Query 022282
Match_columns 300
No_of_seqs 187 out of 949
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 09:25:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022282.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022282hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2605 OTU (ovarian tumor)-li 100.0 3.7E-33 8E-38 270.4 10.2 287 5-296 1-297 (371)
2 PF02338 OTU: OTU-like cystein 99.8 8.3E-22 1.8E-26 158.8 3.9 71 223-299 1-76 (121)
3 KOG2606 OTU (ovarian tumor)-li 99.7 1.4E-17 2.9E-22 157.5 8.3 99 201-299 143-254 (302)
4 KOG3288 OTU-like cysteine prot 99.0 8.2E-11 1.8E-15 110.5 2.9 83 217-299 110-194 (307)
5 PF10275 Peptidase_C65: Peptid 98.8 2.7E-08 5.9E-13 90.8 8.2 54 246-299 141-199 (244)
6 KOG3991 Uncharacterized conser 98.4 2.5E-07 5.3E-12 86.1 4.6 55 245-299 157-214 (256)
7 COG5539 Predicted cysteine pro 98.0 1.7E-06 3.6E-11 82.8 0.8 88 212-299 166-265 (306)
8 COG5539 Predicted cysteine pro 97.4 7.8E-05 1.7E-09 71.5 2.0 74 224-299 119-194 (306)
9 PRK09784 hypothetical protein; 53.5 7.4 0.00016 37.9 1.5 24 211-234 194-217 (417)
10 COG5007 Predicted transcriptio 38.9 31 0.00066 27.9 2.7 46 214-259 13-61 (80)
11 PF05412 Peptidase_C33: Equine 29.5 36 0.00078 28.9 1.8 17 223-239 5-21 (108)
12 PF05415 Peptidase_C36: Beet n 27.8 54 0.0012 27.4 2.5 59 222-298 3-63 (104)
13 KOG0256 1-aminocyclopropane-1- 25.1 79 0.0017 32.8 3.6 56 206-264 88-146 (471)
14 smart00718 DM4_12 DM4/DM12 fam 23.2 1.3E+02 0.0027 24.4 3.9 72 204-287 9-81 (95)
15 KOG2605 OTU (ovarian tumor)-li 21.8 16 0.00035 36.7 -1.9 82 213-294 51-132 (371)
16 COG3081 Nucleoid-associated pr 20.4 1E+02 0.0022 30.4 3.2 36 222-257 194-232 (335)
17 KOG4634 Mitochondrial F1F0-ATP 20.1 93 0.002 26.2 2.5 24 58-81 52-75 (105)
No 1
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.7e-33 Score=270.43 Aligned_cols=287 Identities=27% Similarity=0.330 Sum_probs=214.6
Q ss_pred ccccCCCCeeeecccccCCCCCCCC---CCCCccceeec-CCCCccccccccccccccccccchHHHHHHHHHHHHHHHH
Q 022282 5 ITYEQDPDVLRWGLHQLLDICTLSN---SGSQNVITRYD-RDSSQVGYVRECYSETELAYVENDEVIAHVLQEEFSQVAA 80 (300)
Q Consensus 5 ~~~e~d~dv~~wgl~~l~~~~~~~~---~~~~~~~~~~d-~~~~~~~yv~e~y~~~~~~~v~~d~~ia~~~qee~s~~~~ 80 (300)
+.++++|.+++|.|++|=+..++.- .|.++.+.|.- -++.+.++++++|+......|.+|++||+.+|++++.++.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~~~~~~g~~~~~~~~~r~~~v~~~~~~~~~~~d~~~~~e~ 80 (371)
T KOG2605|consen 1 TFREEVSGDFDWYLWDLGKTKTLGTILELGAMSHVYRRNVIDYEPFGMGTDGYNNKRYGEVDRDFMIARGHQDEVLTVED 80 (371)
T ss_pred CCccccCchHHHHhhcCCCCcccccchhhhhccccccCCCCCcCCccceeccccCccccchhhhhhhhcccccccccccH
Confidence 3588999999999997766555432 55677777664 4556778999999999999999999999999999999999
Q ss_pred HHhcCCCCCCCCcccccCCC-CCCCCCCCCcccccc--cccCCCCCCc--cccccccc-ccccccCCCCccccccCCCCc
Q 022282 81 AEASGSINPEKSSILEQDRV-SPLGIYNNSVCENDR--SAADGSGKNE--EEMDDSGR-MVEADYQSKGEKVELEYDEDN 154 (300)
Q Consensus 81 ~e~~~~~~~~~~~~~~~~w~-~~~~~~~~~~~~~~~--~~~~~~~~~~--~~~~~~~~-~~~~~~~~~s~~~~~~~~~~~ 154 (300)
||.+.....-.-+++.|+-+ .+.....++.|...- ..+.+.++.+ -...-+++ .++...+.++-+ +|.+
T Consensus 81 ~e~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~s~~~~~~~~~~~~~~~~~~~~-----~~sd 155 (371)
T KOG2605|consen 81 AEMAAICQSVLFKVLYQERFKLPSDTPCNGENSPMCSFHSRRGNESFQAASFGGLEIDLEVERNSPEWLGQ-----SPSD 155 (371)
T ss_pred HHHhhHHhhhhhhhhhhhcccCCCCCcccccCCCCCcccccccccccccccccccccchhhhccCchhccc-----cccc
Confidence 99999998888888888843 322221111111000 0111111100 00011111 111111111111 1222
Q ss_pred hhhhhhhhcccccccccchhhhhcccCCCCCCCCCCCCCCCCCCchhhhHHHHHHHHHhhcCcEEEEecCCCchhHHHHH
Q 022282 155 MEDLLHQLDTTDESSVIDGELGKRLNQMVPVPHIPKINGDIPSPDEEISDHQRMLDRLQLYDLVENKVQGDGNCQFRSLS 234 (300)
Q Consensus 155 ~~~~~~~~~~~~~~~~~~g~~gkrls~~~pip~~pk~ng~iPs~de~~~d~~rL~erL~~~GL~i~~V~GDGNCLFRALS 234 (300)
......+...........+++|.+++.+.|++++|++++.+|+..+..++|+++.+++..+|+.+++|.+||||+|||+|
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~g~~in~y~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~g~e~~Kv~edGsC~fra~a 235 (371)
T KOG2605|consen 156 PLRSVPSMEAIHARHPEAKEVGVRINDYNPKVLVPFINGLPPSEEEPQSAHERSAKRKKHFGFEYKKVVEDGSCLFRALA 235 (371)
T ss_pred cccccccccchhhccccchhhcccccCCCccccccccccCCCchHHHHHHHHHHHHHHHHhhhhhhhcccCCchhhhccH
Confidence 22232333222222247789999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCchhHHHHHHHHHHHHhhChhhhcccCCCCHHHHHHHhhcCCccchHHHHHHHHHhc
Q 022282 235 DQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKKMNKSGEWGDHVTLQAAADSV 296 (300)
Q Consensus 235 dQL~g~q~~H~~VRk~vVdyL~~n~d~F~~fV~~~~eeYl~kMsk~GtWGg~IELqAlAdly 296 (300)
+|||++.+.|..+|++++++++++++.|+.|++++|..|+++|++++.||+|+|+||+|+++
T Consensus 236 DQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~ 297 (371)
T KOG2605|consen 236 DQVYGDDEQHDHNRRECVDQLKKERDFYEDYVTEDFTSYIKRKRADGEPGNHIEQQAAADIY 297 (371)
T ss_pred HHhhcCHHHHHHHHHHHHHHHhhcccccccccccchhhcccccccCCCCcchHHHhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999854
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=99.84 E-value=8.3e-22 Score=158.83 Aligned_cols=71 Identities=41% Similarity=0.741 Sum_probs=66.5
Q ss_pred cCCCchhHHHHHHHHh----cCchhHHHHHHHHHHHHh-hChhhhcccCCCCHHHHHHHhhcCCccchHHHHHHHHHhcC
Q 022282 223 QGDGNCQFRSLSDQLY----RSPEHHMFVRQQVVNQLK-AHPEIYEGYVPMAYSDYLKKMNKSGEWGDHVTLQAAADSVW 297 (300)
Q Consensus 223 ~GDGNCLFRALSdQL~----g~q~~H~~VRk~vVdyL~-~n~d~F~~fV~~~~eeYl~kMsk~GtWGg~IELqAlAdly~ 297 (300)
||||||||||||+||+ +++..|.+||++|++||+ +|++.|..|+..+ +|+++|+||+++||+|+|++|+
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~Wg~~~el~a~a~~~~ 74 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD------KMSKPGTWGGEIELQALANVLN 74 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH------HHTSTTSHEEHHHHHHHHHHHT
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh------hhccccccCcHHHHHHHHHHhC
Confidence 7999999999999999 999999999999999999 9999999988644 8999999999999999999999
Q ss_pred CC
Q 022282 298 AT 299 (300)
Q Consensus 298 Vt 299 (300)
++
T Consensus 75 ~~ 76 (121)
T PF02338_consen 75 RP 76 (121)
T ss_dssp SE
T ss_pred Ce
Confidence 85
No 3
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=1.4e-17 Score=157.46 Aligned_cols=99 Identities=16% Similarity=0.360 Sum_probs=89.7
Q ss_pred hhhHHHHHHHHHhhcCcEEEEecCCCchhHHHHHHHHhcC---chhHHHHHHHHHHHHhhChhhhcccCC----------
Q 022282 201 EISDHQRMLDRLQLYDLVENKVQGDGNCQFRSLSDQLYRS---PEHHMFVRQQVVNQLKAHPEIYEGYVP---------- 267 (300)
Q Consensus 201 ~~~d~~rL~erL~~~GL~i~~V~GDGNCLFRALSdQL~g~---q~~H~~VRk~vVdyL~~n~d~F~~fV~---------- 267 (300)
...+.+.|.+.|...||..+.||.||+|||+||++||.-. .-..+.||.++++||++|.++|.+|+.
T Consensus 143 k~~E~~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~ 222 (302)
T KOG2606|consen 143 KSMEKEKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLLDEETGDSLGP 222 (302)
T ss_pred hhhHHHHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhcCccccccCCH
Confidence 3446678999999999999999999999999999999643 367899999999999999999999973
Q ss_pred CCHHHHHHHhhcCCccchHHHHHHHHHhcCCC
Q 022282 268 MAYSDYLKKMNKSGEWGDHVTLQAAADSVWAT 299 (300)
Q Consensus 268 ~~~eeYl~kMsk~GtWGg~IELqAlAdly~Vt 299 (300)
.+|..||+.|+.++.|||+|||.|||.+|.+|
T Consensus 223 ~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~P 254 (302)
T KOG2606|consen 223 EDFDKYCREIRNTAAWGGELELKALSHVLQVP 254 (302)
T ss_pred HHHHHHHHHhhhhccccchHHHHHHHHhhccC
Confidence 14999999999999999999999999999987
No 4
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.05 E-value=8.2e-11 Score=110.47 Aligned_cols=83 Identities=17% Similarity=0.381 Sum_probs=74.3
Q ss_pred cEEEEecCCCchhHHHHHHHHhcCc-hhHHHHHHHHHHHHhhChhhhcc-cCCCCHHHHHHHhhcCCccchHHHHHHHHH
Q 022282 217 LVENKVQGDGNCQFRSLSDQLYRSP-EHHMFVRQQVVNQLKAHPEIYEG-YVPMAYSDYLKKMNKSGEWGDHVTLQAAAD 294 (300)
Q Consensus 217 L~i~~V~GDGNCLFRALSdQL~g~q-~~H~~VRk~vVdyL~~n~d~F~~-fV~~~~eeYl~kMsk~GtWGg~IELqAlAd 294 (300)
|.++.||.|.+|||+||++-+++.- ..-.++|+.|.+.+.+||+.|.. +++..-.+||..+.+...|||.|||..||+
T Consensus 110 l~~~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~ 189 (307)
T KOG3288|consen 110 LSRRVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSD 189 (307)
T ss_pred eEEEeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehh
Confidence 5577899999999999999999853 23379999999999999999975 678899999999999999999999999999
Q ss_pred hcCCC
Q 022282 295 SVWAT 299 (300)
Q Consensus 295 ly~Vt 299 (300)
.|+|-
T Consensus 190 ~ygve 194 (307)
T KOG3288|consen 190 YYGVE 194 (307)
T ss_pred hhcee
Confidence 99873
No 5
>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=98.75 E-value=2.7e-08 Score=90.85 Aligned_cols=54 Identities=22% Similarity=0.419 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhhChhhhcccCC----CCHHHHHH-HhhcCCccchHHHHHHHHHhcCCC
Q 022282 246 FVRQQVVNQLKAHPEIYEGYVP----MAYSDYLK-KMNKSGEWGDHVTLQAAADSVWAT 299 (300)
Q Consensus 246 ~VRk~vVdyL~~n~d~F~~fV~----~~~eeYl~-kMsk~GtWGg~IELqAlAdly~Vt 299 (300)
.+|..+..||+.|++.|++|+. .++++||. .+...+.-++|+.|.|||+.|+|+
T Consensus 141 flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~ 199 (244)
T PF10275_consen 141 FLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVP 199 (244)
T ss_dssp HHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--
T ss_pred HHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCe
Confidence 5777888999999999999997 68999997 478888899999999999999986
No 6
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.41 E-value=2.5e-07 Score=86.11 Aligned_cols=55 Identities=15% Similarity=0.349 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHhhChhhhcccCC--CCHHHHHHH-hhcCCccchHHHHHHHHHhcCCC
Q 022282 245 MFVRQQVVNQLKAHPEIYEGYVP--MAYSDYLKK-MNKSGEWGDHVTLQAAADSVWAT 299 (300)
Q Consensus 245 ~~VRk~vVdyL~~n~d~F~~fV~--~~~eeYl~k-Msk~GtWGg~IELqAlAdly~Vt 299 (300)
+.+|..+-.+|++|+++|++||+ ++...||.. +.-...-.|||+|-||++.+++.
T Consensus 157 ~ylRLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~ 214 (256)
T KOG3991|consen 157 MYLRLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIR 214 (256)
T ss_pred HHHHHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCce
Confidence 45777888899999999999997 589999996 44446679999999999999874
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.00 E-value=1.7e-06 Score=82.77 Aligned_cols=88 Identities=17% Similarity=0.147 Sum_probs=69.0
Q ss_pred HhhcCcEEEEecCCCchhHHHHHHHHhcC-----chhHHHHHHHHHHHHhhChhhhcccCC-------CCHHHHHHHhhc
Q 022282 212 LQLYDLVENKVQGDGNCQFRSLSDQLYRS-----PEHHMFVRQQVVNQLKAHPEIYEGYVP-------MAYSDYLKKMNK 279 (300)
Q Consensus 212 L~~~GL~i~~V~GDGNCLFRALSdQL~g~-----q~~H~~VRk~vVdyL~~n~d~F~~fV~-------~~~eeYl~kMsk 279 (300)
+...+|+-..+.|||+|+|-+||+||--. -+.-+..|-.=..|..++...|.+|.- ..|++|++.|..
T Consensus 166 ~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~t~~m~~~dt~~ne~~~ 245 (306)
T COG5539 166 AYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEETLAMVLWDTYVNEVLF 245 (306)
T ss_pred HHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchhhhhcchHHHHHhhhcc
Confidence 34456666779999999999999999532 122455565556666777777877641 379999999999
Q ss_pred CCccchHHHHHHHHHhcCCC
Q 022282 280 SGEWGDHVTLQAAADSVWAT 299 (300)
Q Consensus 280 ~GtWGg~IELqAlAdly~Vt 299 (300)
+..||..+|++|||.+|+++
T Consensus 246 ~a~~g~~~ei~qLas~lk~~ 265 (306)
T COG5539 246 DASDGITIEIQQLASLLKNP 265 (306)
T ss_pred cccccchHHHHHHHHHhcCc
Confidence 99999999999999999986
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=7.8e-05 Score=71.54 Aligned_cols=74 Identities=15% Similarity=0.216 Sum_probs=67.3
Q ss_pred CCCchhHHHHHHHHhcCchhHHHHHHHHHHHHhhChhhhcccCC-CCHHHHHHHhhcCCccc-hHHHHHHHHHhcCCC
Q 022282 224 GDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVP-MAYSDYLKKMNKSGEWG-DHVTLQAAADSVWAT 299 (300)
Q Consensus 224 GDGNCLFRALSdQL~g~q~~H~~VRk~vVdyL~~n~d~F~~fV~-~~~eeYl~kMsk~GtWG-g~IELqAlAdly~Vt 299 (300)
.|..|+|+|.+.-++.- .-.++|..+...+.+||+.|...+. -+--.|+.++.+.-.|| |+|||.++++.|++.
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~ 194 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVR 194 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEecccccee
Confidence 57999999999999763 5689999999999999999999875 58899999999999999 999999999999863
No 9
>PRK09784 hypothetical protein; Provisional
Probab=53.49 E-value=7.4 Score=37.86 Aligned_cols=24 Identities=33% Similarity=0.564 Sum_probs=21.2
Q ss_pred HHhhcCcEEEEecCCCchhHHHHH
Q 022282 211 RLQLYDLVENKVQGDGNCQFRSLS 234 (300)
Q Consensus 211 rL~~~GL~i~~V~GDGNCLFRALS 234 (300)
.=+.+||+-..|-|||-||.||+-
T Consensus 194 ~n~~~glkyapvdgdgycllrail 217 (417)
T PRK09784 194 INKTYGLKYAPVDGDGYCLLRAIL 217 (417)
T ss_pred hhhhhCceecccCCCchhHHHHHH
Confidence 346899999999999999999974
No 10
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=38.90 E-value=31 Score=27.92 Aligned_cols=46 Identities=17% Similarity=0.250 Sum_probs=36.2
Q ss_pred hcCcEEEEecCCCchhHH-HHHHHHhcC--chhHHHHHHHHHHHHhhCh
Q 022282 214 LYDLVENKVQGDGNCQFR-SLSDQLYRS--PEHHMFVRQQVVNQLKAHP 259 (300)
Q Consensus 214 ~~GL~i~~V~GDGNCLFR-ALSdQL~g~--q~~H~~VRk~vVdyL~~n~ 259 (300)
.+.|....|.|||+=+|- +|++.+-|- -..|+.|-.-+.+||.+|.
T Consensus 13 ~L~~e~v~V~Gdg~Hf~vi~Vs~~F~g~srvkrqq~vYApL~~~i~~~~ 61 (80)
T COG5007 13 ALPLEEVEVEGDGSHFQVIAVSEEFAGKSRVKRQQLVYAPLMAYIADNE 61 (80)
T ss_pred cCCccEEEEecCCceEEEEEehHhhcCccHHHHHHHHHHHHHHHhhcCc
Confidence 577888999999988776 578887763 3578888888888988764
No 11
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 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 corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=29.51 E-value=36 Score=28.93 Aligned_cols=17 Identities=24% Similarity=0.728 Sum_probs=14.8
Q ss_pred cCCCchhHHHHHHHHhc
Q 022282 223 QGDGNCQFRSLSDQLYR 239 (300)
Q Consensus 223 ~GDGNCLFRALSdQL~g 239 (300)
|+||+|-+|.||..+.+
T Consensus 5 P~DG~CG~H~i~aI~n~ 21 (108)
T PF05412_consen 5 PGDGSCGWHCIAAIMNH 21 (108)
T ss_pred CCCCchHHHHHHHHHHH
Confidence 78999999999987763
No 12
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 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 correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=27.82 E-value=54 Score=27.40 Aligned_cols=59 Identities=20% Similarity=0.322 Sum_probs=37.1
Q ss_pred ecCCCchhHHHHHHHHhcCchhHHHHHHHHHHHHhhChhhhcccCCCCHHHHHHHh--hcCCccchHHHHHHHHHhcCC
Q 022282 222 VQGDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKKM--NKSGEWGDHVTLQAAADSVWA 298 (300)
Q Consensus 222 V~GDGNCLFRALSdQL~g~q~~H~~VRk~vVdyL~~n~d~F~~fV~~~~eeYl~kM--sk~GtWGg~IELqAlAdly~V 298 (300)
+..|.|||.-|||.+|.-+-+- |. .-|..|... ...|+..+ +++.+|-|-+ .+|+.++|
T Consensus 3 ~sR~NNCLVVAis~~L~~T~e~---l~----~~M~An~~~--------i~~y~~W~r~~~~STW~DC~---mFA~~LkV 63 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVTLEK---LD----NLMQANVST--------IKKYHTWLRKKRPSTWDDCR---MFADALKV 63 (104)
T ss_pred ccCCCCeEeehHHHHhcchHHH---HH----HHHHhhHHH--------HHHHHHHHhcCCCCcHHHHH---HHHHhhee
Confidence 5679999999999999665322 11 223333333 66777754 4567887754 45666554
No 13
>KOG0256 consensus 1-aminocyclopropane-1-carboxylate synthase, and related proteins [Signal transduction mechanisms]
Probab=25.13 E-value=79 Score=32.83 Aligned_cols=56 Identities=13% Similarity=0.159 Sum_probs=38.7
Q ss_pred HHHHHHHhhcCcEEEEecCCCchhHHHHHHHHhcCchhHHHHHHHHHHHHhhC---hhhhcc
Q 022282 206 QRMLDRLQLYDLVENKVQGDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAH---PEIYEG 264 (300)
Q Consensus 206 ~rL~erL~~~GL~i~~V~GDGNCLFRALSdQL~g~q~~H~~VRk~vVdyL~~n---~d~F~~ 264 (300)
..+..+|++ .-.......||+|.|+.||- |.+=.-+..+|++++++|... +..|.+
T Consensus 88 DL~~~wl~k-~~~~~~~~~eg~~~f~~la~--fqdy~Gl~~frqa~A~Fm~~~r~~~v~fdP 146 (471)
T KOG0256|consen 88 DLIESWLSK-NPEASNCTREGQSSFDELAM--FQDYHGLPSFRQAVAEFMERARGNRVKFDP 146 (471)
T ss_pred HHHHHHHHh-ChhhhhcccccccchhhHhh--cccccCchHHHHHHHHHHHHHhCCCCccCc
Confidence 445567776 33344567899999999863 444445789999999988665 555554
No 14
>smart00718 DM4_12 DM4/DM12 family of domains in Drosophila melanogaster proteins of unknown function.
Probab=23.17 E-value=1.3e+02 Score=24.35 Aligned_cols=72 Identities=15% Similarity=0.301 Sum_probs=40.9
Q ss_pred HHHHHHHHHhhcCcEEEEecCCC-chhHHHHHHHHhcCchhHHHHHHHHHHHHhhChhhhcccCCCCHHHHHHHhhcCCc
Q 022282 204 DHQRMLDRLQLYDLVENKVQGDG-NCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKKMNKSGE 282 (300)
Q Consensus 204 d~~rL~erL~~~GL~i~~V~GDG-NCLFRALSdQL~g~q~~H~~VRk~vVdyL~~n~d~F~~fV~~~~eeYl~kMsk~Gt 282 (300)
=++.|.+.|..+|+ || .|+.|||-+.-.. ...|.-|=..++..|-+=++.-+. .--.+|.+.++ .|.
T Consensus 9 lY~~lE~~l~~~G~-------~g~~ClLR~ICE~a~~-~~~~~Gll~ell~ilftps~~~~~---~~~~~Y~~A~~-~G~ 76 (95)
T smart00718 9 LYEALENLLDQLGF-------NGRACLLRAICESAQK-LDDHRGLLGELLRIVLTPPDELEE---VLDPDYREAYR-AGR 76 (95)
T ss_pred HHHHHHHHHHHcCC-------CchhhHHHHHHHcccc-cccccchHHHHHHHhhcCCcchhh---hchHHHHHHHH-cCC
Confidence 35678888899996 77 9999999776543 223333555556655554411111 11345655443 344
Q ss_pred cchHH
Q 022282 283 WGDHV 287 (300)
Q Consensus 283 WGg~I 287 (300)
-|+++
T Consensus 77 ~g~dC 81 (95)
T smart00718 77 AGGDC 81 (95)
T ss_pred CCCCH
Confidence 45544
No 15
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=21.80 E-value=16 Score=36.67 Aligned_cols=82 Identities=13% Similarity=-0.059 Sum_probs=64.1
Q ss_pred hhcCcEEEEecCCCchhHHHHHHHHhcCchhHHHHHHHHHHHHhhChhhhcccCCCCHHHHHHHhhcCCccchHHHHHHH
Q 022282 213 QLYDLVENKVQGDGNCQFRSLSDQLYRSPEHHMFVRQQVVNQLKAHPEIYEGYVPMAYSDYLKKMNKSGEWGDHVTLQAA 292 (300)
Q Consensus 213 ~~~GL~i~~V~GDGNCLFRALSdQL~g~q~~H~~VRk~vVdyL~~n~d~F~~fV~~~~eeYl~kMsk~GtWGg~IELqAl 292 (300)
..++..+....-+++|.+|...+++...+.-+..-+.++|-|...+.+.|..=-+....-|...|...++|-+...++|+
T Consensus 51 ~~~~~~r~~~v~~~~~~~~~~~d~~~~~e~~e~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~ 130 (371)
T KOG2605|consen 51 DGYNNKRYGEVDRDFMIARGHQDEVLTVEDAEMAAICQSVLFKVLYQERFKLPSDTPCNGENSPMCSFHSRRGNESFQAA 130 (371)
T ss_pred ccccCccccchhhhhhhhcccccccccccHHHHhhHHhhhhhhhhhhhcccCCCCCcccccCCCCCcccccccccccccc
Confidence 45565666667799999999999999999999999999999999999988763333455566677777777777776665
Q ss_pred HH
Q 022282 293 AD 294 (300)
Q Consensus 293 Ad 294 (300)
+.
T Consensus 131 s~ 132 (371)
T KOG2605|consen 131 SF 132 (371)
T ss_pred cc
Confidence 53
No 16
>COG3081 Nucleoid-associated protein [General function prediction only]
Probab=20.38 E-value=1e+02 Score=30.44 Aligned_cols=36 Identities=17% Similarity=0.191 Sum_probs=26.0
Q ss_pred ecCCCchhHHHHHHHHhcC---chhHHHHHHHHHHHHhh
Q 022282 222 VQGDGNCQFRSLSDQLYRS---PEHHMFVRQQVVNQLKA 257 (300)
Q Consensus 222 V~GDGNCLFRALSdQL~g~---q~~H~~VRk~vVdyL~~ 257 (300)
-+.-.-||..||++..-.. .+..+.+|++|++|-..
T Consensus 194 ~~~qnr~LLqAvsDfca~a~l~keq~q~~kkqv~eYc~~ 232 (335)
T COG3081 194 AKAQNRGLLQAVSDFCAEADLDKEERQAVKKQVYEYCNE 232 (335)
T ss_pred cHHhhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHH
Confidence 5566789999999987542 45677888887666543
No 17
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=20.09 E-value=93 Score=26.25 Aligned_cols=24 Identities=25% Similarity=0.283 Sum_probs=21.0
Q ss_pred cccccchHHHHHHHHHHHHHHHHH
Q 022282 58 LAYVENDEVIAHVLQEEFSQVAAA 81 (300)
Q Consensus 58 ~~~v~~d~~ia~~~qee~s~~~~~ 81 (300)
-.-|+.|.-+-+.|+|||-+||-.
T Consensus 52 Gklvds~pe~e~eLk~el~rla~q 75 (105)
T KOG4634|consen 52 GKLVDSDPEYEQELKEELFRLAQQ 75 (105)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHH
Confidence 345999999999999999999873
Done!