Query 031091
Match_columns 166
No_of_seqs 137 out of 481
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 09:06:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031091.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031091hhsearch_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 7.9E-25 1.7E-29 188.6 6.1 88 69-166 157-249 (302)
2 PF02338 OTU: OTU-like cystein 99.7 4.4E-18 9.6E-23 125.9 5.9 69 77-165 1-70 (121)
3 KOG3288 OTU-like cysteine prot 99.7 4E-17 8.6E-22 139.4 4.8 80 70-165 109-188 (307)
4 KOG2605 OTU (ovarian tumor)-li 99.0 1.1E-10 2.5E-15 104.2 2.3 79 69-165 216-294 (371)
5 COG5539 Predicted cysteine pro 98.7 1.2E-09 2.7E-14 94.8 -1.3 86 72-166 172-260 (306)
6 COG5539 Predicted cysteine pro 98.6 7.6E-08 1.7E-12 83.8 5.2 74 74-166 115-189 (306)
7 PF10275 Peptidase_C65: Peptid 98.1 4.9E-06 1.1E-10 69.5 4.9 52 110-165 141-193 (244)
8 KOG3991 Uncharacterized conser 97.6 5E-05 1.1E-09 64.7 3.2 53 108-166 156-209 (256)
9 PF05415 Peptidase_C36: Beet n 81.6 1.8 3.9E-05 32.5 3.1 16 76-91 3-18 (104)
10 PRK09784 hypothetical protein; 79.8 2.6 5.7E-05 37.2 4.1 35 55-89 181-218 (417)
11 COG3426 Butyrate kinase [Energ 52.1 5.8 0.00013 35.6 0.5 25 141-165 315-339 (358)
12 KOG4100 Uncharacterized conser 43.2 50 0.0011 25.8 4.4 59 82-159 14-81 (125)
13 TIGR02934 nifT_nitrog probable 29.5 9.6 0.00021 26.8 -1.3 23 139-161 19-41 (67)
14 PF05412 Peptidase_C33: Equine 28.8 56 0.0012 25.0 2.6 20 77-96 5-24 (108)
15 PF06988 NifT: NifT/FixU prote 27.5 14 0.00031 25.8 -0.8 21 141-161 21-41 (64)
16 PF12091 DUF3567: Protein of u 23.6 1.6E+02 0.0034 21.7 4.0 38 106-153 45-82 (85)
17 PF03466 LysR_substrate: LysR 23.1 3E+02 0.0065 20.0 6.4 103 6-116 44-147 (209)
18 PF05952 ComX: Bacillus compet 22.0 55 0.0012 22.3 1.3 16 5-20 11-26 (57)
19 PF14393 DUF4422: Domain of un 21.3 1.5E+02 0.0032 25.2 4.0 12 139-150 175-186 (231)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=7.9e-25 Score=188.59 Aligned_cols=88 Identities=24% Similarity=0.474 Sum_probs=77.2
Q ss_pred CCcEEEEecCCCChhhHHHHHHHHHccCCCCCCcchhhhHHHHHHHHHHHHhcccCCchhhHHHHHhhh-----hhhhHH
Q 031091 69 ERYSVQRVTGDGRCLFRALVKGMALNKGITLNSRDEREDADDLRMAVKEVICDSGSERRQYEEALIAIT-----IDESLK 143 (166)
Q Consensus 69 ~gl~I~~Ip~DGnCLFrAIadQL~~~~g~~~s~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~-----~~e~fe 143 (166)
++|.+++||+||||||+||+|||..+.+..+ ++..||...|+||+ +|.++|.||+...+ ..++|+
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 7999999999999999999999999876544 47899999999998 48899999986422 235799
Q ss_pred HHHHhhcCCCccccHHHHhhccC
Q 031091 144 RYCQRIGRSDFWGGESELLVSTC 166 (166)
Q Consensus 144 eYC~~I~~t~~WGGeiEL~ALS~ 166 (166)
.||+.|++|++|||+|||.|||+
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=4.4e-18 Score=125.94 Aligned_cols=69 Identities=33% Similarity=0.657 Sum_probs=56.6
Q ss_pred cCCCChhhHHHHHHHHHccCCCCCCcchhhhHHHHHHHHHHHHh-cccCCchhhHHHHHhhhhhhhHHHHHHhhcCCCcc
Q 031091 77 TGDGRCLFRALVKGMALNKGITLNSRDEREDADDLRMAVKEVIC-DSGSERRQYEEALIAITIDESLKRYCQRIGRSDFW 155 (166)
Q Consensus 77 p~DGnCLFrAIadQL~~~~g~~~s~~~~~~~a~eLR~~vad~I~-~~~~~r~~f~efl~~~~~~e~feeYC~~I~~t~~W 155 (166)
|+|||||||||++||...++ ..+..+.+||+.++++|. . +++.|.+++. +. +|+++++|
T Consensus 1 pgDGnClF~Avs~~l~~~~~------~~~~~~~~lR~~~~~~l~~~---~~~~~~~~~~----~~-------~~~~~~~W 60 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGG------GSEDNHQELRKAVVDYLRDK---NRDKFEEFLE----GD-------KMSKPGTW 60 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-S------SSTTTHHHHHHHHHHHHHTH---TTTHHHHHHH----HH-------HHTSTTSH
T ss_pred CCCccHHHHHHHHHHHHhcC------CCHHHHHHHHHHHHHHHHHh---ccchhhhhhh----hh-------hhcccccc
Confidence 79999999999999985432 113468899999999997 5 7788999872 22 99999999
Q ss_pred ccHHHHhhcc
Q 031091 156 GGESELLVST 165 (166)
Q Consensus 156 GGeiEL~ALS 165 (166)
||++||.|||
T Consensus 61 g~~~el~a~a 70 (121)
T PF02338_consen 61 GGEIELQALA 70 (121)
T ss_dssp EEHHHHHHHH
T ss_pred CcHHHHHHHH
Confidence 9999999987
No 3
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.67 E-value=4e-17 Score=139.44 Aligned_cols=80 Identities=26% Similarity=0.469 Sum_probs=69.0
Q ss_pred CcEEEEecCCCChhhHHHHHHHHHccCCCCCCcchhhhHHHHHHHHHHHHhcccCCchhhHHHHHhhhhhhhHHHHHHhh
Q 031091 70 RYSVQRVTGDGRCLFRALVKGMALNKGITLNSRDEREDADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRI 149 (166)
Q Consensus 70 gl~I~~Ip~DGnCLFrAIadQL~~~~g~~~s~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~~e~feeYC~~I 149 (166)
-+..+.||+|++|||+||.+.|....+. ...+||+.++..+.+ +++.|.+++ ++++-.+||.||
T Consensus 109 vl~~~vvp~DNSCLF~ai~yv~~k~~~~---------~~~elR~iiA~~Vas---np~~yn~Ai----LgK~n~eYc~WI 172 (307)
T KOG3288|consen 109 VLSRRVVPDDNSCLFTAIAYVIFKQVSN---------RPYELREIIAQEVAS---NPDKYNDAI----LGKPNKEYCAWI 172 (307)
T ss_pred eeEEEeccCCcchhhhhhhhhhcCccCC---------CcHHHHHHHHHHHhc---ChhhhhHHH----hCCCcHHHHHHH
Confidence 4556778999999999999988643221 125999999999985 789999998 899999999999
Q ss_pred cCCCccccHHHHhhcc
Q 031091 150 GRSDFWGGESELLVST 165 (166)
Q Consensus 150 ~~t~~WGGeiEL~ALS 165 (166)
++...|||.|||.+||
T Consensus 173 ~k~dsWGGaIElsILS 188 (307)
T KOG3288|consen 173 LKMDSWGGAIELSILS 188 (307)
T ss_pred ccccccCceEEeeeeh
Confidence 9999999999999998
No 4
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.01 E-value=1.1e-10 Score=104.24 Aligned_cols=79 Identities=27% Similarity=0.379 Sum_probs=69.9
Q ss_pred CCcEEEEecCCCChhhHHHHHHHHHccCCCCCCcchhhhHHHHHHHHHHHHhcccCCchhhHHHHHhhhhhhhHHHHHHh
Q 031091 69 ERYSVQRVTGDGRCLFRALVKGMALNKGITLNSRDEREDADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQR 148 (166)
Q Consensus 69 ~gl~I~~Ip~DGnCLFrAIadQL~~~~g~~~s~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~~e~feeYC~~ 148 (166)
.++.+++|..||+|+|||++||++.. .+.++..|++++|++. +.++.|..|+ .++|-.|.++
T Consensus 216 ~g~e~~Kv~edGsC~fra~aDQvy~d----------~e~~~~~~~~~~dq~~---~e~~~~~~~v-----t~~~~~y~k~ 277 (371)
T KOG2605|consen 216 FGFEYKKVVEDGSCLFRALADQVYGD----------DEQHDHNRRECVDQLK---KERDFYEDYV-----TEDFTSYIKR 277 (371)
T ss_pred hhhhhhhcccCCchhhhccHHHhhcC----------HHHHHHHHHHHHHHHh---hccccccccc-----ccchhhcccc
Confidence 68899999999999999999999863 3457899999999995 3778888774 6899999999
Q ss_pred hcCCCccccHHHHhhcc
Q 031091 149 IGRSDFWGGESELLVST 165 (166)
Q Consensus 149 I~~t~~WGGeiEL~ALS 165 (166)
++..+.||-.+|++|++
T Consensus 278 kr~~~~~gnhie~Qa~a 294 (371)
T KOG2605|consen 278 KRADGEPGNHIEQQAAA 294 (371)
T ss_pred cccCCCCcchHHHhhhh
Confidence 99999999999999986
No 5
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.72 E-value=1.2e-09 Score=94.82 Aligned_cols=86 Identities=8% Similarity=0.014 Sum_probs=63.5
Q ss_pred EEEEecCCCChhhHHHHHHHHHccC-CCCCCcchhhhHHHHHHHHHHHHhcccCCchhhHHHHHhhhh--hhhHHHHHHh
Q 031091 72 SVQRVTGDGRCLFRALVKGMALNKG-ITLNSRDEREDADDLRMAVKEVICDSGSERRQYEEALIAITI--DESLKRYCQR 148 (166)
Q Consensus 72 ~I~~Ip~DGnCLFrAIadQL~~~~g-~~~s~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~--~e~feeYC~~ 148 (166)
.-.++++||+|+|.+|++||..+.- ..+ ....++|-.-..|..+ +...|+.+..+... -.+|++||+.
T Consensus 172 ~k~d~~~dG~ieia~iS~~l~v~i~~Vdv------~~~~~dr~~~~~~~q~---~~i~f~g~hfD~~t~~m~~~dt~~ne 242 (306)
T COG5539 172 VKPDSQGDGCIEIAIISDQLPVRIHVVDV------DKDSEDRYNSHPYVQR---ISILFTGIHFDEETLAMVLWDTYVNE 242 (306)
T ss_pred hccccCCCceEEEeEeccccceeeeeeec------chhHHhhccCChhhhh---hhhhhcccccchhhhhcchHHHHHhh
Confidence 3347899999999999999976532 222 1235667666666653 66778777653222 2489999999
Q ss_pred hcCCCccccHHHHhhccC
Q 031091 149 IGRSDFWGGESELLVSTC 166 (166)
Q Consensus 149 I~~t~~WGGeiEL~ALS~ 166 (166)
|+.++.||+.||+++|+.
T Consensus 243 ~~~~a~~g~~~ei~qLas 260 (306)
T COG5539 243 VLFDASDGITIEIQQLAS 260 (306)
T ss_pred hcccccccchHHHHHHHH
Confidence 999999999999999973
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.57 E-value=7.6e-08 Score=83.76 Aligned_cols=74 Identities=20% Similarity=0.225 Sum_probs=63.6
Q ss_pred EEecCCCChhhHHHHHHHHHccCCCCCCcchhhhHHHHHHHHHHHHhcccCCchhhHHHHHhhhhhhhHHHHHHhhcCCC
Q 031091 74 QRVTGDGRCLFRALVKGMALNKGITLNSRDEREDADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRIGRSD 153 (166)
Q Consensus 74 ~~Ip~DGnCLFrAIadQL~~~~g~~~s~~~~~~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~~e~feeYC~~I~~t~ 153 (166)
....+|.+|+|+++.+.+.. ....+||.+|+..+.+ +++.|.+++ .+.+--.||.||....
T Consensus 115 ~p~~~d~srl~q~~~~~l~~------------asv~~lrE~vs~Ev~s---nPDl~n~~i----~~~~~i~y~~~i~k~d 175 (306)
T COG5539 115 MPGQDDNSRLFQAERYSLRD------------ASVAKLREVVSLEVLS---NPDLYNPAI----LEIDVIAYATWIVKPD 175 (306)
T ss_pred CCCCCchHHHHHHHHhhhhh------------hhHHHHHHHHHHHHhh---Cccccchhh----cCcchHHHHHhhhccc
Confidence 33458999999999997642 2467999999999985 678999988 6788999999999999
Q ss_pred ccc-cHHHHhhccC
Q 031091 154 FWG-GESELLVSTC 166 (166)
Q Consensus 154 ~WG-GeiEL~ALS~ 166 (166)
.|| |.+||-+||.
T Consensus 176 ~~~dG~ieia~iS~ 189 (306)
T COG5539 176 SQGDGCIEIAIISD 189 (306)
T ss_pred cCCCceEEEeEecc
Confidence 999 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=98.07 E-value=4.9e-06 Score=69.49 Aligned_cols=52 Identities=12% Similarity=0.230 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhcccCCchhhHHHHHhhhhhhhHHHHH-HhhcCCCccccHHHHhhcc
Q 031091 110 DLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYC-QRIGRSDFWGGESELLVST 165 (166)
Q Consensus 110 eLR~~vad~I~~~~~~r~~f~efl~~~~~~e~feeYC-~~I~~t~~WGGeiEL~ALS 165 (166)
.||-.++.||+. |.+.|.+|+.+.. ..++++|| +.|...+.=.+++.+.||+
T Consensus 141 flRLlts~~l~~---~~d~y~~fi~~~~-~~tve~~C~~~Vep~~~Ead~v~i~ALa 193 (244)
T PF10275_consen 141 FLRLLTSAYLKS---NSDEYEPFIDGLE-YLTVEEFCSQEVEPMGKEADHVQIIALA 193 (244)
T ss_dssp HHHHHHHHHHHH---THHHHGGGSSTT---S-HHHHHHHHTSSTT--B-HHHHHHHH
T ss_pred HHHHHHHHHHHh---hHHHHhhhhcccc-cCCHHHHHHhhcccccccchhHHHHHHH
Confidence 788888888885 6788888862110 27899999 4556666777899999986
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.59 E-value=5e-05 Score=64.72 Aligned_cols=53 Identities=11% Similarity=0.102 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHhcccCCchhhHHHHHhhhhhhhHHHHHHhhcCC-CccccHHHHhhccC
Q 031091 108 ADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRIGRS-DFWGGESELLVSTC 166 (166)
Q Consensus 108 a~eLR~~vad~I~~~~~~r~~f~efl~~~~~~e~feeYC~~I~~t-~~WGGeiEL~ALS~ 166 (166)
+.+||-.++-+|+. +.+.|.||+ +-+.+.++||..=..| ..=-|+|+|.|||+
T Consensus 156 V~ylRLvtS~~ik~---~adfy~pFI---~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~ 209 (256)
T KOG3991|consen 156 VMYLRLVTSGFIKS---NADFYQPFI---DEGMTVKAFCTQEVEPMYKESDHIHITALSQ 209 (256)
T ss_pred HHHHHHHHHHHHhh---ChhhhhccC---CCCCcHHHHHHhhcchhhhccCceeHHHHHh
Confidence 45889999999985 668888886 2357999999976655 34567899999985
No 9
>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=81.55 E-value=1.8 Score=32.50 Aligned_cols=16 Identities=19% Similarity=0.426 Sum_probs=14.1
Q ss_pred ecCCCChhhHHHHHHH
Q 031091 76 VTGDGRCLFRALVKGM 91 (166)
Q Consensus 76 Ip~DGnCLFrAIadQL 91 (166)
|.-|+|||.-||+..|
T Consensus 3 ~sR~NNCLVVAis~~L 18 (104)
T PF05415_consen 3 ASRPNNCLVVAISECL 18 (104)
T ss_pred ccCCCCeEeehHHHHh
Confidence 4679999999999977
No 10
>PRK09784 hypothetical protein; Provisional
Probab=79.80 E-value=2.6 Score=37.23 Aligned_cols=35 Identities=37% Similarity=0.573 Sum_probs=25.8
Q ss_pred CCCCCCCc---hhhhccCCcEEEEecCCCChhhHHHHH
Q 031091 55 GPPLGGGS---PAMKKVERYSVQRVTGDGRCLFRALVK 89 (166)
Q Consensus 55 ~~~~~g~~---~~~~k~~gl~I~~Ip~DGnCLFrAIad 89 (166)
|..++|-+ .-.+|..||+-..|.|||-||.|||.-
T Consensus 181 gidlsgisfiqse~n~~~glkyapvdgdgycllrailv 218 (417)
T PRK09784 181 GIDLSGISFIQSEINKTYGLKYAPVDGDGYCLLRAILV 218 (417)
T ss_pred CcCcccchhhHhhhhhhhCceecccCCCchhHHHHHHH
Confidence 44445522 333556899999999999999999975
No 11
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=52.14 E-value=5.8 Score=35.63 Aligned_cols=25 Identities=20% Similarity=0.230 Sum_probs=22.3
Q ss_pred hHHHHHHhhcCCCccccHHHHhhcc
Q 031091 141 SLKRYCQRIGRSDFWGGESELLVST 165 (166)
Q Consensus 141 ~feeYC~~I~~t~~WGGeiEL~ALS 165 (166)
-..+|++||..--..+|+.||.||.
T Consensus 315 ~I~~~v~~iapv~v~PGE~EleALA 339 (358)
T COG3426 315 AIEDRVSWIAPVIVYPGEDELEALA 339 (358)
T ss_pred HHHHHHhhhcceEecCCchHHHHHH
Confidence 4568999999999999999999986
No 12
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.15 E-value=50 Score=25.79 Aligned_cols=59 Identities=19% Similarity=0.385 Sum_probs=34.4
Q ss_pred hhhHHHHHHHHHccCCCCCCcchhhhHHHHHHHHHHHHhc----ccC-CchhhHHHHHhhhhhhhHHHHHHhhcC----C
Q 031091 82 CLFRALVKGMALNKGITLNSRDEREDADDLRMAVKEVICD----SGS-ERRQYEEALIAITIDESLKRYCQRIGR----S 152 (166)
Q Consensus 82 CLFrAIadQL~~~~g~~~s~~~~~~~a~eLR~~vad~I~~----~~~-~r~~f~efl~~~~~~e~feeYC~~I~~----t 152 (166)
-||+.|..+-. |.+ .++|.+=..|+++ +.. ++.+-..|+ .+|+.||.-|.+ .
T Consensus 14 lLYkriLrlHr---~lp----------~~~R~lGD~YVkdEFrrHk~vnp~~~~~Fl------teW~~Ya~~l~qql~~~ 74 (125)
T KOG4100|consen 14 LLYKRILRLHR---GLP----------AELRALGDQYVKDEFRRHKTVNPLEAQGFL------TEWERYAVALSQQLSSA 74 (125)
T ss_pred HHHHHHHHHHc---cCC----------hHHHHHHHHHHHHHHHHhccCChHHHHHHH------HHHHHHHHHHHHHhhhc
Confidence 37888776422 322 2777776666653 100 122222333 479999998887 5
Q ss_pred CccccHH
Q 031091 153 DFWGGES 159 (166)
Q Consensus 153 ~~WGGei 159 (166)
+.|-|++
T Consensus 75 g~~K~~~ 81 (125)
T KOG4100|consen 75 GKWKGEI 81 (125)
T ss_pred Ccccccc
Confidence 7887764
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=29.49 E-value=9.6 Score=26.82 Aligned_cols=23 Identities=22% Similarity=0.578 Sum_probs=17.7
Q ss_pred hhhHHHHHHhhcCCCccccHHHH
Q 031091 139 DESLKRYCQRIGRSDFWGGESEL 161 (166)
Q Consensus 139 ~e~feeYC~~I~~t~~WGGeiEL 161 (166)
-++.|+=+-.|++++.|||.+-|
T Consensus 19 KKDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 19 KKDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred CCcchhheeeeecCccccCEEEE
Confidence 45666667778899999998754
No 14
>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=28.81 E-value=56 Score=25.03 Aligned_cols=20 Identities=30% Similarity=0.546 Sum_probs=16.8
Q ss_pred cCCCChhhHHHHHHHHHccC
Q 031091 77 TGDGRCLFRALVKGMALNKG 96 (166)
Q Consensus 77 p~DGnCLFrAIadQL~~~~g 96 (166)
|+||+|=++.|+.-|.+-.|
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 89999999999997776444
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=27.46 E-value=14 Score=25.76 Aligned_cols=21 Identities=29% Similarity=0.710 Sum_probs=13.9
Q ss_pred hHHHHHHhhcCCCccccHHHH
Q 031091 141 SLKRYCQRIGRSDFWGGESEL 161 (166)
Q Consensus 141 ~feeYC~~I~~t~~WGGeiEL 161 (166)
+.|+=+-.|++++.|||.+.|
T Consensus 21 DLEE~Vv~~E~~~~wGG~v~L 41 (64)
T PF06988_consen 21 DLEEPVVSMEKPELWGGEVTL 41 (64)
T ss_dssp TEEEEEEEESSSSS-SSEEEE
T ss_pred ccccceeeeeccCccCCEEEE
Confidence 344444557799999999876
No 16
>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=23.58 E-value=1.6e+02 Score=21.67 Aligned_cols=38 Identities=18% Similarity=0.244 Sum_probs=27.2
Q ss_pred hhHHHHHHHHHHHHhcccCCchhhHHHHHhhhhhhhHHHHHHhhcCCC
Q 031091 106 EDADDLRMAVKEVICDSGSERRQYEEALIAITIDESLKRYCQRIGRSD 153 (166)
Q Consensus 106 ~~a~eLR~~vad~I~~~~~~r~~f~efl~~~~~~e~feeYC~~I~~t~ 153 (166)
..|...|+.|...|...| ..++ ++.-.+.||..|.+|-
T Consensus 45 ~~Ae~Fr~~V~~li~~~P-t~Ee---------vDdfL~~y~~l~~qPv 82 (85)
T PF12091_consen 45 SWAEMFREDVQALIASEP-TQEE---------VDDFLGGYDALMQQPV 82 (85)
T ss_pred HHHHHHHHHHHHHHhcCC-CHHH---------HHHHHHHHHHHHhCCe
Confidence 458899999999998543 2222 3455789999998873
No 17
>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=23.11 E-value=3e+02 Score=19.96 Aligned_cols=103 Identities=14% Similarity=0.231 Sum_probs=49.7
Q ss_pred hhhHHHHhhccceeEEeecCCCCCCCCCCCCCCCcccccCCccceeeecCCCCC-CCchhhhccCCcEEEEecCCCChhh
Q 031091 6 TEGILEQLRLGVAKFELVSSPVASISNPNSQTFPTAFHRDSNNLFFARIGPPLG-GGSPAMKKVERYSVQRVTGDGRCLF 84 (166)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~-g~~~~~~k~~gl~I~~Ip~DGnCLF 84 (166)
..+++++|++|.+-+-|+..|... +. +-..........+.+.-+..+. ..+-..+.+.++.+.-.+.+. . +
T Consensus 44 ~~~~~~~l~~g~~Dl~i~~~~~~~---~~---~~~~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~-~-~ 115 (209)
T PF03466_consen 44 SDELIEALRSGELDLAITFGPPPP---PG---LESEPLGEEPLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGS-P-Y 115 (209)
T ss_dssp HHHHHHHHHTTSSSEEEESSSSSS---TT---EEEEEEEEEEEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTT-S-H
T ss_pred chhhhHHHhcccccEEEEEeeccc---cc---cccccccceeeeeeeeccccccccccchhhhhhhcccccccccc-c-c
Confidence 468999999999999999877611 11 1111111112223333333231 122234455677766664333 3 5
Q ss_pred HHHHHHHHHccCCCCCCcchhhhHHHHHHHHH
Q 031091 85 RALVKGMALNKGITLNSRDEREDADDLRMAVK 116 (166)
Q Consensus 85 rAIadQL~~~~g~~~s~~~~~~~a~eLR~~va 116 (166)
+...++.....|.......+......+...|.
T Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 147 (209)
T PF03466_consen 116 RDQLDRWLREHGFSPNIVIEVDSFESILSLVA 147 (209)
T ss_dssp HHHHHHHHHHTTEEEEEEEEESSHHHHHHHHH
T ss_pred ccccccccccccccccccccccchhhhccccc
Confidence 55555544444433221122233444444443
No 18
>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=22.01 E-value=55 Score=22.28 Aligned_cols=16 Identities=31% Similarity=0.507 Sum_probs=13.5
Q ss_pred ChhhHHHHhhccceeE
Q 031091 5 PTEGILEQLRLGVAKF 20 (166)
Q Consensus 5 ~~~~~~~~~~~~~~~~ 20 (166)
.|..+|++|++|.|-.
T Consensus 11 ~nPevl~kl~~g~asL 26 (57)
T PF05952_consen 11 QNPEVLEKLKEGEASL 26 (57)
T ss_pred HChHHHHHHHcCCeeE
Confidence 3678999999999976
No 19
>PF14393 DUF4422: Domain of unknown function (DUF4422)
Probab=21.26 E-value=1.5e+02 Score=25.21 Aligned_cols=12 Identities=25% Similarity=0.609 Sum_probs=9.9
Q ss_pred hhhHHHHHHhhc
Q 031091 139 DESLKRYCQRIG 150 (166)
Q Consensus 139 ~e~feeYC~~I~ 150 (166)
.+-|++||+|+-
T Consensus 175 kelF~~Yc~wLF 186 (231)
T PF14393_consen 175 KELFDEYCEWLF 186 (231)
T ss_pred hHHHHHHHHHHH
Confidence 467999999973
Done!