Query 009925
Match_columns 522
No_of_seqs 272 out of 1239
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 18:58:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03189 Protease specific for 100.0 4E-130 9E-135 1030.6 36.5 482 1-522 1-490 (490)
2 KOG0778 Protease, Ulp1 family 100.0 8.3E-69 1.8E-73 569.9 23.7 430 39-521 72-510 (511)
3 COG5160 ULP1 Protease, Ulp1 fa 100.0 6.6E-43 1.4E-47 367.9 13.8 192 316-520 377-568 (578)
4 PF02902 Peptidase_C48: Ulp1 p 100.0 4E-33 8.8E-38 266.2 15.0 185 334-519 1-211 (216)
5 KOG3246 Sentrin-specific cyste 99.9 2E-24 4.4E-29 208.1 13.8 184 318-520 15-215 (223)
6 KOG0779 Protease, Ulp1 family 99.5 4.8E-14 1E-18 156.5 5.4 194 320-518 353-586 (595)
7 PF03290 Peptidase_C57: Vaccin 97.4 0.00022 4.7E-09 75.1 5.5 88 400-498 230-348 (423)
8 PRK14848 deubiquitinase SseL; 96.7 0.0058 1.3E-07 61.6 8.1 85 403-495 190-276 (317)
9 PRK11836 deubiquitinase; Provi 95.7 0.018 3.9E-07 59.2 5.8 94 398-493 216-325 (403)
10 PF00770 Peptidase_C5: Adenovi 94.8 0.049 1.1E-06 52.3 5.2 80 411-495 33-117 (183)
11 PF03421 YopJ: YopJ Serine/Thr 77.6 6.6 0.00014 38.0 6.6 83 404-495 74-163 (177)
12 PRK15371 effector protein YopJ 63.3 17 0.00036 38.1 6.1 26 470-495 161-186 (287)
13 PF12252 SidE: Dot/Icm substra 28.5 95 0.0021 38.0 5.5 36 405-441 49-91 (1439)
14 KOG4110 NADH:ubiquinone oxidor 26.7 50 0.0011 29.9 2.3 33 461-493 16-48 (120)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=4.3e-130 Score=1030.57 Aligned_cols=482 Identities=63% Similarity=1.040 Sum_probs=443.0
Q ss_pred CCcccccCCCCCccc-ccCCCCCCccccCCCCcccccccCCc-ccCcccccccccccCCCCCCcccccccCCcccccccc
Q 009925 1 MGALTSNRKRGDEYL-NYQIPYQNLHISKRPRFNYTQQNQNQ-TLISSNSTVSRMSRYPEAKPPLKREVHAPCRTLKFGF 78 (522)
Q Consensus 1 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 78 (522)
|||||+|+||+++|+ |+++++|+||+||+|||| |+|++.. ..+||||||||||||||+|+||||||||||||+|||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 78 (490)
T PLN03189 1 MGALTSNHKRSDECFNNPLSNSPDFHISKKPRFS-MAQTPDSGNQHSSNSTASRISRYPEVKSPLRREVHAPCRILKFG- 78 (490)
T ss_pred CCcccccccccccccccccccCCccccccCCCcc-ccccccccCCccccccccchhcCCCccchhhhhhcCchhhhhcc-
Confidence 999999999999999 679999999999999999 4555411 128999999999999999999999999999999999
Q ss_pred cccccccccccccCCCCccc-ccccchhhHHHHhHHHHHhhhhhcccccccCceeeecCccccceeeeccCcchhhhhhh
Q 009925 79 ADKSNQAFGSKKANGYGENQ-NLGIRMGNVLRYHLEKAKKSAFGAFRYFSKDKEVIDADNEQEKVEVISDDSSVEEIDAI 157 (522)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (522)
++|+++++++. ++||+|||||++|||+||++||+|+||++|||||||||||.|++++||||||||||+||
T Consensus 79 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (490)
T PLN03189 79 ---------RDKSTDSSEKKQGLGNVMGNFLSRKYDMAKRSALDALRYYRKDKEVVDVGDELGKVEMISDDSSIEEVEAV 149 (490)
T ss_pred ---------cccccchhhhhcchhhhHHHHhhhhhHHHHHHHHHHHHHHhcCCeeeecccccccceeccCccchhhhhee
Confidence 99999999887 79999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCcccccCCCCCCCCCCCCCccccccccccccccccccCCCCCCCccccccCcccchHhhhhcccccc----ccCH
Q 009925 158 EDGREGRSLVFDPRPRGSDENEKPVVDIGEIDGKSAEERNYHTNLQPSSSSVLTDTNNGDVSKMIDLLSLNG----EMTV 233 (522)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~~ 233 (522)
|.+..+ ..++..++.+ +.++|..+ +++|++ +|.++++||+||+|++ ++++
T Consensus 150 ~~~~~~----~~~~~~~~~~------~~~~~~~~-----~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~ 203 (490)
T PLN03189 150 EMDVDE----VEEKAEMGNG------LSSDVKIV-----TKNGNL-----------RVEDTSKMLDSLVLNRPETDVLSV 203 (490)
T ss_pred ecccch----hhhccccCcc------ccccceEe-----ecCCcc-----------cccchhhhhhceeecCcccccccc
Confidence 954422 1222233333 23555554 789999 9999999999999998 8999
Q ss_pred HHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhcCCCCCCchhhhhcCCCCCCCCCCHHHHHHHHHHHcc-CCCcee
Q 009925 234 DVYKKLLQSVQKRGSKLKEIEFEIELNEKRWASLKQLWPLKKPEEEQVEELPREPFIPLTKEEEAAVERAFSA-NWRAVL 312 (522)
Q Consensus 234 ~~~~~~~~~~~~r~~~l~~~~~~~~~~e~r~~~~~~~rp~~~p~~~~~e~~p~e~f~pLs~e~~~~V~~al~~-~~~~vL 312 (522)
++|+++++++++|+.+|++++++++++|++++.+++.+|..+ +++|++++++|+|||+|++++|++||.+ +.++++
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~pLT~e~~~~V~~al~~~~~~~vl 280 (490)
T PLN03189 204 EAYRKLLQSAERRNSKLKDLGFEIELNEKRLSSLRQSRPKPK---EPVEEVPREPFIPLTREEETEVKRAFSANNRRKVL 280 (490)
T ss_pred HHHHHHHHHHHhhcchhhhccceeehhhhHHHHHhhhccCcc---ccccccccccCcCCCHHHHHHHHHHhcCCCcccee
Confidence 999999999999999999999999999999999998888622 3458999999999999999999999998 447899
Q ss_pred eecCCCCeEeccccccccCCCCccCHHHHHHHHHHHHHHhhhCCccccceeeeehhhhhhhccCCCCCchhHHHHhhhcc
Q 009925 313 VSHTETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAK 392 (522)
Q Consensus 313 vs~~~~nI~It~~DL~~L~~~~WLNDeVINfYl~lL~e~~~~~p~~~~k~~~FnSfFy~kL~~~~~~~~y~~VkRWtk~k 392 (522)
+++.+++|+||++||.||.|++||||+||||||.+|.++...+|..+++||+||||||++|...+.+++|.+|+|||+++
T Consensus 281 vs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FNTFFytkL~~~~~~ygY~~VrRWTk~k 360 (490)
T PLN03189 281 VTHENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFNTFFYKKLVSGKSGYDYKAVRRWTTQK 360 (490)
T ss_pred eecCCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEehHHHHHHhhcCCcCChHHHHHHhhhc
Confidence 99988999999999999999999999999999999999877777778999999999999999876778999999999988
Q ss_pred ccccCcccCCceeeeeecCcceEEEEEecCCCcceecccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCceeeccCCC
Q 009925 393 KLGYGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLARYFVEEVRDKCGKDIDVSDWEQEFVLDL 472 (522)
Q Consensus 393 kigidLf~kD~IfIPIn~~sHW~L~VId~k~k~I~~yDSL~~~~~~vl~~L~~yL~~E~k~K~g~~~d~s~W~~~~v~~v 472 (522)
++++++|++|+||||||.+.||+|+|||++.++|.|||||++.+..++..|+.||..|++++.+.+++.+.|...++.++
T Consensus 361 Kigv~Lfs~D~IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~~~vL~~L~rYL~~E~kdK~g~d~D~s~W~~~~~~~v 440 (490)
T PLN03189 361 KLGYHLIDCDKIFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRDPKILDALAKYYVDEVKDKSEKDIDVSSWEQEFVEDL 440 (490)
T ss_pred ccccccccCceEEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHhhhcCCCcchhcceeccCCCC
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999998777899
Q ss_pred CCCCCCCchHHHHHHHHHHHHcCCCCccCCCChHHHHHHHHHHHHHhccC
Q 009925 473 PEQANGFDCGMFMLKYVDFYSRGLGLCFDQSHMPYFRVRTAKEILRMRAD 522 (522)
Q Consensus 473 PqQ~Ng~DCGVFVL~fae~ls~g~~l~FtQ~dMp~fRkrma~EIl~lr~~ 522 (522)
|||.||+|||||||+||+||++|.+++|+|+||++||++|++||+++|+|
T Consensus 441 PQQ~NG~DCGVFVL~yAE~~SrG~~LtFSQeDMp~fRrRma~EIl~~r~~ 490 (490)
T PLN03189 441 PEQKNGYDCGMFMIKYIDFYSRGLGLCFGQEHMPYFRLRTAKEILRLKAD 490 (490)
T ss_pred CCCCCCCCHHHHHHHHHHHHcCCCCCCcChhhhHHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999999999987
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.3e-69 Score=569.92 Aligned_cols=430 Identities=37% Similarity=0.603 Sum_probs=350.7
Q ss_pred CCcccCcccccccccccCCCCCCcccccccCCcc-cccccccccccccccccccCCCCcccccccchhhHHHHhHHHHHh
Q 009925 39 QNQTLISSNSTVSRMSRYPEAKPPLKREVHAPCR-TLKFGFADKSNQAFGSKKANGYGENQNLGIRMGNVLRYHLEKAKK 117 (522)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (522)
...-..++.+..+.|.+||++...++|+.|+|-| ++..+ |.+++.+++.. .+++++.+.+..++.
T Consensus 72 ~~~~~s~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~----------r~~s~~~~s~~----~~~~~~~~~~~~~~~ 137 (511)
T KOG0778|consen 72 VSGRSSSSRPRDPPIPDRPEVSSDTRRKDFESYRWLLRNS----------RTKSNSVGSPY----TSPGLLRRQYDSSAR 137 (511)
T ss_pred cccccccccCCCCCCccchhhccccccccccccccccccc----------ccccccccCCc----cCcchhhhhcchhhh
Confidence 3355677888899999999999999999999998 66666 66777777744 455599999999999
Q ss_pred hhhhcccccccCceeeecCccccceeeeccCcchhhhhhhh-ccccCcccccCCCCCCCCCCCCCccccccccccccccc
Q 009925 118 SAFGAFRYFSKDKEVIDADNEQEKVEVISDDSSVEEIDAIE-DGREGRSLVFDPRPRGSDENEKPVVDIGEIDGKSAEER 196 (522)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (522)
+|+..-.++.+++.+++.+.+.+.+++++.|.+...++..= .|.++ .+++...+... +. .+....
T Consensus 138 ~~~~~s~~v~~~~~~~~~~~s~~~~~~~~~d~s~~~~s~~~~~~~~~-----~~~~~~~~s~~-~~---~~~~~~----- 203 (511)
T KOG0778|consen 138 NALRVSPFVESGPKTVSRGSSVEWTEMVSDDPSELKVSNTLNEGDES-----QEKSEIKDSEK-ST---DEHARI----- 203 (511)
T ss_pred cccccccccCCCcchhcccccccceeecccCCccccccccccccccc-----ccccccccCcC-CC---cchhhh-----
Confidence 99999899999999999999999999999999976655331 11111 01111111111 00 000000
Q ss_pred cccCCCCCCCccccccCcccchHhh-hhcccccc-----ccCHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhc
Q 009925 197 NYHTNLQPSSSSVLTDTNNGDVSKM-IDLLSLNG-----EMTVDVYKKLLQSVQKRGSKLKEIEFEIELNEKRWASLKQL 270 (522)
Q Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~-----~~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~e~r~~~~~~~ 270 (522)
+ ......++++++ .+++..+. ..+.++|+...++++++...++.+++++.........+..+
T Consensus 204 -------~-----n~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~a~q~~~~~~ee~~s~~~~~~~e~~~~~~~~i~l~~~ 271 (511)
T KOG0778|consen 204 -------K-----NGENIKTERAENNFDSLSLRREEESDHRGEKAYQNKEKSLEELVSDLKSLRFEIFQKRGELIPLRSV 271 (511)
T ss_pred -------h-----cccchhhhhhhhhhhhhhhcCccchhhhhHHHHhhhhhhHHHHHHHHHHhhhhhcccccccchhhhh
Confidence 0 001122333333 55555554 78899999988999999999999988877665544444433
Q ss_pred CCCCCCchhhhhcCCCCCCCCCCHHHHHHHHHHHcc-CCCceeeecCCCCeEeccccccccCCCCccCHHHHHHHHHHHH
Q 009925 271 WPLKKPEEEQVEELPREPFIPLTKEEEAAVERAFSA-NWRAVLVSHTETGIDITGKILQCLRPGAWLNDEVINVYLGLLK 349 (522)
Q Consensus 271 rp~~~p~~~~~e~~p~e~f~pLs~e~~~~V~~al~~-~~~~vLvs~~~~nI~It~~DL~~L~~~~WLNDeVINfYl~lL~ 349 (522)
.... ++.+++..+++.|+||+++.+++++++++. +..++++++ ++|+||.+||+||.+++||||+||||||.+|+
T Consensus 272 ~~k~--~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ 347 (511)
T KOG0778|consen 272 QEKL--EKPKVEVKKEDSFPPLTEEREAQVQRAFSSRNSTEILVTH--FNIDITGKDLQTLRPGNWLNDEVINFYMELLK 347 (511)
T ss_pred hccc--ccccccccCccccccccHHHHHHHHHHhccCCcccceehh--ccccccHHHHhhccCccchhHHHHHHHHHHHH
Confidence 2221 112335667789999999999999999996 888999987 46999999999999999999999999999999
Q ss_pred HHhhhCCccccceeeeehhhhhhhccCCCCCchhHHHHhhhccccccCcccCCceeeeeecCcceEEEEEecCCCcceec
Q 009925 350 EREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYL 429 (522)
Q Consensus 350 e~~~~~p~~~~k~~~FnSfFy~kL~~~~~~~~y~~VkRWtk~kkigidLf~kD~IfIPIn~~sHW~L~VId~k~k~I~~y 429 (522)
++....++ +++||+||||||++|... ||++|+|||++ ++||++|+||||||.+.||||+|||+++++|.||
T Consensus 348 ers~~~~~-yp~~h~FnTFFy~kL~~~----gy~~VkRWTk~----v~if~~d~i~vPIH~~vHW~l~vid~r~k~i~y~ 418 (511)
T KOG0778|consen 348 ERSKKDSK-YPKVHAFNTFFYTKLVGR----GYAGVKRWTKK----VDIFDKDIIFVPIHLGVHWCLAVIDLREKTIEYY 418 (511)
T ss_pred hhccccCC-CceEEEEechhhhhhhhc----chHHHHhHhhc----cCccccceeEeeeecCceEEEEEEEcccceEEEe
Confidence 99988776 999999999999999977 99999999984 7999999999999999999999999999999999
Q ss_pred ccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCceeeccCCCCCCCCCCchHHHHHHHHHHHHcCCCCccCCCChHHHH
Q 009925 430 DSLKGRDKKVLGDLARYFVEEVRDKCGKDIDVSDWEQEFVLDLPEQANGFDCGMFMLKYVDFYSRGLGLCFDQSHMPYFR 509 (522)
Q Consensus 430 DSL~~~~~~vl~~L~~yL~~E~k~K~g~~~d~s~W~~~~v~~vPqQ~Ng~DCGVFVL~fae~ls~g~~l~FtQ~dMp~fR 509 (522)
|||++....++..|++||++|+.+|.+.++|.+.|....+.++|||.||+|||||+|+|++|++++.+++|+|+|||+||
T Consensus 419 DS~~~~~nr~~~aL~~Yl~~E~~~k~~~~~d~s~w~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~~ftq~dmp~fR 498 (511)
T KOG0778|consen 419 DSLGGGPNRICDALAKYLQDESRDKSKKDFDVSGWTIEFVQNIPQQRNGSDCGMFVCKYADYISRDVPLTFTQQDMPYFR 498 (511)
T ss_pred eccCCCCcchHHHHHHHHHHHHhhhhcCCCCccchhhhhhhccccccCCCccceEEeeechhhccCCCcccChhhhHHHH
Confidence 99998766666999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcc
Q 009925 510 VRTAKEILRMRA 521 (522)
Q Consensus 510 krma~EIl~lr~ 521 (522)
++||+||++.+.
T Consensus 499 ~~m~~eI~~~~l 510 (511)
T KOG0778|consen 499 KKMAKEILHLKL 510 (511)
T ss_pred HHHHHHHHhhhc
Confidence 999999999875
No 3
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.6e-43 Score=367.87 Aligned_cols=192 Identities=33% Similarity=0.597 Sum_probs=174.7
Q ss_pred CCCCeEeccccccccCCCCccCHHHHHHHHHHHHHHhhhCCccccceeeeehhhhhhhccCCCCCchhHHHHhhhccccc
Q 009925 316 TETGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLG 395 (522)
Q Consensus 316 ~~~nI~It~~DL~~L~~~~WLNDeVINfYl~lL~e~~~~~p~~~~k~~~FnSfFy~kL~~~~~~~~y~~VkRWtk~kkig 395 (522)
+.++|+||.+|+.||.++.||||+||||||+||....+ .+...+++|+||||||++|.+. ||++|+||++ +
T Consensus 377 ~~~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk-~~s~~~~vh~FnTFFYT~Lsrr----Gy~gVrrW~k----k 447 (578)
T COG5160 377 DRSSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISK-NTSKREQVHLFNTFFYTKLSRR----GYSGVRRWTK----K 447 (578)
T ss_pred CcCcceeehHhhhhhccccchhhHHHHHHHHHHHHhcc-CcccccceEEeehhhHHHHHHH----HhHHHHHHHh----c
Confidence 56899999999999999999999999999999965543 3345688999999999999988 9999999998 3
Q ss_pred cCcccCCceeeeeecCcceEEEEEecCCCcceecccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCceeeccCCCCCC
Q 009925 396 YGLIECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLARYFVEEVRDKCGKDIDVSDWEQEFVLDLPEQ 475 (522)
Q Consensus 396 idLf~kD~IfIPIn~~sHW~L~VId~k~k~I~~yDSL~~~~~~vl~~L~~yL~~E~k~K~g~~~d~s~W~~~~v~~vPqQ 475 (522)
++||++++||||||...||+|+|||.+.+.|.|||||++.+..+++.|+.|+.+|++...++ +.|......+||||
T Consensus 448 ~dif~~k~I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y~ldE~k~~~~k----~~~~~~~~~~vPqQ 523 (578)
T COG5160 448 TDIFSKKYIFIPINISYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSYLLDEYKIQHDK----DPQIKMKHCKVPQQ 523 (578)
T ss_pred cCccccceEEEEecccceEEEEEeecCcceeEEecccccCcHHHHHHHHHHHHHHHhcccCC----chhhhhhcCCCCCC
Confidence 68999999999999999999999999999999999999999999999999999998876554 44555556899999
Q ss_pred CCCCchHHHHHHHHHHHHcCCCCccCCCChHHHHHHHHHHHHHhc
Q 009925 476 ANGFDCGMFMLKYVDFYSRGLGLCFDQSHMPYFRVRTAKEILRMR 520 (522)
Q Consensus 476 ~Ng~DCGVFVL~fae~ls~g~~l~FtQ~dMp~fRkrma~EIl~lr 520 (522)
.||+|||||||+|++|++.+.+..|++.||+.+|++|+..|+..+
T Consensus 524 ~Ng~DCGV~vc~~~~~~~~~~p~~f~~nd~~r~Rk~m~h~i~~~q 568 (578)
T COG5160 524 RNGSDCGVFVCMFIRYFLENPPEQFSKNDRPRARKNMAHTIKDLQ 568 (578)
T ss_pred CCCCccceEEEEeeeecccCChhhcCccchHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999998764
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=100.00 E-value=4e-33 Score=266.22 Aligned_cols=185 Identities=31% Similarity=0.611 Sum_probs=146.4
Q ss_pred CccCHHHHHHHHHHHHHHhhhCCccccceeeeehhhhhhhccC-----CC-----------CCchhHHHHhhhccccccC
Q 009925 334 AWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACG-----NK-----------GYDFRAVKRWTSAKKLGYG 397 (522)
Q Consensus 334 ~WLNDeVINfYl~lL~e~~~~~p~~~~k~~~FnSfFy~kL~~~-----~~-----------~~~y~~VkRWtk~kkigid 397 (522)
+||||+|||||+.+|.++....+....++++|+|+|++.|... .. ...+..+.+|++.. ...+
T Consensus 1 ~wLnd~iId~y~~~l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 79 (216)
T PF02902_consen 1 EWLNDSIIDFYLEYLRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKK-NKKN 79 (216)
T ss_dssp --EEHHHHHHHHHHHHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTC-CTST
T ss_pred CcCCHHHHHHHHHHHHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhcc-cccc
Confidence 5999999999999998664333335578999999999999822 00 12467788898753 2347
Q ss_pred cccCCceeeeeec-CcceEEEEEecCCCcceecccCCCCCH-----HHHHHHHHHHHHHHHhhcCCCCCCCCceeeccCC
Q 009925 398 LIECDKIFVPIHK-QIHWCLAVIDRKDKKFQYLDSLKGRDK-----KVLGDLARYFVEEVRDKCGKDIDVSDWEQEFVLD 471 (522)
Q Consensus 398 Lf~kD~IfIPIn~-~sHW~L~VId~k~k~I~~yDSL~~~~~-----~vl~~L~~yL~~E~k~K~g~~~d~s~W~~~~v~~ 471 (522)
++++++||||||. ++||+|+||+++.++|++||||++... ..+..+..+|...+....+...+...|......+
T Consensus 80 l~~~~~i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 159 (216)
T PF02902_consen 80 LFDKDYIFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDPDKSPFKIVRPPN 159 (216)
T ss_dssp GGGSSEEEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTCEEEEECT
T ss_pred ccccCEEEEEEechhhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhccccccccccccceeeeccccc
Confidence 8999999999999 999999999999999999999999987 5678888888888777666666778888887789
Q ss_pred CCCCCCCCchHHHHHHHHHHHHcCCCCc----cCCCChHHHHHHHHHHHHHh
Q 009925 472 LPEQANGFDCGMFMLKYVDFYSRGLGLC----FDQSHMPYFRVRTAKEILRM 519 (522)
Q Consensus 472 vPqQ~Ng~DCGVFVL~fae~ls~g~~l~----FtQ~dMp~fRkrma~EIl~l 519 (522)
+|||.|++|||+|||+||++++.+.+.. |++++|..+|.+++.+|.+.
T Consensus 160 ~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~~i~~~r~~~a~~~~e~ 211 (216)
T PF02902_consen 160 VPQQPNGYDCGVYVLKFMECLLEGPSFDFSQELTEEDIKNFRKKLAVDLYEE 211 (216)
T ss_dssp S-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCSBTGHHHHHHHHHHHH-----
T ss_pred ccCCCCCCCcHHHHHHHHHHHHhCCCCcccccCCHHHHHHHHHHHHhhcccc
Confidence 9999999999999999999999997765 79999999999999887654
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.91 E-value=2e-24 Score=208.07 Aligned_cols=184 Identities=24% Similarity=0.346 Sum_probs=130.3
Q ss_pred CCeEeccccccccCCCCccCHHHHHHHHHHHHHHhhhCCccccceeeeehhhhhhhccCCCCCchhHHHHhhhccccccC
Q 009925 318 TGIDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGNKGYDFRAVKRWTSAKKLGYG 397 (522)
Q Consensus 318 ~nI~It~~DL~~L~~~~WLNDeVINfYl~lL~e~~~~~p~~~~k~~~FnSfFy~kL~~~~~~~~y~~VkRWtk~kkigid 397 (522)
+.+.++.+|++.|.++.||||.+|+||.+||.+..... .+..|++++-....|.... .-+.+...... .+
T Consensus 15 ~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s---~~~~~ll~P~~t~~l~~~~---~~~e~~~~~~p----l~ 84 (223)
T KOG3246|consen 15 FDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRS---EPDLHLLRPSLTFFLRHAP---NPEEIAMVLDP----LD 84 (223)
T ss_pred eehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhccc---CcchhccCHHHHHHHHhCC---CcHHHHHhcCh----hh
Confidence 46789999999999999999999999999998875322 1335777653332233321 23445554432 37
Q ss_pred cccCCceeeeeec---------CcceEEEEEecCCCcceecccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCceeec
Q 009925 398 LIECDKIFVPIHK---------QIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLARYFVEEVRDKCGKDIDVSDWEQEF 468 (522)
Q Consensus 398 Lf~kD~IfIPIn~---------~sHW~L~VId~k~k~I~~yDSL~~~~~~vl~~L~~yL~~E~k~K~g~~~d~s~W~~~~ 468 (522)
+.++++||+|||. |+||+|+|++.++++++||||+.+.|....+.+.+-+...++.+... ..
T Consensus 85 l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~~~~---------~~ 155 (223)
T KOG3246|consen 85 LNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSLMKKLRALLKKKFAK---------RV 155 (223)
T ss_pred cCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHHHHHHHHHHhhhhhh---------cc
Confidence 8999999999994 46999999999999999999999999876666666666555543211 01
Q ss_pred cCCCCCCCCCCchHHHHHHHHHHHHcCC----CCccCC----CChHHHHHHHHHHHHHhc
Q 009925 469 VLDLPEQANGFDCGMFMLKYVDFYSRGL----GLCFDQ----SHMPYFRVRTAKEILRMR 520 (522)
Q Consensus 469 v~~vPqQ~Ng~DCGVFVL~fae~ls~g~----~l~FtQ----~dMp~fRkrma~EIl~lr 520 (522)
...+|||.||||||+|||.+++.++... -.+-.| +.+..+|..+..-|..+.
T Consensus 156 ~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~l~~LI~slg 215 (223)
T KOG3246|consen 156 ECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREELLDLIQSLG 215 (223)
T ss_pred cccChhhhcCCchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHHHHhC
Confidence 3679999999999999999998887542 122233 344555555555555443
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.45 E-value=4.8e-14 Score=156.47 Aligned_cols=194 Identities=24% Similarity=0.395 Sum_probs=136.4
Q ss_pred eEeccccccccCCCCccCHHHHHHHHHHHHHHhhhCCccccceeeeehhhhhhhccCC--------CCCchhHHHHhhhc
Q 009925 320 IDITGKILQCLRPGAWLNDEVINVYLGLLKEREKREPQKFLKCHFFNTFFYNKLACGN--------KGYDFRAVKRWTSA 391 (522)
Q Consensus 320 I~It~~DL~~L~~~~WLNDeVINfYl~lL~e~~~~~p~~~~k~~~FnSfFy~kL~~~~--------~~~~y~~VkRWtk~ 391 (522)
+.++..|+.||.++.+|||.+++||+.++........+....+|+|++|||.++.... .......+++|++
T Consensus 353 ~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f~tffyk~l~~~~~~~~~d~~~~~~~~~~~~~~~- 431 (595)
T KOG0779|consen 353 HQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIFSTFFYKRLCRKLRQKSNDQIQDNRAVRLRTWTR- 431 (595)
T ss_pred cceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhhhhHHHhhhhhhhhhhhhhhhhccccCceeeeee-
Confidence 4688899999999999999999999999988765434456789999999999988761 1224567888987
Q ss_pred cccccCcccCCceeeeeecCcceEEEEEecCCC------cceecccCCCCCH-HHHHHHHHHHHHHHHhhcCC------C
Q 009925 392 KKLGYGLIECDKIFVPIHKQIHWCLAVIDRKDK------KFQYLDSLKGRDK-KVLGDLARYFVEEVRDKCGK------D 458 (522)
Q Consensus 392 kkigidLf~kD~IfIPIn~~sHW~L~VId~k~k------~I~~yDSL~~~~~-~vl~~L~~yL~~E~k~K~g~------~ 458 (522)
++++|.+++|++|+|...||.|++|+.... ....++++..... .....+..++..++...... +
T Consensus 432 ---~~d~~~k~yi~~P~~E~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 (595)
T KOG0779|consen 432 ---HFDLFNKDYVFVPTHERFHWKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNNELIVTEDLE 508 (595)
T ss_pred ---ccccccceeEEecCchHhhhhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccCccccccccc
Confidence 479999999999999999999999998754 3445555544332 22333444444333322111 1
Q ss_pred CCCCCcee------eccCCCCCCCCCCchHHHHHHHHHHHHcCCCC-------------ccCCCChHHHHHHHHHHHHH
Q 009925 459 IDVSDWEQ------EFVLDLPEQANGFDCGMFMLKYVDFYSRGLGL-------------CFDQSHMPYFRVRTAKEILR 518 (522)
Q Consensus 459 ~d~s~W~~------~~v~~vPqQ~Ng~DCGVFVL~fae~ls~g~~l-------------~FtQ~dMp~fRkrma~EIl~ 518 (522)
++..-|.. ..+. .|||.|..|||+|++.|++-+..+.+. +|.+..+-.+|..+-.-+..
T Consensus 509 ~~~~~~~~~~~~~s~~v~-~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~~~~~~r~~~r~~~~~ 586 (595)
T KOG0779|consen 509 LEEELPRRLPRGKSETVR-EPQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPKEILKFRDEIRNLGRK 586 (595)
T ss_pred ccccccccCccccccccc-ccCccCcccchhhHHHHHHHhhhChhhhcccccccccccccCCchHHhhhhhhhhccccc
Confidence 11111111 0112 289999999999999999998765432 37888888888877655443
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=97.38 E-value=0.00022 Score=75.10 Aligned_cols=88 Identities=19% Similarity=0.267 Sum_probs=65.8
Q ss_pred cCCceeeeeecCcceEEEEEecCCCcceecccCCCCCHH-------------------------------HHHHHHHHHH
Q 009925 400 ECDKIFVPIHKQIHWCLAVIDRKDKKFQYLDSLKGRDKK-------------------------------VLGDLARYFV 448 (522)
Q Consensus 400 ~kD~IfIPIn~~sHW~L~VId~k~k~I~~yDSL~~~~~~-------------------------------vl~~L~~yL~ 448 (522)
.+.++.+|.|...||..+|+|.+++-+.+|||-|..... -+..|.+|+.
T Consensus 230 ~~RyvmFgfcY~~Hwkc~IfDk~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~n~dIDVLfrfF~ 309 (423)
T PF03290_consen 230 KKRYVMFGFCYMSHWKCCIFDKEKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNENCDIDVLFRFFE 309 (423)
T ss_pred cccEEEeeeeehhcceEEEEeccccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccccCchHHHHHHHH
Confidence 567999999999999999999999999999998854211 2456777777
Q ss_pred HHHHhhcCCCCCCCCceeeccCCCCCCCCCCchHHHHHHHHHHHHcCCCC
Q 009925 449 EEVRDKCGKDIDVSDWEQEFVLDLPEQANGFDCGMFMLKYVDFYSRGLGL 498 (522)
Q Consensus 449 ~E~k~K~g~~~d~s~W~~~~v~~vPqQ~Ng~DCGVFVL~fae~ls~g~~l 498 (522)
+....+.|- ++ ----|-..++||+|++.||-......|-
T Consensus 310 d~f~~~~gc-iN----------vevnQl~eseCGMF~~iFm~~c~~~ppk 348 (423)
T PF03290_consen 310 DSFGVKYGC-IN----------VEVNQLLESECGMFISIFMILCTLTPPK 348 (423)
T ss_pred hhcccceeE-EE----------hhhhhhcccccchHHHHHHHHHHccCch
Confidence 665444331 11 1124888899999999999988776654
No 8
>PRK14848 deubiquitinase SseL; Provisional
Probab=96.70 E-value=0.0058 Score=61.62 Aligned_cols=85 Identities=13% Similarity=0.246 Sum_probs=50.3
Q ss_pred ceeeeeecCcceEEEEEecC--CCcceecccCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCceeeccCCCCCCCCCCc
Q 009925 403 KIFVPIHKQIHWCLAVIDRK--DKKFQYLDSLKGRDKKVLGDLARYFVEEVRDKCGKDIDVSDWEQEFVLDLPEQANGFD 480 (522)
Q Consensus 403 ~IfIPIn~~sHW~L~VId~k--~k~I~~yDSL~~~~~~vl~~L~~yL~~E~k~K~g~~~d~s~W~~~~v~~vPqQ~Ng~D 480 (522)
.=+||||.++||.|+++..- +-+-.+|.|+..-+....+.+..- ..+.|.. + +-.+.++.-=-||.=...
T Consensus 190 nevF~INtg~HWil~~~~Ki~~kiKC~iFNs~~~l~eNs~~~ii~~-----ak~ag~~-~--e~di~fIe~nLQqnVpng 261 (317)
T PRK14848 190 NEVFLINTGDHWLLCLFYKLAEKIKCLIFNTYYDLNENTKQEIIEA-----AKIAGIS-E--NEDVNFIETNLQNNVPNG 261 (317)
T ss_pred ceEEEecCCCcEEEEEhHHhhhhceEEEeecHhhhhhhHHHHHHHH-----HHhhCcc-c--CCceEEeehhhhhhCCCc
Confidence 44699999999999977432 234567888887665544444321 1122211 0 112222222223444468
Q ss_pred hHHHHHHHHHHHHcC
Q 009925 481 CGMFMLKYVDFYSRG 495 (522)
Q Consensus 481 CGVFVL~fae~ls~g 495 (522)
||.|+|.+++.+...
T Consensus 262 CGlFv~~aIq~l~~~ 276 (317)
T PRK14848 262 CGLFCYHTIQLLSNA 276 (317)
T ss_pred chHHHHHHHHHHHhc
Confidence 999999999988765
No 9
>PRK11836 deubiquitinase; Provisional
Probab=95.71 E-value=0.018 Score=59.19 Aligned_cols=94 Identities=18% Similarity=0.234 Sum_probs=52.3
Q ss_pred cccCCceeeeeecCcceEEEEEec--------CCCcceecccCCCCCH---HHHHHHHHHHHHHHH-----hhcCCCCCC
Q 009925 398 LIECDKIFVPIHKQIHWCLAVIDR--------KDKKFQYLDSLKGRDK---KVLGDLARYFVEEVR-----DKCGKDIDV 461 (522)
Q Consensus 398 Lf~kD~IfIPIn~~sHW~L~VId~--------k~k~I~~yDSL~~~~~---~vl~~L~~yL~~E~k-----~K~g~~~d~ 461 (522)
++-++.-+||||.++||.|+++.. .+.+-.+|.|+..-+. ...+.+..-+..|+. .+... ..
T Consensus 216 ~~~k~~elFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~~~~~ik~--~~ 293 (403)
T PRK11836 216 SWPKEVQLFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSLKRVINSFNSELMGEMSNNNIKV--HL 293 (403)
T ss_pred CCcccceEEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHHHHHHHhhhhhhhhhcchhhhcc--cc
Confidence 455677899999999999998742 2234567777765432 233333333222221 11111 12
Q ss_pred CCceeeccCCCCCCCCCCchHHHHHHHHHHHH
Q 009925 462 SDWEQEFVLDLPEQANGFDCGMFMLKYVDFYS 493 (522)
Q Consensus 462 s~W~~~~v~~vPqQ~Ng~DCGVFVL~fae~ls 493 (522)
.+-.+.++.---||.=...||.|||+.+.-+.
T Consensus 294 ~e~ei~fie~dLQq~vpngCGlFv~~a~Qe~i 325 (403)
T PRK11836 294 TEPEIIFLHADLQQYLSQSCGAFVCMAAQEVI 325 (403)
T ss_pred cCCceEEEechhhhcCCCccceehHHHHHHHH
Confidence 22223333323344445689999999888544
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=94.78 E-value=0.049 Score=52.31 Aligned_cols=80 Identities=13% Similarity=0.203 Sum_probs=40.8
Q ss_pred CcceEEEEEecCCCcceecccCCCCCHHHHHHHH----HHHHHHHHh-hcCCCCCCCCceeeccCCCCCCCCCCchHHHH
Q 009925 411 QIHWCLAVIDRKDKKFQYLDSLKGRDKKVLGDLA----RYFVEEVRD-KCGKDIDVSDWEQEFVLDLPEQANGFDCGMFM 485 (522)
Q Consensus 411 ~sHW~L~VId~k~k~I~~yDSL~~~~~~vl~~L~----~yL~~E~k~-K~g~~~d~s~W~~~~v~~vPqQ~Ng~DCGVFV 485 (522)
|.||.-+..|+..++++.||++|-++.+..+.-. ..|+..... ....-+ +.+...+.-|=+++--||+|.
T Consensus 33 GvHWlA~Aw~P~s~t~YmFDPfGfsd~~L~qiY~FeYe~llrRSAL~~~~dRCv-----~LvkstqtVQ~p~SaaCGLFC 107 (183)
T PF00770_consen 33 GVHWLAFAWDPRSRTFYMFDPFGFSDQKLKQIYQFEYEGLLRRSALSSTPDRCV-----TLVKSTQTVQCPCSAACGLFC 107 (183)
T ss_dssp -S-EEEEEEETTTTEEEEE-TT---HHHHHHHH----HHHHHHHHHHH-TTSEE-----EEEEE-EE-S-TT---HHHHH
T ss_pred ceeEEEEEecCCcceEEEeCCCCCCHHHHHHHHhhhHHHHHHHHhhcCCCCceE-----EEEeccceeeccCchhHHHHH
Confidence 7899999999999999999999988766432211 111111111 100001 111123344556788999999
Q ss_pred HHHHHHHHcC
Q 009925 486 LKYVDFYSRG 495 (522)
Q Consensus 486 L~fae~ls~g 495 (522)
|+|..++..-
T Consensus 108 ~lFL~aF~~~ 117 (183)
T PF00770_consen 108 CLFLHAFVHY 117 (183)
T ss_dssp HHHHHHHHH-
T ss_pred HHHHHHHHhC
Confidence 9999998753
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=77.63 E-value=6.6 Score=38.02 Aligned_cols=83 Identities=19% Similarity=0.250 Sum_probs=48.5
Q ss_pred eeeeeec-CcceEEEEEecC-----CCcceecccCCCCCHHH-HHHHHHHHHHHHHhhcCCCCCCCCceeeccCCCCCCC
Q 009925 404 IFVPIHK-QIHWCLAVIDRK-----DKKFQYLDSLKGRDKKV-LGDLARYFVEEVRDKCGKDIDVSDWEQEFVLDLPEQA 476 (522)
Q Consensus 404 IfIPIn~-~sHW~L~VId~k-----~k~I~~yDSL~~~~~~v-l~~L~~yL~~E~k~K~g~~~d~s~W~~~~v~~vPqQ~ 476 (522)
.++|... +.|. +++|.+ +..|.+++|-...+... +....+.+. +...+.+. .+.+. +.++..|+
T Consensus 74 ~Iv~~~~~~~H~--~a~Dvr~~~~~k~SlI~~Epa~~~~~~~~l~~~~~~~~-~~~~~~~~-----~~~~~-~ie~diQk 144 (177)
T PF03421_consen 74 AIVNLGGDGIHH--VALDVRHTPNGKPSLIVFEPASFYGMKPALAGYTKLAE-EARQKLLP-----NAKFA-VIEMDIQK 144 (177)
T ss_pred EEEeCCCCCCcE--EEEEEeecCCCCceEEEEccccccCCcchhhhHHHHHH-HHHhccCC-----CcEEE-EEeccccc
Confidence 4566443 5565 445544 34689999886443221 222222222 22222222 33332 35788999
Q ss_pred CCCchHHHHHHHHHHHHcC
Q 009925 477 NGFDCGMFMLKYVDFYSRG 495 (522)
Q Consensus 477 Ng~DCGVFVL~fae~ls~g 495 (522)
..+|||+|.|.+|..+...
T Consensus 145 S~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 145 SPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred CcCcchhhHHHHHHHHhhc
Confidence 9999999999999988654
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=63.31 E-value=17 Score=38.06 Aligned_cols=26 Identities=19% Similarity=0.378 Sum_probs=22.0
Q ss_pred CCCCCCCCCCchHHHHHHHHHHHHcC
Q 009925 470 LDLPEQANGFDCGMFMLKYVDFYSRG 495 (522)
Q Consensus 470 ~~vPqQ~Ng~DCGVFVL~fae~ls~g 495 (522)
...-.|+-.+|||+|.|.+|.++...
T Consensus 161 ie~d~QkS~~dC~mFSL~~AkK~~~e 186 (287)
T PRK15371 161 VEMDIQRSSSECGIFSLALAKKLYLE 186 (287)
T ss_pred EecccccCcccchhhhHHHHHHHhhh
Confidence 45667999999999999999988654
No 13
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=28.49 E-value=95 Score=37.97 Aligned_cols=36 Identities=17% Similarity=0.429 Sum_probs=26.4
Q ss_pred eeeeec-------CcceEEEEEecCCCcceecccCCCCCHHHHH
Q 009925 405 FVPIHK-------QIHWCLAVIDRKDKKFQYLDSLKGRDKKVLG 441 (522)
Q Consensus 405 fIPIn~-------~sHW~L~VId~k~k~I~~yDSL~~~~~~vl~ 441 (522)
|+||-. .+||.+++= -+.+..++||+||....+-.+
T Consensus 49 fmpvltgv~p~~~sghwimlik-g~gn~y~lfdplg~~sg~~y~ 91 (1439)
T PF12252_consen 49 FMPVLTGVSPRQDSGHWIMLIK-GQGNQYYLFDPLGKTSGEGYQ 91 (1439)
T ss_pred CceeecCcCCCCcCceeEEEEE-cCCCceEEeccccccccccHH
Confidence 778763 689987654 456788999999977655333
No 14
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=26.66 E-value=50 Score=29.91 Aligned_cols=33 Identities=21% Similarity=0.526 Sum_probs=26.4
Q ss_pred CCCceeeccCCCCCCCCCCchHHHHHHHHHHHH
Q 009925 461 VSDWEQEFVLDLPEQANGFDCGMFMLKYVDFYS 493 (522)
Q Consensus 461 ~s~W~~~~v~~vPqQ~Ng~DCGVFVL~fae~ls 493 (522)
...|.......+|.-.-|+|||.|-..+++|.-
T Consensus 16 ~~r~p~tds~~~p~~~q~r~cg~FE~e~~eC~e 48 (120)
T KOG4110|consen 16 IDRWPTTDSTEQPYKHQGRDCGKFEKEWMECAE 48 (120)
T ss_pred hhhccccccccCccccccccccHHHHHHHHHHH
Confidence 345665555678888889999999999999973
Done!