Query 031210
Match_columns 164
No_of_seqs 137 out of 601
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 10:50:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031210hhsearch_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 1.1E-23 2.4E-28 180.5 6.6 88 67-164 157-249 (302)
2 PF02338 OTU: OTU-like cystein 99.7 5.4E-18 1.2E-22 125.2 6.0 68 75-163 1-70 (121)
3 KOG3288 OTU-like cysteine prot 99.6 3.4E-15 7.4E-20 126.9 4.9 82 67-164 108-189 (307)
4 KOG2605 OTU (ovarian tumor)-li 99.2 4.4E-12 9.6E-17 112.7 2.4 81 65-163 214-294 (371)
5 COG5539 Predicted cysteine pro 98.5 6.9E-09 1.5E-13 89.7 -1.7 89 67-164 169-260 (306)
6 COG5539 Predicted cysteine pro 98.2 3.1E-06 6.7E-11 73.4 5.8 73 73-164 116-189 (306)
7 PF10275 Peptidase_C65: Peptid 98.1 1.1E-05 2.5E-10 67.1 6.7 52 108-163 141-193 (244)
8 KOG3991 Uncharacterized conser 97.3 0.00018 4E-09 61.0 3.3 51 108-164 158-209 (256)
9 PRK09784 hypothetical protein; 66.6 4.3 9.4E-05 35.6 2.2 32 56-87 184-218 (417)
10 PF05412 Peptidase_C33: Equine 61.9 8.4 0.00018 29.3 2.7 20 75-94 5-24 (108)
11 PF05415 Peptidase_C36: Beet n 56.8 15 0.00031 27.5 3.2 18 74-91 3-20 (104)
12 KOG4100 Uncharacterized conser 31.0 87 0.0019 24.3 4.0 20 138-157 58-81 (125)
13 TIGR02934 nifT_nitrog probable 31.0 8.1 0.00018 27.0 -1.5 22 138-159 20-41 (67)
14 PF06988 NifT: NifT/FixU prote 28.5 13 0.00028 25.8 -0.9 15 146-160 28-42 (64)
15 COG3426 Butyrate kinase [Energ 23.6 41 0.00088 30.2 1.1 26 139-164 315-340 (358)
16 PF05952 ComX: Bacillus compet 21.3 46 0.00099 22.5 0.8 17 2-18 10-26 (57)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=1.1e-23 Score=180.54 Aligned_cols=88 Identities=24% Similarity=0.462 Sum_probs=76.4
Q ss_pred cCeEEEEecCCCchhhHHHHHHHHhhcCCCCCcchhhhhHHHHHHHHHHHHhhcccCchhhHHHhhh-----hcchhhHH
Q 031210 67 ERYLVQRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALIS-----ITIDESLK 141 (164)
Q Consensus 67 ~gL~i~eIpgDGnCLFRAIadQL~~~~G~~~~~~~~~~~~~~LR~~vad~I~~~~~~~~d~~e~fi~-----~~~ee~fd 141 (164)
.+|.+++||+||||||+||+|||....+..+ +++.||...|+||+ +|.++|++||.. ...+++|+
T Consensus 157 ~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~-------~v~kLR~~~a~Ymr---~H~~df~pf~~~eet~d~~~~~~f~ 226 (302)
T KOG2606|consen 157 RGLKMFDIPADGHCLYAAISHQLKLRSGKLL-------SVQKLREETADYMR---EHVEDFLPFLLDEETGDSLGPEDFD 226 (302)
T ss_pred ccCccccCCCCchhhHHHHHHHHHhccCCCC-------cHHHHHHHHHHHHH---HHHHHhhhHhcCccccccCCHHHHH
Confidence 7999999999999999999999998766545 48899999999998 477778777764 12345899
Q ss_pred HHHHHhcCCCccccHHhHhhccC
Q 031210 142 RYCQRIGRSDFWGGESELLVSTC 164 (164)
Q Consensus 142 ~Yc~~m~~~~~WGGeiEL~ALS~ 164 (164)
+||++|++++.|||+|||.|||+
T Consensus 227 ~Yc~eI~~t~~WGgelEL~AlSh 249 (302)
T KOG2606|consen 227 KYCREIRNTAAWGGELELKALSH 249 (302)
T ss_pred HHHHHhhhhccccchHHHHHHHH
Confidence 99999999999999999999985
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=99.73 E-value=5.4e-18 Score=125.24 Aligned_cols=68 Identities=34% Similarity=0.667 Sum_probs=52.7
Q ss_pred cCCCchhhHHHHHHHHhhc-CCCCCcchhhhhHHHHHHHHHHHHh-hcccCchhhHHHhhhhcchhhHHHHHHHhcCCCc
Q 031210 75 TGDGRCLFRALVKGMALNK-GINLNSREEREDADDLRMAVKEVIC-DSGSERRQYEEALISITIDESLKRYCQRIGRSDF 152 (164)
Q Consensus 75 pgDGnCLFRAIadQL~~~~-G~~~~~~~~~~~~~~LR~~vad~I~-~~~~~~~d~~e~fi~~~~ee~fd~Yc~~m~~~~~ 152 (164)
|||||||||||++||...+ |. ...+.+||+.++++|. . +++.|.+++ +.+ +|+++++
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~-------~~~~~~lR~~~~~~l~~~---~~~~~~~~~-----~~~------~~~~~~~ 59 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGS-------EDNHQELRKAVVDYLRDK---NRDKFEEFL-----EGD------KMSKPGT 59 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSS-------TTTHHHHHHHHHHHHHTH---TTTHHHHHH-----HHH------HHTSTTS
T ss_pred CCCccHHHHHHHHHHHHhcCCC-------HHHHHHHHHHHHHHHHHh---ccchhhhhh-----hhh------hhccccc
Confidence 7999999999999999543 22 2468999999999997 4 344454444 222 9999999
Q ss_pred cccHHhHhhcc
Q 031210 153 WGGESELLVST 163 (164)
Q Consensus 153 WGGeiEL~ALS 163 (164)
|||++||+|||
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=99.55 E-value=3.4e-15 Score=126.86 Aligned_cols=82 Identities=26% Similarity=0.431 Sum_probs=69.1
Q ss_pred cCeEEEEecCCCchhhHHHHHHHHhhcCCCCCcchhhhhHHHHHHHHHHHHhhcccCchhhHHHhhhhcchhhHHHHHHH
Q 031210 67 ERYLVQRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITIDESLKRYCQR 146 (164)
Q Consensus 67 ~gL~i~eIpgDGnCLFRAIadQL~~~~G~~~~~~~~~~~~~~LR~~vad~I~~~~~~~~d~~e~fi~~~~ee~fd~Yc~~ 146 (164)
.-+..+-||.|++|||+||++.+....+. ...+||+.+++.+. .+++.|.+++ ++++-.+||+|
T Consensus 108 gvl~~~vvp~DNSCLF~ai~yv~~k~~~~---------~~~elR~iiA~~Va---snp~~yn~Ai----LgK~n~eYc~W 171 (307)
T KOG3288|consen 108 GVLSRRVVPDDNSCLFTAIAYVIFKQVSN---------RPYELREIIAQEVA---SNPDKYNDAI----LGKPNKEYCAW 171 (307)
T ss_pred ceeEEEeccCCcchhhhhhhhhhcCccCC---------CcHHHHHHHHHHHh---cChhhhhHHH----hCCCcHHHHHH
Confidence 34667788999999999999988853221 12589999999998 4778899998 58899999999
Q ss_pred hcCCCccccHHhHhhccC
Q 031210 147 IGRSDFWGGESELLVSTC 164 (164)
Q Consensus 147 m~~~~~WGGeiEL~ALS~ 164 (164)
|++...|||.|||.+||.
T Consensus 172 I~k~dsWGGaIElsILS~ 189 (307)
T KOG3288|consen 172 ILKMDSWGGAIELSILSD 189 (307)
T ss_pred HccccccCceEEeeeehh
Confidence 999999999999999984
No 4
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.21 E-value=4.4e-12 Score=112.69 Aligned_cols=81 Identities=25% Similarity=0.349 Sum_probs=67.9
Q ss_pred hhcCeEEEEecCCCchhhHHHHHHHHhhcCCCCCcchhhhhHHHHHHHHHHHHhhcccCchhhHHHhhhhcchhhHHHHH
Q 031210 65 KVERYLVQRVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITIDESLKRYC 144 (164)
Q Consensus 65 k~~gL~i~eIpgDGnCLFRAIadQL~~~~G~~~~~~~~~~~~~~LR~~vad~I~~~~~~~~d~~e~fi~~~~ee~fd~Yc 144 (164)
++.|+.+..|.+||+|+|||++||++.. .+.++..|+++++++. ..+++++-+ +.++|-+|+
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 4479999999999999999999999952 2357788999999994 344444444 478999999
Q ss_pred HHhcCCCccccHHhHhhcc
Q 031210 145 QRIGRSDFWGGESELLVST 163 (164)
Q Consensus 145 ~~m~~~~~WGGeiEL~ALS 163 (164)
++++..+.||.++|++|++
T Consensus 276 k~kr~~~~~gnhie~Qa~a 294 (371)
T KOG2605|consen 276 KRKRADGEPGNHIEQQAAA 294 (371)
T ss_pred cccccCCCCcchHHHhhhh
Confidence 9999999999999999987
No 5
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.55 E-value=6.9e-09 Score=89.67 Aligned_cols=89 Identities=8% Similarity=0.025 Sum_probs=58.9
Q ss_pred cCeEEEEecCCCchhhHHHHHHHHhhcC-CCCCcchhhhhHHHHHHHHHHHHhhcccCchhhHHHhhhhcc--hhhHHHH
Q 031210 67 ERYLVQRVTGDGRCLFRALVKGMALNKG-INLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITI--DESLKRY 143 (164)
Q Consensus 67 ~gL~i~eIpgDGnCLFRAIadQL~~~~G-~~~~~~~~~~~~~~LR~~vad~I~~~~~~~~d~~e~fi~~~~--ee~fd~Y 143 (164)
..+.-.+++|||+|+|.+|+|||....- ..++ ....+|-.-..|.. .+...|..+..+... -.+|++|
T Consensus 169 ~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~------~~~~dr~~~~~~~q---~~~i~f~g~hfD~~t~~m~~~dt~ 239 (306)
T COG5539 169 TWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVD------KDSEDRYNSHPYVQ---RISILFTGIHFDEETLAMVLWDTY 239 (306)
T ss_pred HhhhccccCCCceEEEeEeccccceeeeeeecc------hhHHhhccCChhhh---hhhhhhcccccchhhhhcchHHHH
Confidence 3555568899999999999999996421 1121 12345554444443 123334333321111 2479999
Q ss_pred HHHhcCCCccccHHhHhhccC
Q 031210 144 CQRIGRSDFWGGESELLVSTC 164 (164)
Q Consensus 144 c~~m~~~~~WGGeiEL~ALS~ 164 (164)
|+.|+.++.||+.+|+++||+
T Consensus 240 ~ne~~~~a~~g~~~ei~qLas 260 (306)
T COG5539 240 VNEVLFDASDGITIEIQQLAS 260 (306)
T ss_pred HhhhcccccccchHHHHHHHH
Confidence 999999999999999999985
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.18 E-value=3.1e-06 Score=73.43 Aligned_cols=73 Identities=21% Similarity=0.232 Sum_probs=60.8
Q ss_pred EecCCCchhhHHHHHHHHhhcCCCCCcchhhhhHHHHHHHHHHHHhhcccCchhhHHHhhhhcchhhHHHHHHHhcCCCc
Q 031210 73 RVTGDGRCLFRALVKGMALNKGINLNSREEREDADDLRMAVKEVICDSGSERRQYEEALISITIDESLKRYCQRIGRSDF 152 (164)
Q Consensus 73 eIpgDGnCLFRAIadQL~~~~G~~~~~~~~~~~~~~LR~~vad~I~~~~~~~~d~~e~fi~~~~ee~fd~Yc~~m~~~~~ 152 (164)
....|..|+|++....++- ....+||..|+-.+.. +++.|.++. .+.+--.||.||.++..
T Consensus 116 p~~~d~srl~q~~~~~l~~------------asv~~lrE~vs~Ev~s---nPDl~n~~i----~~~~~i~y~~~i~k~d~ 176 (306)
T COG5539 116 PGQDDNSRLFQAERYSLRD------------ASVAKLREVVSLEVLS---NPDLYNPAI----LEIDVIAYATWIVKPDS 176 (306)
T ss_pred CCCCchHHHHHHHHhhhhh------------hhHHHHHHHHHHHHhh---Cccccchhh----cCcchHHHHHhhhcccc
Confidence 3348899999999998773 1467999999988874 666777776 46678899999999999
Q ss_pred cc-cHHhHhhccC
Q 031210 153 WG-GESELLVSTC 164 (164)
Q Consensus 153 WG-GeiEL~ALS~ 164 (164)
|| |.+|+.+||.
T Consensus 177 ~~dG~ieia~iS~ 189 (306)
T COG5539 177 QGDGCIEIAIISD 189 (306)
T ss_pred CCCceEEEeEecc
Confidence 99 9999999984
No 7
>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=98.05 E-value=1.1e-05 Score=67.05 Aligned_cols=52 Identities=12% Similarity=0.130 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhcccCchhhHHHhhhhcchhhHHHHH-HHhcCCCccccHHhHhhcc
Q 031210 108 DLRMAVKEVICDSGSERRQYEEALISITIDESLKRYC-QRIGRSDFWGGESELLVST 163 (164)
Q Consensus 108 ~LR~~vad~I~~~~~~~~d~~e~fi~~~~ee~fd~Yc-~~m~~~~~WGGeiEL~ALS 163 (164)
.||..++.||+ .+.+++++|+......++++|| +.+.-.+.=.+++.+.||+
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 45667777776 3444445554211127899999 5666777788999999997
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.32 E-value=0.00018 Score=60.95 Aligned_cols=51 Identities=12% Similarity=0.152 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhcccCchhhHHHhhhhcchhhHHHHHHHhcCC-CccccHHhHhhccC
Q 031210 108 DLRMAVKEVICDSGSERRQYEEALISITIDESLKRYCQRIGRS-DFWGGESELLVSTC 164 (164)
Q Consensus 108 ~LR~~vad~I~~~~~~~~d~~e~fi~~~~ee~fd~Yc~~m~~~-~~WGGeiEL~ALS~ 164 (164)
.||-.++-+|+ .+.+++++||. -+.+.++||..=-.| ..=-|+|+|-|||.
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 45666777775 56677788862 246899999986666 34468999999974
No 9
>PRK09784 hypothetical protein; Provisional
Probab=66.60 E-value=4.3 Score=35.64 Aligned_cols=32 Identities=38% Similarity=0.514 Sum_probs=24.4
Q ss_pred CCCCchhhh---hhcCeEEEEecCCCchhhHHHHH
Q 031210 56 LGGGSPVMK---KVERYLVQRVTGDGRCLFRALVK 87 (164)
Q Consensus 56 ~~~~~~~~~---k~~gL~i~eIpgDGnCLFRAIad 87 (164)
|+|-+=+.. |-.||+--+|.|||-||.|||.-
T Consensus 184 lsgisfiqse~n~~~glkyapvdgdgycllrailv 218 (417)
T PRK09784 184 LSGISFIQSEINKTYGLKYAPVDGDGYCLLRAILV 218 (417)
T ss_pred cccchhhHhhhhhhhCceecccCCCchhHHHHHHH
Confidence 455444433 44899999999999999999864
No 10
>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=61.92 E-value=8.4 Score=29.26 Aligned_cols=20 Identities=30% Similarity=0.546 Sum_probs=16.9
Q ss_pred cCCCchhhHHHHHHHHhhcC
Q 031210 75 TGDGRCLFRALVKGMALNKG 94 (164)
Q Consensus 75 pgDGnCLFRAIadQL~~~~G 94 (164)
|+||+|=++.|+.-+.+-.|
T Consensus 5 P~DG~CG~H~i~aI~n~m~~ 24 (108)
T PF05412_consen 5 PGDGSCGWHCIAAIMNHMMG 24 (108)
T ss_pred CCCCchHHHHHHHHHHHhhc
Confidence 89999999999998886444
No 11
>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=56.85 E-value=15 Score=27.45 Aligned_cols=18 Identities=17% Similarity=0.422 Sum_probs=15.1
Q ss_pred ecCCCchhhHHHHHHHHh
Q 031210 74 VTGDGRCLFRALVKGMAL 91 (164)
Q Consensus 74 IpgDGnCLFRAIadQL~~ 91 (164)
+.-|+|||.-||+..|..
T Consensus 3 ~sR~NNCLVVAis~~L~~ 20 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGV 20 (104)
T ss_pred ccCCCCeEeehHHHHhcc
Confidence 456899999999998873
No 12
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.04 E-value=87 Score=24.27 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=15.7
Q ss_pred hhHHHHHHHhcC----CCccccHH
Q 031210 138 ESLKRYCQRIGR----SDFWGGES 157 (164)
Q Consensus 138 e~fd~Yc~~m~~----~~~WGGei 157 (164)
.+|+.||.-+.+ .+.|-|++
T Consensus 58 teW~~Ya~~l~qql~~~g~~K~~~ 81 (125)
T KOG4100|consen 58 TEWERYAVALSQQLSSAGKWKGEI 81 (125)
T ss_pred HHHHHHHHHHHHHhhhcCcccccc
Confidence 469999998887 57887764
No 13
>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=31.00 E-value=8.1 Score=26.99 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=16.7
Q ss_pred hhHHHHHHHhcCCCccccHHhH
Q 031210 138 ESLKRYCQRIGRSDFWGGESEL 159 (164)
Q Consensus 138 e~fd~Yc~~m~~~~~WGGeiEL 159 (164)
.+.|+=+-.|++++.|||.+.|
T Consensus 20 KDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 20 KDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred CcchhheeeeecCccccCEEEE
Confidence 4566666677899999998765
No 14
>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=28.53 E-value=13 Score=25.80 Aligned_cols=15 Identities=33% Similarity=0.933 Sum_probs=10.9
Q ss_pred HhcCCCccccHHhHh
Q 031210 146 RIGRSDFWGGESELL 160 (164)
Q Consensus 146 ~m~~~~~WGGeiEL~ 160 (164)
.|++++.|||.+.|.
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 456899999998763
No 15
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=23.55 E-value=41 Score=30.20 Aligned_cols=26 Identities=19% Similarity=0.183 Sum_probs=22.9
Q ss_pred hHHHHHHHhcCCCccccHHhHhhccC
Q 031210 139 SLKRYCQRIGRSDFWGGESELLVSTC 164 (164)
Q Consensus 139 ~fd~Yc~~m~~~~~WGGeiEL~ALS~ 164 (164)
-..+|+.||..--.+.|+.||.||+.
T Consensus 315 ~I~~~v~~iapv~v~PGE~EleALA~ 340 (358)
T COG3426 315 AIEDRVSWIAPVIVYPGEDELEALAE 340 (358)
T ss_pred HHHHHHhhhcceEecCCchHHHHHHh
Confidence 46789999999999999999999973
No 16
>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=21.28 E-value=46 Score=22.50 Aligned_cols=17 Identities=29% Similarity=0.524 Sum_probs=14.3
Q ss_pred CChhhHHHHHhcCccee
Q 031210 2 INAEGILEQLRLGIAKF 18 (164)
Q Consensus 2 ~~~~~~~~~~~~~~~~~ 18 (164)
+.|+.++++|++|.|--
T Consensus 10 v~nPevl~kl~~g~asL 26 (57)
T PF05952_consen 10 VQNPEVLEKLKEGEASL 26 (57)
T ss_pred HHChHHHHHHHcCCeeE
Confidence 56889999999999754
Done!