Query 014788
Match_columns 418
No_of_seqs 269 out of 779
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:31:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014788.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014788hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5259 RSC8 RSC chromatin rem 100.0 5E-86 1.1E-90 666.7 19.9 345 34-418 46-444 (531)
2 KOG1279 Chromatin remodeling f 100.0 3.9E-77 8.4E-82 620.3 23.7 356 33-417 40-475 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 7.3E-28 1.6E-32 197.8 6.5 85 40-128 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 6.3E-22 1.4E-26 201.0 7.5 104 159-264 13-124 (438)
5 COG5114 Histone acetyltransfer 99.7 1.5E-18 3.2E-23 170.4 4.8 103 160-264 5-115 (432)
6 PF00249 Myb_DNA-binding: Myb- 99.2 2.7E-11 5.8E-16 89.0 5.3 44 214-257 2-47 (48)
7 PF13921 Myb_DNA-bind_6: Myb-l 98.9 1.2E-09 2.6E-14 83.4 5.5 41 216-256 1-41 (60)
8 smart00717 SANT SANT SWI3, AD 98.9 2E-09 4.4E-14 76.7 5.9 44 214-257 2-46 (49)
9 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 5.4E-09 1.2E-13 73.5 5.6 43 215-257 1-44 (45)
10 PLN03000 amine oxidase 98.8 3.3E-09 7.2E-14 118.6 6.6 83 44-131 86-171 (881)
11 PLN02328 lysine-specific histo 98.7 1.2E-08 2.5E-13 113.8 6.7 83 45-131 138-222 (808)
12 cd02336 ZZ_RSC8 Zinc finger, Z 98.5 5.2E-08 1.1E-12 71.3 2.9 44 161-204 1-45 (45)
13 PLN03212 Transcription repress 98.3 5.4E-07 1.2E-11 87.4 5.0 45 213-257 25-71 (249)
14 TIGR01557 myb_SHAQKYF myb-like 98.3 1.6E-06 3.4E-11 66.6 5.2 46 213-258 3-54 (57)
15 PLN02529 lysine-specific histo 98.1 2.9E-06 6.4E-11 94.2 6.2 83 44-131 62-147 (738)
16 PLN03091 hypothetical protein; 98.1 2.7E-06 5.8E-11 88.3 5.1 46 212-257 13-60 (459)
17 KOG0048 Transcription factor, 98.0 6.4E-06 1.4E-10 79.9 4.7 45 213-257 9-55 (238)
18 PLN03212 Transcription repress 98.0 8.1E-06 1.7E-10 79.3 5.0 46 211-256 76-121 (249)
19 KOG0048 Transcription factor, 97.8 2.6E-05 5.6E-10 75.6 5.4 42 213-254 62-103 (238)
20 PLN03091 hypothetical protein; 97.7 4.6E-05 1E-09 79.3 5.5 46 211-256 65-110 (459)
21 KOG0049 Transcription factor, 97.2 0.00041 8.9E-09 74.9 5.3 45 212-256 359-404 (939)
22 cd02335 ZZ_ADA2 Zinc finger, Z 96.9 0.00097 2.1E-08 49.5 3.3 46 161-206 1-49 (49)
23 PLN02976 amine oxidase 96.8 0.0012 2.7E-08 77.8 4.5 81 46-131 452-540 (1713)
24 cd02249 ZZ Zinc finger, ZZ typ 96.5 0.0024 5.2E-08 46.6 3.1 44 161-205 1-45 (46)
25 cd02340 ZZ_NBR1_like Zinc fing 96.2 0.0041 8.9E-08 45.1 2.8 41 162-206 2-43 (43)
26 smart00291 ZnF_ZZ Zinc-binding 96.2 0.0043 9.2E-08 45.0 2.9 39 160-198 4-43 (44)
27 KOG0049 Transcription factor, 96.1 0.0049 1.1E-07 66.9 4.0 44 213-256 412-459 (939)
28 cd02343 ZZ_EF Zinc finger, ZZ 96.0 0.0057 1.2E-07 45.5 2.8 38 162-199 2-40 (48)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.0 0.0039 8.4E-08 50.6 2.1 44 214-257 2-63 (90)
30 cd02338 ZZ_PCMF_like Zinc fing 95.6 0.011 2.4E-07 43.9 2.9 44 162-205 2-48 (49)
31 cd02345 ZZ_dah Zinc finger, ZZ 95.5 0.014 3E-07 43.4 3.2 43 162-204 2-47 (49)
32 cd02341 ZZ_ZZZ3 Zinc finger, Z 95.3 0.015 3.3E-07 43.2 2.9 43 161-205 1-47 (48)
33 PF00569 ZZ: Zinc finger, ZZ t 95.2 0.0074 1.6E-07 44.2 0.8 39 160-198 4-44 (46)
34 cd02334 ZZ_dystrophin Zinc fin 94.9 0.026 5.6E-07 42.2 3.0 42 162-203 2-46 (49)
35 KOG0051 RNA polymerase I termi 94.8 0.034 7.4E-07 60.5 4.6 45 212-257 383-427 (607)
36 cd02344 ZZ_HERC2 Zinc finger, 93.9 0.059 1.3E-06 39.6 2.9 42 162-206 2-45 (45)
37 KOG0051 RNA polymerase I termi 93.5 0.067 1.5E-06 58.3 3.7 53 212-264 435-513 (607)
38 cd02337 ZZ_CBP Zinc finger, ZZ 93.3 0.072 1.6E-06 38.3 2.5 36 161-197 1-37 (41)
39 cd02339 ZZ_Mind_bomb Zinc fing 93.3 0.086 1.9E-06 38.7 2.9 41 162-205 2-44 (45)
40 KOG0050 mRNA splicing protein 92.7 0.1 2.3E-06 55.7 3.6 44 213-256 7-51 (617)
41 PF13873 Myb_DNA-bind_5: Myb/S 92.3 0.29 6.3E-06 38.9 5.1 45 213-257 2-68 (78)
42 KOG4167 Predicted DNA-binding 92.0 0.23 4.9E-06 55.1 5.3 43 213-255 619-661 (907)
43 KOG0050 mRNA splicing protein 89.5 0.3 6.5E-06 52.3 3.3 45 212-257 58-102 (617)
44 COG5118 BDP1 Transcription ini 89.5 0.51 1.1E-05 48.9 4.8 44 213-256 365-408 (507)
45 COG5147 REB1 Myb superfamily p 87.8 0.49 1.1E-05 51.1 3.6 45 212-256 71-115 (512)
46 KOG4329 DNA-binding protein [G 87.8 0.79 1.7E-05 47.4 4.9 51 213-263 277-328 (445)
47 KOG4282 Transcription factor G 87.8 0.63 1.4E-05 47.4 4.3 47 213-259 54-114 (345)
48 cd02342 ZZ_UBA_plant Zinc fing 86.3 0.49 1.1E-05 34.5 1.8 31 162-192 2-34 (43)
49 TIGR02894 DNA_bind_RsfA transc 85.5 0.87 1.9E-05 42.1 3.4 50 213-264 4-60 (161)
50 KOG4468 Polycomb-group transcr 85.3 0.76 1.6E-05 50.1 3.4 45 213-257 88-142 (782)
51 COG5147 REB1 Myb superfamily p 85.1 0.52 1.1E-05 50.9 2.2 42 213-254 20-62 (512)
52 KOG1280 Uncharacterized conser 83.6 0.63 1.4E-05 47.7 1.9 35 160-194 8-44 (381)
53 KOG1279 Chromatin remodeling f 82.6 1.6 3.6E-05 47.1 4.6 118 14-132 154-284 (506)
54 PF09111 SLIDE: SLIDE; InterP 81.7 1.8 4E-05 38.0 3.8 44 212-255 48-107 (118)
55 KOG4582 Uncharacterized conser 77.5 1.5 3.3E-05 43.8 2.2 32 161-192 153-186 (278)
56 PF04504 DUF573: Protein of un 73.0 5.5 0.00012 33.7 4.2 44 213-256 4-60 (98)
57 PLN03142 Probable chromatin-re 70.6 6.3 0.00014 46.3 5.3 40 214-253 825-865 (1033)
58 PF00392 GntR: Bacterial regul 70.2 7.4 0.00016 29.7 4.0 52 75-127 3-55 (64)
59 KOG1194 Predicted DNA-binding 69.3 8.5 0.00019 41.1 5.4 46 211-256 185-230 (534)
60 KOG4286 Dystrophin-like protei 67.9 2.5 5.5E-05 47.4 1.3 41 161-201 604-646 (966)
61 PF12776 Myb_DNA-bind_3: Myb/S 67.6 7 0.00015 31.8 3.6 43 215-257 1-61 (96)
62 smart00345 HTH_GNTR helix_turn 67.3 7.5 0.00016 28.2 3.4 50 78-128 2-52 (60)
63 KOG3554 Histone deacetylase co 66.9 4.8 0.0001 43.0 3.0 52 213-264 285-337 (693)
64 PF12802 MarR_2: MarR family; 64.1 19 0.00042 26.6 5.2 41 89-129 14-54 (62)
65 PRK13923 putative spore coat p 63.8 6.8 0.00015 36.7 3.1 41 213-254 5-52 (170)
66 PF01475 FUR: Ferric uptake re 62.9 12 0.00026 31.9 4.4 49 79-128 7-60 (120)
67 COG1725 Predicted transcriptio 61.7 31 0.00067 30.8 6.7 56 76-131 11-70 (125)
68 PF13404 HTH_AsnC-type: AsnC-t 61.1 20 0.00043 25.7 4.5 38 219-257 3-41 (42)
69 KOG1194 Predicted DNA-binding 61.0 4.6 9.9E-05 43.0 1.6 44 212-256 469-512 (534)
70 PF01022 HTH_5: Bacterial regu 60.7 23 0.00049 25.5 4.8 45 81-128 3-47 (47)
71 smart00550 Zalpha Z-DNA-bindin 59.2 35 0.00076 26.6 6.0 52 80-131 6-57 (68)
72 cd00090 HTH_ARSR Arsenical Res 58.7 24 0.00053 26.0 5.0 44 84-130 11-54 (78)
73 PF02954 HTH_8: Bacterial regu 56.6 17 0.00036 25.7 3.4 25 220-244 6-30 (42)
74 smart00595 MADF subfamily of S 55.7 9.5 0.00021 30.7 2.3 28 234-264 29-56 (89)
75 PF09339 HTH_IclR: IclR helix- 54.9 21 0.00045 26.1 3.9 43 85-128 8-50 (52)
76 PF08914 Myb_DNA-bind_2: Rap1 54.8 22 0.00048 28.0 4.2 43 214-256 3-55 (65)
77 PF13412 HTH_24: Winged helix- 54.7 43 0.00094 23.8 5.5 44 81-126 4-47 (48)
78 PRK09462 fur ferric uptake reg 53.5 24 0.00051 31.5 4.7 46 82-127 19-69 (148)
79 PLN03142 Probable chromatin-re 53.0 19 0.0004 42.5 4.9 45 213-257 926-983 (1033)
80 cd07153 Fur_like Ferric uptake 51.8 29 0.00064 29.1 4.9 46 82-128 3-53 (116)
81 PHA00442 host recBCD nuclease 47.3 20 0.00044 27.5 2.7 26 217-242 24-50 (59)
82 COG5114 Histone acetyltransfer 46.4 30 0.00066 35.6 4.6 70 51-127 360-429 (432)
83 KOG4301 Beta-dystrobrevin [Cyt 43.3 14 0.00029 38.4 1.7 38 159-198 239-280 (434)
84 PF09862 DUF2089: Protein of u 43.3 38 0.00082 29.7 4.2 60 163-243 1-60 (113)
85 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 42.4 72 0.0016 24.0 5.0 40 219-260 7-46 (50)
86 smart00346 HTH_ICLR helix_turn 41.4 54 0.0012 26.0 4.7 44 85-129 10-53 (91)
87 PF03444 HrcA_DNA-bdg: Winged 38.2 1.1E+02 0.0023 25.3 5.8 52 76-128 4-55 (78)
88 PF13463 HTH_27: Winged helix 37.0 1E+02 0.0022 23.0 5.4 40 92-131 14-53 (68)
89 KOG0384 Chromodomain-helicase 36.5 24 0.00051 42.2 2.4 28 212-239 1132-1160(1373)
90 PRK11179 DNA-binding transcrip 36.1 55 0.0012 29.3 4.3 39 218-257 8-47 (153)
91 PF07649 C1_3: C1-like domain; 35.5 19 0.00041 23.6 0.9 27 162-188 2-29 (30)
92 COG0735 Fur Fe2+/Zn2+ uptake r 35.3 63 0.0014 29.0 4.6 50 81-131 22-76 (145)
93 PRK11414 colanic acid/biofilm 35.2 59 0.0013 30.5 4.6 66 63-129 2-67 (221)
94 KOG4479 Transcription factor e 34.6 78 0.0017 26.4 4.4 44 76-123 36-89 (92)
95 PRK06474 hypothetical protein; 34.6 81 0.0018 29.3 5.3 48 81-129 12-60 (178)
96 PF01047 MarR: MarR family; I 34.5 78 0.0017 23.1 4.2 35 97-131 18-52 (59)
97 PRK11639 zinc uptake transcrip 33.5 59 0.0013 29.9 4.1 45 82-127 28-77 (169)
98 PF09286 Pro-kuma_activ: Pro-k 32.2 46 0.00099 29.3 3.1 36 94-129 45-80 (143)
99 smart00426 TEA TEA domain. 32.1 81 0.0018 25.3 4.1 20 213-232 3-22 (68)
100 smart00420 HTH_DEOR helix_turn 32.1 1.3E+02 0.0028 20.8 4.9 34 95-128 13-46 (53)
101 PF09012 FeoC: FeoC like trans 30.0 1.3E+02 0.0028 23.3 5.0 43 79-127 3-45 (69)
102 PRK03837 transcriptional regul 29.8 69 0.0015 30.3 4.1 58 72-130 13-71 (241)
103 cd08310 Death_NFkB-like Death 29.8 43 0.00093 26.8 2.2 23 218-244 2-24 (72)
104 cd07377 WHTH_GntR Winged helix 29.3 99 0.0022 22.5 4.1 52 76-128 5-57 (66)
105 TIGR02702 SufR_cyano iron-sulf 29.2 99 0.0021 29.0 5.0 47 81-129 2-48 (203)
106 KOG2656 DNA methyltransferase 28.7 33 0.00071 36.2 1.7 44 213-256 130-179 (445)
107 PF03979 Sigma70_r1_1: Sigma-7 28.3 1.4E+02 0.0031 24.0 5.1 40 84-125 11-53 (82)
108 PLN03131 hypothetical protein; 28.3 81 0.0018 35.3 4.6 93 161-264 24-122 (705)
109 PRK11169 leucine-responsive tr 28.0 85 0.0018 28.5 4.2 39 218-257 13-52 (164)
110 TIGR03338 phnR_burk phosphonat 27.7 71 0.0015 29.6 3.7 56 74-130 13-68 (212)
111 PLN03119 putative ADP-ribosyla 27.2 70 0.0015 35.5 3.9 93 161-264 24-122 (648)
112 cd00092 HTH_CRP helix_turn_hel 26.8 1.9E+02 0.0041 21.3 5.3 49 81-129 5-58 (67)
113 PF10545 MADF_DNA_bdg: Alcohol 26.7 50 0.0011 25.6 2.1 30 233-264 27-57 (85)
114 PF09420 Nop16: Ribosome bioge 26.7 1E+02 0.0023 28.2 4.5 44 213-256 114-161 (164)
115 PF08100 Dimerisation: Dimeris 26.5 1.2E+02 0.0026 22.7 4.0 27 94-120 20-50 (51)
116 smart00344 HTH_ASNC helix_turn 26.5 1.1E+02 0.0024 25.2 4.3 39 218-257 2-41 (108)
117 PF02082 Rrf2: Transcriptional 26.0 1.2E+02 0.0027 24.1 4.4 44 85-128 14-57 (83)
118 KOG0703 Predicted GTPase-activ 25.6 63 0.0014 32.7 3.1 92 160-264 25-124 (287)
119 PF01978 TrmB: Sugar-specific 25.2 92 0.002 23.7 3.3 35 94-128 20-54 (68)
120 smart00418 HTH_ARSR helix_turn 24.9 1.4E+02 0.003 21.1 4.2 37 94-130 8-44 (66)
121 PF00643 zf-B_box: B-box zinc 24.6 43 0.00092 23.2 1.2 29 161-192 4-33 (42)
122 TIGR02812 fadR_gamma fatty aci 24.6 83 0.0018 29.8 3.6 58 72-130 6-64 (235)
123 PF01388 ARID: ARID/BRIGHT DNA 24.2 1.2E+02 0.0025 24.6 3.9 37 220-256 37-86 (92)
124 PF08279 HTH_11: HTH domain; 24.0 2.7E+02 0.0058 20.0 5.5 41 83-124 3-43 (55)
125 COG5347 GTPase-activating prot 24.0 71 0.0015 32.8 3.1 95 161-264 21-123 (319)
126 PF10440 WIYLD: Ubiquitin-bind 23.8 54 0.0012 26.1 1.8 26 215-240 22-48 (65)
127 PRK00430 fis global DNA-bindin 23.6 98 0.0021 26.0 3.4 26 219-244 55-80 (95)
128 PRK01905 DNA-binding protein F 23.4 1E+02 0.0023 24.6 3.4 28 217-244 35-62 (77)
129 PF11035 SnAPC_2_like: Small n 23.3 1.3E+02 0.0028 31.1 4.8 41 213-253 21-65 (344)
130 smart00419 HTH_CRP helix_turn_ 23.1 96 0.0021 21.3 2.9 34 96-129 8-41 (48)
131 PF00325 Crp: Bacterial regula 22.8 1.2E+02 0.0027 20.7 3.1 27 100-126 6-32 (32)
132 PRK11534 DNA-binding transcrip 22.6 90 0.002 29.3 3.4 57 72-129 7-63 (224)
133 PF08260 Kinin: Insect kinin p 21.7 43 0.00093 16.2 0.5 6 43-48 2-7 (8)
134 PLN02638 cellulose synthase A 21.5 60 0.0013 38.4 2.3 53 155-207 12-73 (1079)
135 PRK10225 DNA-binding transcrip 21.4 1.2E+02 0.0026 29.1 4.1 57 73-130 10-67 (257)
136 PF09538 FYDLN_acid: Protein o 21.2 50 0.0011 28.6 1.3 27 160-191 9-35 (108)
137 PF03107 C1_2: C1 domain; Int 20.9 70 0.0015 21.1 1.6 27 162-188 2-29 (30)
138 PF12674 Zn_ribbon_2: Putative 20.8 40 0.00086 27.7 0.5 35 162-196 2-40 (81)
139 PF14420 Clr5: Clr5 domain 20.8 1.6E+02 0.0034 22.1 3.7 29 76-107 3-31 (54)
140 PF08784 RPA_C: Replication pr 20.7 2.5E+02 0.0053 23.2 5.3 47 80-126 47-95 (102)
141 PF11740 KfrA_N: Plasmid repli 20.6 1.4E+02 0.003 25.2 3.9 29 94-124 17-45 (120)
142 PF01325 Fe_dep_repress: Iron 20.3 1.9E+02 0.0041 22.1 4.2 39 93-131 19-57 (60)
143 cd08312 Death_MyD88 Death doma 20.3 45 0.00098 27.0 0.7 26 219-244 3-28 (79)
144 PRK10906 DNA-binding transcrip 20.3 1.8E+02 0.0039 28.4 5.1 46 80-127 5-50 (252)
145 cd08781 Death_UNC5-like Death 20.1 72 0.0016 26.0 1.9 26 219-244 7-32 (83)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=5e-86 Score=666.75 Aligned_cols=345 Identities=31% Similarity=0.537 Sum_probs=280.6
Q ss_pred CCCCCeeecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHH
Q 014788 34 SSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSI 113 (418)
Q Consensus 34 ~~q~~~iiiPs~s~WF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i 113 (418)
-+|+|+|+||||+.||++.+||+||+++.||||+||+++|||++|++||||||++||+||.+|||+|+||||++|||++|
T Consensus 46 ~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvagDV~ai 125 (531)
T COG5259 46 MEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAGDVAAI 125 (531)
T ss_pred hccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccchhHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhcccccCCCC--cccccccc---------ccccCCcCC--------C----------------CCcc-----
Q 014788 114 RRVFDFLETWGLINYFAS--VKTLKWED---------KETKSSAAS--------A----------------ESSS----- 153 (418)
Q Consensus 114 ~Rvh~FLe~wGlINy~~~--~kP~~~~~---------~~~~~~~~~--------~----------------~~~~----- 153 (418)
.|||+|||+|||||||++ ++|..... .++.....+ + ...|
T Consensus 126 vrvHrFLekWGLINYqvdp~trPs~IgPplt~h~q~l~dtP~gl~p~l~~~~~~~~~~~a~~~e~~~~k~~~~sps~~~~ 205 (531)
T COG5259 126 VRVHRFLEKWGLINYQVDPGTRPSTIGPPLTSHFQDLHDTPRGLSPFLPWGPINQRVLGAKEIEYETHKEENYSPSLKSP 205 (531)
T ss_pred HHHHHHHHHhcceeeccCCCCCccccCCCcchhhHHHhhCccccccccCCCCccccccccchhhhhhhccCCCCchhhhh
Confidence 999999999999999999 66643321 111111110 0 0011
Q ss_pred ---------ccccccc---ccccCCCCccccccccccC-CCccchhhhhccCCCCCCCCCCCccccccCcc-cCCCCCHH
Q 014788 154 ---------ALKETSK---RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRVEISEE-ARSDWTEK 219 (418)
Q Consensus 154 ---------~~~~~~k---~~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~s~dF~ki~~~~~-~~~~WT~~ 219 (418)
...+.+. ..|+.||+.|...+|+... .++.+|..||.+|+|+.+..++||+++++... .+..||.+
T Consensus 206 ~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~~~~~~~dk~WS~q 285 (531)
T COG5259 206 KKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVTISLLIRDKNWSRQ 285 (531)
T ss_pred hhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhhhhcccccccccHH
Confidence 1111222 6799999999877776543 46779999999999999999999999987655 56799999
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCCCCcccCCCCCCcccccccccCCCCCCccccccccCCCCCC
Q 014788 220 ETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESENVGATSPS 299 (418)
Q Consensus 220 E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~LPIeD~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 (418)
|+++|||||++||++|++||.|||+||++|||+|||||||+|+|| ...+ ++. .+ .
T Consensus 286 E~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l-~k~~------~~~-~~-----------------~ 340 (531)
T COG5259 286 ELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYL-SKGD------GKG-DN-----------------S 340 (531)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhh-hccc------CcC-CC-----------------C
Confidence 999999999999999999999999999999999999999999999 2111 010 00 0
Q ss_pred ccCCCcCCcCCCChHHHHHHHHHhhcChHHHHHHHHHHHHHhhccCcccccCccccccccccccccCChhhHHHHHHHHH
Q 014788 300 KRMRLTPLADASNPIMAQAAFLSALAGVEIAEVAARAAVTTLSDVDDRASKGSLMRNTRQQEAGVASNGDATQNALARAS 379 (418)
Q Consensus 300 ~~~~~~Pf~~a~NPvms~vAFLas~V~P~VAaaAA~aAl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~aaa 379 (418)
....||..++|||||+++||+++|.|+|++..+++.++ ..+.....+ ..+ ..-...+..+|++++
T Consensus 341 --~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k-~g~~~~~n~--------e~~----~~~~~~~~~al~s~~ 405 (531)
T COG5259 341 --KGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIK-SGKISHINR--------ESQ----EHIEEVIEYALDSGK 405 (531)
T ss_pred --CCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhh-ccceecCcc--------chh----hHHHHHHHHHHHHHH
Confidence 11379999999999999999999999999888777522 111111000 000 000124567999999
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccC
Q 014788 380 VDASSLIEKEELDVEKAISGIVEVQVRKILGHFFCHIQL 418 (418)
Q Consensus 380 ~kAk~la~~EErei~rLv~~ive~qlkKlelKlk~~~~~ 418 (418)
.+|+++|+.|||+|+||+..+|++||+||++||.+|++|
T Consensus 406 eka~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L 444 (531)
T COG5259 406 EKAKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKEL 444 (531)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999875
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=3.9e-77 Score=620.33 Aligned_cols=356 Identities=35% Similarity=0.619 Sum_probs=280.8
Q ss_pred CCCCCCeeecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHH
Q 014788 33 SSSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGS 112 (418)
Q Consensus 33 ~~~q~~~iiiPs~s~WF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~ 112 (418)
.+.|+|.|+||||++||||++||+||++++||||+|++++|||++|++||||||++||+||.+|||+|+|||+++|||++
T Consensus 40 ~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp~~ylt~ta~rrnl~gDv~a 119 (506)
T KOG1279|consen 40 VSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNPQEYLTFTACRRNLAGDVCA 119 (506)
T ss_pred cccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCcccchhHHHHHhcccchHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhcccccCCCC--cccccccccccc---------CCcCC-CC--Cc--cc-----------ccccccccccC
Q 014788 113 IRRVFDFLETWGLINYFAS--VKTLKWEDKETK---------SSAAS-AE--SS--SA-----------LKETSKRLCNG 165 (418)
Q Consensus 113 i~Rvh~FLe~wGlINy~~~--~kP~~~~~~~~~---------~~~~~-~~--~~--~~-----------~~~~~k~~C~~ 165 (418)
|+|||+|||+||||||+++ ++|..+++..+. ....+ .+ +. +. ..+.....|+.
T Consensus 120 i~Rvh~FlE~WGLINy~~d~e~rp~~~~p~~t~h~~~~~~tp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (506)
T KOG1279|consen 120 IARVHAFLEQWGLINYQVDAESRPHPIEPPETSHFQVLADTPRGLAPLTPEDPQSQPDLGNPRMETLSLESKIKSLHINA 199 (506)
T ss_pred HHHHHhhHHhhcccccccChhhCCcccCCCcccccccccCCCcccccCCCCCccccccccccccccccccccccccccCh
Confidence 9999999999999999999 677665432221 11111 00 00 00 00111233555
Q ss_pred CCCccccccccccC--------CCccchhhhhccCCCCCCCCCCCccccccCcccCCCCCHHHHHHHHHHHHHhCCCHHH
Q 014788 166 CKTLCTIACFACDK--------YDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRK 237 (418)
Q Consensus 166 C~~~c~~~~~~c~k--------~d~~LC~~Cf~~G~~~~~~~s~dF~ki~~~~~~~~~WT~~E~l~LLe~ie~yg~nW~~ 237 (418)
|...|...|+.|.. .++.+|.+||.+|+++..+...||+.+ ....+..||++|+++|||||++||+||.+
T Consensus 200 ~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~--~~~~~~~WT~qE~lLLLE~ie~y~ddW~k 277 (506)
T KOG1279|consen 200 GEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVI--GESARPNWTEQETLLLLEAIEMYGDDWNK 277 (506)
T ss_pred HhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhc--cccCCCCccHHHHHHHHHHHHHhcccHHH
Confidence 55455555555443 357899999999999999999999433 34567899999999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHHhcCCCCCcccCCCCCCcccccccccCCCCCCccccccccCCCCCCccCCCcCCcCCCChHHHH
Q 014788 238 VAQHVSGKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESENVGATSPSKRMRLTPLADASNPIMAQ 317 (418)
Q Consensus 238 IA~~VgtkT~~eC~~hfl~LPIeD~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Pf~~a~NPvms~ 317 (418)
||.|||+||++|||.|||+|||+|+|+ ...+. .+ .+..+.+.||++.+||||++
T Consensus 278 Va~hVg~ks~eqCI~kFL~LPieD~~l-~~~~~-----~~--------------------~~~~~~~~~~sq~gnpv~s~ 331 (506)
T KOG1279|consen 278 VADHVGTKSQEQCILKFLRLPIEDPYL-AKSEA-----SL--------------------GPLSYGPVPFSQDGNPVMST 331 (506)
T ss_pred HHhccCCCCHHHHHHHHHhcCccchhh-hhccc-----cc--------------------CccccCCCccccCCCccccH
Confidence 999999999999999999999999999 43221 01 12234467899999999999
Q ss_pred HHHHHhhcChHHHHHHHHHHHHHhhccCccccc-----------------C--ccc-----cc-----cccc-------c
Q 014788 318 AAFLSALAGVEIAEVAARAAVTTLSDVDDRASK-----------------G--SLM-----RN-----TRQQ-------E 361 (418)
Q Consensus 318 vAFLas~V~P~VAaaAA~aAl~~l~~~~~~~~~-----------------~--~~~-----~~-----~~~~-------~ 361 (418)
++||+++|||+|+..+++.+....++....... + +.+ .+ ...+ +
T Consensus 332 ~~~l~~~vdP~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~e~~k~~~~~~ 411 (506)
T KOG1279|consen 332 VAFLASVVDPVVKSVAAKSAEEKFSKVNEESPLAKIEVSAKGVEEAASKLGGTDKSKFLALSDIACTLPDEEEKLQSKLK 411 (506)
T ss_pred HHHHHhccCchhhhhhhcccchhhhhhhhcccchhhhHHhhhhHHhhhhhccchhhhhhhhhhhhhcccchHHHHHHHhh
Confidence 999999999999999999999988775432210 0 000 00 0000 0
Q ss_pred ccccC---------ChhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcc
Q 014788 362 AGVAS---------NGDATQNALARASVDASSLIEKEELDVEKAISGIVEVQVRKILGHFFCHIQ 417 (418)
Q Consensus 362 ~~~~~---------~~~~~~~aL~aaa~kAk~la~~EErei~rLv~~ive~qlkKlelKlk~~~~ 417 (418)
+.... -+.++..+|++||.+|+.||.+|| +++++++.+++.||+|+|.||++|-+
T Consensus 412 ~~~n~~~~k~~e~~~~~a~~~~ls~aa~k~k~la~~ee-~~~s~~~~~~~~q~~k~E~~l~~~~e 475 (506)
T KOG1279|consen 412 AKLNPNKEKTIELGLSTAANAALSAAAVKAKLLAAQEE-RIKSLVALLEETQLKKLEAKLRHFEE 475 (506)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHHHHhhhhhhhHHH-HHHHHhhhhhhhhhhhhhHHHHHHHH
Confidence 00000 124556789999999999999999 99999999999999999999999865
No 3
>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=99.94 E-value=7.3e-28 Score=197.77 Aligned_cols=85 Identities=47% Similarity=0.897 Sum_probs=78.1
Q ss_pred eecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccc-hhHHHHHHHH
Q 014788 40 VNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVG-DVGSIRRVFD 118 (418)
Q Consensus 40 iiiPs~s~WF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rvh~ 118 (418)
+++|++++||+++.+|++|++.+||||.| ++|+.|+.|||.||+.|+.||.+|||+++||+.+.| |++.+.|||+
T Consensus 1 ~~~~~~~~~~~~~~l~~~E~~~~~e~~~~----~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~ 76 (86)
T PF04433_consen 1 VVIPAHSSWFDPDKLSEIEKQLCPEFFIG----KTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYD 76 (86)
T ss_dssp -HCHCCHTTTTTTSS-HHHHHHCHHCTTS----CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHH
T ss_pred CCCccccCCCCcccCCHHHHHHhHHHhcc----CChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHH
Confidence 46899999999999999999999999998 799999999999999999999999999999999996 9999999999
Q ss_pred hhhhcccccC
Q 014788 119 FLETWGLINY 128 (418)
Q Consensus 119 FLe~wGlINy 128 (418)
||++||+|||
T Consensus 77 FL~~~G~INf 86 (86)
T PF04433_consen 77 FLERWGLINF 86 (86)
T ss_dssp HHHHTTSSSS
T ss_pred HHHHcCccCC
Confidence 9999999998
No 4
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.85 E-value=6.3e-22 Score=200.98 Aligned_cols=104 Identities=27% Similarity=0.629 Sum_probs=94.6
Q ss_pred ccccccCCCCccc----cccccccCCCccchhhhhccCCC-CCCCCCCCccccccC--cccCCCCCHHHHHHHHHHHHHh
Q 014788 159 SKRLCNGCKTLCT----IACFACDKYDLTLCARCYVRGNH-RVGVSSSDFRRVEIS--EEARSDWTEKETLQLLEAIMHF 231 (418)
Q Consensus 159 ~k~~C~~C~~~c~----~~~~~c~k~d~~LC~~Cf~~G~~-~~~~~s~dF~ki~~~--~~~~~~WT~~E~l~LLe~ie~y 231 (418)
.++.|++|..+|+ +.|++|. +++||..||+.|.+ +.|.+.|.|..|+.. .....+||++||++||||+++|
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp--~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~ 90 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECP--DFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETY 90 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCC--CcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHh
Confidence 3789999999886 6788886 57799999999997 778899999999874 3467899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 014788 232 G-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 232 g-~nW~~IA~~VgtkT~~eC~~hfl~LPIeD~~l 264 (418)
| |||++||+|||+||.+||+.||++.+++.++.
T Consensus 91 G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~ 124 (438)
T KOG0457|consen 91 GFGNWQDIADHIGTKTKEECKEHYLKHFVNSPIF 124 (438)
T ss_pred CCCcHHHHHHHHcccchHHHHHHHHHHHhcCccc
Confidence 9 99999999999999999999999999999887
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.73 E-value=1.5e-18 Score=170.37 Aligned_cols=103 Identities=24% Similarity=0.568 Sum_probs=92.7
Q ss_pred cccccCCCCccc----cccccccCCCccchhhhhccCCC-CCCCCCCCccccccC--cccCCCCCHHHHHHHHHHHHHhC
Q 014788 160 KRLCNGCKTLCT----IACFACDKYDLTLCARCYVRGNH-RVGVSSSDFRRVEIS--EEARSDWTEKETLQLLEAIMHFG 232 (418)
Q Consensus 160 k~~C~~C~~~c~----~~~~~c~k~d~~LC~~Cf~~G~~-~~~~~s~dF~ki~~~--~~~~~~WT~~E~l~LLe~ie~yg 232 (418)
+++|+.|..+|+ +.|.+|. +++||..||.+|.+ +.++..|+|+.++.. +....+|++.||++|+++.+..|
T Consensus 5 k~hCdvC~~d~T~~~~i~C~eC~--~~DLC~pCF~~g~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlG 82 (432)
T COG5114 5 KIHCDVCFLDMTDLTFIKCNECP--AVDLCLPCFVNGIETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLG 82 (432)
T ss_pred eeeehHHHHhhhcceeeeeeccc--ccceehhhhhccccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcC
Confidence 689999999987 5677776 56699999999998 567789999999865 35678999999999999999999
Q ss_pred -CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 014788 233 -DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 233 -~nW~~IA~~VgtkT~~eC~~hfl~LPIeD~~l 264 (418)
|||++||+|||.|+++||..||+.+++|..|.
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~y 115 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYY 115 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccc
Confidence 99999999999999999999999999999886
No 6
>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=99.19 E-value=2.7e-11 Score=88.98 Aligned_cols=44 Identities=39% Similarity=0.912 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCC-HHHHHHHhC-CCCHHHHHHHHhcC
Q 014788 214 SDWTEKETLQLLEAIMHFGDD-WRKVAQHVS-GKSEKDCITHFIKL 257 (418)
Q Consensus 214 ~~WT~~E~l~LLe~ie~yg~n-W~~IA~~Vg-tkT~~eC~~hfl~L 257 (418)
..||.+|+.+|+++|.+||.+ |..||++|+ +||..||+.||.++
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 579999999999999999966 999999999 99999999999864
No 7
>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=98.95 E-value=1.2e-09 Score=83.38 Aligned_cols=41 Identities=34% Similarity=0.857 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 216 WTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 216 WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
||.+|+.+|++++.+||.+|..||+++|+||+.+|..||..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999999999999998999999999999
No 8
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.93 E-value=2e-09 Score=76.70 Aligned_cols=44 Identities=30% Similarity=0.810 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 214 ~~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
..||.+|+.+|++++.+|| .+|..||+++++||+.+|..+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5799999999999999999 9999999999999999999999875
No 9
>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=98.85 E-value=5.4e-09 Score=73.48 Aligned_cols=43 Identities=37% Similarity=0.851 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 215 DWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 215 ~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
.||.+|+.+|+.++.+|| ++|..||+.+++||..+|..||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 9999999999999999999999764
No 10
>PLN03000 amine oxidase
Probab=98.84 E-value=3.3e-09 Score=118.55 Aligned_cols=83 Identities=24% Similarity=0.368 Sum_probs=72.2
Q ss_pred CCCCCCCCCCCCHHHHhh--CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccc-hhHHHHHHHHhh
Q 014788 44 SYSRWFSFDSISECEVKF--LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVG-DVGSIRRVFDFL 120 (418)
Q Consensus 44 s~s~WF~~~~ih~iE~~~--lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rvh~FL 120 (418)
.++.-|+.|.+++.|..+ || ... .+.+..|+.|||.||.+|+.||..+||+++|...+.. -...+.++|+||
T Consensus 86 a~~~~~p~d~l~~~e~~~~~~~-~~~----~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L 160 (881)
T PLN03000 86 ALTAGFPADSLTEEEIEFGVVP-IVG----GIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYL 160 (881)
T ss_pred HHHcCCCcccCCHHHHhccccC-ccc----ccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHH
Confidence 457789999999999777 88 222 2578999999999999999999999999999876654 358899999999
Q ss_pred hhcccccCCCC
Q 014788 121 ETWGLINYFAS 131 (418)
Q Consensus 121 e~wGlINy~~~ 131 (418)
.++|+|||++.
T Consensus 161 ~r~G~in~g~~ 171 (881)
T PLN03000 161 VTHGYINFGIA 171 (881)
T ss_pred HHcCcccHHHH
Confidence 99999999998
No 11
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.74 E-value=1.2e-08 Score=113.81 Aligned_cols=83 Identities=22% Similarity=0.306 Sum_probs=74.5
Q ss_pred CCCCCCCCCCCHHHHhh-CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhcc-chhHHHHHHHHhhhh
Q 014788 45 YSRWFSFDSISECEVKF-LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV-GDVGSIRRVFDFLET 122 (418)
Q Consensus 45 ~s~WF~~~~ih~iE~~~-lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~-gDv~~i~Rvh~FLe~ 122 (418)
.+.-|+.+.+|+.|..+ |+....+ ..+..|+.|||.||.+|+.||..|||+++|+..+. -....+.++|.||.+
T Consensus 138 ~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~ 213 (808)
T PLN02328 138 ISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLE 213 (808)
T ss_pred HHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhc
Confidence 46789999999999888 8877765 57899999999999999999999999999997664 356889999999999
Q ss_pred cccccCCCC
Q 014788 123 WGLINYFAS 131 (418)
Q Consensus 123 wGlINy~~~ 131 (418)
.|.|||++.
T Consensus 214 ~g~in~gv~ 222 (808)
T PLN02328 214 HGYINFGVA 222 (808)
T ss_pred cCceeeecc
Confidence 999999998
No 12
>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=98.54 E-value=5.2e-08 Score=71.35 Aligned_cols=44 Identities=32% Similarity=0.555 Sum_probs=39.5
Q ss_pred ccccCCCCccccccccccC-CCccchhhhhccCCCCCCCCCCCcc
Q 014788 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFR 204 (418)
Q Consensus 161 ~~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~s~dF~ 204 (418)
+.|+.|+.+|+..+|+|.+ .+++||+.||.+|+||.++.+.||+
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~Dfv 45 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQSSDFI 45 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhCcCCCCCCcccccC
Confidence 4799999999998998865 3688999999999999999999995
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.33 E-value=5.4e-07 Score=87.36 Aligned_cols=45 Identities=24% Similarity=0.512 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~Vg-tkT~~eC~~hfl~L 257 (418)
+..||.+|+.+|+++|++|| .+|..||+++| +||..||+.||.++
T Consensus 25 Rg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~ 71 (249)
T PLN03212 25 RGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNY 71 (249)
T ss_pred CCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHh
Confidence 57899999999999999999 79999999997 79999999999984
No 14
>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=98.26 E-value=1.6e-06 Score=66.63 Aligned_cols=46 Identities=24% Similarity=0.542 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCH---HHHHHHhC-CC-CHHHHHHHHhcCC
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDW---RKVAQHVS-GK-SEKDCITHFIKLP 258 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW---~~IA~~Vg-tk-T~~eC~~hfl~LP 258 (418)
+..||++|..++|+||+.|| ||| ..|+++++ ++ |+.||..|+-.+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 35799999999999999999 599 99999987 57 9999999987653
No 15
>PLN02529 lysine-specific histone demethylase 1
Probab=98.13 E-value=2.9e-06 Score=94.22 Aligned_cols=83 Identities=25% Similarity=0.343 Sum_probs=70.4
Q ss_pred CCCCCCCCCCCCHHHHhh--CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchh-HHHHHHHHhh
Q 014788 44 SYSRWFSFDSISECEVKF--LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDV-GSIRRVFDFL 120 (418)
Q Consensus 44 s~s~WF~~~~ih~iE~~~--lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv-~~i~Rvh~FL 120 (418)
.++-=|+.+.+.+.|+++ +|+ -..+.+..|+.|||.|+.+|+.||..|||+++++..+.-++ ..|...|+||
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l 136 (738)
T PLN02529 62 ALSVGFPIDALLEEEIRAGVVRE-----LGGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFL 136 (738)
T ss_pred HHHcCCCccccCHHHHhccccCc-----cccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHH
Confidence 456789999999999855 443 23568999999999999999999999999999987765443 4567899999
Q ss_pred hhcccccCCCC
Q 014788 121 ETWGLINYFAS 131 (418)
Q Consensus 121 e~wGlINy~~~ 131 (418)
.+.|.|||++.
T Consensus 137 ~~~~~inc~vn 147 (738)
T PLN02529 137 LYNGYINFGVS 147 (738)
T ss_pred HhCCCcceeec
Confidence 99999999999
No 16
>PLN03091 hypothetical protein; Provisional
Probab=98.12 E-value=2.7e-06 Score=88.30 Aligned_cols=46 Identities=24% Similarity=0.580 Sum_probs=42.4
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 014788 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~Vg-tkT~~eC~~hfl~L 257 (418)
.+..||.+|+.+|+++|++|| ++|..||+++| +||..||+.||.++
T Consensus 13 rKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~Ny 60 (459)
T PLN03091 13 RKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINY 60 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhc
Confidence 356899999999999999999 79999999997 79999999999874
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.99 E-value=6.4e-06 Score=79.85 Aligned_cols=45 Identities=20% Similarity=0.485 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~Vg-tkT~~eC~~hfl~L 257 (418)
+++||.||+.+|.+.|++|| ++|..|+++.| .|+..+|++||+.+
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 58999999999999999999 99999999999 89999999999983
No 18
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.97 E-value=8.1e-06 Score=79.29 Aligned_cols=46 Identities=17% Similarity=0.338 Sum_probs=43.2
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 211 ~~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
....+||.+|+.+||+.+..||..|..||+++.+||..+|..||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 4568999999999999999999999999999999999999999964
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.81 E-value=2.6e-05 Score=75.65 Aligned_cols=42 Identities=17% Similarity=0.554 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHH
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hf 254 (418)
++.||.+||.+|+++...||..|..||.++++||..++..||
T Consensus 62 rg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W 103 (238)
T KOG0048|consen 62 RGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW 103 (238)
T ss_pred CCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH
Confidence 578999999999999999999999999999999999999998
No 20
>PLN03091 hypothetical protein; Provisional
Probab=97.70 E-value=4.6e-05 Score=79.29 Aligned_cols=46 Identities=15% Similarity=0.437 Sum_probs=42.9
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 211 ~~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
..++.||.+|+.+||+.+..||..|.+||+++.+||..+|+.||..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 3467999999999999999999999999999999999999999964
No 21
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.21 E-value=0.00041 Score=74.92 Aligned_cols=45 Identities=31% Similarity=0.731 Sum_probs=42.9
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
..+.||.+|+.+|+-||++|| .+|-+|-+.|.+|+..||+.+|++
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~n 404 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTN 404 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHH
Confidence 468999999999999999999 799999999999999999999987
No 22
>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=96.89 E-value=0.00097 Score=49.49 Aligned_cols=46 Identities=24% Similarity=0.501 Sum_probs=33.2
Q ss_pred ccccCCCCcccc-ccccccC-CCccchhhhhccCCC-CCCCCCCCcccc
Q 014788 161 RLCNGCKTLCTI-ACFACDK-YDLTLCARCYVRGNH-RVGVSSSDFRRV 206 (418)
Q Consensus 161 ~~C~~C~~~c~~-~~~~c~k-~d~~LC~~Cf~~G~~-~~~~~s~dF~ki 206 (418)
+.|++|+..... .++.|.. .|++||..||..|.. ..+..+|.|..+
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 369999987654 4455443 278899999999987 455678888653
No 23
>PLN02976 amine oxidase
Probab=96.76 E-value=0.0012 Score=77.75 Aligned_cols=81 Identities=21% Similarity=0.274 Sum_probs=69.5
Q ss_pred CCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhcc--------chhHHHHHHH
Q 014788 46 SRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV--------GDVGSIRRVF 117 (418)
Q Consensus 46 s~WF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~--------gDv~~i~Rvh 117 (418)
+.-+....+.++||-.|-|...-|. .-+.|+++||.|+-+|-++=.+-|.+++|- +. .-..+|.-|+
T Consensus 452 ~~gl~a~~~~~~e~~~~k~~lkr~~---~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~--v~~~~~~~e~~~~~l~r~~~ 526 (1713)
T PLN02976 452 SAGLKARAVGPIEKIKFKEVLKRKG---GLQEYLECRNMILGLWSKDVSRILPLADCG--VTDTPSEDESPRASLIREVY 526 (1713)
T ss_pred hccccccccChHHHHHHHHHHHhcc---chHHHHHHHHHHHHHhhhhhhhcccHhhcc--ccCCcccccCchhhHHHHHH
Confidence 3445567899999999999997543 578999999999999999999999999993 32 3467899999
Q ss_pred HhhhhcccccCCCC
Q 014788 118 DFLETWGLINYFAS 131 (418)
Q Consensus 118 ~FLe~wGlINy~~~ 131 (418)
.||++.|.||-++.
T Consensus 527 ~fld~~gyin~g~~ 540 (1713)
T PLN02976 527 LFLDQRGYINAGIA 540 (1713)
T ss_pred HHhhccCceecccc
Confidence 99999999999988
No 24
>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=96.52 E-value=0.0024 Score=46.62 Aligned_cols=44 Identities=25% Similarity=0.610 Sum_probs=32.4
Q ss_pred ccccCCCCccccccccccC-CCccchhhhhccCCCCCCCCCCCccc
Q 014788 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRR 205 (418)
Q Consensus 161 ~~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~s~dF~k 205 (418)
+.|++|+..+...+|.|.. .+++||..||..|. ..+...|.|.+
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~~ 45 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFTE 45 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEeE
Confidence 3699999987656666643 36889999999997 44555777764
No 25
>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=96.22 E-value=0.0041 Score=45.06 Aligned_cols=41 Identities=24% Similarity=0.634 Sum_probs=31.3
Q ss_pred cccCCCCccccccccccC-CCccchhhhhccCCCCCCCCCCCcccc
Q 014788 162 LCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRV 206 (418)
Q Consensus 162 ~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~s~dF~ki 206 (418)
.|++|+..+.-.+|.|.. .+++||..||..+ .+ ..|.|.++
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~---~H-~~H~f~~~ 43 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG---VH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC---CC-CCCCEEeC
Confidence 699999977666777654 3788999999988 33 77888653
No 26
>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=96.21 E-value=0.0043 Score=44.97 Aligned_cols=39 Identities=21% Similarity=0.472 Sum_probs=29.9
Q ss_pred cccccCCCCccccccccccC-CCccchhhhhccCCCCCCC
Q 014788 160 KRLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (418)
Q Consensus 160 k~~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~ 198 (418)
...|++|+..+...+|.|.. .|++||.+||..|+++..+
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCCC
Confidence 46799999987766666643 3788999999999876543
No 27
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.13 E-value=0.0049 Score=66.88 Aligned_cols=44 Identities=30% Similarity=0.456 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCH---HHHHHHHhc
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSE---KDCITHFIK 256 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~---~eC~~hfl~ 256 (418)
.+.||-+|+..|+++|++|| |+|-++|-.+|.||. .-|+.+|+.
T Consensus 412 ~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 412 VERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred cCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHH
Confidence 57899999999999999999 999999999999998 779999987
No 28
>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=96.04 E-value=0.0057 Score=45.54 Aligned_cols=38 Identities=26% Similarity=0.764 Sum_probs=28.3
Q ss_pred cccCCCCccccccccccC-CCccchhhhhccCCCCCCCC
Q 014788 162 LCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVS 199 (418)
Q Consensus 162 ~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~ 199 (418)
.|++|.......+|.|.+ .|++||..||..|....++.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCC
Confidence 599999876555555532 47889999999999866553
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.02 E-value=0.0039 Score=50.60 Aligned_cols=44 Identities=25% Similarity=0.675 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHHHHHHH------hC------C--CHHHHHHHhC----CCCHHHHHHHHhcC
Q 014788 214 SDWTEKETLQLLEAIMH------FG------D--DWRKVAQHVS----GKSEKDCITHFIKL 257 (418)
Q Consensus 214 ~~WT~~E~l~LLe~ie~------yg------~--nW~~IA~~Vg----tkT~~eC~~hfl~L 257 (418)
..||++|+..||+.+.. ++ + -|..||+.+. .||+.||..+|-+|
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 1 5999999984 59999999999884
No 30
>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=95.61 E-value=0.011 Score=43.94 Aligned_cols=44 Identities=30% Similarity=0.566 Sum_probs=29.6
Q ss_pred cccCCC-CccccccccccC-CCccchhhhhccCCCCCCC-CCCCccc
Q 014788 162 LCNGCK-TLCTIACFACDK-YDLTLCARCYVRGNHRVGV-SSSDFRR 205 (418)
Q Consensus 162 ~C~~C~-~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~-~s~dF~k 205 (418)
.|++|+ .++...+|.|.. .|++||..||..|.....+ .+|.|..
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEE
Confidence 599999 555544444432 3688999999999765444 4676653
No 31
>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=95.51 E-value=0.014 Score=43.41 Aligned_cols=43 Identities=26% Similarity=0.542 Sum_probs=29.8
Q ss_pred cccCCCC-ccccccccccC-CCccchhhhhccCCCCCC-CCCCCcc
Q 014788 162 LCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRVG-VSSSDFR 204 (418)
Q Consensus 162 ~C~~C~~-~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~-~~s~dF~ 204 (418)
.|++|+. ++.-.+|.|.. .|++||..||..|....+ ...|.|.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~ 47 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMY 47 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcc
Confidence 5999997 66544555532 378899999999986444 3566654
No 32
>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=95.35 E-value=0.015 Score=43.19 Aligned_cols=43 Identities=21% Similarity=0.485 Sum_probs=29.9
Q ss_pred ccccCCCC-ccccccccccC---CCccchhhhhccCCCCCCCCCCCccc
Q 014788 161 RLCNGCKT-LCTIACFACDK---YDLTLCARCYVRGNHRVGVSSSDFRR 205 (418)
Q Consensus 161 ~~C~~C~~-~c~~~~~~c~k---~d~~LC~~Cf~~G~~~~~~~s~dF~k 205 (418)
+.|++|+. .+...+|+|.. .+++||..||..|. .+...|.|.+
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~--~H~~~H~~~~ 47 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE--SHQEDHWLVK 47 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC--CCCCCCceee
Confidence 46999997 55555555543 26889999999997 4555666654
No 33
>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=95.19 E-value=0.0074 Score=44.18 Aligned_cols=39 Identities=28% Similarity=0.612 Sum_probs=23.2
Q ss_pred cccccCCCC-cccccccccc-CCCccchhhhhccCCCCCCC
Q 014788 160 KRLCNGCKT-LCTIACFACD-KYDLTLCARCYVRGNHRVGV 198 (418)
Q Consensus 160 k~~C~~C~~-~c~~~~~~c~-k~d~~LC~~Cf~~G~~~~~~ 198 (418)
.+.|++|+. .....+|.|. -.|++||..||..|.+...+
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~H 44 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKGRHSHNH 44 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH--H-SSS
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCcCCCCCc
Confidence 467999998 4444556654 24788999999999875544
No 34
>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=94.90 E-value=0.026 Score=42.17 Aligned_cols=42 Identities=29% Similarity=0.625 Sum_probs=28.1
Q ss_pred cccCCCCc-cccccccccC-CCccchhhhhccCCCCCCC-CCCCc
Q 014788 162 LCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRVGV-SSSDF 203 (418)
Q Consensus 162 ~C~~C~~~-c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~-~s~dF 203 (418)
.|++|+.. +...+|.|.. .|++||..||..|.....| ..|.+
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~ 46 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPM 46 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCe
Confidence 59999964 4444444432 3688999999999875444 45554
No 35
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.75 E-value=0.034 Score=60.52 Aligned_cols=45 Identities=22% Similarity=0.641 Sum_probs=42.7
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
..+.||.+|+..|-..+.++|++|..|++.+| |.|..|+.+|-++
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~ 427 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQY 427 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHh
Confidence 57899999999999999999999999999997 7999999999985
No 36
>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=93.87 E-value=0.059 Score=39.62 Aligned_cols=42 Identities=26% Similarity=0.761 Sum_probs=28.1
Q ss_pred cccCCCCc-cccccccccC-CCccchhhhhccCCCCCCCCCCCcccc
Q 014788 162 LCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRV 206 (418)
Q Consensus 162 ~C~~C~~~-c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~s~dF~ki 206 (418)
.|++|+.. +.-.+|.|.. .|++||..||..+.. -..|.|.++
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~H---~~~H~F~ri 45 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRKH---NTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCCCc---CCCCceeeC
Confidence 59999864 4334555532 368899999999653 346777653
No 37
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.45 E-value=0.067 Score=58.30 Aligned_cols=53 Identities=25% Similarity=0.481 Sum_probs=45.7
Q ss_pred cCCCCCHHHHHHHHHHHH-------Hh-------C------------CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 014788 212 ARSDWTEKETLQLLEAIM-------HF-------G------------DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie-------~y-------g------------~nW~~IA~~VgtkT~~eC~~hfl~LPIeD~~l 264 (418)
..+.||-+|+.+||..|+ +| | =+|..|++.+|||+..||+.||-+|=+...+-
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 457899999999999995 45 1 17999999999999999999999987777665
No 38
>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=93.32 E-value=0.072 Score=38.27 Aligned_cols=36 Identities=33% Similarity=0.675 Sum_probs=25.8
Q ss_pred ccccCCCCccccccccccC-CCccchhhhhccCCCCCC
Q 014788 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVG 197 (418)
Q Consensus 161 ~~C~~C~~~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~ 197 (418)
+.|++|....+ ..+.|.. .|++||..||..+..+-.
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~~~H~H~ 37 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNTKNHPHK 37 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCCCCCCcc
Confidence 46999988766 4454432 378899999999776543
No 39
>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=93.27 E-value=0.086 Score=38.65 Aligned_cols=41 Identities=22% Similarity=0.546 Sum_probs=26.9
Q ss_pred cccCCCC-ccccccccccC-CCccchhhhhccCCCCCCCCCCCccc
Q 014788 162 LCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRR 205 (418)
Q Consensus 162 ~C~~C~~-~c~~~~~~c~k-~d~~LC~~Cf~~G~~~~~~~s~dF~k 205 (418)
.|++|+. .+...+|.|.. .|++||..||..+. +...|.|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~~---H~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGDK---HDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCCC---CCCCCCEEe
Confidence 6999994 44444555543 26889999999754 344566654
No 40
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=92.66 E-value=0.1 Score=55.69 Aligned_cols=44 Identities=23% Similarity=0.615 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
+..|+..|+..|=-+|.+|| ..|..|+..+..||+.||..+|-.
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e 51 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEE 51 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHH
Confidence 57899999999999999999 779999999999999999999974
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=92.35 E-value=0.29 Score=38.89 Aligned_cols=45 Identities=20% Similarity=0.430 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------CHHHHHHHhC-----CCCHHHHHHHHhcC
Q 014788 213 RSDWTEKETLQLLEAIMHFG----D-------------DWRKVAQHVS-----GKSEKDCITHFIKL 257 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg----~-------------nW~~IA~~Vg-----tkT~~eC~~hfl~L 257 (418)
...||.+|...|++.|++|. + -|..|+..+. .||..|+..+|-+|
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 35799999999999999985 1 5999999983 59999999998764
No 42
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=91.98 E-value=0.23 Score=55.10 Aligned_cols=43 Identities=21% Similarity=0.430 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHh
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFI 255 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl 255 (418)
...||..|..++-.||-.|..|+..|++.|.+||..||+.+|.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHH
Confidence 5789999999999999999999999999999999999999985
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=89.52 E-value=0.3 Score=52.34 Aligned_cols=45 Identities=20% Similarity=0.582 Sum_probs=41.8
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
....|+.+|+.+||.+......-|..|+.-|| ||..||..||..|
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 35789999999999999999999999999997 8999999999875
No 44
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.48 E-value=0.51 Score=48.92 Aligned_cols=44 Identities=23% Similarity=0.477 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
...||.+|..++..|+.++|.|+.-|+....+|...|+..+|++
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999998
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=87.79 E-value=0.49 Score=51.09 Aligned_cols=45 Identities=20% Similarity=0.655 Sum_probs=42.7
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
....|+.+|+..|++.-.++|.-|..||.+++.||..+|..+|+.
T Consensus 71 k~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~ 115 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVN 115 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHH
Confidence 357899999999999999999999999999999999999999995
No 46
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=87.77 E-value=0.79 Score=47.41 Aligned_cols=51 Identities=18% Similarity=0.378 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHH-HhCCCCHHHHHHHHhcCCCCCcc
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQ-HVSGKSEKDCITHFIKLPFGQEF 263 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~-~VgtkT~~eC~~hfl~LPIeD~~ 263 (418)
-..|+.+|=+.+=+||+.||.|+..|-. .|.|||.-||+.+|.+--..+.|
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKkSery 328 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKKSERY 328 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhcCcch
Confidence 4789999999999999999999999976 78999999999998765444433
No 47
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=87.77 E-value=0.63 Score=47.36 Aligned_cols=47 Identities=30% Similarity=0.536 Sum_probs=37.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-----C-----CHHHHHHHh---C-CCCHHHHHHHHhcCCC
Q 014788 213 RSDWTEKETLQLLEAIMHFG-----D-----DWRKVAQHV---S-GKSEKDCITHFIKLPF 259 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-----~-----nW~~IA~~V---g-tkT~~eC~~hfl~LPI 259 (418)
...|+.+|++.||++..... + .|..||..+ | .||+.||..+|-+|..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 37899999999999885432 3 499999944 3 4999999999987643
No 48
>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=86.35 E-value=0.49 Score=34.50 Aligned_cols=31 Identities=35% Similarity=0.743 Sum_probs=21.6
Q ss_pred cccCCCCc-ccccccccc-CCCccchhhhhccC
Q 014788 162 LCNGCKTL-CTIACFACD-KYDLTLCARCYVRG 192 (418)
Q Consensus 162 ~C~~C~~~-c~~~~~~c~-k~d~~LC~~Cf~~G 192 (418)
.|++|+.. +.-.+|.|. ..|++||..||.+.
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 59999863 444455554 34788999999864
No 49
>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=85.47 E-value=0.87 Score=42.10 Aligned_cols=50 Identities=16% Similarity=0.409 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C-----CHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 014788 213 RSDWTEKETLQLLEAIMHFG--D-----DWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg--~-----nW~~IA~~VgtkT~~eC~~hfl~LPIeD~~l 264 (418)
.+.||.+|+++|-|.|-.|= | -.+.|++.++ ||+.-|-.+|..+ +-..|-
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~-VRkqY~ 60 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY-VRKQYE 60 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH-HHHHHH
Confidence 46799999999999998886 3 5889999995 9999999999763 344444
No 50
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=85.33 E-value=0.76 Score=50.14 Aligned_cols=45 Identities=24% Similarity=0.565 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHH----------HHHhCCCCHHHHHHHHhcC
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKV----------AQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~I----------A~~VgtkT~~eC~~hfl~L 257 (418)
+..||.+|+.-+.+||.++|.|+++| -..+..||++|.+.||.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 57899999999999999999999999 3334569999999999764
No 51
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=85.11 E-value=0.52 Score=50.86 Aligned_cols=42 Identities=21% Similarity=0.493 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHH
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHF 254 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hf 254 (418)
.+.|+..|+..|+-+++.|| .+|..||..++.||+++|..||
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw 62 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW 62 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchh
Confidence 46899999999999999999 8999999999999999999999
No 52
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=83.62 E-value=0.63 Score=47.72 Aligned_cols=35 Identities=31% Similarity=0.696 Sum_probs=25.8
Q ss_pred cccccCCCCc-ccccccccc-CCCccchhhhhccCCC
Q 014788 160 KRLCNGCKTL-CTIACFACD-KYDLTLCARCYVRGNH 194 (418)
Q Consensus 160 k~~C~~C~~~-c~~~~~~c~-k~d~~LC~~Cf~~G~~ 194 (418)
...|++|++- .+-.||.|- .+|++||..||.+|.-
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~t 44 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGAT 44 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCCC
Confidence 4679999865 455566653 3578899999999853
No 53
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=82.64 E-value=1.6 Score=47.13 Aligned_cols=118 Identities=11% Similarity=0.018 Sum_probs=85.1
Q ss_pred CCCCCCCCCCCCCCCCCCCC-----CCCCCeeecCCCCCCCCCCCCCHHHHhhCccccCCCC-CCCChHHHHHHHHHHHH
Q 014788 14 SAVNPTTPLAPPPVKPELPS-----SSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRS-PSKNPRVYRYYRDSIVK 87 (418)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~-----~~q~~~iiiPs~s~WF~~~~ih~iE~~~lpeff~~~~-~~ktp~~Y~~~RN~ii~ 87 (418)
-.++.++|+...+-+|..|. -...+. ..+..++-++...=+.-.....++|+.+++ ....+..|+.+|+.++.
T Consensus 154 ~~~~~~tp~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~ 232 (506)
T KOG1279|consen 154 FQVLADTPRGLAPLTPEDPQSQPDLGNPRME-TLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYD 232 (506)
T ss_pred cccccCCCcccccCCCCCccccccccccccc-cccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHh
Confidence 34455555555554444331 112222 677788888888888899999999999973 24567889999999999
Q ss_pred HHHhCCCccee-----HHHHHHhcc--chhHHHHHHHHhhhhcccccCCCCc
Q 014788 88 HYRENPSRKIT-----FTDVRRTLV--GDVGSIRRVFDFLETWGLINYFASV 132 (418)
Q Consensus 88 ~yr~np~~yLT-----~t~~r~~l~--gDv~~i~Rvh~FLe~wGlINy~~~~ 132 (418)
.++---..+.+ -+..+++.. +.+-++.+|+.|.+.|+-|+.+|.+
T Consensus 233 ~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ 284 (506)
T KOG1279|consen 233 QGEFPSEFKKSDFKVIGESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGT 284 (506)
T ss_pred cCCccCccccccchhccccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCC
Confidence 98884444443 445566665 5788999999999999999999983
No 54
>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=81.75 E-value=1.8 Score=38.01 Aligned_cols=44 Identities=18% Similarity=0.443 Sum_probs=35.5
Q ss_pred cCCCCCHHHHHHHHHHHHHhC----CCHHHHHHHhC------------CCCHHHHHHHHh
Q 014788 212 ARSDWTEKETLQLLEAIMHFG----DDWRKVAQHVS------------GKSEKDCITHFI 255 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg----~nW~~IA~~Vg------------tkT~~eC~~hfl 255 (418)
.+..||.+|+.-||-.+.+|| |+|+.|-+.|- +||+.++..|-.
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 357899999999999999999 68999999873 789988877654
No 55
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=77.53 E-value=1.5 Score=43.85 Aligned_cols=32 Identities=28% Similarity=0.563 Sum_probs=23.3
Q ss_pred ccccCCCC-cccccccccc-CCCccchhhhhccC
Q 014788 161 RLCNGCKT-LCTIACFACD-KYDLTLCARCYVRG 192 (418)
Q Consensus 161 ~~C~~C~~-~c~~~~~~c~-k~d~~LC~~Cf~~G 192 (418)
..|++|+. .+.-.+|.|. ..|++||..|+..+
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 57999998 5544455553 23677999999987
No 56
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=72.96 E-value=5.5 Score=33.74 Aligned_cols=44 Identities=20% Similarity=0.505 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHHHHh----C----CCHHHHHHHhCCC-----CHHHHHHHHhc
Q 014788 213 RSDWTEKETLQLLEAIMHF----G----DDWRKVAQHVSGK-----SEKDCITHFIK 256 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~y----g----~nW~~IA~~Vgtk-----T~~eC~~hfl~ 256 (418)
..-||+++|+.||+|+-.| | .||...-++|... |..|-..+.-+
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr 60 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR 60 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 4679999999999999888 4 4888888887532 56666666555
No 57
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=70.57 E-value=6.3 Score=46.28 Aligned_cols=40 Identities=23% Similarity=0.539 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHH
Q 014788 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITH 253 (418)
Q Consensus 214 ~~WT~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~h 253 (418)
..||..+-..++.|.++|| +|-..||..|++||++|...+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 5799999999999999999 999999999999999998864
No 58
>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=70.16 E-value=7.4 Score=29.67 Aligned_cols=52 Identities=19% Similarity=0.318 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchhHHHHHHHHhhhhccccc
Q 014788 75 PRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (418)
Q Consensus 75 p~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (418)
-++|-.+|+.|.+--. -|...| |..+.-+.+.--...+.+.+..|+.+|+|-
T Consensus 3 ~~i~~~l~~~I~~g~~-~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRL-PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp HHHHHHHHHHHHTTSS--TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCC-CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 3578888888887433 378899 999988888888999999999999999984
No 59
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=69.31 E-value=8.5 Score=41.06 Aligned_cols=46 Identities=22% Similarity=0.468 Sum_probs=42.6
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 211 ~~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
.+...||++|..+|=.+.+.||.++.+|-+.+.-||-...+.+|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHH
Confidence 3568999999999999999999999999999999999999998865
No 60
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=67.89 E-value=2.5 Score=47.40 Aligned_cols=41 Identities=20% Similarity=0.459 Sum_probs=27.6
Q ss_pred ccccCCCCc-ccccccccc-CCCccchhhhhccCCCCCCCCCC
Q 014788 161 RLCNGCKTL-CTIACFACD-KYDLTLCARCYVRGNHRVGVSSS 201 (418)
Q Consensus 161 ~~C~~C~~~-c~~~~~~c~-k~d~~LC~~Cf~~G~~~~~~~s~ 201 (418)
-.|++|+.- +.-.+|.|. .+++++|..||..|+-..++..|
T Consensus 604 ~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~ 646 (966)
T KOG4286|consen 604 AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMH 646 (966)
T ss_pred hhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCC
Confidence 359999742 222345554 35788999999999976665443
No 61
>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=67.56 E-value=7 Score=31.79 Aligned_cols=43 Identities=21% Similarity=0.466 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHh-------C------CCHHHHHHHhC-----CCCHHHHHHHHhcC
Q 014788 215 DWTEKETLQLLEAIMHF-------G------DDWRKVAQHVS-----GKSEKDCITHFIKL 257 (418)
Q Consensus 215 ~WT~~E~l~LLe~ie~y-------g------~nW~~IA~~Vg-----tkT~~eC~~hfl~L 257 (418)
.||++++..||+.+... + ..|+.|++.+. ..|..||..||-.|
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 49999999999998544 1 15999999884 36899999998763
No 62
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=67.25 E-value=7.5 Score=28.15 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHhCCCcce-eHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 78 YRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 78 Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
|-.+|+.|+.... .|...| |..+....+.-....+.|...-|+.-|+|-.
T Consensus 2 ~~~l~~~i~~~~~-~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 2 AERLREDIVSGEL-RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHHHcCCC-CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 5667777776433 367778 8998888888788999999999999999853
No 63
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=66.91 E-value=4.8 Score=43.03 Aligned_cols=52 Identities=17% Similarity=0.377 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHH-HhCCCCHHHHHHHHhcCCCCCccc
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQ-HVSGKSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~-~VgtkT~~eC~~hfl~LPIeD~~l 264 (418)
-..|+.-|-.++=||+++||.|+++|-+ ++.=||-..++.+|.-.--.|.|.
T Consensus 285 mEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYv 337 (693)
T KOG3554|consen 285 MEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYV 337 (693)
T ss_pred hhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHH
Confidence 3689999999999999999999999976 556688888988887766666665
No 64
>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=64.13 E-value=19 Score=26.58 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=34.2
Q ss_pred HHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 89 YRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 89 yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
-..+|...+|+++..+.+.-+...+.|+..=|+.+|||--.
T Consensus 14 l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 14 LARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 34456668999999999999999999999999999999543
No 65
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=63.84 E-value=6.8 Score=36.68 Aligned_cols=41 Identities=15% Similarity=0.387 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C-----CHHHHHHHhCCCCHHHHHHHH
Q 014788 213 RSDWTEKETLQLLEAIMHFG--D-----DWRKVAQHVSGKSEKDCITHF 254 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg--~-----nW~~IA~~VgtkT~~eC~~hf 254 (418)
.+.||.+++++|-+.|-.|+ | -...+++.++ ||.-.|-.+|
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~-rt~aac~fRw 52 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK-RTAAACGFRW 52 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh-hhHHHHHhHH
Confidence 46799999999999998888 3 3667777774 8999999999
No 66
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=62.87 E-value=12 Score=31.90 Aligned_cols=49 Identities=27% Similarity=0.392 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHhCCCcceeHHHHHHhcc-----chhHHHHHHHHhhhhcccccC
Q 014788 79 RYYRDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 79 ~~~RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy 128 (418)
-.-|..|++....++. .+|+.+.-..|. -+...|.|...+|+.-|||.=
T Consensus 7 T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 7 TPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp HHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence 4568899998888877 999999887764 367899999999999999974
No 67
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=61.72 E-value=31 Score=30.77 Aligned_cols=56 Identities=16% Similarity=0.348 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHHh---CCCcce-eHHHHHHhccchhHHHHHHHHhhhhcccccCCCC
Q 014788 76 RVYRYYRDSIVKHYRE---NPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (418)
Q Consensus 76 ~~Y~~~RN~ii~~yr~---np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (418)
.+|.+|.|.|...-.. .|...| |+-+--..+.-+.+.+.|.+.-||+-|+|.-...
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg 70 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG 70 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4999999999877654 666655 4444445566689999999999999999985543
No 68
>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=61.12 E-value=20 Score=25.66 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 219 KETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 219 ~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
+=+..||+.++.-+ --|.+||+.+|- |+..|..+.-+|
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHHh
Confidence 44678999999998 789999999985 889998887543
No 69
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=60.96 E-value=4.6 Score=43.03 Aligned_cols=44 Identities=11% Similarity=0.365 Sum_probs=40.1
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 014788 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~ 256 (418)
+.-+||..|-. ++.....||.+...||+-+++||++|....|++
T Consensus 469 ~~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 469 INYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred ecCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 45789998877 888889999999999999999999999999987
No 70
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=60.73 E-value=23 Score=25.45 Aligned_cols=45 Identities=20% Similarity=0.222 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+.|...|||.+
T Consensus 3 ~R~~Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 3 TRLRILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 57788876665 5699999999999999999999999999999974
No 71
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=59.18 E-value=35 Score=26.63 Aligned_cols=52 Identities=15% Similarity=0.126 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCCCC
Q 014788 80 YYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (418)
Q Consensus 80 ~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (418)
..++.|+.....++..-+|..+.-+.|.-+...+.|+..=|+.-|+|.+...
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~ 57 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGG 57 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 3578899988888766799999999999899999999999999999987654
No 72
>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=58.75 E-value=24 Score=25.96 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=34.7
Q ss_pred HHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCCC
Q 014788 84 SIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (418)
Q Consensus 84 ~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (418)
.|+......+ +++.+..+.+.-+...+.|+..-|...|+|+...
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3444433444 8999988888889999999999999999999643
No 73
>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=56.63 E-value=17 Score=25.74 Aligned_cols=25 Identities=20% Similarity=0.201 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHhCC
Q 014788 220 ETLQLLEAIMHFGDDWRKVAQHVSG 244 (418)
Q Consensus 220 E~l~LLe~ie~yg~nW~~IA~~Vgt 244 (418)
|-..|.++++.++||..+.|+.+|-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 6778899999999999999999984
No 74
>smart00595 MADF subfamily of SANT domain.
Probab=55.68 E-value=9.5 Score=30.67 Aligned_cols=28 Identities=18% Similarity=0.531 Sum_probs=24.3
Q ss_pred CHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 014788 234 DWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 234 nW~~IA~~VgtkT~~eC~~hfl~LPIeD~~l 264 (418)
-|..||..+|. |.++|..+|-.| -+.|.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L--R~~y~ 56 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL--RDRYR 56 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH--HHHHH
Confidence 69999999997 999999999984 46665
No 75
>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=54.88 E-value=21 Score=26.12 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=34.7
Q ss_pred HHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 85 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
|++..... ...+|+++.-+.+.-....+.|+..-|+++|+|..
T Consensus 8 iL~~l~~~-~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 8 ILEALAES-GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHCHHCT-BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 55555554 44489999999999999999999999999999854
No 76
>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=54.77 E-value=22 Score=28.01 Aligned_cols=43 Identities=14% Similarity=0.387 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHHHHHHHhC-------CC--HHHHHHHhC-CCCHHHHHHHHhc
Q 014788 214 SDWTEKETLQLLEAIMHFG-------DD--WRKVAQHVS-GKSEKDCITHFIK 256 (418)
Q Consensus 214 ~~WT~~E~l~LLe~ie~yg-------~n--W~~IA~~Vg-tkT~~eC~~hfl~ 256 (418)
...|.+|+..|++-|..+. || |.+.++.-. ..|-.-=..||++
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4689999999999996543 55 999999766 5788888899986
No 77
>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=54.69 E-value=43 Score=23.77 Aligned_cols=44 Identities=32% Similarity=0.403 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccc
Q 014788 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLI 126 (418)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlI 126 (418)
.+-.|++.-+.||. +|.++..+.+.-....+.|...-|+.-|+|
T Consensus 4 ~~~~Il~~l~~~~~--~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKILNYLRENPR--ITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHCTT--S-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 34567776777666 999999988888999999999999999997
No 78
>PRK09462 fur ferric uptake regulator; Provisional
Probab=53.52 E-value=24 Score=31.52 Aligned_cols=46 Identities=17% Similarity=0.381 Sum_probs=38.6
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhcc-----chhHHHHHHHHhhhhccccc
Q 014788 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLIN 127 (418)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlIN 127 (418)
|-.|++.....+.+.+|+.+.-..|. -+...|.|...+|+.-|||.
T Consensus 19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEE
Confidence 77788877766678999999877664 27899999999999999997
No 79
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=52.97 E-value=19 Score=42.52 Aligned_cols=45 Identities=11% Similarity=0.256 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC------------CCCHHHHHHHHhcC
Q 014788 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS------------GKSEKDCITHFIKL 257 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg-~nW~~IA~~Vg------------tkT~~eC~~hfl~L 257 (418)
+..||.+|+..||-.+.+|| |+|+.|-+.|. +||+.++..|...|
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 46799999999999999999 99999988773 79999998876553
No 80
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=51.84 E-value=29 Score=29.10 Aligned_cols=46 Identities=22% Similarity=0.335 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhcc-----chhHHHHHHHHhhhhcccccC
Q 014788 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy 128 (418)
|-.|++..... .+.+|+.+.-..|. -+...+.|..++|+.-|||.-
T Consensus 3 R~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 3 RLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 77788877765 68899999877774 378999999999999999984
No 81
>PHA00442 host recBCD nuclease inhibitor
Probab=47.27 E-value=20 Score=27.52 Aligned_cols=26 Identities=23% Similarity=0.474 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHHHHhC-CCHHHHHHHh
Q 014788 217 TEKETLQLLEAIMHFG-DDWRKVAQHV 242 (418)
Q Consensus 217 T~~E~l~LLe~ie~yg-~nW~~IA~~V 242 (418)
+-+-....|++++..| +||+.+.+.+
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 3456678899999999 9999988765
No 82
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=46.41 E-value=30 Score=35.58 Aligned_cols=70 Identities=19% Similarity=0.353 Sum_probs=55.4
Q ss_pred CCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhccccc
Q 014788 51 FDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (418)
Q Consensus 51 ~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (418)
+.=+++-|.+..--+- -.|..|+.+.-.||..+.. ....+|.++|++.+.-|.+-.-+|++|.-.-|.|-
T Consensus 360 ~~llS~dEq~LC~~l~------i~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 360 YALLSDDEQRLCETLN------ISPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred hhhhcchHHHHHHHhC------CCCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 3345666666554322 3589999999999999887 47789999999877779999999999998888773
No 83
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=43.29 E-value=14 Score=38.37 Aligned_cols=38 Identities=24% Similarity=0.649 Sum_probs=26.3
Q ss_pred ccccccCCCCcc-c---cccccccCCCccchhhhhccCCCCCCC
Q 014788 159 SKRLCNGCKTLC-T---IACFACDKYDLTLCARCYVRGNHRVGV 198 (418)
Q Consensus 159 ~k~~C~~C~~~c-~---~~~~~c~k~d~~LC~~Cf~~G~~~~~~ 198 (418)
+...|++|...- . ..|-.|. ++.+|.+||-.|.-+..|
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~--nyqlcq~cfwrG~~g~~h 280 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCH--NYQLCQQCFWRGHAGGSH 280 (434)
T ss_pred CCccCcceecccccchhhhHhhcC--CccccchhhccccCCCCc
Confidence 356799997542 2 3455565 567999999999975444
No 84
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=43.29 E-value=38 Score=29.73 Aligned_cols=60 Identities=13% Similarity=0.375 Sum_probs=42.0
Q ss_pred ccCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCccccccCcccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHh
Q 014788 163 CNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRKVAQHV 242 (418)
Q Consensus 163 C~~C~~~c~~~~~~c~k~d~~LC~~Cf~~G~~~~~~~s~dF~ki~~~~~~~~~WT~~E~l~LLe~ie~yg~nW~~IA~~V 242 (418)
|..|+....+..+.|...+..+ .|+|.. ..|-. -..|++.+++..-+..||-.+|++.+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i------~G~F~l----~~~~~-----------L~~E~~~Fi~~Fi~~rGnlKe~e~~l 59 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI------EGEFEL----PWFAR-----------LSPEQLEFIKLFIKNRGNLKEMEKEL 59 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE------Eeeecc----chhhc-----------CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 8889988877777666433222 444422 11211 34688999999999999999999999
Q ss_pred C
Q 014788 243 S 243 (418)
Q Consensus 243 g 243 (418)
|
T Consensus 60 g 60 (113)
T PF09862_consen 60 G 60 (113)
T ss_pred C
Confidence 8
No 85
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=42.40 E-value=72 Score=24.01 Aligned_cols=40 Identities=18% Similarity=0.541 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCCC
Q 014788 219 KETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFG 260 (418)
Q Consensus 219 ~E~l~LLe~ie~yg~nW~~IA~~VgtkT~~eC~~hfl~LPIe 260 (418)
..|.-.++++.+-|-.=.+||..+| |+ ..|+.+|++=|+.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i~-RS-r~~Ir~yl~dP~~ 46 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRIG-RS-RTCIRRYLKDPVN 46 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHT----HHHHHHHHHSCCC
T ss_pred HHHHHHHHHHHHhchhHHHHHHHhC-cc-HHHHHHHhcChhh
Confidence 4567788899999999999999997 55 6799999987763
No 86
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=41.39 E-value=54 Score=25.99 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=34.9
Q ss_pred HHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 85 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
|+.....+ ...+|+++.-+.+.-....+.|+...|+.+|+|-..
T Consensus 10 Il~~l~~~-~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 10 VLRALAEE-PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHhC-CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 34433333 247999999888888999999999999999999653
No 87
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.22 E-value=1.1e+02 Score=25.27 Aligned_cols=52 Identities=21% Similarity=0.248 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 76 RVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
++-.+|=..||+.|... .+.+.-.+.-+.|.-+-..|..+..-||..|||-=
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 45667788999999996 78888777777787788999999999999999963
No 88
>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=37.01 E-value=1e+02 Score=22.99 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=31.2
Q ss_pred CCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCCCC
Q 014788 92 NPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (418)
Q Consensus 92 np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (418)
+....+|.++..+.+.-|...+.|+..=|...|||.-..+
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~ 53 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERD 53 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC
Confidence 4789999999999999999999999999999999965433
No 89
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=36.45 E-value=24 Score=42.15 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=25.9
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHH
Q 014788 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVA 239 (418)
Q Consensus 212 ~~~~WT~~E~l~LLe~ie~yg-~nW~~IA 239 (418)
...+|..+++..||=||-+|| |+|+.|-
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhc
Confidence 568999999999999999999 9999873
No 90
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=36.09 E-value=55 Score=29.32 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 218 ~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
++-+..||+.+++-| -.|.+||+.+|. |+..|..++-+|
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL 47 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKM 47 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 457889999999999 799999999985 999999999886
No 91
>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=35.50 E-value=19 Score=23.64 Aligned_cols=27 Identities=22% Similarity=0.602 Sum_probs=11.0
Q ss_pred cccCCCCcccc-ccccccCCCccchhhh
Q 014788 162 LCNGCKTLCTI-ACFACDKYDLTLCARC 188 (418)
Q Consensus 162 ~C~~C~~~c~~-~~~~c~k~d~~LC~~C 188 (418)
.|+.|+..... ..|.|..-|+.+...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 58899888765 7788887778887766
No 92
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=35.34 E-value=63 Score=29.03 Aligned_cols=50 Identities=16% Similarity=0.287 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccc-----hhHHHHHHHHhhhhcccccCCCC
Q 014788 81 YRDSIVKHYRENPSRKITFTDVRRTLVG-----DVGSIRRVFDFLETWGLINYFAS 131 (418)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~g-----Dv~~i~Rvh~FLe~wGlINy~~~ 131 (418)
-|-.|++.-...+.. +|+.+.-+.|.. ....+.|+..||+.-|||+-...
T Consensus 22 qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 22 QRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 377888876665444 999998776652 47889999999999999985544
No 93
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=35.20 E-value=59 Score=30.53 Aligned_cols=66 Identities=11% Similarity=0.070 Sum_probs=48.7
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 63 PEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 63 peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
|-|-.-...+.+..+|-.+|+.|+. -+..|...|+-.+--..+.---..+..-..-|+..|||-..
T Consensus 2 ~~~~~~~~~~~~e~v~~~l~~~I~~-g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 2 PGTEKTQHISLTLQVENDLKHQLSI-GALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHh-CCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEec
Confidence 4444433445567899999999997 55669999998776666665556677777779999999754
No 94
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=34.65 E-value=78 Score=26.41 Aligned_cols=44 Identities=27% Similarity=0.360 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHH-------Hhccchh---HHHHHHHHhhhhc
Q 014788 76 RVYRYYRDSIVKHYRENPSRKITFTDVR-------RTLVGDV---GSIRRVFDFLETW 123 (418)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLT~t~~r-------~~l~gDv---~~i~Rvh~FLe~w 123 (418)
++-..+||-|+.+=-.| +|+.+-. |.|+-|+ ..++||+.||.++
T Consensus 36 ~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 36 DIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKH 89 (92)
T ss_pred HHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHH
Confidence 56678899888765554 7777643 3455564 7899999999876
No 95
>PRK06474 hypothetical protein; Provisional
Probab=34.58 E-value=81 Score=29.33 Aligned_cols=48 Identities=15% Similarity=0.163 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhcc-chhHHHHHHHHhhhhcccccCC
Q 014788 81 YRDSIVKHYRENPSRKITFTDVRRTLV-GDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~-gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
.|-.|+..-..++. .+|++++...+. -....+.|....|+..|||.--
T Consensus 12 ~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~ 60 (178)
T PRK06474 12 VRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVV 60 (178)
T ss_pred HHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence 58888887777654 499999987774 3567899999999999999843
No 96
>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=34.48 E-value=78 Score=23.14 Aligned_cols=35 Identities=26% Similarity=0.281 Sum_probs=30.6
Q ss_pred eeHHHHHHhccchhHHHHHHHHhhhhcccccCCCC
Q 014788 97 ITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (418)
Q Consensus 97 LT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (418)
+|.++--+.+..+-..+.|+..-|++.|||.-..+
T Consensus 18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence 99999988899999999999999999999976544
No 97
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=33.55 E-value=59 Score=29.93 Aligned_cols=45 Identities=20% Similarity=0.293 Sum_probs=37.1
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhcc-----chhHHHHHHHHhhhhccccc
Q 014788 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLIN 127 (418)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlIN 127 (418)
|-.|++..... .+.+|..+.-..|. -+...|.|...+|+.-|||+
T Consensus 28 R~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 28 RLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred HHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEE
Confidence 66677766665 68999999877665 27889999999999999997
No 98
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=32.22 E-value=46 Score=29.33 Aligned_cols=36 Identities=14% Similarity=0.154 Sum_probs=25.3
Q ss_pred CcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
.+|||..+......-+-..+.+|.+||...||=...
T Consensus 45 gk~Lt~~e~~~~~~p~~~~v~~V~~wL~~~G~~~~~ 80 (143)
T PF09286_consen 45 GKYLTPEEFAALFAPSPEDVAAVKSWLKSHGLTVVE 80 (143)
T ss_dssp T----HHHHHHHHS--HHHHHHHHHHHHHCT-EEEE
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCceeE
Confidence 689999999988888888999999999999974444
No 99
>smart00426 TEA TEA domain.
Probab=32.12 E-value=81 Score=25.32 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=18.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC
Q 014788 213 RSDWTEKETLQLLEAIMHFG 232 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg 232 (418)
..-|.++=|..++||++.|-
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~ 22 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYP 22 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcC
Confidence 46799999999999999998
No 100
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=32.07 E-value=1.3e+02 Score=20.82 Aligned_cols=34 Identities=26% Similarity=0.316 Sum_probs=30.3
Q ss_pred cceeHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 95 RKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 95 ~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
..+|..+..+.+.-....+.|....|+.-|+|-.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4589999988888899999999999999999964
No 101
>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=30.01 E-value=1.3e+02 Score=23.29 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhccccc
Q 014788 79 RYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (418)
Q Consensus 79 ~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (418)
.++|++|-+ ...+|+.+--+.+.-+...+.-+.++|++.|.|.
T Consensus 3 ~~i~~~l~~------~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 3 QEIRDYLRE------RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHHH------S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHHH------cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 456666544 6778999999999999999999999999999987
No 102
>PRK03837 transcriptional regulator NanR; Provisional
Probab=29.78 E-value=69 Score=30.26 Aligned_cols=58 Identities=12% Similarity=0.088 Sum_probs=49.7
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchhHHHHHHHHhhhhcccccCCC
Q 014788 72 SKNPRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (418)
Q Consensus 72 ~ktp~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (418)
+....+|..||+.|+.-... |...| +-.+....+.-....+.....-|+.-|||....
T Consensus 13 ~~~~~v~~~l~~~I~~g~l~-pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 13 KLSEEVEERLEQMIRSGEFG-PGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred cHHHHHHHHHHHHHHhCCCC-CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 33567999999999997665 89999 898888888888888999999999999998754
No 103
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=29.75 E-value=43 Score=26.78 Aligned_cols=23 Identities=35% Similarity=0.612 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 014788 218 EKETLQLLEAIMHFGDDWRKVAQHVSG 244 (418)
Q Consensus 218 ~~E~l~LLe~ie~yg~nW~~IA~~Vgt 244 (418)
.++.-+||+. |.||...|+++|-
T Consensus 2 r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 2 RERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred HHHHHHHhCC----CCCHHHHHHHcCc
Confidence 4567778887 9999999999985
No 104
>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=29.34 E-value=99 Score=22.52 Aligned_cols=52 Identities=17% Similarity=0.275 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 76 RVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
+.|-.+++.|+..- ..+...+ |..+..+.+.-....+.+...=|+..|+|-.
T Consensus 5 ~~~~~i~~~i~~~~-~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGE-LKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCC-CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 45566666655531 2333344 4888777777788999999999999999854
No 105
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=29.21 E-value=99 Score=28.97 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=39.4
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
.|+.|+..-..++ .+|+.+..+.+.-+...+.|...-|+.-|||-..
T Consensus 2 tr~~IL~~L~~~~--~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 2 TKEDILSYLLKQG--QATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 3788888665543 3999999988988999999999999999999754
No 106
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=28.71 E-value=33 Score=36.15 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHH-----hCC-CCHHHHHHHHhc
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQH-----VSG-KSEKDCITHFIK 256 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~~-----Vgt-kT~~eC~~hfl~ 256 (418)
++.||.+|+..|.+.-..|.=.|--||+. .++ ||.++-..+|..
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~ 179 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYS 179 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHH
Confidence 57899999999999999999777777775 455 999999999864
No 107
>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=28.29 E-value=1.4e+02 Score=24.05 Aligned_cols=40 Identities=20% Similarity=0.440 Sum_probs=29.3
Q ss_pred HHHHHHHhCCCcceeHHHHHHhccc---hhHHHHHHHHhhhhccc
Q 014788 84 SIVKHYRENPSRKITFTDVRRTLVG---DVGSIRRVFDFLETWGL 125 (418)
Q Consensus 84 ~ii~~yr~np~~yLT~t~~r~~l~g---Dv~~i~Rvh~FLe~wGl 125 (418)
.+|..-+. ..|||..+....|.. +...|-.|+.+|+..|+
T Consensus 11 ~Li~~gK~--~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 11 KLIEKGKK--KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHH--HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHhh--cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 37777776 568999999998883 67889999999999996
No 108
>PLN03131 hypothetical protein; Provisional
Probab=28.26 E-value=81 Score=35.30 Aligned_cols=93 Identities=24% Similarity=0.432 Sum_probs=50.8
Q ss_pred ccccCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCccccccCcccCCCCCHHHHHHHHHH-----HHHhCCCH
Q 014788 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEA-----IMHFGDDW 235 (418)
Q Consensus 161 ~~C~~C~~~c~~~~~~c~k~d~~LC~~Cf~~G~~~~~~~s~dF~ki~~~~~~~~~WT~~E~l~LLe~-----ie~yg~nW 235 (418)
..|.-|+... ..+.|....+.+|..|-.--+.- + | ++.. ..-..||++|...|-.+ =+.|-.+|
T Consensus 24 k~CADCga~~--P~WASiNlGIFICi~CSGIHRsL-g---h---RVKS--VTLD~WtdeEV~~Mk~gGN~~AN~iyeanw 92 (705)
T PLN03131 24 RRCINCNSLG--PQFVCTNFWTFICMTCSGIHREF-T---H---RVKS--VSMSKFTSQDVEALQNGGNQRAREIYLKDW 92 (705)
T ss_pred CccccCCCCC--CCeeEeccceEEchhchhhhccc-C---c---cccc--ccCCCCCHHHHHHHHHhccHHHHHHHHhhc
Confidence 4577776532 33445566788999996543321 1 2 2221 23468999887544311 02233456
Q ss_pred HHHHHHhCCCCHHHHHHHHhc-CCCCCccc
Q 014788 236 RKVAQHVSGKSEKDCITHFIK-LPFGQEFI 264 (418)
Q Consensus 236 ~~IA~~VgtkT~~eC~~hfl~-LPIeD~~l 264 (418)
..--..++..+..+-+..||+ -+++-.|.
T Consensus 93 d~~r~~lP~~sd~ekrr~FIR~KYVeKRFa 122 (705)
T PLN03131 93 DQQRQRLPDNSKVDKIREFIKDIYVDKKYA 122 (705)
T ss_pred ccccCCCCCCccHHHHHHHHHHHHhhhhhh
Confidence 543333444445555677887 46666776
No 109
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=28.03 E-value=85 Score=28.48 Aligned_cols=39 Identities=15% Similarity=0.281 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 218 ~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
++-+.+||.++++-| -.|.+||+.|| -|+..|..++-+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg-lS~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG-LSPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC-cCHHHHHHHHHHH
Confidence 567889999999998 78999999998 4899999999886
No 110
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=27.69 E-value=71 Score=29.63 Aligned_cols=56 Identities=23% Similarity=0.266 Sum_probs=46.2
Q ss_pred ChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCCC
Q 014788 74 NPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (418)
Q Consensus 74 tp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (418)
...+|..+|+.|++- ...|...|+-.+..+.+.---..|.....-|+..|||-+..
T Consensus 13 ~~~v~~~l~~~I~~g-~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 13 TTLVQDEIERAILSG-ELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred HHHHHHHHHHHHHcC-CCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEec
Confidence 457999999999996 44599999888877777767778888888899999997653
No 111
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=27.16 E-value=70 Score=35.47 Aligned_cols=93 Identities=22% Similarity=0.387 Sum_probs=50.8
Q ss_pred ccccCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCccccccCcccCCCCCHHHHHHHHHHH-----HHhCCCH
Q 014788 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAI-----MHFGDDW 235 (418)
Q Consensus 161 ~~C~~C~~~c~~~~~~c~k~d~~LC~~Cf~~G~~~~~~~s~dF~ki~~~~~~~~~WT~~E~l~LLe~i-----e~yg~nW 235 (418)
..|.-|+... ..+.|....+.+|..|-.--+.- + | ++.. ..-..||.+|...|..+= +.|-.+|
T Consensus 24 k~CADCgs~~--P~WASiNlGIFICi~CSGIHRsL-G---h---RVKS--LSLDkWT~EEVe~Mk~gGN~~AN~iyeanw 92 (648)
T PLN03119 24 RRCINCNSLG--PQYVCTTFWTFVCMACSGIHREF-T---H---RVKS--VSMSKFTSKEVEVLQNGGNQRAREIYLKNW 92 (648)
T ss_pred CccccCCCCC--CCceeeccceEEeccchhhhccC-C---c---eeec--cccCCCCHHHHHHHHHhchHHHHHHHHhhc
Confidence 4677777542 34445567788999996533311 1 1 3322 234789998875443211 1222356
Q ss_pred HHHHHHhCCCCHHHHHHHHhc-CCCCCccc
Q 014788 236 RKVAQHVSGKSEKDCITHFIK-LPFGQEFI 264 (418)
Q Consensus 236 ~~IA~~VgtkT~~eC~~hfl~-LPIeD~~l 264 (418)
..--..++..+..+-+..||+ -+++-.|.
T Consensus 93 ~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~ 122 (648)
T PLN03119 93 DHQRQRLPENSNAERVREFIKNVYVQKKYA 122 (648)
T ss_pred ccccCCCCCCccHHHHHHHHHHHHhhhhcc
Confidence 543233343344555668888 46666776
No 112
>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=26.76 E-value=1.9e+02 Score=21.28 Aligned_cols=49 Identities=16% Similarity=0.078 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhC-----CCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 81 YRDSIVKHYREN-----PSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 81 ~RN~ii~~yr~n-----p~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
+..+++...... ....+|..+.-..+......+.|+..-|+..|+|-+.
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 344555544433 2356899998888888999999999999999999654
No 113
>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=26.72 E-value=50 Score=25.60 Aligned_cols=30 Identities=17% Similarity=0.527 Sum_probs=24.3
Q ss_pred CCHHHHHHHhCC-CCHHHHHHHHhcCCCCCccc
Q 014788 233 DDWRKVAQHVSG-KSEKDCITHFIKLPFGQEFI 264 (418)
Q Consensus 233 ~nW~~IA~~Vgt-kT~~eC~~hfl~LPIeD~~l 264 (418)
.-|..||..+|. -+.++|..+|.+ +-+.|-
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~--Lr~~y~ 57 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKN--LRDRYR 57 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHH--HHHHHH
Confidence 369999999985 478999999998 456665
No 114
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=26.71 E-value=1e+02 Score=28.18 Aligned_cols=44 Identities=18% Similarity=0.213 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhC----CCCHHHHHHHHhc
Q 014788 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVS----GKSEKDCITHFIK 256 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~nW~~IA~~Vg----tkT~~eC~~hfl~ 256 (418)
...-|..|..-+-..|++||+|+...+.-.. -.|+.|+...+..
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 3567889999999999999999999998665 2799998876543
No 115
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=26.46 E-value=1.2e+02 Score=22.74 Aligned_cols=27 Identities=11% Similarity=0.324 Sum_probs=23.1
Q ss_pred CcceeHHHHHHhcc----chhHHHHHHHHhh
Q 014788 94 SRKITFTDVRRTLV----GDVGSIRRVFDFL 120 (418)
Q Consensus 94 ~~yLT~t~~r~~l~----gDv~~i~Rvh~FL 120 (418)
..++|..+....|. .+...+.||.+||
T Consensus 20 ~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 20 GGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 58999999988887 6888999999998
No 116
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.46 E-value=1.1e+02 Score=25.20 Aligned_cols=39 Identities=15% Similarity=0.147 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 014788 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (418)
Q Consensus 218 ~~E~l~LLe~ie~yg-~nW~~IA~~VgtkT~~eC~~hfl~L 257 (418)
++.+..+|..+...+ -.|.+||+.+|. ++..|..+..+|
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L 41 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL 41 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 356789999999988 689999999984 888888887775
No 117
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=26.02 E-value=1.2e+02 Score=24.13 Aligned_cols=44 Identities=16% Similarity=0.254 Sum_probs=33.7
Q ss_pred HHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 85 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
|+.....+....+|..+....+.-....+.+|..-|.+-|||.-
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s 57 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIES 57 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEe
Confidence 34444444445599999998888899999999999999999964
No 118
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=25.57 E-value=63 Score=32.73 Aligned_cols=92 Identities=15% Similarity=0.342 Sum_probs=53.9
Q ss_pred cccccCCCCccccccccccCCCccchhhhhccCC-CCCCCCCCCccccccCcccCCCCCHHHHHHHHHHHHHhC-----C
Q 014788 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVRGN-HRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFG-----D 233 (418)
Q Consensus 160 k~~C~~C~~~c~~~~~~c~k~d~~LC~~Cf~~G~-~~~~~~s~dF~ki~~~~~~~~~WT~~E~l~LLe~ie~yg-----~ 233 (418)
-..|.-|+.. +..|.. .+-++.+|.+|-.--+ .+.|+ -++.. ..-+.||+++...|.+ +| -
T Consensus 25 N~~CADC~a~-~P~WaS-wnlGvFiC~~C~giHR~lg~hi-----SkVkS--v~LD~W~~eqv~~m~~----~GN~~an~ 91 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWAS-WNLGVFICLRCAGIHRSLGVHI-----SKVKS--VTLDEWTDEQVDFMIS----MGNAKANS 91 (287)
T ss_pred cCcccccCCC-CCCeEE-eecCeEEEeecccccccccchh-----heeee--eeccccCHHHHHHHHH----Hcchhhhh
Confidence 3568888765 444432 2446889999965322 23222 22221 1236899999877664 34 1
Q ss_pred CHHHH-HHHhCCCCHHHHHHHHhc-CCCCCccc
Q 014788 234 DWRKV-AQHVSGKSEKDCITHFIK-LPFGQEFI 264 (418)
Q Consensus 234 nW~~I-A~~VgtkT~~eC~~hfl~-LPIeD~~l 264 (418)
-|+.= .......++++-+.+||+ =|..-.|+
T Consensus 92 ~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~ 124 (287)
T KOG0703|consen 92 YYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFL 124 (287)
T ss_pred hccccCCccccCCChHHHHHHHHHHHHhhhhhc
Confidence 35532 333334578889999998 35555666
No 119
>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=25.20 E-value=92 Score=23.74 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=31.7
Q ss_pred CcceeHHHHHHhccchhHHHHHHHHhhhhcccccC
Q 014788 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (418)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (418)
...+|+.+..+.+.-+-..+.|+..-|++.|||.-
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 56789999999999999999999999999999964
No 120
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=24.88 E-value=1.4e+02 Score=21.10 Aligned_cols=37 Identities=11% Similarity=0.124 Sum_probs=31.5
Q ss_pred CcceeHHHHHHhccchhHHHHHHHHhhhhcccccCCC
Q 014788 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (418)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (418)
...+|+++..+.+.-....+.|+..=|.++|+|....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence 4678999998888778888999999999999997543
No 121
>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=24.64 E-value=43 Score=23.18 Aligned_cols=29 Identities=28% Similarity=0.658 Sum_probs=18.6
Q ss_pred ccccCCCCc-cccccccccCCCccchhhhhccC
Q 014788 161 RLCNGCKTL-CTIACFACDKYDLTLCARCYVRG 192 (418)
Q Consensus 161 ~~C~~C~~~-c~~~~~~c~k~d~~LC~~Cf~~G 192 (418)
..|..|... ....|..| +..+|..|+..+
T Consensus 4 ~~C~~H~~~~~~~~C~~C---~~~~C~~C~~~~ 33 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDC---NEPLCSECTVSG 33 (42)
T ss_dssp SB-SSTTTSBEEEEETTT---TEEEEHHHHHTS
T ss_pred ccCccCCccceEEEecCC---CCccCccCCCCC
Confidence 456666654 34444444 467999999987
No 122
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=24.61 E-value=83 Score=29.78 Aligned_cols=58 Identities=17% Similarity=0.147 Sum_probs=47.5
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchhHHHHHHHHhhhhcccccCCC
Q 014788 72 SKNPRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (418)
Q Consensus 72 ~ktp~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (418)
+.+..+|-.+|+.|+.- +..|...| |-.+-...+..--..|..-..-|+..|||-...
T Consensus 6 ~~~~~v~~~l~~~I~~g-~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 6 SPAGFAEEYIVESIWNN-RFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred hhHHHHHHHHHHHHHcC-CCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 34568999999999975 45599999 788877788777788888888899999998654
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=24.18 E-value=1.2e+02 Score=24.61 Aligned_cols=37 Identities=27% Similarity=0.528 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhCC--------CHHHHHHHhCCC---C--HHHHHHHHhc
Q 014788 220 ETLQLLEAIMHFGD--------DWRKVAQHVSGK---S--EKDCITHFIK 256 (418)
Q Consensus 220 E~l~LLe~ie~yg~--------nW~~IA~~Vgtk---T--~~eC~~hfl~ 256 (418)
+...|-.+|.+.|| .|..||+.+|-. + ..+...+|.+
T Consensus 37 DL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~ 86 (92)
T PF01388_consen 37 DLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEK 86 (92)
T ss_dssp SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHH
T ss_pred cHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHH
Confidence 35678888999884 799999999842 2 2456666654
No 124
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=24.01 E-value=2.7e+02 Score=20.01 Aligned_cols=41 Identities=29% Similarity=0.385 Sum_probs=33.3
Q ss_pred HHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcc
Q 014788 83 DSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWG 124 (418)
Q Consensus 83 N~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wG 124 (418)
..||.....+.. ++|..+.-..|.-....|.|-...|+.||
T Consensus 3 ~~il~~L~~~~~-~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKE-PITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTT-SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCC-CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 456776655544 49999999999999999999999999999
No 125
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=24.00 E-value=71 Score=32.84 Aligned_cols=95 Identities=14% Similarity=0.201 Sum_probs=52.9
Q ss_pred ccccCCCCccccccccccCCCccchhhhhccCCCCCCCCCCC-ccccccCcccCCCCCHHHHHHHHHHHHHhCCCHHHHH
Q 014788 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSD-FRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRKVA 239 (418)
Q Consensus 161 ~~C~~C~~~c~~~~~~c~k~d~~LC~~Cf~~G~~~~~~~s~d-F~ki~~~~~~~~~WT~~E~l~LLe~ie~yg~nW~~IA 239 (418)
..|.-|+..- ..|..| ..++.||.+|-.--|- +-.|- |+|- ..-+.||.+|.++|.-+=...-+.|-+--
T Consensus 21 k~CaDCga~~-P~W~S~-nlGvfiCi~CagvHRs---LGvhiS~VKS----itLD~wt~~~l~~m~~gGN~~a~~~~e~~ 91 (319)
T COG5347 21 KKCADCGAPN-PTWASV-NLGVFLCIDCAGVHRS---LGVHISKVKS----LTLDNWTEEELRRMEVGGNSNANRFYEKN 91 (319)
T ss_pred CccccCCCCC-CceEec-ccCeEEEeecchhhhc---cccceeeeee----eecccCCHHHHHHHHHhcchhhhhHhccC
Confidence 5688888765 555555 4678999999654331 11221 2221 12368999998887652111112222211
Q ss_pred ------HHhCCCCHHHHHHHHhc-CCCCCccc
Q 014788 240 ------QHVSGKSEKDCITHFIK-LPFGQEFI 264 (418)
Q Consensus 240 ------~~VgtkT~~eC~~hfl~-LPIeD~~l 264 (418)
..+..+.-...+.+|++ ++.+-.+.
T Consensus 92 ~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~ 123 (319)
T COG5347 92 LLDQLLLPIKAKYDSSVAKKYIRKKYELKKFI 123 (319)
T ss_pred CCcccccccccccCHHHHHHHHHHHHHhhhcc
Confidence 11123566778888877 66666665
No 126
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=23.85 E-value=54 Score=26.06 Aligned_cols=26 Identities=12% Similarity=0.447 Sum_probs=17.7
Q ss_pred CCCHHHHHH-HHHHHHHhCCCHHHHHH
Q 014788 215 DWTEKETLQ-LLEAIMHFGDDWRKVAQ 240 (418)
Q Consensus 215 ~WT~~E~l~-LLe~ie~yg~nW~~IA~ 240 (418)
+.+++...- |-+.++.||+||.-|-+
T Consensus 22 G~~~~~v~~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 22 GFSKKQVRPVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred CCCHHHHHHHHHHHHHHHcCCchhhhc
Confidence 344444443 44777899999998864
No 127
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.61 E-value=98 Score=26.02 Aligned_cols=26 Identities=12% Similarity=-0.097 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 014788 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (418)
Q Consensus 219 ~E~l~LLe~ie~yg~nW~~IA~~Vgt 244 (418)
-|...+.++++.++||+.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 47778899999999999999999994
No 128
>PRK01905 DNA-binding protein Fis; Provisional
Probab=23.37 E-value=1e+02 Score=24.58 Aligned_cols=28 Identities=14% Similarity=-0.009 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 014788 217 TEKETLQLLEAIMHFGDDWRKVAQHVSG 244 (418)
Q Consensus 217 T~~E~l~LLe~ie~yg~nW~~IA~~Vgt 244 (418)
..-|...+.++++.+|||+.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 3457778899999999999999999984
No 129
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=23.28 E-value=1.3e+02 Score=31.05 Aligned_cols=41 Identities=24% Similarity=0.411 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCC----CHHHHHHHhCCCCHHHHHHH
Q 014788 213 RSDWTEKETLQLLEAIMHFGD----DWRKVAQHVSGKSEKDCITH 253 (418)
Q Consensus 213 ~~~WT~~E~l~LLe~ie~yg~----nW~~IA~~VgtkT~~eC~~h 253 (418)
...||..|-..||.+++...| |-..++++|.+|+..|+...
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~f 65 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDF 65 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHH
Confidence 468999999999999987754 56678889999998887653
No 130
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=23.14 E-value=96 Score=21.29 Aligned_cols=34 Identities=24% Similarity=0.207 Sum_probs=29.0
Q ss_pred ceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 96 KITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 96 yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
.+|..+..+.+.-....+.|+.+-|+..|+|.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4677787777777889999999999999999754
No 131
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=22.79 E-value=1.2e+02 Score=20.67 Aligned_cols=27 Identities=30% Similarity=0.362 Sum_probs=19.2
Q ss_pred HHHHHhccchhHHHHHHHHhhhhcccc
Q 014788 100 TDVRRTLVGDVGSIRRVFDFLETWGLI 126 (418)
Q Consensus 100 t~~r~~l~gDv~~i~Rvh~FLe~wGlI 126 (418)
.+.-..|.--...+.|++..|++-|||
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 333333334567899999999999998
No 132
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=22.59 E-value=90 Score=29.29 Aligned_cols=57 Identities=18% Similarity=0.307 Sum_probs=46.7
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCC
Q 014788 72 SKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (418)
Q Consensus 72 ~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (418)
+.+..+|-.||+.|++- +..|...|+..+....+.---.-|.....-|+.-|||-..
T Consensus 7 ~~~~~vy~~i~~~I~~g-~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 7 ITALDGYRWLKNDIIRG-NFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred hhhHHHHHHHHHHHHhC-CCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEe
Confidence 34678999999999995 4559999998887777766667888889999999999754
No 133
>PF08260 Kinin: Insect kinin peptide; InterPro: IPR013202 This entry represents neuropeptides that are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterised the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. Insect kinins also mediate visceral muscle contractile activity (myotropic activity) []. These peptides have lengths ranging from 6 to 14 amino acids [].
Probab=21.71 E-value=43 Score=16.19 Aligned_cols=6 Identities=33% Similarity=1.592 Sum_probs=4.4
Q ss_pred CCCCCC
Q 014788 43 PSYSRW 48 (418)
Q Consensus 43 Ps~s~W 48 (418)
|+|.+|
T Consensus 2 pafnsw 7 (8)
T PF08260_consen 2 PAFNSW 7 (8)
T ss_pred cccccc
Confidence 677777
No 134
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=21.48 E-value=60 Score=38.43 Aligned_cols=53 Identities=23% Similarity=0.558 Sum_probs=31.1
Q ss_pred ccccccccccCCCCcccc-----ccccccCCCccchhhhhc----cCCCCCCCCCCCccccc
Q 014788 155 LKETSKRLCNGCKTLCTI-----ACFACDKYDLTLCARCYV----RGNHRVGVSSSDFRRVE 207 (418)
Q Consensus 155 ~~~~~k~~C~~C~~~c~~-----~~~~c~k~d~~LC~~Cf~----~G~~~~~~~s~dF~ki~ 207 (418)
+.+.....|..||.+.+. ....|..+.+-+|..||. +|+----.-...|++..
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CPqCktrYkr~k 73 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTKYKRHK 73 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCCccCCchhhhc
Confidence 344455689999988652 223444445888999985 33332223455666554
No 135
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=21.45 E-value=1.2e+02 Score=29.13 Aligned_cols=57 Identities=23% Similarity=0.256 Sum_probs=46.4
Q ss_pred CChHHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchhHHHHHHHHhhhhcccccCCC
Q 014788 73 KNPRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (418)
Q Consensus 73 ktp~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (418)
..-.+|-.+|+.|++- +..|...| |-.+.-..+.---..+.....-|+..|||-...
T Consensus 10 ~~~~v~~~l~~~I~~g-~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 10 PYQEVGAMIRDLIIKT-PYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHHHHhC-CCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4467999999999984 45599999 688877788777788888888899999997543
No 136
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.25 E-value=50 Score=28.61 Aligned_cols=27 Identities=30% Similarity=0.767 Sum_probs=19.2
Q ss_pred cccccCCCCccccccccccCCCccchhhhhcc
Q 014788 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVR 191 (418)
Q Consensus 160 k~~C~~C~~~c~~~~~~c~k~d~~LC~~Cf~~ 191 (418)
|..|..||. ++|-..+ +.++|+.|-..
T Consensus 9 KR~Cp~CG~----kFYDLnk-~PivCP~CG~~ 35 (108)
T PF09538_consen 9 KRTCPSCGA----KFYDLNK-DPIVCPKCGTE 35 (108)
T ss_pred cccCCCCcc----hhccCCC-CCccCCCCCCc
Confidence 678988864 5676666 56789988553
No 137
>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=20.91 E-value=70 Score=21.07 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=19.5
Q ss_pred cccCCCCccccc-cccccCCCccchhhh
Q 014788 162 LCNGCKTLCTIA-CFACDKYDLTLCARC 188 (418)
Q Consensus 162 ~C~~C~~~c~~~-~~~c~k~d~~LC~~C 188 (418)
.|+.|+...... .|.|...++.+..+|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 588898877665 788876666666655
No 138
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=20.79 E-value=40 Score=27.70 Aligned_cols=35 Identities=20% Similarity=0.516 Sum_probs=22.8
Q ss_pred cccCCCCcccccc-ccc---cCCCccchhhhhccCCCCC
Q 014788 162 LCNGCKTLCTIAC-FAC---DKYDLTLCARCYVRGNHRV 196 (418)
Q Consensus 162 ~C~~C~~~c~~~~-~~c---~k~d~~LC~~Cf~~G~~~~ 196 (418)
.|..||......- +-- ...+-.-|.-||.+|.|..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~ 40 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQ 40 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCceee
Confidence 6899998876433 111 1123447999999999754
No 139
>PF14420 Clr5: Clr5 domain
Probab=20.75 E-value=1.6e+02 Score=22.07 Aligned_cols=29 Identities=14% Similarity=0.256 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHHHhcc
Q 014788 76 RVYRYYRDSIVKHYRENPSRKITFTDVRRTLV 107 (418)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~ 107 (418)
+..-.+|+.|..+|.. +-+|+.++++.+.
T Consensus 3 ~~We~~K~~I~~LY~~---e~~tl~~v~~~M~ 31 (54)
T PF14420_consen 3 EDWEPHKEEIERLYID---ENKTLEEVMEIMK 31 (54)
T ss_pred chHHHHHHHHHHHHHh---CCCcHHHHHHHHH
Confidence 3445789999999984 5678888887664
No 140
>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=20.71 E-value=2.5e+02 Score=23.20 Aligned_cols=47 Identities=19% Similarity=0.425 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhCC--CcceeHHHHHHhccchhHHHHHHHHhhhhcccc
Q 014788 80 YYRDSIVKHYRENP--SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLI 126 (418)
Q Consensus 80 ~~RN~ii~~yr~np--~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlI 126 (418)
.++..|++..+.++ .+=+.+.++.+.|..+...|+.+..||..-|+|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 44556666555523 557999999999976999999999999999998
No 141
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=20.63 E-value=1.4e+02 Score=25.24 Aligned_cols=29 Identities=31% Similarity=0.477 Sum_probs=16.9
Q ss_pred CcceeHHHHHHhccchhHHHHHHHHhhhhcc
Q 014788 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWG 124 (418)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wG 124 (418)
.++.|+..+|..|. .++...|+.||..|.
T Consensus 17 G~~pT~~~Vr~~lG--~GS~~ti~~~l~~w~ 45 (120)
T PF11740_consen 17 GKKPTVRAVRERLG--GGSMSTISKHLKEWR 45 (120)
T ss_pred CCCCCHHHHHHHHC--CCCHHHHHHHHHHHH
Confidence 44557777766655 444555555566664
No 142
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=20.34 E-value=1.9e+02 Score=22.05 Aligned_cols=39 Identities=15% Similarity=0.207 Sum_probs=33.0
Q ss_pred CCcceeHHHHHHhccchhHHHHHHHHhhhhcccccCCCC
Q 014788 93 PSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (418)
Q Consensus 93 p~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (418)
....++.++.-+.|.---.++.....=|+.-|||+|..+
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCC
Confidence 578899999988898888888888888999999998754
No 143
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=20.28 E-value=45 Score=26.96 Aligned_cols=26 Identities=15% Similarity=0.267 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 014788 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (418)
Q Consensus 219 ~E~l~LLe~ie~yg~nW~~IA~~Vgt 244 (418)
++.-.+|+--..+|.||..+|+++|-
T Consensus 3 ~~L~~~Ldp~~~~g~DWr~LA~~Lg~ 28 (79)
T cd08312 3 RRLSLFLNPPRVVAADWTALAEEMGF 28 (79)
T ss_pred HHHHHHcCCCCCcccCHHHHHHHcCC
Confidence 34455666656688999999999983
No 144
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=20.28 E-value=1.8e+02 Score=28.41 Aligned_cols=46 Identities=15% Similarity=0.163 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHhCCCcceeHHHHHHhccchhHHHHHHHHhhhhccccc
Q 014788 80 YYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (418)
Q Consensus 80 ~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (418)
+-|+.|++.-+. ...+|+++..+.|.-....|+|=...||.-|+|-
T Consensus 5 ~R~~~Il~~l~~--~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 5 QRHDAIIELVKQ--QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHH--cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 457778887766 5579999999999888999999999999999984
No 145
>cd08781 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit
Probab=20.09 E-value=72 Score=26.05 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 014788 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (418)
Q Consensus 219 ~E~l~LLe~ie~yg~nW~~IA~~Vgt 244 (418)
++.-.+|+.-...|+||...|+++|-
T Consensus 7 ~~Lc~~LD~~~~~g~dWr~LA~~Lgl 32 (83)
T cd08781 7 QKLCSSLDPPNPRGNDWRLLAKKLSV 32 (83)
T ss_pred HHHHHHcCCCCCCCCCHHHHHHHhCc
Confidence 44555666656678899999999993
Done!