Query 018661
Match_columns 352
No_of_seqs 397 out of 1817
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 02:58:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018661.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018661hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4442 Clathrin coat binding 100.0 1.7E-56 3.8E-61 450.5 16.4 222 37-258 37-265 (729)
2 KOG1082 Histone H3 (Lys9) meth 100.0 5.6E-37 1.2E-41 301.7 12.3 233 20-256 64-357 (364)
3 KOG1080 Histone H3 (Lys4) meth 100.0 2.2E-33 4.8E-38 299.2 11.5 138 115-252 867-1004(1005)
4 KOG1079 Transcriptional repres 100.0 1.8E-30 3.9E-35 261.1 9.5 150 84-235 553-713 (739)
5 smart00317 SET SET (Su(var)3-9 99.9 7.9E-26 1.7E-30 184.7 14.1 115 116-230 2-116 (116)
6 KOG1141 Predicted histone meth 99.9 4.8E-26 1E-30 232.0 3.9 76 177-252 1179-1261(1262)
7 KOG1083 Putative transcription 99.9 3.4E-26 7.3E-31 238.3 2.7 133 103-236 1166-1299(1306)
8 KOG1085 Predicted methyltransf 99.8 1.3E-19 2.8E-24 167.4 10.2 123 111-233 253-379 (392)
9 COG2940 Proteins containing SE 99.8 6.9E-19 1.5E-23 179.5 6.1 151 102-253 320-480 (480)
10 PF00856 SET: SET domain; Int 99.7 2.5E-16 5.5E-21 134.1 9.1 107 125-231 1-162 (162)
11 KOG1081 Transcription factor N 99.5 7.4E-15 1.6E-19 148.4 1.3 157 87-259 286-443 (463)
12 PF09465 LBR_tudor: Lamin-B re 99.5 1.3E-13 2.8E-18 97.8 6.5 47 299-347 7-54 (55)
13 KOG2589 Histone tail methylase 99.2 8.2E-12 1.8E-16 119.4 4.7 126 122-254 135-261 (453)
14 smart00570 AWS associated with 99.2 9.6E-12 2.1E-16 87.7 2.0 49 64-112 2-50 (51)
15 KOG1081 Transcription factor N 98.7 8.9E-09 1.9E-13 104.4 3.5 258 1-261 1-272 (463)
16 PF05033 Pre-SET: Pre-SET moti 98.5 6.5E-08 1.4E-12 78.5 2.3 79 23-106 4-103 (103)
17 KOG2461 Transcription factor B 98.3 3.8E-07 8.3E-12 90.7 4.1 109 113-234 27-146 (396)
18 smart00468 PreSET N-terminal t 97.7 3E-05 6.5E-10 62.4 3.9 55 21-75 4-59 (98)
19 smart00333 TUDOR Tudor domain. 97.5 0.00028 6.1E-09 50.6 5.6 44 299-344 4-49 (57)
20 cd04508 TUDOR Tudor domains ar 97.4 0.00053 1.2E-08 47.4 5.7 42 301-343 1-44 (48)
21 PF09038 53-BP1_Tudor: Tumour 97.2 0.00097 2.1E-08 55.3 6.4 43 297-340 2-45 (122)
22 smart00743 Agenet Tudor-like d 97.2 0.0012 2.5E-08 48.3 5.9 45 298-343 3-51 (61)
23 smart00508 PostSET Cysteine-ri 96.5 0.0012 2.6E-08 40.1 1.2 18 238-255 2-19 (26)
24 KOG1141 Predicted histone meth 95.8 0.027 5.9E-07 59.9 7.7 66 90-155 981-1054(1262)
25 KOG2084 Predicted histone tail 92.5 0.18 4E-06 50.7 5.2 43 190-236 208-251 (482)
26 PF06003 SMN: Survival motor n 91.1 0.6 1.3E-05 44.4 6.6 47 298-344 69-117 (264)
27 KOG4675 Uncharacterized conser 88.0 0.13 2.8E-06 48.5 -0.5 37 295-331 156-193 (273)
28 KOG1337 N-methyltransferase [G 85.5 0.57 1.2E-05 48.1 2.6 39 190-232 239-278 (472)
29 PF15057 DUF4537: Domain of un 83.3 2.8 6.2E-05 35.1 5.5 41 301-342 1-42 (124)
30 KOG1525 Sister chromatid cohes 80.2 0.077 1.7E-06 60.0 -6.6 58 293-350 982-1041(1266)
31 PF00567 TUDOR: Tudor domain; 80.2 6.2 0.00014 31.3 6.3 46 298-344 52-99 (121)
32 PF08863 YolD: YolD-like prote 71.2 15 0.00032 28.4 6.1 42 302-343 45-87 (92)
33 PF08605 Rad9_Rad53_bind: Fung 69.8 11 0.00023 32.1 5.2 34 305-338 15-49 (131)
34 PF03638 TCR: Tesmin/TSO1-like 69.1 3.2 7E-05 28.2 1.5 37 65-107 3-40 (42)
35 cd01735 LSm12_N LSm12 belongs 65.3 29 0.00062 25.5 6.0 33 299-331 4-36 (61)
36 PRK00737 small nuclear ribonuc 64.5 9.3 0.0002 28.8 3.5 31 296-326 9-39 (72)
37 cd00600 Sm_like The eukaryotic 61.4 12 0.00027 26.7 3.6 30 297-326 2-31 (63)
38 PF01423 LSM: LSM domain ; In 60.8 12 0.00027 27.2 3.5 30 297-326 4-33 (67)
39 KOG0644 Uncharacterized conser 59.7 12 0.00025 41.0 4.3 43 300-342 981-1036(1113)
40 PF08666 SAF: SAF domain; Int 58.5 6.2 0.00013 28.2 1.5 15 213-227 3-17 (63)
41 cd01717 Sm_B The eukaryotic Sm 58.3 13 0.00028 28.5 3.3 30 297-326 6-35 (79)
42 cd01731 archaeal_Sm1 The archa 56.4 19 0.00042 26.5 3.9 31 297-327 6-36 (68)
43 COG1958 LSM1 Small nuclear rib 54.9 17 0.00037 27.7 3.5 34 295-328 11-44 (79)
44 KOG2155 Tubulin-tyrosine ligas 54.3 19 0.00041 36.7 4.5 48 186-233 203-252 (631)
45 PF02067 Metallothio_5: Metall 52.9 10 0.00023 25.4 1.7 22 80-103 6-27 (41)
46 cd01719 Sm_G The eukaryotic Sm 52.2 25 0.00055 26.5 4.0 33 294-326 3-35 (72)
47 cd01727 LSm8 The eukaryotic Sm 49.4 24 0.00052 26.6 3.5 30 297-326 5-34 (74)
48 KOG1338 Uncharacterized conser 49.4 10 0.00022 38.0 1.8 40 187-232 218-260 (466)
49 smart00651 Sm snRNP Sm protein 49.1 23 0.0005 25.7 3.3 31 296-326 3-33 (67)
50 cd01726 LSm6 The eukaryotic Sm 48.7 27 0.00058 25.8 3.6 30 297-326 6-35 (67)
51 cd01722 Sm_F The eukaryotic Sm 46.5 30 0.00066 25.6 3.6 31 296-326 6-36 (68)
52 KOG1775 U6 snRNA-associated Sm 45.6 18 0.0004 27.6 2.2 30 297-326 13-42 (84)
53 cd01728 LSm1 The eukaryotic Sm 45.6 28 0.00061 26.4 3.4 30 296-325 7-36 (74)
54 PF05641 Agenet: Agenet domain 44.5 61 0.0013 23.8 5.0 34 300-334 3-40 (68)
55 PRK09618 flgD flagellar basal 42.3 79 0.0017 27.3 6.0 42 295-336 86-127 (142)
56 PF00856 SET: SET domain; Int 41.7 16 0.00035 30.0 1.7 17 212-228 2-18 (162)
57 KOG1079 Transcriptional repres 41.0 11 0.00024 40.0 0.7 30 79-108 511-540 (739)
58 PF07039 DUF1325: SGF29 tudor- 40.6 74 0.0016 26.9 5.5 40 299-338 73-114 (130)
59 cd01729 LSm7 The eukaryotic Sm 39.2 39 0.00084 26.1 3.3 31 296-326 7-37 (81)
60 PF15057 DUF4537: Domain of un 39.1 66 0.0014 26.9 5.0 44 300-343 58-107 (124)
61 cd01732 LSm5 The eukaryotic Sm 38.5 43 0.00093 25.5 3.4 32 297-328 9-40 (76)
62 cd01730 LSm3 The eukaryotic Sm 37.5 44 0.00095 25.7 3.4 29 297-325 7-35 (82)
63 PRK11911 flgD flagellar basal 36.4 95 0.0021 26.7 5.5 43 296-338 88-130 (140)
64 COG0231 Efp Translation elonga 35.9 1E+02 0.0022 26.1 5.6 45 300-350 48-93 (131)
65 PF09910 DUF2139: Uncharacteri 35.6 61 0.0013 31.6 4.6 50 301-350 87-146 (339)
66 PF02237 BPL_C: Biotin protein 34.6 1.5E+02 0.0032 20.2 5.7 39 300-340 2-40 (48)
67 KOG1171 Metallothionein-like p 33.8 12 0.00026 37.7 -0.5 36 64-105 216-252 (406)
68 PF12904 Collagen_bind_2: Puta 31.9 47 0.001 26.5 2.8 27 293-319 38-68 (93)
69 smart00858 SAF This domain fam 31.7 31 0.00067 24.3 1.6 16 213-228 3-18 (64)
70 PF00313 CSD: 'Cold-shock' DNA 31.0 89 0.0019 22.5 4.0 23 316-338 3-25 (66)
71 cd01723 LSm4 The eukaryotic Sm 30.0 1E+02 0.0022 23.3 4.2 33 297-329 7-39 (76)
72 PF02736 Myosin_N: Myosin N-te 29.9 1E+02 0.0022 20.5 3.8 34 305-340 3-38 (42)
73 PF11717 Tudor-knot: RNA bindi 29.3 1.5E+02 0.0033 20.8 4.8 34 300-334 3-39 (55)
74 PF02576 DUF150: Uncharacteris 29.2 1.9E+02 0.004 24.4 6.3 39 295-335 81-123 (141)
75 cd01720 Sm_D2 The eukaryotic S 29.1 82 0.0018 24.7 3.7 31 301-334 14-44 (87)
76 COG1278 CspC Cold shock protei 27.4 57 0.0012 24.4 2.4 23 316-338 4-26 (67)
77 cd06168 LSm9 The eukaryotic Sm 26.4 89 0.0019 23.7 3.4 31 296-326 5-35 (75)
78 smart00317 SET SET (Su(var)3-9 25.9 1.1E+02 0.0024 23.6 4.1 16 126-141 98-113 (116)
79 PRK09507 cspE cold shock prote 24.9 1.2E+02 0.0025 22.6 3.7 22 316-337 6-27 (69)
80 PF03088 Str_synth: Strictosid 24.4 95 0.0021 24.5 3.3 19 316-334 37-55 (89)
81 PF02513 Spin-Ssty: Spin/Ssty 24.3 2.6E+02 0.0057 19.7 5.3 37 300-336 1-42 (50)
82 PRK10943 cold shock-like prote 23.8 1.2E+02 0.0027 22.4 3.7 23 316-338 6-28 (69)
83 PRK06009 flgD flagellar basal 23.8 1.7E+02 0.0036 25.2 4.9 80 258-340 30-133 (140)
84 KOG3026 Splicing factor SPF30 23.7 95 0.0021 29.1 3.6 36 298-333 91-127 (262)
85 PRK14637 hypothetical protein; 22.8 1.8E+02 0.0039 25.2 5.0 33 293-325 90-123 (151)
86 cd01721 Sm_D3 The eukaryotic S 22.7 1.6E+02 0.0035 21.8 4.2 33 296-328 5-37 (70)
87 COG1588 POP4 RNase P/RNase MRP 22.5 2.9E+02 0.0062 22.2 5.6 46 289-338 5-53 (95)
88 TIGR02381 cspD cold shock doma 22.0 1.3E+02 0.0029 22.1 3.5 22 316-337 4-25 (68)
89 PF06613 KorB_C: KorB C-termin 21.9 1.2E+02 0.0026 22.3 3.0 25 323-347 29-54 (60)
90 PF12701 LSM14: Scd6-like Sm d 21.8 2.6E+02 0.0057 22.3 5.4 30 297-326 4-33 (96)
91 COG4697 Uncharacterized protei 21.6 83 0.0018 30.2 2.8 41 295-336 110-154 (319)
92 smart00538 POP4 A domain found 21.5 2.8E+02 0.0061 21.9 5.5 28 292-319 4-34 (92)
93 PF13964 Kelch_6: Kelch motif 21.4 79 0.0017 21.2 2.1 20 333-352 26-45 (50)
94 PRK14998 cold shock-like prote 20.3 1.4E+02 0.0031 22.4 3.5 23 316-338 4-26 (73)
No 1
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-56 Score=450.47 Aligned_cols=222 Identities=41% Similarity=0.808 Sum_probs=205.5
Q ss_pred CCCCCCCcEEecceeeccccccccCCCCCCcccccCCCCC----CCCCCCCCCccceeeeCCC-CCC-CCCCCCCccccc
Q 018661 37 IKPKAIPYVFIKRNIYLTKRIKRRLEDDGIFCSCTASPGS----SGVCDRDCHCGMLLSSCSS-GCK-CGNSCLNKPFQN 110 (352)
Q Consensus 37 ~~~~p~~f~~I~~n~~~~~~~~~~~~~~~~~C~C~~~~~~----~~~C~~~C~c~~~~~eC~~-~C~-C~~~C~Nr~~q~ 110 (352)
....|..|.-|..++|..++.+.....+.+.|+|.+..++ .+.|+.+|.|+++..||++ .|+ ||..|+|++||+
T Consensus 37 k~e~~~~f~~~~e~~y~~krk~~~ee~~~m~Cdc~~~~~d~~n~~~~cg~~CiNr~t~iECs~~~C~~cg~~C~NQRFQk 116 (729)
T KOG4442|consen 37 KEEALTKFENLDEKFYANKRKKKKEENDEMICDCKPKTGDGANGACACGEDCINRMTSIECSDRECPRCGVYCKNQRFQK 116 (729)
T ss_pred hcccchhhhhhhhhhhHHhhccCcccCcceeeecccccccccccccccCccccchhhhcccCCccCCCccccccchhhhh
Confidence 3455788888999999877655444446789999996644 4568999999999999999 899 999999999999
Q ss_pred CCcccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeeccceeEeecccCCcccc
Q 018661 111 RPVKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEINRDMVIDATYKGNKSRY 190 (352)
Q Consensus 111 ~~~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~~~~~IDa~~~GN~aRf 190 (352)
.+..+++||.|+++||||+|.++|++|+||+||.||||+..+++.|...|...+..|+|+|.+..+.+|||+.+||+|||
T Consensus 117 kqyA~vevF~Te~KG~GLRA~~dI~~g~FI~EY~GEVI~~~Ef~kR~~~Y~~d~~kh~Yfm~L~~~e~IDAT~KGnlaRF 196 (729)
T KOG4442|consen 117 KQYAKVEVFLTEKKGCGLRAEEDIPKGQFILEYIGEVIEEKEFEKRVKRYAKDGIKHYYFMALQGGEYIDATKKGNLARF 196 (729)
T ss_pred hccCceeEEEecCcccceeeccccCCCcEEeeeccccccHHHHHHHHHHHHhcCCceEEEEEecCCceecccccCcHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCCCCCCC-ceecCCCCCCccccCcCCCC
Q 018661 191 INHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFVQFGAD-QDCHCGAAGCRRKLGAKPSK 258 (352)
Q Consensus 191 iNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~~~~~-~~C~Cgs~~Crg~l~~~~~~ 258 (352)
|||||+|||.+++|.|++..||+|||.|.|++||||||||+++.|+.. ++|.||+++||||||++|..
T Consensus 197 iNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~rYGr~AQ~CyCgeanC~G~IGgk~q~ 265 (729)
T KOG4442|consen 197 INHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFDRYGRDAQPCYCGEANCRGWIGGKPQT 265 (729)
T ss_pred hcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEecccccccccccccccCCcccccccCCCCcc
Confidence 999999999999999999999999999999999999999999999864 89999999999999999643
No 2
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=5.6e-37 Score=301.74 Aligned_cols=233 Identities=30% Similarity=0.495 Sum_probs=175.4
Q ss_pred HHHhhCCCeEEeCCCCCCCCCCCCcEEecceeeccccccccCCCCCCcccccCCCCCCCCCCCCCCcc------------
Q 018661 20 LLKQIGNPVEFELPDWFIKPKAIPYVFIKRNIYLTKRIKRRLEDDGIFCSCTASPGSSGVCDRDCHCG------------ 87 (352)
Q Consensus 20 ~~~~~~~~~~f~lp~~~~~~~p~~f~~I~~n~~~~~~~~~~~~~~~~~C~C~~~~~~~~~C~~~C~c~------------ 87 (352)
++.+..+..+.++-+.++...++.|+||...++... ..........|.|...+... .|. .|.|.
T Consensus 64 d~~~~~e~~~v~~~n~id~~~~~~f~y~~~~~~~~~--~~~~~~~~~~c~C~~~~~~~-~~~-~C~C~~~n~~~~~~~~~ 139 (364)
T KOG1082|consen 64 DIALGSENLPVPLVNRIDEDAPLYFQYIATEIVDPG--ELSDCENSTGCRCCSSCSSV-LPL-TCLCERHNGGLVAYTCD 139 (364)
T ss_pred cccCccccCceeeeeeccCCccccceeccccccCcc--ccccCccccCCCccCCCCCC-CCc-cccChHhhCCccccccC
Confidence 333444444444444554444478999998877553 12233456779999765432 111 24442
Q ss_pred ----------ceeeeCCCCCCCCCCCCCcccccCCcccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHH
Q 018661 88 ----------MLLSSCSSGCKCGNSCLNKPFQNRPVKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERL 157 (352)
Q Consensus 88 ----------~~~~eC~~~C~C~~~C~Nr~~q~~~~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~ 157 (352)
..++||++.|+|+..|.||++|++...+++|++++.+||||++.+.|++|+||+||+||+++..+++.+.
T Consensus 140 ~~~~~~~~~~~~i~EC~~~C~C~~~C~nRv~q~g~~~~leIfrt~~kGwgvRs~~~I~~G~fvcEyaGe~~t~~e~~~~~ 219 (364)
T KOG1082|consen 140 GDCGTLGKFKEPVFECSVACGCHPDCANRVVQKGLQFHLEVFRTPEKGWGVRTLDPIPAGEFVCEYAGEVLTSEEAQRRT 219 (364)
T ss_pred CccccccccCccccccccCCCCCCcCcchhhccccccceEEEecCCceeeecccccccCCCeeEEEeeEecChHHhhhcc
Confidence 2488999999999999999999999999999999999999999999999999999999999999988763
Q ss_pred HHhhhcCC--cce------E---------------EeeeccceeEeecccCCccccccCCCCCCcceEEEEECC----eE
Q 018661 158 WKMKHLGE--TNF------Y---------------LCEINRDMVIDATYKGNKSRYINHSCCPNTEMQKWIIDG----ET 210 (352)
Q Consensus 158 ~~~~~~~~--~~~------y---------------~~~l~~~~~IDa~~~GN~aRfiNHSC~PN~~~~~~~~~g----~~ 210 (352)
........ ... | .......+.|||...||++|||||||.||+.++.+..++ .+
T Consensus 220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ida~~~GNv~RfinHSC~PN~~~~~v~~~~~~~~~~ 299 (364)
T KOG1082|consen 220 HLREYLDDDCDAYSIADREWVDESPVGNTFVAPSLPGGPGRELLIDAKPHGNVARFINHSCSPNLLYQAVFQDEFVLLYL 299 (364)
T ss_pred ccccccccccccchhhhccccccccccccccccccccCCCcceEEchhhcccccccccCCCCccceeeeeeecCCccchh
Confidence 22211111 000 0 112246689999999999999999999999999888764 37
Q ss_pred EEEEEEccCCCCCCeEEEcCCCCCC------------CCCceecCCCCCCccccCcCC
Q 018661 211 RIGIFATRDIKKGENLTYDYQFVQF------------GADQDCHCGAAGCRRKLGAKP 256 (352)
Q Consensus 211 ~i~i~A~rdI~~GEELT~dY~~~~~------------~~~~~C~Cgs~~Crg~l~~~~ 256 (352)
+++|||+++|.||||||+||+..+. .....|.||+.+||+.+....
T Consensus 300 ~i~ffa~~~I~p~~ELT~dYg~~~~~~~~~~~~~~~~~~~~~c~c~~~~cr~~~~~~~ 357 (364)
T KOG1082|consen 300 RIGFFALRDISPGEELTLDYGKAYKLLVQDGANIYTPVMKKNCNCGLEKCRGLLGSAP 357 (364)
T ss_pred eeeeeeccccCCCcccchhhcccccccccccccccccccchhhcCCCHHhCcccCCCc
Confidence 8999999999999999999996632 123679999999999997654
No 3
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=2.2e-33 Score=299.23 Aligned_cols=138 Identities=40% Similarity=0.698 Sum_probs=132.3
Q ss_pred cEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeeccceeEeecccCCccccccCC
Q 018661 115 KMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEINRDMVIDATYKGNKSRYINHS 194 (352)
Q Consensus 115 ~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~~~~~IDa~~~GN~aRfiNHS 194 (352)
.|...++..+||||||.+.|.+|++|+||+||+|....++.|...|...+....|+|.++...+|||+++||+|||||||
T Consensus 867 ~~~F~~s~iH~wglfa~~~i~~~dmViEY~Ge~vR~~iad~RE~~Y~~~gi~~sYlfrid~~~ViDAtk~gniAr~InHs 946 (1005)
T KOG1080|consen 867 YVKFGRSGIHGWGLFAMENIAAGDMVIEYRGELVRSSIADLREARYERMGIGDSYLFRIDDEVVVDATKKGNIARFINHS 946 (1005)
T ss_pred hhccccccccccceeeccCccccceEEEeeceehhhhHHHHHHHHHhccCcccceeeecccceEEeccccCchhheeecc
Confidence 46777899999999999999999999999999999999999998888888889999999999999999999999999999
Q ss_pred CCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCCCCCCCceecCCCCCCcccc
Q 018661 195 CCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFVQFGADQDCHCGAAGCRRKL 252 (352)
Q Consensus 195 C~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~~~~~~~C~Cgs~~Crg~l 252 (352)
|+|||....+.|+|+.+|+|||.|+|.+||||||||.|...+...+|+|||++|||++
T Consensus 947 C~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYkF~~e~~kipClCgap~Crg~~ 1004 (1005)
T KOG1080|consen 947 CNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYKFPTEDDKIPCLCGAPNCRGFL 1004 (1005)
T ss_pred cCCCceeeEEEecCeeEEEEEEecccccCceeeeeccccccccccccccCCCcccccc
Confidence 9999999999999999999999999999999999999998888899999999999997
No 4
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=99.96 E-value=1.8e-30 Score=261.12 Aligned_cols=150 Identities=35% Similarity=0.642 Sum_probs=137.4
Q ss_pred CCccceeeeCCC-CCCC-C---------CCCCCcccccCCcccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhh
Q 018661 84 CHCGMLLSSCSS-GCKC-G---------NSCLNKPFQNRPVKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQT 152 (352)
Q Consensus 84 C~c~~~~~eC~~-~C~C-~---------~~C~Nr~~q~~~~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e 152 (352)
|+|.+...||.| .|.+ + .+|.|-.+|++.++++.|..+...|||||+.+.+.+++||.||+||+|+++|
T Consensus 553 CpC~~A~rECdPd~Cl~cg~~~~~d~~~~~C~N~~l~~~~qkr~llapSdVaGwGlFlKe~v~KnefisEY~GE~IS~dE 632 (739)
T KOG1079|consen 553 CPCYLAVRECDPDVCLMCGNVDHFDSSKISCKNTNLQRGEQKRVLLAPSDVAGWGLFLKESVSKNEFISEYTGEIISHDE 632 (739)
T ss_pred CchhhhccccCchHHhccCcccccccCccccccchhhhhhhcceeechhhccccceeeccccCCCceeeeecceeccchh
Confidence 677777888986 3644 2 3899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcCCcceEEeeeccceeEeecccCCccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCC
Q 018661 153 CEERLWKMKHLGETNFYLCEINRDMVIDATYKGNKSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQF 232 (352)
Q Consensus 153 ~~~r~~~~~~~~~~~~y~~~l~~~~~IDa~~~GN~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~ 232 (352)
+++|.+.|... ..+|+|+++.+++|||+++||.+||+|||-+|||....+++.|..||+|||.|.|.+||||||||++
T Consensus 633 ADrRGkiYDr~--~cSflFnln~dyviDs~rkGnk~rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrY 710 (739)
T KOG1079|consen 633 ADRRGKIYDRY--MCSFLFNLNNDYVIDSTRKGNKIRFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRY 710 (739)
T ss_pred hhhcccccccc--cceeeeeccccceEeeeeecchhhhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeecc
Confidence 99998777654 3569999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCC
Q 018661 233 VQF 235 (352)
Q Consensus 233 ~~~ 235 (352)
+..
T Consensus 711 s~~ 713 (739)
T KOG1079|consen 711 SPE 713 (739)
T ss_pred Ccc
Confidence 764
No 5
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.94 E-value=7.9e-26 Score=184.66 Aligned_cols=115 Identities=49% Similarity=0.780 Sum_probs=100.9
Q ss_pred EEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeeccceeEeecccCCccccccCCC
Q 018661 116 MKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEINRDMVIDATYKGNKSRYINHSC 195 (352)
Q Consensus 116 l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~~~~~IDa~~~GN~aRfiNHSC 195 (352)
++++.++++|+||||+++|++|++|++|.|.++...+...+...+........|++.....++||++..||++|||||||
T Consensus 2 ~~~~~~~~~G~gl~a~~~i~~g~~i~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~~~~~~~~~iNHsc 81 (116)
T smart00317 2 LEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERSKAYDTDGADSFYLFEIDSDLCIDARRKGNIARFINHSC 81 (116)
T ss_pred cEEEecCCCcEEEEECCccCCCCEEEEEEeEEECHHHHHHHHHHHHhcCCCCEEEEECCCCEEEeCCccCcHHHeeCCCC
Confidence 56788889999999999999999999999999998887766543333333356788887789999999999999999999
Q ss_pred CCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcC
Q 018661 196 CPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDY 230 (352)
Q Consensus 196 ~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY 230 (352)
.||+.+..+..++..++.++|+|+|++|||||+||
T Consensus 82 ~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 82 EPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 99999998888887799999999999999999999
No 6
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=99.92 E-value=4.8e-26 Score=232.01 Aligned_cols=76 Identities=42% Similarity=0.819 Sum_probs=69.0
Q ss_pred eeEeecccCCccccccCCCCCCcceEEEEECCe----EEEEEEEccCCCCCCeEEEcCCCCCC---CCCceecCCCCCCc
Q 018661 177 MVIDATYKGNKSRYINHSCCPNTEMQKWIIDGE----TRIGIFATRDIKKGENLTYDYQFVQF---GADQDCHCGAAGCR 249 (352)
Q Consensus 177 ~~IDa~~~GN~aRfiNHSC~PN~~~~~~~~~g~----~~i~i~A~rdI~~GEELT~dY~~~~~---~~~~~C~Cgs~~Cr 249 (352)
++|||+.-||++||+||||+||+.++.|+++.+ +.++|||.+-|+||+||||||++..- +....|+||+.+||
T Consensus 1179 yvIDAk~eGNlGRfLNHSC~PNl~VQnVfvdTHdlrfPwVAFFt~kyVkAgtELTWDY~Ye~g~v~~keL~C~CGa~~Cr 1258 (1262)
T KOG1141|consen 1179 YVIDAKQEGNLGRFLNHSCDPNLHVQNVFVDTHDLRFPWVAFFTRKYVKAGTELTWDYQYEQGQVATKELTCHCGAENCR 1258 (1262)
T ss_pred EEEecccccchhhhhccCCCccceeeeeeeeccccCCchhhhhhhhhhccCceeeeeccccccccccceEEEecChhhhh
Confidence 789999999999999999999999999999864 67999999999999999999998763 23468999999999
Q ss_pred ccc
Q 018661 250 RKL 252 (352)
Q Consensus 250 g~l 252 (352)
|.|
T Consensus 1259 grL 1261 (1262)
T KOG1141|consen 1259 GRL 1261 (1262)
T ss_pred ccc
Confidence 986
No 7
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=99.92 E-value=3.4e-26 Score=238.27 Aligned_cols=133 Identities=44% Similarity=0.813 Sum_probs=119.4
Q ss_pred CCCcccccCC-cccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeeccceeEee
Q 018661 103 CLNKPFQNRP-VKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEINRDMVIDA 181 (352)
Q Consensus 103 C~Nr~~q~~~-~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~~~~~IDa 181 (352)
|+|+.+|+.. ..+|.+++.+.+||||.|.++|++||||+||+|+|++.++++.++..... ...+.|...+..+++||+
T Consensus 1166 c~nqrm~r~e~cp~L~v~~gp~~G~~v~tk~PikagtfI~EYvGeVit~ke~e~~mmtl~~-~d~~~~cL~I~p~l~id~ 1244 (1306)
T KOG1083|consen 1166 CSNQRMQRHEECPPLEVFRGPKKGWGVRTKEPIKAGTFIMEYVGEVITEKEFEPRMMTLYH-NDDDHYCLVIDPGLFIDI 1244 (1306)
T ss_pred hhhHHhhhhccCCCcceeccCCCCccccccccccccchHHHHHHHHHHHHhhcccccccCC-CCCcccccccCccccCCh
Confidence 8889888754 46899999999999999999999999999999999999988877433322 344578999999999999
Q ss_pred cccCCccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCCCCC
Q 018661 182 TYKGNKSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFVQFG 236 (352)
Q Consensus 182 ~~~GN~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~~~ 236 (352)
.++||.+||+||||.|||+++.|.++|..|++|||+|||.+||||||||++..++
T Consensus 1245 ~R~~n~~RfinhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN~ks~~ 1299 (1306)
T KOG1083|consen 1245 PRMGNGARFINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYNFKSFN 1299 (1306)
T ss_pred hhccccccccccccCCCCccccccccceeeeeeeecCCCCCCceEEEeccccccC
Confidence 9999999999999999999999999999999999999999999999999976654
No 8
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=99.80 E-value=1.3e-19 Score=167.43 Aligned_cols=123 Identities=31% Similarity=0.423 Sum_probs=104.6
Q ss_pred CCcccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCc---ceEEeeeccceeEeeccc-CC
Q 018661 111 RPVKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGET---NFYLCEINRDMVIDATYK-GN 186 (352)
Q Consensus 111 ~~~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~---~~y~~~l~~~~~IDa~~~-GN 186 (352)
+....+.+....++|.||+|+..+.+|+||.||.|.+|.-.++..|...|...... .+|+-..+..++|||+.- +-
T Consensus 253 g~~egl~~~~~dgKGRGv~a~~~F~rgdFVVEY~Gdliei~eAk~rE~~Ya~De~~GcYMYyF~h~sk~yCiDAT~et~~ 332 (392)
T KOG1085|consen 253 GTNEGLLEVYKDGKGRGVRAKVNFERGDFVVEYRGDLIEISEAKVREEQYANDEEIGCYMYYFEHNSKKYCIDATKETPW 332 (392)
T ss_pred ccccceeEEeeccccceeEeecccccCceEEEEecceeeechHHHHHHHhccCcccceEEEeeeccCeeeeeeccccccc
Confidence 34456777777889999999999999999999999999988888877666544333 344445677899999965 45
Q ss_pred ccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCC
Q 018661 187 KSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFV 233 (352)
Q Consensus 187 ~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~ 233 (352)
++|+||||-.+|+....+.++|.++++++|.|||.+||||+||||.-
T Consensus 333 lGRLINHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDR 379 (392)
T KOG1085|consen 333 LGRLINHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDR 379 (392)
T ss_pred chhhhcccccCcceeeEEEecCCceEEEEeccccccchhhhhhcccc
Confidence 78999999999999999999999999999999999999999999963
No 9
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=99.75 E-value=6.9e-19 Score=179.46 Aligned_cols=151 Identities=36% Similarity=0.588 Sum_probs=119.3
Q ss_pred CCCCcccccCCcccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeec-cceeEe
Q 018661 102 SCLNKPFQNRPVKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEIN-RDMVID 180 (352)
Q Consensus 102 ~C~Nr~~q~~~~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~-~~~~ID 180 (352)
.+.|..-+........+..+...|+|+||.+.|++|++|.+|.|+++...++..+...+...+.. +.+..+. ...++|
T Consensus 320 ~~~~~~~~~~~~~~~~~~~~~~~~~g~fa~~~i~~~e~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~d 398 (480)
T COG2940 320 ELLNSNGCKKRREPNVVQESEIKGYGVFALESIKKGEFIIEYHGEIIRRKEAREREENYDLLGNE-FSFGLLEDKDKVRD 398 (480)
T ss_pred chhhhcccccccchhhhhhhcccccceeehhhccchHHHHHhcCcccchHHHHhhhccccccccc-cchhhccccchhhh
Confidence 34444333444556667778999999999999999999999999999998887776555332222 2222333 278899
Q ss_pred ecccCCccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCCCCCC---------CceecCCCCCCccc
Q 018661 181 ATYKGNKSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFVQFGA---------DQDCHCGAAGCRRK 251 (352)
Q Consensus 181 a~~~GN~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~~~~---------~~~C~Cgs~~Crg~ 251 (352)
+...|+.+||+||||.||+........|..++.++|+|||.+|||||+||+...+.. ...|.||+..|++.
T Consensus 399 ~~~~g~~~r~~nHS~~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 478 (480)
T COG2940 399 SQKAGDVARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHT 478 (480)
T ss_pred hhhcccccceeecCCCCCcceecccccccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCC
Confidence 999999999999999999999777666667899999999999999999999776542 36899999999998
Q ss_pred cC
Q 018661 252 LG 253 (352)
Q Consensus 252 l~ 253 (352)
+.
T Consensus 479 ~~ 480 (480)
T COG2940 479 MS 480 (480)
T ss_pred CC
Confidence 63
No 10
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=99.66 E-value=2.5e-16 Score=134.09 Aligned_cols=107 Identities=25% Similarity=0.300 Sum_probs=74.0
Q ss_pred CcEEEeccccCCCceEEEEeeeEechhhHHHH-------------------H-----------------HHhhh------
Q 018661 125 GAGIVADEDIKRGEFVIEYVGEVIDDQTCEER-------------------L-----------------WKMKH------ 162 (352)
Q Consensus 125 G~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r-------------------~-----------------~~~~~------ 162 (352)
|+||||+++|++|++|++..+.+++....... . .....
T Consensus 1 GrGl~At~dI~~Ge~I~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (162)
T PF00856_consen 1 GRGLFATRDIKAGEVILIPRPAILTPDEVSPQPELLRLQLSKALEEQSRSDFSIQKKQKAEKSERSPQLESLHSISLRSE 80 (162)
T ss_dssp SEEEEESS-B-TTEEEEEESEEEEEHHHHHCHHHHSHHTTCSSSCSHHTTHHHHHHHHHHHHHHHHHHHHHHHHHCHTTT
T ss_pred CEEEEECccCCCCCEEEEECcceEEehhhhhcccchhhhhhhhhcccccccccccccccccccccccccccccccccccc
Confidence 89999999999999999989999887665331 0 00000
Q ss_pred cC-------------CcceEEeeeccceeEeecccCCccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEc
Q 018661 163 LG-------------ETNFYLCEINRDMVIDATYKGNKSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYD 229 (352)
Q Consensus 163 ~~-------------~~~~y~~~l~~~~~IDa~~~GN~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~d 229 (352)
.. ...............++.....++.|+||||.|||.+..........+.|+|.|+|++|||||++
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~p~~d~~NHsc~pn~~~~~~~~~~~~~~~~~a~r~I~~GeEi~is 160 (162)
T PF00856_consen 81 LQFSQAFQWSWFISWTRSDFSSRSFSEDDRDGIALYPFADMLNHSCDPNCEVSFDFDGDGGCLVVRATRDIKKGEEIFIS 160 (162)
T ss_dssp CCTCCHHHHHHHHHHHHHEEEEEEETTEEEEEEEEETGGGGSEEESSTSEEEEEEEETTTTEEEEEESS-B-TTSBEEEE
T ss_pred ccccccccchhhccccceeeeccccccccccccccCcHhHheccccccccceeeEeecccceEEEEECCccCCCCEEEEE
Confidence 00 00011112223344566677889999999999999998776667789999999999999999999
Q ss_pred CC
Q 018661 230 YQ 231 (352)
Q Consensus 230 Y~ 231 (352)
||
T Consensus 161 YG 162 (162)
T PF00856_consen 161 YG 162 (162)
T ss_dssp ST
T ss_pred EC
Confidence 97
No 11
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=99.48 E-value=7.4e-15 Score=148.37 Aligned_cols=157 Identities=40% Similarity=0.755 Sum_probs=134.0
Q ss_pred cceeeeCC-CCCCCCCCCCCcccccCCcccEEEEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCC
Q 018661 87 GMLLSSCS-SGCKCGNSCLNKPFQNRPVKKMKLVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGE 165 (352)
Q Consensus 87 ~~~~~eC~-~~C~C~~~C~Nr~~q~~~~~~l~v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~ 165 (352)
.+..++|. ..|.+...|.|+.+....... +.+ +|..+|.+| +|++++..+...++........
T Consensus 286 ~~~~~~~~p~~~~~~~~~~~~~~sk~~~~e------~~~----~~~~~~~k~------vg~~i~~~e~~~~~~~~~~~~~ 349 (463)
T KOG1081|consen 286 KMLAYEVHPKVCSAEERCHNQQFSKESYPE------PQK----TAKADIRKG------VGEVIDDKECKARLQRVKESDL 349 (463)
T ss_pred Hhhhhhhcccccccccccccchhhhhcccc------cch----hhHHhhhcc------cCcccchhhheeehhhhhccch
Confidence 44566665 579999999999876555433 222 888899998 8999999999888888777777
Q ss_pred cceEEeeeccceeEeecccCCccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCCCCCCCceecCCC
Q 018661 166 TNFYLCEINRDMVIDATYKGNKSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFVQFGADQDCHCGA 245 (352)
Q Consensus 166 ~~~y~~~l~~~~~IDa~~~GN~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~~~~~~~C~Cgs 245 (352)
..+|+..+..+..||+..+||.+||+||||+||+...+|.+.+..+++++|.+.|++|||||++|.....+....|.|++
T Consensus 350 ~~~~~~~~e~~~~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t~~~n~~~~~~~~~~~~~~ 429 (463)
T KOG1081|consen 350 VDFYMVFIQKDRIIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELTFNYNGNCEGNEKRCCCGS 429 (463)
T ss_pred hhhhhhhhhcccccccccccchhhhhcccCCCceeechhheecccccccccccccccchhhhheeeccccCCcceEeecc
Confidence 77776666666699999999999999999999999999999999999999999999999999999999888889999999
Q ss_pred CCCccccCcCCCCC
Q 018661 246 AGCRRKLGAKPSKP 259 (352)
Q Consensus 246 ~~Crg~l~~~~~~~ 259 (352)
.+|.++++.+...+
T Consensus 430 e~~~~~~~k~~~~~ 443 (463)
T KOG1081|consen 430 ENCTETKGKKKKKK 443 (463)
T ss_pred cccccCCcccccch
Confidence 99999998765443
No 12
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=99.47 E-value=1.3e-13 Score=97.76 Aligned_cols=47 Identities=28% Similarity=0.584 Sum_probs=38.8
Q ss_pred ccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeecCceeEEeccccce
Q 018661 299 CIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFEDGESEFIDMAKVDW 347 (352)
Q Consensus 299 ~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~dg~~e~~~l~~e~~ 347 (352)
-+|.+|++|||.+..|| |.|.+||+.+++|+|+|+||++ ++|++.+.
T Consensus 7 ~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGte--l~lke~di 54 (55)
T PF09465_consen 7 AIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTE--LELKENDI 54 (55)
T ss_dssp -SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-E--EEEECCCE
T ss_pred cCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCE--EEeccccc
Confidence 47999999999999999 9999999999999999999998 77777654
No 13
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=99.22 E-value=8.2e-12 Score=119.43 Aligned_cols=126 Identities=25% Similarity=0.335 Sum_probs=90.4
Q ss_pred cCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeeccceeEeecccCCccccccCCCCCCcce
Q 018661 122 EKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEINRDMVIDATYKGNKSRYINHSCCPNTEM 201 (352)
Q Consensus 122 ~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~~~~~IDa~~~GN~aRfiNHSC~PN~~~ 201 (352)
...|--|+|++.+.+|+-|-..+|-|+.-.+++++.... .+... |........ =-|...=..|+||||.|.|||++
T Consensus 135 ~~~gAkivst~~w~~ndkIe~LvGcIaeLse~eE~~ll~--~g~nD-FSvmyStRk-~caqLwLGPaafINHDCrpnCkF 210 (453)
T KOG2589|consen 135 SQNGAKIVSTKSWSRNDKIELLVGCIAELSEAEERSLLR--GGGND-FSVMYSTRK-RCAQLWLGPAAFINHDCRPNCKF 210 (453)
T ss_pred cCCCceEEeeccccCCccHHHhhhhhhhcChhhhHHHHh--ccCCc-eeeeeeccc-chhhheeccHHhhcCCCCCCcee
Confidence 356889999999999999999999998776766663221 12222 222211110 01122236789999999999987
Q ss_pred EEEEECCeEEEEEEEccCCCCCCeEEEcCCCCCCCCC-ceecCCCCCCccccCc
Q 018661 202 QKWIIDGETRIGIFATRDIKKGENLTYDYQFVQFGAD-QDCHCGAAGCRRKLGA 254 (352)
Q Consensus 202 ~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~~~~~-~~C~Cgs~~Crg~l~~ 254 (352)
. ..|..++.|.++|||+||||||--||..+|+.. ..|.|-++.=+|.-+.
T Consensus 211 v---s~g~~tacvkvlRDIePGeEITcFYgs~fFG~~N~~CeC~TCER~g~gaF 261 (453)
T KOG2589|consen 211 V---STGRDTACVKVLRDIEPGEEITCFYGSGFFGENNEECECVTCERRGTGAF 261 (453)
T ss_pred e---cCCCceeeeehhhcCCCCceeEEeecccccCCCCceeEEeecccccccch
Confidence 3 345678999999999999999999999999864 6798887766665443
No 14
>smart00570 AWS associated with SET domains. subdomain of PRESET
Probab=99.17 E-value=9.6e-12 Score=87.73 Aligned_cols=49 Identities=43% Similarity=0.944 Sum_probs=44.5
Q ss_pred CCCcccccCCCCCCCCCCCCCCccceeeeCCCCCCCCCCCCCcccccCC
Q 018661 64 DGIFCSCTASPGSSGVCDRDCHCGMLLSSCSSGCKCGNSCLNKPFQNRP 112 (352)
Q Consensus 64 ~~~~C~C~~~~~~~~~C~~~C~c~~~~~eC~~~C~C~~~C~Nr~~q~~~ 112 (352)
+.+.|+|++...+..+|+++|+||++++||++.|+||..|+|++||++.
T Consensus 2 e~~~C~C~~~~~~~~~CgsdClNR~l~~EC~~~C~~G~~C~NqrFqk~~ 50 (51)
T smart00570 2 DIMTCECKPTDDDEGACGSDCLNRMLLIECSSDCPCGSYCSNQRFQKRQ 50 (51)
T ss_pred CCceeeCccCCCCCCCcchHHHHHHHhhhcCCCCCCCcCccCcccccCc
Confidence 4578999998766788999999999999999899999999999999875
No 15
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=98.69 E-value=8.9e-09 Score=104.44 Aligned_cols=258 Identities=25% Similarity=0.199 Sum_probs=194.0
Q ss_pred CCcCccCCchhhHHHHHHHHHHhhCCCeEEeCCCCCCCCCCCCcEEecceeeccccccccCCCCCCcccccCCC-C-CCC
Q 018661 1 MPAAKKNSDNSRIGHAFNKLLKQIGNPVEFELPDWFIKPKAIPYVFIKRNIYLTKRIKRRLEDDGIFCSCTASP-G-SSG 78 (352)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lp~~~~~~~p~~f~~I~~n~~~~~~~~~~~~~~~~~C~C~~~~-~-~~~ 78 (352)
|+..+|+++.+++...+.++.....+...++.|..+...++ ..|.++++....+........++|++..+. + .+.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~n---~~i~~~v~~~~~~~~~~~~~~~g~~~~~s~p~~~~~ 77 (463)
T KOG1081|consen 1 MSKFKKHSDRNQIPQHDLKCPSHNQESCSLETPPGSAPLGN---LKITRTVRLGKDLFESDACGGIGGSVSASEPNHVSP 77 (463)
T ss_pred CCcccccccccccchhhcccccccccccccCCCccccccCC---ceeeeeeecCcChhhcccccccccccccCCccccCC
Confidence 78899999999999999999999999999998888876666 889999998887777777778899999873 2 234
Q ss_pred CCCCCCCccceeeeCCCCCCCCCCCCCcccccCCcccEEEEEecCCCcE---EEeccccCCCceEEEEeeeEechh--hH
Q 018661 79 VCDRDCHCGMLLSSCSSGCKCGNSCLNKPFQNRPVKKMKLVQTEKCGAG---IVADEDIKRGEFVIEYVGEVIDDQ--TC 153 (352)
Q Consensus 79 ~C~~~C~c~~~~~eC~~~C~C~~~C~Nr~~q~~~~~~l~v~~s~~kG~G---lfA~~~I~~G~~I~ey~Gevi~~~--e~ 153 (352)
.|+..+.+....-+|...+.++..+.+...++.....-.-+..+..+++ ..|.+.+..|++|+.++|++.-.. ..
T Consensus 78 ~~~~~~~~~~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~~~~~c~~~~~d~~~~~~~~~~~~vw~~vg~~~~~~c~vc 157 (463)
T KOG1081|consen 78 EPGSRRHPKIEPSECFVCFKGGSLVTCKSRIQAPHRKCKPAQLEKCSKRCTDCRAFKKREVGDLVWSKVGEYPWWPCMVC 157 (463)
T ss_pred CCCchhccCCCcchhccccCCCccceeccccccccccCcCccCcccccCCcceeeeccccceeEEeEEcCccccccccee
Confidence 6888888888877787766666655555444444333344556666776 888889999999999999986554 22
Q ss_pred HHHHHHhhhcC-CcceEEeeeccceeEeecccCCccccccCCCCCCcceEEEEECCeEEEEEEEccCCCCCCe------E
Q 018661 154 EERLWKMKHLG-ETNFYLCEINRDMVIDATYKGNKSRYINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGEN------L 226 (352)
Q Consensus 154 ~~r~~~~~~~~-~~~~y~~~l~~~~~IDa~~~GN~aRfiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GEE------L 226 (352)
........... ...+|....-..+..++...|+..++++|++.|+..+..+...+..++..++.+.++.+.. .
T Consensus 158 ~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~g~~~~~l~~~~~~~s~~~~~~~~~~~r~~~~~~q~~~~~~~~e~k~~~ 237 (463)
T KOG1081|consen 158 HDPLLPKGMKHDHVNFFGCYAWTHEKRVFPYEGQSSKLIPHSKKPASTMSEKIKEAKARFGKLKAQWEAGIKQKELKPEE 237 (463)
T ss_pred cCcccchhhccccceeccchhhHHHhhhhhccchHHHhhhhccccchhhhhhhhcccchhhhcccchhhccchhhccccc
Confidence 33322222222 1333333111223344555899999999999999999999889999999999999998888 7
Q ss_pred EEcCCCCCCCCCceecCCCCCCccccCcCCCCCCC
Q 018661 227 TYDYQFVQFGADQDCHCGAAGCRRKLGAKPSKPKI 261 (352)
Q Consensus 227 T~dY~~~~~~~~~~C~Cgs~~Crg~l~~~~~~~~~ 261 (352)
+-+|....+...+.+.+.+..|...+...+.....
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~ 272 (463)
T KOG1081|consen 238 YKRIKVVCPIGDQQIYSAAVSCIKKLLAKPTDEKP 272 (463)
T ss_pred ccccccccCcCcccccchhhhhhhhcccccccccc
Confidence 77887777777788999999999999888766654
No 16
>PF05033 Pre-SET: Pre-SET motif; InterPro: IPR007728 This region is found in a number of histone lysine methyltransferases (HMTase), N-terminal to the SET domain; it is generally described as the pre-SET domain. 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 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 and stabilising the SET domain. 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: 0008270 zinc ion binding, 0018024 histone-lysine N-methyltransferase activity, 0034968 histone lysine methylation, 0005634 nucleus; PDB: 3K5K_A 2O8J_D 3RJW_B 1ML9_A 1PEG_B 1MVH_A 1MVX_A 3BO5_A 2RFI_B 3MO5_B ....
Probab=98.48 E-value=6.5e-08 Score=78.46 Aligned_cols=79 Identities=20% Similarity=0.381 Sum_probs=41.2
Q ss_pred hhCCCeEEeCCCCCCC-CCCCCcEEecceeeccccccccCCCCCCcccccCCCCCCCCCCCCCCc---------------
Q 018661 23 QIGNPVEFELPDWFIK-PKAIPYVFIKRNIYLTKRIKRRLEDDGIFCSCTASPGSSGVCDRDCHC--------------- 86 (352)
Q Consensus 23 ~~~~~~~f~lp~~~~~-~~p~~f~~I~~n~~~~~~~~~~~~~~~~~C~C~~~~~~~~~C~~~C~c--------------- 86 (352)
...|..++.+-+..+. ..|+.|+||.++++..... .........|+|...+.. ..+|.|
T Consensus 4 ~g~e~~pI~~~N~vd~~~~p~~F~Yi~~~~~~~~~~-~~~~~~~~~C~C~~~C~~----~~~C~C~~~~~~~~~Y~~~g~ 78 (103)
T PF05033_consen 4 RGKENVPIPVVNDVDDEPPPPNFEYIPENIYGEGVP-DIDPEFLQGCDCSGDCSN----PSNCECLQRNGGIFAYDSNGR 78 (103)
T ss_dssp CTSSSS-EEEEESSSS--SSTSSEE-SS-EESTTSS--TBGGGTS----SSSSTC----TTTSHHHCCTSSS-SB-TTSS
T ss_pred CCccCCCEEEEeCCCCCCCCCCeEEeeeEEcCCCcc-ccccccCccCccCCCCCC----CCCCcCccccCccccccCCCc
Confidence 3445555555445443 3469999999999877533 333445678999865422 233433
Q ss_pred -----cceeeeCCCCCCCCCCCCCc
Q 018661 87 -----GMLLSSCSSGCKCGNSCLNK 106 (352)
Q Consensus 87 -----~~~~~eC~~~C~C~~~C~Nr 106 (352)
..+++||++.|.|+..|.||
T Consensus 79 l~~~~~~~i~EC~~~C~C~~~C~NR 103 (103)
T PF05033_consen 79 LRIPDKPPIFECNDNCGCSPSCRNR 103 (103)
T ss_dssp BSSSSTSEEE---TTSSS-TTSTT-
T ss_pred CccCCCCeEEeCCCCCCCCCCCCCC
Confidence 23489999999999999997
No 17
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=98.33 E-value=3.8e-07 Score=90.73 Aligned_cols=109 Identities=24% Similarity=0.247 Sum_probs=81.4
Q ss_pred cccEEEEEe--cCCCcEEEeccccCCCceEEEEeeeEechhhHHHHHHHhhhcCCcceEEeeec----cceeEeec--cc
Q 018661 113 VKKMKLVQT--EKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEERLWKMKHLGETNFYLCEIN----RDMVIDAT--YK 184 (352)
Q Consensus 113 ~~~l~v~~s--~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~r~~~~~~~~~~~~y~~~l~----~~~~IDa~--~~ 184 (352)
...+.|..+ +..|.||++...|++|+--+-|.|+++... ......+.|++.+- .-.+||++ ..
T Consensus 27 P~~l~i~~Ssv~~~~lgV~s~~~i~~G~~FGP~~G~~~~~~---------~~~~~n~~y~W~I~~~d~~~~~iDg~d~~~ 97 (396)
T KOG2461|consen 27 PPELRIKPSSVPVTGLGVWSNASILPGTSFGPFEGEIIASI---------DSKSANNRYMWEIFSSDNGYEYIDGTDEEH 97 (396)
T ss_pred CCceEeeccccCCccccccccccccCcccccCccCcccccc---------ccccccCcceEEEEeCCCceEEeccCChhh
Confidence 446777775 677899999999999999999999982211 12223344555542 23789988 56
Q ss_pred CCccccccCCCCC---CcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCCCC
Q 018661 185 GNKSRYINHSCCP---NTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQFVQ 234 (352)
Q Consensus 185 GN~aRfiNHSC~P---N~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~~~ 234 (352)
.|+.||||-+++. |... +.....|.++|+|+|.+||||.++|+.++
T Consensus 98 sNWmRYV~~Ar~~eeQNL~A----~Q~~~~Ifyrt~r~I~p~eELlVWY~~e~ 146 (396)
T KOG2461|consen 98 SNWMRYVNSARSEEEQNLLA----FQIGENIFYRTIRDIRPNEELLVWYGSEY 146 (396)
T ss_pred cceeeeecccCChhhhhHHH----HhccCceEEEecccCCCCCeEEEEeccch
Confidence 8999999988864 6644 22345789999999999999999998765
No 18
>smart00468 PreSET N-terminal to some SET domains. A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished.
Probab=97.74 E-value=3e-05 Score=62.38 Aligned_cols=55 Identities=18% Similarity=0.203 Sum_probs=37.5
Q ss_pred HHhhCCCeEEeCCCCCCC-CCCCCcEEecceeeccccccccCCCCCCcccccCCCC
Q 018661 21 LKQIGNPVEFELPDWFIK-PKAIPYVFIKRNIYLTKRIKRRLEDDGIFCSCTASPG 75 (352)
Q Consensus 21 ~~~~~~~~~f~lp~~~~~-~~p~~f~~I~~n~~~~~~~~~~~~~~~~~C~C~~~~~ 75 (352)
++...|.+++.+-+..+. ..|+.|+||+++++..............+|+|...+.
T Consensus 4 is~G~E~~pI~~vN~vD~~~~p~~F~Yi~~~~~~~gv~~~~~~~~~~gC~C~~~C~ 59 (98)
T smart00468 4 ISNGKENVPVPLVNEVDEDPPPPDFEYISEYIYGQGVPIDRSPSPLVGCSCSGDCS 59 (98)
T ss_pred ccCCccCCCcceEecCCCCCCCCCcEECcceEcCCCcccccCCCCCCCCcCCCCCC
Confidence 455566677766666654 4569999999999866532234455678999998543
No 19
>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=97.48 E-value=0.00028 Score=50.57 Aligned_cols=44 Identities=18% Similarity=0.301 Sum_probs=39.2
Q ss_pred ccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeec-CceeEEeccc
Q 018661 299 CIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFED-GESEFIDMAK 344 (352)
Q Consensus 299 ~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~d-g~~e~~~l~~ 344 (352)
-+|..+.+.| .|..|| |+|.++++. +...|.|.| |..|.+.+..
T Consensus 4 ~~G~~~~a~~-~d~~wyra~I~~~~~~-~~~~V~f~D~G~~~~v~~~~ 49 (57)
T smart00333 4 KVGDKVAARW-EDGEWYRARIIKVDGE-QLYEVFFIDYGNEEVVPPSD 49 (57)
T ss_pred CCCCEEEEEe-CCCCEEEEEEEEECCC-CEEEEEEECCCccEEEeHHH
Confidence 4789999999 999999 999999998 889999988 9999887543
No 20
>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=97.37 E-value=0.00053 Score=47.35 Aligned_cols=42 Identities=19% Similarity=0.328 Sum_probs=37.8
Q ss_pred ccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeec-CceeEEecc
Q 018661 301 GKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFED-GESEFIDMA 343 (352)
Q Consensus 301 g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~d-g~~e~~~l~ 343 (352)
|..+-+.|+.|..|| |+|.+.++ .++-+|.|.| |.+|.+.++
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~-~~~~~V~f~DyG~~~~v~~~ 44 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS-DGKVEVFFVDYGNTEVVPLS 44 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC-CCcEEEEEEcCCCcEEEeHH
Confidence 667889999999999 99999998 7888999988 999998865
No 21
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=97.21 E-value=0.00097 Score=55.28 Aligned_cols=43 Identities=28% Similarity=0.342 Sum_probs=34.8
Q ss_pred ccccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeecCceeEE
Q 018661 297 QCCIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFEDGESEFI 340 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~dg~~e~~ 340 (352)
..+||.||-.-|..+..|| |+|+. |....|.+|+||||.+-.|
T Consensus 2 ~~~iG~rV~AkWS~n~yyY~G~I~~-~~~~~kykv~FdDG~~~~v 45 (122)
T PF09038_consen 2 SSFIGLRVFAKWSDNGYYYPGKITS-DKGKNKYKVLFDDGYECRV 45 (122)
T ss_dssp --STT-EEEEESSTTSEEEEEEEEE-EETTTEEEEEETTS-EEEE
T ss_pred CcccccEEEEEEccCCcccCceEee-cCCCCeEEEEecCCcccee
Confidence 4689999999999888889 99999 6889999999999987433
No 22
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=97.17 E-value=0.0012 Score=48.26 Aligned_cols=45 Identities=13% Similarity=0.158 Sum_probs=38.0
Q ss_pred cccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeec---CceeEEecc
Q 018661 298 CCIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFED---GESEFIDMA 343 (352)
Q Consensus 298 ~~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~d---g~~e~~~l~ 343 (352)
-.+|..|-++|+.+..|| |+|..++. .+++.|.|.+ |.+|.+..+
T Consensus 3 ~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~~~~~~~~~~e~v~~~ 51 (61)
T smart00743 3 FKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVRYLTESEPLKETVDWS 51 (61)
T ss_pred cCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEEECCCCcccEEEEeHH
Confidence 358999999999999999 99999998 7789999977 556666543
No 23
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=96.53 E-value=0.0012 Score=40.07 Aligned_cols=18 Identities=50% Similarity=1.008 Sum_probs=15.5
Q ss_pred CceecCCCCCCccccCcC
Q 018661 238 DQDCHCGAAGCRRKLGAK 255 (352)
Q Consensus 238 ~~~C~Cgs~~Crg~l~~~ 255 (352)
.+.|+|||.+|||+|+..
T Consensus 2 ~~~C~CGs~~CRG~l~~~ 19 (26)
T smart00508 2 KQPCLCGAPNCRGFLGXX 19 (26)
T ss_pred CeeeeCCCccccceeccc
Confidence 478999999999999654
No 24
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=95.82 E-value=0.027 Score=59.95 Aligned_cols=66 Identities=27% Similarity=0.485 Sum_probs=56.4
Q ss_pred eeeCCCCCCCCCCCCCcccccCCcccEE--------EEEecCCCcEEEeccccCCCceEEEEeeeEechhhHHH
Q 018661 90 LSSCSSGCKCGNSCLNKPFQNRPVKKMK--------LVQTEKCGAGIVADEDIKRGEFVIEYVGEVIDDQTCEE 155 (352)
Q Consensus 90 ~~eC~~~C~C~~~C~Nr~~q~~~~~~l~--------v~~s~~kG~GlfA~~~I~~G~~I~ey~Gevi~~~e~~~ 155 (352)
+++|...|.|...|.|+++|++...+++ |+.+..-|||+.+..+|+.-+||++|+|...+..-+.+
T Consensus 981 f~e~~~hss~~~~e~~~~v~~~~~~~me~~s~~~l~i~~~~~~~~~~~edtD~~~~~~~~~~~~~ppt~~l~~~ 1054 (1262)
T KOG1141|consen 981 FFECNDHSSCHRKEYNRVVQNNIKYPMEVSSFNDLQIFKTAQSGWGVREDTDIPQSTFICTYVGAPPTDDLADE 1054 (1262)
T ss_pred ceeccccchhcccccchhhhcCCccceeeeecccccccccccccccccccccCCCCcccccccCCCCchhhHHH
Confidence 7899999999999999999988766655 45566789999999999999999999999887665544
No 25
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=92.51 E-value=0.18 Score=50.69 Aligned_cols=43 Identities=35% Similarity=0.648 Sum_probs=31.0
Q ss_pred cccCCCCCCcceEEEEECCeEEEEEEEccCCCCCC-eEEEcCCCCCCC
Q 018661 190 YINHSCCPNTEMQKWIIDGETRIGIFATRDIKKGE-NLTYDYQFVQFG 236 (352)
Q Consensus 190 fiNHSC~PN~~~~~~~~~g~~~i~i~A~rdI~~GE-ELT~dY~~~~~~ 236 (352)
++||||.||+.. ..++. ...+.+...+.+++ ||++.|-...++
T Consensus 208 ~~~hsC~pn~~~---~~~~~-~~~~~~~~~~~~~~~~l~~~y~~~~~~ 251 (482)
T KOG2084|consen 208 LFNHSCFPNISV---IFDGR-GLALLVPAGIDAGEEELTISYTDPLLS 251 (482)
T ss_pred hcccCCCCCeEE---EECCc-eeEEEeecccCCCCCEEEEeecccccC
Confidence 889999999972 33443 34456667777776 999999766654
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=91.10 E-value=0.6 Score=44.38 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=38.9
Q ss_pred cccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeec-CceeEEeccc
Q 018661 298 CCIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFED-GESEFIDMAK 344 (352)
Q Consensus 298 ~~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~d-g~~e~~~l~~ 344 (352)
--||-+++.-|-.|..|| ++|.+.|+..+.-.|.|++ |..|++.|..
T Consensus 69 WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~d 117 (264)
T PF06003_consen 69 WKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSD 117 (264)
T ss_dssp --TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGG
T ss_pred CCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhh
Confidence 349999999999999999 9999999999999999954 8888888764
No 27
>KOG4675 consensus Uncharacterized conserved protein, contains ENT domain [General function prediction only]
Probab=87.95 E-value=0.13 Score=48.54 Aligned_cols=37 Identities=24% Similarity=0.475 Sum_probs=30.9
Q ss_pred CcccccccEEEEEeCCCceee-EEEEeeeCCCCeEEEE
Q 018661 295 CPQCCIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVL 331 (352)
Q Consensus 295 ~~~~~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~ 331 (352)
.++.+||++|-.-||.+..|| ++|+.||..+..|+.+
T Consensus 156 pp~slvgr~v~~k~pdk~~~te~iit~~~~~~E~~~~l 193 (273)
T KOG4675|consen 156 PPESLVGRKVWIKWPDKRKFTEAIITQYDAEKEGHHLL 193 (273)
T ss_pred CchhhccccccccCcccccccccccccchhhhhhhhhc
Confidence 556699999999999999999 9999977766655554
No 28
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=85.52 E-value=0.57 Score=48.10 Aligned_cols=39 Identities=23% Similarity=0.288 Sum_probs=30.5
Q ss_pred cccCCCCCCcceEEEEECC-eEEEEEEEccCCCCCCeEEEcCCC
Q 018661 190 YINHSCCPNTEMQKWIIDG-ETRIGIFATRDIKKGENLTYDYQF 232 (352)
Q Consensus 190 fiNHSC~PN~~~~~~~~~g-~~~i~i~A~rdI~~GEELT~dY~~ 232 (352)
+.||++.+.. +..+. ...+.+++.++|.+||||++.||.
T Consensus 239 ~~NH~~~~~~----~~~~~~d~~~~l~~~~~v~~geevfi~YG~ 278 (472)
T KOG1337|consen 239 LLNHSPEVIK----AGYNQEDEAVELVAERDVSAGEEVFINYGP 278 (472)
T ss_pred hhccCchhcc----ccccCCCCcEEEEEeeeecCCCeEEEecCC
Confidence 7899999921 22222 238899999999999999999986
No 29
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=83.30 E-value=2.8 Score=35.15 Aligned_cols=41 Identities=17% Similarity=0.386 Sum_probs=35.5
Q ss_pred ccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeecCceeEEec
Q 018661 301 GKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFEDGESEFIDM 342 (352)
Q Consensus 301 g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~dg~~e~~~l 342 (352)
|.+|=.-|..|.-|| |+|++.- ..+.-.|-|++|+++.+..
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~-~~~~~lV~f~~~~~~~v~~ 42 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV-SSGQFLVEFDDGDTQEVPI 42 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc-CCCEEEEEECCCCEEEeCh
Confidence 678888899999999 9999998 7788888889999987754
No 30
>KOG1525 consensus Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning]
Probab=80.22 E-value=0.077 Score=60.04 Aligned_cols=58 Identities=9% Similarity=0.031 Sum_probs=53.7
Q ss_pred CCCcccccccEEEEEeCCCceee-E-EEEeeeCCCCeEEEEeecCceeEEeccccceEec
Q 018661 293 QICPQCCIGKVIRISHPKNESSF-G-IIRRFDEYSRKHSVLFEDGESEFIDMAKVDWELV 350 (352)
Q Consensus 293 k~~~~~~~g~~i~~~~~~~~~~~-g-~v~~~~~~~~~h~v~y~dg~~e~~~l~~e~~~~~ 350 (352)
.++..++||.++..|||.|..|+ | .|..++...+.|.++|++++.|..++....|+..
T Consensus 982 ~~~~~e~V~~~~~~~la~d~~~~~~edv~~l~~~ke~~~~vl~~l~~~~~n~~~~~~~~~ 1041 (1266)
T KOG1525|consen 982 LAHLPEYVGSYVIHLLAHDPDFVKAEDVDSLSDLKECLWFVLEDLDEENENNQHKFWKRE 1041 (1266)
T ss_pred hhhhhHHhhhhhhhhhccCccccccchhhhHHHHHHhHHHHHhhhhhhhccchhHHHHHH
Confidence 56889999999999999999999 7 8999999999999999999999999999988753
No 31
>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=80.21 E-value=6.2 Score=31.26 Aligned_cols=46 Identities=13% Similarity=0.184 Sum_probs=37.8
Q ss_pred cccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEe-ecCceeEEeccc
Q 018661 298 CCIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLF-EDGESEFIDMAK 344 (352)
Q Consensus 298 ~~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y-~dg~~e~~~l~~ 344 (352)
.-+|...-+.-+.|..|| |+| .-+...+.-+|.| |-|.++.+..++
T Consensus 52 ~~~~~~~~~~~~~~~~w~Ra~I-~~~~~~~~~~V~~iD~G~~~~v~~~~ 99 (121)
T PF00567_consen 52 SNPGEGCLCVVSEDGRWYRAVI-TVDIDENQYKVFLIDYGNTEKVSASD 99 (121)
T ss_dssp --TTEEEEEEETTTSEEEEEEE-EEEECTTEEEEEETTTTEEEEEEGGG
T ss_pred cccCCEEEEEEecCCceeeEEE-EEecccceeEEEEEecCceEEEcHHH
Confidence 346777778888899999 999 8888889999999 999999987653
No 32
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=71.16 E-value=15 Score=28.38 Aligned_cols=42 Identities=31% Similarity=0.338 Sum_probs=33.0
Q ss_pred cEEEEEeCCCceee-EEEEeeeCCCCeEEEEeecCceeEEecc
Q 018661 302 KVIRISHPKNESSF-GIIRRFDEYSRKHSVLFEDGESEFIDMA 343 (352)
Q Consensus 302 ~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~dg~~e~~~l~ 343 (352)
.+|.+|-...-..+ |.|..+|+..+.=.|.-++|+.+++.|+
T Consensus 45 v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~~ 87 (92)
T PF08863_consen 45 VTITYYEDGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPFD 87 (92)
T ss_pred EEEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEhh
Confidence 35667765544455 9999999999888888778999998875
No 33
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=69.80 E-value=11 Score=32.09 Aligned_cols=34 Identities=21% Similarity=0.120 Sum_probs=27.4
Q ss_pred EEEeCCCceee-EEEEeeeCCCCeEEEEeecCcee
Q 018661 305 RISHPKNESSF-GIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 305 ~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
.||=--+..|| |++.+.+....+-.|.||||..|
T Consensus 15 avW~~~~~~yYPa~~~~~~~~~~~~~V~Fedg~~~ 49 (131)
T PF08605_consen 15 AVWAGYNLKYYPATCVGSGVDRDRSLVRFEDGTYE 49 (131)
T ss_pred ceeecCCCeEeeEEEEeecCCCCeEEEEEecCceE
Confidence 35544477789 99999988888899999999943
No 34
>PF03638 TCR: Tesmin/TSO1-like CXC domain, cysteine-rich domain; InterPro: IPR005172 This entry includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin Q9Y4I5 from SWISSPROT [] and TSO1 Q9LE32 from SWISSPROT []. This group of proteins is called a CXC domain in [].
Probab=69.11 E-value=3.2 Score=28.18 Aligned_cols=37 Identities=32% Similarity=0.731 Sum_probs=29.5
Q ss_pred CCcccccCCCCCCCCCC-CCCCccceeeeCCCCCCCCCCCCCcc
Q 018661 65 GIFCSCTASPGSSGVCD-RDCHCGMLLSSCSSGCKCGNSCLNKP 107 (352)
Q Consensus 65 ~~~C~C~~~~~~~~~C~-~~C~c~~~~~eC~~~C~C~~~C~Nr~ 107 (352)
...|+|+.+ .|. ..|.|......|++.|.| ..|.|..
T Consensus 3 ~~gC~Ckks-----~Clk~YC~Cf~~g~~C~~~C~C-~~C~N~~ 40 (42)
T PF03638_consen 3 KKGCNCKKS-----KCLKLYCECFQAGRFCTPNCKC-QNCKNTE 40 (42)
T ss_pred CCCCcccCc-----ChhhhhCHHHHCcCcCCCCccc-CCCCCcC
Confidence 456899864 463 469999999999999999 7898864
No 35
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=65.34 E-value=29 Score=25.54 Aligned_cols=33 Identities=15% Similarity=0.111 Sum_probs=28.7
Q ss_pred ccccEEEEEeCCCceeeEEEEeeeCCCCeEEEE
Q 018661 299 CIGKVIRISHPKNESSFGIIRRFDEYSRKHSVL 331 (352)
Q Consensus 299 ~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h~v~ 331 (352)
-||++|++-=..++.+=|.|..||..+++=.+.
T Consensus 4 ~iGs~V~~kTc~g~~ieGEV~afD~~tk~lIlk 36 (61)
T cd01735 4 SVGSQVSCRTCFEQRLQGEVVAFDYPSKMLILK 36 (61)
T ss_pred ccccEEEEEecCCceEEEEEEEecCCCcEEEEE
Confidence 489999999998888669999999999887766
No 36
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=64.48 E-value=9.3 Score=28.75 Aligned_cols=31 Identities=6% Similarity=0.054 Sum_probs=26.1
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
..+++|++|.|.--.++.|.|++++||+.-.
T Consensus 9 L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mN 39 (72)
T PRK00737 9 LNNALNSPVLVRLKGGREFRGELQGYDIHMN 39 (72)
T ss_pred HHHhCCCEEEEEECCCCEEEEEEEEEcccce
Confidence 4567999999999888776699999998655
No 37
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=61.44 E-value=12 Score=26.68 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=24.9
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
++++|++|.|---.++.|-|++.+||+...
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~N 31 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFDKYMN 31 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEECCCCC
Confidence 467999999998877776699999997753
No 38
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=60.84 E-value=12 Score=27.21 Aligned_cols=30 Identities=27% Similarity=0.454 Sum_probs=24.9
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
++++|.+|+|---.+..|-|++.+||+.-.
T Consensus 4 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~N 33 (67)
T PF01423_consen 4 QKLIGKRVRVELKNGRTYRGTLVSFDQFMN 33 (67)
T ss_dssp HHTTTSEEEEEETTSEEEEEEEEEEETTEE
T ss_pred HHhCCcEEEEEEeCCEEEEEEEEEeechhe
Confidence 568999999999977665599999998654
No 39
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=59.69 E-value=12 Score=40.96 Aligned_cols=43 Identities=16% Similarity=0.174 Sum_probs=34.5
Q ss_pred cccEEEEEeCC----Cceee-EEEEeeeCCCC--------eEEEEeecCceeEEec
Q 018661 300 IGKVIRISHPK----NESSF-GIIRRFDEYSR--------KHSVLFEDGESEFIDM 342 (352)
Q Consensus 300 ~g~~i~~~~~~----~~~~~-g~v~~~~~~~~--------~h~v~y~dg~~e~~~l 342 (352)
++-+.||||.. |.+|. |.|.+-.+++- +..|.||.+++|...-
T Consensus 981 ~~d~crvwwrda~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~~e~~~~sp 1036 (1113)
T KOG0644|consen 981 CRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDNTETELHSP 1036 (1113)
T ss_pred cccceeEEEccCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecCCcccccCc
Confidence 56789999973 34566 99999887774 8899999999987764
No 40
>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=58.48 E-value=6.2 Score=28.17 Aligned_cols=15 Identities=40% Similarity=0.554 Sum_probs=11.5
Q ss_pred EEEEccCCCCCCeEE
Q 018661 213 GIFATRDIKKGENLT 227 (352)
Q Consensus 213 ~i~A~rdI~~GEELT 227 (352)
.++|.|||++|+.|+
T Consensus 3 vvVA~~di~~G~~i~ 17 (63)
T PF08666_consen 3 VVVAARDIPAGTVIT 17 (63)
T ss_dssp EEEESSTB-TT-BEC
T ss_pred EEEEeCccCCCCEEc
Confidence 478999999999995
No 41
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=58.29 E-value=13 Score=28.46 Aligned_cols=30 Identities=17% Similarity=0.181 Sum_probs=25.9
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
..++|++|.|.-..++.+.|+.++||....
T Consensus 6 ~~~l~~~V~V~l~dgR~~~G~L~~~D~~~N 35 (79)
T cd01717 6 LQLINYRLRVTLQDGRQFVGQFLAFDKHMN 35 (79)
T ss_pred HHHcCCEEEEEECCCcEEEEEEEEEcCccC
Confidence 568999999999988776699999997765
No 42
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=56.37 E-value=19 Score=26.54 Aligned_cols=31 Identities=10% Similarity=0.181 Sum_probs=25.8
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCCe
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSRK 327 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~ 327 (352)
++++|++|.|--..++.|.|++++||..-..
T Consensus 6 ~~~~~~~V~V~l~~g~~~~G~L~~~D~~mNl 36 (68)
T cd01731 6 KDSLNKPVLVKLKGGKEVRGRLKSYDQHMNL 36 (68)
T ss_pred HHhcCCEEEEEECCCCEEEEEEEEECCcceE
Confidence 4678999999988777766999999997653
No 43
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=54.86 E-value=17 Score=27.71 Aligned_cols=34 Identities=15% Similarity=0.184 Sum_probs=28.3
Q ss_pred CcccccccEEEEEeCCCceeeEEEEeeeCCCCeE
Q 018661 295 CPQCCIGKVIRISHPKNESSFGIIRRFDEYSRKH 328 (352)
Q Consensus 295 ~~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h 328 (352)
...+++|++|.|+--.++.|.|+.++||..-.-+
T Consensus 11 ~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNlv 44 (79)
T COG1958 11 FLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLV 44 (79)
T ss_pred HHHHhhCCEEEEEECCCCEEEEEEEEEccceeEE
Confidence 3456889999999999988779999999987643
No 44
>KOG2155 consensus Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=54.30 E-value=19 Score=36.72 Aligned_cols=48 Identities=19% Similarity=0.271 Sum_probs=35.6
Q ss_pred CccccccCCCCCCcceEEEEECC--eEEEEEEEccCCCCCCeEEEcCCCC
Q 018661 186 NKSRYINHSCCPNTEMQKWIIDG--ETRIGIFATRDIKKGENLTYDYQFV 233 (352)
Q Consensus 186 N~aRfiNHSC~PN~~~~~~~~~g--~~~i~i~A~rdI~~GEELT~dY~~~ 233 (352)
.++.-+.||-.||..+.....-- -.--.++-+|+...|||+|-|+-..
T Consensus 203 efGsrvrHsdePnf~~aPf~fmPq~vaYsimwp~k~~~tgeE~trDfasg 252 (631)
T KOG2155|consen 203 EFGSRVRHSDEPNFRIAPFMFMPQNVAYSIMWPTKPVNTGEEITRDFASG 252 (631)
T ss_pred hhhhhhccCCCCcceeeeheecchhcceeEEeeccCCCCchHHHHHHhhc
Confidence 45566899999999887654321 1234578999999999999887543
No 45
>PF02067 Metallothio_5: Metallothionein family 5; InterPro: IPR000966 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ] species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class I MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. Diptera (Drosophila, family 5) MTs are 40-43 residue proteins that contain 10 conserved cysteines arranged in five Cys-X-Cys groups. In particular, the consensus pattern C-G-x(2)-C-x-C-x(2)-Q-x(5)-C-x-C-x(2)-D-C-x-C has been found to be diagnostic of family 5 MTs. The protein is found primarily in the alimentary canal, and its induction is stimulated by ingestion of cadmium or copper []. Mercury, silver and zinc induce the protein to a lesser extent. Family 5 includes subfamilies: d1, d2. Only one d2 is known until now. Subfamilies hit the same entry.; GO: 0046872 metal ion binding
Probab=52.89 E-value=10 Score=25.44 Aligned_cols=22 Identities=32% Similarity=1.257 Sum_probs=11.5
Q ss_pred CCCCCCccceeeeCCCCCCCCCCC
Q 018661 80 CDRDCHCGMLLSSCSSGCKCGNSC 103 (352)
Q Consensus 80 C~~~C~c~~~~~eC~~~C~C~~~C 103 (352)
|+.+|.|... .|+.+|.|+..|
T Consensus 6 Cg~~CkC~~~--kcg~~C~C~~dC 27 (41)
T PF02067_consen 6 CGTNCKCSSQ--KCGGNCACNQDC 27 (41)
T ss_pred cCCCCEecCC--ccCCCccCCCCc
Confidence 5556655533 255555555444
No 46
>cd01719 Sm_G The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=52.23 E-value=25 Score=26.45 Aligned_cols=33 Identities=21% Similarity=0.292 Sum_probs=26.5
Q ss_pred CCcccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 294 ICPQCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 294 ~~~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
....+++|++|.|---.++.+.|+..+||+...
T Consensus 3 ~~L~~~i~k~V~V~L~~g~~~~G~L~~~D~~mN 35 (72)
T cd01719 3 PELKKYMDKKLSLKLNGNRKVSGILRGFDPFMN 35 (72)
T ss_pred hhhHHhCCCeEEEEECCCeEEEEEEEEEccccc
Confidence 345678999999998877665599999997665
No 47
>cd01727 LSm8 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm8 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=49.42 E-value=24 Score=26.60 Aligned_cols=30 Identities=13% Similarity=0.319 Sum_probs=24.2
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
.+++++||+|---.++.|.|+.++||+...
T Consensus 5 ~~~l~~~V~V~l~dgr~~~G~L~~~D~~~N 34 (74)
T cd01727 5 EDYLNKTVSVITVDGRVIVGTLKGFDQATN 34 (74)
T ss_pred HHhcCCEEEEEECCCcEEEEEEEEEccccC
Confidence 457899999977766666699999999754
No 48
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=49.38 E-value=10 Score=38.00 Aligned_cols=40 Identities=20% Similarity=0.421 Sum_probs=30.8
Q ss_pred ccccccCC---CCCCcceEEEEECCeEEEEEEEccCCCCCCeEEEcCCC
Q 018661 187 KSRYINHS---CCPNTEMQKWIIDGETRIGIFATRDIKKGENLTYDYQF 232 (352)
Q Consensus 187 ~aRfiNHS---C~PN~~~~~~~~~g~~~i~i~A~rdI~~GEELT~dY~~ 232 (352)
++-|+||- |+.|..+ +...+-++|.|+|++|+|+.-.||.
T Consensus 218 ~ad~lNhd~~k~nanl~y------~~NcL~mva~r~iekgdev~n~dg~ 260 (466)
T KOG1338|consen 218 IADFLNHDGLKANANLRY------EDNCLEMVADRNIEKGDEVDNSDGL 260 (466)
T ss_pred hhhhhccchhhcccceec------cCcceeeeecCCCCCcccccccccc
Confidence 46699995 6666644 2345678999999999999999973
No 49
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=49.09 E-value=23 Score=25.66 Aligned_cols=31 Identities=19% Similarity=0.356 Sum_probs=25.7
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
..+++|++|.|--..++.+.|++.+||+.-.
T Consensus 3 L~~~~~~~V~V~l~~g~~~~G~L~~~D~~~N 33 (67)
T smart00651 3 LKKLIGKRVLVELKNGREYRGTLKGFDQFMN 33 (67)
T ss_pred hHHhCCcEEEEEECCCcEEEEEEEEECcccc
Confidence 4578999999999977776699999998755
No 50
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=48.67 E-value=27 Score=25.78 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=25.0
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
.+++|++|.|---.++.|.|++.+||+.-.
T Consensus 6 ~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mN 35 (67)
T cd01726 6 KAIIGRPVVVKLNSGVDYRGILACLDGYMN 35 (67)
T ss_pred HhhCCCeEEEEECCCCEEEEEEEEEcccee
Confidence 567999999999988776699999997644
No 51
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=46.47 E-value=30 Score=25.57 Aligned_cols=31 Identities=16% Similarity=0.117 Sum_probs=25.2
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
.++++|++|.|---.++.|.|++.+||..-.
T Consensus 6 L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mN 36 (68)
T cd01722 6 LNDLTGKPVIVKLKWGMEYKGTLVSVDSYMN 36 (68)
T ss_pred HHHcCCCEEEEEECCCcEEEEEEEEECCCEE
Confidence 4567999999998888776699999996543
No 52
>KOG1775 consensus U6 snRNA-associated Sm-like protein [RNA processing and modification]
Probab=45.63 E-value=18 Score=27.62 Aligned_cols=30 Identities=27% Similarity=0.522 Sum_probs=26.2
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
..|||++|-|-...|+.+.|+.+.||-+-.
T Consensus 13 DkcIgski~iimksdkE~~GtL~GFDd~VN 42 (84)
T KOG1775|consen 13 DKCIGSKIWIIMKSDKEFVGTLVGFDDFVN 42 (84)
T ss_pred HHhcCceEEEEEccCceeeeEEechHHHHH
Confidence 459999999999999998899999997643
No 53
>cd01728 LSm1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm1 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=45.59 E-value=28 Score=26.44 Aligned_cols=30 Identities=20% Similarity=0.349 Sum_probs=24.5
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCC
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYS 325 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~ 325 (352)
.+++++++|.|--..++.|.|+.++||+..
T Consensus 7 L~~~l~k~v~V~l~~gr~~~G~L~~fD~~~ 36 (74)
T cd01728 7 LVDDLDKKVVVLLRDGRKLIGILRSFDQFA 36 (74)
T ss_pred HHHhcCCEEEEEEcCCeEEEEEEEEECCcc
Confidence 346789999999988877669999999754
No 54
>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=44.45 E-value=61 Score=23.83 Aligned_cols=34 Identities=18% Similarity=0.268 Sum_probs=23.2
Q ss_pred cccEEEEEeCC---Cceee-EEEEeeeCCCCeEEEEeec
Q 018661 300 IGKVIRISHPK---NESSF-GIIRRFDEYSRKHSVLFED 334 (352)
Q Consensus 300 ~g~~i~~~~~~---~~~~~-g~v~~~~~~~~~h~v~y~d 334 (352)
.|..|-|.--. ...|| |+|.+....+ +..|.|+|
T Consensus 3 ~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~ 40 (68)
T PF05641_consen 3 KGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDD 40 (68)
T ss_dssp TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT
T ss_pred CCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECC
Confidence 46677776543 34699 9999999888 99999953
No 55
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=42.35 E-value=79 Score=27.26 Aligned_cols=42 Identities=14% Similarity=0.198 Sum_probs=31.2
Q ss_pred CcccccccEEEEEeCCCceeeEEEEeeeCCCCeEEEEeecCc
Q 018661 295 CPQCCIGKVIRISHPKNESSFGIIRRFDEYSRKHSVLFEDGE 336 (352)
Q Consensus 295 ~~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h~v~y~dg~ 336 (352)
...++||+.|.+--.......|+|.+=.-..+...++++||.
T Consensus 86 ~a~slVGk~V~~~~~~g~~~tG~V~~V~~~~g~~~~~~v~G~ 127 (142)
T PRK09618 86 KYSELIGKEVEWEGEDGEIVSGTVTSVKQKDGDYPLVLDNGT 127 (142)
T ss_pred HHHHHhCCEEEEEeCCCCEEEEEEEEEEEcCCcEEEEEECCE
Confidence 456899999987544444333999988877888778888884
No 56
>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=41.65 E-value=16 Score=29.96 Aligned_cols=17 Identities=59% Similarity=0.860 Sum_probs=13.0
Q ss_pred EEEEEccCCCCCCeEEE
Q 018661 212 IGIFATRDIKKGENLTY 228 (352)
Q Consensus 212 i~i~A~rdI~~GEELT~ 228 (352)
.+|||+|||++||-|.+
T Consensus 2 rGl~At~dI~~Ge~I~~ 18 (162)
T PF00856_consen 2 RGLFATRDIKAGEVILI 18 (162)
T ss_dssp EEEEESS-B-TTEEEEE
T ss_pred EEEEECccCCCCCEEEE
Confidence 37999999999998883
No 57
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=40.96 E-value=11 Score=40.01 Aligned_cols=30 Identities=27% Similarity=0.562 Sum_probs=24.3
Q ss_pred CCCCCCCccceeeeCCCCCCCCCCCCCccc
Q 018661 79 VCDRDCHCGMLLSSCSSGCKCGNSCLNKPF 108 (352)
Q Consensus 79 ~C~~~C~c~~~~~eC~~~C~C~~~C~Nr~~ 108 (352)
.|+.+|.|..--..|..-|.|...|+||..
T Consensus 511 ~c~~~C~C~~n~~~CEk~C~C~~dC~nrF~ 540 (739)
T KOG1079|consen 511 NCGVGCPCIDNETFCEKFCYCSPDCRNRFP 540 (739)
T ss_pred CCCCCCcccccCcchhhcccCCHHHHhcCC
Confidence 378889998888888888888888888753
No 58
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=40.58 E-value=74 Score=26.88 Aligned_cols=40 Identities=18% Similarity=0.190 Sum_probs=29.5
Q ss_pred ccccEEEEEeCCCceee-EEEEee-eCCCCeEEEEeecCcee
Q 018661 299 CIGKVIRISHPKNESSF-GIIRRF-DEYSRKHSVLFEDGESE 338 (352)
Q Consensus 299 ~~g~~i~~~~~~~~~~~-g~v~~~-~~~~~~h~v~y~dg~~e 338 (352)
=.|.+|-.-||.--+|| |+|.+- ...++..+|.|||.+.+
T Consensus 73 ~~g~~VLAlYP~TT~FY~A~V~~~p~~~~~~y~l~Fedd~~~ 114 (130)
T PF07039_consen 73 PKGTKVLALYPDTTCFYPATVVSPPKKKSGEYKLKFEDDEDA 114 (130)
T ss_dssp -TT-EEEEE-TTSSEEEEEEEEEE-SSTTS-EEEEECTTTST
T ss_pred CCCCEEEEECCCCceEEEEEEEeCCCCCCCcEEEEEeCCCCc
Confidence 46889999999999999 988887 44678899999776543
No 59
>cd01729 LSm7 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm7 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=39.22 E-value=39 Score=26.07 Aligned_cols=31 Identities=19% Similarity=0.350 Sum_probs=25.1
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
.+.++|++|+|---.++.|.|+..+||+.-.
T Consensus 7 L~~~i~k~V~V~l~~gr~~~G~L~~~D~~mN 37 (81)
T cd01729 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLN 37 (81)
T ss_pred HHHhcCCeEEEEECCCcEEEEEEEEEcCccc
Confidence 4567999999988877665599999999755
No 60
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=39.09 E-value=66 Score=26.87 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=30.5
Q ss_pred cccEEEEEeC-CCceee-EEEEee----eCCCCeEEEEeecCceeEEecc
Q 018661 300 IGKVIRISHP-KNESSF-GIIRRF----DEYSRKHSVLFEDGESEFIDMA 343 (352)
Q Consensus 300 ~g~~i~~~~~-~~~~~~-g~v~~~----~~~~~~h~v~y~dg~~e~~~l~ 343 (352)
+|-.|=+-|| .+..|+ |+|.+. -...+..+|.|-||.++.+...
T Consensus 58 ~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~vp~~ 107 (124)
T PF15057_consen 58 VGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAKVPRG 107 (124)
T ss_pred CCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCCCCccchh
Confidence 3444444465 455566 999875 6678899999999998765543
No 61
>cd01732 LSm5 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=38.49 E-value=43 Score=25.55 Aligned_cols=32 Identities=28% Similarity=0.485 Sum_probs=24.0
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCCeE
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSRKH 328 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h 328 (352)
..+++++|.|---..+.+.|++++||+.-...
T Consensus 9 ~~~~~~~V~V~l~~gr~~~G~L~g~D~~mNlv 40 (76)
T cd01732 9 DKCIGSRIWIVMKSDKEFVGTLLGFDDYVNMV 40 (76)
T ss_pred HHhCCCEEEEEECCCeEEEEEEEEeccceEEE
Confidence 34578888887776666559999999986543
No 62
>cd01730 LSm3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm3 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=37.55 E-value=44 Score=25.71 Aligned_cols=29 Identities=7% Similarity=0.169 Sum_probs=23.6
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYS 325 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~ 325 (352)
+..++++|.|---.++.|.|++++||..-
T Consensus 7 ~~~~~k~V~V~l~~gr~~~G~L~~fD~~m 35 (82)
T cd01730 7 RLSLDERVYVKLRGDRELRGRLHAYDQHL 35 (82)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEccce
Confidence 34588999998887777669999999854
No 63
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=36.36 E-value=95 Score=26.71 Aligned_cols=43 Identities=19% Similarity=0.165 Sum_probs=31.3
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCCeEEEEeecCcee
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
.-.+||+.|......+...-|+|.+-......-.+..+||+.+
T Consensus 88 a~~lIGk~V~~~~~~g~~~tG~V~sV~~~~~~~~~~v~d~~~~ 130 (140)
T PRK11911 88 AVNFIGKDIKGVSLNGEVISGKVESVQQTTNGVMLKLKDNDSL 130 (140)
T ss_pred HHHhhCceeEEEecCCCEEEEEEEEEEEcCCceEEEEEcCCEE
Confidence 4589999998666655554499998777777777766666654
No 64
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=35.86 E-value=1e+02 Score=26.13 Aligned_cols=45 Identities=18% Similarity=0.301 Sum_probs=32.5
Q ss_pred cccEEEEEeCCCceee-EEEEeeeCCCCeEEEEeecCceeEEeccccceEec
Q 018661 300 IGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFEDGESEFIDMAKVDWELV 350 (352)
Q Consensus 300 ~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~dg~~e~~~l~~e~~~~~ 350 (352)
=|..+..-+|.++.-- ..| ..+.++++|.||+ ..+=|..|.||-+
T Consensus 48 tG~~~e~~f~~~~kve~a~i-----e~~~~q~lY~dg~-~~~FMD~etyeq~ 93 (131)
T COG0231 48 TGKKVEKTFKADDKVEVAIV-----ERKTAQYLYIDGD-FYVFMDLETYEQY 93 (131)
T ss_pred CCCEEEEEEcCCCEEEEeEE-----eeeeEEEEEcCCC-eEEEccCCCceEE
Confidence 3667777777766544 555 4789999999999 5666777777754
No 65
>PF09910 DUF2139: Uncharacterized protein conserved in archaea (DUF2139); InterPro: IPR016675 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=35.63 E-value=61 Score=31.55 Aligned_cols=50 Identities=16% Similarity=0.266 Sum_probs=37.5
Q ss_pred ccEEEEEeC---CCce-eeEEEEe--eeCCCCeEEEEeecCcee----EEeccccceEec
Q 018661 301 GKVIRISHP---KNES-SFGIIRR--FDEYSRKHSVLFEDGESE----FIDMAKVDWELV 350 (352)
Q Consensus 301 g~~i~~~~~---~~~~-~~g~v~~--~~~~~~~h~v~y~dg~~e----~~~l~~e~~~~~ 350 (352)
-.+||+.|. .|+. |+|.|.+ |||++.+=-+.=+||..+ .||.+.-+-|+|
T Consensus 87 ~~~VrLLWkesih~~~~WaGEVSdIlYdP~~D~LLlAR~DGh~nLGvy~ldr~~g~~~~L 146 (339)
T PF09910_consen 87 NDSVRLLWKESIHDKTKWAGEVSDILYDPYEDRLLLARADGHANLGVYSLDRRTGKAEKL 146 (339)
T ss_pred CCeEEEEEecccCCccccccchhheeeCCCcCEEEEEecCCcceeeeEEEcccCCceeec
Confidence 467899996 3444 8898865 999999888888999987 566666555554
No 66
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=34.65 E-value=1.5e+02 Score=20.18 Aligned_cols=39 Identities=26% Similarity=0.354 Sum_probs=29.2
Q ss_pred cccEEEEEeCCCceeeEEEEeeeCCCCeEEEEeecCceeEE
Q 018661 300 IGKVIRISHPKNESSFGIIRRFDEYSRKHSVLFEDGESEFI 340 (352)
Q Consensus 300 ~g~~i~~~~~~~~~~~g~v~~~~~~~~~h~v~y~dg~~e~~ 340 (352)
+|+.|+|..+ ++.+-|++..-|+ .+.=.|..+||..+.+
T Consensus 2 lG~~V~v~~~-~~~~~G~~~gId~-~G~L~v~~~~g~~~~i 40 (48)
T PF02237_consen 2 LGQEVRVETG-DGEIEGIAEGIDD-DGALLVRTEDGSIRTI 40 (48)
T ss_dssp TTSEEEEEET-SCEEEEEEEEEET-TSEEEEEETTEEEEEE
T ss_pred CCCEEEEEEC-CeEEEEEEEEECC-CCEEEEEECCCCEEEE
Confidence 6899999994 6665699999987 4566666777755544
No 67
>KOG1171 consensus Metallothionein-like protein [Inorganic ion transport and metabolism]
Probab=33.80 E-value=12 Score=37.72 Aligned_cols=36 Identities=39% Similarity=0.818 Sum_probs=30.4
Q ss_pred CCCcccccCCCCCCCCCC-CCCCccceeeeCCCCCCCCCCCCC
Q 018661 64 DGIFCSCTASPGSSGVCD-RDCHCGMLLSSCSSGCKCGNSCLN 105 (352)
Q Consensus 64 ~~~~C~C~~~~~~~~~C~-~~C~c~~~~~eC~~~C~C~~~C~N 105 (352)
+..+|+|+.+ .|- ..|.|.+..+-|+.+|+| ..|.|
T Consensus 216 hkkGC~CkkS-----gClKkYCECyQa~vlCS~nCkC-~~CkN 252 (406)
T KOG1171|consen 216 HKKGCNCKKS-----GCLKKYCECYQAGVLCSSNCKC-QGCKN 252 (406)
T ss_pred hcCCCCCccc-----cchHHHHHHHhcCCCccccccC-cCCcc
Confidence 4568999984 574 469999999999999999 68988
No 68
>PF12904 Collagen_bind_2: Putative collagen-binding domain of a collagenase ; InterPro: IPR024749 This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. The structure of one family member, Q8A905 from SWISSPROT, has been characterised. The domain occurs in the C-terminal region of the protein.; PDB: 3KZS_D.
Probab=31.91 E-value=47 Score=26.46 Aligned_cols=27 Identities=15% Similarity=0.143 Sum_probs=18.8
Q ss_pred CCCcccccccEEEEEe--CCCceee--EEEE
Q 018661 293 QICPQCCIGKVIRISH--PKNESSF--GIIR 319 (352)
Q Consensus 293 k~~~~~~~g~~i~~~~--~~~~~~~--g~v~ 319 (352)
.+....+-|.++++|| |.+-.++ |.+.
T Consensus 38 ~vdl~~l~g~~~~a~WfdPR~G~~~~~g~~~ 68 (93)
T PF12904_consen 38 TVDLSKLSGKKVKAWWFDPRTGKYTYIGEFS 68 (93)
T ss_dssp EEEGGGSS-SEEEEEEEETTT-BEEEEEEEE
T ss_pred EEEcccccCCceeEEEEcCCCCCEEEeeeec
Confidence 3456678899999999 8877755 7664
No 69
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=31.72 E-value=31 Score=24.34 Aligned_cols=16 Identities=38% Similarity=0.526 Sum_probs=13.9
Q ss_pred EEEEccCCCCCCeEEE
Q 018661 213 GIFATRDIKKGENLTY 228 (352)
Q Consensus 213 ~i~A~rdI~~GEELT~ 228 (352)
.++|.++|.+|+.|+-
T Consensus 3 v~va~~~i~~G~~i~~ 18 (64)
T smart00858 3 VVVAARDLPAGEVITA 18 (64)
T ss_pred EEEEeCccCCCCCcch
Confidence 4688999999999984
No 70
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=30.97 E-value=89 Score=22.49 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=16.8
Q ss_pred EEEEeeeCCCCeEEEEeecCcee
Q 018661 316 GIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
|+|++||+..+-=-|..++|+..
T Consensus 3 G~V~~~~~~kgyGFI~~~~~~~d 25 (66)
T PF00313_consen 3 GTVKWFDDEKGYGFITSDDGGED 25 (66)
T ss_dssp EEEEEEETTTTEEEEEETTSSSE
T ss_pred EEEEEEECCCCceEEEEccccee
Confidence 88888888777666666766644
No 71
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=29.97 E-value=1e+02 Score=23.33 Aligned_cols=33 Identities=12% Similarity=0.167 Sum_probs=27.4
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCCeEE
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSRKHS 329 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h~ 329 (352)
+.++|++|.|=-..+..+.|++.+||+.-..|-
T Consensus 7 ~~~~g~~V~VeLkng~~~~G~L~~~D~~mNi~L 39 (76)
T cd01723 7 KTAQNHPMLVELKNGETYNGHLVNCDNWMNIHL 39 (76)
T ss_pred HhcCCCEEEEEECCCCEEEEEEEEEcCCCceEE
Confidence 567999999988877776699999999877553
No 72
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=29.86 E-value=1e+02 Score=20.53 Aligned_cols=34 Identities=26% Similarity=0.280 Sum_probs=25.5
Q ss_pred EEEeCCCce-ee-EEEEeeeCCCCeEEEEeecCceeEE
Q 018661 305 RISHPKNES-SF-GIIRRFDEYSRKHSVLFEDGESEFI 340 (352)
Q Consensus 305 ~~~~~~~~~-~~-g~v~~~~~~~~~h~v~y~dg~~e~~ 340 (352)
.||=|..+- |. |.|. +...++-+|...||.+-.+
T Consensus 3 ~vWvpD~~egfv~g~I~--~~~g~~vtV~~~~G~~~tv 38 (42)
T PF02736_consen 3 WVWVPDPKEGFVKGEII--EEEGDKVTVKTEDGKEVTV 38 (42)
T ss_dssp EEEEEESSSSEEEEEEE--EEESSEEEEEETTTEEEEE
T ss_pred EEEEeCCcccEEEEEEE--EEcCCEEEEEECCCCEEEe
Confidence 477786666 55 9999 5667789999999875544
No 73
>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=29.31 E-value=1.5e+02 Score=20.78 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=25.9
Q ss_pred cccEEEEEeCCCceee-EEEEeeeCCCC--eEEEEeec
Q 018661 300 IGKVIRISHPKNESSF-GIIRRFDEYSR--KHSVLFED 334 (352)
Q Consensus 300 ~g~~i~~~~~~~~~~~-g~v~~~~~~~~--~h~v~y~d 334 (352)
||.++.+.| .+..+| +.|.+-....+ ..-|-|..
T Consensus 3 vG~~v~~~~-~~~~~y~A~I~~~r~~~~~~~YyVHY~g 39 (55)
T PF11717_consen 3 VGEKVLCKY-KDGQWYEAKILDIREKNGEPEYYVHYQG 39 (55)
T ss_dssp TTEEEEEEE-TTTEEEEEEEEEEEECTTCEEEEEEETT
T ss_pred cCCEEEEEE-CCCcEEEEEEEEEEecCCCEEEEEEcCC
Confidence 899999999 788888 99988877553 44555653
No 74
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=29.16 E-value=1.9e+02 Score=24.44 Aligned_cols=39 Identities=23% Similarity=0.374 Sum_probs=26.0
Q ss_pred CcccccccEEEEEe--CCC-ceee-EEEEeeeCCCCeEEEEeecC
Q 018661 295 CPQCCIGKVIRISH--PKN-ESSF-GIIRRFDEYSRKHSVLFEDG 335 (352)
Q Consensus 295 ~~~~~~g~~i~~~~--~~~-~~~~-g~v~~~~~~~~~h~v~y~dg 335 (352)
.-...+|+.|+|+. |.+ +..| |.+.+++. ...++.++++
T Consensus 81 ~~~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~--~~i~l~~~~~ 123 (141)
T PF02576_consen 81 DFERFIGRKVKVKLKQPVNGRKEFEGKLLEVDE--DEITLEVEGK 123 (141)
T ss_dssp HHHHH-SEEEEEE-SS-SSS-SEEEEEEEEEET--TEEEEEEE-S
T ss_pred HHHHhcCCeEEEEEeccCCCcEEEEEEEEEEeC--CEEEEEECCc
Confidence 44578999999998 333 3456 99999998 5666767776
No 75
>cd01720 Sm_D2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=29.11 E-value=82 Score=24.72 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=24.6
Q ss_pred ccEEEEEeCCCceeeEEEEeeeCCCCeEEEEeec
Q 018661 301 GKVIRISHPKNESSFGIIRRFDEYSRKHSVLFED 334 (352)
Q Consensus 301 g~~i~~~~~~~~~~~g~v~~~~~~~~~h~v~y~d 334 (352)
|.+|.|.-..++.+.|++++||..-. ++.+|
T Consensus 14 ~~~V~V~lr~~r~~~G~L~~fD~hmN---lvL~d 44 (87)
T cd01720 14 NTQVLINCRNNKKLLGRVKAFDRHCN---MVLEN 44 (87)
T ss_pred CCEEEEEEcCCCEEEEEEEEecCccE---EEEcc
Confidence 78999999988887799999997543 44455
No 76
>COG1278 CspC Cold shock proteins [Transcription]
Probab=27.43 E-value=57 Score=24.45 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=20.2
Q ss_pred EEEEeeeCCCCeEEEEeecCcee
Q 018661 316 GIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
|+|+.||+.++.=-|.=|||...
T Consensus 4 GtVKwfn~~KGfGFI~p~~G~~D 26 (67)
T COG1278 4 GTVKWFNATKGFGFITPEDGGKD 26 (67)
T ss_pred ceEEEeeCCCcceEcCCCCCCcC
Confidence 89999999999999999999544
No 77
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=26.40 E-value=89 Score=23.75 Aligned_cols=31 Identities=16% Similarity=0.295 Sum_probs=24.7
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
.++++|++++|--...+.|.|+...||....
T Consensus 5 L~~~l~~~v~V~l~dgR~~~G~l~~~D~~~N 35 (75)
T cd06168 5 LRSLLGRTMRIHMTDGRTLVGVFLCTDRDCN 35 (75)
T ss_pred HHHhcCCeEEEEEcCCeEEEEEEEEEcCCCc
Confidence 3467899999998877666699999996643
No 78
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=25.87 E-value=1.1e+02 Score=23.58 Aligned_cols=16 Identities=44% Similarity=0.362 Sum_probs=14.3
Q ss_pred cEEEeccccCCCceEE
Q 018661 126 AGIVADEDIKRGEFVI 141 (352)
Q Consensus 126 ~GlfA~~~I~~G~~I~ 141 (352)
..++|+++|++|+=|.
T Consensus 98 ~~~~a~r~I~~GeEi~ 113 (116)
T smart00317 98 IVIFALRDIKPGEELT 113 (116)
T ss_pred EEEEECCCcCCCCEEe
Confidence 7889999999999774
No 79
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=24.87 E-value=1.2e+02 Score=22.59 Aligned_cols=22 Identities=27% Similarity=0.360 Sum_probs=14.2
Q ss_pred EEEEeeeCCCCeEEEEeecCce
Q 018661 316 GIIRRFDEYSRKHSVLFEDGES 337 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~dg~~ 337 (352)
|+|+.||..++-==|.=+||..
T Consensus 6 G~Vk~f~~~kGyGFI~~~~g~~ 27 (69)
T PRK09507 6 GNVKWFNESKGFGFITPEDGSK 27 (69)
T ss_pred eEEEEEeCCCCcEEEecCCCCe
Confidence 7777777777665555556543
No 80
>PF03088 Str_synth: Strictosidine synthase; InterPro: IPR018119 This entry represents a conserved region found in strictosidine synthase (4.3.3.2 from EC), a key enzyme in alkaloid biosynthesis. It catalyses the Pictet-Spengler stereospecific condensation of tryptamine with secologanin to form strictosidine []. The structure of the native enzyme from the Indian medicinal plant Rauvolfia serpentina (Serpentwood) (Devilpepper) represents the first example of a six-bladed four-stranded beta-propeller fold from the plant kingdom [].; GO: 0016844 strictosidine synthase activity, 0009058 biosynthetic process; PDB: 2FPB_A 2V91_B 2FP8_A 3V1S_B 2FPC_A 2VAQ_A 2FP9_B.
Probab=24.39 E-value=95 Score=24.45 Aligned_cols=19 Identities=26% Similarity=0.627 Sum_probs=16.9
Q ss_pred EEEEeeeCCCCeEEEEeec
Q 018661 316 GIIRRFDEYSRKHSVLFED 334 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~d 334 (352)
|.+-.||+.|++-+|+-++
T Consensus 37 GRll~ydp~t~~~~vl~~~ 55 (89)
T PF03088_consen 37 GRLLRYDPSTKETTVLLDG 55 (89)
T ss_dssp EEEEEEETTTTEEEEEEEE
T ss_pred cCEEEEECCCCeEEEehhC
Confidence 8999999999999988654
No 81
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=24.31 E-value=2.6e+02 Score=19.71 Aligned_cols=37 Identities=8% Similarity=0.129 Sum_probs=27.4
Q ss_pred cccEEEEEeCCC----ceeeEEEEeeeCCCC-eEEEEeecCc
Q 018661 300 IGKVIRISHPKN----ESSFGIIRRFDEYSR-KHSVLFEDGE 336 (352)
Q Consensus 300 ~g~~i~~~~~~~----~~~~g~v~~~~~~~~-~h~v~y~dg~ 336 (352)
||++|.-.|-.. ..|-|.|-.-=|... -+-|.||+-+
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~ps~y~Ikyd~d~ 42 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKPSLYYIKYDGDD 42 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTSTTEEEEEETTES
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCCcEEEEEECCCc
Confidence 799999999988 778898877666655 7888886543
No 82
>PRK10943 cold shock-like protein CspC; Provisional
Probab=23.79 E-value=1.2e+02 Score=22.41 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=15.0
Q ss_pred EEEEeeeCCCCeEEEEeecCcee
Q 018661 316 GIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
|+|+.||..++-==|.=+||...
T Consensus 6 G~Vk~f~~~kGfGFI~~~~g~~d 28 (69)
T PRK10943 6 GQVKWFNESKGFGFITPADGSKD 28 (69)
T ss_pred eEEEEEeCCCCcEEEecCCCCee
Confidence 77777777777655555555433
No 83
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=23.78 E-value=1.7e+02 Score=25.24 Aligned_cols=80 Identities=18% Similarity=0.254 Sum_probs=50.4
Q ss_pred CCCCChHHHHHHHHhhhhcCCCcccCCCCCCC------------------------CCcCCCcccccccEEEEEeCCCce
Q 018661 258 KPKISSDAALKLVACQFYQNGDLHIGSSRPPY------------------------NQRQICPQCCIGKVIRISHPKNES 313 (352)
Q Consensus 258 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------------------~q~k~~~~~~~g~~i~~~~~~~~~ 313 (352)
...+..+.=++|...++.....+.+.....=+ .+.....-.+||+.|.+ + |..
T Consensus 30 ~~~L~~d~FLkLLvaQLqnQDPl~P~D~tefiaQlAQfS~lEq~~~mn~~l~~l~~~~~~~qa~slIGk~V~~--~-~~~ 106 (140)
T PRK06009 30 KASVNYDSFLQLLIAQMKNQDPTDPMDATQYVSQLATFSQVEQSIQTNSKLDTLLASSSLTQAEGLIGRTVTS--A-DGS 106 (140)
T ss_pred ccccCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEe--c-CCc
Confidence 34466777777887777666655433221100 01112455789999975 3 344
Q ss_pred eeEEEEeeeCCCCeEEEEeecCceeEE
Q 018661 314 SFGIIRRFDEYSRKHSVLFEDGESEFI 340 (352)
Q Consensus 314 ~~g~v~~~~~~~~~h~v~y~dg~~e~~ 340 (352)
..|+|+++.-+.+......+||.+-.|
T Consensus 107 ~~G~V~sV~~~~~~~~~~~~dg~~v~l 133 (140)
T PRK06009 107 ITGVVKSVTVYSDGVIATLEDGKKVLL 133 (140)
T ss_pred EEEEEEEEEEeCCceEEEEECCEEEEe
Confidence 349999999888888888888875443
No 84
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=23.65 E-value=95 Score=29.10 Aligned_cols=36 Identities=8% Similarity=0.281 Sum_probs=30.6
Q ss_pred cccccEEEEEeCCCceee-EEEEeeeCCCCeEEEEee
Q 018661 298 CCIGKVIRISHPKNESSF-GIIRRFDEYSRKHSVLFE 333 (352)
Q Consensus 298 ~~~g~~i~~~~~~~~~~~-g~v~~~~~~~~~h~v~y~ 333 (352)
--||.++.+-|+.|..|| .+|.+-++....--|.|+
T Consensus 91 w~vg~K~~A~~~ddg~~y~AtIe~ita~~~~~ai~f~ 127 (262)
T KOG3026|consen 91 WKVGDKVQAVFSDDGQIYDATIEHITAMEGTVAIIFA 127 (262)
T ss_pred cccCCEEEEeecCCCceEEeehhhccCCCCceeEEEe
Confidence 358999999999999999 999999987776666664
No 85
>PRK14637 hypothetical protein; Provisional
Probab=22.83 E-value=1.8e+02 Score=25.20 Aligned_cols=33 Identities=15% Similarity=0.119 Sum_probs=26.2
Q ss_pred CCCcccccccEEEEEeCCCceee-EEEEeeeCCC
Q 018661 293 QICPQCCIGKVIRISHPKNESSF-GIIRRFDEYS 325 (352)
Q Consensus 293 k~~~~~~~g~~i~~~~~~~~~~~-g~v~~~~~~~ 325 (352)
..+-...+|+.|+|.....+.|+ |++.++|..+
T Consensus 90 ~~~f~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~ 123 (151)
T PRK14637 90 AAEFSIFVGETVKVWFECTGQWQVGTIAEADETC 123 (151)
T ss_pred HHHHHHhCCCEEEEEECCCCcEEEEEEEEEeCCE
Confidence 34566789999999875567787 9999998863
No 86
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=22.74 E-value=1.6e+02 Score=21.78 Aligned_cols=33 Identities=9% Similarity=0.103 Sum_probs=27.0
Q ss_pred cccccccEEEEEeCCCceeeEEEEeeeCCCCeE
Q 018661 296 PQCCIGKVIRISHPKNESSFGIIRRFDEYSRKH 328 (352)
Q Consensus 296 ~~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~~h 328 (352)
..+++|+.|.|=-..+..|.|++.+||..-..|
T Consensus 5 L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~ 37 (70)
T cd01721 5 LHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQ 37 (70)
T ss_pred HhhCCCCEEEEEECCCcEEEEEEEEEcCCceeE
Confidence 356899999998887777669999999987654
No 87
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=22.48 E-value=2.9e+02 Score=22.21 Aligned_cols=46 Identities=24% Similarity=0.359 Sum_probs=33.1
Q ss_pred CCCcCCCcccccccEEEEEeCCCceee---EEEEeeeCCCCeEEEEeecCcee
Q 018661 289 YNQRQICPQCCIGKVIRISHPKNESSF---GIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 289 ~~q~k~~~~~~~g~~i~~~~~~~~~~~---g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
...+.+..+++||.+++|--..+..|. |.|... -+-++.+++|+-+
T Consensus 5 i~p~~i~~hEliGl~vrVv~s~~~s~vGI~G~VVdE----TkNtLvi~t~~~~ 53 (95)
T COG1588 5 ITPRNIIRHELIGLEVRVVRSTNPSYVGIEGRVVDE----TKNTLVIDTGSRE 53 (95)
T ss_pred ccCCCcChHHhcCcEEEEEecCCCCccceeEEEEee----eccEEEEECCCce
Confidence 344667889999999999999998877 666543 2445666666533
No 88
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=21.98 E-value=1.3e+02 Score=22.13 Aligned_cols=22 Identities=18% Similarity=0.238 Sum_probs=14.9
Q ss_pred EEEEeeeCCCCeEEEEeecCce
Q 018661 316 GIIRRFDEYSRKHSVLFEDGES 337 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~dg~~ 337 (352)
|+|+.||..++-==|.-+||..
T Consensus 4 G~Vk~f~~~kGfGFI~~~~g~~ 25 (68)
T TIGR02381 4 GIVKWFNNAKGFGFICPEGVDG 25 (68)
T ss_pred eEEEEEeCCCCeEEEecCCCCc
Confidence 7777777777766666666543
No 89
>PF06613 KorB_C: KorB C-terminal beta-barrel domain; InterPro: IPR010575 This domain is found in several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This family is found in conjunction with IPR003115 from INTERPRO.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1IGQ_B 1IGU_A.
Probab=21.89 E-value=1.2e+02 Score=22.25 Aligned_cols=25 Identities=24% Similarity=0.310 Sum_probs=16.6
Q ss_pred CCCCeEEEEeec-CceeEEeccccce
Q 018661 323 EYSRKHSVLFED-GESEFIDMAKVDW 347 (352)
Q Consensus 323 ~~~~~h~v~y~d-g~~e~~~l~~e~~ 347 (352)
++.+.-.|.|+| |.+..++|..-.-
T Consensus 29 s~~G~~WiKyED~G~e~E~dl~~v~l 54 (60)
T PF06613_consen 29 SSEGLAWIKYEDDGEEFEVDLGSVQL 54 (60)
T ss_dssp SSTTEEEEEETTT--EEEEEGGG-EE
T ss_pred CcCCeEEEEEccCCcEEEEEccceEE
Confidence 456778999955 9988999876543
No 90
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=21.82 E-value=2.6e+02 Score=22.33 Aligned_cols=30 Identities=20% Similarity=0.207 Sum_probs=26.2
Q ss_pred ccccccEEEEEeCCCceeeEEEEeeeCCCC
Q 018661 297 QCCIGKVIRISHPKNESSFGIIRRFDEYSR 326 (352)
Q Consensus 297 ~~~~g~~i~~~~~~~~~~~g~v~~~~~~~~ 326 (352)
...||++|.|--..|-+|-|++..-|....
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~s 33 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDS 33 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTT
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCC
Confidence 568999999999999887799999998655
No 91
>COG4697 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.60 E-value=83 Score=30.16 Aligned_cols=41 Identities=24% Similarity=0.381 Sum_probs=30.5
Q ss_pred CcccccccEEEEEeCC---Cce-eeEEEEeeeCCCCeEEEEeecCc
Q 018661 295 CPQCCIGKVIRISHPK---NES-SFGIIRRFDEYSRKHSVLFEDGE 336 (352)
Q Consensus 295 ~~~~~~g~~i~~~~~~---~~~-~~g~v~~~~~~~~~h~v~y~dg~ 336 (352)
+.-+++- ||+|-||. |+. |+|.|.-|+|+|+.=...=+||-
T Consensus 110 He~d~~t-~VrllWkek~~dr~~p~geV~lyNpysd~lllir~DG~ 154 (319)
T COG4697 110 HEGDLIT-RVRLLWKEKDVDRLYPFGEVRLYNPYSDRLLLIREDGF 154 (319)
T ss_pred eeecccc-eeEEecccccccccCCCceEEeeCCccccceeccccCc
Confidence 3344555 99999983 444 44999999999998877777764
No 92
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=21.52 E-value=2.8e+02 Score=21.89 Aligned_cols=28 Identities=32% Similarity=0.453 Sum_probs=22.7
Q ss_pred cCCCcccccccEEEEEeCCCceee---EEEE
Q 018661 292 RQICPQCCIGKVIRISHPKNESSF---GIIR 319 (352)
Q Consensus 292 ~k~~~~~~~g~~i~~~~~~~~~~~---g~v~ 319 (352)
+.+...+++|..++|.+..+..+- |.|.
T Consensus 4 ~~l~~~el~G~~v~Vv~s~~ps~vGi~GiVv 34 (92)
T smart00538 4 RKLLRHELIGLKVRVVASKNPSLVGIEGIVV 34 (92)
T ss_pred hhhhhhhhcCCEEEEEEcCCCCccCcEEEEE
Confidence 345667899999999999998876 7664
No 93
>PF13964 Kelch_6: Kelch motif
Probab=21.39 E-value=79 Score=21.20 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=15.8
Q ss_pred ecCceeEEeccccceEeccC
Q 018661 333 EDGESEFIDMAKVDWELVTD 352 (352)
Q Consensus 333 ~dg~~e~~~l~~e~~~~~~~ 352 (352)
.-.++|.+|+...+|+.+++
T Consensus 26 ~~~~v~~yd~~t~~W~~~~~ 45 (50)
T PF13964_consen 26 YSNDVERYDPETNTWEQLPP 45 (50)
T ss_pred ccccEEEEcCCCCcEEECCC
Confidence 34678899999999998763
No 94
>PRK14998 cold shock-like protein CspD; Provisional
Probab=20.31 E-value=1.4e+02 Score=22.42 Aligned_cols=23 Identities=17% Similarity=0.290 Sum_probs=13.4
Q ss_pred EEEEeeeCCCCeEEEEeecCcee
Q 018661 316 GIIRRFDEYSRKHSVLFEDGESE 338 (352)
Q Consensus 316 g~v~~~~~~~~~h~v~y~dg~~e 338 (352)
|+|+.||..++-==|.=+||..+
T Consensus 4 G~Vkwfn~~kGfGFI~~~~g~~d 26 (73)
T PRK14998 4 GTVKWFNNAKGFGFICPEGGGED 26 (73)
T ss_pred eEEEEEeCCCceEEEecCCCCcc
Confidence 66666666666555555555433
Done!