Query 018070
Match_columns 361
No_of_seqs 171 out of 1642
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 05:53:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018070.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018070hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2084 Predicted histone tail 99.8 3.4E-19 7.4E-24 179.5 14.2 244 86-361 22-276 (482)
2 PF00856 SET: SET domain; Int 99.8 1.8E-18 3.9E-23 147.4 10.9 51 281-331 109-162 (162)
3 smart00317 SET SET (Su(var)3-9 99.5 1.4E-14 3.1E-19 117.5 7.7 45 286-330 69-116 (116)
4 KOG1338 Uncharacterized conser 98.5 1.2E-06 2.6E-11 83.8 12.4 91 239-336 173-264 (466)
5 KOG2589 Histone tail methylase 98.5 8.7E-08 1.9E-12 90.6 4.3 64 286-359 191-255 (453)
6 PF01753 zf-MYND: MYND finger; 98.2 3.6E-07 7.9E-12 59.2 1.1 37 123-161 1-37 (37)
7 COG2940 Proteins containing SE 98.1 1.9E-06 4E-11 87.7 3.1 71 290-360 405-478 (480)
8 KOG1080 Histone H3 (Lys4) meth 97.9 9.4E-06 2E-10 87.5 3.9 45 290-334 939-986 (1005)
9 KOG4442 Clathrin coat binding 97.8 1.5E-05 3.3E-10 81.3 4.5 45 292-336 195-242 (729)
10 KOG1337 N-methyltransferase [G 97.6 4.4E-05 9.5E-10 77.6 3.7 95 240-351 197-291 (472)
11 KOG1082 Histone H3 (Lys9) meth 97.2 0.00028 6E-09 69.3 3.2 42 293-334 275-323 (364)
12 KOG1085 Predicted methyltransf 96.6 0.0014 3E-08 60.7 2.8 44 291-334 334-380 (392)
13 KOG1083 Putative transcription 96.4 0.0025 5.5E-08 68.0 3.5 41 292-332 1252-1295(1306)
14 KOG1141 Predicted histone meth 96.1 0.0038 8.2E-08 65.2 3.0 44 291-334 1190-1240(1262)
15 KOG1710 MYND Zn-finger and ank 95.7 0.0028 6.2E-08 58.9 -0.1 44 120-164 319-362 (396)
16 KOG1079 Transcriptional repres 94.4 0.038 8.3E-07 56.9 3.8 42 292-333 667-711 (739)
17 KOG1085 Predicted methyltransf 91.9 0.26 5.5E-06 46.1 4.8 31 78-108 256-286 (392)
18 KOG1081 Transcription factor N 86.7 0.27 5.9E-06 49.8 0.9 52 282-333 362-417 (463)
19 PF09889 DUF2116: Uncharacteri 81.2 0.71 1.5E-05 33.0 0.8 25 121-153 4-28 (59)
20 PF12855 Ecl1: Life-span regul 79.4 0.9 2E-05 30.2 0.9 30 120-154 6-35 (43)
21 KOG3612 PHD Zn-finger protein 77.4 0.62 1.3E-05 47.1 -0.5 37 122-163 529-566 (588)
22 PLN03158 methionine aminopepti 72.9 2.1 4.5E-05 42.7 1.8 39 120-160 9-54 (396)
23 KOG4442 Clathrin coat binding 68.5 4.8 0.0001 42.2 3.4 31 76-106 118-148 (729)
24 PF08666 SAF: SAF domain; Int 67.7 3.6 7.8E-05 29.0 1.7 15 90-104 2-16 (63)
25 smart00317 SET SET (Su(var)3-9 65.5 9.2 0.0002 29.8 3.9 30 77-106 82-114 (116)
26 TIGR02059 swm_rep_I cyanobacte 63.2 10 0.00022 30.0 3.5 25 310-334 75-99 (101)
27 COG2075 RPL24A Ribosomal prote 62.2 4.5 9.8E-05 29.3 1.3 45 121-166 4-52 (66)
28 PF04570 DUF581: Protein of un 61.4 4 8.7E-05 29.0 0.9 34 120-153 16-50 (58)
29 COG4068 Uncharacterized protei 60.9 3.5 7.6E-05 29.1 0.5 23 121-151 9-31 (64)
30 KOG2461 Transcription factor B 55.5 8.8 0.00019 38.2 2.5 27 308-334 120-146 (396)
31 PF08666 SAF: SAF domain; Int 55.1 7.6 0.00017 27.3 1.5 17 313-329 3-19 (63)
32 TIGR03586 PseI pseudaminic aci 48.1 11 0.00025 36.4 1.9 21 88-108 274-294 (327)
33 PF06467 zf-FCS: MYM-type Zinc 46.6 9.6 0.00021 24.7 0.8 33 120-152 6-42 (43)
34 TIGR03569 NeuB_NnaB N-acetylne 46.4 7.3 0.00016 37.8 0.3 23 86-108 274-296 (329)
35 PRK14891 50S ribosomal protein 45.9 12 0.00027 30.8 1.5 32 121-152 5-40 (131)
36 PF00856 SET: SET domain; Int 44.7 29 0.00064 28.2 3.8 29 78-106 128-159 (162)
37 PF13824 zf-Mss51: Zinc-finger 43.1 26 0.00055 24.7 2.5 42 123-164 2-45 (55)
38 KOG2155 Tubulin-tyrosine ligas 42.9 23 0.0005 35.5 3.1 61 285-345 199-264 (631)
39 smart00858 SAF This domain fam 41.1 17 0.00037 25.4 1.5 17 90-106 2-18 (64)
40 PF10013 DUF2256: Uncharacteri 40.9 8.3 0.00018 25.4 -0.2 33 120-152 8-41 (42)
41 PF08394 Arc_trans_TRASH: Arch 40.6 13 0.00028 23.9 0.7 30 123-152 1-32 (37)
42 PF00181 Ribosomal_L2: Ribosom 40.6 21 0.00046 26.7 2.0 41 66-106 37-77 (77)
43 PF04438 zf-HIT: HIT zinc fing 38.5 19 0.00042 21.8 1.2 28 121-151 3-30 (30)
44 PRK00807 50S ribosomal protein 38.2 16 0.00034 25.3 0.9 32 121-152 2-37 (52)
45 PRK01343 zinc-binding protein; 37.6 26 0.00057 24.8 1.9 27 120-153 9-35 (57)
46 COG2089 SpsE Sialic acid synth 36.0 22 0.00047 34.3 1.7 28 87-114 287-314 (347)
47 PLN03144 Carbon catabolite rep 34.8 29 0.00063 36.5 2.6 33 121-159 75-107 (606)
48 KOG2084 Predicted histone tail 34.1 0.48 1E-05 47.6 -10.5 77 283-359 365-449 (482)
49 KOG3362 Predicted BBOX Zn-fing 32.1 19 0.00042 30.3 0.6 30 120-152 118-147 (156)
50 PF04945 YHS: YHS domain; Int 29.5 28 0.0006 23.2 0.9 15 138-152 21-35 (47)
51 KOG2857 Predicted MYND Zn-fing 26.1 34 0.00074 28.8 1.1 31 120-152 5-35 (157)
52 KOG1082 Histone H3 (Lys9) meth 25.9 87 0.0019 30.7 4.1 31 76-106 174-204 (364)
53 PF08189 Meleagrin: Meleagrin/ 23.9 30 0.00065 22.0 0.3 19 139-157 6-25 (39)
54 cd00472 Ribosomal_L24e_L24 Rib 23.3 43 0.00092 23.4 1.0 32 121-152 4-39 (54)
55 PF14353 CpXC: CpXC protein 22.3 1.1E+02 0.0024 24.9 3.5 31 328-359 16-46 (128)
56 smart00746 TRASH metallochaper 22.2 54 0.0012 19.0 1.2 14 139-152 21-34 (39)
No 1
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=99.80 E-value=3.4e-19 Score=179.49 Aligned_cols=244 Identities=21% Similarity=0.298 Sum_probs=139.6
Q ss_pred CCCccEEEEcccCCCCCEEEecCCeEeecCCcccccccccccccccCCCCCCCCcCceecChhhhhhhccchhhhhhhhh
Q 018070 86 ESAGRGVFATRRIRASDLIHTAKPIITHPTLSTLNSVCYFCLRKITSSSQHFQHHNARFCGEVCKDNAKAFYDVERRADW 165 (361)
Q Consensus 86 ~~~GRglvAtrdI~~GevIl~E~P~~~~~~~~~~~~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a~~~H~~EC~~~w 165 (361)
+..|||++|+++|++|++|+.|.|++.+|.. ..|..|+.. ....|-.|....+|+..++...|..|.++|...-
T Consensus 22 ~~~Gr~~~a~~~i~~g~~i~~e~p~~~~p~~----~~~~~c~~~--~~~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 95 (482)
T KOG2084|consen 22 PELGRGLVATQAIEAGEVILEEEPLVVGPAS----KSCSRCLGC--SCDHCRRCLEAIECNKCQQRGWALCGKFACSADL 95 (482)
T ss_pred cccCcceeeecccCCCceEEecCcceeeecc----cCCcccccc--chhhhhcCCccHhhhhhhccCccccchhhcchhh
Confidence 5899999999999999999999999999988 455555554 2234555667777766665555556666654411
Q ss_pred HHhhHHHhhhcCchhHHHHHHHHHHHhcCCCHHHh--------hhcCCCCCChhhHhhHHHHHHHHHHHHHhcCCChHHH
Q 018070 166 SAFNDYCRSQGLKYPLLVKRLACMIISGAESADCI--------DILQPASLSPELILAMEEGFVMLRSAFKKAGIDDEQM 237 (361)
Q Consensus 166 ~~~~~~~~~~~~~~p~l~~Rl~~~~~~~~~~~~~l--------~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~ 237 (361)
............ .+ .++.............+ ..+.... .... .+...+............ .
T Consensus 96 ~~~~~~~~~~~~-~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~----~ 164 (482)
T KOG2084|consen 96 AKLECEPLKLVG-AP---EECLALSSLHEESREAIVLLSLLEECSLSAEK--PRLR-LDLSYLEHGATEDDQSHL----L 164 (482)
T ss_pred ccccccchhhcc-ch---HHHHHhhcCCccccchHHHHHHHHHhhhhccc--ccHh-HHHhhHHHHhhHHhhccc----c
Confidence 100000000000 00 00000000000000000 0000000 0000 000000000000000000 0
Q ss_pred hhhcHHHHHHHHhhhhccceeeeccCcchhHHhhhhhhhccccc--eeeEEEecccccccCCCCCCcEEEEecCCEEEEE
Q 018070 238 KFLNKQWYTNVLAQIRINAFRIELAGGLYEDLLSSAAASIESEI--AVGNAIYMLPSFYNHDCDPNAHIMWIDNADARLM 315 (361)
Q Consensus 238 ~~l~~~~~~~ll~~l~~Nsf~I~~~~~~~~~~~~~~~~~~~~~~--~~g~gLyp~~Sl~NHSC~PN~~~~f~~~~~l~vr 315 (361)
.....+....++..+..+++.+..... ... ..+.|+||..+++||||.||+...| ++....++
T Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~l~~~~~~~~hsC~pn~~~~~-~~~~~~~~ 229 (482)
T KOG2084|consen 165 LVLAADCISKLFPSLLCNSITNASSLR--------------VPEPLFLGRGLFPGSSLFNHSCFPNISVIF-DGRGLALL 229 (482)
T ss_pred chhHHHHHHHHHHHHHHhhhhhhhhhh--------------ccccccceeeecccchhcccCCCCCeEEEE-CCceeEEE
Confidence 011123333344444444443322100 011 4799999999999999999999888 77788888
Q ss_pred EccCCCCCC-eeeeeccCCCCCHHHHHHHHhCCCCeEEeccCCCCCC
Q 018070 316 ALRDVEEGE-ELRICYIDASMARDARQAILTQGFGFQCNCLRCSSGD 361 (361)
Q Consensus 316 A~rdI~~GE-EL~isY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~~d 361 (361)
+...+.+++ ||+++|++..+++..||..|+..|.|.|.|+||.+++
T Consensus 230 ~~~~~~~~~~~l~~~y~~~~~~~~~r~~~l~~~~~f~c~c~rc~d~~ 276 (482)
T KOG2084|consen 230 VPAGIDAGEEELTISYTDPLLSTASRQKQLRQSKLFSCQCPRCLDPT 276 (482)
T ss_pred eecccCCCCCEEEEeecccccCHHHHHHHHhhccceeeecCCCCCCC
Confidence 888888877 9999999999999999999999999999999999753
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=99.77 E-value=1.8e-18 Score=147.44 Aligned_cols=51 Identities=35% Similarity=0.575 Sum_probs=45.3
Q ss_pred ceeeEEEecccccccCCCCCCcEEEEe---cCCEEEEEEccCCCCCCeeeeecc
Q 018070 281 IAVGNAIYMLPSFYNHDCDPNAHIMWI---DNADARLMALRDVEEGEELRICYI 331 (361)
Q Consensus 281 ~~~g~gLyp~~Sl~NHSC~PN~~~~f~---~~~~l~vrA~rdI~~GEEL~isY~ 331 (361)
...+.+|||.++++||||.||+.+.++ ++..++++|.|||++||||||||+
T Consensus 109 ~~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~isYG 162 (162)
T PF00856_consen 109 DRDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFISYG 162 (162)
T ss_dssp EEEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEEST
T ss_pred cccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEEEC
Confidence 446899999999999999999999996 378999999999999999999997
No 3
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.54 E-value=1.4e-14 Score=117.46 Aligned_cols=45 Identities=38% Similarity=0.767 Sum_probs=40.1
Q ss_pred EEecccccccCCCCCCcEEEEec-CC--EEEEEEccCCCCCCeeeeec
Q 018070 286 AIYMLPSFYNHDCDPNAHIMWID-NA--DARLMALRDVEEGEELRICY 330 (361)
Q Consensus 286 gLyp~~Sl~NHSC~PN~~~~f~~-~~--~l~vrA~rdI~~GEEL~isY 330 (361)
.++|.++++||||.||+...+.. ++ .+.++|+|||++|||||++|
T Consensus 69 ~~~~~~~~iNHsc~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 69 RKGNIARFINHSCEPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred ccCcHHHeeCCCCCCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 48899999999999999988754 22 69999999999999999999
No 4
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.52 E-value=1.2e-06 Score=83.82 Aligned_cols=91 Identities=19% Similarity=0.172 Sum_probs=70.2
Q ss_pred hhcHHHHHHHHhhhhccceeeeccCcchhHHhhhhhhhccccceeeEEEecccccccCCCC-CCcEEEEecCCEEEEEEc
Q 018070 239 FLNKQWYTNVLAQIRINAFRIELAGGLYEDLLSSAAASIESEIAVGNAIYMLPSFYNHDCD-PNAHIMWIDNADARLMAL 317 (361)
Q Consensus 239 ~l~~~~~~~ll~~l~~Nsf~I~~~~~~~~~~~~~~~~~~~~~~~~g~gLyp~~Sl~NHSC~-PN~~~~f~~~~~l~vrA~ 317 (361)
.++-+.++.+.+.+..-+|.|....+.. +..-..+....|-.+-|.+.++||.=. -|+...+ +++.+.|+|.
T Consensus 173 ~~slEdF~y~~Al~laysfdve~~~s~~------~~eee~e~e~ngk~m~p~ad~lNhd~~k~nanl~y-~~NcL~mva~ 245 (466)
T KOG1338|consen 173 RPSLEDFMYAYALGLAYSFDVEFLLSLD------NLEEESEIECNGKLMTPIADFLNHDGLKANANLRY-EDNCLEMVAD 245 (466)
T ss_pred ccCHHHHHHHHHHHHHHheeeehhcchh------hhhhhhccccCcccccchhhhhccchhhcccceec-cCcceeeeec
Confidence 3566889999999999999987643211 011112345678899999999999987 7887788 5668999999
Q ss_pred cCCCCCCeeeeeccCCCCC
Q 018070 318 RDVEEGEELRICYIDASMA 336 (361)
Q Consensus 318 rdI~~GEEL~isY~d~~~~ 336 (361)
|+|++|+|++.+|+-..++
T Consensus 246 r~iekgdev~n~dg~~p~~ 264 (466)
T KOG1338|consen 246 RNIEKGDEVDNSDGLKPMG 264 (466)
T ss_pred CCCCCccccccccccCcch
Confidence 9999999999999865554
No 5
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=98.51 E-value=8.7e-08 Score=90.56 Aligned_cols=64 Identities=30% Similarity=0.649 Sum_probs=51.5
Q ss_pred EEecc-cccccCCCCCCcEEEEecCCEEEEEEccCCCCCCeeeeeccCCCCCHHHHHHHHhCCCCeEEeccCCCC
Q 018070 286 AIYML-PSFYNHDCDPNAHIMWIDNADARLMALRDVEEGEELRICYIDASMARDARQAILTQGFGFQCNCLRCSS 359 (361)
Q Consensus 286 gLyp~-~Sl~NHSC~PN~~~~f~~~~~l~vrA~rdI~~GEEL~isY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~ 359 (361)
-|+.. ++++||+|.|||.++-.++.++.|+++|||++|||||-=|++...+. .+ =.|.|.-|..
T Consensus 191 qLwLGPaafINHDCrpnCkFvs~g~~tacvkvlRDIePGeEITcFYgs~fFG~-------~N---~~CeC~TCER 255 (453)
T KOG2589|consen 191 QLWLGPAAFINHDCRPNCKFVSTGRDTACVKVLRDIEPGEEITCFYGSGFFGE-------NN---EECECVTCER 255 (453)
T ss_pred hheeccHHhhcCCCCCCceeecCCCceeeeehhhcCCCCceeEEeecccccCC-------CC---ceeEEeeccc
Confidence 34444 47899999999988874447999999999999999999999877662 22 3699988875
No 6
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=98.24 E-value=3.6e-07 Score=59.19 Aligned_cols=37 Identities=16% Similarity=0.413 Sum_probs=30.2
Q ss_pred cccccccccCCCCCCCCcCceecChhhhhhhccchhhhh
Q 018070 123 CYFCLRKITSSSQHFQHHNARFCGEVCKDNAKAFYDVER 161 (361)
Q Consensus 123 C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a~~~H~~EC 161 (361)
|.+|+++. ...|..|..+.|||++||+.+|..|+.+|
T Consensus 1 C~~C~~~~--~~~C~~C~~~~YCs~~Cq~~~w~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGKPA--LKRCSRCKSVYYCSEECQRADWPYHKFEC 37 (37)
T ss_dssp -TTTSSCS--SEEETTTSSSEESSHHHHHHHHHHHCCTH
T ss_pred CcCCCCCc--CCcCCCCCCEEecCHHHHHHHHHHHhhhC
Confidence 67788833 24667789999999999999999999887
No 7
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=98.08 E-value=1.9e-06 Score=87.70 Aligned_cols=71 Identities=30% Similarity=0.511 Sum_probs=58.2
Q ss_pred ccccccCCCCCCcEEEEecC---CEEEEEEccCCCCCCeeeeeccCCCCCHHHHHHHHhCCCCeEEeccCCCCC
Q 018070 290 LPSFYNHDCDPNAHIMWIDN---ADARLMALRDVEEGEELRICYIDASMARDARQAILTQGFGFQCNCLRCSSG 360 (361)
Q Consensus 290 ~~Sl~NHSC~PN~~~~f~~~---~~l~vrA~rdI~~GEEL~isY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~~ 360 (361)
.+.++||||.||+....... ..+...|+|||++||||++.|........++...+...++..|.|.+|...
T Consensus 405 ~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 405 VARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred ccceeecCCCCCcceecccccccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCC
Confidence 45689999999999886443 389999999999999999999987665444455666778999999999864
No 8
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=97.88 E-value=9.4e-06 Score=87.52 Aligned_cols=45 Identities=29% Similarity=0.524 Sum_probs=36.5
Q ss_pred ccccccCCCCCCcEEE--EecC-CEEEEEEccCCCCCCeeeeeccCCC
Q 018070 290 LPSFYNHDCDPNAHIM--WIDN-ADARLMALRDVEEGEELRICYIDAS 334 (361)
Q Consensus 290 ~~Sl~NHSC~PN~~~~--f~~~-~~l~vrA~rdI~~GEEL~isY~d~~ 334 (361)
.+.++||||.|||... -++| .++++.|.|+|++|||||..|--..
T Consensus 939 iAr~InHsC~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYkF~~ 986 (1005)
T KOG1080|consen 939 IARFINHSCNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYKFPT 986 (1005)
T ss_pred hhheeecccCCCceeeEEEecCeeEEEEEEecccccCceeeeeccccc
Confidence 4678999999999632 2233 4899999999999999999997544
No 9
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.84 E-value=1.5e-05 Score=81.33 Aligned_cols=45 Identities=31% Similarity=0.597 Sum_probs=35.2
Q ss_pred ccccCCCCCCcEE-EEecCC--EEEEEEccCCCCCCeeeeeccCCCCC
Q 018070 292 SFYNHDCDPNAHI-MWIDNA--DARLMALRDVEEGEELRICYIDASMA 336 (361)
Q Consensus 292 Sl~NHSC~PN~~~-~f~~~~--~l~vrA~rdI~~GEEL~isY~d~~~~ 336 (361)
=++||||+|||.+ .|..++ +|=+-|.|+|++|||||..|--...+
T Consensus 195 RFiNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~rYG 242 (729)
T KOG4442|consen 195 RFINHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFDRYG 242 (729)
T ss_pred HhhcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEeccccccc
Confidence 3789999999953 453333 66688999999999999999765544
No 10
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=97.60 E-value=4.4e-05 Score=77.56 Aligned_cols=95 Identities=23% Similarity=0.209 Sum_probs=67.9
Q ss_pred hcHHHHHHHHhhhhccceeeeccCcchhHHhhhhhhhccccceeeEEEecccccccCCCCCCcEEEEecCCEEEEEEccC
Q 018070 240 LNKQWYTNVLAQIRINAFRIELAGGLYEDLLSSAAASIESEIAVGNAIYMLPSFYNHDCDPNAHIMWIDNADARLMALRD 319 (361)
Q Consensus 240 l~~~~~~~ll~~l~~Nsf~I~~~~~~~~~~~~~~~~~~~~~~~~g~gLyp~~Sl~NHSC~PN~~~~f~~~~~l~vrA~rd 319 (361)
.+.+.+...+..+..++|.+....... ......-.++.|...++||++.+........+..+.+++.++
T Consensus 197 ~~~~~~~w~~~~~~sr~~~~~~~~~~~-----------~~~~~~~~~L~P~~D~~NH~~~~~~~~~~~~d~~~~l~~~~~ 265 (472)
T KOG1337|consen 197 FTFSAFKWAYSIVNSRAFYLPSLQRLT-----------AGDPDDNEALAPLIDLLNHSPEVIKAGYNQEDEAVELVAERD 265 (472)
T ss_pred cchHHHHHHHHHHhhhhhccccccccc-----------cCCCCcchhhhhhHHhhccCchhccccccCCCCcEEEEEeee
Confidence 445667777888888888766542100 001122358999999999999994444443355899999999
Q ss_pred CCCCCeeeeeccCCCCCHHHHHHHHhCCCCeE
Q 018070 320 VEEGEELRICYIDASMARDARQAILTQGFGFQ 351 (361)
Q Consensus 320 I~~GEEL~isY~d~~~~~~~Rr~~L~~~y~F~ 351 (361)
|++||||+|+|++..+. .|...|||.
T Consensus 266 v~~geevfi~YG~~~N~------eLL~~YGFv 291 (472)
T KOG1337|consen 266 VSAGEEVFINYGPKSNA------ELLLHYGFV 291 (472)
T ss_pred ecCCCeEEEecCCCchH------HHHHhcCCC
Confidence 99999999999995544 466789995
No 11
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=97.15 E-value=0.00028 Score=69.32 Aligned_cols=42 Identities=38% Similarity=0.578 Sum_probs=35.2
Q ss_pred cccCCCCCCcEEEEec-C------CEEEEEEccCCCCCCeeeeeccCCC
Q 018070 293 FYNHDCDPNAHIMWID-N------ADARLMALRDVEEGEELRICYIDAS 334 (361)
Q Consensus 293 l~NHSC~PN~~~~f~~-~------~~l~vrA~rdI~~GEEL~isY~d~~ 334 (361)
++||||.||+.+.... + -.+.+-|+++|++|+|||..|+...
T Consensus 275 finHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p~~ELT~dYg~~~ 323 (364)
T KOG1082|consen 275 FINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISPGEELTLDYGKAY 323 (364)
T ss_pred cccCCCCccceeeeeeecCCccchheeeeeeccccCCCcccchhhcccc
Confidence 7899999999876542 1 2788999999999999999999764
No 12
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=96.62 E-value=0.0014 Score=60.71 Aligned_cols=44 Identities=34% Similarity=0.407 Sum_probs=36.9
Q ss_pred cccccCCCCCCcEEEEe--c-CCEEEEEEccCCCCCCeeeeeccCCC
Q 018070 291 PSFYNHDCDPNAHIMWI--D-NADARLMALRDVEEGEELRICYIDAS 334 (361)
Q Consensus 291 ~Sl~NHSC~PN~~~~f~--~-~~~l~vrA~rdI~~GEEL~isY~d~~ 334 (361)
+-|+|||=.+|+..... + ...+++.|.|||.+||||+..|+|.+
T Consensus 334 GRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDRS 380 (392)
T KOG1085|consen 334 GRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDRS 380 (392)
T ss_pred hhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhccccc
Confidence 46899999999964332 2 35999999999999999999999965
No 13
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=96.40 E-value=0.0025 Score=68.05 Aligned_cols=41 Identities=44% Similarity=0.752 Sum_probs=33.3
Q ss_pred ccccCCCCCCcEE-EEecCC--EEEEEEccCCCCCCeeeeeccC
Q 018070 292 SFYNHDCDPNAHI-MWIDNA--DARLMALRDVEEGEELRICYID 332 (361)
Q Consensus 292 Sl~NHSC~PN~~~-~f~~~~--~l~vrA~rdI~~GEEL~isY~d 332 (361)
-++||||.|||.. .|.-++ ++.|.|+|||++||||+..|--
T Consensus 1252 RfinhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN~ 1295 (1306)
T KOG1083|consen 1252 RFINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYNF 1295 (1306)
T ss_pred cccccccCCCCccccccccceeeeeeeecCCCCCCceEEEeccc
Confidence 4679999999964 342243 8999999999999999999843
No 14
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=96.11 E-value=0.0038 Score=65.16 Aligned_cols=44 Identities=32% Similarity=0.562 Sum_probs=33.9
Q ss_pred cccccCCCCCCcEEE--EecCC-----EEEEEEccCCCCCCeeeeeccCCC
Q 018070 291 PSFYNHDCDPNAHIM--WIDNA-----DARLMALRDVEEGEELRICYIDAS 334 (361)
Q Consensus 291 ~Sl~NHSC~PN~~~~--f~~~~-----~l~vrA~rdI~~GEEL~isY~d~~ 334 (361)
+-++||||+||..+. |.+.. -+.+-|.+-|++|.|||..|....
T Consensus 1190 GRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~ 1240 (1262)
T KOG1141|consen 1190 GRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQ 1240 (1262)
T ss_pred hhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccc
Confidence 357899999999764 43321 355678899999999999998754
No 15
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=95.67 E-value=0.0028 Score=58.94 Aligned_cols=44 Identities=11% Similarity=0.117 Sum_probs=37.5
Q ss_pred ccccccccccccCCCCCCCCcCceecChhhhhhhccchhhhhhhh
Q 018070 120 NSVCYFCLRKITSSSQHFQHHNARFCGEVCKDNAKAFYDVERRAD 164 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a~~~H~~EC~~~ 164 (361)
..+|+.|..+-.. .+|..|+.+.||+++||+-.|..|+-.|..+
T Consensus 319 ~~fCstCG~~ga~-KrCs~CKav~YCdqeCQk~hWf~HKK~C~~L 362 (396)
T KOG1710|consen 319 CQFCSTCGHPGAK-KRCSQCKAVAYCDQECQKFHWFIHKKVCSFL 362 (396)
T ss_pred cccccccCCCCcc-chhhhhHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 3688888887654 7888999999999999999999999888754
No 16
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=94.40 E-value=0.038 Score=56.87 Aligned_cols=42 Identities=33% Similarity=0.497 Sum_probs=34.0
Q ss_pred ccccCCCCCCcEE--EEec-CCEEEEEEccCCCCCCeeeeeccCC
Q 018070 292 SFYNHDCDPNAHI--MWID-NADARLMALRDVEEGEELRICYIDA 333 (361)
Q Consensus 292 Sl~NHSC~PN~~~--~f~~-~~~l~vrA~rdI~~GEEL~isY~d~ 333 (361)
=+.|||=.|||.. .++. ..++-+.|.|.|.+|||||..|...
T Consensus 667 rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrYs 711 (739)
T KOG1079|consen 667 RFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRYS 711 (739)
T ss_pred hhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeeccC
Confidence 4679999999953 3323 3488899999999999999999863
No 17
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=91.94 E-value=0.26 Score=46.07 Aligned_cols=31 Identities=19% Similarity=0.307 Sum_probs=27.6
Q ss_pred CCeEEEeeCCCccEEEEcccCCCCCEEEecC
Q 018070 78 PPIQVALTESAGRGVFATRRIRASDLIHTAK 108 (361)
Q Consensus 78 ~~veV~~~~~~GRglvAtrdI~~GevIl~E~ 108 (361)
..+.+.+..+|||||+|++.|+.||-|+.-.
T Consensus 256 egl~~~~~dgKGRGv~a~~~F~rgdFVVEY~ 286 (392)
T KOG1085|consen 256 EGLLEVYKDGKGRGVRAKVNFERGDFVVEYR 286 (392)
T ss_pred cceeEEeeccccceeEeecccccCceEEEEe
Confidence 6788999999999999999999999887743
No 18
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=86.69 E-value=0.27 Score=49.82 Aligned_cols=52 Identities=33% Similarity=0.458 Sum_probs=40.2
Q ss_pred eeeEEEecccc-cccCCCCCCcEEEE---ecCCEEEEEEccCCCCCCeeeeeccCC
Q 018070 282 AVGNAIYMLPS-FYNHDCDPNAHIMW---IDNADARLMALRDVEEGEELRICYIDA 333 (361)
Q Consensus 282 ~~g~gLyp~~S-l~NHSC~PN~~~~f---~~~~~l~vrA~rdI~~GEEL~isY~d~ 333 (361)
.+..+-+...| +.||||.||+.-.- .....+.+.|.+.|+.|||+|.+|.-.
T Consensus 362 ~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t~~~n~~ 417 (463)
T KOG1081|consen 362 IIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELTFNYNGN 417 (463)
T ss_pred ccccccccchhhhhcccCCCceeechhheecccccccccccccccchhhhheeecc
Confidence 34456666665 67999999996432 124588999999999999999999754
No 19
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=81.16 E-value=0.71 Score=32.96 Aligned_cols=25 Identities=24% Similarity=0.728 Sum_probs=21.1
Q ss_pred cccccccccccCCCCCCCCcCceecChhhhhhh
Q 018070 121 SVCYFCLRKITSSSQHFQHHNARFCGEVCKDNA 153 (361)
Q Consensus 121 ~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a 153 (361)
.+|-.|.+++++ .-.|||++|++.-
T Consensus 4 kHC~~CG~~Ip~--------~~~fCS~~C~~~~ 28 (59)
T PF09889_consen 4 KHCPVCGKPIPP--------DESFCSPKCREEY 28 (59)
T ss_pred CcCCcCCCcCCc--------chhhhCHHHHHHH
Confidence 689999998886 4789999999863
No 20
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=79.40 E-value=0.9 Score=30.24 Aligned_cols=30 Identities=23% Similarity=0.678 Sum_probs=22.0
Q ss_pred ccccccccccccCCCCCCCCcCceecChhhhhhhc
Q 018070 120 NSVCYFCLRKITSSSQHFQHHNARFCGEVCKDNAK 154 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a~ 154 (361)
..+|-.|-+.+.+ +.-...|||++|+.++.
T Consensus 6 ~~yC~~Cdk~~~~-----~~~~~lYCSe~Cr~~D~ 35 (43)
T PF12855_consen 6 NDYCIVCDKQIDP-----PDDGSLYCSEECRLKDQ 35 (43)
T ss_pred hhHHHHhhccccC-----CCCCccccCHHHHhHhh
Confidence 3567777777643 34578999999998774
No 21
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=77.35 E-value=0.62 Score=47.15 Aligned_cols=37 Identities=22% Similarity=0.425 Sum_probs=26.9
Q ss_pred ccccccccccCCCCCCCCc-CceecChhhhhhhccchhhhhhh
Q 018070 122 VCYFCLRKITSSSQHFQHH-NARFCGEVCKDNAKAFYDVERRA 163 (361)
Q Consensus 122 ~C~~C~~~~~~~~~cc~c~-~~~yCS~~C~~~a~~~H~~EC~~ 163 (361)
=|.+|...-.- .|| ...|||-+||+..|..|+--|..
T Consensus 529 WC~nC~~EAiy-----~CCWNTSYCsveCQQ~HW~~H~ksCrr 566 (588)
T KOG3612|consen 529 WCYNCLDEAIY-----HCCWNTSYCSVECQQGHWPEHRKSCRR 566 (588)
T ss_pred HHHhhhHHHHH-----HhhccccccCcchhhccchhHhhhhcc
Confidence 45555554321 466 79999999999999888888864
No 22
>PLN03158 methionine aminopeptidase; Provisional
Probab=72.91 E-value=2.1 Score=42.67 Aligned_cols=39 Identities=21% Similarity=0.248 Sum_probs=27.3
Q ss_pred ccccccccccccCCCCCCCCc-------CceecChhhhhhhccchhhh
Q 018070 120 NSVCYFCLRKITSSSQHFQHH-------NARFCGEVCKDNAKAFYDVE 160 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c~-------~~~yCS~~C~~~a~~~H~~E 160 (361)
...|..|.++. ...|-.|. ...|||++|.+.+|..|+..
T Consensus 9 ~~~c~~c~~~a--~l~Cp~C~k~~~~~~~s~fCsq~CFk~~w~~Hk~~ 54 (396)
T PLN03158 9 PLACARCSKPA--HLQCPKCLELKLPREGASFCSQDCFKAAWSSHKSV 54 (396)
T ss_pred cccccCCCCcc--cccCccchhcCCCCCCceeECHHHHHHHHHHHHHH
Confidence 35688898753 24443331 37899999999999977543
No 23
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=68.46 E-value=4.8 Score=42.20 Aligned_cols=31 Identities=29% Similarity=0.351 Sum_probs=28.7
Q ss_pred CCCCeEEEeeCCCccEEEEcccCCCCCEEEe
Q 018070 76 SPPPIQVALTESAGRGVFATRRIRASDLIHT 106 (361)
Q Consensus 76 ~~~~veV~~~~~~GRglvAtrdI~~GevIl~ 106 (361)
..-+|+|-.++++|-||.|.+||++|+-|+.
T Consensus 118 qyA~vevF~Te~KG~GLRA~~dI~~g~FI~E 148 (729)
T KOG4442|consen 118 QYAKVEVFLTEKKGCGLRAEEDIPKGQFILE 148 (729)
T ss_pred ccCceeEEEecCcccceeeccccCCCcEEee
Confidence 4568999999999999999999999999987
No 24
>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=67.68 E-value=3.6 Score=29.01 Aligned_cols=15 Identities=47% Similarity=0.534 Sum_probs=11.6
Q ss_pred cEEEEcccCCCCCEE
Q 018070 90 RGVFATRRIRASDLI 104 (361)
Q Consensus 90 RglvAtrdI~~GevI 104 (361)
+-++|++||++|++|
T Consensus 2 ~vvVA~~di~~G~~i 16 (63)
T PF08666_consen 2 RVVVAARDIPAGTVI 16 (63)
T ss_dssp SEEEESSTB-TT-BE
T ss_pred cEEEEeCccCCCCEE
Confidence 468999999999998
No 25
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=65.52 E-value=9.2 Score=29.78 Aligned_cols=30 Identities=23% Similarity=0.417 Sum_probs=22.1
Q ss_pred CCCeEEEeeCCCc---cEEEEcccCCCCCEEEe
Q 018070 77 PPPIQVALTESAG---RGVFATRRIRASDLIHT 106 (361)
Q Consensus 77 ~~~veV~~~~~~G---RglvAtrdI~~GevIl~ 106 (361)
.+..++......| -.++|+|+|++||.|+.
T Consensus 82 ~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i 114 (116)
T smart00317 82 EPNCELLFVEVNGDSRIVIFALRDIKPGEELTI 114 (116)
T ss_pred CCCEEEEEEEECCCcEEEEEECCCcCCCCEEee
Confidence 3556666665554 46689999999998875
No 26
>TIGR02059 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803.
Probab=63.25 E-value=10 Score=30.03 Aligned_cols=25 Identities=28% Similarity=0.480 Sum_probs=22.5
Q ss_pred CEEEEEEccCCCCCCeeeeeccCCC
Q 018070 310 ADARLMALRDVEEGEELRICYIDAS 334 (361)
Q Consensus 310 ~~l~vrA~rdI~~GEEL~isY~d~~ 334 (361)
+++.|.-.++|..||+++++|.+..
T Consensus 75 ktVTLTL~~~V~~Gq~VTVsYt~ps 99 (101)
T TIGR02059 75 TTITLTLAQVVEDGDEVTLSYTKNS 99 (101)
T ss_pred cEEEEEecccccCCCEEEEEeeCCC
Confidence 3888999999999999999998864
No 27
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=62.22 E-value=4.5 Score=29.34 Aligned_cols=45 Identities=27% Similarity=0.589 Sum_probs=31.3
Q ss_pred cccccccccccCCC----CCCCCcCceecChhhhhhhccchhhhhhhhhH
Q 018070 121 SVCYFCLRKITSSS----QHFQHHNARFCGEVCKDNAKAFYDVERRADWS 166 (361)
Q Consensus 121 ~~C~~C~~~~~~~~----~cc~c~~~~yCS~~C~~~a~~~H~~EC~~~w~ 166 (361)
..|++|...+.+.. .--......|||..|.+ .-.+.+.-....|.
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k-~~~~~rnPRk~~WT 52 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK-LFKLGRNPRKLKWT 52 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEechhHHH-HHHccCCCccchhH
Confidence 57999999988742 34456789999999998 33344444455564
No 28
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=61.41 E-value=4 Score=29.01 Aligned_cols=34 Identities=26% Similarity=0.702 Sum_probs=24.6
Q ss_pred ccccccccccccCCC-CCCCCcCceecChhhhhhh
Q 018070 120 NSVCYFCLRKITSSS-QHFQHHNARFCGEVCKDNA 153 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~-~cc~c~~~~yCS~~C~~~a 153 (361)
...|..|-+++.... +.=-.....|||.+|+.+.
T Consensus 16 L~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~q 50 (58)
T PF04570_consen 16 LSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQ 50 (58)
T ss_pred HHHHHccCCCCCCCCCeeeeccccccccHHHHHHH
Confidence 478999999998532 2223456789999999863
No 29
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=60.94 E-value=3.5 Score=29.12 Aligned_cols=23 Identities=26% Similarity=0.764 Sum_probs=19.1
Q ss_pred cccccccccccCCCCCCCCcCceecChhhhh
Q 018070 121 SVCYFCLRKITSSSQHFQHHNARFCGEVCKD 151 (361)
Q Consensus 121 ~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~ 151 (361)
.+|--|.+.++. ...+||++|++
T Consensus 9 ~HC~VCg~aIp~--------de~~CSe~C~e 31 (64)
T COG4068 9 RHCVVCGKAIPP--------DEQVCSEECGE 31 (64)
T ss_pred ccccccCCcCCC--------ccchHHHHHHH
Confidence 688888888876 56799999996
No 30
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=55.51 E-value=8.8 Score=38.18 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=24.4
Q ss_pred cCCEEEEEEccCCCCCCeeeeeccCCC
Q 018070 308 DNADARLMALRDVEEGEELRICYIDAS 334 (361)
Q Consensus 308 ~~~~l~vrA~rdI~~GEEL~isY~d~~ 334 (361)
.+..+..+|+|+|++||||.+=|++..
T Consensus 120 ~~~~Ifyrt~r~I~p~eELlVWY~~e~ 146 (396)
T KOG2461|consen 120 IGENIFYRTIRDIRPNEELLVWYGSEY 146 (396)
T ss_pred ccCceEEEecccCCCCCeEEEEeccch
Confidence 567899999999999999999999864
No 31
>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=55.14 E-value=7.6 Score=27.27 Aligned_cols=17 Identities=24% Similarity=0.354 Sum_probs=12.5
Q ss_pred EEEEccCCCCCCeeeee
Q 018070 313 RLMALRDVEEGEELRIC 329 (361)
Q Consensus 313 ~vrA~rdI~~GEEL~is 329 (361)
+++|.+||++|+.|+-.
T Consensus 3 vvVA~~di~~G~~i~~~ 19 (63)
T PF08666_consen 3 VVVAARDIPAGTVITAE 19 (63)
T ss_dssp EEEESSTB-TT-BECTT
T ss_pred EEEEeCccCCCCEEccC
Confidence 68999999999998543
No 32
>TIGR03586 PseI pseudaminic acid synthase.
Probab=48.11 E-value=11 Score=36.43 Aligned_cols=21 Identities=10% Similarity=0.330 Sum_probs=18.6
Q ss_pred CccEEEEcccCCCCCEEEecC
Q 018070 88 AGRGVFATRRIRASDLIHTAK 108 (361)
Q Consensus 88 ~GRglvAtrdI~~GevIl~E~ 108 (361)
.+|+|||++||++||+|-.+.
T Consensus 274 ~rrsl~a~~di~~G~~it~~~ 294 (327)
T TIGR03586 274 FRRSLYVVKDIKKGETFTEEN 294 (327)
T ss_pred eeEEEEEccCcCCCCEecHHh
Confidence 479999999999999987765
No 33
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=46.60 E-value=9.6 Score=24.73 Aligned_cols=33 Identities=18% Similarity=0.645 Sum_probs=20.7
Q ss_pred ccccccccccccCCCC----CCCCcCceecChhhhhh
Q 018070 120 NSVCYFCLRKITSSSQ----HFQHHNARFCGEVCKDN 152 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~----cc~c~~~~yCS~~C~~~ 152 (361)
...|.+|-+.+..... --....-.|||+.|..+
T Consensus 6 ~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~~ 42 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLSS 42 (43)
T ss_dssp CEE-TTT--EEECCC----EE-TTTTSCCSSHHHHHH
T ss_pred CCcCcccCCcccCCCccccccccCcccChhCHHHHhh
Confidence 4689999998865331 22467789999999863
No 34
>TIGR03569 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine.
Probab=46.36 E-value=7.3 Score=37.77 Aligned_cols=23 Identities=13% Similarity=0.390 Sum_probs=19.3
Q ss_pred CCCccEEEEcccCCCCCEEEecC
Q 018070 86 ESAGRGVFATRRIRASDLIHTAK 108 (361)
Q Consensus 86 ~~~GRglvAtrdI~~GevIl~E~ 108 (361)
....|+|||++||++|++|-.+.
T Consensus 274 ~~~rrsl~a~~di~~G~~lt~~~ 296 (329)
T TIGR03569 274 DVARKSLVAAKDIKKGEIFTEDN 296 (329)
T ss_pred HhcceEEEEccCcCCCCEecHHh
Confidence 34479999999999999987765
No 35
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=45.92 E-value=12 Score=30.84 Aligned_cols=32 Identities=16% Similarity=0.327 Sum_probs=24.8
Q ss_pred cccccccccccCCC----CCCCCcCceecChhhhhh
Q 018070 121 SVCYFCLRKITSSS----QHFQHHNARFCGEVCKDN 152 (361)
Q Consensus 121 ~~C~~C~~~~~~~~----~cc~c~~~~yCS~~C~~~ 152 (361)
..|++|..++.+.. +.-.+....|||.+|.+.
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~ 40 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKN 40 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHH
Confidence 57999999988752 334578899999999753
No 36
>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=44.74 E-value=29 Score=28.21 Aligned_cols=29 Identities=28% Similarity=0.338 Sum_probs=21.6
Q ss_pred CCeEEEee---CCCccEEEEcccCCCCCEEEe
Q 018070 78 PPIQVALT---ESAGRGVFATRRIRASDLIHT 106 (361)
Q Consensus 78 ~~veV~~~---~~~GRglvAtrdI~~GevIl~ 106 (361)
+.+.+... .+..--++|+|+|++||-|+.
T Consensus 128 pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i 159 (162)
T PF00856_consen 128 PNCEVSFDFDGDGGCLVVRATRDIKKGEEIFI 159 (162)
T ss_dssp TSEEEEEEEETTTTEEEEEESS-B-TTSBEEE
T ss_pred cccceeeEeecccceEEEEECCccCCCCEEEE
Confidence 47788887 466677799999999998875
No 37
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.11 E-value=26 Score=24.65 Aligned_cols=42 Identities=10% Similarity=0.068 Sum_probs=28.8
Q ss_pred cccccccccCC--CCCCCCcCceecChhhhhhhccchhhhhhhh
Q 018070 123 CYFCLRKITSS--SQHFQHHNARFCGEVCKDNAKAFYDVERRAD 164 (361)
Q Consensus 123 C~~C~~~~~~~--~~cc~c~~~~yCS~~C~~~a~~~H~~EC~~~ 164 (361)
|..|....... ..|..|....|||++=.+.+..+|..-|..+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipthcS~ehw~~D~e~H~~~c~~L 45 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTHCSEEHWEDDYEEHRQLCERL 45 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCccCHHHHHHhHHHHHHHHHHH
Confidence 66666644332 4566688899999888777766777766543
No 38
>KOG2155 consensus Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=42.93 E-value=23 Score=35.51 Aligned_cols=61 Identities=21% Similarity=0.288 Sum_probs=46.5
Q ss_pred EEEecccccccCCCCCCcEEE---EecC--CEEEEEEccCCCCCCeeeeeccCCCCCHHHHHHHHh
Q 018070 285 NAIYMLPSFYNHDCDPNAHIM---WIDN--ADARLMALRDVEEGEELRICYIDASMARDARQAILT 345 (361)
Q Consensus 285 ~gLyp~~Sl~NHSC~PN~~~~---f~~~--~~l~vrA~rdI~~GEEL~isY~d~~~~~~~Rr~~L~ 345 (361)
.-+--.+|-+.||-.||..+. |-.. ..-.+..+|++.+|||++-.+....-..+.|...|.
T Consensus 199 YvMDefGsrvrHsdePnf~~aPf~fmPq~vaYsimwp~k~~~tgeE~trDfasg~~~p~~Rk~~l~ 264 (631)
T KOG2155|consen 199 YVMDEFGSRVRHSDEPNFRIAPFMFMPQNVAYSIMWPTKPVNTGEEITRDFASGVIHPEWRKYILQ 264 (631)
T ss_pred EEHhhhhhhhccCCCCcceeeeheecchhcceeEEeeccCCCCchHHHHHHhhcCCCHHHHHHHhc
Confidence 344556799999999999754 2111 256788999999999999988876667778887775
No 39
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=41.10 E-value=17 Score=25.39 Aligned_cols=17 Identities=35% Similarity=0.507 Sum_probs=13.8
Q ss_pred cEEEEcccCCCCCEEEe
Q 018070 90 RGVFATRRIRASDLIHT 106 (361)
Q Consensus 90 RglvAtrdI~~GevIl~ 106 (361)
+-++|+++|++|++|-.
T Consensus 2 ~v~va~~~i~~G~~i~~ 18 (64)
T smart00858 2 RVVVAARDLPAGEVITA 18 (64)
T ss_pred CEEEEeCccCCCCCcch
Confidence 45789999999998765
No 40
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=40.95 E-value=8.3 Score=25.44 Aligned_cols=33 Identities=18% Similarity=0.591 Sum_probs=19.6
Q ss_pred ccccccccccccCCCCCCCC-cCceecChhhhhh
Q 018070 120 NSVCYFCLRKITSSSQHFQH-HNARFCGEVCKDN 152 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c-~~~~yCS~~C~~~ 152 (361)
...|..|.+++.=...=-.+ -.+.|||+.|+..
T Consensus 8 ~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR~~ 41 (42)
T PF10013_consen 8 SKICPVCGRPFTWRKKWARCWDEVKYCSDRCRRR 41 (42)
T ss_pred CCcCcccCCcchHHHHHHHhchhhccHHHHhccC
Confidence 35677777776521100112 2589999999863
No 41
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=40.65 E-value=13 Score=23.90 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=20.7
Q ss_pred cccccccccCCCC--CCCCcCceecChhhhhh
Q 018070 123 CYFCLRKITSSSQ--HFQHHNARFCGEVCKDN 152 (361)
Q Consensus 123 C~~C~~~~~~~~~--cc~c~~~~yCS~~C~~~ 152 (361)
|++|.+.+.+..+ .-......||++.|.+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 7788888775422 22466788999999863
No 42
>PF00181 Ribosomal_L2: Ribosomal Proteins L2, RNA binding domain; InterPro: IPR022666 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YIT_A 1Q7Y_C 1YJN_A 3CPW_A 3I56_A 1VQ9_A 1M1K_C 3CC7_A 1YIJ_A 1K9M_C ....
Probab=40.57 E-value=21 Score=26.73 Aligned_cols=41 Identities=17% Similarity=0.242 Sum_probs=29.6
Q ss_pred ccCCCCCCCCCCCCeEEEeeCCCccEEEEcccCCCCCEEEe
Q 018070 66 ATHNGKPSQPSPPPIQVALTESAGRGVFATRRIRASDLIHT 106 (361)
Q Consensus 66 ~~~~~~~~~~~~~~veV~~~~~~GRglvAtrdI~~GevIl~ 106 (361)
+.+.+-|..+..+-..|++..+.-+.++|++.++.||+|.+
T Consensus 37 V~~i~~DP~Rsa~iAlV~~~~g~~~yiiA~eg~~vGd~I~s 77 (77)
T PF00181_consen 37 VIDIEYDPNRSAPIALVKYEDGEKRYIIAPEGMKVGDIIES 77 (77)
T ss_dssp EEEEEEETTTSSEEEEEEETTSEEEEEEEBTTEBTTEEEEE
T ss_pred EEEEEecCCcCccEEEEEecCCcEEEEEeECCCcCCCEEEC
Confidence 33444455566666666766767799999999999999863
No 43
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=38.52 E-value=19 Score=21.85 Aligned_cols=28 Identities=21% Similarity=0.586 Sum_probs=16.4
Q ss_pred cccccccccccCCCCCCCCcCceecChhhhh
Q 018070 121 SVCYFCLRKITSSSQHFQHHNARFCGEVCKD 151 (361)
Q Consensus 121 ~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~ 151 (361)
..|.-|.. .. .--|+.|+..|||-+|.+
T Consensus 3 ~~C~vC~~--~~-kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 3 KLCSVCGN--PA-KYRCPRCGARYCSLACYK 30 (30)
T ss_dssp EEETSSSS--EE-SEE-TTT--EESSHHHHH
T ss_pred CCCccCcC--CC-EEECCCcCCceeCcEeEC
Confidence 34666665 22 345678899999998863
No 44
>PRK00807 50S ribosomal protein L24e; Validated
Probab=38.17 E-value=16 Score=25.33 Aligned_cols=32 Identities=25% Similarity=0.596 Sum_probs=23.8
Q ss_pred cccccccccccCCC----CCCCCcCceecChhhhhh
Q 018070 121 SVCYFCLRKITSSS----QHFQHHNARFCGEVCKDN 152 (361)
Q Consensus 121 ~~C~~C~~~~~~~~----~cc~c~~~~yCS~~C~~~ 152 (361)
..|++|...+.+.. .--......|||..|++.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~ 37 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKN 37 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHH
Confidence 36899988888542 234577899999999864
No 45
>PRK01343 zinc-binding protein; Provisional
Probab=37.62 E-value=26 Score=24.78 Aligned_cols=27 Identities=30% Similarity=0.568 Sum_probs=20.0
Q ss_pred ccccccccccccCCCCCCCCcCceecChhhhhhh
Q 018070 120 NSVCYFCLRKITSSSQHFQHHNARFCGEVCKDNA 153 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a 153 (361)
...|-.|-++... -...|||+.|+.-+
T Consensus 9 ~~~CP~C~k~~~~-------~~rPFCS~RC~~iD 35 (57)
T PRK01343 9 TRPCPECGKPSTR-------EAYPFCSERCRDID 35 (57)
T ss_pred CCcCCCCCCcCcC-------CCCcccCHHHhhhh
Confidence 4567788777543 35689999999865
No 46
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=36.02 E-value=22 Score=34.35 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=21.0
Q ss_pred CCccEEEEcccCCCCCEEEecCCeEeec
Q 018070 87 SAGRGVFATRRIRASDLIHTAKPIITHP 114 (361)
Q Consensus 87 ~~GRglvAtrdI~~GevIl~E~P~~~~~ 114 (361)
..-|+|||++||++||++-.|.-.+.-|
T Consensus 287 ~~~Rsl~~~kdikkGe~ls~~Nl~~~RP 314 (347)
T COG2089 287 FARRSLVATKDIKKGEILSEDNLKVLRP 314 (347)
T ss_pred HHhhheeeecccccCccccccceEEeCC
Confidence 4569999999999999866655444433
No 47
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=34.82 E-value=29 Score=36.54 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=22.5
Q ss_pred cccccccccccCCCCCCCCcCceecChhhhhhhccchhh
Q 018070 121 SVCYFCLRKITSSSQHFQHHNARFCGEVCKDNAKAFYDV 159 (361)
Q Consensus 121 ~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~a~~~H~~ 159 (361)
.-|-.|++.-.+ --...|||++|.+.+|..|+.
T Consensus 75 lqCp~C~k~~~~------~~~s~fCsq~CFk~~w~~Hk~ 107 (606)
T PLN03144 75 LQCVGCVKAKLP------VSKSYHCSPKCFSDAWRHHRV 107 (606)
T ss_pred ccCccchhcCCC------cCcceeeCHHHHHHHHHHHHH
Confidence 455555554431 113689999999999997765
No 48
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=34.05 E-value=0.48 Score=47.56 Aligned_cols=77 Identities=32% Similarity=0.571 Sum_probs=60.4
Q ss_pred eeEEEeccccccc--CCCCCCcEEEEecC---CEEEEEEccCCCCCCeeeeeccCCCCCHHHH---HHHHhCCCCeEEec
Q 018070 283 VGNAIYMLPSFYN--HDCDPNAHIMWIDN---ADARLMALRDVEEGEELRICYIDASMARDAR---QAILTQGFGFQCNC 354 (361)
Q Consensus 283 ~g~gLyp~~Sl~N--HSC~PN~~~~f~~~---~~l~vrA~rdI~~GEEL~isY~d~~~~~~~R---r~~L~~~y~F~C~C 354 (361)
.+.++++..++++ |+|.||........ ....+.+.+++.+|++.++.|.+..+....| ...+...+.+.|.|
T Consensus 365 ~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 444 (482)
T KOG2084|consen 365 KLHLLFILGSLLGAFLSCSPNAELERLLNLFECRELLKALRDVKPGEEPLIAYLDYELGKLARELREKVLAEDALKDCKC 444 (482)
T ss_pred HHHHHHHHHHHHhhhhccchhhHHHHHHHhhhhhHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHHHhhhcCcchhHH
Confidence 4567889999998 99999998765322 2677889999999999999999976655444 45677789999999
Q ss_pred cCCCC
Q 018070 355 LRCSS 359 (361)
Q Consensus 355 ~rC~~ 359 (361)
..|..
T Consensus 445 ~~~~~ 449 (482)
T KOG2084|consen 445 IMCLA 449 (482)
T ss_pred HHHHH
Confidence 87753
No 49
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=32.12 E-value=19 Score=30.31 Aligned_cols=30 Identities=17% Similarity=0.468 Sum_probs=23.2
Q ss_pred ccccccccccccCCCCCCCCcCceecChhhhhh
Q 018070 120 NSVCYFCLRKITSSSQHFQHHNARFCGEVCKDN 152 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~ 152 (361)
...|+-|. . ...-+|..|+..|||..|...
T Consensus 118 r~fCaVCG--~-~S~ysC~~CG~kyCsv~C~~~ 147 (156)
T KOG3362|consen 118 RKFCAVCG--Y-DSKYSCVNCGTKYCSVRCLKT 147 (156)
T ss_pred chhhhhcC--C-CchhHHHhcCCceeechhhhh
Confidence 46888888 2 235678889999999999873
No 50
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=29.54 E-value=28 Score=23.21 Aligned_cols=15 Identities=33% Similarity=0.751 Sum_probs=12.4
Q ss_pred CCcCceecChhhhhh
Q 018070 138 QHHNARFCGEVCKDN 152 (361)
Q Consensus 138 ~c~~~~yCS~~C~~~ 152 (361)
....+.|||+.|++.
T Consensus 21 ~G~~Y~FCS~~C~~~ 35 (47)
T PF04945_consen 21 NGRTYYFCSEGCKEK 35 (47)
T ss_dssp TTEEEEESSHHHHHH
T ss_pred CCEEEEEcCHHHHHH
Confidence 456799999999974
No 51
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=26.08 E-value=34 Score=28.79 Aligned_cols=31 Identities=16% Similarity=0.450 Sum_probs=22.9
Q ss_pred ccccccccccccCCCCCCCCcCceecChhhhhh
Q 018070 120 NSVCYFCLRKITSSSQHFQHHNARFCGEVCKDN 152 (361)
Q Consensus 120 ~~~C~~C~~~~~~~~~cc~c~~~~yCS~~C~~~ 152 (361)
...|.-|++... .-.|+.|.++|||-.|.+.
T Consensus 5 t~tC~ic~e~~~--KYKCpkC~vPYCSl~CfKi 35 (157)
T KOG2857|consen 5 TTTCVICLESEI--KYKCPKCSVPYCSLPCFKI 35 (157)
T ss_pred eeeehhhhcchh--hccCCCCCCccccchhhhh
Confidence 356777877542 3457889999999999874
No 52
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=25.86 E-value=87 Score=30.75 Aligned_cols=31 Identities=23% Similarity=0.219 Sum_probs=28.5
Q ss_pred CCCCeEEEeeCCCccEEEEcccCCCCCEEEe
Q 018070 76 SPPPIQVALTESAGRGVFATRRIRASDLIHT 106 (361)
Q Consensus 76 ~~~~veV~~~~~~GRglvAtrdI~~GevIl~ 106 (361)
...+++|-.++.+|-||.+...|++|+-|..
T Consensus 174 ~~~~leIfrt~~kGwgvRs~~~I~~G~fvcE 204 (364)
T KOG1082|consen 174 LQFHLEVFRTPEKGWGVRTLDPIPAGEFVCE 204 (364)
T ss_pred cccceEEEecCCceeeecccccccCCCeeEE
Confidence 5679999999999999999999999998876
No 53
>PF08189 Meleagrin: Meleagrin/Cygnin family; InterPro: IPR012573 This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contain three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown [].
Probab=23.88 E-value=30 Score=22.01 Aligned_cols=19 Identities=21% Similarity=0.499 Sum_probs=13.7
Q ss_pred CcCceecChhhhhhh-ccch
Q 018070 139 HHNARFCGEVCKDNA-KAFY 157 (361)
Q Consensus 139 c~~~~yCS~~C~~~a-~~~H 157 (361)
|-.+-|||..|.+.+ |.+|
T Consensus 6 cpkiGYCS~~CsKt~vWa~s 25 (39)
T PF08189_consen 6 CPKIGYCSSKCSKTDVWAFS 25 (39)
T ss_pred Ccccceecccccccceeeec
Confidence 445779999999865 6544
No 54
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=23.30 E-value=43 Score=23.44 Aligned_cols=32 Identities=31% Similarity=0.594 Sum_probs=24.3
Q ss_pred cccccccccccCCC----CCCCCcCceecChhhhhh
Q 018070 121 SVCYFCLRKITSSS----QHFQHHNARFCGEVCKDN 152 (361)
Q Consensus 121 ~~C~~C~~~~~~~~----~cc~c~~~~yCS~~C~~~ 152 (361)
..|++|...+.+.. +--......|||..|.+.
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~ 39 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKN 39 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHHHH
Confidence 57999988887642 334577899999999764
No 55
>PF14353 CpXC: CpXC protein
Probab=22.29 E-value=1.1e+02 Score=24.89 Aligned_cols=31 Identities=26% Similarity=0.455 Sum_probs=24.5
Q ss_pred eeccCCCCCHHHHHHHHhCCCCeEEeccCCCC
Q 018070 328 ICYIDASMARDARQAILTQGFGFQCNCLRCSS 359 (361)
Q Consensus 328 isY~d~~~~~~~Rr~~L~~~y~F~C~C~rC~~ 359 (361)
.+.++.....+-|.+.|. .-.|.-.|+.|-.
T Consensus 16 ~~~I~~~~~p~l~e~il~-g~l~~~~CP~Cg~ 46 (128)
T PF14353_consen 16 WTSINADEDPELKEKILD-GSLFSFTCPSCGH 46 (128)
T ss_pred EeEEcCcCCHHHHHHHHc-CCcCEEECCCCCC
Confidence 356777788888999885 4569999999965
No 56
>smart00746 TRASH metallochaperone-like domain.
Probab=22.16 E-value=54 Score=18.99 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=10.6
Q ss_pred CcCceecChhhhhh
Q 018070 139 HHNARFCGEVCKDN 152 (361)
Q Consensus 139 c~~~~yCS~~C~~~ 152 (361)
.....|||..|..+
T Consensus 21 g~~~~FCs~~c~~~ 34 (39)
T smart00746 21 GKVFYFCSSKCLSK 34 (39)
T ss_pred CEEEEEeCHHHHHH
Confidence 45678999988864
Done!