Query 019767
Match_columns 336
No_of_seqs 282 out of 812
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 04:22:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019767hhsearch_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 9.5E-76 2.1E-80 577.1 14.0 274 33-333 45-372 (531)
2 KOG1279 Chromatin remodeling f 100.0 4.2E-70 9.1E-75 551.6 19.9 288 16-331 22-345 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 2.1E-28 4.6E-33 195.0 6.6 85 40-128 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 4.9E-23 1.1E-27 203.4 7.7 104 159-264 13-124 (438)
5 COG5114 Histone acetyltransfer 99.8 1.1E-19 2.4E-24 173.9 5.1 104 159-264 4-115 (432)
6 PF00249 Myb_DNA-binding: Myb- 99.3 2E-12 4.3E-17 92.2 5.2 45 213-257 1-47 (48)
7 PF13921 Myb_DNA-bind_6: Myb-l 99.1 1.5E-10 3.3E-15 85.7 5.5 41 216-256 1-41 (60)
8 smart00717 SANT SANT SWI3, AD 99.1 2.5E-10 5.4E-15 78.9 5.9 44 214-257 2-46 (49)
9 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 7.9E-10 1.7E-14 75.4 5.6 43 215-257 1-44 (45)
10 PLN03000 amine oxidase 98.9 1.4E-09 2.9E-14 118.0 6.7 83 44-131 86-171 (881)
11 PLN02328 lysine-specific histo 98.8 6.4E-09 1.4E-13 112.4 6.7 83 45-131 138-222 (808)
12 PLN03212 Transcription repress 98.7 2.2E-08 4.7E-13 94.2 5.0 46 212-257 24-71 (249)
13 TIGR01557 myb_SHAQKYF myb-like 98.5 1.7E-07 3.6E-12 70.0 5.2 47 213-259 3-55 (57)
14 PLN03091 hypothetical protein; 98.5 1.1E-07 2.5E-12 95.6 5.1 46 212-257 13-60 (459)
15 cd02336 ZZ_RSC8 Zinc finger, Z 98.4 1.2E-07 2.6E-12 67.5 2.8 44 161-204 1-45 (45)
16 KOG0048 Transcription factor, 98.4 2.5E-07 5.5E-12 86.8 4.6 45 213-257 9-55 (238)
17 PLN03212 Transcription repress 98.3 8.6E-07 1.9E-11 83.6 5.0 46 211-256 76-121 (249)
18 PLN02529 lysine-specific histo 98.3 1.1E-06 2.5E-11 94.5 6.2 85 44-131 62-147 (738)
19 PLN03091 hypothetical protein; 98.1 4.9E-06 1.1E-10 84.0 5.6 46 211-256 65-110 (459)
20 KOG0048 Transcription factor, 97.8 2.6E-05 5.6E-10 73.3 5.4 44 212-255 61-104 (238)
21 KOG0049 Transcription factor, 97.6 6E-05 1.3E-09 79.0 5.4 46 211-256 358-404 (939)
22 cd02335 ZZ_ADA2 Zinc finger, Z 97.3 0.00022 4.8E-09 51.4 3.5 46 161-206 1-49 (49)
23 KOG0049 Transcription factor, 96.9 0.00085 1.8E-08 70.7 4.0 45 212-256 411-459 (939)
24 cd02249 ZZ Zinc finger, ZZ typ 96.9 0.0011 2.3E-08 47.1 3.3 44 161-205 1-45 (46)
25 PF13837 Myb_DNA-bind_4: Myb/S 96.6 0.0011 2.4E-08 52.0 2.0 44 214-257 2-63 (90)
26 PLN02976 amine oxidase 96.6 0.0023 4.9E-08 73.5 4.8 82 45-131 451-540 (1713)
27 cd02340 ZZ_NBR1_like Zinc fing 96.5 0.0025 5.5E-08 44.9 3.0 41 162-206 2-43 (43)
28 smart00291 ZnF_ZZ Zinc-binding 96.4 0.0028 6.1E-08 44.6 2.9 38 160-197 4-42 (44)
29 cd02343 ZZ_EF Zinc finger, ZZ 96.4 0.003 6.4E-08 45.7 2.8 37 162-198 2-39 (48)
30 cd02338 ZZ_PCMF_like Zinc fing 96.2 0.0048 1E-07 44.5 3.1 44 162-205 2-48 (49)
31 KOG0051 RNA polymerase I termi 96.2 0.0052 1.1E-07 64.8 4.6 45 212-257 383-427 (607)
32 cd02345 ZZ_dah Zinc finger, ZZ 96.2 0.0051 1.1E-07 44.4 3.1 43 162-204 2-47 (49)
33 cd02334 ZZ_dystrophin Zinc fin 95.8 0.0096 2.1E-07 43.2 3.1 41 162-204 2-47 (49)
34 cd02341 ZZ_ZZZ3 Zinc finger, Z 95.6 0.012 2.7E-07 42.4 3.1 43 161-205 1-47 (48)
35 PF00569 ZZ: Zinc finger, ZZ t 95.5 0.0057 1.2E-07 43.5 0.9 39 160-198 4-44 (46)
36 KOG0050 mRNA splicing protein 95.0 0.022 4.7E-07 59.0 3.6 44 213-256 7-51 (617)
37 cd02337 ZZ_CBP Zinc finger, ZZ 94.9 0.022 4.7E-07 39.8 2.5 37 161-198 1-38 (41)
38 KOG0051 RNA polymerase I termi 94.7 0.027 5.8E-07 59.6 3.6 53 212-264 435-513 (607)
39 cd02344 ZZ_HERC2 Zinc finger, 94.5 0.04 8.6E-07 39.4 3.1 42 162-206 2-45 (45)
40 PF13873 Myb_DNA-bind_5: Myb/S 94.3 0.096 2.1E-06 40.4 5.1 45 213-257 2-68 (78)
41 KOG0050 mRNA splicing protein 94.2 0.035 7.7E-07 57.5 3.1 45 212-257 58-102 (617)
42 cd02339 ZZ_Mind_bomb Zinc fing 93.8 0.059 1.3E-06 38.4 2.8 41 162-205 2-44 (45)
43 KOG4167 Predicted DNA-binding 92.9 0.15 3.3E-06 54.9 5.3 44 213-256 619-662 (907)
44 COG5147 REB1 Myb superfamily p 92.4 0.12 2.5E-06 54.1 3.6 46 211-256 70-115 (512)
45 COG5118 BDP1 Transcription ini 92.4 0.19 4.1E-06 50.6 4.8 44 213-256 365-408 (507)
46 COG5147 REB1 Myb superfamily p 92.0 0.087 1.9E-06 55.0 2.1 43 213-255 20-63 (512)
47 KOG4329 DNA-binding protein [G 91.8 0.23 4.9E-06 49.9 4.7 45 213-257 277-322 (445)
48 TIGR02894 DNA_bind_RsfA transc 91.7 0.18 3.9E-06 45.2 3.5 50 213-264 4-60 (161)
49 KOG4468 Polycomb-group transcr 90.8 0.21 4.5E-06 52.9 3.4 45 213-257 88-142 (782)
50 KOG4282 Transcription factor G 90.5 0.32 6.8E-06 47.9 4.3 45 214-258 55-113 (345)
51 PF09111 SLIDE: SLIDE; InterP 88.5 0.56 1.2E-05 40.0 3.8 45 212-256 48-108 (118)
52 PF08914 Myb_DNA-bind_2: Rap1 83.8 1.8 3.8E-05 33.2 4.0 44 213-256 2-55 (65)
53 KOG1279 Chromatin remodeling f 83.0 1.3 2.9E-05 46.4 4.0 92 41-132 185-284 (506)
54 cd02342 ZZ_UBA_plant Zinc fing 81.9 0.98 2.1E-05 32.1 1.7 31 162-192 2-34 (43)
55 KOG3554 Histone deacetylase co 81.6 1.2 2.6E-05 46.1 3.0 51 214-264 286-337 (693)
56 PF12776 Myb_DNA-bind_3: Myb/S 80.1 2.3 5E-05 33.5 3.6 43 215-257 1-61 (96)
57 KOG1280 Uncharacterized conser 79.9 1 2.2E-05 45.0 1.8 34 160-193 8-43 (381)
58 PRK13923 putative spore coat p 79.7 1.8 3.9E-05 39.3 3.1 42 213-255 5-53 (170)
59 PF04504 DUF573: Protein of un 78.8 3.2 7E-05 34.0 4.2 51 212-264 3-66 (98)
60 PF13404 HTH_AsnC-type: AsnC-t 77.6 5.4 0.00012 27.7 4.4 38 219-257 3-41 (42)
61 PLN03142 Probable chromatin-re 75.8 4.2 9.1E-05 46.2 5.3 40 214-253 825-865 (1033)
62 KOG1194 Predicted DNA-binding 74.7 5.6 0.00012 41.2 5.4 46 211-256 185-230 (534)
63 KOG4582 Uncharacterized conser 71.3 2.6 5.5E-05 40.9 2.0 30 161-192 153-186 (278)
64 KOG4286 Dystrophin-like protei 70.7 2 4.4E-05 46.8 1.2 36 161-196 604-641 (966)
65 PLN03142 Probable chromatin-re 67.9 7.3 0.00016 44.4 4.9 45 213-257 926-983 (1033)
66 PF02954 HTH_8: Bacterial regu 67.5 8.5 0.00018 26.4 3.5 25 220-244 6-30 (42)
67 smart00595 MADF subfamily of S 66.6 4.8 0.0001 31.4 2.3 28 234-264 29-56 (89)
68 smart00345 HTH_GNTR helix_turn 64.6 11 0.00024 26.3 3.8 50 78-128 2-52 (60)
69 PF01475 FUR: Ferric uptake re 63.7 12 0.00026 30.8 4.4 49 79-128 7-60 (120)
70 KOG1194 Predicted DNA-binding 62.7 4.1 9E-05 42.1 1.6 44 212-256 469-512 (534)
71 PF00392 GntR: Bacterial regul 62.5 12 0.00026 27.5 3.8 53 75-128 3-56 (64)
72 COG5347 GTPase-activating prot 61.1 7.8 0.00017 38.5 3.2 97 160-264 20-123 (319)
73 PHA00442 host recBCD nuclease 60.1 9.8 0.00021 28.4 2.7 26 217-242 24-50 (59)
74 PF12802 MarR_2: MarR family; 58.8 30 0.00064 24.7 5.2 41 89-129 14-54 (62)
75 PF09862 DUF2089: Protein of u 58.5 17 0.00036 30.9 4.3 60 163-243 1-60 (113)
76 PLN03119 putative ADP-ribosyla 57.6 8.9 0.00019 40.9 3.0 89 161-264 24-122 (648)
77 PRK11179 DNA-binding transcrip 57.6 17 0.00036 31.6 4.3 45 218-264 8-53 (153)
78 cd07153 Fur_like Ferric uptake 55.5 25 0.00054 28.5 4.8 46 82-128 3-53 (116)
79 cd00090 HTH_ARSR Arsenical Res 55.2 32 0.0007 24.3 5.0 45 84-131 11-55 (78)
80 PLN03131 hypothetical protein; 55.0 12 0.00026 40.3 3.5 92 161-264 24-122 (705)
81 PRK09462 fur ferric uptake reg 55.0 23 0.0005 30.6 4.7 46 82-127 19-69 (148)
82 smart00550 Zalpha Z-DNA-bindin 52.5 56 0.0012 24.6 6.0 52 80-131 6-57 (68)
83 KOG0384 Chromodomain-helicase 51.0 10 0.00023 43.7 2.4 28 212-239 1132-1160(1373)
84 PRK11169 leucine-responsive tr 50.6 24 0.00051 31.1 4.2 39 218-257 13-52 (164)
85 PF01022 HTH_5: Bacterial regu 50.4 42 0.0009 23.3 4.6 45 81-128 3-47 (47)
86 PF09339 HTH_IclR: IclR helix- 50.2 29 0.00062 24.5 3.9 43 85-128 8-50 (52)
87 PF13412 HTH_24: Winged helix- 49.3 63 0.0014 22.1 5.4 43 82-126 5-47 (48)
88 COG1725 Predicted transcriptio 49.2 42 0.00091 29.0 5.4 57 75-131 10-70 (125)
89 PF07649 C1_3: C1-like domain; 48.9 9 0.00019 24.4 0.9 27 162-188 2-29 (30)
90 COG5114 Histone acetyltransfer 46.2 31 0.00068 34.5 4.6 69 52-127 361-429 (432)
91 PF10820 DUF2543: Protein of u 43.9 28 0.0006 27.5 3.1 32 93-124 45-79 (81)
92 PF09420 Nop16: Ribosome bioge 43.3 40 0.00087 29.9 4.5 44 213-256 114-161 (164)
93 smart00344 HTH_ASNC helix_turn 40.6 49 0.0011 26.4 4.3 44 219-264 3-47 (108)
94 smart00105 ArfGap Putative GTP 40.1 32 0.00069 28.6 3.2 91 161-264 4-105 (112)
95 PF01388 ARID: ARID/BRIGHT DNA 39.1 49 0.0011 25.9 4.0 37 220-256 37-86 (92)
96 PF03444 HrcA_DNA-bdg: Winged 38.6 1.1E+02 0.0024 24.4 5.8 52 76-128 4-55 (78)
97 PF10545 MADF_DNA_bdg: Alcohol 38.5 25 0.00054 26.4 2.1 29 234-264 28-57 (85)
98 PF14569 zf-UDP: Zinc-binding 38.2 19 0.00041 28.8 1.4 35 156-190 5-44 (80)
99 COG0735 Fur Fe2+/Zn2+ uptake r 37.8 58 0.0013 28.3 4.6 50 81-131 22-76 (145)
100 cd08310 Death_NFkB-like Death 37.3 28 0.0006 27.0 2.2 23 218-244 2-24 (72)
101 smart00346 HTH_ICLR helix_turn 36.3 72 0.0016 24.4 4.5 44 85-129 10-53 (91)
102 PRK06474 hypothetical protein; 35.8 79 0.0017 28.4 5.3 48 81-129 12-60 (178)
103 PRK01905 DNA-binding protein F 35.5 50 0.0011 25.6 3.4 28 217-244 35-62 (77)
104 PF09286 Pro-kuma_activ: Pro-k 35.3 40 0.00086 28.7 3.1 36 94-129 45-80 (143)
105 PF08074 CHDCT2: CHDCT2 (NUC03 34.8 23 0.00051 32.1 1.6 43 214-256 4-60 (173)
106 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 34.5 1.2E+02 0.0026 22.1 5.0 39 219-259 7-45 (50)
107 PRK11639 zinc uptake transcrip 34.4 58 0.0013 29.0 4.1 45 82-127 28-77 (169)
108 PRK00430 fis global DNA-bindin 34.2 52 0.0011 26.8 3.4 26 219-244 55-80 (95)
109 smart00426 TEA TEA domain. 33.5 79 0.0017 24.6 4.1 20 213-232 3-22 (68)
110 KOG2656 DNA methyltransferase 32.9 25 0.00055 35.9 1.7 45 212-256 129-179 (445)
111 PF11035 SnAPC_2_like: Small n 32.9 71 0.0015 31.9 4.7 40 213-252 21-64 (344)
112 PF13463 HTH_27: Winged helix 32.3 1.5E+02 0.0032 21.3 5.4 40 92-131 14-53 (68)
113 PF01047 MarR: MarR family; I 31.8 97 0.0021 21.8 4.3 35 97-131 18-52 (59)
114 PF09012 FeoC: FeoC like trans 31.6 1.2E+02 0.0026 22.6 4.9 43 79-127 3-45 (69)
115 PLN02638 cellulose synthase A 31.2 31 0.00067 39.5 2.2 35 156-190 13-52 (1079)
116 KOG0703 Predicted GTPase-activ 29.6 54 0.0012 32.2 3.3 93 160-264 25-124 (287)
117 PF01412 ArfGap: Putative GTPa 29.2 24 0.00053 29.4 0.8 59 161-227 14-72 (116)
118 smart00420 HTH_DEOR helix_turn 29.1 1.6E+02 0.0035 19.5 4.9 34 95-128 13-46 (53)
119 KOG0724 Zuotin and related mol 28.9 26 0.00057 34.2 1.0 44 213-256 53-96 (335)
120 KOG4479 Transcription factor e 28.5 1.2E+02 0.0025 24.7 4.4 44 76-123 36-89 (92)
121 PF03979 Sigma70_r1_1: Sigma-7 28.3 1.5E+02 0.0033 23.1 5.1 43 80-125 8-53 (82)
122 cd08311 Death_p75NR Death doma 28.2 50 0.0011 26.0 2.3 26 218-244 2-27 (77)
123 COG1522 Lrp Transcriptional re 27.2 1.1E+02 0.0024 25.8 4.5 39 218-257 7-46 (154)
124 TIGR02702 SufR_cyano iron-sulf 27.1 1.2E+02 0.0026 27.4 5.0 47 81-129 2-48 (203)
125 PF03107 C1_2: C1 domain; Int 26.8 46 0.001 21.2 1.6 27 162-188 2-29 (30)
126 PF08100 Dimerisation: Dimeris 26.3 1.3E+02 0.0028 21.9 4.0 27 94-120 20-50 (51)
127 PRK11414 colanic acid/biofilm 26.3 99 0.0021 28.0 4.3 68 63-131 2-69 (221)
128 cd00092 HTH_CRP helix_turn_hel 26.2 2.1E+02 0.0045 20.3 5.3 49 81-129 5-58 (67)
129 PF11593 Med3: Mediator comple 26.2 78 0.0017 32.2 3.8 46 75-131 64-113 (379)
130 PLN02436 cellulose synthase A 26.1 47 0.001 38.1 2.4 36 156-191 32-72 (1094)
131 PLN02400 cellulose synthase 25.9 46 0.00099 38.2 2.3 53 156-208 32-93 (1085)
132 cd08312 Death_MyD88 Death doma 25.7 31 0.00066 27.1 0.7 26 219-244 3-28 (79)
133 KOG4301 Beta-dystrobrevin [Cyt 25.4 42 0.00092 33.9 1.8 63 159-231 239-306 (434)
134 smart00501 BRIGHT BRIGHT, ARID 25.4 1.2E+02 0.0026 24.0 4.1 37 220-256 33-82 (93)
135 cd07377 WHTH_GntR Winged helix 25.1 1.1E+02 0.0024 21.5 3.5 52 76-128 5-57 (66)
136 PF08281 Sigma70_r4_2: Sigma-7 25.1 1.6E+02 0.0035 20.4 4.4 36 219-255 13-48 (54)
137 PF00643 zf-B_box: B-box zinc 24.7 47 0.001 22.2 1.4 29 161-192 4-33 (42)
138 PF01978 TrmB: Sugar-specific 24.7 1E+02 0.0022 22.7 3.4 35 94-128 20-54 (68)
139 PLN02189 cellulose synthase 24.5 52 0.0011 37.7 2.4 36 156-191 30-70 (1040)
140 PF07750 GcrA: GcrA cell cycle 24.4 1.3E+02 0.0029 26.8 4.6 43 215-258 2-44 (162)
141 KOG0704 ADP-ribosylation facto 24.2 50 0.0011 33.4 2.0 71 162-241 21-103 (386)
142 PF06461 DUF1086: Domain of Un 24.1 1.5E+02 0.0033 26.3 4.8 45 215-260 40-87 (145)
143 cd08319 Death_RAIDD Death doma 23.2 96 0.0021 24.7 3.1 31 223-253 4-35 (83)
144 PF02082 Rrf2: Transcriptional 23.1 1.5E+02 0.0033 22.8 4.2 45 85-129 14-58 (83)
145 PF09538 FYDLN_acid: Protein o 22.9 45 0.00098 28.0 1.3 28 159-191 8-35 (108)
146 PF13325 MCRS_N: N-terminal re 22.3 1.1E+02 0.0024 28.6 3.7 87 215-321 1-90 (199)
147 smart00418 HTH_ARSR helix_turn 22.2 1.8E+02 0.0038 19.8 4.1 37 94-130 8-44 (66)
148 PF12674 Zn_ribbon_2: Putative 21.8 31 0.00068 27.4 0.1 35 162-196 2-40 (81)
149 PRK03837 transcriptional regul 21.6 1.2E+02 0.0026 27.7 3.9 59 72-131 13-72 (241)
150 COG3604 FhlA Transcriptional r 21.6 2E+02 0.0043 30.8 5.8 43 219-262 506-548 (550)
151 smart00419 HTH_CRP helix_turn_ 21.4 1.1E+02 0.0025 20.2 2.9 34 96-129 8-41 (48)
152 PF08784 RPA_C: Replication pr 21.3 2.5E+02 0.0055 22.3 5.3 47 80-126 47-95 (102)
153 KOG2009 Transcription initiati 20.8 75 0.0016 34.2 2.6 44 213-256 409-452 (584)
154 PF14420 Clr5: Clr5 domain 20.6 1.6E+02 0.0035 21.3 3.6 28 77-107 4-31 (54)
155 PF13551 HTH_29: Winged helix- 20.5 1.7E+02 0.0038 22.9 4.2 48 77-124 58-112 (112)
156 PRK14137 recX recombination re 20.0 2.1E+02 0.0046 26.3 5.1 54 75-131 36-92 (195)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=9.5e-76 Score=577.08 Aligned_cols=274 Identities=34% Similarity=0.602 Sum_probs=227.0
Q ss_pred CCCCCceeecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchHHH
Q 019767 33 SSSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGS 112 (336)
Q Consensus 33 ~~~q~~~ivIPs~s~WF~~~~ih~iE~~~lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~ 112 (336)
--+|+|+|+||||+.||++.+||+||+++.||||+||+++|||++|++||||||++||+||++|||+|+||||++|||++
T Consensus 45 l~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvagDV~a 124 (531)
T COG5259 45 LMEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAGDVAA 124 (531)
T ss_pred hhccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccchhHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhcccccCCCC--Cccccccccccc-----Cccc-----------c-C----------------CCcch---
Q 019767 113 IRRVFDFLETWGLINYFAS--VKTLKWEDKETK-----SSAA-----------S-A----------------ESSSA--- 154 (336)
Q Consensus 113 i~Rih~FLe~wGlINy~~~--~kP~~~~~~~~~-----~~~~-----------~-~----------------s~~~~--- 154 (336)
|.|||+|||+|||||||++ ++|....+.-+. .|+. + + ...|.
T Consensus 125 ivrvHrFLekWGLINYqvdp~trPs~IgPplt~h~q~l~dtP~gl~p~l~~~~~~~~~~~a~~~e~~~~k~~~~sps~~~ 204 (531)
T COG5259 125 IVRVHRFLEKWGLINYQVDPGTRPSTIGPPLTSHFQDLHDTPRGLSPFLPWGPINQRVLGAKEIEYETHKEENYSPSLKS 204 (531)
T ss_pred HHHHHHHHHHhcceeeccCCCCCccccCCCcchhhHHHhhCccccccccCCCCccccccccchhhhhhhccCCCCchhhh
Confidence 9999999999999999999 666544321111 0000 0 0 00011
Q ss_pred -----------hhcccc---ccCCCCCCcccccccccc-CCCccchhhhhccCCCCCCCCCCCceecccCcc-cCCCCCH
Q 019767 155 -----------LKETSK---RLCNGCKTLCTIACFACD-KYDLTLCARCYVRGNHRVGVSSSDFRRVEISEE-ARSDWTE 218 (336)
Q Consensus 155 -----------~~~~~k---~~C~~C~~~~~~~~~~c~-k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~-~~~~WT~ 218 (336)
+.+.+. ..|..||+.+...+|+-. ..+..+|..||..|+|+.+..++||+++++... ....||+
T Consensus 205 ~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~~~~~~~dk~WS~ 284 (531)
T COG5259 205 PKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVTISLLIRDKNWSR 284 (531)
T ss_pred hhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhhhhcccccccccH
Confidence 111122 579999999887666543 246779999999999999999999999987655 5669999
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCCCCcccCCCCCCccccccccccCCCCCccccccccCCCCC
Q 019767 219 KETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESENVGATSP 298 (336)
Q Consensus 219 eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 298 (336)
+|+++|||||++||++|++||.|||+||++||+.||++|||+|+||.+ .+ . + ..+
T Consensus 285 qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k-~~---~---~-~~~----------------- 339 (531)
T COG5259 285 QELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSK-GD---G---K-GDN----------------- 339 (531)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhc-cc---C---c-CCC-----------------
Confidence 999999999999999999999999999999999999999999999921 11 0 0 000
Q ss_pred CccCCcccccCCCCcHHHHHHHHHhhhhHHHHHHH
Q 019767 299 SKRMRLTPLADASNPIMAQLSCRLWLVSRLLKLLL 333 (336)
Q Consensus 299 ~~~~~~~Pfs~a~NPvms~vAFLas~V~p~~~~~~ 333 (336)
.....||..++|||||+|+|||++|.|.++...
T Consensus 340 --~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~ 372 (531)
T COG5259 340 --SKGRLPFDGSENPVLSTISFLAGIVNPRVQSEK 372 (531)
T ss_pred --CCCccccccCCCchhhHHHHHHHhcCHHHHHHH
Confidence 012479999999999999999999999976543
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=4.2e-70 Score=551.56 Aligned_cols=288 Identities=36% Similarity=0.654 Sum_probs=228.7
Q ss_pred cCCCCCCCCCC-CCCCCCCCCCCceeecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCC
Q 019767 16 VNPTTPLAPPP-VKPELPSSSEPDVVNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPS 94 (336)
Q Consensus 16 ~~~~~~~~~~~-~~~~~~~~~q~~~ivIPs~s~WF~~~~ih~iE~~~lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~ 94 (336)
-|+++.+.+.. ..++.-.+.|+|.|+||||++||++++||+||++++||||+|++++|||++|++||||||++||+||.
T Consensus 22 ~~~~~~~~~~~~~~~~~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp~ 101 (506)
T KOG1279|consen 22 ESQETLGGPAAHDAAKTVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNPQ 101 (506)
T ss_pred cCcccccccchhhhcccccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCcc
Confidence 56666665322 22222268999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeHHHHHHhccchHHHHHHHHHhhhhcccccCCCC--CcccccccccccC-----cccc-----CC--Cc--c-----
Q 019767 95 RKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS--VKTLKWEDKETKS-----SAAS-----AE--SS--S----- 153 (336)
Q Consensus 95 ~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~--~kP~~~~~~~~~~-----~~~~-----~s--~~--~----- 153 (336)
+|||+|+|||+++|||++|+|||+|||+||||||+++ ++|..+++..+.. +... .+ +. +
T Consensus 102 ~ylt~ta~rrnl~gDv~ai~Rvh~FlE~WGLINy~~d~e~rp~~~~p~~t~h~~~~~~tp~~~~~~~~~~~~~~~~~~~~ 181 (506)
T KOG1279|consen 102 EYLTFTACRRNLAGDVCAIARVHAFLEQWGLINYQVDAESRPHPIEPPETSHFQVLADTPRGLAPLTPEDPQSQPDLGNP 181 (506)
T ss_pred cchhHHHHHhcccchHHHHHHHHhhHHhhcccccccChhhCCcccCCCcccccccccCCCcccccCCCCCcccccccccc
Confidence 9999999999999999999999999999999999999 6777665432221 1110 00 00 0
Q ss_pred ------hhhccccccCCCCCCccccccccccC--------CCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHH
Q 019767 154 ------ALKETSKRLCNGCKTLCTIACFACDK--------YDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEK 219 (336)
Q Consensus 154 ------~~~~~~k~~C~~C~~~~~~~~~~c~k--------~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~e 219 (336)
.-.+.....|+.|...+...|+.|.+ .++.+|..||..|+++..+...||+.+ .+..+..||++
T Consensus 182 ~~~~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~--~~~~~~~WT~q 259 (506)
T KOG1279|consen 182 RMETLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVI--GESARPNWTEQ 259 (506)
T ss_pred ccccccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhc--cccCCCCccHH
Confidence 00111223345444444455554443 357899999999999999999999333 34567899999
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCCCCcccCCCCCCccccccccccCCCCCccccccccCCCCCC
Q 019767 220 ETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESENVGATSPS 299 (336)
Q Consensus 220 E~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 (336)
|+++|||||++||++|.+||.|||+||++||+.||++|||+|+|+ ...+. .+ .+
T Consensus 260 E~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l-~~~~~-----~~--------------------~~ 313 (506)
T KOG1279|consen 260 ETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYL-AKSEA-----SL--------------------GP 313 (506)
T ss_pred HHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhh-hhccc-----cc--------------------Cc
Confidence 999999999999999999999999999999999999999999999 43321 11 12
Q ss_pred ccCCcccccCCCCcHHHHHHHHHhhhhHHHHH
Q 019767 300 KRMRLTPLADASNPIMAQLSCRLWLVSRLLKL 331 (336)
Q Consensus 300 ~~~~~~Pfs~a~NPvms~vAFLas~V~p~~~~ 331 (336)
..+.+.+|++-+|||||+++||+++|||.++.
T Consensus 314 ~~~~~~~~sq~gnpv~s~~~~l~~~vdP~~~~ 345 (506)
T KOG1279|consen 314 LSYGPVPFSQDGNPVMSTVAFLASVVDPVVKS 345 (506)
T ss_pred cccCCCccccCCCccccHHHHHHhccCchhhh
Confidence 23467889999999999999999999996543
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=99.95 E-value=2.1e-28 Score=195.00 Aligned_cols=85 Identities=47% Similarity=0.897 Sum_probs=78.0
Q ss_pred eecCCCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccc-hHHHHHHHHH
Q 019767 40 VNVPSYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVG-DVGSIRRVFD 118 (336)
Q Consensus 40 ivIPs~s~WF~~~~ih~iE~~~lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rih~ 118 (336)
+++|++++||+++.+|++|++.+||||.| ++|+.|+.|||.||+.|+.||.+|||+++||+.+.| |+..+.|||+
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 46899999999999999999999999997 789999999999999999999999999999999996 9999999999
Q ss_pred hhhhcccccC
Q 019767 119 FLETWGLINY 128 (336)
Q Consensus 119 FLe~wGlINy 128 (336)
||++||+|||
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=99.88 E-value=4.9e-23 Score=203.38 Aligned_cols=104 Identities=27% Similarity=0.629 Sum_probs=94.8
Q ss_pred ccccCCCCCCccc----cccccccCCCccchhhhhccCCC-CCCCCCCCceecccC--cccCCCCCHHHHHHHHHHHHHh
Q 019767 159 SKRLCNGCKTLCT----IACFACDKYDLTLCARCYVRGNH-RVGVSSSDFRRVEIS--EEARSDWTEKETLQLLEAIMHF 231 (336)
Q Consensus 159 ~k~~C~~C~~~~~----~~~~~c~k~d~~LC~~CF~~G~~-~~~~~s~df~ki~~~--~~~~~~WT~eE~~~LLeav~~y 231 (336)
.++.|++|..+++ ++|++|. |++||..||+.|.+ +.|..+|.|++++.. .....+||++||++||||+++|
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 5899999999875 6788885 67899999999998 778899999999874 3567899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 232 G-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 232 G-~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
| |||++||+|||+||.++|+.||++.+++.++.
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=99.78 E-value=1.1e-19 Score=173.86 Aligned_cols=104 Identities=24% Similarity=0.559 Sum_probs=93.1
Q ss_pred ccccCCCCCCccc----cccccccCCCccchhhhhccCCC-CCCCCCCCceecccC--cccCCCCCHHHHHHHHHHHHHh
Q 019767 159 SKRLCNGCKTLCT----IACFACDKYDLTLCARCYVRGNH-RVGVSSSDFRRVEIS--EEARSDWTEKETLQLLEAIMHF 231 (336)
Q Consensus 159 ~k~~C~~C~~~~~----~~~~~c~k~d~~LC~~CF~~G~~-~~~~~s~df~ki~~~--~~~~~~WT~eE~~~LLeav~~y 231 (336)
.+++|+.|..+|+ ++|.+|. +++||..||++|.+ +.|...|+|++++.+ .....+|+++||++|+++.+..
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 4789999999987 5666666 57799999999998 567789999999865 4567899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 232 G-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 232 G-~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
| |||++||+|||.|++++|+.||+++++|..|.
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=99.33 E-value=2e-12 Score=92.23 Aligned_cols=45 Identities=40% Similarity=0.927 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-HHHHHHHhC-CCCHHHHHHHHhcC
Q 019767 213 RSDWTEKETLQLLEAIMHFGDD-WRKVAQHVS-GKSEKDCITHFIKL 257 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~n-W~~IA~~Vg-trT~~qC~~hf~~l 257 (336)
+..||.+|+.+|++||.+||.+ |..||++|| +||..||+.||.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 3689999999999999999966 999999999 99999999999864
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.09 E-value=1.5e-10 Score=85.66 Aligned_cols=41 Identities=34% Similarity=0.857 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 216 WTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 216 WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
||.+|+.+|++++.+||.+|.+||+++|+||+.+|..||..
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=99.08 E-value=2.5e-10 Score=78.92 Aligned_cols=44 Identities=30% Similarity=0.810 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 214 ~~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
..||.+|+.+|++++.+|| .+|..||+++++||+.+|+.||..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5799999999999999999 9999999999999999999999875
No 9
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.00 E-value=7.9e-10 Score=75.36 Aligned_cols=43 Identities=37% Similarity=0.851 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 215 DWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 215 ~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
.||.+|+.+|+.++.+|| ++|..||+.+++||..+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 9999999999999999999999764
No 10
>PLN03000 amine oxidase
Probab=98.92 E-value=1.4e-09 Score=118.03 Aligned_cols=83 Identities=24% Similarity=0.368 Sum_probs=72.3
Q ss_pred CCCCCCCCCCCCHHHHhh--CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccc-hHHHHHHHHHhh
Q 019767 44 SYSRWFSFDSISECEVKF--LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVG-DVGSIRRVFDFL 120 (336)
Q Consensus 44 s~s~WF~~~~ih~iE~~~--lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rih~FL 120 (336)
.++.-|+.|.+++.|..+ || -.. ...+..|+.|||.||.+|+.||..+||+++|...+.. -...+.++|+||
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 457899999999999777 77 222 2578999999999999999999999999999977654 358899999999
Q ss_pred hhcccccCCCC
Q 019767 121 ETWGLINYFAS 131 (336)
Q Consensus 121 e~wGlINy~~~ 131 (336)
+++|+|||++.
T Consensus 161 ~r~G~in~g~~ 171 (881)
T PLN03000 161 VTHGYINFGIA 171 (881)
T ss_pred HHcCcccHHHH
Confidence 99999999987
No 11
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.80 E-value=6.4e-09 Score=112.35 Aligned_cols=83 Identities=22% Similarity=0.306 Sum_probs=74.4
Q ss_pred CCCCCCCCCCCHHHHhh-CccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhcc-chHHHHHHHHHhhhh
Q 019767 45 YSRWFSFDSISECEVKF-LPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV-GDVGSIRRVFDFLET 122 (336)
Q Consensus 45 ~s~WF~~~~ih~iE~~~-lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~-gDv~~i~Rih~FLe~ 122 (336)
.+.-|+.+++|+.|..+ |+....+ ..+..|+.|||.||.+|+.||..+||+++|+..+. -....+.++|.||.+
T Consensus 138 ~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~ 213 (808)
T PLN02328 138 ISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLE 213 (808)
T ss_pred HHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhc
Confidence 46789999999999888 7777765 57899999999999999999999999999997765 356889999999999
Q ss_pred cccccCCCC
Q 019767 123 WGLINYFAS 131 (336)
Q Consensus 123 wGlINy~~~ 131 (336)
.|.|||++.
T Consensus 214 ~g~in~gv~ 222 (808)
T PLN02328 214 HGYINFGVA 222 (808)
T ss_pred cCceeeecc
Confidence 999999998
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.67 E-value=2.2e-08 Score=94.21 Aligned_cols=46 Identities=24% Similarity=0.498 Sum_probs=42.8
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 019767 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG-~nW~~IA~~Vg-trT~~qC~~hf~~l 257 (336)
.+..||.+|+.+|+++|++|| .+|..||+++| +||..||++||.++
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~ 71 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNY 71 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHh
Confidence 367899999999999999999 79999999996 89999999999975
No 13
>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=98.52 E-value=1.7e-07 Score=69.97 Aligned_cols=47 Identities=23% Similarity=0.545 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCH---HHHHHHhC-CC-CHHHHHHHHhcCCC
Q 019767 213 RSDWTEKETLQLLEAIMHFG-DDW---RKVAQHVS-GK-SEKDCITHFIKLPF 259 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG-~nW---~~IA~~Vg-tr-T~~qC~~hf~~lPI 259 (336)
+..||++|..++|+||+.|| ||| .+|+++++ ++ |+.||..|+..+.+
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 45799999999999999999 599 99999887 57 99999999987543
No 14
>PLN03091 hypothetical protein; Provisional
Probab=98.50 E-value=1.1e-07 Score=95.56 Aligned_cols=46 Identities=24% Similarity=0.580 Sum_probs=42.7
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 019767 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG-~nW~~IA~~Vg-trT~~qC~~hf~~l 257 (336)
.++.||.+||.+|+++|++|| ++|..||+++| +||.+||++||.++
T Consensus 13 rKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~Ny 60 (459)
T PLN03091 13 RKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINY 60 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhc
Confidence 357899999999999999999 79999999997 89999999999974
No 15
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.45 E-value=1.2e-07 Score=67.53 Aligned_cols=44 Identities=32% Similarity=0.555 Sum_probs=39.2
Q ss_pred ccCCCCCCccccccccccC-CCccchhhhhccCCCCCCCCCCCce
Q 019767 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFR 204 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~~s~df~ 204 (336)
+.|+.|+.+|+..+|+|.+ .+++||..||.+|+++.++.+.||+
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 4699999999988888865 4688999999999999999999984
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.40 E-value=2.5e-07 Score=86.79 Aligned_cols=45 Identities=20% Similarity=0.485 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-CCCHHHHHHHHhcC
Q 019767 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-GKSEKDCITHFIKL 257 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG-~nW~~IA~~Vg-trT~~qC~~hf~~l 257 (336)
+++||.|||.+|.+.|++|| ++|..||++.| .|+..+|++||.++
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~Ny 55 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNY 55 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcc
Confidence 68999999999999999999 99999999999 99999999999985
No 17
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.28 E-value=8.6e-07 Score=83.58 Aligned_cols=46 Identities=17% Similarity=0.338 Sum_probs=43.5
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 211 ~~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
..++.||.+|+.+||+.+..||..|..||+++++||..+|+.||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 4578999999999999999999999999999999999999999965
No 18
>PLN02529 lysine-specific histone demethylase 1
Probab=98.26 E-value=1.1e-06 Score=94.48 Aligned_cols=85 Identities=24% Similarity=0.287 Sum_probs=70.5
Q ss_pred CCCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccch-HHHHHHHHHhhhh
Q 019767 44 SYSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGD-VGSIRRVFDFLET 122 (336)
Q Consensus 44 s~s~WF~~~~ih~iE~~~lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gD-v~~i~Rih~FLe~ 122 (336)
..+.=|+.+.+++.|+++. |-..-..+.++.|+.|||.|+.+|+.||..|||+++++..+.-+ ...|...|+||.+
T Consensus 62 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l~~ 138 (738)
T PLN02529 62 ALSVGFPIDALLEEEIRAG---VVRELGGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLLY 138 (738)
T ss_pred HHHcCCCccccCHHHHhcc---ccCccccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHHHh
Confidence 4567899999999998662 11122356899999999999999999999999999998876543 4557799999999
Q ss_pred cccccCCCC
Q 019767 123 WGLINYFAS 131 (336)
Q Consensus 123 wGlINy~~~ 131 (336)
.|.|||++.
T Consensus 139 ~~~inc~vn 147 (738)
T PLN02529 139 NGYINFGVS 147 (738)
T ss_pred CCCcceeec
Confidence 999999998
No 19
>PLN03091 hypothetical protein; Provisional
Probab=98.07 E-value=4.9e-06 Score=84.00 Aligned_cols=46 Identities=15% Similarity=0.437 Sum_probs=43.3
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 211 ~~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
..++.||.+|+.+||+.+..||..|.+||+++.+||..+|+.||..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 4568999999999999999999999999999999999999999975
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.82 E-value=2.6e-05 Score=73.27 Aligned_cols=44 Identities=16% Similarity=0.505 Sum_probs=41.5
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHh
Q 019767 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFI 255 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~ 255 (336)
.++.||.|||.+|+++...+|..|..||.++++||..++..||.
T Consensus 61 krg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wn 104 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWN 104 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHH
Confidence 36899999999999999999999999999999999999999884
No 21
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.64 E-value=6e-05 Score=79.04 Aligned_cols=46 Identities=30% Similarity=0.701 Sum_probs=43.3
Q ss_pred ccCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 211 EARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 211 ~~~~~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
...+.||.+|+.+|+.||++|| .+|-+|-+.|++|+..||+.||++
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~n 404 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTN 404 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHH
Confidence 3468999999999999999999 699999999999999999999987
No 22
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.34 E-value=0.00022 Score=51.38 Aligned_cols=46 Identities=24% Similarity=0.520 Sum_probs=33.8
Q ss_pred ccCCCCCCcccc-ccccccCC-CccchhhhhccCCC-CCCCCCCCceec
Q 019767 161 RLCNGCKTLCTI-ACFACDKY-DLTLCARCYVRGNH-RVGVSSSDFRRV 206 (336)
Q Consensus 161 ~~C~~C~~~~~~-~~~~c~k~-d~~LC~~CF~~G~~-~~~~~s~df~ki 206 (336)
+.|++|+..+.. .++.|... |++||..||..|.. ..+..+|.|+.+
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 369999988754 44544432 78899999999987 456678888753
No 23
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.89 E-value=0.00085 Score=70.71 Aligned_cols=45 Identities=29% Similarity=0.443 Sum_probs=41.6
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCH---HHHHHHHhc
Q 019767 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSE---KDCITHFIK 256 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~---~qC~~hf~~ 256 (336)
..+.||-+||..||++|++|| |+|-++|..+|.||. .-|+.||+.
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 999999999999999 778888876
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=96.88 E-value=0.0011 Score=47.08 Aligned_cols=44 Identities=25% Similarity=0.610 Sum_probs=32.2
Q ss_pred ccCCCCCCccccccccccC-CCccchhhhhccCCCCCCCCCCCcee
Q 019767 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRR 205 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~~s~df~k 205 (336)
+.|++|+..+.-.+|.|.. .+++||..||+.|. ..+...|.|.+
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 3699999987655666654 36889999999997 44555677754
No 25
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.62 E-value=0.0011 Score=52.05 Aligned_cols=44 Identities=25% Similarity=0.675 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHHHHHHH------hC------C--CHHHHHHHhC----CCCHHHHHHHHhcC
Q 019767 214 SDWTEKETLQLLEAIMH------FG------D--DWRKVAQHVS----GKSEKDCITHFIKL 257 (336)
Q Consensus 214 ~~WT~eE~~~LLeav~~------yG------~--nW~~IA~~Vg----trT~~qC~~hf~~l 257 (336)
..||.+|+..||+.+.. ++ + -|..||+.+. .||+.||..+|-+|
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 57999999999999877 21 1 4999999984 59999999999884
No 26
>PLN02976 amine oxidase
Probab=96.58 E-value=0.0023 Score=73.50 Aligned_cols=82 Identities=21% Similarity=0.267 Sum_probs=70.6
Q ss_pred CCCCCCCCCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhcc--------chHHHHHHH
Q 019767 45 YSRWFSFDSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV--------GDVGSIRRV 116 (336)
Q Consensus 45 ~s~WF~~~~ih~iE~~~lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~--------gDv~~i~Ri 116 (336)
-+.-+....+.++||--|.|..--|. .-+.|+++||.|+-+|-++=.+-|.+++|- ++ +-..+|.-|
T Consensus 451 v~~gl~a~~~~~~e~~~~k~~lkr~~---~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~--v~~~~~~~e~~~~~l~r~~ 525 (1713)
T PLN02976 451 VSAGLKARAVGPIEKIKFKEVLKRKG---GLQEYLECRNMILGLWSKDVSRILPLADCG--VTDTPSEDESPRASLIREV 525 (1713)
T ss_pred hhccccccccChHHHHHHHHHHHhcc---chHHHHHHHHHHHHHhhhhhhhcccHhhcc--ccCCcccccCchhhHHHHH
Confidence 34556678899999999999997543 578999999999999999999999999994 32 347889999
Q ss_pred HHhhhhcccccCCCC
Q 019767 117 FDFLETWGLINYFAS 131 (336)
Q Consensus 117 h~FLe~wGlINy~~~ 131 (336)
+.||++.|.||-|+.
T Consensus 526 ~~fld~~gyin~g~~ 540 (1713)
T PLN02976 526 YLFLDQRGYINAGIA 540 (1713)
T ss_pred HHHhhccCceecccc
Confidence 999999999999987
No 27
>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=96.52 E-value=0.0025 Score=44.86 Aligned_cols=41 Identities=24% Similarity=0.655 Sum_probs=31.0
Q ss_pred cCCCCCCccccccccccCC-CccchhhhhccCCCCCCCCCCCceec
Q 019767 162 LCNGCKTLCTIACFACDKY-DLTLCARCYVRGNHRVGVSSSDFRRV 206 (336)
Q Consensus 162 ~C~~C~~~~~~~~~~c~k~-d~~LC~~CF~~G~~~~~~~s~df~ki 206 (336)
.|++|+..+.-.+|.|... |++||..||..| .+ ..|.|.++
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 5999999876566666553 788999999998 33 67777653
No 28
>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=96.43 E-value=0.0028 Score=44.56 Aligned_cols=38 Identities=21% Similarity=0.502 Sum_probs=29.0
Q ss_pred cccCCCCCCccccccccccC-CCccchhhhhccCCCCCC
Q 019767 160 KRLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVG 197 (336)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k-~d~~LC~~CF~~G~~~~~ 197 (336)
...|+.|+..+...+|.|.. .|++||.+||..|.++..
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~ 42 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGE 42 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCC
Confidence 45799999987655566653 378899999999987643
No 29
>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=96.39 E-value=0.003 Score=45.74 Aligned_cols=37 Identities=27% Similarity=0.783 Sum_probs=27.1
Q ss_pred cCCCCCCccccccccccC-CCccchhhhhccCCCCCCC
Q 019767 162 LCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (336)
Q Consensus 162 ~C~~C~~~~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~ 198 (336)
.|++|...+...+|.|.+ .|++||..||..|.+..++
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H 39 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGH 39 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCC
Confidence 599999876544454432 3788999999999986544
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=96.22 E-value=0.0048 Score=44.54 Aligned_cols=44 Identities=30% Similarity=0.591 Sum_probs=29.3
Q ss_pred cCCCCC-CccccccccccC-CCccchhhhhccCCCCC-CCCCCCcee
Q 019767 162 LCNGCK-TLCTIACFACDK-YDLTLCARCYVRGNHRV-GVSSSDFRR 205 (336)
Q Consensus 162 ~C~~C~-~~~~~~~~~c~k-~d~~LC~~CF~~G~~~~-~~~s~df~k 205 (336)
.|++|+ ..+.-.+|.|.. .|++||.+||..|.... +..+|.|..
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 555533444432 36889999999997644 344777653
No 31
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.21 E-value=0.0052 Score=64.75 Aligned_cols=45 Identities=22% Similarity=0.641 Sum_probs=42.8
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
.++.||.+|+..|-..+.++|++|..|++.+| |.|..|+.||.++
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~ 427 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQY 427 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHh
Confidence 57899999999999999999999999999997 8999999999985
No 32
>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=96.17 E-value=0.0051 Score=44.42 Aligned_cols=43 Identities=26% Similarity=0.539 Sum_probs=29.1
Q ss_pred cCCCCCC-ccccccccccC-CCccchhhhhccCCCCC-CCCCCCce
Q 019767 162 LCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRV-GVSSSDFR 204 (336)
Q Consensus 162 ~C~~C~~-~~~~~~~~c~k-~d~~LC~~CF~~G~~~~-~~~s~df~ 204 (336)
.|++|+. ++.-.+|.|.. .|++||.+||..|.... +...|.|.
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 36889999999998643 34556553
No 33
>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=95.79 E-value=0.0096 Score=43.19 Aligned_cols=41 Identities=29% Similarity=0.680 Sum_probs=28.0
Q ss_pred cCCCCCCc-ccc---ccccccCCCccchhhhhccCCCCC-CCCCCCce
Q 019767 162 LCNGCKTL-CTI---ACFACDKYDLTLCARCYVRGNHRV-GVSSSDFR 204 (336)
Q Consensus 162 ~C~~C~~~-~~~---~~~~c~k~d~~LC~~CF~~G~~~~-~~~s~df~ 204 (336)
.|++|+.. +.. +|..|. |++||..||..|.+.. +...|.++
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~--d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCF--NYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCceeeeEECCCCC--CcCchHHHHhCCCcCCCCCCCCCee
Confidence 59999964 443 444555 6789999999998754 34555543
No 34
>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=95.61 E-value=0.012 Score=42.43 Aligned_cols=43 Identities=23% Similarity=0.512 Sum_probs=29.2
Q ss_pred ccCCCCCC-ccccccccc---cCCCccchhhhhccCCCCCCCCCCCcee
Q 019767 161 RLCNGCKT-LCTIACFAC---DKYDLTLCARCYVRGNHRVGVSSSDFRR 205 (336)
Q Consensus 161 ~~C~~C~~-~~~~~~~~c---~k~d~~LC~~CF~~G~~~~~~~s~df~k 205 (336)
+.|++|+. .+.-..|.| ...+++||..||..|. .+..+|.|.+
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 36999998 454444444 4336889999999996 4555666554
No 35
>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=95.47 E-value=0.0057 Score=43.46 Aligned_cols=39 Identities=28% Similarity=0.607 Sum_probs=22.6
Q ss_pred cccCCCCCCc-cccccccccC-CCccchhhhhccCCCCCCC
Q 019767 160 KRLCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (336)
Q Consensus 160 k~~C~~C~~~-~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~ 198 (336)
...|++|+.. +.-.+|.|.. .|++||..||..|.+...+
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 4679999984 4444555543 4788999999999865443
No 36
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=94.97 E-value=0.022 Score=59.03 Aligned_cols=44 Identities=23% Similarity=0.615 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
.+-|+..||..|--+|.+|| ..|.+|+..+..||+.||..+|..
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 46799999999999999999 679999999999999999999975
No 37
>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=94.93 E-value=0.022 Score=39.80 Aligned_cols=37 Identities=32% Similarity=0.671 Sum_probs=26.4
Q ss_pred ccCCCCCCccccccccccC-CCccchhhhhccCCCCCCC
Q 019767 161 RLCNGCKTLCTIACFACDK-YDLTLCARCYVRGNHRVGV 198 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~ 198 (336)
+.|++|....+ ..+.|.. .|++||..||.++.++..+
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 35999988665 4444433 2788999999998876544
No 38
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.72 E-value=0.027 Score=59.57 Aligned_cols=53 Identities=25% Similarity=0.481 Sum_probs=45.7
Q ss_pred cCCCCCHHHHHHHHHHHH-------Hh-------C------------CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 212 ARSDWTEKETLQLLEAIM-------HF-------G------------DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~-------~y-------G------------~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
.++.||-+|+.+||..|+ +| | =+|..|++.+|||+..||+.||-+|=+...+.
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 567899999999999995 44 1 27999999999999999999999987776665
No 39
>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=94.54 E-value=0.04 Score=39.36 Aligned_cols=42 Identities=26% Similarity=0.781 Sum_probs=28.0
Q ss_pred cCCCCCCc-cccccccccC-CCccchhhhhccCCCCCCCCCCCceec
Q 019767 162 LCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRRV 206 (336)
Q Consensus 162 ~C~~C~~~-~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~~s~df~ki 206 (336)
.|++|+.. +.-..|.|.. .|++||..||..+.+. ..|.|.++
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~H~---~~H~F~ri 45 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRKHN---TRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCCCcC---CCCceeeC
Confidence 59999864 4334444433 3688999999997643 46777654
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.32 E-value=0.096 Score=40.35 Aligned_cols=45 Identities=20% Similarity=0.430 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------CHHHHHHHhC-----CCCHHHHHHHHhcC
Q 019767 213 RSDWTEKETLQLLEAIMHFG----D-------------DWRKVAQHVS-----GKSEKDCITHFIKL 257 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG----~-------------nW~~IA~~Vg-----trT~~qC~~hf~~l 257 (336)
+..||.+|...||+.|++|. + -|.+|++.+. .||..|++.+|.++
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 35799999999999999985 1 4999999883 59999999999764
No 41
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=94.22 E-value=0.035 Score=57.52 Aligned_cols=45 Identities=20% Similarity=0.582 Sum_probs=42.1
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
.+..|+.+||.+||.+......-|..||..|| ||..||..||..+
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 45789999999999999999999999999997 8999999999885
No 42
>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=93.84 E-value=0.059 Score=38.37 Aligned_cols=41 Identities=24% Similarity=0.606 Sum_probs=26.7
Q ss_pred cCCCCCC-ccccccccccC-CCccchhhhhccCCCCCCCCCCCcee
Q 019767 162 LCNGCKT-LCTIACFACDK-YDLTLCARCYVRGNHRVGVSSSDFRR 205 (336)
Q Consensus 162 ~C~~C~~-~~~~~~~~c~k-~d~~LC~~CF~~G~~~~~~~s~df~k 205 (336)
.|++|+. .+.-.+|.|.. .|++||..||..+.+ ...|.|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~~H---~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGDKH---DLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCCCC---CCCCCEEe
Confidence 5999994 44334444443 268899999997553 44566654
No 43
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=92.91 E-value=0.15 Score=54.86 Aligned_cols=44 Identities=20% Similarity=0.422 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
...||..|..++-.|+-.|..|+..|++.|.+||..||++.|.-
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 46899999999999999999999999999999999999998853
No 44
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=92.42 E-value=0.12 Score=54.07 Aligned_cols=46 Identities=20% Similarity=0.621 Sum_probs=43.4
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 211 ~~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
..+..|+.+|+..|++.-..+|.-|..||..++.||..+|..+|+.
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~ 115 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVN 115 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999996
No 45
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.37 E-value=0.19 Score=50.58 Aligned_cols=44 Identities=23% Similarity=0.477 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
...||.+|..++-.|+.++|.++.-||...++|...|+..+|++
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999987
No 46
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=92.04 E-value=0.087 Score=55.02 Aligned_cols=43 Identities=21% Similarity=0.460 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHh
Q 019767 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFI 255 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~ 255 (336)
.+.|+..|+..|+-+++.|| .||..||..++.||++||..||.
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~ 63 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWN 63 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhh
Confidence 46899999999999999999 89999999999999999999993
No 47
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=91.84 E-value=0.23 Score=49.85 Aligned_cols=45 Identities=22% Similarity=0.429 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHH-HHHhCCCCHHHHHHHHhcC
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKV-AQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~I-A~~VgtrT~~qC~~hf~~l 257 (336)
-..||.+|=..+=+|++.||.|+..| +..|.+|+..+|+..|..-
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 36899999999999999999999999 5689999999999988643
No 48
>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=91.69 E-value=0.18 Score=45.18 Aligned_cols=50 Identities=16% Similarity=0.409 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C-----CHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 213 RSDWTEKETLQLLEAIMHFG--D-----DWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG--~-----nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
.+.||.+||++|-|.|-+|= | -.++|++.++ ||+.-|-.||..+ +...|-
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 35799999999999999886 3 5899999995 9999999999875 555565
No 49
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=90.84 E-value=0.21 Score=52.86 Aligned_cols=45 Identities=24% Similarity=0.565 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHH----------HHHhCCCCHHHHHHHHhcC
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKV----------AQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~I----------A~~VgtrT~~qC~~hf~~l 257 (336)
+..||.+|+.-+.+||.++|.|+++| -..+..||.+|.+.||.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 67899999999999999999999999 3344569999999999874
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=90.54 E-value=0.32 Score=47.91 Aligned_cols=45 Identities=31% Similarity=0.581 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHHhC-----C-----CHHHHHHHh---C-CCCHHHHHHHHhcCC
Q 019767 214 SDWTEKETLQLLEAIMHFG-----D-----DWRKVAQHV---S-GKSEKDCITHFIKLP 258 (336)
Q Consensus 214 ~~WT~eE~~~LLeav~~yG-----~-----nW~~IA~~V---g-trT~~qC~~hf~~lP 258 (336)
..|+.+|++.||++-...- + .|..||... | .||+.||..+|-+|.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 6899999999999985433 3 499999943 4 499999999997754
No 51
>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=88.51 E-value=0.56 Score=39.96 Aligned_cols=45 Identities=18% Similarity=0.434 Sum_probs=36.0
Q ss_pred cCCCCCHHHHHHHHHHHHHhC----CCHHHHHHHhC------------CCCHHHHHHHHhc
Q 019767 212 ARSDWTEKETLQLLEAIMHFG----DDWRKVAQHVS------------GKSEKDCITHFIK 256 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG----~nW~~IA~~Vg------------trT~~qC~~hf~~ 256 (336)
.+..||.+||..||-.+.+|| |+|+.|-+.|- +||+.++..|-..
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~t 108 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNT 108 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHH
Confidence 457899999999999999999 68999988773 7999998877543
No 52
>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=83.79 E-value=1.8 Score=33.18 Aligned_cols=44 Identities=16% Similarity=0.413 Sum_probs=30.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC-------CC--HHHHHHHhC-CCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFG-------DD--WRKVAQHVS-GKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG-------~n--W~~IA~~Vg-trT~~qC~~hf~~ 256 (336)
+..+|.+||..|++-|..+. || |++.++.-. .+|-+-=+.||++
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 35789999999999996543 55 999999766 6798999999987
No 53
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=83.00 E-value=1.3 Score=46.37 Aligned_cols=92 Identities=7% Similarity=-0.063 Sum_probs=74.1
Q ss_pred ecCCCCCCCCCCCCCHHHHhhCccccCCCC-CCCChHHHHHHHHHHHHHHHhCCCccee-----HHHHHHhcc--chHHH
Q 019767 41 NVPSYSRWFSFDSISECEVKFLPEFFDSRS-PSKNPRVYRYYRDSIVKHYRENPSRKIT-----FTDVRRTLV--GDVGS 112 (336)
Q Consensus 41 vIPs~s~WF~~~~ih~iE~~~lpEff~~~~-~~ktp~~Y~~~RN~ii~~yr~np~~yLT-----~t~~r~~l~--gDv~~ 112 (336)
..+..+.-++...=+.-.....++|+-+++ ....+..|+.+|..+++.++---..+.+ -+..+++.. +.+-+
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 677778888888888899999999999863 2567888999999999988874444443 455666665 57899
Q ss_pred HHHHHHhhhhcccccCCCCC
Q 019767 113 IRRVFDFLETWGLINYFASV 132 (336)
Q Consensus 113 i~Rih~FLe~wGlINy~~~~ 132 (336)
+.+|+.|.+.|+-|+.+|.+
T Consensus 265 LE~ie~y~ddW~kVa~hVg~ 284 (506)
T KOG1279|consen 265 LEAIEMYGDDWNKVADHVGT 284 (506)
T ss_pred HHHHHHhcccHHHHHhccCC
Confidence 99999999999999999984
No 54
>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=81.87 E-value=0.98 Score=32.06 Aligned_cols=31 Identities=32% Similarity=0.690 Sum_probs=21.0
Q ss_pred cCCCCCCc-cccccccccC-CCccchhhhhccC
Q 019767 162 LCNGCKTL-CTIACFACDK-YDLTLCARCYVRG 192 (336)
Q Consensus 162 ~C~~C~~~-~~~~~~~c~k-~d~~LC~~CF~~G 192 (336)
.|++|+.. +.-..|.|.. .|++||..||.+.
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 59999864 4333444432 4788999999873
No 55
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=81.61 E-value=1.2 Score=46.13 Aligned_cols=51 Identities=16% Similarity=0.386 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHH-HHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 214 SDWTEKETLQLLEAIMHFGDDWRKV-AQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 214 ~~WT~eE~~~LLeav~~yG~nW~~I-A~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
..||+-|-.++-||+++||.|+++| +++++=|+-..+++.|.-.--.|.|.
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYv 337 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYV 337 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHH
Confidence 5899999999999999999999999 55677788888888776655555554
No 56
>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=80.10 E-value=2.3 Score=33.54 Aligned_cols=43 Identities=21% Similarity=0.466 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHh-------C------CCHHHHHHHhC-----CCCHHHHHHHHhcC
Q 019767 215 DWTEKETLQLLEAIMHF-------G------DDWRKVAQHVS-----GKSEKDCITHFIKL 257 (336)
Q Consensus 215 ~WT~eE~~~LLeav~~y-------G------~nW~~IA~~Vg-----trT~~qC~~hf~~l 257 (336)
.||.+++..||+.+... + ..|+.|++.+. ..|..||..||-.|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999998544 1 14999998874 46899999998774
No 57
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=79.87 E-value=1 Score=44.98 Aligned_cols=34 Identities=32% Similarity=0.773 Sum_probs=23.8
Q ss_pred cccCCCCCCc-cccccccccC-CCccchhhhhccCC
Q 019767 160 KRLCNGCKTL-CTIACFACDK-YDLTLCARCYVRGN 193 (336)
Q Consensus 160 k~~C~~C~~~-~~~~~~~c~k-~d~~LC~~CF~~G~ 193 (336)
...|++|++- .+-.+|.|-. +|++||..||.+|.
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~ 43 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGA 43 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCC
Confidence 3569999875 3444444432 37779999999986
No 58
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=79.67 E-value=1.8 Score=39.28 Aligned_cols=42 Identities=14% Similarity=0.347 Sum_probs=35.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C-----CHHHHHHHhCCCCHHHHHHHHh
Q 019767 213 RSDWTEKETLQLLEAIMHFG--D-----DWRKVAQHVSGKSEKDCITHFI 255 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG--~-----nW~~IA~~VgtrT~~qC~~hf~ 255 (336)
.+.||.+++++|-+.|-.|+ | -...+++.+ +||.-.|..||.
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwN 53 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWN 53 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHH
Confidence 46799999999999999998 3 366777777 489999999993
No 59
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=78.77 E-value=3.2 Score=34.05 Aligned_cols=51 Identities=20% Similarity=0.464 Sum_probs=37.2
Q ss_pred cCCCCCHHHHHHHHHHHHHh----C----CCHHHHHHHhCC-----CCHHHHHHHHhcCCCCCccc
Q 019767 212 ARSDWTEKETLQLLEAIMHF----G----DDWRKVAQHVSG-----KSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~y----G----~nW~~IA~~Vgt-----rT~~qC~~hf~~lPIeD~fl 264 (336)
+.+-||+++|..||+|+-.| | .||...-++|.. =|..|...+..+| ...|.
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrL--K~Ky~ 66 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRL--KKKYR 66 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHH--HHHHH
Confidence 34679999999999999888 5 488888887753 2667777766653 44444
No 60
>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=77.58 E-value=5.4 Score=27.70 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 219 KETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 219 eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
+=+.+||+.++.-| --|.+||+.+|- |+..|..|..+|
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHHh
Confidence 45788999999999 789999999985 899998887653
No 61
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=75.76 E-value=4.2 Score=46.22 Aligned_cols=40 Identities=23% Similarity=0.539 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHH
Q 019767 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITH 253 (336)
Q Consensus 214 ~~WT~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~h 253 (336)
.+||..+-..++.|.++|| +|-..||..|++||++|+..+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 5799999999999999999 999999999999999999753
No 62
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=74.70 E-value=5.6 Score=41.20 Aligned_cols=46 Identities=22% Similarity=0.468 Sum_probs=41.7
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 211 EARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 211 ~~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
.+...||+||..+|-.+.+.||.++.+|-+.+.-|+-...+..|..
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 3567899999999999999999999999999999999999888754
No 63
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=71.33 E-value=2.6 Score=40.91 Aligned_cols=30 Identities=30% Similarity=0.703 Sum_probs=22.3
Q ss_pred ccCCCCCC-cccc---ccccccCCCccchhhhhccC
Q 019767 161 RLCNGCKT-LCTI---ACFACDKYDLTLCARCYVRG 192 (336)
Q Consensus 161 ~~C~~C~~-~~~~---~~~~c~k~d~~LC~~CF~~G 192 (336)
..|+.|+. .+.- +|..|. |++||..|+..+
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~--dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCP--DYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCCC--ccchhHHhhcCC
Confidence 57999998 5543 444555 567999999987
No 64
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=70.67 E-value=2 Score=46.82 Aligned_cols=36 Identities=22% Similarity=0.517 Sum_probs=23.8
Q ss_pred ccCCCCCCc-cccccccccC-CCccchhhhhccCCCCC
Q 019767 161 RLCNGCKTL-CTIACFACDK-YDLTLCARCYVRGNHRV 196 (336)
Q Consensus 161 ~~C~~C~~~-~~~~~~~c~k-~d~~LC~~CF~~G~~~~ 196 (336)
-.|++|+.- +.-..|.|.+ +++++|..||..|+-..
T Consensus 604 ~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak 641 (966)
T KOG4286|consen 604 AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAK 641 (966)
T ss_pred hhcchhhhCccceeeeeehhhcChhHHhhHhhhccccc
Confidence 359999763 2222455543 57889999999987533
No 65
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=67.92 E-value=7.3 Score=44.35 Aligned_cols=45 Identities=11% Similarity=0.256 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC------------CCCHHHHHHHHhcC
Q 019767 213 RSDWTEKETLQLLEAIMHFG-DDWRKVAQHVS------------GKSEKDCITHFIKL 257 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG-~nW~~IA~~Vg------------trT~~qC~~hf~~l 257 (336)
+..||.+|+..||-.+.+|| |+|++|-+.|- +||+.++..|-..|
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 46799999999999999999 99999977763 79999998877654
No 66
>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=67.49 E-value=8.5 Score=26.39 Aligned_cols=25 Identities=20% Similarity=0.201 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHhCC
Q 019767 220 ETLQLLEAIMHFGDDWRKVAQHVSG 244 (336)
Q Consensus 220 E~~~LLeav~~yG~nW~~IA~~Vgt 244 (336)
|-..|.++++.+|||..+.|+.+|-
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 7788999999999999999999983
No 67
>smart00595 MADF subfamily of SANT domain.
Probab=66.60 E-value=4.8 Score=31.35 Aligned_cols=28 Identities=18% Similarity=0.531 Sum_probs=24.5
Q ss_pred CHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 234 DWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 234 nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
-|..||..+|. |.++|+.+|..| -+.|.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L--R~~y~ 56 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL--RDRYR 56 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH--HHHHH
Confidence 59999999987 999999999994 56675
No 68
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=64.59 E-value=11 Score=26.30 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHhCCCcce-eHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 78 YRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 78 Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
|-.+|+.|+.... .|...+ |..+....+.-....+.|...-|+.-|+|-.
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 5667777776432 366778 8888877777788999999999999999853
No 69
>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=63.68 E-value=12 Score=30.84 Aligned_cols=49 Identities=27% Similarity=0.392 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHhCCCcceeHHHHHHhcc-----chHHHHHHHHHhhhhcccccC
Q 019767 79 RYYRDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 79 ~~~RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlINy 128 (336)
-.-|..|++.-..++. .+|+.+.-..|. -+...|.|..++|+.-|||.=
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 4568999998888877 999999877764 267899999999999999974
No 70
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=62.71 E-value=4.1 Score=42.15 Aligned_cols=44 Identities=11% Similarity=0.365 Sum_probs=39.5
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
..-+||..|-. ++.....||.+...||+.+++||++|...+|++
T Consensus 469 ~~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 469 INYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred ecCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 34689998866 888889999999999999999999999999987
No 71
>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=62.55 E-value=12 Score=27.53 Aligned_cols=53 Identities=19% Similarity=0.297 Sum_probs=40.6
Q ss_pred hHHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 75 PRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 75 p~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
-++|-.+|+.|.+-- .-|...| |..+--+.+.--...+.+....|+..|+|--
T Consensus 3 ~~i~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 3 EQIYDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 357888888887743 3368899 9988888888788999999999999999853
No 72
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=61.08 E-value=7.8 Score=38.45 Aligned_cols=97 Identities=16% Similarity=0.257 Sum_probs=52.7
Q ss_pred cccCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHHHHhCCCHHHHH
Q 019767 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRKVA 239 (336)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~eE~~~LLeav~~yG~nW~~IA 239 (336)
...|.-|+..- ..|..|. .++.||.+|-. .|+. +-.|-.+ +.. ..-+.||.+|..+|..+=..--..|-+--
T Consensus 20 Nk~CaDCga~~-P~W~S~n-lGvfiCi~Cag--vHRs-LGvhiS~-VKS--itLD~wt~~~l~~m~~gGN~~a~~~~e~~ 91 (319)
T COG5347 20 NKKCADCGAPN-PTWASVN-LGVFLCIDCAG--VHRS-LGVHISK-VKS--LTLDNWTEEELRRMEVGGNSNANRFYEKN 91 (319)
T ss_pred cCccccCCCCC-CceEecc-cCeEEEeecch--hhhc-cccceee-eee--eecccCCHHHHHHHHHhcchhhhhHhccC
Confidence 45799998875 5566554 57889999953 3321 1222221 111 12368999987777652100001222211
Q ss_pred HH----hC--CCCHHHHHHHHhc-CCCCCccc
Q 019767 240 QH----VS--GKSEKDCITHFIK-LPFGQEFI 264 (336)
Q Consensus 240 ~~----Vg--trT~~qC~~hf~~-lPIeD~fl 264 (336)
-- ++ .+.....+.+|++ ++.+-.|.
T Consensus 92 ~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~ 123 (319)
T COG5347 92 LLDQLLLPIKAKYDSSVAKKYIRKKYELKKFI 123 (319)
T ss_pred CCcccccccccccCHHHHHHHHHHHHHhhhcc
Confidence 11 12 3566778888876 56666665
No 73
>PHA00442 host recBCD nuclease inhibitor
Probab=60.09 E-value=9.8 Score=28.42 Aligned_cols=26 Identities=23% Similarity=0.474 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHhC-CCHHHHHHHh
Q 019767 217 TEKETLQLLEAIMHFG-DDWRKVAQHV 242 (336)
Q Consensus 217 T~eE~~~LLeav~~yG-~nW~~IA~~V 242 (336)
+-+-+...|++++.+| +||+.+.+.+
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 4456788999999999 9999987765
No 74
>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=58.82 E-value=30 Score=24.67 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=34.0
Q ss_pred HHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 89 YRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 89 yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
-..+|...+|+++..+.+.-+..++.|+..=|+..|||--.
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 75
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=58.45 E-value=17 Score=30.94 Aligned_cols=60 Identities=13% Similarity=0.376 Sum_probs=42.4
Q ss_pred CCCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHHHHhCCCHHHHHHHh
Q 019767 163 CNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFGDDWRKVAQHV 242 (336)
Q Consensus 163 C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~eE~~~LLeav~~yG~nW~~IA~~V 242 (336)
|..|+..+.+..+.|..++.. .+|.|.. ..|-. -..|++.+++..-+..||-++|++.+
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 CPVCGGELVVTRLKCPSCGTE------IEGEFEL----PWFAR-----------LSPEQLEFIKLFIKNRGNLKEMEKEL 59 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE------EEeeecc----chhhc-----------CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 889999988877777654432 2344322 11212 23488999999999999999999999
Q ss_pred C
Q 019767 243 S 243 (336)
Q Consensus 243 g 243 (336)
|
T Consensus 60 g 60 (113)
T PF09862_consen 60 G 60 (113)
T ss_pred C
Confidence 8
No 76
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=57.63 E-value=8.9 Score=40.90 Aligned_cols=89 Identities=27% Similarity=0.506 Sum_probs=50.1
Q ss_pred ccCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHHHHhC--------
Q 019767 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFG-------- 232 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~eE~~~LLeav~~yG-------- 232 (336)
..|..|+... ..+.|....+.+|..|- |.++.-- | +++. ..-..||.+|...|. ..|
T Consensus 24 k~CADCgs~~--P~WASiNlGIFICi~CS--GIHRsLG--h---RVKS--LSLDkWT~EEVe~Mk----~gGN~~AN~iy 88 (648)
T PLN03119 24 RRCINCNSLG--PQYVCTTFWTFVCMACS--GIHREFT--H---RVKS--VSMSKFTSKEVEVLQ----NGGNQRAREIY 88 (648)
T ss_pred CccccCCCCC--CCceeeccceEEeccch--hhhccCC--c---eeec--cccCCCCHHHHHHHH----HhchHHHHHHH
Confidence 4688887642 33445566788999984 3443321 2 3332 223689998864333 344
Q ss_pred -CCHHHHHHHhCCCCHHHHHHHHhc-CCCCCccc
Q 019767 233 -DDWRKVAQHVSGKSEKDCITHFIK-LPFGQEFI 264 (336)
Q Consensus 233 -~nW~~IA~~VgtrT~~qC~~hf~~-lPIeD~fl 264 (336)
.+|..-...++..+..+-+..|++ -+++..|.
T Consensus 89 eanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~ 122 (648)
T PLN03119 89 LKNWDHQRQRLPENSNAERVREFIKNVYVQKKYA 122 (648)
T ss_pred HhhcccccCCCCCCccHHHHHHHHHHHHhhhhcc
Confidence 346543223343344555667887 46777777
No 77
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=57.60 E-value=17 Score=31.62 Aligned_cols=45 Identities=18% Similarity=0.182 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 218 ~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
++-+.+||+++++-| -.|.+||+.+|- |+..|..|+-+| .++-++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL-~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKM-KQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHH-HHCCCe
Confidence 357899999999999 799999999984 999999999887 334444
No 78
>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=55.50 E-value=25 Score=28.55 Aligned_cols=46 Identities=22% Similarity=0.335 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhcc-----chHHHHHHHHHhhhhcccccC
Q 019767 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlINy 128 (336)
|-.|++.-... .+.+|+.+.-..|. -+...+.|..++|+.-|||.-
T Consensus 3 R~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 3 RLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 77788877765 68899999877774 378999999999999999984
No 79
>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=55.22 E-value=32 Score=24.35 Aligned_cols=45 Identities=22% Similarity=0.311 Sum_probs=34.7
Q ss_pred HHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 84 SIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 84 ~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
.|+......+ ++..+..+.+.-....+.|+..-|++.|+|+....
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 89999888887789999999999999999996433
No 80
>PLN03131 hypothetical protein; Provisional
Probab=55.00 E-value=12 Score=40.27 Aligned_cols=92 Identities=26% Similarity=0.469 Sum_probs=49.6
Q ss_pred ccCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHH------HHhCCC
Q 019767 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAI------MHFGDD 234 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~eE~~~LLeav------~~yG~n 234 (336)
..|..|+... ..+.|....+.+|..|-. .++.- .| +++. ..-..||.+|...| +.+ +.|-.+
T Consensus 24 k~CADCga~~--P~WASiNlGIFICi~CSG--IHRsL--gh---RVKS--VTLD~WtdeEV~~M-k~gGN~~AN~iyean 91 (705)
T PLN03131 24 RRCINCNSLG--PQFVCTNFWTFICMTCSG--IHREF--TH---RVKS--VSMSKFTSQDVEAL-QNGGNQRAREIYLKD 91 (705)
T ss_pred CccccCCCCC--CCeeEeccceEEchhchh--hhccc--Cc---cccc--ccCCCCCHHHHHHH-HHhccHHHHHHHHhh
Confidence 4688887642 333445667889999953 34332 12 3332 12368999886433 221 112235
Q ss_pred HHHHHHHhCCCCHHHHHHHHhc-CCCCCccc
Q 019767 235 WRKVAQHVSGKSEKDCITHFIK-LPFGQEFI 264 (336)
Q Consensus 235 W~~IA~~VgtrT~~qC~~hf~~-lPIeD~fl 264 (336)
|..--..++..+..+-+..|++ -+++..|.
T Consensus 92 wd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa 122 (705)
T PLN03131 92 WDQQRQRLPDNSKVDKIREFIKDIYVDKKYA 122 (705)
T ss_pred cccccCCCCCCccHHHHHHHHHHHHhhhhhh
Confidence 5533233444444555677877 46677777
No 81
>PRK09462 fur ferric uptake regulator; Provisional
Probab=54.97 E-value=23 Score=30.56 Aligned_cols=46 Identities=17% Similarity=0.381 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhcc-----chHHHHHHHHHhhhhccccc
Q 019767 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLIN 127 (336)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlIN 127 (336)
|-.|++.-.....+.+|+.+.-..|. -+...+.|...+|+.-|||.
T Consensus 19 R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~ 69 (148)
T PRK09462 19 RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT 69 (148)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEE
Confidence 77788877766678999999877664 27899999999999999997
No 82
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.52 E-value=56 Score=24.63 Aligned_cols=52 Identities=15% Similarity=0.126 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 80 YYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 80 ~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
..++.|+..-..++..-+|..+.-+.|.-+...+.|+..=|+.-|+|-....
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 3578899988888766799999999998899999999999999999987654
No 83
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=51.00 E-value=10 Score=43.68 Aligned_cols=28 Identities=25% Similarity=0.605 Sum_probs=25.8
Q ss_pred cCCCCCHHHHHHHHHHHHHhC-CCHHHHH
Q 019767 212 ARSDWTEKETLQLLEAIMHFG-DDWRKVA 239 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG-~nW~~IA 239 (336)
...+|..+++..||-||-+|| |+|+.|-
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 84
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=50.55 E-value=24 Score=31.05 Aligned_cols=39 Identities=15% Similarity=0.281 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 218 ~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
++-|.++|.++++-| -.|.+||+.|| -|+..|..|+.+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg-lS~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG-LSPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC-cCHHHHHHHHHHH
Confidence 557899999999999 79999999998 4899999999886
No 85
>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=50.37 E-value=42 Score=23.26 Aligned_cols=45 Identities=20% Similarity=0.222 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+-|+..|||.+
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 47778876555 6699999999998899999999999999999974
No 86
>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=50.24 E-value=29 Score=24.53 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=34.4
Q ss_pred HHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 85 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
|++..... ...+|+++.-+.+.-....+.|+..=|+++|+|..
T Consensus 8 iL~~l~~~-~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 8 ILEALAES-GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHCHHCT-BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 55555554 44589999998888899999999999999999853
No 87
>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=49.28 E-value=63 Score=22.12 Aligned_cols=43 Identities=33% Similarity=0.427 Sum_probs=34.4
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccc
Q 019767 82 RDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLI 126 (336)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlI 126 (336)
+-.|++.-+.||. +|.++..+.+.-....+.|...-|+.-|+|
T Consensus 5 ~~~Il~~l~~~~~--~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 5 QRKILNYLRENPR--ITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHCTT--S-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHcCC--CCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 4567776677665 999999988888899999999999999997
No 88
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=49.24 E-value=42 Score=28.99 Aligned_cols=57 Identities=16% Similarity=0.330 Sum_probs=42.8
Q ss_pred hHHHHHHHHHHHHHHHh---CCCccee-HHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 75 PRVYRYYRDSIVKHYRE---NPSRKIT-FTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 75 p~~Y~~~RN~ii~~yr~---np~~yLT-~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
-.+|.+|.|.|...-.. .|...|- +.+--..+.-+.+.+.|.+.-||+-|+|.-..-
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 45999999999877654 6666664 333333444589999999999999999986543
No 89
>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=48.85 E-value=9 Score=24.44 Aligned_cols=27 Identities=22% Similarity=0.602 Sum_probs=11.4
Q ss_pred cCCCCCCcccc-ccccccCCCccchhhh
Q 019767 162 LCNGCKTLCTI-ACFACDKYDLTLCARC 188 (336)
Q Consensus 162 ~C~~C~~~~~~-~~~~c~k~d~~LC~~C 188 (336)
.|+.|+..... ..|.|...|+.+...|
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 58899988765 7788888888887776
No 90
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=46.16 E-value=31 Score=34.52 Aligned_cols=69 Identities=19% Similarity=0.334 Sum_probs=53.7
Q ss_pred CCCCHHHHhhCccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhccccc
Q 019767 52 DSISECEVKFLPEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (336)
Q Consensus 52 ~~ih~iE~~~lpEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlIN 127 (336)
.=+++-|.+..--+- -.|..|+.+.-.||..+.. ....+|.++|++.+.-|..-.-+|++|.-..|.|-
T Consensus 361 ~llS~dEq~LC~~l~------i~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 361 ALLSDDEQRLCETLN------ISPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred hhhcchHHHHHHHhC------CCCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 345556665543222 2589999999999998887 47789999999877779999999999988877763
No 91
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=43.90 E-value=28 Score=27.47 Aligned_cols=32 Identities=25% Similarity=0.509 Sum_probs=22.4
Q ss_pred CCcceeHHHHHHhc--cc-hHHHHHHHHHhhhhcc
Q 019767 93 PSRKITFTDVRRTL--VG-DVGSIRRVFDFLETWG 124 (336)
Q Consensus 93 p~~yLT~t~~r~~l--~g-Dv~~i~Rih~FLe~wG 124 (336)
-++.++-.+-+..- +| |..-|--|-.||.+||
T Consensus 45 nneeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 45 NNEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred ccHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 35666655443322 35 8888999999999999
No 92
>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=43.32 E-value=40 Score=29.89 Aligned_cols=44 Identities=18% Similarity=0.213 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhC----CCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVS----GKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~IA~~Vg----trT~~qC~~hf~~ 256 (336)
...-|..|...+-..|++||+|+...|.-.. -.|+.|++..+..
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 3567889999999999999999999998654 3799999877654
No 93
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=40.57 E-value=49 Score=26.42 Aligned_cols=44 Identities=16% Similarity=0.113 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcCCCCCccc
Q 019767 219 KETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 219 eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~fl 264 (336)
+.|..+|.+++..| -.|.+||+.+|- ++..+..+..+| .++.++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L-~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL-EEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH-HHCCCe
Confidence 56889999999988 689999999974 888888888776 334444
No 94
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=40.09 E-value=32 Score=28.57 Aligned_cols=91 Identities=18% Similarity=0.280 Sum_probs=44.5
Q ss_pred ccCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCC-CceecccCcccCCCCCHHHHHHHHHHHHHhC-CCHHHH
Q 019767 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSS-DFRRVEISEEARSDWTEKETLQLLEAIMHFG-DDWRKV 238 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~-df~ki~~~~~~~~~WT~eE~~~LLeav~~yG-~nW~~I 238 (336)
..|.-|+... .-+.+...++.+|..|-.--+. +..| .+++ . ..-..||.+|...| +..| ...+++
T Consensus 4 ~~CaDC~~~~--p~w~s~~~GifvC~~CsgiHR~---lg~his~Vk--S--l~md~w~~~~i~~~----~~~GN~~~n~~ 70 (112)
T smart00105 4 KKCFDCGAPN--PTWASVNLGVFLCIECSGIHRS---LGVHISKVR--S--LTLDTWTEEELRLL----QKGGNENANSI 70 (112)
T ss_pred CcccCCCCCC--CCcEEeccceeEhHHhHHHHHh---cCCCcCeee--e--cccCCCCHHHHHHH----HHhhhHHHHHH
Confidence 3577777632 2233445678899999644221 1112 1222 1 12258999875433 3344 223333
Q ss_pred HH-Hh-------CCCCHHHHHHHHhcC-CCCCccc
Q 019767 239 AQ-HV-------SGKSEKDCITHFIKL-PFGQEFI 264 (336)
Q Consensus 239 A~-~V-------gtrT~~qC~~hf~~l-PIeD~fl 264 (336)
=+ ++ +..+..+-+..|++- +.+..|.
T Consensus 71 ~e~~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~ 105 (112)
T smart00105 71 WESNLDDFSLKPPDSDDQQKYESFIAAKYEEKLFV 105 (112)
T ss_pred HHhhCCccccCCCCCchHHHHHHHHHHHHHhhhcc
Confidence 11 11 112346778888773 4444444
No 95
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=39.08 E-value=49 Score=25.92 Aligned_cols=37 Identities=27% Similarity=0.528 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhCC--------CHHHHHHHhCCC---C--HHHHHHHHhc
Q 019767 220 ETLQLLEAIMHFGD--------DWRKVAQHVSGK---S--EKDCITHFIK 256 (336)
Q Consensus 220 E~~~LLeav~~yG~--------nW~~IA~~Vgtr---T--~~qC~~hf~~ 256 (336)
+...|-.+|.+.|| .|..||+.+|-- + ..+.+.+|.+
T Consensus 37 DL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~ 86 (92)
T PF01388_consen 37 DLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEK 86 (92)
T ss_dssp SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHH
T ss_pred cHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHH
Confidence 45788899999984 799999999842 2 2566777765
No 96
>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=38.63 E-value=1.1e+02 Score=24.45 Aligned_cols=52 Identities=21% Similarity=0.248 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 76 RVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
++-.+|=..||+.|... .+.+.-.+.-+.|.-+-..|..+.+-||..|||-=
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~ 55 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVES 55 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccC
Confidence 45677788999999996 78888888777777788899999999999999964
No 97
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=38.53 E-value=25 Score=26.42 Aligned_cols=29 Identities=17% Similarity=0.515 Sum_probs=24.0
Q ss_pred CHHHHHHHhCC-CCHHHHHHHHhcCCCCCccc
Q 019767 234 DWRKVAQHVSG-KSEKDCITHFIKLPFGQEFI 264 (336)
Q Consensus 234 nW~~IA~~Vgt-rT~~qC~~hf~~lPIeD~fl 264 (336)
-|..||..+|. -+.++|..+|.+ +-+.|-
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~--Lr~~y~ 57 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKN--LRDRYR 57 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHH--HHHHHH
Confidence 59999999985 478999999999 456665
No 98
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=38.17 E-value=19 Score=28.81 Aligned_cols=35 Identities=23% Similarity=0.597 Sum_probs=13.8
Q ss_pred hccccccCCCCCCccc-----cccccccCCCccchhhhhc
Q 019767 156 KETSKRLCNGCKTLCT-----IACFACDKYDLTLCARCYV 190 (336)
Q Consensus 156 ~~~~k~~C~~C~~~~~-----~~~~~c~k~d~~LC~~CF~ 190 (336)
.+.....|..|+.+++ ..+..|....+-+|..||.
T Consensus 5 k~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyE 44 (80)
T PF14569_consen 5 KNLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYE 44 (80)
T ss_dssp S--SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHH
T ss_pred hhcCCcccccccCccccCCCCCEEEEEcccCCccchhHHH
Confidence 3445567999998864 3556777777889999984
No 99
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=37.82 E-value=58 Score=28.31 Aligned_cols=50 Identities=16% Similarity=0.287 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccc-----hHHHHHHHHHhhhhcccccCCCC
Q 019767 81 YRDSIVKHYRENPSRKITFTDVRRTLVG-----DVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~g-----Dv~~i~Rih~FLe~wGlINy~~~ 131 (336)
=|-.|++.-...+. ++|+.+.-+.|.. ....+.|...+|+.-|||+--..
T Consensus 22 qR~~vl~~L~~~~~-~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 22 QRLAVLELLLEADG-HLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 37788887666544 4999998776652 47889999999999999985544
No 100
>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=37.33 E-value=28 Score=27.00 Aligned_cols=23 Identities=35% Similarity=0.612 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 019767 218 EKETLQLLEAIMHFGDDWRKVAQHVSG 244 (336)
Q Consensus 218 ~eE~~~LLeav~~yG~nW~~IA~~Vgt 244 (336)
.++..+||+. |.+|...|+++|-
T Consensus 2 r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 2 RERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred HHHHHHHhCC----CCCHHHHHHHcCc
Confidence 4567788887 9999999999985
No 101
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=36.27 E-value=72 Score=24.41 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=34.5
Q ss_pred HHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 85 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
|++....+ ...+|+++.-+.+.-....+.|+...|+.+|+|-..
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 247999999888877999999999999999999653
No 102
>PRK06474 hypothetical protein; Provisional
Probab=35.82 E-value=79 Score=28.43 Aligned_cols=48 Identities=15% Similarity=0.187 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccc-hHHHHHHHHHhhhhcccccCC
Q 019767 81 YRDSIVKHYRENPSRKITFTDVRRTLVG-DVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rih~FLe~wGlINy~ 129 (336)
.|-.|+..-..++. .+|++++...+.+ ....+.|....|+..|||.--
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 58888887777644 4999999887743 567899999999999999843
No 103
>PRK01905 DNA-binding protein Fis; Provisional
Probab=35.48 E-value=50 Score=25.58 Aligned_cols=28 Identities=14% Similarity=-0.009 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 019767 217 TEKETLQLLEAIMHFGDDWRKVAQHVSG 244 (336)
Q Consensus 217 T~eE~~~LLeav~~yG~nW~~IA~~Vgt 244 (336)
..-|...+.++++.+|||+.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 3447778999999999999999999984
No 104
>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=35.28 E-value=40 Score=28.73 Aligned_cols=36 Identities=14% Similarity=0.154 Sum_probs=25.5
Q ss_pred CcceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
.+|||..+......-+-..+.+|.+||...||=...
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 689999999988888888999999999999985544
No 105
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.79 E-value=23 Score=32.09 Aligned_cols=43 Identities=21% Similarity=0.478 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHHHhC-------CCCH------HHHHHHHhc
Q 019767 214 SDWTEKETLQLLEAIMHFG-DDWRKVAQHVS-------GKSE------KDCITHFIK 256 (336)
Q Consensus 214 ~~WT~eE~~~LLeav~~yG-~nW~~IA~~Vg-------trT~------~qC~~hf~~ 256 (336)
.-|-..-+..||-||-.|| +.|++|...-. -||. -+...+|+.
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~~f~IiNEPFk~e~~kgnfle~KNkFLa 60 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDPRFAIINEPFKTESQKGNFLEMKNKFLA 60 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCCceeeecccccccccccchHHHHHHHHH
Confidence 4588999999999999999 99999987531 2333 377777765
No 106
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=34.53 E-value=1.2e+02 Score=22.10 Aligned_cols=39 Identities=15% Similarity=0.534 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCC
Q 019767 219 KETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPF 259 (336)
Q Consensus 219 eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~lPI 259 (336)
.+|...++++.+-|-.=.+||..+| | .+.|+.+|++=|+
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i~-R-Sr~~Ir~yl~dP~ 45 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRIG-R-SRTCIRRYLKDPV 45 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHT----HHHHHHHHHSCC
T ss_pred HHHHHHHHHHHHhchhHHHHHHHhC-c-cHHHHHHHhcChh
Confidence 4567888999999999999999997 4 4679999998775
No 107
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=34.42 E-value=58 Score=28.99 Aligned_cols=45 Identities=20% Similarity=0.293 Sum_probs=37.2
Q ss_pred HHHHHHHHHhCCCcceeHHHHHHhcc-----chHHHHHHHHHhhhhccccc
Q 019767 82 RDSIVKHYRENPSRKITFTDVRRTLV-----GDVGSIRRVFDFLETWGLIN 127 (336)
Q Consensus 82 RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlIN 127 (336)
|-.|++..... .+.+|+.+.-..|. -+...|.|...+|+.-|||+
T Consensus 28 R~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 28 RLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred HHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEE
Confidence 66777766665 68999999877665 27889999999999999997
No 108
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=34.18 E-value=52 Score=26.83 Aligned_cols=26 Identities=12% Similarity=-0.097 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 019767 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (336)
Q Consensus 219 eE~~~LLeav~~yG~nW~~IA~~Vgt 244 (336)
-|...+.++++.+|||+.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 47788999999999999999999994
No 109
>smart00426 TEA TEA domain.
Probab=33.53 E-value=79 Score=24.63 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=18.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC
Q 019767 213 RSDWTEKETLQLLEAIMHFG 232 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG 232 (336)
..-|.++=|..+++|++.|-
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~ 22 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYP 22 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcC
Confidence 45799999999999999998
No 110
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=32.94 E-value=25 Score=35.94 Aligned_cols=45 Identities=16% Similarity=0.304 Sum_probs=37.6
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHHHH-----hCC-CCHHHHHHHHhc
Q 019767 212 ARSDWTEKETLQLLEAIMHFGDDWRKVAQH-----VSG-KSEKDCITHFIK 256 (336)
Q Consensus 212 ~~~~WT~eE~~~LLeav~~yG~nW~~IA~~-----Vgt-rT~~qC~~hf~~ 256 (336)
....||.+|+..|.+.-+.|.=.|--||+. .++ ||.++-.+||..
T Consensus 129 ~dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~ 179 (445)
T KOG2656|consen 129 NDNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYS 179 (445)
T ss_pred ccccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHH
Confidence 347899999999999999999677777765 455 999999999854
No 111
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=32.92 E-value=71 Score=31.93 Aligned_cols=40 Identities=25% Similarity=0.422 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCC----CHHHHHHHhCCCCHHHHHH
Q 019767 213 RSDWTEKETLQLLEAIMHFGD----DWRKVAQHVSGKSEKDCIT 252 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~----nW~~IA~~VgtrT~~qC~~ 252 (336)
...||..|...||.+++...| |-.+++++|.+|+..|++.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~ 64 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRD 64 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHH
Confidence 367999999999999988754 5667888999999988765
No 112
>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=32.29 E-value=1.5e+02 Score=21.34 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=31.3
Q ss_pred CCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 92 NPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 92 np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
+....+|.++..+.+.-|...+.|+..=|...|||.-..+
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 4789999999999999999999999999999999965543
No 113
>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=31.82 E-value=97 Score=21.84 Aligned_cols=35 Identities=26% Similarity=0.281 Sum_probs=30.4
Q ss_pred eeHHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 97 ITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 97 LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
+|.++--+.+.-+-..+-|+.+-|++.|||.-..+
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 99999888888999999999999999999976544
No 114
>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=31.59 E-value=1.2e+02 Score=22.62 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhccccc
Q 019767 79 RYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLIN 127 (336)
Q Consensus 79 ~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlIN 127 (336)
.++|++|-+ ...+|+.+--+.+.-+...+.-+.++|++.|.|.
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 5678999998899999999999999999999986
No 115
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.24 E-value=31 Score=39.53 Aligned_cols=35 Identities=26% Similarity=0.604 Sum_probs=25.9
Q ss_pred hccccccCCCCCCccc-----cccccccCCCccchhhhhc
Q 019767 156 KETSKRLCNGCKTLCT-----IACFACDKYDLTLCARCYV 190 (336)
Q Consensus 156 ~~~~k~~C~~C~~~~~-----~~~~~c~k~d~~LC~~CF~ 190 (336)
.......|..||.+++ ..+..|..+.+-+|..||.
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE 52 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE 52 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchhh
Confidence 3444568999998865 3556777777889999983
No 116
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=29.61 E-value=54 Score=32.20 Aligned_cols=93 Identities=17% Similarity=0.398 Sum_probs=53.3
Q ss_pred cccCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHHHHHhC-----CC
Q 019767 160 KRLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEAIMHFG-----DD 234 (336)
Q Consensus 160 k~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~eE~~~LLeav~~yG-----~n 234 (336)
..+|.-|+.. +-.|..- +.++.||.+|- |.|+.- -. .+-++.. ..-+.||+|+...|.+ +| --
T Consensus 25 N~~CADC~a~-~P~WaSw-nlGvFiC~~C~--giHR~l-g~-hiSkVkS--v~LD~W~~eqv~~m~~----~GN~~an~~ 92 (287)
T KOG0703|consen 25 NKVCADCGAK-GPRWASW-NLGVFICLRCA--GIHRSL-GV-HISKVKS--VTLDEWTDEQVDFMIS----MGNAKANSY 92 (287)
T ss_pred cCcccccCCC-CCCeEEe-ecCeEEEeecc--cccccc-cc-hhheeee--eeccccCHHHHHHHHH----Hcchhhhhh
Confidence 4568888876 3344321 34688999984 444220 00 1122221 1236899999877765 45 12
Q ss_pred HHHH-HHHhCCCCHHHHHHHHhcC-CCCCccc
Q 019767 235 WRKV-AQHVSGKSEKDCITHFIKL-PFGQEFI 264 (336)
Q Consensus 235 W~~I-A~~VgtrT~~qC~~hf~~l-PIeD~fl 264 (336)
|+.- ....-..++++-+++||+- |..-.|+
T Consensus 93 ~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~ 124 (287)
T KOG0703|consen 93 YEAKLPDPFRRPGPDDLVEQFIRDKYERKKFL 124 (287)
T ss_pred ccccCCccccCCChHHHHHHHHHHHHhhhhhc
Confidence 5532 3333345788889999983 4556777
No 117
>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=29.23 E-value=24 Score=29.43 Aligned_cols=59 Identities=24% Similarity=0.494 Sum_probs=27.1
Q ss_pred ccCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCCCceecccCcccCCCCCHHHHHHHHHH
Q 019767 161 RLCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSSDFRRVEISEEARSDWTEKETLQLLEA 227 (336)
Q Consensus 161 ~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~df~ki~~~~~~~~~WT~eE~~~LLea 227 (336)
..|.-|+..- ..+.+..+++.+|..|..- |+. +..|.. ++.. ..-+.||.+|...|.++
T Consensus 14 ~~CaDCg~~~--p~w~s~~~GiflC~~Cag~--HR~-lg~~is-~VkS--i~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 14 KVCADCGAPN--PTWASLNYGIFLCLECAGI--HRS-LGVHIS-RVKS--ITMDNWSPEEVQRMREG 72 (116)
T ss_dssp TB-TTT-SBS----EEETTTTEEE-HHHHHH--HHH-HTTTT---EEE--TTTS---HHHHHHHHHS
T ss_pred CcCCCCCCCC--CCEEEeecChhhhHHHHHH--HHH-hcccch-hccc--cccCCCCHHHHHHHHHH
Confidence 5688887542 2344555788899999754 221 111221 1211 11246999998777654
No 118
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=29.14 E-value=1.6e+02 Score=19.54 Aligned_cols=34 Identities=26% Similarity=0.316 Sum_probs=30.0
Q ss_pred cceeHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 95 RKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 95 ~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
..+|..+-.+.+.-....+.|....|+.-|+|-.
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 4589999888888899999999999999999864
No 119
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=28.88 E-value=26 Score=34.19 Aligned_cols=44 Identities=11% Similarity=-0.126 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
...||.++...+.++|..|+..|+++-+++|.++..+.+.|+..
T Consensus 53 ~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~ 96 (335)
T KOG0724|consen 53 EPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQK 96 (335)
T ss_pred ccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCC
Confidence 34599999999999999998899999999999999999988665
No 120
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=28.55 E-value=1.2e+02 Score=24.69 Aligned_cols=44 Identities=27% Similarity=0.360 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHhCCCcceeHHHHH-------HhccchH---HHHHHHHHhhhhc
Q 019767 76 RVYRYYRDSIVKHYRENPSRKITFTDVR-------RTLVGDV---GSIRRVFDFLETW 123 (336)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yLT~t~~r-------~~l~gDv---~~i~Rih~FLe~w 123 (336)
++-..+||-|+.+=-.| +|+.+-. |.|+-|+ ..++||+.||.++
T Consensus 36 ~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 36 DIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKH 89 (92)
T ss_pred HHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHH
Confidence 56677888888765544 7777643 3455554 6799999999876
No 121
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=28.29 E-value=1.5e+02 Score=23.10 Aligned_cols=43 Identities=19% Similarity=0.411 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhCCCcceeHHHHHHhccc---hHHHHHHHHHhhhhccc
Q 019767 80 YYRDSIVKHYRENPSRKITFTDVRRTLVG---DVGSIRRVFDFLETWGL 125 (336)
Q Consensus 80 ~~RN~ii~~yr~np~~yLT~t~~r~~l~g---Dv~~i~Rih~FLe~wGl 125 (336)
.+|. +|..-+. ..|||..+....|.. +...|-.|+.+|+..|+
T Consensus 8 ~i~~-Li~~gK~--~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 8 AIKK-LIEKGKK--KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHH-HHHHHHH--HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHH-HHHHHhh--cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 3444 7777776 568999999999883 67889999999999986
No 122
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. 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 adaptor
Probab=28.18 E-value=50 Score=25.96 Aligned_cols=26 Identities=35% Similarity=0.539 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCC
Q 019767 218 EKETLQLLEAIMHFGDDWRKVAQHVSG 244 (336)
Q Consensus 218 ~eE~~~LLeav~~yG~nW~~IA~~Vgt 244 (336)
.+|..+||.+= .-|.||...|.++|-
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~LG~ 27 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGELGY 27 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHcCC
Confidence 46778888521 345799999999995
No 123
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.20 E-value=1.1e+02 Score=25.80 Aligned_cols=39 Identities=13% Similarity=0.143 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHhC-CCHHHHHHHhCCCCHHHHHHHHhcC
Q 019767 218 EKETLQLLEAIMHFG-DDWRKVAQHVSGKSEKDCITHFIKL 257 (336)
Q Consensus 218 ~eE~~~LLeav~~yG-~nW~~IA~~VgtrT~~qC~~hf~~l 257 (336)
++-+.++|+.++.-+ -.+.+||+.|| -|+..|..|-.+|
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg-lS~~~v~~Ri~~L 46 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG-LSPSTVLRRIKRL 46 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC-CCHHHHHHHHHHH
Confidence 356789999999998 78999999998 6999999988875
No 124
>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=27.11 E-value=1.2e+02 Score=27.45 Aligned_cols=47 Identities=26% Similarity=0.294 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 81 YRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 81 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
-|+.||..-..+. .+|+++..+.+.-+..++.|...-|++-|||-..
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 3999999888888999999999999999999754
No 125
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=26.82 E-value=46 Score=21.24 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=20.0
Q ss_pred cCCCCCCccccc-cccccCCCccchhhh
Q 019767 162 LCNGCKTLCTIA-CFACDKYDLTLCARC 188 (336)
Q Consensus 162 ~C~~C~~~~~~~-~~~c~k~d~~LC~~C 188 (336)
.|..|+...... .|.|.+.++.+...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 588898887655 888877667766665
No 126
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=26.33 E-value=1.3e+02 Score=21.86 Aligned_cols=27 Identities=11% Similarity=0.324 Sum_probs=22.9
Q ss_pred CcceeHHHHHHhcc----chHHHHHHHHHhh
Q 019767 94 SRKITFTDVRRTLV----GDVGSIRRVFDFL 120 (336)
Q Consensus 94 ~~yLT~t~~r~~l~----gDv~~i~Rih~FL 120 (336)
..++|..+....|. .+...+.||.+||
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 58999999988877 6888999999998
No 127
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=26.26 E-value=99 Score=28.00 Aligned_cols=68 Identities=10% Similarity=0.075 Sum_probs=46.8
Q ss_pred ccccCCCCCCCChHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 63 PEFFDSRSPSKNPRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 63 pEff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
|.|-.-...+.+..+|-.+|+.|++ =+..|...|+-.+--..+.-=-..+..-..-|+.-|||-....
T Consensus 2 ~~~~~~~~~~~~e~v~~~l~~~I~~-g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~ 69 (221)
T PRK11414 2 PGTEKTQHISLTLQVENDLKHQLSI-GALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPA 69 (221)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHh-CCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCC
Confidence 3443333345567899999999997 5667999998766555554344455555556999999976544
No 128
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=26.22 E-value=2.1e+02 Score=20.32 Aligned_cols=49 Identities=16% Similarity=0.078 Sum_probs=36.3
Q ss_pred HHHHHHHHHHhC-----CCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 81 YRDSIVKHYREN-----PSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 81 ~RN~ii~~yr~n-----p~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
+..+++...... ....+|..+.-..+.-....+.|+..-|+..|+|=..
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 344555544433 2356888888888878999999999999999999654
No 129
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=26.18 E-value=78 Score=32.22 Aligned_cols=46 Identities=15% Similarity=0.351 Sum_probs=37.6
Q ss_pred hHHHHHHHHHHHHHHHhCCCcceeHHHHHHhccchHHHHHHHHH----hhhhcccccCCCC
Q 019767 75 PRVYRYYRDSIVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFD----FLETWGLINYFAS 131 (336)
Q Consensus 75 p~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~----FLe~wGlINy~~~ 131 (336)
.|.|+.||+.+|++|. +...|..|+..++-+|+ |.|..|=..|++.
T Consensus 64 qeKFl~IR~KlleL~~-----------~lQ~lS~df~~LqPLF~Ti~eyse~~~~kkF~pL 113 (379)
T PF11593_consen 64 QEKFLLIRSKLLELYN-----------KLQELSSDFQKLQPLFDTIPEYSEKYNSKKFQPL 113 (379)
T ss_pred HHHHHHHHHHHHHHHH-----------HHHHHHHHHHHhchHHhhhHHHhcccCCccceec
Confidence 5999999999999875 45677788888777665 8888888888876
No 130
>PLN02436 cellulose synthase A
Probab=26.09 E-value=47 Score=38.15 Aligned_cols=36 Identities=25% Similarity=0.576 Sum_probs=26.6
Q ss_pred hccccccCCCCCCccc-----cccccccCCCccchhhhhcc
Q 019767 156 KETSKRLCNGCKTLCT-----IACFACDKYDLTLCARCYVR 191 (336)
Q Consensus 156 ~~~~k~~C~~C~~~~~-----~~~~~c~k~d~~LC~~CF~~ 191 (336)
+......|..|+.+++ ..+..|..+.+-+|..||.-
T Consensus 32 ~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey 72 (1094)
T PLN02436 32 QELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEY 72 (1094)
T ss_pred cccCCccccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 3444568999998874 35567777778999999943
No 131
>PLN02400 cellulose synthase
Probab=25.94 E-value=46 Score=38.25 Aligned_cols=53 Identities=21% Similarity=0.473 Sum_probs=33.3
Q ss_pred hccccccCCCCCCccc-----cccccccCCCccchhhhhcc----CCCCCCCCCCCceeccc
Q 019767 156 KETSKRLCNGCKTLCT-----IACFACDKYDLTLCARCYVR----GNHRVGVSSSDFRRVEI 208 (336)
Q Consensus 156 ~~~~k~~C~~C~~~~~-----~~~~~c~k~d~~LC~~CF~~----G~~~~~~~s~df~ki~~ 208 (336)
.......|..|+.+++ ..+..|..+.+-+|..||.= |+----.-...|++.+-
T Consensus 32 ~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYEYERkeGnq~CPQCkTrYkR~Kg 93 (1085)
T PLN02400 32 KNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYEYERKDGTQCCPQCKTRYRRHKG 93 (1085)
T ss_pred cccCCceeeecccccCcCCCCCEEEEEccCCCccccchhheecccCCccCcccCCccccccC
Confidence 3444568999998875 35567777778899999843 22111123456776553
No 132
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=25.71 E-value=31 Score=27.05 Aligned_cols=26 Identities=15% Similarity=0.267 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCC
Q 019767 219 KETLQLLEAIMHFGDDWRKVAQHVSG 244 (336)
Q Consensus 219 eE~~~LLeav~~yG~nW~~IA~~Vgt 244 (336)
++.-.+|+--...|.||..+|+++|-
T Consensus 3 ~~L~~~Ldp~~~~g~DWr~LA~~Lg~ 28 (79)
T cd08312 3 RRLSLFLNPPRVVAADWTALAEEMGF 28 (79)
T ss_pred HHHHHHcCCCCCcccCHHHHHHHcCC
Confidence 34456666666688999999999984
No 133
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=25.42 E-value=42 Score=33.93 Aligned_cols=63 Identities=22% Similarity=0.556 Sum_probs=36.2
Q ss_pred ccccCCCCCCcc-c---cccccccCCCccchhhhhccCCCCCCC-CCCCceecccCcccCCCCCHHHHHHHHHHHHHh
Q 019767 159 SKRLCNGCKTLC-T---IACFACDKYDLTLCARCYVRGNHRVGV-SSSDFRRVEISEEARSDWTEKETLQLLEAIMHF 231 (336)
Q Consensus 159 ~k~~C~~C~~~~-~---~~~~~c~k~d~~LC~~CF~~G~~~~~~-~s~df~ki~~~~~~~~~WT~eE~~~LLeav~~y 231 (336)
....|++|...- . .+|-+|. ++.+|..||-.|.-+..+ ..|.|+.. ..|..- ..+|..|+.+-
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~--nyqlcq~cfwrG~~g~~hsnqh~mke~-------Ss~ksp-~k~Lv~aisks 306 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCH--NYQLCQQCFWRGHAGGSHSNQHQMKEY-------SSWKSP-AKKLVHAISKS 306 (434)
T ss_pred CCccCcceecccccchhhhHhhcC--CccccchhhccccCCCCcchHHHHHHh-------hcccCh-HHHHHHHhhhc
Confidence 346699997653 2 3445555 467999999999864333 33333322 234322 24566666553
No 134
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=25.40 E-value=1.2e+02 Score=23.99 Aligned_cols=37 Identities=14% Similarity=0.394 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhCC--------CHHHHHHHhCCCC-----HHHHHHHHhc
Q 019767 220 ETLQLLEAIMHFGD--------DWRKVAQHVSGKS-----EKDCITHFIK 256 (336)
Q Consensus 220 E~~~LLeav~~yG~--------nW~~IA~~VgtrT-----~~qC~~hf~~ 256 (336)
.-..|-.+|.+.|| .|.+||+.+|-.. ..+-+.+|.+
T Consensus 33 dL~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k 82 (93)
T smart00501 33 DLYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYER 82 (93)
T ss_pred cHHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHH
Confidence 35678889999885 7999999998532 3555666665
No 135
>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=25.10 E-value=1.1e+02 Score=21.51 Aligned_cols=52 Identities=17% Similarity=0.275 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 76 RVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 76 ~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
++|-.+++.|+..- ..+...+ |..+-.+.+.-....+.+...=|+..|+|-.
T Consensus 5 ~~~~~i~~~i~~~~-~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGE-LKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCC-CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 45556666555531 2233344 4777666676678899999999999999854
No 136
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=25.09 E-value=1.6e+02 Score=20.41 Aligned_cols=36 Identities=11% Similarity=0.134 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHh
Q 019767 219 KETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFI 255 (336)
Q Consensus 219 eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~ 255 (336)
+++..++....-.|-.|.+||+.+| .|...+..++.
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ 48 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLR 48 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHH
Confidence 3556666666667789999999997 57777766653
No 137
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=24.72 E-value=47 Score=22.20 Aligned_cols=29 Identities=28% Similarity=0.658 Sum_probs=18.4
Q ss_pred ccCCCCCCc-cccccccccCCCccchhhhhccC
Q 019767 161 RLCNGCKTL-CTIACFACDKYDLTLCARCYVRG 192 (336)
Q Consensus 161 ~~C~~C~~~-~~~~~~~c~k~d~~LC~~CF~~G 192 (336)
..|..|... ....|..| +..+|..|...+
T Consensus 4 ~~C~~H~~~~~~~~C~~C---~~~~C~~C~~~~ 33 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDC---NEPLCSECTVSG 33 (42)
T ss_dssp SB-SSTTTSBEEEEETTT---TEEEEHHHHHTS
T ss_pred ccCccCCccceEEEecCC---CCccCccCCCCC
Confidence 457777654 33444444 467999999987
No 138
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=24.68 E-value=1e+02 Score=22.71 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=31.5
Q ss_pred CcceeHHHHHHhccchHHHHHHHHHhhhhcccccC
Q 019767 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINY 128 (336)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 128 (336)
...+|+.+..+.+.-+-..+.|+..-|++.|||.-
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 56789999998898899999999999999999964
No 139
>PLN02189 cellulose synthase
Probab=24.48 E-value=52 Score=37.66 Aligned_cols=36 Identities=19% Similarity=0.547 Sum_probs=26.5
Q ss_pred hccccccCCCCCCccc-----cccccccCCCccchhhhhcc
Q 019767 156 KETSKRLCNGCKTLCT-----IACFACDKYDLTLCARCYVR 191 (336)
Q Consensus 156 ~~~~k~~C~~C~~~~~-----~~~~~c~k~d~~LC~~CF~~ 191 (336)
.......|..|+.+++ ..+..|..+.+-+|..||.-
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyey 70 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEY 70 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 3444568999998865 35567777778899999943
No 140
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=24.37 E-value=1.3e+02 Score=26.82 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCC
Q 019767 215 DWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLP 258 (336)
Q Consensus 215 ~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~lP 258 (336)
.||+++..+|-+.- .=|-.=.+||+.+|+.|..-.+-+-.+|-
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hRlg 44 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHRLG 44 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhccc
Confidence 69999988776664 45667899999999767777776665553
No 141
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=24.22 E-value=50 Score=33.39 Aligned_cols=71 Identities=24% Similarity=0.520 Sum_probs=36.5
Q ss_pred cCCCCCCccccccccccCCCccchhhhhccCCCCCCCCCC-CceecccCcccCCCCCHHHHHH--------HHHHHHHhC
Q 019767 162 LCNGCKTLCTIACFACDKYDLTLCARCYVRGNHRVGVSSS-DFRRVEISEEARSDWTEKETLQ--------LLEAIMHFG 232 (336)
Q Consensus 162 ~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~G~~~~~~~s~-df~ki~~~~~~~~~WT~eE~~~--------LLeav~~yG 232 (336)
.|.-|+.. .-.|..| .+++.+|++|- |.|+ ++--| .|+|--. =+.|.+.|..+ |-|-++.+|
T Consensus 21 ~CfeC~a~-NPQWvSv-syGIfICLECS--G~HR-gLGVhiSFVRSVT----MD~wkeiel~kMeaGGN~~~~eFL~s~~ 91 (386)
T KOG0704|consen 21 KCFECGAP-NPQWVSV-SYGIFICLECS--GKHR-GLGVHISFVRSVT----MDKWKEIELKKMEAGGNERFREFLSSQG 91 (386)
T ss_pred ceeecCCC-CCCeEee-cccEEEEEecC--Cccc-ccceeeEEEEeee----cccccHHHHHHHHhccchhHHHHHhhCc
Confidence 45555543 1233333 36888999994 4442 22223 3444211 14688887665 344556665
Q ss_pred ---CCHHHHHHH
Q 019767 233 ---DDWRKVAQH 241 (336)
Q Consensus 233 ---~nW~~IA~~ 241 (336)
.-|.-+.++
T Consensus 92 ~~~e~~~i~eKY 103 (386)
T KOG0704|consen 92 IYKETWPIREKY 103 (386)
T ss_pred cccccccHHHhh
Confidence 345544443
No 142
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=24.13 E-value=1.5e+02 Score=26.31 Aligned_cols=45 Identities=27% Similarity=0.557 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHHhC-C--CHHHHHHHhCCCCHHHHHHHHhcCCCC
Q 019767 215 DWTEKETLQLLEAIMHFG-D--DWRKVAQHVSGKSEKDCITHFIKLPFG 260 (336)
Q Consensus 215 ~WT~eE~~~LLeav~~yG-~--nW~~IA~~VgtrT~~qC~~hf~~lPIe 260 (336)
.++..+-..+|.+|..|| | +|......+-.||.++... |..|.+.
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~a-Y~~LFm~ 87 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRA-YGSLFMR 87 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHH-HHHHHHH
Confidence 688999999999999999 4 8999999998999888754 4444333
No 143
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=23.23 E-value=96 Score=24.72 Aligned_cols=31 Identities=13% Similarity=0.276 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCHHHHHHHhCC-CCHHHHHHH
Q 019767 223 QLLEAIMHFGDDWRKVAQHVSG-KSEKDCITH 253 (336)
Q Consensus 223 ~LLeav~~yG~nW~~IA~~Vgt-rT~~qC~~h 253 (336)
.|...-+.-|.+|..+|.++|- .+.-+.+.+
T Consensus 4 ~L~~la~~LG~~W~~Lar~Lgls~~~I~~i~~ 35 (83)
T cd08319 4 ELNQLAQRLGPEWEQVLLDLGLSQTDIYRCKE 35 (83)
T ss_pred HHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHH
Confidence 4555567788999999999994 344444444
No 144
>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=23.08 E-value=1.5e+02 Score=22.82 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=33.7
Q ss_pred HHHHHHhCCCcceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 85 IVKHYRENPSRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 85 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
|+.....+..+.+|..+-...+.-....+.+|..-|.+-|||.-.
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 344444444445999999888888899999999999999999643
No 145
>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=22.88 E-value=45 Score=28.00 Aligned_cols=28 Identities=29% Similarity=0.757 Sum_probs=19.7
Q ss_pred ccccCCCCCCccccccccccCCCccchhhhhcc
Q 019767 159 SKRLCNGCKTLCTIACFACDKYDLTLCARCYVR 191 (336)
Q Consensus 159 ~k~~C~~C~~~~~~~~~~c~k~d~~LC~~CF~~ 191 (336)
.|..|..||. ++|-.++ +.++|+.|-..
T Consensus 8 tKR~Cp~CG~----kFYDLnk-~PivCP~CG~~ 35 (108)
T PF09538_consen 8 TKRTCPSCGA----KFYDLNK-DPIVCPKCGTE 35 (108)
T ss_pred CcccCCCCcc----hhccCCC-CCccCCCCCCc
Confidence 4677888775 5677766 66789988443
No 146
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=22.26 E-value=1.1e+02 Score=28.57 Aligned_cols=87 Identities=9% Similarity=0.149 Sum_probs=56.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHHHhC---CCCHHHHHHHHhcCCCCCcccCCCCCCccccccccccCCCCCcccccc
Q 019767 215 DWTEKETLQLLEAIMHFGDDWRKVAQHVS---GKSEKDCITHFIKLPFGQEFICKESDSEDVDNKFFSINNPSDAVSESE 291 (336)
Q Consensus 215 ~WT~eE~~~LLeav~~yG~nW~~IA~~Vg---trT~~qC~~hf~~lPIeD~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 (336)
.|+..++++|+.||+. |.+=..|+.-|. .-|-.|...||..|=.....- ........++.+...
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is------~~a~~~m~~l~p~~~------ 67 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYDPVIS------RIAVAAMRNLHPELI------ 67 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhH------HHHHHHHHhCCcchh------
Confidence 4999999999999985 567888887775 249999999999963322221 111111222221100
Q ss_pred ccCCCCCCccCCcccccCCCCcHHHHHHHH
Q 019767 292 NVGATSPSKRMRLTPLADASNPIMAQLSCR 321 (336)
Q Consensus 292 ~~~~~~~~~~~~~~Pfs~a~NPvms~vAFL 321 (336)
......+|||.+.+=++..+++-
T Consensus 68 -------~~iq~kalfS~~EE~lL~~v~s~ 90 (199)
T PF13325_consen 68 -------AAIQSKALFSKEEEQLLGTVASS 90 (199)
T ss_pred -------hcccccCCCCHHHHHHHHhhhhc
Confidence 01124589999999998887763
No 147
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=22.15 E-value=1.8e+02 Score=19.77 Aligned_cols=37 Identities=11% Similarity=0.124 Sum_probs=30.9
Q ss_pred CcceeHHHHHHhccchHHHHHHHHHhhhhcccccCCC
Q 019767 94 SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLINYFA 130 (336)
Q Consensus 94 ~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~ 130 (336)
.+.+|+++..+.+.-....+.|+.+=|++.|+|....
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence 4678999998888767788999999999999997543
No 148
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=21.80 E-value=31 Score=27.43 Aligned_cols=35 Identities=20% Similarity=0.490 Sum_probs=22.9
Q ss_pred cCCCCCCcccccc-cc---ccCCCccchhhhhccCCCCC
Q 019767 162 LCNGCKTLCTIAC-FA---CDKYDLTLCARCYVRGNHRV 196 (336)
Q Consensus 162 ~C~~C~~~~~~~~-~~---c~k~d~~LC~~CF~~G~~~~ 196 (336)
.|..||..+...- +. -...+-+-|.-||.+|.|..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~ 40 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQ 40 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCceee
Confidence 6899998876433 11 11123457999999999754
No 149
>PRK03837 transcriptional regulator NanR; Provisional
Probab=21.62 E-value=1.2e+02 Score=27.65 Aligned_cols=59 Identities=12% Similarity=0.089 Sum_probs=48.6
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcce-eHHHHHHhccchHHHHHHHHHhhhhcccccCCCC
Q 019767 72 SKNPRVYRYYRDSIVKHYRENPSRKI-TFTDVRRTLVGDVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 72 ~ktp~~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 131 (336)
+....+|..||+.|+.-.-. |.+.| +-.+-...+.--...+.....-|+.-|||-....
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 33568999999999996655 89999 8888888887777788888888999999987543
No 150
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=21.56 E-value=2e+02 Score=30.78 Aligned_cols=43 Identities=12% Similarity=0.237 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhcCCCCCc
Q 019767 219 KETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIKLPFGQE 262 (336)
Q Consensus 219 eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~lPIeD~ 262 (336)
.|-.++.+++++.|+||.+-|+.+|. |+.+-..+--+|-|+.+
T Consensus 506 ~eR~~I~~aL~~~~~~~a~AAr~LGl-~~~~L~~~~kRlGI~~~ 548 (550)
T COG3604 506 FERQLIIAALEETNGNWAGAARRLGL-TRRTLLYRMKRLGIKVK 548 (550)
T ss_pred HHHHHHHHHHHHhCCcHHHHHHHhCC-CHHHHHHHHHHcCCCcC
Confidence 35567889999999999999999985 78888777777777653
No 151
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=21.39 E-value=1.1e+02 Score=20.17 Aligned_cols=34 Identities=24% Similarity=0.207 Sum_probs=28.3
Q ss_pred ceeHHHHHHhccchHHHHHHHHHhhhhcccccCC
Q 019767 96 KITFTDVRRTLVGDVGSIRRVFDFLETWGLINYF 129 (336)
Q Consensus 96 yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 129 (336)
.+|..+..+.+.-....+.|+.+-|++.|+|.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4677777777777889999999999999999754
No 152
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=21.25 E-value=2.5e+02 Score=22.34 Aligned_cols=47 Identities=19% Similarity=0.425 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHhCC--CcceeHHHHHHhccchHHHHHHHHHhhhhcccc
Q 019767 80 YYRDSIVKHYRENP--SRKITFTDVRRTLVGDVGSIRRVFDFLETWGLI 126 (336)
Q Consensus 80 ~~RN~ii~~yr~np--~~yLT~t~~r~~l~gDv~~i~Rih~FLe~wGlI 126 (336)
.++..|++..+.++ .+=+.+.+..+.|.-+...|..+.+||..-|+|
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 44556666555523 567999999999966999999999999999988
No 153
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=20.83 E-value=75 Score=34.16 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHhc
Q 019767 213 RSDWTEKETLQLLEAIMHFGDDWRKVAQHVSGKSEKDCITHFIK 256 (336)
Q Consensus 213 ~~~WT~eE~~~LLeav~~yG~nW~~IA~~VgtrT~~qC~~hf~~ 256 (336)
...||..|..+.-.++.++|-+..-|++....|+..|.+.+|..
T Consensus 409 ~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 409 TDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 57899999999999999999999999999999999999999954
No 154
>PF14420 Clr5: Clr5 domain
Probab=20.58 E-value=1.6e+02 Score=21.30 Aligned_cols=28 Identities=14% Similarity=0.260 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHHhCCCcceeHHHHHHhcc
Q 019767 77 VYRYYRDSIVKHYRENPSRKITFTDVRRTLV 107 (336)
Q Consensus 77 ~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~ 107 (336)
..-.+|+.|..+|.. +-+|+.++++.+.
T Consensus 4 ~We~~K~~I~~LY~~---e~~tl~~v~~~M~ 31 (54)
T PF14420_consen 4 DWEPHKEEIERLYID---ENKTLEEVMEIMK 31 (54)
T ss_pred hHHHHHHHHHHHHHh---CCCcHHHHHHHHH
Confidence 445789999999984 5678888887664
No 155
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.48 E-value=1.7e+02 Score=22.86 Aligned_cols=48 Identities=23% Similarity=0.271 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHhCCCc---ceeHHHHHHhc-c---chHHHHHHHHHhhhhcc
Q 019767 77 VYRYYRDSIVKHYRENPSR---KITFTDVRRTL-V---GDVGSIRRVFDFLETWG 124 (336)
Q Consensus 77 ~Y~~~RN~ii~~yr~np~~---yLT~t~~r~~l-~---gDv~~i~Rih~FLe~wG 124 (336)
+--+.+..|++.++.+|.. .+|....+..| . |-.-+..-|..+|.+||
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~G 112 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRAG 112 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHCc
Confidence 3456788999999998854 68888887765 2 44445667777788887
No 156
>PRK14137 recX recombination regulator RecX; Provisional
Probab=20.03 E-value=2.1e+02 Score=26.32 Aligned_cols=54 Identities=13% Similarity=0.142 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHHHHHHhCCCcceeHHHHHHhcc--c-hHHHHHHHHHhhhhcccccCCCC
Q 019767 75 PRVYRYYRDSIVKHYRENPSRKITFTDVRRTLV--G-DVGSIRRVFDFLETWGLINYFAS 131 (336)
Q Consensus 75 p~~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~--g-Dv~~i~Rih~FLe~wGlINy~~~ 131 (336)
-+.|.+++++.+. .+. .+.-|..+.++.|. | |-..|-.|.++|...|+||=..+
T Consensus 36 ~e~~~~~~~~Al~--~Ls-~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rf 92 (195)
T PRK14137 36 DEAREALLAYAFR--ALA-ARAMTAAELRAKLERRSEDEALVTEVLERVQELGYQDDAQV 92 (195)
T ss_pred HHHHHHHHHHHHH--HHh-cchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHH
Confidence 4677888888774 221 45567778888776 3 78999999999999999984433
Done!