Query 042337
Match_columns 236
No_of_seqs 120 out of 142
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 05:17:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042337.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042337hhsearch_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 1.4E-18 3E-23 117.4 -0.2 38 163-200 2-39 (39)
2 PF05627 AvrRpt-cleavage: Clea 99.2 1.9E-12 4.1E-17 87.7 -0.0 31 19-49 6-39 (39)
3 PF04939 RRS1: Ribosome biogen 22.2 64 0.0014 28.1 2.0 27 174-200 125-151 (164)
4 PF00469 F-protein: Negative f 16.8 41 0.00088 30.7 -0.3 9 228-236 152-160 (220)
5 COG4262 Predicted spermidine s 13.6 72 0.0016 32.1 0.4 11 19-29 436-446 (508)
6 PF10530 Toxin_35: Toxin with 11.5 90 0.0019 19.3 0.2 8 227-234 12-19 (23)
7 PF02532 PsbI: Photosystem II 9.6 1.6E+02 0.0036 20.0 1.0 9 53-61 25-33 (36)
8 PF10981 DUF2788: Protein of u 9.2 1.7E+02 0.0037 21.2 1.0 14 12-26 15-28 (52)
9 PF08168 NUC205: NUC205 domain 8.9 1.6E+02 0.0035 20.8 0.8 9 51-59 35-43 (44)
10 CHL00024 psbI photosystem II p 8.6 1.8E+02 0.004 19.7 0.9 10 52-61 24-33 (36)
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=99.70 E-value=1.4e-18 Score=117.44 Aligned_cols=38 Identities=50% Similarity=1.026 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCceehhHHHHHHHhcC
Q 042337 163 TDHTAAVPEFGDWDEPDPTSADGYTYIFNQVREERLKG 200 (236)
Q Consensus 163 ~~~~~~vPkFG~WD~~np~s~~~yT~iF~k~reekk~~ 200 (236)
++++.+|||||+||++|++++++|||||+|||+||+++
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 46779999999999999999999999999999999974
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=99.21 E-value=1.9e-12 Score=87.69 Aligned_cols=31 Identities=35% Similarity=0.948 Sum_probs=11.9
Q ss_pred CCCCCCCCCCCCCCcc---cchhhhHHHhhcccC
Q 042337 19 NHVPKFGNWETEEHVP---YSLYFDEARKRRNAA 49 (236)
Q Consensus 19 ~~vPkFG~w~~~~~~p---yT~~fe~ar~~k~~~ 49 (236)
++|||||+||.++..+ ||++|++||++|++|
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 7999999999977666 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=22.19 E-value=64 Score=28.13 Aligned_cols=27 Identities=26% Similarity=0.287 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCCceehhHHHHHHHhcC
Q 042337 174 DWDEPDPTSADGYTYIFNQVREERLKG 200 (236)
Q Consensus 174 ~WD~~np~s~~~yT~iF~k~reekk~~ 200 (236)
+|-.--+..++-|...|.+.|++|+.-
T Consensus 125 ~wiiEv~~~~~~~eDpf~~~~~eKker 151 (164)
T PF04939_consen 125 DWIIEVKPNDDPGEDPFEKKREEKKER 151 (164)
T ss_pred CceEEcCCCCCCCcCHHHHHHHHHHHH
Confidence 455444567789999999999999864
No 4
>PF00469 F-protein: Negative factor, (F-Protein) or Nef; InterPro: IPR001558 Human immunodeficiency virus 1 (HIV-1) negative factor (Nef protein) accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases [].; GO: 0005525 GTP binding; PDB: 4EN2_C 4EMZ_C 3IK5_C 2NEF_A 3REA_C 3REB_A 3RBB_A 3QZW_C 3NFN_C 1QVO_C ....
Probab=16.76 E-value=41 Score=30.66 Aligned_cols=9 Identities=11% Similarity=-0.112 Sum_probs=4.3
Q ss_pred CeeeccCCC
Q 042337 228 KCCCFPVPW 236 (236)
Q Consensus 228 ~ccCF~w~~ 236 (236)
.=-||||||
T Consensus 152 yP~~fGw~~ 160 (220)
T PF00469_consen 152 YPLTFGWLF 160 (220)
T ss_dssp -BSSTT--E
T ss_pred eeeecceeE
Confidence 345888887
No 5
>COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]
Probab=13.64 E-value=72 Score=32.07 Aligned_cols=11 Identities=55% Similarity=1.229 Sum_probs=9.5
Q ss_pred CCCCCCCCCCC
Q 042337 19 NHVPKFGNWET 29 (236)
Q Consensus 19 ~~vPkFG~w~~ 29 (236)
-|||.||+|--
T Consensus 436 v~VPTFGeWGf 446 (508)
T COG4262 436 VHVPTFGEWGF 446 (508)
T ss_pred EecCcccccce
Confidence 48999999974
No 6
>PF10530 Toxin_35: Toxin with inhibitor cystine knot ICK or Knottin scaffold; InterPro: IPR019553 Spider toxins of the CSTX family are ion channel toxins containing an inhibitor cystine knot (ICK) structural motif or Knottin scaffold. The four disulphide bonds present in the CSTX spider toxin family are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7. CSTX-1 is the most important component of Cupiennius salei (Wandering spider) venom in terms of relative abundance and toxicity and therefore is likely to contribute significantly to the overall toxicity of the whole venom. CSTX-1 blocked rat neuronal L-type, but no other types of HVA Cav channels []. Interestingly, the omega-toxins from Phoneutria nigriventer (Brazilian armed spider) venom (another South American species also belonging to the Ctenidae family) are included as they carry the same disulphide bond arrangement. suggested that CSTX-1 may interact with Cav channels. Calcium ion voltage channel heteromultimer containing an L-type pore-forming alpha1-subunit is the most probable candidate for the molecular target of CSTX-1 these toxins [].
Probab=11.47 E-value=90 Score=19.34 Aligned_cols=8 Identities=50% Similarity=1.190 Sum_probs=6.2
Q ss_pred CCeeeccC
Q 042337 227 KKCCCFPV 234 (236)
Q Consensus 227 ~~ccCF~w 234 (236)
+..|||.|
T Consensus 12 k~gCC~~~ 19 (23)
T PF10530_consen 12 KHGCCFKW 19 (23)
T ss_pred CCCceeee
Confidence 66788887
No 7
>PF02532 PsbI: Photosystem II reaction centre I protein (PSII 4.8 kDa protein); InterPro: IPR003686 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbI, which is tightly associated with the D1/D2 heterodimer in PSII. The function of PsbI is unknown, but it may be involved in the assembly, dimerisation or stabilisation of PSII dimers [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_i 3ARC_I 3A0B_i 3BZ2_I 3PRQ_I 3KZI_I 3PRR_I 2AXT_i 4FBY_I 1S5L_i ....
Probab=9.58 E-value=1.6e+02 Score=19.98 Aligned_cols=9 Identities=33% Similarity=0.446 Sum_probs=7.1
Q ss_pred CCCCCCCcc
Q 042337 53 PNDTHENQN 61 (236)
Q Consensus 53 PNDP~eNPe 61 (236)
+|||..||.
T Consensus 25 snDp~RnP~ 33 (36)
T PF02532_consen 25 SNDPGRNPG 33 (36)
T ss_dssp TTCTTSSSS
T ss_pred CCCCCCCCC
Confidence 688888885
No 8
>PF10981 DUF2788: Protein of unknown function (DUF2788); InterPro: IPR021249 This bacterial family of proteins have no known function.
Probab=9.23 E-value=1.7e+02 Score=21.25 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=10.9
Q ss_pred hhhhhcCCCCCCCCC
Q 042337 12 CLFRQRYNHVPKFGN 26 (236)
Q Consensus 12 ~~~~~~~~~vPkFG~ 26 (236)
-+.+.+ +.+||||.
T Consensus 15 ~dl~kk-s~agkfG~ 28 (52)
T PF10981_consen 15 WDLAKK-SKAGKFGT 28 (52)
T ss_pred HHHHHh-cCCCCcch
Confidence 456677 89999995
No 9
>PF08168 NUC205: NUC205 domain; InterPro: IPR012584 This domain is found in a novel family of nucleolar proteins [].; GO: 0005634 nucleus
Probab=8.88 E-value=1.6e+02 Score=20.80 Aligned_cols=9 Identities=56% Similarity=0.959 Sum_probs=8.2
Q ss_pred CCCCCCCCC
Q 042337 51 INPNDTHEN 59 (236)
Q Consensus 51 iNPNDP~eN 59 (236)
|+|.||+||
T Consensus 35 ~~~~d~een 43 (44)
T PF08168_consen 35 ISPKDPEEN 43 (44)
T ss_pred ccCCCcccC
Confidence 899999987
No 10
>CHL00024 psbI photosystem II protein I
Probab=8.61 E-value=1.8e+02 Score=19.75 Aligned_cols=10 Identities=30% Similarity=0.302 Sum_probs=7.5
Q ss_pred CCCCCCCCcc
Q 042337 52 NPNDTHENQN 61 (236)
Q Consensus 52 NPNDP~eNPe 61 (236)
=+|||..||.
T Consensus 24 lsnDp~RnP~ 33 (36)
T CHL00024 24 LSNDPGRNPG 33 (36)
T ss_pred cCCCCCCCCC
Confidence 3688888885
Done!