Query 032310
Match_columns 143
No_of_seqs 130 out of 275
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 12:24:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032310.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032310hhsearch_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 1.9E-43 4.2E-48 251.6 -2.9 78 58-135 1-78 (79)
2 PF14901 Jiv90: Cleavage induc 61.6 4.2 9E-05 30.4 1.0 18 96-113 26-43 (94)
3 TIGR03831 YgiT_finger YgiT-typ 47.8 7.9 0.00017 23.1 0.5 20 86-105 21-40 (46)
4 PF03811 Zn_Tnp_IS1: InsA N-te 38.7 9.7 0.00021 23.5 -0.1 24 80-103 7-35 (36)
5 PRK00241 nudC NADH pyrophospha 37.5 9.7 0.00021 31.8 -0.3 37 71-108 92-128 (256)
6 PF09297 zf-NADH-PPase: NADH p 32.1 11 0.00024 22.0 -0.6 30 77-107 2-31 (32)
7 PF02150 RNA_POL_M_15KD: RNA p 31.5 12 0.00027 22.7 -0.5 33 80-112 3-35 (35)
8 PF13240 zinc_ribbon_2: zinc-r 30.6 17 0.00037 20.3 0.1 10 96-105 12-21 (23)
9 PF12108 SF3a60_bindingd: Spli 29.8 19 0.00041 21.5 0.2 11 68-78 16-26 (28)
10 PRK06424 transcription factor; 26.1 36 0.00079 26.6 1.2 25 88-112 14-39 (144)
11 PF12898 Stc1: Stc1 domain; I 23.5 15 0.00032 26.1 -1.3 31 80-116 39-69 (84)
12 PF10083 DUF2321: Uncharacteri 23.0 37 0.00081 27.6 0.7 31 74-104 3-35 (158)
13 TIGR00270 conserved hypothetic 21.8 47 0.001 26.1 1.1 23 86-108 13-35 (154)
14 KOG0720 Molecular chaperone (D 20.8 43 0.00093 31.5 0.8 17 95-111 347-363 (490)
15 PF14776 UNC-79: Cation-channe 20.2 64 0.0014 30.6 1.8 28 78-105 262-298 (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=1.9e-43 Score=251.65 Aligned_cols=78 Identities=65% Similarity=1.161 Sum_probs=63.1
Q ss_pred ccccCCCcchhccchhhhhhccchhhhcCCCeEeECChhhhHHHhhhhcccccccccccchHHHHHhhHHHhhccCCC
Q 032310 58 SCQVENCRANMTDAKKYHRRHKVCDFHAKAPVVRVEGLAQRFCQQCSRFHELSEFDDTKRSCRRRLAGHNERRRKSSA 135 (143)
Q Consensus 58 ~CqVdGC~adLs~~k~Y~rR~rVCe~H~kA~~V~v~G~~qRFCQQCsrFH~L~eFDg~kRSCR~rLa~Hn~RRRk~~~ 135 (143)
+||||||++||+.+|.||+||+||+.|++||+|+++|+.+||||||++||+|+||||+|||||++|++||+|||++.+
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 599999999999999999999999999999999999999999999999999999999999999999999999999864
No 2
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=61.56 E-value=4.2 Score=30.35 Aligned_cols=18 Identities=44% Similarity=0.752 Sum_probs=14.9
Q ss_pred hhhHHHhhhhcccccccc
Q 032310 96 AQRFCQQCSRFHELSEFD 113 (143)
Q Consensus 96 ~qRFCQQCsrFH~L~eFD 113 (143)
.-|+||+|..+||..+=|
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 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=47.83 E-value=7.9 Score=23.08 Aligned_cols=20 Identities=20% Similarity=0.584 Sum_probs=17.3
Q ss_pred CCCeEeECChhhhHHHhhhh
Q 032310 86 KAPVVRVEGLAQRFCQQCSR 105 (143)
Q Consensus 86 kA~~V~v~G~~qRFCQQCsr 105 (143)
+.-.+++.+++..+|++|+-
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56678899999999999984
No 4
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=38.74 E-value=9.7 Score=23.55 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=16.3
Q ss_pred chhhhcCCCeEeECChh----hhH-HHhh
Q 032310 80 VCDFHAKAPVVRVEGLA----QRF-CQQC 103 (143)
Q Consensus 80 VCe~H~kA~~V~v~G~~----qRF-CQQC 103 (143)
.||....+..|.-+|.. ||| |+.|
T Consensus 7 ~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 7 HCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 36777777767776653 676 7777
No 5
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=37.51 E-value=9.7 Score=31.79 Aligned_cols=37 Identities=14% Similarity=0.319 Sum_probs=28.5
Q ss_pred chhhhhhccchhhhcCCCeEeECChhhhHHHhhhhccc
Q 032310 71 AKKYHRRHKVCDFHAKAPVVRVEGLAQRFCQQCSRFHE 108 (143)
Q Consensus 71 ~k~Y~rR~rVCe~H~kA~~V~v~G~~qRFCQQCsrFH~ 108 (143)
+-.+|++|+-|+.+-....+ ..+...+.|..|+..|-
T Consensus 92 l~~w~~~~~fC~~CG~~~~~-~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 92 LAEFYRSHRFCGYCGHPMHP-SKTEWAMLCPHCRERYY 128 (256)
T ss_pred HHHHhhcCccccccCCCCee-cCCceeEECCCCCCEEC
Confidence 34689999999998876554 45556788999997764
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=32.10 E-value=11 Score=21.98 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=16.1
Q ss_pred hccchhhhcCCCeEeECChhhhHHHhhhhcc
Q 032310 77 RHKVCDFHAKAPVVRVEGLAQRFCQQCSRFH 107 (143)
Q Consensus 77 R~rVCe~H~kA~~V~v~G~~qRFCQQCsrFH 107 (143)
.|+.|... -+|++.+.+...|-|+.|+..|
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 45566554 4567777777788888887543
No 7
>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=31.46 E-value=12 Score=22.67 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=19.1
Q ss_pred chhhhcCCCeEeECChhhhHHHhhhhccccccc
Q 032310 80 VCDFHAKAPVVRVEGLAQRFCQQCSRFHELSEF 112 (143)
Q Consensus 80 VCe~H~kA~~V~v~G~~qRFCQQCsrFH~L~eF 112 (143)
-|+.....+.+.-+....+.|.+|+--++++.|
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 355555555555444433379999988888876
No 8
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=30.65 E-value=17 Score=20.28 Aligned_cols=10 Identities=30% Similarity=1.095 Sum_probs=7.6
Q ss_pred hhhHHHhhhh
Q 032310 96 AQRFCQQCSR 105 (143)
Q Consensus 96 ~qRFCQQCsr 105 (143)
.++||.+|+.
T Consensus 12 ~~~fC~~CG~ 21 (23)
T PF13240_consen 12 DAKFCPNCGT 21 (23)
T ss_pred cCcchhhhCC
Confidence 3678999984
No 9
>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=29.84 E-value=19 Score=21.46 Aligned_cols=11 Identities=45% Similarity=0.915 Sum_probs=6.9
Q ss_pred hccchhhhhhc
Q 032310 68 MTDAKKYHRRH 78 (143)
Q Consensus 68 Ls~~k~Y~rR~ 78 (143)
|..+|.||+||
T Consensus 16 lk~Ike~Hrr~ 26 (28)
T PF12108_consen 16 LKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHS-
T ss_pred HHHHHHHHHhC
Confidence 55667777776
No 10
>PRK06424 transcription factor; Provisional
Probab=26.05 E-value=36 Score=26.57 Aligned_cols=25 Identities=24% Similarity=0.626 Sum_probs=20.5
Q ss_pred CeEeECChhhhHHHhhhhccc-cccc
Q 032310 88 PVVRVEGLAQRFCQQCSRFHE-LSEF 112 (143)
Q Consensus 88 ~~V~v~G~~qRFCQQCsrFH~-L~eF 112 (143)
-.|+|+|....-|..|.+|=. +..+
T Consensus 14 ~~v~ieg~~l~vC~~Ca~~G~~v~~~ 39 (144)
T PRK06424 14 TKVMIDGAILNVCDDCAKFGTPVIEH 39 (144)
T ss_pred eEEEEcCeeeehhHHHHHcCCccccc
Confidence 468899999999999999853 5555
No 11
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=23.49 E-value=15 Score=26.07 Aligned_cols=31 Identities=26% Similarity=0.567 Sum_probs=22.5
Q ss_pred chhhhcCCCeEeECChhhhHHHhhhhccccccccccc
Q 032310 80 VCDFHAKAPVVRVEGLAQRFCQQCSRFHELSEFDDTK 116 (143)
Q Consensus 80 VCe~H~kA~~V~v~G~~qRFCQQCsrFH~L~eFDg~k 116 (143)
+|..|...+++.+ -|-.|++.=||++|-.+.
T Consensus 39 ~C~~ct~~q~~El------~C~~C~~~k~ld~FSK~Q 69 (84)
T PF12898_consen 39 RCRECTGGQVVEL------TCSPCGKTKPLDEFSKNQ 69 (84)
T ss_pred CCccCCCCCcCcC------EeccCCCCcCHHHHhHHh
Confidence 4556665555544 688999999999996553
No 12
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.00 E-value=37 Score=27.57 Aligned_cols=31 Identities=23% Similarity=0.498 Sum_probs=19.6
Q ss_pred hhhhccchhh-hcCCCeEeEC-ChhhhHHHhhh
Q 032310 74 YHRRHKVCDF-HAKAPVVRVE-GLAQRFCQQCS 104 (143)
Q Consensus 74 Y~rR~rVCe~-H~kA~~V~v~-G~~qRFCQQCs 104 (143)
||+-..||.. |.-...+..+ -..+-||.|||
T Consensus 3 ~y~~aqiC~NGH~~t~~~~~~p~~~~~fC~kCG 35 (158)
T PF10083_consen 3 TYRIAQICLNGHVITDSYDKNPELREKFCSKCG 35 (158)
T ss_pred chhHHHHccCccccccccccCchHHHHHHHHhh
Confidence 5566666753 5555555554 45577888887
No 13
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=21.81 E-value=47 Score=26.08 Aligned_cols=23 Identities=26% Similarity=0.615 Sum_probs=19.4
Q ss_pred CCCeEeECChhhhHHHhhhhccc
Q 032310 86 KAPVVRVEGLAQRFCQQCSRFHE 108 (143)
Q Consensus 86 kA~~V~v~G~~qRFCQQCsrFH~ 108 (143)
+.-.|.|+|....-|..|.+|=.
T Consensus 13 ~~~~v~iega~l~vC~~C~k~G~ 35 (154)
T TIGR00270 13 KGFKIVIEGSEMTVCGECRKFGK 35 (154)
T ss_pred CCeEEEEcCeEEehhhhHHhcCC
Confidence 33578899999999999999854
No 14
>KOG0720 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=20.81 E-value=43 Score=31.53 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=14.1
Q ss_pred hhhhHHHhhhhcccccc
Q 032310 95 LAQRFCQQCSRFHELSE 111 (143)
Q Consensus 95 ~~qRFCQQCsrFH~L~e 111 (143)
-.-|.||-|+.+|+-.+
T Consensus 347 s~AR~C~~C~~~H~AKd 363 (490)
T KOG0720|consen 347 SQARWCAECGVKHPAKD 363 (490)
T ss_pred hhhHHHHHhCccCcccc
Confidence 34699999999999655
No 15
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=20.23 E-value=64 Score=30.64 Aligned_cols=28 Identities=36% Similarity=0.617 Sum_probs=21.2
Q ss_pred ccchhhhcCCCeEeE---------CChhhhHHHhhhh
Q 032310 78 HKVCDFHAKAPVVRV---------EGLAQRFCQQCSR 105 (143)
Q Consensus 78 ~rVCe~H~kA~~V~v---------~G~~qRFCQQCsr 105 (143)
++-|.-+.|..+|+- +..+.|+||||..
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 566777777777663 6788999999983
Done!