Query 018176
Match_columns 360
No_of_seqs 64 out of 66
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 06:47:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018176.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018176hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00086 homeodomain Homeodomai 97.9 2.1E-05 4.5E-10 56.1 4.3 42 1-54 15-56 (59)
2 smart00389 HOX Homeodomain. DN 97.8 3.1E-05 6.7E-10 55.1 3.8 41 1-53 15-55 (56)
3 PF00046 Homeobox: Homeobox do 97.7 5.1E-05 1.1E-09 54.8 3.6 42 1-54 15-56 (57)
4 KOG0842 Transcription factor t 96.1 0.0015 3.3E-08 64.4 0.0 28 33-60 188-215 (307)
5 PF11717 Tudor-knot: RNA bindi 95.6 0.0092 2E-07 44.4 2.3 40 130-171 12-51 (55)
6 PF15057 DUF4537: Domain of un 94.6 0.24 5.2E-06 42.6 8.5 108 126-251 6-113 (124)
7 KOG0775 Transcription factor S 93.6 0.22 4.7E-06 49.4 7.2 38 9-56 197-234 (304)
8 KOG0850 Transcription factor D 93.6 0.032 7E-07 53.8 1.4 37 18-54 134-178 (245)
9 PF05920 Homeobox_KN: Homeobox 93.6 0.076 1.6E-06 38.0 2.9 38 4-51 2-39 (40)
10 COG5576 Homeodomain-containing 91.7 0.16 3.4E-06 45.8 3.1 39 11-59 74-112 (156)
11 KOG2251 Homeobox transcription 91.7 0.11 2.5E-06 49.7 2.3 40 1-52 52-91 (228)
12 cd00024 CHROMO Chromatin organ 91.4 0.13 2.9E-06 36.3 1.9 37 135-171 3-40 (55)
13 KOG0485 Transcription factor N 90.6 0.085 1.8E-06 51.0 0.3 44 13-56 111-162 (268)
14 smart00333 TUDOR Tudor domain. 90.5 0.82 1.8E-05 32.8 5.3 54 188-252 2-55 (57)
15 PLN00104 MYST -like histone ac 90.1 1.4 3E-05 46.0 8.5 54 124-179 60-116 (450)
16 KOG0483 Transcription factor H 90.0 0.23 5E-06 46.5 2.6 36 12-57 74-109 (198)
17 KOG0488 Transcription factor B 89.6 0.24 5.1E-06 48.8 2.5 25 19-53 203-227 (309)
18 KOG0491 Transcription factor B 88.8 0.23 5E-06 46.4 1.7 34 12-55 124-157 (194)
19 KOG0843 Transcription factor E 88.4 0.4 8.7E-06 45.2 3.0 46 13-58 109-162 (197)
20 KOG0489 Transcription factor z 87.9 0.28 6.1E-06 46.7 1.7 22 36-57 197-218 (261)
21 smart00298 CHROMO Chromatin or 86.9 0.5 1.1E-05 33.1 2.1 37 135-171 2-38 (55)
22 PF00385 Chromo: Chromo (CHRro 85.5 0.3 6.4E-06 35.2 0.4 37 135-171 1-39 (55)
23 smart00743 Agenet Tudor-like d 84.9 2.7 5.8E-05 30.9 5.2 50 188-247 2-53 (61)
24 cd04508 TUDOR Tudor domains ar 84.5 0.89 1.9E-05 31.6 2.4 36 125-165 5-40 (48)
25 KOG0487 Transcription factor A 84.3 0.3 6.6E-06 48.5 -0.0 35 10-54 257-291 (308)
26 PF06003 SMN: Survival motor n 83.3 2.5 5.4E-05 40.7 5.6 56 187-251 67-122 (264)
27 smart00561 MBT Present in Dros 83.2 1.3 2.8E-05 36.7 3.3 45 122-171 32-76 (96)
28 KOG0492 Transcription factor M 81.7 0.51 1.1E-05 45.5 0.3 20 33-52 179-198 (246)
29 PF12148 DUF3590: Protein of u 79.8 2.8 6E-05 35.1 4.0 48 204-252 9-56 (85)
30 PF02820 MBT: mbt repeat; Int 79.4 1.9 4.2E-05 33.4 2.9 45 122-171 1-45 (73)
31 PF05641 Agenet: Agenet domain 79.3 5.6 0.00012 30.5 5.3 43 189-239 1-44 (68)
32 TIGR01565 homeo_ZF_HD homeobox 78.6 1.1 2.4E-05 34.6 1.2 41 1-51 16-58 (58)
33 KOG0848 Transcription factor C 77.9 0.97 2.1E-05 45.0 1.0 21 34-54 235-255 (317)
34 PF11717 Tudor-knot: RNA bindi 77.6 4.2 9.2E-05 30.2 4.1 38 189-234 1-38 (55)
35 PF12148 DUF3590: Protein of u 77.2 2.9 6.2E-05 35.0 3.4 70 125-197 3-74 (85)
36 KOG0484 Transcription factor P 77.1 1.2 2.7E-05 39.2 1.2 20 33-52 52-71 (125)
37 smart00333 TUDOR Tudor domain. 71.1 4.6 0.0001 28.8 2.8 43 125-176 10-52 (57)
38 KOG0847 Transcription factor, 67.0 4.7 0.0001 39.5 2.7 46 13-58 174-227 (288)
39 PF05641 Agenet: Agenet domain 66.0 3.9 8.5E-05 31.4 1.7 41 131-177 17-63 (68)
40 KOG0493 Transcription factor E 65.8 5.5 0.00012 39.9 3.0 45 13-57 253-305 (342)
41 KOG0490 Transcription factor, 64.8 4.2 9.1E-05 36.0 1.9 24 34-57 96-119 (235)
42 cd04508 TUDOR Tudor domains ar 62.2 20 0.00043 24.8 4.5 45 192-246 1-45 (48)
43 KOG0774 Transcription factor P 61.9 15 0.00033 36.9 5.2 41 3-53 206-246 (334)
44 PF06003 SMN: Survival motor n 60.3 7.5 0.00016 37.5 2.8 43 123-169 74-116 (264)
45 smart00743 Agenet Tudor-like d 58.4 9.9 0.00021 27.9 2.6 34 125-163 10-45 (61)
46 KOG0494 Transcription factor C 55.8 9.1 0.0002 38.4 2.6 22 33-54 176-197 (332)
47 KOG4577 Transcription factor L 55.6 8.4 0.00018 39.1 2.3 39 14-52 175-221 (383)
48 PF00567 TUDOR: Tudor domain; 44.8 19 0.00041 27.8 2.3 52 128-187 62-118 (121)
49 PF11523 DUF3223: Protein of u 39.7 31 0.00067 27.7 2.9 33 212-246 41-74 (76)
50 PF11569 Homez: Homeodomain le 34.7 21 0.00045 27.9 1.1 31 12-52 22-52 (56)
51 PF12824 MRP-L20: Mitochondria 32.0 32 0.0007 31.4 2.1 48 7-54 96-143 (164)
52 PLN00104 MYST -like histone ac 29.4 1.2E+02 0.0027 32.1 6.0 58 187-247 52-111 (450)
53 PTZ00064 histone acetyltransfe 28.7 43 0.00093 36.2 2.6 39 148-188 146-184 (552)
54 COG3458 Acetyl esterase (deace 24.8 1E+02 0.0022 31.5 4.2 94 118-218 55-163 (321)
55 PRK04980 hypothetical protein; 24.8 1.3E+02 0.0028 25.9 4.3 33 188-221 31-63 (102)
56 KOG1911 Heterochromatin-associ 23.8 54 0.0012 31.3 2.1 40 130-170 44-83 (270)
57 PF05506 DUF756: Domain of unk 22.7 88 0.0019 24.8 2.8 23 129-159 66-88 (89)
58 KOG2252 CCAAT displacement pro 21.9 1.7E+02 0.0037 32.0 5.5 42 3-56 437-478 (558)
59 PF15057 DUF4537: Domain of un 20.3 2E+02 0.0043 24.9 4.6 38 192-239 1-38 (124)
No 1
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=97.86 E-value=2.1e-05 Score=56.09 Aligned_cols=42 Identities=38% Similarity=0.605 Sum_probs=36.6
Q ss_pred ChhhhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhh
Q 018176 1 MEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 1 ME~~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~ 54 (360)
||+.|.. +..|+.+-++.||+..+ |+-+||.+||+|||...+
T Consensus 15 Le~~f~~--~~~P~~~~~~~la~~~~----------l~~~qV~~WF~nrR~~~~ 56 (59)
T cd00086 15 LEKEFEK--NPYPSREEREELAKELG----------LTERQVKIWFQNRRAKLK 56 (59)
T ss_pred HHHHHHh--CCCCCHHHHHHHHHHHC----------cCHHHHHHHHHHHHHHHh
Confidence 5677777 67999999999999987 888999999999988754
No 2
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=97.76 E-value=3.1e-05 Score=55.12 Aligned_cols=41 Identities=46% Similarity=0.561 Sum_probs=33.5
Q ss_pred ChhhhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhh
Q 018176 1 MEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAI 53 (360)
Q Consensus 1 ME~~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~ 53 (360)
||..|.. +..|+.+-++.||+..+.+ .+||++||+|||+..
T Consensus 15 L~~~f~~--~~~P~~~~~~~la~~~~l~----------~~qV~~WF~nrR~~~ 55 (56)
T smart00389 15 LEKEFQK--NPYPSREEREELAAKLGLS----------ERQVKVWFQNRRAKW 55 (56)
T ss_pred HHHHHHh--CCCCCHHHHHHHHHHHCcC----------HHHHHHhHHHHhhcc
Confidence 3455554 3489999999999999876 899999999998753
No 3
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=97.65 E-value=5.1e-05 Score=54.80 Aligned_cols=42 Identities=43% Similarity=0.616 Sum_probs=35.6
Q ss_pred ChhhhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhh
Q 018176 1 MEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 1 ME~~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~ 54 (360)
||.+++. +..|+.+-++.||..+ .|.-.||.+||||||...+
T Consensus 15 L~~~f~~--~~~p~~~~~~~la~~l----------~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 15 LEEYFQE--NPYPSKEEREELAKEL----------GLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp HHHHHHH--SSSCHHHHHHHHHHHH----------TSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH--hccccccccccccccc----------cccccccccCHHHhHHHhC
Confidence 5677775 7899999999999998 5678999999999987643
No 4
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=96.10 E-value=0.0015 Score=64.36 Aligned_cols=28 Identities=32% Similarity=0.561 Sum_probs=22.5
Q ss_pred CCcccchhhHHHHHhhhhhhhhhcccCC
Q 018176 33 GKIMVQMKQVWNWFQNRRYAIRAKSIKS 60 (360)
Q Consensus 33 GK~~Vq~kQV~~WFQnrr~~~~~k~~~~ 60 (360)
-++-++.+||..|||||||..|.+-.-.
T Consensus 188 ~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 188 SSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred HhcCCCchheeeeeecchhhhhhhhhhh
Confidence 5677899999999999999976555433
No 5
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=95.56 E-value=0.0092 Score=44.38 Aligned_cols=40 Identities=33% Similarity=0.770 Sum_probs=32.5
Q ss_pred CCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccccc
Q 018176 130 RDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 171 (360)
Q Consensus 130 ~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk 171 (360)
++|.||...+.-. |. ..|+.+..|+|.||..-.||||+..
T Consensus 12 ~~~~~y~A~I~~~-r~-~~~~~~YyVHY~g~nkR~DeWV~~~ 51 (55)
T PF11717_consen 12 KDGQWYEAKILDI-RE-KNGEPEYYVHYQGWNKRLDEWVPES 51 (55)
T ss_dssp TTTEEEEEEEEEE-EE-CTTCEEEEEEETTSTGCC-EEEETT
T ss_pred CCCcEEEEEEEEE-Ee-cCCCEEEEEEcCCCCCCceeeecHH
Confidence 4899999887633 32 6778999999999999999999865
No 6
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=94.58 E-value=0.24 Score=42.63 Aligned_cols=108 Identities=19% Similarity=0.233 Sum_probs=69.4
Q ss_pred eeccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccccccccccCCCcccccccccccCCceEEEeeecCCcc
Q 018176 126 AKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQA 205 (360)
Q Consensus 126 AkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk~rvR~RSiPlE~sEC~~V~pGdlVcCf~eg~d~a 205 (360)
|++.+||-+|--.+- +. + ....+.|.| ...+-+.+... -=|++.+..|+.|++||.||+-.+.. +.
T Consensus 6 AR~~~DG~YY~GtV~-~~--~--~~~~~lV~f---~~~~~~~v~~~-----~iI~~~~~~~~~L~~GD~VLA~~~~~-~~ 71 (124)
T PF15057_consen 6 ARREEDGFYYPGTVK-KC--V--SSGQFLVEF---DDGDTQEVPIS-----DIIALSDAMRHSLQVGDKVLAPWEPD-DC 71 (124)
T ss_pred EeeCCCCcEEeEEEE-Ec--c--CCCEEEEEE---CCCCEEEeChH-----HeEEccCcccCcCCCCCEEEEecCcC-CC
Confidence 778889988865432 22 2 346799999 33333333332 23577888899999999999886655 55
Q ss_pred eEeeEEEeeeeecccCCCCcceEEEEEEecCCccccccCcceeecc
Q 018176 206 LYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRP 251 (360)
Q Consensus 206 lyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpsee~V~l~kvC~rP 251 (360)
.|+-|.|+..-.++ ....=.++|.|-.+. ...|+...+.-.|
T Consensus 72 ~Y~Pg~V~~~~~~~---~~~~~~~~V~f~ng~-~~~vp~~~~~~I~ 113 (124)
T PF15057_consen 72 RYGPGTVIAGPERR---ASEDKEYTVRFYNGK-TAKVPRGEVIWIS 113 (124)
T ss_pred EEeCEEEEECcccc---ccCCceEEEEEECCC-CCccchhhEEECC
Confidence 69999999876665 323335666666554 4445554444443
No 7
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=93.65 E-value=0.22 Score=49.36 Aligned_cols=38 Identities=42% Similarity=0.532 Sum_probs=31.2
Q ss_pred cCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhhhc
Q 018176 9 HNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAK 56 (360)
Q Consensus 9 ~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~~k 56 (360)
.+..|.++--..||+. .-++.+||-|||.|||+.-|+-
T Consensus 197 ~~~YPsp~eKReLA~a----------TgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 197 QNPYPSPREKRELAEA----------TGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred cCCCCChHHHHHHHHH----------hCCchhhhhhhhhhhhhhhhhc
Confidence 5688999888999986 4467899999999999876643
No 8
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=93.59 E-value=0.032 Score=53.78 Aligned_cols=37 Identities=41% Similarity=0.644 Sum_probs=27.8
Q ss_pred HHHHHHHhc-----CCCCCC---CCcccchhhHHHHHhhhhhhhh
Q 018176 18 LVALAEKFS-----ESPERK---GKIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 18 ~q~LAe~Fs-----~S~~Ra---GK~~Vq~kQV~~WFQnrr~~~~ 54 (360)
+|.|-.+|- +=|+|+ -.+-++-+||..||||||...|
T Consensus 134 LqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~K 178 (245)
T KOG0850|consen 134 LQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFK 178 (245)
T ss_pred HHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHH
Confidence 566666665 346665 5677899999999999998765
No 9
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=93.55 E-value=0.076 Score=37.96 Aligned_cols=38 Identities=39% Similarity=0.564 Sum_probs=30.0
Q ss_pred hhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhh
Q 018176 4 ILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRY 51 (360)
Q Consensus 4 ~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~ 51 (360)
++++..+-.|+++..+.||..-+. +-+||.+||-|.|.
T Consensus 2 l~~h~~nPYPs~~ek~~L~~~tgl----------s~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 2 LLEHLHNPYPSKEEKEELAKQTGL----------SRKQISNWFINARR 39 (40)
T ss_dssp HHHTTTSGS--HHHHHHHHHHHTS-----------HHHHHHHHHHHHH
T ss_pred HHHHCCCCCCCHHHHHHHHHHcCC----------CHHHHHHHHHHhHc
Confidence 577888899999999999998754 56799999999874
No 10
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=91.70 E-value=0.16 Score=45.79 Aligned_cols=39 Identities=28% Similarity=0.364 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhhhcccC
Q 018176 11 AMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIK 59 (360)
Q Consensus 11 ~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~~k~~~ 59 (360)
-.|+..--++|+..-| +..|-|+-||||||...+.+...
T Consensus 74 p~Ps~~~r~~L~~~ln----------m~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 74 PYPSSITRIKLSLLLN----------MPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCCHHHHHHHHHhcC----------CChhhhhhhhchHHHHHHHhccc
Confidence 4566677777777665 67789999999999998766653
No 11
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=91.66 E-value=0.11 Score=49.69 Aligned_cols=40 Identities=30% Similarity=0.475 Sum_probs=33.4
Q ss_pred ChhhhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhh
Q 018176 1 MEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYA 52 (360)
Q Consensus 1 ME~~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~ 52 (360)
+|+|+++ .+.|+...-++||.+.|.--.| |+.||+|||-.
T Consensus 52 Le~LF~k--TqYPDv~~rEelAlklnLpeSr----------VqVWFKNRRAK 91 (228)
T KOG2251|consen 52 LEALFAK--TQYPDVFMREELALKLNLPESR----------VQVWFKNRRAK 91 (228)
T ss_pred HHHHHHh--hcCccHHHHHHHHHHhCCchhh----------hhhhhccccch
Confidence 3666665 4679999999999999987776 89999999866
No 12
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=91.42 E-value=0.13 Score=36.28 Aligned_cols=37 Identities=27% Similarity=0.548 Sum_probs=29.1
Q ss_pred eehhhhhhccccCC-CCCeEEEEecCCCcCcccccccc
Q 018176 135 YDVSAFLAQRNFDT-ADPEVQVRFAGFGAEEDEWVNIK 171 (360)
Q Consensus 135 YDV~~fL~~r~l~t-Ge~evrVrF~gFg~EeDEWvnvk 171 (360)
|.|.-.|.+|.... |..++.|++.|++..+++|....
T Consensus 3 ~~ve~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~~ 40 (55)
T cd00024 3 YEVEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEE 40 (55)
T ss_pred ceEeeeeeeeecCCCCcEEEEEEECCCCCccCccccHH
Confidence 44555677775544 78999999999999999998764
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=90.61 E-value=0.085 Score=51.03 Aligned_cols=44 Identities=36% Similarity=0.533 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhc-----CCCCCCC---CcccchhhHHHHHhhhhhhhhhc
Q 018176 13 PSREILVALAEKFS-----ESPERKG---KIMVQMKQVWNWFQNRRYAIRAK 56 (360)
Q Consensus 13 p~r~~~q~LAe~Fs-----~S~~RaG---K~~Vq~kQV~~WFQnrr~~~~~k 56 (360)
+.|.-+-.|-..|- .+.+|+| +..++=+||.-||||||..-+.+
T Consensus 111 FSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 111 FSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred hhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 44444445555444 5777875 77899999999999998764433
No 14
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=90.53 E-value=0.82 Score=32.75 Aligned_cols=54 Identities=19% Similarity=0.287 Sum_probs=40.3
Q ss_pred cccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEecCCccccccCcceeeccc
Q 018176 188 AVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPE 252 (360)
Q Consensus 188 ~V~pGdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpsee~V~l~kvC~rP~ 252 (360)
..++|+.+++.. ++..||.|+|+++... -.+.|+|....+.+.|+...+...|.
T Consensus 2 ~~~~G~~~~a~~---~d~~wyra~I~~~~~~--------~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 2 TFKVGDKVAARW---EDGEWYRARIIKVDGE--------QLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCCEEEEEe---CCCCEEEEEEEEECCC--------CEEEEEEECCCccEEEeHHHeecCCC
Confidence 367898877654 3788999999999743 34678888867777888877776654
No 15
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=90.07 E-value=1.4 Score=46.02 Aligned_cols=54 Identities=22% Similarity=0.399 Sum_probs=39.2
Q ss_pred EEeeccCCCceeehhhhhhcccc---CCCCCeEEEEecCCCcCcccccccccccccCCC
Q 018176 124 FEAKSARDGAWYDVSAFLAQRNF---DTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSL 179 (360)
Q Consensus 124 FEAkSa~DgAWYDV~~fL~~r~l---~tGe~evrVrF~gFg~EeDEWvnvk~rvR~RSi 179 (360)
.-++-..||.||... .++-|.. ..|+.+.+|||.||...-||||+.. |++..++
T Consensus 60 Vla~~~~Dg~~~~A~-VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~-rLdls~~ 116 (450)
T PLN00104 60 VMCRWRFDGKYHPVK-VIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLE-QLDLDTV 116 (450)
T ss_pred EEEEECCCCCEEEEE-EEEEeccCCCCCCCceEEEEEecCCccHhhccCHh-hcccccc
Confidence 445566699999844 4555542 2356789999999999999999975 5655443
No 16
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=89.97 E-value=0.23 Score=46.47 Aligned_cols=36 Identities=36% Similarity=0.410 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhhhcc
Q 018176 12 MPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKS 57 (360)
Q Consensus 12 ~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~~k~ 57 (360)
+|.++=-..||... -+|.-||--||||||-.-+.|.
T Consensus 74 ~L~p~~K~~LAk~L----------gL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 74 KLEPERKKKLAKEL----------GLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccChHHHHHHHHhh----------CCChhHHHHHHhhccccccchh
Confidence 44444456666554 4678999999999987654443
No 17
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=89.58 E-value=0.24 Score=48.78 Aligned_cols=25 Identities=40% Similarity=0.621 Sum_probs=19.0
Q ss_pred HHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhh
Q 018176 19 VALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAI 53 (360)
Q Consensus 19 q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~ 53 (360)
.+||.+.+ ++=.||.-||||||-.-
T Consensus 203 ~~LA~~Lg----------LTdaQVKtWfQNRRtKW 227 (309)
T KOG0488|consen 203 IELAASLG----------LTDAQVKTWFQNRRTKW 227 (309)
T ss_pred HHHHHHcC----------CchhhHHHHHhhhhHHH
Confidence 56666655 45679999999998763
No 18
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=88.78 E-value=0.23 Score=46.37 Aligned_cols=34 Identities=35% Similarity=0.428 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhhh
Q 018176 12 MPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRA 55 (360)
Q Consensus 12 ~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~~ 55 (360)
.|.-.--|.||.-.| +..|||..||||||-.++.
T Consensus 124 YLS~~e~~ELan~L~----------LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 124 YLSTPERQELANALS----------LSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred hcccHHHHHHHHHhh----------hhHHHHHHHHHHHHHHHHH
Confidence 344444566666655 4589999999999877543
No 19
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=88.41 E-value=0.4 Score=45.16 Aligned_cols=46 Identities=26% Similarity=0.300 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhcCCCCCC--------CCcccchhhHHHHHhhhhhhhhhccc
Q 018176 13 PSREILVALAEKFSESPERK--------GKIMVQMKQVWNWFQNRRYAIRAKSI 58 (360)
Q Consensus 13 p~r~~~q~LAe~Fs~S~~Ra--------GK~~Vq~kQV~~WFQnrr~~~~~k~~ 58 (360)
+..+-+++|-..|.-+---. -+..+.-.||.-||||||..+|....
T Consensus 109 ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 109 FTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred cCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 44455556666665432221 24566779999999999988765554
No 20
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=87.91 E-value=0.28 Score=46.71 Aligned_cols=22 Identities=32% Similarity=0.590 Sum_probs=16.8
Q ss_pred ccchhhHHHHHhhhhhhhhhcc
Q 018176 36 MVQMKQVWNWFQNRRYAIRAKS 57 (360)
Q Consensus 36 ~Vq~kQV~~WFQnrr~~~~~k~ 57 (360)
-++=.||..||||||-..+...
T Consensus 197 ~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 197 NLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred chhHHHHHHHHHHHHHHHHHhh
Confidence 4566899999999987765433
No 21
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=86.87 E-value=0.5 Score=33.12 Aligned_cols=37 Identities=27% Similarity=0.517 Sum_probs=28.9
Q ss_pred eehhhhhhccccCCCCCeEEEEecCCCcCcccccccc
Q 018176 135 YDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 171 (360)
Q Consensus 135 YDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk 171 (360)
|.|.-.|.+|....|..++.|+|.|++..++.|+...
T Consensus 2 ~~v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~ 38 (55)
T smart00298 2 YEVEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEE 38 (55)
T ss_pred cchheeeeeeecCCCcEEEEEEECCCCCccCceeeHH
Confidence 3355556666456778899999999999999998764
No 22
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro []. The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [].; PDB: 2H1E_B 3MWY_W 2DY8_A 1KNE_A 1KNA_A 1Q3L_A 2EE1_A 1AP0_A 1GUW_A 1X3P_A ....
Probab=85.50 E-value=0.3 Score=35.21 Aligned_cols=37 Identities=24% Similarity=0.495 Sum_probs=30.1
Q ss_pred eehhhhhhccccCCCC--CeEEEEecCCCcCcccccccc
Q 018176 135 YDVSAFLAQRNFDTAD--PEVQVRFAGFGAEEDEWVNIK 171 (360)
Q Consensus 135 YDV~~fL~~r~l~tGe--~evrVrF~gFg~EeDEWvnvk 171 (360)
|-|.-.|.+|....|. .++.|++.|++.+++.|.+..
T Consensus 1 ~~Ve~Il~~r~~~~~~~~~~ylVkW~g~~~~~~tWe~~~ 39 (55)
T PF00385_consen 1 YEVERILDHRVVKGGNKVYEYLVKWKGYPYSENTWEPEE 39 (55)
T ss_dssp EEEEEEEEEEEETTEESEEEEEEEETTSSGGGEEEEEGG
T ss_pred CEEEEEEEEEEeCCCcccEEEEEEECCCCCCCCeEeeHH
Confidence 5566778888666665 499999999999999998864
No 23
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=84.86 E-value=2.7 Score=30.93 Aligned_cols=50 Identities=24% Similarity=0.419 Sum_probs=37.9
Q ss_pred cccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEec--CCccccccCcce
Q 018176 188 AVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDH--DQSEEIVPLRKV 247 (360)
Q Consensus 188 ~V~pGdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~H--dpsee~V~l~kv 247 (360)
.++.||.|-++... +..||-|.|+++.. .+ +|.|+|.. .+.++.+...+|
T Consensus 2 ~~~~G~~Ve~~~~~--~~~W~~a~V~~~~~-----~~---~~~V~~~~~~~~~~e~v~~~~L 53 (61)
T smart00743 2 DFKKGDRVEVFSKE--EDSWWEAVVTKVLG-----DG---KYLVRYLTESEPLKETVDWSDL 53 (61)
T ss_pred CcCCCCEEEEEECC--CCEEEEEEEEEECC-----CC---EEEEEECCCCcccEEEEeHHHc
Confidence 56899999987743 67899999998865 22 38999998 666677765544
No 24
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=84.46 E-value=0.89 Score=31.57 Aligned_cols=36 Identities=33% Similarity=0.528 Sum_probs=26.5
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcc
Q 018176 125 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEED 165 (360)
Q Consensus 125 EAkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeD 165 (360)
-|+...||.||-..+.--. ++..+.|.|..||+.+.
T Consensus 5 ~a~~~~d~~wyra~V~~~~-----~~~~~~V~f~DyG~~~~ 40 (48)
T cd04508 5 LAKYSDDGKWYRAKITSIL-----SDGKVEVFFVDYGNTEV 40 (48)
T ss_pred EEEECCCCeEEEEEEEEEC-----CCCcEEEEEEcCCCcEE
Confidence 3566678999998765221 25779999999999853
No 25
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=84.32 E-value=0.3 Score=48.53 Aligned_cols=35 Identities=31% Similarity=0.475 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhh
Q 018176 10 NAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 10 ~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~ 54 (360)
|..++||=--.|+...|.+ =.||.-||||||-.-|
T Consensus 257 N~YitkeKR~ElSr~lNLT----------eRQVKIWFQNRRMK~K 291 (308)
T KOG0487|consen 257 NMYITKEKRLELSRTLNLT----------ERQVKIWFQNRRMKEK 291 (308)
T ss_pred HHHHhHHHHHHHHHhcccc----------hhheeeeehhhhhHHh
Confidence 4556666666777776654 5799999999987643
No 26
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=83.25 E-value=2.5 Score=40.68 Aligned_cols=56 Identities=18% Similarity=0.213 Sum_probs=39.5
Q ss_pred ccccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEecCCccccccCcceeecc
Q 018176 187 VAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRP 251 (360)
Q Consensus 187 ~~V~pGdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpsee~V~l~kvC~rP 251 (360)
...++||..++.- .+|-+||.|+|.+|.. .++ +++|+|..-.++|.|.|.+|--..
T Consensus 67 ~~WkvGd~C~A~~--s~Dg~~Y~A~I~~i~~----~~~---~~~V~f~gYgn~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 67 KKWKVGDKCMAVY--SEDGQYYPATIESIDE----EDG---TCVVVFTGYGNEEEVNLSDLKPSE 122 (264)
T ss_dssp T---TT-EEEEE---TTTSSEEEEEEEEEET----TTT---EEEEEETTTTEEEEEEGGGEEETT
T ss_pred cCCCCCCEEEEEE--CCCCCEEEEEEEEEcC----CCC---EEEEEEcccCCeEeeehhhhcccc
Confidence 5789999988763 4466899999999952 222 334999999999999999986653
No 27
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=83.20 E-value=1.3 Score=36.71 Aligned_cols=45 Identities=20% Similarity=0.409 Sum_probs=37.0
Q ss_pred eeEEeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccccc
Q 018176 122 MEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 171 (360)
Q Consensus 122 lEFEAkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk 171 (360)
|-+||...++-..|=|++..+-. | ..|+|+|.|+.+..|.|+++.
T Consensus 32 mkLEavD~~~~~~i~vAtV~~v~----g-~~l~v~~dg~~~~~D~W~~~~ 76 (96)
T smart00561 32 MKLEAVDPRNPSLICVATVVEVK----G-YRLLLHFDGWDDKYDFWCDAD 76 (96)
T ss_pred CEEEEECCCCCceEEEEEEEEEE----C-CEEEEEEccCCCcCCEEEECC
Confidence 78899988887888777765532 3 479999999999999999986
No 28
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=81.70 E-value=0.51 Score=45.54 Aligned_cols=20 Identities=40% Similarity=0.592 Sum_probs=16.8
Q ss_pred CCcccchhhHHHHHhhhhhh
Q 018176 33 GKIMVQMKQVWNWFQNRRYA 52 (360)
Q Consensus 33 GK~~Vq~kQV~~WFQnrr~~ 52 (360)
-...++=+||.-||||||-.
T Consensus 179 sSL~LTeTqVKIWFQNRRAK 198 (246)
T KOG0492|consen 179 SSLELTETQVKIWFQNRRAK 198 (246)
T ss_pred hhhhhhhhheehhhhhhhHH
Confidence 34678999999999999765
No 29
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=79.84 E-value=2.8 Score=35.07 Aligned_cols=48 Identities=17% Similarity=0.358 Sum_probs=35.9
Q ss_pred cceEeeEEEeeeeecccCCCCcceEEEEEEecCCccccccCcceeeccc
Q 018176 204 QALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPE 252 (360)
Q Consensus 204 ~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpsee~V~l~kvC~rP~ 252 (360)
...||+|.|+.|.++. ....+.+.+-|.|+..|..+.+.+.....||-
T Consensus 9 ~gAWfEa~i~~i~~~~-~~~~e~viYhIkyddype~gvv~~~~~~iRpR 56 (85)
T PF12148_consen 9 MGAWFEAQIVTITKKC-MSDDEDVIYHIKYDDYPENGVVEMRSKDIRPR 56 (85)
T ss_dssp T-EEEEEEEEEEEES--SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE-
T ss_pred CcceEEEEEEEeeccC-CCCCCCEEEEEEeccCCCcCceecccccccce
Confidence 4679999999999765 44459999999999999888877777777764
No 30
>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. The crystal structure of the two MBT repeats of human SCM-like 2 protein has been reported. Each repeat consists of an extended "arm" and a globular core. The arm of the first repeat packs against the core of the second repeat and vice versa. The structure of the core-interacting part of each arm consists of an N-terminal alpha-helix and a turn of 310 helix connected by a short beta-strand. The core consists of an Src homology 3-like five-stranded beta-barrel followed by a C-terminal alpha-helix and another short beta-strand. Each arm interacts with its partner core in a similar way, with the orientation of the N-terminal helix relative to the barrel varying slightly. There are also extensive interactions between the two barrels [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P0K_A 3F70_B 3CEY_A 2VYT_A 2BIV_A 1OI1_A 3OQ5_A 2RJE_B 2RJD_A 2RI3_A ....
Probab=79.44 E-value=1.9 Score=33.42 Aligned_cols=45 Identities=24% Similarity=0.448 Sum_probs=34.2
Q ss_pred eeEEeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccccc
Q 018176 122 MEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIK 171 (360)
Q Consensus 122 lEFEAkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk 171 (360)
|-+||....+...|=|++..+-. | ..|+|||.|+.+++|.|+.+.
T Consensus 1 MkLEa~d~~~~~~~~vAtV~~v~----g-~~l~v~~dg~~~~~d~w~~~~ 45 (73)
T PF02820_consen 1 MKLEAVDPRNPSLICVATVVKVC----G-GRLLVRYDGWDDDYDFWCHID 45 (73)
T ss_dssp EEEEEEETTECCEEEEEEEEEEE----T-TEEEEEETTSTGGGEEEEETT
T ss_pred CeEEEECCCCCCeEEEEEEEEEe----C-CEEEEEEcCCCCCccEEEECC
Confidence 56788887787777777655421 3 339999999999999999874
No 31
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=79.35 E-value=5.6 Score=30.53 Aligned_cols=43 Identities=28% Similarity=0.397 Sum_probs=27.7
Q ss_pred ccCCceEEE-eeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEecCCcc
Q 018176 189 VLPGDLILC-FQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSE 239 (360)
Q Consensus 189 V~pGdlVcC-f~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpse 239 (360)
+++|+.|-. .++..-..-||-|.|++..... +|+|+|++-..+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~--------~~~V~Y~~~~~~ 44 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD--------KYLVEYDDLPDE 44 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT---------EEEEEETT-SS-
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc--------EEEEEECCcccc
Confidence 468999984 4455558999999999987665 999999765544
No 32
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=78.55 E-value=1.1 Score=34.65 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=29.0
Q ss_pred ChhhhhhhcCCC--CCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhh
Q 018176 1 MEGILQEHHNAM--PSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRY 51 (360)
Q Consensus 1 ME~~l~e~~~~~--p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~ 51 (360)
||+.++..+-.+ |+.+..+.||.+.+. .-.+|+-||||.+|
T Consensus 16 Le~~fe~~~y~~~~~~~~~r~~la~~lgl----------~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 16 MRDFAEKLGWKLKDKRREEVREFCEEIGV----------TRKVFKVWMHNNKK 58 (58)
T ss_pred HHHHHHHcCCCCCCCCHHHHHHHHHHhCC----------CHHHeeeecccCCC
Confidence 555555544322 888899999988764 45689999999754
No 33
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=77.89 E-value=0.97 Score=44.99 Aligned_cols=21 Identities=43% Similarity=0.610 Sum_probs=15.9
Q ss_pred CcccchhhHHHHHhhhhhhhh
Q 018176 34 KIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 34 K~~Vq~kQV~~WFQnrr~~~~ 54 (360)
...+.=.||.-||||||-.-|
T Consensus 235 ~LgLsERQVKIWFQNRRAKER 255 (317)
T KOG0848|consen 235 TLGLSERQVKIWFQNRRAKER 255 (317)
T ss_pred hhCccHhhhhHhhhhhhHHHH
Confidence 344667899999999986643
No 34
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=77.63 E-value=4.2 Score=30.20 Aligned_cols=38 Identities=21% Similarity=0.560 Sum_probs=27.7
Q ss_pred ccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEe
Q 018176 189 VLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYD 234 (360)
Q Consensus 189 V~pGdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~ 234 (360)
+..|+.|.|+. .+-.+|.|+|+++..+... =.|.|-|.
T Consensus 1 ~~vG~~v~~~~---~~~~~y~A~I~~~r~~~~~-----~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKY---KDGQWYEAKILDIREKNGE-----PEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEE---TTTEEEEEEEEEEEECTTC-----EEEEEEET
T ss_pred CCcCCEEEEEE---CCCcEEEEEEEEEEecCCC-----EEEEEEcC
Confidence 46899999999 4668999999999985433 34556555
No 35
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=77.23 E-value=2.9 Score=34.96 Aligned_cols=70 Identities=13% Similarity=0.288 Sum_probs=38.8
Q ss_pred EeeccCCCceeehhhhhhccccC--CCCCeEEEEecCCCcCcccccccccccccCCCcccccccccccCCceEEE
Q 018176 125 EAKSARDGAWYDVSAFLAQRNFD--TADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILC 197 (360)
Q Consensus 125 EAkSa~DgAWYDV~~fL~~r~l~--tGe~evrVrF~gFg~EeDEWvnvk~rvR~RSiPlE~sEC~~V~pGdlVcC 197 (360)
-|+....|||++-.+.--++.-. ..+.-..|.|.+|.+..-.=+.++ .+|+|..-+= .=..|.+|+.|..
T Consensus 3 D~~d~~~gAWfEa~i~~i~~~~~~~~e~viYhIkyddype~gvv~~~~~-~iRpRARt~l--~w~~L~VG~~VMv 74 (85)
T PF12148_consen 3 DARDRNMGAWFEAQIVTITKKCMSDDEDVIYHIKYDDYPENGVVEMRSK-DIRPRARTIL--KWDELKVGQVVMV 74 (85)
T ss_dssp EEE-TTT-EEEEEEEEEEEES-SSSSTTEEEEEEETT-GGG-EEEEEGG-GEEE---SBE---GGG--TT-EEEE
T ss_pred ccccCCCcceEEEEEEEeeccCCCCCCCEEEEEEeccCCCcCceecccc-cccceeeEec--cHHhCCcccEEEE
Confidence 36677799999976654444322 345667899988876554444444 8888877543 3467889999974
No 36
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=77.05 E-value=1.2 Score=39.15 Aligned_cols=20 Identities=45% Similarity=0.562 Sum_probs=15.7
Q ss_pred CCcccchhhHHHHHhhhhhh
Q 018176 33 GKIMVQMKQVWNWFQNRRYA 52 (360)
Q Consensus 33 GK~~Vq~kQV~~WFQnrr~~ 52 (360)
-|+-++=.-||-||||||-.
T Consensus 52 ~kidLTEARVQVWFQNRRAK 71 (125)
T KOG0484|consen 52 LKIDLTEARVQVWFQNRRAK 71 (125)
T ss_pred HhhhhhHHHHHHHHHhhHHH
Confidence 45677777899999999754
No 37
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=71.08 E-value=4.6 Score=28.85 Aligned_cols=43 Identities=28% Similarity=0.492 Sum_probs=29.8
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCccccccccccccc
Q 018176 125 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQ 176 (360)
Q Consensus 125 EAkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk~rvR~ 176 (360)
.|+- .||.||.+.+. +. .++..+.|.|..||.. ||++.. .+|+
T Consensus 10 ~a~~-~d~~wyra~I~-~~----~~~~~~~V~f~D~G~~--~~v~~~-~l~~ 52 (57)
T smart00333 10 AARW-EDGEWYRARII-KV----DGEQLYEVFFIDYGNE--EVVPPS-DLRP 52 (57)
T ss_pred EEEe-CCCCEEEEEEE-EE----CCCCEEEEEEECCCcc--EEEeHH-Heec
Confidence 3444 59999998754 32 2337799999999998 477754 4443
No 38
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=66.96 E-value=4.7 Score=39.55 Aligned_cols=46 Identities=30% Similarity=0.453 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhcCC-----CCCC---CCcccchhhHHHHHhhhhhhhhhccc
Q 018176 13 PSREILVALAEKFSES-----PERK---GKIMVQMKQVWNWFQNRRYAIRAKSI 58 (360)
Q Consensus 13 p~r~~~q~LAe~Fs~S-----~~Ra---GK~~Vq~kQV~~WFQnrr~~~~~k~~ 58 (360)
..-.-|+.|+.+|... ++|+ -..-.+--||.-||||||..-|.|..
T Consensus 174 f~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 174 FTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 4556788899988854 3332 22336678999999999998776664
No 39
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=65.96 E-value=3.9 Score=31.38 Aligned_cols=41 Identities=20% Similarity=0.447 Sum_probs=21.8
Q ss_pred CCceeehhhhhhccccCCCCCeEEEEecCCCcCccccc------ccccccccC
Q 018176 131 DGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWV------NIKRHVRQR 177 (360)
Q Consensus 131 DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWv------nvk~rvR~R 177 (360)
.||||...+.-... +..++|+|..+..+++++. +.+ ++|+.
T Consensus 17 ~gaWf~a~V~~~~~-----~~~~~V~Y~~~~~~~~~~~~l~e~V~~~-~iRP~ 63 (68)
T PF05641_consen 17 RGAWFPATVLKENG-----DDKYLVEYDDLPDEDGESPPLKEWVDAR-RIRPC 63 (68)
T ss_dssp --EEEEEEEEEEET-----T-EEEEEETT-SS--------EEEEEGG-GEEE-
T ss_pred CcEEEEEEEEEeCC-----CcEEEEEECCcccccccccccEEEechh-eEECc
Confidence 67999988764432 2389999999999966653 333 56664
No 40
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=65.77 E-value=5.5 Score=39.89 Aligned_cols=45 Identities=27% Similarity=0.379 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhcCCCCC--------CCCcccchhhHHHHHhhhhhhhhhcc
Q 018176 13 PSREILVALAEKFSESPER--------KGKIMVQMKQVWNWFQNRRYAIRAKS 57 (360)
Q Consensus 13 p~r~~~q~LAe~Fs~S~~R--------aGK~~Vq~kQV~~WFQnrr~~~~~k~ 57 (360)
+.-|-+|.|-.+|..+.-- +-...+.=-||.-||||||-.++.-+
T Consensus 253 FtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 253 FTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred ccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 3444555555555543211 12234566799999999988775433
No 41
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=64.82 E-value=4.2 Score=36.00 Aligned_cols=24 Identities=33% Similarity=0.401 Sum_probs=16.8
Q ss_pred CcccchhhHHHHHhhhhhhhhhcc
Q 018176 34 KIMVQMKQVWNWFQNRRYAIRAKS 57 (360)
Q Consensus 34 K~~Vq~kQV~~WFQnrr~~~~~k~ 57 (360)
++.+.-..|+.||||||...+...
T Consensus 96 ~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 96 LLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cCCCCeeeeehhhhhhcHhhhhhh
Confidence 344455669999999988765443
No 42
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=62.25 E-value=20 Score=24.76 Aligned_cols=45 Identities=24% Similarity=0.364 Sum_probs=28.0
Q ss_pred CceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEecCCccccccCcc
Q 018176 192 GDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRK 246 (360)
Q Consensus 192 GdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpsee~V~l~k 246 (360)
|+++++.- .++..||-|.|+++.. .-.+.|.|..-.+.+.|+..+
T Consensus 1 G~~c~a~~--~~d~~wyra~V~~~~~--------~~~~~V~f~DyG~~~~v~~~~ 45 (48)
T cd04508 1 GDLCLAKY--SDDGKWYRAKITSILS--------DGKVEVFFVDYGNTEVVPLSD 45 (48)
T ss_pred CCEEEEEE--CCCCeEEEEEEEEECC--------CCcEEEEEEcCCCcEEEeHHH
Confidence 44555432 2378999999999974 234667777744445565544
No 43
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=61.85 E-value=15 Score=36.88 Aligned_cols=41 Identities=32% Similarity=0.476 Sum_probs=33.8
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhh
Q 018176 3 GILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAI 53 (360)
Q Consensus 3 ~~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~ 53 (360)
=.|-+++|-.|..+.-+.||.+-| |+--||-|||-|+|-..
T Consensus 206 yF~~h~~nPYPSee~K~eLAkqCn----------ItvsQvsnwfgnkrIry 246 (334)
T KOG0774|consen 206 YFYSHLSNPYPSEEAKEELAKQCN----------ITVSQVSNWFGNKRIRY 246 (334)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHcC----------ceehhhccccccceeeh
Confidence 356778899999999999999866 45679999999997553
No 44
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=60.30 E-value=7.5 Score=37.49 Aligned_cols=43 Identities=26% Similarity=0.400 Sum_probs=30.2
Q ss_pred eEEeeccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccc
Q 018176 123 EFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVN 169 (360)
Q Consensus 123 EFEAkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvn 169 (360)
.=.|+-+.||-||...+.--+ .......|+|.|||++|..++.
T Consensus 74 ~C~A~~s~Dg~~Y~A~I~~i~----~~~~~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 74 KCMAVYSEDGQYYPATIESID----EEDGTCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp EEEEE-TTTSSEEEEEEEEEE----TTTTEEEEEETTTTEEEEEEGG
T ss_pred EEEEEECCCCCEEEEEEEEEc----CCCCEEEEEEcccCCeEeeehh
Confidence 456777899999998765322 2234688999999999765543
No 45
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=58.45 E-value=9.9 Score=27.91 Aligned_cols=34 Identities=18% Similarity=0.315 Sum_probs=23.3
Q ss_pred EeeccCCCceeehhhhhhccccCCCCCeEEEEecC--CCcC
Q 018176 125 EAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAG--FGAE 163 (360)
Q Consensus 125 EAkSa~DgAWYDV~~fL~~r~l~tGe~evrVrF~g--Fg~E 163 (360)
||++..||+||...+.-- + ++..+.|+|.+ ++.+
T Consensus 10 e~~~~~~~~W~~a~V~~~---~--~~~~~~V~~~~~~~~~~ 45 (61)
T smart00743 10 EVFSKEEDSWWEAVVTKV---L--GDGKYLVRYLTESEPLK 45 (61)
T ss_pred EEEECCCCEEEEEEEEEE---C--CCCEEEEEECCCCcccE
Confidence 555556999998776622 2 24579999998 5543
No 46
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=55.81 E-value=9.1 Score=38.36 Aligned_cols=22 Identities=36% Similarity=0.575 Sum_probs=17.0
Q ss_pred CCcccchhhHHHHHhhhhhhhh
Q 018176 33 GKIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 33 GK~~Vq~kQV~~WFQnrr~~~~ 54 (360)
+|.-|.=.-|+-||||||-.-|
T Consensus 176 ~ktelpEDRIqVWfQNRRAKWR 197 (332)
T KOG0494|consen 176 DKTELPEDRIQVWFQNRRAKWR 197 (332)
T ss_pred hhccCchhhhhHHhhhhhHHhh
Confidence 6666777778899999987644
No 47
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=55.60 E-value=8.4 Score=39.13 Aligned_cols=39 Identities=31% Similarity=0.520 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHhcCCCCCCC--------CcccchhhHHHHHhhhhhh
Q 018176 14 SREILVALAEKFSESPERKG--------KIMVQMKQVWNWFQNRRYA 52 (360)
Q Consensus 14 ~r~~~q~LAe~Fs~S~~RaG--------K~~Vq~kQV~~WFQnrr~~ 52 (360)
.-.-++.|-..++-||--+- ..-+.|.=||-||||||-.
T Consensus 175 tAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAK 221 (383)
T KOG4577|consen 175 TAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAK 221 (383)
T ss_pred eHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHH
Confidence 34455666666666665443 2346778899999999754
No 48
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=44.83 E-value=19 Score=27.81 Aligned_cols=52 Identities=29% Similarity=0.563 Sum_probs=34.7
Q ss_pred ccCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccccccccc-----cCCCcccccccc
Q 018176 128 SARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVR-----QRSLPCEASECV 187 (360)
Q Consensus 128 Sa~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnvk~rvR-----~RSiPlE~sEC~ 187 (360)
...||.||-+.+ ....++..+.|.|..||..+- ++.. .+| ...+|.+...|.
T Consensus 62 ~~~~~~w~Ra~I-----~~~~~~~~~~V~~iD~G~~~~--v~~~-~l~~l~~~~~~~P~~a~~~~ 118 (121)
T PF00567_consen 62 VSEDGRWYRAVI-----TVDIDENQYKVFLIDYGNTEK--VSAS-DLRPLPPEFASLPPQAIKCK 118 (121)
T ss_dssp ETTTSEEEEEEE-----EEEECTTEEEEEETTTTEEEE--EEGG-GEEE--HHHCSSSSSCEEEE
T ss_pred EecCCceeeEEE-----EEecccceeEEEEEecCceEE--EcHH-HhhhhCHHHhhCChhhEEEE
Confidence 345999999988 133466899999999998753 4443 222 234566666664
No 49
>PF11523 DUF3223: Protein of unknown function (DUF3223); InterPro: IPR021602 This family of proteins has no known function. ; PDB: 2K0M_A.
Probab=39.67 E-value=31 Score=27.67 Aligned_cols=33 Identities=39% Similarity=0.486 Sum_probs=22.1
Q ss_pred EeeeeecccCCCC-cceEEEEEEecCCccccccCcc
Q 018176 212 VLDAQRRRHDVRG-CRCRFLVRYDHDQSEEIVPLRK 246 (360)
Q Consensus 212 V~~VqRr~Hd~rg-CrC~FlVrw~Hdpsee~V~l~k 246 (360)
|..|+-+.|...+ .||.|+||= |.+++-.+.+|
T Consensus 41 i~~i~V~~hp~~~~srCF~vvR~--DGs~~DFSy~K 74 (76)
T PF11523_consen 41 IDHIMVRKHPEFKDSRCFFVVRT--DGSEEDFSYRK 74 (76)
T ss_dssp EEEEEEEESSSS---EEEEEEET--TS-EEE--GGG
T ss_pred eeeEEEeecCCCCcceEEEEEEe--CCCeeeeEhhh
Confidence 6788999999765 999999985 66666655543
No 50
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=34.70 E-value=21 Score=27.94 Aligned_cols=31 Identities=29% Similarity=0.411 Sum_probs=17.5
Q ss_pred CCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhh
Q 018176 12 MPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYA 52 (360)
Q Consensus 12 ~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~ 52 (360)
.|.-.=++.|.++ .-+...||+.||-.|+..
T Consensus 22 ~L~E~DL~~L~~k----------S~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 22 QLQEEDLDELCDK----------SRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp ---TTHHHHHHHH----------TT--HHHHHHHHHHHS--
T ss_pred CccHhhHHHHHHH----------HCCCHHHHHHHHHHhccc
Confidence 3444445666664 446789999999988543
No 51
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 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 [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=32.00 E-value=32 Score=31.41 Aligned_cols=48 Identities=23% Similarity=0.141 Sum_probs=35.3
Q ss_pred hhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhh
Q 018176 7 EHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIR 54 (360)
Q Consensus 7 e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~ 54 (360)
++...-|..=-..+||++|++|+-..+-+.=-.+|-..+-+.+.-+.+
T Consensus 96 ~LR~~DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~~~~le~~k 143 (164)
T PF12824_consen 96 RLRAEDPEKWTRKKLAKKFNCSPLFVSMVAPAPKEKKKEMEARLEAIK 143 (164)
T ss_pred HHHHcCchHhhHHHHHHHhCCCHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence 444556667778899999999998887777666777777766655443
No 52
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=29.42 E-value=1.2e+02 Score=32.07 Aligned_cols=58 Identities=17% Similarity=0.281 Sum_probs=39.0
Q ss_pred ccccCCceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEecCCcc--ccccCcce
Q 018176 187 VAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSE--EIVPLRKV 247 (360)
Q Consensus 187 ~~V~pGdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpse--e~V~l~kv 247 (360)
..+..|+.|+|+... +-.||.|+|+++.+..-...+. -.|-|.|..-+.- |=|+..+|
T Consensus 52 ~~~~VGekVla~~~~--Dg~~~~A~VI~~R~~~~~~~~~-~~YYVHY~g~nrRlDEWV~~~rL 111 (450)
T PLN00104 52 LPLEVGTRVMCRWRF--DGKYHPVKVIERRRGGSGGPND-YEYYVHYTEFNRRLDEWVKLEQL 111 (450)
T ss_pred ceeccCCEEEEEECC--CCCEEEEEEEEEeccCCCCCCC-ceEEEEEecCCccHhhccCHhhc
Confidence 456799999999742 4568899999998643001121 2589999876665 55666655
No 53
>PTZ00064 histone acetyltransferase; Provisional
Probab=28.68 E-value=43 Score=36.20 Aligned_cols=39 Identities=26% Similarity=0.346 Sum_probs=27.3
Q ss_pred CCCCeEEEEecCCCcCcccccccccccccCCCccccccccc
Q 018176 148 TADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVA 188 (360)
Q Consensus 148 tGe~evrVrF~gFg~EeDEWvnvk~rvR~RSiPlE~sEC~~ 188 (360)
.|+-|.+|||.||.-.-||||.-. |++... ..+..++..
T Consensus 146 ~~~~eyYVHy~g~nrRlD~WV~~~-ri~~~~-~~~~~~~~~ 184 (552)
T PTZ00064 146 KEDYEFYVHFRGLNRRLDRWVKGK-DIKLSF-DVEELNDPN 184 (552)
T ss_pred CCCeEEEEEecCcCchHhhhcChh-hccccc-ccccccccc
Confidence 356789999999999999999954 665532 333344443
No 54
>COG3458 Acetyl esterase (deacetylase) [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.84 E-value=1e+02 Score=31.51 Aligned_cols=94 Identities=22% Similarity=0.357 Sum_probs=68.7
Q ss_pred CCCceeEEeec-cCCCceeehhhhhhccccCCCCCeEEEEecCCCcCcccccc-----------cccccccCCCcccccc
Q 018176 118 ESTFMEFEAKS-ARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVN-----------IKRHVRQRSLPCEASE 185 (360)
Q Consensus 118 d~~~lEFEAkS-a~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvn-----------vk~rvR~RSiPlE~sE 185 (360)
+-+++.|+.+- .+=.+||-+..- ++|..-+.|+|-||+---++|.+ +.-.+|=.|.--+|+-
T Consensus 55 e~ydvTf~g~~g~rI~gwlvlP~~------~~~~~P~vV~fhGY~g~~g~~~~~l~wa~~Gyavf~MdvRGQg~~~~dt~ 128 (321)
T COG3458 55 EVYDVTFTGYGGARIKGWLVLPRH------EKGKLPAVVQFHGYGGRGGEWHDMLHWAVAGYAVFVMDVRGQGSSSQDTA 128 (321)
T ss_pred EEEEEEEeccCCceEEEEEEeecc------cCCccceEEEEeeccCCCCCccccccccccceeEEEEecccCCCccccCC
Confidence 35678887652 344689988732 23667899999999999988855 2467888888777888
Q ss_pred ccccc---CCceEEEeeecCCcceEeeEEEeeeeec
Q 018176 186 CVAVL---PGDLILCFQEGKDQALYFDAHVLDAQRR 218 (360)
Q Consensus 186 C~~V~---pGdlVcCf~eg~d~alyyDA~V~~VqRr 218 (360)
|.... ||-.+....+++ +..||=.+++|+-|.
T Consensus 129 ~~p~~~s~pG~mtrGilD~k-d~yyyr~v~~D~~~a 163 (321)
T COG3458 129 DPPGGPSDPGFMTRGILDRK-DTYYYRGVFLDAVRA 163 (321)
T ss_pred CCCCCCcCCceeEeecccCC-CceEEeeehHHHHHH
Confidence 87766 677777888888 567777777776544
No 55
>PRK04980 hypothetical protein; Provisional
Probab=24.79 E-value=1.3e+02 Score=25.94 Aligned_cols=33 Identities=18% Similarity=0.234 Sum_probs=26.3
Q ss_pred cccCCceEEEeeecCCcceEeeEEEeeeeecccC
Q 018176 188 AVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHD 221 (360)
Q Consensus 188 ~V~pGdlVcCf~eg~d~alyyDA~V~~VqRr~Hd 221 (360)
..+|||.|..+..+. +..|+++.|++|...+=+
T Consensus 31 ~~~~G~~~~V~~~e~-g~~~c~ieI~sV~~i~f~ 63 (102)
T PRK04980 31 HFKPGDVLRVGTFED-DRYFCTIEVLSVSPVTFD 63 (102)
T ss_pred CCCCCCEEEEEECCC-CcEEEEEEEEEEEEEehh
Confidence 467999999865555 789999999999876543
No 56
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=23.76 E-value=54 Score=31.27 Aligned_cols=40 Identities=20% Similarity=0.419 Sum_probs=33.9
Q ss_pred CCCceeehhhhhhccccCCCCCeEEEEecCCCcCccccccc
Q 018176 130 RDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNI 170 (360)
Q Consensus 130 ~DgAWYDV~~fL~~r~l~tGe~evrVrF~gFg~EeDEWvnv 170 (360)
.+..=|-|...|.+|+ .-|..++.|+..||.++++-|=+.
T Consensus 44 ~~~~~~vvEki~~~r~-~~g~~eYlvkW~Gy~~~~ntWEPe 83 (270)
T KOG1911|consen 44 EEEEEYVVEKILKRRK-KNGKIEYLVKWKGYPDPDNTWEPE 83 (270)
T ss_pred cccchhhhhhhhhccc-cCCCceeeeecCCCCCccccCCch
Confidence 3556688999999995 566689999999999999999775
No 57
>PF05506 DUF756: Domain of unknown function (DUF756); InterPro: IPR008475 This domain is found, normally as a tandem repeat, at the C terminus of bacterial phospholipase C proteins.; GO: 0004629 phospholipase C activity, 0016042 lipid catabolic process
Probab=22.75 E-value=88 Score=24.78 Aligned_cols=23 Identities=39% Similarity=0.726 Sum_probs=16.5
Q ss_pred cCCCceeehhhhhhccccCCCCCeEEEEecC
Q 018176 129 ARDGAWYDVSAFLAQRNFDTADPEVQVRFAG 159 (360)
Q Consensus 129 a~DgAWYDV~~fL~~r~l~tGe~evrVrF~g 159 (360)
+..+-|||+.+...+. ..=||.|
T Consensus 66 ~~s~gwYDl~v~~~~~--------F~rr~aG 88 (89)
T PF05506_consen 66 AASGGWYDLTVTGPNG--------FLRRFAG 88 (89)
T ss_pred cCCCCcEEEEEEcCCC--------EEEEecC
Confidence 4589999999876543 5556665
No 58
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=21.91 E-value=1.7e+02 Score=31.96 Aligned_cols=42 Identities=31% Similarity=0.442 Sum_probs=32.6
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHhcCCCCCCCCcccchhhHHHHHhhhhhhhhhc
Q 018176 3 GILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAK 56 (360)
Q Consensus 3 ~~l~e~~~~~p~r~~~q~LAe~Fs~S~~RaGK~~Vq~kQV~~WFQnrr~~~~~k 56 (360)
.||++ +.-|.++.|+.|+...+... .-|.|||-|-|....-+
T Consensus 437 aiFke--~~RPS~Emq~tIS~qL~L~~----------sTV~NfFmNaRRRsl~~ 478 (558)
T KOG2252|consen 437 AIFKE--NKRPSREMQETISQQLNLEL----------STVINFFMNARRRSLDK 478 (558)
T ss_pred HHHhc--CCCCCHHHHHHHHHHhCCcH----------HHHHHHHHhhhhhcccc
Confidence 35554 67899999999999988654 57999999987664333
No 59
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=20.29 E-value=2e+02 Score=24.89 Aligned_cols=38 Identities=24% Similarity=0.549 Sum_probs=28.1
Q ss_pred CceEEEeeecCCcceEeeEEEeeeeecccCCCCcceEEEEEEecCCcc
Q 018176 192 GDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSE 239 (360)
Q Consensus 192 GdlVcCf~eg~d~alyyDA~V~~VqRr~Hd~rgCrC~FlVrw~Hdpse 239 (360)
|+.|++-.+ .+-.||=+.|.+..+ ...|+|+|+++..+
T Consensus 1 g~~VlAR~~--~DG~YY~GtV~~~~~--------~~~~lV~f~~~~~~ 38 (124)
T PF15057_consen 1 GQKVLARRE--EDGFYYPGTVKKCVS--------SGQFLVEFDDGDTQ 38 (124)
T ss_pred CCeEEEeeC--CCCcEEeEEEEEccC--------CCEEEEEECCCCEE
Confidence 678887665 467799999988773 34699999655554
Done!