Query 031751
Match_columns 153
No_of_seqs 51 out of 53
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:50:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031751.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031751hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3262 H/ACA small nucleolar 23.8 37 0.00081 28.8 0.9 34 2-39 86-124 (215)
2 PF13684 Dak1_2: Dihydroxyacet 12.8 92 0.002 27.1 0.8 11 105-115 297-307 (313)
3 PF11983 DUF3484: Domain of un 12.1 56 0.0012 23.0 -0.6 8 27-34 65-72 (73)
4 PF08765 Mor: Mor transcriptio 10.2 80 0.0017 23.0 -0.4 10 107-116 43-52 (108)
5 TIGR03599 YloV DAK2 domain fus 9.0 1.5E+02 0.0032 28.0 0.8 11 105-115 514-524 (530)
6 KOG2199 Signal transducing ada 8.2 1.4E+02 0.003 28.2 0.2 10 142-151 246-255 (462)
7 TIGR02593 CRISPR_cas5 CRISPR-a 7.1 94 0.002 19.1 -1.0 12 31-42 23-34 (42)
8 KOG2780 Ribosome biogenesis pr 6.3 1.7E+02 0.0036 26.2 -0.2 18 29-46 216-233 (302)
9 PF12206 DUF3599: Domain of un 5.8 1.5E+02 0.0033 23.2 -0.6 9 94-102 44-52 (117)
10 PF05983 Med7: MED7 protein; 5.7 2.2E+02 0.0047 22.7 0.2 9 31-39 3-11 (162)
No 1
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=23.79 E-value=37 Score=28.82 Aligned_cols=34 Identities=35% Similarity=0.632 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCccccccCCCCC-----CCCCcccccccCCCcc
Q 031751 2 EGRKQTGSSSSLTNELFGSKES-----SSSSGIFGSIFSPPSK 39 (153)
Q Consensus 2 E~kKk~~sSsS~~~~LFG~k~s-----ssssgiF~SIFppps~ 39 (153)
|+|+|.+ -+|||||+-.. -.+.+|-.|+|.|=.+
T Consensus 86 enk~qIG----KVDEIfG~i~d~~fsIK~~dgv~assfk~g~k 124 (215)
T KOG3262|consen 86 ENKEQIG----KVDEIFGPINDVHFSIKPSDGVQASSFKPGDK 124 (215)
T ss_pred cchhhhc----chhhhcccccccEEEEecCCCceeecccCCCe
Confidence 4555544 58999999865 4457888888876544
No 2
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=12.82 E-value=92 Score=27.09 Aligned_cols=11 Identities=45% Similarity=1.014 Sum_probs=8.8
Q ss_pred ceeecCccccC
Q 031751 105 SIYYGGQDVYS 115 (153)
Q Consensus 105 SIyYGGqd~Ys 115 (153)
-+|||||.+|.
T Consensus 297 e~~~GgQ~~y~ 307 (313)
T PF13684_consen 297 EVYDGGQPLYP 307 (313)
T ss_pred EEEECCCcceE
Confidence 48899998874
No 3
>PF11983 DUF3484: Domain of unknown function (DUF3484); InterPro: IPR021873 FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains []. This C-terminal domain is found in FtsA from Firmicutes (Gram-positive bacteria). It is typically between 65 to 81 amino acids in length.
Probab=12.13 E-value=56 Score=23.04 Aligned_cols=8 Identities=63% Similarity=1.360 Sum_probs=6.4
Q ss_pred Cccccccc
Q 031751 27 SGIFGSIF 34 (153)
Q Consensus 27 sgiF~SIF 34 (153)
-|||++||
T Consensus 65 R~~fgsmF 72 (73)
T PF11983_consen 65 RGFFGSMF 72 (73)
T ss_pred HHHHhhhc
Confidence 47888888
No 4
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=10.18 E-value=80 Score=23.03 Aligned_cols=10 Identities=60% Similarity=1.544 Sum_probs=3.6
Q ss_pred eecCccccCC
Q 031751 107 YYGGQDVYSP 116 (153)
Q Consensus 107 yYGGqd~Ys~ 116 (153)
||||+.+|-|
T Consensus 43 ~~gG~~iyiP 52 (108)
T PF08765_consen 43 YFGGQQIYIP 52 (108)
T ss_dssp HH-SS-----
T ss_pred HHCCEeEEee
Confidence 7999999983
No 5
>TIGR03599 YloV DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling.
Probab=9.00 E-value=1.5e+02 Score=27.98 Aligned_cols=11 Identities=55% Similarity=1.044 Sum_probs=7.2
Q ss_pred ceeecCccccC
Q 031751 105 SIYYGGQDVYS 115 (153)
Q Consensus 105 SIyYGGqd~Ys 115 (153)
-+|||||..|.
T Consensus 514 e~~~GgQ~~y~ 524 (530)
T TIGR03599 514 EIYEGGQPLYP 524 (530)
T ss_pred EEEECCCCcee
Confidence 46777777663
No 6
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=8.16 E-value=1.4e+02 Score=28.17 Aligned_cols=10 Identities=50% Similarity=1.258 Sum_probs=7.6
Q ss_pred CCCccCCccc
Q 031751 142 SRGNWWQGSL 151 (153)
Q Consensus 142 SRGnWWqGSl 151 (153)
+--|||+|.+
T Consensus 246 s~~~WWKG~~ 255 (462)
T KOG2199|consen 246 SDPNWWKGEN 255 (462)
T ss_pred CCcchhcccc
Confidence 3479999974
No 7
>TIGR02593 CRISPR_cas5 CRISPR-associated protein Cas5, N-terminal domain. This model represents a shared N-terminal domain, about 43 amino acids in length, common to a number of related protein families each of which is associated with a distinct subtype of CRISPR/cas system, where CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeat and Cas is an abbreviation for CRISPR-associated. Members of this family are widely distributed enough that we designated the family Cas5. Homology appears remote, or absent, between the more C-terminal regions different subfamilies of these proteins, which typically are 210 to 265 amino acids in total length. Cas5 proteins of six different CRISPR/cas subtypes so far defined are described by respective full-length models TIGR01868, TIGR01876, TIGR01895, TIGR01874, TIGR02586, and TIGR02592. The best characterized protein in this family is DevS or Myxococcus xanthus, a Cas protein that appears to participate in a species-specific
Probab=7.08 E-value=94 Score=19.09 Aligned_cols=12 Identities=42% Similarity=0.675 Sum_probs=7.8
Q ss_pred ccccCCCccccC
Q 031751 31 GSIFSPPSKVLG 42 (153)
Q Consensus 31 ~SIFppps~v~g 42 (153)
.--||||+++.|
T Consensus 23 ty~~Pp~Stv~G 34 (42)
T TIGR02593 23 TYPVPPPSALLG 34 (42)
T ss_pred cCCCCCHHHHHH
Confidence 345777777665
No 8
>KOG2780 consensus Ribosome biogenesis protein RPF1, contains IMP4 domain [RNA processing and modification]
Probab=6.33 E-value=1.7e+02 Score=26.25 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=14.8
Q ss_pred ccccccCCCccccCccch
Q 031751 29 IFGSIFSPPSKVLGRESL 46 (153)
Q Consensus 29 iF~SIFppps~v~gr~s~ 46 (153)
+|.||||+++.-.||..+
T Consensus 216 ~f~sLfp~~p~f~gRrvv 233 (302)
T KOG2780|consen 216 LFASLFPHDPQFTGRRVV 233 (302)
T ss_pred HHHHhCCCCccccceeEE
Confidence 689999999987777653
No 9
>PF12206 DUF3599: Domain of unknown function (DUF3599); InterPro: IPR024556 This family of bacterial proteins includes phage-like element PBSX protein xkdH from Bacillus subtilis. The function of the family is unknown.; PDB: 3F3B_A.
Probab=5.79 E-value=1.5e+02 Score=23.15 Aligned_cols=9 Identities=33% Similarity=0.667 Sum_probs=6.7
Q ss_pred CCCCCCCcc
Q 031751 94 DQRVQPCHL 102 (153)
Q Consensus 94 ~e~~epc~l 102 (153)
+..-.||||
T Consensus 44 Dl~~vpCyF 52 (117)
T PF12206_consen 44 DLEDVPCYF 52 (117)
T ss_dssp SEEEEEEEE
T ss_pred ccccCccEE
Confidence 445689999
No 10
>PF05983 Med7: MED7 protein; InterPro: IPR009244 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3FBI_C 3FBN_A 1YKH_A 1YKE_A.
Probab=5.71 E-value=2.2e+02 Score=22.67 Aligned_cols=9 Identities=44% Similarity=1.029 Sum_probs=1.5
Q ss_pred ccccCCCcc
Q 031751 31 GSIFSPPSK 39 (153)
Q Consensus 31 ~SIFppps~ 39 (153)
.|.||||+.
T Consensus 3 ~s~fPpPP~ 11 (162)
T PF05983_consen 3 SSLFPPPPP 11 (162)
T ss_dssp ---S----G
T ss_pred CCCCCCchH
Confidence 478888876
Done!