Query 032937
Match_columns 130
No_of_seqs 108 out of 284
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:48:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032937.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032937hhsearch_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 8.2E-44 1.8E-48 250.0 -2.4 78 38-115 1-78 (79)
2 PF14901 Jiv90: Cleavage induc 62.6 3.9 8.6E-05 30.0 1.1 18 76-93 26-43 (94)
3 TIGR03831 YgiT_finger YgiT-typ 47.3 8.1 0.00018 22.7 0.5 20 66-85 21-40 (46)
4 PRK00241 nudC NADH pyrophospha 41.1 9.7 0.00021 31.3 0.2 37 51-88 92-128 (256)
5 PF02150 RNA_POL_M_15KD: RNA p 38.9 6.4 0.00014 23.5 -0.9 33 60-92 3-35 (35)
6 PF12108 SF3a60_bindingd: Spli 36.9 14 0.0003 21.7 0.3 11 48-58 16-26 (28)
7 PHA00437 tail assembly protein 35.1 27 0.00059 25.8 1.7 17 13-29 65-81 (94)
8 PF09297 zf-NADH-PPase: NADH p 34.2 9.3 0.0002 21.9 -0.7 30 57-87 2-31 (32)
9 PF03811 Zn_Tnp_IS1: InsA N-te 33.3 14 0.0003 22.5 -0.1 24 60-83 7-35 (36)
10 PF13240 zinc_ribbon_2: zinc-r 31.0 17 0.00037 19.9 0.1 10 76-85 12-21 (23)
11 PRK06424 transcription factor; 30.6 35 0.00075 26.2 1.7 25 68-92 14-39 (144)
12 PF12898 Stc1: Stc1 domain; I 29.4 9.9 0.00021 26.5 -1.3 32 59-96 38-69 (84)
13 PRK08359 transcription factor; 28.9 61 0.0013 25.9 2.9 20 68-87 21-41 (176)
14 COG2816 NPY1 NTP pyrophosphohy 26.3 21 0.00045 30.7 -0.2 36 51-87 104-139 (279)
15 TIGR00270 conserved hypothetic 25.5 48 0.001 25.6 1.7 22 67-88 14-35 (154)
16 PF14776 UNC-79: Cation-channe 24.6 48 0.001 31.0 1.8 28 58-85 262-298 (525)
17 KOG0720 Molecular chaperone (D 22.2 38 0.00083 31.3 0.7 17 75-91 347-363 (490)
18 PF13248 zf-ribbon_3: zinc-rib 20.2 33 0.00072 18.9 -0.1 10 76-85 15-24 (26)
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=8.2e-44 Score=249.97 Aligned_cols=78 Identities=64% Similarity=1.168 Sum_probs=63.1
Q ss_pred ccccCCCcccccchhhhhhhhcchhhhcCCCEEEECCeehhHHHhhhhcccccccccccchHHHHHhhHHHhhhcCcc
Q 032937 38 CCMVEKCGTDLTDARRYHRRHKVCETHSKAPVVIVAGLRQRFCQQCSRFHELYEFDETKRSCRRRLAGHNERRRKSTA 115 (130)
Q Consensus 38 ~CqVdGC~~dLs~~k~Y~rR~rVCe~H~kAp~V~~~G~~qRFCQQC~rFH~LseFDg~kRSCR~rL~rhn~RRRk~~~ 115 (130)
+||||||++||+.+|.||+||+|||.|++||+|+++|.++||||||++||+|+||||+|||||++|++||+|||+.++
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=62.60 E-value=3.9 Score=29.99 Aligned_cols=18 Identities=39% Similarity=0.656 Sum_probs=14.9
Q ss_pred ehhHHHhhhhcccccccc
Q 032937 76 RQRFCQQCSRFHELYEFD 93 (130)
Q Consensus 76 ~qRFCQQC~rFH~LseFD 93 (130)
..|||+.|+.+||..+=|
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=47.26 E-value=8.1 Score=22.66 Aligned_cols=20 Identities=15% Similarity=0.589 Sum_probs=17.2
Q ss_pred CCCEEEECCeehhHHHhhhh
Q 032937 66 KAPVVIVAGLRQRFCQQCSR 85 (130)
Q Consensus 66 kAp~V~~~G~~qRFCQQC~r 85 (130)
+.-.+++.+.+..+|.+||-
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56678899999999999994
No 4
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=41.14 E-value=9.7 Score=31.27 Aligned_cols=37 Identities=14% Similarity=0.242 Sum_probs=28.7
Q ss_pred hhhhhhhhcchhhhcCCCEEEECCeehhHHHhhhhccc
Q 032937 51 ARRYHRRHKVCETHSKAPVVIVAGLRQRFCQQCSRFHE 88 (130)
Q Consensus 51 ~k~Y~rR~rVCe~H~kAp~V~~~G~~qRFCQQC~rFH~ 88 (130)
+-.+|++|+-|+.+-....+ ..+...+.|..|+..|-
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 44899999999998876554 45566788999997663
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=38.89 E-value=6.4 Score=23.52 Aligned_cols=33 Identities=12% Similarity=0.253 Sum_probs=20.4
Q ss_pred chhhhcCCCEEEECCeehhHHHhhhhccccccc
Q 032937 60 VCETHSKAPVVIVAGLRQRFCQQCSRFHELYEF 92 (130)
Q Consensus 60 VCe~H~kAp~V~~~G~~qRFCQQC~rFH~LseF 92 (130)
-|+.....+.+.-+....+.|..|+--++++.|
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 466666666666544443479999988888876
No 6
>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=36.87 E-value=14 Score=21.70 Aligned_cols=11 Identities=45% Similarity=0.911 Sum_probs=7.0
Q ss_pred ccchhhhhhhh
Q 032937 48 LTDARRYHRRH 58 (130)
Q Consensus 48 Ls~~k~Y~rR~ 58 (130)
|..+|+||+||
T Consensus 16 lk~Ike~Hrr~ 26 (28)
T PF12108_consen 16 LKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHS-
T ss_pred HHHHHHHHHhC
Confidence 55677777776
No 7
>PHA00437 tail assembly protein
Probab=35.05 E-value=27 Score=25.81 Aligned_cols=17 Identities=18% Similarity=0.390 Sum_probs=11.2
Q ss_pred cccchhhHHHhhhcccC
Q 032937 13 DCYADDERKKKATGRRA 29 (130)
Q Consensus 13 ~~~~~~~~~~~~~~~~~ 29 (130)
..++...|+.|.+|||+
T Consensus 65 aqTESgkKKaRA~GKks 81 (94)
T PHA00437 65 AQTESGKKKARAGGKKS 81 (94)
T ss_pred hhhhhhHHHHhhcCccc
Confidence 33445556668899995
No 8
>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=34.21 E-value=9.3 Score=21.91 Aligned_cols=30 Identities=30% Similarity=0.571 Sum_probs=16.6
Q ss_pred hhcchhhhcCCCEEEECCeehhHHHhhhhcc
Q 032937 57 RHKVCETHSKAPVVIVAGLRQRFCQQCSRFH 87 (130)
Q Consensus 57 R~rVCe~H~kAp~V~~~G~~qRFCQQC~rFH 87 (130)
.|+.|... -+|++.+.+...|-|+.|+..|
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 45666654 4677777777888888887543
No 9
>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=33.28 E-value=14 Score=22.50 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=16.5
Q ss_pred chhhhcCCCEEEECCee----hhH-HHhh
Q 032937 60 VCETHSKAPVVIVAGLR----QRF-CQQC 83 (130)
Q Consensus 60 VCe~H~kAp~V~~~G~~----qRF-CQQC 83 (130)
.||....+..|..+|.. ||| |+.|
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 47777777767776653 666 7776
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.02 E-value=17 Score=19.95 Aligned_cols=10 Identities=30% Similarity=1.095 Sum_probs=7.6
Q ss_pred ehhHHHhhhh
Q 032937 76 RQRFCQQCSR 85 (130)
Q Consensus 76 ~qRFCQQC~r 85 (130)
...||.+||.
T Consensus 12 ~~~fC~~CG~ 21 (23)
T PF13240_consen 12 DAKFCPNCGT 21 (23)
T ss_pred cCcchhhhCC
Confidence 3678999983
No 11
>PRK06424 transcription factor; Provisional
Probab=30.60 E-value=35 Score=26.25 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=20.3
Q ss_pred CEEEECCeehhHHHhhhhccc-cccc
Q 032937 68 PVVIVAGLRQRFCQQCSRFHE-LYEF 92 (130)
Q Consensus 68 p~V~~~G~~qRFCQQC~rFH~-LseF 92 (130)
-.|+|+|....-|..|.+|=. +..+
T Consensus 14 ~~v~ieg~~l~vC~~Ca~~G~~v~~~ 39 (144)
T PRK06424 14 TKVMIDGAILNVCDDCAKFGTPVIEH 39 (144)
T ss_pred eEEEEcCeeeehhHHHHHcCCccccc
Confidence 468899999999999999854 4444
No 12
>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=29.36 E-value=9.9 Score=26.55 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=24.7
Q ss_pred cchhhhcCCCEEEECCeehhHHHhhhhccccccccccc
Q 032937 59 KVCETHSKAPVVIVAGLRQRFCQQCSRFHELYEFDETK 96 (130)
Q Consensus 59 rVCe~H~kAp~V~~~G~~qRFCQQC~rFH~LseFDg~k 96 (130)
-+|-.|...+++.+ -|-.|++.=||++|-.+.
T Consensus 38 i~C~~ct~~q~~El------~C~~C~~~k~ld~FSK~Q 69 (84)
T PF12898_consen 38 IRCRECTGGQVVEL------TCSPCGKTKPLDEFSKNQ 69 (84)
T ss_pred CCCccCCCCCcCcC------EeccCCCCcCHHHHhHHh
Confidence 36777776666655 688999999999996553
No 13
>PRK08359 transcription factor; Validated
Probab=28.88 E-value=61 Score=25.91 Aligned_cols=20 Identities=15% Similarity=0.546 Sum_probs=17.5
Q ss_pred CEEEECCeehhHHHhhh-hcc
Q 032937 68 PVVIVAGLRQRFCQQCS-RFH 87 (130)
Q Consensus 68 p~V~~~G~~qRFCQQC~-rFH 87 (130)
-.|.|+|....-|..|. +|=
T Consensus 21 ~~v~ieGael~VC~~Ca~k~G 41 (176)
T PRK08359 21 HRIRIEGAELLVCDRCYEKYG 41 (176)
T ss_pred eEEEEcCeEEehHHHHHHHhC
Confidence 36779999999999999 883
No 14
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.34 E-value=21 Score=30.69 Aligned_cols=36 Identities=22% Similarity=0.438 Sum_probs=29.8
Q ss_pred hhhhhhhhcchhhhcCCCEEEECCeehhHHHhhhhcc
Q 032937 51 ARRYHRRHKVCETHSKAPVVIVAGLRQRFCQQCSRFH 87 (130)
Q Consensus 51 ~k~Y~rR~rVCe~H~kAp~V~~~G~~qRFCQQC~rFH 87 (130)
+-.+++.||.|..+ -+++....|...+-|++|+.-|
T Consensus 104 l~~w~~~~RFCg~C-G~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 104 LLEWYRSHRFCGRC-GTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHHhhCcCCCCC-CCcCccccCceeeeCCCCCCcc
Confidence 44789999999865 5688888999999999999544
No 15
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=25.49 E-value=48 Score=25.62 Aligned_cols=22 Identities=18% Similarity=0.623 Sum_probs=18.9
Q ss_pred CCEEEECCeehhHHHhhhhccc
Q 032937 67 APVVIVAGLRQRFCQQCSRFHE 88 (130)
Q Consensus 67 Ap~V~~~G~~qRFCQQC~rFH~ 88 (130)
.-.|.|+|....-|..|.+|=.
T Consensus 14 ~~~v~iega~l~vC~~C~k~G~ 35 (154)
T TIGR00270 14 GFKIVIEGSEMTVCGECRKFGK 35 (154)
T ss_pred CeEEEEcCeEEehhhhHHhcCC
Confidence 3578899999999999999844
No 16
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=24.63 E-value=48 Score=30.96 Aligned_cols=28 Identities=36% Similarity=0.682 Sum_probs=20.4
Q ss_pred hcchhhhcCCCEEEE---------CCeehhHHHhhhh
Q 032937 58 HKVCETHSKAPVVIV---------AGLRQRFCQQCSR 85 (130)
Q Consensus 58 ~rVCe~H~kAp~V~~---------~G~~qRFCQQC~r 85 (130)
++-|..+.|..+|+- +..+.|+|+||..
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 455666666666653 6788999999983
No 17
>KOG0720 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.24 E-value=38 Score=31.34 Aligned_cols=17 Identities=24% Similarity=0.628 Sum_probs=14.1
Q ss_pred eehhHHHhhhhcccccc
Q 032937 75 LRQRFCQQCSRFHELYE 91 (130)
Q Consensus 75 ~~qRFCQQC~rFH~Lse 91 (130)
..-|+||-|+.+||-.+
T Consensus 347 s~AR~C~~C~~~H~AKd 363 (490)
T KOG0720|consen 347 SQARWCAECGVKHPAKD 363 (490)
T ss_pred hhhHHHHHhCccCcccc
Confidence 34699999999999765
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.23 E-value=33 Score=18.91 Aligned_cols=10 Identities=30% Similarity=1.082 Sum_probs=8.0
Q ss_pred ehhHHHhhhh
Q 032937 76 RQRFCQQCSR 85 (130)
Q Consensus 76 ~qRFCQQC~r 85 (130)
..+||..||.
T Consensus 15 ~~~fC~~CG~ 24 (26)
T PF13248_consen 15 DAKFCPNCGA 24 (26)
T ss_pred ccccChhhCC
Confidence 4789999984
Done!