Query 026716
Match_columns 234
No_of_seqs 175 out of 286
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 11:43:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026716.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026716hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03479 DUF296: Domain of unk 98.6 3.8E-08 8.3E-13 78.3 3.1 56 156-211 1-72 (120)
2 PF02178 AT_hook: AT hook moti 96.6 0.0008 1.7E-08 36.3 0.6 13 88-100 1-13 (13)
3 smart00384 AT_hook DNA binding 96.5 0.0013 2.8E-08 41.5 1.4 15 88-102 1-15 (26)
4 COG1661 Predicted DNA-binding 90.4 0.84 1.8E-05 38.8 6.0 56 158-213 11-83 (141)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 86.3 0.25 5.5E-06 44.1 0.4 12 86-97 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 82.9 0.72 1.6E-05 40.5 1.7 16 85-100 228-243 (273)
7 COG1710 Uncharacterized protei 77.7 1 2.2E-05 38.1 0.9 16 85-100 81-97 (139)
8 PF14869 DUF4488: Domain of un 70.9 6.4 0.00014 33.4 4.0 35 170-206 27-63 (133)
9 COG1777 Predicted transcriptio 53.7 5.6 0.00012 36.2 0.7 23 87-109 63-88 (217)
10 PF13737 DDE_Tnp_1_5: Transpos 34.4 20 0.00044 29.2 1.1 18 85-103 21-38 (112)
11 KOG4565 E93 protein involved i 32.7 14 0.00031 33.0 -0.0 15 86-100 111-125 (206)
12 PF15333 TAF1D: TATA box-bindi 28.5 25 0.00054 32.1 0.8 13 90-102 64-76 (217)
13 PF03211 Pectate_lyase: Pectat 27.8 78 0.0017 28.7 3.7 32 168-199 52-87 (215)
14 cd01287 FabA FabA, beta-hydrox 26.4 1E+02 0.0023 25.7 4.0 35 170-207 82-117 (150)
15 TIGR02656 cyanin_plasto plasto 25.4 1.9E+02 0.0041 21.9 5.0 36 150-188 8-43 (99)
16 smart00412 Cu_FIST Copper-Fist 20.3 46 0.00099 23.0 0.6 8 87-94 31-38 (39)
No 1
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=98.57 E-value=3.8e-08 Score=78.34 Aligned_cols=56 Identities=25% Similarity=0.218 Sum_probs=47.6
Q ss_pred ceeEEEEEcCCC------------CceeEEEecCCCceeEEEEcCCC--CCCCceEEE--EEeEeeeccccc
Q 026716 156 FAPHVISIGVGE------------RPRVVCILSGRGTVSSVTLRQPA--TSVPTVTYE--VEALCLYLFLFW 211 (234)
Q Consensus 156 ftPHVItV~~GE------------g~raICILSA~G~VSnVTLRQP~--ssggtvTyE--FEILSLSGSflp 211 (234)
|+++++.+.+|| .....|++|+.|++++|+|++++ ....+.+|| |||+||+|++.+
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~ 72 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISP 72 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEEC
Confidence 789999999999 34667888999999999999974 334567788 999999999997
No 2
>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=96.56 E-value=0.0008 Score=36.29 Aligned_cols=13 Identities=69% Similarity=1.063 Sum_probs=4.4
Q ss_pred cccCCCCCCCCCC
Q 026716 88 KKKRGRPRKYAPD 100 (234)
Q Consensus 88 KkKRGRPRKYgpd 100 (234)
+||||||+|+..+
T Consensus 1 ~r~RGRP~k~~~~ 13 (13)
T PF02178_consen 1 KRKRGRPRKNAKK 13 (13)
T ss_dssp S--SS--TT----
T ss_pred CCcCCCCccccCC
Confidence 6899999998653
No 3
>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=96.51 E-value=0.0013 Score=41.51 Aligned_cols=15 Identities=60% Similarity=0.933 Sum_probs=13.2
Q ss_pred cccCCCCCCCCCCCC
Q 026716 88 KKKRGRPRKYAPDGQ 102 (234)
Q Consensus 88 KkKRGRPRKYgpdg~ 102 (234)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999998764
No 4
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=90.35 E-value=0.84 Score=38.76 Aligned_cols=56 Identities=16% Similarity=0.198 Sum_probs=41.3
Q ss_pred eEEEEEcCCC------------CceeEEEecCCCceeEEEEcCCCCCCC---ceEEE--EEeEeeeccccccC
Q 026716 158 PHVISIGVGE------------RPRVVCILSGRGTVSSVTLRQPATSVP---TVTYE--VEALCLYLFLFWKK 213 (234)
Q Consensus 158 PHVItV~~GE------------g~raICILSA~G~VSnVTLRQP~ssgg---tvTyE--FEILSLSGSflp~~ 213 (234)
=.++-+..|| ..-...|.++-|++++++|+-=+-... ++++. ||||||.|.+-.+.
T Consensus 11 ~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~ 83 (141)
T COG1661 11 VIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDD 83 (141)
T ss_pred EEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCC
Confidence 3567778888 223348999999999999987543222 33333 99999999998887
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=86.33 E-value=0.25 Score=44.15 Aligned_cols=12 Identities=67% Similarity=1.052 Sum_probs=10.3
Q ss_pred cccccCCCCCCC
Q 026716 86 PVKKKRGRPRKY 97 (234)
Q Consensus 86 ~~KkKRGRPRKY 97 (234)
-.|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 489999999964
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=82.90 E-value=0.72 Score=40.47 Aligned_cols=16 Identities=56% Similarity=0.951 Sum_probs=12.2
Q ss_pred CcccccCCCCCCCCCC
Q 026716 85 DPVKKKRGRPRKYAPD 100 (234)
Q Consensus 85 ~~~KkKRGRPRKYgpd 100 (234)
.+..+|||||||||.-
T Consensus 228 ~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGRR 243 (273)
T ss_pred cccCCCCCCCCCCCCc
Confidence 3455559999999965
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=77.68 E-value=1 Score=38.10 Aligned_cols=16 Identities=69% Similarity=1.099 Sum_probs=13.3
Q ss_pred Cccc-ccCCCCCCCCCC
Q 026716 85 DPVK-KKRGRPRKYAPD 100 (234)
Q Consensus 85 ~~~K-kKRGRPRKYgpd 100 (234)
-|+| |-|||||||.-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 4678 889999999864
No 8
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=70.89 E-value=6.4 Score=33.37 Aligned_cols=35 Identities=29% Similarity=0.187 Sum_probs=27.7
Q ss_pred eeEEEecCCCceeEEEEcCCCCCCCceEEE--EEeEeee
Q 026716 170 RVVCILSGRGTVSSVTLRQPATSVPTVTYE--VEALCLY 206 (234)
Q Consensus 170 raICILSA~G~VSnVTLRQP~ssggtvTyE--FEILSLS 206 (234)
..+=|||.+|++.|+++.+ . ++.++|+. ||+.|=+
T Consensus 27 ~~lKilS~Dgtf~Ni~~~~-~-~~aiIt~~GtY~~~sD~ 63 (133)
T PF14869_consen 27 NVLKILSDDGTFVNITMIP-K-SGAIITGYGTYEQPSDN 63 (133)
T ss_pred ccEEEEcCCCcEEEEEEeC-C-CCcEEEEeEEEEEcCCc
Confidence 3488999999999999944 2 34788877 9988744
No 9
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=53.68 E-value=5.6 Score=36.20 Aligned_cols=23 Identities=52% Similarity=0.751 Sum_probs=15.3
Q ss_pred ccccCCCCCCCCC-CCCccc--ccCC
Q 026716 87 VKKKRGRPRKYAP-DGQVSL--GLSP 109 (234)
Q Consensus 87 ~KkKRGRPRKYgp-dg~~~l--~l~P 109 (234)
.|.+|||||||-- .++++| -++|
T Consensus 63 e~~~Rg~~rKYY~Is~~~rleV~lsp 88 (217)
T COG1777 63 EKIPRGRPRKYYMISRNLRLEVTLSP 88 (217)
T ss_pred cccccCCCcceeeccCCeEEEEEecC
Confidence 5777899999965 444443 4455
No 10
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=34.44 E-value=20 Score=29.18 Aligned_cols=18 Identities=44% Similarity=0.975 Sum_probs=13.4
Q ss_pred CcccccCCCCCCCCCCCCc
Q 026716 85 DPVKKKRGRPRKYAPDGQV 103 (234)
Q Consensus 85 ~~~KkKRGRPRKYgpdg~~ 103 (234)
++...|||||++|- |-.|
T Consensus 21 ~~~~~kRGr~~~yS-D~aI 38 (112)
T PF13737_consen 21 APPRGKRGRPPRYS-DAAI 38 (112)
T ss_pred cCCCCCCCCCcccc-hHHH
Confidence 35578999999996 4443
No 11
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=32.74 E-value=14 Score=33.05 Aligned_cols=15 Identities=47% Similarity=0.795 Sum_probs=12.8
Q ss_pred cccccCCCCCCCCCC
Q 026716 86 PVKKKRGRPRKYAPD 100 (234)
Q Consensus 86 ~~KkKRGRPRKYgpd 100 (234)
.-+|||||=|+|...
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 478999999999763
No 12
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=28.52 E-value=25 Score=32.06 Aligned_cols=13 Identities=46% Similarity=0.974 Sum_probs=9.9
Q ss_pred cCCCCCCCCCCCC
Q 026716 90 KRGRPRKYAPDGQ 102 (234)
Q Consensus 90 KRGRPRKYgpdg~ 102 (234)
|+-+.|||-+.|.
T Consensus 64 KkrkkrKYk~tgr 76 (217)
T PF15333_consen 64 KKRKKRKYKPTGR 76 (217)
T ss_pred HHhhhhccCccCC
Confidence 5566799999775
No 13
>PF03211 Pectate_lyase: Pectate lyase; InterPro: IPR004898 Pectate lyase is responsible for the maceration and soft-rotting of plant tissue. It catalyses the eliminative cleavage of pectate to produce oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends. Pectate lyase is an extracellular enzyme and is induced by pectin. It is subject to self-catabolite repression, and has been implicated in plant disease. The structure and the folding kinetics of one member of this family, pectate lyase C (pelC)1 from Erwinia chrysanthemi has been investigated in some detail []. PelC contains a parallel beta-helix folding motif. The majority of the regular secondary structure is composed of parallel beta-sheets (about 30%). The individual strands of the sheets are connected by unordered loops of varying length. The backbone is then formed by a large helix composed of beta-sheets. There are two disulphide bonds in pelC and 12 proline residues. One of these prolines, Pro220, is involved in a cis peptide bond. he folding mechanism of pelC involves two slow phases that have been attributed to proline isomerization.; GO: 0030570 pectate lyase activity, 0005576 extracellular region; PDB: 3T9G_B 3B90_B 3B8Y_A 3B4N_B 1EE6_A.
Probab=27.77 E-value=78 Score=28.70 Aligned_cols=32 Identities=22% Similarity=0.212 Sum_probs=22.2
Q ss_pred CceeEEEecCCCceeEEEEcCCCCCC----CceEEE
Q 026716 168 RPRVVCILSGRGTVSSVTLRQPATSV----PTVTYE 199 (234)
Q Consensus 168 g~raICILSA~G~VSnVTLRQP~ssg----gtvTyE 199 (234)
.+-+|-||-.-++++||.|-.++..| +.-|+|
T Consensus 52 ~q~~vF~le~GatlkNvIiG~~~~dGIHC~G~Ctl~ 87 (215)
T PF03211_consen 52 DQDPVFILEDGATLKNVIIGANQADGIHCKGSCTLE 87 (215)
T ss_dssp C---SEEEETTEEEEEEEETSS-TT-EEEESCEEEE
T ss_pred ccceEEEecCCCEEEEEEEcCCCcCceEEcCCEEEE
Confidence 56789999999999999998877654 355666
No 14
>cd01287 FabA FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA structure is a homodimer with two independent active sites located at the dimer interface. Each active site is tunnel-shaped and completely inaccessible to solvent. No metal ions or cofactors are required for ligand binding or catalysis.
Probab=26.40 E-value=1e+02 Score=25.67 Aligned_cols=35 Identities=26% Similarity=0.132 Sum_probs=29.0
Q ss_pred eeEEEecCCCceeEEEEcCCCCCCC-ceEEEEEeEeeec
Q 026716 170 RVVCILSGRGTVSSVTLRQPATSVP-TVTYEVEALCLYL 207 (234)
Q Consensus 170 raICILSA~G~VSnVTLRQP~ssgg-tvTyEFEILSLSG 207 (234)
+.+.+| +.|.++..|.+...|. +|+||.||+.+..
T Consensus 82 ~~~~~l---~~~~~~kfr~~v~Pgd~~l~~e~~i~~~~~ 117 (150)
T cd01287 82 RFQGAP---GGPGEWKYRGQITPHNKKVTYEVHIKEVGR 117 (150)
T ss_pred cceeEe---ccceEEEECccCcCCCEEEEEEEEEEEEEc
Confidence 445555 6788999999999998 8999999998863
No 15
>TIGR02656 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts.
Probab=25.38 E-value=1.9e+02 Score=21.93 Aligned_cols=36 Identities=25% Similarity=0.483 Sum_probs=23.7
Q ss_pred cCCCCCceeEEEEEcCCCCceeEEEecCCCceeEEEEcC
Q 026716 150 SSAGIAFAPHVISIGVGERPRVVCILSGRGTVSSVTLRQ 188 (234)
Q Consensus 150 ~s~g~~ftPHVItV~~GEg~raICILSA~G~VSnVTLRQ 188 (234)
...+-.|.|-.|+|.+|+. |-.....+.--||++..
T Consensus 8 ~~g~~~F~P~~i~v~~G~~---V~~~N~~~~~H~~~~~~ 43 (99)
T TIGR02656 8 DKGALVFEPAKISIAAGDT---VEWVNNKGGPHNVVFDE 43 (99)
T ss_pred CCCceeEeCCEEEECCCCE---EEEEECCCCCceEEECC
Confidence 3455789999999999982 33333444556666654
No 16
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=20.27 E-value=46 Score=22.99 Aligned_cols=8 Identities=50% Similarity=0.924 Sum_probs=5.9
Q ss_pred ccccCCCC
Q 026716 87 VKKKRGRP 94 (234)
Q Consensus 87 ~KkKRGRP 94 (234)
.=||||||
T Consensus 31 ~i~kkGRP 38 (39)
T smart00412 31 PVRPRGRP 38 (39)
T ss_pred eecCCCCC
Confidence 44778998
Done!