Query 021093
Match_columns 317
No_of_seqs 141 out of 952
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 07:32:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021093hhsearch_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 100.0 1.5E-30 3.3E-35 245.9 10.4 148 152-315 138-300 (302)
2 PF02338 OTU: OTU-like cystein 99.9 1.5E-24 3.3E-29 177.4 8.7 113 179-307 1-121 (121)
3 KOG3288 OTU-like cysteine prot 99.7 9.9E-18 2.2E-22 156.8 7.0 127 170-314 107-234 (307)
4 PF10275 Peptidase_C65: Peptid 99.6 2.3E-15 4.9E-20 139.0 12.7 101 210-312 138-244 (244)
5 KOG3991 Uncharacterized conser 99.5 6.7E-14 1.4E-18 129.5 9.6 98 210-312 155-255 (256)
6 KOG2605 OTU (ovarian tumor)-li 99.4 2.3E-13 5E-18 134.0 4.9 95 169-274 214-311 (371)
7 COG5539 Predicted cysteine pro 99.1 1.5E-11 3.3E-16 117.1 -0.5 146 151-311 149-305 (306)
8 COG5539 Predicted cysteine pro 98.8 2.6E-09 5.5E-14 102.1 1.9 115 175-311 114-230 (306)
9 PF05415 Peptidase_C36: Beet n 62.3 23 0.00051 29.4 5.6 66 178-272 3-70 (104)
10 KOG2605 OTU (ovarian tumor)-li 45.7 10 0.00023 38.2 1.3 46 229-274 2-47 (371)
11 PRK09784 hypothetical protein; 34.9 21 0.00046 34.8 1.5 26 166-191 193-218 (417)
12 COG5007 Predicted transcriptio 26.1 74 0.0016 25.7 2.9 57 161-226 4-61 (80)
13 PF05381 Peptidase_C21: Tymovi 24.5 1.4E+02 0.003 25.3 4.4 45 255-309 48-94 (104)
14 TIGR02934 nifT_nitrog probable 22.7 8.5 0.00018 30.1 -2.9 34 223-256 6-41 (67)
15 PRK10963 hypothetical protein; 21.0 76 0.0017 29.4 2.5 17 216-232 6-22 (223)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.5e-30 Score=245.86 Aligned_cols=148 Identities=34% Similarity=0.585 Sum_probs=125.0
Q ss_pred hcCCCCCCCchhHHHhhhcCCeEEEEeCCCCchhhHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHhhChhhhhh
Q 021093 152 SKIDGGGGGDDLNVKRCEIINERPFKVTADGRCLFRAIAHGACLRSGEEVPDEERQRELADELRAQVVDELLKRRKETEW 231 (317)
Q Consensus 152 ~~~d~r~~~~~l~~~l~~~~gL~i~~IpgDGNCLFRAVA~qL~~~~G~~~~~~~~~q~~h~eLR~~VvdyI~~n~deFe~ 231 (317)
++.+.|--+++-...++...+|.+++||+||+|||+||+|||..+++..+ ....||..+++||++|.++|.+
T Consensus 138 ~~~~~k~~E~~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~--------~v~kLR~~~a~Ymr~H~~df~p 209 (302)
T KOG2606|consen 138 NQADAKSMEKEKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLL--------SVQKLREETADYMREHVEDFLP 209 (302)
T ss_pred cCCchhhhHHHHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCC--------cHHHHHHHHHHHHHHHHHHhhh
Confidence 34444443433334445599999999999999999999999998876544 4789999999999999999999
Q ss_pred hhc----------ccHHHHHhhhcCCCcccChHHHHHHHHhcCccEEEEEeccCCCcceeEEecCCcccCCCCCeEEEEE
Q 021093 232 FIE----------GDFDTYVKEIQQPYVWGGEPELLMASHVLKKPIAVFMVVQSSGNLVNIANYGEEYQKDKESPINVLF 301 (317)
Q Consensus 232 Fle----------e~feeY~~~Mrk~g~WGGeiEL~ALS~llkv~I~V~~~~~~~~~~~~I~~fGee~~~~~~~pI~LlY 301 (317)
|+. ++|++||++|++++.|||++||.|+|++|++||.||+.+.+ +.+||++|++ .+||+|+|
T Consensus 210 f~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p------~~~~geey~k--d~pL~lvY 281 (302)
T KOG2606|consen 210 FLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGP------ILEYGEEYGK--DKPLILVY 281 (302)
T ss_pred HhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCC------ceeechhhCC--CCCeeeeh
Confidence 983 25999999999999999999999999999999999999854 5789999986 69999999
Q ss_pred cCC----C-CcceeeCCCC
Q 021093 302 HGY----G-HYDILETFSE 315 (317)
Q Consensus 302 hg~----g-HYDSLr~i~d 315 (317)
|+. | |||||.+...
T Consensus 282 ~rH~y~LGeHYNS~~~~~n 300 (302)
T KOG2606|consen 282 HRHAYGLGEHYNSVTPLKN 300 (302)
T ss_pred HHhHHHHHhhhcccccccc
Confidence 985 3 9999988653
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=99.91 E-value=1.5e-24 Score=177.45 Aligned_cols=113 Identities=38% Similarity=0.647 Sum_probs=89.1
Q ss_pred CCCCchhhHHHHHHHHhcC-CCCCCchHHHHHHHHHHHHHHHHHHh-hChhhhhhhhcccHHHHHhhhcCCCcccChHHH
Q 021093 179 TADGRCLFRAIAHGACLRS-GEEVPDEERQRELADELRAQVVDELL-KRRKETEWFIEGDFDTYVKEIQQPYVWGGEPEL 256 (317)
Q Consensus 179 pgDGNCLFRAVA~qL~~~~-G~~~~~~~~~q~~h~eLR~~VvdyI~-~n~deFe~Flee~feeY~~~Mrk~g~WGGeiEL 256 (317)
||||||||||||+||+... |. +..|.+||+++++||+ +|++.|++|++++ +|+++++|||++||
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~--------~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~Wg~~~el 66 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGS--------EDNHQELRKAVVDYLRDKNRDKFEEFLEGD------KMSKPGTWGGEIEL 66 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSS--------TTTHHHHHHHHHHHHHTHTTTHHHHHHHHH------HHTSTTSHEEHHHH
T ss_pred CCCccHHHHHHHHHHHHhcCCC--------HHHHHHHHHHHHHHHHHhccchhhhhhhhh------hhccccccCcHHHH
Confidence 7999999999999998443 22 2579999999999999 9999999999876 99999999999999
Q ss_pred HHHHHhcCccEEEEEeccCCCcceeEEecCC-cccCCCCCeEEEEEcC-----CCCc
Q 021093 257 LMASHVLKKPIAVFMVVQSSGNLVNIANYGE-EYQKDKESPINVLFHG-----YGHY 307 (317)
Q Consensus 257 ~ALS~llkv~I~V~~~~~~~~~~~~I~~fGe-e~~~~~~~pI~LlYhg-----~gHY 307 (317)
+|+|++|+++|+||+..... ....+ .+.. ..+....++|.++|++ .+||
T Consensus 67 ~a~a~~~~~~I~v~~~~~~~-~~~~~-~~~~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 67 QALANVLNRPIIVYSSSDGD-NVVFI-KFTGKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp HHHHHHHTSEEEEECETTTB-EEEEE-EESCEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred HHHHHHhCCeEEEEEcCCCC-cccee-eecCccccCCCCCeEEEEEcCCccCCCCCC
Confidence 99999999999999874331 12222 3322 2112236899999998 7898
No 3
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=9.9e-18 Score=156.79 Aligned_cols=127 Identities=24% Similarity=0.309 Sum_probs=107.3
Q ss_pred cCCeEEEEeCCCCchhhHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHhhChhhh-hhhhcccHHHHHhhhcCCC
Q 021093 170 IINERPFKVTADGRCLFRAIAHGACLRSGEEVPDEERQRELADELRAQVVDELLKRRKET-EWFIEGDFDTYVKEIQQPY 248 (317)
Q Consensus 170 ~~gL~i~~IpgDGNCLFRAVA~qL~~~~G~~~~~~~~~q~~h~eLR~~VvdyI~~n~deF-e~Flee~feeY~~~Mrk~g 248 (317)
.-.+..+.||.|++|||+||+..+....+.. -.+||+.++..+..|++.| +.+++..-++||..|+|+.
T Consensus 107 ~gvl~~~vvp~DNSCLF~ai~yv~~k~~~~~----------~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~d 176 (307)
T KOG3288|consen 107 EGVLSRRVVPDDNSCLFTAIAYVIFKQVSNR----------PYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMD 176 (307)
T ss_pred cceeEEEeccCCcchhhhhhhhhhcCccCCC----------cHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHcccc
Confidence 3456788899999999999999998322221 2689999999999999999 7788889999999999999
Q ss_pred cccChHHHHHHHHhcCccEEEEEeccCCCcceeEEecCCcccCCCCCeEEEEEcCCCCcceeeCCC
Q 021093 249 VWGGEPELLMASHVLKKPIAVFMVVQSSGNLVNIANYGEEYQKDKESPINVLFHGYGHYDILETFS 314 (317)
Q Consensus 249 ~WGGeiEL~ALS~llkv~I~V~~~~~~~~~~~~I~~fGee~~~~~~~pI~LlYhg~gHYDSLr~i~ 314 (317)
.|||.|||..||+.|++.|.|++.... .|..||++..- ...+.|+|.|. |||+|....
T Consensus 177 sWGGaIElsILS~~ygveI~vvDiqt~-----rid~fged~~~--~~rv~llydGI-HYD~l~m~~ 234 (307)
T KOG3288|consen 177 SWGGAIELSILSDYYGVEICVVDIQTV-----RIDRFGEDKNF--DNRVLLLYDGI-HYDPLAMNE 234 (307)
T ss_pred ccCceEEeeeehhhhceeEEEEeccee-----eehhcCCCCCC--CceEEEEeccc-ccChhhhcc
Confidence 999999999999999999999998632 47789987532 67889999886 999987644
No 4
>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=99.63 E-value=2.3e-15 Score=138.98 Aligned_cols=101 Identities=24% Similarity=0.330 Sum_probs=74.1
Q ss_pred HHHHHHHHHHHHHhhChhhhhhhhc----ccHHHHHhh-hcCCCcccChHHHHHHHHhcCccEEEEEeccC-CCcceeEE
Q 021093 210 LADELRAQVVDELLKRRKETEWFIE----GDFDTYVKE-IQQPYVWGGEPELLMASHVLKKPIAVFMVVQS-SGNLVNIA 283 (317)
Q Consensus 210 ~h~eLR~~VvdyI~~n~deFe~Fle----e~feeY~~~-Mrk~g~WGGeiEL~ALS~llkv~I~V~~~~~~-~~~~~~I~ 283 (317)
....+|..++.||+.|.++|++|++ .++++||++ +...+.-.+++.|.|||++|+++|.|+..++. .+......
T Consensus 138 iV~flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~ 217 (244)
T PF10275_consen 138 IVIFLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRH 217 (244)
T ss_dssp HHHHHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEE
T ss_pred HHHHHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccc
Confidence 3558999999999999999999997 579999965 66668899999999999999999999998865 33334444
Q ss_pred ecCCcccCCCCCeEEEEEcCCCCcceeeC
Q 021093 284 NYGEEYQKDKESPINVLFHGYGHYDILET 312 (317)
Q Consensus 284 ~fGee~~~~~~~pI~LlYhg~gHYDSLr~ 312 (317)
.|.++. ......|.|+|.. ||||.|++
T Consensus 218 ~~~~~~-~~~~~~i~LLyrp-gHYdIly~ 244 (244)
T PF10275_consen 218 EFPPDN-ESQEPQITLLYRP-GHYDILYP 244 (244)
T ss_dssp EES-SS-TTSS-SEEEEEET-BEEEEEEE
T ss_pred cCCCcc-CCCCCEEEEEEcC-CccccccC
Confidence 554321 1236789999966 79999985
No 5
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.50 E-value=6.7e-14 Score=129.50 Aligned_cols=98 Identities=24% Similarity=0.299 Sum_probs=78.6
Q ss_pred HHHHHHHHHHHHHhhChhhhhhhhcc--cHHHHHhhhcCC-CcccChHHHHHHHHhcCccEEEEEeccCCCcceeEEecC
Q 021093 210 LADELRAQVVDELLKRRKETEWFIEG--DFDTYVKEIQQP-YVWGGEPELLMASHVLKKPIAVFMVVQSSGNLVNIANYG 286 (317)
Q Consensus 210 ~h~eLR~~VvdyI~~n~deFe~Flee--~feeY~~~Mrk~-g~WGGeiEL~ALS~llkv~I~V~~~~~~~~~~~~I~~fG 286 (317)
....||..+..+|++|+|+|++||++ +.++||.+-..| .+-.|+++|.|||+.+++.|.|...++..++...-..|-
T Consensus 155 iV~ylRLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fp 234 (256)
T KOG3991|consen 155 IVMYLRLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFP 234 (256)
T ss_pred HHHHHHHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCc
Confidence 47889999999999999999999976 799999986665 677999999999999999999999887754322222222
Q ss_pred CcccCCCCCeEEEEEcCCCCcceeeC
Q 021093 287 EEYQKDKESPINVLFHGYGHYDILET 312 (317)
Q Consensus 287 ee~~~~~~~pI~LlYhg~gHYDSLr~ 312 (317)
+. ....|.|+|. .||||.|++
T Consensus 235 -e~---s~P~I~LLYr-pGHYdilY~ 255 (256)
T KOG3991|consen 235 -EA---SAPEIYLLYR-PGHYDILYK 255 (256)
T ss_pred -cc---cCceEEEEec-CCccccccC
Confidence 22 1567889985 489999986
No 6
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.39 E-value=2.3e-13 Score=133.98 Aligned_cols=95 Identities=29% Similarity=0.378 Sum_probs=84.7
Q ss_pred hcCCeEEEEeCCCCchhhHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHhhChhhhhhhhcccHHHHHhhhcCCC
Q 021093 169 EIINERPFKVTADGRCLFRAIAHGACLRSGEEVPDEERQRELADELRAQVVDELLKRRKETEWFIEGDFDTYVKEIQQPY 248 (317)
Q Consensus 169 ~~~gL~i~~IpgDGNCLFRAVA~qL~~~~G~~~~~~~~~q~~h~eLR~~VvdyI~~n~deFe~Flee~feeY~~~Mrk~g 248 (317)
..+|+..+.|.+||||+|||+++|++. + ++.|+.+|+++++++.++++.|+.|+.++|-+|+.++++++
T Consensus 214 ~~~g~e~~Kv~edGsC~fra~aDQvy~---d--------~e~~~~~~~~~~dq~~~e~~~~~~~vt~~~~~y~k~kr~~~ 282 (371)
T KOG2605|consen 214 KHFGFEYKKVVEDGSCLFRALADQVYG---D--------DEQHDHNRRECVDQLKKERDFYEDYVTEDFTSYIKRKRADG 282 (371)
T ss_pred HHhhhhhhhcccCCchhhhccHHHhhc---C--------HHHHHHHHHHHHHHHhhcccccccccccchhhcccccccCC
Confidence 468999999999999999999999994 2 36899999999999999999999999999999999999999
Q ss_pred cccChHHHHHHHH---hcCccEEEEEecc
Q 021093 249 VWGGEPELLMASH---VLKKPIAVFMVVQ 274 (317)
Q Consensus 249 ~WGGeiEL~ALS~---llkv~I~V~~~~~ 274 (317)
+||.++|+||+|. ....++.|.....
T Consensus 283 ~~gnhie~Qa~a~~~~~~~~~~~~~~~~~ 311 (371)
T KOG2605|consen 283 EPGNHIEQQAAADIYEEIEKPLNITSFKD 311 (371)
T ss_pred CCcchHHHhhhhhhhhhccccceeecccc
Confidence 9999999999995 5556666665543
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.08 E-value=1.5e-11 Score=117.10 Aligned_cols=146 Identities=17% Similarity=0.015 Sum_probs=101.8
Q ss_pred hhcCCCC-CCCchhHHHhhhcCCeEEEEeCCCCchhhHHHHHHHHhcCC-CCCCchHHHHHHHHHHHHHHHHHHhhChhh
Q 021093 151 ISKIDGG-GGGDDLNVKRCEIINERPFKVTADGRCLFRAIAHGACLRSG-EEVPDEERQRELADELRAQVVDELLKRRKE 228 (317)
Q Consensus 151 ~~~~d~r-~~~~~l~~~l~~~~gL~i~~IpgDGNCLFRAVA~qL~~~~G-~~~~~~~~~q~~h~eLR~~VvdyI~~n~de 228 (317)
.+++|.. ..+..+..... ...+....++|||+|+|-+|++||..+-- .++ ..-+.+|-.-..|.+++...
T Consensus 149 ~snPDl~n~~i~~~~~i~y-~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv-------~~~~~dr~~~~~~~q~~~i~ 220 (306)
T COG5539 149 LSNPDLYNPAILEIDVIAY-ATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDV-------DKDSEDRYNSHPYVQRISIL 220 (306)
T ss_pred hhCccccchhhcCcchHHH-HHhhhccccCCCceEEEeEeccccceeeeeeec-------chhHHhhccCChhhhhhhhh
Confidence 3555554 22333333333 55667788999999999999999985421 111 12367787888888888888
Q ss_pred hhhhhc-------ccHHHHHhhhcCCCcccChHHHHHHHHhcCccEEEEEeccCCCcceeEEecCCcccCCCCCeEEEEE
Q 021093 229 TEWFIE-------GDFDTYVKEIQQPYVWGGEPELLMASHVLKKPIAVFMVVQSSGNLVNIANYGEEYQKDKESPINVLF 301 (317)
Q Consensus 229 Fe~Fle-------e~feeY~~~Mrk~g~WGGeiEL~ALS~llkv~I~V~~~~~~~~~~~~I~~fGee~~~~~~~pI~LlY 301 (317)
|..|.- ..|++|++.|+-+..||+.+|+++||.+|++|+.+++..+. +++|++=... ....+-++-
T Consensus 221 f~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~------~ik~n~c~~~-~~~e~~~~~ 293 (306)
T COG5539 221 FTGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASP------SIKCNICGTG-FVGEKDYYA 293 (306)
T ss_pred hcccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCc------eEEeeccccc-cchhhHHHH
Confidence 877762 26999999999999999999999999999999999998754 3566532210 122223333
Q ss_pred cCC--CCcceee
Q 021093 302 HGY--GHYDILE 311 (317)
Q Consensus 302 hg~--gHYDSLr 311 (317)
|.+ ||||+++
T Consensus 294 Ha~a~GH~n~~~ 305 (306)
T COG5539 294 HALATGHYNFGE 305 (306)
T ss_pred HHHhhcCccccC
Confidence 433 6999874
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.76 E-value=2.6e-09 Score=102.09 Aligned_cols=115 Identities=26% Similarity=0.215 Sum_probs=94.8
Q ss_pred EEEeCCCCchhhHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHhhChhhhhhhhcc-cHHHHHhhhcCCCccc-C
Q 021093 175 PFKVTADGRCLFRAIAHGACLRSGEEVPDEERQRELADELRAQVVDELLKRRKETEWFIEG-DFDTYVKEIQQPYVWG-G 252 (317)
Q Consensus 175 i~~IpgDGNCLFRAVA~qL~~~~G~~~~~~~~~q~~h~eLR~~VvdyI~~n~deFe~Flee-~feeY~~~Mrk~g~WG-G 252 (317)
..+...|.+|+|++.+..++. ....+||..|+..+.+|||.|.+.+.+ +--.|+.+++++..|| |
T Consensus 114 d~p~~~d~srl~q~~~~~l~~-------------asv~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG 180 (306)
T COG5539 114 DMPGQDDNSRLFQAERYSLRD-------------ASVAKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDG 180 (306)
T ss_pred cCCCCCchHHHHHHHHhhhhh-------------hhHHHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCc
Confidence 334457899999999998861 257899999999999999999888865 7889999999999999 9
Q ss_pred hHHHHHHHHhcCccEEEEEeccCCCcceeEEecCCcccCCCCCeEEEEEcCCCCcceee
Q 021093 253 EPELLMASHVLKKPIAVFMVVQSSGNLVNIANYGEEYQKDKESPINVLFHGYGHYDILE 311 (317)
Q Consensus 253 eiEL~ALS~llkv~I~V~~~~~~~~~~~~I~~fGee~~~~~~~pI~LlYhg~gHYDSLr 311 (317)
.+|+.++|+.|++.|.|++.+... +.+|++..- ...+.++|.++ |||...
T Consensus 181 ~ieia~iS~~l~v~i~~Vdv~~~~-----~dr~~~~~~---~q~~~i~f~g~-hfD~~t 230 (306)
T COG5539 181 CIEIAIISDQLPVRIHVVDVDKDS-----EDRYNSHPY---VQRISILFTGI-HFDEET 230 (306)
T ss_pred eEEEeEeccccceeeeeeecchhH-----HhhccCChh---hhhhhhhhccc-ccchhh
Confidence 999999999999999999987542 346665421 35677888885 999765
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=62.29 E-value=23 Score=29.41 Aligned_cols=66 Identities=18% Similarity=0.315 Sum_probs=43.3
Q ss_pred eCCCCchhhHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHhhChhhhhhhhcccHHHHHhhhc--CCCcccChHH
Q 021093 178 VTADGRCLFRAIAHGACLRSGEEVPDEERQRELADELRAQVVDELLKRRKETEWFIEGDFDTYVKEIQ--QPYVWGGEPE 255 (317)
Q Consensus 178 IpgDGNCLFRAVA~qL~~~~G~~~~~~~~~q~~h~eLR~~VvdyI~~n~deFe~Flee~feeY~~~Mr--k~g~WGGeiE 255 (317)
+..|+|||--||+..|... -+.| -+-|+.|.. +++.|+..++ .+.+|-+
T Consensus 3 ~sR~NNCLVVAis~~L~~T--------------~e~l----~~~M~An~~--------~i~~y~~W~r~~~~STW~D--- 53 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVT--------------LEKL----DNLMQANVS--------TIKKYHTWLRKKRPSTWDD--- 53 (104)
T ss_pred ccCCCCeEeehHHHHhcch--------------HHHH----HHHHHhhHH--------HHHHHHHHHhcCCCCcHHH---
Confidence 5679999999999998521 1111 122333321 3667887665 4578954
Q ss_pred HHHHHHhcCccEEEEEe
Q 021093 256 LLMASHVLKKPIAVFMV 272 (317)
Q Consensus 256 L~ALS~llkv~I~V~~~ 272 (317)
-.++|+.+++.|.|--.
T Consensus 54 C~mFA~~LkVsm~vkV~ 70 (104)
T PF05415_consen 54 CRMFADALKVSMQVKVL 70 (104)
T ss_pred HHHHHHhheeEEEEEEc
Confidence 45899999999887443
No 10
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=45.65 E-value=10 Score=38.24 Aligned_cols=46 Identities=24% Similarity=0.294 Sum_probs=41.0
Q ss_pred hhhhhcccHHHHHhhhcCCCcccChHHHHHHHHhcCccEEEEEecc
Q 021093 229 TEWFIEGDFDTYVKEIQQPYVWGGEPELLMASHVLKKPIAVFMVVQ 274 (317)
Q Consensus 229 Fe~Flee~feeY~~~Mrk~g~WGGeiEL~ALS~llkv~I~V~~~~~ 274 (317)
|..++.++|+.|+.-+.++.+-|+.+||.+++.+++.+...+...+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~~~~~~g 47 (371)
T KOG2605|consen 2 FREEVSGDFDWYLWDLGKTKTLGTILELGAMSHVYRRNVIDYEPFG 47 (371)
T ss_pred CccccCchHHHHhhcCCCCcccccchhhhhccccccCCCCCcCCcc
Confidence 4456678899999999999999999999999999999999988754
No 11
>PRK09784 hypothetical protein; Provisional
Probab=34.88 E-value=21 Score=34.79 Aligned_cols=26 Identities=31% Similarity=0.386 Sum_probs=21.8
Q ss_pred HhhhcCCeEEEEeCCCCchhhHHHHH
Q 021093 166 KRCEIINERPFKVTADGRCLFRAIAH 191 (317)
Q Consensus 166 ~l~~~~gL~i~~IpgDGNCLFRAVA~ 191 (317)
..-+..||+--+|.|||-||.|||--
T Consensus 193 e~n~~~glkyapvdgdgycllrailv 218 (417)
T PRK09784 193 EINKTYGLKYAPVDGDGYCLLRAILV 218 (417)
T ss_pred hhhhhhCceecccCCCchhHHHHHHH
Confidence 44457899999999999999999753
No 12
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=26.10 E-value=74 Score=25.73 Aligned_cols=57 Identities=11% Similarity=0.156 Sum_probs=38.9
Q ss_pred chhHHHhhhcCCeEEEEeCCCCchhhH-HHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHhhCh
Q 021093 161 DDLNVKRCEIINERPFKVTADGRCLFR-AIAHGACLRSGEEVPDEERQRELADELRAQVVDELLKRR 226 (317)
Q Consensus 161 ~~l~~~l~~~~gL~i~~IpgDGNCLFR-AVA~qL~~~~G~~~~~~~~~q~~h~eLR~~VvdyI~~n~ 226 (317)
.++.+-+.+.+.+...+|.|||+-+|- +|++.+. |.. +-..++.+=.-..+||..|.
T Consensus 4 e~Ik~ll~~~L~~e~v~V~Gdg~Hf~vi~Vs~~F~---g~s------rvkrqq~vYApL~~~i~~~~ 61 (80)
T COG5007 4 EEIKSLLENALPLEEVEVEGDGSHFQVIAVSEEFA---GKS------RVKRQQLVYAPLMAYIADNE 61 (80)
T ss_pred HHHHHHHHhcCCccEEEEecCCceEEEEEehHhhc---Ccc------HHHHHHHHHHHHHHHhhcCc
Confidence 356677778899999999999998875 4677765 432 12345555556667777653
No 13
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 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 entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=24.51 E-value=1.4e+02 Score=25.33 Aligned_cols=45 Identities=11% Similarity=0.140 Sum_probs=33.0
Q ss_pred HHHHHHHhcCccEEEEEeccCCCcceeEEecCCcccCCCCCeEEEEEcCC--CCcce
Q 021093 255 ELLMASHVLKKPIAVFMVVQSSGNLVNIANYGEEYQKDKESPINVLFHGY--GHYDI 309 (317)
Q Consensus 255 EL~ALS~llkv~I~V~~~~~~~~~~~~I~~fGee~~~~~~~pI~LlYhg~--gHYDS 309 (317)
.+.|||..|+...+|..... +.+||-... ...+.|.|... +||..
T Consensus 48 hltaLa~~~~~~~~~hs~~~-------~~~~Gi~~a---s~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 48 HLTALAYRYHFQCTFHSDHG-------VLHYGIKDA---STVFTITHTPGPPGHFSL 94 (104)
T ss_pred HHHHHHHHHheEEEEEcCCc-------eEEeecCCC---ceEEEEEeCCCCCCcccc
Confidence 47899999999999998764 358887654 45566665542 49987
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=22.69 E-value=8.5 Score=30.06 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=25.8
Q ss_pred hhChhh-hhhhhc-ccHHHHHhhhcCCCcccChHHH
Q 021093 223 LKRRKE-TEWFIE-GDFDTYVKEIQQPYVWGGEPEL 256 (317)
Q Consensus 223 ~~n~de-Fe~Fle-e~feeY~~~Mrk~g~WGGeiEL 256 (317)
++|.+- +..|+. .|+|+=+-.|.+++.|||.+.|
T Consensus 6 R~~~~g~l~~YvpKKDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 6 RRNRAGELSAYVPKKDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred EeCCCCCEEEEEECCcchhheeeeecCccccCEEEE
Confidence 444443 677775 5899999999999999997654
No 15
>PRK10963 hypothetical protein; Provisional
Probab=21.04 E-value=76 Score=29.36 Aligned_cols=17 Identities=29% Similarity=0.079 Sum_probs=13.9
Q ss_pred HHHHHHHhhChhhhhhh
Q 021093 216 AQVVDELLKRRKETEWF 232 (317)
Q Consensus 216 ~~VvdyI~~n~deFe~F 232 (317)
+.|++|+++|||.|+..
T Consensus 6 ~~V~~yL~~~PdFf~~h 22 (223)
T PRK10963 6 RAVVDYLLQNPDFFIRN 22 (223)
T ss_pred HHHHHHHHHCchHHhhC
Confidence 46889999999999554
Done!