Query 002464
Match_columns 919
No_of_seqs 307 out of 1561
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 00:27:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002464.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002464hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1512 PHD Zn-finger protein 99.0 9.3E-11 2E-15 125.1 2.2 90 741-838 258-362 (381)
2 KOG0956 PHD finger protein AF1 99.0 3E-10 6.6E-15 131.3 3.4 106 742-849 6-190 (900)
3 KOG1244 Predicted transcriptio 98.9 5.5E-10 1.2E-14 118.7 1.3 87 742-834 225-327 (336)
4 KOG4299 PHD Zn-finger protein 98.4 1.1E-07 2.4E-12 110.4 2.7 45 741-785 253-304 (613)
5 KOG4443 Putative transcription 98.4 1.2E-07 2.5E-12 110.5 1.7 89 740-834 17-114 (694)
6 COG5141 PHD zinc finger-contai 98.3 1.4E-07 3.1E-12 106.7 1.6 49 736-784 188-241 (669)
7 KOG0954 PHD finger protein [Ge 98.2 5.6E-07 1.2E-11 105.7 3.1 106 740-848 270-446 (893)
8 KOG4299 PHD Zn-finger protein 98.0 3.5E-06 7.6E-11 98.3 3.6 44 741-784 47-93 (613)
9 KOG0955 PHD finger protein BR1 98.0 3.1E-06 6.6E-11 104.3 3.2 48 737-784 215-267 (1051)
10 KOG1973 Chromatin remodeling p 98.0 3.1E-06 6.7E-11 91.3 2.3 38 747-784 226-266 (274)
11 PF00628 PHD: PHD-finger; Int 98.0 2.2E-06 4.8E-11 69.5 0.8 42 743-784 1-49 (51)
12 smart00249 PHD PHD zinc finger 97.9 8.4E-06 1.8E-10 63.0 2.9 41 743-783 1-47 (47)
13 COG5034 TNG2 Chromatin remodel 97.9 7.5E-06 1.6E-10 87.3 3.0 44 740-784 220-268 (271)
14 KOG1473 Nucleosome remodeling 97.7 1.2E-05 2.5E-10 98.3 0.6 108 737-845 340-485 (1414)
15 KOG0383 Predicted helicase [Ge 97.6 2.4E-05 5.1E-10 93.5 2.8 69 758-836 1-91 (696)
16 KOG1244 Predicted transcriptio 97.6 2.6E-05 5.6E-10 84.0 1.8 45 740-784 280-329 (336)
17 KOG0383 Predicted helicase [Ge 97.5 3.5E-05 7.6E-10 92.1 1.4 51 736-786 42-94 (696)
18 KOG4323 Polycomb-like PHD Zn-f 97.4 6.7E-05 1.4E-09 86.1 2.5 95 741-839 83-225 (464)
19 KOG1512 PHD Zn-finger protein 97.3 0.00011 2.3E-09 79.7 1.8 42 740-781 313-357 (381)
20 smart00249 PHD PHD zinc finger 97.2 0.00028 6E-09 54.5 2.8 44 785-834 2-46 (47)
21 PF15446 zf-PHD-like: PHD/FYVE 97.2 0.00033 7.1E-09 71.4 3.7 80 743-822 1-143 (175)
22 KOG4443 Putative transcription 97.0 0.00019 4.2E-09 84.5 0.9 84 740-823 67-183 (694)
23 KOG0825 PHD Zn-finger protein 97.0 0.0003 6.5E-09 84.0 2.0 45 740-784 214-264 (1134)
24 PF00628 PHD: PHD-finger; Int 96.9 0.0003 6.5E-09 57.1 0.5 44 785-834 2-47 (51)
25 KOG0825 PHD Zn-finger protein 96.6 0.00072 1.6E-08 80.9 1.4 47 785-838 218-265 (1134)
26 KOG0957 PHD finger protein [Ge 96.5 0.00092 2E-08 77.0 1.2 43 742-784 120-177 (707)
27 KOG1973 Chromatin remodeling p 96.1 0.0027 5.7E-08 69.0 2.1 38 800-839 229-269 (274)
28 PF13831 PHD_2: PHD-finger; PD 96.0 0.0017 3.6E-08 50.9 -0.3 34 751-784 2-36 (36)
29 cd04718 BAH_plant_2 BAH, or Br 95.5 0.008 1.7E-07 60.5 2.3 31 762-792 1-33 (148)
30 cd00122 MBD MeCP2, MBD1, MBD2, 95.1 0.014 3.1E-07 50.2 2.5 42 290-331 7-50 (62)
31 KOG1245 Chromatin remodeling c 95.1 0.0051 1.1E-07 79.1 -0.6 45 740-784 1107-1156(1404)
32 KOG4323 Polycomb-like PHD Zn-f 94.9 0.01 2.2E-07 68.7 1.2 44 741-784 168-222 (464)
33 cd01396 MeCP2_MBD MeCP2, MBD1, 94.9 0.021 4.5E-07 51.7 2.8 51 290-340 8-64 (77)
34 KOG0957 PHD finger protein [Ge 93.5 0.042 9E-07 64.0 2.4 45 740-784 543-596 (707)
35 PF01429 MBD: Methyl-CpG bindi 92.6 0.08 1.7E-06 47.5 2.3 43 290-332 12-57 (77)
36 smart00391 MBD Methyl-CpG bind 90.7 0.17 3.8E-06 45.8 2.4 42 290-331 9-53 (77)
37 cd04718 BAH_plant_2 BAH, or Br 90.2 0.15 3.3E-06 51.5 1.8 25 812-836 1-25 (148)
38 COG5034 TNG2 Chromatin remodel 90.1 0.15 3.3E-06 55.4 1.8 37 799-838 230-269 (271)
39 KOG0955 PHD finger protein BR1 89.2 0.2 4.2E-06 63.4 2.0 45 785-835 222-266 (1051)
40 KOG1245 Chromatin remodeling c 87.5 0.17 3.6E-06 65.9 -0.1 49 785-840 1111-1159(1404)
41 cd01397 HAT_MBD Methyl-CpG bin 86.0 0.57 1.2E-05 42.5 2.5 41 290-330 7-49 (73)
42 PF13832 zf-HC5HC2H_2: PHD-zin 84.7 0.63 1.4E-05 43.5 2.2 69 743-823 2-90 (110)
43 PF14446 Prok-RING_1: Prokaryo 84.3 0.51 1.1E-05 40.7 1.3 35 782-821 5-39 (54)
44 KOG1081 Transcription factor N 83.2 0.84 1.8E-05 53.6 2.9 45 739-784 87-131 (463)
45 COG5141 PHD zinc finger-contai 77.9 0.93 2E-05 53.3 1.0 44 785-834 196-239 (669)
46 PF07227 DUF1423: Protein of u 76.1 1.8 3.9E-05 50.6 2.6 62 777-841 123-194 (446)
47 KOG1701 Focal adhesion adaptor 75.3 0.95 2E-05 52.5 0.1 76 742-821 335-431 (468)
48 KOG0956 PHD finger protein AF1 75.1 1.4 2.9E-05 53.7 1.3 47 785-838 8-56 (900)
49 PF14446 Prok-RING_1: Prokaryo 69.0 2.5 5.4E-05 36.6 1.2 29 742-770 6-38 (54)
50 PF12861 zf-Apc11: Anaphase-pr 68.8 2 4.3E-05 40.2 0.6 27 758-784 51-78 (85)
51 KOG1473 Nucleosome remodeling 65.2 1.5 3.2E-05 55.9 -1.3 47 738-784 425-477 (1414)
52 PF11793 FANCL_C: FANCL C-term 64.0 2.9 6.2E-05 37.2 0.7 28 742-769 3-38 (70)
53 PF13831 PHD_2: PHD-finger; PD 62.8 2.6 5.5E-05 33.4 0.1 33 801-834 2-34 (36)
54 KOG0954 PHD finger protein [Ge 61.3 3.5 7.6E-05 50.7 0.9 32 801-834 286-317 (893)
55 smart00258 SAND SAND domain. 59.9 5.3 0.00012 36.5 1.6 38 670-708 22-63 (73)
56 PF10497 zf-4CXXC_R1: Zinc-fin 59.8 4.3 9.3E-05 39.0 1.1 35 757-791 34-79 (105)
57 KOG3576 Ovo and related transc 56.4 3 6.6E-05 44.7 -0.6 61 751-820 115-190 (267)
58 PF13639 zf-RING_2: Ring finge 56.2 2.3 5E-05 33.8 -1.2 38 742-784 1-44 (44)
59 KOG0804 Cytoplasmic Zn-finger 55.9 4.8 0.0001 47.3 0.8 65 739-819 173-253 (493)
60 PF15446 zf-PHD-like: PHD/FYVE 54.5 6.2 0.00013 41.2 1.2 36 785-823 2-37 (175)
61 PF13832 zf-HC5HC2H_2: PHD-zin 53.9 6.5 0.00014 36.8 1.2 31 740-770 54-87 (110)
62 KOG1632 Uncharacterized PHD Zn 53.1 8.2 0.00018 44.0 2.1 60 802-862 74-136 (345)
63 PF13771 zf-HC5HC2H: PHD-like 52.6 4.5 9.9E-05 36.3 -0.0 32 784-823 38-71 (90)
64 PF07897 DUF1675: Protein of u 51.9 18 0.00038 40.6 4.3 30 671-700 253-283 (284)
65 PF13901 DUF4206: Domain of un 51.6 9.7 0.00021 40.1 2.2 35 785-820 155-189 (202)
66 KOG4628 Predicted E3 ubiquitin 50.7 9.9 0.00022 43.6 2.2 43 742-785 230-275 (348)
67 PF13771 zf-HC5HC2H: PHD-like 50.2 8 0.00017 34.8 1.2 30 741-770 36-68 (90)
68 KOG1701 Focal adhesion adaptor 49.2 2.9 6.4E-05 48.7 -2.2 70 742-820 275-363 (468)
69 PF01342 SAND: SAND domain; I 45.7 8.1 0.00018 35.6 0.5 35 671-708 37-72 (82)
70 PF13901 DUF4206: Domain of un 44.9 16 0.00035 38.5 2.6 38 740-784 151-196 (202)
71 KOG1246 DNA-binding protein ju 44.4 15 0.00033 46.5 2.6 50 740-789 154-207 (904)
72 KOG3612 PHD Zn-finger protein 38.0 28 0.0006 42.1 3.3 46 739-784 58-106 (588)
73 PF05502 Dynactin_p62: Dynacti 37.0 21 0.00045 42.5 2.2 30 752-784 4-33 (483)
74 PF11793 FANCL_C: FANCL C-term 36.7 19 0.00041 32.1 1.3 35 784-821 4-40 (70)
75 KOG1829 Uncharacterized conser 35.9 15 0.00032 44.7 0.8 52 779-841 503-561 (580)
76 smart00547 ZnF_RBZ Zinc finger 35.4 20 0.00043 25.7 1.0 9 776-784 1-9 (26)
77 PF00641 zf-RanBP: Zn-finger i 34.0 18 0.00039 27.0 0.7 10 775-784 2-11 (30)
78 KOG1169 Diacylglycerol kinase 32.6 21 0.00046 43.8 1.3 80 739-821 114-212 (634)
79 KOG2752 Uncharacterized conser 32.1 28 0.0006 39.7 2.0 35 788-822 133-168 (345)
80 KOG0269 WD40 repeat-containing 29.9 23 0.0005 44.2 1.0 41 775-822 766-812 (839)
81 PF12678 zf-rbx1: RING-H2 zinc 29.4 20 0.00043 32.0 0.3 24 757-784 48-73 (73)
82 PF07649 C1_3: C1-like domain; 29.1 21 0.00046 26.7 0.3 28 785-818 3-30 (30)
83 PLN03086 PRLI-interacting fact 27.9 41 0.00088 41.1 2.6 27 668-694 405-431 (567)
84 KOG1734 Predicted RING-contain 27.5 19 0.00041 40.3 -0.3 34 737-770 220-263 (328)
85 PLN02400 cellulose synthase 27.4 54 0.0012 42.7 3.6 45 739-784 34-85 (1085)
86 PRK14891 50S ribosomal protein 26.8 27 0.00059 35.2 0.7 29 827-863 28-56 (131)
87 cd01395 HMT_MBD Methyl-CpG bin 25.8 56 0.0012 29.0 2.4 41 291-331 8-49 (60)
88 PRK04023 DNA polymerase II lar 25.3 45 0.00097 43.1 2.3 34 740-784 625-658 (1121)
89 PRK14559 putative protein seri 24.9 52 0.0011 40.7 2.8 43 753-812 1-50 (645)
90 cd00162 RING RING-finger (Real 24.5 20 0.00043 26.9 -0.6 40 744-784 2-42 (45)
91 PLN02436 cellulose synthase A 24.0 65 0.0014 42.0 3.4 45 739-784 34-85 (1094)
92 COG0143 MetG Methionyl-tRNA sy 23.6 41 0.0009 40.9 1.6 36 777-820 126-172 (558)
93 PLN02638 cellulose synthase A 23.4 63 0.0014 42.1 3.1 45 739-784 15-66 (1079)
94 KOG4442 Clathrin coat binding 23.2 32 0.0007 42.6 0.6 55 624-695 208-262 (729)
95 PHA02929 N1R/p28-like protein; 22.7 44 0.00096 36.6 1.4 32 739-770 172-211 (238)
96 PLN02189 cellulose synthase 22.0 74 0.0016 41.4 3.3 45 739-784 32-83 (1040)
97 PF10367 Vps39_2: Vacuolar sor 20.5 60 0.0013 29.5 1.7 30 740-769 77-108 (109)
98 PF12773 DZR: Double zinc ribb 20.5 67 0.0015 26.2 1.8 7 777-783 29-35 (50)
99 KOG3612 PHD Zn-finger protein 20.4 57 0.0012 39.6 1.8 46 775-834 58-104 (588)
100 COG4357 Zinc finger domain con 20.4 51 0.0011 32.0 1.1 29 741-769 62-96 (105)
101 COG5082 AIR1 Arginine methyltr 20.1 1E+02 0.0022 33.0 3.4 49 738-792 57-107 (190)
No 1
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.02 E-value=9.3e-11 Score=125.08 Aligned_cols=90 Identities=27% Similarity=0.592 Sum_probs=74.6
Q ss_pred cccccccccCC---------ceeecCCCCCccccccccC-----CCCCCCCccccccc-ccccCCccCCccccCCCCccc
Q 002464 741 DDSCGICGDGG---------ELICCDNCPSAFHQACLSI-----QDLPTGSWFCSNCT-CWICGDLVNDKEASSSFDALK 805 (919)
Q Consensus 741 dd~C~VCgdGG---------eLLcCD~CpraFHlsCL~~-----~~vPeG~W~Cp~C~-C~iCge~~~Dke~~s~~~lL~ 805 (919)
...|.+|-++. .+|+|..|..++|++|+.+ ..+-...|.|..|+ |.||++++.+ ..+++
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E------~E~~F 331 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIE------SEHLF 331 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccc------hheec
Confidence 35799997743 5999999999999999986 23446789999998 9999999765 45799
Q ss_pred cCcccccCccccccCccCCCCCCcccccccchh
Q 002464 806 CSQCEHKYHGECLKDMSKGAVSEAWFCNQSCQE 838 (919)
Q Consensus 806 CdQCeraYHv~CL~~~~~~~~~g~WFCs~~Cq~ 838 (919)
||.|+|.||..|++.. ..+.|.|.|-..|..
T Consensus 332 CD~CDRG~HT~CVGL~--~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 332 CDVCDRGPHTLCVGLQ--DLPRGEWICDMRCRE 362 (381)
T ss_pred cccccCCCCccccccc--cccCccchhhhHHHH
Confidence 9999999999999864 456899999866653
No 2
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=98.95 E-value=3e-10 Score=131.34 Aligned_cols=106 Identities=31% Similarity=0.806 Sum_probs=82.3
Q ss_pred ccccccccC-----CceeecCC--CCCccccccccCCCCCCCCccccccc------------------------------
Q 002464 742 DSCGICGDG-----GELICCDN--CPSAFHQACLSIQDLPTGSWFCSNCT------------------------------ 784 (919)
Q Consensus 742 d~C~VCgdG-----GeLLcCD~--CpraFHlsCL~~~~vPeG~W~Cp~C~------------------------------ 784 (919)
.-|.||.|. .-|+.||+ |.-+.|+.|+++.++|.|.|||+.|.
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdGALKkTDn~GWAH 85 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDGALKKTDNGGWAH 85 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCcccceecccCCCceE
Confidence 458999883 36999995 99999999999999999999999997
Q ss_pred ----------------------------------ccccCCccCCccccCCCCccccC--cccccCccccccCccCCCC--
Q 002464 785 ----------------------------------CWICGDLVNDKEASSSFDALKCS--QCEHKYHGECLKDMSKGAV-- 826 (919)
Q Consensus 785 ----------------------------------C~iCge~~~Dke~~s~~~lL~Cd--QCeraYHv~CL~~~~~~~~-- 826 (919)
|+||.+......+ ..+..|.|. .|.++||+.|.+-.+....
T Consensus 86 VVCALYIPEVrFgNV~TMEPIiLq~VP~dRfnKtCYIC~E~GrpnkA-~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~ 164 (900)
T KOG0956|consen 86 VVCALYIPEVRFGNVHTMEPIILQDVPHDRFNKTCYICNEEGRPNKA-AKGACMTCNKSGCKQAFHVTCAQRAGLLCEEE 164 (900)
T ss_pred EEEEeeccceeecccccccceeeccCchhhhcceeeeecccCCcccc-ccccceecccccchhhhhhhHhhhhccceecc
Confidence 7777765433222 346788895 8999999999997655322
Q ss_pred ----CCcccccccchhHhhhhhccccc
Q 002464 827 ----SEAWFCNQSCQEVYSGLHSHIGI 849 (919)
Q Consensus 827 ----~g~WFCs~~Cq~I~e~LqklVGv 849 (919)
..--||+ +|+..|..|.+--.+
T Consensus 165 gn~~dNVKYCG-YCk~HfsKlkk~~~~ 190 (900)
T KOG0956|consen 165 GNISDNVKYCG-YCKYHFSKLKKSPAI 190 (900)
T ss_pred ccccccceech-hHHHHHHHhhcCCCc
Confidence 2335775 899999988875443
No 3
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.87 E-value=5.5e-10 Score=118.71 Aligned_cols=87 Identities=32% Similarity=0.754 Sum_probs=73.6
Q ss_pred cccccccc----------CCceeecCCCCCccccccccC-----CCCCCCCccccccc-ccccCCccCCccccCCCCccc
Q 002464 742 DSCGICGD----------GGELICCDNCPSAFHQACLSI-----QDLPTGSWFCSNCT-CWICGDLVNDKEASSSFDALK 805 (919)
Q Consensus 742 d~C~VCgd----------GGeLLcCD~CpraFHlsCL~~-----~~vPeG~W~Cp~C~-C~iCge~~~Dke~~s~~~lL~ 805 (919)
.+|-.|-. +.+|+-|..|+++-|++||.. ..+-...|+|..|+ |.|||...+| ..+++
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsend------dqllf 298 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSEND------DQLLF 298 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCC------ceeEe
Confidence 46767743 348999999999999999984 34567899999998 8999987544 67899
Q ss_pred cCcccccCccccccCccCCCCCCcccccc
Q 002464 806 CSQCEHKYHGECLKDMSKGAVSEAWFCNQ 834 (919)
Q Consensus 806 CdQCeraYHv~CL~~~~~~~~~g~WFCs~ 834 (919)
||-|+|.||.+||.|+....++|.|-|--
T Consensus 299 cddcdrgyhmyclsppm~eppegswsc~K 327 (336)
T KOG1244|consen 299 CDDCDRGYHMYCLSPPMVEPPEGSWSCHL 327 (336)
T ss_pred ecccCCceeeEecCCCcCCCCCCchhHHH
Confidence 99999999999999988788899999964
No 4
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.41 E-value=1.1e-07 Score=110.43 Aligned_cols=45 Identities=49% Similarity=1.354 Sum_probs=41.1
Q ss_pred cccccccccCCce---eecCCCCCccccccccC----CCCCCCCcccccccc
Q 002464 741 DDSCGICGDGGEL---ICCDNCPSAFHQACLSI----QDLPTGSWFCSNCTC 785 (919)
Q Consensus 741 dd~C~VCgdGGeL---LcCD~CpraFHlsCL~~----~~vPeG~W~Cp~C~C 785 (919)
.++|..|+..|.. ||||+||++||+.||.| +.+|.|.|+|+.|.|
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~ 304 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKI 304 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCee
Confidence 5699999998866 99999999999999986 579999999999994
No 5
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.37 E-value=1.2e-07 Score=110.54 Aligned_cols=89 Identities=29% Similarity=0.813 Sum_probs=73.3
Q ss_pred ccccccccccC-----CceeecCCCCCccccccccC---CCCCCCCccccccc-ccccCCccCCccccCCCCccccCccc
Q 002464 740 NDDSCGICGDG-----GELICCDNCPSAFHQACLSI---QDLPTGSWFCSNCT-CWICGDLVNDKEASSSFDALKCSQCE 810 (919)
Q Consensus 740 ndd~C~VCgdG-----GeLLcCD~CpraFHlsCL~~---~~vPeG~W~Cp~C~-C~iCge~~~Dke~~s~~~lL~CdQCe 810 (919)
....|.+|+.. |.|+-|..|...||.+|+.. ..+-.+.|.|+.|+ |..|+... +....++|+.|+
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~g------D~~kf~~Ck~cD 90 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTG------DPKKFLLCKRCD 90 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccC------Cccccccccccc
Confidence 45788899874 46899999999999999985 22234459999998 99999542 235678999999
Q ss_pred ccCccccccCccCCCCCCcccccc
Q 002464 811 HKYHGECLKDMSKGAVSEAWFCNQ 834 (919)
Q Consensus 811 raYHv~CL~~~~~~~~~g~WFCs~ 834 (919)
-.||.+|..|.....+.+.|+|..
T Consensus 91 vsyh~yc~~P~~~~v~sg~~~ckk 114 (694)
T KOG4443|consen 91 VSYHCYCQKPPNDKVPSGPWLCKK 114 (694)
T ss_pred ccccccccCCccccccCcccccHH
Confidence 999999999998888999999976
No 6
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=98.34 E-value=1.4e-07 Score=106.73 Aligned_cols=49 Identities=39% Similarity=0.954 Sum_probs=42.8
Q ss_pred CCcccccccccccc-----CCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 736 EDDKNDDSCGICGD-----GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 736 ~~d~ndd~C~VCgd-----GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
++++-++.|.+|.. ...+++||+|.-+.|+.|+++..+|+|.|.|..|.
T Consensus 188 ~~d~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi 241 (669)
T COG5141 188 PSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCI 241 (669)
T ss_pred CchhhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCcchhhhhhhc
Confidence 34456788999875 24699999999999999999999999999999997
No 7
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=98.22 E-value=5.6e-07 Score=105.75 Aligned_cols=106 Identities=26% Similarity=0.690 Sum_probs=75.4
Q ss_pred ccccccccccC-----CceeecCCCCCccccccccCCCCCCCCccccccc------ccccCCccC------Cc-------
Q 002464 740 NDDSCGICGDG-----GELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT------CWICGDLVN------DK------- 795 (919)
Q Consensus 740 ndd~C~VCgdG-----GeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~------C~iCge~~~------Dk------- 795 (919)
++..|-+|..+ .+|++||.|....|+.|+++..+|+|.|.|..|. |..|-+..- ++
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg~~ppCvLCPkkGGamK~~~sgT~wAHvs 349 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALGIEPPCVLCPKKGGAMKPTKSGTKWAHVS 349 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCCCCeeehhccccCCCCeeeccccCCcccccCCCCeeeEee
Confidence 67788888764 5899999999999999999999999999999998 777744221 00
Q ss_pred ----------------ccc--------------------CCCCccccC--cccccCccccccCccCCCC---------CC
Q 002464 796 ----------------EAS--------------------SSFDALKCS--QCEHKYHGECLKDMSKGAV---------SE 828 (919)
Q Consensus 796 ----------------e~~--------------------s~~~lL~Cd--QCeraYHv~CL~~~~~~~~---------~g 828 (919)
++. ..+..+.|. .|.-+||+.|....++.+. ..
T Consensus 350 CALwIPEVsie~~ekmePItkfs~IpesRwslvC~LCk~k~GACIqCs~k~C~t~fHv~CA~~aG~~~~~~~~~~D~v~~ 429 (893)
T KOG0954|consen 350 CALWIPEVSIECPEKMEPITKFSHIPESRWSLVCNLCKVKSGACIQCSNKTCRTAFHVTCAFEAGLEMKTILKENDEVKF 429 (893)
T ss_pred eeeccceeeccCHhhcCcccccCCCcHHHHHHHHHHhcccCcceEEecccchhhhccchhhhhcCCeeeeeeccCCchhh
Confidence 000 123445564 7888999999998876431 55
Q ss_pred cccccccchhHhhhhhcccc
Q 002464 829 AWFCNQSCQEVYSGLHSHIG 848 (919)
Q Consensus 829 ~WFCs~~Cq~I~e~LqklVG 848 (919)
.-||+. |..+.+ .+.+|
T Consensus 430 ~s~c~k-hs~~~~--~~s~g 446 (893)
T KOG0954|consen 430 KSYCSK-HSDHRE--GKSLG 446 (893)
T ss_pred eeeccc-cccccc--ccccc
Confidence 668875 444443 45555
No 8
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.00 E-value=3.5e-06 Score=98.26 Aligned_cols=44 Identities=48% Similarity=1.139 Sum_probs=36.0
Q ss_pred cccccccccCCceeecCCCCCccccccccCC---CCCCCCccccccc
Q 002464 741 DDSCGICGDGGELICCDNCPSAFHQACLSIQ---DLPTGSWFCSNCT 784 (919)
Q Consensus 741 dd~C~VCgdGGeLLcCD~CpraFHlsCL~~~---~vPeG~W~Cp~C~ 784 (919)
...|.+|..||++++|+.|+.+||+.|-.+. ..+.+.|.|..|.
T Consensus 47 ~ts~~~~~~~gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~ 93 (613)
T KOG4299|consen 47 ATSCGICKSGGNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCP 93 (613)
T ss_pred hhhcchhhhcCCccccccCccccchhccCcccCcccccccccccCCC
Confidence 5789999999999999999999999998863 3334567776665
No 9
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.00 E-value=3.1e-06 Score=104.29 Aligned_cols=48 Identities=40% Similarity=0.941 Sum_probs=42.9
Q ss_pred CccccccccccccC-----CceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 737 DDKNDDSCGICGDG-----GELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 737 ~d~ndd~C~VCgdG-----GeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
..+.|..|.||.++ ..++.||+|..++|+.|++..-+|+|.|.|..|.
T Consensus 215 ~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipeg~WlCr~Cl 267 (1051)
T KOG0955|consen 215 LLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCL 267 (1051)
T ss_pred ccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCCCcEeehhhc
Confidence 34567899999985 3689999999999999999989999999999997
No 10
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.97 E-value=3.1e-06 Score=91.26 Aligned_cols=38 Identities=39% Similarity=1.082 Sum_probs=35.3
Q ss_pred cccCCceeecCC--CC-CccccccccCCCCCCCCccccccc
Q 002464 747 CGDGGELICCDN--CP-SAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 747 CgdGGeLLcCD~--Cp-raFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
|..+|+||-||. |+ .+||..|+++...|.|.|||+.|+
T Consensus 226 qvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~ 266 (274)
T KOG1973|consen 226 QVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCK 266 (274)
T ss_pred ccccccccccCCCCCCcceEEEeccccccCCCCcccchhhh
Confidence 456999999997 99 899999999999999999999886
No 11
>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=97.96 E-value=2.2e-06 Score=69.50 Aligned_cols=42 Identities=40% Similarity=1.272 Sum_probs=35.5
Q ss_pred ccccccc---CCceeecCCCCCccccccccCC----CCCCCCccccccc
Q 002464 743 SCGICGD---GGELICCDNCPSAFHQACLSIQ----DLPTGSWFCSNCT 784 (919)
Q Consensus 743 ~C~VCgd---GGeLLcCD~CpraFHlsCL~~~----~vPeG~W~Cp~C~ 784 (919)
+|.+|+. .+++|.|+.|.++||..|+++. ..+.+.|+|+.|.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 4788887 6789999999999999999984 3345699999986
No 12
>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 COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.87 E-value=7.5e-06 Score=87.30 Aligned_cols=44 Identities=34% Similarity=1.068 Sum_probs=39.5
Q ss_pred cccccccccc--CCceeecCC--CCC-ccccccccCCCCCCCCccccccc
Q 002464 740 NDDSCGICGD--GGELICCDN--CPS-AFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgd--GGeLLcCD~--Cpr-aFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
+..+|+ |.+ .|+|+-||+ |.+ +||+.|+++...|+|.|||+.|+
T Consensus 220 e~lYCf-CqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk 268 (271)
T COG5034 220 EELYCF-CQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECK 268 (271)
T ss_pred ceeEEE-ecccccccceecCCCCCchhheeccccccCCCCCCcEeCHHhH
Confidence 446777 887 689999995 999 99999999999999999999996
No 14
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=97.66 E-value=1.2e-05 Score=98.25 Aligned_cols=108 Identities=26% Similarity=0.527 Sum_probs=73.5
Q ss_pred CccccccccccccCCceeecCCCCCccccccccC--CCCCCCCccccccc-ccccCC-----c-------------cCCc
Q 002464 737 DDKNDDSCGICGDGGELICCDNCPSAFHQACLSI--QDLPTGSWFCSNCT-CWICGD-----L-------------VNDK 795 (919)
Q Consensus 737 ~d~ndd~C~VCgdGGeLLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~-C~iCge-----~-------------~~Dk 795 (919)
...-++.|.+|.+.|.++||..||+.||+.|+.+ ..+|...|.|--|. |.+=|- + ..|.
T Consensus 340 ~~~~ddhcrf~~d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvngvvd~vl~~~K~~~~iR~~~iG~dr 419 (1414)
T KOG1473|consen 340 EIEYDDHCRFCHDLGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVNGVVDCVLPPSKNVDSIRHTPIGRDR 419 (1414)
T ss_pred ceeecccccccCcccceeecccCCceEEeeecCCccccCCCccchhhhhhhhccCcccccccChhhcccceeccCCCcCc
Confidence 3445789999999999999999999999999986 56788999999887 211110 0 0000
Q ss_pred cc-------------cCCCCccccCc-ccccCcc-ccccCccCC--CCCCcccccccchhHhhhhhc
Q 002464 796 EA-------------SSSFDALKCSQ-CEHKYHG-ECLKDMSKG--AVSEAWFCNQSCQEVYSGLHS 845 (919)
Q Consensus 796 e~-------------~s~~~lL~CdQ-CeraYHv-~CL~~~~~~--~~~g~WFCs~~Cq~I~e~Lqk 845 (919)
.. .-.++.+.|+. |+..||. .|++....+ ...+.|+|.. |-.-.++|..
T Consensus 420 ~gr~ywfi~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~e-e~~rqM~lT~ 485 (1414)
T KOG1473|consen 420 YGRKYWFISRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERRE-EIIRQMGLTE 485 (1414)
T ss_pred cccchhceeeeeEEecCCCcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHH-HHHHhccchh
Confidence 00 01245566765 9999999 999954433 3478999974 4444444443
No 15
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.64 E-value=2.4e-05 Score=93.51 Aligned_cols=69 Identities=30% Similarity=0.766 Sum_probs=59.3
Q ss_pred CCCCccccccccC--CCCCCCCccccccc--------------------ccccCCccCCccccCCCCccccCcccccCcc
Q 002464 758 NCPSAFHQACLSI--QDLPTGSWFCSNCT--------------------CWICGDLVNDKEASSSFDALKCSQCEHKYHG 815 (919)
Q Consensus 758 ~CpraFHlsCL~~--~~vPeG~W~Cp~C~--------------------C~iCge~~~Dke~~s~~~lL~CdQCeraYHv 815 (919)
.|++.||..|+.+ ...|+++|.||.|. |.+|+.. +.++.|+.|..+||.
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~---------g~~l~c~tC~~s~h~ 71 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADG---------GELLWCDTCPASFHA 71 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCC---------CcEEEeccccHHHHH
Confidence 4899999999997 55668999999997 8888864 678889999999999
Q ss_pred ccccCccCCCCCCcccccccc
Q 002464 816 ECLKDMSKGAVSEAWFCNQSC 836 (919)
Q Consensus 816 ~CL~~~~~~~~~g~WFCs~~C 836 (919)
.|+.+.....+.+.|.|+ .|
T Consensus 72 ~cl~~pl~~~p~~~~~c~-Rc 91 (696)
T KOG0383|consen 72 SCLGPPLTPQPNGEFICP-RC 91 (696)
T ss_pred HccCCCCCcCCccceeee-ee
Confidence 999998887776669999 45
No 16
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.58 E-value=2.6e-05 Score=83.95 Aligned_cols=45 Identities=40% Similarity=1.007 Sum_probs=38.3
Q ss_pred ccccccccccC---CceeecCCCCCccccccccC--CCCCCCCccccccc
Q 002464 740 NDDSCGICGDG---GELICCDNCPSAFHQACLSI--QDLPTGSWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgdG---GeLLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~ 784 (919)
...+|.+||.. .+|++||.|.+.||.+||.| .+.|+|.|.|..|.
T Consensus 280 eck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 280 ECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred ecceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence 35688999874 47999999999999999997 67899999987774
No 17
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.49 E-value=3.5e-05 Score=92.09 Aligned_cols=51 Identities=45% Similarity=1.139 Sum_probs=44.2
Q ss_pred CCccccccccccccCCceeecCCCCCccccccccC--CCCCCCCccccccccc
Q 002464 736 EDDKNDDSCGICGDGGELICCDNCPSAFHQACLSI--QDLPTGSWFCSNCTCW 786 (919)
Q Consensus 736 ~~d~ndd~C~VCgdGGeLLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~C~ 786 (919)
..+.+...|.+|+++|++++||.|+.+||.+|+++ ...|.+.|.|+.|.|.
T Consensus 42 ~~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p 94 (696)
T KOG0383|consen 42 WDDAEQEACRICADGGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCP 94 (696)
T ss_pred cchhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCCcCCccceeeeeeccC
Confidence 45667789999999999999999999999999986 5667778999988754
No 18
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.43 E-value=6.7e-05 Score=86.06 Aligned_cols=95 Identities=21% Similarity=0.447 Sum_probs=68.7
Q ss_pred ccccccccc-----CCceeecCCCCCccccccccCCCCCCCCccccccc-------------------------------
Q 002464 741 DDSCGICGD-----GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT------------------------------- 784 (919)
Q Consensus 741 dd~C~VCgd-----GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~------------------------------- 784 (919)
...|.+|.. +.++..|+.|.++||..|..+.....+.|.+..|.
T Consensus 83 e~~~nv~~s~~~~p~~e~~~~~r~~~~~~q~~~i~~~~~~~~~~~~~c~~~~~~~~g~a~K~g~~a~~~l~y~~~~l~wD 162 (464)
T KOG4323|consen 83 ELNPNVLTSETVLPENEKVICGRCKSGYHQGCNIPRFPSLDIGESTECVFPIFSQEGGALKKGRLARPSLPYPEASLDWD 162 (464)
T ss_pred ccCCcccccccccCchhhhhhhhhccCcccccCccCcCcCCccccccccccccccccccccccccccccccCcccccccC
Confidence 345666654 44688899999999999987655555566666555
Q ss_pred --------ccccCCccCCccccCCCCccccCcccccCccccccCccCCC----CCCcccccccchhH
Q 002464 785 --------CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKGA----VSEAWFCNQSCQEV 839 (919)
Q Consensus 785 --------C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~----~~g~WFCs~~Cq~I 839 (919)
|.+|...+.. .+..|++|+.|..+||..|.++....+ +...|||..|+...
T Consensus 163 ~~~~~n~qc~vC~~g~~~----~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 163 SGHKVNLQCSVCYCGGPG----AGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred ccccccceeeeeecCCcC----ccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 6666654221 235899999999999999999875433 37899999877643
No 19
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.27 E-value=0.00011 Score=79.71 Aligned_cols=42 Identities=38% Similarity=0.935 Sum_probs=37.9
Q ss_pred ccccccccccC---CceeecCCCCCccccccccCCCCCCCCcccc
Q 002464 740 NDDSCGICGDG---GELICCDNCPSAFHQACLSIQDLPTGSWFCS 781 (919)
Q Consensus 740 ndd~C~VCgdG---GeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp 781 (919)
....|.+|+.+ .++++||.|+++||.+|+++..+|.|.|.|-
T Consensus 313 ~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL~~lP~G~WICD 357 (381)
T KOG1512|consen 313 SCELCRICLGPVIESEHLFCDVCDRGPHTLCVGLQDLPRGEWICD 357 (381)
T ss_pred ccHhhhccCCcccchheeccccccCCCCccccccccccCccchhh
Confidence 35689999984 5899999999999999999999999999995
No 20
>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 PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=97.15 E-value=0.00033 Score=71.41 Aligned_cols=80 Identities=28% Similarity=0.662 Sum_probs=57.3
Q ss_pred ccccccc------CCceeecCCCCCccccccccCC--------CCCCCC--ccccccc---------------ccccCCc
Q 002464 743 SCGICGD------GGELICCDNCPSAFHQACLSIQ--------DLPTGS--WFCSNCT---------------CWICGDL 791 (919)
Q Consensus 743 ~C~VCgd------GGeLLcCD~CpraFHlsCL~~~--------~vPeG~--W~Cp~C~---------------C~iCge~ 791 (919)
.|.+|+. .|.||.|-+|..+||..||++. .+..+. -+|.+|. |..|...
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~~~~C~~C~~~ 80 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPHHGMCQQCKKP 80 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCCCCCCCcccccCCC
Confidence 3677742 4689999999999999999972 233343 5788887 8888764
Q ss_pred cCCc-------------------ccc-------------CCCCccccCcccccCccccccCcc
Q 002464 792 VNDK-------------------EAS-------------SSFDALKCSQCEHKYHGECLKDMS 822 (919)
Q Consensus 792 ~~Dk-------------------e~~-------------s~~~lL~CdQCeraYHv~CL~~~~ 822 (919)
...- .+. ....++.|..|.|+||...|++..
T Consensus 81 G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~~HLP~~~ 143 (175)
T PF15446_consen 81 GPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHFEHLPPPS 143 (175)
T ss_pred CCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeehhhCCCCc
Confidence 4211 000 123578999999999999999864
No 22
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.03 E-value=0.00019 Score=84.55 Aligned_cols=84 Identities=29% Similarity=0.760 Sum_probs=60.9
Q ss_pred ccccccccccCC---ceeecCCCCCccccccccC--CCCCCCCccccccc-ccccCCccCC----cc-------c-----
Q 002464 740 NDDSCGICGDGG---ELICCDNCPSAFHQACLSI--QDLPTGSWFCSNCT-CWICGDLVND----KE-------A----- 797 (919)
Q Consensus 740 ndd~C~VCgdGG---eLLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~-C~iCge~~~D----ke-------~----- 797 (919)
..-.|..|+.+| .+++|+.|.-+||-+|..| ..+|.|.|+|++|. |.-|...+-. -. +
T Consensus 67 ~crvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~qc~~~lpg~s~~~~~~~~~~~~c~s~~ 146 (694)
T KOG4443|consen 67 SCRVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTRCRQCDSTLPGLSLDLQEGYLQCAPCASLS 146 (694)
T ss_pred CceeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHhhhhccccccccchhhhccCcccccccccc
Confidence 445777887544 7899999999999999987 78999999999997 6666543211 00 0
Q ss_pred -----------cCCCCccccCcccccCccccccCccC
Q 002464 798 -----------SSSFDALKCSQCEHKYHGECLKDMSK 823 (919)
Q Consensus 798 -----------~s~~~lL~CdQCeraYHv~CL~~~~~ 823 (919)
.....++.|++|.++-|..|-.....
T Consensus 147 ~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd 183 (694)
T KOG4443|consen 147 YCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDD 183 (694)
T ss_pred cCchHHHhhhhccchhhHHHHHhcccccCCCCccchH
Confidence 00123478889999999999776544
No 23
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.00 E-value=0.0003 Score=83.95 Aligned_cols=45 Identities=33% Similarity=0.983 Sum_probs=38.9
Q ss_pred ccccccccccC---CceeecCCCCCc-cccccccC--CCCCCCCccccccc
Q 002464 740 NDDSCGICGDG---GELICCDNCPSA-FHQACLSI--QDLPTGSWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgdG---GeLLcCD~Cpra-FHlsCL~~--~~vPeG~W~Cp~C~ 784 (919)
...-|.+|... .-||+||.|..+ ||.+||.+ .++|-+.|||+.|.
T Consensus 214 E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~ 264 (1134)
T KOG0825|consen 214 EEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCS 264 (1134)
T ss_pred ccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcch
Confidence 34569999864 369999999998 99999998 56999999999997
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=96.88 E-value=0.0003 Score=57.11 Aligned_cols=44 Identities=32% Similarity=0.849 Sum_probs=34.1
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccccCccCCC--CCCcccccc
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKGA--VSEAWFCNQ 834 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~--~~g~WFCs~ 834 (919)
|.+|++. .....++.|+.|.+.||..|+++..... +.+.|+|+.
T Consensus 2 C~vC~~~------~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~ 47 (51)
T PF00628_consen 2 CPVCGQS------DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPN 47 (51)
T ss_dssp BTTTTSS------CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHH
T ss_pred CcCCCCc------CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcC
Confidence 6788873 2236789999999999999999976532 356999974
No 25
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.63 E-value=0.00072 Score=80.90 Aligned_cols=47 Identities=32% Similarity=0.695 Sum_probs=37.2
Q ss_pred ccccCCccCCccccCCCCccccCccccc-CccccccCccCCCCCCcccccccchh
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHK-YHGECLKDMSKGAVSEAWFCNQSCQE 838 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCera-YHv~CL~~~~~~~~~g~WFCs~~Cq~ 838 (919)
|.||+.+ |.+ ..+|.|+.|... ||.+||++.+.+.+-+.|||. .|..
T Consensus 218 C~IC~~~--DpE----dVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~-NC~d 265 (1134)
T KOG0825|consen 218 CDICTVH--DPE----DVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCT-NCSL 265 (1134)
T ss_pred ceeeccC--ChH----HhheeecccccceeeccccCcccccccccceecC-cchh
Confidence 6777754 222 458899999999 999999998877888999997 4653
No 26
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=96.51 E-value=0.00092 Score=76.95 Aligned_cols=43 Identities=33% Similarity=1.010 Sum_probs=35.3
Q ss_pred cccccccc-----CCceeecCCCCCccccccccC---CCCCC-------CCccccccc
Q 002464 742 DSCGICGD-----GGELICCDNCPSAFHQACLSI---QDLPT-------GSWFCSNCT 784 (919)
Q Consensus 742 d~C~VCgd-----GGeLLcCD~CpraFHlsCL~~---~~vPe-------G~W~Cp~C~ 784 (919)
..|.||-. .|+++-||.|+-..|..|++. ..+|. ..|||.-|.
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
Confidence 48999954 689999999999999999985 23332 479999998
No 27
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=96.13 E-value=0.0027 Score=68.98 Aligned_cols=38 Identities=18% Similarity=0.467 Sum_probs=31.1
Q ss_pred CCCccccCc--cc-ccCccccccCccCCCCCCcccccccchhH
Q 002464 800 SFDALKCSQ--CE-HKYHGECLKDMSKGAVSEAWFCNQSCQEV 839 (919)
Q Consensus 800 ~~~lL~CdQ--Ce-raYHv~CL~~~~~~~~~g~WFCs~~Cq~I 839 (919)
.+.|+.||. |+ .+||..|++.. ..|.|.|||++|+...
T Consensus 229 yg~Mi~CDn~~C~~eWFH~~CVGL~--~~PkgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 229 YGKMIGCDNPGCPIEWFHFTCVGLK--TKPKGKWYCPRCKAEN 269 (274)
T ss_pred cccccccCCCCCCcceEEEeccccc--cCCCCcccchhhhhhh
Confidence 478899997 99 99999999964 4568999999766543
No 28
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=95.96 E-value=0.0017 Score=50.94 Aligned_cols=34 Identities=41% Similarity=1.195 Sum_probs=20.5
Q ss_pred CceeecCCCCCccccccccCCCCCCC-Cccccccc
Q 002464 751 GELICCDNCPSAFHQACLSIQDLPTG-SWFCSNCT 784 (919)
Q Consensus 751 GeLLcCD~CpraFHlsCL~~~~vPeG-~W~Cp~C~ 784 (919)
..|+.|+.|.-.+|..|++...+|.+ +|+|..|+
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 36899999999999999999888877 89998884
No 29
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=95.48 E-value=0.008 Score=60.49 Aligned_cols=31 Identities=32% Similarity=0.863 Sum_probs=26.5
Q ss_pred ccccccccC--CCCCCCCcccccccccccCCcc
Q 002464 762 AFHQACLSI--QDLPTGSWFCSNCTCWICGDLV 792 (919)
Q Consensus 762 aFHlsCL~~--~~vPeG~W~Cp~C~C~iCge~~ 792 (919)
+||+.||.| ..+|+|+|+||.|.....++..
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~~~~~~~ 33 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSA 33 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCCCCCCcc
Confidence 599999996 7899999999999977666653
No 30
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=95.14 E-value=0.014 Score=50.21 Aligned_cols=42 Identities=33% Similarity=0.434 Sum_probs=37.9
Q ss_pred HcCceeccccCCC--ccccceeeeCCCccccccchhHHHHhccc
Q 002464 290 AAGWAVERRKRPS--RKYMDTIYRSPEGRLFREFPKVWRVCGEN 331 (919)
Q Consensus 290 ~agW~i~~r~R~~--r~~~~~~y~sp~~~~~r~~~~aWk~cG~~ 331 (919)
-.||+-+-+.|.. +.++|.||.||.|+.||+.+++=+.++++
T Consensus 7 p~GW~R~~~~r~~g~~~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~~ 50 (62)
T cd00122 7 PPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKT 50 (62)
T ss_pred CCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhC
Confidence 3699999888885 89999999999999999999999998875
No 31
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=95.06 E-value=0.0051 Score=79.14 Aligned_cols=45 Identities=33% Similarity=0.980 Sum_probs=40.1
Q ss_pred ccccccccccCC---ceeecCCCCCccccccccC--CCCCCCCccccccc
Q 002464 740 NDDSCGICGDGG---ELICCDNCPSAFHQACLSI--QDLPTGSWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgdGG---eLLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~ 784 (919)
....|.+|...+ .+++|+.|..+||..|+.+ ..+|.|+|+||.|+
T Consensus 1107 ~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~ 1156 (1404)
T KOG1245|consen 1107 VNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCR 1156 (1404)
T ss_pred chhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccc
Confidence 456899998744 6899999999999999987 78999999999998
No 32
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.91 E-value=0.01 Score=68.73 Aligned_cols=44 Identities=36% Similarity=0.928 Sum_probs=35.5
Q ss_pred cccccccccCC-----ceeecCCCCCccccccccC------CCCCCCCccccccc
Q 002464 741 DDSCGICGDGG-----ELICCDNCPSAFHQACLSI------QDLPTGSWFCSNCT 784 (919)
Q Consensus 741 dd~C~VCgdGG-----eLLcCD~CpraFHlsCL~~------~~vPeG~W~Cp~C~ 784 (919)
+..|.+|..|+ .||.|+.|...||..|..+ ..-+.+.|+|..|.
T Consensus 168 n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~ 222 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCN 222 (464)
T ss_pred cceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhc
Confidence 34599987644 8999999999999999986 23367799998886
No 33
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=94.85 E-value=0.021 Score=51.69 Aligned_cols=51 Identities=29% Similarity=0.391 Sum_probs=42.5
Q ss_pred HcCceeccccCCC--ccccceeeeCCCccccccchhHHHHhccc----ccccCCCCC
Q 002464 290 AAGWAVERRKRPS--RKYMDTIYRSPEGRLFREFPKVWRVCGEN----LLADGSNVV 340 (919)
Q Consensus 290 ~agW~i~~r~R~~--r~~~~~~y~sp~~~~~r~~~~aWk~cG~~----L~~~~~~~~ 340 (919)
-.||..+-+.|.+ ..++|.||.||.|+.||+.+++=++++.+ |-++.-+|.
T Consensus 8 p~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~~~~~~~~FdF~ 64 (77)
T cd01396 8 PPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFT 64 (77)
T ss_pred CCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCCCCCcHhHcccC
Confidence 3699999988886 89999999999999999999999999874 544444444
No 34
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.52 E-value=0.042 Score=63.96 Aligned_cols=45 Identities=42% Similarity=0.945 Sum_probs=36.4
Q ss_pred ccccccccccCC---ceeecCCCCCccccccccC--CCCCCC----Cccccccc
Q 002464 740 NDDSCGICGDGG---ELICCDNCPSAFHQACLSI--QDLPTG----SWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgdGG---eLLcCD~CpraFHlsCL~~--~~vPeG----~W~Cp~C~ 784 (919)
-...|.||...- -|+.||.|...||+.||.| ..+|.. .|+|..|.
T Consensus 543 ~~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred cceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence 347899998754 4889999999999999986 566643 69998883
No 35
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=92.59 E-value=0.08 Score=47.49 Aligned_cols=43 Identities=37% Similarity=0.446 Sum_probs=36.2
Q ss_pred HcCceeccccCCC---ccccceeeeCCCccccccchhHHHHhcccc
Q 002464 290 AAGWAVERRKRPS---RKYMDTIYRSPEGRLFREFPKVWRVCGENL 332 (919)
Q Consensus 290 ~agW~i~~r~R~~---r~~~~~~y~sp~~~~~r~~~~aWk~cG~~L 332 (919)
-.||+.+-+.|.+ .-+++.||.||.|+.||++.++=+++++.-
T Consensus 12 p~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~ 57 (77)
T PF01429_consen 12 PDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENP 57 (77)
T ss_dssp TTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS
T ss_pred CCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCC
Confidence 3699999987773 358999999999999999999999988765
No 36
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=90.69 E-value=0.17 Score=45.78 Aligned_cols=42 Identities=31% Similarity=0.502 Sum_probs=36.1
Q ss_pred HcCceeccccCC---CccccceeeeCCCccccccchhHHHHhccc
Q 002464 290 AAGWAVERRKRP---SRKYMDTIYRSPEGRLFREFPKVWRVCGEN 331 (919)
Q Consensus 290 ~agW~i~~r~R~---~r~~~~~~y~sp~~~~~r~~~~aWk~cG~~ 331 (919)
-.||.=+-+.|. ++.++|-||.||.|+.+|+.+++=+.++++
T Consensus 9 p~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~ 53 (77)
T smart00391 9 PCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKN 53 (77)
T ss_pred CCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhC
Confidence 369987777666 467999999999999999999999999865
No 37
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=90.25 E-value=0.15 Score=51.54 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=22.4
Q ss_pred cCccccccCccCCCCCCcccccccc
Q 002464 812 KYHGECLKDMSKGAVSEAWFCNQSC 836 (919)
Q Consensus 812 aYHv~CL~~~~~~~~~g~WFCs~~C 836 (919)
.||..||+|++...+.|+|+||.|-
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~ 25 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCE 25 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCc
Confidence 4999999999988899999999753
No 38
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=90.14 E-value=0.15 Score=55.39 Aligned_cols=37 Identities=27% Similarity=0.779 Sum_probs=29.1
Q ss_pred CCCCccccC--ccccc-CccccccCccCCCCCCcccccccchh
Q 002464 799 SSFDALKCS--QCEHK-YHGECLKDMSKGAVSEAWFCNQSCQE 838 (919)
Q Consensus 799 s~~~lL~Cd--QCera-YHv~CL~~~~~~~~~g~WFCs~~Cq~ 838 (919)
+.+.|+.|| -|+++ ||..|++. ...|+|.|||+ .|+.
T Consensus 230 SyGqMVaCDn~nCkrEWFH~~CVGL--k~pPKG~WYC~-eCk~ 269 (271)
T COG5034 230 SYGQMVACDNANCKREWFHLECVGL--KEPPKGKWYCP-ECKK 269 (271)
T ss_pred ccccceecCCCCCchhheecccccc--CCCCCCcEeCH-HhHh
Confidence 347889998 79886 89999986 34568999995 5764
No 39
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=89.21 E-value=0.2 Score=63.42 Aligned_cols=45 Identities=27% Similarity=0.527 Sum_probs=34.0
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccccCccCCCCCCccccccc
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKGAVSEAWFCNQS 835 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~~~g~WFCs~~ 835 (919)
|.||.+.. ..+...+++||.|..++|..|+.- ...++|.|+|-+|
T Consensus 222 C~iC~~~~----~~n~n~ivfCD~Cnl~VHq~Cygi--~~ipeg~WlCr~C 266 (1051)
T KOG0955|consen 222 CCICLDGE----CQNSNVIVFCDGCNLAVHQECYGI--PFIPEGQWLCRRC 266 (1051)
T ss_pred ceeecccc----cCCCceEEEcCCCcchhhhhccCC--CCCCCCcEeehhh
Confidence 67777652 233467899999999999999992 3456899999643
No 40
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=87.47 E-value=0.17 Score=65.95 Aligned_cols=49 Identities=22% Similarity=0.612 Sum_probs=39.1
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccccCccCCCCCCcccccccchhHh
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKGAVSEAWFCNQSCQEVY 840 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~~~g~WFCs~~Cq~I~ 840 (919)
|.+|..... ...++.|++|...||..|+++.....+.+.|+|+. |..-+
T Consensus 1111 c~~cr~k~~------~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~-c~~e~ 1159 (1404)
T KOG1245|consen 1111 CKVCRRKKQ------DEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPS-CRKEH 1159 (1404)
T ss_pred hhhhhhccc------chhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCc-cchhh
Confidence 888887521 24688999999999999999988778899999986 44433
No 41
>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.
Probab=85.99 E-value=0.57 Score=42.52 Aligned_cols=41 Identities=29% Similarity=0.572 Sum_probs=37.9
Q ss_pred HcCceeccccCC--CccccceeeeCCCccccccchhHHHHhcc
Q 002464 290 AAGWAVERRKRP--SRKYMDTIYRSPEGRLFREFPKVWRVCGE 330 (919)
Q Consensus 290 ~agW~i~~r~R~--~r~~~~~~y~sp~~~~~r~~~~aWk~cG~ 330 (919)
..||+=|.+.|. +|.+.|-||.||-|+.+|+.+.+=+.+++
T Consensus 7 ~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~ 49 (73)
T cd01397 7 ELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSK 49 (73)
T ss_pred CCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHh
Confidence 479999998888 69999999999999999999999999986
No 42
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=84.67 E-value=0.63 Score=43.51 Aligned_cols=69 Identities=26% Similarity=0.599 Sum_probs=44.5
Q ss_pred cccccccC-CceeecCCCCCccccccccC-----------------CCCCCCCcccccccccccCCccCCccccCCCCcc
Q 002464 743 SCGICGDG-GELICCDNCPSAFHQACLSI-----------------QDLPTGSWFCSNCTCWICGDLVNDKEASSSFDAL 804 (919)
Q Consensus 743 ~C~VCgdG-GeLLcCD~CpraFHlsCL~~-----------------~~vPeG~W~Cp~C~C~iCge~~~Dke~~s~~~lL 804 (919)
.|.+|... |-|.. ..-....|..|... ..++...| .=.|.+|++. .+..+
T Consensus 2 ~C~lC~~~~Galk~-t~~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~---~~~C~iC~~~--------~G~~i 69 (110)
T PF13832_consen 2 SCVLCPKRGGALKR-TSDGQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRF---KLKCSICGKS--------GGACI 69 (110)
T ss_pred ccEeCCCCCCcccC-ccCCcEEEeEccceeCccEEeechhcCcccceeecchhc---CCcCcCCCCC--------CceeE
Confidence 47888764 44443 33577889999642 01111111 1237788875 25678
Q ss_pred ccCc--ccccCccccccCccC
Q 002464 805 KCSQ--CEHKYHGECLKDMSK 823 (919)
Q Consensus 805 ~CdQ--CeraYHv~CL~~~~~ 823 (919)
.|.. |.+.||+.|....+.
T Consensus 70 ~C~~~~C~~~fH~~CA~~~g~ 90 (110)
T PF13832_consen 70 KCSHPGCSTAFHPTCARKAGL 90 (110)
T ss_pred EcCCCCCCcCCCHHHHHHCCC
Confidence 9987 999999999987543
No 43
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=84.34 E-value=0.51 Score=40.69 Aligned_cols=35 Identities=31% Similarity=0.879 Sum_probs=28.3
Q ss_pred cccccccCCccCCccccCCCCccccCcccccCccccccCc
Q 002464 782 NCTCWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDM 821 (919)
Q Consensus 782 ~C~C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~ 821 (919)
.++|.+||+...+. ..+++|..|...||..|....
T Consensus 5 ~~~C~~Cg~~~~~~-----dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG-----DDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CccChhhCCcccCC-----CCEEECCCCCCcccHHHHhhC
Confidence 45799999986543 457999999999999998654
No 44
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=83.15 E-value=0.84 Score=53.55 Aligned_cols=45 Identities=29% Similarity=0.612 Sum_probs=31.1
Q ss_pred cccccccccccCCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 739 KNDDSCGICGDGGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 739 ~ndd~C~VCgdGGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
.+.++|++|.+||.+++|+.|+.++|..|... ..|...|.|..|.
T Consensus 87 ~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~-~~~~c~~~~~d~~ 131 (463)
T KOG1081|consen 87 IEPSECFVCFKGGSLVTCKSRIQAPHRKCKPA-QLEKCSKRCTDCR 131 (463)
T ss_pred CCcchhccccCCCccceeccccccccccCcCc-cCcccccCCccee
Confidence 46789999999999999997666666666654 2344444444443
No 45
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=77.92 E-value=0.93 Score=53.27 Aligned_cols=44 Identities=25% Similarity=0.505 Sum_probs=33.3
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccccCccCCCCCCcccccc
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKGAVSEAWFCNQ 834 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~~~g~WFCs~ 834 (919)
|.+|.....+ +...+++|+.|+-+.|..|++-. -.++|.|||-+
T Consensus 196 C~~c~~t~~e----N~naiVfCdgC~i~VHq~CYGI~--f~peG~WlCrk 239 (669)
T COG5141 196 CTKCTSTHNE----NSNAIVFCDGCEICVHQSCYGIQ--FLPEGFWLCRK 239 (669)
T ss_pred hHhccccccC----CcceEEEecCcchhhhhhcccce--ecCcchhhhhh
Confidence 5567665333 34789999999999999999864 34579999965
No 46
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=76.12 E-value=1.8 Score=50.58 Aligned_cols=62 Identities=23% Similarity=0.547 Sum_probs=41.6
Q ss_pred CcccccccccccCCccCCccccCCCCccccCcccccCccccccCccCC---C-C------CCcccccccchhHhh
Q 002464 777 SWFCSNCTCWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKG---A-V------SEAWFCNQSCQEVYS 841 (919)
Q Consensus 777 ~W~Cp~C~C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~---~-~------~g~WFCs~~Cq~I~e 841 (919)
+=||..|.|.+|++...+ .++-.-+.|+.|.++.|..|.=..... . . .+--|++..|....+
T Consensus 123 ~gFC~~C~C~iC~kfD~~---~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 123 PGFCRRCMCCICSKFDDN---KNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred CCccccCCccccCCcccC---CCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 347999999999985322 233456899999999999997554321 1 1 233466677886644
No 47
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=75.34 E-value=0.95 Score=52.49 Aligned_cols=76 Identities=18% Similarity=0.650 Sum_probs=45.6
Q ss_pred ccccccccC--CceeecCCCCCcccccccc-------CCCCC-----CCCccccccc-------ccccCCccCCccccCC
Q 002464 742 DSCGICGDG--GELICCDNCPSAFHQACLS-------IQDLP-----TGSWFCSNCT-------CWICGDLVNDKEASSS 800 (919)
Q Consensus 742 d~C~VCgdG--GeLLcCD~CpraFHlsCL~-------~~~vP-----eG~W~Cp~C~-------C~iCge~~~Dke~~s~ 800 (919)
+.|.+|+.. ..+| -.|+++||..|-. +..+| +..-||-.|- |.+|++++...++.+
T Consensus 335 ekC~~Cg~~I~d~iL--rA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~- 411 (468)
T KOG1701|consen 335 EKCNKCGEPIMDRIL--RALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKD- 411 (468)
T ss_pred HHHhhhhhHHHHHHH--HhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCc-
Confidence 456666642 2222 3578888888743 22232 3467777664 999999876544432
Q ss_pred CCccccCcccccCccccccCc
Q 002464 801 FDALKCSQCEHKYHGECLKDM 821 (919)
Q Consensus 801 ~~lL~CdQCeraYHv~CL~~~ 821 (919)
+.+.-.-=+|.||+.|++-.
T Consensus 412 -etvRvvamdr~fHv~CY~CE 431 (468)
T KOG1701|consen 412 -ETVRVVAMDRDFHVNCYKCE 431 (468)
T ss_pred -ceEEEEEccccccccceehh
Confidence 12233334788999998753
No 48
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=75.11 E-value=1.4 Score=53.71 Aligned_cols=47 Identities=23% Similarity=0.737 Sum_probs=34.7
Q ss_pred ccccCCccCCccccCCCCccccC--cccccCccccccCccCCCCCCcccccccchh
Q 002464 785 CWICGDLVNDKEASSSFDALKCS--QCEHKYHGECLKDMSKGAVSEAWFCNQSCQE 838 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~Cd--QCeraYHv~CL~~~~~~~~~g~WFCs~~Cq~ 838 (919)
|.+|-+ ..+.....++.|| .|.-+.|+.|+... ..+.|.|||- .|..
T Consensus 8 CCVCSD----ErGWaeNPLVYCDG~nCsVAVHQaCYGIv--qVPtGpWfCr-KCes 56 (900)
T KOG0956|consen 8 CCVCSD----ERGWAENPLVYCDGHNCSVAVHQACYGIV--QVPTGPWFCR-KCES 56 (900)
T ss_pred eeeecC----cCCCccCceeeecCCCceeeeehhcceeE--ecCCCchhhh-hhhh
Confidence 555653 3345567899998 89999999999863 4668999995 4653
No 49
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=68.97 E-value=2.5 Score=36.59 Aligned_cols=29 Identities=28% Similarity=1.011 Sum_probs=25.6
Q ss_pred cccccccc----CCceeecCCCCCccccccccC
Q 002464 742 DSCGICGD----GGELICCDNCPSAFHQACLSI 770 (919)
Q Consensus 742 d~C~VCgd----GGeLLcCD~CpraFHlsCL~~ 770 (919)
..|.+|++ +++++.|..|...||..|...
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 57999986 789999999999999999854
No 50
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=68.80 E-value=2 Score=40.20 Aligned_cols=27 Identities=22% Similarity=0.584 Sum_probs=17.7
Q ss_pred CCCCccccccccC-CCCCCCCccccccc
Q 002464 758 NCPSAFHQACLSI-QDLPTGSWFCSNCT 784 (919)
Q Consensus 758 ~CpraFHlsCL~~-~~vPeG~W~Cp~C~ 784 (919)
.|...||..|+.. -..+...=.||.|+
T Consensus 51 ~C~H~FH~hCI~kWl~~~~~~~~CPmCR 78 (85)
T PF12861_consen 51 KCSHNFHMHCILKWLSTQSSKGQCPMCR 78 (85)
T ss_pred cCccHHHHHHHHHHHccccCCCCCCCcC
Confidence 4999999999874 11122233677776
No 51
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=65.22 E-value=1.5 Score=55.87 Aligned_cols=47 Identities=23% Similarity=0.293 Sum_probs=41.6
Q ss_pred ccccccccccccCCceeecCC-CCCcccc-ccccC----CCCCCCCccccccc
Q 002464 738 DKNDDSCGICGDGGELICCDN-CPSAFHQ-ACLSI----QDLPTGSWFCSNCT 784 (919)
Q Consensus 738 d~ndd~C~VCgdGGeLLcCD~-CpraFHl-sCL~~----~~vPeG~W~Cp~C~ 784 (919)
.-+.+.|.+|+..+.++||++ ||..||+ .|++- ..++++-|+|+.|.
T Consensus 425 wfi~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~ 477 (1414)
T KOG1473|consen 425 WFISRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEI 477 (1414)
T ss_pred hceeeeeEEecCCCcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHH
Confidence 345678999999999999997 9999998 99993 57899999999997
No 52
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=64.00 E-value=2.9 Score=37.17 Aligned_cols=28 Identities=46% Similarity=1.010 Sum_probs=11.5
Q ss_pred cccccccc----CCc--eeecC--CCCCcccccccc
Q 002464 742 DSCGICGD----GGE--LICCD--NCPSAFHQACLS 769 (919)
Q Consensus 742 d~C~VCgd----GGe--LLcCD--~CpraFHlsCL~ 769 (919)
..|.||.. .++ .+.|+ .|...||..||.
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~ 38 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLS 38 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGH
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHH
Confidence 46888865 232 47798 899999999996
No 53
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=62.82 E-value=2.6 Score=33.36 Aligned_cols=33 Identities=21% Similarity=0.601 Sum_probs=16.9
Q ss_pred CCccccCcccccCccccccCccCCCCCCcccccc
Q 002464 801 FDALKCSQCEHKYHGECLKDMSKGAVSEAWFCNQ 834 (919)
Q Consensus 801 ~~lL~CdQCeraYHv~CL~~~~~~~~~g~WFCs~ 834 (919)
+.++.|+.|.-..|..|++-..... ...|+|-.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~-~~~W~C~~ 34 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPD-GDDWLCDR 34 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--S-S-----HH
T ss_pred CceEEeCCCCCcCChhhCCcccCCC-CCcEECCc
Confidence 3578999999999999999754332 33599953
No 54
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=61.29 E-value=3.5 Score=50.75 Aligned_cols=32 Identities=19% Similarity=0.541 Sum_probs=25.4
Q ss_pred CCccccCcccccCccccccCccCCCCCCcccccc
Q 002464 801 FDALKCSQCEHKYHGECLKDMSKGAVSEAWFCNQ 834 (919)
Q Consensus 801 ~~lL~CdQCeraYHv~CL~~~~~~~~~g~WFCs~ 834 (919)
..|++|+.|.-..|..|+.. .+.+.+.|.|..
T Consensus 286 neMVfCd~Cn~cVHqaCyGI--le~p~gpWlCr~ 317 (893)
T KOG0954|consen 286 NEMVFCDKCNICVHQACYGI--LEVPEGPWLCRT 317 (893)
T ss_pred ceeEEeccchhHHHHhhhce--eecCCCCeeehh
Confidence 56888999999999999885 345578999964
No 55
>smart00258 SAND SAND domain.
Probab=59.94 E-value=5.3 Score=36.48 Aligned_cols=38 Identities=24% Similarity=0.468 Sum_probs=26.1
Q ss_pred CeEeccc---CcccchhhhhhhcCCCCCcccc-cccccCCCcc
Q 002464 670 GIICKCC---NLVFSVSQFKIHAGFKPNRPCL-NLVMESGKPF 708 (919)
Q Consensus 670 GI~C~CC---~kv~SpS~FE~HAG~~~rRP~~-nI~LedGkSL 708 (919)
||.+.|- ++.|||++||.+||.....-|. +|.+ +|.+|
T Consensus 22 G~~~kCI~~~~~~~TP~eFe~~~g~~~~K~WK~sIR~-~g~~L 63 (73)
T smart00258 22 GISVKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRC-GGSSL 63 (73)
T ss_pred CcccCCccCCCEEEChHHHHhhcCCcccCCcchheeE-CCccH
Confidence 6665553 6889999999999987765553 3433 35554
No 56
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=59.79 E-value=4.3 Score=38.97 Aligned_cols=35 Identities=29% Similarity=0.783 Sum_probs=23.8
Q ss_pred CCCCCccccccccC-------CCCCCCCccccccc----ccccCCc
Q 002464 757 DNCPSAFHQACLSI-------QDLPTGSWFCSNCT----CWICGDL 791 (919)
Q Consensus 757 D~CpraFHlsCL~~-------~~vPeG~W~Cp~C~----C~iCge~ 791 (919)
..|...|-..||-- +.+.++.|.||.|+ |..|.+.
T Consensus 34 ~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCnCs~Crrk 79 (105)
T PF10497_consen 34 RGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICNCSFCRRK 79 (105)
T ss_pred ccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeCCHhhhcc
Confidence 33466777777642 33457789999998 7777664
No 57
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=56.40 E-value=3 Score=44.72 Aligned_cols=61 Identities=28% Similarity=0.592 Sum_probs=38.5
Q ss_pred CceeecCCCCCcc--------ccccccCCCCCCCCcccccccccccCCccCCccc-------cCCCCccccCcccccCcc
Q 002464 751 GELICCDNCPSAF--------HQACLSIQDLPTGSWFCSNCTCWICGDLVNDKEA-------SSSFDALKCSQCEHKYHG 815 (919)
Q Consensus 751 GeLLcCD~CpraF--------HlsCL~~~~vPeG~W~Cp~C~C~iCge~~~Dke~-------~s~~~lL~CdQCeraYHv 815 (919)
++...|+.|.+.| |+.|...- ....|.+||+..+|--. -.+..-+.|.+|+++|-.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~v---------kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDV---------KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHH---------HHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 5666777777777 55555431 12348889986543111 112345899999999999
Q ss_pred ccccC
Q 002464 816 ECLKD 820 (919)
Q Consensus 816 ~CL~~ 820 (919)
.|--+
T Consensus 186 rcsle 190 (267)
T KOG3576|consen 186 RCSLE 190 (267)
T ss_pred hccHH
Confidence 88644
No 58
>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=56.17 E-value=2.3 Score=33.80 Aligned_cols=38 Identities=29% Similarity=0.747 Sum_probs=23.8
Q ss_pred cccccccc----CCceeecCCCCCccccccccC--CCCCCCCccccccc
Q 002464 742 DSCGICGD----GGELICCDNCPSAFHQACLSI--QDLPTGSWFCSNCT 784 (919)
Q Consensus 742 d~C~VCgd----GGeLLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~ 784 (919)
|.|.||.+ +..++.. .|+..||..|+.. ... -.||.|+
T Consensus 1 d~C~IC~~~~~~~~~~~~l-~C~H~fh~~Ci~~~~~~~----~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKL-PCGHVFHRSCIKEWLKRN----NSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEE-TTSEEEEHHHHHHHHHHS----SB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEc-cCCCeeCHHHHHHHHHhC----CcCCccC
Confidence 46888876 2344444 4999999999874 221 2677774
No 59
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=55.92 E-value=4.8 Score=47.27 Aligned_cols=65 Identities=26% Similarity=0.502 Sum_probs=39.8
Q ss_pred cccccccccccC----CceeecCCCCCccccccccCCCCCCCCccccccc------------ccccCCccCCccccCCCC
Q 002464 739 KNDDSCGICGDG----GELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT------------CWICGDLVNDKEASSSFD 802 (919)
Q Consensus 739 ~ndd~C~VCgdG----GeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~------------C~iCge~~~Dke~~s~~~ 802 (919)
.....|.||-.. -..|.---|..+||-.|+.. -++-.||-|+ |..|+.. ..
T Consensus 173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~----w~~~scpvcR~~q~p~~ve~~~c~~c~~~---------~~ 239 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMK----WWDSSCPVCRYCQSPSVVESSLCLACGCT---------ED 239 (493)
T ss_pred ccCCCcchhHhhcCccccceeeeecccccchHHHhh----cccCcChhhhhhcCcchhhhhhhhhhccc---------cc
Confidence 345789999752 12344456899999999864 2223466665 5555543 34
Q ss_pred ccccCcccccCcccccc
Q 002464 803 ALKCSQCEHKYHGECLK 819 (919)
Q Consensus 803 lL~CdQCeraYHv~CL~ 819 (919)
+..|--|+ |++|-+
T Consensus 240 LwicliCg---~vgcgr 253 (493)
T KOG0804|consen 240 LWICLICG---NVGCGR 253 (493)
T ss_pred EEEEEEcc---ceeccc
Confidence 56677665 555544
No 60
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=54.48 E-value=6.2 Score=41.21 Aligned_cols=36 Identities=31% Similarity=0.611 Sum_probs=26.6
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccccCccC
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSK 823 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~ 823 (919)
|..|+....+ ...+.++.|..|..+||..||.+...
T Consensus 2 C~~C~~~g~~---~~kG~Lv~CQGCs~sYHk~CLG~Rs~ 37 (175)
T PF15446_consen 2 CDTCGYEGDD---RNKGPLVYCQGCSSSYHKACLGPRSQ 37 (175)
T ss_pred cccccCCCCC---ccCCCeEEcCccChHHHhhhcCCccc
Confidence 6677643222 22368999999999999999998654
No 61
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=53.92 E-value=6.5 Score=36.78 Aligned_cols=31 Identities=42% Similarity=0.981 Sum_probs=26.6
Q ss_pred cccccccccc-CCceeecCC--CCCccccccccC
Q 002464 740 NDDSCGICGD-GGELICCDN--CPSAFHQACLSI 770 (919)
Q Consensus 740 ndd~C~VCgd-GGeLLcCD~--CpraFHlsCL~~ 770 (919)
....|.+|+. +|-.+-|.. |..+||+.|...
T Consensus 54 ~~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKSGGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHH
Confidence 4578999998 688999987 999999999753
No 62
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=53.09 E-value=8.2 Score=43.96 Aligned_cols=60 Identities=28% Similarity=0.485 Sum_probs=45.8
Q ss_pred CccccCcccccCcccc--ccCccCCCC-CCcccccccchhHhhhhhcccccccCCCCCcceeec
Q 002464 802 DALKCSQCEHKYHGEC--LKDMSKGAV-SEAWFCNQSCQEVYSGLHSHIGIINHAADGFSWTLL 862 (919)
Q Consensus 802 ~lL~CdQCeraYHv~C--L~~~~~~~~-~g~WFCs~~Cq~I~e~LqklVGv~nei~dg~sWtLL 862 (919)
.+..|+.|+.+||..| ++......+ ...|+| ..|+....+++..-+........++|.+.
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c-~~c~~~~~~~~~~~~l~~~~~~~~~~~~s 136 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVC-DECKEAQDGMSESDGLSCVCRQDDSELLS 136 (345)
T ss_pred hhhccccccccccccccccCchhhcCCccccccc-cccchhhhhhhhhccceeecccccccccc
Confidence 4578999999999999 877665555 789999 78999988777765555555555666644
No 63
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=52.57 E-value=4.5 Score=36.34 Aligned_cols=32 Identities=25% Similarity=0.636 Sum_probs=24.5
Q ss_pred cccccCCccCCccccCCCCccccC--cccccCccccccCccC
Q 002464 784 TCWICGDLVNDKEASSSFDALKCS--QCEHKYHGECLKDMSK 823 (919)
Q Consensus 784 ~C~iCge~~~Dke~~s~~~lL~Cd--QCeraYHv~CL~~~~~ 823 (919)
.|.+|++. .+..+.|. .|.+.||+.|......
T Consensus 38 ~C~~C~~~--------~Ga~i~C~~~~C~~~fH~~CA~~~~~ 71 (90)
T PF13771_consen 38 KCSICKKK--------GGACIGCSHPGCSRSFHVPCARKAGC 71 (90)
T ss_pred CCcCCCCC--------CCeEEEEeCCCCCcEEChHHHccCCe
Confidence 47888865 25568896 5999999999987643
No 64
>PF07897 DUF1675: Protein of unknown function (DUF1675); InterPro: IPR012463 The members of this family are sequences derived from hypothetical plant proteins of unknown function. One member of this family (Q9SFV5 from SWISSPROT) is annotated as a putative RNA-binding protein, but no evidence was found to support this.
Probab=51.94 E-value=18 Score=40.57 Aligned_cols=30 Identities=30% Similarity=0.523 Sum_probs=25.4
Q ss_pred eEecccCcccchhhhhhhcCCCCCc-ccccc
Q 002464 671 IICKCCNLVFSVSQFKIHAGFKPNR-PCLNL 700 (919)
Q Consensus 671 I~C~CC~kv~SpS~FE~HAG~~~rR-P~~nI 700 (919)
|+|.|-+.-++|.+|-.|||....- |-.+|
T Consensus 253 i~c~chg~~~~~~efv~h~~~~~~~~p~~hi 283 (284)
T PF07897_consen 253 IVCVCHGSFLSPAEFVKHAGGGDVANPLRHI 283 (284)
T ss_pred EEEEecCCCCCHHHHHHhcCCCCcCCchhcc
Confidence 8999999999999999999986543 65555
No 65
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=51.57 E-value=9.7 Score=40.09 Aligned_cols=35 Identities=20% Similarity=0.520 Sum_probs=23.2
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccccC
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKD 820 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~ 820 (919)
|.+|.... -.-+.....+..|..|..-||..|...
T Consensus 155 Ce~C~~~~-~IfPF~~~~~~~C~~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 155 CEICNSDD-IIFPFQIDTTVRCPKCKSVFHKSCFRK 189 (202)
T ss_pred CccCCCCC-CCCCCCCCCeeeCCcCccccchhhcCC
Confidence 66665431 011222346789999999999999984
No 66
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.69 E-value=9.9 Score=43.56 Aligned_cols=43 Identities=30% Similarity=0.652 Sum_probs=28.2
Q ss_pred cccccccc---CCceeecCCCCCccccccccCCCCCCCCcccccccc
Q 002464 742 DSCGICGD---GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCTC 785 (919)
Q Consensus 742 d~C~VCgd---GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~C 785 (919)
+.|.||-+ .|+.+-==-|...||..|+++=-... .=+||-|++
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~-r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT-RTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc-CccCCCCCC
Confidence 79999987 35444334689999999998711111 224666665
No 67
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=50.24 E-value=8 Score=34.75 Aligned_cols=30 Identities=33% Similarity=0.826 Sum_probs=26.0
Q ss_pred cccccccccC-CceeecC--CCCCccccccccC
Q 002464 741 DDSCGICGDG-GELICCD--NCPSAFHQACLSI 770 (919)
Q Consensus 741 dd~C~VCgdG-GeLLcCD--~CpraFHlsCL~~ 770 (919)
...|.+|+.. |-.+-|. +|...||..|...
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHcc
Confidence 4689999998 9999997 5999999999753
No 68
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=49.21 E-value=2.9 Score=48.66 Aligned_cols=70 Identities=23% Similarity=0.601 Sum_probs=49.2
Q ss_pred cccccccc--CCceeecCCCCCccccccccC-------C----CCCCCCccccccc------ccccCCccCCccccCCCC
Q 002464 742 DSCGICGD--GGELICCDNCPSAFHQACLSI-------Q----DLPTGSWFCSNCT------CWICGDLVNDKEASSSFD 802 (919)
Q Consensus 742 d~C~VCgd--GGeLLcCD~CpraFHlsCL~~-------~----~vPeG~W~Cp~C~------C~iCge~~~Dke~~s~~~ 802 (919)
..|.-|+. .|+-.-|..=.+.||..|-.- . -.-++.-||..|- |..|++.+.|+
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~------- 347 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDR------- 347 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHH-------
Confidence 48999987 466666777788899988642 1 1236678898885 99999876442
Q ss_pred ccccCcccccCccccccC
Q 002464 803 ALKCSQCEHKYHGECLKD 820 (919)
Q Consensus 803 lL~CdQCeraYHv~CL~~ 820 (919)
| =.-|+++||..|+.-
T Consensus 348 i--LrA~GkayHp~CF~C 363 (468)
T KOG1701|consen 348 I--LRALGKAYHPGCFTC 363 (468)
T ss_pred H--HHhcccccCCCceEE
Confidence 2 246788899888753
No 69
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=45.75 E-value=8.1 Score=35.63 Aligned_cols=35 Identities=26% Similarity=0.517 Sum_probs=23.9
Q ss_pred eEecccCcccchhhhhhhcCCCCCccc-ccccccCCCcc
Q 002464 671 IICKCCNLVFSVSQFKIHAGFKPNRPC-LNLVMESGKPF 708 (919)
Q Consensus 671 I~C~CC~kv~SpS~FE~HAG~~~rRP~-~nI~LedGkSL 708 (919)
|.+. ++.+||++||.|||....+-| .+|.+ .|.+|
T Consensus 37 I~~~--g~~~TP~eFE~~~G~~~sK~WK~SIr~-~g~~L 72 (82)
T PF01342_consen 37 IQCE--GRWFTPSEFERHGGKGSSKDWKRSIRC-GGEPL 72 (82)
T ss_dssp EEET--TEEE-HHHHHHHHTTCTCS-HHHHSEE-TTEEH
T ss_pred EeeC--CcEECHHHHHhhcCcccCCCCCccEEE-CCEEH
Confidence 4455 899999999999999877544 34555 55554
No 70
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=44.93 E-value=16 Score=38.46 Aligned_cols=38 Identities=29% Similarity=0.846 Sum_probs=28.9
Q ss_pred ccccccccccCC--------ceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 740 NDDSCGICGDGG--------ELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgdGG--------eLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
....|.+|.+.+ ....|..|...||..|.... .||.|.
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~~-------~CpkC~ 196 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRKK-------SCPKCA 196 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCCC-------CCCCcH
Confidence 356888998643 57889999999999999741 277774
No 71
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=44.38 E-value=15 Score=46.52 Aligned_cols=50 Identities=32% Similarity=0.847 Sum_probs=40.5
Q ss_pred ccccccccccCCc--eeecCCCCCccccccccC--CCCCCCCcccccccccccC
Q 002464 740 NDDSCGICGDGGE--LICCDNCPSAFHQACLSI--QDLPTGSWFCSNCTCWICG 789 (919)
Q Consensus 740 ndd~C~VCgdGGe--LLcCD~CpraFHlsCL~~--~~vPeG~W~Cp~C~C~iCg 789 (919)
....|..|..+.+ ++.|++|...||..|..+ +.+++|.|.|+.|...-|.
T Consensus 154 ~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 207 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEEKLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPTPES 207 (904)
T ss_pred cchhhhccccCCCccceecccccCcccccccCCCCCcCCcCcccCCcccccccC
Confidence 4467888987662 349999999999999986 7889999999999866444
No 72
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.99 E-value=28 Score=42.09 Aligned_cols=46 Identities=22% Similarity=0.278 Sum_probs=38.3
Q ss_pred cccccccccccCCceeecCCCCCccccccccC-CCCC--CCCccccccc
Q 002464 739 KNDDSCGICGDGGELICCDNCPSAFHQACLSI-QDLP--TGSWFCSNCT 784 (919)
Q Consensus 739 ~ndd~C~VCgdGGeLLcCD~CpraFHlsCL~~-~~vP--eG~W~Cp~C~ 784 (919)
..+.+|+.|.-.|..+-|+.|-+.||..|+.+ .+.+ ...|.|+.|.
T Consensus 58 N~d~~cfechlpg~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~ 106 (588)
T KOG3612|consen 58 NIDPFCFECHLPGAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPY 106 (588)
T ss_pred CCCcccccccCCcceeeeehhhccccccccCcchhhccccccccCCccc
Confidence 45678999999999999999999999999987 3333 3479999887
No 73
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=37.04 E-value=21 Score=42.47 Aligned_cols=30 Identities=33% Similarity=0.857 Sum_probs=17.8
Q ss_pred ceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 752 ELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 752 eLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
+|.+|..|...=...|+..+ -..||||.|.
T Consensus 4 ~L~fC~~C~~irc~~c~~~E---i~~~yCp~CL 33 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPRCVSEE---IDSYYCPNCL 33 (483)
T ss_pred cceecccccccCChhhcccc---cceeECcccc
Confidence 46667776665555555432 2357777775
No 74
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=36.70 E-value=19 Score=32.08 Aligned_cols=35 Identities=29% Similarity=0.637 Sum_probs=13.3
Q ss_pred cccccCCccCCccccCCCCccccC--cccccCccccccCc
Q 002464 784 TCWICGDLVNDKEASSSFDALKCS--QCEHKYHGECLKDM 821 (919)
Q Consensus 784 ~C~iCge~~~Dke~~s~~~lL~Cd--QCeraYHv~CL~~~ 821 (919)
.|.||.....+.+ ....+.|+ +|.+.||..||..-
T Consensus 4 ~C~IC~~~~~~~~---~~p~~~C~n~~C~~~fH~~CL~~w 40 (70)
T PF11793_consen 4 ECGICYSYRLDDG---EIPDVVCPNPSCGKKFHLLCLSEW 40 (70)
T ss_dssp S-SSS--SS-TT--------B--S-TT----B-SGGGHHH
T ss_pred CCCcCCcEecCCC---CcCceEcCCcccCCHHHHHHHHHH
Confidence 3778876543211 13458897 99999999999753
No 75
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=35.92 E-value=15 Score=44.67 Aligned_cols=52 Identities=27% Similarity=0.678 Sum_probs=33.0
Q ss_pred cccccc-----ccccCCc--cCCccccCCCCccccCcccccCccccccCccCCCCCCcccccccchhHhh
Q 002464 779 FCSNCT-----CWICGDL--VNDKEASSSFDALKCSQCEHKYHGECLKDMSKGAVSEAWFCNQSCQEVYS 841 (919)
Q Consensus 779 ~Cp~C~-----C~iCge~--~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~~~g~WFCs~~Cq~I~e 841 (919)
.|..|. |.+|... ++. +...+...|.+|...||..|+.-... -|| .|..+.+
T Consensus 503 ~C~lC~~~gfiCe~Cq~~~iiyP---F~~~~~~rC~~C~avfH~~C~~r~s~-------~CP-rC~R~q~ 561 (580)
T KOG1829|consen 503 ECDLCTGKGFICELCQHNDIIYP---FETRNTRRCSTCLAVFHKKCLRRKSP-------CCP-RCERRQK 561 (580)
T ss_pred hchhhccCeeeeeeccCCCcccc---cccccceeHHHHHHHHHHHHHhccCC-------CCC-chHHHHH
Confidence 366665 6677322 121 11346788999999999999986421 166 4776654
No 76
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=35.45 E-value=20 Score=25.71 Aligned_cols=9 Identities=56% Similarity=1.590 Sum_probs=7.4
Q ss_pred CCccccccc
Q 002464 776 GSWFCSNCT 784 (919)
Q Consensus 776 G~W~Cp~C~ 784 (919)
|+|.|+.|.
T Consensus 1 g~W~C~~C~ 9 (26)
T smart00547 1 GDWECPACT 9 (26)
T ss_pred CcccCCCCC
Confidence 579999885
No 77
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=34.01 E-value=18 Score=27.02 Aligned_cols=10 Identities=50% Similarity=1.487 Sum_probs=8.4
Q ss_pred CCCccccccc
Q 002464 775 TGSWFCSNCT 784 (919)
Q Consensus 775 eG~W~Cp~C~ 784 (919)
.|+|.|+.|.
T Consensus 2 ~g~W~C~~C~ 11 (30)
T PF00641_consen 2 EGDWKCPSCT 11 (30)
T ss_dssp SSSEEETTTT
T ss_pred CcCccCCCCc
Confidence 5799998887
No 78
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=32.60 E-value=21 Score=43.81 Aligned_cols=80 Identities=28% Similarity=0.684 Sum_probs=51.7
Q ss_pred cccccccccccC-CceeecCCCCCccccccccC---C------------CCCCCCccccccc---ccccCCccCCccccC
Q 002464 739 KNDDSCGICGDG-GELICCDNCPSAFHQACLSI---Q------------DLPTGSWFCSNCT---CWICGDLVNDKEASS 799 (919)
Q Consensus 739 ~ndd~C~VCgdG-GeLLcCD~CpraFHlsCL~~---~------------~vPeG~W~Cp~C~---C~iCge~~~Dke~~s 799 (919)
....+|.+|+.+ +..++|+-|+...|..|+.- + .+-...|.+-.+. |..|..... ...
T Consensus 114 ~c~~~c~~~~~~~~~g~~C~~C~~~vh~~C~~~~~~~~~~~~~~~~~r~~v~~~~~~~~~~~~~~~~~~~~~~~---~~~ 190 (634)
T KOG1169|consen 114 VCPKSCGSCGVGIKQGLCCDWCGRTVHERCVRRADPECQCKCDLGRLRKIVLDHPWVKGNAGEAKCDQCLKSVK---ADQ 190 (634)
T ss_pred eccccccchhhcccCceeeccccchHHHHHHhhcCcccccccccccccceeecCcccccccCCccchhhhcccc---ccc
Confidence 344567777765 57899999999999999863 1 1113345555553 444443321 122
Q ss_pred CCCccccCcccccCccccccCc
Q 002464 800 SFDALKCSQCEHKYHGECLKDM 821 (919)
Q Consensus 800 ~~~lL~CdQCeraYHv~CL~~~ 821 (919)
+.+...|..|-+.+|..|....
T Consensus 191 ~~~~~~c~~~~~~~h~~~~~~~ 212 (634)
T KOG1169|consen 191 GLTGPRCGWCQIRVHDKCKSEL 212 (634)
T ss_pred cccccccceeeeeeecchHHHH
Confidence 3457789999999999997643
No 79
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=32.15 E-value=28 Score=39.66 Aligned_cols=35 Identities=23% Similarity=0.561 Sum_probs=24.1
Q ss_pred cCCccCCccccCCCCccccCcccccCc-cccccCcc
Q 002464 788 CGDLVNDKEASSSFDALKCSQCEHKYH-GECLKDMS 822 (919)
Q Consensus 788 Cge~~~Dke~~s~~~lL~CdQCeraYH-v~CL~~~~ 822 (919)
|..+..+....-.+.++.|-.|+-+|| .+|++...
T Consensus 133 Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~~~ 168 (345)
T KOG2752|consen 133 CDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQAKT 168 (345)
T ss_pred ecCCCCCccccccceeeeEEeccchhcccccCcccc
Confidence 445444322223467899999999999 89988653
No 80
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=29.85 E-value=23 Score=44.16 Aligned_cols=41 Identities=29% Similarity=0.644 Sum_probs=32.5
Q ss_pred CCCccccccc------ccccCCccCCccccCCCCccccCcccccCccccccCcc
Q 002464 775 TGSWFCSNCT------CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMS 822 (919)
Q Consensus 775 eG~W~Cp~C~------C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~ 822 (919)
.+.|+|..|. |.+|+..+. +...-|.+|++.=|..|+..-.
T Consensus 766 ~~~~~c~rc~s~a~~~CtVC~~vi~-------G~~~~c~~C~H~gH~sh~~sw~ 812 (839)
T KOG0269|consen 766 TKLWQCDRCESRASAKCTVCDLVIR-------GVDVWCQVCGHGGHDSHLKSWF 812 (839)
T ss_pred ccceeechHHHHhhcCceeecceee-------eeEeecccccccccHHHHHHHH
Confidence 3349999997 999998753 3457899999999999998643
No 81
>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=29.36 E-value=20 Score=32.01 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=16.1
Q ss_pred CCCCCccccccccC--CCCCCCCccccccc
Q 002464 757 DNCPSAFHQACLSI--QDLPTGSWFCSNCT 784 (919)
Q Consensus 757 D~CpraFHlsCL~~--~~vPeG~W~Cp~C~ 784 (919)
..|+..||..|+.. ... ..||.|+
T Consensus 48 ~~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp ETTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred cccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 35999999999973 222 2677774
No 82
>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=29.10 E-value=21 Score=26.70 Aligned_cols=28 Identities=32% Similarity=0.789 Sum_probs=12.0
Q ss_pred ccccCCccCCccccCCCCccccCcccccCccccc
Q 002464 785 CWICGDLVNDKEASSSFDALKCSQCEHKYHGECL 818 (919)
Q Consensus 785 C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL 818 (919)
|..|+++... ...+.|.+|+-..|..|.
T Consensus 3 C~~C~~~~~~------~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 3 CDACGKPIDG------GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp -TTTS----S--------EEE-TTT-----HHHH
T ss_pred CCcCCCcCCC------CceEECccCCCccChhcC
Confidence 6778876321 357899999999999884
No 83
>PLN03086 PRLI-interacting factor K; Provisional
Probab=27.90 E-value=41 Score=41.05 Aligned_cols=27 Identities=11% Similarity=0.425 Sum_probs=21.9
Q ss_pred cCCeEecccCcccchhhhhhhcCCCCC
Q 002464 668 NNGIICKCCNLVFSVSQFKIHAGFKPN 694 (919)
Q Consensus 668 ~~GI~C~CC~kv~SpS~FE~HAG~~~r 694 (919)
.+-++|..|...+....++.|-.+-.+
T Consensus 405 ~~~V~C~NC~~~i~l~~l~lHe~~C~r 431 (567)
T PLN03086 405 VDTVECRNCKHYIPSRSIALHEAYCSR 431 (567)
T ss_pred CCeEECCCCCCccchhHHHHHHhhCCC
Confidence 445789999999999999999765443
No 84
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.47 E-value=19 Score=40.31 Aligned_cols=34 Identities=26% Similarity=0.575 Sum_probs=22.5
Q ss_pred CccccccccccccCC------c----eeecCCCCCccccccccC
Q 002464 737 DDKNDDSCGICGDGG------E----LICCDNCPSAFHQACLSI 770 (919)
Q Consensus 737 ~d~ndd~C~VCgdGG------e----LLcCD~CpraFHlsCL~~ 770 (919)
...++..|.+|++.= + -+.==.|...||..|..-
T Consensus 220 khl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrG 263 (328)
T KOG1734|consen 220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRG 263 (328)
T ss_pred CCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhh
Confidence 345778999998721 1 111125899999999864
No 85
>PLN02400 cellulose synthase
Probab=27.43 E-value=54 Score=42.67 Aligned_cols=45 Identities=29% Similarity=0.835 Sum_probs=35.9
Q ss_pred ccccccccccc-------CCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 739 KNDDSCGICGD-------GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 739 ~ndd~C~VCgd-------GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
.+...|+|||| |.--+.|..|.-...-.|+.- +..+|.=.||+|+
T Consensus 34 ~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEY-ERkeGnq~CPQCk 85 (1085)
T PLN02400 34 LNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEY-ERKDGTQCCPQCK 85 (1085)
T ss_pred cCCceeeecccccCcCCCCCEEEEEccCCCccccchhhe-ecccCCccCcccC
Confidence 46679999998 334688999988887888844 5678888999998
No 86
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=26.75 E-value=27 Score=35.16 Aligned_cols=29 Identities=21% Similarity=0.547 Sum_probs=20.9
Q ss_pred CCcccccccchhHhhhhhcccccccCCCCCcceeece
Q 002464 827 SEAWFCNQSCQEVYSGLHSHIGIINHAADGFSWTLLR 863 (919)
Q Consensus 827 ~g~WFCs~~Cq~I~e~LqklVGv~nei~dg~sWtLLr 863 (919)
..-|||+..|...|. ....+..+.||.+-
T Consensus 28 kvf~FcssKC~k~f~--------~kRnPRKlkWT~~y 56 (131)
T PRK14891 28 TVLHFVDSKCEKNYD--------LGREARDLEWTEAG 56 (131)
T ss_pred CEEEEecHHHHHHHH--------ccCCCccchhHHHH
Confidence 567999999988874 12234578999883
No 87
>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
Probab=25.82 E-value=56 Score=28.97 Aligned_cols=41 Identities=24% Similarity=0.447 Sum_probs=32.1
Q ss_pred cCceeccccCC-CccccceeeeCCCccccccchhHHHHhccc
Q 002464 291 AGWAVERRKRP-SRKYMDTIYRSPEGRLFREFPKVWRVCGEN 331 (919)
Q Consensus 291 agW~i~~r~R~-~r~~~~~~y~sp~~~~~r~~~~aWk~cG~~ 331 (919)
-||.=..++|+ +.-+-+=+|+||-|+.+|.++.+=+.+=++
T Consensus 8 ~gw~R~~~~~~~~~~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t 49 (60)
T cd01395 8 CGFQRMKYRARVGKVKKHVIYKAPCGRSLRNMSEVHRYLRET 49 (60)
T ss_pred cCeEEEEEeccCCCcccceEEECCcchhhhcHHHHHHHHHhc
Confidence 58987777776 345666899999999999999887776544
No 88
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.34 E-value=45 Score=43.14 Aligned_cols=34 Identities=21% Similarity=0.544 Sum_probs=24.6
Q ss_pred ccccccccccCCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 740 NDDSCGICGDGGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 740 ndd~C~VCgdGGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
....|..||..+....|..|+.. +...|+||.|.
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~-----------Te~i~fCP~CG 658 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTH-----------TEPVYRCPRCG 658 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCC-----------CCcceeCcccc
Confidence 45689999988777778888753 34457788875
No 89
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.88 E-value=52 Score=40.71 Aligned_cols=43 Identities=28% Similarity=0.845 Sum_probs=0.0
Q ss_pred eeecCCCCCccccccccCCCCCCCCccccccc-------ccccCCccCCccccCCCCccccCccccc
Q 002464 753 LICCDNCPSAFHQACLSIQDLPTGSWFCSNCT-------CWICGDLVNDKEASSSFDALKCSQCEHK 812 (919)
Q Consensus 753 LLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~-------C~iCge~~~Dke~~s~~~lL~CdQCera 812 (919)
|+.|-.|+. ..|.+.-||+.|- |..||.. .....-+|..|+..
T Consensus 1 M~~Cp~Cg~----------~n~~~akFC~~CG~~l~~~~Cp~CG~~-------~~~~~~fC~~CG~~ 50 (645)
T PRK14559 1 MLICPQCQF----------ENPNNNRFCQKCGTSLTHKPCPQCGTE-------VPVDEAHCPNCGAE 50 (645)
T ss_pred CCcCCCCCC----------cCCCCCccccccCCCCCCCcCCCCCCC-------CCcccccccccCCc
No 90
>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=24.50 E-value=20 Score=26.86 Aligned_cols=40 Identities=25% Similarity=0.503 Sum_probs=24.2
Q ss_pred ccccccCC-ceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 744 CGICGDGG-ELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 744 C~VCgdGG-eLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
|.+|.+.- +.+.-..|+..||..|+..-.. .+...||.|+
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~-~~~~~Cp~C~ 42 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK-SGKNTCPLCR 42 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH-hCcCCCCCCC
Confidence 67777643 4444456999999999864110 1445566664
No 91
>PLN02436 cellulose synthase A
Probab=23.98 E-value=65 Score=41.97 Aligned_cols=45 Identities=27% Similarity=0.816 Sum_probs=35.2
Q ss_pred ccccccccccc-------CCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 739 KNDDSCGICGD-------GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 739 ~ndd~C~VCgd-------GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
.+...|+|||| |.--+-|..|.-.....|+. .+..+|.=.||+|+
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-yer~eg~~~Cpqck 85 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-YERREGNQACPQCK 85 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchhh-hhhhcCCccCcccC
Confidence 45679999998 33468899998888888884 35678888899997
No 92
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.56 E-value=41 Score=40.90 Aligned_cols=36 Identities=22% Similarity=0.607 Sum_probs=25.0
Q ss_pred Cccccccc-----------ccccCCccCCccccCCCCccccCcccccCccccccC
Q 002464 777 SWFCSNCT-----------CWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKD 820 (919)
Q Consensus 777 ~W~Cp~C~-----------C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~ 820 (919)
.|||+.|. |..||.... .--.|+.|++.|++.++..
T Consensus 126 ~~Yc~~~e~fl~dr~v~g~cp~cg~~~a--------rGD~Ce~Cg~~~~P~~l~~ 172 (558)
T COG0143 126 GLYCVSCERFLPDRYVEGTCPKCGGEDA--------RGDQCENCGRTLDPTELIN 172 (558)
T ss_pred eeEcccccccccchheeccCCCcCcccc--------CcchhhhccCcCCchhcCC
Confidence 57777776 777774311 1126999999999988654
No 93
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=23.41 E-value=63 Score=42.11 Aligned_cols=45 Identities=29% Similarity=0.803 Sum_probs=35.8
Q ss_pred ccccccccccc-------CCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 739 KNDDSCGICGD-------GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 739 ~ndd~C~VCgd-------GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
.+...|++||+ |.--+-|..|.-.....|+.- +..+|.=.||+|+
T Consensus 15 ~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEY-Er~eG~q~CPqCk 66 (1079)
T PLN02638 15 GGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEY-ERKDGNQSCPQCK 66 (1079)
T ss_pred cCCceeeecccccCcCCCCCEEEEeccCCCccccchhhh-hhhcCCccCCccC
Confidence 45679999998 334688999988888888843 5678888999998
No 94
>KOG4442 consensus Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.18 E-value=32 Score=42.60 Aligned_cols=55 Identities=16% Similarity=0.182 Sum_probs=45.1
Q ss_pred CccccccCchhhhHHHHhCccccCCceeeeCCCCccccccceeecCCeEecccCcccchhhhhhhcCCCCCc
Q 002464 624 GMWFMEGTRTVLSWLIIAGIIALNDVIQYRNPKDDAVIKDGLVTNNGIICKCCNLVFSVSQFKIHAGFKPNR 695 (919)
Q Consensus 624 gk~~~~g~rTVLSWLID~Glv~~~dkvqY~~~k~~~~Ll~G~it~~GI~C~CC~kv~SpS~FE~HAG~~~rR 695 (919)
+||+|.+.-+| |+|+-+.+.-..+.+++|... +-.++-..|-| +-.++.||.+..
T Consensus 208 ~KWtV~~~lRv-------GiFakk~I~~GEEITFDYqf~--rYGr~AQ~CyC--------geanC~G~IGgk 262 (729)
T KOG4442|consen 208 QKWTVPDELRV-------GIFAKKVIKPGEEITFDYQFD--RYGRDAQPCYC--------GEANCRGWIGGK 262 (729)
T ss_pred eeeeeCCeeEE-------EEeEecccCCCceeeEecccc--ccccccccccc--------CCcccccccCCC
Confidence 99999999999 999999999999999998875 44567788998 666777765544
No 95
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.67 E-value=44 Score=36.60 Aligned_cols=32 Identities=31% Similarity=0.672 Sum_probs=22.2
Q ss_pred cccccccccccCC---c-----eeecCCCCCccccccccC
Q 002464 739 KNDDSCGICGDGG---E-----LICCDNCPSAFHQACLSI 770 (919)
Q Consensus 739 ~ndd~C~VCgdGG---e-----LLcCD~CpraFHlsCL~~ 770 (919)
..+..|.+|.+.- + ...=..|...||..|+..
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~ 211 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDI 211 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHH
Confidence 3467999998741 1 112247899999999975
No 96
>PLN02189 cellulose synthase
Probab=22.02 E-value=74 Score=41.38 Aligned_cols=45 Identities=27% Similarity=0.783 Sum_probs=35.1
Q ss_pred ccccccccccc-------CCceeecCCCCCccccccccCCCCCCCCccccccc
Q 002464 739 KNDDSCGICGD-------GGELICCDNCPSAFHQACLSIQDLPTGSWFCSNCT 784 (919)
Q Consensus 739 ~ndd~C~VCgd-------GGeLLcCD~CpraFHlsCL~~~~vPeG~W~Cp~C~ 784 (919)
.+...|.+||+ |.--+-|..|.-.....|+. .+..+|.=.||+|+
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye-yer~eg~q~CpqCk 83 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE-YERREGTQNCPQCK 83 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchhh-hhhhcCCccCcccC
Confidence 35679999998 33568899998877788884 35678888899997
No 97
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.55 E-value=60 Score=29.53 Aligned_cols=30 Identities=23% Similarity=0.771 Sum_probs=20.8
Q ss_pred cccccccccc--CCceeecCCCCCcccccccc
Q 002464 740 NDDSCGICGD--GGELICCDNCPSAFHQACLS 769 (919)
Q Consensus 740 ndd~C~VCgd--GGeLLcCD~CpraFHlsCL~ 769 (919)
.+..|.+|+. +...+.---|+..||..|..
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 3567999998 44444334566899999973
No 98
>PF12773 DZR: Double zinc ribbon
Probab=20.46 E-value=67 Score=26.15 Aligned_cols=7 Identities=43% Similarity=1.180 Sum_probs=3.3
Q ss_pred Ccccccc
Q 002464 777 SWFCSNC 783 (919)
Q Consensus 777 ~W~Cp~C 783 (919)
.++|+.|
T Consensus 29 ~~~C~~C 35 (50)
T PF12773_consen 29 KKICPNC 35 (50)
T ss_pred CCCCcCC
Confidence 4554444
No 99
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=20.41 E-value=57 Score=39.60 Aligned_cols=46 Identities=24% Similarity=0.312 Sum_probs=34.0
Q ss_pred CCCcccccccccccCCccCCccccCCCCccccCcccccCccccccCccCCCC-CCcccccc
Q 002464 775 TGSWFCSNCTCWICGDLVNDKEASSSFDALKCSQCEHKYHGECLKDMSKGAV-SEAWFCNQ 834 (919)
Q Consensus 775 eG~W~Cp~C~C~iCge~~~Dke~~s~~~lL~CdQCeraYHv~CL~~~~~~~~-~g~WFCs~ 834 (919)
.-+|+|-.|. -+ +..+.|..|-|.||..|+.+...... ...|-|+.
T Consensus 58 N~d~~cfech-----lp---------g~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~ 104 (588)
T KOG3612|consen 58 NIDPFCFECH-----LP---------GAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQ 104 (588)
T ss_pred CCCccccccc-----CC---------cceeeeehhhccccccccCcchhhccccccccCCc
Confidence 3478887775 32 66789999999999999987543332 66777775
No 100
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=20.40 E-value=51 Score=32.01 Aligned_cols=29 Identities=31% Similarity=0.724 Sum_probs=19.9
Q ss_pred ccccccccc------CCceeecCCCCCcccccccc
Q 002464 741 DDSCGICGD------GGELICCDNCPSAFHQACLS 769 (919)
Q Consensus 741 dd~C~VCgd------GGeLLcCD~CpraFHlsCL~ 769 (919)
.-.|++|.. -+....|..|.+.|-+.|-.
T Consensus 62 ~iiCGvC~~~LT~~EY~~~~~Cp~C~spFNp~Ck~ 96 (105)
T COG4357 62 AIICGVCRKLLTRAEYGMCGSCPYCQSPFNPGCKN 96 (105)
T ss_pred cEEhhhhhhhhhHHHHhhcCCCCCcCCCCCccccc
Confidence 467888875 35566677777777777743
No 101
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.14 E-value=1e+02 Score=33.03 Aligned_cols=49 Identities=29% Similarity=0.725 Sum_probs=30.7
Q ss_pred ccccccccccccCCceeecCCCCCccccccccCCCCC-CCCcccccc-cccccCCcc
Q 002464 738 DKNDDSCGICGDGGELICCDNCPSAFHQACLSIQDLP-TGSWFCSNC-TCWICGDLV 792 (919)
Q Consensus 738 d~ndd~C~VCgdGGeLLcCD~CpraFHlsCL~~~~vP-eG~W~Cp~C-~C~iCge~~ 792 (919)
.+....|..|++-|.+. -.|| |.-|..- ... -..-.|+++ .|.+||+..
T Consensus 57 ~~~~~~C~nCg~~GH~~--~DCP---~~iC~~C-~~~~H~s~~C~~~~~C~~Cg~~G 107 (190)
T COG5082 57 REENPVCFNCGQNGHLR--RDCP---HSICYNC-SWDGHRSNHCPKPKKCYNCGETG 107 (190)
T ss_pred cccccccchhcccCccc--ccCC---hhHhhhc-CCCCcccccCCcccccccccccC
Confidence 34557899999999887 4677 3444332 111 112347777 588888764
Done!