Query 002944
Match_columns 863
No_of_seqs 359 out of 1402
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 13:54:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002944.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002944hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5141 PHD zinc finger-contai 99.4 4.6E-14 1E-18 156.9 1.9 122 714-849 191-342 (669)
2 KOG0956 PHD finger protein AF1 99.3 9E-13 1.9E-17 151.1 3.8 141 714-862 3-179 (900)
3 KOG0955 PHD finger protein BR1 99.2 3E-12 6.6E-17 154.8 4.3 130 711-853 214-375 (1051)
4 KOG0954 PHD finger protein [Ge 99.1 2E-11 4.3E-16 141.3 0.5 119 714-846 269-416 (893)
5 KOG1244 Predicted transcriptio 98.9 6.1E-10 1.3E-14 117.7 1.6 93 714-862 222-330 (336)
6 KOG4299 PHD Zn-finger protein 98.9 2.6E-09 5.7E-14 123.0 6.4 46 716-761 253-305 (613)
7 KOG1244 Predicted transcriptio 98.7 2.7E-09 5.8E-14 113.0 1.3 80 656-760 244-330 (336)
8 KOG1512 PHD Zn-finger protein 98.6 2.8E-08 6E-13 106.0 2.5 85 716-858 258-357 (381)
9 KOG1512 PHD Zn-finger protein 98.4 5E-08 1.1E-12 104.1 0.1 93 643-760 264-362 (381)
10 KOG0825 PHD Zn-finger protein 98.2 1.4E-07 3E-12 110.5 -2.1 127 634-760 122-265 (1134)
11 KOG1473 Nucleosome remodeling 98.1 6.9E-07 1.5E-11 108.0 1.0 125 713-861 341-477 (1414)
12 KOG4299 PHD Zn-finger protein 98.0 5.3E-06 1.2E-10 96.3 4.5 45 716-760 47-94 (613)
13 KOG0957 PHD finger protein [Ge 98.0 2.5E-06 5.3E-11 96.7 1.6 122 717-846 120-278 (707)
14 PF00628 PHD: PHD-finger; Int 97.9 3.4E-06 7.5E-11 68.0 1.3 43 718-760 1-50 (51)
15 KOG4443 Putative transcription 97.9 2.8E-06 6.1E-11 98.9 -0.1 159 657-860 34-199 (694)
16 smart00249 PHD PHD zinc finger 97.8 1.3E-05 2.9E-10 61.6 3.1 41 718-758 1-47 (47)
17 KOG4443 Putative transcription 97.6 1.4E-05 3.1E-10 93.3 1.0 93 715-863 17-118 (694)
18 KOG1973 Chromatin remodeling p 97.6 2.5E-05 5.3E-10 84.1 1.6 45 716-760 219-267 (274)
19 smart00249 PHD PHD zinc finger 97.5 0.00011 2.4E-09 56.5 3.3 46 807-860 2-47 (47)
20 KOG0383 Predicted helicase [Ge 97.4 0.00011 2.4E-09 87.6 4.2 89 733-861 1-92 (696)
21 KOG0825 PHD Zn-finger protein 97.4 6.1E-05 1.3E-09 89.1 1.7 52 802-863 213-266 (1134)
22 PF00628 PHD: PHD-finger; Int 97.2 0.00015 3.2E-09 58.6 1.4 47 807-860 2-48 (51)
23 KOG0383 Predicted helicase [Ge 97.2 0.00011 2.4E-09 87.6 0.9 51 713-763 44-96 (696)
24 KOG4323 Polycomb-like PHD Zn-f 97.1 0.00026 5.5E-09 81.0 3.2 130 717-861 84-222 (464)
25 COG5034 TNG2 Chromatin remodel 97.0 0.0003 6.5E-09 75.0 2.0 45 715-760 220-269 (271)
26 PF13831 PHD_2: PHD-finger; PD 96.8 0.0002 4.3E-09 55.7 -0.9 34 726-759 2-36 (36)
27 PF15446 zf-PHD-like: PHD/FYVE 96.7 0.0024 5.3E-08 64.8 5.3 44 718-761 1-60 (175)
28 COG5034 TNG2 Chromatin remodel 96.4 0.0014 3E-08 70.1 1.6 46 801-860 218-267 (271)
29 smart00258 SAND SAND domain. 95.8 0.0047 1E-07 55.2 2.0 43 659-702 25-68 (73)
30 KOG1973 Chromatin remodeling p 95.6 0.0047 1E-07 66.8 1.4 33 822-860 229-265 (274)
31 cd04718 BAH_plant_2 BAH, or Br 95.6 0.0061 1.3E-07 60.9 2.0 25 737-761 1-27 (148)
32 KOG0957 PHD finger protein [Ge 95.4 0.0051 1.1E-07 70.7 0.9 47 804-860 544-592 (707)
33 PF01342 SAND: SAND domain; I 95.3 0.005 1.1E-07 55.8 0.2 44 656-702 34-77 (82)
34 KOG4323 Polycomb-like PHD Zn-f 95.0 0.0095 2.1E-07 68.6 1.5 45 717-761 169-224 (464)
35 KOG1245 Chromatin remodeling c 94.7 0.0074 1.6E-07 77.5 -0.7 51 711-761 1103-1158(1404)
36 smart00258 SAND SAND domain. 94.6 0.029 6.2E-07 50.3 3.0 51 441-493 18-69 (73)
37 KOG0955 PHD finger protein BR1 94.6 0.022 4.7E-07 71.2 3.1 52 801-862 216-268 (1051)
38 PF13832 zf-HC5HC2H_2: PHD-zin 93.4 0.046 1E-06 50.8 2.2 37 803-847 54-92 (110)
39 PF13771 zf-HC5HC2H: PHD-like 89.4 0.22 4.8E-06 44.5 2.0 49 804-860 36-86 (90)
40 PF01342 SAND: SAND domain; I 88.9 0.083 1.8E-06 48.1 -1.1 55 437-493 18-78 (82)
41 KOG0954 PHD finger protein [Ge 86.4 0.35 7.5E-06 58.5 1.7 52 801-861 268-319 (893)
42 PF14446 Prok-RING_1: Prokaryo 86.4 0.47 1E-05 40.6 2.0 39 805-848 6-44 (54)
43 KOG1245 Chromatin remodeling c 85.8 0.19 4.1E-06 65.2 -0.9 50 801-860 1105-1155(1404)
44 COG5141 PHD zinc finger-contai 84.3 0.47 1E-05 55.3 1.4 49 804-862 193-242 (669)
45 PF07897 DUF1675: Protein of u 81.8 3.1 6.8E-05 46.0 6.4 62 411-479 215-283 (284)
46 PF15446 zf-PHD-like: PHD/FYVE 75.7 4.6 9.9E-05 41.8 5.0 19 728-746 124-142 (175)
47 KOG1081 Transcription factor N 70.5 2.9 6.3E-05 49.0 2.5 47 713-760 86-132 (463)
48 PF07897 DUF1675: Protein of u 66.8 7.3 0.00016 43.2 4.5 32 658-689 252-283 (284)
49 PF13831 PHD_2: PHD-finger; PD 66.5 1.9 4E-05 33.8 -0.0 33 823-860 2-35 (36)
50 PF14446 Prok-RING_1: Prokaryo 66.2 2.9 6.3E-05 35.9 1.1 29 716-744 5-37 (54)
51 PF07227 DUF1423: Protein of u 62.8 5 0.00011 46.8 2.4 37 807-846 131-167 (446)
52 KOG2752 Uncharacterized conser 57.0 9.8 0.00021 42.8 3.3 37 809-845 132-169 (345)
53 PF11793 FANCL_C: FANCL C-term 55.0 6.4 0.00014 34.8 1.3 46 717-762 3-65 (70)
54 PF11793 FANCL_C: FANCL C-term 52.8 7.5 0.00016 34.3 1.3 34 806-842 4-39 (70)
55 PF05502 Dynactin_p62: Dynacti 50.7 14 0.0003 43.7 3.5 32 727-761 4-35 (483)
56 PF13832 zf-HC5HC2H_2: PHD-zin 47.9 8.8 0.00019 35.7 1.1 30 715-744 54-86 (110)
57 KOG1473 Nucleosome remodeling 46.1 12 0.00025 48.1 1.9 42 806-860 346-388 (1414)
58 KOG1246 DNA-binding protein ju 44.9 25 0.00055 44.4 4.7 47 715-761 154-204 (904)
59 KOG4628 Predicted E3 ubiquitin 44.3 14 0.00031 42.1 2.2 47 717-764 230-279 (348)
60 PF12861 zf-Apc11: Anaphase-pr 44.1 7.9 0.00017 36.0 0.1 32 728-761 47-80 (85)
61 PF13771 zf-HC5HC2H: PHD-like 40.2 14 0.0003 33.0 1.1 28 717-744 37-67 (90)
62 KOG3612 PHD Zn-finger protein 37.8 25 0.00053 42.2 2.8 48 713-760 57-107 (588)
63 PF13901 DUF4206: Domain of un 36.0 26 0.00057 36.7 2.5 38 716-760 152-197 (202)
64 KOG1734 Predicted RING-contain 34.6 17 0.00036 40.4 0.8 51 711-761 219-279 (328)
65 KOG1080 Histone H3 (Lys4) meth 34.2 48 0.001 42.8 4.7 45 716-760 573-623 (1005)
66 PF13901 DUF4206: Domain of un 33.6 38 0.00083 35.5 3.2 36 806-842 154-189 (202)
67 KOG1829 Uncharacterized conser 33.3 16 0.00034 44.3 0.4 39 806-845 513-551 (580)
68 PF07649 C1_3: C1-like domain; 30.7 22 0.00047 26.4 0.6 28 807-840 3-30 (30)
69 PF10367 Vps39_2: Vacuolar sor 30.3 43 0.00093 30.3 2.6 30 805-841 79-108 (109)
70 PF00130 C1_1: Phorbol esters/ 26.6 53 0.0011 26.7 2.3 36 804-843 11-46 (53)
71 PF13639 zf-RING_2: Ring finge 22.5 24 0.00051 27.8 -0.5 31 806-842 2-32 (44)
72 PF10497 zf-4CXXC_R1: Zinc-fin 22.1 37 0.0008 32.5 0.6 48 712-759 3-68 (105)
73 COG5194 APC11 Component of SCF 21.8 35 0.00077 31.8 0.4 20 830-849 53-76 (88)
74 PF10080 DUF2318: Predicted me 21.1 2.3E+02 0.0049 27.4 5.6 57 620-680 3-75 (102)
75 cd00162 RING RING-finger (Real 21.0 20 0.00043 26.7 -1.2 41 719-760 2-43 (45)
76 KOG1701 Focal adhesion adaptor 20.2 97 0.0021 36.6 3.5 25 717-743 335-361 (468)
77 cd00029 C1 Protein kinase C co 20.0 69 0.0015 25.2 1.7 36 804-843 11-46 (50)
No 1
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=99.41 E-value=4.6e-14 Score=156.89 Aligned_cols=122 Identities=31% Similarity=0.663 Sum_probs=96.5
Q ss_pred cccccccccccCC-----ceEEcCCCCCccccCCCCCCCCCCCCcccccccc-----------cccchhhhh-------c
Q 002944 714 ENDDLCGICMDGG-----DLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMN-----------TFQKEKFVE-------Y 770 (863)
Q Consensus 714 endd~C~VC~dgG-----dLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~-----------~~~keKfve-------~ 770 (863)
.-++.|.+|.... -+++||+|.-++|+.|++++.+|+|.|+|..|.. +...|+|.. |
T Consensus 191 ~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~peG~WlCrkCi~~~~~i~~C~fCps~dGaFkqT~dgrW~H 270 (669)
T COG5141 191 EFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGH 270 (669)
T ss_pred hhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCcchhhhhhhcccccceeEEEeccCCCCceeeccCCchHh
Confidence 4678899998653 4999999999999999999999999999999963 223344433 3
Q ss_pred cccccc-----cCcccccCchhcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecc--cccccccccccccC
Q 002944 771 NANARA-----AGRIEGVDPFAQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCD--QCEREYHVGCLKDH 843 (863)
Q Consensus 771 n~nava-----~Gri~GvdPieQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CD--qCeraYHV~CLr~a 843 (863)
+.+|.| ++....++|++.+.. + ...+|..+|.+|+.. .|++|+|. .|-++|||+|++++
T Consensus 271 ~iCA~~~pelsF~~l~~~dpI~~i~s-----V-s~srwkl~C~iCk~~--------~GtcIqCs~~nC~~aYHVtCArra 336 (669)
T COG5141 271 VICAMFNPELSFGHLLSKDPIDNIAS-----V-SSSRWKLGCLICKEF--------GGTCIQCSYFNCTRAYHVTCARRA 336 (669)
T ss_pred HhHHHhcchhccccccccchhhhhcc-----c-chhhHhheeeEEccc--------Ccceeeecccchhhhhhhhhhhhc
Confidence 444443 567778889887542 1 235788999999984 48999999 59999999999999
Q ss_pred CCCCCC
Q 002944 844 GMEDLQ 849 (863)
Q Consensus 844 GL~dLK 849 (863)
|+-+++
T Consensus 337 g~f~~~ 342 (669)
T COG5141 337 GYFDLN 342 (669)
T ss_pred chhhhh
Confidence 998886
No 2
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=99.30 E-value=9e-13 Score=151.05 Aligned_cols=141 Identities=23% Similarity=0.513 Sum_probs=98.7
Q ss_pred cccccccccccC-----CceEEcCC--CCCccccCCCCCCCCCCCCccccccccc-----------ccc-hhhh------
Q 002944 714 ENDDLCGICMDG-----GDLLCCDS--CPRAFHIDCVSLPGIPSGTWHCRYCMNT-----------FQK-EKFV------ 768 (863)
Q Consensus 714 endd~C~VC~dg-----GdLL~CD~--CpraFH~~CL~L~~vP~G~W~C~~C~~~-----------~~k-eKfv------ 768 (863)
+...-|.||.|. .-|++||+ |..++|+.||++.++|.|.|||..|... +++ ++.+
T Consensus 3 EMVGGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPtGpWfCrKCesqeraarvrCeLCP~kdGALKkTDn~G 82 (900)
T KOG0956|consen 3 EMVGGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPTGPWFCRKCESQERAARVRCELCPHKDGALKKTDNGG 82 (900)
T ss_pred ccccceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCCCchhhhhhhhhhhhccceeecccCcccceecccCCC
Confidence 445679999985 26999996 9999999999999999999999999631 111 2211
Q ss_pred -hccccccc-----cCcccccCchhcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecc--ccccccccccc
Q 002944 769 -EYNANARA-----AGRIEGVDPFAQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCD--QCEREYHVGCL 840 (863)
Q Consensus 769 -e~n~nava-----~Gri~GvdPieQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CD--qCeraYHV~CL 840 (863)
+|-+++++ +|.+..|+||--- .+ ..++....||||..-.... .-..+++|.|+ .|.++|||.|+
T Consensus 83 WAHVVCALYIPEVrFgNV~TMEPIiLq------~V-P~dRfnKtCYIC~E~Grpn-kA~~GACMtCNKs~CkqaFHVTCA 154 (900)
T KOG0956|consen 83 WAHVVCALYIPEVRFGNVHTMEPIILQ------DV-PHDRFNKTCYICNEEGRPN-KAAKGACMTCNKSGCKQAFHVTCA 154 (900)
T ss_pred ceEEEEEeeccceeecccccccceeec------cC-chhhhcceeeeecccCCcc-ccccccceecccccchhhhhhhHh
Confidence 23344433 5566667775310 11 1244566799998753211 22357999998 79999999999
Q ss_pred ccCCC-CCCC--CCCCCcceeeeee
Q 002944 841 KDHGM-EDLQ--VPQLLVYDTISFW 862 (863)
Q Consensus 841 r~aGL-~dLK--lPe~~wy~~iC~~ 862 (863)
..+|| |.-. .-+.+.||-+|=|
T Consensus 155 Q~~GLLCEE~gn~~dNVKYCGYCk~ 179 (900)
T KOG0956|consen 155 QRAGLLCEEEGNISDNVKYCGYCKY 179 (900)
T ss_pred hhhccceeccccccccceechhHHH
Confidence 99996 3333 6778899999854
No 3
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=99.25 E-value=3e-12 Score=154.79 Aligned_cols=130 Identities=28% Similarity=0.623 Sum_probs=97.7
Q ss_pred CCccccccccccccCC-----ceEEcCCCCCccccCCCCCCCCCCCCcccccccccccc-----------hhhh------
Q 002944 711 SSKENDDLCGICMDGG-----DLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMNTFQK-----------EKFV------ 768 (863)
Q Consensus 711 s~~endd~C~VC~dgG-----dLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~~~~k-----------eKfv------ 768 (863)
...+.|.+|.||.++. .+|+||.|+.++|++|++.+.+|+|.|+|..|....+. ++|.
T Consensus 214 ~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipeg~WlCr~Cl~s~~~~v~c~~cp~~~gAFkqt~dgr 293 (1051)
T KOG0955|consen 214 ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPEGQWLCRRCLQSPQRPVRCLLCPSKGGAFKQTDDGR 293 (1051)
T ss_pred cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCCCcEeehhhccCcCcccceEeccCCCCcceeccCCc
Confidence 3446788999999864 59999999999999999999999999999999764332 3332
Q ss_pred -hccccccccC-----cccccCchhcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecc--ccccccccccc
Q 002944 769 -EYNANARAAG-----RIEGVDPFAQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCD--QCEREYHVGCL 840 (863)
Q Consensus 769 -e~n~nava~G-----ri~GvdPieQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CD--qCeraYHV~CL 840 (863)
.|..++.|.+ ....++||+.+ +.+ .+.+|...|++|+... .+++|+|. .|-.+|||+|+
T Consensus 294 w~Hv~caiwipev~F~nt~~~E~I~~i-----~~i-~~aRwkL~cy~cK~~~-------~gaciqcs~~~c~~a~hvtca 360 (1051)
T KOG0955|consen 294 WAHVVCAIWIPEVSFANTVFLEPIDSI-----ENI-PPARWKLTCYICKQKG-------LGACIQCSKANCYTAFHVTCA 360 (1051)
T ss_pred eeeeehhhcccccccccchhhccccch-----hcC-cHhhhhceeeeeccCC-------CCcceecchhhhhhhhhhhhH
Confidence 2445555533 33455565543 222 2356899999999853 58999999 79999999999
Q ss_pred ccCCCCCC-C-CCCC
Q 002944 841 KDHGMEDL-Q-VPQL 853 (863)
Q Consensus 841 r~aGL~dL-K-lPe~ 853 (863)
+++|+... . +++.
T Consensus 361 ~~agl~m~~~~~~~~ 375 (1051)
T KOG0955|consen 361 RRAGLYMKSNTVKEL 375 (1051)
T ss_pred hhcCceEeecccccc
Confidence 99998765 3 6665
No 4
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=99.08 E-value=2e-11 Score=141.26 Aligned_cols=119 Identities=25% Similarity=0.578 Sum_probs=90.5
Q ss_pred cccccccccccC-----CceEEcCCCCCccccCCCCCCCCCCCCccccccccccc--------chh---------hhhcc
Q 002944 714 ENDDLCGICMDG-----GDLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMNTFQ--------KEK---------FVEYN 771 (863)
Q Consensus 714 endd~C~VC~dg-----GdLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~~~~--------keK---------fve~n 771 (863)
+++-.|.||..+ .+|++||.|...+|+.|+++..+|+|.|.|..|...+. +|. -.+|.
T Consensus 269 dedviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg~~ppCvLCPkkGGamK~~~sgT~wAHv 348 (893)
T KOG0954|consen 269 DEDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALGIEPPCVLCPKKGGAMKPTKSGTKWAHV 348 (893)
T ss_pred cccceeceecCCCccccceeEEeccchhHHHHhhhceeecCCCCeeehhccccCCCCeeeccccCCcccccCCCCeeeEe
Confidence 367889999976 47999999999999999999999999999999975322 111 12344
Q ss_pred ccccc-----cCcccccCchhcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecc--cccccccccccccCC
Q 002944 772 ANARA-----AGRIEGVDPFAQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCD--QCEREYHVGCLKDHG 844 (863)
Q Consensus 772 ~nava-----~Gri~GvdPieQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CD--qCeraYHV~CLr~aG 844 (863)
.+++| .+....|.||..+- +|. ..+|...|.+|+.. -|++|+|. .|...||+.|+.++|
T Consensus 349 sCALwIPEVsie~~ekmePItkfs----~Ip--esRwslvC~LCk~k--------~GACIqCs~k~C~t~fHv~CA~~aG 414 (893)
T KOG0954|consen 349 SCALWIPEVSIECPEKMEPITKFS----HIP--ESRWSLVCNLCKVK--------SGACIQCSNKTCRTAFHVTCAFEAG 414 (893)
T ss_pred eeeeccceeeccCHhhcCcccccC----CCc--HHHHHHHHHHhccc--------CcceEEecccchhhhccchhhhhcC
Confidence 56666 33445566765432 222 25788889999984 37899998 899999999999999
Q ss_pred CC
Q 002944 845 ME 846 (863)
Q Consensus 845 L~ 846 (863)
+.
T Consensus 415 ~~ 416 (893)
T KOG0954|consen 415 LE 416 (893)
T ss_pred Ce
Confidence 85
No 5
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.86 E-value=6.1e-10 Score=117.73 Aligned_cols=93 Identities=24% Similarity=0.710 Sum_probs=77.0
Q ss_pred cccccccccccC----------CceEEcCCCCCccccCCCCCC-----CCCCCCcccccccccccchhhhhccccccccC
Q 002944 714 ENDDLCGICMDG----------GDLLCCDSCPRAFHIDCVSLP-----GIPSGTWHCRYCMNTFQKEKFVEYNANARAAG 778 (863)
Q Consensus 714 endd~C~VC~dg----------GdLL~CD~CpraFH~~CL~L~-----~vP~G~W~C~~C~~~~~keKfve~n~nava~G 778 (863)
....+|..|..+ .+|+.|..|.|+-|+.||..+ .+-...|+|..|+.
T Consensus 222 ~Pn~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~------------------ 283 (336)
T KOG1244|consen 222 QPNPYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKY------------------ 283 (336)
T ss_pred cCCcccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecce------------------
Confidence 345677777643 379999999999999999633 45678999999985
Q ss_pred cccccCchhcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcce
Q 002944 779 RIEGVDPFAQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYD 857 (863)
Q Consensus 779 ri~GvdPieQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~ 857 (863)
|.||+-.+ .+..+++||-|++.||.+||. +.|- -|++.|.|
T Consensus 284 ----------------------------csicgtse------nddqllfcddcdrgyhmycls----ppm~eppegswsc 325 (336)
T KOG1244|consen 284 ----------------------------CSICGTSE------NDDQLLFCDDCDRGYHMYCLS----PPMVEPPEGSWSC 325 (336)
T ss_pred ----------------------------eccccCcC------CCceeEeecccCCceeeEecC----CCcCCCCCCchhH
Confidence 88998743 468999999999999999999 4666 99999999
Q ss_pred eeeee
Q 002944 858 TISFW 862 (863)
Q Consensus 858 ~iC~~ 862 (863)
++|+-
T Consensus 326 ~KOG~ 330 (336)
T KOG1244|consen 326 HLCLE 330 (336)
T ss_pred HHHHH
Confidence 99973
No 6
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.86 E-value=2.6e-09 Score=122.98 Aligned_cols=46 Identities=43% Similarity=1.234 Sum_probs=41.2
Q ss_pred cccccccccCCce---EEcCCCCCccccCCCCCC----CCCCCCccccccccc
Q 002944 716 DDLCGICMDGGDL---LCCDSCPRAFHIDCVSLP----GIPSGTWHCRYCMNT 761 (863)
Q Consensus 716 dd~C~VC~dgGdL---L~CD~CpraFH~~CL~L~----~vP~G~W~C~~C~~~ 761 (863)
.++|..|...|.. +|||+||++||++||.+| .+|.|.|+|+.|...
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 5799999999865 999999999999999655 789999999999763
No 7
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.73 E-value=2.7e-09 Score=112.99 Aligned_cols=80 Identities=31% Similarity=0.703 Sum_probs=64.4
Q ss_pred CCeeEeCCCCCccChhhhhhccCc--ccCCCCCceeEecCCccchhhhhhhccCCCCCCccccccccccccC---CceEE
Q 002944 656 GFGILCTCCNSEVSPSQFEAHAGW--ASRRKPFQHIYTSNGVSLHELSIKLSLERPFSSKENDDLCGICMDG---GDLLC 730 (863)
Q Consensus 656 G~GI~CsCCn~~~SPSeFEaHAG~--~srRkPy~sIytsnG~SL~elai~Lsk~r~~s~~endd~C~VC~dg---GdLL~ 730 (863)
.+.|.|+.|++.-|||++.-.+.+ +.++.-|+.|.+ .+|.+|+.. .+||+
T Consensus 244 eelvscsdcgrsghpsclqft~nm~~avk~yrwqciec-------------------------k~csicgtsenddqllf 298 (336)
T KOG1244|consen 244 EELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIEC-------------------------KYCSICGTSENDDQLLF 298 (336)
T ss_pred hhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeec-------------------------ceeccccCcCCCceeEe
Confidence 378999999999999865544443 455566777765 678999854 47999
Q ss_pred cCCCCCccccCCCCC--CCCCCCCcccccccc
Q 002944 731 CDSCPRAFHIDCVSL--PGIPSGTWHCRYCMN 760 (863)
Q Consensus 731 CD~CpraFH~~CL~L--~~vP~G~W~C~~C~~ 760 (863)
||.|+|+||++||.+ ...|+|.|.|..|..
T Consensus 299 cddcdrgyhmyclsppm~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 299 CDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLE 330 (336)
T ss_pred ecccCCceeeEecCCCcCCCCCCchhHHHHHH
Confidence 999999999999974 478899999999975
No 8
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.55 E-value=2.8e-08 Score=106.00 Aligned_cols=85 Identities=25% Similarity=0.508 Sum_probs=71.0
Q ss_pred cccccccccCC---------ceEEcCCCCCccccCCCCCC-----CCCCCCcccccccccccchhhhhccccccccCccc
Q 002944 716 DDLCGICMDGG---------DLLCCDSCPRAFHIDCVSLP-----GIPSGTWHCRYCMNTFQKEKFVEYNANARAAGRIE 781 (863)
Q Consensus 716 dd~C~VC~dgG---------dLL~CD~CpraFH~~CL~L~-----~vP~G~W~C~~C~~~~~keKfve~n~nava~Gri~ 781 (863)
...|.+|.++- .+++|..|-.++|++|+.++ .+-...|.|..|+.
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~l--------------------- 316 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCEL--------------------- 316 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHh---------------------
Confidence 35678887753 58999999999999999754 34467999999984
Q ss_pred ccCchhcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCccee
Q 002944 782 GVDPFAQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDT 858 (863)
Q Consensus 782 GvdPieQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~ 858 (863)
|.||.++.- ...+++||.|++.||..|+. |+ ||.+.|-|-
T Consensus 317 -------------------------C~IC~~P~~------E~E~~FCD~CDRG~HT~CVG------L~~lP~G~WICD 357 (381)
T KOG1512|consen 317 -------------------------CRICLGPVI------ESEHLFCDVCDRGPHTLCVG------LQDLPRGEWICD 357 (381)
T ss_pred -------------------------hhccCCccc------chheeccccccCCCCccccc------cccccCccchhh
Confidence 999999762 46899999999999999987 77 999999764
No 9
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.41 E-value=5e-08 Score=104.07 Aligned_cols=93 Identities=25% Similarity=0.559 Sum_probs=69.9
Q ss_pred EeCCeEEeeceeeCCeeEeCCCCCccChhhhhhccCcccC--CCCCceeEecCCccchhhhhhhccCCCCCCcccccccc
Q 002944 643 FVRGEKFLVGYKKGFGILCTCCNSEVSPSQFEAHAGWASR--RKPFQHIYTSNGVSLHELSIKLSLERPFSSKENDDLCG 720 (863)
Q Consensus 643 y~~Gq~lL~G~k~G~GI~CsCCn~~~SPSeFEaHAG~~sr--RkPy~sIytsnG~SL~elai~Lsk~r~~s~~endd~C~ 720 (863)
+.+||.-+.-.+....|.|+.|....||++.+........ -.+|..+ ....|.
T Consensus 264 ~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~-------------------------~C~lC~ 318 (381)
T KOG1512|consen 264 FWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCS-------------------------SCELCR 318 (381)
T ss_pred hhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhc-------------------------ccHhhh
Confidence 4456655555567789999999999999987755443321 1233322 236789
Q ss_pred ccccC---CceEEcCCCCCccccCCCCCCCCCCCCcccc-cccc
Q 002944 721 ICMDG---GDLLCCDSCPRAFHIDCVSLPGIPSGTWHCR-YCMN 760 (863)
Q Consensus 721 VC~dg---GdLL~CD~CpraFH~~CL~L~~vP~G~W~C~-~C~~ 760 (863)
+|+.+ .++++||.|+|+||.+|++|..+|.|.|+|. .|..
T Consensus 319 IC~~P~~E~E~~FCD~CDRG~HT~CVGL~~lP~G~WICD~~C~~ 362 (381)
T KOG1512|consen 319 ICLGPVIESEHLFCDVCDRGPHTLCVGLQDLPRGEWICDMRCRE 362 (381)
T ss_pred ccCCcccchheeccccccCCCCccccccccccCccchhhhHHHH
Confidence 99976 4799999999999999999999999999998 4653
No 10
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.22 E-value=1.4e-07 Score=110.48 Aligned_cols=127 Identities=18% Similarity=0.316 Sum_probs=73.2
Q ss_pred CCCCceeEEEeCCeEEeeceeeCCeeEeCCCC-Cc--------cChhhhhhccC--cccCCCCCceeEecCCccchhhhh
Q 002944 634 LEDGAEVGYFVRGEKFLVGYKKGFGILCTCCN-SE--------VSPSQFEAHAG--WASRRKPFQHIYTSNGVSLHELSI 702 (863)
Q Consensus 634 L~dgt~V~Yy~~Gq~lL~G~k~G~GI~CsCCn-~~--------~SPSeFEaHAG--~~srRkPy~sIytsnG~SL~elai 702 (863)
+...+..+.....+.|+.-.++..+|||..|- .| +...+|-...- ....+.+|..+.........++..
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v~V~eS~~~~~~vR~lP~EEs~~~~e~~~ 201 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGEVKVLESTGIEANVRCLPSEESENILEKGG 201 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhheeeeeccccccceeEecchhhhhhhhhhcc
Confidence 33444444445577888889999999998883 33 33344532211 111122333332222111111110
Q ss_pred hhccCCCCCCccccccccccccCC---ceEEcCCCCCc-cccCCCCC--CCCCCCCcccccccc
Q 002944 703 KLSLERPFSSKENDDLCGICMDGG---DLLCCDSCPRA-FHIDCVSL--PGIPSGTWHCRYCMN 760 (863)
Q Consensus 703 ~Lsk~r~~s~~endd~C~VC~dgG---dLL~CD~Cpra-FH~~CL~L--~~vP~G~W~C~~C~~ 760 (863)
.-..+...........|.+|.... -||+||.|+.+ ||.+||.+ ..+|-+.|||+.|..
T Consensus 202 d~~~d~~~~~~~E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 202 DEKQDQISGLSQEEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred ccccccccCcccccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 000001111223345699998654 59999999999 99999975 469999999999964
No 11
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=98.12 E-value=6.9e-07 Score=108.00 Aligned_cols=125 Identities=27% Similarity=0.509 Sum_probs=84.2
Q ss_pred ccccccccccccCCceEEcCCCCCccccCCCCC--CCCCCCCcccccccccccchhhhhccccccccCcccccCchhccc
Q 002944 713 KENDDLCGICMDGGDLLCCDSCPRAFHIDCVSL--PGIPSGTWHCRYCMNTFQKEKFVEYNANARAAGRIEGVDPFAQMV 790 (863)
Q Consensus 713 ~endd~C~VC~dgGdLL~CD~CpraFH~~CL~L--~~vP~G~W~C~~C~~~~~keKfve~n~nava~Gri~GvdPieQi~ 790 (863)
..-+|.|.+|.+.|+++||..||+.||..|+.. ..+|...|.|-.|.. +.+|.+ +..+-|.+.-
T Consensus 341 ~~~ddhcrf~~d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~---------hkvngv----vd~vl~~~K~- 406 (1414)
T KOG1473|consen 341 IEYDDHCRFCHDLGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNI---------HKVNGV----VDCVLPPSKN- 406 (1414)
T ss_pred eeecccccccCcccceeecccCCceEEeeecCCccccCCCccchhhhhhh---------hccCcc----cccccChhhc-
Confidence 345689999999999999999999999999964 478999999999984 112211 1111111100
Q ss_pred cccccccc------CCCCC--cCccccCCCCCcCCCCCCCCceEeccc-ccccccc-cccccCCCCCCCCCCCCcceeee
Q 002944 791 SRCIRIVQ------TPDTE--LGGCVLCRGRDFCKSRFGRRTVILCDQ-CEREYHV-GCLKDHGMEDLQVPQLLVYDTIS 860 (863)
Q Consensus 791 kRC~RIvk------~~~~e--~~~C~ICkk~dfsks~f~~gtII~CDq-CeraYHV-~CLr~aGL~dLKlPe~~wy~~iC 860 (863)
...+|.-. ..+.| .-.|.||.. +++.+.|+. |++.||. .||... ...+.||+.+|++.-|
T Consensus 407 ~~~iR~~~iG~dr~gr~ywfi~rrl~Ie~~---------det~l~yysT~pqly~ll~cLd~~-~~e~~L~d~i~~~~ee 476 (1414)
T KOG1473|consen 407 VDSIRHTPIGRDRYGRKYWFISRRLRIEGM---------DETLLWYYSTCPQLYHLLRCLDRT-YVEMYLCDGIWERREE 476 (1414)
T ss_pred ccceeccCCCcCccccchhceeeeeEEecC---------CCcEEEEecCcHHHHHHHHHhchH-HHHHhhccchhhhHHH
Confidence 00011111 11222 234999986 478999996 9999999 999832 2234499999999877
Q ss_pred e
Q 002944 861 F 861 (863)
Q Consensus 861 ~ 861 (863)
|
T Consensus 477 ~ 477 (1414)
T KOG1473|consen 477 I 477 (1414)
T ss_pred H
Confidence 6
No 12
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.98 E-value=5.3e-06 Score=96.35 Aligned_cols=45 Identities=42% Similarity=1.147 Sum_probs=37.6
Q ss_pred cccccccccCCceEEcCCCCCccccCCCCCC---CCCCCCcccccccc
Q 002944 716 DDLCGICMDGGDLLCCDSCPRAFHIDCVSLP---GIPSGTWHCRYCMN 760 (863)
Q Consensus 716 dd~C~VC~dgGdLL~CD~CpraFH~~CL~L~---~vP~G~W~C~~C~~ 760 (863)
.+.|.+|..+|++++|+.|+-+||..|.... ..+.+.|.|..|..
T Consensus 47 ~ts~~~~~~~gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSGGNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhhcCCccccccCccccchhccCcccCcccccccccccCCCc
Confidence 4779999999999999999999999999744 33457788888854
No 13
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=97.97 E-value=2.5e-06 Score=96.68 Aligned_cols=122 Identities=29% Similarity=0.650 Sum_probs=77.8
Q ss_pred cccccccc-----CCceEEcCCCCCccccCCCCCC---CCCC-------CCccccccccccc----------chhhhhcc
Q 002944 717 DLCGICMD-----GGDLLCCDSCPRAFHIDCVSLP---GIPS-------GTWHCRYCMNTFQ----------KEKFVEYN 771 (863)
Q Consensus 717 d~C~VC~d-----gGdLL~CD~CpraFH~~CL~L~---~vP~-------G~W~C~~C~~~~~----------keKfve~n 771 (863)
..|.||-. .|++|-||.|+..+|..|++.. ++|. ..|||..|+.... .|.|.+.+
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElCPn~~GifKetD 199 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELCPNRFGIFKETD 199 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCCCCCccccCCCcCCcccccc
Confidence 38999984 5789999999999999999733 3443 4899999986432 13333332
Q ss_pred c-------cccccCcccccCchhcccccccccccCCC---CCcCccccCCCCCcCCCCCCCCceEecc--cccccccccc
Q 002944 772 A-------NARAAGRIEGVDPFAQMVSRCIRIVQTPD---TELGGCVLCRGRDFCKSRFGRRTVILCD--QCEREYHVGC 839 (863)
Q Consensus 772 ~-------nava~Gri~GvdPieQi~kRC~RIvk~~~---~e~~~C~ICkk~dfsks~f~~gtII~CD--qCeraYHV~C 839 (863)
+ ++++ +.|+. +.|+.+.|.-.+..++ .-...|.+|-..-|+++ |-+|.|| .|..+|||+|
T Consensus 200 igrWvH~iCALY---vpGVa-fg~~~~l~~Vtl~em~ysk~Gak~Cs~Ced~~fARt----Gvci~CdaGMCk~YfHVTC 271 (707)
T KOG0957|consen 200 IGRWVHAICALY---VPGVA-FGQTHTLCGVTLEEMDYSKFGAKTCSACEDKIFART----GVCIRCDAGMCKEYFHVTC 271 (707)
T ss_pred hhhHHHHHHHhh---cCccc-cccccccccccHHHhhhhhhccchhccccchhhhhc----ceeeeccchhhhhhhhhhH
Confidence 2 2222 11111 1111122211111111 12446999999888874 4789999 8999999999
Q ss_pred cccCCCC
Q 002944 840 LKDHGME 846 (863)
Q Consensus 840 Lr~aGL~ 846 (863)
+...|+-
T Consensus 272 AQk~GlL 278 (707)
T KOG0957|consen 272 AQKLGLL 278 (707)
T ss_pred Hhhhcce
Confidence 9998873
No 14
>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=97.93 E-value=3.4e-06 Score=68.01 Aligned_cols=43 Identities=47% Similarity=1.152 Sum_probs=36.0
Q ss_pred ccccccc---CCceEEcCCCCCccccCCCCCC----CCCCCCcccccccc
Q 002944 718 LCGICMD---GGDLLCCDSCPRAFHIDCVSLP----GIPSGTWHCRYCMN 760 (863)
Q Consensus 718 ~C~VC~d---gGdLL~CD~CpraFH~~CL~L~----~vP~G~W~C~~C~~ 760 (863)
+|.+|+. .+++|.|+.|.+.||..|++++ .++.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 4788887 5689999999999999999876 33456999999974
No 15
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.87 E-value=2.8e-06 Score=98.93 Aligned_cols=159 Identities=23% Similarity=0.419 Sum_probs=90.7
Q ss_pred CeeEeCCCCCccChhhhhhccCcccCCCCCceeEecCCccchhhhhhhccCCCCCCccccccccccccCC---ceEEcCC
Q 002944 657 FGILCTCCNSEVSPSQFEAHAGWASRRKPFQHIYTSNGVSLHELSIKLSLERPFSSKENDDLCGICMDGG---DLLCCDS 733 (863)
Q Consensus 657 ~GI~CsCCn~~~SPSeFEaHAG~~srRkPy~sIytsnG~SL~elai~Lsk~r~~s~~endd~C~VC~dgG---dLL~CD~ 733 (863)
-...|.+|...+|+.+.-.-+-.. -+..||.- .....|..|+.+| .+++|+.
T Consensus 34 ~m~ac~~c~~~yH~~cvt~~~~~~---------~l~~gWrC----------------~~crvCe~c~~~gD~~kf~~Ck~ 88 (694)
T KOG4443|consen 34 RLLACSDCGQKYHPYCVTSWAQHA---------VLSGGWRC----------------PSCRVCEACGTTGDPKKFLLCKR 88 (694)
T ss_pred cchhhhhhcccCCcchhhHHHhHH---------HhcCCccc----------------CCceeeeeccccCCccccccccc
Confidence 346799999999987654322221 11122111 1235677787554 6999999
Q ss_pred CCCccccCCCC--CCCCCCCCcccccccccccchhhhhccccccccC-cccccCchhcccccccccccCCCCCcCccccC
Q 002944 734 CPRAFHIDCVS--LPGIPSGTWHCRYCMNTFQKEKFVEYNANARAAG-RIEGVDPFAQMVSRCIRIVQTPDTELGGCVLC 810 (863)
Q Consensus 734 CpraFH~~CL~--L~~vP~G~W~C~~C~~~~~keKfve~n~nava~G-ri~GvdPieQi~kRC~RIvk~~~~e~~~C~IC 810 (863)
|+-+||.+|.. ...+|.|.|+|+.|....+.+ ...+| ...-....-+. -.|.+ ...|.+|
T Consensus 89 cDvsyh~yc~~P~~~~v~sg~~~ckk~~~c~qc~--------~~lpg~s~~~~~~~~~~-~~c~s--------~~~cPvc 151 (694)
T KOG4443|consen 89 CDVSYHCYCQKPPNDKVPSGPWLCKKCTRCRQCD--------STLPGLSLDLQEGYLQC-APCAS--------LSYCPVC 151 (694)
T ss_pred ccccccccccCCccccccCcccccHHHHhhhhcc--------ccccccchhhhccCccc-ccccc--------cccCchH
Confidence 99999999995 458999999999987533322 22222 00000000000 01221 2347777
Q ss_pred CCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeee
Q 002944 811 RGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTIS 860 (863)
Q Consensus 811 kk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC 860 (863)
..-+... ..-.++.|++|.+|-|..|-.-..+..+. .=+....|-+|
T Consensus 152 ~~~Y~~~---e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~C 199 (694)
T KOG4443|consen 152 LIVYQDS---ESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTC 199 (694)
T ss_pred HHhhhhc---cchhhHHHHHhcccccCCCCccchHHHHHHhhhhhccccee
Confidence 6533221 12345899999999999997655543333 22234444444
No 16
>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 KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.65 E-value=1.4e-05 Score=93.27 Aligned_cols=93 Identities=28% Similarity=0.591 Sum_probs=73.7
Q ss_pred ccccccccccCC-----ceEEcCCCCCccccCCCCCC--C-CCCCCcccccccccccchhhhhccccccccCcccccCch
Q 002944 715 NDDLCGICMDGG-----DLLCCDSCPRAFHIDCVSLP--G-IPSGTWHCRYCMNTFQKEKFVEYNANARAAGRIEGVDPF 786 (863)
Q Consensus 715 ndd~C~VC~dgG-----dLL~CD~CpraFH~~CL~L~--~-vP~G~W~C~~C~~~~~keKfve~n~nava~Gri~GvdPi 786 (863)
....|.+|+..| .|+.|..|..-||.+|+.+. . +=.+-|.|+.|+.
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv-------------------------- 70 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV-------------------------- 70 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCcee--------------------------
Confidence 346788888755 59999999999999999732 1 1234499999984
Q ss_pred hcccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeeeeeC
Q 002944 787 AQMVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTISFWL 863 (863)
Q Consensus 787 eQi~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC~~~ 863 (863)
|..|+. ..++...++|+.|+-.||.+|.. +.++ +|.+-|.|.-|||+
T Consensus 71 --------------------Ce~c~~------~gD~~kf~~Ck~cDvsyh~yc~~----P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 71 --------------------CEACGT------TGDPKKFLLCKRCDVSYHCYCQK----PPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred --------------------eeeccc------cCCcccccccccccccccccccC----CccccccCcccccHHHHhh
Confidence 667764 23567899999999999999998 4566 99999999998874
No 18
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.58 E-value=2.5e-05 Score=84.09 Aligned_cols=45 Identities=36% Similarity=0.882 Sum_probs=39.0
Q ss_pred cccccc-cccCCceEEcCC--CC-CccccCCCCCCCCCCCCcccccccc
Q 002944 716 DDLCGI-CMDGGDLLCCDS--CP-RAFHIDCVSLPGIPSGTWHCRYCMN 760 (863)
Q Consensus 716 dd~C~V-C~dgGdLL~CD~--Cp-raFH~~CL~L~~vP~G~W~C~~C~~ 760 (863)
..+|.. |...|+|+-||. |+ .-||+.|++|...|.|.|||+.|..
T Consensus 219 ~~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 219 PTYCICNQVSYGKMIGCDNPGCPIEWFHFTCVGLKTKPKGKWYCPRCKA 267 (274)
T ss_pred CEEEEecccccccccccCCCCCCcceEEEeccccccCCCCcccchhhhh
Confidence 344443 557899999997 99 9999999999999999999999985
No 19
>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 KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.41 E-value=0.00011 Score=87.60 Aligned_cols=89 Identities=27% Similarity=0.558 Sum_probs=64.5
Q ss_pred CCCCccccCCCC--CCCCCCCCcccccccccccchhhhhccccccccCcccccCchhcccccccccccCCCCCcCccccC
Q 002944 733 SCPRAFHIDCVS--LPGIPSGTWHCRYCMNTFQKEKFVEYNANARAAGRIEGVDPFAQMVSRCIRIVQTPDTELGGCVLC 810 (863)
Q Consensus 733 ~CpraFH~~CL~--L~~vP~G~W~C~~C~~~~~keKfve~n~nava~Gri~GvdPieQi~kRC~RIvk~~~~e~~~C~IC 810 (863)
.|+|+||..|+. +...|+++|.|+.|...... +.+.++- -.+.+...|.+|
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~------------------~~~~~~~---------~~~~~~e~c~ic 53 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQ------------------VEAKDDD---------WDDAEQEACRIC 53 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhhcccc------------------cccccCC---------cchhhhhhhhhh
Confidence 499999999997 44566899999999752110 0000000 123446679999
Q ss_pred CCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeeee
Q 002944 811 RGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTISF 861 (863)
Q Consensus 811 kk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC~ 861 (863)
.. .++++.||.|+.+||..|+. .++. .|..-|.|.-||
T Consensus 54 ~~---------~g~~l~c~tC~~s~h~~cl~----~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 54 AD---------GGELLWCDTCPASFHASCLG----PPLTPQPNGEFICPRCF 92 (696)
T ss_pred cC---------CCcEEEeccccHHHHHHccC----CCCCcCCccceeeeeec
Confidence 87 47899999999999999998 4555 888778888875
No 21
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.39 E-value=6.1e-05 Score=89.14 Aligned_cols=52 Identities=37% Similarity=0.608 Sum_probs=43.8
Q ss_pred CCcCccccCCCCCcCCCCCCCCceEeccccccc-ccccccccCCCCCCC-CCCCCcceeeeeeC
Q 002944 802 TELGGCVLCRGRDFCKSRFGRRTVILCDQCERE-YHVGCLKDHGMEDLQ-VPQLLVYDTISFWL 863 (863)
Q Consensus 802 ~e~~~C~ICkk~dfsks~f~~gtII~CDqCera-YHV~CLr~aGL~dLK-lPe~~wy~~iC~~~ 863 (863)
.+...|.||..++- ..-+|+||.|... ||++||+ ++|. +|-+-|||.-|-.|
T Consensus 213 ~E~~~C~IC~~~Dp------EdVLLLCDsCN~~~YH~YCLD----Pdl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDP------EDVLLLCDSCNKVYYHVYCLD----PDLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred cccccceeeccCCh------HHhheeecccccceeeccccC----cccccccccceecCcchhh
Confidence 34667999998763 4678999999988 9999999 6787 99999999999543
No 22
>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=97.19 E-value=0.00015 Score=58.59 Aligned_cols=47 Identities=26% Similarity=0.489 Sum_probs=35.3
Q ss_pred cccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCCCCCCCcceeee
Q 002944 807 CVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQVPQLLVYDTIS 860 (863)
Q Consensus 807 C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLKlPe~~wy~~iC 860 (863)
|.+|++. ...+.+|+|+.|.++||..|+...... ..+|...|+++.|
T Consensus 2 C~vC~~~------~~~~~~i~C~~C~~~~H~~C~~~~~~~-~~~~~~~w~C~~C 48 (51)
T PF00628_consen 2 CPVCGQS------DDDGDMIQCDSCNRWYHQECVGPPEKA-EEIPSGDWYCPNC 48 (51)
T ss_dssp BTTTTSS------CTTSSEEEBSTTSCEEETTTSTSSHSH-HSHHSSSBSSHHH
T ss_pred CcCCCCc------CCCCCeEEcCCCChhhCcccCCCChhh-ccCCCCcEECcCC
Confidence 8899883 246789999999999999999943321 1245558888876
No 23
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.18 E-value=0.00011 Score=87.58 Aligned_cols=51 Identities=39% Similarity=1.012 Sum_probs=43.2
Q ss_pred ccccccccccccCCceEEcCCCCCccccCCCC--CCCCCCCCccccccccccc
Q 002944 713 KENDDLCGICMDGGDLLCCDSCPRAFHIDCVS--LPGIPSGTWHCRYCMNTFQ 763 (863)
Q Consensus 713 ~endd~C~VC~dgGdLL~CD~CpraFH~~CL~--L~~vP~G~W~C~~C~~~~~ 763 (863)
..+...|.+|.++|.+++||.|+.+||.+|++ +..+|.+.|.|+.|..+..
T Consensus 44 ~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 44 DAEQEACRICADGGELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCFCPKN 96 (696)
T ss_pred hhhhhhhhhhcCCCcEEEeccccHHHHHHccCCCCCcCCccceeeeeeccCCC
Confidence 34557899999999999999999999999996 4467778899999965544
No 24
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.15 E-value=0.00026 Score=81.05 Aligned_cols=130 Identities=16% Similarity=0.240 Sum_probs=79.8
Q ss_pred cccccccc-----CCceEEcCCCCCccccCCCCCCCCCCCCcccccccccccchhhhhccccccccCcccccC---chhc
Q 002944 717 DLCGICMD-----GGDLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMNTFQKEKFVEYNANARAAGRIEGVD---PFAQ 788 (863)
Q Consensus 717 d~C~VC~d-----gGdLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~~~~keKfve~n~nava~Gri~Gvd---PieQ 788 (863)
-.|.+|.. +..+..|+.|.++||+.|........+.|.+..|.....--.-+ +.-.|+..++. +...
T Consensus 84 ~~~nv~~s~~~~p~~e~~~~~r~~~~~~q~~~i~~~~~~~~~~~~~c~~~~~~~~g~-----a~K~g~~a~~~l~y~~~~ 158 (464)
T KOG4323|consen 84 LNPNVLTSETVLPENEKVICGRCKSGYHQGCNIPRFPSLDIGESTECVFPIFSQEGG-----ALKKGRLARPSLPYPEAS 158 (464)
T ss_pred cCCcccccccccCchhhhhhhhhccCcccccCccCcCcCCccccccccccccccccc-----cccccccccccccCcccc
Confidence 34555553 34688999999999999998777778899999987642110000 01112222100 0000
Q ss_pred ccccccccccCCCCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeeee
Q 002944 789 MVSRCIRIVQTPDTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTISF 861 (863)
Q Consensus 789 i~kRC~RIvk~~~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC~ 861 (863)
+-. .....-...|.+|....... .+ .|++|+.|..+||-.|..+---..|- -|...|||-.|-
T Consensus 159 l~w------D~~~~~n~qc~vC~~g~~~~---~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~ 222 (464)
T KOG4323|consen 159 LDW------DSGHKVNLQCSVCYCGGPGA---GN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCN 222 (464)
T ss_pred ccc------CccccccceeeeeecCCcCc---cc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhc
Confidence 000 00011122399998754322 23 89999999999999999865554444 788888888884
No 25
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.01 E-value=0.0003 Score=75.01 Aligned_cols=45 Identities=36% Similarity=0.960 Sum_probs=38.4
Q ss_pred cccccccccc--CCceEEcCC--CC-CccccCCCCCCCCCCCCcccccccc
Q 002944 715 NDDLCGICMD--GGDLLCCDS--CP-RAFHIDCVSLPGIPSGTWHCRYCMN 760 (863)
Q Consensus 715 ndd~C~VC~d--gGdLL~CD~--Cp-raFH~~CL~L~~vP~G~W~C~~C~~ 760 (863)
+.-+|+ |.+ .|+|+-||. |. ..||..|++|...|.|.|||+.|+.
T Consensus 220 e~lYCf-CqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~ 269 (271)
T COG5034 220 EELYCF-CQQVSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKK 269 (271)
T ss_pred ceeEEE-ecccccccceecCCCCCchhheeccccccCCCCCCcEeCHHhHh
Confidence 345675 665 489999996 98 6899999999999999999999974
No 26
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.82 E-value=0.0002 Score=55.66 Aligned_cols=34 Identities=38% Similarity=0.988 Sum_probs=20.8
Q ss_pred CceEEcCCCCCccccCCCCCCCCCCC-Cccccccc
Q 002944 726 GDLLCCDSCPRAFHIDCVSLPGIPSG-TWHCRYCM 759 (863)
Q Consensus 726 GdLL~CD~CpraFH~~CL~L~~vP~G-~W~C~~C~ 759 (863)
+.|+.|+.|.-++|+.|+++..+|.+ .|+|..|+
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 46899999999999999999988887 89999884
No 27
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.68 E-value=0.0024 Score=64.85 Aligned_cols=44 Identities=25% Similarity=0.765 Sum_probs=31.9
Q ss_pred ccccccc------CCceEEcCCCCCccccCCCCCCC--------CCCCC--ccccccccc
Q 002944 718 LCGICMD------GGDLLCCDSCPRAFHIDCVSLPG--------IPSGT--WHCRYCMNT 761 (863)
Q Consensus 718 ~C~VC~d------gGdLL~CD~CpraFH~~CL~L~~--------vP~G~--W~C~~C~~~ 761 (863)
.|.+|.. -|.||+|.+|-.+||..||+..+ |-.+. .+|..|.-.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~ 60 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGI 60 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcCh
Confidence 3778853 35799999999999999998542 22333 468888653
No 28
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.38 E-value=0.0014 Score=70.08 Aligned_cols=46 Identities=26% Similarity=0.621 Sum_probs=37.3
Q ss_pred CCCcCccccCCCCCcCCCCCCCCceEecc--cccc-cccccccccCCCCCCC-CCCCCcceeee
Q 002944 801 DTELGGCVLCRGRDFCKSRFGRRTVILCD--QCER-EYHVGCLKDHGMEDLQ-VPQLLVYDTIS 860 (863)
Q Consensus 801 ~~e~~~C~ICkk~dfsks~f~~gtII~CD--qCer-aYHV~CLr~aGL~dLK-lPe~~wy~~iC 860 (863)
+.+...| +|.+..| +.||-|| .|++ |||..|+. |+ .|++.|||.-|
T Consensus 218 e~e~lYC-fCqqvSy-------GqMVaCDn~nCkrEWFH~~CVG------Lk~pPKG~WYC~eC 267 (271)
T COG5034 218 EGEELYC-FCQQVSY-------GQMVACDNANCKREWFHLECVG------LKEPPKGKWYCPEC 267 (271)
T ss_pred cCceeEE-Eeccccc-------ccceecCCCCCchhheeccccc------cCCCCCCcEeCHHh
Confidence 3445568 7888643 5799999 7997 67999987 88 99999999877
No 29
>smart00258 SAND SAND domain.
Probab=95.84 E-value=0.0047 Score=55.24 Aligned_cols=43 Identities=23% Similarity=0.333 Sum_probs=35.4
Q ss_pred eEeCCC-CCccChhhhhhccCcccCCCCCceeEecCCccchhhhh
Q 002944 659 ILCTCC-NSEVSPSQFEAHAGWASRRKPFQHIYTSNGVSLHELSI 702 (863)
Q Consensus 659 I~CsCC-n~~~SPSeFEaHAG~~srRkPy~sIytsnG~SL~elai 702 (863)
-.|..+ ++||||++||.++|.....+|..+|++ +|.+|..+..
T Consensus 25 ~kCI~~~~~~~TP~eFe~~~g~~~~K~WK~sIR~-~g~~Lr~L~~ 68 (73)
T smart00258 25 VKCIQYEDKWFTPKEFEIEGGKGKSKDWKRSIRC-GGSSLRTLME 68 (73)
T ss_pred cCCccCCCEEEChHHHHhhcCCcccCCcchheeE-CCccHHHHHH
Confidence 344445 678999999999999888999999987 8899887653
No 30
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=95.63 E-value=0.0047 Score=66.84 Aligned_cols=33 Identities=27% Similarity=0.516 Sum_probs=29.7
Q ss_pred CCceEeccc--cc-ccccccccccCCCCCCC-CCCCCcceeee
Q 002944 822 RRTVILCDQ--CE-REYHVGCLKDHGMEDLQ-VPQLLVYDTIS 860 (863)
Q Consensus 822 ~gtII~CDq--Ce-raYHV~CLr~aGL~dLK-lPe~~wy~~iC 860 (863)
-+.||.||. |+ .|||..|+. |+ -|++-|||+-|
T Consensus 229 yg~Mi~CDn~~C~~eWFH~~CVG------L~~~PkgkWyC~~C 265 (274)
T KOG1973|consen 229 YGKMIGCDNPGCPIEWFHFTCVG------LKTKPKGKWYCPRC 265 (274)
T ss_pred cccccccCCCCCCcceEEEeccc------cccCCCCcccchhh
Confidence 368999997 99 999999997 66 89999999987
No 31
>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=95.62 E-value=0.0061 Score=60.95 Aligned_cols=25 Identities=36% Similarity=1.081 Sum_probs=22.0
Q ss_pred ccccCCCC--CCCCCCCCccccccccc
Q 002944 737 AFHIDCVS--LPGIPSGTWHCRYCMNT 761 (863)
Q Consensus 737 aFH~~CL~--L~~vP~G~W~C~~C~~~ 761 (863)
+||++||. |..+|+|+|+|+.|...
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~ 27 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVE 27 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCC
Confidence 59999995 66999999999999863
No 32
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.44 E-value=0.0051 Score=70.70 Aligned_cols=47 Identities=26% Similarity=0.626 Sum_probs=39.1
Q ss_pred cCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCC-cceeee
Q 002944 804 LGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLL-VYDTIS 860 (863)
Q Consensus 804 ~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~-wy~~iC 860 (863)
.-.|.||++.. +.--+++||.|.+-||++||. ++|. +|+.- -|.|+|
T Consensus 544 ~ysCgiCkks~------dQHll~~CDtC~lhYHlGCL~----PPLTR~Pkk~kn~gWqC 592 (707)
T KOG0957|consen 544 NYSCGICKKST------DQHLLTQCDTCHLHYHLGCLS----PPLTRLPKKNKNFGWQC 592 (707)
T ss_pred ceeeeeeccch------hhHHHhhcchhhceeeccccC----CccccCcccccCcceee
Confidence 45699999853 456789999999999999999 6888 99876 777777
No 33
>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=95.30 E-value=0.005 Score=55.84 Aligned_cols=44 Identities=32% Similarity=0.402 Sum_probs=34.5
Q ss_pred CCeeEeCCCCCccChhhhhhccCcccCCCCCceeEecCCccchhhhh
Q 002944 656 GFGILCTCCNSEVSPSQFEAHAGWASRRKPFQHIYTSNGVSLHELSI 702 (863)
Q Consensus 656 G~GI~CsCCn~~~SPSeFEaHAG~~srRkPy~sIytsnG~SL~elai 702 (863)
+..|.+. +.|+||++||.|+|....++|..+|++ +|.+|..+..
T Consensus 34 ~kCI~~~--g~~~TP~eFE~~~G~~~sK~WK~SIr~-~g~~L~~li~ 77 (82)
T PF01342_consen 34 GKCIQCE--GRWFTPSEFERHGGKGSSKDWKRSIRC-GGEPLGKLIE 77 (82)
T ss_dssp SS-EEET--TEEE-HHHHHHHHTTCTCS-HHHHSEE-TTEEHHHHHH
T ss_pred CceEeeC--CcEECHHHHHhhcCcccCCCCCccEEE-CCEEHHHHHh
Confidence 3445555 889999999999999998899999999 8999887653
No 34
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.04 E-value=0.0095 Score=68.61 Aligned_cols=45 Identities=33% Similarity=0.832 Sum_probs=37.0
Q ss_pred ccccccccCC-----ceEEcCCCCCccccCCCCC------CCCCCCCccccccccc
Q 002944 717 DLCGICMDGG-----DLLCCDSCPRAFHIDCVSL------PGIPSGTWHCRYCMNT 761 (863)
Q Consensus 717 d~C~VC~dgG-----dLL~CD~CpraFH~~CL~L------~~vP~G~W~C~~C~~~ 761 (863)
-.|.||..|+ .||.|+.|..-||+.|+-+ ..-|...|||..|...
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~ 224 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRG 224 (464)
T ss_pred ceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccc
Confidence 3489998654 7999999999999999953 2457889999999864
No 35
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=94.67 E-value=0.0074 Score=77.46 Aligned_cols=51 Identities=31% Similarity=0.886 Sum_probs=43.2
Q ss_pred CCccccccccccccCC---ceEEcCCCCCccccCCCC--CCCCCCCCccccccccc
Q 002944 711 SSKENDDLCGICMDGG---DLLCCDSCPRAFHIDCVS--LPGIPSGTWHCRYCMNT 761 (863)
Q Consensus 711 s~~endd~C~VC~dgG---dLL~CD~CpraFH~~CL~--L~~vP~G~W~C~~C~~~ 761 (863)
........|.+|...+ .++.|+.|...||++|+. +..+|.|+|+|+.|+..
T Consensus 1103 ~~s~~~~~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1103 DRSAVNALCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKE 1158 (1404)
T ss_pred ccccchhhhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchh
Confidence 3445567899999755 689999999999999995 66899999999999864
No 36
>smart00258 SAND SAND domain.
Probab=94.62 E-value=0.029 Score=50.33 Aligned_cols=51 Identities=29% Similarity=0.394 Sum_probs=40.4
Q ss_pred EeCCeEEeecCCCCCCeeeChhhHhhhcCCC-CCCCCCceeccCCCcHHHHHHH
Q 002944 441 VKGSGISCFCDDCKGNQVVTPAVFELHAGSS-NKRPPEYIYLENGKTLRDIMNV 493 (863)
Q Consensus 441 I~~~GIlC~Cc~C~g~kVvS~s~FE~HAGs~-~r~P~~~IyLeNGkSL~dvl~a 493 (863)
....|+.+.|-.+++ +-+||++||.|||.. ++.=-..|. -||.+|+.+|+.
T Consensus 18 kf~~G~~~kCI~~~~-~~~TP~eFe~~~g~~~~K~WK~sIR-~~g~~Lr~L~~~ 69 (73)
T smart00258 18 KFKCGISVKCIQYED-KWFTPKEFEIEGGKGKSKDWKRSIR-CGGSSLRTLMEN 69 (73)
T ss_pred hhhcCcccCCccCCC-EEEChHHHHhhcCCcccCCcchhee-ECCccHHHHHHc
Confidence 345699999999877 899999999999975 444334554 479999999875
No 37
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=94.60 E-value=0.022 Score=71.23 Aligned_cols=52 Identities=17% Similarity=0.397 Sum_probs=44.5
Q ss_pred CCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeeeee
Q 002944 801 DTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTISFW 862 (863)
Q Consensus 801 ~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC~~ 862 (863)
..+...|.||.+++. +....+++||.|..++|.+|.. .+ +|++.|.|--|.|
T Consensus 216 ~~~D~~C~iC~~~~~----~n~n~ivfCD~Cnl~VHq~Cyg------i~~ipeg~WlCr~Cl~ 268 (1051)
T KOG0955|consen 216 LEEDAVCCICLDGEC----QNSNVIVFCDGCNLAVHQECYG------IPFIPEGQWLCRRCLQ 268 (1051)
T ss_pred cCCCccceeeccccc----CCCceEEEcCCCcchhhhhccC------CCCCCCCcEeehhhcc
Confidence 456778999999864 3457899999999999999997 55 9999999999986
No 38
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=93.44 E-value=0.046 Score=50.76 Aligned_cols=37 Identities=22% Similarity=0.535 Sum_probs=31.5
Q ss_pred CcCccccCCCCCcCCCCCCCCceEeccc--ccccccccccccCCCCC
Q 002944 803 ELGGCVLCRGRDFCKSRFGRRTVILCDQ--CEREYHVGCLKDHGMED 847 (863)
Q Consensus 803 e~~~C~ICkk~dfsks~f~~gtII~CDq--CeraYHV~CLr~aGL~d 847 (863)
....|.+|++. .+.+++|.. |.++||+.|+..+|+..
T Consensus 54 ~~~~C~iC~~~--------~G~~i~C~~~~C~~~fH~~CA~~~g~~~ 92 (110)
T PF13832_consen 54 FKLKCSICGKS--------GGACIKCSHPGCSTAFHPTCARKAGLYF 92 (110)
T ss_pred cCCcCcCCCCC--------CceeEEcCCCCCCcCCCHHHHHHCCCeE
Confidence 45669999984 478999998 99999999999999753
No 39
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=89.37 E-value=0.22 Score=44.50 Aligned_cols=49 Identities=20% Similarity=0.419 Sum_probs=34.3
Q ss_pred cCccccCCCCCcCCCCCCCCceEeccc--ccccccccccccCCCCCCCCCCCCcceeee
Q 002944 804 LGGCVLCRGRDFCKSRFGRRTVILCDQ--CEREYHVGCLKDHGMEDLQVPQLLVYDTIS 860 (863)
Q Consensus 804 ~~~C~ICkk~dfsks~f~~gtII~CDq--CeraYHV~CLr~aGL~dLKlPe~~wy~~iC 860 (863)
...|++|++. .|..|.|.. |.+.||+.|+..++......-+..++..+|
T Consensus 36 ~~~C~~C~~~--------~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C 86 (90)
T PF13771_consen 36 KLKCSICKKK--------GGACIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFC 86 (90)
T ss_pred CCCCcCCCCC--------CCeEEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEEC
Confidence 3459999984 268999994 999999999998886422122333454444
No 40
>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=88.92 E-value=0.083 Score=48.08 Aligned_cols=55 Identities=27% Similarity=0.492 Sum_probs=38.4
Q ss_pred eeEEEe-----CCeEEeecCCCCCCeeeChhhHhhhcCCCC-CCCCCceeccCCCcHHHHHHH
Q 002944 437 LRGVVK-----GSGISCFCDDCKGNQVVTPAVFELHAGSSN-KRPPEYIYLENGKTLRDIMNV 493 (863)
Q Consensus 437 L~G~I~-----~~GIlC~Cc~C~g~kVvS~s~FE~HAGs~~-r~P~~~IyLeNGkSL~dvl~a 493 (863)
+.|++. ..|+...|-.+. .+-+||.+||.|||... ++=-..|.. +|.+|..+|+.
T Consensus 18 ~~G~L~~~k~~~~g~~~kCI~~~-g~~~TP~eFE~~~G~~~sK~WK~SIr~-~g~~L~~li~~ 78 (82)
T PF01342_consen 18 VKGTLYKKKFVKQGICGKCIQCE-GRWFTPSEFERHGGKGSSKDWKRSIRC-GGEPLGKLIEK 78 (82)
T ss_dssp EEEEEEHHHH-TTGTTSS-EEET-TEEE-HHHHHHHHTTCTCS-HHHHSEE-TTEEHHHHHHT
T ss_pred eEEEEEHHHhhcccccCceEeeC-CcEECHHHHHhhcCcccCCCCCccEEE-CCEEHHHHHhh
Confidence 466655 345555566666 47899999999999864 444467877 99999998765
No 41
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=86.45 E-value=0.35 Score=58.55 Aligned_cols=52 Identities=25% Similarity=0.365 Sum_probs=43.3
Q ss_pred CCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCCCCCCCcceeeee
Q 002944 801 DTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQVPQLLVYDTISF 861 (863)
Q Consensus 801 ~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLKlPe~~wy~~iC~ 861 (863)
.++...|-+|+.+|. .....|++||.|....|.-|+. .|++|++-|.|-.|-
T Consensus 268 ~dedviCDvCrspD~----e~~neMVfCd~Cn~cVHqaCyG-----Ile~p~gpWlCr~Ca 319 (893)
T KOG0954|consen 268 YDEDVICDVCRSPDS----EEANEMVFCDKCNICVHQACYG-----ILEVPEGPWLCRTCA 319 (893)
T ss_pred ccccceeceecCCCc----cccceeEEeccchhHHHHhhhc-----eeecCCCCeeehhcc
Confidence 346677999999863 3467899999999999999997 567999999998883
No 42
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.42 E-value=0.47 Score=40.56 Aligned_cols=39 Identities=21% Similarity=0.512 Sum_probs=31.9
Q ss_pred CccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCC
Q 002944 805 GGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDL 848 (863)
Q Consensus 805 ~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dL 848 (863)
..|.+|++. ....+.+++|..|...||-.|....|-+.+
T Consensus 6 ~~C~~Cg~~-----~~~~dDiVvCp~CgapyHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 6 CKCPVCGKK-----FKDGDDIVVCPECGAPYHRDCWEKAGGCIN 44 (54)
T ss_pred ccChhhCCc-----ccCCCCEEECCCCCCcccHHHHhhCCceEe
Confidence 459999984 223678999999999999999998887754
No 43
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=85.80 E-value=0.19 Score=65.17 Aligned_cols=50 Identities=26% Similarity=0.506 Sum_probs=43.1
Q ss_pred CCCcCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeee
Q 002944 801 DTELGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTIS 860 (863)
Q Consensus 801 ~~e~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC 860 (863)
......|-+|+.. ++...++.|+.|...||..|++ +.|. +|.+=|+|+-|
T Consensus 1105 s~~~~~c~~cr~k------~~~~~m~lc~~c~~~~h~~C~r----p~~~~~~~~dW~C~~c 1155 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRK------KQDEKMLLCDECLSGFHLFCLR----PALSSVPPGDWMCPSC 1155 (1404)
T ss_pred ccchhhhhhhhhc------ccchhhhhhHhhhhhHHHHhhh----hhhccCCcCCccCCcc
Confidence 4556789999983 3567899999999999999999 6788 99999999988
No 44
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=84.30 E-value=0.47 Score=55.30 Aligned_cols=49 Identities=20% Similarity=0.453 Sum_probs=40.1
Q ss_pred cCccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeeeee
Q 002944 804 LGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTISFW 862 (863)
Q Consensus 804 ~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC~~ 862 (863)
...|++|...+.. ...+++.||.|+.+.|..|.. .. ||++.|.|--|++
T Consensus 193 d~~C~~c~~t~~e----N~naiVfCdgC~i~VHq~CYG------I~f~peG~WlCrkCi~ 242 (669)
T COG5141 193 DDICTKCTSTHNE----NSNAIVFCDGCEICVHQSCYG------IQFLPEGFWLCRKCIY 242 (669)
T ss_pred hhhhHhccccccC----CcceEEEecCcchhhhhhccc------ceecCcchhhhhhhcc
Confidence 4558888876533 246999999999999999987 45 8999999988875
No 45
>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=81.81 E-value=3.1 Score=46.00 Aligned_cols=62 Identities=29% Similarity=0.547 Sum_probs=41.4
Q ss_pred HhcCCCCCcEEEEEeCCccCCCcccceeEEEeCCe------EEeecCCCCCCeeeChhhHhhhcCCC-CCCCCCce
Q 002944 411 LESGILEGMSVMYIRGSKVKGPGVSGLRGVVKGSG------ISCFCDDCKGNQVVTPAVFELHAGSS-NKRPPEYI 479 (863)
Q Consensus 411 l~tGlLeG~~V~Y~~~~~~~~~g~~~L~G~I~~~G------IlC~Cc~C~g~kVvS~s~FE~HAGs~-~r~P~~~I 479 (863)
+.+.+++.+|-.+-.+. |+.-+.+.|+.+.-| |.|-|.- ..+||.+|=.|||.. .-||-.||
T Consensus 215 ~~~~~~~~mp~v~t~g~---gpng~~i~g~ly~y~~~~~v~i~c~chg----~~~~~~efv~h~~~~~~~~p~~hi 283 (284)
T PF07897_consen 215 GSRNMMEDMPCVSTTGD---GPNGKRIEGFLYKYGKGEEVRIVCVCHG----SFLSPAEFVKHAGGGDVANPLRHI 283 (284)
T ss_pred ccccccccCCceeeccC---CCCCceeeEEEEEecCCCeEEEEEEecC----CCCCHHHHHHhcCCCCcCCchhcc
Confidence 33445566664443321 122245677765542 8888886 569999999999986 58999998
No 46
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=75.72 E-value=4.6 Score=41.84 Aligned_cols=19 Identities=42% Similarity=0.955 Sum_probs=16.7
Q ss_pred eEEcCCCCCccccCCCCCC
Q 002944 728 LLCCDSCPRAFHIDCVSLP 746 (863)
Q Consensus 728 LL~CD~CpraFH~~CL~L~ 746 (863)
|..|..|.|+||..-|+..
T Consensus 124 LFRC~~C~RawH~~HLP~~ 142 (175)
T PF15446_consen 124 LFRCTSCHRAWHFEHLPPP 142 (175)
T ss_pred EEecCCccceeehhhCCCC
Confidence 6889999999999999643
No 47
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=70.49 E-value=2.9 Score=49.00 Aligned_cols=47 Identities=28% Similarity=0.561 Sum_probs=40.1
Q ss_pred ccccccccccccCCceEEcCCCCCccccCCCCCCCCCCCCcccccccc
Q 002944 713 KENDDLCGICMDGGDLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMN 760 (863)
Q Consensus 713 ~endd~C~VC~dgGdLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~ 760 (863)
..+.++|.+|.++|.+++|+.|..++|..|... ..|...|.|..|..
T Consensus 86 ~~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~-~~~~c~~~~~d~~~ 132 (463)
T KOG1081|consen 86 KIEPSECFVCFKGGSLVTCKSRIQAPHRKCKPA-QLEKCSKRCTDCRA 132 (463)
T ss_pred CCCcchhccccCCCccceeccccccccccCcCc-cCcccccCCcceee
Confidence 456689999999999999999999999999864 56778888888875
No 48
>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=66.81 E-value=7.3 Score=43.21 Aligned_cols=32 Identities=41% Similarity=0.787 Sum_probs=29.6
Q ss_pred eeEeCCCCCccChhhhhhccCcccCCCCCcee
Q 002944 658 GILCTCCNSEVSPSQFEAHAGWASRRKPFQHI 689 (863)
Q Consensus 658 GI~CsCCn~~~SPSeFEaHAG~~srRkPy~sI 689 (863)
-|+|.|=+.-++|.+|-.|||...--+|..||
T Consensus 252 ~i~c~chg~~~~~~efv~h~~~~~~~~p~~hi 283 (284)
T PF07897_consen 252 RIVCVCHGSFLSPAEFVKHAGGGDVANPLRHI 283 (284)
T ss_pred EEEEEecCCCCCHHHHHHhcCCCCcCCchhcc
Confidence 58999999999999999999998888999888
No 49
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=66.55 E-value=1.9 Score=33.82 Aligned_cols=33 Identities=21% Similarity=0.405 Sum_probs=17.3
Q ss_pred CceEecccccccccccccccCCCCCCCCCCC-Ccceeee
Q 002944 823 RTVILCDQCEREYHVGCLKDHGMEDLQVPQL-LVYDTIS 860 (863)
Q Consensus 823 gtII~CDqCeraYHV~CLr~aGL~dLKlPe~-~wy~~iC 860 (863)
..+|.|+.|...+|..|..-.. +|.. .|+|-.|
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~-----~~~~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSE-----VPDGDDWLCDRC 35 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS-------SS-----HHH
T ss_pred CceEEeCCCCCcCChhhCCccc-----CCCCCcEECCcC
Confidence 3689999999999999997222 3443 5776544
No 50
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=66.18 E-value=2.9 Score=35.87 Aligned_cols=29 Identities=31% Similarity=0.866 Sum_probs=25.3
Q ss_pred ccccccccc----CCceEEcCCCCCccccCCCC
Q 002944 716 DDLCGICMD----GGDLLCCDSCPRAFHIDCVS 744 (863)
Q Consensus 716 dd~C~VC~d----gGdLL~CD~CpraFH~~CL~ 744 (863)
...|.+|++ +++++.|..|...||..|+.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 357999985 67999999999999999994
No 51
>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=62.84 E-value=5 Score=46.81 Aligned_cols=37 Identities=30% Similarity=0.557 Sum_probs=29.6
Q ss_pred cccCCCCCcCCCCCCCCceEecccccccccccccccCCCC
Q 002944 807 CVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGME 846 (863)
Q Consensus 807 C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~ 846 (863)
|.+|.+-|+++ ++-.-|.||.|+.|-|.+|+-.+++.
T Consensus 131 C~iC~kfD~~~---n~~~Wi~Cd~CgH~cH~dCALr~~~i 167 (446)
T PF07227_consen 131 CCICSKFDDNK---NTCSWIGCDVCGHWCHLDCALRHELI 167 (446)
T ss_pred ccccCCcccCC---CCeeEEeccCCCceehhhhhcccccc
Confidence 88998866554 34457889999999999998877764
No 52
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=56.96 E-value=9.8 Score=42.81 Aligned_cols=37 Identities=22% Similarity=0.443 Sum_probs=25.8
Q ss_pred cCCCCCcCCCCCCCCceEeccccccccc-ccccccCCC
Q 002944 809 LCRGRDFCKSRFGRRTVILCDQCEREYH-VGCLKDHGM 845 (863)
Q Consensus 809 ICkk~dfsks~f~~gtII~CDqCeraYH-V~CLr~aGL 845 (863)
.|..++-....-..+.+++|--|+-||| -+|++...+
T Consensus 132 ~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~~~~ 169 (345)
T KOG2752|consen 132 KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQAKTF 169 (345)
T ss_pred EecCCCCCccccccceeeeEEeccchhcccccCcccch
Confidence 4555443322334679999999999999 899885443
No 53
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=54.96 E-value=6.4 Score=34.76 Aligned_cols=46 Identities=35% Similarity=0.765 Sum_probs=18.2
Q ss_pred ccccccccC----Cc--eEEcC--CCCCccccCCCC-----CC----CCCCCCcccccccccc
Q 002944 717 DLCGICMDG----GD--LLCCD--SCPRAFHIDCVS-----LP----GIPSGTWHCRYCMNTF 762 (863)
Q Consensus 717 d~C~VC~dg----Gd--LL~CD--~CpraFH~~CL~-----L~----~vP~G~W~C~~C~~~~ 762 (863)
..|.||... +. .+.|+ .|...||..||. ++ ..-.-.+.||.|...+
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 458888743 22 47897 899999999993 11 1112346799998754
No 54
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=52.83 E-value=7.5 Score=34.34 Aligned_cols=34 Identities=24% Similarity=0.730 Sum_probs=13.3
Q ss_pred ccccCCCCCcCCCCCCCCceEecc--ccccccccccccc
Q 002944 806 GCVLCRGRDFCKSRFGRRTVILCD--QCEREYHVGCLKD 842 (863)
Q Consensus 806 ~C~ICkk~dfsks~f~~gtII~CD--qCeraYHV~CLr~ 842 (863)
.|.||...-. ..+....+.|+ .|.+.||..||..
T Consensus 4 ~C~IC~~~~~---~~~~~p~~~C~n~~C~~~fH~~CL~~ 39 (70)
T PF11793_consen 4 ECGICYSYRL---DDGEIPDVVCPNPSCGKKFHLLCLSE 39 (70)
T ss_dssp S-SSS--SS----TT-----B--S-TT----B-SGGGHH
T ss_pred CCCcCCcEec---CCCCcCceEcCCcccCCHHHHHHHHH
Confidence 4999987432 12334678998 9999999999974
No 55
>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=50.74 E-value=14 Score=43.66 Aligned_cols=32 Identities=25% Similarity=0.632 Sum_probs=23.6
Q ss_pred ceEEcCCCCCccccCCCCCCCCCCCCccccccccc
Q 002944 727 DLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMNT 761 (863)
Q Consensus 727 dLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~~ 761 (863)
+|++|..|..--+..|+.. .-..|||+.|...
T Consensus 4 ~L~fC~~C~~irc~~c~~~---Ei~~~yCp~CL~~ 35 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPRCVSE---EIDSYYCPNCLFE 35 (483)
T ss_pred cceecccccccCChhhccc---ccceeECcccccc
Confidence 5788988887777777743 2247999999863
No 56
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=47.86 E-value=8.8 Score=35.72 Aligned_cols=30 Identities=37% Similarity=0.831 Sum_probs=25.6
Q ss_pred cccccccccc-CCceEEcCC--CCCccccCCCC
Q 002944 715 NDDLCGICMD-GGDLLCCDS--CPRAFHIDCVS 744 (863)
Q Consensus 715 ndd~C~VC~d-gGdLL~CD~--CpraFH~~CL~ 744 (863)
....|.+|+. .|-.+-|.. |..+||..|..
T Consensus 54 ~~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 54 FKLKCSICGKSGGACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred cCCcCcCCCCCCceeEEcCCCCCCcCCCHHHHH
Confidence 3468999998 588999987 99999999983
No 57
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=46.05 E-value=12 Score=48.14 Aligned_cols=42 Identities=21% Similarity=0.537 Sum_probs=35.7
Q ss_pred ccccCCCCCcCCCCCCCCceEecccccccccccccccCCCCCCC-CCCCCcceeee
Q 002944 806 GCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGMEDLQ-VPQLLVYDTIS 860 (863)
Q Consensus 806 ~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL~dLK-lPe~~wy~~iC 860 (863)
.|.+|.+ .+.+++|..|++-||..|+. ..+- +|+..|-|-+|
T Consensus 346 hcrf~~d---------~~~~lc~Et~prvvhlEcv~----hP~~~~~s~~~e~evc 388 (1414)
T KOG1473|consen 346 HCRFCHD---------LGDLLCCETCPRVVHLECVF----HPRFAVPSAFWECEVC 388 (1414)
T ss_pred cccccCc---------ccceeecccCCceEEeeecC----CccccCCCccchhhhh
Confidence 4999987 36789999999999999998 3455 89999998887
No 58
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=44.90 E-value=25 Score=44.38 Aligned_cols=47 Identities=38% Similarity=1.022 Sum_probs=38.0
Q ss_pred ccccccccccCCc--eEEcCCCCCccccCCCC--CCCCCCCCccccccccc
Q 002944 715 NDDLCGICMDGGD--LLCCDSCPRAFHIDCVS--LPGIPSGTWHCRYCMNT 761 (863)
Q Consensus 715 ndd~C~VC~dgGd--LL~CD~CpraFH~~CL~--L~~vP~G~W~C~~C~~~ 761 (863)
....|..|..+.. ++.|+.|...||..|.. ++.+++|.|.|+.|...
T Consensus 154 ~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 204 (904)
T KOG1246|consen 154 DYPQCNTCSKGKEEKLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIPT 204 (904)
T ss_pred cchhhhccccCCCccceecccccCcccccccCCCCCcCCcCcccCCccccc
Confidence 3456888887652 33999999999999995 66899999999999753
No 59
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.26 E-value=14 Score=42.07 Aligned_cols=47 Identities=28% Similarity=0.681 Sum_probs=34.8
Q ss_pred ccccccccC---CceEEcCCCCCccccCCCCCCCCCCCCcccccccccccc
Q 002944 717 DLCGICMDG---GDLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMNTFQK 764 (863)
Q Consensus 717 d~C~VC~dg---GdLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~~~~k 764 (863)
+.|.+|.+. |+.|-==-|...||..|+++.-... .-+||.|+..+.+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~-r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT-RTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc-CccCCCCCCcCCC
Confidence 699999974 6655556799999999998543333 3479999986554
No 60
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=44.13 E-value=7.9 Score=36.05 Aligned_cols=32 Identities=28% Similarity=0.725 Sum_probs=22.1
Q ss_pred eEEcCCCCCccccCCCC--CCCCCCCCccccccccc
Q 002944 728 LLCCDSCPRAFHIDCVS--LPGIPSGTWHCRYCMNT 761 (863)
Q Consensus 728 LL~CD~CpraFH~~CL~--L~~vP~G~W~C~~C~~~ 761 (863)
|++ ..|...||..|+- +.. +...=.||.|+..
T Consensus 47 lv~-g~C~H~FH~hCI~kWl~~-~~~~~~CPmCR~~ 80 (85)
T PF12861_consen 47 LVW-GKCSHNFHMHCILKWLST-QSSKGQCPMCRQP 80 (85)
T ss_pred eee-ccCccHHHHHHHHHHHcc-ccCCCCCCCcCCe
Confidence 443 3499999999994 322 2334599999974
No 61
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=40.23 E-value=14 Score=33.00 Aligned_cols=28 Identities=36% Similarity=0.973 Sum_probs=24.8
Q ss_pred ccccccccC-CceEEcC--CCCCccccCCCC
Q 002944 717 DLCGICMDG-GDLLCCD--SCPRAFHIDCVS 744 (863)
Q Consensus 717 d~C~VC~dg-GdLL~CD--~CpraFH~~CL~ 744 (863)
..|.+|... |-.+-|. .|.+.||..|.-
T Consensus 37 ~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~ 67 (90)
T PF13771_consen 37 LKCSICKKKGGACIGCSHPGCSRSFHVPCAR 67 (90)
T ss_pred CCCcCCCCCCCeEEEEeCCCCCcEEChHHHc
Confidence 579999998 9999996 499999999984
No 62
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.77 E-value=25 Score=42.25 Aligned_cols=48 Identities=27% Similarity=0.353 Sum_probs=39.2
Q ss_pred ccccccccccccCCceEEcCCCCCccccCCCCCC-CCC--CCCcccccccc
Q 002944 713 KENDDLCGICMDGGDLLCCDSCPRAFHIDCVSLP-GIP--SGTWHCRYCMN 760 (863)
Q Consensus 713 ~endd~C~VC~dgGdLL~CD~CpraFH~~CL~L~-~vP--~G~W~C~~C~~ 760 (863)
...+.+|+-|.-.|..+.|+.|.|+||..|.... +.+ .-.|.|+.|..
T Consensus 57 ~N~d~~cfechlpg~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s 107 (588)
T KOG3612|consen 57 SNIDPFCFECHLPGAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYS 107 (588)
T ss_pred cCCCcccccccCCcceeeeehhhccccccccCcchhhccccccccCCcccc
Confidence 3456789999999999999999999999999643 333 45799998875
No 63
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=36.01 E-value=26 Score=36.70 Aligned_cols=38 Identities=26% Similarity=0.699 Sum_probs=29.4
Q ss_pred cccccccccCC--------ceEEcCCCCCccccCCCCCCCCCCCCcccccccc
Q 002944 716 DDLCGICMDGG--------DLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMN 760 (863)
Q Consensus 716 dd~C~VC~dgG--------dLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~ 760 (863)
...|.+|.+.+ ....|..|...||..|... -.||.|..
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~-------~~CpkC~R 197 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK-------KSCPKCAR 197 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC-------CCCCCcHh
Confidence 36788888654 4689999999999999973 23888864
No 64
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.58 E-value=17 Score=40.39 Aligned_cols=51 Identities=25% Similarity=0.454 Sum_probs=34.3
Q ss_pred CCccccccccccccCCc----------eEEcCCCCCccccCCCCCCCCCCCCccccccccc
Q 002944 711 SSKENDDLCGICMDGGD----------LLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMNT 761 (863)
Q Consensus 711 s~~endd~C~VC~dgGd----------LL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~~ 761 (863)
...-++..|.||++.=+ -+.=-.|+..||..|..-.-+-.-.-.||.|+..
T Consensus 219 tkhl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKek 279 (328)
T KOG1734|consen 219 TKHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEK 279 (328)
T ss_pred CCCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHH
Confidence 45667899999996311 1112259999999999644333445689999863
No 65
>KOG1080 consensus Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics; Transcription]
Probab=34.17 E-value=48 Score=42.76 Aligned_cols=45 Identities=27% Similarity=0.737 Sum_probs=36.3
Q ss_pred cccccccccC-----CceEEcCCCCCccccCCCCCCCCC-CCCcccccccc
Q 002944 716 DDLCGICMDG-----GDLLCCDSCPRAFHIDCVSLPGIP-SGTWHCRYCMN 760 (863)
Q Consensus 716 dd~C~VC~dg-----GdLL~CD~CpraFH~~CL~L~~vP-~G~W~C~~C~~ 760 (863)
-+-|.+|.+- ...+.|+.|.++.|..|++....+ .-.|.|..|..
T Consensus 573 t~~c~~~~~~~~~~~n~~~~~~~~~~~~~s~~~g~~~~~~~~~~~~~~~~~ 623 (1005)
T KOG1080|consen 573 TERCAVCRDDEDWEKNVSIICDRCTRSVHSECYGNLKSYDGTSWVCDSCET 623 (1005)
T ss_pred cccccccccccccccceeeeeccccccCCCcccccCCCCCCCcchhhcccc
Confidence 3679999863 358899999999999999855444 45799999986
No 66
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=33.65 E-value=38 Score=35.52 Aligned_cols=36 Identities=25% Similarity=0.702 Sum_probs=28.2
Q ss_pred ccccCCCCCcCCCCCCCCceEeccccccccccccccc
Q 002944 806 GCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKD 842 (863)
Q Consensus 806 ~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~ 842 (863)
.|-+|...+. .=.|...+++.|..|...||..|...
T Consensus 154 iCe~C~~~~~-IfPF~~~~~~~C~~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 154 ICEICNSDDI-IFPFQIDTTVRCPKCKSVFHKSCFRK 189 (202)
T ss_pred CCccCCCCCC-CCCCCCCCeeeCCcCccccchhhcCC
Confidence 4888876532 22566779999999999999999985
No 67
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=33.33 E-value=16 Score=44.28 Aligned_cols=39 Identities=28% Similarity=0.593 Sum_probs=27.9
Q ss_pred ccccCCCCCcCCCCCCCCceEecccccccccccccccCCC
Q 002944 806 GCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDHGM 845 (863)
Q Consensus 806 ~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~aGL 845 (863)
.|.+|...+ -.=.|..+++..|+.|...||..|++....
T Consensus 513 iCe~Cq~~~-iiyPF~~~~~~rC~~C~avfH~~C~~r~s~ 551 (580)
T KOG1829|consen 513 ICELCQHND-IIYPFETRNTRRCSTCLAVFHKKCLRRKSP 551 (580)
T ss_pred eeeeccCCC-cccccccccceeHHHHHHHHHHHHHhccCC
Confidence 466663221 122444678999999999999999997776
No 68
>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=30.70 E-value=22 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=12.7
Q ss_pred cccCCCCCcCCCCCCCCceEeccccccccccccc
Q 002944 807 CVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCL 840 (863)
Q Consensus 807 C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CL 840 (863)
|.+|++.. .......|.+|+-..|..|+
T Consensus 3 C~~C~~~~------~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 3 CDACGKPI------DGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp -TTTS----------S--EEE-TTT-----HHHH
T ss_pred CCcCCCcC------CCCceEECccCCCccChhcC
Confidence 88898853 22478999999999999985
No 69
>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=30.34 E-value=43 Score=30.32 Aligned_cols=30 Identities=23% Similarity=0.693 Sum_probs=20.4
Q ss_pred CccccCCCCCcCCCCCCCCceEecccccccccccccc
Q 002944 805 GGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLK 841 (863)
Q Consensus 805 ~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr 841 (863)
..|.+|+++ ++...+... -|+..||..|++
T Consensus 79 ~~C~vC~k~------l~~~~f~~~-p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKP------LGNSVFVVF-PCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCc------CCCceEEEe-CCCeEEeccccc
Confidence 459999994 333333333 456999999986
No 70
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=26.63 E-value=53 Score=26.69 Aligned_cols=36 Identities=19% Similarity=0.296 Sum_probs=25.6
Q ss_pred cCccccCCCCCcCCCCCCCCceEecccccccccccccccC
Q 002944 804 LGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDH 843 (863)
Q Consensus 804 ~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~a 843 (863)
...|.+|++.-. + ....-+.|..|...+|-.|+...
T Consensus 11 ~~~C~~C~~~i~---g-~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 11 PTYCDVCGKFIW---G-LGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp TEB-TTSSSBEC---S-SSSCEEEETTTT-EEETTGGCTS
T ss_pred CCCCcccCcccC---C-CCCCeEEECCCCChHhhhhhhhc
Confidence 345999998431 1 34678999999999999999843
No 71
>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=22.53 E-value=24 Score=27.83 Aligned_cols=31 Identities=23% Similarity=0.571 Sum_probs=21.7
Q ss_pred ccccCCCCCcCCCCCCCCceEeccccccccccccccc
Q 002944 806 GCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKD 842 (863)
Q Consensus 806 ~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~ 842 (863)
.|.||...-. ....++... |...||..|+..
T Consensus 2 ~C~IC~~~~~-----~~~~~~~l~-C~H~fh~~Ci~~ 32 (44)
T PF13639_consen 2 ECPICLEEFE-----DGEKVVKLP-CGHVFHRSCIKE 32 (44)
T ss_dssp CETTTTCBHH-----TTSCEEEET-TSEEEEHHHHHH
T ss_pred CCcCCChhhc-----CCCeEEEcc-CCCeeCHHHHHH
Confidence 3899987321 234555555 999999999873
No 72
>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=22.13 E-value=37 Score=32.48 Aligned_cols=48 Identities=23% Similarity=0.505 Sum_probs=0.0
Q ss_pred Ccccccccccccc--CCceEEc------CCC---CCccccCCC-------CCCCCCCCCccccccc
Q 002944 712 SKENDDLCGICMD--GGDLLCC------DSC---PRAFHIDCV-------SLPGIPSGTWHCRYCM 759 (863)
Q Consensus 712 ~~endd~C~VC~d--gGdLL~C------D~C---praFH~~CL-------~L~~vP~G~W~C~~C~ 759 (863)
...+...|..|.. .+....| ..| ...|-..|| ....+..+.|.||.|+
T Consensus 3 d~~~g~~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Cr 68 (105)
T PF10497_consen 3 DSVNGKTCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCR 68 (105)
T ss_pred cCCCCCCchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCC
No 73
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=21.80 E-value=35 Score=31.81 Aligned_cols=20 Identities=30% Similarity=0.738 Sum_probs=15.5
Q ss_pred cccccccccc----cccCCCCCCC
Q 002944 830 QCEREYHVGC----LKDHGMEDLQ 849 (863)
Q Consensus 830 qCeraYHV~C----Lr~aGL~dLK 849 (863)
.|..+||..| |...|+++|.
T Consensus 53 ~CnHaFH~HCI~rWL~Tk~~CPld 76 (88)
T COG5194 53 VCNHAFHDHCIYRWLDTKGVCPLD 76 (88)
T ss_pred ecchHHHHHHHHHHHhhCCCCCCC
Confidence 4888999999 5557777765
No 74
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=21.10 E-value=2.3e+02 Score=27.37 Aligned_cols=57 Identities=26% Similarity=0.609 Sum_probs=40.1
Q ss_pred ccccceeeeeecCCCCCCceeEEEe--C--CeE--E--------eece-eeCCeeEeCCCCCccChhhhh-hccCcc
Q 002944 620 KDLRMHKLVFEEGGLEDGAEVGYFV--R--GEK--F--------LVGY-KKGFGILCTCCNSEVSPSQFE-AHAGWA 680 (863)
Q Consensus 620 rD~~LHkllf~~g~L~dgt~V~Yy~--~--Gq~--l--------L~G~-k~G~GI~CsCCn~~~SPSeFE-aHAG~~ 680 (863)
+|.+||+--+. .+|++|.+++ + |.. - -.|| .+|+.+.|.-|+..++...+. ...|+.
T Consensus 3 ~Dgklh~y~y~----~~G~~vrff~i~~~dg~~~va~daCeiC~~~GY~q~g~~lvC~~C~~~~~~~~ig~~~GGCN 75 (102)
T PF10080_consen 3 KDGKLHRYAYT----DDGKEVRFFAIKKPDGSYRVAFDACEICGPKGYYQEGDQLVCKNCGVRFNLPTIGGKSGGCN 75 (102)
T ss_pred cCCcEEEEEEc----CCCEEEEEEEEECCCCCEEEEEEeccccCCCceEEECCEEEEecCCCEEehhhcccccCCCC
Confidence 57888887773 3567777776 1 221 1 1244 578999999999999988888 677764
No 75
>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=21.02 E-value=20 Score=26.69 Aligned_cols=41 Identities=24% Similarity=0.519 Sum_probs=26.4
Q ss_pred ccccccCC-ceEEcCCCCCccccCCCCCCCCCCCCcccccccc
Q 002944 719 CGICMDGG-DLLCCDSCPRAFHIDCVSLPGIPSGTWHCRYCMN 760 (863)
Q Consensus 719 C~VC~dgG-dLL~CD~CpraFH~~CL~L~~vP~G~W~C~~C~~ 760 (863)
|.+|.+.- +.+.-..|...||..|+..... .+...|+.|+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~-~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK-SGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH-hCcCCCCCCCC
Confidence 67777653 4444556888999999851110 15667888874
No 76
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=20.24 E-value=97 Score=36.59 Aligned_cols=25 Identities=24% Similarity=0.655 Sum_probs=15.5
Q ss_pred ccccccccC--CceEEcCCCCCccccCCC
Q 002944 717 DLCGICMDG--GDLLCCDSCPRAFHIDCV 743 (863)
Q Consensus 717 d~C~VC~dg--GdLL~CD~CpraFH~~CL 743 (863)
+.|.+|+.. ..|| -.|.++||..|.
T Consensus 335 ekC~~Cg~~I~d~iL--rA~GkayHp~CF 361 (468)
T KOG1701|consen 335 EKCNKCGEPIMDRIL--RALGKAYHPGCF 361 (468)
T ss_pred HHHhhhhhHHHHHHH--HhcccccCCCce
Confidence 457777643 1222 257889998876
No 77
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=20.04 E-value=69 Score=25.22 Aligned_cols=36 Identities=19% Similarity=0.382 Sum_probs=26.8
Q ss_pred cCccccCCCCCcCCCCCCCCceEecccccccccccccccC
Q 002944 804 LGGCVLCRGRDFCKSRFGRRTVILCDQCEREYHVGCLKDH 843 (863)
Q Consensus 804 ~~~C~ICkk~dfsks~f~~gtII~CDqCeraYHV~CLr~a 843 (863)
...|.+|.+.-. + ....-+.|+.|...+|..|.+..
T Consensus 11 ~~~C~~C~~~i~---~-~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 11 PTFCDVCRKSIW---G-LFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CCChhhcchhhh---c-cccceeEcCCCCCchhhhhhccC
Confidence 345999988421 1 13577899999999999999854
Done!