Query 041979
Match_columns 254
No_of_seqs 127 out of 149
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 12:44:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041979.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041979hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05627 AvrRpt-cleavage: Clea 99.7 6.4E-19 1.4E-23 120.0 0.0 38 184-221 2-39 (39)
2 PF05627 AvrRpt-cleavage: Clea 99.3 4.4E-13 9.6E-18 91.5 1.2 31 5-35 6-39 (39)
3 PF04939 RRS1: Ribosome biogen 22.4 63 0.0014 28.5 2.1 27 195-221 125-151 (164)
4 PF10380 CRF1: Transcription f 14.2 89 0.0019 26.5 1.1 19 6-24 36-54 (123)
5 TIGR02689 ars_reduc_gluta arse 9.8 2.7E+02 0.0058 22.3 2.5 26 190-217 92-117 (126)
6 cd05806 CBM20_laforin Laforin 9.3 1.3E+02 0.0028 24.7 0.5 14 5-18 22-35 (112)
7 PF08168 NUC205: NUC205 domain 9.2 1.6E+02 0.0035 21.0 0.9 11 36-46 33-43 (44)
8 cd05808 CBM20_alpha_amylase Al 8.8 1.1E+02 0.0023 22.9 -0.2 16 5-20 21-36 (95)
9 PF00686 CBM_20: Starch bindin 8.6 1.1E+02 0.0024 23.2 -0.1 15 6-20 23-37 (96)
10 COG0394 Wzb Protein-tyrosine-p 8.4 2E+02 0.0043 24.1 1.3 28 192-219 103-132 (139)
No 1
>PF05627 AvrRpt-cleavage: Cleavage site for pathogenic type III effector avirulence factor Avr; InterPro: IPR008700 This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium []. The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain []. ; PDB: 2NUD_C.
Probab=99.72 E-value=6.4e-19 Score=120.05 Aligned_cols=38 Identities=63% Similarity=1.235 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCceehhHHHHHHHhhc
Q 041979 184 PDKGAAVPKFGDWDENNPSSADGYTHIFNQVREERNSA 221 (254)
Q Consensus 184 ~~~~~~vPkFG~WD~~np~s~~~yT~iF~k~r~ekk~~ 221 (254)
+.++.+|||||+||++||++|++|||||+|||+|||++
T Consensus 2 ~~~~~~vPkFG~WD~~~~~~~~~yT~iF~kar~~Kk~~ 39 (39)
T PF05627_consen 2 PQKGSHVPKFGEWDENNPASAEGYTVIFEKAREEKKTG 39 (39)
T ss_dssp ----------SGGGTT-TT---SS-EEEE---------
T ss_pred CcCCCCCCCCCcccCCCCCCCCCeeehHHHHhhhccCC
Confidence 56789999999999999999999999999999999974
No 2
>PF05627 AvrRpt-cleavage: Cleavage site for pathogenic type III effector avirulence factor Avr; InterPro: IPR008700 This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium []. The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain []. ; PDB: 2NUD_C.
Probab=99.31 E-value=4.4e-13 Score=91.53 Aligned_cols=31 Identities=48% Similarity=1.045 Sum_probs=11.9
Q ss_pred CCCCCCCCccCCCCcc---ceeeecccccCCCCC
Q 041979 5 SHVPKFGNWENEDNVP---YTMYFDKARKGRTGG 35 (254)
Q Consensus 5 ~~vPkFG~Wd~~~~~p---yT~~Fe~aR~~k~~g 35 (254)
++|||||+||.++..+ ||+||++||++|++|
T Consensus 6 ~~vPkFG~WD~~~~~~~~~yT~iF~kar~~Kk~~ 39 (39)
T PF05627_consen 6 SHVPKFGEWDENNPASAEGYTVIFEKAREEKKTG 39 (39)
T ss_dssp ------SGGGTT-TT---SS-EEEE---------
T ss_pred CCCCCCCcccCCCCCCCCCeeehHHHHhhhccCC
Confidence 5899999999987655 999999999999864
No 3
>PF04939 RRS1: Ribosome biogenesis regulatory protein (RRS1); InterPro: IPR007023 This is a family of eukaryotic ribosomal biogenesis regulatory proteins.; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=22.35 E-value=63 Score=28.46 Aligned_cols=27 Identities=26% Similarity=0.384 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCCceehhHHHHHHHhhc
Q 041979 195 DWDENNPSSADGYTHIFNQVREERNSA 221 (254)
Q Consensus 195 ~WD~~np~s~~~yT~iF~k~r~ekk~~ 221 (254)
+|=.--+..++-|...|.+.|++|+..
T Consensus 125 ~wiiEv~~~~~~~eDpf~~~~~eKker 151 (164)
T PF04939_consen 125 DWIIEVKPNDDPGEDPFEKKREEKKER 151 (164)
T ss_pred CceEEcCCCCCCCcCHHHHHHHHHHHH
Confidence 455554667789999999999999864
No 4
>PF10380 CRF1: Transcription factor CRF1; InterPro: IPR018837 CRF1 is a transcription factor that co-represses ribosomal genes with FHL1 via the TOR signalling pathway and protein kinase A [].
Probab=14.22 E-value=89 Score=26.52 Aligned_cols=19 Identities=26% Similarity=0.768 Sum_probs=16.3
Q ss_pred CCCCCCCccCCCCccceee
Q 041979 6 HVPKFGNWENEDNVPYTMY 24 (254)
Q Consensus 6 ~vPkFG~Wd~~~~~pyT~~ 24 (254)
..|++|.|-..++-||..+
T Consensus 36 rPP~LGtWv~~d~KPFgII 54 (123)
T PF10380_consen 36 RPPVLGTWVTTDSKPFGII 54 (123)
T ss_pred CCCeeeeeeccCCccceee
Confidence 5799999976699999876
No 5
>TIGR02689 ars_reduc_gluta arsenate reductase, glutathione/glutaredoxin type. Members of this protein family represent a novel form of arsenate reductase, using glutathione and glutaredoxin rather than thioredoxin for reducing equivalents as do some homologous arsenate reductases. An example of this type is Synechocystis sp. strain PCC 6803 slr0946, and of latter type (excluded from this model) is Staphylococcus aureus plasmid pI258 ArsC. Both are among the subset of arsenate reductases that belong the the low-molecular-weight protein-tyrosine phosphatase superfamily.
Probab=9.85 E-value=2.7e+02 Score=22.29 Aligned_cols=26 Identities=31% Similarity=0.685 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCCCCCCCceehhHHHHHH
Q 041979 190 VPKFGDWDENNPSSADGYTHIFNQVREE 217 (254)
Q Consensus 190 vPkFG~WD~~np~s~~~yT~iF~k~r~e 217 (254)
+..++.||..||.. +....|.+++++
T Consensus 92 ~~~~~~w~i~DP~~--~~~~~f~~~~~~ 117 (126)
T TIGR02689 92 REIFEDWQLEDPDG--QSIEVFRRVRDE 117 (126)
T ss_pred CceeecCCCCCCCC--CcHHHHHHHHHH
Confidence 45679999999953 345566666665
No 6
>cd05806 CBM20_laforin Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding laforin result in Lafora disease, a fatal autosomal recessive neurodegenerative disorder characterized by the presence of intracellular deposits of insoluble, abnormally branched, glycogen-like polymers, known as Lafora bodies, in neurons, muscle, liver, and other tissues. The molecular basis for the formation of these Lafora bodies is unknown. Laforin is one of the only phosphatases that contains a carbohydrate-binding module. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen
Probab=9.34 E-value=1.3e+02 Score=24.66 Aligned_cols=14 Identities=21% Similarity=0.800 Sum_probs=10.7
Q ss_pred CCCCCCCCccCCCC
Q 041979 5 SHVPKFGNWENEDN 18 (254)
Q Consensus 5 ~~vPkFG~Wd~~~~ 18 (254)
+.+|.+|+|+....
T Consensus 22 GsipeLG~Wd~~~A 35 (112)
T cd05806 22 GSRPELGSWDPQRA 35 (112)
T ss_pred ECchhcCCCCcccc
Confidence 46999999986443
No 7
>PF08168 NUC205: NUC205 domain; InterPro: IPR012584 This domain is found in a novel family of nucleolar proteins [].; GO: 0005634 nucleus
Probab=9.16 E-value=1.6e+02 Score=21.02 Aligned_cols=11 Identities=55% Similarity=0.960 Sum_probs=9.6
Q ss_pred CcCCCCCCCCC
Q 041979 36 TMINPNDPQEN 46 (254)
Q Consensus 36 ~~~NPNDP~en 46 (254)
.+|+|.||+||
T Consensus 33 ip~~~~d~een 43 (44)
T PF08168_consen 33 IPISPKDPEEN 43 (44)
T ss_pred ccccCCCcccC
Confidence 57899999987
No 8
>cd05808 CBM20_alpha_amylase Alpha-amylase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. This domain is found in several bacterial and fungal alpha-amylases including the maltopentaose-forming amylases (G5-amylases). Most alpha-amylases have, in addition to the C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13, which hydrolyzes internal alpha-1,4-glucosidic bonds in starch and related saccharides, yielding maltotriose and maltose. Two types of soluble substrates are used by alpha-amylases including long substrates (e.g. amylose) and short substrates (e.g. maltodextrins or maltooligosaccharides). The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. lafo
Probab=8.76 E-value=1.1e+02 Score=22.94 Aligned_cols=16 Identities=38% Similarity=0.943 Sum_probs=10.9
Q ss_pred CCCCCCCCccCCCCcc
Q 041979 5 SHVPKFGNWENEDNVP 20 (254)
Q Consensus 5 ~~vPkFG~Wd~~~~~p 20 (254)
+.+|.||+|+....++
T Consensus 21 G~~~~lG~W~~~~a~~ 36 (95)
T cd05808 21 GNVPELGNWSPANAVA 36 (95)
T ss_pred eCcHHhCCCChhhCcc
Confidence 3578999998644333
No 9
>PF00686 CBM_20: Starch binding domain; InterPro: IPR002044 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain binds to starch, and is found often at the C terminus of a variety of glycosyl hydrolases acting on polysaccharides more rapidly than on oligosaccharides. Reations include: the hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose, the degradation of starch to cyclodextrins by formation of a 1,4-alpha-D-glucosidic bond, and hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides to remove successive maltose units from the non-reducing ends of the chains.; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1KUL_A 1ACZ_A 1AC0_A 1KUM_A 2Z0B_C 9CGT_A 3CGT_A 6CGT_A 4CGT_A 1CGT_A ....
Probab=8.61 E-value=1.1e+02 Score=23.18 Aligned_cols=15 Identities=40% Similarity=1.097 Sum_probs=11.0
Q ss_pred CCCCCCCccCCCCcc
Q 041979 6 HVPKFGNWENEDNVP 20 (254)
Q Consensus 6 ~vPkFG~Wd~~~~~p 20 (254)
..|.+|+|+....++
T Consensus 23 s~~~LG~W~~~~a~~ 37 (96)
T PF00686_consen 23 SCPELGNWDPKKAVP 37 (96)
T ss_dssp SSGGGTTTSGGGSBE
T ss_pred CcHHhCCCChHhccc
Confidence 578999999754443
No 10
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=8.37 E-value=2e+02 Score=24.06 Aligned_cols=28 Identities=7% Similarity=0.514 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCCC--CceehhHHHHHHHh
Q 041979 192 KFGDWDENNPSSAD--GYTHIFNQVREERN 219 (254)
Q Consensus 192 kFG~WD~~np~s~~--~yT~iF~k~r~ekk 219 (254)
.+-.||..||..+. .|...|..|++.=+
T Consensus 103 ~~~~~~v~DP~~~~~e~~~~~~~~i~~~~~ 132 (139)
T COG0394 103 EYEHWEVPDPYYGSGEEFEEVYRLIEDAIK 132 (139)
T ss_pred cccCCCCCCCCCCchHHHHHHHHHHHHHHH
Confidence 34449999998754 89999999988643
Done!