Query 040838
Match_columns 430
No_of_seqs 121 out of 225
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 12:18:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040838.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040838hhsearch_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 6.2E-32 1.3E-36 213.9 7.6 65 352-416 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 2.2E-30 4.8E-35 201.0 7.2 59 358-416 1-59 (59)
3 smart00544 MA3 Domain in DAP-5 61.8 10 0.00022 30.9 3.5 46 365-412 1-46 (113)
4 PF13724 DNA_binding_2: DNA-bi 48.9 9.4 0.0002 29.9 1.2 23 16-38 6-28 (49)
5 PF08132 AdoMetDC_leader: S-ad 25.1 38 0.00082 27.1 1.1 14 4-17 5-18 (54)
6 PF10273 WGG: Pre-rRNA-process 23.0 1E+02 0.0022 25.4 3.3 37 357-393 28-64 (82)
7 PF02847 MA3: MA3 domain; Int 22.8 1.2E+02 0.0025 24.7 3.6 24 383-406 17-40 (113)
8 PRK10072 putative transcriptio 22.6 1.2E+02 0.0026 26.0 3.7 31 358-388 3-42 (96)
9 PF02979 NHase_alpha: Nitrile 17.9 1.9E+02 0.004 28.2 4.3 48 362-409 5-53 (188)
10 PF08887 GAD-like: GAD-like do 17.5 41 0.0009 29.3 -0.1 45 367-411 34-92 (109)
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=6.2e-32 Score=213.85 Aligned_cols=65 Identities=48% Similarity=0.675 Sum_probs=62.6
Q ss_pred EEEEeecCCchHHHHHHHHHHHHhcCCC-ChhHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHhhh
Q 040838 352 FAVVKCSFDPQKDFRDSMIEMILEKRFS-QPQELEELLACYLTLNSDEYHDLIIKVFRQVWFDLNQ 416 (430)
Q Consensus 352 vAVvK~S~DPy~DFR~SMvEMI~e~gI~-d~ddLEELL~CYLsLNs~ehH~~IV~AF~DVw~~L~s 416 (430)
|||+++|.|||.|||+||+|||+++|+. +|++|||||+|||+||+++||++|++||+|||.+|++
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 6999999999999999999999999999999999874
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=99.96 E-value=2.2e-30 Score=200.98 Aligned_cols=59 Identities=53% Similarity=0.870 Sum_probs=57.6
Q ss_pred cCCchHHHHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHhhh
Q 040838 358 SFDPQKDFRDSMIEMILEKRFSQPQELEELLACYLTLNSDEYHDLIIKVFRQVWFDLNQ 416 (430)
Q Consensus 358 S~DPy~DFR~SMvEMI~e~gI~d~ddLEELL~CYLsLNs~ehH~~IV~AF~DVw~~L~s 416 (430)
|.|||.|||+||+|||+++||.+|++|||||+|||+||+++||++||+||+|||.+|++
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
>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=61.79 E-value=10 Score=30.94 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCCCchhhHHHHHHHHHH
Q 040838 365 FRDSMIEMILEKRFSQPQELEELLACYLTLNSDEYHDLIIKVFRQVWF 412 (430)
Q Consensus 365 FR~SMvEMI~e~gI~d~ddLEELL~CYLsLNs~ehH~~IV~AF~DVw~ 412 (430)
||+++...|.+- .+..|+.|...|.+.||.+.+|+.++........
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 345555555432 2335778888888888877777766665555444
No 4
>PF13724 DNA_binding_2: DNA-binding domain
Probab=48.86 E-value=9.4 Score=29.88 Aligned_cols=23 Identities=26% Similarity=0.518 Sum_probs=19.2
Q ss_pred cccccccchhhhhhhhccccCcc
Q 040838 16 SLISHVFPVSWLSKFKQKSRDVE 38 (430)
Q Consensus 16 s~iS~v~p~SWlsKfk~ms~ns~ 38 (430)
+=+|+..|=+||=|+|-|+....
T Consensus 6 FRLSdMmPNaWFYKLkDM~k~r~ 28 (49)
T PF13724_consen 6 FRLSDMMPNAWFYKLKDMSKPRK 28 (49)
T ss_pred eeccccCchHHHHHHhhcccCCC
Confidence 44799999999999999985543
No 5
>PF08132 AdoMetDC_leader: S-adenosyl-l-methionine decarboxylase leader peptide; InterPro: IPR012511 This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism [].
Probab=25.11 E-value=38 Score=27.06 Aligned_cols=14 Identities=50% Similarity=0.439 Sum_probs=7.4
Q ss_pred CCCCCCCCCCcccc
Q 040838 4 GRKKISSESSRNSL 17 (430)
Q Consensus 4 g~kk~ss~SS~~s~ 17 (430)
|+||.+|+||++.+
T Consensus 5 ggkkkssssss~~s 18 (54)
T PF08132_consen 5 GGKKKSSSSSSSNS 18 (54)
T ss_pred cCcccccccccccc
Confidence 56666554444433
No 6
>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=22.98 E-value=1e+02 Score=25.44 Aligned_cols=37 Identities=14% Similarity=0.242 Sum_probs=31.2
Q ss_pred ecCCchHHHHHHHHHHHHhcCCCChhHHHHHHHHHHh
Q 040838 357 CSFDPQKDFRDSMIEMILEKRFSQPQELEELLACYLT 393 (430)
Q Consensus 357 ~S~DPy~DFR~SMvEMI~e~gI~d~ddLEELL~CYLs 393 (430)
.|.+....|...+.++...+.-.+.++|+++|.-||.
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 4677788888888898888877779999999998883
No 7
>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=22.81 E-value=1.2e+02 Score=24.68 Aligned_cols=24 Identities=25% Similarity=0.523 Sum_probs=11.1
Q ss_pred HHHHHHHHHHhcCCCCchhhHHHH
Q 040838 383 ELEELLACYLTLNSDEYHDLIIKV 406 (430)
Q Consensus 383 dLEELL~CYLsLNs~ehH~~IV~A 406 (430)
|.+|...|-..||.+.+|..++..
T Consensus 17 d~~ea~~~l~el~~~~~~~~vv~~ 40 (113)
T PF02847_consen 17 DVDEAVECLKELKLPSQHHEVVKV 40 (113)
T ss_dssp -HHHHHHHHHHTT-GGGHHHHHHH
T ss_pred CHHHHHHHHHHhCCCccHHHHHHH
Confidence 455555555555555444444433
No 8
>PRK10072 putative transcriptional regulator; Provisional
Probab=22.62 E-value=1.2e+02 Score=26.00 Aligned_cols=31 Identities=19% Similarity=0.301 Sum_probs=23.9
Q ss_pred cCCchHHHHHHHHHHHHhcCC-----C----ChhHHHHHH
Q 040838 358 SFDPQKDFRDSMIEMILEKRF-----S----QPQELEELL 388 (430)
Q Consensus 358 S~DPy~DFR~SMvEMI~e~gI-----~----d~ddLEELL 388 (430)
-.||..|..+||.|||.++|- . ...++.+|.
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~eik~LR 42 (96)
T PRK10072 3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLR 42 (96)
T ss_pred cCCHHHHHHHHHHHHHHhcCCccceeecccCChHHHHHHH
Confidence 369999999999999997762 1 556677663
No 9
>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=17.90 E-value=1.9e+02 Score=28.21 Aligned_cols=48 Identities=10% Similarity=0.283 Sum_probs=38.2
Q ss_pred hHHHHHHHHHHHHhcCCCChhHHHHHHHHHHhc-CCCCchhhHHHHHHH
Q 040838 362 QKDFRDSMIEMILEKRFSQPQELEELLACYLTL-NSDEYHDLIIKVFRQ 409 (430)
Q Consensus 362 y~DFR~SMvEMI~e~gI~d~ddLEELL~CYLsL-Ns~ehH~~IV~AF~D 409 (430)
+..--..+++++.++|+.+.+++..++..|-+. ++..--++|-+|.+|
T Consensus 5 ~~~~~~al~~ll~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~D 53 (188)
T PF02979_consen 5 IAARVRALESLLIEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTD 53 (188)
T ss_dssp HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCC
Confidence 334456788999999999999999999999998 777777788887766
No 10
>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=17.53 E-value=41 Score=29.30 Aligned_cols=45 Identities=24% Similarity=0.533 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCC----------CChhHHHHHHHHHHh----cCCCCchhhHHHHHHHHH
Q 040838 367 DSMIEMILEKRF----------SQPQELEELLACYLT----LNSDEYHDLIIKVFRQVW 411 (430)
Q Consensus 367 ~SMvEMI~e~gI----------~d~ddLEELL~CYLs----LNs~ehH~~IV~AF~DVw 411 (430)
+++.+.-.+.|. .++++.+++|..-|. ++...+|.+.+.||-||+
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 467777777765 479999999999886 788999999999999975
Done!