Query psy14934
Match_columns 87
No_of_seqs 109 out of 120
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 16:12:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14934.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14934hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5092 NMT1 N-myristoyl trans 98.8 3.4E-09 7.3E-14 86.6 2.6 45 42-86 6-53 (451)
2 KOG2779|consensus 98.7 3.6E-09 7.7E-14 86.6 2.1 44 43-86 12-55 (421)
3 PF15017 AF1Q: Drug resistance 60.2 4.8 0.0001 27.2 1.0 20 64-84 16-35 (87)
4 PF14002 YniB: YniB-like prote 37.1 17 0.00037 27.2 1.0 14 71-84 55-68 (166)
5 PF08761 dUTPase_2: dUTPase; 31.5 21 0.00046 25.3 0.7 10 69-78 54-63 (167)
6 PHA02047 phage lambda Rz1-like 26.4 31 0.00068 24.0 0.8 13 69-81 76-88 (101)
7 PF10404 BHD_2: Rad4 beta-hair 18.2 34 0.00074 20.8 -0.3 11 69-79 51-61 (64)
8 PF09562 RE_LlaMI: LlaMI restr 16.1 71 0.0015 25.5 0.9 15 69-83 113-127 (271)
9 PF05627 AvrRpt-cleavage: Clea 15.5 57 0.0012 19.1 0.2 8 77-84 6-13 (39)
10 KOG2422|consensus 14.6 79 0.0017 28.3 0.9 7 72-78 214-220 (665)
No 1
>COG5092 NMT1 N-myristoyl transferase [Lipid metabolism]
Probab=98.77 E-value=3.4e-09 Score=86.56 Aligned_cols=45 Identities=20% Similarity=0.469 Sum_probs=34.2
Q ss_pred cHHHHHHHHHHHhhccCCCC---ChHHHhcCCCcccCCcCCCCCCcCC
Q psy14934 42 SIQEIRKAMEVFSLQQRSAK---TPEEALQKQYQFWSTQPVPKIVVTI 86 (87)
Q Consensus 42 k~k~i~~lL~lLsl~~~~~k---~~~~k~~k~yKFW~TQPVPKldE~V 86 (87)
+...|+++|++|+|+.-..+ +.+.+.+++|+||+|||||+|||++
T Consensus 6 ~a~~l~~ll~~l~l~~~~~~~~t~~~~k~~kdhKFW~TQPV~~fdee~ 53 (451)
T COG5092 6 KAKKLENLLKLLQLNNDDTSKFTQEQKKMGKDHKFWSTQPVDRFDEEA 53 (451)
T ss_pred hHHHHHHHHHHHhccCcchhhhhhcchhhcccccceecCCCCccchhh
Confidence 45679999999998643322 2445566889999999999999964
No 2
>KOG2779|consensus
Probab=98.75 E-value=3.6e-09 Score=86.60 Aligned_cols=44 Identities=41% Similarity=0.701 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhhccCCCCChHHHhcCCCcccCCcCCCCCCcCC
Q psy14934 43 IQEIRKAMEVFSLQQRSAKTPEEALQKQYQFWSTQPVPKIVVTI 86 (87)
Q Consensus 43 ~k~i~~lL~lLsl~~~~~k~~~~k~~k~yKFW~TQPVPKldE~V 86 (87)
.+.+..+++++++.++.+..++++..++|+||+|||||++||.|
T Consensus 12 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~fw~tqpV~k~de~~ 55 (421)
T KOG2779|consen 12 LRNALKALELMSVIQGPATMMDEAAKKDFKFWSTQPVPKLDEVV 55 (421)
T ss_pred HHHHHHHHHhcccccCcccccccccccccceeecccccccCccc
Confidence 45556666666667788888999999999999999999999954
No 3
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=60.16 E-value=4.8 Score=27.16 Aligned_cols=20 Identities=30% Similarity=0.788 Sum_probs=15.3
Q ss_pred HHHhcCCCcccCCcCCCCCCc
Q psy14934 64 EEALQKQYQFWSTQPVPKIVV 84 (87)
Q Consensus 64 ~~k~~k~yKFW~TQPVPKldE 84 (87)
......+|.||+. |+|.||.
T Consensus 16 ~~~~f~sF~fWR~-PlP~id~ 35 (87)
T PF15017_consen 16 EDEEFNSFLFWRN-PLPDIDL 35 (87)
T ss_pred ccccccceeeccC-CCCCCCH
Confidence 3345678999985 9999974
No 4
>PF14002 YniB: YniB-like protein
Probab=37.13 E-value=17 Score=27.24 Aligned_cols=14 Identities=36% Similarity=0.805 Sum_probs=12.3
Q ss_pred CcccCCcCCCCCCc
Q psy14934 71 YQFWSTQPVPKIVV 84 (87)
Q Consensus 71 yKFW~TQPVPKldE 84 (87)
--||+--|||.+++
T Consensus 55 n~FW~nSPvP~~~~ 68 (166)
T PF14002_consen 55 NFFWNNSPVPDFDN 68 (166)
T ss_pred hhhccCCCCCCccc
Confidence 35999999999986
No 5
>PF08761 dUTPase_2: dUTPase; InterPro: IPR014871 2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyses the hydrolysis of dUTP to dUMP and pyrophosphate (3.6.1.23 from EC). Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organisms. This family contains both dUTPase homologues of dUTPase including dCTPase of phage T4. ; PDB: 2YB0_E 2YAZ_B 2YAY_A 2CJE_A 1OGK_A 1OGL_A 1W2Y_B 2CIC_A.
Probab=31.51 E-value=21 Score=25.27 Aligned_cols=10 Identities=10% Similarity=0.909 Sum_probs=5.9
Q ss_pred CCCcccCCcC
Q psy14934 69 KQYQFWSTQP 78 (87)
Q Consensus 69 k~yKFW~TQP 78 (87)
..||||++++
T Consensus 54 ~~fK~Wk~~~ 63 (167)
T PF08761_consen 54 RCFKYWKKKK 63 (167)
T ss_dssp ----SSSSTT
T ss_pred cchHhhcCCC
Confidence 5799999999
No 6
>PHA02047 phage lambda Rz1-like protein
Probab=26.38 E-value=31 Score=24.03 Aligned_cols=13 Identities=38% Similarity=0.879 Sum_probs=11.5
Q ss_pred CCCcccCCcCCCC
Q psy14934 69 KQYQFWSTQPVPK 81 (87)
Q Consensus 69 k~yKFW~TQPVPK 81 (87)
.+|+=|.-||||-
T Consensus 76 ~~n~~WaD~PVPp 88 (101)
T PHA02047 76 DQNRPWADRPVPP 88 (101)
T ss_pred HhCCCcccCCCCh
Confidence 5699999999994
No 7
>PF10404 BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR018327 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=18.24 E-value=34 Score=20.82 Aligned_cols=11 Identities=36% Similarity=0.782 Sum_probs=7.3
Q ss_pred CCCcccCCcCC
Q psy14934 69 KQYQFWSTQPV 79 (87)
Q Consensus 69 k~yKFW~TQPV 79 (87)
.=|-||.|+|.
T Consensus 51 ~LYg~wQTe~y 61 (64)
T PF10404_consen 51 PLYGEWQTEPY 61 (64)
T ss_dssp EEB-GGGEEE-
T ss_pred cCCCHHHCccc
Confidence 44999999874
No 8
>PF09562 RE_LlaMI: LlaMI restriction endonuclease; InterPro: IPR019063 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the restriction endonuclease LlaMI, which recognises and cleaves the double-stranded sequence CC^NGG.
Probab=16.06 E-value=71 Score=25.54 Aligned_cols=15 Identities=40% Similarity=0.755 Sum_probs=12.1
Q ss_pred CCCcccCCcCCCCCC
Q psy14934 69 KQYQFWSTQPVPKIV 83 (87)
Q Consensus 69 k~yKFW~TQPVPKld 83 (87)
..-.=|+-+|||++.
T Consensus 113 ~~R~SWSGspiPk~~ 127 (271)
T PF09562_consen 113 NNRYSWSGSPIPKIN 127 (271)
T ss_pred CCcccccCCcCCCcc
Confidence 445669999999985
No 9
>PF05627 AvrRpt-cleavage: Cleavage site for pathogenic type III effector avirulence factor Avr; InterPro: IPR008700 This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium []. The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain []. ; PDB: 2NUD_C.
Probab=15.49 E-value=57 Score=19.06 Aligned_cols=8 Identities=38% Similarity=0.380 Sum_probs=1.4
Q ss_pred cCCCCCCc
Q psy14934 77 QPVPKIVV 84 (87)
Q Consensus 77 QPVPKldE 84 (87)
-+||+|.+
T Consensus 6 ~~vPkFG~ 13 (39)
T PF05627_consen 6 SHVPKFGE 13 (39)
T ss_dssp ------SG
T ss_pred CCCCCCCc
Confidence 37999976
No 10
>KOG2422|consensus
Probab=14.55 E-value=79 Score=28.33 Aligned_cols=7 Identities=29% Similarity=0.297 Sum_probs=4.0
Q ss_pred cccCCcC
Q psy14934 72 QFWSTQP 78 (87)
Q Consensus 72 KFW~TQP 78 (87)
+-|-|+|
T Consensus 214 r~vl~kP 220 (665)
T KOG2422|consen 214 RTVLTKP 220 (665)
T ss_pred eeEecCc
Confidence 5555655
Done!