Query 019578
Match_columns 339
No_of_seqs 96 out of 98
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 02:52:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019578.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019578hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1079 Transcriptional repres 98.9 4E-09 8.7E-14 110.7 8.5 126 95-328 595-728 (739)
2 smart00317 SET SET (Su(var)3-9 98.9 1.4E-08 3E-13 79.9 8.6 32 107-138 9-40 (116)
3 KOG1080 Histone H3 (Lys4) meth 96.6 0.0068 1.5E-07 67.7 8.9 68 96-168 868-937 (1005)
4 KOG1082 Histone H3 (Lys9) meth 95.2 0.057 1.2E-06 53.6 7.2 148 92-317 174-322 (364)
5 KOG2461 Transcription factor B 94.1 0.066 1.4E-06 54.5 4.7 62 96-167 30-95 (396)
6 PF00856 SET: SET domain; Int 93.5 0.059 1.3E-06 43.5 2.7 27 109-135 1-27 (162)
7 KOG1085 Predicted methyltransf 89.1 0.27 5.9E-06 49.0 2.6 47 85-133 243-291 (392)
8 KOG4442 Clathrin coat binding 86.5 3 6.4E-05 45.6 8.5 60 107-168 129-191 (729)
9 COG2940 Proteins containing SE 79.7 0.61 1.3E-05 47.9 0.2 30 105-134 339-368 (480)
10 PF00856 SET: SET domain; Int 60.1 6.2 0.00013 31.7 1.9 21 295-315 141-162 (162)
11 KOG3489 Mitochondrial import i 59.0 9.6 0.00021 31.7 2.8 18 8-26 20-38 (86)
12 KOG1083 Putative transcription 51.2 9.6 0.00021 43.8 2.1 23 296-318 1274-1297(1306)
13 PF14398 ATPgrasp_YheCD: YheC/ 42.0 64 0.0014 30.7 5.9 87 71-165 34-134 (262)
14 KOG0404 Thioredoxin reductase 36.0 15 0.00033 36.2 0.7 51 52-118 242-292 (322)
15 KOG1337 N-methyltransferase [G 33.2 30 0.00065 35.6 2.3 21 296-316 257-278 (472)
16 PF08666 SAF: SAF domain; Int 30.8 34 0.00074 24.7 1.7 13 298-310 3-16 (63)
17 PRK05254 uracil-DNA glycosylas 28.8 54 0.0012 31.2 3.1 49 54-114 75-123 (224)
18 TIGR00628 ung uracil-DNA glyco 28.6 57 0.0012 30.9 3.2 49 54-114 69-118 (212)
19 PHA03200 uracil DNA glycosylas 28.6 69 0.0015 31.4 3.8 49 54-114 100-149 (255)
20 COG0692 Ung Uracil DNA glycosy 27.5 60 0.0013 31.3 3.1 58 39-114 63-121 (223)
21 PF01870 Hjc: Archaeal hollida 26.9 1.7E+02 0.0037 24.1 5.3 34 83-133 5-38 (88)
22 COG1485 Predicted ATPase [Gene 25.9 44 0.00096 34.3 2.0 41 295-335 160-228 (367)
23 PHA03199 uracil DNA glycosylas 24.0 72 0.0016 32.1 3.0 49 54-114 156-205 (304)
24 PF07626 PSD3: Protein of unkn 22.3 76 0.0016 24.7 2.3 26 77-102 1-26 (67)
25 TIGR00768 rimK_fam alpha-L-glu 22.0 98 0.0021 28.1 3.4 38 73-114 103-141 (277)
26 PHA03201 uracil DNA glycosylas 20.6 91 0.002 31.5 3.0 49 54-114 170-219 (318)
27 PF08443 RimK: RimK-like ATP-g 20.4 66 0.0014 28.6 1.9 39 73-114 18-57 (190)
28 PHA03347 uracil DNA glycosylas 20.0 67 0.0015 31.4 1.9 50 53-114 93-143 (252)
No 1
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=98.89 E-value=4e-09 Score=110.69 Aligned_cols=126 Identities=29% Similarity=0.334 Sum_probs=91.9
Q ss_pred EEEecCCCCCcCCCCceeEEeeecCCCcEEEEecCeeeCcccccccCCCCCCCCCC-CeeeeecCCeEEecCCCCCCCCc
Q 019578 95 TLDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGIIYSPAYYRYIPGYPRVDAQN-PYLITRYDGTVINAQPWGSGWDT 173 (339)
Q Consensus 95 s~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~VY~p~~~~~ipgyP~vd~~N-~Yli~r~DG~vIDg~~wg~gg~s 173 (339)
.+.+++|.| ||.|+|+|-.|.++++|+.|.|.+-+..-...- |- ..|..+ +|||-.+++.|||++-.|
T Consensus 595 r~llapSdV----aGwGlFlKe~v~KnefisEY~GE~IS~dEADrR-Gk-iYDr~~cSflFnln~dyviDs~rkG----- 663 (739)
T KOG1079|consen 595 RVLLAPSDV----AGWGLFLKESVSKNEFISEYTGEIISHDEADRR-GK-IYDRYMCSFLFNLNNDYVIDSTRKG----- 663 (739)
T ss_pred ceeechhhc----cccceeeccccCCCceeeeecceeccchhhhhc-cc-ccccccceeeeeccccceEeeeeec-----
Confidence 489999987 579999999999999999999998873211100 00 013334 799999999999999553
Q ss_pred ccccCCCCcCccCCCCCCcCcCchhHHHhhcCCcCCCCCCCCcccccccChhhhhhhhcCCCCCCCCCeEEEeecCCCCc
Q 019578 174 RELWDGLTLPEIMPNSKGAEKGSDQFWKLLSKPMDNKRGGSGSEMLERRNPLALAHFANHPAKGMVPNVMICPYDFPLTE 253 (339)
Q Consensus 174 r~~~~g~~~~~~~~~~~~a~~~~D~~w~~ls~Pl~~s~~~~~~~~le~~NPLAlGH~aNHpp~g~~pNV~~~~yDfP~~~ 253 (339)
.++|||||-. .||..+.-+=++-
T Consensus 664 ----------------------------------------------------nk~rFANHS~---nPNCYAkvm~V~G-- 686 (739)
T KOG1079|consen 664 ----------------------------------------------------NKIRFANHSF---NPNCYAKVMMVAG-- 686 (739)
T ss_pred ----------------------------------------------------chhhhccCCC---CCCcEEEEEEecC--
Confidence 1368999987 5887776654441
Q ss_pred ccccccCCceecCCchhhhhhhccccceecCCCCCCCCCceEEEEEEEeccc-CCceeEeecccCCCC------CCCCcc
Q 019578 254 KDMRPYIPNISFGNAEEVNMRRFGSFWFKWGSGSGSSTPVLKTLALVATRAI-CDEEVLLNYRLSNSK------RRPVWY 326 (339)
Q Consensus 254 ~~Lr~YIPNv~~~~~~~~~m~r~g~~w~~~~~~~~~~~~vlr~vVLVAtRdI-~dEELflNYRls~~~------~~P~WY 326 (339)
-+=+.+.|.|+| .|||||.+|||++.. .-++||
T Consensus 687 ----------------------------------------dhRIGifAkRaIeagEELffDYrYs~~~~~k~~~~~~~s~ 726 (739)
T KOG1079|consen 687 ----------------------------------------DHRIGIFAKRAIEAGEELFFDYRYSPEHALKFVGIERESY 726 (739)
T ss_pred ----------------------------------------CcceeeeehhhcccCceeeeeeccCccccccccccCcccc
Confidence 122347899999 889999999999865 234666
Q ss_pred cc
Q 019578 327 SP 328 (339)
Q Consensus 327 ~p 328 (339)
.+
T Consensus 727 k~ 728 (739)
T KOG1079|consen 727 KV 728 (739)
T ss_pred cc
Confidence 54
No 2
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=98.85 E-value=1.4e-08 Score=79.89 Aligned_cols=32 Identities=22% Similarity=0.250 Sum_probs=28.8
Q ss_pred CCCceeEEeeecCCCcEEEEecCeeeCccccc
Q 019578 107 EAGQGLFLCGEANVGAVIAIYPGIIYSPAYYR 138 (339)
Q Consensus 107 ~AG~GvF~~G~v~~G~Vva~YPG~VY~p~~~~ 138 (339)
++|.|||++-.+++|++|.-|+|.+..+....
T Consensus 9 ~~G~gl~a~~~i~~g~~i~~~~g~~~~~~~~~ 40 (116)
T smart00317 9 GKGWGVRATEDIPKGEFIGEYVGEIITSEEAE 40 (116)
T ss_pred CCcEEEEECCccCCCCEEEEEEeEEECHHHHH
Confidence 99999999999999999999999999864443
No 3
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=96.64 E-value=0.0068 Score=67.68 Aligned_cols=68 Identities=28% Similarity=0.414 Sum_probs=51.2
Q ss_pred EEecCCCCCcCCCCceeEEeeecCCCcEEEEecCeeeCc--ccccccCCCCCCCCCCCeeeeecCCeEEecCCCC
Q 019578 96 LDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGIIYSP--AYYRYIPGYPRVDAQNPYLITRYDGTVINAQPWG 168 (339)
Q Consensus 96 ~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~VY~p--~~~~~ipgyP~vd~~N~Yli~r~DG~vIDg~~wg 168 (339)
|.-.+|.|. |-|||+.+.+.+|.-|--|=|.++.+ +=+|-+ .|=+.-..-.|||+-=|++||||...|
T Consensus 868 ~~F~~s~iH----~wglfa~~~i~~~dmViEY~Ge~vR~~iad~RE~-~Y~~~gi~~sYlfrid~~~ViDAtk~g 937 (1005)
T KOG1080|consen 868 VKFGRSGIH----GWGLFAMENIAAGDMVIEYRGELVRSSIADLREA-RYERMGIGDSYLFRIDDEVVVDATKKG 937 (1005)
T ss_pred hcccccccc----ccceeeccCccccceEEEeeceehhhhHHHHHHH-HHhccCcccceeeecccceEEeccccC
Confidence 677889885 78999999999999999999999984 112221 222223356799987789999999653
No 4
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=95.18 E-value=0.057 Score=53.61 Aligned_cols=148 Identities=20% Similarity=0.238 Sum_probs=89.0
Q ss_pred hCeEEEecCCCCCcCCCCceeEEeeecCCCcEEEEecCeeeCcccccccCCCCCCCCCCCeeeeecCCeEEecCCCCCCC
Q 019578 92 IGYTLDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGIIYSPAYYRYIPGYPRVDAQNPYLITRYDGTVINAQPWGSGW 171 (339)
Q Consensus 92 lGfs~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~VY~p~~~~~ipgyP~vd~~N~Yli~r~DG~vIDg~~wg~gg 171 (339)
+=|.|.|-.+ + ..|=||-..-.+++|+-|+-|.|.+-+-.-.+... ..+.|++...|++.+.-.+|..
T Consensus 174 ~~~~leIfrt--~--~kGwgvRs~~~I~~G~fvcEyaGe~~t~~e~~~~~------~~~~~~~~~~~~~~~~~~~~~~-- 241 (364)
T KOG1082|consen 174 LQFHLEVFRT--P--EKGWGVRTLDPIPAGEFVCEYAGEVLTSEEAQRRT------HLREYLDDDCDAYSIADREWVD-- 241 (364)
T ss_pred cccceEEEec--C--CceeeecccccccCCCeeEEEeeEecChHHhhhcc------ccccccccccccchhhhccccc--
Confidence 4445555554 2 36777777678999999999999998854444331 2456766555655555454421
Q ss_pred CcccccCCCCcCccCCCCCCcCcCchhHHHhhcCCcCCCCCCCCcccccccChhhhhhhhcCCCCCCCCCeEEEeecCCC
Q 019578 172 DTRELWDGLTLPEIMPNSKGAEKGSDQFWKLLSKPMDNKRGGSGSEMLERRNPLALAHFANHPAKGMVPNVMICPYDFPL 251 (339)
Q Consensus 172 ~sr~~~~g~~~~~~~~~~~~a~~~~D~~w~~ls~Pl~~s~~~~~~~~le~~NPLAlGH~aNHpp~g~~pNV~~~~yDfP~ 251 (339)
+.+.+. .....+++...+.+ ..+...+=-.+|+|+||- -+|||+++.+-.
T Consensus 242 ---~~~~~~------------~~~~~~~~~~~~~~----------~~ida~~~GNv~RfinHS---C~PN~~~~~v~~-- 291 (364)
T KOG1082|consen 242 ---ESPVGN------------TFVAPSLPGGPGRE----------LLIDAKPHGNVARFINHS---CSPNLLYQAVFQ-- 291 (364)
T ss_pred ---cccccc------------cccccccccCCCcc----------eEEchhhcccccccccCC---CCccceeeeeee--
Confidence 111110 01111111111110 223455556788999997 579999987711
Q ss_pred CcccccccCCceecCCchhhhhhhccccceecCCCCCCCCCceEEEEEEEeccc-CCceeEeecccC
Q 019578 252 TEKDMRPYIPNISFGNAEEVNMRRFGSFWFKWGSGSGSSTPVLKTLALVATRAI-CDEEVLLNYRLS 317 (339)
Q Consensus 252 ~~~~Lr~YIPNv~~~~~~~~~m~r~g~~w~~~~~~~~~~~~vlr~vVLVAtRdI-~dEELflNYRls 317 (339)
+ + ..+.+--++|.|+++| ..|||=++|-..
T Consensus 292 --------------~--~--------------------~~~~~~~i~ffa~~~I~p~~ELT~dYg~~ 322 (364)
T KOG1082|consen 292 --------------D--E--------------------FVLLYLRIGFFALRDISPGEELTLDYGKA 322 (364)
T ss_pred --------------c--C--------------------CccchheeeeeeccccCCCcccchhhccc
Confidence 1 0 1233556789999999 889999999865
No 5
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=94.07 E-value=0.066 Score=54.47 Aligned_cols=62 Identities=24% Similarity=0.406 Sum_probs=46.5
Q ss_pred EEecCCCCCcCCCCceeEEeeecCCCcEEEEecCeeeCcccccccCCCCCCCCCCCeeeeecC-C---eEEecCCC
Q 019578 96 LDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGIIYSPAYYRYIPGYPRVDAQNPYLITRYD-G---TVINAQPW 167 (339)
Q Consensus 96 ~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~VY~p~~~~~ipgyP~vd~~N~Yli~r~D-G---~vIDg~~w 167 (339)
+.+++|+|+ .+|.||+-+..+++|+.-+=|=|-+ |+-+..-.++|.|+..-|. + .+|||.+.
T Consensus 30 l~i~~Ssv~--~~~lgV~s~~~i~~G~~FGP~~G~~--------~~~~~~~~~n~~y~W~I~~~d~~~~~iDg~d~ 95 (396)
T KOG2461|consen 30 LRIKPSSVP--VTGLGVWSNASILPGTSFGPFEGEI--------IASIDSKSANNRYMWEIFSSDNGYEYIDGTDE 95 (396)
T ss_pred eEeeccccC--CccccccccccccCcccccCccCcc--------ccccccccccCcceEEEEeCCCceEEeccCCh
Confidence 789999999 9999999999999999999998887 2222222345677665443 2 68999864
No 6
>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=93.54 E-value=0.059 Score=43.54 Aligned_cols=27 Identities=37% Similarity=0.605 Sum_probs=21.5
Q ss_pred CceeEEeeecCCCcEEEEecCeeeCcc
Q 019578 109 GQGLFLCGEANVGAVIAIYPGIIYSPA 135 (339)
Q Consensus 109 G~GvF~~G~v~~G~Vva~YPG~VY~p~ 135 (339)
|.|||++-.+++|++|....+.+.++.
T Consensus 1 GrGl~At~dI~~Ge~I~~p~~~~~~~~ 27 (162)
T PF00856_consen 1 GRGLFATRDIKAGEVILIPRPAILTPD 27 (162)
T ss_dssp SEEEEESS-B-TTEEEEEESEEEEEHH
T ss_pred CEEEEECccCCCCCEEEEECcceEEeh
Confidence 899999999999998888878777753
No 7
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=89.14 E-value=0.27 Score=48.97 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=32.3
Q ss_pred HHHHHHHh--CeEEEecCCCCCcCCCCceeEEeeecCCCcEEEEecCeeeC
Q 019578 85 SQRLKDAI--GYTLDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGIIYS 133 (339)
Q Consensus 85 s~~l~~~l--Gfs~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~VY~ 133 (339)
-+.|.+.. |=+--...-.+. +.|+||-.+.....|..|--|-|..-.
T Consensus 243 ~~~l~~~vl~g~~egl~~~~~d--gKGRGv~a~~~F~rgdFVVEY~Gdlie 291 (392)
T KOG1085|consen 243 KHALRDTVLKGTNEGLLEVYKD--GKGRGVRAKVNFERGDFVVEYRGDLIE 291 (392)
T ss_pred HHHHHHHHHhccccceeEEeec--cccceeEeecccccCceEEEEecceee
Confidence 34444443 333333334455 789999999999999999999998654
No 8
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.46 E-value=3 Score=45.65 Aligned_cols=60 Identities=22% Similarity=0.310 Sum_probs=41.1
Q ss_pred CCCceeEEeeecCCCcEEEEecCeeeCcccccc-cCCCCCCCCCC--CeeeeecCCeEEecCCCC
Q 019578 107 EAGQGLFLCGEANVGAVIAIYPGIIYSPAYYRY-IPGYPRVDAQN--PYLITRYDGTVINAQPWG 168 (339)
Q Consensus 107 ~AG~GvF~~G~v~~G~Vva~YPG~VY~p~~~~~-ipgyP~vd~~N--~Yli~r~DG~vIDg~~wg 168 (339)
..|-||=+.-.+++|+.|--|=|-|-+-.-|+. +.-|-+ ..| -|.|+.--|.+|||.-.|
T Consensus 129 ~KG~GLRA~~dI~~g~FI~EY~GEVI~~~Ef~kR~~~Y~~--d~~kh~Yfm~L~~~e~IDAT~KG 191 (729)
T KOG4442|consen 129 KKGCGLRAEEDIPKGQFILEYIGEVIEEKEFEKRVKRYAK--DGIKHYYFMALQGGEYIDATKKG 191 (729)
T ss_pred CcccceeeccccCCCcEEeeeccccccHHHHHHHHHHHHh--cCCceEEEEEecCCceecccccC
Confidence 667777777799999999999999988544431 111110 122 366666689999999774
No 9
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=79.73 E-value=0.61 Score=47.87 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=25.0
Q ss_pred cCCCCceeEEeeecCCCcEEEEecCeeeCc
Q 019578 105 HEEAGQGLFLCGEANVGAVIAIYPGIIYSP 134 (339)
Q Consensus 105 H~~AG~GvF~~G~v~~G~Vva~YPG~VY~p 134 (339)
++.-|.|||+.=.++.|+.|-.|-|.+-..
T Consensus 339 ~~~~~~g~fa~~~i~~~e~i~~~~~~~~~~ 368 (480)
T COG2940 339 SEIKGYGVFALESIKKGEFIIEYHGEIIRR 368 (480)
T ss_pred hcccccceeehhhccchHHHHHhcCcccch
Confidence 557789999999999999988888886664
No 10
>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=60.10 E-value=6.2 Score=31.72 Aligned_cols=21 Identities=38% Similarity=0.567 Sum_probs=17.9
Q ss_pred EEEEEEEeccc-CCceeEeecc
Q 019578 295 KTLALVATRAI-CDEEVLLNYR 315 (339)
Q Consensus 295 r~vVLVAtRdI-~dEELflNYR 315 (339)
.+++++|+|+| .|||||++|.
T Consensus 141 ~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 141 GCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp TEEEEEESS-B-TTSBEEEEST
T ss_pred ceEEEEECCccCCCCEEEEEEC
Confidence 46889999999 8999999994
No 11
>KOG3489 consensus Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=58.99 E-value=9.6 Score=31.69 Aligned_cols=18 Identities=28% Similarity=0.711 Sum_probs=14.3
Q ss_pred hHHHHH-HHHHHHHHHHHHH
Q 019578 8 SDQQQQ-VLDNIHSQIKRFC 26 (339)
Q Consensus 8 ~~qq~q-vq~nih~qi~~~c 26 (339)
+||||| ||+.|| |..++|
T Consensus 20 ~E~qk~k~~~~VH-qft~~C 38 (86)
T KOG3489|consen 20 AETQKQKFQEQVH-QFTEIC 38 (86)
T ss_pred HHHHHHHHHHHHH-HHHHHH
Confidence 588998 999999 556666
No 12
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=51.21 E-value=9.6 Score=43.83 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=19.7
Q ss_pred EEEEEEeccc-CCceeEeecccCC
Q 019578 296 TLALVATRAI-CDEEVLLNYRLSN 318 (339)
Q Consensus 296 ~vVLVAtRdI-~dEELflNYRls~ 318 (339)
-++|+|+||| +||||..+|-+.-
T Consensus 1274 Rv~L~A~rDi~kGEELtYDYN~ks 1297 (1306)
T KOG1083|consen 1274 RVGLFALRDLPKGEELTYDYNFKS 1297 (1306)
T ss_pred eeeeeecCCCCCCceEEEeccccc
Confidence 3678999999 9999999987653
No 13
>PF14398 ATPgrasp_YheCD: YheC/D like ATP-grasp
Probab=41.96 E-value=64 Score=30.73 Aligned_cols=87 Identities=23% Similarity=0.399 Sum_probs=50.8
Q ss_pred CCCcccccccH-HHHHHHHHHHhCeEEEecCCCCCcCCCCceeEEeeecCCCcEEEEecCe-----eeC--cccccccCC
Q 019578 71 PVVPQTRQLTR-TELSQRLKDAIGYTLDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGI-----IYS--PAYYRYIPG 142 (339)
Q Consensus 71 ~~~~~~~~l~~-~~vs~~l~~~lGfs~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~-----VY~--p~~~~~ipg 142 (339)
+-+|+|..++. ++|.+.| +..+ +|++||+.= .-|.|++-=-..+.+-.+..+-+. ++. -.+.+.+..
T Consensus 34 ~~LP~T~~~~~~~~l~~~L-~~y~-~vylKP~~G---s~G~gI~ri~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 108 (262)
T PF14398_consen 34 PYLPETELLTSFEDLREML-NKYK-SVYLKPDNG---SKGKGIIRIEKKGGGYRIQYRNKKKNVRRTFSSLEELEQFLKE 108 (262)
T ss_pred hhCCCceEcCCHHHHHHHH-HHCC-EEEEEeCCC---CCCccEEEEEEeCCEEEEEEccCCceeEEEeCCHHHHHHHHHH
Confidence 44999999987 6664444 4445 899999853 899999852222223333333222 233 122222311
Q ss_pred CCCCCCCCCeeee------ecCCeEEecC
Q 019578 143 YPRVDAQNPYLIT------RYDGTVINAQ 165 (339)
Q Consensus 143 yP~vd~~N~Yli~------r~DG~vIDg~ 165 (339)
+...+.||++ ++||..+|-+
T Consensus 109 ---~~~~~~yIiQq~I~l~~~~gr~fD~R 134 (262)
T PF14398_consen 109 ---LLGKRRYIIQQGIPLATYDGRPFDFR 134 (262)
T ss_pred ---hcCCCcEEEeCCccccccCCCeEEEE
Confidence 1235689988 6678877764
No 14
>KOG0404 consensus Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]
Probab=36.04 E-value=15 Score=36.19 Aligned_cols=51 Identities=29% Similarity=0.486 Sum_probs=36.0
Q ss_pred CCCCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHhCeEEEecCCCCCcCCCCceeEEeeec
Q 019578 52 PRRSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAIGYTLDLKPSQIPHEEAGQGLFLCGEA 118 (339)
Q Consensus 52 ~r~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~lGfs~~v~~S~i~H~~AG~GvF~~G~v 118 (339)
-..|||.||+|-+ |+|+.|+- +| =.|.-||-+.+..++. -.=.|||+.|.|
T Consensus 242 l~v~GlFf~IGH~---------Pat~~l~g-qv---e~d~~GYi~t~pgts~---TsvpG~FAAGDV 292 (322)
T KOG0404|consen 242 LPVSGLFFAIGHS---------PATKFLKG-QV---ELDEDGYIVTRPGTSL---TSVPGVFAAGDV 292 (322)
T ss_pred cccceeEEEecCC---------chhhHhcC-ce---eeccCceEEeccCccc---ccccceeecccc
Confidence 4579999999975 88888866 44 4578899888744332 122399987754
No 15
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=33.22 E-value=30 Score=35.57 Aligned_cols=21 Identities=43% Similarity=0.697 Sum_probs=19.5
Q ss_pred EEEEEEeccc-CCceeEeeccc
Q 019578 296 TLALVATRAI-CDEEVLLNYRL 316 (339)
Q Consensus 296 ~vVLVAtRdI-~dEELflNYRl 316 (339)
++.++++++| +|||+|.||+-
T Consensus 257 ~~~l~~~~~v~~geevfi~YG~ 278 (472)
T KOG1337|consen 257 AVELVAERDVSAGEEVFINYGP 278 (472)
T ss_pred cEEEEEeeeecCCCeEEEecCC
Confidence 8899999999 99999999984
No 16
>PF08666 SAF: SAF domain; InterPro: IPR013974 This entry includes a range of different proteins, such as antifreeze proteins, flagellar FlgA proteins, and CpaB pilus proteins. ; PDB: 1C89_A 3NLA_A 3RDN_A 1C8A_A 3FRN_A 1WVO_A 3K3S_H 3G8R_B 1XUU_A 1XUZ_A ....
Probab=30.82 E-value=34 Score=24.70 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=10.3
Q ss_pred EEEEeccc-CCcee
Q 019578 298 ALVATRAI-CDEEV 310 (339)
Q Consensus 298 VLVAtRdI-~dEEL 310 (339)
|+||+||| .|+.|
T Consensus 3 vvVA~~di~~G~~i 16 (63)
T PF08666_consen 3 VVVAARDIPAGTVI 16 (63)
T ss_dssp EEEESSTB-TT-BE
T ss_pred EEEEeCccCCCCEE
Confidence 68999999 77666
No 17
>PRK05254 uracil-DNA glycosylase; Provisional
Probab=28.85 E-value=54 Score=31.24 Aligned_cols=49 Identities=29% Similarity=0.500 Sum_probs=31.3
Q ss_pred CCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHhCeEEEecCCCCCcCCCCceeEE
Q 019578 54 RSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAIGYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 54 ~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~lGfs~~v~~S~i~H~~AG~GvF~ 114 (339)
-.||+|+|.++.+ +| -|-..|-++|.+.+||...-.-.+.. =|-+||++
T Consensus 75 A~GLaFSv~~~~~------~P----pSL~NI~kel~~d~~~~~p~~g~L~~--Wa~QGVLL 123 (224)
T PRK05254 75 AHGLSFSVPPGVP------IP----PSLRNIFKELEDDLGFPIPNHGDLTS--WAEQGVLL 123 (224)
T ss_pred cceEeeeCCCCCC------CC----ccHHHHHHHHHHhcCCCCCCCCChHH--HHhCCEEe
Confidence 4599999885431 12 35667888899998866532112222 47888887
No 18
>TIGR00628 ung uracil-DNA glycosylase. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.64 E-value=57 Score=30.94 Aligned_cols=49 Identities=20% Similarity=0.295 Sum_probs=31.5
Q ss_pred CCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHh-CeEEEecCCCCCcCCCCceeEE
Q 019578 54 RSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAI-GYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 54 ~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~l-Gfs~~v~~S~i~H~~AG~GvF~ 114 (339)
-.||+|+|.++.+ + |-|-..|-++|++.+ ||.+.-.-.+.. =|-+||++
T Consensus 69 A~GLaFSv~~~~~------~----PpSL~NI~kEl~~d~~~~~~p~~g~L~~--WA~QGVLL 118 (212)
T TIGR00628 69 AHGLAFSVKPGVP------I----PPSLKNIFKELEADYPDFPPPKHGCLEA--WARQGVLL 118 (212)
T ss_pred cceeeeECCCCCC------C----CchHHHHHHHHHHHcCCCCCCCCCChHH--HHhcCEEe
Confidence 4599999865432 2 235678889999998 476432223332 48889886
No 19
>PHA03200 uracil DNA glycosylase; Provisional
Probab=28.62 E-value=69 Score=31.41 Aligned_cols=49 Identities=14% Similarity=0.179 Sum_probs=34.1
Q ss_pred CCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHh-CeEEEecCCCCCcCCCCceeEE
Q 019578 54 RSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAI-GYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 54 ~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~l-Gfs~~v~~S~i~H~~AG~GvF~ 114 (339)
-.||+|+|-++.+ + |=|-..|-++|++.+ ||..--.-.+.. =|-+||++
T Consensus 100 A~GLaFSV~~~~~------~----PpSL~NIfKEL~~d~~g~~~p~~G~L~~--WAkQGVLL 149 (255)
T PHA03200 100 ACGLAFGTVRGRS------A----PPSLKNVFRELERTVPNFSRPDSGCLDS--WCRQGVLL 149 (255)
T ss_pred cceEEEEeCCCCC------C----CccHHHHHHHHHhhcCCCCCCCCCChhh--HHhCCEEE
Confidence 4599999865432 2 236678888899988 888543334444 78899998
No 20
>COG0692 Ung Uracil DNA glycosylase [DNA replication, recombination, and repair]
Probab=27.45 E-value=60 Score=31.33 Aligned_cols=58 Identities=24% Similarity=0.414 Sum_probs=38.4
Q ss_pred CCCCCccccccCCCCCCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHhC-eEEEecCCCCCcCCCCceeEE
Q 019578 39 NVPIESSAQSNAAPRRSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAIG-YTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 39 ~~~~~~~~~~~~~~r~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~lG-fs~~v~~S~i~H~~AG~GvF~ 114 (339)
-||-+.+-|+. ||+|+|-.+++- |=|-..|-++|+..+| +.+--..-+.+ =|-+||.+
T Consensus 63 QDPYh~p~qAh------GLsFSV~~~v~~----------PpSL~NI~kEL~~dl~~~~~~~~g~L~~--WA~QGVLL 121 (223)
T COG0692 63 QDPYHGPGQAH------GLSFSVPPGVKI----------PPSLKNIYKELEADLGGFPIPNHGDLTS--WAEQGVLL 121 (223)
T ss_pred cCCCCCCCccc------eeeeecCCCCCC----------CchHHHHHHHHHhhhCCCCCCCCCccHH--HHHhchhh
Confidence 46666666655 999999765432 2266788888888888 55544444444 67788876
No 21
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=26.89 E-value=1.7e+02 Score=24.06 Aligned_cols=34 Identities=24% Similarity=0.218 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCeEEEecCCCCCcCCCCceeEEeeecCCCcEEEEecCeeeC
Q 019578 83 ELSQRLKDAIGYTLDLKPSQIPHEEAGQGLFLCGEANVGAVIAIYPGIIYS 133 (339)
Q Consensus 83 ~vs~~l~~~lGfs~~v~~S~i~H~~AG~GvF~~G~v~~G~Vva~YPG~VY~ 133 (339)
||.+.|.+ .||.+.+.+.+-. + +|||+.+|++|.
T Consensus 5 el~~~L~~-~Gf~v~R~~~Sg~----~------------DiiA~~~~~~l~ 38 (88)
T PF01870_consen 5 ELVKILWE-RGFAVVRAAGSGG----G------------DIIAGKGGRYLA 38 (88)
T ss_dssp HHHHHHHH-TT-EEEEBSCCSS----S------------SEEEEETTEEEE
T ss_pred HHHHHHHh-CCcEEEEecCCCC----c------------CEEEECCCEEEE
Confidence 56566664 7999999887532 2 999999999776
No 22
>COG1485 Predicted ATPase [General function prediction only]
Probab=25.86 E-value=44 Score=34.32 Aligned_cols=41 Identities=34% Similarity=0.655 Sum_probs=32.7
Q ss_pred EEEEEEEecccCCc---------eeEe-------------------ecccCCCCCCCCccccCCHHHHh
Q 019578 295 KTLALVATRAICDE---------EVLL-------------------NYRLSNSKRRPVWYSPVDEEEDR 335 (339)
Q Consensus 295 r~vVLVAtRdI~dE---------ELfl-------------------NYRls~~~~~P~WY~pvD~eed~ 335 (339)
++|+||||-.+.=+ |.|| +||+-...+-|-|++|.|.|.++
T Consensus 160 ~GV~lvaTSN~~P~~LY~dGlqR~~FLP~I~li~~~~~v~~vD~~~DYR~r~l~~a~~y~~Pl~~~~~~ 228 (367)
T COG1485 160 RGVVLVATSNTAPDNLYKDGLQRERFLPAIDLIKSHFEVVNVDGPVDYRLRKLEQAPVYLTPLDAEAEA 228 (367)
T ss_pred CCcEEEEeCCCChHHhcccchhHHhhHHHHHHHHHheEEEEecCCccccccccccCceeecCCcHHHHH
Confidence 67889999877333 3343 89999999999999999998774
No 23
>PHA03199 uracil DNA glycosylase; Provisional
Probab=23.96 E-value=72 Score=32.08 Aligned_cols=49 Identities=22% Similarity=0.266 Sum_probs=32.5
Q ss_pred CCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHh-CeEEEecCCCCCcCCCCceeEE
Q 019578 54 RSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAI-GYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 54 ~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~l-Gfs~~v~~S~i~H~~AG~GvF~ 114 (339)
-.||+|+|.++++ +| =|...|-++|++.+ ||.+--.-.+.. =|-+||++
T Consensus 156 A~GLaFSV~~gv~------iP----PSL~NIfKEL~~dl~g~~~p~~G~L~~--WAkQGVLL 205 (304)
T PHA03199 156 AHGLAFSVKRGIP------IP----PSLKNIFAALMESYPHLPLPTHGCLDN--WARQGVLL 205 (304)
T ss_pred cceEEEecCCCCC------CC----ccHHHHHHHHHHhcCCCCCCCCCCHHH--HHhcCEEe
Confidence 4499999875431 22 26678888899988 886532223333 67788887
No 24
>PF07626 PSD3: Protein of unknown function (DUF1587); InterPro: IPR013036 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=22.27 E-value=76 Score=24.68 Aligned_cols=26 Identities=31% Similarity=0.510 Sum_probs=22.0
Q ss_pred ccccHHHHHHHHHHHhCeEEEecCCC
Q 019578 77 RQLTRTELSQRLKDAIGYTLDLKPSQ 102 (339)
Q Consensus 77 ~~l~~~~vs~~l~~~lGfs~~v~~S~ 102 (339)
|.|++.|-.+.|+|.+|..+.+..+.
T Consensus 1 RRLtr~EY~nTvrDLlg~~~~~~~~l 26 (67)
T PF07626_consen 1 RRLTRREYQNTVRDLLGVDVDPADGL 26 (67)
T ss_pred CCCCHHHHHHHHHHHhCCCCchhccC
Confidence 67999999999999999996666543
No 25
>TIGR00768 rimK_fam alpha-L-glutamate ligases, RimK family. This family, related to bacterial glutathione synthetases, contains at least two different alpha-L-glutamate ligases. One is RimK, as in E. coli, which adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6, but not to Lys-Glu mutants. Most species with a member of this subfamily lack an S6 homolog ending in Glu-Glu, however. Members in Methanococcus jannaschii act instead as a tetrahydromethanopterin:alpha-l-glutamate ligase (MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase (MJ1001).
Probab=22.03 E-value=98 Score=28.13 Aligned_cols=38 Identities=29% Similarity=0.326 Sum_probs=27.2
Q ss_pred Cccccccc-HHHHHHHHHHHhCeEEEecCCCCCcCCCCceeEE
Q 019578 73 VPQTRQLT-RTELSQRLKDAIGYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 73 ~~~~~~l~-~~~vs~~l~~~lGfs~~v~~S~i~H~~AG~GvF~ 114 (339)
+|+|..+. .+++ ..+.+.+||.+.+||..- ..|.|+++
T Consensus 103 ~P~t~~~~~~~~~-~~~~~~~~~p~vvKP~~g---~~g~gv~~ 141 (277)
T TIGR00768 103 QPRTGLAGSPEEA-LKLIEEIGFPVVLKPVFG---SWGRLVSL 141 (277)
T ss_pred CCCEEEeCCHHHH-HHHHHhcCCCEEEEECcC---CCCCceEE
Confidence 56776654 4444 455677899999999863 67889885
No 26
>PHA03201 uracil DNA glycosylase; Provisional
Probab=20.58 E-value=91 Score=31.53 Aligned_cols=49 Identities=16% Similarity=0.223 Sum_probs=31.2
Q ss_pred CCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHh-CeEEEecCCCCCcCCCCceeEE
Q 019578 54 RSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAI-GYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 54 ~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~l-Gfs~~v~~S~i~H~~AG~GvF~ 114 (339)
-.||+|+|.++++ + +=|...|-++|++.+ ||...-.-.+.. =|-+||++
T Consensus 170 A~GLaFSV~~gv~------~----PpSLrNIfKEL~~d~~g~~~p~~G~L~~--WAkQGVLL 219 (318)
T PHA03201 170 AHGLAFSVRPGTP------A----PPSLRNILAAVRNCCPDARMSGHGCLEK--WARGGVLL 219 (318)
T ss_pred cceEeeecCCCCC------C----ChhHHHHHHHHHHhccCCCCCCCcCHHH--HhhcCEEe
Confidence 4599999976542 1 236678888898888 875431112222 47778886
No 27
>PF08443 RimK: RimK-like ATP-grasp domain; InterPro: IPR013651 This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK []. It has an unusual nucleotide-binding fold referred to as palmate, or ATP-grasp fold. This domain is found in a number of enzymes of known structure as well as in urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis.; PDB: 1UC8_B 1UC9_A.
Probab=20.39 E-value=66 Score=28.60 Aligned_cols=39 Identities=31% Similarity=0.639 Sum_probs=18.4
Q ss_pred CcccccccHHHHHHHHHHHh-CeEEEecCCCCCcCCCCceeEE
Q 019578 73 VPQTRQLTRTELSQRLKDAI-GYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 73 ~~~~~~l~~~~vs~~l~~~l-Gfs~~v~~S~i~H~~AG~GvF~ 114 (339)
+|+|......+-.+.+.+.+ ||.+.+|+..= ..|.|||+
T Consensus 18 vP~t~~~~~~~~~~~~~~~~~~~p~ViKp~~g---~~G~gV~~ 57 (190)
T PF08443_consen 18 VPETRVTNSPEEAKEFIEELGGFPVVIKPLRG---SSGRGVFL 57 (190)
T ss_dssp ---EEEESSHHHHHHHHHHH--SSEEEE-SB----------EE
T ss_pred CCCEEEECCHHHHHHHHHHhcCCCEEEeeCCC---CCCCEEEE
Confidence 67876664444445566666 99999999752 77999997
No 28
>PHA03347 uracil DNA glycosylase; Provisional
Probab=20.03 E-value=67 Score=31.41 Aligned_cols=50 Identities=22% Similarity=0.291 Sum_probs=33.9
Q ss_pred CCCCcccccCCCCCCCCCCCCcccccccHHHHHHHHHHHh-CeEEEecCCCCCcCCCCceeEE
Q 019578 53 RRSGLSFAVGPTARPTDSPVVPQTRQLTRTELSQRLKDAI-GYTLDLKPSQIPHEEAGQGLFL 114 (339)
Q Consensus 53 r~sgl~fa~~~~~~~~~~~~~~~~~~l~~~~vs~~l~~~l-Gfs~~v~~S~i~H~~AG~GvF~ 114 (339)
.-.||+|+|.++.+ +| =|-..|-++|++.+ ||..--.-.+.. =|-+||++
T Consensus 93 qA~GLaFSV~~~~~------~P----pSL~NIfKEL~~d~~~~~~p~~G~L~~--WA~QGVLL 143 (252)
T PHA03347 93 QANGLAFSVAYGFP------VP----PSLRNIFAELHRSVPDFSPPDHGCLDA--WARQGVLL 143 (252)
T ss_pred ccceEEEecCCCCC------CC----ccHHHHHHHHHhhccCCCCCCCCChHH--HHhcCEEe
Confidence 35699999976532 22 36667888888888 887432234444 68899997
Done!