Query 029650
Match_columns 190
No_of_seqs 144 out of 282
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 16:19:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029650.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029650hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03110 SBP: SBP domain; Int 100.0 3.2E-42 7E-47 254.9 -1.1 78 65-142 1-78 (79)
2 PF14901 Jiv90: Cleavage induc 50.3 6.2 0.00013 30.8 0.4 18 103-120 26-43 (94)
3 TIGR03831 YgiT_finger YgiT-typ 42.5 14 0.0003 23.0 1.0 20 93-112 21-40 (46)
4 PRK00241 nudC NADH pyrophospha 37.0 15 0.00032 32.0 0.7 37 78-115 92-128 (256)
5 PF02150 RNA_POL_M_15KD: RNA p 30.5 18 0.0004 22.9 0.2 33 87-119 3-35 (35)
6 PF09297 zf-NADH-PPase: NADH p 28.6 25 0.00054 21.4 0.5 30 84-114 2-31 (32)
7 PF12108 SF3a60_bindingd: Spli 28.4 18 0.00039 22.6 -0.1 11 75-85 16-26 (28)
8 PF13240 zinc_ribbon_2: zinc-r 26.1 25 0.00054 20.6 0.2 9 104-112 13-21 (23)
9 PF14803 Nudix_N_2: Nudix N-te 26.0 38 0.00082 21.7 1.1 15 100-114 18-32 (34)
10 PRK06424 transcription factor; 24.7 47 0.001 27.1 1.6 20 96-115 15-34 (144)
11 COG2816 NPY1 NTP pyrophosphohy 21.2 38 0.00083 30.9 0.5 36 78-114 104-139 (279)
12 TIGR00270 conserved hypothetic 20.8 63 0.0014 26.5 1.7 22 94-115 14-35 (154)
13 PF10161 DDDD: Putative mitoch 20.7 48 0.001 25.3 0.9 10 22-31 70-79 (79)
14 PF14776 UNC-79: Cation-channe 20.4 51 0.0011 32.7 1.2 28 85-112 262-298 (525)
No 1
>PF03110 SBP: SBP domain; InterPro: IPR004333 The SBP plant protein domain is a sequence specific DNA-binding domain []. Proteins with this domain probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1UL4_A 1WJ0_A 1UL5_A.
Probab=100.00 E-value=3.2e-42 Score=254.92 Aligned_cols=78 Identities=71% Similarity=1.197 Sum_probs=63.2
Q ss_pred ccccCCCCcccccchhhhhhccchhhhhcccEEEECCeeeehhhhhcccccccccccccchHHHHHhhHHHHhccccc
Q 029650 65 SCQVDKCGADLSDAKQYHRRHKVCEVHAKAQVVLMGGIRQRFCQQCSRFHELSEFDETKRSCRRRLAGHNERRRKNAA 142 (190)
Q Consensus 65 ~CQVeGC~adLs~~K~YhrRhrVCe~H~KAp~V~v~G~~qRFCQQCsRFH~L~EFDg~KRSCR~rLarHn~RRRk~~~ 142 (190)
+||||||++||+++|.||+||+|||.|++||+|+++|.++||||||++||+|+||||+|||||++|++||+|||++++
T Consensus 1 ~CqV~gC~~dL~~~k~Y~rR~rICe~H~ka~~V~~~G~~~RFCQQC~rfh~l~eFdg~kRSCr~~L~~h~~RRr~~~~ 78 (79)
T PF03110_consen 1 RCQVDGCGADLSGAKEYHRRYRICEEHAKAPVVVVDGVEQRFCQQCGRFHPLSEFDGGKRSCRARLARHNERRRKRQQ 78 (79)
T ss_dssp C-SSTTEE-EETS--SSCCCTT--HHHHTHSEEEETTEEEEE-TTTSSEEETTCB-SSTTSBSTTTT-SSS---S-S-
T ss_pred CCcCCCCCcchhhhHHHhhccCcchhhcCCCeEEECChhHHHHHHHHcCCCHHHHcchhhhHHHHHHHHHHHhccccC
Confidence 599999999999999999999999999999999999999999999999999999999999999999999999999875
No 2
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=50.34 E-value=6.2 Score=30.79 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=14.4
Q ss_pred eeehhhhhcccccccccc
Q 029650 103 RQRFCQQCSRFHELSEFD 120 (190)
Q Consensus 103 ~qRFCQQCsRFH~L~EFD 120 (190)
.-|+||+|+.+||..+=|
T Consensus 26 ~AR~C~~C~~~H~Ak~gD 43 (94)
T PF14901_consen 26 AARYCQDCKIRHPAKEGD 43 (94)
T ss_pred hhHhHHHhhhhcccccCC
Confidence 469999999999876533
No 3
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=42.53 E-value=14 Score=23.02 Aligned_cols=20 Identities=15% Similarity=0.602 Sum_probs=17.2
Q ss_pred cccEEEECCeeeehhhhhcc
Q 029650 93 KAQVVLMGGIRQRFCQQCSR 112 (190)
Q Consensus 93 KAp~V~v~G~~qRFCQQCsR 112 (190)
+.-.+++.+++..+|++|+.
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56678889999999999984
No 4
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=36.99 E-value=15 Score=32.04 Aligned_cols=37 Identities=14% Similarity=0.261 Sum_probs=28.9
Q ss_pred chhhhhhccchhhhhcccEEEECCeeeehhhhhccccc
Q 029650 78 AKQYHRRHKVCEVHAKAQVVLMGGIRQRFCQQCSRFHE 115 (190)
Q Consensus 78 ~K~YhrRhrVCe~H~KAp~V~v~G~~qRFCQQCsRFH~ 115 (190)
+-.+|++|+-|+.+-....+. .+...+.|..|+..|-
T Consensus 92 l~~w~~~~~fC~~CG~~~~~~-~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 92 LAEFYRSHRFCGYCGHPMHPS-KTEWAMLCPHCRERYY 128 (256)
T ss_pred HHHHhhcCccccccCCCCeec-CCceeEECCCCCCEEC
Confidence 457899999999988866554 4556789999997763
No 5
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=30.46 E-value=18 Score=22.94 Aligned_cols=33 Identities=15% Similarity=0.288 Sum_probs=19.7
Q ss_pred chhhhhcccEEEECCeeeehhhhhccccccccc
Q 029650 87 VCEVHAKAQVVLMGGIRQRFCQQCSRFHELSEF 119 (190)
Q Consensus 87 VCe~H~KAp~V~v~G~~qRFCQQCsRFH~L~EF 119 (190)
-|+.....+.+.-+....+.|.+|+--++++.|
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~~ 35 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPISQF 35 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-SS-
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCCCCC
Confidence 366666666655544444489999988888776
No 6
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=28.62 E-value=25 Score=21.41 Aligned_cols=30 Identities=27% Similarity=0.437 Sum_probs=15.5
Q ss_pred hccchhhhhcccEEEECCeeeehhhhhcccc
Q 029650 84 RHKVCEVHAKAQVVLMGGIRQRFCQQCSRFH 114 (190)
Q Consensus 84 RhrVCe~H~KAp~V~v~G~~qRFCQQCsRFH 114 (190)
.|+-|... -+|++.+.+...|-|+.|+..|
T Consensus 2 ~~rfC~~C-G~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 2 NHRFCGRC-GAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TTSB-TTT---BEEE-SSSS-EEESSSS-EE
T ss_pred CCcccCcC-CccccCCCCcCEeECCCCcCEe
Confidence 34555543 4566667677788888887543
No 7
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=28.37 E-value=18 Score=22.62 Aligned_cols=11 Identities=55% Similarity=0.966 Sum_probs=6.6
Q ss_pred cccchhhhhhc
Q 029650 75 LSDAKQYHRRH 85 (190)
Q Consensus 75 Ls~~K~YhrRh 85 (190)
|..+|+||+||
T Consensus 16 lk~Ike~Hrr~ 26 (28)
T PF12108_consen 16 LKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHS-
T ss_pred HHHHHHHHHhC
Confidence 45567777765
No 8
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=26.15 E-value=25 Score=20.56 Aligned_cols=9 Identities=33% Similarity=1.228 Sum_probs=7.4
Q ss_pred eehhhhhcc
Q 029650 104 QRFCQQCSR 112 (190)
Q Consensus 104 qRFCQQCsR 112 (190)
.+||.+||.
T Consensus 13 ~~fC~~CG~ 21 (23)
T PF13240_consen 13 AKFCPNCGT 21 (23)
T ss_pred CcchhhhCC
Confidence 689999984
No 9
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.04 E-value=38 Score=21.70 Aligned_cols=15 Identities=20% Similarity=0.543 Sum_probs=9.4
Q ss_pred CCeeeehhhhhcccc
Q 029650 100 GGIRQRFCQQCSRFH 114 (190)
Q Consensus 100 ~G~~qRFCQQCsRFH 114 (190)
++.+-.+|..|+..|
T Consensus 18 d~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 18 DDRERLVCPACGFIH 32 (34)
T ss_dssp -SS-EEEETTTTEEE
T ss_pred CCccceECCCCCCEE
Confidence 555667788888766
No 10
>PRK06424 transcription factor; Provisional
Probab=24.69 E-value=47 Score=27.11 Aligned_cols=20 Identities=25% Similarity=0.723 Sum_probs=18.3
Q ss_pred EEEECCeeeehhhhhccccc
Q 029650 96 VVLMGGIRQRFCQQCSRFHE 115 (190)
Q Consensus 96 ~V~v~G~~qRFCQQCsRFH~ 115 (190)
.|.|+|....-|..|.+|=.
T Consensus 15 ~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 15 KVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred EEEEcCeeeehhHHHHHcCC
Confidence 68999999999999999965
No 11
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=21.24 E-value=38 Score=30.88 Aligned_cols=36 Identities=22% Similarity=0.468 Sum_probs=29.1
Q ss_pred chhhhhhccchhhhhcccEEEECCeeeehhhhhcccc
Q 029650 78 AKQYHRRHKVCEVHAKAQVVLMGGIRQRFCQQCSRFH 114 (190)
Q Consensus 78 ~K~YhrRhrVCe~H~KAp~V~v~G~~qRFCQQCsRFH 114 (190)
+-.+|+.||.|.. .-++.....|...+-|++|+.-|
T Consensus 104 l~~w~~~~RFCg~-CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 104 LLEWYRSHRFCGR-CGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHHhhCcCCCC-CCCcCccccCceeeeCCCCCCcc
Confidence 3468899999985 46777788888899999999655
No 12
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.83 E-value=63 Score=26.52 Aligned_cols=22 Identities=18% Similarity=0.605 Sum_probs=18.9
Q ss_pred ccEEEECCeeeehhhhhccccc
Q 029650 94 AQVVLMGGIRQRFCQQCSRFHE 115 (190)
Q Consensus 94 Ap~V~v~G~~qRFCQQCsRFH~ 115 (190)
.-.|.|+|....-|..|.+|=.
T Consensus 14 ~~~v~iega~l~vC~~C~k~G~ 35 (154)
T TIGR00270 14 GFKIVIEGSEMTVCGECRKFGK 35 (154)
T ss_pred CeEEEEcCeEEehhhhHHhcCC
Confidence 3478999999999999999843
No 13
>PF10161 DDDD: Putative mitochondrial precursor protein; InterPro: IPR018782 This entry represents a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. These proteins have been putatively designated as mitochondrial precursor proteins but this has not been confirmed.
Probab=20.67 E-value=48 Score=25.28 Aligned_cols=10 Identities=80% Similarity=1.268 Sum_probs=5.6
Q ss_pred ccccCCCCCC
Q 029650 22 FVDSDDDDDD 31 (190)
Q Consensus 22 ~~~~~~~~~~ 31 (190)
||-+|||||+
T Consensus 70 FvP~DDDDDd 79 (79)
T PF10161_consen 70 FVPEDDDDDD 79 (79)
T ss_pred cCCCcCCCCC
Confidence 4555666654
No 14
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=20.39 E-value=51 Score=32.66 Aligned_cols=28 Identities=39% Similarity=0.688 Sum_probs=21.8
Q ss_pred ccchhhhhcccEEEE---------CCeeeehhhhhcc
Q 029650 85 HKVCEVHAKAQVVLM---------GGIRQRFCQQCSR 112 (190)
Q Consensus 85 hrVCe~H~KAp~V~v---------~G~~qRFCQQCsR 112 (190)
.+-|..+.|..+|+- ++.+.|+||||..
T Consensus 262 nK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~ 298 (525)
T PF14776_consen 262 NKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHS 298 (525)
T ss_pred CCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhh
Confidence 566777777777763 7789999999983
Done!