Query 012334
Match_columns 466
No_of_seqs 243 out of 756
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 01:32:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012334.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012334hhsearch_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 3.5E-90 7.6E-95 705.5 24.8 373 34-446 46-475 (531)
2 KOG1279 Chromatin remodeling f 100.0 3.1E-81 6.7E-86 659.9 27.2 385 33-446 40-504 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 1.6E-27 3.6E-32 198.5 6.4 85 40-128 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 2.6E-22 5.7E-27 206.4 7.5 104 159-264 13-124 (438)
5 COG5114 Histone acetyltransfer 99.7 5.9E-19 1.3E-23 175.2 5.0 104 159-264 4-115 (432)
6 PF00249 Myb_DNA-binding: Myb- 99.1 5.8E-11 1.3E-15 88.4 5.2 44 214-257 2-47 (48)
7 PF13921 Myb_DNA-bind_6: Myb-l 98.9 1.8E-09 3.9E-14 83.6 5.4 41 216-256 1-41 (60)
8 smart00717 SANT SANT SWI3, AD 98.9 4.1E-09 9E-14 76.3 5.8 44 214-257 2-46 (49)
9 PLN03000 amine oxidase 98.8 5E-09 1.1E-13 118.8 6.7 83 44-131 86-171 (881)
10 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 1E-08 2.2E-13 73.1 5.6 43 215-257 1-44 (45)
11 PLN02328 lysine-specific histo 98.7 2.1E-08 4.5E-13 113.5 6.7 83 45-131 138-222 (808)
12 cd02336 ZZ_RSC8 Zinc finger, Z 98.5 8.3E-08 1.8E-12 71.2 2.8 44 161-204 1-45 (45)
13 PLN03212 Transcription repress 98.3 9.7E-07 2.1E-11 86.7 4.9 45 213-257 25-71 (249)
14 TIGR01557 myb_SHAQKYF myb-like 98.2 2.1E-06 4.5E-11 66.9 4.8 46 213-258 3-54 (57)
15 PLN02529 lysine-specific histo 98.1 3.5E-06 7.6E-11 95.1 6.3 83 44-131 62-147 (738)
16 PLN03091 hypothetical protein; 98.0 4.6E-06 9.9E-11 87.7 5.1 45 213-257 14-60 (459)
17 KOG0048 Transcription factor, 97.8 1.5E-05 3.3E-10 78.4 4.7 44 213-256 9-54 (238)
18 PLN03212 Transcription repress 97.8 2.9E-05 6.4E-10 76.5 4.9 46 211-256 76-121 (249)
19 PLN03091 hypothetical protein; 97.4 0.00016 3.5E-09 76.4 5.3 45 212-256 66-110 (459)
20 KOG0048 Transcription factor, 97.4 0.00024 5.3E-09 70.0 5.4 42 213-254 62-103 (238)
21 cd02335 ZZ_ADA2 Zinc finger, Z 97.0 0.00079 1.7E-08 50.7 3.4 46 161-206 1-49 (49)
22 KOG0049 Transcription factor, 96.9 0.00099 2.1E-08 73.0 5.3 45 212-256 359-404 (939)
23 PLN02976 amine oxidase 96.5 0.0041 8.8E-08 74.6 6.5 86 43-131 449-540 (1713)
24 cd02249 ZZ Zinc finger, ZZ typ 96.5 0.0026 5.5E-08 47.2 3.2 44 161-205 1-45 (46)
25 KOG0049 Transcription factor, 96.1 0.0053 1.1E-07 67.5 4.0 45 212-256 411-459 (939)
26 cd02343 ZZ_EF Zinc finger, ZZ 96.1 0.0051 1.1E-07 46.4 2.7 38 162-199 2-40 (48)
27 smart00291 ZnF_ZZ Zinc-binding 96.0 0.0058 1.3E-07 44.9 2.8 39 160-198 4-43 (44)
28 cd02340 ZZ_NBR1_like Zinc fing 96.0 0.0061 1.3E-07 44.8 2.9 41 162-206 2-43 (43)
29 PF13837 Myb_DNA-bind_4: Myb/S 95.6 0.0067 1.5E-07 50.0 2.0 44 214-257 2-63 (90)
30 cd02338 ZZ_PCMF_like Zinc fing 95.6 0.011 2.5E-07 44.5 2.9 44 162-205 2-48 (49)
31 cd02345 ZZ_dah Zinc finger, ZZ 95.5 0.013 2.8E-07 44.2 3.0 43 162-204 2-47 (49)
32 cd02334 ZZ_dystrophin Zinc fin 95.2 0.02 4.3E-07 43.4 3.0 43 162-204 2-47 (49)
33 cd02341 ZZ_ZZZ3 Zinc finger, Z 95.1 0.022 4.7E-07 43.0 3.0 43 161-205 1-47 (48)
34 PF00569 ZZ: Zinc finger, ZZ t 95.0 0.0093 2E-07 44.3 0.9 39 160-198 4-44 (46)
35 KOG0051 RNA polymerase I termi 94.2 0.053 1.1E-06 59.9 4.6 45 212-257 383-427 (607)
36 cd02337 ZZ_CBP Zinc finger, ZZ 93.7 0.053 1.1E-06 39.5 2.4 37 161-198 1-38 (41)
37 cd02344 ZZ_HERC2 Zinc finger, 93.6 0.067 1.4E-06 39.9 2.8 42 162-206 2-45 (45)
38 cd02339 ZZ_Mind_bomb Zinc fing 93.6 0.074 1.6E-06 39.6 3.0 41 162-205 2-44 (45)
39 KOG0051 RNA polymerase I termi 93.1 0.078 1.7E-06 58.6 3.6 53 212-264 435-513 (607)
40 KOG0050 mRNA splicing protein 91.5 0.17 3.7E-06 54.8 3.6 44 213-256 7-51 (617)
41 KOG4167 Predicted DNA-binding 91.0 0.33 7E-06 54.6 5.3 44 213-256 619-662 (907)
42 PF13873 Myb_DNA-bind_5: Myb/S 90.8 0.51 1.1E-05 38.1 5.1 44 214-257 3-68 (78)
43 KOG0050 mRNA splicing protein 88.9 0.34 7.5E-06 52.6 3.3 44 213-257 59-102 (617)
44 COG5118 BDP1 Transcription ini 88.2 0.7 1.5E-05 48.5 4.9 44 213-256 365-408 (507)
45 KOG4282 Transcription factor G 88.1 0.63 1.4E-05 48.2 4.6 46 214-259 55-114 (345)
46 TIGR02894 DNA_bind_RsfA transc 86.2 0.74 1.6E-05 43.2 3.4 50 213-264 4-60 (161)
47 KOG4329 DNA-binding protein [G 85.5 1.1 2.4E-05 47.0 4.5 50 213-262 277-327 (445)
48 cd02342 ZZ_UBA_plant Zinc fing 84.4 0.67 1.5E-05 34.3 1.8 31 162-192 2-34 (43)
49 COG5147 REB1 Myb superfamily p 84.4 0.9 2E-05 49.8 3.6 45 212-256 71-115 (512)
50 KOG4468 Polycomb-group transcr 84.3 0.87 1.9E-05 50.3 3.4 44 213-256 88-141 (782)
51 COG5147 REB1 Myb superfamily p 82.2 0.81 1.7E-05 50.2 2.1 42 213-254 20-62 (512)
52 KOG1279 Chromatin remodeling f 79.9 2.3 5.1E-05 46.6 4.7 92 41-132 185-284 (506)
53 KOG1280 Uncharacterized conser 79.3 1 2.2E-05 46.8 1.7 35 160-194 8-44 (381)
54 PRK00409 recombination and DNA 76.5 15 0.00033 42.5 10.2 64 379-443 504-567 (782)
55 TIGR01069 mutS2 MutS2 family p 76.2 17 0.00037 42.1 10.4 64 379-443 499-562 (771)
56 KOG4582 Uncharacterized conser 74.2 2.1 4.6E-05 43.5 2.3 42 161-205 153-196 (278)
57 PF09111 SLIDE: SLIDE; InterP 71.8 4.9 0.00011 35.9 3.8 44 212-255 48-107 (118)
58 PF04504 DUF573: Protein of un 68.5 7.6 0.00016 33.4 4.1 44 213-256 4-60 (98)
59 PLN03142 Probable chromatin-re 68.5 7.3 0.00016 46.5 5.3 40 214-253 825-865 (1033)
60 KOG1194 Predicted DNA-binding 65.7 11 0.00024 40.8 5.4 46 211-256 185-230 (534)
61 PRK13923 putative spore coat p 63.2 6.9 0.00015 37.1 3.1 41 213-254 5-52 (170)
62 PF00392 GntR: Bacterial regul 63.1 12 0.00026 29.0 4.0 52 75-127 3-55 (64)
63 smart00345 HTH_GNTR helix_turn 62.4 13 0.00027 27.4 3.9 50 78-128 2-52 (60)
64 KOG4286 Dystrophin-like protei 61.5 3.8 8.1E-05 46.7 1.1 41 161-201 604-646 (966)
65 KOG3554 Histone deacetylase co 57.6 9.5 0.00021 41.4 3.3 52 213-264 285-337 (693)
66 PF01475 FUR: Ferric uptake re 57.6 17 0.00036 31.6 4.3 49 79-128 7-60 (120)
67 PF09862 DUF2089: Protein of u 57.0 19 0.00042 32.0 4.6 61 163-244 1-61 (113)
68 PF12776 Myb_DNA-bind_3: Myb/S 56.7 14 0.0003 30.5 3.6 42 215-256 1-60 (96)
69 PF12802 MarR_2: MarR family; 56.2 31 0.00068 25.9 5.2 41 89-129 14-54 (62)
70 PF13404 HTH_AsnC-type: AsnC-t 54.8 28 0.0006 25.3 4.4 37 219-256 3-40 (42)
71 PF02954 HTH_8: Bacterial regu 54.3 19 0.00041 25.9 3.4 26 219-244 5-30 (42)
72 KOG3647 Predicted coiled-coil 54.1 76 0.0016 32.5 8.7 61 374-436 92-156 (338)
73 smart00307 ILWEQ I/LWEQ domain 53.0 81 0.0018 30.8 8.6 38 399-437 160-197 (200)
74 PF01022 HTH_5: Bacterial regu 52.9 36 0.00077 24.8 4.8 45 81-128 3-47 (47)
75 KOG1194 Predicted DNA-binding 52.5 7.6 0.00017 42.0 1.6 43 213-256 470-512 (534)
76 cd00090 HTH_ARSR Arsenical Res 52.0 35 0.00075 25.6 4.9 45 84-131 11-55 (78)
77 smart00595 MADF subfamily of S 51.4 12 0.00026 30.6 2.3 28 234-264 29-56 (89)
78 PHA00442 host recBCD nuclease 49.8 17 0.00038 28.3 2.7 25 218-242 25-50 (59)
79 PF09339 HTH_IclR: IclR helix- 49.5 28 0.00061 25.8 3.9 43 85-128 8-50 (52)
80 smart00550 Zalpha Z-DNA-bindin 49.1 61 0.0013 25.7 6.0 52 80-131 6-57 (68)
81 PRK09462 fur ferric uptake reg 48.2 31 0.00067 31.3 4.7 46 82-127 19-69 (148)
82 cd07153 Fur_like Ferric uptake 46.4 39 0.00084 28.9 4.8 46 82-128 3-53 (116)
83 PF13412 HTH_24: Winged helix- 46.4 67 0.0015 23.1 5.4 44 81-126 4-47 (48)
84 KOG3859 Septins (P-loop GTPase 46.0 1.5E+02 0.0033 30.9 9.5 49 401-449 353-402 (406)
85 KOG4479 Transcription factor e 43.4 45 0.00098 28.1 4.4 45 76-124 36-90 (92)
86 PF08914 Myb_DNA-bind_2: Rap1 43.1 42 0.0009 26.9 4.1 43 214-256 3-55 (65)
87 cd04779 HTH_MerR-like_sg4 Heli 40.9 1.6E+02 0.0035 26.7 8.1 46 399-446 84-129 (134)
88 PLN03142 Probable chromatin-re 40.6 37 0.00079 40.8 4.9 44 213-256 926-982 (1033)
89 KOG0384 Chromodomain-helicase 39.4 20 0.00043 43.3 2.4 28 212-239 1132-1160(1373)
90 PF03444 HrcA_DNA-bdg: Winged 38.8 97 0.0021 25.9 5.7 53 76-129 4-56 (78)
91 KOG4301 Beta-dystrobrevin [Cyt 38.7 18 0.00038 38.0 1.7 38 159-198 239-280 (434)
92 PF07649 C1_3: C1-like domain; 38.0 16 0.00035 24.4 0.9 27 162-188 2-29 (30)
93 PF01608 I_LWEQ: I/LWEQ domain 37.9 2.1E+02 0.0044 26.9 8.4 39 400-438 111-150 (152)
94 PF04111 APG6: Autophagy prote 37.0 3.5E+02 0.0077 28.0 10.9 49 399-447 74-122 (314)
95 COG5114 Histone acetyltransfer 36.8 50 0.0011 34.5 4.5 53 74-127 377-429 (432)
96 smart00346 HTH_ICLR helix_turn 36.7 64 0.0014 26.0 4.5 44 85-129 10-53 (91)
97 KOG3915 Transcription regulato 33.9 2.7E+02 0.0058 30.8 9.5 39 74-112 175-217 (641)
98 PF12958 DUF3847: Protein of u 33.9 2.4E+02 0.0053 23.9 7.5 51 401-451 6-60 (86)
99 TIGR02449 conserved hypothetic 33.7 1.8E+02 0.004 23.4 6.4 42 405-446 2-43 (65)
100 PF13463 HTH_27: Winged helix 32.8 1.3E+02 0.0027 22.8 5.4 40 92-131 14-53 (68)
101 COG2916 Hns DNA-binding protei 32.4 3.9E+02 0.0085 24.4 9.2 37 393-429 5-41 (128)
102 COG0735 Fur Fe2+/Zn2+ uptake r 31.7 75 0.0016 29.0 4.5 49 82-131 23-76 (145)
103 COG1725 Predicted transcriptio 31.7 1.3E+02 0.0028 27.3 5.8 57 75-131 10-70 (125)
104 PRK06474 hypothetical protein; 31.1 91 0.002 29.5 5.1 48 81-129 12-60 (178)
105 cd08310 Death_NFkB-like Death 31.0 39 0.00085 27.4 2.2 24 217-244 1-24 (72)
106 PF01047 MarR: MarR family; I 30.6 96 0.0021 23.0 4.3 35 97-131 18-52 (59)
107 PF07795 DUF1635: Protein of u 28.9 3.1E+02 0.0067 27.2 8.3 47 401-447 24-70 (214)
108 COG3883 Uncharacterized protei 28.8 3.9E+02 0.0084 27.3 9.3 59 390-449 51-115 (265)
109 PRK11179 DNA-binding transcrip 28.3 86 0.0019 28.5 4.3 39 218-257 8-47 (153)
110 PF09286 Pro-kuma_activ: Pro-k 28.2 57 0.0012 29.2 3.1 36 94-129 45-80 (143)
111 smart00420 HTH_DEOR helix_turn 27.9 1.6E+02 0.0034 20.7 4.9 34 95-128 13-46 (53)
112 PRK11639 zinc uptake transcrip 27.8 79 0.0017 29.5 4.0 50 72-127 23-77 (169)
113 PRK00846 hypothetical protein; 27.7 3.6E+02 0.0078 22.4 8.5 53 395-447 5-63 (77)
114 PF08100 Dimerisation: Dimeris 27.5 1.1E+02 0.0024 23.2 4.1 27 94-120 20-50 (51)
115 PF15346 ARGLU: Arginine and g 27.0 4.8E+02 0.01 24.4 8.9 38 408-445 71-108 (149)
116 PF04102 SlyX: SlyX; InterPro 26.2 2.7E+02 0.0058 22.2 6.3 35 401-435 2-40 (69)
117 PF00643 zf-B_box: B-box zinc 26.2 44 0.00096 23.5 1.6 29 161-192 4-33 (42)
118 PF11278 DUF3079: Protein of u 25.8 63 0.0014 24.7 2.3 23 156-178 9-31 (52)
119 cd07377 WHTH_GntR Winged helix 25.5 1E+02 0.0023 22.8 3.7 53 75-128 4-57 (66)
120 PF09012 FeoC: FeoC like trans 25.1 1.5E+02 0.0033 23.2 4.6 43 79-127 3-45 (69)
121 PRK11414 colanic acid/biofilm 24.5 1.1E+02 0.0024 29.1 4.5 67 63-130 2-68 (221)
122 PRK06800 fliH flagellar assemb 24.4 2.8E+02 0.006 27.1 6.9 26 418-443 85-110 (228)
123 PF10820 DUF2543: Protein of u 24.0 55 0.0012 26.9 1.9 31 94-124 46-79 (81)
124 PF08112 ATP-synt_E_2: ATP syn 23.9 3.5E+02 0.0077 21.1 6.5 22 416-437 33-54 (56)
125 COG5347 GTPase-activating prot 23.8 77 0.0017 33.1 3.4 96 160-264 20-123 (319)
126 PF14569 zf-UDP: Zinc-binding 23.6 47 0.001 27.8 1.4 53 156-208 5-66 (80)
127 PF01412 ArfGap: Putative GTPa 23.4 24 0.00053 30.9 -0.3 59 161-227 14-72 (116)
128 KOG0706 Predicted GTPase-activ 23.0 57 0.0012 35.4 2.3 56 160-224 23-79 (454)
129 PF09538 FYDLN_acid: Protein o 22.9 45 0.00098 29.3 1.3 27 160-191 9-35 (108)
130 cd00092 HTH_CRP helix_turn_hel 22.8 2.4E+02 0.0051 21.1 5.3 50 81-130 5-59 (67)
131 cd08781 Death_UNC5-like Death 22.5 58 0.0013 27.0 1.8 26 219-244 7-32 (83)
132 PF09444 MRC1: MRC1-like domai 22.3 1.8E+02 0.0039 27.1 5.1 64 376-439 57-127 (145)
133 PRK11169 leucine-responsive tr 22.1 1.2E+02 0.0027 27.9 4.1 39 218-257 13-52 (164)
134 TIGR02702 SufR_cyano iron-sulf 22.0 1.6E+02 0.0034 28.1 4.9 47 81-129 2-48 (203)
135 KOG2656 DNA methyltransferase 21.5 54 0.0012 35.1 1.7 44 213-256 130-179 (445)
136 PRK06800 fliH flagellar assemb 21.4 4E+02 0.0086 26.0 7.3 25 423-447 58-82 (228)
137 PF08279 HTH_11: HTH domain; 21.3 3.2E+02 0.0068 20.0 5.5 41 83-124 3-43 (55)
138 PRK00430 fis global DNA-bindin 21.2 1.2E+02 0.0025 26.0 3.4 26 219-244 55-80 (95)
139 smart00418 HTH_ARSR helix_turn 21.0 1.8E+02 0.0038 20.9 4.1 37 94-130 8-44 (66)
140 PF06034 DUF919: Nucleopolyhed 20.9 3.2E+02 0.0069 21.9 5.6 45 401-446 13-57 (62)
141 PF09420 Nop16: Ribosome bioge 20.8 1.5E+02 0.0033 27.5 4.5 43 213-255 114-160 (164)
142 TIGR01843 type_I_hlyD type I s 20.8 9.3E+02 0.02 24.8 11.5 47 409-455 235-281 (423)
143 PF10440 WIYLD: Ubiquitin-bind 20.6 69 0.0015 25.9 1.8 18 223-240 31-48 (65)
144 PF03979 Sigma70_r1_1: Sigma-7 20.5 2.4E+02 0.0052 23.1 5.1 40 84-125 11-53 (82)
145 smart00344 HTH_ASNC helix_turn 20.5 1.6E+02 0.0035 24.6 4.3 38 219-257 3-41 (108)
146 COG4942 Membrane-bound metallo 20.5 5E+02 0.011 28.3 8.7 59 389-451 71-131 (420)
147 PF12674 Zn_ribbon_2: Putative 20.4 61 0.0013 27.0 1.5 36 161-196 1-40 (81)
148 PF02082 Rrf2: Transcriptional 20.3 1.8E+02 0.004 23.5 4.4 45 85-129 14-58 (83)
149 PRK03837 transcriptional regul 20.0 1.3E+02 0.0029 28.8 4.0 59 72-131 13-72 (241)
150 PRK01905 DNA-binding protein F 20.0 1.6E+02 0.0035 23.8 4.0 28 217-244 35-62 (77)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=3.5e-90 Score=705.45 Aligned_cols=373 Identities=29% Similarity=0.514 Sum_probs=300.0
Q ss_pred CCCCCceecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccchHHHH
Q 012334 34 SSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSI 113 (466)
Q Consensus 34 ~~q~~~ivIPs~~~wF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i 113 (466)
-+|+|+|+||||+.||++.+||+||+++.||||+||+++|||++|++||||||++||+||++|||+|+||||++||||+|
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 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhcccccCCCC--Cccccccc---------ccccCCcCCC------------------------CCcc-----
Q 012334 114 RRVFDFLETWGLINYFAS--VKTLKWED---------KETKSSAASA------------------------ESSS----- 153 (466)
Q Consensus 114 ~Rvh~FLe~wGlINy~~~--~kP~~~~~---------~~~~~~~~~~------------------------s~~~----- 153 (466)
.|||+||++|||||||++ ++|..... .++.....+. ...|
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 66644321 1111111100 0011
Q ss_pred ---------ccccccc---ccccCCCCccccccccccC-CCcccchhhhccCCCCCCCCCCCceecccCcc-cCCCCCHH
Q 012334 154 ---------ALKETSK---RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRVEISEE-ARSDWTEK 219 (466)
Q Consensus 154 ---------~~~~~~k---~~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~s~dF~~~~~~~~-~~~~WT~~ 219 (466)
...+.+. ..|+.||+.+...+|+... .++++|..||.+|+||.+..++||++++.... .+..||++
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 0111222 5799999999877776543 56789999999999999999999999987655 56699999
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCCCCcccCCCCCCcccccccccCCCCCCCcccccccCCCCCC
Q 012334 220 ETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESENVGATSPS 299 (466)
Q Consensus 220 E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflqLPIeD~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 (466)
|+++|||||++||++|++||.|||+||++|||+|||+|||+|.||. ..+ ++. .+
T Consensus 286 E~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~-k~~------~~~-~~------------------ 339 (531)
T COG5259 286 ELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLS-KGD------GKG-DN------------------ 339 (531)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhh-ccc------CcC-CC------------------
Confidence 9999999999999999999999999999999999999999999992 111 010 00
Q ss_pred cccCcccccCCCChhHHHHHHHHhhcChHHHHHHHHHHHHHhhccCcccccCcccccchhhcccccCCchhHHHHHHHHH
Q 012334 300 KRMRLTPLADASNPIMAQAAFLSALAGVEIAEVAARAAVTTLSDVDDRASKGSLMRNTRQQEAGVASNGDATQNALARAS 379 (466)
Q Consensus 300 ~~~~~~Pfs~~~NPVms~vAFLas~V~P~VAaaAA~aAl~~l~~~~~~~~~~~~~~~~~~~~~~~~~ng~~~~~aL~aAa 379 (466)
.....||..++|||||+++||+++|.|+|++..+++.++.-.... ... ..++ --......+|++++
T Consensus 340 -~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k~g~~~~-~n~--------e~~~----~~~~~~~~al~s~~ 405 (531)
T COG5259 340 -SKGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIKSGKISH-INR--------ESQE----HIEEVIEYALDSGK 405 (531)
T ss_pred -CCCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhhccceec-Ccc--------chhh----HHHHHHHHHHHHHH
Confidence 011369999999999999999999999999888777532111000 000 0000 00012446899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Q 012334 380 VDASSLIEKEELDVEKAISGIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQ---VKNLLFVDQLSVLFH 446 (466)
Q Consensus 380 ~kAk~la~~EErei~~Lv~~iie~QlkKlelKLk~feeLE~~le~Er~~Le~---~r~~l~~dRl~~~~~ 446 (466)
.+|+++++.|||+|++|+..+|++||+||++||.+|++||+.++.||++|+. .|+..+.+.+-+...
T Consensus 406 eka~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L~~~~~L~rqeLd~nlll~rl~~~e~l~~~~e 475 (531)
T COG5259 406 EKAKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKSTSLERQELDANLLLRRLNAEEKLFAIDE 475 (531)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999 555544444443333
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=3.1e-81 Score=659.94 Aligned_cols=385 Identities=35% Similarity=0.618 Sum_probs=308.6
Q ss_pred CCCCCCceecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccchHHH
Q 012334 33 SSSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGS 112 (466)
Q Consensus 33 ~~~q~~~ivIPs~~~wF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~ 112 (466)
.+.|+|.|+||||++||+|++||+||++++||||+|++++|||++|++||||||++||+||.+|||+|+||||++||||+
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 58899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhcccccCCCC--Cccccccccccc---------CCcCC-CC--Cc--cc-----------ccccccccccC
Q 012334 113 IRRVFDFLETWGLINYFAS--VKTLKWEDKETK---------SSAAS-AE--SS--SA-----------LKETSKRLCNG 165 (466)
Q Consensus 113 i~Rvh~FLe~wGlINy~~~--~kP~~~~~~~~~---------~~~~~-~s--~~--~~-----------~~~~~k~~C~~ 165 (466)
|+|||+|||+||||||+++ ++|..+++..+. ....+ .+ +. +. ..+.....|+.
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 677666432221 11111 00 00 00 00112234555
Q ss_pred CCCccccccccccC--------CCcccchhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHHHHhCCCHHH
Q 012334 166 CKTLCTIACFACDK--------YDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRK 237 (466)
Q Consensus 166 C~~~~~~~~~~c~k--------~d~~lC~~Cf~~G~~~~~~~s~dF~~~~~~~~~~~~WT~~E~l~LLEaIe~yg~nW~~ 237 (466)
|...|...|+.|.. .++.+|.+||.+|+++..+...||+.+ ....+..||++|+++|||||++||+||++
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 55555555555543 357899999999999999999999333 34567899999999999999999999999
Q ss_pred HHHHhCCCCHHHHHHHHhcCCCCCcccCCCCCCcccccccccCCCCCCCcccccccCCCCCCcccCcccccCCCChhHHH
Q 012334 238 VAQHVSGKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESENVGATSPSKRMRLTPLADASNPIMAQ 317 (466)
Q Consensus 238 IA~~VgtKT~~eCi~hflqLPIeD~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Pfs~~~NPVms~ 317 (466)
||.|||+||++|||+|||+|||+|+|+ ...+. .+ .+..+.+.||++.+||||++
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 33221 01 01224467899889999999
Q ss_pred HHHHHhhcChHHHHHHHHHHHHHhhccCccccc-----------------C--cccc-------------cchh-hc---
Q 012334 318 AAFLSALAGVEIAEVAARAAVTTLSDVDDRASK-----------------G--SLMR-------------NTRQ-QE--- 361 (466)
Q Consensus 318 vAFLas~V~P~VAaaAA~aAl~~l~~~~~~~~~-----------------~--~~~~-------------~~~~-~~--- 361 (466)
++||+++|||+|+..+++.+.....+....... + +.+. ...+ +.
T Consensus 332 ~~~l~~~vdP~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~e~~k~~~~~~ 411 (506)
T KOG1279|consen 332 VAFLASVVDPVVKSVAAKSAEEKFSKVNEESPLAKIEVSAKGVEEAASKLGGTDKSKFLALSDIACTLPDEEEKLQSKLK 411 (506)
T ss_pred HHHHHhccCchhhhhhhcccchhhhhhhhcccchhhhHHhhhhHHhhhhhccchhhhhhhhhhhhhcccchHHHHHHHhh
Confidence 999999999999999999999988765432210 0 0000 0000 00
Q ss_pred ccccCC---------chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 012334 362 AGVASN---------GDATQNALARASVDASSLIEKEELDVEKAISGIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQV 432 (466)
Q Consensus 362 ~~~~~n---------g~~~~~aL~aAa~kAk~la~~EErei~~Lv~~iie~QlkKlelKLk~feeLE~~le~Er~~Le~~ 432 (466)
....-+ +.++..+|++||.+|+.+|.+|| +++.+++.+++.||+|+|.||++|++.|+++.+|+++++..
T Consensus 412 ~~~n~~~~k~~e~~~~~a~~~~ls~aa~k~k~la~~ee-~~~s~~~~~~~~q~~k~E~~l~~~~e~e~~~~~e~e~~~~~ 490 (506)
T KOG1279|consen 412 AKLNPNKEKTIELGLSTAANAALSAAAVKAKLLAAQEE-RIKSLVALLEETQLKKLEAKLRHFEEAETLLMREREQLERV 490 (506)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHHHHhhhhhhhHHH-HHHHHhhhhhhhhhhhhhHHHHHHHHHHhhhhhhhhhHHHH
Confidence 000001 23455689999999999999999 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 012334 433 KNLLFVDQLSVLFH 446 (466)
Q Consensus 433 r~~l~~dRl~~~~~ 446 (466)
|+.+..+|..+.-.
T Consensus 491 ~~~~~~~~~~~~~~ 504 (506)
T KOG1279|consen 491 RQRLKAERQQFHMA 504 (506)
T ss_pred HHHHHhcchhhhhh
Confidence 99999999887643
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=1.6e-27 Score=198.51 Aligned_cols=85 Identities=47% Similarity=0.897 Sum_probs=78.2
Q ss_pred eecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccc-hHHHHHHHHH
Q 012334 40 VNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVG-DVGSIRRVFD 118 (466)
Q Consensus 40 ivIPs~~~wF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~g-Dv~~i~Rvh~ 118 (466)
+++|++++||+++.+|++|++.+||||.| ++|+.|+.|||.||..|+.||.+|||+++||+.+.| |++.+.|||+
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 47899999999999999999999999998 799999999999999999999999999999999996 9999999999
Q ss_pred hhhhcccccC
Q 012334 119 FLETWGLINY 128 (466)
Q Consensus 119 FLe~wGlINy 128 (466)
||++||+|||
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=99.86 E-value=2.6e-22 Score=206.37 Aligned_cols=104 Identities=27% Similarity=0.629 Sum_probs=94.6
Q ss_pred ccccccCCCCccc----cccccccCCCcccchhhhccCCC-CCCCCCCCceecccC--cccCCCCCHHHHHHHHHHHHHh
Q 012334 159 SKRLCNGCKTLCT----IACFACDKYDLTLCARCYVRGNH-RVGVSSSDFRRVEIS--EEARSDWTEKETLQLLEAIMHF 231 (466)
Q Consensus 159 ~k~~C~~C~~~~~----~~~~~c~k~d~~lC~~Cf~~G~~-~~~~~s~dF~~~~~~--~~~~~~WT~~E~l~LLEaIe~y 231 (466)
.+++|++|..+++ +.|+.|. +++||..||+.|.+ +.|.++|+|..++.. .....+||++||++||||+++|
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 4899999999886 6788886 57799999999997 788899999999874 3567899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 012334 232 G-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (466)
Q Consensus 232 g-~nW~~IA~~VgtKT~~eCi~hflqLPIeD~fl 264 (466)
| |||.+||+|||+||.+||+.||+...++.++.
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=99.75 E-value=5.9e-19 Score=175.18 Aligned_cols=104 Identities=24% Similarity=0.559 Sum_probs=93.4
Q ss_pred ccccccCCCCccc----cccccccCCCcccchhhhccCCC-CCCCCCCCceecccC--cccCCCCCHHHHHHHHHHHHHh
Q 012334 159 SKRLCNGCKTLCT----IACFACDKYDLTLCARCYVRGNH-RVGVSSSDFRRVEIS--EEARSDWTEKETLQLLEAIMHF 231 (466)
Q Consensus 159 ~k~~C~~C~~~~~----~~~~~c~k~d~~lC~~Cf~~G~~-~~~~~s~dF~~~~~~--~~~~~~WT~~E~l~LLEaIe~y 231 (466)
.+++|+.|..+|+ +.|..|. +++||..||.+|.+ +.|+.+|+|++++.. +....+|++.||++|+++.+..
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~--~~DLC~pCF~~g~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~Tl 81 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECP--AVDLCLPCFVNGIETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTL 81 (432)
T ss_pred ceeeehHHHHhhhcceeeeeeccc--ccceehhhhhccccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhc
Confidence 3689999999987 5677776 57799999999998 667789999999865 3567899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 012334 232 G-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (466)
Q Consensus 232 g-~nW~~IA~~VgtKT~~eCi~hflqLPIeD~fl 264 (466)
| |||++||+|||.|+++||..||+.+++|..|.
T Consensus 82 GlGNW~dIadyiGsr~kee~k~HylK~y~es~~y 115 (432)
T COG5114 82 GLGNWEDIADYIGSRAKEEIKSHYLKMYDESKYY 115 (432)
T ss_pred CCCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccc
Confidence 9 99999999999999999999999999999887
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=99.14 E-value=5.8e-11 Score=88.43 Aligned_cols=44 Identities=39% Similarity=0.912 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCC-HHHHHHHhC-CCCHHHHHHHHhcC
Q 012334 214 SDWTEKETLQLLEAIMHFGDD-WRKVAQHVS-GKSEKDCITHFIKL 257 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~yg~n-W~~IA~~Vg-tKT~~eCi~hflqL 257 (466)
..||.+|+.+|++||.+||.+ |..||++|| +||..||+.||.++
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 579999999999999999965 999999999 99999999999764
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=98.91 E-value=1.8e-09 Score=83.58 Aligned_cols=41 Identities=34% Similarity=0.857 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 216 WTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 216 WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
||.+|+.+|++++..||.+|..||+++|+||+.+|..||..
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=98.87 E-value=4.1e-09 Score=76.28 Aligned_cols=44 Identities=30% Similarity=0.810 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
..||.+|+.+|+.++.+|| ++|..||.++++||+.+|..+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5799999999999999999 9999999999999999999999874
No 9
>PLN03000 amine oxidase
Probab=98.81 E-value=5e-09 Score=118.83 Aligned_cols=83 Identities=24% Similarity=0.382 Sum_probs=72.4
Q ss_pred CCCCCCCCCCCCHHHHhh--CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccch-HHHHHHHHHhh
Q 012334 44 SYSRWFSFDSISECEVKF--LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGD-VGSIRRVFDFL 120 (466)
Q Consensus 44 s~~~wF~~~~ih~iE~~~--lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gD-v~~i~Rvh~FL 120 (466)
.++.-|+.+.+++.|..+ || ... ...+..|+.|||.||.+|+.||..|||+++|...+..+ ...+.++|+||
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 456789999999999777 88 222 35789999999999999999999999999999776643 48899999999
Q ss_pred hhcccccCCCC
Q 012334 121 ETWGLINYFAS 131 (466)
Q Consensus 121 e~wGlINy~~~ 131 (466)
.++|+|||++.
T Consensus 161 ~r~G~in~g~~ 171 (881)
T PLN03000 161 VTHGYINFGIA 171 (881)
T ss_pred HHcCcccHHHH
Confidence 99999999998
No 10
>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=98.80 E-value=1e-08 Score=73.13 Aligned_cols=43 Identities=37% Similarity=0.851 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 215 DWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 215 ~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
.||.+|+.+|+.++.+|| ++|..||+.+++||..+|..||..+
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 11
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.69 E-value=2.1e-08 Score=113.52 Aligned_cols=83 Identities=22% Similarity=0.306 Sum_probs=74.3
Q ss_pred CCCCCCCCCCCHHHHhh-CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhcc-chHHHHHHHHHhhhh
Q 012334 45 YSRWFSFDSISECEVKF-LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV-GDVGSIRRVFDFLET 122 (466)
Q Consensus 45 ~~~wF~~~~ih~iE~~~-lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~-gDv~~i~Rvh~FLe~ 122 (466)
.+.-|+.+.+|+.|..+ |+....+ ..+..|+.|||.||.+|+.||..|||+++|+..+. -....+.++|.||.+
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 45789999999999887 7777665 57899999999999999999999999999997765 356899999999999
Q ss_pred cccccCCCC
Q 012334 123 WGLINYFAS 131 (466)
Q Consensus 123 wGlINy~~~ 131 (466)
.|.|||++.
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=98.48 E-value=8.3e-08 Score=71.18 Aligned_cols=44 Identities=32% Similarity=0.555 Sum_probs=39.5
Q ss_pred ccccCCCCccccccccccC-CCcccchhhhccCCCCCCCCCCCce
Q 012334 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFR 204 (466)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~s~dF~ 204 (466)
+.|+.|+.+|+..+|+|.+ .+++||+.||.+|+||.++.+.||+
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 4799999999988888865 4688999999999999999999995
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.25 E-value=9.7e-07 Score=86.74 Aligned_cols=45 Identities=24% Similarity=0.512 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~Vg-tKT~~eCi~hflqL 257 (466)
...||.+|+.+|+++|++|| .+|..||+++| +||..||+.||.++
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 56899999999999999999 79999999997 79999999999983
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=98.20 E-value=2.1e-06 Score=66.86 Aligned_cols=46 Identities=24% Similarity=0.542 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCH---HHHHHHhC-CC-CHHHHHHHHhcCC
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDW---RKVAQHVS-GK-SEKDCITHFIKLP 258 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW---~~IA~~Vg-tK-T~~eCi~hflqLP 258 (466)
...||++|..++|+||+.|| ||| ..|+++++ ++ |+.||..|+-.+.
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 699 99999987 57 9999999986543
No 15
>PLN02529 lysine-specific histone demethylase 1
Probab=98.11 E-value=3.5e-06 Score=95.05 Aligned_cols=83 Identities=25% Similarity=0.343 Sum_probs=70.7
Q ss_pred CCCCCCCCCCCCHHHHhh--CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccchH-HHHHHHHHhh
Q 012334 44 SYSRWFSFDSISECEVKF--LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDV-GSIRRVFDFL 120 (466)
Q Consensus 44 s~~~wF~~~~ih~iE~~~--lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv-~~i~Rvh~FL 120 (466)
.++-=|+.+.+++.|+++ +|+ -..+.+..|+.|||.|+.+|+.||..|||+++++..+.-++ ..|...|+||
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 23578999999999999999999999999999987766544 5677899999
Q ss_pred hhcccccCCCC
Q 012334 121 ETWGLINYFAS 131 (466)
Q Consensus 121 e~wGlINy~~~ 131 (466)
.+.|.|||++.
T Consensus 137 ~~~~~inc~vn 147 (738)
T PLN02529 137 LYNGYINFGVS 147 (738)
T ss_pred HhCCCcceeec
Confidence 99999999998
No 16
>PLN03091 hypothetical protein; Provisional
Probab=98.04 E-value=4.6e-06 Score=87.75 Aligned_cols=45 Identities=24% Similarity=0.597 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~Vg-tKT~~eCi~hflqL 257 (466)
+..||.+|+.+|+++|++|| ++|..||+++| +||..||+.||..+
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~Ny 60 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINY 60 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhc
Confidence 46799999999999999999 89999999998 79999999999873
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.85 E-value=1.5e-05 Score=78.41 Aligned_cols=44 Identities=20% Similarity=0.496 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~Vg-tKT~~eCi~hflq 256 (466)
++.||.+|+.+|.+-|++|| ++|..|+++.| .|+-.+|+++|+.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~N 54 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTN 54 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhc
Confidence 58999999999999999999 99999999999 8999999999987
No 18
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.76 E-value=2.9e-05 Score=76.47 Aligned_cols=46 Identities=17% Similarity=0.338 Sum_probs=43.0
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 211 ~~~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
.....||.+|+.+||+.+..||..|..||++|.+||..+|..||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 3468999999999999999999999999999999999999999964
No 19
>PLN03091 hypothetical protein; Provisional
Probab=97.44 E-value=0.00016 Score=76.38 Aligned_cols=45 Identities=16% Similarity=0.468 Sum_probs=42.2
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
.+..||.+|+.+||+.+..||..|.+||++|.+||..+|..||..
T Consensus 66 kKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 66 KRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 457899999999999999999999999999999999999998864
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.37 E-value=0.00024 Score=69.98 Aligned_cols=42 Identities=17% Similarity=0.554 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHH
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHF 254 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hf 254 (466)
+..||.+||.+|+++-..||.-|..||.|+++||..+...||
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 578999999999999999999999999999999999998887
No 21
>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=96.97 E-value=0.00079 Score=50.68 Aligned_cols=46 Identities=24% Similarity=0.501 Sum_probs=33.6
Q ss_pred ccccCCCCcccc-ccccccC-CCcccchhhhccCCC-CCCCCCCCceec
Q 012334 161 RLCNGCKTLCTI-ACFACDK-YDLTLCARCYVRGNH-RVGVSSSDFRRV 206 (466)
Q Consensus 161 ~~C~~C~~~~~~-~~~~c~k-~d~~lC~~Cf~~G~~-~~~~~s~dF~~~ 206 (466)
+.|++|+..+.. .++.|.. .|++||..||..|.. ..+..+|.|..+
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 369999987653 4454443 278899999999987 456678888753
No 22
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.95 E-value=0.00099 Score=72.97 Aligned_cols=45 Identities=31% Similarity=0.731 Sum_probs=42.6
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
..+.||.+|+.+|+-||++|| .+|-+|-+.|.+||-.||+.+|++
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 457899999999999999999 699999999999999999999986
No 23
>PLN02976 amine oxidase
Probab=96.51 E-value=0.0041 Score=74.58 Aligned_cols=86 Identities=20% Similarity=0.230 Sum_probs=72.1
Q ss_pred CCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHh------hccchHHHHHHH
Q 012334 43 PSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRR------TLVGDVGSIRRV 116 (466)
Q Consensus 43 Ps~~~wF~~~~ih~iE~~~lpeff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~------~l~gDv~~i~Rv 116 (466)
..-+.-+....+.+|||-.|.|...-|. .-+-|+++||.|+-+|-++=.+-|.+++|-= .-.+-...|.-|
T Consensus 449 aav~~gl~a~~~~~~e~~~~k~~lkr~~---~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~ 525 (1713)
T PLN02976 449 AAVSAGLKARAVGPIEKIKFKEVLKRKG---GLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREV 525 (1713)
T ss_pred hhhhccccccccChHHHHHHHHHHHhcc---chHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHH
Confidence 3444566678899999999999997543 5799999999999999999999999999931 111456889999
Q ss_pred HHhhhhcccccCCCC
Q 012334 117 FDFLETWGLINYFAS 131 (466)
Q Consensus 117 h~FLe~wGlINy~~~ 131 (466)
+.||++.|.||-++.
T Consensus 526 ~~fld~~gyin~g~~ 540 (1713)
T PLN02976 526 YLFLDQRGYINAGIA 540 (1713)
T ss_pred HHHhhccCceecccc
Confidence 999999999999988
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=96.51 E-value=0.0026 Score=47.17 Aligned_cols=44 Identities=25% Similarity=0.610 Sum_probs=32.6
Q ss_pred ccccCCCCccccccccccC-CCcccchhhhccCCCCCCCCCCCcee
Q 012334 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRR 205 (466)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~s~dF~~ 205 (466)
+.|++|+..+.-.+|.|.. .+++||..||..|. ..+...|.|.+
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 45555777765
No 25
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.08 E-value=0.0053 Score=67.50 Aligned_cols=45 Identities=29% Similarity=0.443 Sum_probs=41.5
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCH---HHHHHHHhc
Q 012334 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSE---KDCITHFIK 256 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~---~eCi~hflq 256 (466)
..+.||-+|+..||++|++|| |+|-++|-.+|.||. .-|+.+|+.
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHH
Confidence 357899999999999999999 999999999999998 778888876
No 26
>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=96.06 E-value=0.0051 Score=46.38 Aligned_cols=38 Identities=26% Similarity=0.764 Sum_probs=28.1
Q ss_pred cccCCCCccccccccccC-CCcccchhhhccCCCCCCCC
Q 012334 162 LCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVS 199 (466)
Q Consensus 162 ~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~ 199 (466)
.|++|+..+...+|.|.. .|++||..||..|....++.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCC
Confidence 599999876544555532 47889999999999865553
No 27
>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=96.01 E-value=0.0058 Score=44.91 Aligned_cols=39 Identities=21% Similarity=0.472 Sum_probs=29.5
Q ss_pred cccccCCCCccccccccccC-CCcccchhhhccCCCCCCC
Q 012334 160 KRLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (466)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~ 198 (466)
...|++|+..+.-.+|.|.. .|++||.+||..|.++..+
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 45799999977655666643 3788999999999876543
No 28
>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=96.01 E-value=0.0061 Score=44.79 Aligned_cols=41 Identities=24% Similarity=0.634 Sum_probs=31.1
Q ss_pred cccCCCCccccccccccC-CCcccchhhhccCCCCCCCCCCCceec
Q 012334 162 LCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRV 206 (466)
Q Consensus 162 ~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~s~dF~~~ 206 (466)
.|++|+..+.-.+|.|.. .+++||..||..| .+ ..|.|.++
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 599999977656666654 3788999999998 33 77888753
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.64 E-value=0.0067 Score=49.99 Aligned_cols=44 Identities=25% Similarity=0.675 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHHHHHHH------hC------C--CHHHHHHHhC----CCCHHHHHHHHhcC
Q 012334 214 SDWTEKETLQLLEAIMH------FG------D--DWRKVAQHVS----GKSEKDCITHFIKL 257 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~------yg------~--nW~~IA~~Vg----tKT~~eCi~hflqL 257 (466)
..||++|+..||+.+.. ++ + -|..||+.+. .||+.||..+|-.|
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 47999999999999977 21 1 4999999984 49999999999883
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=95.59 E-value=0.011 Score=44.49 Aligned_cols=44 Identities=30% Similarity=0.566 Sum_probs=29.5
Q ss_pred cccCCC-CccccccccccC-CCcccchhhhccCCCCCCC-CCCCcee
Q 012334 162 LCNGCK-TLCTIACFACDK-YDLTLCARCYVRGNHRVGV-SSSDFRR 205 (466)
Q Consensus 162 ~C~~C~-~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~-~s~dF~~ 205 (466)
.|++|+ .++.-.+|.|.. .|++||..||..|.....| .+|.|..
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 555534444432 3688999999999764444 4777653
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=95.49 E-value=0.013 Score=44.19 Aligned_cols=43 Identities=26% Similarity=0.542 Sum_probs=29.4
Q ss_pred cccCCCC-ccccccccccC-CCcccchhhhccCCCCCC-CCCCCce
Q 012334 162 LCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRVG-VSSSDFR 204 (466)
Q Consensus 162 ~C~~C~~-~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~-~~s~dF~ 204 (466)
.|++|+. ++.-.+|.|.. .|++||..||..|....+ ..+|.|.
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 5999998 66544444432 478899999999976443 4566654
No 32
>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=95.16 E-value=0.02 Score=43.37 Aligned_cols=43 Identities=28% Similarity=0.631 Sum_probs=28.2
Q ss_pred cccCCCCc-cccccccccC-CCcccchhhhccCCCCCCC-CCCCce
Q 012334 162 LCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRVGV-SSSDFR 204 (466)
Q Consensus 162 ~C~~C~~~-~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~-~s~dF~ 204 (466)
.|++|+.. +.-.+|.|.. .|++||..||..|.....| ..|.++
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 59999964 4433444432 3688999999999875444 555553
No 33
>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=95.09 E-value=0.022 Score=42.98 Aligned_cols=43 Identities=21% Similarity=0.485 Sum_probs=29.7
Q ss_pred ccccCCCC-ccccccccccC---CCcccchhhhccCCCCCCCCCCCcee
Q 012334 161 RLCNGCKT-LCTIACFACDK---YDLTLCARCYVRGNHRVGVSSSDFRR 205 (466)
Q Consensus 161 ~~C~~C~~-~~~~~~~~c~k---~d~~lC~~Cf~~G~~~~~~~s~dF~~ 205 (466)
+.|++|+. .+.-.+|.|.. .+++||..||..|. .+..+|.|.+
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 55544455543 36889999999996 4556666654
No 34
>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=95.01 E-value=0.0093 Score=44.27 Aligned_cols=39 Identities=28% Similarity=0.622 Sum_probs=22.9
Q ss_pred cccccCCCC-ccccccccccC-CCcccchhhhccCCCCCCC
Q 012334 160 KRLCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (466)
Q Consensus 160 k~~C~~C~~-~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~ 198 (466)
...|++|+. .+.-.+|.|.. .|++||..||..|.+...+
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 44444555542 4788999999999875544
No 35
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.18 E-value=0.053 Score=59.89 Aligned_cols=45 Identities=22% Similarity=0.641 Sum_probs=42.4
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
..+.||.+|+..|-.-+.++|++|..|++.|| |.|..|+.+|-++
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 56889999999999999999999999999998 7999999999884
No 36
>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=93.71 E-value=0.053 Score=39.52 Aligned_cols=37 Identities=32% Similarity=0.671 Sum_probs=26.5
Q ss_pred ccccCCCCccccccccccC-CCcccchhhhccCCCCCCC
Q 012334 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (466)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~ 198 (466)
+.|++|.+..+ ..+.|.. .|++||..||..+.++..+
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~~~H~H~~ 38 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNTKNHPHKM 38 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCCCCCCccc
Confidence 36999988766 4444432 3788999999998876543
No 37
>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=93.62 E-value=0.067 Score=39.86 Aligned_cols=42 Identities=26% Similarity=0.761 Sum_probs=28.3
Q ss_pred cccCCCCc-cccccccccC-CCcccchhhhccCCCCCCCCCCCceec
Q 012334 162 LCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRV 206 (466)
Q Consensus 162 ~C~~C~~~-~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~s~dF~~~ 206 (466)
.|++|+.. +.-.+|.|.. .|++||..||..+.+ ...|.|.|+
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 3334454432 368899999999664 356777664
No 38
>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=93.58 E-value=0.074 Score=39.56 Aligned_cols=41 Identities=22% Similarity=0.546 Sum_probs=27.0
Q ss_pred cccCCCC-ccccccccccC-CCcccchhhhccCCCCCCCCCCCcee
Q 012334 162 LCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRR 205 (466)
Q Consensus 162 ~C~~C~~-~~~~~~~~c~k-~d~~lC~~Cf~~G~~~~~~~s~dF~~ 205 (466)
.|++|+. .+.-.+|.|.. .|++||..||..+. +...|.|.+
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 5999994 44344444443 26889999999755 345566654
No 39
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.13 E-value=0.078 Score=58.61 Aligned_cols=53 Identities=25% Similarity=0.481 Sum_probs=45.7
Q ss_pred cCCCCCHHHHHHHHHHHH-------Hh-------C------------CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 012334 212 ARSDWTEKETLQLLEAIM-------HF-------G------------DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe-------~y-------g------------~nW~~IA~~VgtKT~~eCi~hflqLPIeD~fl 264 (466)
....||-+|+.+||..|+ +| | =+|..|++.+|||++.||+.||-+|=+...+-
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 17999999999999999999999988877665
No 40
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.47 E-value=0.17 Score=54.82 Aligned_cols=44 Identities=23% Similarity=0.615 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
+..|+..|+..|--+|.+|| ..|..|+..+..||+.||..+|-.
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 56899999999999999999 779999999999999999999974
No 41
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=90.98 E-value=0.33 Score=54.64 Aligned_cols=44 Identities=20% Similarity=0.422 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
..-||..|..++-.||-.|..|+..|++.|.+||..||+..|.-
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 46799999999999999999999999999999999999999853
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=90.79 E-value=0.51 Score=38.08 Aligned_cols=44 Identities=20% Similarity=0.419 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHHhC----C-------------CHHHHHHHhC-----CCCHHHHHHHHhcC
Q 012334 214 SDWTEKETLQLLEAIMHFG----D-------------DWRKVAQHVS-----GKSEKDCITHFIKL 257 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~yg----~-------------nW~~IA~~Vg-----tKT~~eCi~hflqL 257 (466)
..||.+|...||+.|+.|. + -|..|+..+. .||..|+..+|-.|
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 5799999999999999985 1 5999999993 48999999988654
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=88.86 E-value=0.34 Score=52.56 Aligned_cols=44 Identities=20% Similarity=0.598 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
...|+.+|+.+||.+.......|-.|+.-|| ||..||..||..|
T Consensus 59 ~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 59 KTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 4689999999999999999999999999998 8999999999874
No 44
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=88.22 E-value=0.7 Score=48.53 Aligned_cols=44 Identities=23% Similarity=0.477 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
...||..|..++..|+.++|.|+.-|+....+|...|+..+|++
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999998
No 45
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=88.14 E-value=0.63 Score=48.18 Aligned_cols=46 Identities=30% Similarity=0.544 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHHHHHHhC-----C-----CHHHHHHHh---C-CCCHHHHHHHHhcCCC
Q 012334 214 SDWTEKETLQLLEAIMHFG-----D-----DWRKVAQHV---S-GKSEKDCITHFIKLPF 259 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~yg-----~-----nW~~IA~~V---g-tKT~~eCi~hflqLPI 259 (466)
..|+.+|++.||++..... + .|..||..+ | .||+.||..+|-.|..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 6899999999999985332 4 499999944 4 3999999999977554
No 46
>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=86.22 E-value=0.74 Score=43.16 Aligned_cols=50 Identities=16% Similarity=0.409 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C-----CHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 012334 213 RSDWTEKETLQLLEAIMHFG--D-----DWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg--~-----nW~~IA~~VgtKT~~eCi~hflqLPIeD~fl 264 (466)
.+.||.+|+++|-|.|-.|= | -++.|++.++ ||+.-|-.+|... +-..|-
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 36799999999999999886 3 5899999995 9999999999763 344443
No 47
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=85.50 E-value=1.1 Score=47.03 Aligned_cols=50 Identities=20% Similarity=0.377 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHH-HHHhCCCCHHHHHHHHhcCCCCCc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKV-AQHVSGKSEKDCITHFIKLPFGQE 262 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~I-A~~VgtKT~~eCi~hflqLPIeD~ 262 (466)
-..|+.+|=..+=+||+.||.|+..| +..|.+||.-||+..|.+--....
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKkSer 327 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKKSER 327 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhcCcc
Confidence 47899999999999999999999999 467899999999999876544443
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=84.39 E-value=0.67 Score=34.26 Aligned_cols=31 Identities=35% Similarity=0.743 Sum_probs=21.3
Q ss_pred cccCCCCc-ccccccccc-CCCcccchhhhccC
Q 012334 162 LCNGCKTL-CTIACFACD-KYDLTLCARCYVRG 192 (466)
Q Consensus 162 ~C~~C~~~-~~~~~~~c~-k~d~~lC~~Cf~~G 192 (466)
.|++|+.. +.-..|.|. ..|++||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 59999964 433445554 34788999999864
No 49
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=84.38 E-value=0.9 Score=49.81 Aligned_cols=45 Identities=20% Similarity=0.655 Sum_probs=42.6
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
....|+.+|+-.|++.=..+|.-|..||..++.+|..+|..+|+.
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 50
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=84.32 E-value=0.87 Score=50.33 Aligned_cols=44 Identities=23% Similarity=0.548 Sum_probs=38.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHH----------HHHhCCCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKV----------AQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~I----------A~~VgtKT~~eCi~hflq 256 (466)
+..||.+|+.-+.+||.+||.|+++| -..+..||..|...||.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~ 141 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYR 141 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHH
Confidence 57899999999999999999999999 333446899999999976
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=82.20 E-value=0.81 Score=50.17 Aligned_cols=42 Identities=21% Similarity=0.493 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHH
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHF 254 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hf 254 (466)
.+.|+..|+.-|+-+++.|| .||..||..++.+|+++|..|+
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
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=79.89 E-value=2.3 Score=46.64 Aligned_cols=92 Identities=7% Similarity=-0.063 Sum_probs=75.0
Q ss_pred ecCCCCCCCCCCCCCHHHHhhCccccCCCC-CCCChHHHHHHHHHHHHHHHhCCCccee-----HHHHHhhcc--chHHH
Q 012334 41 NVPSYSRWFSFDSISECEVKFLPEFFDSRS-PSKNPRVYRYYRDSIVKHYRENPSRKIT-----FTDVRRTLV--GDVGS 112 (466)
Q Consensus 41 vIPs~~~wF~~~~ih~iE~~~lpeff~~~~-~~ktp~~Y~~~RN~ii~~yr~np~~yLt-----~t~~r~~l~--gDv~~ 112 (466)
..+..++-++...=+.-....+++|+-+++ ....+..|+.+|+.++..++---.-+.+ -+..+++.. +.+-+
T Consensus 185 ~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLL 264 (506)
T KOG1279|consen 185 TLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLL 264 (506)
T ss_pred cccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHH
Confidence 667778888888888899999999999873 2567888999999999998885444443 455666665 68899
Q ss_pred HHHHHHhhhhcccccCCCCC
Q 012334 113 IRRVFDFLETWGLINYFASV 132 (466)
Q Consensus 113 i~Rvh~FLe~wGlINy~~~~ 132 (466)
+-+|+.|.+.|+-|+.+|.+
T Consensus 265 LE~ie~y~ddW~kVa~hVg~ 284 (506)
T KOG1279|consen 265 LEAIEMYGDDWNKVADHVGT 284 (506)
T ss_pred HHHHHHhcccHHHHHhccCC
Confidence 99999999999999999983
No 53
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=79.28 E-value=1 Score=46.83 Aligned_cols=35 Identities=31% Similarity=0.696 Sum_probs=25.6
Q ss_pred cccccCCCCc-ccccccccc-CCCcccchhhhccCCC
Q 012334 160 KRLCNGCKTL-CTIACFACD-KYDLTLCARCYVRGNH 194 (466)
Q Consensus 160 k~~C~~C~~~-~~~~~~~c~-k~d~~lC~~Cf~~G~~ 194 (466)
...|++|++- .+..||.|- .+|++||..||.+|.-
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 3579999865 455566553 3478899999999853
No 54
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=76.53 E-value=15 Score=42.53 Aligned_cols=64 Identities=22% Similarity=0.262 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 379 SVDASSLIEKEELDVEKAISGIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSV 443 (466)
Q Consensus 379 a~kAk~la~~EErei~~Lv~~iie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~ 443 (466)
..+|+.+...++.++++|+..+.+. -+.+|.+...++.+...+++.+++|++.++.|-.+|-.+
T Consensus 504 i~~A~~~~~~~~~~~~~li~~l~~~-~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~ 567 (782)
T PRK00409 504 IEEAKKLIGEDKEKLNELIASLEEL-ERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKL 567 (782)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988653 333555555555555555555555555555444444433
No 55
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=76.19 E-value=17 Score=42.14 Aligned_cols=64 Identities=20% Similarity=0.140 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 379 SVDASSLIEKEELDVEKAISGIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSV 443 (466)
Q Consensus 379 a~kAk~la~~EErei~~Lv~~iie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~ 443 (466)
..+|+.+...++.++++|+..+.+. .+++|.+...++.+...+++.+++|++.++.|-.+|-.+
T Consensus 499 i~~A~~~~~~~~~~~~~li~~L~~~-~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~ 562 (771)
T TIGR01069 499 IEQAKTFYGEFKEEINVLIEKLSAL-EKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNK 562 (771)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999988653 334566665555555555555555555555544444433
No 56
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=74.17 E-value=2.1 Score=43.49 Aligned_cols=42 Identities=24% Similarity=0.434 Sum_probs=27.0
Q ss_pred ccccCCCC-cccccccccc-CCCcccchhhhccCCCCCCCCCCCcee
Q 012334 161 RLCNGCKT-LCTIACFACD-KYDLTLCARCYVRGNHRVGVSSSDFRR 205 (466)
Q Consensus 161 ~~C~~C~~-~~~~~~~~c~-k~d~~lC~~Cf~~G~~~~~~~s~dF~~ 205 (466)
..|+.|+. .+.-..|.|. ..|++||..|+..+ .++..|-|.+
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~---~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN---EHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC---CCCcccceee
Confidence 57999998 5543444443 23677999999987 2334444444
No 57
>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=71.80 E-value=4.9 Score=35.85 Aligned_cols=44 Identities=18% Similarity=0.443 Sum_probs=35.0
Q ss_pred cCCCCCHHHHHHHHHHHHHhC----CCHHHHHHHhC------------CCCHHHHHHHHh
Q 012334 212 ARSDWTEKETLQLLEAIMHFG----DDWRKVAQHVS------------GKSEKDCITHFI 255 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg----~nW~~IA~~Vg------------tKT~~eCi~hfl 255 (466)
.+..||.+|+--||-.+.+|| |+|+.|-+.+- +||+.++..|-.
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 788888866643
No 58
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=68.52 E-value=7.6 Score=33.41 Aligned_cols=44 Identities=20% Similarity=0.505 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHHHHh----C----CCHHHHHHHhCCC-----CHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHF----G----DDWRKVAQHVSGK-----SEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~y----g----~nW~~IA~~VgtK-----T~~eCi~hflq 256 (466)
..-||.++|+.||+|+-.| | .||...-++|... |..|-..+.-+
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 4888888888542 55565555444
No 59
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=68.49 E-value=7.3 Score=46.49 Aligned_cols=40 Identities=23% Similarity=0.539 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHH
Q 012334 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITH 253 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~h 253 (466)
.+||..+-..++.|.++|| +|-..||..|++||++|...+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 6799999999999999999 999999999999999998643
No 60
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=65.72 E-value=11 Score=40.85 Aligned_cols=46 Identities=22% Similarity=0.468 Sum_probs=42.4
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 211 ~~~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
.+...||++|..+|=.+.+.||.++.+|-+.+.-||-...+..|..
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 3568999999999999999999999999999999999999988864
No 61
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=63.24 E-value=6.9 Score=37.15 Aligned_cols=41 Identities=15% Similarity=0.387 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C-----CHHHHHHHhCCCCHHHHHHHH
Q 012334 213 RSDWTEKETLQLLEAIMHFG--D-----DWRKVAQHVSGKSEKDCITHF 254 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg--~-----nW~~IA~~VgtKT~~eCi~hf 254 (466)
.+.||.+++++|-+.|-.|+ | -...+++.++ ||...|-.+|
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 36799999999999999988 3 3667777774 8999999999
No 62
>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=63.15 E-value=12 Score=28.97 Aligned_cols=52 Identities=19% Similarity=0.318 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHHHHHHhCCCcce-eHHHHHhhccchHHHHHHHHHhhhhccccc
Q 012334 75 PRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (466)
Q Consensus 75 p~~Y~~~RN~ii~~yr~np~~yL-t~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (466)
-++|-.+++.|.+--. -|...| |..+.-+.+.--...+.+....|+.+|+|-
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 3678888888877433 378899 999988888888999999999999999985
No 63
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=62.42 E-value=13 Score=27.39 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHhCCCcce-eHHHHHhhccchHHHHHHHHHhhhhcccccC
Q 012334 78 YRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 78 Y~~~RN~ii~~yr~np~~yL-t~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (466)
|-.+|+.|+.... .|...| |..+....+.-....+.|...-|+.-|+|-.
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 8999888888789999999999999999853
No 64
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=61.48 E-value=3.8 Score=46.70 Aligned_cols=41 Identities=20% Similarity=0.459 Sum_probs=27.0
Q ss_pred ccccCCCCc-ccccccccc-CCCcccchhhhccCCCCCCCCCC
Q 012334 161 RLCNGCKTL-CTIACFACD-KYDLTLCARCYVRGNHRVGVSSS 201 (466)
Q Consensus 161 ~~C~~C~~~-~~~~~~~c~-k~d~~lC~~Cf~~G~~~~~~~s~ 201 (466)
-.|++|..- +.-..|.|. .+++++|..||..|+-..+|..|
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 369999753 222334554 35788999999999876555443
No 65
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=57.62 E-value=9.5 Score=41.38 Aligned_cols=52 Identities=17% Similarity=0.369 Sum_probs=45.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHh-CCCCHHHHHHHHhcCCCCCccc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHV-SGKSEKDCITHFIKLPFGQEFI 264 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~V-gtKT~~eCi~hflqLPIeD~fl 264 (466)
-..|+.-|-.++=||+++||.|+++|-+.. .=||-..++..|.-.--.|.|.
T Consensus 285 mEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYv 337 (693)
T KOG3554|consen 285 MEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYV 337 (693)
T ss_pred hhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHH
Confidence 368999999999999999999999996554 5599999999998888888887
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=57.60 E-value=17 Score=31.59 Aligned_cols=49 Identities=27% Similarity=0.392 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHhCCCcceeHHHHHhhcc-----chHHHHHHHHHhhhhcccccC
Q 012334 79 RYYRDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 79 ~~~RN~ii~~yr~np~~yLt~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy 128 (466)
-.-|..|++....++. .+|+.+.-..|. -+..+|.|..++|+.-|||.=
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 999999877764 377899999999999999974
No 67
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=57.03 E-value=19 Score=32.00 Aligned_cols=61 Identities=13% Similarity=0.344 Sum_probs=43.7
Q ss_pred ccCCCCccccccccccCCCcccchhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHh
Q 012334 163 CNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRKVAQHV 242 (466)
Q Consensus 163 C~~C~~~~~~~~~~c~k~d~~lC~~Cf~~G~~~~~~~s~dF~~~~~~~~~~~~WT~~E~l~LLEaIe~yg~nW~~IA~~V 242 (466)
|..|+..+.+..+.|..++..+ .|.|.. ..|.. =..|++.+++..-+..||-.+|++.+
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 8899998888877776544332 455422 12222 23588999999999999999999999
Q ss_pred CC
Q 012334 243 SG 244 (466)
Q Consensus 243 gt 244 (466)
|-
T Consensus 60 gi 61 (113)
T PF09862_consen 60 GI 61 (113)
T ss_pred CC
Confidence 83
No 68
>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=56.65 E-value=14 Score=30.51 Aligned_cols=42 Identities=19% Similarity=0.446 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHHh-------C------CCHHHHHHHhC-----CCCHHHHHHHHhc
Q 012334 215 DWTEKETLQLLEAIMHF-------G------DDWRKVAQHVS-----GKSEKDCITHFIK 256 (466)
Q Consensus 215 ~WT~~E~l~LLEaIe~y-------g------~nW~~IA~~Vg-----tKT~~eCi~hflq 256 (466)
.||.+.+..||+.+... + ..|+.|++.+. ..|..||..||-.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 49999999999998544 1 15899999885 3589999999866
No 69
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=56.20 E-value=31 Score=25.85 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=34.2
Q ss_pred HHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCC
Q 012334 89 YRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 89 yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
-..+|...+|+++..+.+.-+..++.|+..=|+.+|||--.
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 70
>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=54.84 E-value=28 Score=25.28 Aligned_cols=37 Identities=14% Similarity=0.202 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 219 KETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 219 ~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
+=+..||..++.-| --|.+||+.||- |+..|..+.-+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 34678999999988 789999999995 88888877654
No 71
>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=54.31 E-value=19 Score=25.87 Aligned_cols=26 Identities=19% Similarity=0.151 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 012334 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (466)
Q Consensus 219 ~E~l~LLEaIe~yg~nW~~IA~~Vgt 244 (466)
-|-..|.++++.++||..+.|+.+|-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 37788999999999999999999984
No 72
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=54.14 E-value=76 Score=32.48 Aligned_cols=61 Identities=21% Similarity=0.312 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH----HHHHHHHHHHHHHHHHHHHHH
Q 012334 374 ALARASVDASSLIEKEELDVEKAISGIVEVQMKEIQDKIIRF----ESLDLQMEEEWKQLEQVKNLL 436 (466)
Q Consensus 374 aL~aAa~kAk~la~~EErei~~Lv~~iie~QlkKlelKLk~f----eeLE~~le~Er~~Le~~r~~l 436 (466)
.+-.||.|+-.|++-| ++-+..-+-|.+|++++..+|+.- .+|+.-+++-+.+||+.|+.|
T Consensus 92 ~~~~aa~Rplel~e~E--kvlk~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRl 156 (338)
T KOG3647|consen 92 SLMSAAQRPLELLEVE--KVLKSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRL 156 (338)
T ss_pred HHHHHHcCCccHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777777543 344455556788999999999864 678889999999999988875
No 73
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=52.96 E-value=81 Score=30.79 Aligned_cols=38 Identities=16% Similarity=0.379 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 399 GIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLF 437 (466)
Q Consensus 399 ~iie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~ 437 (466)
.+++...+.+|...+-| +||+.|+.+|+.|-..|+.-+
T Consensus 160 ~~~~~k~~emE~Qv~IL-~lE~~L~~ar~~L~~lRk~~Y 197 (200)
T smart00307 160 SLHEGKTQEMEQQVEIL-KLENELEAARKKLAEIRKQHY 197 (200)
T ss_pred chHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence 34555555566666677 789999999999999887644
No 74
>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=52.91 E-value=36 Score=24.80 Aligned_cols=45 Identities=20% Similarity=0.222 Sum_probs=37.9
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccC
Q 012334 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 81 ~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (466)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+.|...|||.+
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 47788876655 5699999999999999999999999999999974
No 75
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=52.53 E-value=7.6 Score=41.96 Aligned_cols=43 Identities=12% Similarity=0.380 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~VgtKT~~eCi~hflq 256 (466)
.-+||..|-. ++.....||++...||+-+++|||+|....|++
T Consensus 470 ~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred cCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 4789998877 788888999999999999999999999999987
No 76
>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=52.03 E-value=35 Score=25.55 Aligned_cols=45 Identities=22% Similarity=0.311 Sum_probs=35.1
Q ss_pred HHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCCCC
Q 012334 84 SIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 84 ~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
.|+......+ +++.+..+.+.-+...+.|+..-|...|+|+....
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~ 55 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE 55 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence 3444433444 89999888888899999999999999999996443
No 77
>smart00595 MADF subfamily of SANT domain.
Probab=51.44 E-value=12 Score=30.61 Aligned_cols=28 Identities=14% Similarity=0.507 Sum_probs=24.3
Q ss_pred CHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 012334 234 DWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (466)
Q Consensus 234 nW~~IA~~VgtKT~~eCi~hflqLPIeD~fl 264 (466)
-|..||..+|. |.++|..+|-. +-+.|.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~--LR~~y~ 56 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKN--LRDRYR 56 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHH--HHHHHH
Confidence 69999999997 99999999998 446665
No 78
>PHA00442 host recBCD nuclease inhibitor
Probab=49.78 E-value=17 Score=28.26 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHh
Q 012334 218 EKETLQLLEAIMHFG-DDWRKVAQHV 242 (466)
Q Consensus 218 ~~E~l~LLEaIe~yg-~nW~~IA~~V 242 (466)
-+-....|++++.+| +||+.+.+.+
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 355678899999999 9999988765
No 79
>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=49.48 E-value=28 Score=25.83 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=34.8
Q ss_pred HHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccC
Q 012334 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 85 ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (466)
|++..... ...+|+++.-+.+.-....+.|+..-|+.+|++..
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 55655554 44489999999999999999999999999999864
No 80
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=49.13 E-value=61 Score=25.67 Aligned_cols=52 Identities=15% Similarity=0.126 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCCCC
Q 012334 80 YYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 80 ~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
..++.|+.....++..-+|..+.-+.|.-+...+.|+..=|+.-|+|.+...
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 81
>PRK09462 fur ferric uptake regulator; Provisional
Probab=48.18 E-value=31 Score=31.30 Aligned_cols=46 Identities=17% Similarity=0.381 Sum_probs=38.6
Q ss_pred HHHHHHHHHhCCCcceeHHHHHhhcc-----chHHHHHHHHHhhhhccccc
Q 012334 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLIN 127 (466)
Q Consensus 82 RN~ii~~yr~np~~yLt~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlIN 127 (466)
|-.|++.....+...+|+.+.-..|. -+..+|.|...+|+.-|||.
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 77788877766678999999876664 27899999999999999997
No 82
>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=46.41 E-value=39 Score=28.86 Aligned_cols=46 Identities=22% Similarity=0.335 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCCcceeHHHHHhhcc-----chHHHHHHHHHhhhhcccccC
Q 012334 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 82 RN~ii~~yr~np~~yLt~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy 128 (466)
|-.|++....+ ...+|+.+.-..|. -+..++.|..++|..-|||.-
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 67788877765 68999999877773 378999999999999999984
No 83
>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=46.40 E-value=67 Score=23.12 Aligned_cols=44 Identities=32% Similarity=0.403 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccc
Q 012334 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLI 126 (466)
Q Consensus 81 ~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlI 126 (466)
.+-.|++.-+.||. +|.++..+.+.-....+.|...-|+.-|+|
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 34567776777766 999999988888999999999999999997
No 84
>KOG3859 consensus Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]
Probab=45.97 E-value=1.5e+02 Score=30.91 Aligned_cols=49 Identities=24% Similarity=0.311 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHH-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 012334 401 VEVQMKEIQDKII-RFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFHKSN 449 (466)
Q Consensus 401 ie~QlkKlelKLk-~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~~~~ 449 (466)
-+..||+.|--|- .|+.|-..-..|+..||..|.+|=.|+..|.+++..
T Consensus 353 kE~elke~Ekel~~kf~~lkr~h~eEk~kle~~rr~Leee~~~f~~rk~~ 402 (406)
T KOG3859|consen 353 KEAELKEAEKELHEKFDRLKRLHQEEKKKLEEKRKQLEEEVNAFQRRKTA 402 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667888887775 799999999999999999999999999999887543
No 85
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=43.37 E-value=45 Score=28.13 Aligned_cols=45 Identities=27% Similarity=0.355 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHH-------hhccchH---HHHHHHHHhhhhcc
Q 012334 76 RVYRYYRDSIVKHYRENPSRKITFTDVR-------RTLVGDV---GSIRRVFDFLETWG 124 (466)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLt~t~~r-------~~l~gDv---~~i~Rvh~FLe~wG 124 (466)
++-..+||-|+.+=-.| +|+.+.. |-|+-|+ ..++|||.||.++.
T Consensus 36 ~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~~ 90 (92)
T KOG4479|consen 36 DIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKHA 90 (92)
T ss_pred HHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHHh
Confidence 56778999998876555 7777643 3556565 78999999998763
No 86
>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=43.06 E-value=42 Score=26.86 Aligned_cols=43 Identities=14% Similarity=0.387 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHHHHHHHhC-------CC--HHHHHHHhC-CCCHHHHHHHHhc
Q 012334 214 SDWTEKETLQLLEAIMHFG-------DD--WRKVAQHVS-GKSEKDCITHFIK 256 (466)
Q Consensus 214 ~~WT~~E~l~LLEaIe~yg-------~n--W~~IA~~Vg-tKT~~eCi~hflq 256 (466)
...|.+|+..|++-|..+. || |.+.++.-. ..|-+-=..||++
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 4689999999999996553 55 999999877 5788888899976
No 87
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=40.92 E-value=1.6e+02 Score=26.67 Aligned_cols=46 Identities=13% Similarity=0.214 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 399 GIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFH 446 (466)
Q Consensus 399 ~iie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~ 446 (466)
..++.|+++||.+++.+.++-..|+++ +=..++.++.-+-+++.++
T Consensus 84 ~~l~~~i~~Le~~l~~L~~~~~~l~~~--~~~~~~~~~~~~~~~~~~~ 129 (134)
T cd04779 84 QLVCDQIDGLEHRLKQLKPIASQTDRA--QRMKMTKELSQQVLTLIQS 129 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHhcCHHhHHHHHH
Confidence 358899999999999999999988874 5667888888888777764
No 88
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=40.60 E-value=37 Score=40.78 Aligned_cols=44 Identities=9% Similarity=0.232 Sum_probs=37.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC------------CCCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS------------GKSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg-~nW~~IA~~Vg------------tKT~~eCi~hflq 256 (466)
+..||.+|+..||-.+.+|| |+|+.|-+.+- +||+.++..|...
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~ 982 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDT 982 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHH
Confidence 46799999999999999999 99999988773 7899998766543
No 89
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=39.36 E-value=20 Score=43.28 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=25.9
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHH
Q 012334 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVA 239 (466)
Q Consensus 212 ~~~~WT~~E~l~LLEaIe~yg-~nW~~IA 239 (466)
...+|..+++..||=||-+|| |+|+.|-
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
>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=38.77 E-value=97 Score=25.88 Aligned_cols=53 Identities=21% Similarity=0.228 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCC
Q 012334 76 RVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
++-.+|=..||+.|... .+.+.-.+.-+.|.-+-..|..+..-|+..|||-=+
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 45667788999999996 788887777777777889999999999999999643
No 91
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=38.66 E-value=18 Score=38.04 Aligned_cols=38 Identities=24% Similarity=0.649 Sum_probs=26.0
Q ss_pred ccccccCCCCcc-c---cccccccCCCcccchhhhccCCCCCCC
Q 012334 159 SKRLCNGCKTLC-T---IACFACDKYDLTLCARCYVRGNHRVGV 198 (466)
Q Consensus 159 ~k~~C~~C~~~~-~---~~~~~c~k~d~~lC~~Cf~~G~~~~~~ 198 (466)
+...|++|.... . ..|-.|. .+.+|.+||-.|.-+..|
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 356799997553 2 3444555 577999999999875433
No 92
>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=37.98 E-value=16 Score=24.37 Aligned_cols=27 Identities=22% Similarity=0.602 Sum_probs=11.2
Q ss_pred cccCCCCcccc-ccccccCCCcccchhh
Q 012334 162 LCNGCKTLCTI-ACFACDKYDLTLCARC 188 (466)
Q Consensus 162 ~C~~C~~~~~~-~~~~c~k~d~~lC~~C 188 (466)
.|+.|+..... ..|.|...|+.+...|
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 68899988765 7788888788887766
No 93
>PF01608 I_LWEQ: I/LWEQ domain; InterPro: IPR002558 I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin P26039 from SWISSPROT and yeast Sla2p P33338 from SWISSPROT interact with F-actin []. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks []. I/LWEQ domains can be placed into four major groups based on sequence similarity: Metazoan talin. Dictyostelium discoideum (Slime mould) TalA/TalB P54633 from SWISSPROT and SLA110. Metazoan Hip1p O00291 from SWISSPROT. Saccharomyces cerevisiae Sla2p P33338 from SWISSPROT. ; GO: 0003779 actin binding; PDB: 2QDQ_A 2JSW_A 1R0D_B.
Probab=37.94 E-value=2.1e+02 Score=26.86 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHH-hHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 400 IVEVQMKEIQDKII-RFESLDLQMEEEWKQLEQVKNLLFV 438 (466)
Q Consensus 400 iie~QlkKlelKLk-~feeLE~~le~Er~~Le~~r~~l~~ 438 (466)
+-.+|.|++|+--+ ..=+||+.|+.+|+.|-..|+.-+-
T Consensus 111 ls~~~~k~~eMe~Qv~iL~lE~eLe~ar~kL~~lRk~~Y~ 150 (152)
T PF01608_consen 111 LSLHQAKRQEMEAQVRILKLEKELEKARKKLAELRKAHYH 150 (152)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---
T ss_pred hcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 34444444443322 2335789999999999888876543
No 94
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=37.00 E-value=3.5e+02 Score=27.95 Aligned_cols=49 Identities=8% Similarity=0.122 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012334 399 GIVEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFHK 447 (466)
Q Consensus 399 ~iie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~~ 447 (466)
.-++.++++++.++..+++.|..+.+++..+.....++..+|.++..+.
T Consensus 74 ~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q~ 122 (314)
T PF04111_consen 74 EELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQY 122 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788899999999999999999999988888888777777776553
No 95
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=36.84 E-value=50 Score=34.50 Aligned_cols=53 Identities=21% Similarity=0.411 Sum_probs=46.5
Q ss_pred ChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhccccc
Q 012334 74 NPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (466)
Q Consensus 74 tp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (466)
.|..|+.+.-.||..+.. ....+|.++|++.+.-|.+-.-+|++|.-.-|.|-
T Consensus 377 ~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 377 SPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred CCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 589999999999999887 47789999999777769999999999998888773
No 96
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=36.67 E-value=64 Score=26.02 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=35.0
Q ss_pred HHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCC
Q 012334 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 85 ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
|++....+ ...+|+++.-+.+.-....+.|....|+.+|+|-..
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 247999999988888999999999999999999654
No 97
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=33.94 E-value=2.7e+02 Score=30.77 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=25.2
Q ss_pred ChHHHHHHHHHHHHHHHhCCCcceeHHHH----HhhccchHHH
Q 012334 74 NPRVYRYYRDSIVKHYRENPSRKITFTDV----RRTLVGDVGS 112 (466)
Q Consensus 74 tp~~Y~~~RN~ii~~yr~np~~yLt~t~~----r~~l~gDv~~ 112 (466)
..-..++||-.=|..|..+-.+-|.+-.+ .++|+|-...
T Consensus 175 necKmVd~rG~kVAsF~i~g~emiCLPQafdlFLKhlVGGLHT 217 (641)
T KOG3915|consen 175 NECKMVDLRGAKVASFTIEGCELICLPQAFDLFLKHLVGGLHT 217 (641)
T ss_pred cceeeeeecCceeeEEEecCceEEecHHHHHHHHHHHhchHHH
Confidence 34466777777777777777777666554 4566665444
No 98
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=33.86 E-value=2.4e+02 Score=23.92 Aligned_cols=51 Identities=16% Similarity=0.196 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHhhcCC
Q 012334 401 VEVQMKEIQDKIIRFESLDLQMEEEWKQLE----QVKNLLFVDQLSVLFHKSNAR 451 (466)
Q Consensus 401 ie~QlkKlelKLk~feeLE~~le~Er~~Le----~~r~~l~~dRl~~~~~~~~~~ 451 (466)
++.++++++.||.+.++=.++|+.-...|+ +.|-.-+..|-.++-+-+.-+
T Consensus 6 l~~e~e~~~~kl~q~e~~~k~L~nr~k~l~k~eRK~RtHRLi~rGa~lEsi~~e~ 60 (86)
T PF12958_consen 6 LQAEIEKAEKKLEQAEHKIKQLENRKKKLEKKERKERTHRLIERGAILESIFPEP 60 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHhhcc
Confidence 467788888888888888888888888775 577778888888888766544
No 99
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=33.74 E-value=1.8e+02 Score=23.40 Aligned_cols=42 Identities=7% Similarity=0.096 Sum_probs=29.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 405 MKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFH 446 (466)
Q Consensus 405 lkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~ 446 (466)
|+.|+.||.++=.+-.-+..|-..|-.+...+-.||..+..+
T Consensus 2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ek 43 (65)
T TIGR02449 2 LQALAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEK 43 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566777777777777777777777777777777777666654
No 100
>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=32.80 E-value=1.3e+02 Score=22.84 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=31.5
Q ss_pred CCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCCCC
Q 012334 92 NPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 92 np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
+....+|.++..+.+.-|...+.|+..=|...|||.-..+
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 4789999999999999999999999999999999965544
No 101
>COG2916 Hns DNA-binding protein H-NS [General function prediction only]
Probab=32.38 E-value=3.9e+02 Score=24.37 Aligned_cols=37 Identities=11% Similarity=0.061 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 012334 393 VEKAISGIVEVQMKEIQDKIIRFESLDLQMEEEWKQL 429 (466)
Q Consensus 393 i~~Lv~~iie~QlkKlelKLk~feeLE~~le~Er~~L 429 (466)
|..|...+-+.+++-||..++.|+.+...-..|....
T Consensus 5 ~r~l~~~~~e~~~e~lee~~ek~eq~~~~r~~e~~~~ 41 (128)
T COG2916 5 IRTLRAMARETYLELLEEMLEKEEQVVQERQEEEAAA 41 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6677888888999999888888777665555444433
No 102
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=31.73 E-value=75 Score=29.01 Aligned_cols=49 Identities=16% Similarity=0.304 Sum_probs=38.6
Q ss_pred HHHHHHHHHhCCCcceeHHHHHhhccc-----hHHHHHHHHHhhhhcccccCCCC
Q 012334 82 RDSIVKHYRENPSRKITFTDVRRTLVG-----DVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 82 RN~ii~~yr~np~~yLt~t~~r~~l~g-----Dv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
|-.|++....++.. +|+.+.-+.|.. ....+.|+..||+.-|||+-...
T Consensus 23 R~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 23 RLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 77888866665444 999998776652 47899999999999999985544
No 103
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=31.72 E-value=1.3e+02 Score=27.27 Aligned_cols=57 Identities=16% Similarity=0.338 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHHHHHHh---CCCcce-eHHHHHhhccchHHHHHHHHHhhhhcccccCCCC
Q 012334 75 PRVYRYYRDSIVKHYRE---NPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 75 p~~Y~~~RN~ii~~yr~---np~~yL-t~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
-.+|.+|.|.|...-.. .|...| |+.+--..+.-+.+.+.|.+.-||+-|+|.-...
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg 70 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG 70 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 46999999999887654 666655 5555555566789999999999999999985543
No 104
>PRK06474 hypothetical protein; Provisional
Probab=31.08 E-value=91 Score=29.47 Aligned_cols=48 Identities=15% Similarity=0.163 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHhhcc-chHHHHHHHHHhhhhcccccCC
Q 012334 81 YRDSIVKHYRENPSRKITFTDVRRTLV-GDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 81 ~RN~ii~~yr~np~~yLt~t~~r~~l~-gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
.|-.|+..-..++. .+|++++...+. -....+.|....|+..|||.--
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 58889987777654 499999988774 3568899999999999999843
No 105
>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=31.01 E-value=39 Score=27.43 Aligned_cols=24 Identities=38% Similarity=0.621 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 012334 217 TEKETLQLLEAIMHFGDDWRKVAQHVSG 244 (466)
Q Consensus 217 T~~E~l~LLEaIe~yg~nW~~IA~~Vgt 244 (466)
|.++.-+||+. |.||...|+++|-
T Consensus 1 ~r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 1 TRERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred CHHHHHHHhCC----CCCHHHHHHHcCc
Confidence 34677788887 9999999999985
No 106
>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=30.62 E-value=96 Score=23.02 Aligned_cols=35 Identities=26% Similarity=0.281 Sum_probs=30.8
Q ss_pred eeHHHHHhhccchHHHHHHHHHhhhhcccccCCCC
Q 012334 97 ITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 97 Lt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
+|.++.-+.+..+...+.|+.+-|++.|||.-..+
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 99999988999999999999999999999976544
No 107
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=28.93 E-value=3.1e+02 Score=27.16 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012334 401 VEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFHK 447 (466)
Q Consensus 401 ie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~~ 447 (466)
.+.+|+|-|..+.++.+|=+..-+||.+...+=|.|+.+-+.+.++.
T Consensus 24 A~EElRk~eeqi~~L~~Ll~~a~~ERDEAr~qlq~Ll~~~~~l~~~~ 70 (214)
T PF07795_consen 24 ANEELRKREEQIAHLKDLLKKAYQERDEAREQLQKLLLEKLSLQQQQ 70 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccC
Confidence 45567888888999999999999999999999999998887777655
No 108
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.77 E-value=3.9e+02 Score=27.31 Aligned_cols=59 Identities=14% Similarity=0.208 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH---HHHHHHHHHH---HHHHHHHHHHHHHHHHhhc
Q 012334 390 ELDVEKAISGIVEVQMKEIQDKIIRFESLDL---QMEEEWKQLE---QVKNLLFVDQLSVLFHKSN 449 (466)
Q Consensus 390 Erei~~Lv~~iie~QlkKlelKLk~feeLE~---~le~Er~~Le---~~r~~l~~dRl~~~~~~~~ 449 (466)
+.+|++|.+.|=+.| +|++.+=+.+++++. .++.|-..|+ ..|+.+|.+|++-++....
T Consensus 51 q~ei~~L~~qi~~~~-~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I~~r~~~l~~raRAmq~nG~ 115 (265)
T COG3883 51 QNEIESLDNQIEEIQ-SKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQVNGT 115 (265)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 456777776653332 333333333444333 3444444444 5788899999998876544
No 109
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.25 E-value=86 Score=28.54 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 218 ~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
++-+..||+.++.-| -.|.+||+.+|- |+..|..++-+|
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 356889999999998 799999999985 999999998885
No 110
>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=28.19 E-value=57 Score=29.20 Aligned_cols=36 Identities=14% Similarity=0.154 Sum_probs=25.5
Q ss_pred CcceeHHHHHhhccchHHHHHHHHHhhhhcccccCC
Q 012334 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 94 ~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
.+|||..+......-+-..+..|.+||...||=...
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 689999999988888889999999999999985544
No 111
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=27.90 E-value=1.6e+02 Score=20.69 Aligned_cols=34 Identities=26% Similarity=0.316 Sum_probs=30.4
Q ss_pred cceeHHHHHhhccchHHHHHHHHHhhhhcccccC
Q 012334 95 RKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 95 ~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (466)
..+|+.+..+.+.-....+.|....|+.-|+|-.
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 112
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=27.82 E-value=79 Score=29.54 Aligned_cols=50 Identities=20% Similarity=0.312 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhcc-----chHHHHHHHHHhhhhccccc
Q 012334 72 SKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLIN 127 (466)
Q Consensus 72 ~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlIN 127 (466)
-.||. |-.|++....+ .+.+|..+.-..|. -+..+|.|...+|+.-|||+
T Consensus 23 R~T~q-----R~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 23 RLTPQ-----RLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred CCCHH-----HHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEE
Confidence 45665 66677766665 68999999876664 27899999999999999997
No 113
>PRK00846 hypothetical protein; Provisional
Probab=27.67 E-value=3.6e+02 Score=22.44 Aligned_cols=53 Identities=11% Similarity=0.144 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHH----HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHh
Q 012334 395 KAISGIVEVQMKEIQDKIIRFE----SLDLQMEEEWKQLEQVKNL--LFVDQLSVLFHK 447 (466)
Q Consensus 395 ~Lv~~iie~QlkKlelKLk~fe----eLE~~le~Er~~Le~~r~~--l~~dRl~~~~~~ 447 (466)
.|-..-++..+-.||.||.|-+ +|...+-+-.+++++++++ ++.+||.=+...
T Consensus 5 ~~~~~~le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~~s 63 (77)
T PRK00846 5 SLRDQALEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVRST 63 (77)
T ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3445667788999999999764 5566666666677765554 667777666643
No 114
>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=27.53 E-value=1.1e+02 Score=23.24 Aligned_cols=27 Identities=11% Similarity=0.324 Sum_probs=23.2
Q ss_pred CcceeHHHHHhhcc----chHHHHHHHHHhh
Q 012334 94 SRKITFTDVRRTLV----GDVGSIRRVFDFL 120 (466)
Q Consensus 94 ~~yLt~t~~r~~l~----gDv~~i~Rvh~FL 120 (466)
..++|..+....|. .+...+.||.+||
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 7889999999998
No 115
>PF15346 ARGLU: Arginine and glutamate-rich 1
Probab=27.03 E-value=4.8e+02 Score=24.39 Aligned_cols=38 Identities=18% Similarity=0.243 Sum_probs=22.7
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 408 IQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLF 445 (466)
Q Consensus 408 lelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~ 445 (466)
-+-.-+.-++||.+|+.-++.++..++.+..+|++++-
T Consensus 71 eEeer~~~eELe~ileen~rkvEEAQrk~aeEr~~~~E 108 (149)
T PF15346_consen 71 EEEERKKREELEKILEENRRKVEEAQRKLAEERLRMEE 108 (149)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555666666666666666666666666665543
No 116
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=26.24 E-value=2.7e+02 Score=22.25 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHhHHH----HHHHHHHHHHHHHHHHHH
Q 012334 401 VEVQMKEIQDKIIRFES----LDLQMEEEWKQLEQVKNL 435 (466)
Q Consensus 401 ie~QlkKlelKLk~fee----LE~~le~Er~~Le~~r~~ 435 (466)
++..|..||.||.|.++ |...+-+--+++++.+.+
T Consensus 2 le~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~ 40 (69)
T PF04102_consen 2 LEERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQ 40 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788899999998754 444444445555554443
No 117
>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=26.18 E-value=44 Score=23.48 Aligned_cols=29 Identities=28% Similarity=0.658 Sum_probs=19.3
Q ss_pred ccccCCCCc-cccccccccCCCcccchhhhccC
Q 012334 161 RLCNGCKTL-CTIACFACDKYDLTLCARCYVRG 192 (466)
Q Consensus 161 ~~C~~C~~~-~~~~~~~c~k~d~~lC~~Cf~~G 192 (466)
..|..|... ....|..|. ..+|..|+..+
T Consensus 4 ~~C~~H~~~~~~~~C~~C~---~~~C~~C~~~~ 33 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCN---EPLCSECTVSG 33 (42)
T ss_dssp SB-SSTTTSBEEEEETTTT---EEEEHHHHHTS
T ss_pred ccCccCCccceEEEecCCC---CccCccCCCCC
Confidence 457777764 445555554 67999999987
No 118
>PF11278 DUF3079: Protein of unknown function (DUF3079); InterPro: IPR021430 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=25.76 E-value=63 Score=24.72 Aligned_cols=23 Identities=30% Similarity=0.902 Sum_probs=14.9
Q ss_pred cccccccccCCCCcccccccccc
Q 012334 156 KETSKRLCNGCKTLCTIACFACD 178 (466)
Q Consensus 156 ~~~~k~~C~~C~~~~~~~~~~c~ 178 (466)
+..|+..|-+|...|...-..|.
T Consensus 9 P~hPERiCWGCD~YC~a~~l~CG 31 (52)
T PF11278_consen 9 PKHPERICWGCDRYCPADSLACG 31 (52)
T ss_pred CCCccceeeccccccChhhhccc
Confidence 34567889999887655444443
No 119
>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=25.47 E-value=1e+02 Score=22.78 Aligned_cols=53 Identities=17% Similarity=0.266 Sum_probs=36.9
Q ss_pred hHHHHHHHHHHHHHHHhCCCcce-eHHHHHhhccchHHHHHHHHHhhhhcccccC
Q 012334 75 PRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (466)
Q Consensus 75 p~~Y~~~RN~ii~~yr~np~~yL-t~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 128 (466)
.++|-.+++.|+..- ..+...+ |..+..+.+.-....+.+...=|+..|+|-.
T Consensus 4 ~~~~~~i~~~i~~~~-~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 4 EQIADQLREAILSGE-LKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHHHHHHHHHHHcCC-CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 355666666665531 2333344 4888777777788999999999999999854
No 120
>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=25.12 E-value=1.5e+02 Score=23.25 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhccccc
Q 012334 79 RYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (466)
Q Consensus 79 ~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 127 (466)
.+||++|-+ ...+|+.+--+.+.-+...+.-+.++|++-|.|.
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 456666654 6678999999999999999999999999999986
No 121
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=24.52 E-value=1.1e+02 Score=29.11 Aligned_cols=67 Identities=10% Similarity=0.071 Sum_probs=48.9
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCCC
Q 012334 63 PEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (466)
Q Consensus 63 peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (466)
|.|=+-...+.+..+|-.||..|+. -+..|...|+-.+....+.---..+..-..-|+.-|||-...
T Consensus 2 ~~~~~~~~~~~~e~v~~~l~~~I~~-g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 2 PGTEKTQHISLTLQVENDLKHQLSI-GALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHh-CCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence 4444433445667899999999997 566799999987766666655566677777799999997543
No 122
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=24.44 E-value=2.8e+02 Score=27.08 Aligned_cols=26 Identities=8% Similarity=0.033 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 418 LDLQMEEEWKQLEQVKNLLFVDQLSV 443 (466)
Q Consensus 418 LE~~le~Er~~Le~~r~~l~~dRl~~ 443 (466)
-+..|+.+|.+-++.+++.+...-.|
T Consensus 85 ~~~~~e~~r~~fekekqq~~~~~t~~ 110 (228)
T PRK06800 85 QMKEIEAARQQFQKEQQETAYEWTEL 110 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666666655444433
No 123
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=24.03 E-value=55 Score=26.91 Aligned_cols=31 Identities=26% Similarity=0.535 Sum_probs=21.8
Q ss_pred CcceeHHHHHhhc--cc-hHHHHHHHHHhhhhcc
Q 012334 94 SRKITFTDVRRTL--VG-DVGSIRRVFDFLETWG 124 (466)
Q Consensus 94 ~~yLt~t~~r~~l--~g-Dv~~i~Rvh~FLe~wG 124 (466)
++.++-.+-+..- +| |..-|--|-.||.+||
T Consensus 46 neeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 46 NEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred cHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 5666654433322 25 8888999999999999
No 124
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=23.89 E-value=3.5e+02 Score=21.06 Aligned_cols=22 Identities=23% Similarity=0.323 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 012334 416 ESLDLQMEEEWKQLEQVKNLLF 437 (466)
Q Consensus 416 eeLE~~le~Er~~Le~~r~~l~ 437 (466)
.|++++|..-|.+||..|...+
T Consensus 33 ~EY~kiLk~r~~~lEevKrk~L 54 (56)
T PF08112_consen 33 MEYEKILKQRRKELEEVKRKAL 54 (56)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 5788999999999998887654
No 125
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=23.76 E-value=77 Score=33.06 Aligned_cols=96 Identities=16% Similarity=0.221 Sum_probs=53.1
Q ss_pred cccccCCCCccccccccccCCCcccchhhhccCCCCCCCCCCC-ceecccCcccCCCCCHHHHHHHHHHHHHhCCCHHHH
Q 012334 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSD-FRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRKV 238 (466)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k~d~~lC~~Cf~~G~~~~~~~s~d-F~~~~~~~~~~~~WT~~E~l~LLEaIe~yg~nW~~I 238 (466)
-..|.-|+..- ..|..| ...+.||.+|-.- ++. +-.|- |+| ...-+.||.+|..+|.-+=...-+.|.+-
T Consensus 20 Nk~CaDCga~~-P~W~S~-nlGvfiCi~Cagv--HRs-LGvhiS~VK----SitLD~wt~~~l~~m~~gGN~~a~~~~e~ 90 (319)
T COG5347 20 NKKCADCGAPN-PTWASV-NLGVFLCIDCAGV--HRS-LGVHISKVK----SLTLDNWTEEELRRMEVGGNSNANRFYEK 90 (319)
T ss_pred cCccccCCCCC-CceEec-ccCeEEEeecchh--hhc-cccceeeee----eeecccCCHHHHHHHHHhcchhhhhHhcc
Confidence 35798898875 666665 4678899999653 211 11222 222 12346899999887765211111233322
Q ss_pred HHHh----C--CCCHHHHHHHHhc-CCCCCccc
Q 012334 239 AQHV----S--GKSEKDCITHFIK-LPFGQEFI 264 (466)
Q Consensus 239 A~~V----g--tKT~~eCi~hflq-LPIeD~fl 264 (466)
---+ . .+.-...+.+|++ ++.+-.|.
T Consensus 91 ~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~ 123 (319)
T COG5347 91 NLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFI 123 (319)
T ss_pred CCCcccccccccccCHHHHHHHHHHHHHhhhcc
Confidence 1111 2 2456667777776 66665555
No 126
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=23.55 E-value=47 Score=27.76 Aligned_cols=53 Identities=21% Similarity=0.492 Sum_probs=16.2
Q ss_pred cccccccccCCCCccc-----cccccccCCCcccchhhhc----cCCCCCCCCCCCceeccc
Q 012334 156 KETSKRLCNGCKTLCT-----IACFACDKYDLTLCARCYV----RGNHRVGVSSSDFRRVEI 208 (466)
Q Consensus 156 ~~~~k~~C~~C~~~~~-----~~~~~c~k~d~~lC~~Cf~----~G~~~~~~~s~dF~~~~~ 208 (466)
.+.....|..|+.+++ .....|....+.+|..||. .|+----.-...|++..-
T Consensus 5 k~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kg 66 (80)
T PF14569_consen 5 KNLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRHKG 66 (80)
T ss_dssp S--SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----TT
T ss_pred hhcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccccC
Confidence 3444568999998865 2344555556888999985 233211122356666554
No 127
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=23.44 E-value=24 Score=30.90 Aligned_cols=59 Identities=24% Similarity=0.493 Sum_probs=27.0
Q ss_pred ccccCCCCccccccccccCCCcccchhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHH
Q 012334 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEA 227 (466)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k~d~~lC~~Cf~~G~~~~~~~s~dF~~~~~~~~~~~~WT~~E~l~LLEa 227 (466)
..|.-|+..-. .+.+..+.+.+|..|..- ++. +..|.. ++.. ..-+.||.+|...|.++
T Consensus 14 ~~CaDCg~~~p--~w~s~~~GiflC~~Cag~--HR~-lg~~is-~VkS--i~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 14 KVCADCGAPNP--TWASLNYGIFLCLECAGI--HRS-LGVHIS-RVKS--ITMDNWSPEEVQRMREG 72 (116)
T ss_dssp TB-TTT-SBS----EEETTTTEEE-HHHHHH--HHH-HTTTT---EEE--TTTS---HHHHHHHHHS
T ss_pred CcCCCCCCCCC--CEEEeecChhhhHHHHHH--HHH-hcccch-hccc--cccCCCCHHHHHHHHHH
Confidence 56888875322 334445678899999853 211 111211 1111 12346999998887654
No 128
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=22.99 E-value=57 Score=35.42 Aligned_cols=56 Identities=21% Similarity=0.435 Sum_probs=32.4
Q ss_pred cccccCCCCccccccccccCCCcccchhhhcc-CCCCCCCCCCCceecccCcccCCCCCHHHHHHH
Q 012334 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVR-GNHRVGVSSSDFRRVEISEEARSDWTEKETLQL 224 (466)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k~d~~lC~~Cf~~-G~~~~~~~s~dF~~~~~~~~~~~~WT~~E~l~L 224 (466)
.+.|.-|++.-.. |. ...|.+.||.+|-.. .+.+.|++ |+|-.+ . +.||-.+...+
T Consensus 23 NKvCFDCgAknPt-Wa-SVTYGIFLCiDCSAvHRnLGVHiS---FVRSTn---L-DsWs~~qLR~M 79 (454)
T KOG0706|consen 23 NKVCFDCGAKNPT-WA-SVTYGIFLCIDCSAVHRNLGVHIS---FVRSTN---L-DSWSWEQLRRM 79 (454)
T ss_pred CceecccCCCCCC-ce-eecceEEEEEecchhhhccccceE---EEeecc---c-ccCCHHHHhHh
Confidence 3567777754211 11 124678899999764 33455544 776432 2 34998886644
No 129
>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=22.85 E-value=45 Score=29.34 Aligned_cols=27 Identities=30% Similarity=0.767 Sum_probs=19.7
Q ss_pred cccccCCCCccccccccccCCCcccchhhhcc
Q 012334 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVR 191 (466)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k~d~~lC~~Cf~~ 191 (466)
|..|..||. ++|-.++ +.++|+.|-..
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 678988875 5776666 66789988654
No 130
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=22.77 E-value=2.4e+02 Score=21.10 Aligned_cols=50 Identities=16% Similarity=0.080 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhC-----CCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCCC
Q 012334 81 YRDSIVKHYREN-----PSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (466)
Q Consensus 81 ~RN~ii~~yr~n-----p~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (466)
+..+++..+... ....+|..+.-..+......+.|+..-|+..|+|-+..
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 344555544433 23568999988888889999999999999999997543
No 131
>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=22.55 E-value=58 Score=27.02 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 012334 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (466)
Q Consensus 219 ~E~l~LLEaIe~yg~nW~~IA~~Vgt 244 (466)
++.-.+|+.-...|+||...|+++|-
T Consensus 7 ~~Lc~~LD~~~~~g~dWr~LA~~Lgl 32 (83)
T cd08781 7 QKLCSSLDPPNPRGNDWRLLAKKLSV 32 (83)
T ss_pred HHHHHHcCCCCCCCCCHHHHHHHhCc
Confidence 45566677666678899999999993
No 132
>PF09444 MRC1: MRC1-like domain; InterPro: IPR018564 This putative domain is found in the most conserved region in mediator of replication checkpoint protein 1. This protein is a component of the replisome and is required for Rad3-dependent activation of the checkpoint kinase Cds1 in response to replication fork arrest [].
Probab=22.35 E-value=1.8e+02 Score=27.08 Aligned_cols=64 Identities=16% Similarity=0.174 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHhH-HHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 376 ARASVDASSLIEKEELDVEKAISGIVEVQMKEIQ------DKIIRF-ESLDLQMEEEWKQLEQVKNLLFVD 439 (466)
Q Consensus 376 ~aAa~kAk~la~~EErei~~Lv~~iie~QlkKle------lKLk~f-eeLE~~le~Er~~Le~~r~~l~~d 439 (466)
..++..|......-++++++|+..|++-.+.|=- +=|.-= ++.+.-..+-|+++.++|+.++.+
T Consensus 57 el~~~~~~~~~~~D~k~v~kl~~Di~~G~lRrRr~~~g~d~dlsDseDe~~~~~R~krr~~~~~rk~ll~d 127 (145)
T PF09444_consen 57 ELAALFADEEREQDEKEVEKLLKDITTGGLRRRRGRNGDDLDLSDSEDEDLARRRRKRREFAKMRKRLLED 127 (145)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHhcchhhcccCCCCcCccCccchHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4456777778888999999999999999888542 111110 344445555577888888877764
No 133
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.12 E-value=1.2e+02 Score=27.88 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 218 ~~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
++-+.++|..++.-| -.|.+||+.||- |+..|..++-+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 556889999999998 789999999984 888998888875
No 134
>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=22.00 E-value=1.6e+02 Score=28.10 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCC
Q 012334 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 81 ~RN~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
.|+.||..-..++ .+|+.+....+.-+..++.|...-|+.-|||-..
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 3778888665543 3999999988988999999999999999999754
No 135
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=21.49 E-value=54 Score=35.11 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=37.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHH-----hCC-CCHHHHHHHHhc
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQH-----VSG-KSEKDCITHFIK 256 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~-----Vgt-KT~~eCi~hflq 256 (466)
+..||.+|+..|.+.-..|.=.|--||+. .++ ||.++-..+|..
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 57899999999999999999667666665 455 999999999965
No 136
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=21.37 E-value=4e+02 Score=26.04 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 012334 423 EEEWKQLEQVKNLLFVDQLSVLFHK 447 (466)
Q Consensus 423 e~Er~~Le~~r~~l~~dRl~~~~~~ 447 (466)
+.|++.|+..|++|++||-.+-.+.
T Consensus 58 ~~eqQ~l~~er~~l~~er~~~~~~~ 82 (228)
T PRK06800 58 RQEQQKLERERQQLLADREQFQEHV 82 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556666666666666555443
No 137
>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=21.26 E-value=3.2e+02 Score=19.97 Aligned_cols=41 Identities=29% Similarity=0.385 Sum_probs=33.3
Q ss_pred HHHHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcc
Q 012334 83 DSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWG 124 (466)
Q Consensus 83 N~ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wG 124 (466)
..||.....+.. ++|..+.-..|.-...+|.|-...|+.||
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 138
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=21.16 E-value=1.2e+02 Score=26.00 Aligned_cols=26 Identities=12% Similarity=-0.097 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 012334 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (466)
Q Consensus 219 ~E~l~LLEaIe~yg~nW~~IA~~Vgt 244 (466)
-|...+.++++.++||+.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 47778999999999999999999995
No 139
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.96 E-value=1.8e+02 Score=20.90 Aligned_cols=37 Identities=11% Similarity=0.124 Sum_probs=31.5
Q ss_pred CcceeHHHHHhhccchHHHHHHHHHhhhhcccccCCC
Q 012334 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (466)
Q Consensus 94 ~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 130 (466)
...+|+++..+.+.-....+.++..=|.++|+|....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence 5678999998888778889999999999999997544
No 140
>PF06034 DUF919: Nucleopolyhedrovirus protein of unknown function (DUF919); InterPro: IPR009265 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short baculovirus proteins of unknown function.
Probab=20.88 E-value=3.2e+02 Score=21.90 Aligned_cols=45 Identities=16% Similarity=0.157 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012334 401 VEVQMKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFH 446 (466)
Q Consensus 401 ie~QlkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~ 446 (466)
|+..-++|..|..|+|.|-++ ++--.+|+...+.|..-|..++.-
T Consensus 13 I~~~K~~l~ik~~H~Ekl~ki-tK~p~El~~i~~kl~~~R~~FLn~ 57 (62)
T PF06034_consen 13 INQMKRQLTIKSQHWEKLKKI-TKNPKELQEIEKKLQELRQNFLNF 57 (62)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHHHHHHHHH
Confidence 344556799999999988654 555566777777777777777653
No 141
>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=20.78 E-value=1.5e+02 Score=27.52 Aligned_cols=43 Identities=16% Similarity=0.204 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhC-C---CCHHHHHHHHh
Q 012334 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVS-G---KSEKDCITHFI 255 (466)
Q Consensus 213 ~~~WT~~E~l~LLEaIe~yg~nW~~IA~~Vg-t---KT~~eCi~hfl 255 (466)
...-|..|..-+--.|++||+|+..++.-.. + .|+.|+...+.
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHH
Confidence 3456888999999999999999999998765 3 69999876654
No 142
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=20.77 E-value=9.3e+02 Score=24.78 Aligned_cols=47 Identities=13% Similarity=0.005 Sum_probs=30.7
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCC
Q 012334 409 QDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFHKSNARKNGD 455 (466)
Q Consensus 409 elKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~~~~~~~~~~ 455 (466)
+.+.....+++..+..-+.+|+..+.++-.-+..+-...-.||.+|-
T Consensus 235 ~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~l~~~~i~AP~dG~ 281 (423)
T TIGR01843 235 QIEQTFREEVLEELTEAQARLAELRERLNKARDRLQRLIIRSPVDGT 281 (423)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcEEECCCCcE
Confidence 33444445555555555667777777776666667777888887775
No 143
>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=20.57 E-value=69 Score=25.87 Aligned_cols=18 Identities=11% Similarity=0.453 Sum_probs=13.6
Q ss_pred HHHHHHHHhCCCHHHHHH
Q 012334 223 QLLEAIMHFGDDWRKVAQ 240 (466)
Q Consensus 223 ~LLEaIe~yg~nW~~IA~ 240 (466)
.|-+.++.||+||.-|-+
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 355667889999998864
No 144
>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=20.52 E-value=2.4e+02 Score=23.12 Aligned_cols=40 Identities=20% Similarity=0.410 Sum_probs=29.1
Q ss_pred HHHHHHHhCCCcceeHHHHHhhcc---chHHHHHHHHHhhhhccc
Q 012334 84 SIVKHYRENPSRKITFTDVRRTLV---GDVGSIRRVFDFLETWGL 125 (466)
Q Consensus 84 ~ii~~yr~np~~yLt~t~~r~~l~---gDv~~i~Rvh~FLe~wGl 125 (466)
.+|..-+. ..|||..+....|. -+...|-.|+.+|+..|+
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 36777776 56899999998887 477889999999999996
No 145
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.50 E-value=1.6e+02 Score=24.59 Aligned_cols=38 Identities=16% Similarity=0.128 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 012334 219 KETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (466)
Q Consensus 219 ~E~l~LLEaIe~yg-~nW~~IA~~VgtKT~~eCi~hflqL 257 (466)
+.+..+|..+...+ -.|.+||+.+|- ++..|..+..+|
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L 41 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL 41 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 46788999999988 689999999984 788887777664
No 146
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=20.45 E-value=5e+02 Score=28.26 Aligned_cols=59 Identities=14% Similarity=0.216 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHH--HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 012334 389 EELDVEKAISGIVEVQ--MKEIQDKIIRFESLDLQMEEEWKQLEQVKNLLFVDQLSVLFHKSNAR 451 (466)
Q Consensus 389 EErei~~Lv~~iie~Q--lkKlelKLk~feeLE~~le~Er~~Le~~r~~l~~dRl~~~~~~~~~~ 451 (466)
=|.+|.++-..|++.+ +++++-+|... +..+++...+. +.|+.++++.|+-+++....|
T Consensus 71 ~e~~i~~~~~ql~~s~~~l~~~~~~I~~~---~~~l~~l~~q~-r~qr~~La~~L~A~~r~g~~p 131 (420)
T COG4942 71 LETEIASLEAQLIETADDLKKLRKQIADL---NARLNALEVQE-REQRRRLAEQLAALQRSGRNP 131 (420)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHhhHHHH---HHHHHHHHHHH-HHHHHHHHHHHHHHHhccCCC
Confidence 4567888888887765 45666555544 44444443333 677888889999888864444
No 147
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=20.36 E-value=61 Score=27.03 Aligned_cols=36 Identities=19% Similarity=0.502 Sum_probs=23.0
Q ss_pred ccccCCCCcccccc-cc---ccCCCcccchhhhccCCCCC
Q 012334 161 RLCNGCKTLCTIAC-FA---CDKYDLTLCARCYVRGNHRV 196 (466)
Q Consensus 161 ~~C~~C~~~~~~~~-~~---c~k~d~~lC~~Cf~~G~~~~ 196 (466)
+.|-.||..+...- +. -....-.-|.-||.+|.|..
T Consensus 1 k~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~ 40 (81)
T PF12674_consen 1 KFCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQ 40 (81)
T ss_pred CcCCcCcCccCCccccccccCCCCchhHHHHHhcCCceee
Confidence 36899998876433 11 11123446999999999744
No 148
>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=20.35 E-value=1.8e+02 Score=23.52 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=34.3
Q ss_pred HHHHHHhCCCcceeHHHHHhhccchHHHHHHHHHhhhhcccccCC
Q 012334 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (466)
Q Consensus 85 ii~~yr~np~~yLt~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 129 (466)
|+.....+....+|..+....+.-....+.+|..-|.+-|||.-.
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 344444444455999999988988999999999999999999743
No 149
>PRK03837 transcriptional regulator NanR; Provisional
Probab=20.01 E-value=1.3e+02 Score=28.84 Aligned_cols=59 Identities=12% Similarity=0.089 Sum_probs=50.0
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcce-eHHHHHhhccchHHHHHHHHHhhhhcccccCCCC
Q 012334 72 SKNPRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (466)
Q Consensus 72 ~ktp~~Y~~~RN~ii~~yr~np~~yL-t~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 131 (466)
+....+|..||+.|+.-... |...| +-.+....+.-....+.....-|+.-|||.....
T Consensus 13 ~~~~~v~~~l~~~I~~g~l~-pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 13 KLSEEVEERLEQMIRSGEFG-PGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred cHHHHHHHHHHHHHHhCCCC-CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34568999999999997665 89999 8999888888888888889999999999987543
No 150
>PRK01905 DNA-binding protein Fis; Provisional
Probab=20.00 E-value=1.6e+02 Score=23.85 Aligned_cols=28 Identities=14% Similarity=-0.009 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 012334 217 TEKETLQLLEAIMHFGDDWRKVAQHVSG 244 (466)
Q Consensus 217 T~~E~l~LLEaIe~yg~nW~~IA~~Vgt 244 (466)
..-|...+.++++.+|||+.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 3457778999999999999999999995
Done!