Query 043071
Match_columns 194
No_of_seqs 107 out of 126
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 12:34:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043071.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043071hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05078 DUF679: Protein of un 100.0 1.1E-81 2.3E-86 521.8 15.3 166 16-194 1-166 (170)
2 PF13127 DUF3955: Protein of u 66.8 6 0.00013 28.3 2.6 33 51-83 2-35 (63)
3 PF10894 DUF2689: Protein of u 42.4 12 0.00027 27.0 0.9 8 134-141 22-29 (61)
4 PF13511 DUF4124: Domain of un 38.7 20 0.00043 24.0 1.4 14 76-89 19-32 (60)
5 PRK13724 conjugal transfer pro 36.4 17 0.00037 26.5 0.9 9 133-141 21-29 (65)
6 PF15601 Imm42: Immunity prote 33.1 27 0.00059 28.6 1.6 23 124-146 6-28 (134)
7 PF03770 IPK: Inositol polypho 32.4 17 0.00038 30.3 0.4 92 34-140 84-175 (197)
8 PRK04989 psbM photosystem II r 31.7 9.8 0.00021 24.9 -0.9 15 178-192 6-20 (35)
9 CHL00080 psbM photosystem II p 30.5 11 0.00023 24.6 -0.9 15 178-192 6-20 (34)
10 PF11395 DUF2873: Protein of u 29.6 51 0.0011 22.2 2.2 23 129-151 3-25 (43)
11 KOG4833 Uncharacterized conser 29.3 17 0.00037 35.4 -0.2 26 131-165 499-524 (573)
12 PF15623 CT47: Cancer/testis g 24.9 31 0.00068 31.6 0.7 19 126-144 114-132 (279)
13 PF10726 DUF2518: Protein of f 24.7 59 0.0013 27.2 2.2 76 57-138 44-129 (145)
14 TIGR03038 PS_II_psbM photosyst 24.2 16 0.00035 23.6 -0.9 15 178-192 6-20 (33)
15 PF03022 MRJP: Major royal jel 23.4 52 0.0011 29.1 1.8 31 72-102 188-219 (287)
16 PLN02667 inositol polyphosphat 23.3 52 0.0011 29.7 1.8 15 125-139 235-249 (286)
17 KOG4054 Uncharacterized conser 22.5 62 0.0013 28.1 2.0 26 124-149 31-56 (183)
18 PF05381 Peptidase_C21: Tymovi 22.2 95 0.0021 24.7 2.8 37 62-98 49-85 (104)
19 PRK14094 psbM photosystem II r 21.2 22 0.00047 24.9 -0.8 15 178-192 6-20 (50)
No 1
>PF05078 DUF679: Protein of unknown function (DUF679); InterPro: IPR007770 This family contains uncharacterised plant proteins of unknown function.
Probab=100.00 E-value=1.1e-81 Score=521.80 Aligned_cols=166 Identities=48% Similarity=0.798 Sum_probs=157.5
Q ss_pred hhhHHHHhhhCchhHHHHHHhhccccccCCccccchhHHHHHHHHHhhhhhhcccccceeecCCCcEEEEEEeccceeee
Q 043071 16 CPSAANLANLLPTGTVLAYQALMPSLSNNGTCLAAHKYLSIVALAGCSIVCFLSSFTDSYYSSKGKLYYGIATTTGLHIF 95 (194)
Q Consensus 16 lssta~La~LLPTGTvLaFQ~LsP~fTN~G~C~~~nr~Lt~~Ll~~ca~sCff~sFTDS~~~~dGkvyYG~aT~~Gl~~f 95 (194)
|+++|||+||||||||||||+|+|+|||||+|+++|||||++||++||+||||+||||||+|+|||+|||+||+||||+|
T Consensus 1 ls~ta~La~LLPTGTvlaFq~L~P~~Tn~G~C~~~nr~lt~~Ll~lca~sC~f~sFTDS~~~~dGkvyYG~aT~~Gl~~f 80 (170)
T PF05078_consen 1 LSSTANLAKLLPTGTVLAFQILSPSFTNNGECDTANRWLTAALLALCAASCFFFSFTDSFRGSDGKVYYGFATPRGLWVF 80 (170)
T ss_pred CccHHHHHHhCcchHHHHHHHhhhhcccCCccCcchHHHHHHHHHHHHHHHHHeeecceeECCCCCEEEEEEEcccceec
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCccccccccCCCCCCCCCCCCCCCcccccceeeehhhhHHHHHHHHHHHHhccCCCceeeCCCCCCCHHHHHHHhh
Q 043071 96 NKKDSEDEGEKADNNIEDGDKGTEKEGVCLDTYKIRWIDFVHAFTSLLVFLVFATTNSDARRCFFPHPGPNTNVLLMHLP 175 (194)
Q Consensus 96 ~~~~~~~~~e~~~~~~~~g~~~~~~~~~~~~~yrLr~~DfvHA~lS~~VF~avAl~D~~v~~CffP~~~~~~~ell~~lP 175 (194)
|.+++++ ++.+.++++++||||||+|||||++|++||++||++|+|||+||||.+++++||+|+++|
T Consensus 81 ~~~~~~~-------------g~~~~~~~~~~~yrlr~~DfvHA~lS~~VF~aval~d~~v~~Cf~P~~~~~~~~~l~~lP 147 (170)
T PF05078_consen 81 NYPGPEE-------------GGGELKPRDLSKYRLRFIDFVHAFLSVVVFLAVALSDQNVVSCFFPSPSSETKEVLMNLP 147 (170)
T ss_pred CCCCccc-------------cccCCCccccccceEehhhhhHHHHHHHHHHHhheeCCCcceecCCCCchhHHHHHHHhH
Confidence 9875532 123456789999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHhhhheeeecccCCC
Q 043071 176 ILVGVLQASYSCFSPLIGE 194 (194)
Q Consensus 176 l~vG~l~S~vF~iFPt~~~ 194 (194)
++||++||+|||+|||+|.
T Consensus 148 ~~vG~~~S~vF~~FPt~R~ 166 (170)
T PF05078_consen 148 LGVGVLCSMVFMIFPTTRH 166 (170)
T ss_pred HHHHHhHeeEEEECCCCCC
Confidence 9999999999999999984
No 2
>PF13127 DUF3955: Protein of unknown function (DUF3955)
Probab=66.83 E-value=6 Score=28.32 Aligned_cols=33 Identities=27% Similarity=0.440 Sum_probs=26.9
Q ss_pred hhHHHHHHHHHhhhhhhccc-ccceeecCCCcEE
Q 043071 51 HKYLSIVALAGCSIVCFLSS-FTDSYYSSKGKLY 83 (194)
Q Consensus 51 nr~Lt~~Ll~~ca~sCff~s-FTDS~~~~dGkvy 83 (194)
+++..+.++.+.++.|++.. ...||+|+||-++
T Consensus 2 ~~~~l~~~~~llg~~~l~i~~~~~syVd~~G~L~ 35 (63)
T PF13127_consen 2 KKYILSLILLLLGVVCLFIFNIIGSYVDEDGVLH 35 (63)
T ss_pred cchHHHHHHHHHHHHHHHHHhcccceECCCCeEe
Confidence 46778888889999998764 5569999999775
No 3
>PF10894 DUF2689: Protein of unknown function (DUF2689); InterPro: IPR024396 Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Probab=42.42 E-value=12 Score=26.99 Aligned_cols=8 Identities=63% Similarity=0.945 Sum_probs=7.7
Q ss_pred hhhhHHHH
Q 043071 134 DFVHAFTS 141 (194)
Q Consensus 134 DfvHA~lS 141 (194)
||+||++|
T Consensus 22 DFmhaVlS 29 (61)
T PF10894_consen 22 DFMHAVLS 29 (61)
T ss_pred HHHHHHHh
Confidence 89999998
No 4
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=38.72 E-value=20 Score=24.03 Aligned_cols=14 Identities=14% Similarity=0.242 Sum_probs=10.6
Q ss_pred ecCCCcEEEEEEec
Q 043071 76 YSSKGKLYYGIATT 89 (194)
Q Consensus 76 ~~~dGkvyYG~aT~ 89 (194)
+|.+|+++|.=.=+
T Consensus 19 ~D~~G~v~ysd~P~ 32 (60)
T PF13511_consen 19 VDENGVVHYSDTPP 32 (60)
T ss_pred ECCCCCEEECccCC
Confidence 58999999975533
No 5
>PRK13724 conjugal transfer protein TrbD; Provisional
Probab=36.38 E-value=17 Score=26.48 Aligned_cols=9 Identities=56% Similarity=0.700 Sum_probs=8.0
Q ss_pred ehhhhHHHH
Q 043071 133 IDFVHAFTS 141 (194)
Q Consensus 133 ~DfvHA~lS 141 (194)
-||+||++|
T Consensus 21 DDF~h~VlS 29 (65)
T PRK13724 21 DDFMHAVLS 29 (65)
T ss_pred HHHHHHHHh
Confidence 399999998
No 6
>PF15601 Imm42: Immunity protein 42
Probab=33.05 E-value=27 Score=28.58 Aligned_cols=23 Identities=30% Similarity=0.470 Sum_probs=19.0
Q ss_pred cccccceeeehhhhHHHHHHHHH
Q 043071 124 CLDTYKIRWIDFVHAFTSLLVFL 146 (194)
Q Consensus 124 ~~~~yrLr~~DfvHA~lS~~VF~ 146 (194)
+..-|.+.-.||+|+|+|.+..-
T Consensus 6 ~~~~~eiG~~dfl~sFFsti~~~ 28 (134)
T PF15601_consen 6 GFSWYEIGPPDFLHSFFSTISYR 28 (134)
T ss_pred CceEEEeCCHHHHHHHHHHHHHH
Confidence 45679999999999999977543
No 7
>PF03770 IPK: Inositol polyphosphate kinase ; InterPro: IPR005522 ArgRIII has been demonstrated to be an inositol polyphosphate kinase [] which catalyses the reaction ATP + 1D-myo-inositol 1,4,5-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate .; GO: 0008440 inositol trisphosphate 3-kinase activity; PDB: 2IF8_B 2IEW_B 1W2C_A 1W2F_A 1W2D_A 2A98_A 2AQX_A 1TZD_A.
Probab=32.37 E-value=17 Score=30.32 Aligned_cols=92 Identities=15% Similarity=0.190 Sum_probs=38.0
Q ss_pred HHhhccccccCCccccchhHHHHHHHHHhhhhhhcccccceeecCCCcEEEEEEeccceeeecCCCCccccccccCCCCC
Q 043071 34 YQALMPSLSNNGTCLAAHKYLSIVALAGCSIVCFLSSFTDSYYSSKGKLYYGIATTTGLHIFNKKDSEDEGEKADNNIED 113 (194)
Q Consensus 34 FQ~LsP~fTN~G~C~~~nr~Lt~~Ll~~ca~sCff~sFTDS~~~~dGkvyYG~aT~~Gl~~f~~~~~~~~~e~~~~~~~~ 113 (194)
.+.|..-|.+++.-....+.+..++--+-.+--+|-.-+. |=+-...=|.++++..... |. ++..
T Consensus 84 ~~~l~~Ff~~~~~~~~~~~~~~~~l~~L~~L~~~~~~~~~----------~~f~sSSLLivYd~~~~~~--~~---~~~~ 148 (197)
T PF03770_consen 84 RDALKKFFNNGSSPRRRRELLRSILKQLEQLREWFESQRS----------FRFYSSSLLIVYDGDPSRL--EN---ESSS 148 (197)
T ss_dssp HHHHHHHHT-TT-HHTHHHHHHHHHHHHHHHHHHHCC-CC----------EEEESEEEEEEEETTHHHH--HH---C---
T ss_pred HHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHHHHHhccc----------CeeecceEEEEEcCCcccc--cc---cccc
Confidence 4455555665543333344555555555555555554443 2222233366777652111 00 0000
Q ss_pred CCCCCCCCCCcccccceeeehhhhHHH
Q 043071 114 GDKGTEKEGVCLDTYKIRWIDFVHAFT 140 (194)
Q Consensus 114 g~~~~~~~~~~~~~yrLr~~DfvHA~l 140 (194)
.....+........+++|+|||.|+..
T Consensus 149 ~~~~~~~~~~~~~~~~vklIDFAH~~~ 175 (197)
T PF03770_consen 149 SSTSTSDSDDPPNKVDVKLIDFAHVFP 175 (197)
T ss_dssp ------------S-EEEEEE--TTEEE
T ss_pred cccccccccCCCCcccEEEEECCCccc
Confidence 011111233455689999999999987
No 8
>PRK04989 psbM photosystem II reaction center protein M; Provisional
Probab=31.74 E-value=9.8 Score=24.89 Aligned_cols=15 Identities=13% Similarity=0.372 Sum_probs=12.8
Q ss_pred HHHhhhheeeecccC
Q 043071 178 VGVLQASYSCFSPLI 192 (194)
Q Consensus 178 vG~l~S~vF~iFPt~ 192 (194)
.|++++.+|+..||.
T Consensus 6 lgfiAt~Lfi~iPt~ 20 (35)
T PRK04989 6 LGFVASLLFVLVPTV 20 (35)
T ss_pred HHHHHHHHHHHHHHH
Confidence 489999999999973
No 9
>CHL00080 psbM photosystem II protein M
Probab=30.49 E-value=11 Score=24.55 Aligned_cols=15 Identities=7% Similarity=0.208 Sum_probs=12.9
Q ss_pred HHHhhhheeeecccC
Q 043071 178 VGVLQASYSCFSPLI 192 (194)
Q Consensus 178 vG~l~S~vF~iFPt~ 192 (194)
.|++++.+|+..||.
T Consensus 6 lgfiAt~LFi~iPt~ 20 (34)
T CHL00080 6 LAFIATALFILVPTA 20 (34)
T ss_pred HHHHHHHHHHHHHHH
Confidence 489999999999973
No 10
>PF11395 DUF2873: Protein of unknown function (DUF2873); InterPro: IPR021532 This entry is represented by the human SARS coronavirus, Orf7b; it is a family of uncharacterised viral proteins.
Probab=29.55 E-value=51 Score=22.18 Aligned_cols=23 Identities=35% Similarity=0.596 Sum_probs=19.9
Q ss_pred ceeeehhhhHHHHHHHHHHHHhc
Q 043071 129 KIRWIDFVHAFTSLLVFLVFATT 151 (194)
Q Consensus 129 rLr~~DfvHA~lS~~VF~avAl~ 151 (194)
.|+.+||--.++|.+.|+++.+.
T Consensus 3 ~ltl~dfylc~l~~llflv~iml 25 (43)
T PF11395_consen 3 HLTLFDFYLCFLSFLLFLVIIML 25 (43)
T ss_pred ceehhHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998764
No 11
>KOG4833 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.29 E-value=17 Score=35.45 Aligned_cols=26 Identities=31% Similarity=0.572 Sum_probs=20.6
Q ss_pred eeehhhhHHHHHHHHHHHHhccCCCceeeCCCCCC
Q 043071 131 RWIDFVHAFTSLLVFLVFATTNSDARRCFFPHPGP 165 (194)
Q Consensus 131 r~~DfvHA~lS~~VF~avAl~D~~v~~CffP~~~~ 165 (194)
+.+||+||+ .++|-|+..||||..+.
T Consensus 499 piidfnhaV---------cfsdLnIadcflpieSr 524 (573)
T KOG4833|consen 499 PIIDFNHAV---------CFSDLNIADCFLPIESR 524 (573)
T ss_pred HHHHHHHHH---------HHhcccHhHheehhHhh
Confidence 357888875 46899999999998764
No 12
>PF15623 CT47: Cancer/testis gene family 47
Probab=24.85 E-value=31 Score=31.60 Aligned_cols=19 Identities=16% Similarity=0.534 Sum_probs=15.6
Q ss_pred cccceeeehhhhHHHHHHH
Q 043071 126 DTYKIRWIDFVHAFTSLLV 144 (194)
Q Consensus 126 ~~yrLr~~DfvHA~lS~~V 144 (194)
..||+.|+|.||+.|-=+-
T Consensus 114 aGfR~~fLDLVhslL~RiY 132 (279)
T PF15623_consen 114 AGFRFMFLDLVHSLLNRIY 132 (279)
T ss_pred ccceeeHHHHHHHHHHHHh
Confidence 4599999999999887443
No 13
>PF10726 DUF2518: Protein of function (DUF2518); InterPro: IPR019664 This entry contains the Ycf51 protein family, which is conserved in Cyanobacteria. The function is not known.
Probab=24.72 E-value=59 Score=27.24 Aligned_cols=76 Identities=20% Similarity=0.230 Sum_probs=46.2
Q ss_pred HHHHHhhhhhhcccccceeecC-CCcEEEEEEeccce--eeecCCCCcccc------ccccCCCCCC-CCCCCCCCCccc
Q 043071 57 VALAGCSIVCFLSSFTDSYYSS-KGKLYYGIATTTGL--HIFNKKDSEDEG------EKADNNIEDG-DKGTEKEGVCLD 126 (194)
Q Consensus 57 ~Ll~~ca~sCff~sFTDS~~~~-dGkvyYG~aT~~Gl--~~f~~~~~~~~~------e~~~~~~~~g-~~~~~~~~~~~~ 126 (194)
.+..+++++||-+++.=.-+-. .|.+||=++=-+|- -++.-+.+..|+ |+++.|+..+ +-| . ..
T Consensus 44 ~F~~vLt~g~fal~~~~~~r~~IpGA~~~~~VyDnG~~~vVi~v~~~i~~~~leaTL~QaA~nL~s~GR~~-----~-~~ 117 (145)
T PF10726_consen 44 SFMLVLTVGCFALSLSYFPRVVIPGAVRYPIVYDNGADQVVIAVPPDITPEALEATLEQAASNLFSGGRSG-----R-DN 117 (145)
T ss_pred HHHHHHHHHHHHheeccCCCccccCceEeeEEEECCCcEEEEEcCCCCCHHHHHHHHHHHHHhccccCccC-----C-CC
Confidence 5667888899887775544433 89999999998884 455443333321 2345555532 211 1 33
Q ss_pred ccceeeehhhhH
Q 043071 127 TYKIRWIDFVHA 138 (194)
Q Consensus 127 ~yrLr~~DfvHA 138 (194)
+..+|.+-..|.
T Consensus 118 ~~~IR~R~l~h~ 129 (145)
T PF10726_consen 118 QVTIRARTLIHP 129 (145)
T ss_pred eEEEEEEEeEcC
Confidence 677777776664
No 14
>TIGR03038 PS_II_psbM photosystem II reaction center protein PsbM. Members of this protein family are the photosystem II reaction center M protein, product of the psbM gene, in Cyanobacteria and their derived organelles in plants. This model resembles Pfam model pfam05151 but has cutoffs set to avoid false-positive matches to similar (not necessarily homologous) sequences in species that are not photosynthetic.
Probab=24.18 E-value=16 Score=23.62 Aligned_cols=15 Identities=13% Similarity=0.359 Sum_probs=12.4
Q ss_pred HHHhhhheeeecccC
Q 043071 178 VGVLQASYSCFSPLI 192 (194)
Q Consensus 178 vG~l~S~vF~iFPt~ 192 (194)
.|++++.+|+..||.
T Consensus 6 l~fiAt~Lfi~iPt~ 20 (33)
T TIGR03038 6 LGFIATLLFILVPTV 20 (33)
T ss_pred HHHHHHHHHHHHHHH
Confidence 488999999998873
No 15
>PF03022 MRJP: Major royal jelly protein; InterPro: IPR003534 The major royal jelly proteins (MRJPs) comprise 12.5% of the mass, and 82-90% of the protein content [], of honeybee (Apis mellifera) royal jelly. Royal jelly is a substance secreted by the cephalic glands of nurse bees [] and it is used to trigger development of a queen bee from a bee larva. The biological function of the MRJPs is unknown, but they are believed to play a major role in nutrition due to their high essential amino acid content []. Two royal jelly proteins, MRJP3 and MRJP5, contain a tandem repeat that results from a high genetic variablility. This polymorphism may be useful for genotyping individual bees [].; PDB: 3Q6P_B 3Q6K_A 3Q6T_A 2QE8_B.
Probab=23.42 E-value=52 Score=29.12 Aligned_cols=31 Identities=13% Similarity=0.341 Sum_probs=24.4
Q ss_pred ccee-ecCCCcEEEEEEeccceeeecCCCCcc
Q 043071 72 TDSY-YSSKGKLYYGIATTTGLHIFNKKDSED 102 (194)
Q Consensus 72 TDS~-~~~dGkvyYG~aT~~Gl~~f~~~~~~~ 102 (194)
+|.. .|++|.+||+.+..++++..+...+..
T Consensus 188 s~g~~~D~~G~ly~~~~~~~aI~~w~~~~~~~ 219 (287)
T PF03022_consen 188 SDGMAIDPNGNLYFTDVEQNAIGCWDPDGPYT 219 (287)
T ss_dssp ECEEEEETTTEEEEEECCCTEEEEEETTTSB-
T ss_pred CceEEECCCCcEEEecCCCCeEEEEeCCCCcC
Confidence 3444 578999999999999999999766443
No 16
>PLN02667 inositol polyphosphate multikinase
Probab=23.27 E-value=52 Score=29.73 Aligned_cols=15 Identities=20% Similarity=0.545 Sum_probs=13.1
Q ss_pred ccccceeeehhhhHH
Q 043071 125 LDTYKIRWIDFVHAF 139 (194)
Q Consensus 125 ~~~yrLr~~DfvHA~ 139 (194)
..+.++|+|||-|++
T Consensus 235 ~~~v~VkmIDFAH~~ 249 (286)
T PLN02667 235 DSRVEVKLVDFAHVL 249 (286)
T ss_pred CCcceEEEEeCcccc
Confidence 458999999999985
No 17
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.48 E-value=62 Score=28.06 Aligned_cols=26 Identities=19% Similarity=0.292 Sum_probs=19.4
Q ss_pred cccccceeeehhhhHHHHHHHHHHHH
Q 043071 124 CLDTYKIRWIDFVHAFTSLLVFLVFA 149 (194)
Q Consensus 124 ~~~~yrLr~~DfvHA~lS~~VF~avA 149 (194)
...|||||+.=||||..=++--+=+.
T Consensus 31 ~~~Ks~lK~lifvh~lI~v~mlak~~ 56 (183)
T KOG4054|consen 31 VTLKSRLKKLIFVHALIWVLMLAKMS 56 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45689999999999987655544443
No 18
>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=22.22 E-value=95 Score=24.66 Aligned_cols=37 Identities=19% Similarity=0.387 Sum_probs=30.6
Q ss_pred hhhhhhcccccceeecCCCcEEEEEEeccceeeecCC
Q 043071 62 CSIVCFLSSFTDSYYSSKGKLYYGIATTTGLHIFNKK 98 (194)
Q Consensus 62 ca~sCff~sFTDS~~~~dGkvyYG~aT~~Gl~~f~~~ 98 (194)
+++.|+.++|-=.++...|.++||+.+..-...+...
T Consensus 49 ltaLa~~~~~~~~~hs~~~~~~~Gi~~as~~~~I~ht 85 (104)
T PF05381_consen 49 LTALAYRYHFQCTFHSDHGVLHYGIKDASTVFTITHT 85 (104)
T ss_pred HHHHHHHHheEEEEEcCCceEEeecCCCceEEEEEeC
Confidence 4567899999999999999999999998766666543
No 19
>PRK14094 psbM photosystem II reaction center protein M; Provisional
Probab=21.16 E-value=22 Score=24.87 Aligned_cols=15 Identities=20% Similarity=0.195 Sum_probs=12.9
Q ss_pred HHHhhhheeeecccC
Q 043071 178 VGVLQASYSCFSPLI 192 (194)
Q Consensus 178 vG~l~S~vF~iFPt~ 192 (194)
.|++++.+|+..||.
T Consensus 6 lgfiAtaLFi~iPT~ 20 (50)
T PRK14094 6 FGFVASLLFVGVPTI 20 (50)
T ss_pred HHHHHHHHHHHHHHH
Confidence 589999999999974
Done!