Query 029706
Match_columns 189
No_of_seqs 116 out of 166
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 17:12:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029706.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029706hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02178 AT_hook: AT hook moti 96.7 0.00048 1E-08 36.1 0.5 12 88-99 1-12 (13)
2 smart00384 AT_hook DNA binding 96.7 0.00083 1.8E-08 41.2 1.3 15 88-102 1-15 (26)
3 PF14621 RFX5_DNA_bdg: RFX5 DN 89.0 0.14 3.1E-06 44.4 0.4 16 86-101 66-82 (219)
4 PF13546 DDE_5: DDE superfamil 86.1 0.41 8.9E-06 40.6 1.6 16 85-100 228-243 (273)
5 COG1710 Uncharacterized protei 80.7 0.73 1.6E-05 37.9 0.9 16 85-100 81-97 (139)
6 COG1777 Predicted transcriptio 60.8 3.6 7.7E-05 36.3 0.6 19 87-105 63-82 (217)
7 PF13737 DDE_Tnp_1_5: Transpos 40.5 14 0.0003 29.2 1.0 15 85-99 21-35 (112)
8 PF00127 Copper-bind: Copper b 38.3 18 0.00039 26.6 1.2 19 152-170 10-28 (99)
9 KOG4565 E93 protein involved i 37.8 11 0.00023 32.9 -0.1 15 86-100 111-125 (206)
10 PF14601 TFX_C: DNA_binding pr 30.5 25 0.00055 26.5 0.9 15 156-170 12-26 (84)
11 TIGR02657 amicyanin amicyanin. 27.1 35 0.00075 24.4 1.2 18 153-170 5-22 (83)
12 smart00412 Cu_FIST Copper-Fist 24.3 33 0.00072 22.9 0.6 8 87-94 31-38 (39)
No 1
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=96.75 E-value=0.00048 Score=36.13 Aligned_cols=12 Identities=75% Similarity=1.138 Sum_probs=4.4
Q ss_pred ccccCCCCCCCC
Q 029706 88 KKKRGRPRKYAP 99 (189)
Q Consensus 88 KKKRGRPRKYgp 99 (189)
+|+||||+|+..
T Consensus 1 ~r~RGRP~k~~~ 12 (13)
T PF02178_consen 1 KRKRGRPRKNAK 12 (13)
T ss_dssp S--SS--TT---
T ss_pred CCcCCCCccccC
Confidence 689999999865
No 2
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=96.68 E-value=0.00083 Score=41.24 Aligned_cols=15 Identities=60% Similarity=0.933 Sum_probs=13.2
Q ss_pred ccccCCCCCCCCCCC
Q 029706 88 KKKRGRPRKYAPDGQ 102 (189)
Q Consensus 88 KKKRGRPRKYgpDG~ 102 (189)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999998864
No 3
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=89.01 E-value=0.14 Score=44.44 Aligned_cols=16 Identities=56% Similarity=0.918 Sum_probs=12.3
Q ss_pred ccccccCCCCC-CCCCC
Q 029706 86 PVKKKRGRPRK-YAPDG 101 (189)
Q Consensus 86 ~~KKKRGRPRK-YgpDG 101 (189)
..||||||||| -|-.+
T Consensus 66 dAKRKRGRPRKKsggsg 82 (219)
T PF14621_consen 66 DAKRKRGRPRKKSGGSG 82 (219)
T ss_pred hhhhhcCCCccCCCCCc
Confidence 58999999995 45444
No 4
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=86.14 E-value=0.41 Score=40.57 Aligned_cols=16 Identities=56% Similarity=0.951 Sum_probs=12.2
Q ss_pred cccccccCCCCCCCCC
Q 029706 85 DPVKKKRGRPRKYAPD 100 (189)
Q Consensus 85 e~~KKKRGRPRKYgpD 100 (189)
.+..+|||||||||.-
T Consensus 228 ~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGRR 243 (273)
T ss_pred cccCCCCCCCCCCCCc
Confidence 3455559999999965
No 5
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=80.70 E-value=0.73 Score=37.85 Aligned_cols=16 Identities=69% Similarity=1.099 Sum_probs=13.5
Q ss_pred cccc-cccCCCCCCCCC
Q 029706 85 DPVK-KKRGRPRKYAPD 100 (189)
Q Consensus 85 e~~K-KKRGRPRKYgpD 100 (189)
-|+| |-|||||||.-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 4778 889999999874
No 6
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=60.76 E-value=3.6 Score=36.30 Aligned_cols=19 Identities=47% Similarity=0.686 Sum_probs=13.7
Q ss_pred cccccCCCCCCCC-CCCccc
Q 029706 87 VKKKRGRPRKYAP-DGQVSL 105 (189)
Q Consensus 87 ~KKKRGRPRKYgp-DG~vsl 105 (189)
.|.+|||||||-- .++++|
T Consensus 63 e~~~Rg~~rKYY~Is~~~rl 82 (217)
T COG1777 63 EKIPRGRPRKYYMISRNLRL 82 (217)
T ss_pred cccccCCCcceeeccCCeEE
Confidence 5777899999965 455544
No 7
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=40.45 E-value=14 Score=29.20 Aligned_cols=15 Identities=47% Similarity=0.975 Sum_probs=12.1
Q ss_pred cccccccCCCCCCCC
Q 029706 85 DPVKKKRGRPRKYAP 99 (189)
Q Consensus 85 e~~KKKRGRPRKYgp 99 (189)
++...|||||++|-.
T Consensus 21 ~~~~~kRGr~~~ySD 35 (112)
T PF13737_consen 21 APPRGKRGRPPRYSD 35 (112)
T ss_pred cCCCCCCCCCcccch
Confidence 356789999999954
No 8
>PF00127 Copper-bind: Copper binding proteins, plastocyanin/azurin family; InterPro: IPR000923 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. This pollen protein is evolutionary related to the above proteins, but seems to have lost the ability to bind copper. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1UAT_A 1CUO_A 1PLC_A 4PCY_A 3PCY_A 1PND_A 1PNC_A 1JXG_A 6PCY_A 1TKW_A ....
Probab=38.27 E-value=18 Score=26.56 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=16.3
Q ss_pred CcccccceEEEecCCCccc
Q 029706 152 AGIAFAPHVISIGVGEVCY 170 (189)
Q Consensus 152 aG~~FTPHVITVnaGEDVa 170 (189)
.+..|.|..|+|++||-|.
T Consensus 10 ~~~~F~P~~i~V~~G~tV~ 28 (99)
T PF00127_consen 10 GDMAFDPSEITVKAGDTVT 28 (99)
T ss_dssp STSSEESSEEEEETTEEEE
T ss_pred CccEEeCCEEEECCCCEEE
Confidence 4689999999999998654
No 9
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=37.77 E-value=11 Score=32.91 Aligned_cols=15 Identities=47% Similarity=0.795 Sum_probs=13.1
Q ss_pred ccccccCCCCCCCCC
Q 029706 86 PVKKKRGRPRKYAPD 100 (189)
Q Consensus 86 ~~KKKRGRPRKYgpD 100 (189)
.-+|||||=|+|...
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 578999999999874
No 10
>PF14601 TFX_C: DNA_binding protein, TFX, C-term; PDB: 1NR3_A.
Probab=30.48 E-value=25 Score=26.54 Aligned_cols=15 Identities=33% Similarity=0.403 Sum_probs=9.1
Q ss_pred ccceEEEecCCCccc
Q 029706 156 FAPHVISIGVGEVCY 170 (189)
Q Consensus 156 FTPHVITVnaGEDVa 170 (189)
-.|+.|+|.+|+|+.
T Consensus 12 ~Apv~i~i~~GtDl~ 26 (84)
T PF14601_consen 12 NAPVRITIPAGTDLF 26 (84)
T ss_dssp ---EEEEE--GGGHH
T ss_pred CCCEEEEEcCCCcHH
Confidence 369999999999974
No 11
>TIGR02657 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc.
Probab=27.11 E-value=35 Score=24.36 Aligned_cols=18 Identities=11% Similarity=0.346 Sum_probs=15.3
Q ss_pred cccccceEEEecCCCccc
Q 029706 153 GIAFAPHVISIGVGEVCY 170 (189)
Q Consensus 153 G~~FTPHVITVnaGEDVa 170 (189)
+..|.|..|+|.+|+-|.
T Consensus 5 ~~~F~P~~i~v~~GdtVt 22 (83)
T TIGR02657 5 KMKYETPELHVKVGDTVT 22 (83)
T ss_pred eeEEcCCEEEECCCCEEE
Confidence 567999999999999774
No 12
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=24.31 E-value=33 Score=22.94 Aligned_cols=8 Identities=50% Similarity=0.924 Sum_probs=5.9
Q ss_pred cccccCCC
Q 029706 87 VKKKRGRP 94 (189)
Q Consensus 87 ~KKKRGRP 94 (189)
.=||||||
T Consensus 31 ~i~kkGRP 38 (39)
T smart00412 31 PVRPRGRP 38 (39)
T ss_pred eecCCCCC
Confidence 44778998
Done!