Query 015381
Match_columns 408
No_of_seqs 135 out of 230
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 05:46:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015381.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015381hhsearch_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 1.5E-32 3.3E-37 216.9 7.6 65 339-403 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 7E-31 1.5E-35 203.5 7.1 59 345-403 1-59 (59)
3 PF13724 DNA_binding_2: DNA-bi 99.9 2.7E-25 5.9E-30 167.1 3.0 32 1-32 1-32 (49)
4 smart00544 MA3 Domain in DAP-5 69.4 5.8 0.00013 32.6 3.4 46 352-399 1-46 (113)
5 PF02847 MA3: MA3 domain; Int 33.1 53 0.0012 26.8 3.3 43 352-396 1-43 (113)
6 PF09388 SpoOE-like: Spo0E lik 31.7 88 0.0019 22.9 3.9 32 350-381 7-44 (45)
7 PRK10072 putative transcriptio 28.0 78 0.0017 27.0 3.6 30 345-374 3-41 (96)
8 PF14551 MCM_N: MCM N-terminal 27.5 1.3E+02 0.0028 24.5 4.7 51 352-402 18-74 (121)
9 PF10273 WGG: Pre-rRNA-process 22.3 1E+02 0.0022 25.4 3.2 37 344-380 28-64 (82)
10 PF02979 NHase_alpha: Nitrile 22.2 1.6E+02 0.0034 28.6 4.8 47 350-396 6-53 (188)
11 PF04994 TfoX_C: TfoX C-termin 21.3 1E+02 0.0022 25.4 2.9 31 354-384 13-45 (81)
12 cd00982 gltB_C gltb_C. This do 21.2 1.1E+02 0.0024 30.5 3.7 61 335-398 178-242 (251)
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=99.97 E-value=1.5e-32 Score=216.93 Aligned_cols=65 Identities=46% Similarity=0.717 Sum_probs=62.7
Q ss_pred EEEEeecCChHHHHHHHHHHHHHHCCCC-CchhHHHHHHHHHhcCCCcchhhHHHHHHHHHHHhcc
Q 015381 339 FAIVKSSFDPQRDFRESMVEMIVENNIR-ASKDLEDLLACYLSLNSDEYHELIIKVFKQIWFDLTD 403 (408)
Q Consensus 339 vAVvk~S~DPy~DFR~SM~EMI~e~~i~-~~~dLEELL~CYLsLNs~e~H~~Iv~AF~dIw~~L~~ 403 (408)
|||+|+|.|||.|||+||+|||+++||. +|++|||||+|||+||+++||++|++||+|||.+|++
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 6899999999999999999999999999999999974
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=7e-31 Score=203.48 Aligned_cols=59 Identities=61% Similarity=0.968 Sum_probs=57.6
Q ss_pred cCChHHHHHHHHHHHHHHCCCCCchhHHHHHHHHHhcCCCcchhhHHHHHHHHHHHhcc
Q 015381 345 SFDPQRDFRESMVEMIVENNIRASKDLEDLLACYLSLNSDEYHELIIKVFKQIWFDLTD 403 (408)
Q Consensus 345 S~DPy~DFR~SM~EMI~e~~i~~~~dLEELL~CYLsLNs~e~H~~Iv~AF~dIw~~L~~ 403 (408)
|.|||+|||+||+|||+++||.+|++|||||+|||+||+++||++||+||+|||.+|++
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=2.7e-25 Score=167.14 Aligned_cols=32 Identities=69% Similarity=1.250 Sum_probs=30.0
Q ss_pred CCCCcccccCCCcchhhhhcccccCcCCCCCC
Q 015381 1 MGNHRFRFSDMMPNAWFYRLKDMGKARSHNST 32 (408)
Q Consensus 1 MGN~rFrLSDMiPNAWFyKLkDM~k~r~~~~~ 32 (408)
|||||||||||||||||||||||+|+|+++.+
T Consensus 1 Mgn~rFRLSdMmPNaWFYKLkDM~k~r~~~~~ 32 (49)
T PF13724_consen 1 MGNYRFRLSDMMPNAWFYKLKDMSKPRKKSPS 32 (49)
T ss_pred CCccceeccccCchHHHHHHhhcccCCCCCCC
Confidence 99999999999999999999999999998543
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=69.43 E-value=5.8 Score=32.62 Aligned_cols=46 Identities=24% Similarity=0.395 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHCCCCCchhHHHHHHHHHhcCCCcchhhHHHHHHHHHH
Q 015381 352 FRESMVEMIVENNIRASKDLEDLLACYLSLNSDEYHELIIKVFKQIWF 399 (408)
Q Consensus 352 FR~SM~EMI~e~~i~~~~dLEELL~CYLsLNs~e~H~~Iv~AF~dIw~ 399 (408)
||+++...|.+- ....|++|...|.+.||.+++|+.++........
T Consensus 1 ~~k~i~~~l~ey--~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~l 46 (113)
T smart00544 1 LKKKIFLIIEEY--LSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCAL 46 (113)
T ss_pred ChhHHHHHHHHH--HHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHH
Confidence 455666655532 2235888899999999987777776666555444
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=33.05 E-value=53 Score=26.79 Aligned_cols=43 Identities=21% Similarity=0.454 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHCCCCCchhHHHHHHHHHhcCCCcchhhHHHHHHH
Q 015381 352 FRESMVEMIVENNIRASKDLEDLLACYLSLNSDEYHELIIKVFKQ 396 (408)
Q Consensus 352 FR~SM~EMI~e~~i~~~~dLEELL~CYLsLNs~e~H~~Iv~AF~d 396 (408)
||+.+-..|.|- ..-.|.+|...|-..||.+.+|..++.....
T Consensus 1 ~rk~i~~~l~ey--~~~~d~~ea~~~l~el~~~~~~~~vv~~~l~ 43 (113)
T PF02847_consen 1 LRKKIFSILMEY--FSSGDVDEAVECLKELKLPSQHHEVVKVILE 43 (113)
T ss_dssp HHHHHHHHHHHH--HHHT-HHHHHHHHHHTT-GGGHHHHHHHHHH
T ss_pred ChHHHHHHHHHH--hcCCCHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence 455555555532 1113667777777777766555555554443
No 6
>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=31.73 E-value=88 Score=22.88 Aligned_cols=32 Identities=19% Similarity=0.480 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHCCCCCch------hHHHHHHHHHhc
Q 015381 350 RDFRESMVEMIVENNIRASK------DLEDLLACYLSL 381 (408)
Q Consensus 350 ~DFR~SM~EMI~e~~i~~~~------dLEELL~CYLsL 381 (408)
+.-|+-|.+++...|+.+++ +|-+|+..|..+
T Consensus 7 e~~R~~L~~~~~~~~l~~~~vl~~Sq~LD~lI~~y~~~ 44 (45)
T PF09388_consen 7 EELRQELNELAEKKGLTDPEVLELSQELDKLINEYQKL 44 (45)
T ss_dssp HHHHHHHHHHHHHCCTTCHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 35688999999999998876 688999888643
No 7
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.01 E-value=78 Score=27.03 Aligned_cols=30 Identities=17% Similarity=0.348 Sum_probs=23.0
Q ss_pred cCChHHHHHHHHHHHHHHCCC---C------CchhHHHH
Q 015381 345 SFDPQRDFRESMVEMIVENNI---R------ASKDLEDL 374 (408)
Q Consensus 345 S~DPy~DFR~SM~EMI~e~~i---~------~~~dLEEL 374 (408)
=.||..|..+||.|||+++|- + ...+|.+|
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~eik~L 41 (96)
T PRK10072 3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQL 41 (96)
T ss_pred cCCHHHHHHHHHHHHHHhcCCccceeecccCChHHHHHH
Confidence 359999999999999997762 1 44566666
No 8
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=27.51 E-value=1.3e+02 Score=24.50 Aligned_cols=51 Identities=27% Similarity=0.291 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHCCC---CCchhHHH---HHHHHHhcCCCcchhhHHHHHHHHHHHhc
Q 015381 352 FRESMVEMIVENNI---RASKDLED---LLACYLSLNSDEYHELIIKVFKQIWFDLT 402 (408)
Q Consensus 352 FR~SM~EMI~e~~i---~~~~dLEE---LL~CYLsLNs~e~H~~Iv~AF~dIw~~L~ 402 (408)
+++.+.+|+..+.- -++++|.+ -|+-.|.-|+.++..++-+|..+++..+.
T Consensus 18 Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~~ 74 (121)
T PF14551_consen 18 YMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKELF 74 (121)
T ss_dssp CHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT-
T ss_pred HHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677777776432 26667655 68889999999999999999999998754
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=22.26 E-value=1e+02 Score=25.43 Aligned_cols=37 Identities=27% Similarity=0.329 Sum_probs=29.1
Q ss_pred ecCChHHHHHHHHHHHHHHCCCCCchhHHHHHHHHHh
Q 015381 344 SSFDPQRDFRESMVEMIVENNIRASKDLEDLLACYLS 380 (408)
Q Consensus 344 ~S~DPy~DFR~SM~EMI~e~~i~~~~dLEELL~CYLs 380 (408)
.|.+-...|...+.++..++.--+.++||++|.-||.
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 3566677788888888888766668899999998883
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=22.20 E-value=1.6e+02 Score=28.60 Aligned_cols=47 Identities=6% Similarity=0.261 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHCCCCCchhHHHHHHHHHhc-CCCcchhhHHHHHHH
Q 015381 350 RDFRESMVEMIVENNIRASKDLEDLLACYLSL-NSDEYHELIIKVFKQ 396 (408)
Q Consensus 350 ~DFR~SM~EMI~e~~i~~~~dLEELL~CYLsL-Ns~e~H~~Iv~AF~d 396 (408)
..--..+++.+.|+|+.+.++++.++..|-+. .+..--++|-+|..|
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 766677777777665
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=21.30 E-value=1e+02 Score=25.44 Aligned_cols=31 Identities=26% Similarity=0.483 Sum_probs=24.1
Q ss_pred HHHHHHHHHCCCCCchhHHHH--HHHHHhcCCC
Q 015381 354 ESMVEMIVENNIRASKDLEDL--LACYLSLNSD 384 (408)
Q Consensus 354 ~SM~EMI~e~~i~~~~dLEEL--L~CYLsLNs~ 384 (408)
--|++|..+-||.+.++|+++ .+||+.|-..
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 358899999999999999998 6788887654
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=21.24 E-value=1.1e+02 Score=30.51 Aligned_cols=61 Identities=20% Similarity=0.291 Sum_probs=43.7
Q ss_pred CCCeEEEEeecCChHHHHHHH-HHHHHHHCCCC---CchhHHHHHHHHHhcCCCcchhhHHHHHHHHH
Q 015381 335 LSDSFAIVKSSFDPQRDFRES-MVEMIVENNIR---ASKDLEDLLACYLSLNSDEYHELIIKVFKQIW 398 (408)
Q Consensus 335 ~~~svAVvk~S~DPy~DFR~S-M~EMI~e~~i~---~~~dLEELL~CYLsLNs~e~H~~Iv~AF~dIw 398 (408)
..++++++. ||..+|.+- -.+||.-..+. ++++|++||..|+..-..+....|+.-|.+..
T Consensus 178 M~gG~iyv~---~~~~~~~~~~n~~~V~~~~l~~~~d~~~l~~ll~~h~~~t~s~~a~~iL~~~~~~~ 242 (251)
T cd00982 178 MSGGVAYVL---DEDGDFEKKVNHEMVDLERLEDAEDEEQLKELIEEHVEYTGSEKAKEILANWEAYL 242 (251)
T ss_pred CCCCEEEEE---CCcCChhhhcCHhhEeeccCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHh
Confidence 567777775 666677532 22555543443 66789999999999999999888988876544
Done!