 (194)
Q Consensus 152 ~e----~~~~~~~~~f~~~d~~~~r~~~wf~~~~i~~~R~~i~~~ 192 (194)
-. .+..+.+..-..+-- ..-..+||+..+..+.|..+..+
T Consensus 293 ~~~~~~~~~~~~s~~q~~s~~-~~~~~~~~~~~~~~~~~~l~~~~ 336 (595)
T KOG0779|consen 293 PLDKPFEWLLANSPNQSESRS-RDSLDNWFPVKEADKQRTLIVKL 336 (595)
T ss_pred ccccchhhhhhcCcccchhcc-cccccccccccccccccchHHHh
Confidence 21 122111111111101 11126899998888888776653
No 15
>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=40.53 E-value=19 Score=25.86 Aligned_cols=22 Identities=23% Similarity=0.451 Sum_probs=14.9
Q ss_pred CCCCCCCCCcHHHHHHHHHHHh
Q 029358 135 VPQQRNGEECGNFVLYFINLFV 156 (194)
Q Consensus 135 ~P~Q~N~~DCGvfvl~~~e~~~ 156 (194)
+=.|....|||+-.|.++-...
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 4578899999999999887664
No 16
>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=40.39 E-value=75 Score=32.07 Aligned_cols=35 Identities=23% Similarity=0.421 Sum_probs=25.1
Q ss_pred EEeccC-------CCcceeEEEecCCCCcCcCCCCCeEEEeeCCCCCCCcch
Q 029358 57 LVPIVC-------WRHWNLLILCNFGGSFESKTRTPCMLLLDSLEMSNPWRF 101 (194)
Q Consensus 57 ~iPin~-------~~HW~L~vi~~p~~~~~~~~~~~~i~~~DSl~~~~~~~~ 101 (194)
|.||-. ..||.+++- .+ .+..++||+||..+....
T Consensus 49 fmpvltgv~p~~~sghwimlik-g~---------gn~y~lfdplg~~sg~~y 90 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLIK-GQ---------GNQYYLFDPLGKTSGEGY 90 (1439)
T ss_pred CceeecCcCCCCcCceeEEEEE-cC---------CCceEEeccccccccccH
Confidence 566654 489998886 33 257899999998766443
No 17
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.60 E-value=25 Score=27.60 Aligned_cols=28 Identities=25% Similarity=0.459 Sum_probs=24.8
Q ss_pred CCCCCCCCCCCCcHHHHHHHHHHHhcCC
Q 029358 132 VPKVPQQRNGEECGNFVLYFINLFVEGA 159 (194)
Q Consensus 132 ~~~~P~Q~N~~DCGvfvl~~~e~~~~~~ 159 (194)
...+|.-.|+.+|+-||+-.++.++.+.
T Consensus 130 fISVPke~~~lnc~~fvaGIiea~L~~a 157 (191)
T KOG3315|consen 130 FISVPKENGTLNCAAFVAGIIEAVLDNA 157 (191)
T ss_pred ceecccccCcccHHHHHHHHHHHHHHhC
Confidence 4578999999999999999999998664
No 18
>PHA02130 hypothetical protein
Probab=35.91 E-value=16 Score=24.01 Aligned_cols=36 Identities=17% Similarity=0.363 Sum_probs=30.6
Q ss_pred CchhHHHhhh-ccCCCccceEEEeccCCCcceeEEEe
Q 029358 37 SKAKVLTWIK-RKHIFSKKYVLVPIVCWRHWNLLILC 72 (194)
Q Consensus 37 ~~~~v~rw~k-~~~if~~d~i~iPin~~~HW~L~vi~ 72 (194)
..++++.|.. +.|-++.|++=||.-.-.||-|+-.+
T Consensus 15 s~~sl~~wl~~~~dswdddil~ipfkstv~w~lcp~~ 51 (81)
T PHA02130 15 SWESLREWLDERFDSWDDDILSIPFKSTVYWDLCPYA 51 (81)
T ss_pred HHHHHHHHHHhcccccccchhcccccceeeeccCcch
Confidence 4678999975 56888999999999999999998764
No 19
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=31.12 E-value=49 Score=24.01 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=23.9
Q ss_pred Cccc-cCCCCCCCCCCCCcHHHHHHHHHHHhc
Q 029358 127 RIPL-LVPKVPQQRNGEECGNFVLYFINLFVE 157 (194)
Q Consensus 127 ~~~~-~~~~~P~Q~N~~DCGvfvl~~~e~~~~ 157 (194)
+|+. -...+|.-.-+.|||.|=..++||+-.
T Consensus 18 r~p~tds~~~p~~~q~r~cg~FE~e~~eC~ea 49 (120)
T KOG4110|consen 18 RWPTTDSTEQPYKHQGRDCGKFEKEWMECAEA 49 (120)
T ss_pred hccccccccCccccccccccHHHHHHHHHHHH
Confidence 4553 345677777799999999999998764
No 20
>COG5019 CDC3 Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]
Probab=22.37 E-value=74 Score=28.10 Aligned_cols=37 Identities=16% Similarity=0.261 Sum_probs=27.1
Q ss_pred HHHHHHHhcCCCCCcCCCCCcchhhhCCCCHHHHHHHHHHhhh
Q 029358 149 LYFINLFVEGAPENFNLEDYPYFMEKNWFTAEDLDCFCERLNS 191 (194)
Q Consensus 149 l~~~e~~~~~~~~~f~~~d~~~~r~~~wf~~~~i~~~R~~i~~ 191 (194)
+.+|..++... +-+|-+-+.+-+++++....|+.|++
T Consensus 153 Ie~Mk~ls~~v------NlIPVI~KaD~lT~~El~~~K~~I~~ 189 (373)
T COG5019 153 IEAMKRLSKRV------NLIPVIAKADTLTDDELAEFKERIRE 189 (373)
T ss_pred HHHHHHHhccc------CeeeeeeccccCCHHHHHHHHHHHHH
Confidence 45666666553 23566677888999999999988875
No 21
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=22.18 E-value=57 Score=23.42 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=15.0
Q ss_pred CCCCCCCcHHHHHHHHHHH
Q 029358 137 QQRNGEECGNFVLYFINLF 155 (194)
Q Consensus 137 ~Q~N~~DCGvfvl~~~e~~ 155 (194)
.|.+..|||+..|..+-..
T Consensus 5 ~q~~~~dcgla~l~~i~~~ 23 (129)
T cd02424 5 KQTDLNDCGIAVIQMLYNH 23 (129)
T ss_pred EecCccchHHHHHHHHHHH
Confidence 4667779999999877665
No 22
>KOG0271 consensus Notchless-like WD40 repeat-containing protein [Function unknown]
Probab=20.61 E-value=1.4e+02 Score=26.74 Aligned_cols=36 Identities=17% Similarity=0.271 Sum_probs=28.3
Q ss_pred CCCcceeEEEecCCC-CcCcCCCCCeEEEeeCCCCCC
Q 029358 62 CWRHWNLLILCNFGG-SFESKTRTPCMLLLDSLEMSN 97 (194)
Q Consensus 62 ~~~HW~L~vi~~p~~-~~~~~~~~~~i~~~DSl~~~~ 97 (194)
...||.|+|-.-|.. .+.|+++...|.++|+-.+..
T Consensus 155 gH~~WVlcvawsPDgk~iASG~~dg~I~lwdpktg~~ 191 (480)
T KOG0271|consen 155 GHKNWVLCVAWSPDGKKIASGSKDGSIRLWDPKTGQQ 191 (480)
T ss_pred CCccEEEEEEECCCcchhhccccCCeEEEecCCCCCc
Confidence 368999999988854 457788889999999766653
No 23
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=20.13 E-value=1.3e+02 Score=21.08 Aligned_cols=22 Identities=18% Similarity=0.193 Sum_probs=16.6
Q ss_pred CCCCCCCCcHHHHHHHHHHHhc
Q 029358 136 PQQRNGEECGNFVLYFINLFVE 157 (194)
Q Consensus 136 P~Q~N~~DCGvfvl~~~e~~~~ 157 (194)
-.|++..|||+..+.++-....
T Consensus 4 ~~q~~~~~~~l~~l~~~~~~~g 25 (129)
T cd02423 4 VRQSYDFSCGPAALATLLRYYG 25 (129)
T ss_pred eecCCCCChHHHHHHHHHHhcC
Confidence 3566777999999887766665
Done!