Query 038692
Match_columns 443
No_of_seqs 300 out of 1496
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 13:37:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038692hhsearch_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 1.5E-46 3.3E-51 396.8 14.3 170 251-420 92-266 (729)
2 KOG1080 Histone H3 (Lys4) meth 100.0 1.8E-32 4E-37 305.6 11.2 139 276-414 867-1005(1005)
3 KOG1082 Histone H3 (Lys9) meth 100.0 2.8E-31 6.1E-36 272.4 10.3 168 253-420 152-360 (364)
4 smart00317 SET SET (Su(var)3-9 99.9 1.6E-24 3.5E-29 183.0 13.9 115 277-391 2-116 (116)
5 KOG1079 Transcriptional repres 99.9 6.2E-24 1.3E-28 224.6 8.7 130 265-396 582-713 (739)
6 KOG1083 Putative transcription 99.9 5.6E-23 1.2E-27 224.5 1.6 133 265-398 1165-1300(1306)
7 KOG1085 Predicted methyltransf 99.8 3.7E-19 8E-24 173.2 9.8 119 276-394 257-379 (392)
8 KOG1141 Predicted histone meth 99.8 1.5E-19 3.2E-24 193.8 7.3 162 252-413 980-1261(1262)
9 KOG1081 Transcription factor N 99.7 2E-17 4.4E-22 174.5 3.0 324 78-426 117-449 (463)
10 COG2940 Proteins containing SE 99.6 3.8E-17 8.3E-22 173.7 1.9 138 277-414 334-480 (480)
11 PF00856 SET: SET domain; Int 99.6 1.3E-15 2.7E-20 133.8 8.2 107 286-392 1-162 (162)
12 KOG2589 Histone tail methylase 99.2 1.2E-11 2.6E-16 124.5 5.7 122 284-412 136-258 (453)
13 KOG2461 Transcription factor B 98.3 6.2E-07 1.3E-11 93.5 4.4 108 275-395 28-146 (396)
14 KOG1141 Predicted histone meth 97.9 2.6E-06 5.5E-11 93.5 -0.0 65 253-317 774-841 (1262)
15 smart00570 AWS associated with 96.5 0.0013 2.7E-08 49.6 1.5 25 251-275 26-50 (51)
16 smart00508 PostSET Cysteine-ri 95.9 0.0043 9.4E-08 40.3 1.3 19 399-417 2-20 (26)
17 smart00249 PHD PHD zinc finger 95.2 0.016 3.5E-07 40.8 2.5 45 116-162 2-47 (47)
18 KOG1081 Transcription factor N 94.6 0.027 5.9E-07 60.4 3.5 163 254-417 96-267 (463)
19 PF13771 zf-HC5HC2H: PHD-like 94.6 0.013 2.8E-07 48.3 0.8 51 110-162 33-89 (90)
20 KOG4443 Putative transcription 93.9 0.021 4.6E-07 62.5 0.9 77 114-190 19-101 (694)
21 PF13832 zf-HC5HC2H_2: PHD-zin 91.5 0.093 2E-06 44.9 1.4 40 107-148 49-88 (110)
22 KOG2084 Predicted histone tail 90.0 0.46 1E-05 49.6 5.2 43 351-397 208-251 (482)
23 PF05033 Pre-SET: Pre-SET moti 89.3 0.25 5.4E-06 41.6 2.2 96 134-269 3-103 (103)
24 PF00628 PHD: PHD-finger; Int 87.1 0.29 6.3E-06 35.9 1.1 44 115-160 1-46 (51)
25 KOG1337 N-methyltransferase [G 81.9 0.95 2.1E-05 48.6 2.6 41 350-393 238-278 (472)
26 COG5141 PHD zinc finger-contai 81.8 0.58 1.3E-05 50.1 0.8 34 113-148 303-336 (669)
27 PF13832 zf-HC5HC2H_2: PHD-zin 75.3 1.2 2.6E-05 38.0 0.7 72 114-190 1-88 (110)
28 smart00468 PreSET N-terminal t 68.1 11 0.00023 31.6 4.9 35 133-167 4-38 (98)
29 PF13639 zf-RING_2: Ring finge 67.6 1.6 3.5E-05 31.0 -0.1 35 114-150 1-35 (44)
30 PF08746 zf-RING-like: RING-li 64.9 3 6.4E-05 30.2 0.8 41 116-160 1-41 (43)
31 smart00249 PHD PHD zinc finger 60.6 6.5 0.00014 27.2 1.9 27 164-190 2-32 (47)
32 PF08666 SAF: SAF domain; Int 56.9 7 0.00015 29.4 1.7 16 374-389 3-18 (63)
33 KOG1338 Uncharacterized conser 51.6 10 0.00022 40.1 2.2 40 347-392 217-259 (466)
34 PF11793 FANCL_C: FANCL C-term 49.5 7.7 0.00017 30.9 0.8 38 113-150 2-42 (70)
35 PF00130 C1_1: Phorbol esters/ 44.7 23 0.00049 25.9 2.7 37 111-149 9-47 (53)
36 cd00162 RING RING-finger (Real 41.7 12 0.00025 25.3 0.7 32 115-150 1-32 (45)
37 KOG0383 Predicted helicase [Ge 40.4 11 0.00024 42.7 0.5 53 136-188 2-75 (696)
38 KOG1973 Chromatin remodeling p 37.8 17 0.00036 36.5 1.3 49 108-160 214-263 (274)
39 PF00412 LIM: LIM domain; Int 36.0 30 0.00064 25.4 2.2 28 116-146 1-28 (58)
40 smart00744 RINGv The RING-vari 35.9 15 0.00033 27.2 0.5 39 115-153 1-41 (49)
41 PF15446 zf-PHD-like: PHD/FYVE 35.8 12 0.00027 35.0 0.0 29 168-196 13-41 (175)
42 PF13445 zf-RING_UBOX: RING-ty 34.1 11 0.00025 27.2 -0.4 43 116-160 1-43 (43)
43 KOG2155 Tubulin-tyrosine ligas 34.1 24 0.00052 38.0 1.8 48 347-394 203-252 (631)
44 PF00856 SET: SET domain; Int 33.7 21 0.00045 30.5 1.2 17 373-389 2-18 (162)
45 KOG1244 Predicted transcriptio 32.0 12 0.00027 37.6 -0.6 69 120-190 238-314 (336)
46 KOG3970 Predicted E3 ubiquitin 31.1 21 0.00045 35.1 0.8 53 104-159 41-97 (299)
47 KOG0956 PHD finger protein AF1 30.7 26 0.00056 39.5 1.4 32 116-147 120-156 (900)
48 KOG1952 Transcription factor N 30.4 19 0.00041 41.4 0.4 49 110-160 188-240 (950)
49 smart00858 SAF This domain fam 29.8 35 0.00077 25.4 1.7 16 374-389 3-18 (64)
50 smart00132 LIM Zinc-binding do 29.5 38 0.00082 22.3 1.7 29 115-146 1-29 (39)
51 PF12861 zf-Apc11: Anaphase-pr 27.2 35 0.00075 28.6 1.3 22 133-154 49-70 (85)
52 PF00097 zf-C3HC4: Zinc finger 25.6 33 0.00072 23.5 0.8 40 116-161 1-40 (41)
53 PF07649 C1_3: C1-like domain; 25.5 35 0.00075 22.4 0.8 29 115-145 2-30 (30)
54 PRK10781 rcsF outer membrane l 24.6 1.3E+02 0.0029 27.2 4.6 35 71-105 75-112 (133)
55 smart00184 RING Ring finger. E 24.5 27 0.0006 22.4 0.2 20 131-150 11-30 (39)
56 PHA02929 N1R/p28-like protein; 24.2 47 0.001 32.9 1.8 40 111-150 172-214 (238)
57 KOG0954 PHD finger protein [Ge 22.7 36 0.00079 38.7 0.8 35 112-148 379-413 (893)
58 PF12678 zf-rbx1: RING-H2 zinc 20.4 46 0.001 26.5 0.8 20 132-151 46-65 (73)
59 PHA02862 5L protein; Provision 20.4 44 0.00096 30.7 0.8 38 113-152 2-40 (156)
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=1.5e-46 Score=396.83 Aligned_cols=170 Identities=44% Similarity=0.884 Sum_probs=163.5
Q ss_pred eeEEecCC-CCC-CCCCCCCCccccCc--eEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCc
Q 038692 251 VQYISCSK-ACH-CSETCNNRPFRKEK--KIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGV 326 (443)
Q Consensus 251 ~~~~EC~~-~C~-C~~~C~Nr~~q~~~--kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~ 326 (443)
+.++||++ .|+ |+.+|.|+.||+.+ +++||.|+++||||+|.++|++|+||+||.||||+..+++.|+..|...+.
T Consensus 92 ~t~iECs~~~C~~cg~~C~NQRFQkkqyA~vevF~Te~KG~GLRA~~dI~~g~FI~EY~GEVI~~~Ef~kR~~~Y~~d~~ 171 (729)
T KOG4442|consen 92 MTSIECSDRECPRCGVYCKNQRFQKKQYAKVEVFLTEKKGCGLRAEEDIPKGQFILEYIGEVIEEKEFEKRVKRYAKDGI 171 (729)
T ss_pred hhhcccCCccCCCccccccchhhhhhccCceeEEEecCcccceeeccccCCCcEEeeeccccccHHHHHHHHHHHHhcCC
Confidence 45689998 999 99999999999975 799999999999999999999999999999999999999999999999999
Q ss_pred cceeeeeeceeEEEecccccCccccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCCCCCC-CeeeecC
Q 038692 327 QNFYMCEIRKDFTIDATFKGNFSRFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFVQFGP-EVKCYCG 405 (443)
Q Consensus 327 ~~~y~~~~~~~~~IDa~~~GN~aRFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~~~~-~~~C~CG 405 (443)
.+||+|.+..+++|||+.+||++|||||||+|||++++|.|.+..||+|||.|+|.+||||||||+++++|. .++|+||
T Consensus 172 kh~Yfm~L~~~e~IDAT~KGnlaRFiNHSC~PNa~~~KWtV~~~lRvGiFakk~I~~GEEITFDYqf~rYGr~AQ~CyCg 251 (729)
T KOG4442|consen 172 KHYYFMALQGGEYIDATKKGNLARFINHSCDPNAEVQKWTVPDELRVGIFAKKVIKPGEEITFDYQFDRYGRDAQPCYCG 251 (729)
T ss_pred ceEEEEEecCCceecccccCcHHHhhcCCCCCCceeeeeeeCCeeEEEEeEecccCCCceeeEecccccccccccccccC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999986 4899999
Q ss_pred CCCCccccCCccccc
Q 038692 406 ASSCQGYLGTKRKIG 420 (443)
Q Consensus 406 S~~Crg~L~~~~~~~ 420 (443)
+++|+||||++++.+
T Consensus 252 eanC~G~IGgk~q~d 266 (729)
T KOG4442|consen 252 EANCRGWIGGKPQTD 266 (729)
T ss_pred CcccccccCCCCccc
Confidence 999999999997764
No 2
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=99.97 E-value=1.8e-32 Score=305.56 Aligned_cols=139 Identities=39% Similarity=0.809 Sum_probs=134.1
Q ss_pred eEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeeceeEEEecccccCccccccCC
Q 038692 276 KIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIRKDFTIDATFKGNFSRFLNHS 355 (443)
Q Consensus 276 kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~IDa~~~GN~aRFINHS 355 (443)
+|...++.++||||||+++|.+|++|+||.||+|....++.|...|...+....|+|.++++.+|||+..||+|||||||
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 47788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCCCCCCCeeeecCCCCCccccC
Q 038692 356 CDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFVQFGPEVKCYCGASSCQGYLG 414 (443)
Q Consensus 356 C~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~~~~~~~C~CGS~~Crg~L~ 414 (443)
|+|||....+.|+|..+|+|||.|||.+||||||||.|...+.+.+|+||+++|||+|+
T Consensus 947 C~PNCyakvi~V~g~~~IvIyakr~I~~~EElTYDYkF~~e~~kipClCgap~Crg~~n 1005 (1005)
T KOG1080|consen 947 CNPNCYAKVITVEGDKRIVIYSKRDIAAGEELTYDYKFPTEDDKIPCLCGAPNCRGFLN 1005 (1005)
T ss_pred cCCCceeeEEEecCeeEEEEEEecccccCceeeeeccccccccccccccCCCccccccC
Confidence 99999999999999999999999999999999999999998889999999999999984
No 3
>KOG1082 consensus Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics; Transcription]
Probab=99.97 E-value=2.8e-31 Score=272.44 Aligned_cols=168 Identities=35% Similarity=0.658 Sum_probs=138.5
Q ss_pred EEecCCCCCCCCCCCCCccccCc--eEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcC--ccc
Q 038692 253 YISCSKACHCSETCNNRPFRKEK--KIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRG--VQN 328 (443)
Q Consensus 253 ~~EC~~~C~C~~~C~Nr~~q~~~--kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~--~~~ 328 (443)
++||+..|+|+..|.||++|++. +|+||+++.+||||++.+.|++|+||+||+||+++..+++.+........ ...
T Consensus 152 i~EC~~~C~C~~~C~nRv~q~g~~~~leIfrt~~kGwgvRs~~~I~~G~fvcEyaGe~~t~~e~~~~~~~~~~~~~~~~~ 231 (364)
T KOG1082|consen 152 VFECSVACGCHPDCANRVVQKGLQFHLEVFRTPEKGWGVRTLDPIPAGEFVCEYAGEVLTSEEAQRRTHLREYLDDDCDA 231 (364)
T ss_pred ccccccCCCCCCcCcchhhccccccceEEEecCCceeeecccccccCCCeeEEEeeEecChHHhhhcccccccccccccc
Confidence 58999999999999999999984 69999999999999999999999999999999999999887732211111 110
Q ss_pred e------e---------------eeeeceeEEEecccccCccccccCCCCCceeEEEEEECC----eeEEEEEEccCCCC
Q 038692 329 F------Y---------------MCEIRKDFTIDATFKGNFSRFLNHSCDPNCILEKWQVEG----ETRVGVFAARSIKA 383 (443)
Q Consensus 329 ~------y---------------~~~~~~~~~IDa~~~GN~aRFINHSC~PNc~~~~~~v~g----~~ri~l~A~RdI~a 383 (443)
+ | .......+.|||...||++|||||||.||+.+..+..+. ..+++|||+++|.+
T Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ida~~~GNv~RfinHSC~PN~~~~~v~~~~~~~~~~~i~ffa~~~I~p 311 (364)
T KOG1082|consen 232 YSIADREWVDESPVGNTFVAPSLPGGPGRELLIDAKPHGNVARFINHSCSPNLLYQAVFQDEFVLLYLRIGFFALRDISP 311 (364)
T ss_pred chhhhccccccccccccccccccccCCCcceEEchhhcccccccccCCCCccceeeeeeecCCccchheeeeeeccccCC
Confidence 1 1 112246799999999999999999999999888777663 36999999999999
Q ss_pred CCcEeEecCCCCC------------CCCeeeecCCCCCccccCCccccc
Q 038692 384 GEPLTYDYRFVQF------------GPEVKCYCGASSCQGYLGTKRKIG 420 (443)
Q Consensus 384 GEELT~DYg~~~~------------~~~~~C~CGS~~Crg~L~~~~~~~ 420 (443)
|||||+||+..+. ..+..|.||+.+||+.+...+.+.
T Consensus 312 ~~ELT~dYg~~~~~~~~~~~~~~~~~~~~~c~c~~~~cr~~~~~~~~~~ 360 (364)
T KOG1082|consen 312 GEELTLDYGKAYKLLVQDGANIYTPVMKKNCNCGLEKCRGLLGSAPCVA 360 (364)
T ss_pred CcccchhhcccccccccccccccccccchhhcCCCHHhCcccCCCcccc
Confidence 9999999997642 124679999999999998776554
No 4
>smart00317 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues
Probab=99.92 E-value=1.6e-24 Score=183.00 Aligned_cols=115 Identities=49% Similarity=0.833 Sum_probs=100.7
Q ss_pred EEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeeceeEEEecccccCccccccCCC
Q 038692 277 IKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIRKDFTIDATFKGNFSRFLNHSC 356 (443)
Q Consensus 277 l~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~IDa~~~GN~aRFINHSC 356 (443)
++++.++++|+||||+++|++|++|++|.|.++...+...+...+........|++.....++||+...||++|||||||
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 57888899999999999999999999999999988877776543444443356777777789999999999999999999
Q ss_pred CCceeEEEEEECCeeEEEEEEccCCCCCCcEeEec
Q 038692 357 DPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDY 391 (443)
Q Consensus 357 ~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DY 391 (443)
.||+.+......+..++.++|+|||++|||||+||
T Consensus 82 ~pN~~~~~~~~~~~~~~~~~a~r~I~~GeEi~i~Y 116 (116)
T smart00317 82 EPNCELLFVEVNGDSRIVIFALRDIKPGEELTIDY 116 (116)
T ss_pred CCCEEEEEEEECCCcEEEEEECCCcCCCCEEeecC
Confidence 99999988877777789999999999999999999
No 5
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=99.89 E-value=6.2e-24 Score=224.62 Aligned_cols=130 Identities=36% Similarity=0.677 Sum_probs=120.5
Q ss_pred CCCCCccccC--ceEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeeceeEEEec
Q 038692 265 TCNNRPFRKE--KKIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIRKDFTIDA 342 (443)
Q Consensus 265 ~C~Nr~~q~~--~kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~IDa 342 (443)
.|.|-.+|++ +++.+..+...|||||+.+.+.+++||.||+||+|++.|+++|.+.|.... -.|+|++..+|+|||
T Consensus 582 ~C~N~~l~~~~qkr~llapSdVaGwGlFlKe~v~KnefisEY~GE~IS~dEADrRGkiYDr~~--cSflFnln~dyviDs 659 (739)
T KOG1079|consen 582 SCKNTNLQRGEQKRVLLAPSDVAGWGLFLKESVSKNEFISEYTGEIISHDEADRRGKIYDRYM--CSFLFNLNNDYVIDS 659 (739)
T ss_pred ccccchhhhhhhcceeechhhccccceeeccccCCCceeeeecceeccchhhhhccccccccc--ceeeeeccccceEee
Confidence 7989888876 468999999999999999999999999999999999999999988775443 568889999999999
Q ss_pred ccccCccccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCCCC
Q 038692 343 TFKGNFSRFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFVQF 396 (443)
Q Consensus 343 ~~~GN~aRFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~~ 396 (443)
+++||.+||+|||-+|||....+.|.|..+|.|||.|+|++||||||||++...
T Consensus 660 ~rkGnk~rFANHS~nPNCYAkvm~V~GdhRIGifAkRaIeagEELffDYrYs~~ 713 (739)
T KOG1079|consen 660 TRKGNKIRFANHSFNPNCYAKVMMVAGDHRIGIFAKRAIEAGEELFFDYRYSPE 713 (739)
T ss_pred eeecchhhhccCCCCCCcEEEEEEecCCcceeeeehhhcccCceeeeeeccCcc
Confidence 999999999999999999999999999999999999999999999999998754
No 6
>KOG1083 consensus Putative transcription factor ASH1/LIN-59 [Transcription]
Probab=99.86 E-value=5.6e-23 Score=224.54 Aligned_cols=133 Identities=41% Similarity=0.809 Sum_probs=119.1
Q ss_pred CCCCCccccC---ceEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeeceeEEEe
Q 038692 265 TCNNRPFRKE---KKIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIRKDFTID 341 (443)
Q Consensus 265 ~C~Nr~~q~~---~kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~ID 341 (443)
.|.|+.+|+. ..|++++.+.+||||.|.++|++||||+||+|+|+...+.+.+|-.+. ....+.|.+.++.+.+||
T Consensus 1165 ~c~nqrm~r~e~cp~L~v~~gp~~G~~v~tk~PikagtfI~EYvGeVit~ke~e~~mmtl~-~~d~~~~cL~I~p~l~id 1243 (1306)
T KOG1083|consen 1165 SCSNQRMQRHEECPPLEVFRGPKKGWGVRTKEPIKAGTFIMEYVGEVITEKEFEPRMMTLY-HNDDDHYCLVIDPGLFID 1243 (1306)
T ss_pred hhhhHHhhhhccCCCcceeccCCCCccccccccccccchHHHHHHHHHHHHhhcccccccC-CCCCcccccccCccccCC
Confidence 3889999874 579999999999999999999999999999999999998888743332 234466788899999999
Q ss_pred cccccCccccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCCCCCC
Q 038692 342 ATFKGNFSRFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFVQFGP 398 (443)
Q Consensus 342 a~~~GN~aRFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~~~~ 398 (443)
+.+.||.+||+||+|.|||+++.|.++|+.|++|||+|||.+||||||||++..++.
T Consensus 1244 ~~R~~n~~RfinhscKPNc~~qkwSVNG~~Rv~L~A~rDi~kGEELtYDYN~ks~~~ 1300 (1306)
T KOG1083|consen 1244 IPRMGNGARFINHSCKPNCEMQKWSVNGEYRVGLFALRDLPKGEELTYDYNFKSFNY 1300 (1306)
T ss_pred hhhccccccccccccCCCCccccccccceeeeeeeecCCCCCCceEEEeccccccCC
Confidence 999999999999999999999999999999999999999999999999998876553
No 7
>KOG1085 consensus Predicted methyltransferase (contains a SET domain) [General function prediction only]
Probab=99.78 E-value=3.7e-19 Score=173.15 Aligned_cols=119 Identities=29% Similarity=0.411 Sum_probs=104.3
Q ss_pred eEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhc---CccceeeeeeceeEEEecccc-cCcccc
Q 038692 276 KIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYR---GVQNFYMCEIRKDFTIDATFK-GNFSRF 351 (443)
Q Consensus 276 kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~---~~~~~y~~~~~~~~~IDa~~~-GN~aRF 351 (443)
.+.+....++|.||+|+.++.+|+||+||.|.+|...++..|...|... +-+.|||-..+..|+|||+.- +-.+|.
T Consensus 257 gl~~~~~dgKGRGv~a~~~F~rgdFVVEY~Gdliei~eAk~rE~~Ya~De~~GcYMYyF~h~sk~yCiDAT~et~~lGRL 336 (392)
T KOG1085|consen 257 GLLEVYKDGKGRGVRAKVNFERGDFVVEYRGDLIEISEAKVREEQYANDEEIGCYMYYFEHNSKKYCIDATKETPWLGRL 336 (392)
T ss_pred ceeEEeeccccceeEeecccccCceEEEEecceeeechHHHHHHHhccCcccceEEEeeeccCeeeeeecccccccchhh
Confidence 3666677779999999999999999999999999888888877666543 345567777788999999984 667999
Q ss_pred ccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCC
Q 038692 352 LNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFV 394 (443)
Q Consensus 352 INHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~ 394 (443)
||||=.+|+....+.+++.++++++|.|||.+||||+||||+.
T Consensus 337 INHS~~gNl~TKvv~Idg~pHLiLvA~rdIa~GEELlYDYGDR 379 (392)
T KOG1085|consen 337 INHSVRGNLKTKVVEIDGSPHLILVARRDIAQGEELLYDYGDR 379 (392)
T ss_pred hcccccCcceeeEEEecCCceEEEEeccccccchhhhhhcccc
Confidence 9999999999999999999999999999999999999999965
No 8
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=99.78 E-value=1.5e-19 Score=193.84 Aligned_cols=162 Identities=34% Similarity=0.601 Sum_probs=124.9
Q ss_pred eEEecCCCCCCCCCCCCCccccCc----------eEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHh
Q 038692 252 QYISCSKACHCSETCNNRPFRKEK----------KIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDM 321 (443)
Q Consensus 252 ~~~EC~~~C~C~~~C~Nr~~q~~~----------kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~ 321 (443)
..+||+.+|.|...|.|++.|.+. .|.|+++...|||+++..+|+.-+||++|.|...++.-+.+....+
T Consensus 980 ~f~e~~~hss~~~~e~~~~v~~~~~~~me~~s~~~l~i~~~~~~~~~~~edtD~~~~~~~~~~~~~ppt~~l~~~~r~aq 1059 (1262)
T KOG1141|consen 980 FFFECNDHSSCHRKEYNRVVQNNIKYPMEVSSFNDLQIFKTAQSGWGVREDTDIPQSTFICTYVGAPPTDDLADELRNAQ 1059 (1262)
T ss_pred cceeccccchhcccccchhhhcCCccceeeeecccccccccccccccccccccCCCCcccccccCCCCchhhHHHHhhhh
Confidence 347999999999999999998853 2678889999999999999999999999999986543332210000
Q ss_pred hhc-------------------------Ccccee----------------------------------------------
Q 038692 322 KYR-------------------------GVQNFY---------------------------------------------- 330 (443)
Q Consensus 322 ~~~-------------------------~~~~~y---------------------------------------------- 330 (443)
... +...-|
T Consensus 1060 ad~~sn~~D~~~~~~l~es~~~~~T~~r~~t~~~~~~~~~d~dd~q~I~k~ve~qd~~~~~~~T~~~~RQ~~~~s~k~~~ 1139 (1262)
T KOG1141|consen 1060 ADQYSNDLDLKDTVELEESREDHETDFRGDTSDYDDEEGSDGDDGQDIMKMVERQDSSESGEETKRLTRQKRKQSKKSGK 1139 (1262)
T ss_pred hccccCccchhhhhhhhhcccccccccCCCCCCCcccccccCccHHHHHHHhhcccccccccccchhhhhhhhhhhhccc
Confidence 000 000000
Q ss_pred -------------eeeec-------------------eeEEEecccccCccccccCCCCCceeEEEEEECC----eeEEE
Q 038692 331 -------------MCEIR-------------------KDFTIDATFKGNFSRFLNHSCDPNCILEKWQVEG----ETRVG 374 (443)
Q Consensus 331 -------------~~~~~-------------------~~~~IDa~~~GN~aRFINHSC~PNc~~~~~~v~g----~~ri~ 374 (443)
+++.+ .-|+|||+..||++||+||||.||+.++.++++. .+.++
T Consensus 1140 ~~s~~~~~~ts~~~~~~dkges~~~~~~~~~~y~~~~~~yvIDAk~eGNlGRfLNHSC~PNl~VQnVfvdTHdlrfPwVA 1219 (1262)
T KOG1141|consen 1140 GGSVEKDDTTSRDSMEKDKGESKDEPVFNWDKYFEPFPLYVIDAKQEGNLGRFLNHSCDPNLHVQNVFVDTHDLRFPWVA 1219 (1262)
T ss_pred CccccccccCccchhhhccCccCcccccchhhccCCCceEEEecccccchhhhhccCCCccceeeeeeeeccccCCchhh
Confidence 00011 1378999999999999999999999999998875 36899
Q ss_pred EEEccCCCCCCcEeEecCCCCC---CCCeeeecCCCCCcccc
Q 038692 375 VFAARSIKAGEPLTYDYRFVQF---GPEVKCYCGASSCQGYL 413 (443)
Q Consensus 375 l~A~RdI~aGEELT~DYg~~~~---~~~~~C~CGS~~Crg~L 413 (443)
|||.|-|++|+|||+||+++.- +....|+||+.+|||.|
T Consensus 1220 FFt~kyVkAgtELTWDY~Ye~g~v~~keL~C~CGa~~CrgrL 1261 (1262)
T KOG1141|consen 1220 FFTRKYVKAGTELTWDYQYEQGQVATKELTCHCGAENCRGRL 1261 (1262)
T ss_pred hhhhhhhccCceeeeeccccccccccceEEEecChhhhhccc
Confidence 9999999999999999998753 34578999999999987
No 9
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=99.66 E-value=2e-17 Score=174.49 Aligned_cols=324 Identities=28% Similarity=0.368 Sum_probs=218.3
Q ss_pred CcChHHHHHHHHhhhhhcCCCccccccceeccCcCceecccccccccC-cceee-eeecCCCccccccchhcccCCCCCC
Q 038692 78 ISGLEDHVAAWVKKKMELGVPQSNCSLPFLVGAKKMIECRACHRFIYH-GEEVF-CSVRGCGGVYHFICVKERLGISNPR 155 (443)
Q Consensus 78 ~~~~~~~~~~~~~~~~~~g~~~~~~~lp~l~~a~~~~~C~~C~~~~~~-ge~i~-Csv~~C~~~yH~~C~~~~~~~~~~~ 155 (443)
...+++.++-|...+++. ..++..+..+.+|.-....|-+|.+..+. ++... +..-.| ..|+..+....- ..+.+
T Consensus 117 ~~~~~~c~~~~~d~~~~~-~~~~~~~vw~~vg~~~~~~c~vc~~~~~~~~~~~~~~~f~~~-~~~~~~~~~~~~-~g~~~ 193 (463)
T KOG1081|consen 117 PAQLEKCSKRCTDCRAFK-KREVGDLVWSKVGEYPWWPCMVCHDPLLPKGMKHDHVNFFGC-YAWTHEKRVFPY-EGQSS 193 (463)
T ss_pred CccCcccccCCcceeeec-cccceeEEeEEcCcccccccceecCcccchhhccccceeccc-hhhHHHhhhhhc-cchHH
Confidence 345778888888889888 88889999999999999999999998777 66663 777767 666666544322 22222
Q ss_pred CCcc------CCCceeeecccccccceeccccccCCCCCCCcceeEeccCCCceeeecCCcchhcccccccccCCCCCCc
Q 038692 156 NFKC------PQHACFICRQRLQWRCVRCTIASHDKCAPWPDRVIHLKDQPGRAVCWRHPAKWLLDKQEVFCRLPLPYAD 229 (443)
Q Consensus 156 ~f~C------p~H~C~~c~~~~~~rC~rC~~a~h~~C~p~~~~~~~l~~~~~~~~c~rhp~~W~~~~~~~f~~~~~p~~~ 229 (443)
.+.+ +++.+..+.....+++.++..+-+..= .+......+.....||.++..-....-..+..+ ..+..
T Consensus 194 ~~l~~~~~~~s~~~~~~~~~~~r~~~~~~q~~~~~~~----~e~k~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-~~~~~ 268 (463)
T KOG1081|consen 194 KLIPHSKKPASTMSEKIKEAKARFGKLKAQWEAGIKQ----KELKPEEYKRIKVVCPIGDQQIYSAAVSCIKKL-LAKPT 268 (463)
T ss_pred Hhhhhccccchhhhhhhhcccchhhhcccchhhccch----hhcccccccccccccCcCcccccchhhhhhhhc-ccccc
Confidence 2222 222222222234555555544433111 222333444455566665444110000000000 00000
Q ss_pred cccccccchhhccccccCCCCeeEEe-cCCCCCCCCCCCCCccccCceEEEEEcCCCccEEEeccccCCCcEEEEEccee
Q 038692 230 EEFKIDLTWKDLMENKVGPPPVQYIS-CSKACHCSETCNNRPFRKEKKIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEV 308 (443)
Q Consensus 230 ~~~~~~~~~~~~~~~~~~p~~~~~~E-C~~~C~C~~~C~Nr~~q~~~kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeV 308 (443)
. .+ ...+.......++..+..++ ++..|.+...|.|+.+......+ +.. +|.++|.+| .|++
T Consensus 269 ~-~~--~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~sk~~~~e----~~~----~~~~~~~k~------vg~~ 331 (463)
T KOG1081|consen 269 D-EK--PNSRGASEEATKSEKMLAYEVHPKVCSAEERCHNQQFSKESYPE----PQK----TAKADIRKG------VGEV 331 (463)
T ss_pred c-cc--cccCCcHHHhhhhHHhhhhhhcccccccccccccchhhhhcccc----cch----hhHHhhhcc------cCcc
Confidence 0 00 00000000011111122234 46799999999999987765444 222 888999999 8999
Q ss_pred cCHHHHHHHHHHhhhcCccceeeeeeceeEEEecccccCccccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEe
Q 038692 309 IDDALCEQRLWDMKYRGVQNFYMCEIRKDFTIDATFKGNFSRFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLT 388 (443)
Q Consensus 309 i~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~IDa~~~GN~aRFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT 388 (443)
++..+...+++........++|+..+..+..||+..+||.+||+||||+||++...+++.+..++.++|.++|++|||||
T Consensus 332 i~~~e~~~~~~~~~~~~~~~~~~~~~e~~~~id~~~~~n~sr~~nh~~~~~v~~~k~~~~~~t~~~~~a~~~i~~g~e~t 411 (463)
T KOG1081|consen 332 IDDKECKARLQRVKESDLVDFYMVFIQKDRIIDAGPKGNYSRFLNHSCQPNVETEKWQVIGDTRVGLFAPRQIEAGEELT 411 (463)
T ss_pred cchhhheeehhhhhccchhhhhhhhhhcccccccccccchhhhhcccCCCceeechhheecccccccccccccccchhhh
Confidence 99999999988888888888887777777799999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCCCCCeeeecCCCCCccccCCccccccccccc
Q 038692 389 YDYRFVQFGPEVKCYCGASSCQGYLGTKRKIGKLELCW 426 (443)
Q Consensus 389 ~DYg~~~~~~~~~C~CGS~~Crg~L~~~~~~~~~~~~w 426 (443)
++|.....+..+.|.||+.+|.++++.+.+.++..+.|
T Consensus 412 ~~~n~~~~~~~~~~~~~~e~~~~~~~k~~~~~~~~~~~ 449 (463)
T KOG1081|consen 412 FNYNGNCEGNEKRCCCGSENCTETKGKKKKKKKQLRSR 449 (463)
T ss_pred heeeccccCCcceEeecccccccCCcccccchhhhhhh
Confidence 99999988888999999999999999998888555555
No 10
>COG2940 Proteins containing SET domain [General function prediction only]
Probab=99.64 E-value=3.8e-17 Score=173.66 Aligned_cols=138 Identities=37% Similarity=0.586 Sum_probs=111.7
Q ss_pred EEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeeceeEEEecccccCccccccCCC
Q 038692 277 IKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIRKDFTIDATFKGNFSRFLNHSC 356 (443)
Q Consensus 277 l~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~IDa~~~GN~aRFINHSC 356 (443)
..+..+..+|+|+||.+.|++|++|.+|.|+++...+...+...+...+...++....+...++|+...|+.+||+||||
T Consensus 334 ~~~~~~~~~~~g~fa~~~i~~~e~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~g~~~r~~nHS~ 413 (480)
T COG2940 334 NVVQESEIKGYGVFALESIKKGEFIIEYHGEIIRRKEAREREENYDLLGNEFSFGLLEDKDKVRDSQKAGDVARFINHSC 413 (480)
T ss_pred hhhhhhcccccceeehhhccchHHHHHhcCcccchHHHHhhhccccccccccchhhccccchhhhhhhcccccceeecCC
Confidence 44567788999999999999999999999999988887777655422222222222222378999999999999999999
Q ss_pred CCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCCCCCC---------CeeeecCCCCCccccC
Q 038692 357 DPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFVQFGP---------EVKCYCGASSCQGYLG 414 (443)
Q Consensus 357 ~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~~~~---------~~~C~CGS~~Crg~L~ 414 (443)
.||+......+.+..++.++|+|||.+||||++||+...+.. ...|.||+..|++++.
T Consensus 414 ~pN~~~~~~~~~g~~~~~~~~~rDI~~geEl~~dy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 480 (480)
T COG2940 414 TPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPSLEDNRELKKLLEKRWGCACGEDRCSHTMS 480 (480)
T ss_pred CCCcceecccccccceeeecccccchhhhhhccccccccccchhhhhhhhhhhccccCCCccCCCCC
Confidence 999998776666667899999999999999999999887652 3689999999998863
No 11
>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=99.61 E-value=1.3e-15 Score=133.79 Aligned_cols=107 Identities=26% Similarity=0.313 Sum_probs=72.3
Q ss_pred ccEEEeccccCCCcEEEEEcceecCHHHHHHH-------------------H-----------------HHhh---hc-C
Q 038692 286 GWGVEAAEPINKGEFIIEYIGEVIDDALCEQR-------------------L-----------------WDMK---YR-G 325 (443)
Q Consensus 286 G~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r-------------------~-----------------~~~~---~~-~ 325 (443)
|+||||+++|++|++|++..+.+++....... . .... .. .
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 89999999999999999888888876655331 0 0000 00 0
Q ss_pred cc---------------ceeeeeeceeEEEecccccCccccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEe
Q 038692 326 VQ---------------NFYMCEIRKDFTIDATFKGNFSRFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYD 390 (443)
Q Consensus 326 ~~---------------~~y~~~~~~~~~IDa~~~GN~aRFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~D 390 (443)
.. .............++....+++.|+||||.|||.+..........+.|+|.|||++|||||++
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 000111112234556667788999999999999887766667889999999999999999999
Q ss_pred cC
Q 038692 391 YR 392 (443)
Q Consensus 391 Yg 392 (443)
||
T Consensus 161 YG 162 (162)
T PF00856_consen 161 YG 162 (162)
T ss_dssp ST
T ss_pred EC
Confidence 97
No 12
>KOG2589 consensus Histone tail methylase [Chromatin structure and dynamics]
Probab=99.21 E-value=1.2e-11 Score=124.48 Aligned_cols=122 Identities=23% Similarity=0.330 Sum_probs=89.8
Q ss_pred CCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeeceeEEEecccccCccccccCCCCCceeEE
Q 038692 284 FCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIRKDFTIDATFKGNFSRFLNHSCDPNCILE 363 (443)
Q Consensus 284 ~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~~~~~IDa~~~GN~aRFINHSC~PNc~~~ 363 (443)
..|--|.+++.+.+|+-|...+|-|+.-.+.+++.. ...+..+|-+|.....-+ +...-..++||||.|.|||+|.
T Consensus 136 ~~gAkivst~~w~~ndkIe~LvGcIaeLse~eE~~l--l~~g~nDFSvmyStRk~c--aqLwLGPaafINHDCrpnCkFv 211 (453)
T KOG2589|consen 136 QNGAKIVSTKSWSRNDKIELLVGCIAELSEAEERSL--LRGGGNDFSVMYSTRKRC--AQLWLGPAAFINHDCRPNCKFV 211 (453)
T ss_pred CCCceEEeeccccCCccHHHhhhhhhhcChhhhHHH--HhccCCceeeeeecccch--hhheeccHHhhcCCCCCCceee
Confidence 468889999999999999999999887666666532 223333444443322111 2223467899999999999985
Q ss_pred EEEECCeeEEEEEEccCCCCCCcEeEecCCCCCCCC-eeeecCCCCCccc
Q 038692 364 KWQVEGETRVGVFAARSIKAGEPLTYDYRFVQFGPE-VKCYCGASSCQGY 412 (443)
Q Consensus 364 ~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~~~~~-~~C~CGS~~Crg~ 412 (443)
..|..++.+.++|||++|||||.-||..+|++. ..|.|-+..=+|.
T Consensus 212 ---s~g~~tacvkvlRDIePGeEITcFYgs~fFG~~N~~CeC~TCER~g~ 258 (453)
T KOG2589|consen 212 ---STGRDTACVKVLRDIEPGEEITCFYGSGFFGENNEECECVTCERRGT 258 (453)
T ss_pred ---cCCCceeeeehhhcCCCCceeEEeecccccCCCCceeEEeecccccc
Confidence 356689999999999999999999999999864 6788865444444
No 13
>KOG2461 consensus Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription]
Probab=98.28 E-value=6.2e-07 Score=93.54 Aligned_cols=108 Identities=24% Similarity=0.250 Sum_probs=79.9
Q ss_pred ceEEEEEc--CCCccEEEeccccCCCcEEEEEcceecCHHHHHHHHHHhhhcCccceeeeeec----eeEEEeccc--cc
Q 038692 275 KKIKIVKT--EFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQRLWDMKYRGVQNFYMCEIR----KDFTIDATF--KG 346 (443)
Q Consensus 275 ~kl~V~~s--~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r~~~~~~~~~~~~y~~~~~----~~~~IDa~~--~G 346 (443)
..+.|+.+ +..|.||++...|++|+-.+-|.|+++... ........|++.+- ..++||++. ..
T Consensus 28 ~~l~i~~Ssv~~~~lgV~s~~~i~~G~~FGP~~G~~~~~~---------~~~~~n~~y~W~I~~~d~~~~~iDg~d~~~s 98 (396)
T KOG2461|consen 28 PELRIKPSSVPVTGLGVWSNASILPGTSFGPFEGEIIASI---------DSKSANNRYMWEIFSSDNGYEYIDGTDEEHS 98 (396)
T ss_pred CceEeeccccCCccccccccccccCcccccCccCcccccc---------ccccccCcceEEEEeCCCceEEeccCChhhc
Confidence 34666655 667899999999999999999999972111 11223344555542 338899877 68
Q ss_pred CccccccCCCC---CceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCCCC
Q 038692 347 NFSRFLNHSCD---PNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRFVQ 395 (443)
Q Consensus 347 N~aRFINHSC~---PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~~~ 395 (443)
|++||||=+++ -|.... .....|+++|+|+|.+||||.+.|+.++
T Consensus 99 NWmRYV~~Ar~~eeQNL~A~----Q~~~~Ifyrt~r~I~p~eELlVWY~~e~ 146 (396)
T KOG2461|consen 99 NWMRYVNSARSEEEQNLLAF----QIGENIFYRTIRDIRPNEELLVWYGSEY 146 (396)
T ss_pred ceeeeecccCChhhhhHHHH----hccCceEEEecccCCCCCeEEEEeccch
Confidence 99999998885 465432 2346799999999999999999998765
No 14
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=97.89 E-value=2.6e-06 Score=93.46 Aligned_cols=65 Identities=28% Similarity=0.588 Sum_probs=58.1
Q ss_pred EEecCCCCCCC-CCCCCCccccCc--eEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHHHHHHH
Q 038692 253 YISCSKACHCS-ETCNNRPFRKEK--KIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDALCEQR 317 (443)
Q Consensus 253 ~~EC~~~C~C~-~~C~Nr~~q~~~--kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~e~~~r 317 (443)
.|||+..|+|. ..|.||.+|.+. ++.+|++..+|||++...+|.+|.||+.|.|.++++.-.+..
T Consensus 774 ~yEc~k~ckc~~~~C~nrmvqhg~qvRlq~fkt~~kGWg~rclddi~~g~fVciy~g~~l~~~~sdks 841 (1262)
T KOG1141|consen 774 PYECLKACKCCGPDCLNRMVQHGYQVRLQRFKTIHKGWGRRCLDDITGGNFVCIYPGGALLHQISDKS 841 (1262)
T ss_pred HHHHHHhhccCcHHHHHHHhhcCceeEeeeccccccccceEeeeecCCceEEEEecchhhhhhhchhh
Confidence 58999999984 689999999985 688899999999999999999999999999999877665554
No 15
>smart00570 AWS associated with SET domains. subdomain of PRESET
Probab=96.50 E-value=0.0013 Score=49.62 Aligned_cols=25 Identities=36% Similarity=0.915 Sum_probs=22.1
Q ss_pred eeEEecCCCCCCCCCCCCCccccCc
Q 038692 251 VQYISCSKACHCSETCNNRPFRKEK 275 (443)
Q Consensus 251 ~~~~EC~~~C~C~~~C~Nr~~q~~~ 275 (443)
++++||+..|+|++.|+||.||+..
T Consensus 26 ~l~~EC~~~C~~G~~C~NqrFqk~~ 50 (51)
T smart00570 26 MLLIECSSDCPCGSYCSNQRFQKRQ 50 (51)
T ss_pred HHhhhcCCCCCCCcCccCcccccCc
Confidence 5568999999999999999999853
No 16
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=95.85 E-value=0.0043 Score=40.32 Aligned_cols=19 Identities=42% Similarity=1.106 Sum_probs=16.1
Q ss_pred CeeeecCCCCCccccCCcc
Q 038692 399 EVKCYCGASSCQGYLGTKR 417 (443)
Q Consensus 399 ~~~C~CGS~~Crg~L~~~~ 417 (443)
.+.|+|||.+|||+|+...
T Consensus 2 ~~~C~CGs~~CRG~l~~~~ 20 (26)
T smart00508 2 KQPCLCGAPNCRGFLGXXX 20 (26)
T ss_pred CeeeeCCCccccceecccc
Confidence 4799999999999996553
No 17
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=94.62 E-value=0.027 Score=60.39 Aligned_cols=163 Identities=18% Similarity=0.177 Sum_probs=103.7
Q ss_pred EecCCCCCCCCCCCCCccccCceEEEEEcCCCccEEEeccccCCCcEEEEEcceecCHH--HHHHHHHHhhhcCc-ccee
Q 038692 254 ISCSKACHCSETCNNRPFRKEKKIKIVKTEFCGWGVEAAEPINKGEFIIEYIGEVIDDA--LCEQRLWDMKYRGV-QNFY 330 (443)
Q Consensus 254 ~EC~~~C~C~~~C~Nr~~q~~~kl~V~~s~~kG~GLfA~e~I~kGt~I~eY~GeVi~~~--e~~~r~~~~~~~~~-~~~y 330 (443)
+++...+-|...+.+- .....+++.-.....+-=..|.+.+..|++|+.+.|+..-+. ......+....... ..||
T Consensus 96 ~~ggs~v~~~s~~~~~-~r~c~~~~~~~c~~~~~d~~~~~~~~~~~~vw~~vg~~~~~~c~vc~~~~~~~~~~~~~~~f~ 174 (463)
T KOG1081|consen 96 FKGGSLVTCKSRIQAP-HRKCKPAQLEKCSKRCTDCRAFKKREVGDLVWSKVGEYPWWPCMVCHDPLLPKGMKHDHVNFF 174 (463)
T ss_pred cCCCccceeccccccc-cccCcCccCcccccCCcceeeeccccceeEEeEEcCcccccccceecCcccchhhccccceec
Confidence 4444555555444443 333333333333333333888889999999999999986544 22222222111111 2222
Q ss_pred eeeeceeEEEecccccCccccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCc------EeEecCCCCCCCCeeeec
Q 038692 331 MCEIRKDFTIDATFKGNFSRFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEP------LTYDYRFVQFGPEVKCYC 404 (443)
Q Consensus 331 ~~~~~~~~~IDa~~~GN~aRFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEE------LT~DYg~~~~~~~~~C~C 404 (443)
....-.....++...|+..++++|++.|+-.+..+......++..++.+.++-+.. .+.+|....+..++.+.+
T Consensus 175 ~~~~~~~~~~~~~~~g~~~~~l~~~~~~~s~~~~~~~~~~~r~~~~~~q~~~~~~~~e~k~~~~~~~~~~~~~~~~~~~~ 254 (463)
T KOG1081|consen 175 GCYAWTHEKRVFPYEGQSSKLIPHSKKPASTMSEKIKEAKARFGKLKAQWEAGIKQKELKPEEYKRIKVVCPIGDQQIYS 254 (463)
T ss_pred cchhhHHHhhhhhccchHHHhhhhccccchhhhhhhhcccchhhhcccchhhccchhhcccccccccccccCcCcccccc
Confidence 22111123344555999999999999999888888888889999999998888877 777887777766677888
Q ss_pred CCCCCccccCCcc
Q 038692 405 GASSCQGYLGTKR 417 (443)
Q Consensus 405 GS~~Crg~L~~~~ 417 (443)
...+|..-++...
T Consensus 255 ~~~~~~~k~~~~~ 267 (463)
T KOG1081|consen 255 AAVSCIKKLLAKP 267 (463)
T ss_pred hhhhhhhhccccc
Confidence 8888876665544
No 19
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=94.59 E-value=0.013 Score=48.26 Aligned_cols=51 Identities=24% Similarity=0.617 Sum_probs=38.7
Q ss_pred CcCceecccccccccCcceeeeeecCCCccccccchhcccCCC------CCCCCccCCC
Q 038692 110 AKKMIECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLGIS------NPRNFKCPQH 162 (443)
Q Consensus 110 a~~~~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~~~------~~~~f~Cp~H 162 (443)
..++-.|.+|++. .|=.|+|...+|...||+.|+....... ....+.||.|
T Consensus 33 ~~~~~~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C~~H 89 (90)
T PF13771_consen 33 RRRKLKCSICKKK--GGACIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFCPKH 89 (90)
T ss_pred HHhCCCCcCCCCC--CCeEEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEEChhc
Confidence 3455689999887 6889999999999999999999843311 1335666666
No 20
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=93.90 E-value=0.021 Score=62.46 Aligned_cols=77 Identities=23% Similarity=0.504 Sum_probs=56.0
Q ss_pred eecccccccccCcceeeeeecCCCccccccchhcccC-CCCCCCCccCCCc-eeeec----ccccccceeccccccCCCC
Q 038692 114 IECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLG-ISNPRNFKCPQHA-CFICR----QRLQWRCVRCTIASHDKCA 187 (443)
Q Consensus 114 ~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~-~~~~~~f~Cp~H~-C~~c~----~~~~~rC~rC~~a~h~~C~ 187 (443)
..|++|.-++.+.+.-.=+...|+.+||.-|++-+.. .-....|+||.|. |..|. .+.++-|-+|-++||.-|.
T Consensus 19 ~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~ 98 (694)
T KOG4443|consen 19 LMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDVSYHCYCQ 98 (694)
T ss_pred hhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCccccccccccccccccccc
Confidence 4566665554444433334567899999999996543 2234459999986 99998 4699999999999999997
Q ss_pred CCC
Q 038692 188 PWP 190 (443)
Q Consensus 188 p~~ 190 (443)
-+.
T Consensus 99 ~P~ 101 (694)
T KOG4443|consen 99 KPP 101 (694)
T ss_pred CCc
Confidence 544
No 21
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=91.50 E-value=0.093 Score=44.86 Aligned_cols=40 Identities=23% Similarity=0.624 Sum_probs=34.7
Q ss_pred eccCcCceecccccccccCcceeeeeecCCCccccccchhcc
Q 038692 107 LVGAKKMIECRACHRFIYHGEEVFCSVRGCGGVYHFICVKER 148 (443)
Q Consensus 107 l~~a~~~~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~ 148 (443)
+..+..+.+|.+|++. .|..|+|+..+|...||+.|+...
T Consensus 49 i~~~~~~~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 49 IPPSRFKLKCSICGKS--GGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred ecchhcCCcCcCCCCC--CceeEEcCCCCCCcCCCHHHHHHC
Confidence 3345678899999998 789999999999999999999874
No 22
>KOG2084 consensus Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics]
Probab=89.96 E-value=0.46 Score=49.64 Aligned_cols=43 Identities=33% Similarity=0.550 Sum_probs=30.6
Q ss_pred cccCCCCCceeEEEEEECCeeEEEEEEccCCCCCC-cEeEecCCCCCC
Q 038692 351 FLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGE-PLTYDYRFVQFG 397 (443)
Q Consensus 351 FINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGE-ELT~DYg~~~~~ 397 (443)
++||||.||+.. ..++ ....+.+..++.+++ ||++.|-...++
T Consensus 208 ~~~hsC~pn~~~---~~~~-~~~~~~~~~~~~~~~~~l~~~y~~~~~~ 251 (482)
T KOG2084|consen 208 LFNHSCFPNISV---IFDG-RGLALLVPAGIDAGEEELTISYTDPLLS 251 (482)
T ss_pred hcccCCCCCeEE---EECC-ceeEEEeecccCCCCCEEEEeecccccC
Confidence 789999999862 2333 345566667777776 999999876653
No 23
>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=89.28 E-value=0.25 Score=41.62 Aligned_cols=96 Identities=19% Similarity=0.370 Sum_probs=43.2
Q ss_pred cCCCccccccchhcccCCCCCCCCccCCCceeeecc-----cccccceeccccccCCCCCCCcceeEeccCCCceeeecC
Q 038692 134 RGCGGVYHFICVKERLGISNPRNFKCPQHACFICRQ-----RLQWRCVRCTIASHDKCAPWPDRVIHLKDQPGRAVCWRH 208 (443)
Q Consensus 134 ~~C~~~yH~~C~~~~~~~~~~~~f~Cp~H~C~~c~~-----~~~~rC~rC~~a~h~~C~p~~~~~~~l~~~~~~~~c~rh 208 (443)
++..+-+++..++..+....+..|.+...+-..-+. .++..| .| ...|. .+....|.+.
T Consensus 3 s~g~e~~pI~~~N~vd~~~~p~~F~Yi~~~~~~~~~~~~~~~~~~~C-~C----~~~C~-----------~~~~C~C~~~ 66 (103)
T PF05033_consen 3 SRGKENVPIPVVNDVDDEPPPPNFEYIPENIYGEGVPDIDPEFLQGC-DC----SGDCS-----------NPSNCECLQR 66 (103)
T ss_dssp TCTSSSS-EEEEESSSS--SSTSSEE-SS-EESTTSS-TBGGGTS---------SSSST-----------CTTTSHHHCC
T ss_pred CCCccCCCEEEEeCCCCCCCCCCeEEeeeEEcCCCccccccccCccC-cc----CCCCC-----------CCCCCcCccc
Confidence 445566667777777777667888887775544422 244444 33 23351 1133344443
Q ss_pred CcchhcccccccccCCCCCCccccccccchhhccccccCCCCeeEEecCCCCCCCCCCCCC
Q 038692 209 PAKWLLDKQEVFCRLPLPYADEEFKIDLTWKDLMENKVGPPPVQYISCSKACHCSETCNNR 269 (443)
Q Consensus 209 p~~W~~~~~~~f~~~~~p~~~~~~~~~~~~~~~~~~~~~p~~~~~~EC~~~C~C~~~C~Nr 269 (443)
-.. -++|++++... .+....+|||++.|.|+..|+||
T Consensus 67 ~~~------------~~~Y~~~g~l~------------~~~~~~i~EC~~~C~C~~~C~NR 103 (103)
T PF05033_consen 67 NGG------------IFAYDSNGRLR------------IPDKPPIFECNDNCGCSPSCRNR 103 (103)
T ss_dssp TSS------------S-SB-TTSSBS------------SSSTSEEE---TTSSS-TTSTT-
T ss_pred cCc------------cccccCCCcCc------------cCCCCeEEeCCCCCCCCCCCCCC
Confidence 211 12554432111 11234579999999999999997
No 24
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=87.14 E-value=0.29 Score=35.89 Aligned_cols=44 Identities=25% Similarity=0.553 Sum_probs=32.7
Q ss_pred ecccccccccCcceeeeeecCCCccccccchhcccC--CCCCCCCccC
Q 038692 115 ECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLG--ISNPRNFKCP 160 (443)
Q Consensus 115 ~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~--~~~~~~f~Cp 160 (443)
.|.+|++....++.|.|. .|+..||..|+.-... ......|.||
T Consensus 1 ~C~vC~~~~~~~~~i~C~--~C~~~~H~~C~~~~~~~~~~~~~~w~C~ 46 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD--SCNRWYHQECVGPPEKAEEIPSGDWYCP 46 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS--TTSCEEETTTSTSSHSHHSHHSSSBSSH
T ss_pred eCcCCCCcCCCCCeEEcC--CCChhhCcccCCCChhhccCCCCcEECc
Confidence 378899877778899997 7999999999987544 1122367663
No 25
>KOG1337 consensus N-methyltransferase [General function prediction only]
Probab=81.90 E-value=0.95 Score=48.60 Aligned_cols=41 Identities=27% Similarity=0.294 Sum_probs=31.2
Q ss_pred ccccCCCCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecCC
Q 038692 350 RFLNHSCDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYRF 393 (443)
Q Consensus 350 RFINHSC~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg~ 393 (443)
-+.||++++.- ..+......+.+++.++|.+||||+++||.
T Consensus 238 D~~NH~~~~~~---~~~~~~d~~~~l~~~~~v~~geevfi~YG~ 278 (472)
T KOG1337|consen 238 DLLNHSPEVIK---AGYNQEDEAVELVAERDVSAGEEVFINYGP 278 (472)
T ss_pred HhhccCchhcc---ccccCCCCcEEEEEeeeecCCCeEEEecCC
Confidence 46899999821 112222338999999999999999999986
No 26
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=81.76 E-value=0.58 Score=50.10 Aligned_cols=34 Identities=29% Similarity=0.764 Sum_probs=30.8
Q ss_pred ceecccccccccCcceeeeeecCCCccccccchhcc
Q 038692 113 MIECRACHRFIYHGEEVFCSVRGCGGVYHFICVKER 148 (443)
Q Consensus 113 ~~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~ 148 (443)
+-.|.+||+. +|..|+|+..+|...||+.|+.+.
T Consensus 303 kl~C~iCk~~--~GtcIqCs~~nC~~aYHVtCArra 336 (669)
T COG5141 303 KLGCLICKEF--GGTCIQCSYFNCTRAYHVTCARRA 336 (669)
T ss_pred hheeeEEccc--Ccceeeecccchhhhhhhhhhhhc
Confidence 3459999999 899999999999999999999874
No 27
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=75.34 E-value=1.2 Score=37.97 Aligned_cols=72 Identities=22% Similarity=0.395 Sum_probs=45.5
Q ss_pred eecccccccccCcceeeeeecCCCccccccchhcccCCC--C---CCCCc-------cCCCceeeecc--ccccccee--
Q 038692 114 IECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLGIS--N---PRNFK-------CPQHACFICRQ--RLQWRCVR-- 177 (443)
Q Consensus 114 ~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~~~--~---~~~f~-------Cp~H~C~~c~~--~~~~rC~r-- 177 (443)
+.|.+|.+. +| .++-... +...|..|+.-.+.+. + ..++. =-...|..|++ |..++|.+
T Consensus 1 ~~C~lC~~~--~G-alk~t~~--~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~~~~C~iC~~~~G~~i~C~~~~ 75 (110)
T PF13832_consen 1 ASCVLCPKR--GG-ALKRTSD--GQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRFKLKCSICGKSGGACIKCSHPG 75 (110)
T ss_pred CccEeCCCC--CC-cccCccC--CcEEEeEccceeCccEEeechhcCcccceeecchhcCCcCcCCCCCCceeEEcCCCC
Confidence 368888765 33 3443333 7899999987633210 0 00000 01346799966 68999999
Q ss_pred ccccccCCCCCCC
Q 038692 178 CTIASHDKCAPWP 190 (443)
Q Consensus 178 C~~a~h~~C~p~~ 190 (443)
|..+||..|+-..
T Consensus 76 C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 76 CSTAFHPTCARKA 88 (110)
T ss_pred CCcCCCHHHHHHC
Confidence 9999999997543
No 28
>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=68.06 E-value=11 Score=31.60 Aligned_cols=35 Identities=11% Similarity=-0.024 Sum_probs=25.0
Q ss_pred ecCCCccccccchhcccCCCCCCCCccCCCceeee
Q 038692 133 VRGCGGVYHFICVKERLGISNPRNFKCPQHACFIC 167 (443)
Q Consensus 133 v~~C~~~yH~~C~~~~~~~~~~~~f~Cp~H~C~~c 167 (443)
+++..+-+.+.+++..+....+..|.+..+....-
T Consensus 4 is~G~E~~pI~~vN~vD~~~~p~~F~Yi~~~~~~~ 38 (98)
T smart00468 4 ISNGKENVPVPLVNEVDEDPPPPDFEYISEYIYGQ 38 (98)
T ss_pred ccCCccCCCcceEecCCCCCCCCCcEECcceEcCC
Confidence 34556667777888887766668899887776544
No 29
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=67.65 E-value=1.6 Score=31.01 Aligned_cols=35 Identities=40% Similarity=0.693 Sum_probs=25.1
Q ss_pred eecccccccccCcceeeeeecCCCccccccchhcccC
Q 038692 114 IECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLG 150 (443)
Q Consensus 114 ~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~ 150 (443)
++|-+|-+....++.+. ...|+..||..|+.++..
T Consensus 1 d~C~IC~~~~~~~~~~~--~l~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVV--KLPCGHVFHRSCIKEWLK 35 (44)
T ss_dssp -CETTTTCBHHTTSCEE--EETTSEEEEHHHHHHHHH
T ss_pred CCCcCCChhhcCCCeEE--EccCCCeeCHHHHHHHHH
Confidence 36888987665455444 334999999999999754
No 30
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=64.90 E-value=3 Score=30.20 Aligned_cols=41 Identities=32% Similarity=0.657 Sum_probs=21.8
Q ss_pred cccccccccCcceeeeeecCCCccccccchhcccCCCCCCCCccC
Q 038692 116 CRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLGISNPRNFKCP 160 (443)
Q Consensus 116 C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~~~~~~~f~Cp 160 (443)
|.+|+++. .-.++|+-..|..-+|..|+..+-+..... +||
T Consensus 1 C~~C~~iv--~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~--~CP 41 (43)
T PF08746_consen 1 CEACKEIV--TQGQRCSNRDCNVRLHDDCFKKYFRHRSNP--KCP 41 (43)
T ss_dssp -TTT-SB---SSSEE-SS--S--EE-HHHHHHHTTT-SS---B-T
T ss_pred CcccchhH--eeeccCCCCccCchHHHHHHHHHHhcCCCC--CCc
Confidence 67898874 455789988999999999999975543322 555
No 31
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=56.91 E-value=7 Score=29.41 Aligned_cols=16 Identities=50% Similarity=0.497 Sum_probs=12.0
Q ss_pred EEEEccCCCCCCcEeE
Q 038692 374 GVFAARSIKAGEPLTY 389 (443)
Q Consensus 374 ~l~A~RdI~aGEELT~ 389 (443)
.++|.|||++|+.|+-
T Consensus 3 vvVA~~di~~G~~i~~ 18 (63)
T PF08666_consen 3 VVVAARDIPAGTVITA 18 (63)
T ss_dssp EEEESSTB-TT-BECT
T ss_pred EEEEeCccCCCCEEcc
Confidence 4799999999999963
No 33
>KOG1338 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.62 E-value=10 Score=40.13 Aligned_cols=40 Identities=23% Similarity=0.388 Sum_probs=30.5
Q ss_pred CccccccCC---CCCceeEEEEEECCeeEEEEEEccCCCCCCcEeEecC
Q 038692 347 NFSRFLNHS---CDPNCILEKWQVEGETRVGVFAARSIKAGEPLTYDYR 392 (443)
Q Consensus 347 N~aRFINHS---C~PNc~~~~~~v~g~~ri~l~A~RdI~aGEELT~DYg 392 (443)
.++.|+||- |+.|..+ +...+-++|.|+|++|+|+.-.||
T Consensus 217 p~ad~lNhd~~k~nanl~y------~~NcL~mva~r~iekgdev~n~dg 259 (466)
T KOG1338|consen 217 PIADFLNHDGLKANANLRY------EDNCLEMVADRNIEKGDEVDNSDG 259 (466)
T ss_pred chhhhhccchhhcccceec------cCcceeeeecCCCCCccccccccc
Confidence 457899995 4455433 345667899999999999999997
No 34
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=49.47 E-value=7.7 Score=30.87 Aligned_cols=38 Identities=29% Similarity=0.755 Sum_probs=17.2
Q ss_pred ceecccccccccCcce---eeeeecCCCccccccchhcccC
Q 038692 113 MIECRACHRFIYHGEE---VFCSVRGCGGVYHFICVKERLG 150 (443)
Q Consensus 113 ~~~C~~C~~~~~~ge~---i~Csv~~C~~~yH~~C~~~~~~ 150 (443)
..+|-+|.......+. +.|.-..|+..||..|+.++..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~ 42 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFL 42 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHH
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHH
Confidence 3679999886552332 4599999999999999999744
No 35
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=44.73 E-value=23 Score=25.92 Aligned_cols=37 Identities=32% Similarity=0.577 Sum_probs=28.0
Q ss_pred cCceecccccccc--cCcceeeeeecCCCccccccchhccc
Q 038692 111 KKMIECRACHRFI--YHGEEVFCSVRGCGGVYHFICVKERL 149 (443)
Q Consensus 111 ~~~~~C~~C~~~~--~~ge~i~Csv~~C~~~yH~~C~~~~~ 149 (443)
.+...|.+|++.+ .....++|+ .|+-.+|..|+...+
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~--~C~~~~H~~C~~~~~ 47 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCS--WCGLVCHKKCLSKVP 47 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEET--TTT-EEETTGGCTSS
T ss_pred CCCCCCcccCcccCCCCCCeEEEC--CCCChHhhhhhhhcC
Confidence 5778899999988 445666776 799999999998753
No 36
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=41.70 E-value=12 Score=25.33 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=21.7
Q ss_pred ecccccccccCcceeeeeecCCCccccccchhcccC
Q 038692 115 ECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLG 150 (443)
Q Consensus 115 ~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~ 150 (443)
+|.+|.+.. ...-.+..|+..||..|+..+..
T Consensus 1 ~C~iC~~~~----~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 1 ECPICLEEF----REPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCCcCchhh----hCceEecCCCChhcHHHHHHHHH
Confidence 467776552 12334566999999999997643
No 37
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=40.42 E-value=11 Score=42.68 Aligned_cols=53 Identities=30% Similarity=0.662 Sum_probs=39.3
Q ss_pred CCccccccchhcccCCCCCCCCccCCC--------------------ceeeecc-cccccceeccccccCCCCC
Q 038692 136 CGGVYHFICVKERLGISNPRNFKCPQH--------------------ACFICRQ-RLQWRCVRCTIASHDKCAP 188 (443)
Q Consensus 136 C~~~yH~~C~~~~~~~~~~~~f~Cp~H--------------------~C~~c~~-~~~~rC~rC~~a~h~~C~p 188 (443)
|.+.||..|+...-.....++|+||-. .|-.|.. +.++.|-.|+.+||.+|.-
T Consensus 2 ~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~ 75 (696)
T KOG0383|consen 2 CPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGELLWCDTCPASFHASCLG 75 (696)
T ss_pred CCcccCcCCCCcccccCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCcEEEeccccHHHHHHccC
Confidence 678899888886444444678888722 2666655 4888899999999999983
No 38
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=37.85 E-value=17 Score=36.54 Aligned_cols=49 Identities=29% Similarity=0.711 Sum_probs=36.9
Q ss_pred ccCcCceecccccccccCcceeeeeecCCC-ccccccchhcccCCCCCCCCccC
Q 038692 108 VGAKKMIECRACHRFIYHGEEVFCSVRGCG-GVYHFICVKERLGISNPRNFKCP 160 (443)
Q Consensus 108 ~~a~~~~~C~~C~~~~~~ge~i~Csv~~C~-~~yH~~C~~~~~~~~~~~~f~Cp 160 (443)
.....+.-|+ |++.+| |+.|.|-=.+|. +-||..||-=. .....+|.||
T Consensus 214 ~d~~e~~yC~-Cnqvsy-g~Mi~CDn~~C~~eWFH~~CVGL~--~~PkgkWyC~ 263 (274)
T KOG1973|consen 214 VDPDEPTYCI-CNQVSY-GKMIGCDNPGCPIEWFHFTCVGLK--TKPKGKWYCP 263 (274)
T ss_pred cCCCCCEEEE-eccccc-ccccccCCCCCCcceEEEeccccc--cCCCCcccch
Confidence 3445566675 667665 999999999999 99999999743 3445569887
No 39
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=35.96 E-value=30 Score=25.43 Aligned_cols=28 Identities=36% Similarity=0.681 Sum_probs=19.3
Q ss_pred cccccccccCcceeeeeecCCCccccccchh
Q 038692 116 CRACHRFIYHGEEVFCSVRGCGGVYHFICVK 146 (443)
Q Consensus 116 C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~ 146 (443)
|..|++.+++++.+. ++ -++.||+.|..
T Consensus 1 C~~C~~~I~~~~~~~-~~--~~~~~H~~Cf~ 28 (58)
T PF00412_consen 1 CARCGKPIYGTEIVI-KA--MGKFWHPECFK 28 (58)
T ss_dssp BTTTSSBESSSSEEE-EE--TTEEEETTTSB
T ss_pred CCCCCCCccCcEEEE-Ee--CCcEEEccccc
Confidence 678999888666542 23 37889977643
No 40
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=35.90 E-value=15 Score=27.18 Aligned_cols=39 Identities=26% Similarity=0.480 Sum_probs=25.6
Q ss_pred ecccccccccCccee--eeeecCCCccccccchhcccCCCC
Q 038692 115 ECRACHRFIYHGEEV--FCSVRGCGGVYHFICVKERLGISN 153 (443)
Q Consensus 115 ~C~~C~~~~~~ge~i--~Csv~~C~~~yH~~C~~~~~~~~~ 153 (443)
.|.+|.....+++.+ +|.=.+-.+++|..|+.++-....
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~ 41 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG 41 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC
Confidence 377887633334433 466555579999999999855443
No 41
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=35.76 E-value=12 Score=35.03 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=22.4
Q ss_pred cccccccceeccccccCCCCCCCcceeEe
Q 038692 168 RQRLQWRCVRCTIASHDKCAPWPDRVIHL 196 (443)
Q Consensus 168 ~~~~~~rC~rC~~a~h~~C~p~~~~~~~l 196 (443)
++|.++-|+-|+.+||..|+-....-.+|
T Consensus 13 ~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHl 41 (175)
T PF15446_consen 13 NKGPLVYCQGCSSSYHKACLGPRSQREHL 41 (175)
T ss_pred cCCCeEEcCccChHHHhhhcCCcccccee
Confidence 56799999999999999998554443333
No 42
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=34.13 E-value=11 Score=27.21 Aligned_cols=43 Identities=28% Similarity=0.597 Sum_probs=22.0
Q ss_pred cccccccccCcceeeeeecCCCccccccchhcccCCCCCCCCccC
Q 038692 116 CRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLGISNPRNFKCP 160 (443)
Q Consensus 116 C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~~~~~~~f~Cp 160 (443)
|-+|++ ....+..+=+.. ||..|=..|+.+.........|+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence 667877 334556666666 9999999999986554435678887
No 43
>KOG2155 consensus Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=34.09 E-value=24 Score=37.97 Aligned_cols=48 Identities=19% Similarity=0.318 Sum_probs=35.2
Q ss_pred CccccccCCCCCceeEEEEEECC--eeEEEEEEccCCCCCCcEeEecCCC
Q 038692 347 NFSRFLNHSCDPNCILEKWQVEG--ETRVGVFAARSIKAGEPLTYDYRFV 394 (443)
Q Consensus 347 N~aRFINHSC~PNc~~~~~~v~g--~~ri~l~A~RdI~aGEELT~DYg~~ 394 (443)
.++.-|.||-+||........-. -..-.++-+|+...|||+|-|+...
T Consensus 203 efGsrvrHsdePnf~~aPf~fmPq~vaYsimwp~k~~~tgeE~trDfasg 252 (631)
T KOG2155|consen 203 EFGSRVRHSDEPNFRIAPFMFMPQNVAYSIMWPTKPVNTGEEITRDFASG 252 (631)
T ss_pred hhhhhhccCCCCcceeeeheecchhcceeEEeeccCCCCchHHHHHHhhc
Confidence 34566899999998765443322 2355688999999999999988543
No 44
>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=33.73 E-value=21 Score=30.50 Aligned_cols=17 Identities=53% Similarity=0.792 Sum_probs=12.8
Q ss_pred EEEEEccCCCCCCcEeE
Q 038692 373 VGVFAARSIKAGEPLTY 389 (443)
Q Consensus 373 i~l~A~RdI~aGEELT~ 389 (443)
.+|||+|||++||-|.+
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 46899999999998873
No 45
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=31.95 E-value=12 Score=37.55 Aligned_cols=69 Identities=26% Similarity=0.463 Sum_probs=49.6
Q ss_pred cccccCcceeeeeecCCCccccccchhcccC-CCC--CCCCccCC-Cceeeeccc----ccccceeccccccCCCCCCC
Q 038692 120 HRFIYHGEEVFCSVRGCGGVYHFICVKERLG-ISN--PRNFKCPQ-HACFICRQR----LQWRCVRCTIASHDKCAPWP 190 (443)
Q Consensus 120 ~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~-~~~--~~~f~Cp~-H~C~~c~~~----~~~rC~rC~~a~h~~C~p~~ 190 (443)
|+++-+.|.|.|+ .||+-=|+.|+.-... +.. .-.|-|.. ..|+.|+.+ +++-|-.|-.-||--|+.++
T Consensus 238 kkt~~peelvscs--dcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcddcdrgyhmyclspp 314 (336)
T KOG1244|consen 238 KKTGMPEELVSCS--DCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPP 314 (336)
T ss_pred cccCCchhhcchh--hcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeecccCCceeeEecCCC
Confidence 4566677888886 5899999999875322 111 11566654 457777543 99999999999999998776
No 46
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.09 E-value=21 Score=35.07 Aligned_cols=53 Identities=25% Similarity=0.621 Sum_probs=40.5
Q ss_pred cceeccCcCceecccccccccCcceeeeeecCCCccccccchhcccC----CCCCCCCcc
Q 038692 104 LPFLVGAKKMIECRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLG----ISNPRNFKC 159 (443)
Q Consensus 104 lp~l~~a~~~~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~----~~~~~~f~C 159 (443)
|-||+..-..--|.+|+-+...|| |..-.|+.+||=.|.+++.. .--+.++.|
T Consensus 41 LqWL~DsDY~pNC~LC~t~La~gd---t~RLvCyhlfHW~ClneraA~lPanTAPaGyqC 97 (299)
T KOG3970|consen 41 LQWLQDSDYNPNCRLCNTPLASGD---TTRLVCYHLFHWKCLNERAANLPANTAPAGYQC 97 (299)
T ss_pred HHHHhhcCCCCCCceeCCccccCc---ceeehhhhhHHHHHhhHHHhhCCCcCCCCcccC
Confidence 579999999999999987754454 66678999999999999654 222555655
No 47
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=30.67 E-value=26 Score=39.53 Aligned_cols=32 Identities=25% Similarity=0.684 Sum_probs=25.7
Q ss_pred cccccccc-----cCcceeeeeecCCCccccccchhc
Q 038692 116 CRACHRFI-----YHGEEVFCSVRGCGGVYHFICVKE 147 (443)
Q Consensus 116 C~~C~~~~-----~~ge~i~Csv~~C~~~yH~~C~~~ 147 (443)
|.+|++.+ .-|-.|.|-..+|...||+.|+..
T Consensus 120 CYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~ 156 (900)
T KOG0956|consen 120 CYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQR 156 (900)
T ss_pred eeeecccCCccccccccceecccccchhhhhhhHhhh
Confidence 99999872 124456699999999999999875
No 48
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=30.39 E-value=19 Score=41.37 Aligned_cols=49 Identities=27% Similarity=0.653 Sum_probs=36.2
Q ss_pred CcCceecccccccccCccee-eeeecCCCccccccchhcccCC---CCCCCCccC
Q 038692 110 AKKMIECRACHRFIYHGEEV-FCSVRGCGGVYHFICVKERLGI---SNPRNFKCP 160 (443)
Q Consensus 110 a~~~~~C~~C~~~~~~ge~i-~Csv~~C~~~yH~~C~~~~~~~---~~~~~f~Cp 160 (443)
..+..+|.+|-+.+-...-| -|.- |+.+||..|+..|.+. .....|+||
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~s--CYhVFHl~CI~~WArs~ek~~~~~WrCP 240 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKS--CYHVFHLNCIKKWARSSEKTGQDGWRCP 240 (950)
T ss_pred hcCceEEEEeeeeccccCCceecch--hhhhhhHHHHHHHHHHhhhccCccccCC
Confidence 68899999997655333333 4655 9999999999998773 224589886
No 49
>smart00858 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Probab=29.82 E-value=35 Score=25.38 Aligned_cols=16 Identities=50% Similarity=0.549 Sum_probs=14.1
Q ss_pred EEEEccCCCCCCcEeE
Q 038692 374 GVFAARSIKAGEPLTY 389 (443)
Q Consensus 374 ~l~A~RdI~aGEELT~ 389 (443)
.++|.+||.+|+.|+-
T Consensus 3 v~va~~~i~~G~~i~~ 18 (64)
T smart00858 3 VVVAARDLPAGEVITA 18 (64)
T ss_pred EEEEeCccCCCCCcch
Confidence 4789999999999984
No 50
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=29.52 E-value=38 Score=22.33 Aligned_cols=29 Identities=41% Similarity=0.758 Sum_probs=18.6
Q ss_pred ecccccccccCcceeeeeecCCCccccccchh
Q 038692 115 ECRACHRFIYHGEEVFCSVRGCGGVYHFICVK 146 (443)
Q Consensus 115 ~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~ 146 (443)
.|..|++.+.+++.+ +..=++.||..|..
T Consensus 1 ~C~~C~~~i~~~~~~---~~~~~~~~H~~Cf~ 29 (39)
T smart00132 1 KCAGCGKPIRGGELV---LRALGKVWHPECFK 29 (39)
T ss_pred CccccCCcccCCcEE---EEeCCccccccCCC
Confidence 377899988766333 22237888887643
No 51
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=27.24 E-value=35 Score=28.56 Aligned_cols=22 Identities=18% Similarity=0.478 Sum_probs=17.7
Q ss_pred ecCCCccccccchhcccCCCCC
Q 038692 133 VRGCGGVYHFICVKERLGISNP 154 (443)
Q Consensus 133 v~~C~~~yH~~C~~~~~~~~~~ 154 (443)
...|+..||..|+.++.....+
T Consensus 49 ~g~C~H~FH~hCI~kWl~~~~~ 70 (85)
T PF12861_consen 49 WGKCSHNFHMHCILKWLSTQSS 70 (85)
T ss_pred eccCccHHHHHHHHHHHccccC
Confidence 5569999999999998775443
No 52
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=25.59 E-value=33 Score=23.52 Aligned_cols=40 Identities=25% Similarity=0.564 Sum_probs=26.1
Q ss_pred cccccccccCcceeeeeecCCCccccccchhcccCCCCCCCCccCC
Q 038692 116 CRACHRFIYHGEEVFCSVRGCGGVYHFICVKERLGISNPRNFKCPQ 161 (443)
Q Consensus 116 C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~~~~~~~~~f~Cp~ 161 (443)
|-+|.+.. .+.+ .+..|+..|...|+.++... ...+.||+
T Consensus 1 C~iC~~~~--~~~~--~~~~C~H~fC~~C~~~~~~~--~~~~~CP~ 40 (41)
T PF00097_consen 1 CPICLEPF--EDPV--ILLPCGHSFCRDCLRKWLEN--SGSVKCPL 40 (41)
T ss_dssp ETTTSSBC--SSEE--EETTTSEEEEHHHHHHHHHH--TSSSBTTT
T ss_pred CCcCCccc--cCCC--EEecCCCcchHHHHHHHHHh--cCCccCCc
Confidence 45665542 2222 78899999999999986443 45566764
No 53
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=25.45 E-value=35 Score=22.39 Aligned_cols=29 Identities=31% Similarity=0.482 Sum_probs=11.0
Q ss_pred ecccccccccCcceeeeeecCCCccccccch
Q 038692 115 ECRACHRFIYHGEEVFCSVRGCGGVYHFICV 145 (443)
Q Consensus 115 ~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~ 145 (443)
.|-+|++.++++-...| ..|.=.+|..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C--~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRC--SECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE---TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEEC--ccCCCccChhcC
Confidence 58889888665344466 678888888875
No 54
>PRK10781 rcsF outer membrane lipoprotein; Reviewed
Probab=24.65 E-value=1.3e+02 Score=27.20 Aligned_cols=35 Identities=6% Similarity=0.079 Sum_probs=18.5
Q ss_pred eccCCCCCcChHHHHHHHHhhhhh---cCCCccccccc
Q 038692 71 RCRGAKNISGLEDHVAAWVKKKME---LGVPQSNCSLP 105 (443)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~---~g~~~~~~~lp 105 (443)
+++..+..+++.+--+...-+.+. .|+..++|...
T Consensus 75 q~~~~~~p~s~~~Ar~~~r~kAa~~gaN~Vvl~~C~~~ 112 (133)
T PRK10781 75 QASNQDSPPSIPTARKRMQINASKMKANAVLLHSCEIT 112 (133)
T ss_pred ccCCCCCCCCHHHHHHHHHHHHHHcCCCEEEEEEeecc
Confidence 444556667777644444333343 44456566654
No 55
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=24.55 E-value=27 Score=22.43 Aligned_cols=20 Identities=25% Similarity=0.514 Sum_probs=15.5
Q ss_pred eeecCCCccccccchhcccC
Q 038692 131 CSVRGCGGVYHFICVKERLG 150 (443)
Q Consensus 131 Csv~~C~~~yH~~C~~~~~~ 150 (443)
-.+..|+..||..|+..+..
T Consensus 11 ~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 11 PVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred cEEecCCChHHHHHHHHHHH
Confidence 34567999999999987644
No 56
>PHA02929 N1R/p28-like protein; Provisional
Probab=24.21 E-value=47 Score=32.89 Aligned_cols=40 Identities=25% Similarity=0.484 Sum_probs=29.1
Q ss_pred cCceecccccccccCcce---eeeeecCCCccccccchhcccC
Q 038692 111 KKMIECRACHRFIYHGEE---VFCSVRGCGGVYHFICVKERLG 150 (443)
Q Consensus 111 ~~~~~C~~C~~~~~~ge~---i~Csv~~C~~~yH~~C~~~~~~ 150 (443)
.+..+|.+|.+.....+. ..-.+..|+..||..|+.++..
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 456899999886544331 1245778999999999998743
No 57
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=22.69 E-value=36 Score=38.70 Aligned_cols=35 Identities=26% Similarity=0.589 Sum_probs=30.7
Q ss_pred CceecccccccccCcceeeeeecCCCccccccchhcc
Q 038692 112 KMIECRACHRFIYHGEEVFCSVRGCGGVYHFICVKER 148 (443)
Q Consensus 112 ~~~~C~~C~~~~~~ge~i~Csv~~C~~~yH~~C~~~~ 148 (443)
..-.|.+|+.. -|-.|+|++..|...||+.|+-+.
T Consensus 379 wslvC~LCk~k--~GACIqCs~k~C~t~fHv~CA~~a 413 (893)
T KOG0954|consen 379 WSLVCNLCKVK--SGACIQCSNKTCRTAFHVTCAFEA 413 (893)
T ss_pred HHHHHHHhccc--CcceEEecccchhhhccchhhhhc
Confidence 34459999987 699999999999999999999873
No 58
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=20.43 E-value=46 Score=26.51 Aligned_cols=20 Identities=30% Similarity=0.755 Sum_probs=16.4
Q ss_pred eecCCCccccccchhcccCC
Q 038692 132 SVRGCGGVYHFICVKERLGI 151 (443)
Q Consensus 132 sv~~C~~~yH~~C~~~~~~~ 151 (443)
....|+..||..|+.++...
T Consensus 46 ~~~~C~H~FH~~Ci~~Wl~~ 65 (73)
T PF12678_consen 46 VWGPCGHIFHFHCISQWLKQ 65 (73)
T ss_dssp EEETTSEEEEHHHHHHHHTT
T ss_pred EecccCCCEEHHHHHHHHhc
Confidence 45779999999999987543
No 59
>PHA02862 5L protein; Provisional
Probab=20.42 E-value=44 Score=30.72 Aligned_cols=38 Identities=24% Similarity=0.411 Sum_probs=29.4
Q ss_pred ceecccccccccCccee-eeeecCCCccccccchhcccCCC
Q 038692 113 MIECRACHRFIYHGEEV-FCSVRGCGGVYHFICVKERLGIS 152 (443)
Q Consensus 113 ~~~C~~C~~~~~~ge~i-~Csv~~C~~~yH~~C~~~~~~~~ 152 (443)
...|.+|.+. ++|.+ +|.=.+-.++.|..|+.++-..+
T Consensus 2 ~diCWIC~~~--~~e~~~PC~C~GS~K~VHq~CL~~WIn~S 40 (156)
T PHA02862 2 SDICWICNDV--CDERNNFCGCNEEYKVVHIKCMQLWINYS 40 (156)
T ss_pred CCEEEEecCc--CCCCcccccccCcchhHHHHHHHHHHhcC
Confidence 3579999887 34544 68877889999999999986443
Done!