Query 045719
Match_columns 384
No_of_seqs 239 out of 303
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 04:52:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045719.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045719hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02338 OTU: OTU-like cystein 99.7 5.9E-18 1.3E-22 143.5 6.7 109 200-323 1-121 (121)
2 KOG2606 OTU (ovarian tumor)-li 99.4 3.1E-13 6.7E-18 130.3 8.2 134 183-329 148-298 (302)
3 KOG2605 OTU (ovarian tumor)-li 98.6 3.4E-08 7.3E-13 99.8 4.1 132 184-329 208-344 (371)
4 PF10275 Peptidase_C65: Peptid 98.1 1.4E-05 3E-10 76.5 8.8 32 181-213 29-60 (244)
5 KOG3288 OTU-like cysteine prot 97.8 4.2E-05 9.2E-10 73.2 6.3 121 193-330 109-234 (307)
6 KOG3991 Uncharacterized conser 97.4 0.0007 1.5E-08 64.1 9.2 87 231-329 166-256 (256)
7 COG5539 Predicted cysteine pro 95.6 0.012 2.7E-07 57.5 4.0 117 176-299 153-280 (306)
8 smart00575 ZnF_PMZ plant mutat 94.6 0.025 5.5E-07 36.4 2.0 25 18-42 2-26 (28)
9 PF05412 Peptidase_C33: Equine 93.4 0.13 2.8E-06 43.5 4.5 63 198-293 3-65 (108)
10 PF04434 SWIM: SWIM zinc finge 88.8 0.28 6.2E-06 33.6 1.8 28 13-40 11-38 (40)
11 COG5539 Predicted cysteine pro 79.4 1.8 4E-05 42.7 3.3 111 201-328 119-231 (306)
12 KOG4345 NF-kappa B regulator A 65.3 5.5 0.00012 43.7 3.1 52 274-327 225-290 (774)
13 PRK09784 hypothetical protein; 51.5 9 0.0002 37.3 1.8 39 188-227 194-232 (417)
14 PF04545 Sigma70_r4: Sigma-70, 41.8 57 0.0012 22.9 4.4 47 183-233 3-49 (50)
15 PF07506 RepB: RepB plasmid pa 36.0 1.3E+02 0.0028 27.5 6.8 62 194-256 52-113 (185)
16 PF03412 Peptidase_C39: Peptid 30.4 1.7E+02 0.0036 24.2 6.2 52 268-331 44-95 (131)
17 TIGR03277 methan_mark_9 putati 29.6 50 0.0011 28.1 2.7 31 204-234 77-108 (109)
18 PF09607 BrkDBD: Brinker DNA-b 29.2 49 0.0011 25.2 2.3 18 201-218 20-39 (58)
19 KOG4844 Mitochondrial ribosoma 28.1 23 0.00049 29.4 0.4 18 115-132 82-100 (102)
20 PLN03097 FHY3 Protein FAR-RED 26.8 34 0.00075 38.9 1.6 43 16-58 578-621 (846)
21 PF05381 Peptidase_C21: Tymovi 25.5 3.8E+02 0.0082 22.8 7.2 89 203-325 3-94 (104)
22 PF05415 Peptidase_C36: Beet n 25.1 77 0.0017 26.3 2.9 20 199-218 3-22 (104)
No 1
>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=5.9e-18 Score=143.55 Aligned_cols=109 Identities=21% Similarity=0.392 Sum_probs=85.6
Q ss_pred CCCCCcchHHHHhHhc----CCchhHHHHHHHHHHHHH-HhhhhcccccCChhHHHHHHHHhccCCCCCCCCccccccch
Q 045719 200 APDGNCGFRAIADLMG----FGENGWLQVRKDLLNELH-LNMEHYSHLYGTYERVNELIHAISYFENCPGSDKWMTMPDM 274 (384)
Q Consensus 200 ~gDGnCgFRAiA~~Lg----~~ed~~~~VR~~li~el~-~~~~~Y~~~~~~~~~~~~~l~~L~~~~~~a~~~kWl~~p~~ 274 (384)
+|||||+|||||.+|+ .+++.|..||++++++|+ .+++.|..++.++ .+ ..++.|++.+++
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~--------~~------~~~~~Wg~~~el 66 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD--------KM------SKPGTWGGEIEL 66 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH--------HH------TSTTSHEEHHHH
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh--------hh------ccccccCcHHHH
Confidence 6999999999999999 999999999999999999 9999888887543 34 557899999976
Q ss_pred hHHhhhhcceEEEEEccCcc--eecccCCCCCCCCCCCCeEEEEEec-----CCcc
Q 045719 275 GHLIASAYNIVVFHLSMKQC--LTFLPLRSNPVPTDSRKEIAIGFVN-----NNHF 323 (384)
Q Consensus 275 g~iiAn~ynrpVi~ls~~~s--~tffPl~~~P~~~~~~~pI~La~v~-----~nHF 323 (384)
+++|+.|+|+|++|+.... ..+.+..+.-+.....++|+|+|.. ++||
T Consensus 67 -~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 67 -QALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp -HHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred -HHHHHHhCCeEEEEEcCCCCccceeeecCccccCCCCCeEEEEEcCCccCCCCCC
Confidence 9999999999999886332 2333322200112236899999997 8998
No 2
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.42 E-value=3.1e-13 Score=130.33 Aligned_cols=134 Identities=13% Similarity=0.217 Sum_probs=111.6
Q ss_pred hhhhHHHHhhhhcccccCCCCCcchHHHHhHhcCCc---hhHHHHHHHHHHHHHHhhhhcccccCCh--------hHHHH
Q 045719 183 NEFPAALQSYIHHIKDVAPDGNCGFRAIADLMGFGE---NGWLQVRKDLLNELHLNMEHYSHLYGTY--------ERVNE 251 (384)
Q Consensus 183 ~q~p~~l~~~i~~i~dV~gDGnCgFRAiA~~Lg~~e---d~~~~VR~~li~el~~~~~~Y~~~~~~~--------~~~~~ 251 (384)
..+-..|..-.+.++|++.||||.|+||++||.+.. -+-..+|++..++|..|.++|.+|+-++ .+|+.
T Consensus 148 ~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~ 227 (302)
T KOG2606|consen 148 EKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDK 227 (302)
T ss_pred HHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHH
Confidence 357788999999999999999999999999998763 4688999999999999999999986553 47999
Q ss_pred HHHHhccCCCCCCCCccccccchhHHhhhhcceEEEEEccCcc-eecccCCCCCCCCCCCCeEEEEEe-----cCCcceE
Q 045719 252 LIHAISYFENCPGSDKWMTMPDMGHLIASAYNIVVFHLSMKQC-LTFLPLRSNPVPTDSRKEIAIGFV-----NNNHFVE 325 (384)
Q Consensus 252 ~l~~L~~~~~~a~~~kWl~~p~~g~iiAn~ynrpVi~ls~~~s-~tffPl~~~P~~~~~~~pI~La~v-----~~nHFvs 325 (384)
|++.+ +.+..||+.++. ++++++|.+||.+|..+++ .+|-+-.+. .+||+|+|+ -|.||+|
T Consensus 228 Yc~eI------~~t~~WGgelEL-~AlShvL~~PI~Vy~~~~p~~~~geey~k------d~pL~lvY~rH~y~LGeHYNS 294 (302)
T KOG2606|consen 228 YCREI------RNTAAWGGELEL-KALSHVLQVPIEVYQADGPILEYGEEYGK------DKPLILVYHRHAYGLGEHYNS 294 (302)
T ss_pred HHHHh------hhhccccchHHH-HHHHHhhccCeEEeecCCCceeechhhCC------CCCeeeehHHhHHHHHhhhcc
Confidence 99988 567899999975 8999999999999998655 555544431 478999986 2588988
Q ss_pred eecC
Q 045719 326 VFLL 329 (384)
Q Consensus 326 l~lk 329 (384)
+..-
T Consensus 295 ~~~~ 298 (302)
T KOG2606|consen 295 VTPL 298 (302)
T ss_pred cccc
Confidence 8753
No 3
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.59 E-value=3.4e-08 Score=99.80 Aligned_cols=132 Identities=17% Similarity=0.178 Sum_probs=101.8
Q ss_pred hhhHHHHhhhhcccccCCCCCcchHHHHhHhcCCchhHHHHHHHHHHHHHHhhhhcccccCChhHHHHHHHHhccCCCCC
Q 045719 184 EFPAALQSYIHHIKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYSHLYGTYERVNELIHAISYFENCP 263 (384)
Q Consensus 184 q~p~~l~~~i~~i~dV~gDGnCgFRAiA~~Lg~~ed~~~~VR~~li~el~~~~~~Y~~~~~~~~~~~~~l~~L~~~~~~a 263 (384)
.....+..|+..+..|.+||+|.|||+|+++.++.|.|..+|++..++++.++++|..++.. .|..+++.. .
T Consensus 208 ~~~~~~~~~g~e~~Kv~edGsC~fra~aDQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt~--~~~~y~k~k------r 279 (371)
T KOG2605|consen 208 RSAKRKKHFGFEYKKVVEDGSCLFRALADQVYGDDEQHDHNRRECVDQLKKERDFYEDYVTE--DFTSYIKRK------R 279 (371)
T ss_pred HHHHHHHHhhhhhhhcccCCchhhhccHHHhhcCHHHHHHHHHHHHHHHhhccccccccccc--chhhccccc------c
Confidence 34566788999999999999999999999999999999999999999999999999998875 477777755 3
Q ss_pred CCCccccccchhHHhhh---hcceEEEEEccC-cc-eecccCCCCCCCCCCCCeEEEEEecCCcceEeecC
Q 045719 264 GSDKWMTMPDMGHLIAS---AYNIVVFHLSMK-QC-LTFLPLRSNPVPTDSRKEIAIGFVNNNHFVEVFLL 329 (384)
Q Consensus 264 ~~~kWl~~p~~g~iiAn---~ynrpVi~ls~~-~s-~tffPl~~~P~~~~~~~pI~La~v~~nHFvsl~lk 329 (384)
-.+.||++..+ |++|. -..+|++..+.+ .| ....|-. ..+...+++.||...||..+...
T Consensus 280 ~~~~~gnhie~-Qa~a~~~~~~~~~~~~~~~~~t~~~~~~~~~-----~~~~~~~~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 280 ADGEPGNHIEQ-QAAADIYEEIEKPLNITSFKDTCYIQTPPAI-----EESVKMEKYNFWVEVHYNTARHS 344 (371)
T ss_pred cCCCCcchHHH-hhhhhhhhhccccceeecccccceeccCccc-----ccchhhhhhcccchhhhhhcccc
Confidence 45799999865 89995 344555555432 33 2233222 22345699999989999988763
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=98.08 E-value=1.4e-05 Score=76.47 Aligned_cols=32 Identities=31% Similarity=0.457 Sum_probs=23.9
Q ss_pred chhhhhHHHHhhhhcccccCCCCCcchHHHHhH
Q 045719 181 FVNEFPAALQSYIHHIKDVAPDGNCGFRAIADL 213 (384)
Q Consensus 181 ~~~q~p~~l~~~i~~i~dV~gDGnCgFRAiA~~ 213 (384)
|..++ +.|......++.|.|||||.|||++-+
T Consensus 29 ~~~ki-~~L~~~y~~~R~vRGDGNCFYRAf~F~ 60 (244)
T PF10275_consen 29 FQKKI-KKLSQKYSGIRRVRGDGNCFYRAFGFS 60 (244)
T ss_dssp HHHHH-HHHHHHEEEEE-B-SSSTHHHHHHHHH
T ss_pred HHHHH-HHHHhhhhheEeecCCccHHHHHHHHH
Confidence 33444 667777889999999999999999877
No 5
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=97.79 E-value=4.2e-05 Score=73.17 Aligned_cols=121 Identities=14% Similarity=0.216 Sum_probs=88.8
Q ss_pred hhcccccCCCCCcchHHHHhHhcCCchhH-HHHHHHHHHHHHHhhhhcccccCCh--hHHHHHHHHhccCCCCCCCCccc
Q 045719 193 IHHIKDVAPDGNCGFRAIADLMGFGENGW-LQVRKDLLNELHLNMEHYSHLYGTY--ERVNELIHAISYFENCPGSDKWM 269 (384)
Q Consensus 193 i~~i~dV~gDGnCgFRAiA~~Lg~~ed~~-~~VR~~li~el~~~~~~Y~~~~~~~--~~~~~~l~~L~~~~~~a~~~kWl 269 (384)
|+..+=|+.|--|+|+||+.-+....+.- .++|+-+.+|+-++++.|..-+-+. ..|..++.+ .+.|+
T Consensus 109 vl~~~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k---------~dsWG 179 (307)
T KOG3288|consen 109 VLSRRVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILK---------MDSWG 179 (307)
T ss_pred eeEEEeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHcc---------ccccC
Confidence 33445689999999999988775543222 6899999999999999999764442 355555543 57999
Q ss_pred cccchhHHhhhhcceEEEEEccCc--ceecccCCCCCCCCCCCCeEEEEEecCCcceEeecCC
Q 045719 270 TMPDMGHLIASAYNIVVFHLSMKQ--CLTFLPLRSNPVPTDSRKEIAIGFVNNNHFVEVFLLP 330 (384)
Q Consensus 270 ~~p~~g~iiAn~ynrpVi~ls~~~--s~tffPl~~~P~~~~~~~pI~La~v~~nHFvsl~lk~ 330 (384)
+-.+. -||++.|++-|++++... +..|-+-. ....-++|-| +|-||.+|.+..
T Consensus 180 GaIEl-sILS~~ygveI~vvDiqt~rid~fged~------~~~~rv~lly-dGIHYD~l~m~~ 234 (307)
T KOG3288|consen 180 GAIEL-SILSDYYGVEICVVDIQTVRIDRFGEDK------NFDNRVLLLY-DGIHYDPLAMNE 234 (307)
T ss_pred ceEEe-eeehhhhceeEEEEecceeeehhcCCCC------CCCceEEEEe-cccccChhhhcc
Confidence 99876 599999999999999753 34455321 1245667777 599999999854
No 6
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.45 E-value=0.0007 Score=64.08 Aligned_cols=87 Identities=17% Similarity=0.069 Sum_probs=55.6
Q ss_pred HHHHhhhhcccccCChhHHHHHHHHhccCCCCCCCCccccccchhH--Hhhhhcce--EEEEEccCcceecccCCCCCCC
Q 045719 231 ELHLNMEHYSHLYGTYERVNELIHAISYFENCPGSDKWMTMPDMGH--LIASAYNI--VVFHLSMKQCLTFLPLRSNPVP 306 (384)
Q Consensus 231 el~~~~~~Y~~~~~~~~~~~~~l~~L~~~~~~a~~~kWl~~p~~g~--iiAn~ynr--pVi~ls~~~s~tffPl~~~P~~ 306 (384)
+|+++.++|.+++.++..+++++..- ++.+ .+ -.++.+ +|+++.++ -|.+++-+..-++.+..-| .
T Consensus 166 ~ik~~adfy~pFI~e~~tV~~fC~~e--VEPm---~k---esdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fp-e- 235 (256)
T KOG3991|consen 166 FIKSNADFYQPFIDEGMTVKAFCTQE--VEPM---YK---ESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFP-E- 235 (256)
T ss_pred HHhhChhhhhccCCCCCcHHHHHHhh--cchh---hh---ccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCc-c-
Confidence 47788899999988877888888752 2211 11 123334 47788884 5667765444455544332 1
Q ss_pred CCCCCeEEEEEecCCcceEeecC
Q 045719 307 TDSRKEIAIGFVNNNHFVEVFLL 329 (384)
Q Consensus 307 ~~~~~pI~La~v~~nHFvsl~lk 329 (384)
-+.|-|.|.|- +-||..|+.+
T Consensus 236 -~s~P~I~LLYr-pGHYdilY~~ 256 (256)
T KOG3991|consen 236 -ASAPEIYLLYR-PGHYDILYKK 256 (256)
T ss_pred -ccCceEEEEec-CCccccccCC
Confidence 23678999996 7999988753
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=95.60 E-value=0.012 Score=57.53 Aligned_cols=117 Identities=9% Similarity=-0.095 Sum_probs=71.4
Q ss_pred CCCCCchhhhhHHHHhhhhcccccCCCCCcchHHHHhHhcCCc-----hhHHHHHHHHHHHHHHhhhhcccccCCh----
Q 045719 176 LKSNPFVNEFPAALQSYIHHIKDVAPDGNCGFRAIADLMGFGE-----NGWLQVRKDLLNELHLNMEHYSHLYGTY---- 246 (384)
Q Consensus 176 ~~~~p~~~q~p~~l~~~i~~i~dV~gDGnCgFRAiA~~Lg~~e-----d~~~~VR~~li~el~~~~~~Y~~~~~~~---- 246 (384)
..-.+++-.+|.....--..-.|..|||||.|-+|+++|+..- +.=...|..=......+...|.++.-++
T Consensus 153 Dl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~t~~ 232 (306)
T COG5539 153 DLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEETLA 232 (306)
T ss_pred cccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchhhhh
Confidence 3334455555555555455557889999999999999998741 1112222222223333445555542222
Q ss_pred -hHHHHHHHHhccCCCCCCCCccccccchhHHhhhhcceEEEEEccC-cceeccc
Q 045719 247 -ERVNELIHAISYFENCPGSDKWMTMPDMGHLIASAYNIVVFHLSMK-QCLTFLP 299 (384)
Q Consensus 247 -~~~~~~l~~L~~~~~~a~~~kWl~~p~~g~iiAn~ynrpVi~ls~~-~s~tffP 299 (384)
..|+.+.+.+ -....|+..+. .+.||+.+..|+-++... .++-|-+
T Consensus 233 m~~~dt~~ne~------~~~a~~g~~~e-i~qLas~lk~~~~~~nT~~~~ik~n~ 280 (306)
T COG5539 233 MVLWDTYVNEV------LFDASDGITIE-IQQLASLLKNPHYYTNTASPSIKCNI 280 (306)
T ss_pred cchHHHHHhhh------cccccccchHH-HHHHHHHhcCceEEeecCCceEEeec
Confidence 2467777766 34679987664 488999999999888754 3444443
No 8
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=94.61 E-value=0.025 Score=36.44 Aligned_cols=25 Identities=24% Similarity=0.632 Sum_probs=21.8
Q ss_pred ccCceeecccccchhHHHHHHHhcC
Q 045719 18 VCGCTIRSTHGLPCAHEIVEYKRES 42 (384)
Q Consensus 18 ~C~~~~~~~~GlPCah~l~~~l~~~ 42 (384)
.|+|-.....||||+|-|+.+...|
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~~ 26 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHIG 26 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHhC
Confidence 6899888999999999999887654
No 9
>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=93.40 E-value=0.13 Score=43.50 Aligned_cols=63 Identities=22% Similarity=0.342 Sum_probs=39.8
Q ss_pred ccCCCCCcchHHHHhHhcCCchhHHHHHHHHHHHHHHhhhhcccccCChhHHHHHHHHhccCCCCCCCCccccccchhHH
Q 045719 198 DVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYSHLYGTYERVNELIHAISYFENCPGSDKWMTMPDMGHL 277 (384)
Q Consensus 198 dV~gDGnCgFRAiA~~Lg~~ed~~~~VR~~li~el~~~~~~Y~~~~~~~~~~~~~l~~L~~~~~~a~~~kWl~~p~~g~i 277 (384)
.+++||+||+|+||.-+.. | ++++ |.. . ++.-..+.+.|++--+++++
T Consensus 3 sPP~DG~CG~H~i~aI~n~---------------m----------~~~~--~t~---~--l~~~~r~~d~W~~dedl~~~ 50 (108)
T PF05412_consen 3 SPPGDGSCGWHCIAAIMNH---------------M----------MGGE--FTT---P--LPQRNRPSDDWADDEDLYQV 50 (108)
T ss_pred CCCCCCchHHHHHHHHHHH---------------h----------hccC--CCc---c--ccccCCChHHccChHHHHHH
Confidence 5799999999999876532 1 2211 000 0 11123467899999999999
Q ss_pred hhhhcceEEEEEccCc
Q 045719 278 IASAYNIVVFHLSMKQ 293 (384)
Q Consensus 278 iAn~ynrpVi~ls~~~ 293 (384)
|-.. +.|+-+-..+.
T Consensus 51 iq~l-~lPat~~~~~~ 65 (108)
T PF05412_consen 51 IQSL-RLPATLDRNGA 65 (108)
T ss_pred HHHc-cCceeccCCCC
Confidence 8766 77776544433
No 10
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=88.76 E-value=0.28 Score=33.63 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=24.1
Q ss_pred CCCCCccCceeecccccchhHHHHHHHh
Q 045719 13 GIDVSVCGCTIRSTHGLPCAHEIVEYKR 40 (384)
Q Consensus 13 ~~~~~~C~~~~~~~~GlPCah~l~~~l~ 40 (384)
+.+...|+|......|.||.|.+|.++.
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~ 38 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLA 38 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHh
Confidence 4457899999888899999999998874
No 11
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=79.38 E-value=1.8 Score=42.73 Aligned_cols=111 Identities=16% Similarity=0.031 Sum_probs=77.8
Q ss_pred CCCCcchHHHHhHhcCCchhHHHHHHHHHHHHHHhhhhcccccCChhHHHHHHHHhccCCCCCCCCccccccchhHHhhh
Q 045719 201 PDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYSHLYGTYERVNELIHAISYFENCPGSDKWMTMPDMGHLIAS 280 (384)
Q Consensus 201 gDGnCgFRAiA~~Lg~~ed~~~~VR~~li~el~~~~~~Y~~~~~~~~~~~~~l~~L~~~~~~a~~~kWl~~p~~g~iiAn 280 (384)
.|--|.|+|.+..++-- +=..+|+.+..|+.+++|.|...+.+. +.-.++..| ..++-|++--.---+|.+
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~-~~i~y~~~i------~k~d~~~dG~ieia~iS~ 189 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEI-DVIAYATWI------VKPDSQGDGCIEIAIISD 189 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCc-chHHHHHhh------hccccCCCceEEEeEecc
Confidence 45789999999988753 778899999999999999999877654 233334444 456788843333357899
Q ss_pred hcceEEEEEccCcc--eecccCCCCCCCCCCCCeEEEEEecCCcceEeec
Q 045719 281 AYNIVVFHLSMKQC--LTFLPLRSNPVPTDSRKEIAIGFVNNNHFVEVFL 328 (384)
Q Consensus 281 ~ynrpVi~ls~~~s--~tffPl~~~P~~~~~~~pI~La~v~~nHFvsl~l 328 (384)
.+++-|.+...... ..|.+- +...-|++-|. +-||.++++
T Consensus 190 ~l~v~i~~Vdv~~~~~dr~~~~-------~~~q~~~i~f~-g~hfD~~t~ 231 (306)
T COG5539 190 QLPVRIHVVDVDKDSEDRYNSH-------PYVQRISILFT-GIHFDEETL 231 (306)
T ss_pred ccceeeeeeecchhHHhhccCC-------hhhhhhhhhhc-ccccchhhh
Confidence 99988887775422 334421 11234777775 899987775
No 12
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=65.27 E-value=5.5 Score=43.72 Aligned_cols=52 Identities=15% Similarity=0.222 Sum_probs=38.5
Q ss_pred hhHHhhhhcceEEEEEccC-----cc---------eecccCCCCCCCCCCCCeEEEEEecCCcceEee
Q 045719 274 MGHLIASAYNIVVFHLSMK-----QC---------LTFLPLRSNPVPTDSRKEIAIGFVNNNHFVEVF 327 (384)
Q Consensus 274 ~g~iiAn~ynrpVi~ls~~-----~s---------~tffPl~~~P~~~~~~~pI~La~v~~nHFvsl~ 327 (384)
+.+++|+...|||++++.. .+ ..|+|+-.++..+ .--||+|+|- .-||..++
T Consensus 225 hifvl~~ilRrpivvvsd~mlR~s~~~sfap~~~ggiylpLe~p~~~c-~r~pLvl~yd-~~hf~~lv 290 (774)
T KOG4345|consen 225 HIFVLAHILRRPIVVVSDTMLRDSGGESFAPIPVGGIYLPLEVPAQEC-HRSPLVLAYD-QAHFSALV 290 (774)
T ss_pred HHHHHHHHhhCCeeEecccccccCCCcccccCccCceEEeccCchhhc-ccchhhhhhH-hhhhhhhh
Confidence 6788999999999999841 11 4678887766443 3468999994 68998883
No 13
>PRK09784 hypothetical protein; Provisional
Probab=51.48 E-value=9 Score=37.33 Aligned_cols=39 Identities=26% Similarity=0.311 Sum_probs=28.1
Q ss_pred HHHhhhhcccccCCCCCcchHHHHhHhcCCchhHHHHHHH
Q 045719 188 ALQSYIHHIKDVAPDGNCGFRAIADLMGFGENGWLQVRKD 227 (384)
Q Consensus 188 ~l~~~i~~i~dV~gDGnCgFRAiA~~Lg~~ed~~~~VR~~ 227 (384)
.=+.|+++-.-|.|||-|..|||-..- ..+-+|..+-..
T Consensus 194 ~n~~~glkyapvdgdgycllrailvlk-~h~yswal~s~k 232 (417)
T PRK09784 194 INKTYGLKYAPVDGDGYCLLRAILVLK-QHDYSWALGSHK 232 (417)
T ss_pred hhhhhCceecccCCCchhHHHHHHHhh-hcccchhhccch
Confidence 346688899999999999999996543 234566655433
No 14
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.78 E-value=57 Score=22.94 Aligned_cols=47 Identities=17% Similarity=0.228 Sum_probs=30.6
Q ss_pred hhhhHHHHhhhhcccccCCCCCcchHHHHhHhcCCchhHHHHHHHHHHHHH
Q 045719 183 NEFPAALQSYIHHIKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELH 233 (384)
Q Consensus 183 ~q~p~~l~~~i~~i~dV~gDGnCgFRAiA~~Lg~~ed~~~~VR~~li~el~ 233 (384)
+++|..-+..|.... ..+.-+..||..||.+...=..+....++.|+
T Consensus 3 ~~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 3 DQLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp CTS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hhCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 344444444444333 55678999999999997777777777777665
No 15
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=35.99 E-value=1.3e+02 Score=27.46 Aligned_cols=62 Identities=16% Similarity=0.239 Sum_probs=49.8
Q ss_pred hcccccCCCCCcchHHHHhHhcCCchhHHHHHHHHHHHHHHhhhhcccccCChhHHHHHHHHh
Q 045719 194 HHIKDVAPDGNCGFRAIADLMGFGENGWLQVRKDLLNELHLNMEHYSHLYGTYERVNELIHAI 256 (384)
Q Consensus 194 ~~i~dV~gDGnCgFRAiA~~Lg~~ed~~~~VR~~li~el~~~~~~Y~~~~~~~~~~~~~l~~L 256 (384)
..+++.-.|+.||..+|..+-+.+.+.|..+.+.|+.. ..-...|..-...+.+|+.+++.+
T Consensus 52 ~e~~~ll~~~~~~~~~ig~A~~igr~Rw~ela~l~~~~-~~~~~~~~~~~~s~~rf~~l~~~l 113 (185)
T PF07506_consen 52 PEEVRLLADVEVGIIAIGPAPKIGRPRWIELAELMIAA-NNFTSAYFRALLSDTRFEALVRAL 113 (185)
T ss_pred HHHHHHHhhccccHHHHHHHHHCCCcCHHHHHHHHHHH-HhhhHHHHHhcccCCcHHHHHHHH
Confidence 45677889999999999999999999999999999333 333455666666677999999987
No 16
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 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 sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=30.40 E-value=1.7e+02 Score=24.23 Aligned_cols=52 Identities=17% Similarity=0.252 Sum_probs=27.7
Q ss_pred cccccchhHHhhhhcceEEEEEccCcceecccCCCCCCCCCCCCeEEEEEecCCcceEeecCCC
Q 045719 268 WMTMPDMGHLIASAYNIVVFHLSMKQCLTFLPLRSNPVPTDSRKEIAIGFVNNNHFVEVFLLPG 331 (384)
Q Consensus 268 Wl~~p~~g~iiAn~ynrpVi~ls~~~s~tffPl~~~P~~~~~~~pI~La~v~~nHFvsl~lk~~ 331 (384)
-.++.++ ..+|..||...-.+..... -|... .-| +|.++..+||+.|...++
T Consensus 44 g~s~~~L-~~~~~~~gl~~~~~~~~~~--~l~~~--------~~P-~I~~~~~~h~vVi~~~~~ 95 (131)
T PF03412_consen 44 GTSLADL-KRAARKYGLKAKAVKLNFE--KLKRL--------PLP-AIAHLKDGHFVVIYKIDD 95 (131)
T ss_dssp B--CCCH-HHHHHHTTEEEEEEE--GG--GCTCG--------GSS-EEEEECCCEEEEEEEECC
T ss_pred CCCHHHH-HHHHHhcccceeeeecchh--hhhhc--------ccc-EEEEecCcceEEEEeEcC
Confidence 3455544 4678899987766653222 12111 123 334447899999887543
No 17
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=29.64 E-value=50 Score=28.13 Aligned_cols=31 Identities=23% Similarity=0.520 Sum_probs=27.4
Q ss_pred CcchH-HHHhHhcCCchhHHHHHHHHHHHHHH
Q 045719 204 NCGFR-AIADLMGFGENGWLQVRKDLLNELHL 234 (384)
Q Consensus 204 nCgFR-AiA~~Lg~~ed~~~~VR~~li~el~~ 234 (384)
.|-|| ..-.++|++.+.+..+.+++.+||..
T Consensus 77 PCplrd~aL~~igls~~EYm~lKkelae~i~~ 108 (109)
T TIGR03277 77 PCPLRDSALQRIGMSPEEYMELKKKLAEELLK 108 (109)
T ss_pred CCcCchHHHHHcCCCHHHHHHHHHHHHHHHhc
Confidence 47899 67788999999999999999999864
No 18
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=29.25 E-value=49 Score=25.21 Aligned_cols=18 Identities=33% Similarity=0.470 Sum_probs=14.5
Q ss_pred CCCCcc--hHHHHhHhcCCc
Q 045719 201 PDGNCG--FRAIADLMGFGE 218 (384)
Q Consensus 201 gDGnCg--FRAiA~~Lg~~e 218 (384)
-||||. +||.|...|.++
T Consensus 20 ~~~nc~~~~RAaarkf~V~r 39 (58)
T PF09607_consen 20 KDNNCKGNQRAAARKFNVSR 39 (58)
T ss_dssp H-TTTTT-HHHHHHHTTS-H
T ss_pred HccchhhhHHHHHHHhCccH
Confidence 689998 999999999974
No 19
>KOG4844 consensus Mitochondrial ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=28.11 E-value=23 Score=29.43 Aligned_cols=18 Identities=28% Similarity=0.536 Sum_probs=12.3
Q ss_pred cccCCCCCCc-cCCCCccC
Q 045719 115 KKNTRGRPNS-KANASTCR 132 (384)
Q Consensus 115 K~~tKG~pk~-k~~~stkR 132 (384)
|...||+||+ ++.+..+|
T Consensus 82 kRrgKGapKk~kk~~aa~~ 100 (102)
T KOG4844|consen 82 KRRGKGAPKKGKKKRAAKR 100 (102)
T ss_pred HHccCCCCcccchhhhhhc
Confidence 6788999998 44444444
No 20
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=26.78 E-value=34 Score=38.92 Aligned_cols=43 Identities=26% Similarity=0.467 Sum_probs=34.3
Q ss_pred CCccCceeecccccchhHHHHHHHhcC-CCCCCCcccccccccc
Q 045719 16 VSVCGCTIRSTHGLPCAHEIVEYKRES-RPIPLECIDSHWKKLD 58 (384)
Q Consensus 16 ~~~C~~~~~~~~GlPCah~l~~~l~~~-~~l~~~~~H~~W~~L~ 58 (384)
.-.|+|-..-..||||.|.|.-+...| ..|+..-|=.-|.+-.
T Consensus 578 ~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTKdA 621 (846)
T PLN03097 578 EVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTKDA 621 (846)
T ss_pred eEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchhhh
Confidence 678999999999999999998665443 5677777778888543
No 21
>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=25.54 E-value=3.8e+02 Score=22.82 Aligned_cols=89 Identities=19% Similarity=0.146 Sum_probs=55.1
Q ss_pred CCcchHHHHhHhcCCc-hhHHHHHHHHHHHHHHhhhhcccccCChhHHHHHHHHhccCCCCCCCCccccccchhHHhhhh
Q 045719 203 GNCGFRAIADLMGFGE-NGWLQVRKDLLNELHLNMEHYSHLYGTYERVNELIHAISYFENCPGSDKWMTMPDMGHLIASA 281 (384)
Q Consensus 203 GnCgFRAiA~~Lg~~e-d~~~~VR~~li~el~~~~~~Y~~~~~~~~~~~~~l~~L~~~~~~a~~~kWl~~p~~g~iiAn~ 281 (384)
-+|..-||+.+++.++ +=|..+...+=+-|-.+.+ + ..-|=-.|+.-++|-.
T Consensus 3 ~~CLL~A~s~at~~~~~~LW~~L~~~lPDSlL~n~e---------------i------------~~~GLSTDhltaLa~~ 55 (104)
T PF05381_consen 3 LDCLLVAISQATSISPETLWATLCEILPDSLLDNPE---------------I------------RTLGLSTDHLTALAYR 55 (104)
T ss_pred cceeHHhhhhhhCCCHHHHHHHHHHhCchhhcCchh---------------h------------hhcCCcHHHHHHHHHH
Confidence 4799999999999984 4565554443332221111 0 1111123678899999
Q ss_pred cceEEEEEccCcceecccCCCCCCCCCCCCeEEEEEecC--CcceE
Q 045719 282 YNIVVFHLSMKQCLTFLPLRSNPVPTDSRKEIAIGFVNN--NHFVE 325 (384)
Q Consensus 282 ynrpVi~ls~~~s~tffPl~~~P~~~~~~~pI~La~v~~--nHFvs 325 (384)
|+--+.+.+......|-... ....+.|-|-.| -||..
T Consensus 56 ~~~~~~~hs~~~~~~~Gi~~-------as~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 56 YHFQCTFHSDHGVLHYGIKD-------ASTVFTITHTPGPPGHFSL 94 (104)
T ss_pred HheEEEEEcCCceEEeecCC-------CceEEEEEeCCCCCCcccc
Confidence 99888888876665555322 245677777533 78876
No 22
>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=25.06 E-value=77 Score=26.34 Aligned_cols=20 Identities=25% Similarity=0.390 Sum_probs=17.2
Q ss_pred cCCCCCcchHHHHhHhcCCc
Q 045719 199 VAPDGNCGFRAIADLMGFGE 218 (384)
Q Consensus 199 V~gDGnCgFRAiA~~Lg~~e 218 (384)
+..|.||..-|||.+||.+=
T Consensus 3 ~sR~NNCLVVAis~~L~~T~ 22 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVTL 22 (104)
T ss_pred ccCCCCeEeehHHHHhcchH
Confidence 45689999999999999873
Done!