Query 031037
Match_columns 167
No_of_seqs 131 out of 587
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:18:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031037.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031037hhsearch_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 99.9 1.8E-23 3.9E-28 179.9 6.5 97 61-167 145-249 (302)
2 PF02338 OTU: OTU-like cystein 99.7 1.1E-17 2.4E-22 124.0 5.2 68 78-166 1-70 (121)
3 KOG3288 OTU-like cysteine prot 99.5 1.1E-14 2.3E-19 124.3 4.9 79 72-166 110-188 (307)
4 KOG2605 OTU (ovarian tumor)-li 99.2 5.2E-12 1.1E-16 112.7 2.7 81 68-166 214-294 (371)
5 COG5539 Predicted cysteine pro 98.4 2.9E-08 6.2E-13 86.2 -1.3 88 71-167 170-260 (306)
6 PF10275 Peptidase_C65: Peptid 98.1 6.1E-06 1.3E-10 68.9 6.6 52 111-166 141-193 (244)
7 COG5539 Predicted cysteine pro 97.9 1.1E-05 2.4E-10 70.4 3.9 74 75-167 115-189 (306)
8 KOG3991 Uncharacterized conser 97.5 0.00015 3.3E-09 61.7 4.7 51 111-167 158-209 (256)
9 PRK09784 hypothetical protein; 62.4 5.7 0.00012 35.1 2.2 22 69-90 197-218 (417)
10 PF05415 Peptidase_C36: Beet n 55.6 14 0.00031 27.6 3.0 18 77-94 3-20 (104)
11 PF05412 Peptidase_C33: Equine 50.6 25 0.00053 26.9 3.6 22 78-99 5-26 (108)
12 KOG4100 Uncharacterized conser 43.8 32 0.00068 26.8 3.3 45 111-160 29-81 (125)
13 PF05952 ComX: Bacillus compet 25.9 44 0.00095 22.7 1.4 16 6-21 11-26 (57)
14 TIGR02934 nifT_nitrog probable 24.3 13 0.00029 26.0 -1.4 22 141-162 20-41 (67)
15 PF06988 NifT: NifT/FixU prote 21.8 19 0.00041 25.1 -1.0 15 149-163 28-42 (64)
16 cd08486 PBP2_CbnR The C-termin 21.4 3.4E+02 0.0074 20.0 7.5 105 6-116 38-143 (198)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.8e-23 Score=179.89 Aligned_cols=97 Identities=22% Similarity=0.418 Sum_probs=79.5
Q ss_pred CChhhhhhc---cCeEEEEecCCCchhhHHHHHhHHhccCCCCCcchhhhhHHHHHHHHHHHHHhhcccchhhHHHhhhc
Q 031037 61 GGSPVMKKV---ERYLVQRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISI 137 (167)
Q Consensus 61 ~~~~~~kk~---~gl~i~eIpgDGnCLFRAIadQL~~~~g~~~~~~~~~~~a~~LR~~vad~i~~~~~~~~~~~e~fi~~ 137 (167)
.+...+.++ ++|.++.||+||||||+||+|||..+.+..+ .+..||...++||+ ++.++|.++|..-
T Consensus 145 ~E~~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~-------~v~kLR~~~a~Ymr---~H~~df~pf~~~e 214 (302)
T KOG2606|consen 145 MEKEKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLL-------SVQKLREETADYMR---EHVEDFLPFLLDE 214 (302)
T ss_pred hHHHHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCC-------cHHHHHHHHHHHHH---HHHHHhhhHhcCc
Confidence 455555555 6999999999999999999999998765545 48899999999997 4566777776531
Q ss_pred -----cccchHHHHHHHhcCCCccccHHHHhhccC
Q 031037 138 -----TIDESLKRYCQRIGRSDFWGGESELLVSTC 167 (167)
Q Consensus 138 -----~~e~~fd~Yc~~m~~~~~WGGeiEL~ALS~ 167 (167)
..+++|++||++|++++.|||+|||.|||+
T Consensus 215 et~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlSh 249 (302)
T KOG2606|consen 215 ETGDSLGPEDFDKYCREIRNTAAWGGELELKALSH 249 (302)
T ss_pred cccccCCHHHHHHHHHHhhhhccccchHHHHHHHH
Confidence 123579999999999999999999999985
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=99.71 E-value=1.1e-17 Score=123.99 Aligned_cols=68 Identities=34% Similarity=0.648 Sum_probs=51.8
Q ss_pred cCCCchhhHHHHHhHHhcc-CCCCCcchhhhhHHHHHHHHHHHHH-hhcccchhhHHHhhhccccchHHHHHHHhcCCCc
Q 031037 78 TGDGRCLFRALVKGMALNK-GINLNSREEREDADDLRMAVKEVIC-DSGSERRQYEEALISITIDESLKRYCQRIGRSDF 155 (167)
Q Consensus 78 pgDGnCLFRAIadQL~~~~-g~~~~~~~~~~~a~~LR~~vad~i~-~~~~~~~~~~e~fi~~~~e~~fd~Yc~~m~~~~~ 155 (167)
|||||||||||++||.... |.. ..+.+||+.++++|. . +++.|.+++. + . +|+++++
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~-------~~~~~lR~~~~~~l~~~---~~~~~~~~~~----~-~------~~~~~~~ 59 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSE-------DNHQELRKAVVDYLRDK---NRDKFEEFLE----G-D------KMSKPGT 59 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSST-------TTHHHHHHHHHHHHHTH---TTTHHHHHHH----H-H------HHTSTTS
T ss_pred CCCccHHHHHHHHHHHHhcCCCH-------HHHHHHHHHHHHHHHHh---ccchhhhhhh----h-h------hhccccc
Confidence 7999999999999999543 222 358999999999996 2 3344444441 1 1 9999999
Q ss_pred cccHHHHhhcc
Q 031037 156 WGGESELLVST 166 (167)
Q Consensus 156 WGGeiEL~ALS 166 (167)
|||++||+|||
T Consensus 60 Wg~~~el~a~a 70 (121)
T PF02338_consen 60 WGGEIELQALA 70 (121)
T ss_dssp HEEHHHHHHHH
T ss_pred cCcHHHHHHHH
Confidence 99999999997
No 3
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.52 E-value=1.1e-14 Score=124.34 Aligned_cols=79 Identities=27% Similarity=0.472 Sum_probs=67.5
Q ss_pred eEEEEecCCCchhhHHHHHhHHhccCCCCCcchhhhhHHHHHHHHHHHHHhhcccchhhHHHhhhccccchHHHHHHHhc
Q 031037 72 YLVQRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITIDESLKRYCQRIG 151 (167)
Q Consensus 72 l~i~eIpgDGnCLFRAIadQL~~~~g~~~~~~~~~~~a~~LR~~vad~i~~~~~~~~~~~e~fi~~~~e~~fd~Yc~~m~ 151 (167)
+..+-||.|++|||+||+..+....+. ...+||..|+.-+. .+++.|.+++ ++++-.+||+||+
T Consensus 110 l~~~vvp~DNSCLF~ai~yv~~k~~~~---------~~~elR~iiA~~Va---snp~~yn~Ai----LgK~n~eYc~WI~ 173 (307)
T KOG3288|consen 110 LSRRVVPDDNSCLFTAIAYVIFKQVSN---------RPYELREIIAQEVA---SNPDKYNDAI----LGKPNKEYCAWIL 173 (307)
T ss_pred eEEEeccCCcchhhhhhhhhhcCccCC---------CcHHHHHHHHHHHh---cChhhhhHHH----hCCCcHHHHHHHc
Confidence 666778999999999999988753221 13599999999997 5677889998 5899999999999
Q ss_pred CCCccccHHHHhhcc
Q 031037 152 RSDFWGGESELLVST 166 (167)
Q Consensus 152 ~~~~WGGeiEL~ALS 166 (167)
+...|||.|||.+||
T Consensus 174 k~dsWGGaIElsILS 188 (307)
T KOG3288|consen 174 KMDSWGGAIELSILS 188 (307)
T ss_pred cccccCceEEeeeeh
Confidence 999999999999998
No 4
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.21 E-value=5.2e-12 Score=112.66 Aligned_cols=81 Identities=25% Similarity=0.349 Sum_probs=68.1
Q ss_pred hccCeEEEEecCCCchhhHHHHHhHHhccCCCCCcchhhhhHHHHHHHHHHHHHhhcccchhhHHHhhhccccchHHHHH
Q 031037 68 KVERYLVQRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITIDESLKRYC 147 (167)
Q Consensus 68 k~~gl~i~eIpgDGnCLFRAIadQL~~~~g~~~~~~~~~~~a~~LR~~vad~i~~~~~~~~~~~e~fi~~~~e~~fd~Yc 147 (167)
+..|+.+.+|.+||+|+|||++||++.. .+.++..|+++++++. ..+++++-+ +.++|-+|+
T Consensus 214 ~~~g~e~~Kv~edGsC~fra~aDQvy~d----------~e~~~~~~~~~~dq~~----~e~~~~~~~----vt~~~~~y~ 275 (371)
T KOG2605|consen 214 KHFGFEYKKVVEDGSCLFRALADQVYGD----------DEQHDHNRRECVDQLK----KERDFYEDY----VTEDFTSYI 275 (371)
T ss_pred HHhhhhhhhcccCCchhhhccHHHhhcC----------HHHHHHHHHHHHHHHh----hcccccccc----cccchhhcc
Confidence 3468999999999999999999999962 1347889999999983 455555555 478999999
Q ss_pred HHhcCCCccccHHHHhhcc
Q 031037 148 QRIGRSDFWGGESELLVST 166 (167)
Q Consensus 148 ~~m~~~~~WGGeiEL~ALS 166 (167)
+.++.++.||.++|++|++
T Consensus 276 k~kr~~~~~gnhie~Qa~a 294 (371)
T KOG2605|consen 276 KRKRADGEPGNHIEQQAAA 294 (371)
T ss_pred cccccCCCCcchHHHhhhh
Confidence 9999999999999999986
No 5
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.42 E-value=2.9e-08 Score=86.20 Aligned_cols=88 Identities=9% Similarity=0.035 Sum_probs=55.0
Q ss_pred CeEEEEecCCCchhhHHHHHhHHhccC-CCCCcchhhhhHHHHHHHHHHHHHhhcccchhhHHHhhhc-c-ccchHHHHH
Q 031037 71 RYLVQRVTGDGRCLFRALVKGMALNKG-INLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISI-T-IDESLKRYC 147 (167)
Q Consensus 71 gl~i~eIpgDGnCLFRAIadQL~~~~g-~~~~~~~~~~~a~~LR~~vad~i~~~~~~~~~~~e~fi~~-~-~e~~fd~Yc 147 (167)
.+.-.+++|||+|+|.+|++||....- ..++ ....+|-.-..|.. .+...|..+..+. + --.+|++||
T Consensus 170 ~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~------~~~~dr~~~~~~~q---~~~i~f~g~hfD~~t~~m~~~dt~~ 240 (306)
T COG5539 170 WIVKPDSQGDGCIEIAIISDQLPVRIHVVDVD------KDSEDRYNSHPYVQ---RISILFTGIHFDEETLAMVLWDTYV 240 (306)
T ss_pred hhhccccCCCceEEEeEeccccceeeeeeecc------hhHHhhccCChhhh---hhhhhhcccccchhhhhcchHHHHH
Confidence 445568899999999999999986421 1121 12333322222221 1222333322210 0 124799999
Q ss_pred HHhcCCCccccHHHHhhccC
Q 031037 148 QRIGRSDFWGGESELLVSTC 167 (167)
Q Consensus 148 ~~m~~~~~WGGeiEL~ALS~ 167 (167)
+.|+.++.||+.||+++||.
T Consensus 241 ne~~~~a~~g~~~ei~qLas 260 (306)
T COG5539 241 NEVLFDASDGITIEIQQLAS 260 (306)
T ss_pred hhhcccccccchHHHHHHHH
Confidence 99999999999999999973
No 6
>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=98.13 E-value=6.1e-06 Score=68.94 Aligned_cols=52 Identities=12% Similarity=0.130 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhcccchhhHHHhhhccccchHHHHH-HHhcCCCccccHHHHhhcc
Q 031037 111 DLRMAVKEVICDSGSERRQYEEALISITIDESLKRYC-QRIGRSDFWGGESELLVST 166 (167)
Q Consensus 111 ~LR~~vad~i~~~~~~~~~~~e~fi~~~~e~~fd~Yc-~~m~~~~~WGGeiEL~ALS 166 (167)
.||..++.||+ .+.+++++|+......++++|| +.+.-.+.=.+|+.+.||+
T Consensus 141 flRLlts~~l~----~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa 193 (244)
T PF10275_consen 141 FLRLLTSAYLK----SNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALA 193 (244)
T ss_dssp HHHHHHHHHHH----HTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHH
T ss_pred HHHHHHHHHHH----hhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHH
Confidence 56666667775 3444445554211127899999 4566677788999999986
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=97.89 E-value=1.1e-05 Score=70.35 Aligned_cols=74 Identities=22% Similarity=0.232 Sum_probs=61.2
Q ss_pred EEecCCCchhhHHHHHhHHhccCCCCCcchhhhhHHHHHHHHHHHHHhhcccchhhHHHhhhccccchHHHHHHHhcCCC
Q 031037 75 QRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITIDESLKRYCQRIGRSD 154 (167)
Q Consensus 75 ~eIpgDGnCLFRAIadQL~~~~g~~~~~~~~~~~a~~LR~~vad~i~~~~~~~~~~~e~fi~~~~e~~fd~Yc~~m~~~~ 154 (167)
.....|.+|+|+++...+.. ....+||.+|+.-+. ++++.|.++. .+.+--.||.||.+..
T Consensus 115 ~p~~~d~srl~q~~~~~l~~------------asv~~lrE~vs~Ev~---snPDl~n~~i----~~~~~i~y~~~i~k~d 175 (306)
T COG5539 115 MPGQDDNSRLFQAERYSLRD------------ASVAKLREVVSLEVL---SNPDLYNPAI----LEIDVIAYATWIVKPD 175 (306)
T ss_pred CCCCCchHHHHHHHHhhhhh------------hhHHHHHHHHHHHHh---hCccccchhh----cCcchHHHHHhhhccc
Confidence 34458899999999997773 147899999998887 4566777766 4678889999999999
Q ss_pred ccc-cHHHHhhccC
Q 031037 155 FWG-GESELLVSTC 167 (167)
Q Consensus 155 ~WG-GeiEL~ALS~ 167 (167)
.|| |.+|+.+||.
T Consensus 176 ~~~dG~ieia~iS~ 189 (306)
T COG5539 176 SQGDGCIEIAIISD 189 (306)
T ss_pred cCCCceEEEeEecc
Confidence 999 9999999984
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.48 E-value=0.00015 Score=61.66 Aligned_cols=51 Identities=12% Similarity=0.152 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHhhcccchhhHHHhhhccccchHHHHHHHhcCC-CccccHHHHhhccC
Q 031037 111 DLRMAVKEVICDSGSERRQYEEALISITIDESLKRYCQRIGRS-DFWGGESELLVSTC 167 (167)
Q Consensus 111 ~LR~~vad~i~~~~~~~~~~~e~fi~~~~e~~fd~Yc~~m~~~-~~WGGeiEL~ALS~ 167 (167)
.||-.++-+|+ ++.+++++||. -+.+.++||.+=-.| ..=-|+|+|.|||.
T Consensus 158 ylRLvtS~~ik----~~adfy~pFI~--e~~tV~~fC~~eVEPm~kesdhi~I~ALs~ 209 (256)
T KOG3991|consen 158 YLRLVTSGFIK----SNADFYQPFID--EGMTVKAFCTQEVEPMYKESDHIHITALSQ 209 (256)
T ss_pred HHHHHHHHHHh----hChhhhhccCC--CCCcHHHHHHhhcchhhhccCceeHHHHHh
Confidence 45666666664 67788888873 347999999987666 23468999999984
No 9
>PRK09784 hypothetical protein; Provisional
Probab=62.43 E-value=5.7 Score=35.05 Aligned_cols=22 Identities=36% Similarity=0.591 Sum_probs=19.3
Q ss_pred ccCeEEEEecCCCchhhHHHHH
Q 031037 69 VERYLVQRVTGDGRCLFRALVK 90 (167)
Q Consensus 69 ~~gl~i~eIpgDGnCLFRAIad 90 (167)
-.||+--.|.|||-||.|||.-
T Consensus 197 ~~glkyapvdgdgycllrailv 218 (417)
T PRK09784 197 TYGLKYAPVDGDGYCLLRAILV 218 (417)
T ss_pred hhCceecccCCCchhHHHHHHH
Confidence 3689999999999999999964
No 10
>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=55.56 E-value=14 Score=27.60 Aligned_cols=18 Identities=17% Similarity=0.422 Sum_probs=15.2
Q ss_pred ecCCCchhhHHHHHhHHh
Q 031037 77 VTGDGRCLFRALVKGMAL 94 (167)
Q Consensus 77 IpgDGnCLFRAIadQL~~ 94 (167)
|.-|+|||.-||+..|..
T Consensus 3 ~sR~NNCLVVAis~~L~~ 20 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGV 20 (104)
T ss_pred ccCCCCeEeehHHHHhcc
Confidence 467999999999998873
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=50.58 E-value=25 Score=26.88 Aligned_cols=22 Identities=27% Similarity=0.442 Sum_probs=17.6
Q ss_pred cCCCchhhHHHHHhHHhccCCC
Q 031037 78 TGDGRCLFRALVKGMALNKGIN 99 (167)
Q Consensus 78 pgDGnCLFRAIadQL~~~~g~~ 99 (167)
|+||+|=++.|+.-|.+..|..
T Consensus 5 P~DG~CG~H~i~aI~n~m~~~~ 26 (108)
T PF05412_consen 5 PGDGSCGWHCIAAIMNHMMGGE 26 (108)
T ss_pred CCCCchHHHHHHHHHHHhhccC
Confidence 8999999999998777644433
No 12
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.80 E-value=32 Score=26.78 Aligned_cols=45 Identities=18% Similarity=0.389 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhhcccchhh----HHHhhhccccchHHHHHHHhcC----CCccccHH
Q 031037 111 DLRMAVKEVICDSGSERRQY----EEALISITIDESLKRYCQRIGR----SDFWGGES 160 (167)
Q Consensus 111 ~LR~~vad~i~~~~~~~~~~----~e~fi~~~~e~~fd~Yc~~m~~----~~~WGGei 160 (167)
++|..=.+|+.+....|.+- ...|+ .+|+.||.-|.+ .+.|-|++
T Consensus 29 ~~R~lGD~YVkdEFrrHk~vnp~~~~~Fl-----teW~~Ya~~l~qql~~~g~~K~~~ 81 (125)
T KOG4100|consen 29 ELRALGDQYVKDEFRRHKTVNPLEAQGFL-----TEWERYAVALSQQLSSAGKWKGEI 81 (125)
T ss_pred HHHHHHHHHHHHHHHHhccCChHHHHHHH-----HHHHHHHHHHHHHhhhcCcccccc
Confidence 77877777776544344333 22332 469999998876 57887764
No 13
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=25.94 E-value=44 Score=22.69 Aligned_cols=16 Identities=31% Similarity=0.490 Sum_probs=13.6
Q ss_pred CchhHHHHhhccceeE
Q 031037 6 PTEGILEQLRLGIAKF 21 (167)
Q Consensus 6 ~~~~~~~~~~~~~~~~ 21 (167)
.|..+|++|++|.|-.
T Consensus 11 ~nPevl~kl~~g~asL 26 (57)
T PF05952_consen 11 QNPEVLEKLKEGEASL 26 (57)
T ss_pred HChHHHHHHHcCCeeE
Confidence 3778999999999975
No 14
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=24.31 E-value=13 Score=26.03 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=16.3
Q ss_pred chHHHHHHHhcCCCccccHHHH
Q 031037 141 ESLKRYCQRIGRSDFWGGESEL 162 (167)
Q Consensus 141 ~~fd~Yc~~m~~~~~WGGeiEL 162 (167)
.+.++=+-.|.+++.|||.+.|
T Consensus 20 KDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 20 KDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred CcchhheeeeecCccccCEEEE
Confidence 4555666667799999998765
No 15
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=21.75 E-value=19 Score=25.05 Aligned_cols=15 Identities=33% Similarity=0.933 Sum_probs=10.6
Q ss_pred HhcCCCccccHHHHh
Q 031037 149 RIGRSDFWGGESELL 163 (167)
Q Consensus 149 ~m~~~~~WGGeiEL~ 163 (167)
.|.+++.|||.+.|.
T Consensus 28 ~~E~~~~wGG~v~L~ 42 (64)
T PF06988_consen 28 SMEKPELWGGEVTLA 42 (64)
T ss_dssp EESSSSS-SSEEEET
T ss_pred eeeccCccCCEEEEC
Confidence 455899999988763
No 16
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=21.42 E-value=3.4e+02 Score=19.95 Aligned_cols=105 Identities=14% Similarity=0.084 Sum_probs=51.1
Q ss_pred CchhHHHHhhccceeEEEecCCCCCCCCCCCCCCCCcccCCCCCceeeeccCCCC-CChhhhhhccCeEEEEecCCCchh
Q 031037 6 PTEGILEQLRLGIAKFELVSSPVASISNPNSQTCPTAFHRDSNHLFFARIGPPLG-GGSPVMKKVERYLVQRVTGDGRCL 84 (167)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ar~~~~~~-~~~~~~kk~~gl~i~eIpgDGnCL 84 (167)
.+..++++|++|.+.+=|+..|.. .++. .-..++. -...++.+-+..+. ..+-.++.+.++.+.-.+...+|-
T Consensus 38 ~~~~l~~~l~~g~~D~~~~~~~~~---~~~~--~~~~l~~-~~~~lv~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~ 111 (198)
T cd08486 38 TKDEQVEGLLAGTIHVGFSRFFPR---HPGI--EIVNIAQ-EDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPS 111 (198)
T ss_pred CHHHHHHHHHcCCceEEEecCCCC---CCce--EEEEEee-ccEEEEecCCCccccCCcccHHHHcCCCeEeecCCcCch
Confidence 457899999999999988754321 1111 0111221 12223333333332 223334455666665554444565
Q ss_pred hHHHHHhHHhccCCCCCcchhhhhHHHHHHHH
Q 031037 85 FRALVKGMALNKGINLNSREEREDADDLRMAV 116 (167)
Q Consensus 85 FRAIadQL~~~~g~~~~~~~~~~~a~~LR~~v 116 (167)
++.....+....|...+...+-.+...++..|
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v 143 (198)
T cd08486 112 FADEVIGLFKHAGIEPRIARVVEDATAALALT 143 (198)
T ss_pred HHHHHHHHHHHcCCCcceEEEeccHHHHHHHH
Confidence 56555555544454443222223445555544
Done!