Query 046185
Match_columns 380
No_of_seqs 252 out of 340
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:30:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046185.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046185hhsearch_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 2.2E-17 4.7E-22 139.9 5.1 109 254-377 1-121 (121)
2 KOG2606 OTU (ovarian tumor)-li 99.4 1.1E-13 2.3E-18 132.8 6.5 130 237-380 148-295 (302)
3 KOG2605 OTU (ovarian tumor)-li 98.3 3.9E-07 8.5E-12 91.8 4.2 126 240-379 210-340 (371)
4 PF10275 Peptidase_C65: Peptid 97.8 3.7E-05 7.9E-10 73.4 6.9 27 241-267 34-60 (244)
5 KOG3288 OTU-like cysteine prot 97.7 0.0001 2.2E-09 70.3 6.6 119 247-380 109-230 (307)
6 COG5539 Predicted cysteine pro 97.3 0.00011 2.4E-09 71.2 2.6 121 227-355 150-282 (306)
7 KOG3991 Uncharacterized conser 97.2 0.0024 5.1E-08 60.2 9.6 86 282-380 163-253 (256)
8 smart00575 ZnF_PMZ plant mutat 95.1 0.012 2.7E-07 37.6 1.5 24 79-102 2-25 (28)
9 PF05412 Peptidase_C33: Equine 92.5 0.13 2.8E-06 43.2 3.3 61 251-344 2-62 (108)
10 PF04434 SWIM: SWIM zinc finge 89.6 0.19 4.1E-06 34.3 1.4 25 77-101 14-38 (40)
11 COG5539 Predicted cysteine pro 72.6 7.2 0.00016 38.5 5.3 107 255-379 119-228 (306)
12 PLN03097 FHY3 Protein FAR-RED 64.9 13 0.00029 42.0 6.2 111 6-117 475-619 (846)
13 KOG4345 NF-kappa B regulator A 52.3 8 0.00017 42.3 1.7 50 328-379 225-288 (774)
14 PRK09784 hypothetical protein; 49.5 11 0.00024 36.5 2.0 40 243-283 195-234 (417)
15 PF04545 Sigma70_r4: Sigma-70, 44.1 35 0.00076 23.9 3.5 47 237-287 3-49 (50)
16 TIGR03277 methan_mark_9 putati 36.2 31 0.00068 29.2 2.5 34 256-289 75-109 (109)
17 PF07506 RepB: RepB plasmid pa 31.5 72 0.0016 29.0 4.4 61 248-309 52-113 (185)
18 cd00258 GM2-AP GM2 activator p 30.4 25 0.00054 31.9 1.1 22 75-97 89-110 (162)
19 PF09607 BrkDBD: Brinker DNA-b 28.8 46 0.001 25.1 2.1 19 254-272 19-39 (58)
20 PF05379 Peptidase_C23: Carlav 24.7 48 0.001 27.0 1.7 69 258-353 4-72 (89)
21 smart00412 Cu_FIST Copper-Fist 23.7 41 0.00088 23.4 0.9 13 160-172 27-39 (39)
22 KOG3146 Dolichyl pyrophosphate 23.7 57 0.0012 31.0 2.2 42 48-95 58-102 (228)
23 PF05415 Peptidase_C36: Beet n 20.2 66 0.0014 26.5 1.6 21 253-273 3-23 (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=99.69 E-value=2.2e-17 Score=139.88 Aligned_cols=109 Identities=25% Similarity=0.403 Sum_probs=84.4
Q ss_pred CCCCCccHHHHHHHhc----cCCchHHHHHHHHHHHHh-hcccccccccCChhHHHHHHHhccCCCCCCCcccccccccc
Q 046185 254 VADGNCGFRAIADLIG----LGEDGWVQVRKDLLNELY-SHLDDYGKLYGPERVNELIHILSYYENWPASSDRWMTMPDM 328 (380)
Q Consensus 254 ~gDGhCgFraiA~~lg----~~e~~~~~VR~~l~~el~-~~~~~y~~~~~~~~~~~~~~~L~~~~~~~~~~~~Wl~~p~~ 328 (380)
+|||||+|||||++|+ .+++.|..||++++++|+ .+++.|.+++.++ .| .....|++.+++
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 9988887766422 44 356799999876
Q ss_pred hhhhhhccceEEEEEeCCcc--eeeecCCCCCCCCCCCCcEEEEEec-----CCcc
Q 046185 329 GHLIASCYNVVLFHLSSVQC--LTFLPLRSEPVHILSRRNIALGYVF-----GNHF 377 (380)
Q Consensus 329 G~iiA~~y~~pI~~ls~~~s--~t~~P~~~~p~~~~~~~~I~L~~~~-----~nHf 377 (380)
+++|+.|+|+|++++.... ..+.+..+.-++....++|+|+|.. +|||
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 9999999999999875332 3343332211122234789999998 9998
No 2
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.44 E-value=1.1e-13 Score=132.82 Aligned_cols=130 Identities=16% Similarity=0.255 Sum_probs=107.7
Q ss_pred cccchhhhhhcccccccCCCCCccHHHHHHHhccCC---chHHHHHHHHHHHHhhcccccccccCC---------hhHHH
Q 046185 237 DEFPVGLQSYIHHIKDVVADGNCGFRAIADLIGLGE---DGWVQVRKDLLNELYSHLDDYGKLYGP---------ERVNE 304 (380)
Q Consensus 237 ~q~p~~l~~~i~~i~dv~gDGhCgFraiA~~lg~~e---~~~~~VR~~l~~el~~~~~~y~~~~~~---------~~~~~ 304 (380)
..+...|..-.+..+|+++||||.|+||++||.+.. -+...+|+..++||++|.++|.+|+-+ ++|+.
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 467788999999999999999999999999998874 568999999999999999999998761 36999
Q ss_pred HHHHhccCCCCCCCcccccccccchhhhhhccceEEEEEeCCcc-eeeecCCCCCCCCCCCCcEEEEEec-----CCccc
Q 046185 305 LIHILSYYENWPASSDRWMTMPDMGHLIASCYNVVLFHLSSVQC-LTFLPLRSEPVHILSRRNIALGYVF-----GNHFV 378 (380)
Q Consensus 305 ~~~~L~~~~~~~~~~~~Wl~~p~~G~iiA~~y~~pI~~ls~~~s-~t~~P~~~~p~~~~~~~~I~L~~~~-----~nHfv 378 (380)
|++.+. .++.|++.++. ++|+++|++||.||+.+++ .+|.+..+. .+||+|.|+- +-||+
T Consensus 228 Yc~eI~-------~t~~WGgelEL-~AlShvL~~PI~Vy~~~~p~~~~geey~k------d~pL~lvY~rH~y~LGeHYN 293 (302)
T KOG2606|consen 228 YCREIR-------NTAAWGGELEL-KALSHVLQVPIEVYQADGPILEYGEEYGK------DKPLILVYHRHAYGLGEHYN 293 (302)
T ss_pred HHHHhh-------hhccccchHHH-HHHHHhhccCeEEeecCCCceeechhhCC------CCCeeeehHHhHHHHHhhhc
Confidence 999995 67899999876 8999999999999997655 556554432 2578888862 36666
Q ss_pred cC
Q 046185 379 EV 380 (380)
Q Consensus 379 ~v 380 (380)
.|
T Consensus 294 S~ 295 (302)
T KOG2606|consen 294 SV 295 (302)
T ss_pred cc
Confidence 53
No 3
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.33 E-value=3.9e-07 Score=91.81 Aligned_cols=126 Identities=19% Similarity=0.172 Sum_probs=94.5
Q ss_pred chhhhhhcccccccCCCCCccHHHHHHHhccCCchHHHHHHHHHHHHhhcccccccccCChhHHHHHHHhccCCCCCCCc
Q 046185 240 PVGLQSYIHHIKDVVADGNCGFRAIADLIGLGEDGWVQVRKDLLNELYSHLDDYGKLYGPERVNELIHILSYYENWPASS 319 (380)
Q Consensus 240 p~~l~~~i~~i~dv~gDGhCgFraiA~~lg~~e~~~~~VR~~l~~el~~~~~~y~~~~~~~~~~~~~~~L~~~~~~~~~~ 319 (380)
-..+..|+..+..|.+||+|.|||+|+|+.++.|.|..+|++..++++.++++|..+.. +.|..+++.... .
T Consensus 210 ~~~~~~~g~e~~Kv~edGsC~fra~aDQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt-~~~~~y~k~kr~-------~ 281 (371)
T KOG2605|consen 210 AKRKKHFGFEYKKVVEDGSCLFRALADQVYGDDEQHDHNRRECVDQLKKERDFYEDYVT-EDFTSYIKRKRA-------D 281 (371)
T ss_pred HHHHHHhhhhhhhcccCCchhhhccHHHhhcCHHHHHHHHHHHHHHHhhcccccccccc-cchhhccccccc-------C
Confidence 35567889999999999999999999999999999999999999999999999988874 678888887763 3
Q ss_pred ccccccccchhhhhh---ccceEEEEEeCCc-c-eeeecCCCCCCCCCCCCcEEEEEecCCcccc
Q 046185 320 DRWMTMPDMGHLIAS---CYNVVLFHLSSVQ-C-LTFLPLRSEPVHILSRRNIALGYVFGNHFVE 379 (380)
Q Consensus 320 ~~Wl~~p~~G~iiA~---~y~~pI~~ls~~~-s-~t~~P~~~~p~~~~~~~~I~L~~~~~nHfv~ 379 (380)
+.|++..++ +++|. -...|+++.+.+. | .... |...+....+++.|+...||..
T Consensus 282 ~~~gnhie~-Qa~a~~~~~~~~~~~~~~~~~t~~~~~~-----~~~~~~~~~~~~n~~~~~h~~~ 340 (371)
T KOG2605|consen 282 GEPGNHIEQ-QAAADIYEEIEKPLNITSFKDTCYIQTP-----PAIEESVKMEKYNFWVEVHYNT 340 (371)
T ss_pred CCCcchHHH-hhhhhhhhhccccceeecccccceeccC-----cccccchhhhhhcccchhhhhh
Confidence 578887765 88885 3445555554322 1 1112 2333333458888888888864
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=97.83 E-value=3.7e-05 Score=73.42 Aligned_cols=27 Identities=33% Similarity=0.421 Sum_probs=21.0
Q ss_pred hhhhhhcccccccCCCCCccHHHHHHH
Q 046185 241 VGLQSYIHHIKDVVADGNCGFRAIADL 267 (380)
Q Consensus 241 ~~l~~~i~~i~dv~gDGhCgFraiA~~ 267 (380)
+.|......+..|.|||||+|||++-+
T Consensus 34 ~~L~~~y~~~R~vRGDGNCFYRAf~F~ 60 (244)
T PF10275_consen 34 KKLSQKYSGIRRVRGDGNCFYRAFGFS 60 (244)
T ss_dssp HHHHHHEEEEE-B-SSSTHHHHHHHHH
T ss_pred HHHHhhhhheEeecCCccHHHHHHHHH
Confidence 556666788899999999999999876
No 5
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=97.66 E-value=0.0001 Score=70.29 Aligned_cols=119 Identities=20% Similarity=0.245 Sum_probs=80.9
Q ss_pred cccccccCCCCCccHHHHHHHhccCCchH-HHHHHHHHHHHhhcccccccccCChhHHHHHHHhccCCCCCCCccccccc
Q 046185 247 IHHIKDVVADGNCGFRAIADLIGLGEDGW-VQVRKDLLNELYSHLDDYGKLYGPERVNELIHILSYYENWPASSDRWMTM 325 (380)
Q Consensus 247 i~~i~dv~gDGhCgFraiA~~lg~~e~~~-~~VR~~l~~el~~~~~~y~~~~~~~~~~~~~~~L~~~~~~~~~~~~Wl~~ 325 (380)
++...-|+.|--|+|+||+--+....+.- .++|+-+.+|+-++++.|..-+-...=++|+.=+. ..+.|++-
T Consensus 109 vl~~~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~-------k~dsWGGa 181 (307)
T KOG3288|consen 109 VLSRRVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWIL-------KMDSWGGA 181 (307)
T ss_pred eeEEEeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHc-------cccccCce
Confidence 34456688899999999988775543222 68999999999999999975333222233343332 33677776
Q ss_pred ccchhhhhhccceEEEEEeC--CcceeeecCCCCCCCCCCCCcEEEEEecCCccccC
Q 046185 326 PDMGHLIASCYNVVLFHLSS--VQCLTFLPLRSEPVHILSRRNIALGYVFGNHFVEV 380 (380)
Q Consensus 326 p~~G~iiA~~y~~pI~~ls~--~~s~t~~P~~~~p~~~~~~~~I~L~~~~~nHfv~v 380 (380)
.+. .||++.|++-|++++. ..+..|.+-. +- ..-++|.| ++-||.++
T Consensus 182 IEl-sILS~~ygveI~vvDiqt~rid~fged~-----~~-~~rv~lly-dGIHYD~l 230 (307)
T KOG3288|consen 182 IEL-SILSDYYGVEICVVDIQTVRIDRFGEDK-----NF-DNRVLLLY-DGIHYDPL 230 (307)
T ss_pred EEe-eeehhhhceeEEEEecceeeehhcCCCC-----CC-CceEEEEe-cccccChh
Confidence 654 5899999999999985 4556666432 11 12466765 69999863
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=0.00011 Score=71.21 Aligned_cols=121 Identities=12% Similarity=-0.068 Sum_probs=88.1
Q ss_pred CCCccCcccccccchhhhhhcccccccCCCCCccHHHHHHHhccCC-----chHHHHHHHHHHHHhhcccccccccCCh-
Q 046185 227 STPVKSITFIDEFPVGLQSYIHHIKDVVADGNCGFRAIADLIGLGE-----DGWVQVRKDLLNELYSHLDDYGKLYGPE- 300 (380)
Q Consensus 227 ~~p~~~~~~~~q~p~~l~~~i~~i~dv~gDGhCgFraiA~~lg~~e-----~~~~~VR~~l~~el~~~~~~y~~~~~~~- 300 (380)
+.|..-.+++-.+|.....--..-.|..|||||.|.+|+++|+..- +-=...|..-..+...+...|.++..|+
T Consensus 150 snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~ 229 (306)
T COG5539 150 SNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEE 229 (306)
T ss_pred hCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchh
Confidence 4566666677777777776666678999999999999999999863 2224555555666666777787766532
Q ss_pred -----hHHHHHHHhccCCCCCCCcccccccccchhhhhhccceEEEEEeC-CcceeeecCC
Q 046185 301 -----RVNELIHILSYYENWPASSDRWMTMPDMGHLIASCYNVVLFHLSS-VQCLTFLPLR 355 (380)
Q Consensus 301 -----~~~~~~~~L~~~~~~~~~~~~Wl~~p~~G~iiA~~y~~pI~~ls~-~~s~t~~P~~ 355 (380)
.|+.+++.+. ..+.|+..++. ++||+.+.+|+.++.. +.+..|.+-.
T Consensus 230 t~~m~~~dt~~ne~~-------~~a~~g~~~ei-~qLas~lk~~~~~~nT~~~~ik~n~c~ 282 (306)
T COG5539 230 TLAMVLWDTYVNEVL-------FDASDGITIEI-QQLASLLKNPHYYTNTASPSIKCNICG 282 (306)
T ss_pred hhhcchHHHHHhhhc-------ccccccchHHH-HHHHHHhcCceEEeecCCceEEeeccc
Confidence 4777888775 56789866654 8999999999999975 4556666543
No 7
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.20 E-value=0.0024 Score=60.23 Aligned_cols=86 Identities=14% Similarity=-0.012 Sum_probs=51.4
Q ss_pred HHHHHhhcccccccccC-ChhHHHHHHHhccCCCCCCCcccccccccchh--hhhhccceE--EEEEeCCcceeeecCCC
Q 046185 282 LLNELYSHLDDYGKLYG-PERVNELIHILSYYENWPASSDRWMTMPDMGH--LIASCYNVV--LFHLSSVQCLTFLPLRS 356 (380)
Q Consensus 282 l~~el~~~~~~y~~~~~-~~~~~~~~~~L~~~~~~~~~~~~Wl~~p~~G~--iiA~~y~~p--I~~ls~~~s~t~~P~~~ 356 (380)
.-.+|+++.|.|.+|+. +..+++++..=- . |+.+ ..+|-+ +|+++.++- |.+++-+..-|+.++.-
T Consensus 163 tS~~ik~~adfy~pFI~e~~tV~~fC~~eV-E-----Pm~k---esdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~f 233 (256)
T KOG3991|consen 163 TSGFIKSNADFYQPFIDEGMTVKAFCTQEV-E-----PMYK---ESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDF 233 (256)
T ss_pred HHHHHhhChhhhhccCCCCCcHHHHHHhhc-c-----hhhh---ccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcC
Confidence 34567788888888887 467777776541 1 1111 123334 688888864 44455444445554432
Q ss_pred CCCCCCCCCcEEEEEecCCccccC
Q 046185 357 EPVHILSRRNIALGYVFGNHFVEV 380 (380)
Q Consensus 357 ~p~~~~~~~~I~L~~~~~nHfv~v 380 (380)
| ....|.|+|.|- +-||..+
T Consensus 234 p---e~s~P~I~LLYr-pGHYdil 253 (256)
T KOG3991|consen 234 P---EASAPEIYLLYR-PGHYDIL 253 (256)
T ss_pred c---cccCceEEEEec-CCccccc
Confidence 2 223478999986 8899753
No 8
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=95.10 E-value=0.012 Score=37.63 Aligned_cols=24 Identities=29% Similarity=0.711 Sum_probs=21.0
Q ss_pred CccceeeccccccchhhhHHHHhc
Q 046185 79 ACGCVICQTHGLPCAHEITEYKRE 102 (380)
Q Consensus 79 ~C~~~~~~~~GlPCaH~i~~~l~~ 102 (380)
.|+|--....||||+|.|+.+...
T Consensus 2 ~CsC~~~~~~gipC~H~i~v~~~~ 25 (28)
T smart00575 2 TCSCRKFQLSGIPCRHALAAAIHI 25 (28)
T ss_pred cccCCCcccCCccHHHHHHHHHHh
Confidence 589999999999999999987654
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=92.53 E-value=0.13 Score=43.17 Aligned_cols=61 Identities=20% Similarity=0.349 Sum_probs=37.6
Q ss_pred cccCCCCCccHHHHHHHhccCCchHHHHHHHHHHHHhhcccccccccCChhHHHHHHHhccCCCCCCCcccccccccchh
Q 046185 251 KDVVADGNCGFRAIADLIGLGEDGWVQVRKDLLNELYSHLDDYGKLYGPERVNELIHILSYYENWPASSDRWMTMPDMGH 330 (380)
Q Consensus 251 ~dv~gDGhCgFraiA~~lg~~e~~~~~VR~~l~~el~~~~~~y~~~~~~~~~~~~~~~L~~~~~~~~~~~~Wl~~p~~G~ 330 (380)
+.+++||+||+++||.-+.. |.. ..|..-+ +.-..+.+.|++--++++
T Consensus 2 ysPP~DG~CG~H~i~aI~n~---------------m~~--~~~t~~l---------------~~~~r~~d~W~~dedl~~ 49 (108)
T PF05412_consen 2 YSPPGDGSCGWHCIAAIMNH---------------MMG--GEFTTPL---------------PQRNRPSDDWADDEDLYQ 49 (108)
T ss_pred CCCCCCCchHHHHHHHHHHH---------------hhc--cCCCccc---------------cccCCChHHccChHHHHH
Confidence 46899999999999876532 111 1111111 122246788999888888
Q ss_pred hhhhccceEEEEEe
Q 046185 331 LIASCYNVVLFHLS 344 (380)
Q Consensus 331 iiA~~y~~pI~~ls 344 (380)
+|-.. +.|+-+.-
T Consensus 50 ~iq~l-~lPat~~~ 62 (108)
T PF05412_consen 50 VIQSL-RLPATLDR 62 (108)
T ss_pred HHHHc-cCceeccC
Confidence 87666 55655433
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=89.64 E-value=0.19 Score=34.32 Aligned_cols=25 Identities=28% Similarity=0.643 Sum_probs=22.1
Q ss_pred CCCccceeeccccccchhhhHHHHh
Q 046185 77 RSACGCVICQTHGLPCAHEITEYKR 101 (380)
Q Consensus 77 ~~~C~~~~~~~~GlPCaH~i~~~l~ 101 (380)
...|+|......|.||.|.++.++.
T Consensus 14 ~~~CsC~~~~~~~~~CkHi~av~~~ 38 (40)
T PF04434_consen 14 QASCSCPYFQFRGGPCKHIVAVLLA 38 (40)
T ss_pred ccEeeCCCccccCCcchhHHHHHHh
Confidence 5789999999999999999998764
No 11
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=72.57 E-value=7.2 Score=38.49 Aligned_cols=107 Identities=17% Similarity=0.117 Sum_probs=73.1
Q ss_pred CCCCccHHHHHHHhccCCchHHHHHHHHHHHHhhcccccccccCChhHHHHHHHhccCCCCCCCcccccc-cccchhhhh
Q 046185 255 ADGNCGFRAIADLIGLGEDGWVQVRKDLLNELYSHLDDYGKLYGPERVNELIHILSYYENWPASSDRWMT-MPDMGHLIA 333 (380)
Q Consensus 255 gDGhCgFraiA~~lg~~e~~~~~VR~~l~~el~~~~~~y~~~~~~~~~~~~~~~L~~~~~~~~~~~~Wl~-~p~~G~iiA 333 (380)
.|--|.|+|.+-.++-- +-..+|+.+..|+.+++|.|.+...+-..-.++..|. .++-|.+ --+. .+|.
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~-------k~d~~~dG~iei-a~iS 188 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIV-------KPDSQGDGCIEI-AIIS 188 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCcchHHHHHhhh-------ccccCCCceEEE-eEec
Confidence 56789999998888653 7889999999999999999987766444444455552 4455552 1111 3799
Q ss_pred hccceEEEEEeCC--cceeeecCCCCCCCCCCCCcEEEEEecCCcccc
Q 046185 334 SCYNVVLFHLSSV--QCLTFLPLRSEPVHILSRRNIALGYVFGNHFVE 379 (380)
Q Consensus 334 ~~y~~pI~~ls~~--~s~t~~P~~~~p~~~~~~~~I~L~~~~~nHfv~ 379 (380)
+.+++-|.++... .-..|.+. |-. .-|++.|. +-||.+
T Consensus 189 ~~l~v~i~~Vdv~~~~~dr~~~~---~~~----q~~~i~f~-g~hfD~ 228 (306)
T COG5539 189 DQLPVRIHVVDVDKDSEDRYNSH---PYV----QRISILFT-GIHFDE 228 (306)
T ss_pred cccceeeeeeecchhHHhhccCC---hhh----hhhhhhhc-ccccch
Confidence 9999999988743 33555542 111 23777764 888864
No 12
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=64.89 E-value=13 Score=41.95 Aligned_cols=111 Identities=16% Similarity=0.223 Sum_probs=64.7
Q ss_pred CcCcHHHHHHHHHHHHHHHHH-HHHHHHhhhhceeeccccc-ccccccccchhHHHHHHHHHHHHHhhhc----------
Q 046185 6 SQGNFETSWAKIHNLLELQHT-DIKASFEKSLTVVQHQFKP-AKFKHIRGFISIIALNITLSELKRAISI---------- 73 (380)
Q Consensus 6 S~gDL~~v~~~i~~~v~~Q~~-~i~~s~~~~~~~~~~~~~~-~~~~~l~g~IS~~AL~~i~~q~~~~~~~---------- 73 (380)
+.-+|..-++....+++.... |.++.+.......... .+ .+-....+.-++..-.+..+|+..+..+
T Consensus 475 ~~tsL~~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~-t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~ 553 (846)
T PLN03097 475 KKTTVQEFVKQYETILQDRYEEEAKADSDTWNKQPALK-SPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDET 553 (846)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHhhhhcccCCcccc-cccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCc
Confidence 344577788888888876553 3444444322111110 11 1222233444455556666666544211
Q ss_pred -------------------CC--CCCCccceeeccccccchhhhHHHHhc-CCCcCCCcccccccc
Q 046185 74 -------------------GV--DRSACGCVICQTHGLPCAHEITEYKRE-CHPIPLERIDLHWKK 117 (380)
Q Consensus 74 -------------------~~--~~~~C~~~~~~~~GlPCaH~i~~~l~~-~~~l~~~~~h~hW~l 117 (380)
+. ..-.|+|-.....||||+|.|.-+... -..|+..-|=..|..
T Consensus 554 ~~~y~V~~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~~v~~IP~~YILkRWTK 619 (846)
T PLN03097 554 SITFRVQDFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMCQLSAIPSQYILKRWTK 619 (846)
T ss_pred eEEEEEEEecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhcCcccCchhhhhhhchh
Confidence 11 133899999999999999999866543 366777777778875
No 13
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=52.32 E-value=8 Score=42.29 Aligned_cols=50 Identities=20% Similarity=0.236 Sum_probs=35.7
Q ss_pred chhhhhhccceEEEEEeC-----Ccc---------eeeecCCCCCCCCCCCCcEEEEEecCCcccc
Q 046185 328 MGHLIASCYNVVLFHLSS-----VQC---------LTFLPLRSEPVHILSRRNIALGYVFGNHFVE 379 (380)
Q Consensus 328 ~G~iiA~~y~~pI~~ls~-----~~s---------~t~~P~~~~p~~~~~~~~I~L~~~~~nHfv~ 379 (380)
+-+++|+...+||+|++. ..+ ..|+|+..++.... ..||.|+|- .-||++
T Consensus 225 hifvl~~ilRrpivvvsd~mlR~s~~~sfap~~~ggiylpLe~p~~~c~-r~pLvl~yd-~~hf~~ 288 (774)
T KOG4345|consen 225 HIFVLAHILRRPIVVVSDTMLRDSGGESFAPIPVGGIYLPLEVPAQECH-RSPLVLAYD-QAHFSA 288 (774)
T ss_pred HHHHHHHHhhCCeeEecccccccCCCcccccCccCceEEeccCchhhcc-cchhhhhhH-hhhhhh
Confidence 567899999999999984 111 45777776666553 347888874 678865
No 14
>PRK09784 hypothetical protein; Provisional
Probab=49.50 E-value=11 Score=36.55 Aligned_cols=40 Identities=25% Similarity=0.283 Sum_probs=28.3
Q ss_pred hhhhcccccccCCCCCccHHHHHHHhccCCchHHHHHHHHH
Q 046185 243 LQSYIHHIKDVVADGNCGFRAIADLIGLGEDGWVQVRKDLL 283 (380)
Q Consensus 243 l~~~i~~i~dv~gDGhCgFraiA~~lg~~e~~~~~VR~~l~ 283 (380)
=+.|+++-.-|.|||-|+.|||-..- ..+-+|..+-..-.
T Consensus 195 n~~~glkyapvdgdgycllrailvlk-~h~yswal~s~ktq 234 (417)
T PRK09784 195 NKTYGLKYAPVDGDGYCLLRAILVLK-QHDYSWALGSHKTQ 234 (417)
T ss_pred hhhhCceecccCCCchhHHHHHHHhh-hcccchhhccchhH
Confidence 35678888899999999999997643 33456665544333
No 15
>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=44.07 E-value=35 Score=23.92 Aligned_cols=47 Identities=19% Similarity=0.222 Sum_probs=31.3
Q ss_pred cccchhhhhhcccccccCCCCCccHHHHHHHhccCCchHHHHHHHHHHHHh
Q 046185 237 DEFPVGLQSYIHHIKDVVADGNCGFRAIADLIGLGEDGWVQVRKDLLNELY 287 (380)
Q Consensus 237 ~q~p~~l~~~i~~i~dv~gDGhCgFraiA~~lg~~e~~~~~VR~~l~~el~ 287 (380)
+++|+.-+..|...+ ..+.-+.-||+.||.+...-..+....++.|+
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 344444444444433 56678999999999998777777777777765
No 16
>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=36.16 E-value=31 Score=29.15 Aligned_cols=34 Identities=24% Similarity=0.542 Sum_probs=29.2
Q ss_pred CCCccHH-HHHHHhccCCchHHHHHHHHHHHHhhc
Q 046185 256 DGNCGFR-AIADLIGLGEDGWVQVRKDLLNELYSH 289 (380)
Q Consensus 256 DGhCgFr-aiA~~lg~~e~~~~~VR~~l~~el~~~ 289 (380)
--.|-|| ...+++|++.+.|..+.+++.+||.++
T Consensus 75 ~KPCplrd~aL~~igls~~EYm~lKkelae~i~~~ 109 (109)
T TIGR03277 75 TKPCPLRDSALQRIGMSPEEYMELKKKLAEELLKK 109 (109)
T ss_pred CCCCcCchHHHHHcCCCHHHHHHHHHHHHHHHhcC
Confidence 3458899 688899999999999999999998753
No 17
>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=31.53 E-value=72 Score=29.02 Aligned_cols=61 Identities=18% Similarity=0.297 Sum_probs=47.6
Q ss_pred ccccccCCCCCccHHHHHHHhccCCchHHHHHHHHHHHHhhcccccccccC-ChhHHHHHHHh
Q 046185 248 HHIKDVVADGNCGFRAIADLIGLGEDGWVQVRKDLLNELYSHLDDYGKLYG-PERVNELIHIL 309 (380)
Q Consensus 248 ~~i~dv~gDGhCgFraiA~~lg~~e~~~~~VR~~l~~el~~~~~~y~~~~~-~~~~~~~~~~L 309 (380)
..+++.-.|+.||..+|-.+-+++.+.|..+.+.|+.. ..-...|..-.. +.+++.+.+.+
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 35577889999999999999999999999999999333 333334444333 78999999988
No 18
>cd00258 GM2-AP GM2 activator protein (GM2-AP) is a non-enzymatic lysosomal protein that acts as cofactor in the sequential degradation of gangliosides. GM2A is an essential cofactor for beta-hexosaminidase A (Hex A) in the enzymatic hydrolysis of GM2 ganglioside to GM3. Mutation of the gene results in the AB variant of Tay-Sachs disease. GM2-AP and similar proteins belong to the ML domain family.
Probab=30.36 E-value=25 Score=31.95 Aligned_cols=22 Identities=27% Similarity=0.522 Sum_probs=16.9
Q ss_pred CCCCCccceeeccccccchhhhH
Q 046185 75 VDRSACGCVICQTHGLPCAHEIT 97 (380)
Q Consensus 75 ~~~~~C~~~~~~~~GlPCaH~i~ 97 (380)
++...|--.+ .+||+||.|-+.
T Consensus 89 ~~~~~Cp~~l-~~~g~pC~CP~~ 110 (162)
T cd00258 89 PPGQQCPEPL-RTYGLPCHCPFK 110 (162)
T ss_pred CCCCCCCchh-hccCCccCCCCC
Confidence 3456777777 889999999875
No 19
>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=28.84 E-value=46 Score=25.14 Aligned_cols=19 Identities=32% Similarity=0.435 Sum_probs=15.1
Q ss_pred CCCCCcc--HHHHHHHhccCC
Q 046185 254 VADGNCG--FRAIADLIGLGE 272 (380)
Q Consensus 254 ~gDGhCg--FraiA~~lg~~e 272 (380)
.-|+||- +||.|...|.++
T Consensus 19 ~~~~nc~~~~RAaarkf~V~r 39 (58)
T PF09607_consen 19 EKDNNCKGNQRAAARKFNVSR 39 (58)
T ss_dssp HH-TTTTT-HHHHHHHTTS-H
T ss_pred HHccchhhhHHHHHHHhCccH
Confidence 3789998 999999999975
No 20
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 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 belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=24.66 E-value=48 Score=27.01 Aligned_cols=69 Identities=17% Similarity=0.187 Sum_probs=40.0
Q ss_pred CccHHHHHHHhccCCchHHHHHHHHHHHHhhcccccccccCChhHHHHHHHhccCCCCCCCcccccccccchhhhhhccc
Q 046185 258 NCGFRAIADLIGLGEDGWVQVRKDLLNELYSHLDDYGKLYGPERVNELIHILSYYENWPASSDRWMTMPDMGHLIASCYN 337 (380)
Q Consensus 258 hCgFraiA~~lg~~e~~~~~VR~~l~~el~~~~~~y~~~~~~~~~~~~~~~L~~~~~~~~~~~~Wl~~p~~G~iiA~~y~ 337 (380)
.|-.+|||.+||+++.+ +++-|.+.. -..+...|. .+.+ +++ +.-..+.+.|+
T Consensus 4 ~Cvi~AiA~aL~R~~~d-------Vl~Vl~~~~-----------~~~~~~~l~-~G~G-------l~l-~~le~~f~~F~ 56 (89)
T PF05379_consen 4 GCVIRAIAEALGRREQD-------VLAVLSRKC-----------GEELLEELW-SGEG-------LDL-EDLEELFELFD 56 (89)
T ss_pred cchhHHHHHHhCCCHHH-------HHHHHHhcc-----------CHHHHHHHH-cCCC-------cCH-HHHHHHHHHcC
Confidence 59999999999998533 222233221 112222231 1111 111 22357888999
Q ss_pred eEEEEEeCCcceeeec
Q 046185 338 VVLFHLSSVQCLTFLP 353 (380)
Q Consensus 338 ~pI~~ls~~~s~t~~P 353 (380)
.--.+...+....+.|
T Consensus 57 I~A~v~~~g~~~~lN~ 72 (89)
T PF05379_consen 57 ICAHVNFGGETFVLNE 72 (89)
T ss_pred eEEEEEECCEEEEECC
Confidence 8888888777777665
No 21
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=23.74 E-value=41 Score=23.42 Aligned_cols=13 Identities=54% Similarity=0.963 Sum_probs=11.0
Q ss_pred CCcccccCCCCCC
Q 046185 160 DPEVKTRTRGRPS 172 (380)
Q Consensus 160 ~Pp~k~~tKG~p~ 172 (380)
-|..++++||||.
T Consensus 27 RpL~~i~kkGRP~ 39 (39)
T smart00412 27 RPLIPVRPRGRPS 39 (39)
T ss_pred ccceeecCCCCCC
Confidence 4778999999994
No 22
>KOG3146 consensus Dolichyl pyrophosphate phosphatase and related acid phosphatases [Lipid transport and metabolism]
Probab=23.73 E-value=57 Score=31.03 Aligned_cols=42 Identities=14% Similarity=0.226 Sum_probs=29.6
Q ss_pred ccccccchhHHHHHHHHHHHHHhhhcCCCCCCccc---eeeccccccchhh
Q 046185 48 FKHIRGFISIIALNITLSELKRAISIGVDRSACGC---VICQTHGLPCAHE 95 (380)
Q Consensus 48 ~~~l~g~IS~~AL~~i~~q~~~~~~~~~~~~~C~~---~~~~~~GlPCaH~ 95 (380)
+.-+.|.|+...++.+..- .+++ +.||+| +++..||.|-+|.
T Consensus 58 ~~~~~G~v~Ne~in~viK~--il~q----pRP~~~~~~t~~s~yGMPSSHS 102 (228)
T KOG3146|consen 58 IWFVIGQVSNEFINVVIKN--ILKQ----PRPVSFPDTTLRSGYGMPSSHS 102 (228)
T ss_pred HHHHHHHHHHHHHHHHHHH--HhcC----CCCCCCCccccccCCCCCchHH
Confidence 4447889999888877542 2222 467877 4567899999996
No 23
>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=20.17 E-value=66 Score=26.49 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=17.6
Q ss_pred cCCCCCccHHHHHHHhccCCc
Q 046185 253 VVADGNCGFRAIADLIGLGED 273 (380)
Q Consensus 253 v~gDGhCgFraiA~~lg~~e~ 273 (380)
+..|.||+.-|||.+||.+=|
T Consensus 3 ~sR~NNCLVVAis~~L~~T~e 23 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVTLE 23 (104)
T ss_pred ccCCCCeEeehHHHHhcchHH
Confidence 346889999999999999833
Done!