Query 035345
Match_columns 67
No_of_seqs 101 out of 141
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 11:07:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035345.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035345hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05627 AvrRpt-cleavage: Clea 99.9 7.3E-23 1.6E-27 116.1 0.2 37 3-39 3-39 (39)
2 PF04939 RRS1: Ribosome biogen 65.3 4.8 0.0001 28.4 1.9 34 5-38 107-150 (164)
3 smart00107 BTK Bruton's tyrosi 40.5 13 0.00027 20.4 0.5 11 53-63 15-25 (36)
4 COG4262 Predicted spermidine s 34.4 16 0.00034 30.2 0.4 11 6-16 436-446 (508)
5 cd05806 CBM20_laforin Laforin 34.3 20 0.00044 23.5 0.8 13 6-18 22-34 (112)
6 PF00779 BTK: BTK motif; Inte 33.7 14 0.00029 19.8 -0.0 11 53-63 10-20 (32)
7 TIGR02689 ars_reduc_gluta arse 28.2 44 0.00095 21.2 1.7 24 10-35 94-117 (126)
8 PF00686 CBM_20: Starch bindin 24.2 23 0.00051 21.3 -0.2 12 7-18 23-34 (96)
9 PF13197 DUF4013: Protein of u 22.8 39 0.00084 22.3 0.7 14 3-16 32-45 (169)
10 cd05808 CBM20_alpha_amylase Al 21.3 28 0.00062 20.6 -0.2 13 6-18 21-33 (95)
11 COG0394 Wzb Protein-tyrosine-p 20.8 64 0.0014 21.4 1.4 27 9-35 102-130 (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=99.85 E-value=7.3e-23 Score=116.06 Aligned_cols=37 Identities=76% Similarity=1.278 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCceehhHHHHHhhhcC
Q 035345 3 DKGRPLPKFGEWDVNDPASAEGFTVIFNKARDEKKTG 39 (67)
Q Consensus 3 ~~~~~VPKFG~WD~~~p~sa~~yTviF~KaReeKk~~ 39 (67)
+++++|||||+||++||+++++|||||+|||++||++
T Consensus 3 ~~~~~vPkFG~WD~~~~~~~~~yT~iF~kar~~Kk~~ 39 (39)
T PF05627_consen 3 QKGSHVPKFGEWDENNPASAEGYTVIFEKAREEKKTG 39 (39)
T ss_dssp ---------SGGGTT-TT---SS-EEEE---------
T ss_pred cCCCCCCCCCcccCCCCCCCCCeeehHHHHhhhccCC
Confidence 5679999999999999999999999999999999974
No 2
>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=65.27 E-value=4.8 Score=28.43 Aligned_cols=34 Identities=29% Similarity=0.561 Sum_probs=28.4
Q ss_pred CCCCCCCC----------CCCCCCCCCCCCceehhHHHHHhhhc
Q 035345 5 GRPLPKFG----------EWDVNDPASAEGFTVIFNKARDEKKT 38 (67)
Q Consensus 5 ~~~VPKFG----------~WD~~~p~sa~~yTviF~KaReeKk~ 38 (67)
+.=||+|| +|-.+-+..+..|.-.|.+.|++||.
T Consensus 107 ~eW~prwGyk~~nkd~~~~wiiEv~~~~~~~eDpf~~~~~eKke 150 (164)
T PF04939_consen 107 GEWVPRWGYKRANKDKEKDWIIEVKPNDDPGEDPFEKKREEKKE 150 (164)
T ss_pred cchhhcccccccccccccCceEEcCCCCCCCcCHHHHHHHHHHH
Confidence 44578888 78877777889999999999999985
No 3
>smart00107 BTK Bruton's tyrosine kinase Cys-rich motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
Probab=40.46 E-value=13 Score=20.36 Aligned_cols=11 Identities=45% Similarity=1.177 Sum_probs=8.6
Q ss_pred CcceeeeecCC
Q 035345 53 RHGWFCCIQSP 63 (67)
Q Consensus 53 ~~k~~cc~~~~ 63 (67)
..+|.||.+..
T Consensus 15 ~G~W~CC~q~~ 25 (36)
T smart00107 15 DGKWLCCQQSE 25 (36)
T ss_pred CCeEccCCCcC
Confidence 57899998754
No 4
>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]
Probab=34.42 E-value=16 Score=30.17 Aligned_cols=11 Identities=45% Similarity=1.150 Sum_probs=9.2
Q ss_pred CCCCCCCCCCC
Q 035345 6 RPLPKFGEWDV 16 (67)
Q Consensus 6 ~~VPKFG~WD~ 16 (67)
.+||-||||-=
T Consensus 436 v~VPTFGeWGf 446 (508)
T COG4262 436 VHVPTFGEWGF 446 (508)
T ss_pred EecCcccccce
Confidence 47999999964
No 5
>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=34.29 E-value=20 Score=23.52 Aligned_cols=13 Identities=31% Similarity=0.828 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCCC
Q 035345 6 RPLPKFGEWDVND 18 (67)
Q Consensus 6 ~~VPKFG~WD~~~ 18 (67)
..+|.+|+||...
T Consensus 22 GsipeLG~Wd~~~ 34 (112)
T cd05806 22 GSRPELGSWDPQR 34 (112)
T ss_pred ECchhcCCCCccc
Confidence 4689999999765
No 6
>PF00779 BTK: BTK motif; InterPro: IPR001562 The Btk-type zinc finger or Btk motif (BM) is a conserved zinc-binding motif containing conserved cysteines and a histidine that is present in certain eukaryotic signalling proteins. The motif is named after Bruton's tyrosine kinase (Btk), an enzyme which is essential for B cell maturation in humans and mice [, ]. Btk is a member of the Tec family of protein tyrosine kinases (PTK). These kinases contain a conserved Tec homology (TH) domain between the N-terminal pleckstrin homology (PH) domain (IPR001849 from INTERPRO) and the Src homology 3 (SH3) domain (IPR001452 from INTERPRO). The N-terminal of the TH domain is highly conserved and known as the Btf motif, while the C-terminal region of the TH domain contains a proline-rich region (PRR). The Btk motif contains a conserved His and three Cys residues that form a zinc finger (although these differ from known zinc finger topologies), while PRRs are commonly involved in protein-protein interactions, including interactions with G proteins [, ]. The TH domain may be of functional importance in various signalling pathways in different species []. A complete TH domain, containing both the Btk and PRR regions, has not been found outside the Tec family; however, the Btk motif on its own does occur in other proteins, usually C-terminal to a PH domain (note that although a Btk motif always occurs C-terminal to a PH domain, not all PH domains are followed by a Btk motif). The crystal structures of Btk show that the Btk-type zinc finger has a globular core, formed by a long loop which is held together by a zinc ion, and that the Btk motif is packed against the PH domain []. The zinc-binding residues are a histidine and three cysteines, which are fully conserved in the Btk motif []. Proteins known to contain a Btk-type zinc finger include: Mammalian Bruton's tyrosine kinase (Btk), a protein tyrosine kinase involved in modulation of diverse cellular processes. Mutations affecting Btk are the cause of X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency in mice. Mammalian Tec, Bmx, and Itk proteins, which are tyrosine protein kinases of the Tec subfamily. Drosophila tyrosine-protein kinase Btk29A, which is required for the development of proper ring canals and of male genitalia and required for adult survival. Mammalian Ras GTPase-activating proteins (RasGAP), which regulate the activation of inactive GDP-bound Ras by converting GDP to GTP. ; GO: 0035556 intracellular signal transduction; PDB: 2E6I_A 2YS2_A 2Z0P_A 1B55_A 1BTK_B 1BWN_A.
Probab=33.66 E-value=14 Score=19.80 Aligned_cols=11 Identities=36% Similarity=1.123 Sum_probs=7.7
Q ss_pred CcceeeeecCC
Q 035345 53 RHGWFCCIQSP 63 (67)
Q Consensus 53 ~~k~~cc~~~~ 63 (67)
..+|.||.+..
T Consensus 10 ~g~W~CC~q~~ 20 (32)
T PF00779_consen 10 GGKWLCCKQTD 20 (32)
T ss_dssp TTCESSSS-SS
T ss_pred CCcCcCCCCcC
Confidence 46899998743
No 7
>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=28.24 E-value=44 Score=21.20 Aligned_cols=24 Identities=33% Similarity=0.790 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCCCCCceehhHHHHHh
Q 035345 10 KFGEWDVNDPASAEGFTVIFNKARDE 35 (67)
Q Consensus 10 KFG~WD~~~p~sa~~yTviF~KaRee 35 (67)
.++.|+-.||.+ ...-.|.++|++
T Consensus 94 ~~~~w~i~DP~~--~~~~~f~~~~~~ 117 (126)
T TIGR02689 94 IFEDWQLEDPDG--QSIEVFRRVRDE 117 (126)
T ss_pred eeecCCCCCCCC--CcHHHHHHHHHH
Confidence 468999999964 345566666654
No 8
>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=24.21 E-value=23 Score=21.32 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=9.8
Q ss_pred CCCCCCCCCCCC
Q 035345 7 PLPKFGEWDVND 18 (67)
Q Consensus 7 ~VPKFG~WD~~~ 18 (67)
..|.+|+||.+.
T Consensus 23 s~~~LG~W~~~~ 34 (96)
T PF00686_consen 23 SCPELGNWDPKK 34 (96)
T ss_dssp SSGGGTTTSGGG
T ss_pred CcHHhCCCChHh
Confidence 479999999853
No 9
>PF13197 DUF4013: Protein of unknown function (DUF4013)
Probab=22.77 E-value=39 Score=22.26 Aligned_cols=14 Identities=36% Similarity=0.999 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCCC
Q 035345 3 DKGRPLPKFGEWDV 16 (67)
Q Consensus 3 ~~~~~VPKFG~WD~ 16 (67)
++...+|+|.+|..
T Consensus 32 g~~~~lP~~~~~~~ 45 (169)
T PF13197_consen 32 GGSDPLPEFNDWGE 45 (169)
T ss_pred cCCCCCCCchHHHH
Confidence 34478999888754
No 10
>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=21.31 E-value=28 Score=20.57 Aligned_cols=13 Identities=23% Similarity=0.846 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCCC
Q 035345 6 RPLPKFGEWDVND 18 (67)
Q Consensus 6 ~~VPKFG~WD~~~ 18 (67)
...|.||+|+...
T Consensus 21 G~~~~lG~W~~~~ 33 (95)
T cd05808 21 GNVPELGNWSPAN 33 (95)
T ss_pred eCcHHhCCCChhh
Confidence 3579999999653
No 11
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=20.84 E-value=64 Score=21.44 Aligned_cols=27 Identities=22% Similarity=0.578 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCCCCC--CceehhHHHHHh
Q 035345 9 PKFGEWDVNDPASAE--GFTVIFNKARDE 35 (67)
Q Consensus 9 PKFG~WD~~~p~sa~--~yTviF~KaRee 35 (67)
..+-.||..||..+. .|-..|..+|+.
T Consensus 102 ~~~~~~~v~DP~~~~~e~~~~~~~~i~~~ 130 (139)
T COG0394 102 LEYEHWEVPDPYYGSGEEFEEVYRLIEDA 130 (139)
T ss_pred ccccCCCCCCCCCCchHHHHHHHHHHHHH
Confidence 355569999998654 788888888875
Done!