Query psy5299
Match_columns 75
No_of_seqs 42 out of 44
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 22:59:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5299.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5299hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1337|consensus 98.8 1.3E-09 2.8E-14 84.5 1.6 59 1-59 210-274 (472)
2 PF00856 SET: SET domain; Int 98.4 6E-08 1.3E-12 59.1 0.7 45 15-59 111-159 (162)
3 smart00317 SET SET (Su(var)3-9 94.5 0.024 5.2E-07 33.6 1.6 41 19-59 70-114 (116)
4 KOG1338|consensus 69.6 3.2 6.8E-05 34.9 1.9 44 16-59 212-256 (466)
5 PF15114 UPF0640: Uncharacteri 45.2 4 8.6E-05 26.6 -1.2 17 23-40 39-55 (69)
6 KOG0196|consensus 32.4 12 0.00026 34.1 -0.6 21 20-40 833-854 (996)
7 COG1915 Uncharacterized conser 32.1 16 0.00035 30.3 0.1 20 41-60 131-150 (415)
8 TIGR00300 conserved hypothetic 28.8 28 0.00062 28.9 1.0 19 41-59 131-149 (407)
9 PF06211 BAMBI: BMP and activi 27.9 23 0.0005 24.7 0.3 6 24-29 98-103 (107)
10 KOG3437|consensus 21.0 41 0.00089 25.3 0.6 8 25-32 139-146 (184)
11 PLN02684 Probable galactinol-- 20.5 35 0.00076 30.3 0.1 48 19-70 476-526 (750)
No 1
>KOG1337|consensus
Probab=98.82 E-value=1.3e-09 Score=84.47 Aligned_cols=59 Identities=19% Similarity=0.266 Sum_probs=53.6
Q ss_pred CcccccccCc-----CCCCceeeccccccccCCCCCCCCcccccc-cceeeecccCCCCCCcchh
Q psy5299 1 MTRLNAVPSV-----NEDSEVHALIPVWDMCNHENGRSEPKEKTR-NRSLLLSPHNAPMAIPVVV 59 (75)
Q Consensus 1 MTRQN~VP~~-----~~~~~i~ALIPlWDM~NH~~G~itT~yd~~-~r~ec~A~~d~~~~~~v~~ 59 (75)
+||++..|+. .+.....+|+|+||||||.++.+..+|+.+ .+.+|.+.+++++|+||..
T Consensus 210 ~sr~~~~~~~~~~~~~~~~~~~~L~P~~D~~NH~~~~~~~~~~~~d~~~~l~~~~~v~~geevfi 274 (472)
T KOG1337|consen 210 NSRAFYLPSLQRLTAGDPDDNEALAPLIDLLNHSPEVIKAGYNQEDEAVELVAERDVSAGEEVFI 274 (472)
T ss_pred hhhhhccccccccccCCCCcchhhhhhHHhhccCchhccccccCCCCcEEEEEeeeecCCCeEEE
Confidence 5889988876 456679999999999999999999999999 6999999999999999974
No 2
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=98.43 E-value=6e-08 Score=59.14 Aligned_cols=45 Identities=18% Similarity=0.157 Sum_probs=36.4
Q ss_pred ceeeccccccccCCCC-CCCCcccc--cc-cceeeecccCCCCCCcchh
Q psy5299 15 EVHALIPVWDMCNHEN-GRSEPKEK--TR-NRSLLLSPHNAPMAIPVVV 59 (75)
Q Consensus 15 ~i~ALIPlWDM~NH~~-G~itT~yd--~~-~r~ec~A~~d~~~~~~v~~ 59 (75)
...+|+|++||+||+. +.....|+ .. .+....|.+|.++||+|.+
T Consensus 111 ~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i 159 (162)
T PF00856_consen 111 DGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFI 159 (162)
T ss_dssp EEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEE
T ss_pred cccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEE
Confidence 4689999999999998 46666776 34 9999999999999999864
No 3
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=94.49 E-value=0.024 Score=33.61 Aligned_cols=41 Identities=7% Similarity=-0.039 Sum_probs=30.0
Q ss_pred ccccccccCCCCCCCC-cccccc---cceeeecccCCCCCCcchh
Q psy5299 19 LIPVWDMCNHENGRSE-PKEKTR---NRSLLLSPHNAPMAIPVVV 59 (75)
Q Consensus 19 LIPlWDM~NH~~G~it-T~yd~~---~r~ec~A~~d~~~~~~v~~ 59 (75)
+.|+.+++||+...=. ..+... .+..-.|.+|.++||++.+
T Consensus 70 ~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i 114 (116)
T smart00317 70 KGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTI 114 (116)
T ss_pred cCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEee
Confidence 7899999999984422 122221 2588899999999999865
No 4
>KOG1338|consensus
Probab=69.56 E-value=3.2 Score=34.89 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=34.8
Q ss_pred eeeccccccccCCCCCCCCcccccc-cceeeecccCCCCCCcchh
Q psy5299 16 VHALIPVWDMCNHENGRSEPKEKTR-NRSLLLSPHNAPMAIPVVV 59 (75)
Q Consensus 16 i~ALIPlWDM~NH~~G~itT~yd~~-~r~ec~A~~d~~~~~~v~~ 59 (75)
-.+-+|.=||.||..-+....---+ ||.+-.|.++.+||++|--
T Consensus 212 gk~m~p~ad~lNhd~~k~nanl~y~~NcL~mva~r~iekgdev~n 256 (466)
T KOG1338|consen 212 GKLMTPIADFLNHDGLKANANLRYEDNCLEMVADRNIEKGDEVDN 256 (466)
T ss_pred cccccchhhhhccchhhcccceeccCcceeeeecCCCCCcccccc
Confidence 4678999999999887655443333 7778899999999999864
No 5
>PF15114 UPF0640: Uncharacterised protein family UPF0640
Probab=45.17 E-value=4 Score=26.60 Aligned_cols=17 Identities=35% Similarity=0.517 Sum_probs=15.7
Q ss_pred ccccCCCCCCCCcccccc
Q psy5299 23 WDMCNHENGRSEPKEKTR 40 (75)
Q Consensus 23 WDM~NH~~G~itT~yd~~ 40 (75)
|-|+|-..|+ +|+||+-
T Consensus 39 ~~MIn~~vG~-~~FY~ty 55 (69)
T PF15114_consen 39 WSMINWRVGK-ENFYDTY 55 (69)
T ss_pred EEEEEEeeCc-eeHHHHH
Confidence 8999999999 9999975
No 6
>KOG0196|consensus
Probab=32.39 E-value=12 Score=34.15 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=14.5
Q ss_pred cccccccCCCC-CCCCcccccc
Q psy5299 20 IPVWDMCNHEN-GRSEPKEKTR 40 (75)
Q Consensus 20 IPlWDM~NH~~-G~itT~yd~~ 40 (75)
=|+|||.|+.. --|.-+|-.-
T Consensus 833 RPYWdmSNQdVIkaIe~gyRLP 854 (996)
T KOG0196|consen 833 RPYWDMSNQDVIKAIEQGYRLP 854 (996)
T ss_pred CcccccchHHHHHHHHhccCCC
Confidence 49999999976 3355555543
No 7
>COG1915 Uncharacterized conserved protein [Function unknown]
Probab=32.13 E-value=16 Score=30.32 Aligned_cols=20 Identities=20% Similarity=-0.007 Sum_probs=18.5
Q ss_pred cceeeecccCCCCCCcchhH
Q psy5299 41 NRSLLLSPHNAPMAIPVVVP 60 (75)
Q Consensus 41 ~r~ec~A~~d~~~~~~v~~~ 60 (75)
++..|.-++|+++|++|||-
T Consensus 131 ~~A~ck~ire~k~Gd~VvVg 150 (415)
T COG1915 131 RRARCKPIRELKKGDLVVVG 150 (415)
T ss_pred CcceeeEhhHhccCCEEEEc
Confidence 78899999999999999974
No 8
>TIGR00300 conserved hypothetical protein TIGR00300. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family.
Probab=28.83 E-value=28 Score=28.87 Aligned_cols=19 Identities=21% Similarity=0.031 Sum_probs=17.5
Q ss_pred cceeeecccCCCCCCcchh
Q psy5299 41 NRSLLLSPHNAPMAIPVVV 59 (75)
Q Consensus 41 ~r~ec~A~~d~~~~~~v~~ 59 (75)
.+.+|.-++|+|+|+.|||
T Consensus 131 ~~~~~~~~r~lk~GD~VVv 149 (407)
T TIGR00300 131 PRARCKPIREIKKGDRVVV 149 (407)
T ss_pred CeEEEEEccccCCCCEEEE
Confidence 6788999999999999987
No 9
>PF06211 BAMBI: BMP and activin membrane-bound inhibitor (BAMBI) N-terminal domain; InterPro: IPR009345 This family consists of several eukaryotic BMP and activin membrane-bound inhibitor (BAMBI) proteins. Members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-beta, bone morphogenetic proteins (BMPs), activins and nodals, are vital for regulating growth and differentiation. BAMBI is related to TGF-beta-family type I receptors but lacks an intracellular kinase domain. BAMBI is co-expressed with the ventralising morphogen BMP4 during Xenopus embryogenesis and requires BMP signalling for its expression. The protein stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling [].
Probab=27.86 E-value=23 Score=24.67 Aligned_cols=6 Identities=67% Similarity=1.248 Sum_probs=5.4
Q ss_pred cccCCC
Q psy5299 24 DMCNHE 29 (75)
Q Consensus 24 DM~NH~ 29 (75)
|||||+
T Consensus 98 DMCNyr 103 (107)
T PF06211_consen 98 DMCNYR 103 (107)
T ss_pred hhcccC
Confidence 999996
No 10
>KOG3437|consensus
Probab=21.00 E-value=41 Score=25.33 Aligned_cols=8 Identities=50% Similarity=1.145 Sum_probs=7.6
Q ss_pred ccCCCCCC
Q psy5299 25 MCNHENGR 32 (75)
Q Consensus 25 M~NH~~G~ 32 (75)
|.||.+|+
T Consensus 139 ~~NHq~Gk 146 (184)
T KOG3437|consen 139 LSNHQNGK 146 (184)
T ss_pred ecccccCc
Confidence 89999998
No 11
>PLN02684 Probable galactinol--sucrose galactosyltransferase
Probab=20.47 E-value=35 Score=30.28 Aligned_cols=48 Identities=21% Similarity=0.351 Sum_probs=32.6
Q ss_pred ccccccccCCCCCCCCcccccccceeeec---ccCCCCCCcchhHHHHHHHHhhh
Q psy5299 19 LIPVWDMCNHENGRSEPKEKTRNRSLLLS---PHNAPMAIPVVVPILRRLILQDC 70 (75)
Q Consensus 19 LIPlWDM~NH~~G~itT~yd~~~r~ec~A---~~d~~~~~~v~~~~~~~~~~~~~ 70 (75)
.+|=|||+ |+..... .|...-|+.|.. ..| +.|+- ...+|++|++.|-
T Consensus 476 v~PDWDMF-qS~hp~A-~~HAaaRAisGGPIYvSD-~PG~H-df~LLk~LvlpDG 526 (750)
T PLN02684 476 MQPDWDMF-HSLHPAA-EYHASARAISGGPLYVSD-APGKH-NFELLKKLVLPDG 526 (750)
T ss_pred cccCcccc-eecCccH-HHHHHHHhhcCCceEEec-CCCCc-cHHHHHhhhCCCC
Confidence 69999999 7776643 677766666543 356 44443 4578888888764
Done!