Query 021420
Match_columns 312
No_of_seqs 171 out of 333
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 02:49:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021420.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021420hhsearch_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 1.6E-40 3.5E-45 262.1 -0.1 78 23-100 1-78 (79)
2 PRK06424 transcription factor; 46.3 12 0.00027 32.8 1.7 21 53-73 14-34 (144)
3 PF14901 Jiv90: Cleavage induc 45.0 8 0.00017 32.3 0.3 18 61-78 26-43 (94)
4 PF09297 zf-NADH-PPase: NADH p 35.4 19 0.00041 23.6 0.9 30 42-72 2-31 (32)
5 PRK00241 nudC NADH pyrophospha 32.0 17 0.00037 34.3 0.3 36 37-73 93-128 (256)
6 PF14776 UNC-79: Cation-channe 31.3 23 0.0005 37.4 1.1 27 43-69 262-297 (525)
7 TIGR03831 YgiT_finger YgiT-typ 26.4 36 0.00079 22.9 1.1 20 51-70 21-40 (46)
8 COG2816 NPY1 NTP pyrophosphohy 23.8 32 0.0007 33.6 0.6 35 37-72 105-139 (279)
9 PF02150 RNA_POL_M_15KD: RNA p 23.8 27 0.00058 23.8 0.0 33 45-77 3-35 (35)
10 TIGR00270 conserved hypothetic 22.2 55 0.0012 29.0 1.7 22 51-72 13-34 (154)
11 PF09526 DUF2387: Probable met 20.4 68 0.0015 25.3 1.7 26 44-69 9-37 (71)
12 PF12108 SF3a60_bindingd: Spli 20.1 19 0.00042 23.9 -1.2 11 33-43 16-26 (28)
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=1.6e-40 Score=262.13 Aligned_cols=78 Identities=63% Similarity=1.158 Sum_probs=63.2
Q ss_pred ceecCCCcccccccccccccccchhhhcCCCeEEECCeeeehhhhcccccccccccCcchhHHHHHhHHHhhhcCCCC
Q 021420 23 SCLVDGCTADLGKCRDYHRRHKVCEIHSKTPKVTIHGREQRFCQQCSRFHSLEEFDEGKRSCRKRLDGHNRRRRKPQP 100 (312)
Q Consensus 23 ~CqV~GC~~dLs~~k~Y~rR~rvCe~H~ka~~V~v~G~~~RFCQQC~rFH~L~eFDg~kRSCR~rL~~hn~RRRk~q~ 100 (312)
+||||||++||+.+|+||+||||||.|+|||+|+++|+++||||||+|||+|+||||+|||||++|++||+||||+++
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 599999999999999999999999999999999999999999999999999999999999999999999999999876
No 2
>PRK06424 transcription factor; Provisional
Probab=46.27 E-value=12 Score=32.83 Aligned_cols=21 Identities=33% Similarity=0.767 Sum_probs=18.6
Q ss_pred CeEEECCeeeehhhhcccccc
Q 021420 53 PKVTIHGREQRFCQQCSRFHS 73 (312)
Q Consensus 53 ~~V~v~G~~~RFCQQC~rFH~ 73 (312)
-.|+|+|.+.+-|..|.+|=.
T Consensus 14 ~~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 14 TKVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred eEEEEcCeeeehhHHHHHcCC
Confidence 468899999999999998854
No 3
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=45.04 E-value=8 Score=32.28 Aligned_cols=18 Identities=39% Similarity=0.744 Sum_probs=14.7
Q ss_pred eeehhhhccccccccccc
Q 021420 61 EQRFCQQCSRFHSLEEFD 78 (312)
Q Consensus 61 ~~RFCQQC~rFH~L~eFD 78 (312)
.-|+||+|..+|+..|=|
T Consensus 26 ~AR~C~~C~~~H~Ak~gD 43 (94)
T PF14901_consen 26 AARYCQDCKIRHPAKEGD 43 (94)
T ss_pred hhHhHHHhhhhcccccCC
Confidence 469999999999876644
No 4
>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=35.41 E-value=19 Score=23.63 Aligned_cols=30 Identities=27% Similarity=0.540 Sum_probs=17.5
Q ss_pred cccchhhhcCCCeEEECCeeeehhhhccccc
Q 021420 42 RHKVCEIHSKTPKVTIHGREQRFCQQCSRFH 72 (312)
Q Consensus 42 R~rvCe~H~ka~~V~v~G~~~RFCQQC~rFH 72 (312)
+||.|... -++++.+.+...|-|+.|+..|
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 56667654 5677778888888899888644
No 5
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=32.04 E-value=17 Score=34.31 Aligned_cols=36 Identities=14% Similarity=0.328 Sum_probs=26.8
Q ss_pred ccccccccchhhhcCCCeEEECCeeeehhhhcccccc
Q 021420 37 RDYHRRHKVCEIHSKTPKVTIHGREQRFCQQCSRFHS 73 (312)
Q Consensus 37 k~Y~rR~rvCe~H~ka~~V~v~G~~~RFCQQC~rFH~ 73 (312)
..+|++||-|..+-....+ ..+...|.|..|++.|-
T Consensus 93 ~~w~~~~~fC~~CG~~~~~-~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 93 AEFYRSHRFCGYCGHPMHP-SKTEWAMLCPHCRERYY 128 (256)
T ss_pred HHHhhcCccccccCCCCee-cCCceeEECCCCCCEEC
Confidence 4678899999988775544 45556788999997663
No 6
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=31.26 E-value=23 Score=37.43 Aligned_cols=27 Identities=41% Similarity=0.703 Sum_probs=21.5
Q ss_pred ccchhhhcCCCeEEE---------CCeeeehhhhcc
Q 021420 43 HKVCEIHSKTPKVTI---------HGREQRFCQQCS 69 (312)
Q Consensus 43 ~rvCe~H~ka~~V~v---------~G~~~RFCQQC~ 69 (312)
+|-|.-+.|..+|+- ++++.|+||||.
T Consensus 262 nK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch 297 (525)
T PF14776_consen 262 NKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCH 297 (525)
T ss_pred CCCCcCCCCCeEEEEechhhccccCCCcchhHHHHh
Confidence 566777778777753 678899999997
No 7
>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=26.39 E-value=36 Score=22.85 Aligned_cols=20 Identities=20% Similarity=0.411 Sum_probs=17.4
Q ss_pred CCCeEEECCeeeehhhhccc
Q 021420 51 KTPKVTIHGREQRFCQQCSR 70 (312)
Q Consensus 51 ka~~V~v~G~~~RFCQQC~r 70 (312)
+...+++.+.+..+|.+|+.
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56778899999999999984
No 8
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.81 E-value=32 Score=33.64 Aligned_cols=35 Identities=26% Similarity=0.527 Sum_probs=29.0
Q ss_pred ccccccccchhhhcCCCeEEECCeeeehhhhccccc
Q 021420 37 RDYHRRHKVCEIHSKTPKVTIHGREQRFCQQCSRFH 72 (312)
Q Consensus 37 k~Y~rR~rvCe~H~ka~~V~v~G~~~RFCQQC~rFH 72 (312)
-++|++||.|.. +-+++...+|...|-|++|+.-|
T Consensus 105 ~~w~~~~RFCg~-CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 105 LEWYRSHRFCGR-CGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHhhCcCCCC-CCCcCccccCceeeeCCCCCCcc
Confidence 467899999986 46678888999999999998654
No 9
>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=23.77 E-value=27 Score=23.82 Aligned_cols=33 Identities=12% Similarity=0.284 Sum_probs=20.4
Q ss_pred chhhhcCCCeEEECCeeeehhhhcccccccccc
Q 021420 45 VCEIHSKTPKVTIHGREQRFCQQCSRFHSLEEF 77 (312)
Q Consensus 45 vCe~H~ka~~V~v~G~~~RFCQQC~rFH~L~eF 77 (312)
-|+.....+.+.-+....+.|..|+--++++.|
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 466666666666554444489999988888776
No 10
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.15 E-value=55 Score=29.01 Aligned_cols=22 Identities=36% Similarity=0.753 Sum_probs=18.8
Q ss_pred CCCeEEECCeeeehhhhccccc
Q 021420 51 KTPKVTIHGREQRFCQQCSRFH 72 (312)
Q Consensus 51 ka~~V~v~G~~~RFCQQC~rFH 72 (312)
+.-.|.|+|.+..-|..|.+|=
T Consensus 13 ~~~~v~iega~l~vC~~C~k~G 34 (154)
T TIGR00270 13 KGFKIVIEGSEMTVCGECRKFG 34 (154)
T ss_pred CCeEEEEcCeEEehhhhHHhcC
Confidence 3457889999999999999883
No 11
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=20.37 E-value=68 Score=25.29 Aligned_cols=26 Identities=23% Similarity=0.508 Sum_probs=23.2
Q ss_pred cchhhhcCCCeEEE---CCeeeehhhhcc
Q 021420 44 KVCEIHSKTPKVTI---HGREQRFCQQCS 69 (312)
Q Consensus 44 rvCe~H~ka~~V~v---~G~~~RFCQQC~ 69 (312)
-+|+.+....+|++ +|.+.|.|=.|+
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CG 37 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECG 37 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCC
Confidence 47999999998875 899999999998
No 12
>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=20.11 E-value=19 Score=23.95 Aligned_cols=11 Identities=45% Similarity=0.890 Sum_probs=7.1
Q ss_pred ccccccccccc
Q 021420 33 LGKCRDYHRRH 43 (312)
Q Consensus 33 Ls~~k~Y~rR~ 43 (312)
|..+|+||+||
T Consensus 16 lk~Ike~Hrr~ 26 (28)
T PF12108_consen 16 LKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHS-
T ss_pred HHHHHHHHHhC
Confidence 55667788776
Done!