Query 012858
Match_columns 455
No_of_seqs 274 out of 689
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 07:02:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012858.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012858hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5259 RSC8 RSC chromatin rem 100.0 3.3E-83 7.1E-88 653.2 15.9 325 11-401 46-378 (531)
2 KOG1279 Chromatin remodeling f 100.0 8.9E-74 1.9E-78 601.8 19.5 318 8-408 38-360 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 1.3E-27 2.7E-32 198.6 6.1 85 17-105 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 9.2E-23 2E-27 209.3 8.6 109 194-303 13-125 (438)
5 COG5114 Histone acetyltransfer 99.8 1.7E-19 3.7E-24 178.8 5.7 110 194-304 4-117 (432)
6 PF00249 Myb_DNA-binding: Myb- 99.2 3.8E-11 8.1E-16 89.3 4.9 44 252-295 2-47 (48)
7 cd02336 ZZ_RSC8 Zinc finger, Z 99.1 7.4E-11 1.6E-15 87.3 3.6 44 196-239 1-45 (45)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.9 1.6E-09 3.5E-14 83.6 5.5 41 254-294 1-41 (60)
9 smart00717 SANT SANT SWI3, AD 98.9 3.2E-09 6.9E-14 76.6 5.8 44 252-295 2-46 (49)
10 PLN03000 amine oxidase 98.8 3.9E-09 8.5E-14 119.3 6.8 84 22-110 87-173 (881)
11 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 9E-09 2E-13 73.2 5.6 43 253-295 1-44 (45)
12 PLN02328 lysine-specific histo 98.7 1.2E-08 2.5E-13 115.1 6.9 85 22-110 138-224 (808)
13 PLN03212 Transcription repress 98.4 4.5E-07 9.8E-12 88.9 5.3 45 250-294 24-70 (249)
14 PLN02529 lysine-specific histo 98.3 1.4E-06 3E-11 98.0 6.8 84 22-110 63-149 (738)
15 TIGR01557 myb_SHAQKYF myb-like 98.2 2.4E-06 5.2E-11 66.4 5.7 44 251-294 3-52 (57)
16 PLN03091 hypothetical protein; 98.2 1.9E-06 4.2E-11 90.3 5.2 45 250-294 13-59 (459)
17 cd02335 ZZ_ADA2 Zinc finger, Z 98.0 5.1E-06 1.1E-10 62.5 4.1 46 196-241 1-49 (49)
18 PLN03212 Transcription repress 98.0 8.6E-06 1.9E-10 80.0 5.2 46 249-294 76-121 (249)
19 KOG0048 Transcription factor, 97.9 8.5E-06 1.8E-10 80.0 4.7 50 251-306 9-60 (238)
20 cd02249 ZZ Zinc finger, ZZ typ 97.9 1.2E-05 2.5E-10 59.6 3.8 45 196-241 1-46 (46)
21 smart00291 ZnF_ZZ Zinc-binding 97.8 2.7E-05 5.9E-10 57.2 3.6 40 194-233 3-43 (44)
22 PLN03091 hypothetical protein; 97.7 4.3E-05 9.2E-10 80.4 5.8 46 249-294 65-110 (459)
23 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.6 5E-05 1.1E-09 57.1 3.6 44 196-241 1-48 (48)
24 cd02345 ZZ_dah Zinc finger, ZZ 97.6 5.7E-05 1.2E-09 56.9 3.3 43 197-239 2-47 (49)
25 cd02340 ZZ_NBR1_like Zinc fing 97.6 6.6E-05 1.4E-09 55.1 3.5 41 197-241 2-43 (43)
26 cd02338 ZZ_PCMF_like Zinc fing 97.5 0.00011 2.4E-09 55.3 3.7 44 197-240 2-48 (49)
27 cd02343 ZZ_EF Zinc finger, ZZ 97.5 0.00011 2.3E-09 55.3 3.4 37 197-233 2-39 (48)
28 PF00569 ZZ: Zinc finger, ZZ t 97.5 6.6E-05 1.4E-09 55.7 2.1 40 194-233 3-44 (46)
29 cd02334 ZZ_dystrophin Zinc fin 97.4 0.00014 3E-09 55.0 3.6 43 197-239 2-47 (49)
30 KOG0048 Transcription factor, 97.4 0.00021 4.5E-09 70.2 5.8 43 251-293 62-104 (238)
31 cd02344 ZZ_HERC2 Zinc finger, 97.1 0.00063 1.4E-08 50.6 3.5 42 197-241 2-45 (45)
32 KOG0049 Transcription factor, 97.0 0.00077 1.7E-08 73.7 5.1 46 249-294 358-404 (939)
33 cd02339 ZZ_Mind_bomb Zinc fing 96.9 0.0011 2.4E-08 49.2 3.6 41 197-240 2-44 (45)
34 cd02337 ZZ_CBP Zinc finger, ZZ 96.5 0.0024 5.2E-08 46.5 2.8 34 196-230 1-35 (41)
35 PLN02976 amine oxidase 96.4 0.0032 6.8E-08 75.3 4.5 83 25-110 454-542 (1713)
36 cd02342 ZZ_UBA_plant Zinc fing 96.1 0.0045 9.7E-08 45.5 2.5 31 197-227 2-34 (43)
37 KOG0049 Transcription factor, 96.1 0.0055 1.2E-07 67.2 4.0 53 250-305 411-467 (939)
38 PF13837 Myb_DNA-bind_4: Myb/S 95.8 0.0043 9.3E-08 51.0 1.5 43 252-294 2-62 (90)
39 KOG0051 RNA polymerase I termi 94.7 0.032 7E-07 61.4 4.4 44 250-294 383-426 (607)
40 KOG0050 mRNA splicing protein 93.6 0.057 1.2E-06 58.3 3.4 43 251-293 7-50 (617)
41 KOG0051 RNA polymerase I termi 93.3 0.076 1.6E-06 58.6 3.7 53 250-302 435-513 (607)
42 KOG4582 Uncharacterized conser 92.6 0.085 1.8E-06 53.4 2.8 43 196-241 153-197 (278)
43 KOG4167 Predicted DNA-binding 91.1 0.33 7.1E-06 54.5 5.4 44 250-293 618-661 (907)
44 PF13873 Myb_DNA-bind_5: Myb/S 90.9 0.37 8.1E-06 38.8 4.3 44 252-295 3-68 (78)
45 KOG0050 mRNA splicing protein 90.8 0.19 4.1E-06 54.4 3.2 45 250-295 58-102 (617)
46 KOG1280 Uncharacterized conser 90.0 0.23 4.9E-06 51.5 2.8 36 193-228 6-43 (381)
47 COG5118 BDP1 Transcription ini 89.7 0.47 1E-05 49.7 4.8 45 250-294 364-408 (507)
48 KOG4329 DNA-binding protein [G 88.4 0.65 1.4E-05 48.6 4.8 44 251-294 277-321 (445)
49 COG5147 REB1 Myb superfamily p 88.2 0.47 1E-05 51.8 3.9 46 249-294 70-115 (512)
50 TIGR02894 DNA_bind_RsfA transc 87.6 0.49 1.1E-05 44.3 3.1 42 251-293 4-52 (161)
51 KOG4468 Polycomb-group transcr 86.9 0.56 1.2E-05 51.7 3.4 44 251-294 88-141 (782)
52 COG5147 REB1 Myb superfamily p 85.6 0.46 1E-05 51.9 2.0 42 251-292 20-62 (512)
53 KOG4282 Transcription factor G 85.0 0.92 2E-05 46.8 3.8 44 252-295 55-112 (345)
54 KOG4286 Dystrophin-like protei 83.3 0.64 1.4E-05 52.5 1.9 40 195-234 603-644 (966)
55 PF09111 SLIDE: SLIDE; InterP 76.7 3.1 6.7E-05 37.1 3.7 45 249-293 47-107 (118)
56 KOG3554 Histone deacetylase co 72.7 2.8 6.1E-05 45.2 2.8 52 252-303 286-338 (693)
57 PF12776 Myb_DNA-bind_3: Myb/S 72.2 4.9 0.00011 33.2 3.7 42 253-294 1-60 (96)
58 PF04504 DUF573: Protein of un 71.8 5.3 0.00011 34.3 3.8 45 250-294 3-60 (98)
59 PF13404 HTH_AsnC-type: AsnC-t 65.1 12 0.00026 27.1 4.0 38 257-295 3-41 (42)
60 smart00345 HTH_GNTR helix_turn 63.7 9.8 0.00021 27.9 3.5 50 55-105 2-52 (60)
61 KOG4301 Beta-dystrobrevin [Cyt 63.6 3.5 7.5E-05 43.0 1.3 40 194-233 239-280 (434)
62 KOG0703 Predicted GTPase-activ 63.2 7.4 0.00016 39.8 3.5 98 195-304 25-126 (287)
63 PF12802 MarR_2: MarR family; 62.1 20 0.00044 26.8 5.0 43 67-109 15-57 (62)
64 PLN03142 Probable chromatin-re 61.7 11 0.00024 44.9 5.0 40 252-291 825-865 (1033)
65 PRK13923 putative spore coat p 60.7 7.2 0.00016 37.0 2.7 41 251-292 5-52 (170)
66 PLN03119 putative ADP-ribosyla 60.4 10 0.00022 42.2 4.1 96 195-304 23-124 (648)
67 KOG1279 Chromatin remodeling f 59.7 5.7 0.00012 43.6 2.1 92 19-110 186-285 (506)
68 KOG1194 Predicted DNA-binding 59.3 17 0.00036 39.4 5.4 46 249-294 185-230 (534)
69 PF03107 C1_2: C1 domain; Int 58.6 9.7 0.00021 25.6 2.4 27 197-223 2-29 (30)
70 PF01475 FUR: Ferric uptake re 56.8 19 0.00041 31.1 4.6 50 56-106 7-61 (120)
71 PF00392 GntR: Bacterial regul 55.9 22 0.00048 27.4 4.4 52 53-105 4-56 (64)
72 PF07649 C1_3: C1-like domain; 55.8 8.1 0.00018 25.8 1.6 27 197-223 2-29 (30)
73 PLN03131 hypothetical protein; 55.5 17 0.00038 40.8 4.9 94 195-303 23-123 (705)
74 cd00090 HTH_ARSR Arsenical Res 54.5 30 0.00065 25.8 4.9 44 61-107 11-54 (78)
75 PF01022 HTH_5: Bacterial regu 52.9 38 0.00083 24.6 5.0 45 58-105 3-47 (47)
76 PF13412 HTH_24: Winged helix- 50.6 51 0.0011 23.7 5.3 44 58-103 4-47 (48)
77 PF09339 HTH_IclR: IclR helix- 50.3 27 0.00059 25.8 3.9 43 62-105 8-50 (52)
78 PF12674 Zn_ribbon_2: Putative 49.0 9.5 0.00021 31.8 1.3 35 197-231 2-40 (81)
79 smart00595 MADF subfamily of S 49.0 13 0.00028 30.3 2.2 28 272-302 29-56 (89)
80 PLN03142 Probable chromatin-re 48.2 25 0.00054 42.0 5.1 45 249-293 924-981 (1033)
81 COG1725 Predicted transcriptio 48.2 38 0.00082 30.6 5.1 54 53-106 11-68 (125)
82 PF02954 HTH_8: Bacterial regu 48.0 22 0.00049 25.4 3.0 25 257-281 5-29 (42)
83 cd07153 Fur_like Ferric uptake 47.2 34 0.00073 29.1 4.6 47 58-105 2-53 (116)
84 PRK09462 fur ferric uptake reg 46.6 32 0.0007 31.1 4.5 48 58-105 18-70 (148)
85 smart00105 ArfGap Putative GTP 45.9 37 0.0008 29.5 4.6 82 197-294 5-96 (112)
86 smart00550 Zalpha Z-DNA-bindin 45.8 54 0.0012 25.9 5.2 50 58-107 7-56 (68)
87 KOG1194 Predicted DNA-binding 45.2 11 0.00023 40.8 1.3 44 250-294 469-512 (534)
88 PF03444 HrcA_DNA-bdg: Winged 42.1 75 0.0016 26.5 5.5 53 53-106 4-56 (78)
89 PF13463 HTH_27: Winged helix 42.0 74 0.0016 24.1 5.4 42 69-110 14-55 (68)
90 PRK11179 DNA-binding transcrip 41.1 38 0.00083 30.7 4.2 39 256-295 8-47 (153)
91 PF09862 DUF2089: Protein of u 38.8 50 0.0011 29.4 4.3 74 198-295 1-79 (113)
92 PF08914 Myb_DNA-bind_2: Rap1 38.0 61 0.0013 25.9 4.3 43 252-294 3-55 (65)
93 COG5114 Histone acetyltransfer 37.8 42 0.00091 35.0 4.2 68 30-104 362-429 (432)
94 KOG4479 Transcription factor e 37.2 67 0.0015 27.1 4.5 44 53-100 36-89 (92)
95 PF01412 ArfGap: Putative GTPa 36.6 26 0.00056 30.7 2.2 58 196-265 14-72 (116)
96 PHA00442 host recBCD nuclease 36.5 36 0.00077 26.6 2.6 25 256-280 25-50 (59)
97 PF06689 zf-C4_ClpX: ClpX C4-t 36.3 22 0.00049 25.7 1.5 31 196-226 2-33 (41)
98 smart00346 HTH_ICLR helix_turn 35.6 64 0.0014 25.9 4.3 34 72-105 19-52 (91)
99 COG0735 Fur Fe2+/Zn2+ uptake r 34.8 62 0.0014 29.5 4.5 52 57-109 21-77 (145)
100 KOG0384 Chromodomain-helicase 34.6 27 0.00059 42.2 2.5 27 250-276 1132-1159(1373)
101 PF01047 MarR: MarR family; I 34.3 65 0.0014 23.9 3.8 37 74-110 18-54 (59)
102 PRK06474 hypothetical protein; 34.2 77 0.0017 29.9 5.1 50 58-108 12-62 (178)
103 PRK11169 leucine-responsive tr 33.8 55 0.0012 30.1 4.0 39 256-295 13-52 (164)
104 PF14471 DUF4428: Domain of un 33.3 27 0.00058 26.6 1.5 30 197-227 1-30 (51)
105 PF00643 zf-B_box: B-box zinc 31.2 70 0.0015 22.4 3.4 31 196-228 4-34 (42)
106 smart00420 HTH_DEOR helix_turn 30.0 1.3E+02 0.0029 21.0 4.8 34 72-105 13-46 (53)
107 PHA03082 DNA-dependent RNA pol 30.0 11 0.00025 29.6 -1.0 18 196-213 5-22 (63)
108 PF09286 Pro-kuma_activ: Pro-k 29.8 51 0.0011 29.4 3.0 38 71-108 45-82 (143)
109 COG5347 GTPase-activating prot 29.8 53 0.0011 34.2 3.5 98 195-304 20-125 (319)
110 PF05864 Chordopox_RPO7: Chord 29.0 15 0.00032 29.0 -0.6 18 196-213 5-22 (63)
111 cd07377 WHTH_GntR Winged helix 28.5 91 0.002 23.1 3.8 52 53-105 5-57 (66)
112 PF04182 B-block_TFIIIC: B-blo 27.4 69 0.0015 25.8 3.1 43 63-108 11-53 (75)
113 PRK11639 zinc uptake transcrip 27.4 79 0.0017 29.5 3.9 46 58-104 27-77 (169)
114 PF09012 FeoC: FeoC like trans 26.9 1.1E+02 0.0023 24.0 4.1 47 56-108 3-49 (69)
115 TIGR00270 conserved hypothetic 26.6 2.5E+02 0.0054 26.1 7.0 32 197-228 2-35 (154)
116 TIGR02702 SufR_cyano iron-sulf 26.6 1.1E+02 0.0024 29.1 4.8 49 58-108 2-50 (203)
117 KOG2656 DNA methyltransferase 26.4 42 0.00092 35.8 2.1 45 249-293 128-178 (445)
118 PF10820 DUF2543: Protein of u 26.4 49 0.0011 27.2 2.0 30 71-101 46-79 (81)
119 smart00344 HTH_ASNC helix_turn 26.0 1E+02 0.0022 25.7 4.1 38 256-294 2-40 (108)
120 KOG0818 GTPase-activating prot 25.5 46 0.001 36.7 2.2 68 196-276 9-79 (669)
121 PF08100 Dimerisation: Dimeris 25.5 1.2E+02 0.0027 23.0 3.9 27 71-97 20-50 (51)
122 cd08310 Death_NFkB-like Death 25.1 58 0.0013 26.4 2.3 23 256-282 2-24 (72)
123 KOG0724 Zuotin and related mol 24.0 34 0.00073 35.1 0.8 44 251-294 53-96 (335)
124 PF00412 LIM: LIM domain; Int 24.0 51 0.0011 24.4 1.6 33 193-226 24-56 (58)
125 PF08074 CHDCT2: CHDCT2 (NUC03 23.3 50 0.0011 31.3 1.7 29 252-280 4-33 (173)
126 PF01978 TrmB: Sugar-specific 23.3 1.1E+02 0.0023 23.7 3.4 36 71-106 20-55 (68)
127 PF09420 Nop16: Ribosome bioge 23.2 1.4E+02 0.003 27.8 4.7 43 251-293 114-160 (164)
128 PF09986 DUF2225: Uncharacteri 22.7 1.3E+02 0.0028 29.2 4.6 77 194-293 4-101 (214)
129 cd00092 HTH_CRP helix_turn_hel 22.5 2.2E+02 0.0049 21.2 5.0 50 58-107 5-59 (67)
130 cd08311 Death_p75NR Death doma 22.4 74 0.0016 26.2 2.4 26 256-282 2-27 (77)
131 KOG0706 Predicted GTPase-activ 22.2 1.4E+02 0.003 32.5 5.0 56 195-262 23-79 (454)
132 PF02082 Rrf2: Transcriptional 21.3 1.7E+02 0.0038 23.6 4.4 45 62-106 14-58 (83)
133 PF10545 MADF_DNA_bdg: Alcohol 21.1 69 0.0015 25.1 2.0 24 271-294 27-51 (85)
134 PRK11414 colanic acid/biofilm 20.9 1.3E+02 0.0029 28.5 4.3 66 40-106 2-67 (221)
135 PF11035 SnAPC_2_like: Small n 20.8 1.6E+02 0.0034 30.9 4.8 40 251-290 21-64 (344)
136 PF10440 WIYLD: Ubiquitin-bind 20.7 65 0.0014 26.0 1.7 25 254-278 23-48 (65)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=3.3e-83 Score=653.17 Aligned_cols=325 Identities=28% Similarity=0.534 Sum_probs=268.1
Q ss_pred CCCceeEecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHH
Q 012858 11 KPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLL 90 (455)
Q Consensus 11 ~~~~e~ivIPsy~~WF~~~~Ih~iEk~~lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i 90 (455)
-++.++|+||||+.||++.+||+||+++.||||+|++++|||++|+.||||||++||+||.+|||+|+|||||+|||++|
T Consensus 46 ~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvagDV~ai 125 (531)
T COG5259 46 MEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAGDVAAI 125 (531)
T ss_pred hccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccchhHHHH
Confidence 35788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhccccccCCCCCCCCCCCCCCCCCccccccceeecCCCCCcccccCCCCCCCCcCCCCCCCCCCCCccccc
Q 012858 91 HKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVA 170 (455)
Q Consensus 91 ~Rvh~FLe~wGlINy~~~~~~~~~~~~~~~lg~p~~tg~f~v~~dtP~Gl~~~~~p~~~kp~~~~~~~~~~s~~~~~~~~ 170 (455)
.|||+|||+|||||||+++. ++|+.+||| +|+||++++|||+||+|+.+++...... .++..- +....
T Consensus 126 vrvHrFLekWGLINYqvdp~-----trPs~IgPp-lt~h~q~l~dtP~gl~p~l~~~~~~~~~---~~a~~~---e~~~~ 193 (531)
T COG5259 126 VRVHRFLEKWGLINYQVDPG-----TRPSTIGPP-LTSHFQDLHDTPRGLSPFLPWGPINQRV---LGAKEI---EYETH 193 (531)
T ss_pred HHHHHHHHHhcceeeccCCC-----CCccccCCC-cchhhHHHhhCccccccccCCCCccccc---cccchh---hhhhh
Confidence 99999999999999999994 778778875 7899999999999999997655432211 111100 00000
Q ss_pred CCCCCCCCCcccchh----hccccc---ccCCccCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCceecc
Q 012858 171 GETGVKLPPLASYLD----VFGDLV---KLKGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFSD 242 (455)
Q Consensus 171 ~~~~~~~~~l~~~~~----~~~~~~---~~~~~~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~i~ 242 (455)
.+..+ .|++..... .+.++. ......|..||+.+..+||+..+ .++++|..||.+|+||+...+.||..++
T Consensus 194 k~~~~-sps~~~~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~ 272 (531)
T COG5259 194 KEENY-SPSLKSPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVT 272 (531)
T ss_pred ccCCC-CchhhhhhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhh
Confidence 11111 122211110 112222 23348999999999999999998 8899999999999999999999999998
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHcCCCCCccCCCccccCCCCCCCCCCCccc
Q 012858 243 LGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLK 322 (455)
Q Consensus 243 ~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflqLPIeD~~L~~~~~~~~~~~~~~~~~~~~ 322 (455)
...+ ..+..||++|+++|||||++||++|++||.|||+||++|||+|||||||+|.||...++...+
T Consensus 273 ~~~~--~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~~~~~----------- 339 (531)
T COG5259 273 ISLL--IRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDGKGDN----------- 339 (531)
T ss_pred hhcc--cccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccCcCCC-----------
Confidence 7664 256799999999999999999999999999999999999999999999999999876641110
Q ss_pred ccccccccccccchhhhhhhhhccccccCCCCCcCCCccccCCCccCCCCCChHHHHHHHHhhccChHHHHHHHHHHHH
Q 012858 323 EGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVA 401 (455)
Q Consensus 323 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~P~~k~~~~~PFs~a~NPVMs~vAFLas~V~P~VAaAAA~aAl~ 401 (455)
.+ ..+||..+.||||++|+||+++|.|+|++..+++.++
T Consensus 340 -----------------------------------~~-----G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k 378 (531)
T COG5259 340 -----------------------------------SK-----GRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIK 378 (531)
T ss_pred -----------------------------------CC-----CccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhh
Confidence 11 3479999999999999999999999999888877643
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=8.9e-74 Score=601.78 Aligned_cols=318 Identities=31% Similarity=0.567 Sum_probs=257.9
Q ss_pred CCCCCCceeEecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchH
Q 012858 8 PNTKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDV 87 (455)
Q Consensus 8 ~~~~~~~e~ivIPsy~~WF~~~~Ih~iEk~~lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv 87 (455)
+....+.+.|+||||++||+|++||+||++++||||+|++++|||++|++||||||++||+||.+|||+|+|||+++|||
T Consensus 38 ~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp~~ylt~ta~rrnl~gDv 117 (506)
T KOG1279|consen 38 TVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNPQEYLTFTACRRNLAGDV 117 (506)
T ss_pred cccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCcccchhHHHHHhcccchH
Confidence 34467899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhccccccCCCCCCCCCCCCCCCCCccccccceeecCCCCCcccccCCCCCCCCcCCCCCCCCCCCCcc
Q 012858 88 SLLHKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKV 167 (455)
Q Consensus 88 ~~i~Rvh~FLe~wGlINy~~~~~~~~~~~~~~~lg~p~~tg~f~v~~dtP~Gl~~~~~p~~~kp~~~~~~~~~~s~~~~~ 167 (455)
++|+|||+|||+||||||+++++ .+|..++||. ++||+++.++|+|+.++.++... .....+...-
T Consensus 118 ~ai~Rvh~FlE~WGLINy~~d~e-----~rp~~~~p~~-t~h~~~~~~tp~~~~~~~~~~~~---~~~~~~~~~~----- 183 (506)
T KOG1279|consen 118 CAIARVHAFLEQWGLINYQVDAE-----SRPHPIEPPE-TSHFQVLADTPRGLAPLTPEDPQ---SQPDLGNPRM----- 183 (506)
T ss_pred HHHHHHHhhHHhhcccccccChh-----hCCcccCCCc-ccccccccCCCcccccCCCCCcc---cccccccccc-----
Confidence 99999999999999999999994 6666677764 69999999999999887543322 1111111100
Q ss_pred cccCCCCCCCCCcccchhhccccc----ccCCccCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCceecc
Q 012858 168 AVAGETGVKLPPLASYLDVFGDLV----KLKGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFSD 242 (455)
Q Consensus 168 ~~~~~~~~~~~~l~~~~~~~~~~~----~~~~~~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~i~ 242 (455)
+ .+...++...... .....+|..|+.. ||+..+ ..+.+|.+||.+|+|+..+...||..+.
T Consensus 184 ----~------~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~ 249 (506)
T KOG1279|consen 184 ----E------TLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIG 249 (506)
T ss_pred ----c------cccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccchhcc
Confidence 0 1111111111111 1344566666555 555544 6789999999999999999999993332
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHcCCCCCccCCCccccCCCCCCCCCCCccc
Q 012858 243 LGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLK 322 (455)
Q Consensus 243 ~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflqLPIeD~~L~~~~~~~~~~~~~~~~~~~~ 322 (455)
...+..||++|+++|||||++||++|.+||.|||+||++||+.|||||||+|.||....+.
T Consensus 250 -----~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l~~~~~~-------------- 310 (506)
T KOG1279|consen 250 -----ESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYLAKSEAS-------------- 310 (506)
T ss_pred -----ccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhhhhcccc--------------
Confidence 2457899999999999999999999999999999999999999999999999999874321
Q ss_pred ccccccccccccchhhhhhhhhccccccCCCCCcCCCccccCCCccCCCCCChHHHHHHHHhhccChHHHHHHHHHHHHH
Q 012858 323 EGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAA 402 (455)
Q Consensus 323 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~P~~k~~~~~PFs~a~NPVMs~vAFLas~V~P~VAaAAA~aAl~~ 402 (455)
.+|+ ++ +..+|++-+||||++++||+++|+|+|+..++++++..
T Consensus 311 ----------------------------------~~~~-~~-~~~~~sq~gnpv~s~~~~l~~~vdP~~~~~~~k~~~~~ 354 (506)
T KOG1279|consen 311 ----------------------------------LGPL-SY-GPVPFSQDGNPVMSTVAFLASVVDPVVKSVAAKSAEEK 354 (506)
T ss_pred ----------------------------------cCcc-cc-CCCccccCCCccccHHHHHHhccCchhhhhhhcccchh
Confidence 1332 34 35788888899999999999999999999999999988
Q ss_pred HhcCCC
Q 012858 403 LCNESS 408 (455)
Q Consensus 403 l~~e~~ 408 (455)
....+.
T Consensus 355 ~~~~~~ 360 (506)
T KOG1279|consen 355 FSKVNE 360 (506)
T ss_pred hhhhhh
Confidence 765543
No 3
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.94 E-value=1.3e-27 Score=198.63 Aligned_cols=85 Identities=41% Similarity=0.829 Sum_probs=78.1
Q ss_pred EecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccc-hHHHHHHHHH
Q 012858 17 YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFR 95 (455)
Q Consensus 17 ivIPsy~~WF~~~~Ih~iEk~~lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rvh~ 95 (455)
+++|.+++||+++.+|++|++.|||||.| ++|+.||+|||.||+.|+.||.+|||+++||+.+.| |++.+.|||+
T Consensus 1 ~~~~~~~~~~~~~~l~~~E~~~~~e~~~~----~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~ 76 (86)
T PF04433_consen 1 VVIPAHSSWFDPDKLSEIEKQLCPEFFIG----KTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYD 76 (86)
T ss_dssp -HCHCCHTTTTTTSS-HHHHHHCHHCTTS----CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHH
T ss_pred CCCccccCCCCcccCCHHHHHHhHHHhcc----CChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHH
Confidence 47899999999999999999999999998 799999999999999999999999999999999996 9999999999
Q ss_pred Hhhhhccccc
Q 012858 96 LLDEWGLINF 105 (455)
Q Consensus 96 FLe~wGlINy 105 (455)
||++||+|||
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=99.87 E-value=9.2e-23 Score=209.30 Aligned_cols=109 Identities=23% Similarity=0.495 Sum_probs=99.3
Q ss_pred CCccCCCCCCCCCC-ceeeecc-CCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 012858 194 KGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 270 (455)
Q Consensus 194 ~~~~C~~Cg~dc~~-~~y~c~k-~~~~LC~~CF~~G~-~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g 270 (455)
.+++|++|..+|+. ++++|.. .+|+||..||+.|. .+.|.+.|+|.+|++..++ .....||++||.+||||+++||
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~-i~~~~WtadEEilLLea~~t~G 91 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFP-ILDPSWTADEEILLLEAAETYG 91 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCC-CCCCCCChHHHHHHHHHHHHhC
Confidence 57999999999998 4799999 78999999999996 5889999999999997765 4578999999999999999999
Q ss_pred -CCHHHHHhHCCCCCHHHHHHHHHcCCCCCccCC
Q 012858 271 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMG 303 (455)
Q Consensus 271 -~nW~~Ia~~VgtKT~~eC~~hflqLPIeD~~L~ 303 (455)
|||++||+|||+||+++|+.||+...++..+..
T Consensus 92 ~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~ 125 (438)
T KOG0457|consen 92 FGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFP 125 (438)
T ss_pred CCcHHHHHHHHcccchHHHHHHHHHHHhcCcccc
Confidence 999999999999999999999998777776644
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.77 E-value=1.7e-19 Score=178.78 Aligned_cols=110 Identities=20% Similarity=0.350 Sum_probs=101.0
Q ss_pred CCccCCCCCCCCCC-ceeeecc-CCcccchhhhhcCCC-CCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 012858 194 KGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 270 (455)
Q Consensus 194 ~~~~C~~Cg~dc~~-~~y~c~k-~~~~LC~~CF~~G~~-~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g 270 (455)
.+++|++|..+|+. +++.|.. .+++||..||++|.+ +.|+-.|+|.+++.+..+ .....|++.||++|+++.+..|
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsyp-I~~e~WgadEEllli~~~~TlG 82 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYP-IGEEGWGADEELLLIECLDTLG 82 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCcc-ccCCCcCchHHHHHHHHHHhcC
Confidence 46899999999998 7999999 799999999999976 677789999999988876 4578999999999999999999
Q ss_pred -CCHHHHHhHCCCCCHHHHHHHHHcCCCCCccCCC
Q 012858 271 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGS 304 (455)
Q Consensus 271 -~nW~~Ia~~VgtKT~~eC~~hflqLPIeD~~L~~ 304 (455)
|||++||.|||.|+++||..||+.+++|..|..-
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~ypl 117 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYPL 117 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccccc
Confidence 9999999999999999999999999999888543
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=99.16 E-value=3.8e-11 Score=89.26 Aligned_cols=44 Identities=34% Similarity=0.700 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHcCCC-HHHHHhHCC-CCCHHHHHHHHHcC
Q 012858 252 ATWTEAETLLLLESVMRHGDN-WELVAQNVP-TKSKLDCISKLIEL 295 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g~n-W~~Ia~~Vg-tKT~~eC~~hflqL 295 (455)
..||.+|+.+|+++|.+||.+ |..||++|+ +||..||..||.++
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 579999999999999999966 999999999 99999999999763
No 7
>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=99.09 E-value=7.4e-11 Score=87.29 Aligned_cols=44 Identities=25% Similarity=0.767 Sum_probs=41.7
Q ss_pred ccCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCce
Q 012858 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFR 239 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~ 239 (455)
++|+.||.||+.+||||++ .+++||+.||.+|+||.++++.||+
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 5799999999999999999 7799999999999999999999985
No 8
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.93 E-value=1.6e-09 Score=83.63 Aligned_cols=41 Identities=29% Similarity=0.659 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 254 WTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 254 WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
||.+|+.+|++++.+||.+|..||+++|.||+.+|..||..
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 99999999999999999999999999988999999999997
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.89 E-value=3.2e-09 Score=76.58 Aligned_cols=44 Identities=36% Similarity=0.728 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 012858 252 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflqL 295 (455)
..||.+|+.+|+.++.+|| .+|..||+++++||+.+|..+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5799999999999999999 9999999999999999999999864
No 10
>PLN03000 amine oxidase
Probab=98.84 E-value=3.9e-09 Score=119.35 Aligned_cols=84 Identities=27% Similarity=0.332 Sum_probs=73.3
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccch-HHHHHHHHHHhh
Q 012858 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGD-VSLLHKVFRLLD 98 (455)
Q Consensus 22 y~~WF~~~~Ih~iEk~~--lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gD-v~~i~Rvh~FLe 98 (455)
++.-|+.+.+++.|..+ || ...+ ..+..||.|||.||.+|+.||..+||+++|...+..+ ...+.++|+||.
T Consensus 87 ~~~~~p~d~l~~~e~~~~~~~-~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~ 161 (881)
T PLN03000 87 LTAGFPADSLTEEEIEFGVVP-IVGG----IEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLV 161 (881)
T ss_pred HHcCCCcccCCHHHHhccccC-cccc----cchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHH
Confidence 45789999999999777 88 3333 4789999999999999999999999999999888653 578999999999
Q ss_pred hhccccccCCCC
Q 012858 99 EWGLINFGAVSR 110 (455)
Q Consensus 99 ~wGlINy~~~~~ 110 (455)
++|+|||++...
T Consensus 162 r~G~in~g~~~~ 173 (881)
T PLN03000 162 THGYINFGIAQA 173 (881)
T ss_pred HcCcccHHHHHH
Confidence 999999999854
No 11
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.81 E-value=9e-09 Score=73.18 Aligned_cols=43 Identities=40% Similarity=0.784 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 012858 253 TWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (455)
Q Consensus 253 ~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflqL 295 (455)
.||.+|+.+|+.++.+|| .+|..||+.+++||..+|..||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 499999999999999999 9999999999999999999999763
No 12
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.75 E-value=1.2e-08 Score=115.14 Aligned_cols=85 Identities=26% Similarity=0.355 Sum_probs=76.2
Q ss_pred CCCCCCCCCCCHHHHhh-cccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhcc-chHHHHHHHHHHhhh
Q 012858 22 HSSWFRWDDIHETERTA-LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLV-GDVSLLHKVFRLLDE 99 (455)
Q Consensus 22 y~~WF~~~~Ih~iEk~~-lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~-gDv~~i~Rvh~FLe~ 99 (455)
.+.-|+.+.+|+.|..+ |+....+ ..+..||.|||.||.+|+.||..+||+++|+..+- -....+.++|.||.+
T Consensus 138 ~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~ 213 (808)
T PLN02328 138 ISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLE 213 (808)
T ss_pred HHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhc
Confidence 45789999999999887 8877766 47899999999999999999999999999998874 356899999999999
Q ss_pred hccccccCCCC
Q 012858 100 WGLINFGAVSR 110 (455)
Q Consensus 100 wGlINy~~~~~ 110 (455)
.|.|||++.+.
T Consensus 214 ~g~in~gv~~~ 224 (808)
T PLN02328 214 HGYINFGVAPV 224 (808)
T ss_pred cCceeeecccc
Confidence 99999999986
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.36 E-value=4.5e-07 Score=88.88 Aligned_cols=45 Identities=16% Similarity=0.443 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCC-CCCHHHHHHHHHc
Q 012858 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~Vg-tKT~~eC~~hflq 294 (455)
.+..||.+|+.+|+++|++|| .+|..||+++| +||..||++||.+
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N 70 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMN 70 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHH
Confidence 467899999999999999999 79999999997 8999999999985
No 14
>PLN02529 lysine-specific histone demethylase 1
Probab=98.25 E-value=1.4e-06 Score=97.97 Aligned_cols=84 Identities=23% Similarity=0.350 Sum_probs=71.9
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchH-HHHHHHHHHhh
Q 012858 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDV-SLLHKVFRLLD 98 (455)
Q Consensus 22 y~~WF~~~~Ih~iEk~~--lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv-~~i~Rvh~FLe 98 (455)
++-=|+.+.+.+.|+++ +|+. ..+.++.||.|||.|+.+|+.||..+||+++++..+.-++ ..|...|.||.
T Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l~ 137 (738)
T PLN02529 63 LSVGFPIDALLEEEIRAGVVREL-----GGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLL 137 (738)
T ss_pred HHcCCCccccCHHHHhccccCcc-----ccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHHH
Confidence 45679999999999855 5543 3568999999999999999999999999999998876543 45779999999
Q ss_pred hhccccccCCCC
Q 012858 99 EWGLINFGAVSR 110 (455)
Q Consensus 99 ~wGlINy~~~~~ 110 (455)
+.|.|||++.+.
T Consensus 138 ~~~~inc~vnp~ 149 (738)
T PLN02529 138 YNGYINFGVSPS 149 (738)
T ss_pred hCCCcceeeccc
Confidence 999999999986
No 15
>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=98.23 E-value=2.4e-06 Score=66.40 Aligned_cols=44 Identities=20% Similarity=0.371 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCH---HHHHhHCC-CC-CHHHHHHHHHc
Q 012858 251 GATWTEAETLLLLESVMRHG-DNW---ELVAQNVP-TK-SKLDCISKLIE 294 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW---~~Ia~~Vg-tK-T~~eC~~hflq 294 (455)
+..||++|..++|+||+.|| ++| ..|+++++ ++ |+.||..|+-.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QK 52 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQK 52 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHH
Confidence 45799999999999999999 599 99999987 57 99999999864
No 16
>PLN03091 hypothetical protein; Provisional
Probab=98.17 E-value=1.9e-06 Score=90.33 Aligned_cols=45 Identities=20% Similarity=0.441 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCC-CCCHHHHHHHHHc
Q 012858 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~Vg-tKT~~eC~~hflq 294 (455)
.+..||.+|+.+|+++|++|| .+|..||+++| +||..||++||++
T Consensus 13 rKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~N 59 (459)
T PLN03091 13 RKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWIN 59 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHh
Confidence 356899999999999999999 79999999998 7999999999984
No 17
>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=98.05 E-value=5.1e-06 Score=62.47 Aligned_cols=46 Identities=20% Similarity=0.625 Sum_probs=40.5
Q ss_pred ccCCCCCCCCCC-ceeeecc-CCcccchhhhhcCCC-CCCCCCCCceec
Q 012858 196 FKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRFS 241 (455)
Q Consensus 196 ~~C~~Cg~dc~~-~~y~c~k-~~~~LC~~CF~~G~~-~~~~ss~dF~~i 241 (455)
+.|++|++++.. .||+|.. .+++||..||..|.. +.|...|.|+.+
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 469999999888 7999999 899999999999975 678888998764
No 18
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.97 E-value=8.6e-06 Score=80.04 Aligned_cols=46 Identities=20% Similarity=0.282 Sum_probs=43.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
.....||.+|+.+||+.+..||..|..||+++.+||..+|..||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999964
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.94 E-value=8.5e-06 Score=79.95 Aligned_cols=50 Identities=16% Similarity=0.262 Sum_probs=45.5
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCC-CCCHHHHHHHHHcCCCCCccCCCcc
Q 012858 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIELPFGEFMMGSAH 306 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~Vg-tKT~~eC~~hflqLPIeD~~L~~~~ 306 (455)
++.||.||+.+|.+.|++|| ++|..|+++.| .|+..+|++||+ -||....
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~------NyLrP~i 60 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWT------NYLRPDL 60 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhh------cccCCCc
Confidence 58999999999999999999 89999999999 999999999998 4665543
No 20
>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=97.91 E-value=1.2e-05 Score=59.62 Aligned_cols=45 Identities=18% Similarity=0.478 Sum_probs=39.2
Q ss_pred ccCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCceec
Q 012858 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~i 241 (455)
+.|+.|+.++...||+|.. .+++||..||..|. +.|...|.|.++
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEeEC
Confidence 4699999999999999999 88999999999998 666667888754
No 21
>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=97.76 E-value=2.7e-05 Score=57.20 Aligned_cols=40 Identities=23% Similarity=0.703 Sum_probs=35.0
Q ss_pred CCccCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCC
Q 012858 194 KGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (455)
Q Consensus 194 ~~~~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ 233 (455)
..+.|+.|+..+...||+|.. .+++||.+||..|.++..+
T Consensus 3 ~~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 3 HSYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CCcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCCC
Confidence 357899999999999999998 8999999999999876543
No 22
>PLN03091 hypothetical protein; Provisional
Probab=97.73 E-value=4.3e-05 Score=80.45 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=42.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
...+.||.+|+.+||+.+..||..|.+||+++.+||..+|..||..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999964
No 23
>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=97.65 E-value=5e-05 Score=57.09 Aligned_cols=44 Identities=27% Similarity=0.589 Sum_probs=37.1
Q ss_pred ccCCCCCC-CCCCceeeecc-C--CcccchhhhhcCCCCCCCCCCCceec
Q 012858 196 FKCGSCGE-QCNSGCYEYSK-G--SFVICEKCFKNGNYGEDKSKDDFRFS 241 (455)
Q Consensus 196 ~~C~~Cg~-dc~~~~y~c~k-~--~~~LC~~CF~~G~~~~~~ss~dF~~i 241 (455)
+.|+.|+. .+...||+|+. . +++||..||..|. .|...|.|.++
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~--~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE--SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC--CCCCCCceeeC
Confidence 46999998 78889999998 6 8999999999997 56667777653
No 24
>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=97.60 E-value=5.7e-05 Score=56.90 Aligned_cols=43 Identities=14% Similarity=0.424 Sum_probs=36.6
Q ss_pred cCCCCCC-CCCCceeeecc-CCcccchhhhhcCCC-CCCCCCCCce
Q 012858 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFR 239 (455)
Q Consensus 197 ~C~~Cg~-dc~~~~y~c~k-~~~~LC~~CF~~G~~-~~~~ss~dF~ 239 (455)
.|+.|.+ ++...||+|+. .+++||..||..|.. ..|...|.|.
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 99989999999 999999999999975 4555667664
No 25
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=97.59 E-value=6.6e-05 Score=55.09 Aligned_cols=41 Identities=17% Similarity=0.358 Sum_probs=36.1
Q ss_pred cCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCceec
Q 012858 197 KCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (455)
Q Consensus 197 ~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~i 241 (455)
.|+.|+..+...||+|.. .+++||..||..| .| ..|.|+++
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 699999999999999999 7999999999988 44 77888764
No 26
>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=97.50 E-value=0.00011 Score=55.33 Aligned_cols=44 Identities=16% Similarity=0.485 Sum_probs=36.9
Q ss_pred cCCCCC-CCCCCceeeecc-CCcccchhhhhcCCC-CCCCCCCCcee
Q 012858 197 KCGSCG-EQCNSGCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRF 240 (455)
Q Consensus 197 ~C~~Cg-~dc~~~~y~c~k-~~~~LC~~CF~~G~~-~~~~ss~dF~~ 240 (455)
.|+.|+ .++...||+|+. .+++||.+||..|.. +.|...|+|..
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 699999 788888999999 899999999999965 45555777764
No 27
>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=97.48 E-value=0.00011 Score=55.32 Aligned_cols=37 Identities=24% Similarity=0.547 Sum_probs=32.5
Q ss_pred cCCCCCCCCCCceeeecc-CCcccchhhhhcCCCCCCC
Q 012858 197 KCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (455)
Q Consensus 197 ~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ 233 (455)
.|++|.+.+...||+|++ .+++||..||..|.....+
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H 39 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGH 39 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCC
Confidence 599999988889999999 8999999999999875433
No 28
>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=97.46 E-value=6.6e-05 Score=55.69 Aligned_cols=40 Identities=25% Similarity=0.703 Sum_probs=28.7
Q ss_pred CCccCCCCCC-CCCCceeeecc-CCcccchhhhhcCCCCCCC
Q 012858 194 KGFKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (455)
Q Consensus 194 ~~~~C~~Cg~-dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ 233 (455)
..+.|+.|+. .+...||+|+. .+++||..||..|.+...+
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~H 44 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKGRHSHNH 44 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH--H-SSS
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCcCCCCCc
Confidence 4578999999 56778999998 8999999999999876543
No 29
>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=97.44 E-value=0.00014 Score=55.00 Aligned_cols=43 Identities=26% Similarity=0.563 Sum_probs=35.4
Q ss_pred cCCCCCC-CCCCceeeecc-CCcccchhhhhcCCCC-CCCCCCCce
Q 012858 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYG-EDKSKDDFR 239 (455)
Q Consensus 197 ~C~~Cg~-dc~~~~y~c~k-~~~~LC~~CF~~G~~~-~~~ss~dF~ 239 (455)
.|+.|+. .+...||+|++ .+++||..||..|... .|...|+++
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 5999997 57889999999 8999999999999764 455566654
No 30
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.43 E-value=0.00021 Score=70.21 Aligned_cols=43 Identities=16% Similarity=0.390 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hfl 293 (455)
++.||.+||.+|+++...+|..|..||.++++||..+...||-
T Consensus 62 rg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wn 104 (238)
T KOG0048|consen 62 RGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWN 104 (238)
T ss_pred CCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHH
Confidence 6789999999999999999999999999999999999998884
No 31
>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=97.07 E-value=0.00063 Score=50.57 Aligned_cols=42 Identities=24% Similarity=0.608 Sum_probs=34.4
Q ss_pred cCCCCCC-CCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCceec
Q 012858 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (455)
Q Consensus 197 ~C~~Cg~-dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~i 241 (455)
.|+.|+. .+...||+|+. .+++||..||..+. |...|.|.+|
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~---H~~~H~F~ri 45 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRK---HNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCCC---cCCCCceeeC
Confidence 5999986 56678999999 89999999999853 4457888764
No 32
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.01 E-value=0.00077 Score=73.70 Aligned_cols=46 Identities=33% Similarity=0.660 Sum_probs=43.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
...+.||++|+.+|+.||++|| .+|.+|-+.|.+||..||+.+|++
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 4567899999999999999999 699999999999999999999984
No 33
>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=96.90 E-value=0.0011 Score=49.24 Aligned_cols=41 Identities=12% Similarity=0.455 Sum_probs=32.9
Q ss_pred cCCCCC-CCCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCcee
Q 012858 197 KCGSCG-EQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRF 240 (455)
Q Consensus 197 ~C~~Cg-~dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~ 240 (455)
.|+.|+ ..+...||+|+. .+++||.+||..+ .|...|.|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~---~H~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGD---KHDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCC---CCCCCCCEEe
Confidence 699999 566678999999 7999999999964 3445677765
No 34
>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=96.47 E-value=0.0024 Score=46.48 Aligned_cols=34 Identities=15% Similarity=0.599 Sum_probs=28.8
Q ss_pred ccCCCCCCCCCCceeeecc-CCcccchhhhhcCCCC
Q 012858 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYG 230 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~k-~~~~LC~~CF~~G~~~ 230 (455)
+.|+.|.+..+ .||+|+. .+|+||..||..+.-|
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~~~H~ 35 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNTKNHP 35 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCCCCCC
Confidence 46999998654 9999999 8999999999886544
No 35
>PLN02976 amine oxidase
Probab=96.37 E-value=0.0032 Score=75.31 Aligned_cols=83 Identities=23% Similarity=0.355 Sum_probs=70.8
Q ss_pred CCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhh------ccchHHHHHHHHHHhh
Q 012858 25 WFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKS------LVGDVSLLHKVFRLLD 98 (455)
Q Consensus 25 WF~~~~Ih~iEk~~lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~------l~gDv~~i~Rvh~FLe 98 (455)
=+....+.+|||-.|.|...-+ ..-+.||++||.|+-+|-++=.+-|.+++|-=. -.+-..+|.-|+.||+
T Consensus 454 gl~a~~~~~~e~~~~k~~lkr~---~~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~~~fld 530 (1713)
T PLN02976 454 GLKARAVGPIEKIKFKEVLKRK---GGLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREVYLFLD 530 (1713)
T ss_pred cccccccChHHHHHHHHHHHhc---cchHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHHHHHhh
Confidence 4556789999999999998754 367899999999999999999999999999421 1245788999999999
Q ss_pred hhccccccCCCC
Q 012858 99 EWGLINFGAVSR 110 (455)
Q Consensus 99 ~wGlINy~~~~~ 110 (455)
+.|.||-++...
T Consensus 531 ~~gyin~g~~s~ 542 (1713)
T PLN02976 531 QRGYINAGIASE 542 (1713)
T ss_pred ccCceecccccc
Confidence 999999999875
No 36
>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=96.11 E-value=0.0045 Score=45.54 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=27.3
Q ss_pred cCCCCCC-CCCCceeeecc-CCcccchhhhhcC
Q 012858 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNG 227 (455)
Q Consensus 197 ~C~~Cg~-dc~~~~y~c~k-~~~~LC~~CF~~G 227 (455)
.|+.|+. .+...||+|.. .+++||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 5999997 67778999998 8999999999765
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.05 E-value=0.0055 Score=67.25 Aligned_cols=53 Identities=26% Similarity=0.357 Sum_probs=45.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCH---HHHHHHHHcCCCCCccCCCc
Q 012858 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSK---LDCISKLIELPFGEFMMGSA 305 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~---~eC~~hflqLPIeD~~L~~~ 305 (455)
..+.||-+|+..||++|++|| |+|.++|-.+|.||. .-|+.+|+.. ..+|...
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~---k~rl~~~ 467 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAA---KLRLAAG 467 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHH---HHHHhcC
Confidence 467899999999999999999 999999999999999 7789998852 3455443
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.81 E-value=0.0043 Score=50.99 Aligned_cols=43 Identities=26% Similarity=0.530 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHHHHHHH------cC------C--CHHHHHhHCC----CCCHHHHHHHHHc
Q 012858 252 ATWTEAETLLLLESVMR------HG------D--NWELVAQNVP----TKSKLDCISKLIE 294 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~------~g------~--nW~~Ia~~Vg----tKT~~eC~~hflq 294 (455)
..||++|+..||+.+.. ++ + -|..||+.+. .||+.||..+|-+
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~ 62 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKN 62 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 46999999999999877 21 1 5999999875 5999999999975
No 39
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.71 E-value=0.032 Score=61.38 Aligned_cols=44 Identities=23% Similarity=0.564 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
.++.||.+|+..|-..+.++|++|..|++.+| |.|..|+.||-|
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~ 426 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQ 426 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHH
Confidence 57889999999999999999999999999997 799999999986
No 40
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=93.62 E-value=0.057 Score=58.27 Aligned_cols=43 Identities=26% Similarity=0.577 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLI 293 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hfl 293 (455)
+..|+..|+..|--+|.+|| ..|.+|+..+..||+.||..+|.
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~ 50 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWE 50 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHH
Confidence 56899999999999999999 78999999999999999999996
No 41
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.25 E-value=0.076 Score=58.60 Aligned_cols=53 Identities=26% Similarity=0.441 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc------------------C-CCHHHHHhHCCCCCHHHHHHHHHcCCCCCccC
Q 012858 250 HGATWTEAETLLLLESVM-------RH------------------G-DNWELVAQNVPTKSKLDCISKLIELPFGEFMM 302 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie-------~~------------------g-~nW~~Ia~~VgtKT~~eC~~hflqLPIeD~~L 302 (455)
....||-+|+.+||..|+ +| . -+|..|++.+|||+..||+.||-+|=+...+-
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 467899999999999995 44 1 28999999999999999999999876666553
No 42
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=92.61 E-value=0.085 Score=53.35 Aligned_cols=43 Identities=19% Similarity=0.491 Sum_probs=34.4
Q ss_pred ccCCCCCC-CCCCceeeecc-CCcccchhhhhcCCCCCCCCCCCceec
Q 012858 196 FKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (455)
Q Consensus 196 ~~C~~Cg~-dc~~~~y~c~k-~~~~LC~~CF~~G~~~~~~ss~dF~~i 241 (455)
..|+.|+. .+...||+|+. .+|+||..|+..+ .++-.|.+.++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~---~~h~~H~~lR~ 197 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN---EHHAAHAMLRL 197 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC---CCCcccceeec
Confidence 68999999 88889999999 8999999999887 22334555553
No 43
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=91.10 E-value=0.33 Score=54.52 Aligned_cols=44 Identities=18% Similarity=0.358 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHH
Q 012858 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hfl 293 (455)
....||..|..++-.||-.|..|+..|++.|.+||..||++.|.
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHH
Confidence 35679999999999999999999999999999999999999986
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=90.92 E-value=0.37 Score=38.78 Aligned_cols=44 Identities=27% Similarity=0.424 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHcC-----------------CCHHHHHhHCC-----CCCHHHHHHHHHcC
Q 012858 252 ATWTEAETLLLLESVMRHG-----------------DNWELVAQNVP-----TKSKLDCISKLIEL 295 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-----------------~nW~~Ia~~Vg-----tKT~~eC~~hflqL 295 (455)
..||.+|...||+.|++|. .-|..|++.+. .||..|+..+|-.|
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 5799999999999999984 16999998873 59999999998653
No 45
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=90.83 E-value=0.19 Score=54.37 Aligned_cols=45 Identities=18% Similarity=0.422 Sum_probs=41.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHcC
Q 012858 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIEL 295 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflqL 295 (455)
....|+.+|+.+||.+-.....-|..|+..|| ||..||.+||..|
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 35689999999999999999999999999997 8999999999853
No 46
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=89.97 E-value=0.23 Score=51.47 Aligned_cols=36 Identities=25% Similarity=0.775 Sum_probs=30.7
Q ss_pred cCCccCCCCCCCCCC-ceeeecc-CCcccchhhhhcCC
Q 012858 193 LKGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGN 228 (455)
Q Consensus 193 ~~~~~C~~Cg~dc~~-~~y~c~k-~~~~LC~~CF~~G~ 228 (455)
...+.|+.|++.--. -+|+|+. .||+||..||.+|.
T Consensus 6 He~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~ 43 (381)
T KOG1280|consen 6 HEGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGA 43 (381)
T ss_pred cCCceeccccccceeeeeeEeeeecchhHHHHHhhcCC
Confidence 456789999987544 6899998 89999999999995
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.68 E-value=0.47 Score=49.70 Aligned_cols=45 Identities=16% Similarity=0.392 Sum_probs=42.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
....||..|..++..|+.++|.++..|++..++|...|...+|++
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 346899999999999999999999999999999999999999986
No 48
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=88.43 E-value=0.65 Score=48.58 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHH-HhHCCCCCHHHHHHHHHc
Q 012858 251 GATWTEAETLLLLESVMRHGDNWELV-AQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~I-a~~VgtKT~~eC~~hflq 294 (455)
-..|+.+|=+.+-+||+.||.|+..| +..|.|||--||+..|.+
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 35799999999999999999999999 678999999999999874
No 49
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=88.22 E-value=0.47 Score=51.81 Aligned_cols=46 Identities=17% Similarity=0.478 Sum_probs=43.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
.....|+.+|+..|++.-..+|.-|..||..++.||..+|..+|+.
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~ 115 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVN 115 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999984
No 50
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=87.61 E-value=0.49 Score=44.25 Aligned_cols=42 Identities=31% Similarity=0.510 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHhHCCCCCHHHHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKLI 293 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g--~-----nW~~Ia~~VgtKT~~eC~~hfl 293 (455)
...||.+|+++|-|.|.+|- | -.+.|++.++ ||+.-|-.||.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWN 52 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWN 52 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHH
Confidence 46799999999999999995 2 5788888885 99999999995
No 51
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=86.87 E-value=0.56 Score=51.66 Aligned_cols=44 Identities=20% Similarity=0.353 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHH----------HhHCCCCCHHHHHHHHHc
Q 012858 251 GATWTEAETLLLLESVMRHGDNWELV----------AQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~I----------a~~VgtKT~~eC~~hflq 294 (455)
+..||.+|+.-+.+||.++|.|+++| -..+..||+.|.+.||.|
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~ 141 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYR 141 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHH
Confidence 67899999999999999999999999 345557999999999986
No 52
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=85.56 E-value=0.46 Score=51.87 Aligned_cols=42 Identities=24% Similarity=0.417 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKL 292 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hf 292 (455)
.+.|+..|+..|+-+++.|| .+|..||...+.||+++|..||
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw 62 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW 62 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchh
Confidence 56899999999999999999 8999999999999999999999
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=85.02 E-value=0.92 Score=46.79 Aligned_cols=44 Identities=34% Similarity=0.547 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHHcC----------CCHHHHHh---HCC-CCCHHHHHHHHHcC
Q 012858 252 ATWTEAETLLLLESVMRHG----------DNWELVAQ---NVP-TKSKLDCISKLIEL 295 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g----------~nW~~Ia~---~Vg-tKT~~eC~~hflqL 295 (455)
..|+.+|++.||++....- ..|..||. ..| .||+.||..+|-.|
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl 112 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENL 112 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 6799999999999985432 35999998 344 59999999998653
No 54
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=83.34 E-value=0.64 Score=52.49 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=32.1
Q ss_pred CccCCCCCCC-CCCceeeecc-CCcccchhhhhcCCCCCCCC
Q 012858 195 GFKCGSCGEQ-CNSGCYEYSK-GSFVICEKCFKNGNYGEDKS 234 (455)
Q Consensus 195 ~~~C~~Cg~d-c~~~~y~c~k-~~~~LC~~CF~~G~~~~~~s 234 (455)
...|+.|..- +...||+|.+ -+++||..||-.|+.+.++.
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk 644 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHK 644 (966)
T ss_pred hhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCC
Confidence 3569999654 5567999999 89999999999998765443
No 55
>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=76.66 E-value=3.1 Score=37.07 Aligned_cols=45 Identities=20% Similarity=0.400 Sum_probs=35.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC----CCHHHHHhHC------------CCCCHHHHHHHHH
Q 012858 249 THGATWTEAETLLLLESVMRHG----DNWELVAQNV------------PTKSKLDCISKLI 293 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g----~nW~~Ia~~V------------gtKT~~eC~~hfl 293 (455)
..+..||.+|+..||-.+.+|| |.|+.|-+.+ .+||+.+...|--
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 4478899999999999999999 5999997765 3899998877653
No 56
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=72.73 E-value=2.8 Score=45.19 Aligned_cols=52 Identities=15% Similarity=0.241 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHH-hHCCCCCHHHHHHHHHcCCCCCccCC
Q 012858 252 ATWTEAETLLLLESVMRHGDNWELVA-QNVPTKSKLDCISKLIELPFGEFMMG 303 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g~nW~~Ia-~~VgtKT~~eC~~hflqLPIeD~~L~ 303 (455)
..|++-|-.++-|++++||.|+++|- +++.=||-...++.|.-.--.|.|..
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYvq 338 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQ 338 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHHH
Confidence 57999999999999999999999994 67777888888888876555565543
No 57
>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=72.25 E-value=4.9 Score=33.17 Aligned_cols=42 Identities=21% Similarity=0.425 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHHc-------C------CCHHHHHhHCC-----CCCHHHHHHHHHc
Q 012858 253 TWTEAETLLLLESVMRH-------G------DNWELVAQNVP-----TKSKLDCISKLIE 294 (455)
Q Consensus 253 ~WT~~E~~~LLe~Ie~~-------g------~nW~~Ia~~Vg-----tKT~~eC~~hflq 294 (455)
.||++++..||+.+... + ..|+.|++.+. ..|+.||..||-.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 49999999999998544 1 15889988775 4689999999864
No 58
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=71.82 E-value=5.3 Score=34.31 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=34.8
Q ss_pred CCCCCCHHHHHHHHHHHHHc----C----CCHHHHHhHCCCC-----CHHHHHHHHHc
Q 012858 250 HGATWTEAETLLLLESVMRH----G----DNWELVAQNVPTK-----SKLDCISKLIE 294 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~----g----~nW~~Ia~~VgtK-----T~~eC~~hflq 294 (455)
..+.||+++|..||+|+-.| | .||...-++|... |..|-..+.-+
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr 60 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR 60 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 35679999999999999888 4 4888888777532 66777666654
No 59
>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=65.13 E-value=12 Score=27.13 Aligned_cols=38 Identities=13% Similarity=0.177 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 012858 257 AETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (455)
Q Consensus 257 ~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflqL 295 (455)
+=+..||..++.-+ -.|.+||+.||- |+..|..+.-+|
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 44678999999999 799999999995 888888887543
No 60
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.68 E-value=9.8 Score=27.91 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHhCCCcee-eHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 55 YKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 55 Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
|-.+|+.|+.... .|...| |..+....+.-....+.|...-|+.-|+|-.
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 5677887777533 467788 8999888887678999999999999999863
No 61
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=63.61 E-value=3.5 Score=43.02 Aligned_cols=40 Identities=20% Similarity=0.594 Sum_probs=32.4
Q ss_pred CCccCCCCCCCCC-Cceeeecc-CCcccchhhhhcCCCCCCC
Q 012858 194 KGFKCGSCGEQCN-SGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (455)
Q Consensus 194 ~~~~C~~Cg~dc~-~~~y~c~k-~~~~LC~~CF~~G~~~~~~ 233 (455)
-...|++|..... ..+|+|.. ..+.+|..||-.|+-+..+
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~h 280 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSH 280 (434)
T ss_pred CCccCcceecccccchhhhHhhcCCccccchhhccccCCCCc
Confidence 3567999977654 46899998 8899999999999986544
No 62
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=63.23 E-value=7.4 Score=39.76 Aligned_cols=98 Identities=12% Similarity=0.179 Sum_probs=59.3
Q ss_pred CccCCCCCCCCCCceeeeccCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CC
Q 012858 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DN 272 (455)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~-~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~n 272 (455)
-.+|.-||.. .++.-.-.-++.||.+|-.--+ +|.|. .++... .-..||+++...|.+.=..-. .-
T Consensus 25 N~~CADC~a~--~P~WaSwnlGvFiC~~C~giHR~lg~hi-----SkVkSv-----~LD~W~~eqv~~m~~~GN~~an~~ 92 (287)
T KOG0703|consen 25 NKVCADCGAK--GPRWASWNLGVFICLRCAGIHRSLGVHI-----SKVKSV-----TLDEWTDEQVDFMISMGNAKANSY 92 (287)
T ss_pred cCcccccCCC--CCCeEEeecCeEEEeecccccccccchh-----heeeee-----eccccCHHHHHHHHHHcchhhhhh
Confidence 5679988887 4555555678999999986553 44433 333332 235799999887765321111 24
Q ss_pred HHHH-HhHCCCCCHHHHHHHHHc-CCCCCccCCC
Q 012858 273 WELV-AQNVPTKSKLDCISKLIE-LPFGEFMMGS 304 (455)
Q Consensus 273 W~~I-a~~VgtKT~~eC~~hflq-LPIeD~~L~~ 304 (455)
|+.- ....-..++++-+++||+ =+....|+..
T Consensus 93 ~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~ 126 (287)
T KOG0703|consen 93 YEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDP 126 (287)
T ss_pred ccccCCccccCCChHHHHHHHHHHHHhhhhhccc
Confidence 5533 333334677888999997 3333445554
No 63
>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=62.06 E-value=20 Score=26.83 Aligned_cols=43 Identities=19% Similarity=0.266 Sum_probs=35.8
Q ss_pred HhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCCC
Q 012858 67 REEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVS 109 (455)
Q Consensus 67 r~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~~ 109 (455)
..+|...+|+++..+.+.-+-.++.|+..=|+.+|||--..++
T Consensus 15 ~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 15 ARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 3466668999999999999999999999999999999766554
No 64
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=61.72 E-value=11 Score=44.90 Aligned_cols=40 Identities=13% Similarity=0.301 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHH
Q 012858 252 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISK 291 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~h 291 (455)
..||..+-..++.|.++|| ++-..||..|++||++|....
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 4699999999999999999 899999999999999998753
No 65
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=60.68 E-value=7.2 Score=36.99 Aligned_cols=41 Identities=27% Similarity=0.445 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHhHCCCCCHHHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKL 292 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g--~-----nW~~Ia~~VgtKT~~eC~~hf 292 (455)
...||.+++++|-+.|..|+ | -.+.+++.+ .||...|-.+|
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRw 52 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRW 52 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHH
Confidence 46799999999999998887 2 345556666 48999999999
No 66
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=60.44 E-value=10 Score=42.20 Aligned_cols=96 Identities=16% Similarity=0.183 Sum_probs=54.2
Q ss_pred CccCCCCCCCCCCceeeeccCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH-----HHc
Q 012858 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV-----MRH 269 (455)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~I-----e~~ 269 (455)
-..|.-|+.. ...+-|..-++.||.+|-.--+--. + ++... .-..||.+|...|..+= +.|
T Consensus 23 Nk~CADCgs~--~P~WASiNlGIFICi~CSGIHRsLG----h---RVKSL-----SLDkWT~EEVe~Mk~gGN~~AN~iy 88 (648)
T PLN03119 23 NRRCINCNSL--GPQYVCTTFWTFVCMACSGIHREFT----H---RVKSV-----SMSKFTSKEVEVLQNGGNQRAREIY 88 (648)
T ss_pred CCccccCCCC--CCCceeeccceEEeccchhhhccCC----c---eeecc-----ccCCCCHHHHHHHHHhchHHHHHHH
Confidence 3568888864 3677788888999999986543211 1 33332 23679998875443211 112
Q ss_pred CCCHHHHHhHCCCCCHHHHHHHHHc-CCCCCccCCC
Q 012858 270 GDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMGS 304 (455)
Q Consensus 270 g~nW~~Ia~~VgtKT~~eC~~hflq-LPIeD~~L~~ 304 (455)
-.+|..-...++..+..+-+..||+ -+++..|...
T Consensus 89 eanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~ 124 (648)
T PLN03119 89 LKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGA 124 (648)
T ss_pred HhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCc
Confidence 2356543333444444566678887 3344444433
No 67
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=59.68 E-value=5.7 Score=43.62 Aligned_cols=92 Identities=9% Similarity=-0.021 Sum_probs=71.8
Q ss_pred cCCCCCCCCCCCCCHHHHhhcccccCCCC-CCCChhHHHHHHHHHHHHHHhCCCceee-----HHHHHhhcc--chHHHH
Q 012858 19 IPSHSSWFRWDDIHETERTALKEFFDGSS-ISRTPKIYKEYRDFMINKYREEPSRRLT-----FTQVRKSLV--GDVSLL 90 (455)
Q Consensus 19 IPsy~~WF~~~~Ih~iEk~~lpefF~g~~-~~ktpe~Y~~~RN~ii~~yr~np~~yLT-----~t~~r~~l~--gDv~~i 90 (455)
.+.+++-++...=+.-....+++|+.+++ ....+..|+.+|+.+++.++.--.-+.+ -+..+++.. +.+-++
T Consensus 186 ~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLLL 265 (506)
T KOG1279|consen 186 LSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLLL 265 (506)
T ss_pred ccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHHH
Confidence 44566777777777888999999999873 2457788999999999999954333443 455666664 688999
Q ss_pred HHHHHHhhhhccccccCCCC
Q 012858 91 HKVFRLLDEWGLINFGAVSR 110 (455)
Q Consensus 91 ~Rvh~FLe~wGlINy~~~~~ 110 (455)
-+|+.|.+.|+-|+.+|-.+
T Consensus 266 E~ie~y~ddW~kVa~hVg~k 285 (506)
T KOG1279|consen 266 EAIEMYGDDWNKVADHVGTK 285 (506)
T ss_pred HHHHHhcccHHHHHhccCCC
Confidence 99999999999999999864
No 68
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=59.32 E-value=17 Score=39.43 Aligned_cols=46 Identities=15% Similarity=0.340 Sum_probs=42.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
.+...||++|..+|-.+.+.||.+..+|-+.+.-||-...+..|..
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 3467899999999999999999999999999999999999998863
No 69
>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=58.57 E-value=9.7 Score=25.57 Aligned_cols=27 Identities=22% Similarity=0.556 Sum_probs=22.8
Q ss_pred cCCCCCCCCCCc-eeeeccCCcccchhh
Q 012858 197 KCGSCGEQCNSG-CYEYSKGSFVICEKC 223 (455)
Q Consensus 197 ~C~~Cg~dc~~~-~y~c~k~~~~LC~~C 223 (455)
.|..|++..... .|+|.+-.+.+.++|
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 699999999988 999977668877766
No 70
>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=56.84 E-value=19 Score=31.12 Aligned_cols=50 Identities=24% Similarity=0.297 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhcccccc
Q 012858 56 KEYRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINFG 106 (455)
Q Consensus 56 ~~~RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy~ 106 (455)
-.-|..|++....++. .+|+.+....|. -+...|.|...+|+.-|||.=-
T Consensus 7 T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~ 61 (120)
T PF01475_consen 7 TPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKI 61 (120)
T ss_dssp HHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEE
Confidence 4568899998888876 999999987773 2678999999999999999843
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=55.95 E-value=22 Score=27.38 Aligned_cols=52 Identities=21% Similarity=0.335 Sum_probs=40.9
Q ss_pred hHHHHHHHHHHHHHHhCCCcee-eHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 53 KIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 53 e~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
++|-.+|+.|.+--. -|...| +..+..+.+.--...+.+.+..|+.+|+|--
T Consensus 4 ~i~~~l~~~I~~g~~-~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 4 QIYDQLRQAILSGRL-PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHTTSS--TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHcCCC-CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 578888888887433 578899 9999888887778899999999999999953
No 72
>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=55.82 E-value=8.1 Score=25.79 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=12.4
Q ss_pred cCCCCCCCCCC-ceeeeccCCcccchhh
Q 012858 197 KCGSCGEQCNS-GCYEYSKGSFVICEKC 223 (455)
Q Consensus 197 ~C~~Cg~dc~~-~~y~c~k~~~~LC~~C 223 (455)
.|+.|+..... ..|+|..=+|.|..+|
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 59999999988 8999998888888777
No 73
>PLN03131 hypothetical protein; Provisional
Probab=55.51 E-value=17 Score=40.75 Aligned_cols=94 Identities=17% Similarity=0.197 Sum_probs=54.1
Q ss_pred CccCCCCCCCCCCceeeeccCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH------HH
Q 012858 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV------MR 268 (455)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~I------e~ 268 (455)
-..|.-|+.. ...+-|..-++.||.+|-.--+--. + ++... .-..||++|...|- .+ +.
T Consensus 23 Nk~CADCga~--~P~WASiNlGIFICi~CSGIHRsLg----h---RVKSV-----TLD~WtdeEV~~Mk-~gGN~~AN~i 87 (705)
T PLN03131 23 NRRCINCNSL--GPQFVCTNFWTFICMTCSGIHREFT----H---RVKSV-----SMSKFTSQDVEALQ-NGGNQRAREI 87 (705)
T ss_pred CCccccCCCC--CCCeeEeccceEEchhchhhhcccC----c---ccccc-----cCCCCCHHHHHHHH-HhccHHHHHH
Confidence 3468888864 3667777888999999986554211 1 33332 23579998875442 21 12
Q ss_pred cCCCHHHHHhHCCCCCHHHHHHHHHc-CCCCCccCC
Q 012858 269 HGDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMG 303 (455)
Q Consensus 269 ~g~nW~~Ia~~VgtKT~~eC~~hflq-LPIeD~~L~ 303 (455)
|-.+|..--..++..+..+-+..||+ -+++..|+.
T Consensus 88 yeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~ 123 (705)
T PLN03131 88 YLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAG 123 (705)
T ss_pred HHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhc
Confidence 22456543334444455566778886 334444444
No 74
>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=54.46 E-value=30 Score=25.82 Aligned_cols=44 Identities=23% Similarity=0.293 Sum_probs=34.6
Q ss_pred HHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 012858 61 FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (455)
Q Consensus 61 ~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 107 (455)
.|+......+ +++.+..+.+.-....+.|+..-|...|+|+...
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3444333344 8999998888778999999999999999998643
No 75
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=52.92 E-value=38 Score=24.59 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+-|...|||.+
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 57888887665 5699999999999899999999999999999974
No 76
>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=50.58 E-value=51 Score=23.71 Aligned_cols=44 Identities=27% Similarity=0.386 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccc
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLI 103 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlI 103 (455)
.+-.|++.-+.||. +|.++..+.+.-....+.|...-|+.-|+|
T Consensus 4 ~~~~Il~~l~~~~~--~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKILNYLRENPR--ITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHCTT--S-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 34567776677775 999999999988899999999999999997
No 77
>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=50.28 E-value=27 Score=25.85 Aligned_cols=43 Identities=21% Similarity=0.316 Sum_probs=35.0
Q ss_pred HHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 62 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
|++.....+ ..+|+++..+.+.-....+.|+..=|+.+|+|..
T Consensus 8 iL~~l~~~~-~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 8 ILEALAESG-GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHCHHCTB-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 556555544 4589999999998899999999999999999864
No 78
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=49.03 E-value=9.5 Score=31.78 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=25.6
Q ss_pred cCCCCCCCCCCceeeecc----CCcccchhhhhcCCCCC
Q 012858 197 KCGSCGEQCNSGCYEYSK----GSFVICEKCFKNGNYGE 231 (455)
Q Consensus 197 ~C~~Cg~dc~~~~y~c~k----~~~~LC~~CF~~G~~~~ 231 (455)
.|..||..+......=+. ..-+-|.-||.+|.|-.
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 699999999876532222 34567999999998753
No 79
>smart00595 MADF subfamily of SANT domain.
Probab=49.02 E-value=13 Score=30.26 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=23.1
Q ss_pred CHHHHHhHCCCCCHHHHHHHHHcCCCCCccC
Q 012858 272 NWELVAQNVPTKSKLDCISKLIELPFGEFMM 302 (455)
Q Consensus 272 nW~~Ia~~VgtKT~~eC~~hflqLPIeD~~L 302 (455)
-|..||..+|. |.++|..+|..| -+.|.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L--R~~y~ 56 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL--RDRYR 56 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH--HHHHH
Confidence 69999999997 999999999763 34453
No 80
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=48.24 E-value=25 Score=42.01 Aligned_cols=45 Identities=16% Similarity=0.316 Sum_probs=38.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHC------------CCCCHHHHHHHHH
Q 012858 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNV------------PTKSKLDCISKLI 293 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~V------------gtKT~~eC~~hfl 293 (455)
..+..||.+|+..||-.+.+|| ++|+.|-+.+ .+||+.++..|..
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 4467899999999999999999 9999996655 3899999877764
No 81
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=48.18 E-value=38 Score=30.60 Aligned_cols=54 Identities=15% Similarity=0.330 Sum_probs=42.0
Q ss_pred hHHHHHHHHHHHHHH---hCCCceee-HHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 012858 53 KIYKEYRDFMINKYR---EEPSRRLT-FTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (455)
Q Consensus 53 e~Y~~~RN~ii~~yr---~np~~yLT-~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 106 (455)
-+|.+|.|.|...-. +.|...|- +.+--..+.-..+.+.|.+.-||+-|+|.-.
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 499999999988766 36777664 4444445555889999999999999999843
No 82
>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=48.00 E-value=22 Score=25.42 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHcCCCHHHHHhHCC
Q 012858 257 AETLLLLESVMRHGDNWELVAQNVP 281 (455)
Q Consensus 257 ~E~~~LLe~Ie~~g~nW~~Ia~~Vg 281 (455)
-|-..|.++++.++||..+.|+.+|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHC
Confidence 3667899999999999999999999
No 83
>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=47.24 E-value=34 Score=29.12 Aligned_cols=47 Identities=21% Similarity=0.258 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhccccc
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy 105 (455)
-|-.|++..... .+.+|+.+.-..|. -+...+.|...+|..-|||.-
T Consensus 2 qR~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 2 QRLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 367788877665 58899999987773 378999999999999999984
No 84
>PRK09462 fur ferric uptake regulator; Provisional
Probab=46.63 E-value=32 Score=31.07 Aligned_cols=48 Identities=15% Similarity=0.251 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhccccc
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlINy 105 (455)
-|-.|++.....+.+.+|+.+.-..|. -+...|.|...+|+.-|||.=
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence 467788877655678999999877773 268999999999999999973
No 85
>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=45.90 E-value=37 Score=29.54 Aligned_cols=82 Identities=22% Similarity=0.307 Sum_probs=46.8
Q ss_pred cCCCCCCCCCCceeeeccCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CCHH
Q 012858 197 KCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DNWE 274 (455)
Q Consensus 197 ~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~-~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~nW~ 274 (455)
.|.-|+.. .+.+-+..-+..+|..|-.--+ ++.|. .+++ .. .-..||.+|.+.| +..| ...+
T Consensus 5 ~CaDC~~~--~p~w~s~~~GifvC~~CsgiHR~lg~hi---s~Vk--Sl-----~md~w~~~~i~~~----~~~GN~~~n 68 (112)
T smart00105 5 KCFDCGAP--NPTWASVNLGVFLCIECSGIHRSLGVHI---SKVR--SL-----TLDTWTEEELRLL----QKGGNENAN 68 (112)
T ss_pred cccCCCCC--CCCcEEeccceeEhHHhHHHHHhcCCCc---Ceee--ec-----ccCCCCHHHHHHH----HHhhhHHHH
Confidence 57778763 4566677788999999987654 34332 1222 21 1247999886433 3444 2333
Q ss_pred HHHhHC--------CCCCHHHHHHHHHc
Q 012858 275 LVAQNV--------PTKSKLDCISKLIE 294 (455)
Q Consensus 275 ~Ia~~V--------gtKT~~eC~~hflq 294 (455)
++=+.- +..+..+-+..||+
T Consensus 69 ~~~e~~~~~~~~~~~~~~~~~~~~~fI~ 96 (112)
T smart00105 69 SIWESNLDDFSLKPPDSDDQQKYESFIA 96 (112)
T ss_pred HHHHhhCCccccCCCCCchHHHHHHHHH
Confidence 332111 11235678888886
No 86
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.79 E-value=54 Score=25.91 Aligned_cols=50 Identities=14% Similarity=0.088 Sum_probs=44.2
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 107 (455)
.++.|+.....++..-+|..+.-+.|.-+...+.|+..=|+.-|+|-...
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 57889998888876679999999999889999999999999999998754
No 87
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=45.16 E-value=11 Score=40.81 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=39.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
..-+||..|-. ++.-...|+.+...||+.+++||++|....|++
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 34589998887 777778999999999999999999999999985
No 88
>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=42.06 E-value=75 Score=26.52 Aligned_cols=53 Identities=15% Similarity=0.203 Sum_probs=44.7
Q ss_pred hHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 012858 53 KIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (455)
Q Consensus 53 e~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 106 (455)
++-.+|=..||+.|... .+.+...+.-+.|.-+-..|..+..-|+..|||-=+
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 45667888999999976 688888888777876889999999999999999743
No 89
>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=42.04 E-value=74 Score=24.10 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=33.8
Q ss_pred CCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCCCC
Q 012858 69 EPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (455)
Q Consensus 69 np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~~~ 110 (455)
+....+|.++..+.+.-|...+.|+..=|...|||.-..++.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 478999999999999999999999999999999998776663
No 90
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=41.10 E-value=38 Score=30.74 Aligned_cols=39 Identities=13% Similarity=0.145 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 012858 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (455)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflqL 295 (455)
++-+.+||+.+++-| -.|.+||+.+|. |+..|..++-+|
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL 47 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKM 47 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 456889999999999 799999999985 899999998654
No 91
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=38.75 E-value=50 Score=29.39 Aligned_cols=74 Identities=16% Similarity=0.288 Sum_probs=48.0
Q ss_pred CCCCCCCCCCceeeeccCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHH
Q 012858 198 CGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVA 277 (455)
Q Consensus 198 C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia 277 (455)
|..||..+.-.+++|...+..+ +|+|.. ..| .--..|++.+++..-+..||-++|+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i------~G~F~l----~~~--------------~~L~~E~~~Fi~~Fi~~rGnlKe~e 56 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI------EGEFEL----PWF--------------ARLSPEQLEFIKLFIKNRGNLKEME 56 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE------Eeeecc----chh--------------hcCCHHHHHHHHHHHHhcCCHHHHH
Confidence 7889998888888875422221 344321 011 1235688889999999999999999
Q ss_pred hHCCC-----CCHHHHHHHHHcC
Q 012858 278 QNVPT-----KSKLDCISKLIEL 295 (455)
Q Consensus 278 ~~Vgt-----KT~~eC~~hflqL 295 (455)
+.+|- |.+-+=+..=|.+
T Consensus 57 ~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 57 KELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHCCCcHHHHHHHHHHHHHhCC
Confidence 99992 4554444444443
No 92
>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=37.96 E-value=61 Score=25.90 Aligned_cols=43 Identities=19% Similarity=0.387 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHHHHHHHcC-------CC--HHHHHhHCC-CCCHHHHHHHHHc
Q 012858 252 ATWTEAETLLLLESVMRHG-------DN--WELVAQNVP-TKSKLDCISKLIE 294 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-------~n--W~~Ia~~Vg-tKT~~eC~~hflq 294 (455)
...|.+|+..|++-|..+. || |++.++.-. ..|-.-=..||++
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4689999999999996553 33 999988766 6788888899985
No 93
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=37.77 E-value=42 Score=34.99 Aligned_cols=68 Identities=16% Similarity=0.244 Sum_probs=54.2
Q ss_pred CCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccc
Q 012858 30 DIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLIN 104 (455)
Q Consensus 30 ~Ih~iEk~~lpefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlIN 104 (455)
=+++-|++..--+ .-.|..||.+.--||..+.. ....+|.++|++.+.-|+.-.-+|+.|.-.-|.|-
T Consensus 362 llS~dEq~LC~~l------~i~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 362 LLSDDEQRLCETL------NISPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred hhcchHHHHHHHh------CCCCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 4455565555433 23689999999999999885 45789999999999889999999999998888773
No 94
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=37.22 E-value=67 Score=27.12 Aligned_cols=44 Identities=30% Similarity=0.450 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHHHhCCCceeeHHHHH-------hhccchH---HHHHHHHHHhhhh
Q 012858 53 KIYKEYRDFMINKYREEPSRRLTFTQVR-------KSLVGDV---SLLHKVFRLLDEW 100 (455)
Q Consensus 53 e~Y~~~RN~ii~~yr~np~~yLT~t~~r-------~~l~gDv---~~i~Rvh~FLe~w 100 (455)
++-..+||-|+.+=-.| +|+.+.. |-|+-|+ ..++||+.||+++
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 56778999998865544 7877754 3344454 6899999999986
No 95
>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=36.60 E-value=26 Score=30.68 Aligned_cols=58 Identities=17% Similarity=0.259 Sum_probs=31.5
Q ss_pred ccCCCCCCCCCCceeeeccCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHH
Q 012858 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLES 265 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~-~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~ 265 (455)
..|.-|+.. ...+.+..-++.||..|..--+ ++.+.+ +++ ... -..|+.+|..+|.++
T Consensus 14 ~~CaDCg~~--~p~w~s~~~GiflC~~Cag~HR~lg~~is---~Vk--Si~-----~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 14 KVCADCGAP--NPTWASLNYGIFLCLECAGIHRSLGVHIS---RVK--SIT-----MDNWSPEEVQRMREG 72 (116)
T ss_dssp TB-TTT-SB--S--EEETTTTEEE-HHHHHHHHHHTTTT-----EE--ETT-----TS---HHHHHHHHHS
T ss_pred CcCCCCCCC--CCCEEEeecChhhhHHHHHHHHHhcccch---hcc--ccc-----cCCCCHHHHHHHHHH
Confidence 568888744 3477788888999999997653 454322 222 211 235999998887654
No 96
>PHA00442 host recBCD nuclease inhibitor
Probab=36.53 E-value=36 Score=26.58 Aligned_cols=25 Identities=24% Similarity=0.387 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHC
Q 012858 256 EAETLLLLESVMRHG-DNWELVAQNV 280 (455)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~V 280 (455)
-+-....|++++..| +||+.+.+.+
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 345667899999999 9999987654
No 97
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=36.31 E-value=22 Score=25.68 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=18.8
Q ss_pred ccCCCCCCCCCCc-eeeeccCCcccchhhhhc
Q 012858 196 FKCGSCGEQCNSG-CYEYSKGSFVICEKCFKN 226 (455)
Q Consensus 196 ~~C~~Cg~dc~~~-~y~c~k~~~~LC~~CF~~ 226 (455)
..|++||+.-..+ .+.....+..+|..|...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 5799999998775 444333478899999753
No 98
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=35.60 E-value=64 Score=25.94 Aligned_cols=34 Identities=24% Similarity=0.326 Sum_probs=31.0
Q ss_pred ceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 72 ~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
..+|+++.-+.+.-....+.|+...|+.+|+|-.
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 4799999999998789999999999999999964
No 99
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=34.80 E-value=62 Score=29.46 Aligned_cols=52 Identities=17% Similarity=0.232 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHhCCCceeeHHHHHhhccc-----hHHHHHHHHHHhhhhccccccCCC
Q 012858 57 EYRDFMINKYREEPSRRLTFTQVRKSLVG-----DVSLLHKVFRLLDEWGLINFGAVS 109 (455)
Q Consensus 57 ~~RN~ii~~yr~np~~yLT~t~~r~~l~g-----Dv~~i~Rvh~FLe~wGlINy~~~~ 109 (455)
.-|-.|++.-...+. ++|+.+.-+.|.. -+..+.|...+|+.-|||+-....
T Consensus 21 ~qR~~vl~~L~~~~~-~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~ 77 (145)
T COG0735 21 PQRLAVLELLLEADG-HLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFE 77 (145)
T ss_pred HHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeC
Confidence 347788886665554 4999998777742 478999999999999999966664
No 100
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=34.56 E-value=27 Score=42.16 Aligned_cols=27 Identities=26% Similarity=0.777 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHH
Q 012858 250 HGATWTEAETLLLLESVMRHG-DNWELV 276 (455)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~I 276 (455)
....|..+++..||=||-+|| |+|+.|
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHh
Confidence 578999999999999999999 999998
No 101
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=34.30 E-value=65 Score=23.92 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=33.4
Q ss_pred eeHHHHHhhccchHHHHHHHHHHhhhhccccccCCCC
Q 012858 74 LTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (455)
Q Consensus 74 LT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~~~ 110 (455)
+|.++.-+.+..+...+.|+..-|++.|||.-..++.
T Consensus 18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 9999999999999999999999999999999887764
No 102
>PRK06474 hypothetical protein; Provisional
Probab=34.20 E-value=77 Score=29.87 Aligned_cols=50 Identities=14% Similarity=0.083 Sum_probs=40.1
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccc-hHHHHHHHHHHhhhhccccccCC
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFRLLDEWGLINFGAV 108 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~g-Dv~~i~Rvh~FLe~wGlINy~~~ 108 (455)
.|-.|+..-..++. .+|++++...+.+ ....+.|....|+..|||.--..
T Consensus 12 ~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 12 VRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred HHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 68889987776654 4999999888843 56789999999999999995433
No 103
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.82 E-value=55 Score=30.15 Aligned_cols=39 Identities=15% Similarity=0.234 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 012858 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (455)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflqL 295 (455)
++-+.+||.++++-| -.|.+||+.||- |...|..|+-+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 667889999999999 799999999984 888898888653
No 104
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=33.34 E-value=27 Score=26.59 Aligned_cols=30 Identities=30% Similarity=0.520 Sum_probs=20.3
Q ss_pred cCCCCCCCCCCceeeeccCCcccchhhhhcC
Q 012858 197 KCGSCGEQCNSGCYEYSKGSFVICEKCFKNG 227 (455)
Q Consensus 197 ~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G 227 (455)
.|..||+.++...-.-.+++ .+|.+|+..-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 48999999876421112234 6999999765
No 105
>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=31.17 E-value=70 Score=22.37 Aligned_cols=31 Identities=19% Similarity=0.319 Sum_probs=22.7
Q ss_pred ccCCCCCCCCCCceeeeccCCcccchhhhhcCC
Q 012858 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN 228 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~ 228 (455)
..|..|... ...|.|..-+..+|..|+..+.
T Consensus 4 ~~C~~H~~~--~~~~~C~~C~~~~C~~C~~~~H 34 (42)
T PF00643_consen 4 PKCPEHPEE--PLSLFCEDCNEPLCSECTVSGH 34 (42)
T ss_dssp SB-SSTTTS--BEEEEETTTTEEEEHHHHHTST
T ss_pred ccCccCCcc--ceEEEecCCCCccCccCCCCCC
Confidence 456666642 2678888888899999999883
No 106
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=30.05 E-value=1.3e+02 Score=21.03 Aligned_cols=34 Identities=15% Similarity=0.218 Sum_probs=30.4
Q ss_pred ceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 72 ~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
..+|+.+..+.+.-....+.|....|+.-|+|-.
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 3589999999998899999999999999999974
No 107
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=30.03 E-value=11 Score=29.59 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.7
Q ss_pred ccCCCCCCCCCCceeeec
Q 012858 196 FKCGSCGEQCNSGCYEYS 213 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~ 213 (455)
..|+.||.|++..+|+-.
T Consensus 5 lVCsTCGrDlSeeRy~Ll 22 (63)
T PHA03082 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCcchhHHHHHHH
Confidence 579999999999998754
No 108
>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=29.80 E-value=51 Score=29.44 Aligned_cols=38 Identities=16% Similarity=0.072 Sum_probs=26.7
Q ss_pred CceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 012858 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (455)
Q Consensus 71 ~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 108 (455)
.+|||..+......-+-..+.+|.+||...||=.....
T Consensus 45 gk~Lt~~e~~~~~~p~~~~v~~V~~wL~~~G~~~~~~~ 82 (143)
T PF09286_consen 45 GKYLTPEEFAALFAPSPEDVAAVKSWLKSHGLTVVEVS 82 (143)
T ss_dssp T----HHHHHHHHS--HHHHHHHHHHHHHCT-EEEEEE
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCceeEEe
Confidence 68999999999999888899999999999998555533
No 109
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=29.76 E-value=53 Score=34.19 Aligned_cols=98 Identities=16% Similarity=0.127 Sum_probs=55.3
Q ss_pred CccCCCCCCCCCCceeeeccCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCH
Q 012858 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNW 273 (455)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~-~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW 273 (455)
-..|.-||..- -.| -...-++.||.+|-.--+ .|.|.+ |+| .. .=..||.+|..+|.-+=...-..|
T Consensus 20 Nk~CaDCga~~-P~W-~S~nlGvfiCi~CagvHRsLGvhiS---~VK--Si-----tLD~wt~~~l~~m~~gGN~~a~~~ 87 (319)
T COG5347 20 NKKCADCGAPN-PTW-ASVNLGVFLCIDCAGVHRSLGVHIS---KVK--SL-----TLDNWTEEELRRMEVGGNSNANRF 87 (319)
T ss_pred cCccccCCCCC-Cce-EecccCeEEEeecchhhhcccccee---eee--ee-----ecccCCHHHHHHHHHhcchhhhhH
Confidence 35698888875 223 333467899999987664 353332 222 21 135799998877765211111233
Q ss_pred HHHHh---H-CC--CCCHHHHHHHHHc-CCCCCccCCC
Q 012858 274 ELVAQ---N-VP--TKSKLDCISKLIE-LPFGEFMMGS 304 (455)
Q Consensus 274 ~~Ia~---~-Vg--tKT~~eC~~hflq-LPIeD~~L~~ 304 (455)
-+--- + +. .+.-...+.+|++ ++.+-.|...
T Consensus 88 ~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 88 YEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 22211 1 22 4567788999986 6666666554
No 110
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=28.95 E-value=15 Score=29.00 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.5
Q ss_pred ccCCCCCCCCCCceeeec
Q 012858 196 FKCGSCGEQCNSGCYEYS 213 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~ 213 (455)
..|+.||.|++..+|.-.
T Consensus 5 lvCSTCGrDlSeeRy~Ll 22 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCCcchHHHHHHH
Confidence 579999999999988754
No 111
>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=28.53 E-value=91 Score=23.05 Aligned_cols=52 Identities=19% Similarity=0.307 Sum_probs=36.5
Q ss_pred hHHHHHHHHHHHHHHhCCCcee-eHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 012858 53 KIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (455)
Q Consensus 53 e~Y~~~RN~ii~~yr~np~~yL-T~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy 105 (455)
++|-.+++.|+..-. .+...+ |..+..+.+.-.-..+.++..=|+..|+|-.
T Consensus 5 ~~~~~i~~~i~~~~~-~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGEL-KPGDRLPSERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCCC-CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 455666666655422 333344 4888777776678999999999999999853
No 112
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=27.38 E-value=69 Score=25.79 Aligned_cols=43 Identities=26% Similarity=0.224 Sum_probs=32.0
Q ss_pred HHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 012858 63 INKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (455)
Q Consensus 63 i~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 108 (455)
|...|.+. ++..+-.+.+..|...+..+...|+..|||==+..
T Consensus 11 I~rsR~~G---i~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 11 IARSRYNG---ITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHhcCCCC---EehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 44455443 56666667777899999999999999999954433
No 113
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=27.36 E-value=79 Score=29.48 Aligned_cols=46 Identities=11% Similarity=0.105 Sum_probs=37.4
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhcccc
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLIN 104 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~-----gDv~~i~Rvh~FLe~wGlIN 104 (455)
-|-.|++..... .+.+|..+.-..|. -+...|.|...+|+.-|||+
T Consensus 27 qR~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 27 QRLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEE
Confidence 366777766655 58999999877773 26889999999999999997
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=26.93 E-value=1.1e+02 Score=24.04 Aligned_cols=47 Identities=15% Similarity=0.244 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 012858 56 KEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (455)
Q Consensus 56 ~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 108 (455)
++||++|-+ ...+|+.+..+.+.-+...+.-+.++|++.|.|.=...
T Consensus 3 ~~i~~~l~~------~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRE------RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHH------S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHH------cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 456666654 46789999999999999999999999999999984333
No 115
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=26.63 E-value=2.5e+02 Score=26.09 Aligned_cols=32 Identities=22% Similarity=0.671 Sum_probs=23.4
Q ss_pred cCCCCCCCCCCceeee--ccCCcccchhhhhcCC
Q 012858 197 KCGSCGEQCNSGCYEY--SKGSFVICEKCFKNGN 228 (455)
Q Consensus 197 ~C~~Cg~dc~~~~y~c--~k~~~~LC~~CF~~G~ 228 (455)
.|-.||..+...-|.- ......+|..|+.=|.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKFGK 35 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhcCC
Confidence 4999999987653322 2256789999997776
No 116
>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=26.56 E-value=1.1e+02 Score=29.07 Aligned_cols=49 Identities=16% Similarity=0.235 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 012858 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (455)
Q Consensus 58 ~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~~ 108 (455)
.|+.||..-..++. +|+++..+.+.-+..++.|...-|++-|||-....
T Consensus 2 tr~~IL~~L~~~~~--~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~ 50 (203)
T TIGR02702 2 TKEDILSYLLKQGQ--ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAV 50 (203)
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeec
Confidence 47788886655433 99999999998899999999999999999976543
No 117
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=26.44 E-value=42 Score=35.81 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=38.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhH-----CCC-CCHHHHHHHHH
Q 012858 249 THGATWTEAETLLLLESVMRHGDNWELVAQN-----VPT-KSKLDCISKLI 293 (455)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~-----Vgt-KT~~eC~~hfl 293 (455)
+.+..||.+|+..|.+.-+.|.=.|--||+. .++ ||-++-.++|.
T Consensus 128 l~dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY 178 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYY 178 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHH
Confidence 3457899999999999999999888888765 455 99999999996
No 118
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=26.41 E-value=49 Score=27.21 Aligned_cols=30 Identities=17% Similarity=0.565 Sum_probs=21.1
Q ss_pred CceeeHHHHHhhc---cc-hHHHHHHHHHHhhhhc
Q 012858 71 SRRLTFTQVRKSL---VG-DVSLLHKVFRLLDEWG 101 (455)
Q Consensus 71 ~~yLT~t~~r~~l---~g-Dv~~i~Rvh~FLe~wG 101 (455)
++.++-.+ ++-+ +| |..-|--|-.||.+||
T Consensus 46 neeIsEea-Q~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 46 NEEISEEA-QQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred cHhhhHHH-HHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 45555433 3333 35 8888999999999999
No 119
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=25.96 E-value=1e+02 Score=25.74 Aligned_cols=38 Identities=13% Similarity=0.110 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
++.+..+|..++..+ -.|.+||+.+|. ++..+..+..+
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~ 40 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKR 40 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHH
Confidence 356789999999988 699999999984 77778777765
No 120
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=25.53 E-value=46 Score=36.69 Aligned_cols=68 Identities=18% Similarity=0.404 Sum_probs=45.6
Q ss_pred ccCCCCCCCCCCceeeeccCCcccchhhhhcCCC-CCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCC--C
Q 012858 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGNY-GEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGD--N 272 (455)
Q Consensus 196 ~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~~-~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~--n 272 (455)
-.|.-||.. .+...+.+.+..||.+||+--++ |.|.+ +++- .....| +.+.+.|++++...|. =
T Consensus 9 evC~DC~~~--dp~WASvnrGt~lC~eCcsvHrsLGrhIS---~vrh-------LR~s~W-~pt~l~~V~tLn~~gaNsI 75 (669)
T KOG0818|consen 9 EVCADCSGP--DPSWASVNRGTFLCDECCSVHRSLGRHIS---QVRH-------LRHTPW-PPTLLQMVETLNNNGANSI 75 (669)
T ss_pred hhhcccCCC--CCcceeecCceEehHhhhHHHhhhcchHH---HHHH-------hccCCC-CHHHHHHHHHHHhcCcchh
Confidence 468888765 23344556788999999998765 44432 2221 335679 5678889999999984 4
Q ss_pred HHHH
Q 012858 273 WELV 276 (455)
Q Consensus 273 W~~I 276 (455)
|+.-
T Consensus 76 WEh~ 79 (669)
T KOG0818|consen 76 WEHS 79 (669)
T ss_pred hhhh
Confidence 8753
No 121
>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=25.53 E-value=1.2e+02 Score=23.00 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=23.2
Q ss_pred CceeeHHHHHhhcc----chHHHHHHHHHHh
Q 012858 71 SRRLTFTQVRKSLV----GDVSLLHKVFRLL 97 (455)
Q Consensus 71 ~~yLT~t~~r~~l~----gDv~~i~Rvh~FL 97 (455)
...+|..+....|. .+...+.||.+||
T Consensus 20 ~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 20 GGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 58999999988887 6889999999998
No 122
>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=25.11 E-value=58 Score=26.38 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHhHCCC
Q 012858 256 EAETLLLLESVMRHGDNWELVAQNVPT 282 (455)
Q Consensus 256 ~~E~~~LLe~Ie~~g~nW~~Ia~~Vgt 282 (455)
-++.-+||+. |.+|..+|+++|-
T Consensus 2 r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 2 RERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred HHHHHHHhCC----CCCHHHHHHHcCc
Confidence 3556678887 9999999999985
No 123
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=24.02 E-value=34 Score=35.06 Aligned_cols=44 Identities=5% Similarity=-0.146 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 012858 251 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hflq 294 (455)
...||.++...++++|..|+..|+.|-++++.++..+.+.|...
T Consensus 53 ~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~ 96 (335)
T KOG0724|consen 53 EPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQK 96 (335)
T ss_pred ccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCC
Confidence 34599999999999999999999999999999999999999754
No 124
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=23.98 E-value=51 Score=24.36 Aligned_cols=33 Identities=30% Similarity=0.778 Sum_probs=24.3
Q ss_pred cCCccCCCCCCCCCCceeeeccCCcccchhhhhc
Q 012858 193 LKGFKCGSCGEQCNSGCYEYSKGSFVICEKCFKN 226 (455)
Q Consensus 193 ~~~~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~ 226 (455)
..=+.|..|+..+....+. ...+...|..||.+
T Consensus 24 ~~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGDFY-EKDGKPYCKDCYQK 56 (58)
T ss_dssp TTTSBETTTTCBTTTSSEE-EETTEEEEHHHHHH
T ss_pred ccccccCCCCCccCCCeeE-eECCEEECHHHHhh
Confidence 4567899999999886532 23557899999864
No 125
>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=23.27 E-value=50 Score=31.31 Aligned_cols=29 Identities=21% Similarity=0.661 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHhHC
Q 012858 252 ATWTEAETLLLLESVMRHG-DNWELVAQNV 280 (455)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~V 280 (455)
.-|-..-+..||-||-+|| +.|++|....
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~ 33 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDP 33 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCC
Confidence 4688999999999999999 9999997643
No 126
>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=23.27 E-value=1.1e+02 Score=23.72 Aligned_cols=36 Identities=19% Similarity=0.201 Sum_probs=32.2
Q ss_pred CceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 012858 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (455)
Q Consensus 71 ~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 106 (455)
...+|+.+..+.+.-+-..+.|+..-|++.|||.-.
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 357999999999998999999999999999999744
No 127
>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=23.23 E-value=1.4e+02 Score=27.77 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHhHCC----CCCHHHHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHGDNWELVAQNVP----TKSKLDCISKLI 293 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~Vg----tKT~~eC~~hfl 293 (455)
...-|..|...+-..|++||+|+...|.-.. ..|+.|+...+.
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHH
Confidence 4568899999999999999999999987554 479999887664
No 128
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=22.70 E-value=1.3e+02 Score=29.21 Aligned_cols=77 Identities=16% Similarity=0.329 Sum_probs=46.9
Q ss_pred CCccCCCCCCCCCCceeeecc-----C----------------CcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCC
Q 012858 194 KGFKCGSCGEQCNSGCYEYSK-----G----------------SFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGA 252 (455)
Q Consensus 194 ~~~~C~~Cg~dc~~~~y~c~k-----~----------------~~~LC~~CF~~G~~~~~~ss~dF~~i~~~~~~~~~~~ 252 (455)
+...|..|++.-....++... . .+.+|++|.-..- ..||.
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~------~~~F~------------- 64 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF------EEDFE------------- 64 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc------ccccc-------------
Confidence 567899999887665444432 1 2456777764332 12222
Q ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHH
Q 012858 253 TWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (455)
Q Consensus 253 ~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eC~~hfl 293 (455)
..+..+..+|.+.|.. .|... +.-+.||.++-+..|.
T Consensus 65 ~l~~~~~~~i~~~i~~---~~~~~-~~~~~Rt~~~ai~~Yk 101 (214)
T PF09986_consen 65 KLSPEQKEKIKENISS---RWKPR-DFSGERTLEEAIESYK 101 (214)
T ss_pred cCCHHHHHHHHHHHHh---hcccC-CCCCCCCHHHHHHHHH
Confidence 3555566666665554 56655 5666789988888775
No 129
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=22.46 E-value=2.2e+02 Score=21.17 Aligned_cols=50 Identities=20% Similarity=0.178 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhC-----CCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 012858 58 YRDFMINKYREE-----PSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (455)
Q Consensus 58 ~RN~ii~~yr~n-----p~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~~ 107 (455)
+..+++...... -...+|.++....+.-....+.|+..-|+..|+|=+..
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 344555544432 23468999988888889999999999999999997543
No 130
>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=22.36 E-value=74 Score=26.18 Aligned_cols=26 Identities=35% Similarity=0.487 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHhHCCC
Q 012858 256 EAETLLLLESVMRHGDNWELVAQNVPT 282 (455)
Q Consensus 256 ~~E~~~LLe~Ie~~g~nW~~Ia~~Vgt 282 (455)
.+|..+||..= .-|.||...|.++|-
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~LG~ 27 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGELGY 27 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHcCC
Confidence 46777888521 446899999999995
No 131
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=22.17 E-value=1.4e+02 Score=32.47 Aligned_cols=56 Identities=18% Similarity=0.282 Sum_probs=35.3
Q ss_pred CccCCCCCCCCCCceeeeccCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHH
Q 012858 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLL 262 (455)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~c~k~~~~LC~~CF~~G~-~~~~~ss~dF~~i~~~~~~~~~~~~WT~~E~~~L 262 (455)
-..|.-|+..-.. | -...-++.||.+|-..-+ .|-|.+ |++-.+ .+. ||-.|...+
T Consensus 23 NKvCFDCgAknPt-W-aSVTYGIFLCiDCSAvHRnLGVHiS---FVRSTn------LDs-Ws~~qLR~M 79 (454)
T KOG0706|consen 23 NKVCFDCGAKNPT-W-ASVTYGIFLCIDCSAVHRNLGVHIS---FVRSTN------LDS-WSWEQLRRM 79 (454)
T ss_pred CceecccCCCCCC-c-eeecceEEEEEecchhhhccccceE---EEeecc------ccc-CCHHHHhHh
Confidence 3568888876321 1 122257899999998774 577765 776432 233 998876543
No 132
>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=21.27 E-value=1.7e+02 Score=23.58 Aligned_cols=45 Identities=20% Similarity=0.271 Sum_probs=33.9
Q ss_pred HHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 012858 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (455)
Q Consensus 62 ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 106 (455)
|+.....+....+|..+....+.--...+.+|..-|.+-|||.-.
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 334444344445999999999988899999999999999999743
No 133
>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=21.11 E-value=69 Score=25.13 Aligned_cols=24 Identities=21% Similarity=0.444 Sum_probs=20.5
Q ss_pred CCHHHHHhHCCC-CCHHHHHHHHHc
Q 012858 271 DNWELVAQNVPT-KSKLDCISKLIE 294 (455)
Q Consensus 271 ~nW~~Ia~~Vgt-KT~~eC~~hflq 294 (455)
.-|..||..+|. -+.++|..+|.+
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~ 51 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKN 51 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHH
Confidence 369999999995 478999999986
No 134
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=20.93 E-value=1.3e+02 Score=28.47 Aligned_cols=66 Identities=12% Similarity=0.074 Sum_probs=47.3
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 012858 40 KEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (455)
Q Consensus 40 pefF~g~~~~ktpe~Y~~~RN~ii~~yr~np~~yLT~t~~r~~l~gDv~~i~Rvh~FLe~wGlINy~ 106 (455)
|.|=.-...+.+..+|-.+|..|+. -+..|...|+-.+....+.-=-..+..-..-|+..|||-..
T Consensus 2 ~~~~~~~~~~~~e~v~~~l~~~I~~-g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 2 PGTEKTQHISLTLQVENDLKHQLSI-GALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVA 67 (221)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHh-CCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEec
Confidence 3343333344567899999999997 45689999998766666643345677777789999999753
No 135
>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=20.77 E-value=1.6e+02 Score=30.90 Aligned_cols=40 Identities=20% Similarity=0.317 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCC----CHHHHHhHCCCCCHHHHHH
Q 012858 251 GATWTEAETLLLLESVMRHGD----NWELVAQNVPTKSKLDCIS 290 (455)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~----nW~~Ia~~VgtKT~~eC~~ 290 (455)
...||..|...||.+++--.| |-..|+++|.+|+..|+..
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 467999999999999987653 6667888999999888654
No 136
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=20.72 E-value=65 Score=25.96 Aligned_cols=25 Identities=20% Similarity=0.461 Sum_probs=18.4
Q ss_pred CCHHHHH-HHHHHHHHcCCCHHHHHh
Q 012858 254 WTEAETL-LLLESVMRHGDNWELVAQ 278 (455)
Q Consensus 254 WT~~E~~-~LLe~Ie~~g~nW~~Ia~ 278 (455)
..++... .|-+.++.||+||.-|-+
T Consensus 23 ~~~~~v~~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 23 FSKKQVRPVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred CCHHHHHHHHHHHHHHHcCCchhhhc
Confidence 4444444 677888999999999864
Done!