Query 009788
Match_columns 525
No_of_seqs 219 out of 938
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 17:20:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009788.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009788hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0457 Histone acetyltransfer 100.0 3E-104 6E-109 813.9 32.2 420 45-524 13-437 (438)
2 COG5114 Histone acetyltransfer 100.0 4.3E-98 9E-103 737.0 27.7 420 44-524 3-429 (432)
3 COG5259 RSC8 RSC chromatin rem 99.7 2.7E-17 5.7E-22 171.5 6.3 108 44-155 222-329 (531)
4 cd02335 ZZ_ADA2 Zinc finger, Z 99.5 3.9E-14 8.4E-19 107.3 4.2 49 47-95 1-49 (49)
5 PF04433 SWIRM: SWIRM domain; 99.5 8.6E-14 1.9E-18 117.5 6.7 78 447-524 3-85 (86)
6 KOG1279 Chromatin remodeling f 99.3 1.3E-12 2.8E-17 141.3 7.1 81 69-155 223-303 (506)
7 cd02343 ZZ_EF Zinc finger, ZZ 99.3 2.6E-12 5.6E-17 96.1 3.5 46 47-93 1-46 (48)
8 cd02338 ZZ_PCMF_like Zinc fing 99.3 3.7E-12 8.1E-17 96.5 3.8 48 47-95 1-49 (49)
9 cd02334 ZZ_dystrophin Zinc fin 99.2 4.9E-12 1.1E-16 95.6 3.7 46 47-93 1-47 (49)
10 cd02345 ZZ_dah Zinc finger, ZZ 99.2 7.2E-12 1.6E-16 94.9 3.5 46 48-94 2-48 (49)
11 PF00249 Myb_DNA-binding: Myb- 99.1 8.7E-11 1.9E-15 88.3 5.2 45 105-149 2-47 (48)
12 cd02249 ZZ Zinc finger, ZZ typ 99.1 6.7E-11 1.5E-15 88.4 3.8 46 47-95 1-46 (46)
13 cd02340 ZZ_NBR1_like Zinc fing 99.0 2.7E-10 5.8E-15 84.0 3.6 43 47-95 1-43 (43)
14 cd02341 ZZ_ZZZ3 Zinc finger, Z 99.0 3E-10 6.6E-15 85.5 3.6 45 47-95 1-48 (48)
15 cd02336 ZZ_RSC8 Zinc finger, Z 98.9 5.9E-10 1.3E-14 82.8 3.4 42 47-89 1-42 (45)
16 cd02344 ZZ_HERC2 Zinc finger, 98.9 9.4E-10 2E-14 81.6 3.5 44 47-95 1-45 (45)
17 cd02339 ZZ_Mind_bomb Zinc fing 98.9 1.6E-09 3.5E-14 80.6 3.5 43 47-94 1-44 (45)
18 smart00291 ZnF_ZZ Zinc-binding 98.8 2.2E-09 4.7E-14 79.5 3.6 41 45-86 3-43 (44)
19 PF00569 ZZ: Zinc finger, ZZ t 98.8 3.3E-09 7.1E-14 79.3 2.4 42 45-87 3-45 (46)
20 smart00717 SANT SANT SWI3, AD 98.7 3.8E-08 8.3E-13 72.3 5.8 46 105-150 2-47 (49)
21 cd00167 SANT 'SWI3, ADA2, N-Co 98.7 5.1E-08 1.1E-12 70.6 5.6 44 106-149 1-44 (45)
22 TIGR01557 myb_SHAQKYF myb-like 98.6 7.5E-08 1.6E-12 75.3 5.6 49 104-152 3-56 (57)
23 PF13921 Myb_DNA-bind_6: Myb-l 98.6 1.2E-07 2.7E-12 74.2 6.1 41 107-148 1-41 (60)
24 cd02337 ZZ_CBP Zinc finger, ZZ 98.5 7.2E-08 1.6E-12 70.4 2.2 33 47-81 1-33 (41)
25 cd02342 ZZ_UBA_plant Zinc fing 98.4 1.6E-07 3.4E-12 68.5 2.4 34 47-81 1-35 (43)
26 PLN03212 Transcription repress 98.2 1.4E-06 3E-11 86.3 5.3 49 102-150 23-72 (249)
27 KOG1280 Uncharacterized conser 98.1 1.7E-06 3.8E-11 88.6 2.8 51 44-95 6-57 (381)
28 PLN03091 hypothetical protein; 98.0 8E-06 1.7E-10 86.6 5.2 49 102-150 12-61 (459)
29 KOG4582 Uncharacterized conser 97.9 7.3E-06 1.6E-10 83.8 3.6 46 47-97 153-199 (278)
30 KOG0048 Transcription factor, 97.8 1.4E-05 3E-10 80.0 4.3 46 104-149 9-55 (238)
31 KOG4286 Dystrophin-like protei 97.8 6.5E-06 1.4E-10 91.2 0.3 55 40-95 597-652 (966)
32 PLN03212 Transcription repress 97.6 8.2E-05 1.8E-09 73.9 5.4 48 101-149 75-122 (249)
33 PLN03091 hypothetical protein; 97.2 0.00046 9.9E-09 73.6 6.1 48 101-149 64-111 (459)
34 KOG4301 Beta-dystrobrevin [Cyt 97.1 0.00012 2.5E-09 75.3 -0.5 52 41-93 235-287 (434)
35 KOG0048 Transcription factor, 96.9 0.0015 3.2E-08 65.5 5.7 48 101-149 59-106 (238)
36 KOG0049 Transcription factor, 96.1 0.0088 1.9E-07 66.2 5.6 52 101-152 357-408 (939)
37 KOG0049 Transcription factor, 95.6 0.012 2.6E-07 65.3 4.3 49 100-148 408-459 (939)
38 KOG0051 RNA polymerase I termi 94.2 0.049 1.1E-06 60.7 4.3 90 60-154 339-432 (607)
39 PF13837 Myb_DNA-bind_4: Myb/S 93.6 0.051 1.1E-06 45.4 2.5 45 105-149 2-63 (90)
40 PF07649 C1_3: C1-like domain; 92.5 0.079 1.7E-06 35.8 1.6 28 48-76 2-29 (30)
41 KOG0050 mRNA splicing protein 90.3 0.27 5.9E-06 53.7 3.9 48 104-152 7-54 (617)
42 PF03107 C1_2: C1 domain; Int 89.9 0.24 5.2E-06 33.5 2.1 29 47-76 1-29 (30)
43 KOG0051 RNA polymerase I termi 88.6 0.44 9.5E-06 53.4 4.0 51 103-153 435-510 (607)
44 PF02207 zf-UBR: Putative zinc 86.2 0.57 1.2E-05 38.1 2.4 43 51-98 2-48 (71)
45 COG5147 REB1 Myb superfamily p 86.1 0.55 1.2E-05 52.0 3.0 45 104-148 20-64 (512)
46 KOG0050 mRNA splicing protein 83.7 0.97 2.1E-05 49.5 3.4 45 102-148 57-101 (617)
47 PF09111 SLIDE: SLIDE; InterP 82.8 1.6 3.5E-05 39.3 4.0 43 104-146 49-106 (118)
48 KOG4282 Transcription factor G 81.2 2 4.3E-05 45.3 4.6 47 105-151 55-114 (345)
49 COG5118 BDP1 Transcription ini 81.1 2.6 5.6E-05 44.7 5.2 44 104-148 365-408 (507)
50 TIGR02894 DNA_bind_RsfA transc 77.8 1.7 3.7E-05 41.0 2.5 44 105-149 5-54 (161)
51 KOG1778 CREB binding protein/P 76.7 1.3 2.8E-05 46.5 1.5 45 44-96 167-211 (319)
52 KOG4468 Polycomb-group transcr 75.8 3 6.4E-05 46.6 4.0 45 104-149 88-142 (782)
53 KOG4167 Predicted DNA-binding 74.1 4.3 9.3E-05 46.4 4.8 44 104-148 619-662 (907)
54 COG5147 REB1 Myb superfamily p 73.3 3.4 7.4E-05 45.9 3.7 50 102-152 70-119 (512)
55 smart00396 ZnF_UBR1 Putative z 73.0 4.5 9.7E-05 33.0 3.5 42 51-97 2-47 (71)
56 PHA00442 host recBCD nuclease 72.2 4.3 9.2E-05 31.4 2.9 27 109-135 25-51 (59)
57 PF08914 Myb_DNA-bind_2: Rap1 71.7 6.1 0.00013 31.8 3.9 47 105-151 3-58 (65)
58 PF13412 HTH_24: Winged helix- 71.3 11 0.00024 27.6 5.1 44 481-524 5-48 (48)
59 smart00420 HTH_DEOR helix_turn 71.1 10 0.00022 27.5 4.8 36 489-524 10-45 (53)
60 COG3935 DnaD Putative primosom 70.9 10 0.00022 38.5 6.2 58 337-394 134-210 (246)
61 PLN03000 amine oxidase 70.7 7.8 0.00017 46.0 6.1 72 452-524 90-167 (881)
62 KOG0384 Chromodomain-helicase 69.4 3.1 6.7E-05 50.2 2.5 28 103-130 1132-1159(1373)
63 PF09862 DUF2089: Protein of u 67.4 11 0.00023 33.8 4.9 60 49-135 1-60 (113)
64 PF13873 Myb_DNA-bind_5: Myb/S 64.6 9.1 0.0002 31.1 3.7 45 105-149 3-68 (78)
65 PLN03142 Probable chromatin-re 64.3 8.5 0.00018 46.5 4.8 58 105-164 825-882 (1033)
66 PF14569 zf-UDP: Zinc-binding 63.9 3.7 8.1E-05 34.2 1.2 33 46-79 9-45 (80)
67 PF09012 FeoC: FeoC like trans 63.2 8.9 0.00019 30.7 3.4 40 485-524 5-45 (69)
68 PF00643 zf-B_box: B-box zinc 62.2 7.8 0.00017 27.7 2.6 39 46-94 3-41 (42)
69 PF12802 MarR_2: MarR family; 60.5 18 0.0004 27.5 4.6 50 470-524 1-52 (62)
70 PF07975 C1_4: TFIIH C1-like d 59.6 6.2 0.00014 30.3 1.7 30 48-78 1-37 (51)
71 PF08394 Arc_trans_TRASH: Arch 59.2 6.2 0.00013 28.3 1.5 31 49-79 1-32 (37)
72 PF01047 MarR: MarR family; I 57.3 11 0.00024 28.6 2.8 35 490-524 14-48 (59)
73 PF13404 HTH_AsnC-type: AsnC-t 56.0 34 0.00073 24.9 5.0 37 111-148 4-40 (42)
74 PLN03142 Probable chromatin-re 54.2 16 0.00035 44.2 4.9 45 104-148 926-982 (1033)
75 TIGR01889 Staph_reg_Sar staphy 51.8 45 0.00098 28.9 6.2 64 460-524 11-74 (109)
76 KOG4329 DNA-binding protein [G 50.7 18 0.00039 38.5 3.9 43 105-148 278-321 (445)
77 TIGR02337 HpaR homoprotocatech 50.7 53 0.0012 28.6 6.5 61 459-524 13-73 (118)
78 PF08074 CHDCT2: CHDCT2 (NUC03 49.7 9.3 0.0002 36.3 1.5 30 105-134 4-33 (173)
79 PF04504 DUF573: Protein of un 49.2 19 0.0004 31.3 3.2 32 103-134 3-41 (98)
80 KOG1356 Putative transcription 47.6 10 0.00022 44.3 1.7 36 43-80 226-261 (889)
81 PF12776 Myb_DNA-bind_3: Myb/S 46.8 42 0.0009 28.0 5.0 44 106-149 1-61 (96)
82 PLN02328 lysine-specific histo 46.5 35 0.00075 40.4 5.8 69 456-524 144-218 (808)
83 PF04703 FaeA: FaeA-like prote 45.7 27 0.00058 27.9 3.3 44 481-524 2-46 (62)
84 PLN02638 cellulose synthase A 45.3 18 0.00039 43.6 3.3 32 47-79 18-53 (1079)
85 PF06461 DUF1086: Domain of Un 45.3 38 0.00083 31.6 4.8 55 105-160 39-95 (145)
86 PRK03573 transcriptional regul 45.3 61 0.0013 29.2 6.2 56 465-524 22-77 (144)
87 TIGR00270 conserved hypothetic 45.0 78 0.0017 29.7 7.0 40 48-87 2-41 (154)
88 PF09397 Ftsk_gamma: Ftsk gamm 43.9 44 0.00095 26.9 4.4 45 477-525 8-52 (65)
89 smart00595 MADF subfamily of S 43.9 23 0.00051 29.2 3.0 23 126-149 29-51 (89)
90 KOG3993 Transcription factor ( 42.7 6.6 0.00014 42.4 -0.7 50 38-94 259-322 (500)
91 PLN02436 cellulose synthase A 42.1 15 0.00033 44.2 2.0 34 47-81 37-74 (1094)
92 KOG1194 Predicted DNA-binding 41.5 17 0.00036 39.7 2.1 43 104-148 470-512 (534)
93 PF13730 HTH_36: Helix-turn-he 41.3 74 0.0016 23.7 5.2 53 471-523 2-55 (55)
94 PF15614 WHIM3: WSTF, HB1, Itc 41.2 52 0.0011 24.8 4.1 28 344-371 4-36 (46)
95 PF07261 DnaB_2: Replication i 41.2 5.8 0.00013 31.9 -1.1 23 367-389 54-76 (77)
96 PRK13923 putative spore coat p 40.8 23 0.0005 33.9 2.7 45 104-149 5-55 (170)
97 PF10925 DUF2680: Protein of u 40.7 95 0.0021 24.5 5.7 45 476-524 15-59 (59)
98 PF03979 Sigma70_r1_1: Sigma-7 40.2 52 0.0011 27.3 4.5 41 482-522 10-53 (82)
99 PF08513 LisH: LisH; InterPro 40.0 19 0.00041 23.7 1.4 13 511-523 5-17 (27)
100 PRK11512 DNA-binding transcrip 39.9 63 0.0014 29.3 5.4 52 468-524 34-85 (144)
101 PF13463 HTH_27: Winged helix 39.4 59 0.0013 25.1 4.5 34 490-523 15-48 (68)
102 PF05290 Baculo_IE-1: Baculovi 38.5 12 0.00025 34.5 0.3 53 45-100 79-131 (140)
103 smart00345 HTH_GNTR helix_turn 38.1 50 0.0011 24.4 3.8 46 479-524 4-51 (60)
104 cd00090 HTH_ARSR Arsenical Res 38.0 67 0.0014 24.4 4.7 34 490-524 18-51 (78)
105 PLN02915 cellulose synthase A 37.8 25 0.00055 42.3 3.0 35 45-80 14-52 (1044)
106 KOG3579 Predicted E3 ubiquitin 37.0 53 0.0011 34.0 4.7 42 38-79 260-301 (352)
107 COG5347 GTPase-activating prot 36.8 21 0.00045 37.6 1.9 58 47-118 21-78 (319)
108 PF02954 HTH_8: Bacterial regu 36.7 48 0.001 23.9 3.3 25 111-136 6-30 (42)
109 KOG1194 Predicted DNA-binding 34.9 51 0.0011 36.2 4.4 48 100-148 183-230 (534)
110 PLN02189 cellulose synthase 34.5 24 0.00051 42.5 2.1 34 47-81 35-72 (1040)
111 PF08784 RPA_C: Replication pr 33.8 35 0.00077 29.2 2.6 32 491-523 64-95 (102)
112 COG4008 Predicted metal-bindin 33.7 94 0.002 28.4 5.2 25 468-492 87-111 (153)
113 PLN02400 cellulose synthase 33.6 25 0.00054 42.5 2.0 33 47-80 37-73 (1085)
114 smart00347 HTH_MARR helix_turn 32.8 73 0.0016 26.0 4.3 51 469-524 5-55 (101)
115 TIGR01446 DnaD_dom DnaD and ph 32.7 32 0.0007 27.5 2.0 18 368-385 55-72 (73)
116 smart00843 Ftsk_gamma This dom 31.8 1.2E+02 0.0027 24.3 5.1 45 477-525 7-51 (63)
117 KOG3554 Histone deacetylase co 31.6 56 0.0012 35.9 4.1 42 105-147 286-328 (693)
118 PF14471 DUF4428: Domain of un 31.4 28 0.00062 26.6 1.4 30 48-80 1-30 (51)
119 PF09107 SelB-wing_3: Elongati 31.1 96 0.0021 23.6 4.2 39 485-523 1-40 (50)
120 smart00346 HTH_ICLR helix_turn 30.5 1.1E+02 0.0024 24.9 5.1 40 485-524 10-51 (91)
121 PRK08359 transcription factor; 30.4 40 0.00086 32.5 2.5 40 47-86 7-48 (176)
122 PF01978 TrmB: Sugar-specific 30.4 49 0.0011 26.0 2.7 35 490-524 19-53 (68)
123 PF01388 ARID: ARID/BRIGHT DNA 30.0 1.1E+02 0.0023 25.6 4.8 38 113-150 39-88 (92)
124 KOG2807 RNA polymerase II tran 29.5 33 0.00071 36.1 1.9 34 43-77 327-360 (378)
125 PLN02195 cellulose synthase A 28.6 37 0.00081 40.7 2.4 33 47-80 7-43 (977)
126 TIGR03277 methan_mark_9 putati 28.5 60 0.0013 28.7 3.1 23 468-490 86-108 (109)
127 COG1725 Predicted transcriptio 27.7 1.5E+02 0.0033 27.0 5.6 50 475-524 11-66 (125)
128 PF13076 DUF3940: Protein of u 26.1 77 0.0017 22.9 2.7 34 481-515 3-36 (38)
129 smart00550 Zalpha Z-DNA-bindin 26.0 1.8E+02 0.0038 23.2 5.2 44 481-524 8-53 (68)
130 PRK10870 transcriptional repre 25.9 1.6E+02 0.0036 27.8 5.9 58 464-524 45-102 (176)
131 PF09339 HTH_IclR: IclR helix- 25.2 92 0.002 23.2 3.3 43 482-524 5-49 (52)
132 PF00130 C1_1: Phorbol esters/ 24.9 63 0.0014 24.0 2.3 24 45-68 10-35 (53)
133 KOG0006 E3 ubiquitin-protein l 24.7 53 0.0012 34.5 2.4 24 45-68 133-156 (446)
134 COG3058 FdhE Uncharacterized p 24.7 15 0.00032 37.9 -1.6 31 37-68 202-232 (308)
135 PF10123 Mu-like_Pro: Mu-like 24.4 57 0.0012 34.2 2.6 25 454-478 301-325 (326)
136 PRK00420 hypothetical protein; 24.0 48 0.001 29.6 1.7 29 46-74 23-53 (112)
137 PF07875 Coat_F: Coat F domain 23.6 66 0.0014 25.2 2.3 25 501-525 38-62 (64)
138 PF12488 DUF3704: Protein of u 23.3 29 0.00063 23.2 0.1 9 252-260 7-15 (27)
139 smart00418 HTH_ARSR helix_turn 23.2 1.6E+02 0.0034 21.6 4.3 34 491-524 8-41 (66)
140 TIGR00622 ssl1 transcription f 23.2 68 0.0015 28.7 2.5 30 47-77 56-96 (112)
141 COG1813 Predicted transcriptio 23.2 97 0.0021 29.6 3.6 96 49-148 6-114 (165)
142 cd04766 HTH_HspR Helix-Turn-He 23.2 3.2E+02 0.0069 22.8 6.6 61 313-373 22-87 (91)
143 PF13325 MCRS_N: N-terminal re 22.6 1.3E+02 0.0029 29.6 4.6 46 106-153 1-49 (199)
144 PF12674 Zn_ribbon_2: Putative 22.4 47 0.001 27.9 1.3 35 48-83 2-39 (81)
145 cd00092 HTH_CRP helix_turn_hel 22.2 1.2E+02 0.0025 23.2 3.4 35 490-524 22-56 (67)
146 PRK11179 DNA-binding transcrip 21.9 1.8E+02 0.004 26.7 5.3 43 110-153 9-51 (153)
147 PF03374 ANT: Phage antirepres 21.7 1.6E+02 0.0035 25.3 4.6 35 486-523 16-51 (111)
148 COG5207 UBP14 Isopeptidase T [ 21.3 40 0.00086 37.6 0.8 36 45-90 21-56 (749)
149 PRK14890 putative Zn-ribbon RN 21.2 99 0.0021 24.6 2.7 36 45-80 6-46 (59)
150 COG2956 Predicted N-acetylgluc 20.8 58 0.0013 34.6 1.8 26 44-70 352-377 (389)
151 PRK13777 transcriptional regul 20.7 2.2E+02 0.0048 27.5 5.7 52 468-524 39-90 (185)
152 cd07377 WHTH_GntR Winged helix 20.6 1.8E+02 0.0038 21.8 4.2 31 494-524 26-56 (66)
153 PF10545 MADF_DNA_bdg: Alcohol 20.6 94 0.002 24.8 2.7 24 126-149 28-52 (85)
154 PF00392 GntR: Bacterial regul 20.4 1.2E+02 0.0026 23.5 3.2 32 493-524 23-55 (64)
155 PF05584 Sulfolobus_pRN: Sulfo 20.2 2.7E+02 0.0058 23.1 5.1 46 478-524 4-49 (72)
No 1
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=2.9e-104 Score=813.89 Aligned_cols=420 Identities=50% Similarity=0.838 Sum_probs=368.6
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhCC
Q 009788 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGL 124 (525)
Q Consensus 45 ~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wta~Eel~LLeai~~~G~ 124 (525)
..|+|++|..+|++.+||+|++|++||||+.||+.|+|++.|+++|+|+||++++||+..++|||+||++||+|++.|||
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~ 92 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGF 92 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCCccccccchHHHHHHhccCcccccccccCCCCCCCCCccCCCCC
Q 009788 125 GNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKVAVAGPSKPGEATVKEESPF 204 (525)
Q Consensus 125 gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~plp~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~p~ 204 (525)
|||++||+|||+||.+||++||.++|++++++|+|+++..+++++.+++++.+... .|+
T Consensus 93 GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~---------------------~~~ 151 (438)
T KOG0457|consen 93 GNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRA---------------------EPF 151 (438)
T ss_pred CcHHHHHHHHcccchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhccccc---------------------ccC
Confidence 99999999999999999999999999999999999999999999999988765421 233
Q ss_pred CCchhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCCC
Q 009788 205 SPSRVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDADS 284 (525)
Q Consensus 205 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFE~EydNdAE~li~dmeF~~~D~ 284 (525)
.|... .|+.++.++|..++++||||+|.|||.||||+||++|+||+|.++|+
T Consensus 152 ~~~~~----------------------------~pr~p~~~~p~~~e~~gyMp~R~dFd~Eydn~AE~li~dm~f~e~D~ 203 (438)
T KOG0457|consen 152 QPTDL----------------------------VPRKPGVSNPLRREISGYMPGRLDFDEEYDNEAEQLIRDMEFEEDDT 203 (438)
T ss_pred CCCCC----------------------------CCCCCCCCCchHHHHhhhCccchhhhhhhcchhhhhHhhcccCCCCc
Confidence 33210 12333345788999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC---CCCCCCCChHHHHHHHhhcccccCCChhHHHHHHHHHHHHH
Q 009788 285 EEERDIKLRVLRIYSKRLDERKRRKDFILERNLLYP---NPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISEH 361 (525)
Q Consensus 285 ~~e~elKL~~l~iYn~rL~ER~rRK~~v~e~~Ll~~---~~~~k~~s~eer~~~~~l~~farf~~~~~~e~l~~~l~~E~ 361 (525)
|.+.+||+++|+|||+||+||.|||++|++|||+++ ++.++++|+|+|++++++|+||||+|+.||++|+.+++.|.
T Consensus 204 ~~d~elKla~ldiY~srl~eR~RRK~~I~d~nLl~~rk~q~~e~~~skEer~l~~s~k~fAR~~t~~d~~kfl~~~~eE~ 283 (438)
T KOG0457|consen 204 EEDHELKLAVLDIYNSRLKERKRRKRFIRDRNLLDYRKNQAMEKRLSKEERELYNSIKVFARFLTKSDHDKFLGSVAEEK 283 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHhhccHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999995 78899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCC--CCCCCC
Q 009788 362 RTLKRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSN--SRPSGQ 439 (525)
Q Consensus 362 ~Lr~rI~~Lq~~R~~Gi~tl~e~~~Ye~~k~~Re~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 439 (525)
+|+.||++||+||.+|+||++++.+|+.+|.++. +........+++. .. +.+ +.....++. +....+
T Consensus 284 ~L~~ri~~lqE~R~ag~tt~~e~~ky~~~k~~~~-~~s~~~~~~~~~~---~~-i~~------~~~~~~~~~~~~~v~~~ 352 (438)
T KOG0457|consen 284 ELRKRISDLQEYRSAGLTTNAEPNKYERLKFKEF-RESTALLLSSGAL---RY-IKN------SNQEASGSASKRPVQQQ 352 (438)
T ss_pred HHHHHHHHHHHHHHhcceeccccchhHHHHHHHH-HHHhhhccccchh---hh-hhc------cccccccccccCccccc
Confidence 9999999999999999999999999999994432 2221111111100 00 000 011111111 122233
Q ss_pred CCCCCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHH
Q 009788 440 ASSSHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVK 519 (525)
Q Consensus 440 ~~~~~~~~l~i~~~pg~~LLs~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~ 519 (525)
...++++++++.++++.++||+.|+.||+.++|+|++||.+|++|++|..++|.+++.+|+.++|||++|+++|||||++
T Consensus 353 ~~~~~~~~~~~~~~~~~q~Lse~E~~lc~~~~~~p~~yLe~~~vl~~e~~k~~~~kks~a~~l~Kid~~Kvd~vyd~~~~ 432 (438)
T KOG0457|consen 353 SIYKSATPLDISGAPDTQLLSEDEKRLCQELKILPKLYLELKEVLSREIKKGGTLKKSDAYRLFKIDPRKVDRVYDFLIA 432 (438)
T ss_pred ccccCCCHHHHhcchhhhhhhhhHHHHHHHHHhccHHHHHHHHHHHHHHhccCcccchhHHHHhcCCcchHHHHHHHHHH
Confidence 45667899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCC
Q 009788 520 KGLAP 524 (525)
Q Consensus 520 ~Gwi~ 524 (525)
+||+.
T Consensus 433 ~~~~~ 437 (438)
T KOG0457|consen 433 QGWIG 437 (438)
T ss_pred hhhcc
Confidence 99996
No 2
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=4.3e-98 Score=737.02 Aligned_cols=420 Identities=32% Similarity=0.535 Sum_probs=362.0
Q ss_pred cCCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhC
Q 009788 44 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 123 (525)
Q Consensus 44 ~~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wta~Eel~LLeai~~~G 123 (525)
...++||+|..+||..++|+|++|++||||+.||.+|.+.+.|.+.|+|+||+.+++||+.++|+++||++|+++++.+|
T Consensus 3 ~~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlG 82 (432)
T COG5114 3 GVKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLG 82 (432)
T ss_pred CceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcC
Confidence 37899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCCccccccchHHHHHHhccCcccccccccCCCCCCCCCccCCCC
Q 009788 124 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKVAVAGPSKPGEATVKEESP 203 (525)
Q Consensus 124 ~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~plp~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~p 203 (525)
+|||++||+|||+|+.+||+.||.++|+++.++|||++...+.....+|++....+++... .+|
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~ypl~~i~~~~~v~q~~f~~qrr~rie~f~----------------~pp 146 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYPLPDITQNIHVPQDEFLEQRRHRIETFE----------------LPP 146 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccccccccccCCCCchHHHHHHHHhhhhhcc----------------CCC
Confidence 9999999999999999999999999999999999999998888889999887554432211 122
Q ss_pred CCCchhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCC
Q 009788 204 FSPSRVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDAD 283 (525)
Q Consensus 204 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFE~EydNdAE~li~dmeF~~~D 283 (525)
..| .||..| +|.+++++||||+|.|||+||+|+||..|+||.|++|+
T Consensus 147 i~p------------------------------rkP~aS---~P~cheiqgyMPgRleFd~EymnEaE~pikDm~fd~d~ 193 (432)
T COG5114 147 INP------------------------------RKPKAS---NPYCHEIQGYMPGRLEFDVEYMNEAEVPIKDMSFDGDK 193 (432)
T ss_pred CCC------------------------------CCCCCC---CCchhhhhccCCCccccchhhhhcccccccccccCCch
Confidence 222 145544 69999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC---CCCCCCCCChHHHHHHHhhcccccCCChhHHHHHHHHHHHH
Q 009788 284 SEEERDIKLRVLRIYSKRLDERKRRKDFILERNLLY---PNPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISE 360 (525)
Q Consensus 284 ~~~e~elKL~~l~iYn~rL~ER~rRK~~v~e~~Ll~---~~~~~k~~s~eer~~~~~l~~farf~~~~~~e~l~~~l~~E 360 (525)
.+.+++||+++|+|||+||.-|.+||+.|++++|+| -++.+|++||||+.++++++||||++|+.||+.|+.+++.+
T Consensus 194 ~el~~~lk~a~LdiYnsrlt~Ra~rK~~if~~nLmDyr~Lqa~dkk~skEe~~l~N~iK~fAr~lT~~Df~~F~~~~~e~ 273 (432)
T COG5114 194 EELKKKLKNATLDIYNSRLTFRARRKHAIFGKNLMDYRNLQAKDKKRSKEECGLVNSIKWFARYLTKSDFNVFFRDILEG 273 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhhhccHHHHhHHHhhhHHHHhhcchhHHHHHHHHhhh
Confidence 999999999999999999999999999999999999 47889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCCCCCC---
Q 009788 361 HRTLKRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSNSRPS--- 437 (525)
Q Consensus 361 ~~Lr~rI~~Lq~~R~~Gi~tl~e~~~Ye~~k~~Re~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 437 (525)
.-+++||++||+||.||+|||+.|-+||++|-.+ .....+ .+...+.+. ..+++.+ +++...+..
T Consensus 274 v~~~kri~~LqewR~~glttle~g~kyeRDk~ek---f~~s~a-as~~e~~~r-------~~~n~~~-~sna~~s~~d~~ 341 (432)
T COG5114 274 VYIEKRIHELQEWRNNGLTTLEAGLKYERDKFEK---FGASTA-ASLSEGNSR-------YRSNSAH-RSNAEYSQMDVK 341 (432)
T ss_pred hhHHHHHHHHHHHHhcCchhhhhhhhhhhhHHHh---hccchh-hhhcccchh-------hhccccc-ccCcchhHHHHH
Confidence 9999999999999999999999999999997321 100000 000001111 1111111 000000000
Q ss_pred CCCCCCCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHh-CCCCCHHHHhhhhccCchhHHHHHHH
Q 009788 438 GQASSSHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDM 516 (525)
Q Consensus 438 ~~~~~~~~~~l~i~~~pg~~LLs~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~-~G~lkk~dA~~l~kiD~~K~~rIydF 516 (525)
....++...+-+|..+|++.|||++|++||++|+|.|++||.+|.++|+++++ +|.+++++++.||+||.+|+.+||||
T Consensus 342 ni~p~K~~t~s~~q~a~d~~llS~dEq~LC~~l~i~PkpyL~LK~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~Ydf 421 (432)
T COG5114 342 NILPSKNMTISDIQHAPDYALLSDDEQRLCETLNISPKPYLELKKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDF 421 (432)
T ss_pred hccCCCCCChhhhhccchhhhhcchHHHHHHHhCCCCccHHHHHHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHH
Confidence 01134455677899999999999999999999999999999999999999995 89999999999999999999999999
Q ss_pred HHHCCCCC
Q 009788 517 LVKKGLAP 524 (525)
Q Consensus 517 lv~~Gwi~ 524 (525)
|.+.|||-
T Consensus 422 F~~~~Wi~ 429 (432)
T COG5114 422 FLERGWIH 429 (432)
T ss_pred HHhccccC
Confidence 99999995
No 3
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=99.68 E-value=2.7e-17 Score=171.47 Aligned_cols=108 Identities=30% Similarity=0.613 Sum_probs=95.0
Q ss_pred cCCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhC
Q 009788 44 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 123 (525)
Q Consensus 44 ~~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wta~Eel~LLeai~~~G 123 (525)
.+..+|+.|+..+.. .||+-..-.++++|..||.+|.++....++ +|..++...+. ....|+.+|.++|||||++||
T Consensus 222 ~~~~~C~~cG~~~~~-t~y~nlra~~~n~C~~C~~qg~f~s~~~ss-Df~~v~~~~~~-~dk~WS~qE~~LLLEGIe~yg 298 (531)
T COG5259 222 KHPSSCSCCGNKSFN-TRYHNLRAEKYNSCSECYDQGRFPSEFTSS-DFKPVTISLLI-RDKNWSRQELLLLLEGIEMYG 298 (531)
T ss_pred cCCceeeccCccccc-hhhhhhhhhhcccchHHHhcCcCCCccccc-cchhhhhhccc-ccccccHHHHHHHHHHHHHhh
Confidence 356899999999887 899988878999999999999998887665 78777654433 456999999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCC
Q 009788 124 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPF 155 (525)
Q Consensus 124 ~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~ 155 (525)
++|..||.|||+||++||+.||.+.++.+++
T Consensus 299 -DdW~kVA~HVgtKt~EqCIl~FL~LPieD~~ 329 (531)
T COG5259 299 -DDWDKVARHVGTKTKEQCILHFLQLPIEDNY 329 (531)
T ss_pred -hhHHHHHHHhCCCCHHHHHHHHHcCCcchhh
Confidence 8999999999999999999999999998864
No 4
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.47 E-value=3.9e-14 Score=107.33 Aligned_cols=49 Identities=69% Similarity=1.499 Sum_probs=46.6
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
++|++|.+++...+||+|++|+|||||..||+.|.+.+.|+++|+|++|
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~~~~~ 49 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHNYRVV 49 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCCeEeC
Confidence 5799999999877999999999999999999999999999999999986
No 5
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.46 E-value=8.6e-14 Score=117.46 Aligned_cols=78 Identities=33% Similarity=0.477 Sum_probs=68.6
Q ss_pred cccccCCCccCCCCHHHHHHHHHhCC--CchHHHHHHHHHHHHHH--hCCCCCHHHHhhhhc-cCchhHHHHHHHHHHCC
Q 009788 447 DLYIMGFNETQLLSEAEKRLCCEIRL--APPLYLRMQEVMSREIF--SGNVNNKADAHHLFK-IEPSKIDRVYDMLVKKG 521 (525)
Q Consensus 447 ~l~i~~~pg~~LLs~~Ek~LC~~lrL--~P~~YL~iK~~LirE~~--~~G~lkk~dA~~l~k-iD~~K~~rIydFlv~~G 521 (525)
++++++.++.+.||+.|+++|..+++ .|..||.||..||.+.. .++.+++++|+++++ +|++++.+||+||.+.|
T Consensus 3 ~~~~~~~~~~~~l~~~E~~~~~e~~~~~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G 82 (86)
T PF04433_consen 3 IPAHSSWFDPDKLSEIEKQLCPEFFIGKTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWG 82 (86)
T ss_dssp CHCCHTTTTTTSS-HHHHHHCHHCTTSCHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTT
T ss_pred CccccCCCCcccCCHHHHHHhHHHhccCChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcC
Confidence 45667788999999999999999999 99999999999999954 578999999999999 99999999999999999
Q ss_pred CCC
Q 009788 522 LAP 524 (525)
Q Consensus 522 wi~ 524 (525)
||.
T Consensus 83 ~IN 85 (86)
T PF04433_consen 83 LIN 85 (86)
T ss_dssp SSS
T ss_pred ccC
Confidence 995
No 6
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=99.34 E-value=1.3e-12 Score=141.26 Aligned_cols=81 Identities=36% Similarity=0.862 Sum_probs=71.6
Q ss_pred CcccchhhhhcccccCCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 69 DFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 69 dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
++.+|..||..|.....++.+ +|.++.. .....||.+|+++||+||++|| .+|..||.|||+||++||+.||.+
T Consensus 223 ~~~~c~~c~~~g~~~~~~~~~-Df~~~~~----~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 223 DVNLCADCYDQGEFPSEFKKS-DFKVIGE----SARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred hhhhhHHHHhcCCccCccccc-cchhccc----cCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHh
Confidence 388999999999999988776 5755443 2357999999999999999999 899999999999999999999999
Q ss_pred hccCCCC
Q 009788 149 VYMNSPF 155 (525)
Q Consensus 149 ~yi~~~~ 155 (525)
.++.+++
T Consensus 297 LPieD~~ 303 (506)
T KOG1279|consen 297 LPIEDPY 303 (506)
T ss_pred cCccchh
Confidence 9998864
No 7
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.27 E-value=2.6e-12 Score=96.14 Aligned_cols=46 Identities=33% Similarity=0.717 Sum_probs=42.7
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCee
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 93 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~ 93 (525)
+.||+|.+.+.+ +||+|++|+|||||..||..|.+.+.|+.+|+.+
T Consensus 1 i~CdgC~~~~~~-~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~ 46 (48)
T cd02343 1 ISCDGCDEIAPW-HRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMV 46 (48)
T ss_pred CCCCCCCCcCCC-ceEECCCCCCchhHHHHHhCCccCCCCCCCCCcc
Confidence 369999998876 8999999999999999999999999999999865
No 8
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=99.26 E-value=3.7e-12 Score=96.45 Aligned_cols=48 Identities=38% Similarity=0.953 Sum_probs=44.8
Q ss_pred ccccccc-cccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 47 YHCNYCN-KDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 47 ~~C~~C~-~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
+.|++|+ .+|.+ .||+|++|+|||||..||+.|.+.+.|+++|+|+++
T Consensus 1 i~C~~C~~~~i~g-~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~~ 49 (49)
T cd02338 1 VSCDGCGKSNFTG-RRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQCI 49 (49)
T ss_pred CCCCCCcCCCcEE-eeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEEC
Confidence 4699999 78997 999999999999999999999999999999999874
No 9
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=99.24 E-value=4.9e-12 Score=95.63 Aligned_cols=46 Identities=41% Similarity=0.977 Sum_probs=42.9
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCee
Q 009788 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 93 (525)
Q Consensus 47 ~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~ 93 (525)
+.|++|++ +|.+ .||+|++|.|||||..||..|.+.+.|+++|+|+
T Consensus 1 ~~Cd~C~~~pi~g-~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 1 AKCNICKEFPITG-FRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCCcee-eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 36999997 5887 9999999999999999999999999999999986
No 10
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=99.22 E-value=7.2e-12 Score=94.89 Aligned_cols=46 Identities=43% Similarity=0.969 Sum_probs=43.5
Q ss_pred ccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeee
Q 009788 48 HCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (525)
Q Consensus 48 ~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~v 94 (525)
.|++|.+ +|++ +||+|++|+|||||..||+.|.+.+.|+++|+|..
T Consensus 2 ~C~~C~~~~i~g-~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02345 2 SCSACRKQDISG-IRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48 (49)
T ss_pred cCCCCCCCCceE-eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCccc
Confidence 6999998 9997 99999999999999999999999999999998864
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.12 E-value=8.7e-11 Score=88.34 Aligned_cols=45 Identities=31% Similarity=0.716 Sum_probs=41.1
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 009788 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 149 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~ 149 (525)
..||.+|+.+|++||.+||.+||..||.+|+ +||+.||+.||.++
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 5799999999999999999877999999999 99999999999875
No 12
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=99.10 E-value=6.7e-11 Score=88.41 Aligned_cols=46 Identities=41% Similarity=1.024 Sum_probs=42.5
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
+.|++|+++|.+ .||+|.+|++||||..||+.+. +.|.++|+|+.|
T Consensus 1 ~~C~~C~~~i~g-~r~~C~~C~d~dLC~~Cf~~~~--~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLKPIVG-VRYHCLVCEDFDLCSSCYAKGK--KGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCCCCcC-CEEECCCCCCCcCHHHHHCcCc--CCCCCCCCEeEC
Confidence 579999999998 9999999999999999999998 789999998764
No 13
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=99.00 E-value=2.7e-10 Score=83.99 Aligned_cols=43 Identities=42% Similarity=0.943 Sum_probs=39.1
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
+.|++|+.+|.+ .||+|++|++||||..||..+ .| +.|+|..|
T Consensus 1 v~Cd~C~~~i~G-~ry~C~~C~d~dLC~~C~~~~----~H-~~H~f~~~ 43 (43)
T cd02340 1 VICDGCQGPIVG-VRYKCLVCPDYDLCESCEAKG----VH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCCcCcC-CeEECCCCCCccchHHhhCcC----CC-CCCCEEeC
Confidence 469999999998 999999999999999999998 68 89998754
No 14
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.99 E-value=3e-10 Score=85.53 Aligned_cols=45 Identities=36% Similarity=0.882 Sum_probs=41.0
Q ss_pred cccccccc-ccCCceeEEcCCCC--CcccchhhhhcccccCCCCCCCCeeec
Q 009788 47 YHCNYCNK-DITGKIRIKCAVCP--DFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 47 ~~C~~C~~-~i~~~~ri~C~~C~--dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
|.|++|+. +|.+ +||+|.+|+ +||||..||..|. .|+.+|.+..|
T Consensus 1 y~Cd~C~~~pI~G-~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPG-TRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCcccc-ceEECCCCCCCCCccCHHHHhCcC---CCCCCCceeeC
Confidence 57999998 8897 999999999 9999999999997 79999988754
No 15
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.94 E-value=5.9e-10 Score=82.78 Aligned_cols=42 Identities=31% Similarity=0.648 Sum_probs=39.8
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCC
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSN 89 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~ 89 (525)
++|+.|+.|++. +||+|+.+.++|||+.||.+|.++..|.++
T Consensus 1 y~C~~Cg~D~t~-vryh~~~~~~~dLC~~CF~~G~f~~~~~s~ 42 (45)
T cd02336 1 YHCFTCGNDCTR-VRYHNLKAKKYDLCPSCYQEGRFPSNFQSS 42 (45)
T ss_pred CcccCCCCccCc-eEEEecCCCccccChHHHhCcCCCCCCccc
Confidence 689999999996 999999999999999999999999999876
No 16
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.91 E-value=9.4e-10 Score=81.62 Aligned_cols=44 Identities=36% Similarity=0.906 Sum_probs=38.9
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 47 ~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
+.||+|+. +|.+ .||+|++|.|||||..||..+ .|...|.|..|
T Consensus 1 V~Cd~C~~~pI~G-~RykC~~C~dyDLC~~Cf~~~----~H~~~H~F~ri 45 (45)
T cd02344 1 VTCDGCQMFPING-PRFKCRNCDDFDFCENCFKTR----KHNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCCcc-CeEECCCCCCccchHHhhCCC----CcCCCCceeeC
Confidence 46999996 6887 999999999999999999995 49889998765
No 17
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=98.87 E-value=1.6e-09 Score=80.55 Aligned_cols=43 Identities=42% Similarity=0.981 Sum_probs=37.3
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeee
Q 009788 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (525)
Q Consensus 47 ~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~v 94 (525)
+.||+|++ +|.+ .||+|++|+|||||..||.. +.|+.+|+|..
T Consensus 1 i~Cd~C~~~~i~G-~RykC~~C~dyDLC~~C~~~----~~H~~~H~f~r 44 (45)
T cd02339 1 IICDTCRKQGIIG-IRWKCAECPNYDLCTTCYHG----DKHDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCCccc-CeEECCCCCCccchHHHhCC----CCCCCCCCEEe
Confidence 36999994 6777 99999999999999999996 45999999863
No 18
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=98.85 E-value=2.2e-09 Score=79.54 Aligned_cols=41 Identities=46% Similarity=1.093 Sum_probs=37.3
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCC
Q 009788 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPH 86 (525)
Q Consensus 45 ~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H 86 (525)
..+.|++|+.+|++ .||+|+.|+|||||..||+.|.+.+.|
T Consensus 3 ~~~~C~~C~~~i~g-~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 3 HSYSCDTCGKPIVG-VRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CCcCCCCCCCCCcC-CEEECCCCCCccchHHHHhCcCcCCCC
Confidence 46789999999998 899999999999999999999877666
No 19
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=98.77 E-value=3.3e-09 Score=79.35 Aligned_cols=42 Identities=50% Similarity=1.118 Sum_probs=31.9
Q ss_pred CCcccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCC
Q 009788 45 ALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 87 (525)
Q Consensus 45 ~~~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~ 87 (525)
..+.|++|+. .|.+ .||+|..|+|||||..||..|.....|+
T Consensus 3 ~~~~C~~C~~~~i~g-~Ry~C~~C~d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIG-VRYHCLVCPDYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SSCE-SSS-SSSEES-SEEEESSSSS-EEEHHHHHH--H-SSSS
T ss_pred CCeECcCCCCCcCcC-CeEECCCCCCCchhhHHHhCcCCCCCcC
Confidence 4688999998 6777 9999999999999999999998777764
No 20
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.69 E-value=3.8e-08 Score=72.34 Aligned_cols=46 Identities=33% Similarity=0.749 Sum_probs=43.1
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhc
Q 009788 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVY 150 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~y 150 (525)
..||.+|+..|+.++..||.++|..||.++++||+.+|+.+|..+.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 5799999999999999999889999999999999999999998653
No 21
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.65 E-value=5.1e-08 Score=70.60 Aligned_cols=44 Identities=34% Similarity=0.791 Sum_probs=41.8
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 106 DWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 106 ~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
.||.+|+..|+.++..||.++|..||..+++||+.+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 49999999999999999988999999999999999999999765
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.61 E-value=7.5e-08 Score=75.25 Aligned_cols=49 Identities=18% Similarity=0.317 Sum_probs=44.9
Q ss_pred CCCCCchhHHHHHHHHHHhCCCCh---HHHHHHhC-CC-CHHHHHHHHHhhccC
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNW---AEIAEHVG-TK-TKELCIEHYTNVYMN 152 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW---~~Ia~~vg-tk-t~~ec~~hy~~~yi~ 152 (525)
+..||++|...+|+||+.+|.||| ..|+++|+ ++ |+.||+.|+.+||+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 357999999999999999999999 99999998 57 999999999999864
No 23
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.57 E-value=1.2e-07 Score=74.16 Aligned_cols=41 Identities=39% Similarity=0.920 Sum_probs=37.1
Q ss_pred CCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 107 WNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 107 Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
||.+|+.+|+.++..|| .+|..||++||+||+.+|+.||..
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999 699999999988999999999998
No 24
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=98.47 E-value=7.2e-08 Score=70.36 Aligned_cols=33 Identities=42% Similarity=1.111 Sum_probs=29.2
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhccc
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGV 81 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~ 81 (525)
|+|++|.+. .+ +||+|++|+|||||..||..+.
T Consensus 1 y~C~~C~~~-~~-~r~~C~~C~dfDLC~~C~~~~~ 33 (41)
T cd02337 1 YTCNECKHH-VE-TRWHCTVCEDYDLCITCYNTKN 33 (41)
T ss_pred CcCCCCCCc-CC-CceECCCCcchhhHHHHhCCCC
Confidence 579999884 44 9999999999999999999955
No 25
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.40 E-value=1.6e-07 Score=68.50 Aligned_cols=34 Identities=44% Similarity=0.743 Sum_probs=30.4
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhccc
Q 009788 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGV 81 (525)
Q Consensus 47 ~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~ 81 (525)
+.||+|+. +|.+ .||+|.+|.|||||..||....
T Consensus 1 I~CDgCg~~PI~G-~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 1 IQCDGCGVLPITG-PRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCCcccc-cceEeCCCCCCccHHHHhhhhc
Confidence 46999996 7898 9999999999999999999843
No 26
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.22 E-value=1.4e-06 Score=86.34 Aligned_cols=49 Identities=18% Similarity=0.472 Sum_probs=45.2
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 009788 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 150 (525)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~y 150 (525)
+-+..||.+|+.+|+++|+.||.+||..||.+++ +||+.||++||.++.
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 4568899999999999999999999999999997 799999999999774
No 27
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.08 E-value=1.7e-06 Score=88.56 Aligned_cols=51 Identities=33% Similarity=0.771 Sum_probs=45.9
Q ss_pred cCCccccccccc-cCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 44 RALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 44 ~~~~~C~~C~~~-i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
.-.+.|++|++. +++ .||+|..|.|||||..||-.|+-+..|.-+|+.+.|
T Consensus 6 He~v~CdgC~k~~~t~-rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqci 57 (381)
T KOG1280|consen 6 HEGVSCDGCGKTAFTF-RRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCI 57 (381)
T ss_pred cCCceeccccccceee-eeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEE
Confidence 346889999987 455 999999999999999999999999999999998866
No 28
>PLN03091 hypothetical protein; Provisional
Probab=97.97 E-value=8e-06 Score=86.64 Aligned_cols=49 Identities=24% Similarity=0.545 Sum_probs=44.7
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 009788 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 150 (525)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~y 150 (525)
+-...||.+||.+|+++|.+||.+||..||.+++ +||+.||++||.++.
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 3457899999999999999999999999999998 799999999998764
No 29
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=97.91 E-value=7.3e-06 Score=83.79 Aligned_cols=46 Identities=39% Similarity=0.890 Sum_probs=39.0
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccC
Q 009788 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDN 97 (525)
Q Consensus 47 ~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~ 97 (525)
..||.|+. .|.+ .||+|++|+|||||..|++.+ .|+-.|.+..|..
T Consensus 153 v~CD~C~~~~IvG-~RyKC~~C~dYDLCe~Ce~~~----~~h~~H~~lR~~t 199 (278)
T KOG4582|consen 153 VPCDNCGKPGIVG-ARYKCTVCPDYDLCERCEAGN----EHHAAHAMLRLHT 199 (278)
T ss_pred ccCCCccCCcccc-ceeeecCCCccchhHHhhcCC----CCCcccceeeccc
Confidence 68999999 8998 999999999999999999986 3556777766543
No 30
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.85 E-value=1.4e-05 Score=80.01 Aligned_cols=46 Identities=17% Similarity=0.427 Sum_probs=44.4
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 149 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~ 149 (525)
.+.||.+||..|.+.|+.||-|||..||++.| .|+...|+.+|.+|
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~Ny 55 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNY 55 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcc
Confidence 58999999999999999999999999999999 89999999999976
No 31
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=97.75 E-value=6.5e-06 Score=91.25 Aligned_cols=55 Identities=27% Similarity=0.556 Sum_probs=47.3
Q ss_pred CCCCcCCcccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeec
Q 009788 40 GEGKRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (525)
Q Consensus 40 ~~~~~~~~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi 95 (525)
+|.-.+.-.|++|.+ +|.+ +||+|..|.++|||..||..|..-+.|+..|+..-.
T Consensus 597 aE~~kH~~kCniCk~~pIvG-~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey 652 (966)
T KOG4286|consen 597 AETAKHQAKCNICKECPIIG-FRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEY 652 (966)
T ss_pred HHHHHhhhhcchhhhCccce-eeeeehhhcChhHHhhHhhhcccccCCCCCCCceee
Confidence 444556778999986 6888 999999999999999999999999999998876644
No 32
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.60 E-value=8.2e-05 Score=73.94 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=44.4
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 101 p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
.+..+.||.+|+.+||+++..|| ..|..||.+|.+||..+|+.||..+
T Consensus 75 ~I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~LpGRTDnqIKNRWns~ 122 (249)
T PLN03212 75 SVKRGGITSDEEDLILRLHRLLG-NRWSLIAGRIPGRTDNEIKNYWNTH 122 (249)
T ss_pred hcccCCCChHHHHHHHHHHHhcc-ccHHHHHhhcCCCCHHHHHHHHHHH
Confidence 35678999999999999999999 7899999999999999999999864
No 33
>PLN03091 hypothetical protein; Provisional
Probab=97.25 E-value=0.00046 Score=73.62 Aligned_cols=48 Identities=19% Similarity=0.351 Sum_probs=44.5
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 101 p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
.+..+.||.+||.+||+.+..|| ..|..||.+|.+||..+|+.||..+
T Consensus 64 ~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~LPGRTDnqIKNRWnsl 111 (459)
T PLN03091 64 DLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQLPGRTDNEIKNLWNSC 111 (459)
T ss_pred cccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhcCCCCHHHHHHHHHHH
Confidence 35678999999999999999999 7999999999999999999999864
No 34
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=97.06 E-value=0.00012 Score=75.27 Aligned_cols=52 Identities=29% Similarity=0.752 Sum_probs=45.6
Q ss_pred CCCcCCcccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCee
Q 009788 41 EGKRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 93 (525)
Q Consensus 41 ~~~~~~~~C~~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~ 93 (525)
+.....+.|++|.. .+++ .||+|..|.+|.+|.+||-.|..-+.|.+.|.+.
T Consensus 235 ~nv~hpv~cs~c~srs~~g-fry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mk 287 (434)
T KOG4301|consen 235 ENVFHPVECSYCRSRSMMG-FRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMK 287 (434)
T ss_pred cccCCCccCcceecccccc-hhhhHhhcCCccccchhhccccCCCCcchHHHHH
Confidence 44467889999985 5776 9999999999999999999999999999999665
No 35
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.89 E-value=0.0015 Score=65.48 Aligned_cols=48 Identities=19% Similarity=0.368 Sum_probs=43.4
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 101 p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
-+-++.||.+||.+|+++...+| .-|..||.++++||..+++.||...
T Consensus 59 ~ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 59 DLKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred CccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCCCcCHHHHHHHHHHH
Confidence 34578999999999999999999 5699999999999999999999643
No 36
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.05 E-value=0.0088 Score=66.24 Aligned_cols=52 Identities=27% Similarity=0.639 Sum_probs=47.4
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 009788 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 152 (525)
Q Consensus 101 p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~ 152 (525)
.+-.+.||.+|+.+|+.||+.||--+|-.|-+.|.+|+..||+++|.+..-.
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 4557899999999999999999988999999999999999999999986543
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.61 E-value=0.012 Score=65.27 Aligned_cols=49 Identities=24% Similarity=0.348 Sum_probs=43.7
Q ss_pred CCCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCH---HHHHHHHHh
Q 009788 100 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTK---ELCIEHYTN 148 (525)
Q Consensus 100 ~p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~---~ec~~hy~~ 148 (525)
+..-.+.|+-.||..|+++|++||.|+|..+|..+|.||. .-|+.+++.
T Consensus 408 ~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 408 RSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred HhhccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHH
Confidence 4455689999999999999999999999999999999998 678888875
No 38
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.16 E-value=0.049 Score=60.70 Aligned_cols=90 Identities=13% Similarity=0.198 Sum_probs=60.9
Q ss_pred eeEEcCCC-CCcccchhhhhcccccCCCCCCCCeeeccCCCCCC---CCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC
Q 009788 60 IRIKCAVC-PDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPL---ICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG 135 (525)
Q Consensus 60 ~ri~C~~C-~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~---~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg 135 (525)
-|+.|..| +...-|-.|...-.-.. ...-.|.-|.. .+.+ .++.||.+|+..|-..+..+| +.|.+|++.||
T Consensus 339 ~~i~s~~~~~~~~~l~n~~~~~Lp~R--~~~siy~~~rR-~y~~FE~~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg 414 (607)
T KOG0051|consen 339 QRIWSKDWKTIIRNLYNNLYKLLPYR--DRKSIYHHLRR-AYTPFENKRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG 414 (607)
T ss_pred hheeccCcchHHHHHHHhhhhhcCcc--cchhHHHHHHh-cCCccccccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc
Confidence 35555555 44455666665533110 11112332222 2222 458999999999999999999 89999999997
Q ss_pred CCCHHHHHHHHHhhccCCC
Q 009788 136 TKTKELCIEHYTNVYMNSP 154 (525)
Q Consensus 136 tkt~~ec~~hy~~~yi~~~ 154 (525)
|.|..|+.+|.++-..+.
T Consensus 415 -r~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 415 -RMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred -cCcHHHHHHHHHhhcccc
Confidence 799999999998866653
No 39
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=93.61 E-value=0.051 Score=45.41 Aligned_cols=45 Identities=29% Similarity=0.614 Sum_probs=33.2
Q ss_pred CCCCchhHHHHHHHHHH--hC--CC---------ChHHHHHHhC----CCCHHHHHHHHHhh
Q 009788 105 PDWNADDEILLLEGIEM--YG--LG---------NWAEIAEHVG----TKTKELCIEHYTNV 149 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~--~G--~g---------nW~~Ia~~vg----tkt~~ec~~hy~~~ 149 (525)
..||.+|...||+++.. +. ++ -|..||+.|. .||+.||+.+|.++
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 47999999999999877 21 11 3999999985 59999999999875
No 40
>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=92.45 E-value=0.079 Score=35.81 Aligned_cols=28 Identities=43% Similarity=0.967 Sum_probs=12.9
Q ss_pred cccccccccCCceeEEcCCCCCcccchhh
Q 009788 48 HCNYCNKDITGKIRIKCAVCPDFDLCIEC 76 (525)
Q Consensus 48 ~C~~C~~~i~~~~ri~C~~C~dfdLC~~C 76 (525)
.|+.|+..+.+...|+|.+|. |+|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cd-f~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECD-FDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT------HHH
T ss_pred cCCcCCCcCCCCceEECccCC-CccChhc
Confidence 699999999866899999994 9998887
No 41
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=90.31 E-value=0.27 Score=53.65 Aligned_cols=48 Identities=21% Similarity=0.524 Sum_probs=43.7
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 152 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~ 152 (525)
...|+.-||..|-.||..||-..|..||..+..+|+.+|..+|. -+|+
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~-e~ld 54 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWE-EWLD 54 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHH-HHhC
Confidence 46799999999999999999888999999999999999999999 4444
No 42
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=89.94 E-value=0.24 Score=33.54 Aligned_cols=29 Identities=31% Similarity=0.907 Sum_probs=24.3
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhh
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIEC 76 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~C 76 (525)
+.|+.|.+.+.+...|+|..|. |++.+.|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCC-CeEcCcc
Confidence 4699999999872299999998 9888777
No 43
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=88.61 E-value=0.44 Score=53.41 Aligned_cols=51 Identities=20% Similarity=0.378 Sum_probs=42.7
Q ss_pred CCCCCCchhHHHHHHHHH-------Hh------------------CCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 009788 103 ICPDWNADDEILLLEGIE-------MY------------------GLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 153 (525)
Q Consensus 103 ~~~~Wta~Eel~LLeai~-------~~------------------G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~ 153 (525)
-...||-+|+..||..|+ ++ ..=||..|++.+|||+..+|+.||.++-...
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~ 510 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSP 510 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhH
Confidence 467999999999999995 33 1128999999999999999999999875543
No 44
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=86.20 E-value=0.57 Score=38.07 Aligned_cols=43 Identities=28% Similarity=0.557 Sum_probs=28.5
Q ss_pred ccccccC-CceeEEcCCCCC---cccchhhhhcccccCCCCCCCCeeeccCC
Q 009788 51 YCNKDIT-GKIRIKCAVCPD---FDLCIECFSVGVEVHPHKSNHPYRVMDNL 98 (525)
Q Consensus 51 ~C~~~i~-~~~ri~C~~C~d---fdLC~~CF~~G~e~~~H~~~H~y~vi~~~ 98 (525)
.|+..++ +.+.|+|..|.. ..+|..||..+. |. .|.|.++...
T Consensus 2 ~C~~~~~~~q~~y~C~tC~~~~~~~iC~~CF~~~~----H~-gH~~~~~~~~ 48 (71)
T PF02207_consen 2 KCTYVWTSGQIFYRCLTCSLDESSGICEECFANSC----HE-GHRVVYYRSS 48 (71)
T ss_dssp SS--B--TT-EEEEETTTBSSTT-BBEHHHHCTSG----GG-GSSEEEEE--
T ss_pred cCCCCCcCCCEEEECccCCCCCCEEEchhhCCCCC----cC-CCcEEEEEeC
Confidence 3666553 368999999964 679999999965 75 7999988654
No 45
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=86.10 E-value=0.55 Score=51.97 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=42.4
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
.+.|+..|+..|+-++..||..||..||..+..+++++|+.||..
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~ 64 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNN 64 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhh
Confidence 468999999999999999999999999999999999999999954
No 46
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=83.69 E-value=0.97 Score=49.55 Aligned_cols=45 Identities=27% Similarity=0.634 Sum_probs=40.8
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
|-...|+.+||.+||.+....- ..|..||..|| +|..+|.+||++
T Consensus 57 i~~tews~eederlLhlakl~p-~qwrtIa~i~g-r~~~qc~eRy~~ 101 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEP-TQWRTIADIMG-RTSQQCLERYNN 101 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcC-CccchHHHHhh-hhHHHHHHHHHH
Confidence 4457899999999999999887 78999999997 899999999987
No 47
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=82.81 E-value=1.6 Score=39.26 Aligned_cols=43 Identities=21% Similarity=0.441 Sum_probs=34.4
Q ss_pred CCCCCchhHHHHHHHHHHhCC---CChHHHHHHhC------------CCCHHHHHHHH
Q 009788 104 CPDWNADDEILLLEGIEMYGL---GNWAEIAEHVG------------TKTKELCIEHY 146 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~---gnW~~Ia~~vg------------tkt~~ec~~hy 146 (525)
...||.+||.-||-.+..||+ |+|+.|-..|- +||+.|+..|=
T Consensus 49 ~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~ 106 (118)
T PF09111_consen 49 KKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRC 106 (118)
T ss_dssp -SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHH
T ss_pred CCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHH
Confidence 478999999999999999999 99999988763 67777776553
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=81.22 E-value=2 Score=45.27 Aligned_cols=47 Identities=23% Similarity=0.575 Sum_probs=37.9
Q ss_pred CCCCchhHHHHHHHHHHh----CCCC-----hHHHHHHh---C-CCCHHHHHHHHHhhcc
Q 009788 105 PDWNADDEILLLEGIEMY----GLGN-----WAEIAEHV---G-TKTKELCIEHYTNVYM 151 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~----G~gn-----W~~Ia~~v---g-tkt~~ec~~hy~~~yi 151 (525)
..|+.+|.+.||++.... +-|+ |++||..+ | .||+.||+..|.+++.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 689999999999987533 3345 99999954 3 4999999999998654
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=81.06 E-value=2.6 Score=44.68 Aligned_cols=44 Identities=7% Similarity=0.314 Sum_probs=41.4
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
...|++.|-.++..|++++| .++.-||...++|+..|++..|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCchhHHHHHHHHHH
Confidence 47899999999999999999 699999999999999999998875
No 50
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=77.81 E-value=1.7 Score=41.03 Aligned_cols=44 Identities=20% Similarity=0.480 Sum_probs=36.9
Q ss_pred CCCCchhHHHHHHHHHHh---C---CCChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 105 PDWNADDEILLLEGIEMY---G---LGNWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~---G---~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
..||.+||++|-+.|-.| | +--.++|++.++ ||+.-|-.+|+.+
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~ 54 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY 54 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH
Confidence 579999999999998766 3 124789999985 9999999999876
No 51
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=76.75 E-value=1.3 Score=46.46 Aligned_cols=45 Identities=33% Similarity=0.812 Sum_probs=36.6
Q ss_pred cCCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeecc
Q 009788 44 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 96 (525)
Q Consensus 44 ~~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~ 96 (525)
...+.|+.|..+. ..+|+|.+|++||.|..|+.... | .|.|..+.
T Consensus 167 ~~~~~c~~c~~~~--~~~~~c~~~~d~d~~~~~~~k~~----h--~h~~~~~~ 211 (319)
T KOG1778|consen 167 WFAYTCPICKLEV--LTAWHCEVCPDYDRCRACEEKPL----H--PHLYEAME 211 (319)
T ss_pred ceeeecCcccccc--ccccccccCCchhhhhcccCCCC----C--Ccchhccc
Confidence 3568899999988 37899999999999999999865 4 36666554
No 52
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=75.82 E-value=3 Score=46.63 Aligned_cols=45 Identities=18% Similarity=0.413 Sum_probs=39.0
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHH----------HhCCCCHHHHHHHHHhh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAE----------HVGTKTKELCIEHYTNV 149 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~----------~vgtkt~~ec~~hy~~~ 149 (525)
...||.+|+..+.+||.++| -|++.|-+ .+..||..+++.||++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 46899999999999999999 79999933 34569999999999874
No 53
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=74.07 E-value=4.3 Score=46.44 Aligned_cols=44 Identities=20% Similarity=0.423 Sum_probs=40.6
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
...||..|-.++-+|+-.|. -++.-|+..|.+||..||.+.|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 36899999999999999998 799999999999999999998864
No 54
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=73.25 E-value=3.4 Score=45.91 Aligned_cols=50 Identities=24% Similarity=0.548 Sum_probs=44.6
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 009788 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 152 (525)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~ 152 (525)
+-...|+.+|+-.|++.-..+| .-|..||..|+++|..+|.++|....=.
T Consensus 70 lk~~~~~~eed~~li~l~~~~~-~~wstia~~~d~rt~~~~~ery~~~~~~ 119 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELG-TQWSTIADYKDRRTAQQCVERYVNTLED 119 (512)
T ss_pred cccccccHHHHHHHHHHHHhcC-chhhhhccccCccchHHHHHHHHHHhhh
Confidence 3468999999999999999999 4699999999999999999999976533
No 55
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=72.97 E-value=4.5 Score=33.00 Aligned_cols=42 Identities=29% Similarity=0.757 Sum_probs=30.3
Q ss_pred ccccccC-CceeEEcCCCC---CcccchhhhhcccccCCCCCCCCeeeccC
Q 009788 51 YCNKDIT-GKIRIKCAVCP---DFDLCIECFSVGVEVHPHKSNHPYRVMDN 97 (525)
Q Consensus 51 ~C~~~i~-~~~ri~C~~C~---dfdLC~~CF~~G~e~~~H~~~H~y~vi~~ 97 (525)
.|+..++ +...|+|..|. ..-+|..||..+. | ..|.|.+...
T Consensus 2 ~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~----H-~gH~~~~~~~ 47 (71)
T smart00396 2 VCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNC----H-KGHDYSLKTS 47 (71)
T ss_pred CCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCC----C-CCCCEEEEEe
Confidence 4666653 44779999995 2459999999754 7 4788887754
No 56
>PHA00442 host recBCD nuclease inhibitor
Probab=72.16 E-value=4.3 Score=31.43 Aligned_cols=27 Identities=19% Similarity=0.462 Sum_probs=22.9
Q ss_pred chhHHHHHHHHHHhCCCChHHHHHHhC
Q 009788 109 ADDEILLLEGIEMYGLGNWAEIAEHVG 135 (525)
Q Consensus 109 a~Eel~LLeai~~~G~gnW~~Ia~~vg 135 (525)
-+-+..+|++++.+|..||+.+.+.+.
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~e 51 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAVE 51 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHHH
Confidence 356778999999999999999987663
No 57
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=71.73 E-value=6.1 Score=31.80 Aligned_cols=47 Identities=23% Similarity=0.408 Sum_probs=32.4
Q ss_pred CCCCchhHHHHHHHHHHh---C---CCC--hHHHHHHhC-CCCHHHHHHHHHhhcc
Q 009788 105 PDWNADDEILLLEGIEMY---G---LGN--WAEIAEHVG-TKTKELCIEHYTNVYM 151 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~---G---~gn--W~~Ia~~vg-tkt~~ec~~hy~~~yi 151 (525)
..+|++||..|++.|..+ | -|| |.++++.-. ..|-+--++||.+...
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~ 58 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLR 58 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence 468999999999999543 3 367 999999887 5888888999988754
No 58
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=71.35 E-value=11 Score=27.57 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=35.5
Q ss_pred HHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 481 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 481 K~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
+..++.....+|.++..+.-..+.+....+.+...-|++.|||.
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 34455666678889999999999999999999999999999984
No 59
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=71.09 E-value=10 Score=27.55 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=31.9
Q ss_pred HhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 489 FSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 489 ~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..++.++..+....+.+....+.+..+.|.+.|||.
T Consensus 10 ~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 10 AQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 345678999999999999999999999999999984
No 60
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=70.91 E-value=10 Score=38.46 Aligned_cols=58 Identities=21% Similarity=0.182 Sum_probs=39.2
Q ss_pred hhcccccCCChhHHHHHHHHHHHH--------HHHHHHH-----------HHHHHHHHhCCcchHHHHHHHHHHHhh
Q 009788 337 RYDVFMRFHSKEDHEDLLQTVISE--------HRTLKRI-----------QDLKEARAAGCRTSAEADRYLELKRGR 394 (525)
Q Consensus 337 ~l~~farf~~~~~~e~l~~~l~~E--------~~Lr~rI-----------~~Lq~~R~~Gi~tl~e~~~Ye~~k~~R 394 (525)
-..-|.+++||-+.|.|..-|..= ..|+.-. .-|..|+.+||+|++++..|+++.+.|
T Consensus 134 F~~e~Gr~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~n~~YI~~IL~nW~k~gvkTv~dv~~~~~~~~~~ 210 (246)
T COG3935 134 FEEEFGRMLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKLNFKYIDAILRNWKKNGVKTVEDVRAREEERRTR 210 (246)
T ss_pred HHHHcCCcCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHH
Confidence 345567788888887776544311 1232222 238899999999999999998776544
No 61
>PLN03000 amine oxidase
Probab=70.69 E-value=7.8 Score=45.97 Aligned_cols=72 Identities=18% Similarity=0.142 Sum_probs=55.7
Q ss_pred CCCccCCCCHHHHHHH--H-HhCCCchHHHHHHHHHHHHHHhCC--CCCHHHHhhhhccCc-hhHHHHHHHHHHCCCCC
Q 009788 452 GFNETQLLSEAEKRLC--C-EIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKIEP-SKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 452 ~~pg~~LLs~~Ek~LC--~-~lrL~P~~YL~iK~~LirE~~~~G--~lkk~dA~~l~kiD~-~K~~rIydFlv~~Gwi~ 524 (525)
++| .+-||++|.+.- . .-++.+..||.|...||+=...+- .+++++|...++.+- +-+..+|+||+.+|+|.
T Consensus 90 ~~p-~d~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r~G~in 167 (881)
T PLN03000 90 GFP-ADSLTEEEIEFGVVPIVGGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVTHGYIN 167 (881)
T ss_pred CCC-cccCCHHHHhccccCcccccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHHcCccc
Confidence 345 678999997751 1 124678999999999998777554 578888988876433 77889999999999985
No 62
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=69.42 E-value=3.1 Score=50.20 Aligned_cols=28 Identities=39% Similarity=0.763 Sum_probs=26.8
Q ss_pred CCCCCCchhHHHHHHHHHHhCCCChHHH
Q 009788 103 ICPDWNADDEILLLEGIEMYGLGNWAEI 130 (525)
Q Consensus 103 ~~~~Wta~Eel~LLeai~~~G~gnW~~I 130 (525)
+..+|+.+++-.||-||=.||+|+|+.|
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHh
Confidence 6789999999999999999999999998
No 63
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=67.36 E-value=11 Score=33.84 Aligned_cols=60 Identities=22% Similarity=0.465 Sum_probs=41.9
Q ss_pred ccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhCCCChH
Q 009788 49 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWA 128 (525)
Q Consensus 49 C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wta~Eel~LLeai~~~G~gnW~ 128 (525)
|-.|+.++.- .+++|..|.. .+.+ .|.+-.-.--..|++.+++..-... ||-.
T Consensus 1 CPvCg~~l~v-t~l~C~~C~t------------~i~G-------------~F~l~~~~~L~~E~~~Fi~~Fi~~r-GnlK 53 (113)
T PF09862_consen 1 CPVCGGELVV-TRLKCPSCGT------------EIEG-------------EFELPWFARLSPEQLEFIKLFIKNR-GNLK 53 (113)
T ss_pred CCCCCCceEE-EEEEcCCCCC------------EEEe-------------eeccchhhcCCHHHHHHHHHHHHhc-CCHH
Confidence 8899999885 7899998861 1111 1111111123468899999888887 8999
Q ss_pred HHHHHhC
Q 009788 129 EIAEHVG 135 (525)
Q Consensus 129 ~Ia~~vg 135 (525)
+|++.+|
T Consensus 54 e~e~~lg 60 (113)
T PF09862_consen 54 EMEKELG 60 (113)
T ss_pred HHHHHHC
Confidence 9999998
No 64
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=64.57 E-value=9.1 Score=31.10 Aligned_cols=45 Identities=22% Similarity=0.480 Sum_probs=37.0
Q ss_pred CCCCchhHHHHHHHHHHh-----C-----------CCChHHHHHHhC-----CCCHHHHHHHHHhh
Q 009788 105 PDWNADDEILLLEGIEMY-----G-----------LGNWAEIAEHVG-----TKTKELCIEHYTNV 149 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~-----G-----------~gnW~~Ia~~vg-----tkt~~ec~~hy~~~ 149 (525)
..||.+|...|++.|+.| | -.-|++|+..+. .||..+++..|.++
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 579999999999998876 2 024999999884 59999999999765
No 65
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=64.29 E-value=8.5 Score=46.53 Aligned_cols=58 Identities=24% Similarity=0.377 Sum_probs=46.4
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCCccc
Q 009788 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHV 164 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~plp~~~~~ 164 (525)
.+|+..+=..++.|+++||-.+-+.||..|++||++|++. |.+.|.... -.+.+..+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~-y~~~f~~~~-~~~~~~~~~ 882 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVER-YAKVFWERY-KELNDYDRI 882 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHH-HHHHHHHhh-hhhccHHHH
Confidence 4899999999999999999999999999999999999985 555555442 234554443
No 66
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=63.91 E-value=3.7 Score=34.16 Aligned_cols=33 Identities=27% Similarity=0.881 Sum_probs=16.4
Q ss_pred Ccccccccccc----CCceeEEcCCCCCcccchhhhhc
Q 009788 46 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSV 79 (525)
Q Consensus 46 ~~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~ 79 (525)
...|.+|+.++ .+.+++-|.+|. |-+|-.||..
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~-fPvCr~CyEY 45 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECA-FPVCRPCYEY 45 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS------HHHHHH
T ss_pred CcccccccCccccCCCCCEEEEEcccC-CccchhHHHH
Confidence 35699999775 466999999997 9999999976
No 67
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=63.19 E-value=8.9 Score=30.67 Aligned_cols=40 Identities=20% Similarity=0.384 Sum_probs=32.0
Q ss_pred HHHHH-hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 485 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 485 irE~~-~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
|++++ .+|..+..+.-.-|.+++.-+..+.++|+++|.|.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 44555 78899999888889999999999999999999983
No 68
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=62.17 E-value=7.8 Score=27.67 Aligned_cols=39 Identities=28% Similarity=0.531 Sum_probs=28.0
Q ss_pred CccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeee
Q 009788 46 LYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (525)
Q Consensus 46 ~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~v 94 (525)
...|..|... ...+-|..|. .-+|..|+..+ |+. |.++.
T Consensus 3 ~~~C~~H~~~---~~~~~C~~C~-~~~C~~C~~~~-----H~~-H~~~~ 41 (42)
T PF00643_consen 3 EPKCPEHPEE---PLSLFCEDCN-EPLCSECTVSG-----HKG-HKIVP 41 (42)
T ss_dssp SSB-SSTTTS---BEEEEETTTT-EEEEHHHHHTS-----TTT-SEEEE
T ss_pred CccCccCCcc---ceEEEecCCC-CccCccCCCCC-----CCC-CEEeE
Confidence 3568877754 2568999997 57999999986 654 76654
No 69
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=60.52 E-value=18 Score=27.49 Aligned_cols=50 Identities=20% Similarity=0.297 Sum_probs=38.2
Q ss_pred hCCCchHHHHHHHHHHHHHHhCCC--CCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 470 IRLAPPLYLRMQEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 470 lrL~P~~YL~iK~~LirE~~~~G~--lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
++|.|.+|..+--+. ..+. ++..+....+.+++.-+.++.+=|++.|||.
T Consensus 1 ~glt~~q~~vL~~l~-----~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 1 LGLTPSQFRVLMALA-----RHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp TTSTHHHHHHHHHHH-----HSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CccCHHHHHHHHHHH-----HCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 356777776554433 3333 8888999999999999999999999999983
No 70
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=59.61 E-value=6.2 Score=30.31 Aligned_cols=30 Identities=30% Similarity=0.738 Sum_probs=18.6
Q ss_pred cccccccccCCc-------eeEEcCCCCCcccchhhhh
Q 009788 48 HCNYCNKDITGK-------IRIKCAVCPDFDLCIECFS 78 (525)
Q Consensus 48 ~C~~C~~~i~~~-------~ri~C~~C~dfdLC~~CF~ 78 (525)
.|.+|...+... .+|+|..|. -.+|..|=.
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~-~~FC~dCD~ 37 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCK-NHFCIDCDV 37 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT---B-HHHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCC-CccccCcCh
Confidence 488898887653 699999997 568888843
No 71
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=59.18 E-value=6.2 Score=28.34 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=19.3
Q ss_pred ccccccccCCceeEEcCCCCCccc-chhhhhc
Q 009788 49 CNYCNKDITGKIRIKCAVCPDFDL-CIECFSV 79 (525)
Q Consensus 49 C~~C~~~i~~~~ri~C~~C~dfdL-C~~CF~~ 79 (525)
||+|++.|.+.+.+.=..=..|-+ |..|...
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 999999998765544332222444 4777654
No 72
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=57.28 E-value=11 Score=28.60 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=29.6
Q ss_pred hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 490 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 490 ~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..|.++..+.-..+.++...+.++.+-|++.|||.
T Consensus 14 ~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 14 ENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 45558888888889999999999999999999984
No 73
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=55.96 E-value=34 Score=24.93 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 111 DEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 111 Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
=+..||..++.-|--.|.+||+.+|- |+..|..++..
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 36789999999888899999999984 88888887654
No 74
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=54.24 E-value=16 Score=44.20 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=37.0
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhC------------CCCHHHHHHHHHh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG------------TKTKELCIEHYTN 148 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg------------tkt~~ec~~hy~~ 148 (525)
...||.+|+.-||-.+..||+|+|+.|-..|. +||+.|+..+-..
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~ 982 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDT 982 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHH
Confidence 35799999999999999999999999977663 6777777665443
No 75
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=51.83 E-value=45 Score=28.92 Aligned_cols=64 Identities=16% Similarity=0.055 Sum_probs=49.3
Q ss_pred CHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 460 SEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 460 s~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..-+..|=..++|.|..|..+..+-. -...+|.++..+....+.++...+.++.+=|+++|||.
T Consensus 11 ~~~~~~l~~~~~ls~~q~~vL~~l~~-~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 11 KSLKRYLKKEFNLSLEELLILYYLGK-LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh-hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 33445555567999999987754432 11245788889999999999999999999999999984
No 76
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=50.71 E-value=18 Score=38.52 Aligned_cols=43 Identities=28% Similarity=0.499 Sum_probs=37.3
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHH-HHHhCCCCHHHHHHHHHh
Q 009788 105 PDWNADDEILLLEGIEMYGLGNWAEI-AEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~I-a~~vgtkt~~ec~~hy~~ 148 (525)
..|+.+|=+.+=+|++.|| -|+.-| +..|.||+..||...|+.
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHHH
Confidence 5899999999999999999 566666 668999999999988764
No 77
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=50.66 E-value=53 Score=28.64 Aligned_cols=61 Identities=8% Similarity=0.025 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 459 LSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 459 Ls~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
++..-..+...++|.|..|..+-.+ ..+|.++..+.-..+.++..-+.++.+=|.+.|||.
T Consensus 13 ~~~~~~~~l~~~~lt~~q~~iL~~l-----~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~ 73 (118)
T TIGR02337 13 AMSFFRPILAQHGLTEQQWRILRIL-----AEQGSMEFTQLANQACILRPSLTGILARLERDGLVT 73 (118)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH-----HHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence 3444456667889999999866332 356778888888888999999999999999999984
No 78
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=49.72 E-value=9.3 Score=36.25 Aligned_cols=30 Identities=30% Similarity=0.650 Sum_probs=25.8
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHh
Q 009788 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHV 134 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~v 134 (525)
.-|-..-+.-||.||-.||+|.|++|...-
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~ 33 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDP 33 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCC
Confidence 358888889999999999999999997643
No 79
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=49.24 E-value=19 Score=31.27 Aligned_cols=32 Identities=25% Similarity=0.558 Sum_probs=24.2
Q ss_pred CCCCCCchhHHHHHHHHHHh----CCC---ChHHHHHHh
Q 009788 103 ICPDWNADDEILLLEGIEMY----GLG---NWAEIAEHV 134 (525)
Q Consensus 103 ~~~~Wta~Eel~LLeai~~~----G~g---nW~~Ia~~v 134 (525)
|..-||.++|+.||+|+-.| |.+ +|...-++|
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~v 41 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFV 41 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHH
Confidence 56789999999999999887 643 555555554
No 80
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=47.61 E-value=10 Score=44.27 Aligned_cols=36 Identities=25% Similarity=0.763 Sum_probs=30.8
Q ss_pred CcCCccccccccccCCceeEEcCCCCCcccchhhhhcc
Q 009788 43 KRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 80 (525)
Q Consensus 43 ~~~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G 80 (525)
+-....|+.|.+.+.. +.++|..|. |-+|+.|+-.-
T Consensus 226 ~g~~~mC~~C~~tlfn-~hw~C~~C~-~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 226 KGIREMCDRCETTLFN-IHWRCPRCG-FGVCLDCYRKW 261 (889)
T ss_pred cCcchhhhhhcccccc-eeEEccccC-Ceeeecchhhc
Confidence 3456789999999987 899999997 66999999775
No 81
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=46.79 E-value=42 Score=28.01 Aligned_cols=44 Identities=23% Similarity=0.412 Sum_probs=32.7
Q ss_pred CCCchhHHHHHHHHHHh---CCC---------ChHHHHHHhC-----CCCHHHHHHHHHhh
Q 009788 106 DWNADDEILLLEGIEMY---GLG---------NWAEIAEHVG-----TKTKELCIEHYTNV 149 (525)
Q Consensus 106 ~Wta~Eel~LLeai~~~---G~g---------nW~~Ia~~vg-----tkt~~ec~~hy~~~ 149 (525)
.||.+.+..||+++... |.. .|+.|+..+. ..|..+|+.||..+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999987332 111 3888888775 47899999998753
No 82
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=46.48 E-value=35 Score=40.42 Aligned_cols=69 Identities=14% Similarity=0.156 Sum_probs=53.6
Q ss_pred cCCCCHHHHHH---HHHhCCCchHHHHHHHHHHHHHHhCC--CCCHHHHhhhhcc-CchhHHHHHHHHHHCCCCC
Q 009788 456 TQLLSEAEKRL---CCEIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKI-EPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 456 ~~LLs~~Ek~L---C~~lrL~P~~YL~iK~~LirE~~~~G--~lkk~dA~~l~ki-D~~K~~rIydFlv~~Gwi~ 524 (525)
.+-||++|.+. =.-.+.-+..||.|...||+=..++- .+++.+|...++. ..+-+..+|+||+..|+|.
T Consensus 144 ~~~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~~g~in 218 (808)
T PLN02328 144 VDSLTEEEIEANVVSTIGGTEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLEHGYIN 218 (808)
T ss_pred CccCCHHHHhhcCcchhcccceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhccCcee
Confidence 56789988664 22334788999999999998777543 5888899887752 3468999999999999985
No 83
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=45.67 E-value=27 Score=27.88 Aligned_cols=44 Identities=11% Similarity=0.061 Sum_probs=33.1
Q ss_pred HHHHHHHHHh-CCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 481 QEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 481 K~~LirE~~~-~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
|+.++.=... ++.++-.+.-+.+.|....++++..+|.+.|.|.
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 5555433333 6778888888889999999999999999999874
No 84
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=45.34 E-value=18 Score=43.59 Aligned_cols=32 Identities=28% Similarity=0.926 Sum_probs=27.2
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhc
Q 009788 47 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSV 79 (525)
Q Consensus 47 ~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~ 79 (525)
-.|.+|+-++ .+.+++-|.+|. |-+|-.||.-
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~-FPVCrpCYEY 53 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCA-FPVCRPCYEY 53 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCC-Cccccchhhh
Confidence 3799999875 456999999997 9999999965
No 85
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=45.29 E-value=38 Score=31.57 Aligned_cols=55 Identities=20% Similarity=0.403 Sum_probs=45.9
Q ss_pred CCCCchhHHHHHHHHHHhCCC--ChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCC
Q 009788 105 PDWNADDEILLLEGIEMYGLG--NWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPD 160 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~g--nW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~plp~ 160 (525)
-+++..+-..+|.+|..||+| +|......+-.||.+|.+ .|...|+..-+.|..+
T Consensus 39 lGFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~-aY~~LFm~HL~E~~~d 95 (145)
T PF06461_consen 39 LGFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIR-AYGSLFMRHLCEPGTD 95 (145)
T ss_pred eccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHH-HHHHHHHHHhcCCCcC
Confidence 378999999999999999998 799999999999998887 5777877766555433
No 86
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=45.27 E-value=61 Score=29.22 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=44.7
Q ss_pred HHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 465 RLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 465 ~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.....++|.|.+|..+-.+. ..++.++..+....+.++..-+.++.+=|++.|||.
T Consensus 22 ~~l~~~glt~~q~~vL~~l~----~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 22 HRLKPLELTQTHWVTLHNIH----QLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHhcCCCHHHHHHHHHHH----HcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 45578999999998764443 134456777888888999999999999999999985
No 87
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=44.99 E-value=78 Score=29.75 Aligned_cols=40 Identities=25% Similarity=0.498 Sum_probs=26.5
Q ss_pred cccccccccCCceeEEcCCCCCcccchhhhhcccccCCCC
Q 009788 48 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 87 (525)
Q Consensus 48 ~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~ 87 (525)
.|-.|+++|.+..+.-=.+=....+|..|+--|.++..+.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~G~~~~~~~ 41 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKFGKEIIKKP 41 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhcCCccccCC
Confidence 3999999998752222222223779999998888765443
No 88
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=43.92 E-value=44 Score=26.94 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCCC
Q 009788 477 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 525 (525)
Q Consensus 477 YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~~ 525 (525)
|-..++.++ ..|..+..-...-|+|.-|++.+|.|-|.+.|+|+|
T Consensus 8 y~~a~~~V~----~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 8 YEEAVEFVI----EEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp HHHHHHHHH----HCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred HHHHHHHHH----HcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 445555554 467778777888899999999999999999999975
No 89
>smart00595 MADF subfamily of SANT domain.
Probab=43.89 E-value=23 Score=29.22 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=20.8
Q ss_pred ChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 126 NWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 126 nW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
-|..||..+|. |.++|+.+|.++
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 49999999997 999999999875
No 90
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=42.69 E-value=6.6 Score=42.37 Aligned_cols=50 Identities=20% Similarity=0.432 Sum_probs=33.1
Q ss_pred CCCCCCcCCccccccccc--------------cCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeee
Q 009788 38 GAGEGKRALYHCNYCNKD--------------ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (525)
Q Consensus 38 ~~~~~~~~~~~C~~C~~~--------------i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~v 94 (525)
++...+...|.|..|... |.. +-|+|.+|....-|.. ....|+++|.=+.
T Consensus 259 ~~i~n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~-vEYrCPEC~KVFsCPA------NLASHRRWHKPR~ 322 (500)
T KOG3993|consen 259 AGIPNVIGDYICQLCKEKYEDAFALAQHRCPRIVH-VEYRCPECDKVFSCPA------NLASHRRWHKPRP 322 (500)
T ss_pred ccCcccHHHHHHHHHHHhhhhHHHHhhccCCeeEE-eeecCCcccccccCch------hhhhhhcccCCch
Confidence 445566777999999743 222 5567777777655554 4456999997654
No 91
>PLN02436 cellulose synthase A
Probab=42.09 E-value=15 Score=44.18 Aligned_cols=34 Identities=26% Similarity=0.823 Sum_probs=28.3
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 009788 47 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (525)
Q Consensus 47 ~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 81 (525)
-.|.+|+-++ .+.+++-|.+|. |-+|..||.--.
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~-fpvCr~Cyeyer 74 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECA-FPVCRPCYEYER 74 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCC-Cccccchhhhhh
Confidence 4799999775 456999999997 999999996543
No 92
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=41.49 E-value=17 Score=39.73 Aligned_cols=43 Identities=26% Similarity=0.422 Sum_probs=36.4
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
.-+||..|-- ++..-..|| .|.+-||+.++++||+|+...|++
T Consensus 470 ~~~wSp~e~s-~ircf~~y~-~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYK-DNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred cCCCCCcccc-cccCchhhc-cchHHHHHHhcCCCHHHHHHHhcC
Confidence 3689987655 777788999 899999999999999999987653
No 93
>PF13730 HTH_36: Helix-turn-helix domain
Probab=41.28 E-value=74 Score=23.68 Aligned_cols=53 Identities=19% Similarity=0.209 Sum_probs=36.1
Q ss_pred CCCchHHHHHHHHHHHHHHhCC-CCCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 009788 471 RLAPPLYLRMQEVMSREIFSGN-VNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 523 (525)
Q Consensus 471 rL~P~~YL~iK~~LirE~~~~G-~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 523 (525)
+|.|...+.+=-++-.-...++ ..+.+..-..+.+-.+.+.+..+-|++.|||
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 4555555555443322212333 3467777788899999999999999999997
No 94
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=41.25 E-value=52 Score=24.79 Aligned_cols=28 Identities=18% Similarity=0.431 Sum_probs=23.6
Q ss_pred CCChhHHHHHHHHH-----HHHHHHHHHHHHHH
Q 009788 344 FHSKEDHEDLLQTV-----ISEHRTLKRIQDLK 371 (525)
Q Consensus 344 f~~~~~~e~l~~~l-----~~E~~Lr~rI~~Lq 371 (525)
+.+++++++|++.| ++|.+|++.+.+..
T Consensus 4 ~~~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~ 36 (46)
T PF15614_consen 4 YDDPEELDELLKALENPRGKRESKLKKELDKHR 36 (46)
T ss_pred ccCHHHHHHHHHHHcCcccHhHHHHHHHHHHHh
Confidence 56789999999999 79999988877654
No 95
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=41.15 E-value=5.8 Score=31.91 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCCcchHHHHHHHH
Q 009788 367 IQDLKEARAAGCRTSAEADRYLE 389 (525)
Q Consensus 367 I~~Lq~~R~~Gi~tl~e~~~Ye~ 389 (525)
..-|..|++.||+|++++..|++
T Consensus 54 ~~Il~~W~~~gi~t~e~~~~~~k 76 (77)
T PF07261_consen 54 EKILNNWKQKGIKTVEDAEEYEK 76 (77)
T ss_dssp HHHHHHHHHCT--SCCCCT----
T ss_pred HHHHHHHHHcCCCCHHHHHHHhh
Confidence 35688999999999999988754
No 96
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=40.83 E-value=23 Score=33.91 Aligned_cols=45 Identities=18% Similarity=0.282 Sum_probs=33.5
Q ss_pred CCCCCchhHHHHHHHHHHhCC------CChHHHHHHhCCCCHHHHHHHHHhh
Q 009788 104 CPDWNADDEILLLEGIEMYGL------GNWAEIAEHVGTKTKELCIEHYTNV 149 (525)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~------gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (525)
...||.+++++|-+.|-.|+- .-.+.+++.+ .||+..|..+|+.+
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~ 55 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSV 55 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHH
Confidence 367999999999888776652 1245566666 48999999999543
No 97
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=40.65 E-value=95 Score=24.53 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 476 LYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 476 ~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.=|.+|..+|...+..|.|+.++|-.+. +.+..-+++...+|++.
T Consensus 15 qm~e~kK~~idk~Ve~G~iTqeqAd~ik----~~id~~~~~~~qnGf~p 59 (59)
T PF10925_consen 15 QMLELKKQIIDKYVEAGVITQEQADAIK----KHIDQRQEYMQQNGFVP 59 (59)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHH----HHHHHHHHHHHHcCCCC
Confidence 3478899999999999999999998864 56668899999999863
No 98
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=40.22 E-value=52 Score=27.33 Aligned_cols=41 Identities=17% Similarity=0.355 Sum_probs=30.0
Q ss_pred HHHHHHHHhCCCCCHHHHhhhhc---cCchhHHHHHHHHHHCCC
Q 009788 482 EVMSREIFSGNVNNKADAHHLFK---IEPSKIDRVYDMLVKKGL 522 (525)
Q Consensus 482 ~~LirE~~~~G~lkk~dA~~l~k---iD~~K~~rIydFlv~~Gw 522 (525)
..||....+.|.++-.+....|+ +++..+..||++|...|.
T Consensus 10 ~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 10 KKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 33676677889999999888887 899999999999999885
No 99
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=40.02 E-value=19 Score=23.73 Aligned_cols=13 Identities=38% Similarity=0.761 Sum_probs=10.0
Q ss_pred HHHHHHHHHCCCC
Q 009788 511 DRVYDMLVKKGLA 523 (525)
Q Consensus 511 ~rIydFlv~~Gwi 523 (525)
.-|||||+++|+.
T Consensus 5 ~lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 5 QLIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHHCT-H
T ss_pred HHHHHHHHHCCcH
Confidence 3589999999974
No 100
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.91 E-value=63 Score=29.29 Aligned_cols=52 Identities=12% Similarity=0.261 Sum_probs=43.4
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 468 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 468 ~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..++|.|.+|..+..+- .+|.++..+....+.+|..-+.++.+=|++.|||.
T Consensus 34 ~~~glt~~q~~vL~~l~-----~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 34 SPLDITAAQFKVLCSIR-----CAACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred cccCCCHHHHHHHHHHH-----HcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 56789999998776432 45668888888889999999999999999999984
No 101
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=39.41 E-value=59 Score=25.06 Aligned_cols=34 Identities=26% Similarity=0.359 Sum_probs=28.4
Q ss_pred hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 009788 490 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 523 (525)
Q Consensus 490 ~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 523 (525)
.++.++..+..+.+.++..-+.++.+=|++.|||
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 4788888999999999999999999999999998
No 102
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=38.49 E-value=12 Score=34.50 Aligned_cols=53 Identities=23% Similarity=0.442 Sum_probs=39.1
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCC
Q 009788 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSF 100 (525)
Q Consensus 45 ~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~ 100 (525)
..|.|+.|...-++..+.+=.+|-+|.+|-.||+.-. .|-+.|+-=.+...+|
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LW---K~~~~ypvCPvCkTSF 131 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLW---KFCNLYPVCPVCKTSF 131 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHH---HHcccCCCCCcccccc
Confidence 6799999998777766677778999999999999855 3555565444444343
No 103
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=38.06 E-value=50 Score=24.41 Aligned_cols=46 Identities=13% Similarity=0.250 Sum_probs=33.7
Q ss_pred HHHHHHHHHHH-hCCCC-CHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 479 RMQEVMSREIF-SGNVN-NKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 479 ~iK~~LirE~~-~~G~l-kk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.++..++...+ .+..+ +..+.-..+.+..+-+++.+.-|.+.|||.
T Consensus 4 ~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34455544433 23455 777888888999999999999999999984
No 104
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=38.05 E-value=67 Score=24.35 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=29.6
Q ss_pred hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 490 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 490 ~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.++ ++..++...+.+....+.++.+-|++.|||.
T Consensus 18 ~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 18 EGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred HCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 444 8888888888999999999999999999984
No 105
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=37.79 E-value=25 Score=42.27 Aligned_cols=35 Identities=26% Similarity=0.818 Sum_probs=28.5
Q ss_pred CCcccccccccc----CCceeEEcCCCCCcccchhhhhcc
Q 009788 45 ALYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVG 80 (525)
Q Consensus 45 ~~~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G 80 (525)
....|.+|+.++ .+.+++-|.+|. |-+|-.||.--
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~-fpvCr~cyeye 52 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCG-FPVCKPCYEYE 52 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCC-Cccccchhhhh
Confidence 345699999774 466999999997 99999999653
No 106
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.95 E-value=53 Score=33.98 Aligned_cols=42 Identities=19% Similarity=0.587 Sum_probs=31.6
Q ss_pred CCCCCCcCCccccccccccCCceeEEcCCCCCcccchhhhhc
Q 009788 38 GAGEGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSV 79 (525)
Q Consensus 38 ~~~~~~~~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~ 79 (525)
.++..+....+|..|..-+..+.+++|..-+--.+|--|--.
T Consensus 260 ~s~~A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 260 DSGAAPSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred ccccCCCCceeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 344455667999999999998899998876666677776543
No 107
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=36.84 E-value=21 Score=37.58 Aligned_cols=58 Identities=21% Similarity=0.407 Sum_probs=34.6
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHH
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEG 118 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wta~Eel~LLea 118 (525)
-.|-=|+..-. .|.-|. -++.||+.|-+.....|.|..- |.. +.-..|+.+| ++.|+.
T Consensus 21 k~CaDCga~~P--~W~S~n--lGvfiCi~CagvHRsLGvhiS~-----VKS----itLD~wt~~~-l~~m~~ 78 (319)
T COG5347 21 KKCADCGAPNP--TWASVN--LGVFLCIDCAGVHRSLGVHISK-----VKS----LTLDNWTEEE-LRRMEV 78 (319)
T ss_pred CccccCCCCCC--ceEecc--cCeEEEeecchhhhccccceee-----eee----eecccCCHHH-HHHHHH
Confidence 34666887652 343333 4678999999998877766422 111 2235699865 444443
No 108
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=36.74 E-value=48 Score=23.86 Aligned_cols=25 Identities=28% Similarity=0.502 Sum_probs=21.0
Q ss_pred hHHHHHHHHHHhCCCChHHHHHHhCC
Q 009788 111 DEILLLEGIEMYGLGNWAEIAEHVGT 136 (525)
Q Consensus 111 Eel~LLeai~~~G~gnW~~Ia~~vgt 136 (525)
|-..|.++++.+| ||....|+.+|-
T Consensus 6 E~~~i~~aL~~~~-gn~~~aA~~Lgi 30 (42)
T PF02954_consen 6 EKQLIRQALERCG-GNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHTT-T-HHHHHHHHTS
T ss_pred HHHHHHHHHHHhC-CCHHHHHHHHCC
Confidence 5567888999999 999999999983
No 109
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=34.88 E-value=51 Score=36.17 Aligned_cols=48 Identities=15% Similarity=0.400 Sum_probs=41.8
Q ss_pred CCCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 100 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 100 ~p~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
+.-+...||++|-.+|-.+.+.|| -+...|-..+.-|+-...+..|..
T Consensus 183 r~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 183 RTEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred cCCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHH
Confidence 334568999999888889999999 799999999999999999988764
No 110
>PLN02189 cellulose synthase
Probab=34.53 E-value=24 Score=42.50 Aligned_cols=34 Identities=26% Similarity=0.836 Sum_probs=28.3
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 009788 47 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (525)
Q Consensus 47 ~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 81 (525)
..|..|+.++ .+.+++-|.+|. |-+|..||.--.
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~-fpvCr~Cyeyer 72 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECG-FPVCRPCYEYER 72 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCC-Cccccchhhhhh
Confidence 4799999874 466999999997 999999996543
No 111
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=33.82 E-value=35 Score=29.17 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=24.3
Q ss_pred CCCCCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 009788 491 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 523 (525)
Q Consensus 491 ~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 523 (525)
.|+-...-|.+| .++.++++.+.+||+..|+|
T Consensus 64 ~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 64 EGVHVDEIAQQL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TTEEHHHHHHHS-TS-HHHHHHHHHHHHHTTSE
T ss_pred CcccHHHHHHHh-CcCHHHHHHHHHHHHhCCeE
Confidence 354444445555 99999999999999999997
No 112
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=33.66 E-value=94 Score=28.41 Aligned_cols=25 Identities=16% Similarity=0.449 Sum_probs=21.2
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCC
Q 009788 468 CEIRLAPPLYLRMQEVMSREIFSGN 492 (525)
Q Consensus 468 ~~lrL~P~~YL~iK~~LirE~~~~G 492 (525)
+.++|+|..|+.+|..|-.+.+...
T Consensus 87 ~ri~mS~~EYM~lKkqLae~il~~s 111 (153)
T COG4008 87 NRINMSPEEYMELKKQLAEYILGHS 111 (153)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhccC
Confidence 5789999999999999988877443
No 113
>PLN02400 cellulose synthase
Probab=33.62 E-value=25 Score=42.53 Aligned_cols=33 Identities=30% Similarity=0.936 Sum_probs=27.6
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhcc
Q 009788 47 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVG 80 (525)
Q Consensus 47 ~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G 80 (525)
-.|.+|+-++ .+.+++-|.+|. |-+|-.||..-
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCa-FPVCRpCYEYE 73 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECA-FPVCRPCYEYE 73 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCC-Cccccchhhee
Confidence 3799999775 466999999997 99999999653
No 114
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=32.80 E-value=73 Score=26.03 Aligned_cols=51 Identities=25% Similarity=0.409 Sum_probs=38.0
Q ss_pred HhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 469 EIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 469 ~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..+|.+..+..+.-+. .+|.++..+....+.+....+.++++=|++.|||.
T Consensus 5 ~~~l~~~~~~il~~l~-----~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 5 PLGLTPTQFLVLRILY-----EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred ccCCCHHHHHHHHHHH-----HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 4456666555554433 35567777777888899999999999999999984
No 115
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=32.71 E-value=32 Score=27.47 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=15.7
Q ss_pred HHHHHHHHhCCcchHHHH
Q 009788 368 QDLKEARAAGCRTSAEAD 385 (525)
Q Consensus 368 ~~Lq~~R~~Gi~tl~e~~ 385 (525)
.-|..|+..||+|+++++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 458899999999999875
No 116
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=31.81 E-value=1.2e+02 Score=24.26 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCCC
Q 009788 477 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 525 (525)
Q Consensus 477 YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~~ 525 (525)
|-..++.++ ..|..+..-...-|+|--|+..+|.|-|.+.|.|+|
T Consensus 7 y~~a~~~V~----~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 7 YDEAVELVI----ETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred HHHHHHHHH----HhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 444444444 446666666777799999999999999999999975
No 117
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=31.55 E-value=56 Score=35.91 Aligned_cols=42 Identities=26% Similarity=0.519 Sum_probs=33.5
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHH-HhCCCCHHHHHHHHH
Q 009788 105 PDWNADDEILLLEGIEMYGLGNWAEIAE-HVGTKTKELCIEHYT 147 (525)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~-~vgtkt~~ec~~hy~ 147 (525)
+.|++.|-.++-||+++|| .++++|-. ++.=|+-..+.+.|.
T Consensus 286 EEWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHHHHH
Confidence 6899999999999999999 67777754 445577777776665
No 118
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=31.43 E-value=28 Score=26.57 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=21.3
Q ss_pred cccccccccCCceeEEcCCCCCcccchhhhhcc
Q 009788 48 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 80 (525)
Q Consensus 48 ~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G 80 (525)
.|+.|++.+.-..+++ =.|..+|..||..-
T Consensus 1 ~C~iCg~kigl~~~~k---~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK---IKDGYICKDCLKKL 30 (51)
T ss_pred CCCcccccccccccee---ccCccchHHHHHHh
Confidence 4999999986433333 23456999999874
No 119
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=31.07 E-value=96 Score=23.61 Aligned_cols=39 Identities=15% Similarity=0.249 Sum_probs=32.4
Q ss_pred HHHHH-hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 009788 485 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 523 (525)
Q Consensus 485 irE~~-~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 523 (525)
|++++ .+|.++..+++.++.+--.-+-.|.+||=..||.
T Consensus 1 i~~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T 40 (50)
T PF09107_consen 1 IRELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREGIT 40 (50)
T ss_dssp HHHHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred ChHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCE
Confidence 34555 6899999999999988888888999999999984
No 120
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.53 E-value=1.1e+02 Score=24.89 Aligned_cols=40 Identities=13% Similarity=0.108 Sum_probs=33.3
Q ss_pred HHHHH-hC-CCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 485 SREIF-SG-NVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 485 irE~~-~~-G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
|-+++ .. |.++..+.-..+.+...-+.++.+.|++.|||.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 44444 33 689998888888999999999999999999984
No 121
>PRK08359 transcription factor; Validated
Probab=30.41 E-value=40 Score=32.53 Aligned_cols=40 Identities=18% Similarity=0.380 Sum_probs=26.6
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhh-hccc-ccCCC
Q 009788 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECF-SVGV-EVHPH 86 (525)
Q Consensus 47 ~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF-~~G~-e~~~H 86 (525)
..|-.|+.+|.+..+.-=.+=...++|..|+ --|. +++.+
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G~~~~~~~ 48 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYGRKKPGTF 48 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhCCCccCCc
Confidence 4599999999875222222222378999999 6687 55544
No 122
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=30.41 E-value=49 Score=26.00 Aligned_cols=35 Identities=20% Similarity=0.240 Sum_probs=31.5
Q ss_pred hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 490 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 490 ~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..|..+..+.-..+.++.+.+.++.+-|.+.|||.
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 67888888888888999999999999999999984
No 123
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=30.01 E-value=1.1e+02 Score=25.58 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCC-------CChHHHHHHhCCCC-----HHHHHHHHHhhc
Q 009788 113 ILLLEGIEMYGL-------GNWAEIAEHVGTKT-----KELCIEHYTNVY 150 (525)
Q Consensus 113 l~LLeai~~~G~-------gnW~~Ia~~vgtkt-----~~ec~~hy~~~y 150 (525)
..|-.+|...|- +.|..||..+|-.+ ..+.+.+|.++-
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L 88 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYL 88 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHh
Confidence 556667777761 36999999998422 367788887763
No 124
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=29.50 E-value=33 Score=36.10 Aligned_cols=34 Identities=21% Similarity=0.592 Sum_probs=25.6
Q ss_pred CcCCccccccccccCCceeEEcCCCCCcccchhhh
Q 009788 43 KRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECF 77 (525)
Q Consensus 43 ~~~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF 77 (525)
.....+|.+|+.......+|+|..|. -.+|+.|=
T Consensus 327 ~~~~~~Cf~C~~~~~~~~~y~C~~Ck-~~FCldCD 360 (378)
T KOG2807|consen 327 YNGSRFCFACQGELLSSGRYRCESCK-NVFCLDCD 360 (378)
T ss_pred cCCCcceeeeccccCCCCcEEchhcc-ceeeccch
Confidence 34455699997777666999999997 44788873
No 125
>PLN02195 cellulose synthase A
Probab=28.59 E-value=37 Score=40.67 Aligned_cols=33 Identities=24% Similarity=0.810 Sum_probs=27.2
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhcc
Q 009788 47 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVG 80 (525)
Q Consensus 47 ~~C~~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G 80 (525)
..|..|+.++ .+.+++-|.+|. |-+|-.||.--
T Consensus 7 ~~c~~cgd~~~~~~~g~~fvaC~eC~-~pvCrpCyeye 43 (977)
T PLN02195 7 PICATCGEEVGVDSNGEAFVACHECS-YPLCKACLEYE 43 (977)
T ss_pred ccceecccccCcCCCCCeEEEeccCC-Cccccchhhhh
Confidence 4699999754 456999999997 99999999653
No 126
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=28.50 E-value=60 Score=28.70 Aligned_cols=23 Identities=17% Similarity=0.534 Sum_probs=20.4
Q ss_pred HHhCCCchHHHHHHHHHHHHHHh
Q 009788 468 CEIRLAPPLYLRMQEVMSREIFS 490 (525)
Q Consensus 468 ~~lrL~P~~YL~iK~~LirE~~~ 490 (525)
.+++|.|+.|+.+|..|..|.++
T Consensus 86 ~~igls~~EYm~lKkelae~i~~ 108 (109)
T TIGR03277 86 QRIGMSPEEYMELKKKLAEELLK 108 (109)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhc
Confidence 46899999999999999988874
No 127
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=27.71 E-value=1.5e+02 Score=27.02 Aligned_cols=50 Identities=18% Similarity=0.446 Sum_probs=37.4
Q ss_pred hHHHHHHHHHHHHHHh----CC--CCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 475 PLYLRMQEVMSREIFS----GN--VNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 475 ~~YL~iK~~LirE~~~----~G--~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.-|.-|.+.+....++ .| .++..+.-..+.+.+|-+.|.|.-|.+.|+|.
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~ 66 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVE 66 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 3577787777766663 23 45655555667899999999999999999874
No 128
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=26.14 E-value=77 Score=22.89 Aligned_cols=34 Identities=15% Similarity=0.538 Sum_probs=28.2
Q ss_pred HHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHH
Q 009788 481 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYD 515 (525)
Q Consensus 481 K~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIyd 515 (525)
|+.||...+..|+.+..+ +.|..+...-..+.|.
T Consensus 3 K~~lI~~Li~~Giyk~~d-rqL~Eltl~ELe~ey~ 36 (38)
T PF13076_consen 3 KDFLIEKLIQSGIYKKED-RQLYELTLSELEKEYE 36 (38)
T ss_pred HHHHHHHHHHcCCcCccc-hHHHHcCHHHHHHHHH
Confidence 677888888999999988 8888888777777764
No 129
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=26.03 E-value=1.8e+02 Score=23.19 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=34.3
Q ss_pred HHHHHHHHHhCCC--CCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 481 QEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 481 K~~LirE~~~~G~--lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
++.++.=....|. ++..+.-..+.|+...++++..=|.+.|+|.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444443445555 8888888888999999999999999999983
No 130
>PRK10870 transcriptional repressor MprA; Provisional
Probab=25.94 E-value=1.6e+02 Score=27.85 Aligned_cols=58 Identities=10% Similarity=0.160 Sum_probs=46.0
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 464 KRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 464 k~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
...-..++|.|.+|..+..+. ...++.++..+....+.++..-+.++.+=|++.|||.
T Consensus 45 ~~~l~~~gLt~~q~~iL~~L~---~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 45 NKMLKAQGINETLFMALITLE---SQENHSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred HHHHHHCCCCHHHHHHHHHHh---cCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 445578999999999875543 1234667777777788899999999999999999984
No 131
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=25.19 E-value=92 Score=23.19 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=33.2
Q ss_pred HHHHHHHH--hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 482 EVMSREIF--SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 482 ~~LirE~~--~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.+-|-|++ .++.++..+.-.-+.+....+-++..-|++.||+.
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 33444555 34457888888888999999999999999999984
No 132
>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=24.89 E-value=63 Score=24.03 Aligned_cols=24 Identities=33% Similarity=0.665 Sum_probs=18.4
Q ss_pred CCcccccccccc--CCceeEEcCCCC
Q 009788 45 ALYHCNYCNKDI--TGKIRIKCAVCP 68 (525)
Q Consensus 45 ~~~~C~~C~~~i--~~~~ri~C~~C~ 68 (525)
....|++|++.| ....-++|..|.
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~ 35 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCG 35 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT
T ss_pred CCCCCcccCcccCCCCCCeEEECCCC
Confidence 456899999999 445789999986
No 133
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=24.74 E-value=53 Score=34.45 Aligned_cols=24 Identities=29% Similarity=0.771 Sum_probs=18.9
Q ss_pred CCccccccccccCCceeEEcCCCC
Q 009788 45 ALYHCNYCNKDITGKIRIKCAVCP 68 (525)
Q Consensus 45 ~~~~C~~C~~~i~~~~ri~C~~C~ 68 (525)
..++|..|..-..+..|++|+.|.
T Consensus 133 FyV~Ck~Cd~v~~GKLRV~C~~C~ 156 (446)
T KOG0006|consen 133 FYVWCKNCDDVKRGKLRVYCQKCS 156 (446)
T ss_pred eEEEecchhhccCCceEEEeeccc
Confidence 346888888888777888888875
No 134
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=24.71 E-value=15 Score=37.85 Aligned_cols=31 Identities=29% Similarity=0.702 Sum_probs=17.3
Q ss_pred CCCCCCCcCCccccccccccCCceeEEcCCCC
Q 009788 37 QGAGEGKRALYHCNYCNKDITGKIRIKCAVCP 68 (525)
Q Consensus 37 ~~~~~~~~~~~~C~~C~~~i~~~~ri~C~~C~ 68 (525)
+|.++.+..-.+|+.|..+... +|++|+.|.
T Consensus 202 ~g~~~~GlRYL~CslC~teW~~-VR~KC~nC~ 232 (308)
T COG3058 202 IGETEQGLRYLHCSLCETEWHY-VRVKCSNCE 232 (308)
T ss_pred ecCccccchhhhhhhHHHHHHH-HHHHhcccc
Confidence 3334444445566666666554 666666664
No 135
>PF10123 Mu-like_Pro: Mu-like prophage I protein; InterPro: IPR012106 This entry is represented by the Bacteriophage Mu, Gp32. The characteristics of the protein distribution suggest prophage matches.
Probab=24.39 E-value=57 Score=34.22 Aligned_cols=25 Identities=16% Similarity=0.446 Sum_probs=22.4
Q ss_pred CccCCCCHHHHHHHHHhCCCchHHH
Q 009788 454 NETQLLSEAEKRLCCEIRLAPPLYL 478 (525)
Q Consensus 454 pg~~LLs~~Ek~LC~~lrL~P~~YL 478 (525)
.+..-||.+|+..|.+|+|.|..|+
T Consensus 301 ~~~~~Lt~ee~av~~~lGis~edf~ 325 (326)
T PF10123_consen 301 DGSAALTAEELAVCRQLGISPEDFA 325 (326)
T ss_pred CCCCCCCHHHHHHHHHcCCCHHHhc
Confidence 3456799999999999999999996
No 136
>PRK00420 hypothetical protein; Validated
Probab=24.00 E-value=48 Score=29.64 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=21.0
Q ss_pred CccccccccccCC--ceeEEcCCCCCcccch
Q 009788 46 LYHCNYCNKDITG--KIRIKCAVCPDFDLCI 74 (525)
Q Consensus 46 ~~~C~~C~~~i~~--~~ri~C~~C~dfdLC~ 74 (525)
..+|..|+.++.. ...+.|..|.....|.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCeeeec
Confidence 3689999998763 4677788777655553
No 137
>PF07875 Coat_F: Coat F domain; InterPro: IPR012851 The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination []. Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus [].
Probab=23.58 E-value=66 Score=25.25 Aligned_cols=25 Identities=12% Similarity=0.278 Sum_probs=18.9
Q ss_pred hhhccCchhHHHHHHHHHHCCCCCC
Q 009788 501 HLFKIEPSKIDRVYDMLVKKGLAPP 525 (525)
Q Consensus 501 ~l~kiD~~K~~rIydFlv~~Gwi~~ 525 (525)
.++.-...-...||+++.++||-++
T Consensus 38 ~~~~~~~~~~~~l~~~m~~kGwY~~ 62 (64)
T PF07875_consen 38 QILNECQQMQYELFNYMNQKGWYQP 62 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcCC
Confidence 3344455667799999999999865
No 138
>PF12488 DUF3704: Protein of unknown function (DUF3704) ; InterPro: IPR022173 This domain family is found in eukaryotes, and is approximately 30 amino acids in length.
Probab=23.30 E-value=29 Score=23.20 Aligned_cols=9 Identities=22% Similarity=0.342 Sum_probs=7.2
Q ss_pred cccccCCCC
Q 009788 252 LSGYNSKRQ 260 (525)
Q Consensus 252 ~~GYmP~R~ 260 (525)
-.||||.|+
T Consensus 7 S~gyMp~s~ 15 (27)
T PF12488_consen 7 SFGYMPRSG 15 (27)
T ss_pred ccceeeecc
Confidence 479999885
No 139
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=23.25 E-value=1.6e+02 Score=21.55 Aligned_cols=34 Identities=12% Similarity=0.158 Sum_probs=26.9
Q ss_pred CCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 491 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 491 ~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
++.++..+....+.+....+.++.+-|.+.|||.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 5667777777777788888888888888888874
No 140
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.25 E-value=68 Score=28.70 Aligned_cols=30 Identities=30% Similarity=0.685 Sum_probs=22.6
Q ss_pred ccccccccccCC-----------ceeEEcCCCCCcccchhhh
Q 009788 47 YHCNYCNKDITG-----------KIRIKCAVCPDFDLCIECF 77 (525)
Q Consensus 47 ~~C~~C~~~i~~-----------~~ri~C~~C~dfdLC~~CF 77 (525)
..|.+|+..+.. ..+|+|..|. .++|.+|=
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~-~~FC~dCD 96 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCK-NVFCVDCD 96 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCC-Cccccccc
Confidence 459999987642 3589999997 56788773
No 141
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=23.22 E-value=97 Score=29.61 Aligned_cols=96 Identities=14% Similarity=0.189 Sum_probs=49.3
Q ss_pred ccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCeeeccCCCCCCC-CCCCCch----hHHH--------H
Q 009788 49 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLI-CPDWNAD----DEIL--------L 115 (525)
Q Consensus 49 C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~-~~~Wta~----Eel~--------L 115 (525)
|-.|++.+... ..--.+=...+.|..|+--|.....|...-.-........+.. ...|-.. +... +
T Consensus 6 CEiCG~~i~~~-~~v~vegsel~VC~~Cak~G~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~d~~~elvedY~e~I 84 (165)
T COG1813 6 CELCGREIDKP-IKVKVEGAELTVCDDCAKFGTAAKTASGDPRKEPARRNQAQKPRGSPRRERRDNDELPELVEDYGERI 84 (165)
T ss_pred eeccccccCCC-eeEEeecceeehhHHHHHhccCccccCCCccccccccccccCCCCCccccCCccchHHHHHHHHHHHH
Confidence 99999998742 2222223347899999977765555543211111001111111 1245442 2222 3
Q ss_pred HHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009788 116 LEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (525)
Q Consensus 116 Leai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (525)
-+|-++-|+ .=+++|..++- ...+...|..
T Consensus 85 r~ARE~~G~-SqedLA~ki~e--k~svI~~iE~ 114 (165)
T COG1813 85 REAREKRGL-SQEDLAAKLKE--KVSVIRRIER 114 (165)
T ss_pred HHHHHHcCC-CHHHHHHHhcc--cHHHHHHHHh
Confidence 335566674 56788888864 2345555543
No 142
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.20 E-value=3.2e+02 Score=22.77 Aligned_cols=61 Identities=15% Similarity=0.100 Sum_probs=45.5
Q ss_pred HhhccCCCC---CCCCCCChHHHHHHHhhccccc--CCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009788 313 LERNLLYPN---PFEKDLSPEERELCRRYDVFMR--FHSKEDHEDLLQTVISEHRTLKRIQDLKEA 373 (525)
Q Consensus 313 ~e~~Ll~~~---~~~k~~s~eer~~~~~l~~far--f~~~~~~e~l~~~l~~E~~Lr~rI~~Lq~~ 373 (525)
.+.|||.+. ...+.++.++-.....++.+.+ -++-.+...++..+-+-..|+.+|.+|++.
T Consensus 22 e~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~~l~~l~~~ 87 (91)
T cd04766 22 ERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRAR 87 (91)
T ss_pred HHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356898742 2345678887777777777765 678888889998888888888888888743
No 143
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=22.60 E-value=1.3e+02 Score=29.57 Aligned_cols=46 Identities=17% Similarity=0.356 Sum_probs=38.8
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHhC---CCCHHHHHHHHHhhccCC
Q 009788 106 DWNADDEILLLEGIEMYGLGNWAEIAEHVG---TKTKELCIEHYTNVYMNS 153 (525)
Q Consensus 106 ~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg---tkt~~ec~~hy~~~yi~~ 153 (525)
.|++.++++|+.||++-. +-..|+.-|. .-|..|+..+|.....+.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 499999999999999864 8999988776 479999999999875443
No 144
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=22.39 E-value=47 Score=27.88 Aligned_cols=35 Identities=17% Similarity=0.323 Sum_probs=25.0
Q ss_pred cccccccccCCceeEEcCC---CCCcccchhhhhccccc
Q 009788 48 HCNYCNKDITGKIRIKCAV---CPDFDLCIECFSVGVEV 83 (525)
Q Consensus 48 ~C~~C~~~i~~~~ri~C~~---C~dfdLC~~CF~~G~e~ 83 (525)
.|..|+.+++... ..-++ ...-+-|.-||..|.++
T Consensus 2 ~CQSCGMPl~~~~-~~Gte~dGs~s~~YC~yCy~~G~Ft 39 (81)
T PF12674_consen 2 FCQSCGMPLSKDE-DFGTEADGSKSEDYCSYCYQNGEFT 39 (81)
T ss_pred cCCcCcCccCCcc-ccccccCCCCchhHHHHHhcCCcee
Confidence 5999999998633 33333 23457899999999854
No 145
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=22.18 E-value=1.2e+02 Score=23.16 Aligned_cols=35 Identities=11% Similarity=0.185 Sum_probs=30.6
Q ss_pred hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 490 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 490 ~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..+.++..+.-..+.+....+.+++.-|.+.|||.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34568888888999999999999999999999984
No 146
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=21.87 E-value=1.8e+02 Score=26.68 Aligned_cols=43 Identities=14% Similarity=0.122 Sum_probs=36.6
Q ss_pred hhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 009788 110 DDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 153 (525)
Q Consensus 110 ~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~ 153 (525)
+-|..||++++.-|--.|.+||+.+|. |+..|..++...-=.+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCC
Confidence 568999999999998899999999984 8889999998764443
No 147
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=21.72 E-value=1.6e+02 Score=25.31 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=27.0
Q ss_pred HHHH-hCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 009788 486 REIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 523 (525)
Q Consensus 486 rE~~-~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 523 (525)
-.++ ..|.++..++-+++.|- ..++++||.+.|||
T Consensus 16 d~~~~~~~~~ti~~~AK~L~i~---~~~l~~~Lr~~g~l 51 (111)
T PF03374_consen 16 DAFVDSDGLYTIREAAKLLGIG---RNKLFQWLREKGWL 51 (111)
T ss_pred HHHHcCCCCccHHHHHHHhCCC---HHHHHHHHHhCCce
Confidence 3344 56888888888887554 67889999999997
No 148
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=21.30 E-value=40 Score=37.59 Aligned_cols=36 Identities=28% Similarity=0.669 Sum_probs=25.4
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCC
Q 009788 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNH 90 (525)
Q Consensus 45 ~~~~C~~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H~~~H 90 (525)
.+-.|-+|...+... ...++|+.||.++.+ .|..-|
T Consensus 21 ~reeC~yCf~S~~~e--------~si~vClnCfqs~C~--~h~~~H 56 (749)
T COG5207 21 FREECCYCFRSIGDE--------HSISVCLNCFQSFCE--KHRGIH 56 (749)
T ss_pred hhhhhheeeccCCCC--------cceehHHHHhHhhhh--hcccee
Confidence 345788898887653 358899999999763 344444
No 149
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.16 E-value=99 Score=24.57 Aligned_cols=36 Identities=19% Similarity=0.561 Sum_probs=23.4
Q ss_pred CCccccccccccC--C-ceeEEcCCCCCc--ccchhhhhcc
Q 009788 45 ALYHCNYCNKDIT--G-KIRIKCAVCPDF--DLCIECFSVG 80 (525)
Q Consensus 45 ~~~~C~~C~~~i~--~-~~ri~C~~C~df--dLC~~CF~~G 80 (525)
....|..|+..|. + .+.+.|..|... --|..|-..+
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 3456888887774 2 367788888643 2377776655
No 150
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=20.83 E-value=58 Score=34.56 Aligned_cols=26 Identities=19% Similarity=0.653 Sum_probs=20.0
Q ss_pred cCCccccccccccCCceeEEcCCCCCc
Q 009788 44 RALYHCNYCNKDITGKIRIKCAVCPDF 70 (525)
Q Consensus 44 ~~~~~C~~C~~~i~~~~ri~C~~C~df 70 (525)
...|+|..|+-.... .+|+|..|..+
T Consensus 352 ~~~YRC~~CGF~a~~-l~W~CPsC~~W 377 (389)
T COG2956 352 KPRYRCQNCGFTAHT-LYWHCPSCRAW 377 (389)
T ss_pred cCCceecccCCccee-eeeeCCCcccc
Confidence 467889999887664 78898888754
No 151
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=20.71 E-value=2.2e+02 Score=27.53 Aligned_cols=52 Identities=8% Similarity=-0.089 Sum_probs=40.6
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 468 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 468 ~~lrL~P~~YL~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
..++|.|.+|..+-.+ ..++.++.++....+.++..-+.++.+=|.+.|||.
T Consensus 39 ~~~gLt~~q~~iL~~L-----~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~ 90 (185)
T PRK13777 39 KPYDLNINEHHILWIA-----YHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLT 90 (185)
T ss_pred HHCCCCHHHHHHHHHH-----HhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEE
Confidence 4689999999766322 244566777777788899999999999999999984
No 152
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=20.63 E-value=1.8e+02 Score=21.81 Aligned_cols=31 Identities=10% Similarity=0.194 Sum_probs=25.5
Q ss_pred CCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 494 NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 494 lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.+..+....+.+..+.+++.+.=|.+.|||.
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3367777778899999999999999999984
No 153
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=20.63 E-value=94 Score=24.78 Aligned_cols=24 Identities=29% Similarity=0.684 Sum_probs=20.5
Q ss_pred ChHHHHHHhCC-CCHHHHHHHHHhh
Q 009788 126 NWAEIAEHVGT-KTKELCIEHYTNV 149 (525)
Q Consensus 126 nW~~Ia~~vgt-kt~~ec~~hy~~~ 149 (525)
-|..||..+|. -+.++|+.+|.++
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHH
Confidence 49999999985 5789999999874
No 154
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=20.42 E-value=1.2e+02 Score=23.51 Aligned_cols=32 Identities=9% Similarity=0.178 Sum_probs=25.3
Q ss_pred CC-CHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 493 VN-NKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 493 ~l-kk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
.| +..+.-+.+.+-.+-+++.++.|.+.|||.
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 45 777777778888899999999999999974
No 155
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=20.21 E-value=2.7e+02 Score=23.05 Aligned_cols=46 Identities=13% Similarity=0.109 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 009788 478 LRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 524 (525)
Q Consensus 478 L~iK~~LirE~~~~G~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 524 (525)
|++.+.++-= +.++..++++......|+.+++.....-|.+.|+|.
T Consensus 4 lt~~~~IL~~-ls~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 4 LTVTQKILII-LSKRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred hhHHHHHHHH-HHhccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 4455555533 344489999999999999999999999999999985
Done!