Query 039447
Match_columns 307
No_of_seqs 127 out of 235
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:43:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039447hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01568 A_thal_3678 uncharac 100.0 6.9E-34 1.5E-38 217.6 7.7 65 240-304 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 3.6E-32 7.8E-37 204.1 7.3 59 246-304 1-59 (59)
3 PF13724 DNA_binding_2: DNA-bi 99.9 1.9E-25 4.1E-30 162.6 2.0 31 1-31 1-31 (49)
4 smart00544 MA3 Domain in DAP-5 74.0 5 0.00011 31.9 3.9 47 253-301 1-47 (113)
5 PF02847 MA3: MA3 domain; Int 37.8 45 0.00097 26.2 3.5 28 270-297 16-43 (113)
6 PRK10072 putative transcriptio 34.8 55 0.0012 26.9 3.7 30 246-275 3-41 (96)
7 PF14551 MCM_N: MCM N-terminal 34.7 97 0.0021 24.3 5.0 50 253-302 18-73 (121)
8 PF09388 SpoOE-like: Spo0E lik 34.5 84 0.0018 22.0 4.1 31 252-282 8-44 (45)
9 PF10273 WGG: Pre-rRNA-process 33.3 53 0.0011 26.1 3.2 37 245-281 28-64 (82)
10 PF02979 NHase_alpha: Nitrile 30.7 68 0.0015 29.9 3.9 47 251-297 6-53 (188)
11 PF04994 TfoX_C: TfoX C-termin 29.9 61 0.0013 25.7 3.1 31 255-285 13-45 (81)
12 cd00982 gltB_C gltb_C. This do 29.6 66 0.0014 30.9 3.8 63 234-299 176-242 (251)
13 PF08887 GAD-like: GAD-like do 27.1 16 0.00034 30.7 -0.8 45 255-299 34-92 (109)
14 PF10524 NfI_DNAbd_pre-N: Nucl 23.5 35 0.00075 25.1 0.6 25 281-305 4-34 (44)
15 TIGR02835 spore_sigmaE RNA pol 21.7 1.7E+02 0.0036 26.4 4.7 36 268-303 50-95 (234)
16 PRK05572 sporulation sigma fac 20.2 2.3E+02 0.005 25.8 5.4 48 256-303 18-75 (252)
No 1
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=100.00 E-value=6.9e-34 Score=217.61 Aligned_cols=65 Identities=45% Similarity=0.695 Sum_probs=62.7
Q ss_pred EEEEeecCChHHHHHHHHHHHHHhCCCC-ChhhHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhhc
Q 039447 240 FVVVKSSFDPQRDFRESMVEMIVENNLR-GSQDLEDLLACYFSLNSNEYHEVIVKAFEQVWLDITN 304 (307)
Q Consensus 240 vAVvk~S~DPy~DFR~SM~EMI~e~~i~-~~~dLeeLL~CYLsLNs~~~H~~Iv~AF~diw~~L~~ 304 (307)
|||+|+|.|||.|||+||+|||+++||. +|++|||||+|||+||+++||++|++||+|||.+|++
T Consensus 1 vAv~k~S~DPy~DFr~SM~EMI~~~~i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~dl~~~L~~ 66 (66)
T TIGR01568 1 VAVAKESDDPYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFVDILSALLS 66 (66)
T ss_pred CeeeeCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHhC
Confidence 6999999999999999999999999995 7999999999999999999999999999999999974
No 2
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=99.97 E-value=3.6e-32 Score=204.14 Aligned_cols=59 Identities=61% Similarity=0.963 Sum_probs=57.5
Q ss_pred cCChHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhhc
Q 039447 246 SFDPQRDFRESMVEMIVENNLRGSQDLEDLLACYFSLNSNEYHEVIVKAFEQVWLDITN 304 (307)
Q Consensus 246 S~DPy~DFR~SM~EMI~e~~i~~~~dLeeLL~CYLsLNs~~~H~~Iv~AF~diw~~L~~ 304 (307)
|.|||+|||+||+|||+|+||.+|++|||||+|||+||+++||++||+||+|||.+|++
T Consensus 1 S~DP~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~dv~~~l~s 59 (59)
T PF04844_consen 1 SSDPYEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFVDVWVELFS 59 (59)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHhC
Confidence 78999999999999999999999999999999999999999999999999999999874
No 3
>PF13724 DNA_binding_2: DNA-binding domain
Probab=99.91 E-value=1.9e-25 Score=162.62 Aligned_cols=31 Identities=71% Similarity=1.253 Sum_probs=30.0
Q ss_pred CCCCcccccCCCcchhhhcccccCCCcCcch
Q 039447 1 MGKNRFRFSDMLPNAWFYKLKDMSKTRTQQQ 31 (307)
Q Consensus 1 Mgn~rFrLSdMmPNaWFYKLkDM~k~R~~~~ 31 (307)
|||||||||||||||||||||||+|+|++++
T Consensus 1 Mgn~rFRLSdMmPNaWFYKLkDM~k~r~~~~ 31 (49)
T PF13724_consen 1 MGNYRFRLSDMMPNAWFYKLKDMSKPRKKSP 31 (49)
T ss_pred CCccceeccccCchHHHHHHhhcccCCCCCC
Confidence 9999999999999999999999999999876
No 4
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=74.03 E-value=5 Score=31.87 Aligned_cols=47 Identities=23% Similarity=0.388 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCCChhhHHHHHHHHHhcCCCcchhHHHHHHHHHHHH
Q 039447 253 FRESMVEMIVENNLRGSQDLEDLLACYFSLNSNEYHEVIVKAFEQVWLD 301 (307)
Q Consensus 253 FR~SM~EMI~e~~i~~~~dLeeLL~CYLsLNs~~~H~~Iv~AF~diw~~ 301 (307)
||+++...|.|- .+..|++|...|.+.||.+++|..++........+
T Consensus 1 ~~k~i~~~l~ey--~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~le 47 (113)
T smart00544 1 LKKKIFLIIEEY--LSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCALE 47 (113)
T ss_pred ChhHHHHHHHHH--HHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHHc
Confidence 455666655532 23358888889999999887777776666554443
No 5
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=37.76 E-value=45 Score=26.25 Aligned_cols=28 Identities=21% Similarity=0.411 Sum_probs=13.8
Q ss_pred hhHHHHHHHHHhcCCCcchhHHHHHHHH
Q 039447 270 QDLEDLLACYFSLNSNEYHEVIVKAFEQ 297 (307)
Q Consensus 270 ~dLeeLL~CYLsLNs~~~H~~Iv~AF~d 297 (307)
.|.+|...|-..||.+.+|..++.....
T Consensus 16 ~d~~ea~~~l~el~~~~~~~~vv~~~l~ 43 (113)
T PF02847_consen 16 GDVDEAVECLKELKLPSQHHEVVKVILE 43 (113)
T ss_dssp T-HHHHHHHHHHTT-GGGHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence 3555666666666666555544444433
No 6
>PRK10072 putative transcriptional regulator; Provisional
Probab=34.84 E-value=55 Score=26.88 Aligned_cols=30 Identities=17% Similarity=0.331 Sum_probs=23.1
Q ss_pred cCChHHHHHHHHHHHHHhCCC---C------ChhhHHHH
Q 039447 246 SFDPQRDFRESMVEMIVENNL---R------GSQDLEDL 275 (307)
Q Consensus 246 S~DPy~DFR~SM~EMI~e~~i---~------~~~dLeeL 275 (307)
=.||..|..+||.|||+++|- . ...+|.+|
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~eik~L 41 (96)
T PRK10072 3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQL 41 (96)
T ss_pred cCCHHHHHHHHHHHHHHhcCCccceeecccCChHHHHHH
Confidence 359999999999999997772 1 45566666
No 7
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=34.74 E-value=97 Score=24.34 Aligned_cols=50 Identities=24% Similarity=0.321 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCC---CCChhhHHH---HHHHHHhcCCCcchhHHHHHHHHHHHHh
Q 039447 253 FRESMVEMIVENN---LRGSQDLED---LLACYFSLNSNEYHEVIVKAFEQVWLDI 302 (307)
Q Consensus 253 FR~SM~EMI~e~~---i~~~~dLee---LL~CYLsLNs~~~H~~Iv~AF~diw~~L 302 (307)
+++.+.+|+..+. ..++++|.+ -|+-.|--|+.++..++-+|..+++..+
T Consensus 18 Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~ 73 (121)
T PF14551_consen 18 YMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKEL 73 (121)
T ss_dssp CHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT
T ss_pred HHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4567777777654 247777765 7889999999999999999999998865
No 8
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=34.53 E-value=84 Score=22.05 Aligned_cols=31 Identities=23% Similarity=0.503 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhCCCCChh------hHHHHHHHHHhc
Q 039447 252 DFRESMVEMIVENNLRGSQ------DLEDLLACYFSL 282 (307)
Q Consensus 252 DFR~SM~EMI~e~~i~~~~------dLeeLL~CYLsL 282 (307)
.-|+-|.+++...|+.+++ +|.+|+..|..+
T Consensus 8 ~~R~~L~~~~~~~~l~~~~vl~~Sq~LD~lI~~y~~~ 44 (45)
T PF09388_consen 8 ELRQELNELAEKKGLTDPEVLELSQELDKLINEYQKL 44 (45)
T ss_dssp HHHHHHHHHHHHCCTTCHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 4688999999999998876 688999888653
No 9
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=33.28 E-value=53 Score=26.07 Aligned_cols=37 Identities=27% Similarity=0.323 Sum_probs=30.4
Q ss_pred ecCChHHHHHHHHHHHHHhCCCCChhhHHHHHHHHHh
Q 039447 245 SSFDPQRDFRESMVEMIVENNLRGSQDLEDLLACYFS 281 (307)
Q Consensus 245 ~S~DPy~DFR~SM~EMI~e~~i~~~~dLeeLL~CYLs 281 (307)
.|.+-...|...+.++..++.-.+.++||++|.-||.
T Consensus 28 ~s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~~m~ 64 (82)
T PF10273_consen 28 DSQEKADWLAEVIVDWFTENKDPDADDLEDFLEDIMD 64 (82)
T ss_pred cHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 3566777888888888888877779999999999884
No 10
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=30.70 E-value=68 Score=29.90 Aligned_cols=47 Identities=13% Similarity=0.287 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhCCCCChhhHHHHHHHHHhc-CCCcchhHHHHHHHH
Q 039447 251 RDFRESMVEMIVENNLRGSQDLEDLLACYFSL-NSNEYHEVIVKAFEQ 297 (307)
Q Consensus 251 ~DFR~SM~EMI~e~~i~~~~dLeeLL~CYLsL-Ns~~~H~~Iv~AF~d 297 (307)
..--..+++++.|+|+.+.++++.++..|-+. .+..--++|-+|.+|
T Consensus 6 ~~~~~al~~ll~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~D 53 (188)
T PF02979_consen 6 AARVRALESLLIEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTD 53 (188)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCC
Confidence 34456788999999999999999999999998 666667777777665
No 11
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=29.94 E-value=61 Score=25.68 Aligned_cols=31 Identities=19% Similarity=0.440 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCCChhhHHHH--HHHHHhcCCC
Q 039447 255 ESMVEMIVENNLRGSQDLEDL--LACYFSLNSN 285 (307)
Q Consensus 255 ~SM~EMI~e~~i~~~~dLeeL--L~CYLsLNs~ 285 (307)
--|++|..+-||.+.+||+++ .+||+.|-..
T Consensus 13 ~~~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~ 45 (81)
T PF04994_consen 13 PKSERMLAKVGIHTVEDLRELGAVEAYLRLKAS 45 (81)
T ss_dssp HHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH
Confidence 458999999999999999988 6788887655
No 12
>cd00982 gltB_C gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear to occur in other domains within the protein, and not the domain in this CD. This particular domain has no known function, but it likely has a structural role as it interacts with the amidotransferase and FMN-binding domains of gltS.
Probab=29.64 E-value=66 Score=30.92 Aligned_cols=63 Identities=21% Similarity=0.286 Sum_probs=45.1
Q ss_pred CcccceEEEEeecCChHHHHHHH-HHHHHHhCCCC---ChhhHHHHHHHHHhcCCCcchhHHHHHHHHHH
Q 039447 234 KSISESFVVVKSSFDPQRDFRES-MVEMIVENNLR---GSQDLEDLLACYFSLNSNEYHEVIVKAFEQVW 299 (307)
Q Consensus 234 ~~~~~svAVvk~S~DPy~DFR~S-M~EMI~e~~i~---~~~dLeeLL~CYLsLNs~~~H~~Iv~AF~diw 299 (307)
....++++++. ||..+|.+- -.|||.-..+. ++++|++||..|+..-..+..+.|+.-|.+..
T Consensus 176 aGM~gG~iyv~---~~~~~~~~~~n~~~V~~~~l~~~~d~~~l~~ll~~h~~~t~s~~a~~iL~~~~~~~ 242 (251)
T cd00982 176 AGMSGGVAYVL---DEDGDFEKKVNHEMVDLERLEDAEDEEQLKELIEEHVEYTGSEKAKEILANWEAYL 242 (251)
T ss_pred cCCCCCEEEEE---CCcCChhhhcCHhhEeeccCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHh
Confidence 45667888885 666677532 22555543343 67789999999999999999999988876543
No 13
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=27.05 E-value=16 Score=30.72 Aligned_cols=45 Identities=20% Similarity=0.462 Sum_probs=37.4
Q ss_pred HHHHHHHHhCCC----------CChhhHHHHHHHHHh----cCCCcchhHHHHHHHHHH
Q 039447 255 ESMVEMIVENNL----------RGSQDLEDLLACYFS----LNSNEYHEVIVKAFEQVW 299 (307)
Q Consensus 255 ~SM~EMI~e~~i----------~~~~dLeeLL~CYLs----LNs~~~H~~Iv~AF~diw 299 (307)
+.+.+.-.+.|. .+++|.+++|..-|. +....+|.+.+.||-||+
T Consensus 34 ~~Ll~~W~~~G~g~~~dG~f~~vnP~dy~~vl~~~~~~~~~~~~~~~~~ia~tAFGdl~ 92 (109)
T PF08887_consen 34 DELLEYWKEYGFGGYGDGLFWLVNPDDYEDVLDEWLGGTPLFDPDNYIPIARTAFGDLY 92 (109)
T ss_pred HHHHHHHHHcCCchhcCcEEEEECHHHHHHHHHHHhcCCccccCceEEEEEEcccccEE
Confidence 467777777763 578999999999886 888999999999999975
No 14
>PF10524 NfI_DNAbd_pre-N: Nuclear factor I protein pre-N-terminus; InterPro: IPR019548 Nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF) [, ] (also known as TGGCA-binding proteins) are a family of vertebrate nuclear proteins which recognise and bind, as dimers, the palindromic DNA sequence 5'-TGGCANNNTGCCA-3'. CTF/NF-I binding sites are present in viral and cellular promoters and in the origin of DNA replication of Human adenovirus 2 (HAdV-2). The CTF/NF-I proteins were first identified as nuclear factor I, a collection of proteins that activate the replication of several Adenovirus serotypes (together with NF-II and NF-III) []. The family of proteins was also identified as the CTF transcription factors, before the NFI and CTF families were found to be identical []. The CTF/NF-I proteins are individually capable of activating transcription and DNA replication. In a given species, there are a large number of different CTF/NF-I proteins, generated both by alternative splicing and by the occurrence of four different genes. CTF/NF-1 proteins contain 400 to 600 amino acids. The N-terminal 200 amino-acid sequence, almost perfectly conserved in all species and genes sequenced, mediates site-specific DNA recognition, protein dimerisation and Adenovirus DNA replication. The C-terminal 100 amino acids contain the transcriptional activation domain. This activation domain is the target of gene expression regulatory pathways elicited by growth factors and it interacts with basal transcription factors and with histone H3 []. This entry represents the N terminus, of which 200 residues contain the DNA-binding and dimerisation domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerisation-ability and the stimulation of adenovirus DNA replication [].
Probab=23.53 E-value=35 Score=25.06 Aligned_cols=25 Identities=36% Similarity=0.740 Sum_probs=17.6
Q ss_pred hcCCCcchhHH------HHHHHHHHHHhhcc
Q 039447 281 SLNSNEYHEVI------VKAFEQVWLDITNL 305 (307)
Q Consensus 281 sLNs~~~H~~I------v~AF~diw~~L~~~ 305 (307)
+.-..++|.+| |++|.=+|+.|-.+
T Consensus 4 ~~~~de~hpFiEalLP~Vk~fay~WfnLQA~ 34 (44)
T PF10524_consen 4 SSQQDEFHPFIEALLPYVKAFAYTWFNLQAA 34 (44)
T ss_pred CchHHHhhhHHHHHHHHHHHHHHHHHhHHHH
Confidence 33445566666 78999999998544
No 15
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=21.73 E-value=1.7e+02 Score=26.39 Aligned_cols=36 Identities=6% Similarity=0.045 Sum_probs=28.8
Q ss_pred ChhhHHHHHHHHHhc----------CCCcchhHHHHHHHHHHHHhh
Q 039447 268 GSQDLEDLLACYFSL----------NSNEYHEVIVKAFEQVWLDIT 303 (307)
Q Consensus 268 ~~~dLeeLL~CYLsL----------Ns~~~H~~Iv~AF~diw~~L~ 303 (307)
+...+++|+..|..+ |..+..+++.++|..||..+.
T Consensus 50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~ 95 (234)
T TIGR02835 50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVN 95 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHH
Confidence 567788887777554 777889999999999998875
No 16
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.19 E-value=2.3e+02 Score=25.77 Aligned_cols=48 Identities=8% Similarity=0.026 Sum_probs=33.8
Q ss_pred HHHHHHHhCCCCChhhHHHHHHHHH----------hcCCCcchhHHHHHHHHHHHHhh
Q 039447 256 SMVEMIVENNLRGSQDLEDLLACYF----------SLNSNEYHEVIVKAFEQVWLDIT 303 (307)
Q Consensus 256 SM~EMI~e~~i~~~~dLeeLL~CYL----------sLNs~~~H~~Iv~AF~diw~~L~ 303 (307)
...++|....-.+.+.+++|+..|. ..|..+..+++.++|..+|..+.
T Consensus 18 ~~~~li~~~~~gd~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~ 75 (252)
T PRK05572 18 ENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVD 75 (252)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence 4455555433446677777776664 34777888999999999998775
Done!