Query psy2584
Match_columns 397
No_of_seqs 230 out of 822
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 19:55:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2584.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2584hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01088 Peptidase_C12: Ubiqui 100.0 5.1E-70 1.1E-74 512.5 19.7 207 74-323 3-214 (214)
2 KOG1415|consensus 100.0 1.3E-67 2.7E-72 488.4 21.9 213 70-333 4-218 (222)
3 KOG2778|consensus 100.0 1.7E-58 3.7E-63 445.3 14.5 209 69-333 1-220 (328)
4 KOG1415|consensus 99.8 2.6E-19 5.7E-24 167.0 4.3 61 333-397 44-104 (222)
5 PF01088 Peptidase_C12: Ubiqui 99.7 2.4E-17 5.2E-22 155.7 4.4 65 333-397 41-105 (214)
6 KOG2778|consensus 92.0 0.075 1.6E-06 53.3 1.6 27 370-396 69-95 (328)
7 COG3271 Predicted double-glyci 30.3 68 0.0015 30.9 4.0 96 195-291 36-137 (201)
8 PHA02744 hypothetical protein; 30.0 31 0.00067 29.2 1.5 13 272-284 4-16 (88)
9 PF06715 Gp5_C: Gp5 C-terminal 28.2 60 0.0013 21.0 2.3 18 22-39 6-23 (24)
10 PRK14848 deubiquitinase SseL; 24.1 97 0.0021 31.3 3.9 25 364-388 239-267 (317)
11 cd08596 PI-PLCc_epsilon Cataly 20.8 1.3E+02 0.0028 30.0 4.1 62 251-319 13-82 (254)
No 1
>PF01088 Peptidase_C12: Ubiquitin carboxyl-terminal hydrolase, family 1; InterPro: IPR001578 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 peptidases belong to the MEROPS peptidase family C12 (ubiquitin C-terminal hydrolase family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. The type example is the human ubiquitin C-terminal hydrolase UCH-L1. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa and 100-200 kDa, IPR001394 from INTERPRO) []: this family are the 20-30 kDa ppeptides which includes the yeast yuh1. Yeast yuh1 protease is known to be active only against small ubiquitin conjugates, being inactive against conjugated beta-galactosidase []. A mammalian homologue, UCH (ubiquitin conjugate hydrolase), is one of the most abundant proteins in the brain []. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process, 0005622 intracellular; PDB: 1CMX_A 4DM9_A 2ETL_A 3IRT_A 3KW5_A 3IFW_A 2LEN_A 3KVF_A 2WDT_C 2WE6_B ....
Probab=100.00 E-value=5.1e-70 Score=512.51 Aligned_cols=207 Identities=47% Similarity=0.781 Sum_probs=179.7
Q ss_pred cccCCChhHH-HHHHHcCCCCccEEEEeecCCh-hHhhccCCCceEEEEEecCChhhHHHHHHHhhhhhhhccccchhhh
Q psy2584 74 VNRLSTPGSL-AFLVALGVPSKWQIVDVYGTDP-DMLAIVPQPVLALIMLFPCTEKYEEHCKEQEKEIEEKGQTISSELF 151 (397)
Q Consensus 74 i~~ESnPeVF-~ll~~LGv~~~~~f~DVysLD~-dlLa~iP~PV~alIfLFP~~~~~e~~~~~~~~~~~~~~~~i~~~~~ 151 (397)
++|||||+|| +|+++||| ++++|+||||||+ ++|+|+|+|||||||||||++++++.+..++....
T Consensus 3 ~pLESnP~vfn~l~~~lGv-~~~~f~Dv~sld~~~lL~~ip~Pv~alI~lfp~~~~~~~~~~~~~~~~~----------- 70 (214)
T PF01088_consen 3 IPLESNPEVFNELLRKLGV-SGVQFEDVYSLDDPELLAMIPRPVYALIFLFPWTEEYEERRAEEDAKIE----------- 70 (214)
T ss_dssp --EESSHHHHHHHHHHTTB-TSEEEEEESTSSHHHHHTTSSSSEEEEEEEEE--HHHHHHHHHHHHHHC-----------
T ss_pred ccccCCHHHHHHHHHHcCC-ceeEEEEcccccchHhhhhcCccceeEEEEEecchhhhhhhcccccccc-----------
Confidence 4459999999 99999999 5999999999998 78999999999999999999999888766543221
Q ss_pred hhhhhhccccccchhhhhhhhhhhhhHHHHhhhccCCCCceEEEeecccchhHHHHHHHhhccCCCccccCCc-hHHHHH
Q psy2584 152 FMKQFVHNACGTIALIHSYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLNNVKLEDG-KLKSFL 230 (397)
Q Consensus 152 ~~~~~~~~~~g~~~~~h~y~~~~ke~~~~~~~~~~~~~~~v~f~KQtI~NACGTiALLHaLlN~~~~i~l~~~-~L~~f~ 230 (397)
..++..++++|||||||+||||||||||+|+|+++.+.+..| .|++|+
T Consensus 71 -------------------------------~~~~~~~~~v~f~kQti~NACgt~AlLh~l~N~~~~~~i~~gs~L~~f~ 119 (214)
T PF01088_consen 71 -------------------------------EKGQDIPENVFFAKQTIGNACGTIALLHALLNNPDRIEIEPGSILDQFK 119 (214)
T ss_dssp -------------------------------CHSCTCGTTS-EES-SSBTGHHHHHHHHHHHTCCCTTCBBTTSHHHHHH
T ss_pred -------------------------------ccccCCCCCceEeeecCCchhhHHHHHHHHhcccccccccCCchHHHHH
Confidence 123456789999999999999999999999999876556545 599999
Q ss_pred HHhcCCChHHHHhhhccChHHHHHHHhhcccCCCCCCC--CCCCCCceEEEEEeeCCeEEEecCCCCCceeecCCCCCch
Q psy2584 231 DEAKDLSPERRGKLLDENQSISDVHKVIAQEGQTAPPE--DREPVPYHFVALVHKEGALYELDGRKGFPINHGATSPETL 308 (397)
Q Consensus 231 ~~t~~lsP~~Rg~~L~ns~~l~~aHns~A~~g~T~~p~--~~~~v~~HFVafV~~~G~LyELDG~k~gPI~~G~~~~d~~ 308 (397)
++|++|+|++||++|+++++|+++|+++|++|+|+.|. .+++++|||||||+++|+||||||||+|||+||++++++|
T Consensus 120 ~~t~~~~p~~Rg~~l~~~~~l~~aH~s~A~~g~t~~~~~~~~~~~~~HFI~fV~~~G~LyELDG~k~~Pi~~G~~~~~~~ 199 (214)
T PF01088_consen 120 EFTKDLSPEERGKALENSKELRKAHNSFARQGQTEAPDDEADDEVDFHFIAFVPVDGHLYELDGRKSGPIDHGPCSDEDW 199 (214)
T ss_dssp HHHTTSTHHHHHHHHHTHHHHHHHHHHHHCHCSSTS-H--TTSCGCEEEEEEEEETTEEEEEETTSSS-EEEEE-BTTSH
T ss_pred HHHhcCCHHHHHHHHhCcHHHHHHHHHHhccCCcCCCccccCCCCCccEEEEEeECCeEEEcCCCCCCCeEcCcCCCccH
Confidence 99999999999999999999999999999999999876 5789999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcC
Q psy2584 309 LADATQVAKKYMQRD 323 (397)
Q Consensus 309 l~~a~~vIq~~m~~~ 323 (397)
+++|+++||+||+++
T Consensus 200 l~~a~~vik~~m~~y 214 (214)
T PF01088_consen 200 LSDARPVIKERMERY 214 (214)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhcC
Confidence 999999999999874
No 2
>KOG1415|consensus
Probab=100.00 E-value=1.3e-67 Score=488.38 Aligned_cols=213 Identities=54% Similarity=0.870 Sum_probs=198.2
Q ss_pred cccccccCCChhHH-HHHHHcCCCCccEEEEeecCChhHhhccCCCceEEEEEecCChhhHHHHHHHhhhhhhhccccch
Q psy2584 70 KRHPVNRLSTPGSL-AFLVALGVPSKWQIVDVYGTDPDMLAIVPQPVLALIMLFPCTEKYEEHCKEQEKEIEEKGQTISS 148 (397)
Q Consensus 70 ~~~~i~~ESnPeVF-~ll~~LGv~~~~~f~DVysLD~dlLa~iP~PV~alIfLFP~~~~~e~~~~~~~~~~~~~~~~i~~ 148 (397)
.|.|+ ||||+|+ .|+++|||++.|+|.||||||+++|+||||||+|||||||++++++..+.++.+.+
T Consensus 4 ~w~PL--EsNPEv~n~~l~klGv~~~~~~~DVy~ldee~L~~vPrPv~A~lllFP~~e~~e~~~~~~~e~~--------- 72 (222)
T KOG1415|consen 4 RWTPL--ESNPEVLNPFLHKLGVAGEWSVVDVYGLDEESLEFVPRPVKALLLLFPITEKREEFRKEQIEEI--------- 72 (222)
T ss_pred ccccc--cCCHHHHHHHHHHhCCCCceEEEEeeecChhhhhhcCccceEEEEEecccchhhHhhhhhHhhh---------
Confidence 56666 9999999 99999999977999999999999999999999999999999999998887764321
Q ss_pred hhhhhhhhhccccccchhhhhhhhhhhhhHHHHhhhccCCCCceEEEeecccchhHHHHHHHhhccCCCccccCCch-HH
Q psy2584 149 ELFFMKQFVHNACGTIALIHSYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLNNVKLEDGK-LK 227 (397)
Q Consensus 149 ~~~~~~~~~~~~~g~~~~~h~y~~~~ke~~~~~~~~~~~~~~~v~f~KQtI~NACGTiALLHaLlN~~~~i~l~~~~-L~ 227 (397)
+++ +++||||||||+|||||+||||+|+|+.+++.+++|+ |+
T Consensus 73 -----------------------------------k~~--~~~V~fmkQti~NACGTiaLlHslaN~~~r~~l~~Gs~l~ 115 (222)
T KOG1415|consen 73 -----------------------------------KEQ--SDKVFFMKQTIGNACGTIALLHSLANNEDRVKLEDGSFLK 115 (222)
T ss_pred -----------------------------------hcC--CCceEEEeccccchhHHHHHHHHHhccccccccCCchHHH
Confidence 122 7899999999999999999999999999889999895 99
Q ss_pred HHHHHhcCCChHHHHhhhccChHHHHHHHhhcccCCCCCCCCCCCCCceEEEEEeeCCeEEEecCCCCCceeecCCCCCc
Q psy2584 228 SFLDEAKDLSPERRGKLLDENQSISDVHKVIAQEGQTAPPEDREPVPYHFVALVHKEGALYELDGRKGFPINHGATSPET 307 (397)
Q Consensus 228 ~f~~~t~~lsP~~Rg~~L~ns~~l~~aHns~A~~g~T~~p~~~~~v~~HFVafV~~~G~LyELDG~k~gPI~~G~~~~d~ 307 (397)
+|++.+.++||++|+++|+++++|+.+|..+|..|||++ ++++++||||||.+||+|||||||++|||.||++++++
T Consensus 116 ~fl~~~~~~s~eeRa~~le~d~~l~~~H~a~a~eGqte~---~~~vd~HFI~~v~~~G~lYELDgR~~fPi~hG~ts~~t 192 (222)
T KOG1415|consen 116 KFLEEAEKMSPEERADLLENDEELEAAHEAAAQEGQTEA---DEDVDLHFICFVNKNGHLYELDGRKPFPINHGPTSDDT 192 (222)
T ss_pred HHHHHhhcCCHHHHHHHhcccHHHHHHHHHHHhcCCCCC---ccccceEEEEEEccCCeEEEecCCcCCCccCCCCchHH
Confidence 999999999999999999999999999999999999984 67899999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhcCCCCceeeeec
Q psy2584 308 LLADATQVAKKYMQRDPDNGRKGFPI 333 (397)
Q Consensus 308 ~l~~a~~vIq~~m~~~~~~vrFslpi 333 (397)
++++|.+|||+||++.+++++||+..
T Consensus 193 l~kda~~v~k~~~~~~~nel~Fs~iA 218 (222)
T KOG1415|consen 193 LLKDAAKVCKEFIERNPNELRFSAIA 218 (222)
T ss_pred HHHHHHHHHHHHHHcCCCccceEEEE
Confidence 99999999999999999999999854
No 3
>KOG2778|consensus
Probab=100.00 E-value=1.7e-58 Score=445.34 Aligned_cols=209 Identities=30% Similarity=0.457 Sum_probs=183.5
Q ss_pred ecccccccCCChhHH-HHHHHcCCCCccEEEEeecCChhHhhccCCCceEEEEEecCChhhHHHHHHHhhhhhhhccccc
Q psy2584 69 VKRHPVNRLSTPGSL-AFLVALGVPSKWQIVDVYGTDPDMLAIVPQPVLALIMLFPCTEKYEEHCKEQEKEIEEKGQTIS 147 (397)
Q Consensus 69 ~~~~~i~~ESnPeVF-~ll~~LGv~~~~~f~DVysLD~dlLa~iP~PV~alIfLFP~~~~~e~~~~~~~~~~~~~~~~i~ 147 (397)
+.||.| ||||+|| ++++.+||+ ++++++|||||.+.+..+ +||||+||||+|.++.+... ..+
T Consensus 1 ~~W~~i--ESDPGvFTeli~~fgv~-gvQVEElysLd~~~~~~~-~piyGlIFLFKW~~ed~~~g-----------~v~- 64 (328)
T KOG2778|consen 1 MSWCLI--ESDPGVFTELIEGFGVK-GVQVEELYSLDSDSLRPL-RPIYGLIFLFKWIEEDKPAG-----------SVI- 64 (328)
T ss_pred CCceee--ccCCcHHHHHHHhcCCC-ceeEeeeeccCcchhccC-CCceeEEEEEEeccCCCCCc-----------ccc-
Confidence 469999 9999999 999999999 999999999999999998 99999999999986421100 000
Q ss_pred hhhhhhhhhhccccccchhhhhhhhhhhhhHHHHhhhccCCCCceEEEeecccchhHHHHHHHhhccCC-CccccCCchH
Q psy2584 148 SELFFMKQFVHNACGTIALIHSYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNL-NNVKLEDGKL 226 (397)
Q Consensus 148 ~~~~~~~~~~~~~~g~~~~~h~y~~~~ke~~~~~~~~~~~~~~~v~f~KQtI~NACGTiALLHaLlN~~-~~i~l~~~~L 226 (397)
++.-+++||+||+|+|||||+|||++|+|+. ++|.|| .+|
T Consensus 65 --------------------------------------~D~~~niFFA~QvInNACATqAlLsvLlN~~~~~idLG-~tL 105 (328)
T KOG2778|consen 65 --------------------------------------DDSVSNIFFAKQVINNACATQALLSVLLNCSHEDIDLG-PTL 105 (328)
T ss_pred --------------------------------------cccccchhhhhhhcccHHHHHHHHHHHHcCCccccchh-hHH
Confidence 1113689999999999999999999999986 568897 689
Q ss_pred HHHHHHhcCCChHHHHhhhccChHHHHHHHhhcccCC-------CCCCCCCCCCCceEEEEEeeCCeEEEecCCCCCcee
Q psy2584 227 KSFLDEAKDLSPERRGKLLDENQSISDVHKVIAQEGQ-------TAPPEDREPVPYHFVALVHKEGALYELDGRKGFPIN 299 (397)
Q Consensus 227 ~~f~~~t~~lsP~~Rg~~L~ns~~l~~aHns~A~~g~-------T~~p~~~~~v~~HFVafV~~~G~LyELDG~k~gPI~ 299 (397)
.+|+++|++|+|+.||.+|+|+++||.+||||||+.- ++.+ ..+++.||||+|||++|+||||||+|.|||+
T Consensus 106 s~~K~f~k~f~Pe~KGlal~Nse~Ir~~HNSfARp~~~~~~e~~a~~~-~~~dd~yHFVsyvPI~g~lyELDGLke~PI~ 184 (328)
T KOG2778|consen 106 SELKEFTKGFDPELKGLALGNSEEIRCAHNSFARPEPFRPEEVDAATS-AKEDDVYHFVSYVPINGRLYELDGLKEGPID 184 (328)
T ss_pred HHHHHHhhcCChhhcccccCCcHHHHHHhccccCCCCcchhhhhcccc-cccccceeEEEEEeeCCEEEeccCCccCCcc
Confidence 9999999999999999999999999999999999865 2222 2377889999999999999999999999999
Q ss_pred ecCCCCC-chHHHHHHHHHHHHhcC-CCCceeeeec
Q psy2584 300 HGATSPE-TLLADATQVAKKYMQRD-PDNGRKGFPI 333 (397)
Q Consensus 300 ~G~~~~d-~~l~~a~~vIq~~m~~~-~~~vrFslpi 333 (397)
||+|..+ +|++.+++|||++|+++ +|++|||++.
T Consensus 185 lg~~~~eqeW~d~vrpVIqeRi~~ys~gEIrFNLMA 220 (328)
T KOG2778|consen 185 LGPCEKEQEWLDKVRPVIQERIQRYSEGEIRFNLMA 220 (328)
T ss_pred cCCCCccHhHHHHHHHHHHHHHhhCCcceeEEEEEE
Confidence 9999854 89999999999999998 4899999965
No 4
>KOG1415|consensus
Probab=99.76 E-value=2.6e-19 Score=167.02 Aligned_cols=61 Identities=46% Similarity=0.608 Sum_probs=56.4
Q ss_pred cCCCCCccchhcccchhHHHHHHHHHHHHHhhccCCCCcceeecccccchhhHHHHHHHhhcCCC
Q psy2584 333 INHGATSPETLLADATQYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLN 397 (397)
Q Consensus 333 i~~pa~a~~~lfP~t~~~e~~r~~e~~~~~~~g~~~~~~v~~~KQtI~NACGtiALLHalaN~~~ 397 (397)
+++|+.|..++||.+++++.+|+++.++++ ++ +++||||||||+|||||||||||||||.+
T Consensus 44 vPrPv~A~lllFP~~e~~e~~~~~~~e~~k--~~--~~~V~fmkQti~NACGTiaLlHslaN~~~ 104 (222)
T KOG1415|consen 44 VPRPVKALLLLFPITEKREEFRKEQIEEIK--EQ--SDKVFFMKQTIGNACGTIALLHSLANNED 104 (222)
T ss_pred cCccceEEEEEecccchhhHhhhhhHhhhh--cC--CCceEEEeccccchhHHHHHHHHHhcccc
Confidence 699999999999999999999999988766 33 88999999999999999999999999864
No 5
>PF01088 Peptidase_C12: Ubiquitin carboxyl-terminal hydrolase, family 1; InterPro: IPR001578 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 peptidases belong to the MEROPS peptidase family C12 (ubiquitin C-terminal hydrolase family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. The type example is the human ubiquitin C-terminal hydrolase UCH-L1. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa and 100-200 kDa, IPR001394 from INTERPRO) []: this family are the 20-30 kDa ppeptides which includes the yeast yuh1. Yeast yuh1 protease is known to be active only against small ubiquitin conjugates, being inactive against conjugated beta-galactosidase []. A mammalian homologue, UCH (ubiquitin conjugate hydrolase), is one of the most abundant proteins in the brain []. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process, 0005622 intracellular; PDB: 1CMX_A 4DM9_A 2ETL_A 3IRT_A 3KW5_A 3IFW_A 2LEN_A 3KVF_A 2WDT_C 2WE6_B ....
Probab=99.67 E-value=2.4e-17 Score=155.72 Aligned_cols=65 Identities=43% Similarity=0.637 Sum_probs=55.7
Q ss_pred cCCCCCccchhcccchhHHHHHHHHHHHHHhhccCCCCcceeecccccchhhHHHHHHHhhcCCC
Q psy2584 333 INHGATSPETLLADATQYEEHCKEQEKEIEEKGQTISSELFFMKQFVHNACGTIALIHSVANNLN 397 (397)
Q Consensus 333 i~~pa~a~~~lfP~t~~~e~~r~~e~~~~~~~g~~~~~~v~~~KQtI~NACGtiALLHalaN~~~ 397 (397)
++.|+.+.++|||.++.|+++|.+++++..+.++..+++||||||||+||||||||||+|+|+++
T Consensus 41 ip~Pv~alI~lfp~~~~~~~~~~~~~~~~~~~~~~~~~~v~f~kQti~NACgt~AlLh~l~N~~~ 105 (214)
T PF01088_consen 41 IPRPVYALIFLFPWTEEYEERRAEEDAKIEEKGQDIPENVFFAKQTIGNACGTIALLHALLNNPD 105 (214)
T ss_dssp SSSSEEEEEEEEE--HHHHHHHHHHHHHHCCHSCTCGTTS-EES-SSBTGHHHHHHHHHHHTCCC
T ss_pred cCccceeEEEEEecchhhhhhhccccccccccccCCCCCceEeeecCCchhhHHHHHHHHhcccc
Confidence 58999999999999999999999888877766777899999999999999999999999999864
No 6
>KOG2778|consensus
Probab=92.04 E-value=0.075 Score=53.29 Aligned_cols=27 Identities=44% Similarity=0.701 Sum_probs=25.1
Q ss_pred CcceeecccccchhhHHHHHHHhhcCC
Q psy2584 370 SELFFMKQFVHNACGTIALIHSVANNL 396 (397)
Q Consensus 370 ~~v~~~KQtI~NACGtiALLHalaN~~ 396 (397)
+++||-||+|.|||-|=|||-.|.|..
T Consensus 69 ~niFFA~QvInNACATqAlLsvLlN~~ 95 (328)
T KOG2778|consen 69 SNIFFAKQVINNACATQALLSVLLNCS 95 (328)
T ss_pred cchhhhhhhcccHHHHHHHHHHHHcCC
Confidence 689999999999999999999999963
No 7
>COG3271 Predicted double-glycine peptidase [General function prediction only]
Probab=30.26 E-value=68 Score=30.92 Aligned_cols=96 Identities=16% Similarity=0.152 Sum_probs=49.5
Q ss_pred EeecccchhHHHHHHHhhccCCCccccCCch-HHHHHHHhcCCChHHHHhhhccChHHHHHH-HhhcccCCCCCCC---C
Q psy2584 195 MKQFVHNACGTIALIHSVANNLNNVKLEDGK-LKSFLDEAKDLSPERRGKLLDENQSISDVH-KVIAQEGQTAPPE---D 269 (397)
Q Consensus 195 ~KQtI~NACGTiALLHaLlN~~~~i~l~~~~-L~~f~~~t~~lsP~~Rg~~L~ns~~l~~aH-ns~A~~g~T~~p~---~ 269 (397)
++|+..-+||-.|+...|-|--... ..++. +..........|...-..+++....=++.. +.+..-.|+..|. .
T Consensus 36 Irq~~d~ScGaaalatll~n~~gk~-~~e~~~~~~m~~~~~~~s~~g~~~~~~~~g~~a~~~~~~~~~l~q~~~p~iV~~ 114 (201)
T COG3271 36 IRQTTDFSCGAAALATLLNNDYGKL-ADESLVLIEMNLEEFGESFSGMARAIKSLGNRAQGYENEFESLAQLKIPVIVTL 114 (201)
T ss_pred HHhhhccCchHHHHHHHHHhhcccc-CCHHHHHHHhhHHHhhhcHHHHHHHhhCCCCcccccccchhhhhhccCCeeEEe
Confidence 7999999999999999888843211 22221 333322222233333333332221111111 1111112333333 3
Q ss_pred CCCCCceEEEEEeeC-CeEEEec
Q psy2584 270 REPVPYHFVALVHKE-GALYELD 291 (397)
Q Consensus 270 ~~~v~~HFVafV~~~-G~LyELD 291 (397)
++....||+.-+-++ +.++-.|
T Consensus 115 ~~~~~~hf~v~~~v~~~~v~l~D 137 (201)
T COG3271 115 KYPANNHFDVVIGVDGDNVTLAD 137 (201)
T ss_pred ecCCCceeEEEEeccCCeeEEcC
Confidence 567789999988865 5677666
No 8
>PHA02744 hypothetical protein; Provisional
Probab=29.99 E-value=31 Score=29.21 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.8
Q ss_pred CCCceEEEEEeeC
Q psy2584 272 PVPYHFVALVHKE 284 (397)
Q Consensus 272 ~v~~HFVafV~~~ 284 (397)
+..+|||||||..
T Consensus 4 ~~~~~y~CiVPkE 16 (88)
T PHA02744 4 DGKYHYICIAPKE 16 (88)
T ss_pred CCceeEEEEecHH
Confidence 4569999999965
No 9
>PF06715 Gp5_C: Gp5 C-terminal repeat (3 copies); InterPro: IPR010609 This repeat composes the C-terminal part of the Bacteriophage T4 baseplate protein Gp5. This region of the protein forms a needle like projection from the baseplate that is presumed to puncture the bacterial cell membrane. Structurally three copies of the repeated region trimerise to form a beta solenoid type structure []. This family also includes repeats from bacterial Vgr proteins.; PDB: 3A1M_F 1K28_A 1WTH_A 2Z6B_A.
Probab=28.17 E-value=60 Score=21.01 Aligned_cols=18 Identities=33% Similarity=0.370 Sum_probs=14.6
Q ss_pred eeCcceeEEeeCceeeEE
Q psy2584 22 YGGNNRLYTVHGDHLIKL 39 (397)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~ 39 (397)
+=|+||--||.|++.+.+
T Consensus 6 ~V~gnrT~tV~gn~T~tV 23 (24)
T PF06715_consen 6 TVGGNRTITVGGNETETV 23 (24)
T ss_dssp EESSBEEEEESSEEEEEE
T ss_pred EeCCcEEEEeCCceEEEc
Confidence 347789999999998764
No 10
>PRK14848 deubiquitinase SseL; Provisional
Probab=24.09 E-value=97 Score=31.27 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=18.5
Q ss_pred hccCCCCcceee----cccccchhhHHHH
Q psy2584 364 KGQTISSELFFM----KQFVHNACGTIAL 388 (397)
Q Consensus 364 ~g~~~~~~v~~~----KQtI~NACGtiAL 388 (397)
.|....++|.|+ .|.++|.||+.++
T Consensus 239 ag~~~e~di~fIe~nLQqnVpngCGlFv~ 267 (317)
T PRK14848 239 AGISENEDVNFIETNLQNNVPNGCGLFCY 267 (317)
T ss_pred hCcccCCceEEeehhhhhhCCCcchHHHH
Confidence 333335678875 7899999999875
No 11
>cd08596 PI-PLCc_epsilon Catalytic domain of metazoan phosphoinositide-specific phospholipase C-epsilon. This family corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-epsilon isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-epsilon represents a class of mammalian PI-PLC that has an N-terminal CDC25 homology domain with a guanyl-nucleotide exchange factor (GFF) activity, a pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core
Probab=20.76 E-value=1.3e+02 Score=30.04 Aligned_cols=62 Identities=24% Similarity=0.331 Sum_probs=38.6
Q ss_pred HHHHHHhhcccCCCCCCCCCCCCCceEEEEEe---eCCeEEEec---CCCCCce-eecCC-CCCchHHHHHHHHHHH
Q psy2584 251 ISDVHKVIAQEGQTAPPEDREPVPYHFVALVH---KEGALYELD---GRKGFPI-NHGAT-SPETLLADATQVAKKY 319 (397)
Q Consensus 251 l~~aHns~A~~g~T~~p~~~~~v~~HFVafV~---~~G~LyELD---G~k~gPI-~~G~~-~~d~~l~~a~~vIq~~ 319 (397)
|...||++-...|-...+. + -+|+. .+=|..||| |....|| .||-+ +..-.+.++.+.|++|
T Consensus 13 I~SSHNTYL~g~Ql~~~ss---~----~~y~~aL~~GcRcvElD~wdG~~~eP~V~HG~tlts~i~f~dv~~~I~~~ 82 (254)
T cd08596 13 IESSHNTYLTGHQLKGESS---V----ELYSQVLLTGCRCVELDCWDGDDGMPIIYHGHTLTTKIPFKDVVEAINRS 82 (254)
T ss_pred eecCccccccCCccCCccC---H----HHHHHHHHcCCcEEEEEeecCCCCCcEEeeCCCcccCcCHHHHHHHHHHH
Confidence 4456888876665432211 1 13333 466888997 8888887 78854 3455677888888863
Done!