Query 030553
Match_columns 175
No_of_seqs 140 out of 448
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 15:29:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030553hhsearch_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 9.1E-26 2E-30 196.7 5.8 96 61-175 146-249 (302)
2 PF02338 OTU: OTU-like cystein 99.7 1E-17 2.2E-22 124.9 6.2 68 77-174 1-70 (121)
3 KOG3288 OTU-like cysteine prot 99.7 2.1E-17 4.5E-22 143.0 4.8 80 71-175 110-189 (307)
4 KOG2605 OTU (ovarian tumor)-li 98.9 2.3E-10 5.1E-15 103.4 1.5 81 67-174 214-294 (371)
5 COG5539 Predicted cysteine pro 98.7 1.3E-09 2.8E-14 95.9 -1.3 87 71-175 171-260 (306)
6 COG5539 Predicted cysteine pro 98.5 1.3E-07 2.8E-12 83.4 5.2 74 74-175 115-189 (306)
7 PF10275 Peptidase_C65: Peptid 97.7 3.5E-05 7.6E-10 64.9 4.2 53 118-174 140-193 (244)
8 KOG3991 Uncharacterized conser 97.4 9E-05 2E-09 64.0 2.7 53 117-175 156-209 (256)
9 PRK09784 hypothetical protein; 58.4 6.9 0.00015 35.1 2.0 32 58-89 184-218 (417)
10 PF05415 Peptidase_C36: Beet n 54.4 12 0.00027 28.5 2.5 17 76-92 3-19 (104)
11 PF03466 LysR_substrate: LysR 39.3 1.5E+02 0.0033 21.7 6.7 84 6-97 44-128 (209)
12 PF12091 DUF3567: Protein of u 32.1 1E+02 0.0023 23.0 4.4 36 117-162 47-82 (85)
13 PF05412 Peptidase_C33: Equine 29.5 51 0.0011 25.6 2.5 21 76-96 4-24 (108)
14 PF02330 MAM33: Mitochondrial 29.1 80 0.0017 25.8 3.8 47 113-160 153-199 (204)
15 cd08486 PBP2_CbnR The C-termin 28.3 2.5E+02 0.0055 20.9 8.8 88 5-98 38-126 (198)
16 PF06858 NOG1: Nucleolar GTP-b 24.5 1.1E+02 0.0024 21.1 3.3 29 64-93 9-37 (58)
17 TIGR02934 nifT_nitrog probable 23.8 15 0.00033 26.2 -1.2 22 149-170 20-41 (67)
18 KOG4100 Uncharacterized conser 22.7 2.2E+02 0.0048 22.6 4.9 44 119-168 29-81 (125)
19 PF06988 NifT: NifT/FixU prote 22.3 22 0.00047 25.2 -0.6 18 153-170 24-41 (64)
20 cd08463 PBP2_DntR_like_4 The C 21.8 3.5E+02 0.0076 20.3 7.2 86 5-97 38-124 (203)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=9.1e-26 Score=196.72 Aligned_cols=96 Identities=22% Similarity=0.451 Sum_probs=81.8
Q ss_pred Cchhhhhc---cCcEEEEeCCCCchhhHHHHHHHHhccCCCCCCccccccccCCcccchHHHHHHHHHHHHhhccCCchh
Q 030553 61 GSPAMKKV---ERYSVQRVTGDGRCLFRALVKGMALNKGITLNSRDEREDAAFPLFFTNADDLRMAVKEVICDSGSERRQ 137 (175)
Q Consensus 61 ~~~~~~k~---~gL~I~eIp~DG~CLFrAIadQL~~~~g~~~~~~~er~~~~~~~~~~~a~eLR~~vad~I~~~~~~r~~ 137 (175)
+....+++ ++|.+++||+||||||+||+|||..+++..++ +..||...|+||+ .|.++
T Consensus 146 E~~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~----------------v~kLR~~~a~Ymr---~H~~d 206 (302)
T KOG2606|consen 146 EKEKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLS----------------VQKLREETADYMR---EHVED 206 (302)
T ss_pred HHHHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCc----------------HHHHHHHHHHHHH---HHHHH
Confidence 34444444 69999999999999999999999998765443 8899999999998 58999
Q ss_pred hHHHHHhh-----hhhhhHHHHHHhhcCCCcccchHhHhhccC
Q 030553 138 YEEALIAI-----TIDESLKRYCQRIGRSDFWGGESELLVSTC 175 (175)
Q Consensus 138 f~efl~~~-----~~ee~fdeYC~~I~~t~~WGGeiEL~ALS~ 175 (175)
|.+|+... ...++|++||+.|++|+.|||+|||.|||+
T Consensus 207 f~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlSh 249 (302)
T KOG2606|consen 207 FLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSH 249 (302)
T ss_pred hhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHH
Confidence 99999742 224589999999999999999999999995
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=99.72 E-value=1e-17 Score=124.95 Aligned_cols=68 Identities=35% Similarity=0.662 Sum_probs=55.4
Q ss_pred CCCCchhhHHHHHHHHhccC-CCCCCccccccccCCcccchHHHHHHHHHHHHh-hccCCchhhHHHHHhhhhhhhHHHH
Q 030553 77 TGDGRCLFRALVKGMALNKG-ITLNSRDEREDAAFPLFFTNADDLRMAVKEVIC-DSGSERRQYEEALIAITIDESLKRY 154 (175)
Q Consensus 77 p~DG~CLFrAIadQL~~~~g-~~~~~~~er~~~~~~~~~~~a~eLR~~vad~I~-~~~~~r~~f~efl~~~~~ee~fdeY 154 (175)
|+|||||||||++||...++ .. . .+.+||+.+++||. . +++.|.+++. ++
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~-------~---------~~~~lR~~~~~~l~~~---~~~~~~~~~~----~~----- 52 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSE-------D---------NHQELRKAVVDYLRDK---NRDKFEEFLE----GD----- 52 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSST-------T---------THHHHHHHHHHHHHTH---TTTHHHHHHH----HH-----
T ss_pred CCCccHHHHHHHHHHHHhcCCCH-------H---------HHHHHHHHHHHHHHHh---ccchhhhhhh----hh-----
Confidence 79999999999999975432 11 1 28899999999997 4 7899999872 22
Q ss_pred HHhhcCCCcccchHhHhhcc
Q 030553 155 CQRIGRSDFWGGESELLVST 174 (175)
Q Consensus 155 C~~I~~t~~WGGeiEL~ALS 174 (175)
+|+++++|||++||+|||
T Consensus 53 --~~~~~~~Wg~~~el~a~a 70 (121)
T PF02338_consen 53 --KMSKPGTWGGEIELQALA 70 (121)
T ss_dssp --HHTSTTSHEEHHHHHHHH
T ss_pred --hhccccccCcHHHHHHHH
Confidence 999999999999999997
No 3
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.68 E-value=2.1e-17 Score=142.99 Aligned_cols=80 Identities=28% Similarity=0.471 Sum_probs=68.7
Q ss_pred cEEEEeCCCCchhhHHHHHHHHhccCCCCCCccccccccCCcccchHHHHHHHHHHHHhhccCCchhhHHHHHhhhhhhh
Q 030553 71 YSVQRVTGDGRCLFRALVKGMALNKGITLNSRDEREDAAFPLFFTNADDLRMAVKEVICDSGSERRQYEEALIAITIDES 150 (175)
Q Consensus 71 L~I~eIp~DG~CLFrAIadQL~~~~g~~~~~~~er~~~~~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~ee~ 150 (175)
+..+-||+|++|||+||++.|....+.. ..+||+++|..+. ++++.|.+++ ++++
T Consensus 110 l~~~vvp~DNSCLF~ai~yv~~k~~~~~------------------~~elR~iiA~~Va---snp~~yn~Ai----LgK~ 164 (307)
T KOG3288|consen 110 LSRRVVPDDNSCLFTAIAYVIFKQVSNR------------------PYELREIIAQEVA---SNPDKYNDAI----LGKP 164 (307)
T ss_pred eEEEeccCCcchhhhhhhhhhcCccCCC------------------cHHHHHHHHHHHh---cChhhhhHHH----hCCC
Confidence 6677899999999999999775321110 3599999999887 5899999998 7899
Q ss_pred HHHHHHhhcCCCcccchHhHhhccC
Q 030553 151 LKRYCQRIGRSDFWGGESELLVSTC 175 (175)
Q Consensus 151 fdeYC~~I~~t~~WGGeiEL~ALS~ 175 (175)
..+||.||++...|||.|||.+||.
T Consensus 165 n~eYc~WI~k~dsWGGaIElsILS~ 189 (307)
T KOG3288|consen 165 NKEYCAWILKMDSWGGAIELSILSD 189 (307)
T ss_pred cHHHHHHHccccccCceEEeeeehh
Confidence 9999999999999999999999984
No 4
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=2.3e-10 Score=103.41 Aligned_cols=81 Identities=28% Similarity=0.400 Sum_probs=70.2
Q ss_pred hccCcEEEEeCCCCchhhHHHHHHHHhccCCCCCCccccccccCCcccchHHHHHHHHHHHHhhccCCchhhHHHHHhhh
Q 030553 67 KVERYSVQRVTGDGRCLFRALVKGMALNKGITLNSRDEREDAAFPLFFTNADDLRMAVKEVICDSGSERRQYEEALIAIT 146 (175)
Q Consensus 67 k~~gL~I~eIp~DG~CLFrAIadQL~~~~g~~~~~~~er~~~~~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~ 146 (175)
++.|+.++.|..||+|+|||++||++.. .+ .++..|++++|++. .+++.|+.+
T Consensus 214 ~~~g~e~~Kv~edGsC~fra~aDQvy~d--------~e-----------~~~~~~~~~~dq~~---~e~~~~~~~----- 266 (371)
T KOG2605|consen 214 KHFGFEYKKVVEDGSCLFRALADQVYGD--------DE-----------QHDHNRRECVDQLK---KERDFYEDY----- 266 (371)
T ss_pred HHhhhhhhhcccCCchhhhccHHHhhcC--------HH-----------HHHHHHHHHHHHHh---hcccccccc-----
Confidence 3468999999999999999999999853 11 26799999999996 478888887
Q ss_pred hhhhHHHHHHhhcCCCcccchHhHhhcc
Q 030553 147 IDESLKRYCQRIGRSDFWGGESELLVST 174 (175)
Q Consensus 147 ~ee~fdeYC~~I~~t~~WGGeiEL~ALS 174 (175)
+.++|-+|.++++....||-++|++|++
T Consensus 267 vt~~~~~y~k~kr~~~~~gnhie~Qa~a 294 (371)
T KOG2605|consen 267 VTEDFTSYIKRKRADGEPGNHIEQQAAA 294 (371)
T ss_pred cccchhhcccccccCCCCcchHHHhhhh
Confidence 4688999999999999999999999986
No 5
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=1.3e-09 Score=95.88 Aligned_cols=87 Identities=8% Similarity=0.011 Sum_probs=62.6
Q ss_pred cEEEEeCCCCchhhHHHHHHHHhccC-CCCCCccccccccCCcccchHHHHHHHHHHHHhhccCCchhhHHHHHhhhh--
Q 030553 71 YSVQRVTGDGRCLFRALVKGMALNKG-ITLNSRDEREDAAFPLFFTNADDLRMAVKEVICDSGSERRQYEEALIAITI-- 147 (175)
Q Consensus 71 L~I~eIp~DG~CLFrAIadQL~~~~g-~~~~~~~er~~~~~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~-- 147 (175)
+.-.++++||+|+|.+|+|||..+.- ..++ ....+|-.-..|.. .+...|+.+..+...
T Consensus 171 i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~---------------~~~~dr~~~~~~~q---~~~i~f~g~hfD~~t~~ 232 (306)
T COG5539 171 IVKPDSQGDGCIEIAIISDQLPVRIHVVDVD---------------KDSEDRYNSHPYVQ---RISILFTGIHFDEETLA 232 (306)
T ss_pred hhccccCCCceEEEeEeccccceeeeeeecc---------------hhHHhhccCChhhh---hhhhhhcccccchhhhh
Confidence 34466899999999999999976521 1111 13466666666664 356777776543222
Q ss_pred hhhHHHHHHhhcCCCcccchHhHhhccC
Q 030553 148 DESLKRYCQRIGRSDFWGGESELLVSTC 175 (175)
Q Consensus 148 ee~fdeYC~~I~~t~~WGGeiEL~ALS~ 175 (175)
--+|++||+.|+.++.||+.||+++|++
T Consensus 233 m~~~dt~~ne~~~~a~~g~~~ei~qLas 260 (306)
T COG5539 233 MVLWDTYVNEVLFDASDGITIEIQQLAS 260 (306)
T ss_pred cchHHHHHhhhcccccccchHHHHHHHH
Confidence 2479999999999999999999999974
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=1.3e-07 Score=83.44 Aligned_cols=74 Identities=22% Similarity=0.233 Sum_probs=62.4
Q ss_pred EEeCCCCchhhHHHHHHHHhccCCCCCCccccccccCCcccchHHHHHHHHHHHHhhccCCchhhHHHHHhhhhhhhHHH
Q 030553 74 QRVTGDGRCLFRALVKGMALNKGITLNSRDEREDAAFPLFFTNADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKR 153 (175)
Q Consensus 74 ~eIp~DG~CLFrAIadQL~~~~g~~~~~~~er~~~~~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~ee~fde 153 (175)
....+|.+|+|+++.+.+... ...+||..|+--+. ++++.|.+++ .+.+--.
T Consensus 115 ~p~~~d~srl~q~~~~~l~~a---------------------sv~~lrE~vs~Ev~---snPDl~n~~i----~~~~~i~ 166 (306)
T COG5539 115 MPGQDDNSRLFQAERYSLRDA---------------------SVAKLREVVSLEVL---SNPDLYNPAI----LEIDVIA 166 (306)
T ss_pred CCCCCchHHHHHHHHhhhhhh---------------------hHHHHHHHHHHHHh---hCccccchhh----cCcchHH
Confidence 334489999999999965321 27899999998886 5899999998 6777889
Q ss_pred HHHhhcCCCccc-chHhHhhccC
Q 030553 154 YCQRIGRSDFWG-GESELLVSTC 175 (175)
Q Consensus 154 YC~~I~~t~~WG-GeiEL~ALS~ 175 (175)
||.||.+...|| |.+|+-+||.
T Consensus 167 y~~~i~k~d~~~dG~ieia~iS~ 189 (306)
T COG5539 167 YATWIVKPDSQGDGCIEIAIISD 189 (306)
T ss_pred HHHhhhccccCCCceEEEeEecc
Confidence 999999999999 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=97.72 E-value=3.5e-05 Score=64.95 Aligned_cols=53 Identities=11% Similarity=0.202 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhhccCCchhhHHHHHhhhhhhhHHHHH-HhhcCCCcccchHhHhhcc
Q 030553 118 DDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYC-QRIGRSDFWGGESELLVST 174 (175)
Q Consensus 118 ~eLR~~vad~I~~~~~~r~~f~efl~~~~~ee~fdeYC-~~I~~t~~WGGeiEL~ALS 174 (175)
-.||-.++.||+. |.+.|.+|+.+.. ..++++|| +.|...+.=.+++.+.||+
T Consensus 140 ~flRLlts~~l~~---~~d~y~~fi~~~~-~~tve~~C~~~Vep~~~Ead~v~i~ALa 193 (244)
T PF10275_consen 140 IFLRLLTSAYLKS---NSDEYEPFIDGLE-YLTVEEFCSQEVEPMGKEADHVQIIALA 193 (244)
T ss_dssp HHHHHHHHHHHHH---THHHHGGGSSTT---S-HHHHHHHHTSSTT--B-HHHHHHHH
T ss_pred HHHHHHHHHHHHh---hHHHHhhhhcccc-cCCHHHHHHhhcccccccchhHHHHHHH
Confidence 3678888889984 6788888862111 27899999 4566666777899999986
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.42 E-value=9e-05 Score=64.04 Aligned_cols=53 Identities=13% Similarity=0.112 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHhhccCCchhhHHHHHhhhhhhhHHHHHHhhcCC-CcccchHhHhhccC
Q 030553 117 ADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRIGRS-DFWGGESELLVSTC 175 (175)
Q Consensus 117 a~eLR~~vad~I~~~~~~r~~f~efl~~~~~ee~fdeYC~~I~~t-~~WGGeiEL~ALS~ 175 (175)
+..||-.++-+|+ .+.+.|.+|+ +-+.+.++||+.=-.| ..=-|+|+|-|||+
T Consensus 156 V~ylRLvtS~~ik---~~adfy~pFI---~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~ 209 (256)
T KOG3991|consen 156 VMYLRLVTSGFIK---SNADFYQPFI---DEGMTVKAFCTQEVEPMYKESDHIHITALSQ 209 (256)
T ss_pred HHHHHHHHHHHHh---hChhhhhccC---CCCCcHHHHHHhhcchhhhccCceeHHHHHh
Confidence 5678888999998 4678888886 2357899999864443 44567899999984
No 9
>PRK09784 hypothetical protein; Provisional
Probab=58.36 E-value=6.9 Score=35.14 Aligned_cols=32 Identities=34% Similarity=0.508 Sum_probs=24.6
Q ss_pred CCCCchhhhhc---cCcEEEEeCCCCchhhHHHHH
Q 030553 58 LGGGSPAMKKV---ERYSVQRVTGDGRCLFRALVK 89 (175)
Q Consensus 58 ~~~~~~~~~k~---~gL~I~eIp~DG~CLFrAIad 89 (175)
|+|-+=....+ .||+.-.|.+||-||.|||.-
T Consensus 184 lsgisfiqse~n~~~glkyapvdgdgycllrailv 218 (417)
T PRK09784 184 LSGISFIQSEINKTYGLKYAPVDGDGYCLLRAILV 218 (417)
T ss_pred cccchhhHhhhhhhhCceecccCCCchhHHHHHHH
Confidence 45655544433 699999999999999999965
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=54.35 E-value=12 Score=28.49 Aligned_cols=17 Identities=18% Similarity=0.411 Sum_probs=14.3
Q ss_pred eCCCCchhhHHHHHHHH
Q 030553 76 VTGDGRCLFRALVKGMA 92 (175)
Q Consensus 76 Ip~DG~CLFrAIadQL~ 92 (175)
|.-|+|||--||+.+|.
T Consensus 3 ~sR~NNCLVVAis~~L~ 19 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLG 19 (104)
T ss_pred ccCCCCeEeehHHHHhc
Confidence 45799999999999873
No 11
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=39.32 E-value=1.5e+02 Score=21.74 Aligned_cols=84 Identities=13% Similarity=0.271 Sum_probs=48.0
Q ss_pred hhhHHHHhhccceeEEEecCCCCCCCCCCCCCCCcccccCCCceeeeeeCCCC-CCCchhhhhccCcEEEEeCCCCchhh
Q 030553 6 TEGILEQLRLGVAKFELVSSPVASISNPNSQTFPTAFHRDSNNLFFARIGPPL-GGGSPAMKKVERYSVQRVTGDGRCLF 84 (175)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~-~~~~~~~~k~~gL~I~eIp~DG~CLF 84 (175)
...++++|++|.+-+-|+..|.. .+. +...........+.++-+.++ .+..-..+.+.++.+.-.+.+.. +
T Consensus 44 ~~~~~~~l~~g~~Dl~i~~~~~~---~~~---~~~~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~--~ 115 (209)
T PF03466_consen 44 SDELIEALRSGELDLAITFGPPP---PPG---LESEPLGEEPLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGSP--Y 115 (209)
T ss_dssp HHHHHHHHHTTSSSEEEESSSSS---STT---EEEEEEEEEEEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTS--H
T ss_pred chhhhHHHhcccccEEEEEeecc---ccc---cccccccceeeeeeeeccccccccccchhhhhhhccccccccccc--c
Confidence 46899999999999999987761 111 111111222333565655545 33344556667777777754444 5
Q ss_pred HHHHHHHHhccCC
Q 030553 85 RALVKGMALNKGI 97 (175)
Q Consensus 85 rAIadQL~~~~g~ 97 (175)
+...++.....|.
T Consensus 116 ~~~~~~~~~~~~~ 128 (209)
T PF03466_consen 116 RDQLDRWLREHGF 128 (209)
T ss_dssp HHHHHHHHHHTTE
T ss_pred ccccccccccccc
Confidence 5555554444343
No 12
>PF12091 DUF3567: Protein of unknown function (DUF3567); InterPro: IPR021951 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.
Probab=32.11 E-value=1e+02 Score=22.97 Aligned_cols=36 Identities=19% Similarity=0.265 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhhccCCchhhHHHHHhhhhhhhHHHHHHhhcCCC
Q 030553 117 ADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRIGRSD 162 (175)
Q Consensus 117 a~eLR~~vad~I~~~~~~r~~f~efl~~~~~ee~fdeYC~~I~~t~ 162 (175)
|...|+.|...|.+.| ..++. ++-.+.||..|.+|-
T Consensus 47 Ae~Fr~~V~~li~~~P-t~Eev---------DdfL~~y~~l~~qPv 82 (85)
T PF12091_consen 47 AEMFREDVQALIASEP-TQEEV---------DDFLGGYDALMQQPV 82 (85)
T ss_pred HHHHHHHHHHHHhcCC-CHHHH---------HHHHHHHHHHHhCCe
Confidence 7889999999997532 22333 344788999998763
No 13
>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=51 Score=25.63 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=16.6
Q ss_pred eCCCCchhhHHHHHHHHhccC
Q 030553 76 VTGDGRCLFRALVKGMALNKG 96 (175)
Q Consensus 76 Ip~DG~CLFrAIadQL~~~~g 96 (175)
=|+||+|=++.|+.=|+.-.|
T Consensus 4 PP~DG~CG~H~i~aI~n~m~~ 24 (108)
T PF05412_consen 4 PPGDGSCGWHCIAAIMNHMMG 24 (108)
T ss_pred CCCCCchHHHHHHHHHHHhhc
Confidence 389999999999987765433
No 14
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=29.14 E-value=80 Score=25.83 Aligned_cols=47 Identities=13% Similarity=0.179 Sum_probs=34.9
Q ss_pred ccchHHHHHHHHHHHHhhccCCchhhHHHHHhhhhhhhHHHHHHhhcC
Q 030553 113 FFTNADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRIGR 160 (175)
Q Consensus 113 ~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~ee~fdeYC~~I~~ 160 (175)
|...-..|....-+||.. +.=..++..|+........-.+|++|+.+
T Consensus 153 f~~LDe~Lq~~~~~yLee-RGId~~la~fl~~y~~~kEq~eYi~wL~~ 199 (204)
T PF02330_consen 153 FDELDENLQDAFMNYLEE-RGIDEELANFLHDYSTDKEQREYIRWLKN 199 (204)
T ss_dssp GGGSBHHHHHHHHHHHHH-TT-SHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333456999999999975 34557788888766667788999999864
No 15
>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=28.32 E-value=2.5e+02 Score=20.86 Aligned_cols=88 Identities=13% Similarity=0.080 Sum_probs=46.3
Q ss_pred ChhhHHHHhhccceeEEEecCCCCCCCCCCCCCCCcccccCCCceeeeeeCCCCCC-CchhhhhccCcEEEEeCCCCchh
Q 030553 5 PTEGILEQLRLGVAKFELVSSPVASISNPNSQTFPTAFHRDSNNLFFARIGPPLGG-GSPAMKKVERYSVQRVTGDGRCL 83 (175)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~-~~~~~~k~~gL~I~eIp~DG~CL 83 (175)
.+..++++|++|.+.+=|+..|.. .++ +......+-...+.++-+..+.+ .+-..+.+.++.+.-.+...+|-
T Consensus 38 ~~~~l~~~l~~g~~D~~~~~~~~~---~~~---~~~~~l~~~~~~lv~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~ 111 (198)
T cd08486 38 TKDEQVEGLLAGTIHVGFSRFFPR---HPG---IEIVNIAQEDLYLAVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPS 111 (198)
T ss_pred CHHHHHHHHHcCCceEEEecCCCC---CCc---eEEEEEeeccEEEEecCCCccccCCcccHHHHcCCCeEeecCCcCch
Confidence 467899999999999988754321 111 11111111233344444444432 23334556666666665555565
Q ss_pred hHHHHHHHHhccCCC
Q 030553 84 FRALVKGMALNKGIT 98 (175)
Q Consensus 84 FrAIadQL~~~~g~~ 98 (175)
++.....+....|..
T Consensus 112 ~~~~~~~~~~~~~~~ 126 (198)
T cd08486 112 FADEVIGLFKHAGIE 126 (198)
T ss_pred HHHHHHHHHHHcCCC
Confidence 665555554544543
No 16
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=24.53 E-value=1.1e+02 Score=21.15 Aligned_cols=29 Identities=10% Similarity=0.285 Sum_probs=20.7
Q ss_pred hhhhccCcEEEEeCCCCchhhHHHHHHHHh
Q 030553 64 AMKKVERYSVQRVTGDGRCLFRALVKGMAL 93 (175)
Q Consensus 64 ~~~k~~gL~I~eIp~DG~CLFrAIadQL~~ 93 (175)
||+-+++..++-+-+-|.|-| +|.+|+.+
T Consensus 9 AL~hL~~~ilfi~D~Se~CGy-sie~Q~~L 37 (58)
T PF06858_consen 9 ALAHLADAILFIIDPSEQCGY-SIEEQLSL 37 (58)
T ss_dssp GGGGT-SEEEEEE-TT-TTSS--HHHHHHH
T ss_pred HHHhhcceEEEEEcCCCCCCC-CHHHHHHH
Confidence 556667888899999999999 89999865
No 17
>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=23.77 E-value=15 Score=26.22 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=16.2
Q ss_pred hhHHHHHHhhcCCCcccchHhH
Q 030553 149 ESLKRYCQRIGRSDFWGGESEL 170 (175)
Q Consensus 149 e~fdeYC~~I~~t~~WGGeiEL 170 (175)
.|.++=+-.+++++.|||.+-|
T Consensus 20 KDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 20 KDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred CcchhheeeeecCccccCEEEE
Confidence 4555556677899999998754
No 18
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.73 E-value=2.2e+02 Score=22.60 Aligned_cols=44 Identities=20% Similarity=0.346 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhh----c-cCCchhhHHHHHhhhhhhhHHHHHHhhcC----CCcccchH
Q 030553 119 DLRMAVKEVICD----S-GSERRQYEEALIAITIDESLKRYCQRIGR----SDFWGGES 168 (175)
Q Consensus 119 eLR~~vad~I~~----~-~~~r~~f~efl~~~~~ee~fdeYC~~I~~----t~~WGGei 168 (175)
++|.+=..|+++ + ..++.+-..|+ .+|+.||.-|.+ .+.|-|++
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 777776666642 1 01233333343 459999998887 57787764
No 19
>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=22.35 E-value=22 Score=25.23 Aligned_cols=18 Identities=28% Similarity=0.722 Sum_probs=12.5
Q ss_pred HHHHhhcCCCcccchHhH
Q 030553 153 RYCQRIGRSDFWGGESEL 170 (175)
Q Consensus 153 eYC~~I~~t~~WGGeiEL 170 (175)
+=+-.+++++.|||.+.|
T Consensus 24 E~Vv~~E~~~~wGG~v~L 41 (64)
T PF06988_consen 24 EPVVSMEKPELWGGEVTL 41 (64)
T ss_dssp EEEEEESSSSS-SSEEEE
T ss_pred cceeeeeccCccCCEEEE
Confidence 334556799999999876
No 20
>cd08463 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=21.77 E-value=3.5e+02 Score=20.27 Aligned_cols=86 Identities=13% Similarity=0.095 Sum_probs=45.6
Q ss_pred ChhhHHHHhhccceeEEEecCCCCCCCCCCCCCCCcccccCCCceeeeeeCCCCCC-CchhhhhccCcEEEEeCCCCchh
Q 030553 5 PTEGILEQLRLGVAKFELVSSPVASISNPNSQTFPTAFHRDSNNLFFARIGPPLGG-GSPAMKKVERYSVQRVTGDGRCL 83 (175)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~-~~~~~~k~~gL~I~eIp~DG~CL 83 (175)
++..++++|.+|.+.+=|+.+|.... . ..-..++ .....++++-+..+.+ .+-.++.+.++.....+ ++.|.
T Consensus 38 ~~~~l~~~L~~g~lDl~i~~~~~~~~---~--l~~~~l~-~~~~~lv~~~~h~l~~~~~i~~~~l~~~~~i~~~-~~~~~ 110 (203)
T cd08463 38 PDFDYERALASGELDLVIGNWPEPPE---H--LHLSPLF-SDEIVCLMRADHPLARRGLMTLDDYLEAPHLAPT-PYSVG 110 (203)
T ss_pred cchhHHHHHhcCCeeEEEeccccCCC---C--cEEeEee-cCceEEEEeCCCCcccCCCCCHHHHhhCCcEEEE-cCCCC
Confidence 35789999999999998886554211 0 0001122 2233366676766632 22334555566655553 33455
Q ss_pred hHHHHHHHHhccCC
Q 030553 84 FRALVKGMALNKGI 97 (175)
Q Consensus 84 FrAIadQL~~~~g~ 97 (175)
++.+...+....|.
T Consensus 111 ~~~~~~~~~~~~~~ 124 (203)
T cd08463 111 QRGVIDSHLARLGL 124 (203)
T ss_pred CCchHHHHHHHcCC
Confidence 55555554443343
Done!