Query 025530
Match_columns 251
No_of_seqs 61 out of 63
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:47:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025530hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2606 OTU (ovarian tumor)-li 99.0 5.4E-13 1.2E-17 123.0 -13.6 215 1-251 2-216 (302)
2 PF02338 OTU: OTU-like cystein 98.7 5E-09 1.1E-13 79.3 2.3 44 200-250 1-45 (121)
3 PF10275 Peptidase_C65: Peptid 93.9 0.041 8.9E-07 47.8 2.5 23 195-217 42-64 (244)
4 KOG2605 OTU (ovarian tumor)-li 90.9 0.16 3.5E-06 48.8 2.5 49 189-248 213-261 (371)
5 KOG3991 Uncharacterized conser 89.3 0.18 3.8E-06 46.8 1.3 20 197-216 67-86 (256)
6 KOG3288 OTU-like cysteine prot 78.0 3.4 7.5E-05 39.3 4.5 53 186-248 102-154 (307)
7 PRK09784 hypothetical protein; 50.1 16 0.00035 35.2 3.1 46 192-237 198-243 (417)
8 PF05347 Complex1_LYR: Complex 39.8 71 0.0015 21.7 4.3 36 206-250 6-41 (59)
9 PF07418 PCEMA1: Acidic phosph 20.5 64 0.0014 30.8 1.8 39 13-56 2-45 (282)
10 PTZ00091 40S ribosomal protein 17.3 42 0.00092 30.2 -0.1 36 211-251 144-186 (193)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.99 E-value=5.4e-13 Score=122.95 Aligned_cols=215 Identities=17% Similarity=0.086 Sum_probs=152.0
Q ss_pred CeeeccccccccceEEecccccccccceeeeeeecCCCceeeeeeccCcccccccceeEEeecCCccccccccccccccc
Q 025530 1 MIVSTSICACAKNVVNLGGRFQGQMGGNICGVTYRGPSSSCCFYLCSGQSKKNYAGISRTISSSSLNVLQPFQATCFSPG 80 (251)
Q Consensus 1 mi~~~~i~~~~~n~v~l~g~~~~~mgs~i~~~~~~g~s~s~c~~~~~g~s~~~y~~~s~~~s~~s~~~~q~~~~~~~~S~ 80 (251)
|+++.++..|.+|...| .+|-+.+-......+..+..|.... ++.++.|.+.-..++. -+-|++++.+++..
T Consensus 2 ~~~~~~~~~~~~~e~iL----aRHr~E~keLq~ki~~mKk~a~k~~-k~~rK~~~~~~~~le~---el~qkH~kEL~~~~ 73 (302)
T KOG2606|consen 2 MTCMDSEQDEESNEEIL----ARHRRERKELQAKITSMKKAAPKGN-KKKRKELTEDIAKLEK---ELSQKHKKELEKLK 73 (302)
T ss_pred cCCccchhhhhhHHHHH----HHHHHHHHHHHHHHHHHHHhhhhcc-HHHHHHHHHHHHHHHh---HHHHHHHHHHHhhc
Confidence 67888899999998888 8899999999999999999999887 8999999995555554 24579999999999
Q ss_pred ccCCCCCCCCceeeeeecccCccceeeeeeecccceeeeecccccCccccccCCcccccCCCCCCcceeeeeeeeeccCc
Q 025530 81 LTKPRCNLRPLTIRSFIGSRGSQKRHIEISLACRSMKMRLLVPSQGVLPKLKLNAGPIDWPKGCASAGLICGLLVCYSSS 160 (251)
Q Consensus 81 l~k~~~~~~~~tvk~~~~s~G~~kr~~~ISl~c~~ln~r~~~p~~~~~ski~~n~~~~~w~~g~~s~gL~fg~~vc~ss~ 160 (251)
+.... +| .++....-++..+..||.++---. -|. ..+.+.-|...+-....-..-..+|+++.
T Consensus 74 ~~~~~------e~--------~~~e~~~~s~l~~~a~~~~~~~ee--~P~-~sKa~k~r~k~r~e~r~~e~~~~~e~~~~ 136 (302)
T KOG2606|consen 74 LINES------EV--------TPKENLIESVLSPIANMSLENKEE--TPR-QSKARKRREKKRKEERKREAEKIAEEESL 136 (302)
T ss_pred ccCcc------cc--------Cccccchhhhhccccccccccccc--CCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 98766 45 677878888888888876432110 000 12233333333444444333444444333
Q ss_pred ccccccccccccCCCccccccccCCCCceeEEeeeEeeecCCcchhhHHHHhHHhHHhCCCCCChhhhhhhHHHHHHHHH
Q 025530 161 KAHAEAADEKEDGEEDYDLSNVKYSHGKKVYTDYSVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVA 240 (251)
Q Consensus 161 ~a~ae~~~~~~~~~~~~~~s~~~~~~g~k~~~~ysV~gI~GDGRCLFRSvAhGa~~~~G~~~p~~~eqrelADeLR~~Va 240 (251)
. +-..+...++. . -..+=......+..||.||.|||+||.|+++++.+..++-+.++++.||.+|..|.
T Consensus 137 ~-~~~~~k~~E~~--k--------~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~ 205 (302)
T KOG2606|consen 137 S-NQADAKSMEKE--K--------LAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVE 205 (302)
T ss_pred h-cCCchhhhHHH--H--------HHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHH
Confidence 1 10000000000 0 00011123467889999999999999999999999999999999999999999999
Q ss_pred HHHhhcccccC
Q 025530 241 DEFIKRREETE 251 (251)
Q Consensus 241 DeL~kRReEtE 251 (251)
|+|.-++.|++
T Consensus 206 df~pf~~~eet 216 (302)
T KOG2606|consen 206 DFLPFLLDEET 216 (302)
T ss_pred HhhhHhcCccc
Confidence 99998888865
No 2
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=98.73 E-value=5e-09 Score=79.35 Aligned_cols=44 Identities=39% Similarity=0.640 Sum_probs=35.2
Q ss_pred cCCcchhhHHHHhHHhHHhCCCCCChhhhhhhHHHHHHHHHHHHh-hccccc
Q 025530 200 PGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFI-KRREET 250 (251)
Q Consensus 200 ~GDGRCLFRSvAhGa~~~~G~~~p~~~eqrelADeLR~~VaDeL~-kRReEt 250 (251)
||||+||||||++++....+ . ....+.+||.+|++.|. +.+++.
T Consensus 1 pgDGnClF~Avs~~l~~~~~---~----~~~~~~~lR~~~~~~l~~~~~~~~ 45 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGG---G----SEDNHQELRKAVVDYLRDKNRDKF 45 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-S---S----STTTHHHHHHHHHHHHHTHTTTHH
T ss_pred CCCccHHHHHHHHHHHHhcC---C----CHHHHHHHHHHHHHHHHHhccchh
Confidence 79999999999999997665 1 13479999999999999 877753
No 3
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 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 family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=93.90 E-value=0.041 Score=47.77 Aligned_cols=23 Identities=26% Similarity=0.611 Sum_probs=17.6
Q ss_pred eEeeecCCcchhhHHHHhHHhHH
Q 025530 195 SVIGIPGDGRCLFRAVAHGACLR 217 (251)
Q Consensus 195 sV~gI~GDGRCLFRSvAhGa~~~ 217 (251)
.+.+|+|||+|.|||++-+.--.
T Consensus 42 ~~R~vRGDGNCFYRAf~F~ylE~ 64 (244)
T PF10275_consen 42 GIRRVRGDGNCFYRAFGFSYLEQ 64 (244)
T ss_dssp EEE-B-SSSTHHHHHHHHHHHHH
T ss_pred heEeecCCccHHHHHHHHHHHHH
Confidence 45689999999999999996653
No 4
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=90.91 E-value=0.16 Score=48.78 Aligned_cols=49 Identities=31% Similarity=0.416 Sum_probs=40.6
Q ss_pred eeEEeeeEeeecCCcchhhHHHHhHHhHHhCCCCCChhhhhhhHHHHHHHHHHHHhhccc
Q 025530 189 KVYTDYSVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRRE 248 (251)
Q Consensus 189 k~~~~ysV~gI~GDGRCLFRSvAhGa~~~~G~~~p~~~eqrelADeLR~~VaDeL~kRRe 248 (251)
++.-.|-..+|.+||.|+|||++-.+.. . .|..|..|..++|.+-+.|.
T Consensus 213 ~~~~g~e~~Kv~edGsC~fra~aDQvy~--------d---~e~~~~~~~~~~dq~~~e~~ 261 (371)
T KOG2605|consen 213 KKHFGFEYKKVVEDGSCLFRALADQVYG--------D---DEQHDHNRRECVDQLKKERD 261 (371)
T ss_pred HHHhhhhhhhcccCCchhhhccHHHhhc--------C---HHHHHHHHHHHHHHHhhccc
Confidence 4667788999999999999999998876 2 34678899999999966664
No 5
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.32 E-value=0.18 Score=46.83 Aligned_cols=20 Identities=35% Similarity=0.552 Sum_probs=17.2
Q ss_pred eeecCCcchhhHHHHhHHhH
Q 025530 197 IGIPGDGRCLFRAVAHGACL 216 (251)
Q Consensus 197 ~gI~GDGRCLFRSvAhGa~~ 216 (251)
.++.|||+|+|||++.+..-
T Consensus 67 R~trgDGNCfyra~~~s~lE 86 (256)
T KOG3991|consen 67 RKTRGDGNCFYRAFAYSYLE 86 (256)
T ss_pred heecCCCceehHHHHHHHHH
Confidence 36789999999999998764
No 6
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=78.02 E-value=3.4 Score=39.26 Aligned_cols=53 Identities=25% Similarity=0.283 Sum_probs=37.5
Q ss_pred CCceeEEeeeEeeecCCcchhhHHHHhHHhHHhCCCCCChhhhhhhHHHHHHHHHHHHhhccc
Q 025530 186 HGKKVYTDYSVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRRE 248 (251)
Q Consensus 186 ~g~k~~~~ysV~gI~GDGRCLFRSvAhGa~~~~G~~~p~~~eqrelADeLR~~VaDeL~kRRe 248 (251)
.+-.-.-...++-||.|--|||+||+.++-.-.+.+ .-|||..|+.|..-..+
T Consensus 102 ~~g~~~gvl~~~vvp~DNSCLF~ai~yv~~k~~~~~----------~~elR~iiA~~Vasnp~ 154 (307)
T KOG3288|consen 102 IGGSGEGVLSRRVVPDDNSCLFTAIAYVIFKQVSNR----------PYELREIIAQEVASNPD 154 (307)
T ss_pred CCCCccceeEEEeccCCcchhhhhhhhhhcCccCCC----------cHHHHHHHHHHHhcChh
Confidence 344444567788899999999999999986532221 24788888888765543
No 7
>PRK09784 hypothetical protein; Provisional
Probab=50.09 E-value=16 Score=35.25 Aligned_cols=46 Identities=22% Similarity=0.245 Sum_probs=30.7
Q ss_pred EeeeEeeecCCcchhhHHHHhHHhHHhCCCCCChhhhhhhHHHHHH
Q 025530 192 TDYSVIGIPGDGRCLFRAVAHGACLRAGKPAPSVSIQRELADDLRA 237 (251)
Q Consensus 192 ~~ysV~gI~GDGRCLFRSvAhGa~~~~G~~~p~~~eqrelADeLR~ 237 (251)
-...-..|.|||-||.|||..=-.+.---.+-+-..|+|.-||.-.
T Consensus 198 ~glkyapvdgdgycllrailvlk~h~yswal~s~ktqk~vy~efik 243 (417)
T PRK09784 198 YGLKYAPVDGDGYCLLRAILVLKQHDYSWALGSHKTQKEVYEEFIK 243 (417)
T ss_pred hCceecccCCCchhHHHHHHHhhhcccchhhccchhHHHHHHHHHH
Confidence 3445568999999999999764444434445556667776666543
No 8
>PF05347 Complex1_LYR: Complex 1 protein (LYR family); InterPro: IPR008011 This family of short proteins includes proteins from the NADH-ubiquinone oxidoreductase complex I. The family includes the B14 subunit from bovine NADH-ubiquinone oxidoreductase B14 subunit Q02366 from SWISSPROT, and the B22 subunit from the human enzyme Q9Y6M9 from SWISSPROT. The family has been named LYR after a highly conserved tripeptide motif close to the N terminus of these proteins. Members of this family also found in yeast which do contain this complex. In these organisms they are believed to be be required for iron-sulphur custer biogenesis.
Probab=39.80 E-value=71 Score=21.67 Aligned_cols=36 Identities=36% Similarity=0.491 Sum_probs=25.8
Q ss_pred hhHHHHhHHhHHhCCCCCChhhhhhhHHHHHHHHHHHHhhccccc
Q 025530 206 LFRAVAHGACLRAGKPAPSVSIQRELADDLRAKVADEFIKRREET 250 (251)
Q Consensus 206 LFRSvAhGa~~~~G~~~p~~~eqrelADeLR~~VaDeL~kRReEt 250 (251)
|||.+...+.. +|+.+ .-+.+|..|-++|.++++++
T Consensus 6 LYR~lLR~~~~-----~~~~~----~r~~~~~~iR~~Fr~n~~~~ 41 (59)
T PF05347_consen 6 LYRQLLRAARS-----FPDDS----EREYIRAEIRQEFRKNRNET 41 (59)
T ss_pred HHHHHHHHHHH-----cCCcc----hHHHHHHHHHHHHHhcCCCC
Confidence 57776665533 55544 35677999999999999876
No 9
>PF07418 PCEMA1: Acidic phosphoprotein precursor PCEMA1; InterPro: IPR010882 This family consists of several acidic phosphoprotein precursor PCEMA1 sequences which appear to be found exclusively in Plasmodium chabaudi. PCEMA1 is an antigen that is associated with the membrane of the infected erythrocyte throughout the entire intraerythrocytic cycle []. The exact function of this family is unclear.
Probab=20.49 E-value=64 Score=30.85 Aligned_cols=39 Identities=26% Similarity=0.465 Sum_probs=30.6
Q ss_pred ceEEecccccccccceeeeeeec-----CCCceeeeeeccCcccccccc
Q 025530 13 NVVNLGGRFQGQMGGNICGVTYR-----GPSSSCCFYLCSGQSKKNYAG 56 (251)
Q Consensus 13 n~v~l~g~~~~~mgs~i~~~~~~-----g~s~s~c~~~~~g~s~~~y~~ 56 (251)
|||.| ++..|-||-+|-. --||--||+.|.-+.++.++-
T Consensus 2 k~isl-----glissiifsivlakn~s~s~sttgcF~f~rkK~kk~~~~ 45 (282)
T PF07418_consen 2 KVISL-----GLISSIIFSIVLAKNSSGSGSTTGCFGFCRKKPKKIHKT 45 (282)
T ss_pred ceeee-----cchhhhheeeEEeccCCCCCCccceehhhcccccccccc
Confidence 67888 5888999988743 345678999999999988764
No 10
>PTZ00091 40S ribosomal protein S5; Provisional
Probab=17.32 E-value=42 Score=30.20 Aligned_cols=36 Identities=31% Similarity=0.371 Sum_probs=24.3
Q ss_pred HhHHhH---HhCCCCCChhhhhhhHHHHHHHHHHH----HhhcccccC
Q 025530 211 AHGACL---RAGKPAPSVSIQRELADDLRAKVADE----FIKRREETE 251 (251)
Q Consensus 211 AhGa~~---~~G~~~p~~~eqrelADeLR~~VaDe----L~kRReEtE 251 (251)
+.|+.. ++++.+ +..|||||=.+.-.. -+|.|||+|
T Consensus 144 ~~~ar~~~fR~~ks~-----~e~LA~Eli~Aa~~~~~s~AikKKeE~h 186 (193)
T PTZ00091 144 CKGAREAAFRNIKTI-----AECLADEIINASKESSNSYAIKKKDEVE 186 (193)
T ss_pred HHHHHhhcccCCCCH-----HHHHHHHHHHHHhCCCCCcceehHHHHH
Confidence 555544 444433 355999998888776 678888875
Done!