Query 035469
Match_columns 62
No_of_seqs 94 out of 96
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 03:11:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035469.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035469hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12734 CYSTM: Cysteine-rich 99.2 1.2E-11 2.6E-16 68.4 2.9 21 35-55 17-37 (37)
2 PF06689 zf-C4_ClpX: ClpX C4-t 59.5 4.7 0.0001 21.9 0.8 15 15-29 1-15 (41)
3 PF10685 KGG: Stress-induced b 50.6 13 0.00027 18.9 1.4 15 2-16 5-20 (23)
4 PF13719 zinc_ribbon_5: zinc-r 32.1 18 0.0004 19.0 0.3 17 10-26 20-36 (37)
5 TIGR03602 streptolysinS bacter 32.0 6.9 0.00015 23.9 -1.5 14 46-59 26-39 (56)
6 PF13717 zinc_ribbon_4: zinc-r 14.8 67 0.0015 16.9 0.3 17 9-25 19-35 (36)
7 PF13771 zf-HC5HC2H: PHD-like 14.0 1.1E+02 0.0023 17.6 1.1 19 6-24 27-45 (90)
8 KOG4101 Cysteine-rich hydropho 13.4 92 0.002 22.7 0.8 10 43-52 99-108 (175)
9 PF10204 DuoxA: Dual oxidase m 11.3 1.1E+02 0.0025 23.2 0.8 13 2-14 130-142 (281)
10 PF02069 Metallothio_Pro: Prok 11.0 37 0.00081 20.1 -1.5 13 7-19 20-32 (52)
No 1
>PF12734 CYSTM: Cysteine-rich TM module stress tolerance
Probab=99.20 E-value=1.2e-11 Score=68.36 Aligned_cols=21 Identities=48% Similarity=1.244 Sum_probs=19.8
Q ss_pred cchHHHHHHHHHHHhhhhccc
Q 035469 35 RSFIEGCLFALCCCWICDACF 55 (62)
Q Consensus 35 ~GcL~gCLAALCCCCllD~Cf 55 (62)
.|||+||||||||||++|+||
T Consensus 17 ~g~l~gClaaLcCCc~ld~cc 37 (37)
T PF12734_consen 17 DGCLAGCLAALCCCCLLDECC 37 (37)
T ss_pred CChHHHHHHHHHHHHHHHHhC
Confidence 389999999999999999987
No 2
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=59.49 E-value=4.7 Score=21.94 Aligned_cols=15 Identities=27% Similarity=0.744 Sum_probs=7.3
Q ss_pred ccccccccccccccc
Q 035469 15 KRKCSMCARGFARTK 29 (62)
Q Consensus 15 ~~~~~~~~~~~~et~ 29 (62)
|++||+|.+...+..
T Consensus 1 ~~~CSFCgr~~~~v~ 15 (41)
T PF06689_consen 1 EKRCSFCGRPESEVG 15 (41)
T ss_dssp --B-TTT--BTTTSS
T ss_pred CCCccCCCCCHHHHh
Confidence 578999998766543
No 3
>PF10685 KGG: Stress-induced bacterial acidophilic repeat motif; InterPro: IPR019626 This repeat contains a highly conserved, characteristic sequence motif, KGG, that is recognised by plants and lower eukaryotes. Further downstream from this motif is a Walker A, nucleotide binding motif. YciG is expressed as part of a three-gene operon, yciGFE and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress [].
Probab=50.59 E-value=13 Score=18.88 Aligned_cols=15 Identities=53% Similarity=0.776 Sum_probs=10.2
Q ss_pred cchh-HHHHHhhCCcc
Q 035469 2 MDHE-HEEAQRKGGKR 16 (62)
Q Consensus 2 ~~~~-~~~~~~~~~~~ 16 (62)
||+| -.|+-||||+-
T Consensus 5 ~d~e~~~eig~kGG~a 20 (23)
T PF10685_consen 5 MDPEKAREIGRKGGQA 20 (23)
T ss_pred cCHHHHHHHHHhcCcc
Confidence 4544 36788999973
No 4
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=32.10 E-value=18 Score=19.05 Aligned_cols=17 Identities=29% Similarity=0.663 Sum_probs=13.6
Q ss_pred HhhCCcccccccccccc
Q 035469 10 QRKGGKRKCSMCARGFA 26 (62)
Q Consensus 10 ~~~~~~~~~~~~~~~~~ 26 (62)
..+|++-+|+-|..++.
T Consensus 20 ~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 20 PAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ccCCcEEECCCCCcEee
Confidence 46788999999987653
No 5
>TIGR03602 streptolysinS bacteriocin protoxin, streptolysin S family. Members of this family are bacteriocin precursors. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. This family belongs to a class of heterocycle-containing bacteriocins, including streptolysin S from Streptococcus pyogenes, and related bacteriocins from Streptococcus iniae and Clostridium botulinum. Streptolysin S is hemolytic. Bacteriocin genes in general are small and highly diverse, with odd sequence composition, and are easily missed by many gene-finding programs.
Probab=32.00 E-value=6.9 Score=23.94 Aligned_cols=14 Identities=43% Similarity=1.518 Sum_probs=7.1
Q ss_pred HHHhhhhccccchh
Q 035469 46 CCCWICDACFDVTV 59 (62)
Q Consensus 46 CCCCllD~Cfd~~~ 59 (62)
||||++-.||+..+
T Consensus 26 cccccc~cc~si~~ 39 (56)
T TIGR03602 26 CCCCCCCCCFSIAT 39 (56)
T ss_pred eEEEeccEEEEEEe
Confidence 44444545666543
No 6
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=14.83 E-value=67 Score=16.91 Aligned_cols=17 Identities=41% Similarity=0.772 Sum_probs=13.0
Q ss_pred HHhhCCccccccccccc
Q 035469 9 AQRKGGKRKCSMCARGF 25 (62)
Q Consensus 9 ~~~~~~~~~~~~~~~~~ 25 (62)
...+|.+-+|+-|...+
T Consensus 19 ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 19 IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CCCCCcEEECCCCCCEe
Confidence 34678889999998754
No 7
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=13.99 E-value=1.1e+02 Score=17.61 Aligned_cols=19 Identities=32% Similarity=0.656 Sum_probs=14.6
Q ss_pred HHHHHhhCCcccccccccc
Q 035469 6 HEEAQRKGGKRKCSMCARG 24 (62)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~ 24 (62)
-+++.+++-+.+|+.|.+.
T Consensus 27 v~~~~~~~~~~~C~~C~~~ 45 (90)
T PF13771_consen 27 VEKEIKRRRKLKCSICKKK 45 (90)
T ss_pred HHHHHHHHhCCCCcCCCCC
Confidence 3567778888999999753
No 8
>KOG4101 consensus Cysteine-rich hydrophobic proteins [General function prediction only]
Probab=13.37 E-value=92 Score=22.65 Aligned_cols=10 Identities=40% Similarity=1.025 Sum_probs=6.5
Q ss_pred HHHHHHhhhh
Q 035469 43 FALCCCWICD 52 (62)
Q Consensus 43 AALCCCCllD 52 (62)
..+||||.+.
T Consensus 99 Gc~cCCCtlG 108 (175)
T KOG4101|consen 99 GCLCCCCTLG 108 (175)
T ss_pred hHHHHhhccC
Confidence 3467887764
No 9
>PF10204 DuoxA: Dual oxidase maturation factor; InterPro: IPR018469 DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases. DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N terminus (type III) and two N-glycosylation sites []. It is conserved from nematodes to humans.; GO: 0015031 protein transport, 0005789 endoplasmic reticulum membrane, 0016021 integral to membrane
Probab=11.35 E-value=1.1e+02 Score=23.20 Aligned_cols=13 Identities=46% Similarity=0.422 Sum_probs=10.9
Q ss_pred cchhHHHHHhhCC
Q 035469 2 MDHEHEEAQRKGG 14 (62)
Q Consensus 2 ~~~~~~~~~~~~~ 14 (62)
|++|-+||++||=
T Consensus 130 ~~~ey~~al~kGL 142 (281)
T PF10204_consen 130 MAEEYREALEKGL 142 (281)
T ss_pred HHHHHHHHHHcCC
Confidence 6788899999984
No 10
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=10.98 E-value=37 Score=20.07 Aligned_cols=13 Identities=62% Similarity=0.823 Sum_probs=0.0
Q ss_pred HHHHhhCCccccc
Q 035469 7 EEAQRKGGKRKCS 19 (62)
Q Consensus 7 ~~~~~~~~~~~~~ 19 (62)
++|.+++||..||
T Consensus 20 ~~Ai~~dGk~YCS 32 (52)
T PF02069_consen 20 EEAIQKDGKYYCS 32 (52)
T ss_dssp TTSEESSS-EESS
T ss_pred hHhHHhCCEeeec
Done!