Query 016971
Match_columns 379
No_of_seqs 190 out of 334
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:28:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016971.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016971hhsearch_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 5.8E-40 1.3E-44 264.9 -1.0 78 87-164 1-78 (79)
2 PF14901 Jiv90: Cleavage induc 44.1 9.4 0.0002 32.7 0.6 18 125-142 26-43 (94)
3 PRK06424 transcription factor; 44.1 13 0.00028 33.6 1.5 21 117-137 14-34 (144)
4 PRK00241 nudC NADH pyrophospha 34.2 14 0.0003 35.9 0.1 37 100-137 92-128 (256)
5 PF14776 UNC-79: Cation-channe 33.2 22 0.00047 38.6 1.3 27 107-133 262-297 (525)
6 TIGR03831 YgiT_finger YgiT-typ 22.4 45 0.00097 23.1 1.0 20 115-134 21-40 (46)
7 TIGR00270 conserved hypothetic 21.4 53 0.0012 29.9 1.5 22 115-136 13-34 (154)
8 PF12108 SF3a60_bindingd: Spli 21.4 18 0.00039 24.8 -1.2 11 97-107 16-26 (28)
9 COG2816 NPY1 NTP pyrophosphohy 21.0 38 0.00081 34.1 0.5 36 100-136 104-139 (279)
10 PF05485 THAP: THAP domain; I 17.8 65 0.0014 25.0 1.1 14 106-119 48-61 (84)
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=5.8e-40 Score=264.92 Aligned_cols=78 Identities=62% Similarity=1.141 Sum_probs=63.2
Q ss_pred ceeeCCCccccccccccccccccchhhcCCCeEeEcCeeehhhhhccccccccccccchhHHHHHHhHHHhhhcCCCC
Q 016971 87 SCLVDGCDSDLSNCRDYHRRHKVCELHSKTPQVLICGQKQRFCQQCSRFHCLEEFDEGKRSCRKRLDGHNRRRRKPQP 164 (379)
Q Consensus 87 ~CqV~GC~~dLs~~k~Y~rR~rVCe~H~ka~~V~v~G~~qRFCQQC~rFH~L~eFD~~kRSCR~rL~~hn~RRRk~q~ 164 (379)
+||||||++||+.+|+||+||||||.|+||++|+++|+++||||||+|||+|+||||+|||||++|++||+||||.++
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 699999999999999999999999999999999999999999999999999999999999999999999999999875
No 2
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=44.12 E-value=9.4 Score=32.74 Aligned_cols=18 Identities=39% Similarity=0.672 Sum_probs=14.6
Q ss_pred eehhhhhccccccccccc
Q 016971 125 KQRFCQQCSRFHCLEEFD 142 (379)
Q Consensus 125 ~qRFCQQC~rFH~L~eFD 142 (379)
.-|+||+|..+|+..|=|
T Consensus 26 ~AR~C~~C~~~H~Ak~gD 43 (94)
T PF14901_consen 26 AARYCQDCKIRHPAKEGD 43 (94)
T ss_pred hhHhHHHhhhhcccccCC
Confidence 469999999999876544
No 3
>PRK06424 transcription factor; Provisional
Probab=44.06 E-value=13 Score=33.58 Aligned_cols=21 Identities=29% Similarity=0.721 Sum_probs=18.7
Q ss_pred CeEeEcCeeehhhhhcccccc
Q 016971 117 PQVLICGQKQRFCQQCSRFHC 137 (379)
Q Consensus 117 ~~V~v~G~~qRFCQQC~rFH~ 137 (379)
..|+|+|.+.+-|..|.+|=.
T Consensus 14 ~~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 14 TKVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred eEEEEcCeeeehhHHHHHcCC
Confidence 578999999999999998854
No 4
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=34.17 E-value=14 Score=35.86 Aligned_cols=37 Identities=14% Similarity=0.316 Sum_probs=28.9
Q ss_pred ccccccccccchhhcCCCeEeEcCeeehhhhhcccccc
Q 016971 100 CRDYHRRHKVCELHSKTPQVLICGQKQRFCQQCSRFHC 137 (379)
Q Consensus 100 ~k~Y~rR~rVCe~H~ka~~V~v~G~~qRFCQQC~rFH~ 137 (379)
+..+|++||-|..+-....+. .+...|.|..|++.|-
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 468999999999988765554 5556788999997664
No 5
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=33.20 E-value=22 Score=38.59 Aligned_cols=27 Identities=33% Similarity=0.607 Sum_probs=20.3
Q ss_pred cccchhhcCCCeEeE---------cCeeehhhhhcc
Q 016971 107 HKVCELHSKTPQVLI---------CGQKQRFCQQCS 133 (379)
Q Consensus 107 ~rVCe~H~ka~~V~v---------~G~~qRFCQQC~ 133 (379)
+|-|.-+.|..+|+- +++..|+||||.
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 456666667666653 788999999997
No 6
>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=22.41 E-value=45 Score=23.07 Aligned_cols=20 Identities=20% Similarity=0.400 Sum_probs=17.4
Q ss_pred CCCeEeEcCeeehhhhhccc
Q 016971 115 KTPQVLICGQKQRFCQQCSR 134 (379)
Q Consensus 115 ka~~V~v~G~~qRFCQQC~r 134 (379)
+...+++.++...+|.+|+.
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56778899999999999994
No 7
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=21.40 E-value=53 Score=29.92 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=19.0
Q ss_pred CCCeEeEcCeeehhhhhccccc
Q 016971 115 KTPQVLICGQKQRFCQQCSRFH 136 (379)
Q Consensus 115 ka~~V~v~G~~qRFCQQC~rFH 136 (379)
+.-.|.|+|.+..-|..|.+|=
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 8
>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=21.39 E-value=18 Score=24.80 Aligned_cols=11 Identities=45% Similarity=0.918 Sum_probs=7.2
Q ss_pred ccccccccccc
Q 016971 97 LSNCRDYHRRH 107 (379)
Q Consensus 97 Ls~~k~Y~rR~ 107 (379)
|..+|+||+||
T Consensus 16 lk~Ike~Hrr~ 26 (28)
T PF12108_consen 16 LKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHS-
T ss_pred HHHHHHHHHhC
Confidence 55677788776
No 9
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=20.99 E-value=38 Score=34.10 Aligned_cols=36 Identities=25% Similarity=0.454 Sum_probs=29.4
Q ss_pred ccccccccccchhhcCCCeEeEcCeeehhhhhccccc
Q 016971 100 CRDYHRRHKVCELHSKTPQVLICGQKQRFCQQCSRFH 136 (379)
Q Consensus 100 ~k~Y~rR~rVCe~H~ka~~V~v~G~~qRFCQQC~rFH 136 (379)
+-++|++||.|.. .-+++...+|...|-|++|+.-|
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 4578999999985 45677888899999999998554
No 10
>PF05485 THAP: THAP domain; InterPro: IPR006612 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. The THAP domain is an ~90-residue domain restricted to animals, which is shared between the THAP family of cellular DNA-binding proteins, and transposases from mobile genomic parasites. The defined THAP domain includes: a C2CH signature (consensus: C-x(2,4)-C-x(35,50)-C-x(2)-H); three additional key residues that are strictly conserved in all THAP domains that have been found to date (THAP1 amino acids P26, W36, F58); a C-terminal AVPTIF box; and several other conserved amino acid positions with distinct physicochemical properties (e.g. hydrophobic and polar). The THAP domain can be found in one or more copies and can be associated with other domains, such as the C2H2-type zinc finger. The THAP domain is supposed to be a DNA-binding domain (DBD) [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding; PDB: 3KDE_C 2D8R_A 2JM3_A 2KO0_A 2JTG_A 2L1G_A.
Probab=17.76 E-value=65 Score=25.01 Aligned_cols=14 Identities=14% Similarity=0.482 Sum_probs=9.0
Q ss_pred ccccchhhcCCCeE
Q 016971 106 RHKVCELHSKTPQV 119 (379)
Q Consensus 106 R~rVCe~H~ka~~V 119 (379)
..+||..|.....+
T Consensus 48 ~~~ICs~HF~~~~~ 61 (84)
T PF05485_consen 48 NSRICSRHFEPDDF 61 (84)
T ss_dssp TSEEEGGGSTGGGB
T ss_pred CccchhhhCchhhc
Confidence 45777777765444
Done!