Query 013569
Match_columns 440
No_of_seqs 266 out of 705
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:10:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013569hhsearch_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 7.4E-85 1.6E-89 662.1 15.9 325 11-401 46-378 (531)
2 KOG1279 Chromatin remodeling f 100.0 1.1E-74 2.5E-79 605.8 18.5 316 10-408 40-360 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 1.4E-27 3E-32 197.5 6.1 85 17-105 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 1.2E-22 2.7E-27 207.4 8.7 111 194-305 13-127 (438)
5 COG5114 Histone acetyltransfer 99.8 1.8E-19 3.9E-24 177.7 5.8 110 194-304 4-117 (432)
6 PF00249 Myb_DNA-binding: Myb- 99.2 4.4E-11 9.4E-16 88.5 4.9 44 252-295 2-47 (48)
7 cd02336 ZZ_RSC8 Zinc finger, Z 99.1 7.4E-11 1.6E-15 86.8 3.7 44 196-239 1-45 (45)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.9 1.4E-09 3E-14 83.6 5.5 41 254-294 1-41 (60)
9 smart00717 SANT SANT SWI3, AD 98.9 3.2E-09 7E-14 76.2 5.8 44 252-295 2-46 (49)
10 PLN03000 amine oxidase 98.8 4.3E-09 9.3E-14 118.5 6.9 84 22-110 87-173 (881)
11 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 8.7E-09 1.9E-13 72.9 5.6 43 253-295 1-44 (45)
12 PLN02328 lysine-specific histo 98.7 1.5E-08 3.3E-13 113.7 6.9 85 22-110 138-224 (808)
13 PLN03212 Transcription repress 98.4 4.1E-07 8.8E-12 88.7 5.3 45 250-294 24-70 (249)
14 PLN02529 lysine-specific histo 98.3 1.4E-06 3E-11 97.5 6.8 84 22-110 63-149 (738)
15 PLN03091 hypothetical protein; 98.2 1.9E-06 4E-11 90.0 5.2 45 250-294 13-59 (459)
16 TIGR01557 myb_SHAQKYF myb-like 98.2 3.9E-06 8.4E-11 64.9 5.7 44 251-294 3-52 (57)
17 cd02335 ZZ_ADA2 Zinc finger, Z 98.0 8.3E-06 1.8E-10 61.0 4.1 46 196-241 1-49 (49)
18 KOG0048 Transcription factor, 97.9 9.7E-06 2.1E-10 79.2 4.7 44 251-294 9-54 (238)
19 PLN03212 Transcription repress 97.9 1.3E-05 2.8E-10 78.4 5.2 46 249-294 76-121 (249)
20 cd02249 ZZ Zinc finger, ZZ typ 97.9 1.4E-05 3E-10 58.8 3.9 45 196-241 1-46 (46)
21 smart00291 ZnF_ZZ Zinc-binding 97.7 3.2E-05 7E-10 56.5 3.7 39 195-233 4-43 (44)
22 PLN03091 hypothetical protein; 97.7 6.2E-05 1.3E-09 78.8 5.8 46 249-294 65-110 (459)
23 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.6 5.3E-05 1.2E-09 56.6 3.7 44 196-241 1-48 (48)
24 cd02340 ZZ_NBR1_like Zinc fing 97.6 7.3E-05 1.6E-09 54.6 3.5 41 197-241 2-43 (43)
25 cd02345 ZZ_dah Zinc finger, ZZ 97.6 7.3E-05 1.6E-09 56.0 3.5 43 197-239 2-47 (49)
26 cd02338 ZZ_PCMF_like Zinc fing 97.5 0.00013 2.9E-09 54.5 3.8 44 197-240 2-48 (49)
27 cd02343 ZZ_EF Zinc finger, ZZ 97.4 0.00013 2.9E-09 54.5 3.5 37 197-233 2-39 (48)
28 PF00569 ZZ: Zinc finger, ZZ t 97.4 7.4E-05 1.6E-09 55.1 2.0 40 194-233 3-44 (46)
29 cd02334 ZZ_dystrophin Zinc fin 97.3 0.00025 5.5E-09 53.2 3.7 43 197-239 2-47 (49)
30 KOG0048 Transcription factor, 97.1 0.00071 1.5E-08 66.2 5.8 43 251-293 62-104 (238)
31 cd02344 ZZ_HERC2 Zinc finger, 97.1 0.00057 1.2E-08 50.5 3.6 42 197-241 2-45 (45)
32 KOG0049 Transcription factor, 97.1 0.00058 1.3E-08 74.2 5.1 46 249-294 358-404 (939)
33 cd02339 ZZ_Mind_bomb Zinc fing 96.9 0.0011 2.3E-08 49.0 3.6 41 197-240 2-44 (45)
34 cd02337 ZZ_CBP Zinc finger, ZZ 96.5 0.0025 5.4E-08 46.1 2.8 36 196-232 1-37 (41)
35 PLN02976 amine oxidase 96.3 0.0034 7.3E-08 74.7 4.5 83 25-110 454-542 (1713)
36 cd02342 ZZ_UBA_plant Zinc fing 96.1 0.0047 1E-07 45.1 2.6 31 197-227 2-34 (43)
37 KOG0049 Transcription factor, 96.0 0.0061 1.3E-07 66.6 4.0 54 249-305 410-467 (939)
38 PF13837 Myb_DNA-bind_4: Myb/S 95.9 0.0039 8.4E-08 51.0 1.5 44 252-295 2-63 (90)
39 KOG0051 RNA polymerase I termi 94.7 0.034 7.4E-07 60.9 4.4 44 250-294 383-426 (607)
40 KOG0050 mRNA splicing protein 93.7 0.055 1.2E-06 58.1 3.4 43 251-293 7-50 (617)
41 KOG0051 RNA polymerase I termi 93.4 0.07 1.5E-06 58.5 3.7 54 250-303 435-514 (607)
42 KOG4582 Uncharacterized conser 92.9 0.074 1.6E-06 53.5 2.9 43 196-241 153-197 (278)
43 KOG0050 mRNA splicing protein 91.9 0.13 2.8E-06 55.3 3.2 45 250-295 58-102 (617)
44 PF13873 Myb_DNA-bind_5: Myb/S 91.5 0.3 6.6E-06 39.1 4.3 44 252-295 3-68 (78)
45 KOG4167 Predicted DNA-binding 91.1 0.32 6.9E-06 54.4 5.3 44 250-293 618-661 (907)
46 KOG1280 Uncharacterized conser 89.5 0.25 5.4E-06 50.9 2.7 36 193-228 6-43 (381)
47 COG5118 BDP1 Transcription ini 89.1 0.56 1.2E-05 48.9 4.8 45 250-294 364-408 (507)
48 COG5147 REB1 Myb superfamily p 88.9 0.4 8.7E-06 52.1 3.9 45 250-294 71-115 (512)
49 TIGR02894 DNA_bind_RsfA transc 88.5 0.4 8.6E-06 44.6 3.1 42 251-293 4-52 (161)
50 KOG4329 DNA-binding protein [G 88.0 0.73 1.6E-05 47.9 4.8 44 251-294 277-321 (445)
51 KOG4286 Dystrophin-like protei 87.3 0.32 6.9E-06 54.5 1.9 40 195-234 603-644 (966)
52 KOG4282 Transcription factor G 86.6 0.7 1.5E-05 47.4 3.8 44 252-295 55-112 (345)
53 KOG4468 Polycomb-group transcr 86.2 0.65 1.4E-05 50.9 3.4 44 251-294 88-141 (782)
54 COG5147 REB1 Myb superfamily p 85.4 0.48 1E-05 51.5 2.0 42 251-292 20-62 (512)
55 PF09111 SLIDE: SLIDE; InterP 78.9 2.5 5.4E-05 37.4 3.7 45 249-293 47-107 (118)
56 KOG0703 Predicted GTPase-activ 74.2 3.1 6.7E-05 42.2 3.4 98 195-304 25-126 (287)
57 PF12776 Myb_DNA-bind_3: Myb/S 71.7 5.1 0.00011 32.9 3.7 42 253-294 1-60 (96)
58 KOG3554 Histone deacetylase co 70.2 3.2 6.9E-05 44.6 2.5 52 252-303 286-338 (693)
59 PF04504 DUF573: Protein of un 68.9 6.7 0.00015 33.5 3.8 45 250-294 3-60 (98)
60 PF13404 HTH_AsnC-type: AsnC-t 68.7 9.4 0.0002 27.5 4.0 38 257-295 3-41 (42)
61 KOG4301 Beta-dystrobrevin [Cyt 68.4 2.5 5.3E-05 43.8 1.3 41 194-234 239-281 (434)
62 PLN03142 Probable chromatin-re 65.8 8.4 0.00018 45.6 5.0 40 252-291 825-865 (1033)
63 PRK13923 putative spore coat p 63.3 6 0.00013 37.3 2.7 41 251-292 5-52 (170)
64 smart00345 HTH_GNTR helix_turn 63.1 10 0.00022 27.6 3.5 50 55-105 2-52 (60)
65 PF12802 MarR_2: MarR family; 62.5 20 0.00043 26.7 5.0 43 67-109 15-57 (62)
66 PF07649 C1_3: C1-like domain; 61.2 6 0.00013 26.2 1.7 27 197-223 2-29 (30)
67 PF03107 C1_2: C1 domain; Int 59.8 9 0.0002 25.5 2.4 27 197-223 2-29 (30)
68 KOG1194 Predicted DNA-binding 59.4 17 0.00036 39.2 5.4 46 249-294 185-230 (534)
69 KOG1279 Chromatin remodeling f 58.2 6.2 0.00013 43.1 2.1 92 19-110 186-285 (506)
70 PF01475 FUR: Ferric uptake re 57.5 18 0.0004 31.0 4.6 50 56-106 7-61 (120)
71 PF00392 GntR: Bacterial regul 55.7 23 0.00049 27.1 4.4 53 52-105 3-56 (64)
72 cd00090 HTH_ARSR Arsenical Res 54.1 31 0.00067 25.6 4.9 44 61-107 11-54 (78)
73 PF01022 HTH_5: Bacterial regu 53.7 37 0.0008 24.5 5.0 45 58-105 3-47 (47)
74 PLN03119 putative ADP-ribosyla 53.5 19 0.0004 40.0 4.7 96 195-305 23-125 (648)
75 PF12674 Zn_ribbon_2: Putative 53.3 7.3 0.00016 32.2 1.3 34 197-230 2-39 (81)
76 PLN03131 hypothetical protein; 53.1 20 0.00044 40.0 4.9 94 195-304 23-124 (705)
77 PLN03142 Probable chromatin-re 52.0 20 0.00044 42.5 5.1 46 249-294 924-982 (1033)
78 smart00595 MADF subfamily of S 51.8 11 0.00024 30.5 2.2 28 272-302 29-56 (89)
79 PF02954 HTH_8: Bacterial regu 49.4 21 0.00045 25.4 3.0 25 257-281 5-29 (42)
80 PF13412 HTH_24: Winged helix- 49.3 56 0.0012 23.3 5.4 44 58-103 4-47 (48)
81 PF09339 HTH_IclR: IclR helix- 49.2 29 0.00064 25.5 3.9 43 62-105 8-50 (52)
82 cd07153 Fur_like Ferric uptake 47.5 34 0.00073 29.0 4.6 47 58-105 2-53 (116)
83 COG1725 Predicted transcriptio 47.0 41 0.00089 30.2 5.1 54 53-106 11-68 (125)
84 PRK09462 fur ferric uptake reg 46.4 33 0.00071 30.8 4.5 48 58-105 18-70 (148)
85 KOG1194 Predicted DNA-binding 46.2 10 0.00022 40.8 1.3 44 250-294 469-512 (534)
86 smart00550 Zalpha Z-DNA-bindin 45.5 56 0.0012 25.7 5.2 50 58-107 7-56 (68)
87 PRK11179 DNA-binding transcrip 43.7 33 0.00072 31.0 4.2 39 256-295 8-47 (153)
88 KOG4479 Transcription factor e 43.4 48 0.001 27.8 4.5 44 53-100 36-89 (92)
89 PF13463 HTH_27: Winged helix 42.5 73 0.0016 24.0 5.4 42 69-110 14-55 (68)
90 COG5114 Histone acetyltransfer 41.7 34 0.00073 35.5 4.2 68 30-104 362-429 (432)
91 KOG0384 Chromodomain-helicase 39.9 20 0.00043 43.0 2.5 27 250-276 1132-1159(1373)
92 smart00105 ArfGap Putative GTP 39.5 54 0.0012 28.3 4.6 83 196-294 4-96 (112)
93 PF09862 DUF2089: Protein of u 39.3 49 0.0011 29.2 4.3 74 198-295 1-79 (113)
94 PF03444 HrcA_DNA-bdg: Winged 38.9 91 0.002 25.8 5.5 54 53-107 4-57 (78)
95 PF08914 Myb_DNA-bind_2: Rap1 38.8 58 0.0013 25.8 4.3 43 252-294 3-55 (65)
96 PRK11169 leucine-responsive tr 35.2 51 0.0011 30.2 4.0 39 256-295 13-52 (164)
97 smart00346 HTH_ICLR helix_turn 34.4 74 0.0016 25.4 4.5 34 72-105 19-52 (91)
98 COG0735 Fur Fe2+/Zn2+ uptake r 33.3 69 0.0015 29.0 4.5 51 58-109 22-77 (145)
99 PHA00442 host recBCD nuclease 33.3 43 0.00094 25.9 2.6 24 257-280 26-50 (59)
100 PF01047 MarR: MarR family; I 33.0 75 0.0016 23.4 4.0 37 74-110 18-54 (59)
101 PRK06474 hypothetical protein; 32.7 86 0.0019 29.4 5.2 50 58-108 12-62 (178)
102 PF01412 ArfGap: Putative GTPa 32.3 34 0.00074 29.7 2.2 84 195-294 13-105 (116)
103 PF00643 zf-B_box: B-box zinc 31.1 71 0.0015 22.2 3.4 31 196-228 4-34 (42)
104 PHA03082 DNA-dependent RNA pol 31.0 10 0.00023 29.6 -1.0 18 196-213 5-22 (63)
105 PF14471 DUF4428: Domain of un 30.7 32 0.0007 25.9 1.6 29 197-227 1-30 (51)
106 PF05864 Chordopox_RPO7: Chord 30.6 13 0.00029 29.0 -0.6 18 196-213 5-22 (63)
107 PF09286 Pro-kuma_activ: Pro-k 30.5 49 0.0011 29.4 3.0 38 71-108 45-82 (143)
108 PF06689 zf-C4_ClpX: ClpX C4-t 29.9 31 0.00067 24.8 1.3 31 196-226 2-33 (41)
109 smart00420 HTH_DEOR helix_turn 29.5 1.4E+02 0.003 20.8 4.8 34 72-105 13-46 (53)
110 PF09986 DUF2225: Uncharacteri 28.2 84 0.0018 30.4 4.4 77 194-293 4-101 (214)
111 PF09420 Nop16: Ribosome bioge 28.2 96 0.0021 28.6 4.6 43 251-293 114-160 (164)
112 cd07377 WHTH_GntR Winged helix 27.9 96 0.0021 22.8 3.8 52 53-105 5-57 (66)
113 cd08310 Death_NFkB-like Death 27.8 49 0.0011 26.6 2.3 23 256-282 2-24 (72)
114 smart00344 HTH_ASNC helix_turn 27.8 92 0.002 25.9 4.1 39 256-295 2-41 (108)
115 PF08100 Dimerisation: Dimeris 27.2 1.1E+02 0.0024 23.1 4.0 27 71-97 20-50 (51)
116 PRK11639 zinc uptake transcrip 26.9 82 0.0018 29.2 3.9 46 58-104 27-77 (169)
117 PF04182 B-block_TFIIIC: B-blo 26.5 74 0.0016 25.4 3.1 43 63-108 11-53 (75)
118 cd08311 Death_p75NR Death doma 26.1 61 0.0013 26.5 2.6 26 256-282 2-27 (77)
119 TIGR02702 SufR_cyano iron-sulf 25.4 1.2E+02 0.0026 28.6 4.8 49 58-108 2-50 (203)
120 PF10820 DUF2543: Protein of u 25.2 53 0.0012 26.8 2.0 30 71-101 46-79 (81)
121 COG5347 GTPase-activating prot 25.1 70 0.0015 33.1 3.4 98 195-304 20-125 (319)
122 PF00412 LIM: LIM domain; Int 25.0 46 0.001 24.4 1.6 33 193-226 24-56 (58)
123 PF09012 FeoC: FeoC like trans 24.8 1.3E+02 0.0027 23.5 4.1 46 56-107 3-48 (69)
124 PF01978 TrmB: Sugar-specific 23.4 1.1E+02 0.0023 23.6 3.4 36 71-106 20-55 (68)
125 TIGR00270 conserved hypothetic 23.3 3.1E+02 0.0068 25.3 7.0 32 197-228 2-35 (154)
126 PF10545 MADF_DNA_bdg: Alcohol 22.7 61 0.0013 25.3 2.0 25 271-295 27-52 (85)
127 cd00092 HTH_CRP helix_turn_hel 22.1 2.3E+02 0.0051 20.9 5.1 36 72-107 24-59 (67)
128 PF09538 FYDLN_acid: Protein o 21.9 44 0.00096 29.2 1.0 26 194-224 8-33 (108)
129 PF14569 zf-UDP: Zinc-binding 21.9 55 0.0012 27.2 1.5 50 194-243 8-66 (80)
130 PF08074 CHDCT2: CHDCT2 (NUC03 21.7 56 0.0012 30.8 1.7 29 252-280 4-33 (173)
131 KOG2656 DNA methyltransferase 21.4 58 0.0013 34.6 1.9 45 249-293 128-178 (445)
132 PF02082 Rrf2: Transcriptional 21.3 1.7E+02 0.0038 23.4 4.4 45 62-106 14-58 (83)
133 PRK11414 colanic acid/biofilm 21.3 1.3E+02 0.0029 28.4 4.3 66 40-106 2-67 (221)
134 PF01388 ARID: ARID/BRIGHT DNA 20.5 1.9E+02 0.004 23.5 4.5 37 258-294 37-86 (92)
135 KOG0724 Zuotin and related mol 20.5 42 0.00091 34.2 0.7 44 251-294 53-96 (335)
136 smart00418 HTH_ARSR helix_turn 20.4 1.8E+02 0.0038 20.7 3.9 36 71-106 8-43 (66)
137 PF00325 Crp: Bacterial regula 20.2 1.6E+02 0.0034 20.3 3.2 27 77-103 6-32 (32)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=7.4e-85 Score=662.06 Aligned_cols=325 Identities=27% Similarity=0.533 Sum_probs=268.5
Q ss_pred CCCceeEecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHH
Q 013569 11 KPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLL 90 (440)
Q Consensus 11 ~~~~~~ivIPsy~~WF~~~~ih~iEk~~lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i 90 (440)
-+|.++|+||||+.||++.+||+||+++.||||+|++++|||++|+.||||||++||+||.+|||+|+|||||+||||+|
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 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhccccccCCCCCCCCCCCCCCCCCccccccceeecCCCCCcccccCCCCCCCCcCCCCCCCCCCCCccccc
Q 013569 91 HKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVA 170 (440)
Q Consensus 91 ~Rih~FLe~wGlINy~~~~~~~~~~~~~~~lg~p~~tg~f~v~~dtP~Gl~~~~~p~~~k~~~~~~~~~~~s~~~~~~~~ 170 (440)
.|||+|||+|||||||+++. ++|+.+||| +||||++++|||+||+|+.+++.........++.. ....
T Consensus 126 vrvHrFLekWGLINYqvdp~-----trPs~IgPp-lt~h~q~l~dtP~gl~p~l~~~~~~~~~~~a~~~e------~~~~ 193 (531)
T COG5259 126 VRVHRFLEKWGLINYQVDPG-----TRPSTIGPP-LTSHFQDLHDTPRGLSPFLPWGPINQRVLGAKEIE------YETH 193 (531)
T ss_pred HHHHHHHHHhcceeeccCCC-----CCccccCCC-cchhhHHHhhCccccccccCCCCccccccccchhh------hhhh
Confidence 99999999999999999994 777778875 78999999999999999976544322111111100 0000
Q ss_pred CCCCCCCCCcccch----hhccccc---ccCCccCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCceecc
Q 013569 171 GETGVKLPPLASYL----DVFGDLV---KLKGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFSD 242 (440)
Q Consensus 171 ~~~~~~~~~l~~~~----~~~~~~~---~~~~~~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~i~ 242 (440)
.+..+ .|++.... ..+.++. ......|..||+.|..+||+..+ ..+.+|..||.+|+||+...+.||++++
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 11221110 0112222 22348999999999999999998 8899999999999999999999999998
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHcCCcCCCCCCCcccCCCCCCCCCCCCccc
Q 013569 243 LGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLK 322 (440)
Q Consensus 243 ~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flqLPIeD~fL~~~~~~~~~~~~~~~~~~~~ 322 (440)
...+ ..+..||.+|+++|||||++||++|++||.|||+||++|||+|||||||+|.||...++...+
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 256799999999999999999999999999999999999999999999999999987641100
Q ss_pred ccccccccccccchhhhhhhhhccccccCCCCCcCCCccccCCCCcCCCCCChHHHHHHHHhhccChHHHHHHHHHHHH
Q 013569 323 EGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVA 401 (440)
Q Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~PFs~a~NPVMs~vAFLas~V~P~VAaAAA~aAl~ 401 (440)
+ .+.+||..++|||||+|+|||++|.|+|++..+++.++
T Consensus 340 -----------------------------------~-----~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k 378 (531)
T COG5259 340 -----------------------------------S-----KGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIK 378 (531)
T ss_pred -----------------------------------C-----CCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhh
Confidence 1 13589999999999999999999999999888877533
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=1.1e-74 Score=605.75 Aligned_cols=316 Identities=30% Similarity=0.560 Sum_probs=256.2
Q ss_pred CCCCceeEecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHH
Q 013569 10 TKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSL 89 (440)
Q Consensus 10 ~~~~~~~ivIPsy~~WF~~~~ih~iEk~~lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~ 89 (440)
...+.|.|+||||++||+|++||+||++++||||+|++++|||++|++||||||++||+||.+|||+|+|||+|+||||+
T Consensus 40 ~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp~~ylt~ta~rrnl~gDv~a 119 (506)
T KOG1279|consen 40 VSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNPQEYLTFTACRRNLAGDVCA 119 (506)
T ss_pred cccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCcccchhHHHHHhcccchHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhhccccccCCCCCCCCCCCCCCCCCccccccceeecCCCCCcccccCCCCCCCCcCCCCCCCCCCCCcccc
Q 013569 90 LHKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAV 169 (440)
Q Consensus 90 i~Rih~FLe~wGlINy~~~~~~~~~~~~~~~lg~p~~tg~f~v~~dtP~Gl~~~~~p~~~k~~~~~~~~~~~s~~~~~~~ 169 (440)
|+|||+|||+||||||+++++ .+|..++|| .++||+++.+||+|+.++.++... .....+...-+
T Consensus 120 i~Rvh~FlE~WGLINy~~d~e-----~rp~~~~p~-~t~h~~~~~~tp~~~~~~~~~~~~---~~~~~~~~~~~------ 184 (506)
T KOG1279|consen 120 IARVHAFLEQWGLINYQVDAE-----SRPHPIEPP-ETSHFQVLADTPRGLAPLTPEDPQ---SQPDLGNPRME------ 184 (506)
T ss_pred HHHHHhhHHhhcccccccChh-----hCCcccCCC-cccccccccCCCcccccCCCCCcc---ccccccccccc------
Confidence 999999999999999999995 666667766 469999999999999987543322 11111111000
Q ss_pred cCCCCCCCCCcccchhhccccc----ccCCccCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCceeccCC
Q 013569 170 AGETGVKLPPLASYLDVFGDLV----KLKGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFSDLG 244 (440)
Q Consensus 170 ~~~~~~~~~~l~~~~~~~~~~~----~~~~~~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~i~~~ 244 (440)
. +...++..+... .....+|..|+.. ||+..+ ..+.+|..||.+|+|+..+...||+.+.
T Consensus 185 -------~--~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~-- 249 (506)
T KOG1279|consen 185 -------T--LSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIG-- 249 (506)
T ss_pred -------c--ccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccchhcc--
Confidence 0 111111111111 1334556665554 455444 6789999999999999999999993222
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHcCCcCCCCCCCcccCCCCCCCCCCCCccccc
Q 013569 245 GNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLKEG 324 (440)
Q Consensus 245 ~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flqLPIeD~fL~~~~~~~~~~~~~~~~~~~~~~ 324 (440)
...+..||++|+++|||||++||++|.+||.|||+||++|||.|||||||+|+||....+.
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 2457899999999999999999999999999999999999999999999999999985421
Q ss_pred ccccccccccchhhhhhhhhccccccCCCCCcCCCccccCCCCcCCCCCChHHHHHHHHhhccChHHHHHHHHHHHHHHh
Q 013569 325 QSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALC 404 (440)
Q Consensus 325 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~PFs~a~NPVMs~vAFLas~V~P~VAaAAA~aAl~~l~ 404 (440)
.+|. ++ +..+|++-+||||++++||+++|+|+|+..++++++....
T Consensus 311 --------------------------------~~~~-~~-~~~~~sq~gnpv~s~~~~l~~~vdP~~~~~~~k~~~~~~~ 356 (506)
T KOG1279|consen 311 --------------------------------LGPL-SY-GPVPFSQDGNPVMSTVAFLASVVDPVVKSVAAKSAEEKFS 356 (506)
T ss_pred --------------------------------cCcc-cc-CCCccccCCCccccHHHHHHhccCchhhhhhhcccchhhh
Confidence 1332 33 3578888899999999999999999999999999998876
Q ss_pred cCCC
Q 013569 405 NESS 408 (440)
Q Consensus 405 ~e~~ 408 (440)
..+.
T Consensus 357 ~~~~ 360 (506)
T KOG1279|consen 357 KVNE 360 (506)
T ss_pred hhhh
Confidence 5543
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=1.4e-27 Score=197.45 Aligned_cols=85 Identities=41% Similarity=0.829 Sum_probs=78.1
Q ss_pred EecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccc-hHHHHHHHHH
Q 013569 17 YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFR 95 (440)
Q Consensus 17 ivIPsy~~WF~~~~ih~iEk~~lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~g-Dv~~i~Rih~ 95 (440)
+++|.+++||+++.+|++|++.+||||.| ++|+.|+.|||.||+.|+.||.+|||+++||+.+.| |++.+.|||+
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 013569 96 LLDEWGLINF 105 (440)
Q Consensus 96 FLe~wGlINy 105 (440)
||++||+|||
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=1.2e-22 Score=207.39 Aligned_cols=111 Identities=23% Similarity=0.481 Sum_probs=100.0
Q ss_pred CCccCCCCCCCCCC-ceeEecC-CCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 013569 194 KGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 270 (440)
Q Consensus 194 ~~~~C~~Cg~dc~~-~~y~~~k-~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g 270 (440)
.++.|++|..+|+. ++++|.. .+++||..||+.|. ++.|.+.|+|.+|+...++ .....||++||.+||||+++||
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 5799999 77999999999995 6899999999999997665 4578999999999999999999
Q ss_pred -CCHHHHHhHCCCCCHHHHHHHHHcCCcCCCCCCCc
Q 013569 271 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSA 305 (440)
Q Consensus 271 -~nW~~Ia~~VgtKT~~eCi~~flqLPIeD~fL~~~ 305 (440)
|||++||+|||+||++||..||++..++.++..-.
T Consensus 92 ~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~~ 127 (438)
T KOG0457|consen 92 FGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPLP 127 (438)
T ss_pred CCcHHHHHHHHcccchHHHHHHHHHHHhcCcccccc
Confidence 99999999999999999999999987777765443
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.77 E-value=1.8e-19 Score=177.73 Aligned_cols=110 Identities=20% Similarity=0.350 Sum_probs=100.5
Q ss_pred CCccCCCCCCCCCC-ceeEecC-CCcccchhhhhcCCC-CCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 013569 194 KGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 270 (440)
Q Consensus 194 ~~~~C~~Cg~dc~~-~~y~~~k-~~~~LC~~CF~~G~~-~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g 270 (440)
.+++|+.|..+|+. +++.|.. ++++||..||++|.+ +.|+-.|+|.+++.+.++ ....+|++.||++|+++.+..|
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 699999999999975 677779999999988876 4578999999999999999999
Q ss_pred -CCHHHHHhHCCCCCHHHHHHHHHcCCcCCCCCCC
Q 013569 271 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGS 304 (440)
Q Consensus 271 -~nW~~Ia~~VgtKT~~eCi~~flqLPIeD~fL~~ 304 (440)
|||++||.|||.|+++||..||+++++|..|..-
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~ypl 117 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYPL 117 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccccc
Confidence 9999999999999999999999999999988543
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=99.15 E-value=4.4e-11 Score=88.45 Aligned_cols=44 Identities=34% Similarity=0.700 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCC-HHHHHhHCC-CCCHHHHHHHHHcC
Q 013569 252 ATWTEAETLLLLESVMRHGDN-WELVAQNVP-TKSKLDCISKLIEL 295 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g~n-W~~Ia~~Vg-tKT~~eCi~~flqL 295 (440)
..||.+|+.+|+++|.+||.+ |..||++|+ +||..||..||.++
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=86.77 Aligned_cols=44 Identities=25% Similarity=0.767 Sum_probs=41.6
Q ss_pred ccCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCce
Q 013569 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFR 239 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~ 239 (440)
++|+.||.||+.+||||++ .+++||+.||.+|+||.++++.||+
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 6799999999999999999999995
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=98.94 E-value=1.4e-09 Score=83.58 Aligned_cols=41 Identities=29% Similarity=0.659 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 254 WTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 254 WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
||.+|+.+|++++++||.+|..||+++|+||+.+|..||..
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 99999999999999999999999999998999999999997
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.89 E-value=3.2e-09 Score=76.22 Aligned_cols=44 Identities=36% Similarity=0.728 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 252 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
..||.+|+.+|+.++.+|| .+|..||+++++||+.+|..+|..+
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=98.83 E-value=4.3e-09 Score=118.47 Aligned_cols=84 Identities=27% Similarity=0.332 Sum_probs=73.2
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccch-HHHHHHHHHHhh
Q 013569 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGD-VSLLHKVFRLLD 98 (440)
Q Consensus 22 y~~WF~~~~ih~iEk~~--lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gD-v~~i~Rih~FLe 98 (440)
++.-|+.+++++.|..+ || ...+ ..+..||.|||.||.+|+.||..+||+++|...+..+ ...+.++|+||.
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 4789999999999999999999999999999888643 488999999999
Q ss_pred hhccccccCCCC
Q 013569 99 EWGLINFGAVSR 110 (440)
Q Consensus 99 ~wGlINy~~~~~ 110 (440)
++|+|||++...
T Consensus 162 r~G~in~g~~~~ 173 (881)
T PLN03000 162 THGYINFGIAQA 173 (881)
T ss_pred HcCcccHHHHHH
Confidence 999999999853
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=8.7e-09 Score=72.92 Aligned_cols=43 Identities=40% Similarity=0.784 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 253 TWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 253 ~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
.||.+|+.+|+.++++|| .+|..||+.+++||..+|..||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 499999999999999999 9999999999999999999999753
No 12
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.72 E-value=1.5e-08 Score=113.70 Aligned_cols=85 Identities=26% Similarity=0.355 Sum_probs=76.0
Q ss_pred CCCCCCCCCCCHHHHhh-cccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhcc-chHHHHHHHHHHhhh
Q 013569 22 HSSWFRWDDIHETERTA-LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLV-GDVSLLHKVFRLLDE 99 (440)
Q Consensus 22 y~~WF~~~~ih~iEk~~-lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~-gDv~~i~Rih~FLe~ 99 (440)
.+.-|+.+++|+.|..+ |++...+ ..+..||.|||.||.+|+.||..+||+++|+..+- -....+.++|.||.+
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 7877665 47899999999999999999999999999998874 356789999999999
Q ss_pred hccccccCCCC
Q 013569 100 WGLINFGAVSR 110 (440)
Q Consensus 100 wGlINy~~~~~ 110 (440)
.|.|||++.+.
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=98.37 E-value=4.1e-07 Score=88.74 Aligned_cols=45 Identities=16% Similarity=0.443 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCC-CCCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~Vg-tKT~~eCi~~flq 294 (440)
....||.+|+.+|+++|++|| .+|..||++++ +||..||++||.+
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=97.49 Aligned_cols=84 Identities=23% Similarity=0.350 Sum_probs=71.6
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchH-HHHHHHHHHhh
Q 013569 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDV-SLLHKVFRLLD 98 (440)
Q Consensus 22 y~~WF~~~~ih~iEk~~--lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv-~~i~Rih~FLe 98 (440)
++-=|+.+.+.+-|+++ +|+. ..+.++.||.|||.|+.+|+.||..+||+++++..+.-++ .+|.+.|.||.
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 45679999999988855 5543 3568999999999999999999999999999998876543 55679999999
Q ss_pred hhccccccCCCC
Q 013569 99 EWGLINFGAVSR 110 (440)
Q Consensus 99 ~wGlINy~~~~~ 110 (440)
+.|.|||++.+.
T Consensus 138 ~~~~inc~vnp~ 149 (738)
T PLN02529 138 YNGYINFGVSPS 149 (738)
T ss_pred hCCCcceeeccc
Confidence 999999999986
No 15
>PLN03091 hypothetical protein; Provisional
Probab=98.17 E-value=1.9e-06 Score=89.99 Aligned_cols=45 Identities=20% Similarity=0.441 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCC-CCCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~Vg-tKT~~eCi~~flq 294 (440)
.+..||.+|+.+|+++|++|| .+|..||++++ +||.+||++||++
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 79999999997 8999999999984
No 16
>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=98.17 E-value=3.9e-06 Score=64.86 Aligned_cols=44 Identities=20% Similarity=0.371 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCH---HHHHhHCC-CC-CHHHHHHHHHc
Q 013569 251 GATWTEAETLLLLESVMRHG-DNW---ELVAQNVP-TK-SKLDCISKLIE 294 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW---~~Ia~~Vg-tK-T~~eCi~~flq 294 (440)
+..||++|..++|+||+.+| ++| .+|+++++ ++ |+.||..|+-.
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 67 99999999864
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=97.98 E-value=8.3e-06 Score=60.97 Aligned_cols=46 Identities=20% Similarity=0.625 Sum_probs=40.0
Q ss_pred ccCCCCCCCCCC-ceeEecC-CCcccchhhhhcCCC-CCCCCCCCceec
Q 013569 196 FKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRFS 241 (440)
Q Consensus 196 ~~C~~Cg~dc~~-~~y~~~k-~~~~LC~~CF~~G~~-~~~~s~~df~~i 241 (440)
+.|++|+.++.. .||+|.. .+++||..||..|.. +.|...|.|+.+
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 8999999 799999999999964 678888988764
No 18
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.92 E-value=9.7e-06 Score=79.18 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCC-CCCHHHHHHHHHc
Q 013569 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~Vg-tKT~~eCi~~flq 294 (440)
.+.||.+|+.+|.+.|++|| ++|..|+++.| .|+-++|++||+.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~N 54 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTN 54 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhc
Confidence 57899999999999999999 89999999999 9999999999984
No 19
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.91 E-value=1.3e-05 Score=78.38 Aligned_cols=46 Identities=20% Similarity=0.282 Sum_probs=43.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
.....||.+|+.+||+.+..||..|..||+++.+||..+|..||..
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 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=97.89 E-value=1.4e-05 Score=58.83 Aligned_cols=45 Identities=18% Similarity=0.478 Sum_probs=39.1
Q ss_pred ccCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 013569 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~i 241 (440)
+.|+.|+.++...+|+|.. .+++||..||..|. +.|...|.|.++
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 666667888653
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=97.74 E-value=3.2e-05 Score=56.46 Aligned_cols=39 Identities=23% Similarity=0.716 Sum_probs=34.6
Q ss_pred CccCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCC
Q 013569 195 GFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (440)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~ 233 (440)
.+.|+.|+..+...||+|.. .+++||.+||..|+++..+
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCCC
Confidence 57899999999999999998 8999999999999876543
No 22
>PLN03091 hypothetical protein; Provisional
Probab=97.66 E-value=6.2e-05 Score=78.84 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=42.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
...+.||.+|+.+||+.+..||..|.+||+++.+||..+|..||..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999864
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=5.3e-05 Score=56.61 Aligned_cols=44 Identities=27% Similarity=0.589 Sum_probs=36.9
Q ss_pred ccCCCCCC-CCCCceeEecC-C--CcccchhhhhcCCCCCCCCCCCceec
Q 013569 196 FKCGSCGE-QCNSGCYEYSK-G--SFVICEKCFKNGNYGEDKSKDDFRFS 241 (440)
Q Consensus 196 ~~C~~Cg~-dc~~~~y~~~k-~--~~~LC~~CF~~G~~~~~~s~~df~~i 241 (440)
+.|+.|+. .+...||+|+. . +++||..||..|. .|...|.|.++
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 5 8999999999997 56666777653
No 24
>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=97.58 E-value=7.3e-05 Score=54.56 Aligned_cols=41 Identities=17% Similarity=0.358 Sum_probs=36.0
Q ss_pred cCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 013569 197 KCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (440)
Q Consensus 197 ~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~i 241 (440)
.|+.|+..+...||+|.. .+++||..||..| .| ..|.|.++
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 25
>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=97.56 E-value=7.3e-05 Score=55.99 Aligned_cols=43 Identities=14% Similarity=0.424 Sum_probs=36.3
Q ss_pred cCCCCCC-CCCCceeEecC-CCcccchhhhhcCCC-CCCCCCCCce
Q 013569 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFR 239 (440)
Q Consensus 197 ~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G~~-~~~~s~~df~ 239 (440)
.|+.|+. ++...||+|++ .+++||..||..|.. ..|...|.|.
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 6999998 99989999999 899999999999974 4555567664
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=97.46 E-value=0.00013 Score=54.53 Aligned_cols=44 Identities=16% Similarity=0.483 Sum_probs=36.5
Q ss_pred cCCCCC-CCCCCceeEecC-CCcccchhhhhcCCCC-CCCCCCCcee
Q 013569 197 KCGSCG-EQCNSGCYEYSK-GSFVICEKCFKNGNYG-EDKSKDDFRF 240 (440)
Q Consensus 197 ~C~~Cg-~dc~~~~y~~~k-~~~~LC~~CF~~G~~~-~~~s~~df~~ 240 (440)
.|+.|+ .++...||+|.. .+++||..||..|... .|...|+|..
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 8999999999999654 4555777654
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=97.44 E-value=0.00013 Score=54.46 Aligned_cols=37 Identities=24% Similarity=0.547 Sum_probs=32.5
Q ss_pred cCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCCC
Q 013569 197 KCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (440)
Q Consensus 197 ~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~ 233 (440)
.|+.|...+...||+|++ .+++||..||..|.....+
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 8999999999999865443
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=97.43 E-value=7.4e-05 Score=55.10 Aligned_cols=40 Identities=25% Similarity=0.703 Sum_probs=28.6
Q ss_pred CCccCCCCCC-CCCCceeEecC-CCcccchhhhhcCCCCCCC
Q 013569 194 KGFKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (440)
Q Consensus 194 ~~~~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~ 233 (440)
..+.|+.|+. .+...||+|+. .+++||..||..|++...+
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=97.32 E-value=0.00025 Score=53.23 Aligned_cols=43 Identities=26% Similarity=0.563 Sum_probs=35.0
Q ss_pred cCCCCCC-CCCCceeEecC-CCcccchhhhhcCCCC-CCCCCCCce
Q 013569 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYG-EDKSKDDFR 239 (440)
Q Consensus 197 ~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G~~~-~~~s~~df~ 239 (440)
.|+.|+. .+...||+|++ .+++||..||..|... .|...|+++
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 5999996 57889999999 8999999999999764 455556553
No 30
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.14 E-value=0.00071 Score=66.18 Aligned_cols=43 Identities=16% Similarity=0.390 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHH
Q 013569 251 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~fl 293 (440)
.+.||.+||.+|+++-..+|..|..||.++++||..+...||-
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 6789999999999999999999999999999999999988884
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=97.10 E-value=0.00057 Score=50.47 Aligned_cols=42 Identities=24% Similarity=0.608 Sum_probs=34.4
Q ss_pred cCCCCCC-CCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 013569 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (440)
Q Consensus 197 ~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~i 241 (440)
.|+.|+. .+...||+|+. .+++||..||..+. |...|.|.+|
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 6999986 56678999999 89999999999853 4457888764
No 32
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.09 E-value=0.00058 Score=74.20 Aligned_cols=46 Identities=33% Similarity=0.660 Sum_probs=43.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
...+.||.+|+.+|+.||++|| .+|-+|-+.|.+||..||+.+|++
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=96.91 E-value=0.0011 Score=48.97 Aligned_cols=41 Identities=12% Similarity=0.455 Sum_probs=32.9
Q ss_pred cCCCCC-CCCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCcee
Q 013569 197 KCGSCG-EQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRF 240 (440)
Q Consensus 197 ~C~~Cg-~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~ 240 (440)
.|+.|+ ..+...||+|.. .+++||..||..+ .|...|.|.+
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 566688999999 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=96.46 E-value=0.0025 Score=46.10 Aligned_cols=36 Identities=14% Similarity=0.575 Sum_probs=29.7
Q ss_pred ccCCCCCCCCCCceeEecC-CCcccchhhhhcCCCCCC
Q 013569 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGED 232 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~ 232 (440)
+.|+.|....+ .+|+|+. .+|+||..||..+.-|-.
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~~~H~H~ 37 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNTKNHPHK 37 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCCCCCCcc
Confidence 46999988654 9999999 899999999998765433
No 35
>PLN02976 amine oxidase
Probab=96.35 E-value=0.0034 Score=74.72 Aligned_cols=83 Identities=23% Similarity=0.351 Sum_probs=70.7
Q ss_pred CCCCCCCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHh------hccchHHHHHHHHHHhh
Q 013569 25 WFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRK------SLVGDVSLLHKVFRLLD 98 (440)
Q Consensus 25 WF~~~~ih~iEk~~lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~------~l~gDv~~i~Rih~FLe 98 (440)
=+....+.+|||-.|-|...-+ ..-+.||++||.|+-+|-++=.+-|.+++|-= .-.+-..+|.-|+.||+
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 36789999999999999999999999999942 11245788999999999
Q ss_pred hhccccccCCCC
Q 013569 99 EWGLINFGAVSR 110 (440)
Q Consensus 99 ~wGlINy~~~~~ 110 (440)
+.|.||-++...
T Consensus 531 ~~gyin~g~~s~ 542 (1713)
T PLN02976 531 QRGYINAGIASE 542 (1713)
T ss_pred ccCceecccccc
Confidence 999999998865
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=96.09 E-value=0.0047 Score=45.11 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=27.2
Q ss_pred cCCCCCC-CCCCceeEecC-CCcccchhhhhcC
Q 013569 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNG 227 (440)
Q Consensus 197 ~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G 227 (440)
.|+.|+. .+...||+|.. .+++||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 6999996 67778999998 8999999999754
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.00 E-value=0.0061 Score=66.58 Aligned_cols=54 Identities=26% Similarity=0.354 Sum_probs=45.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCH---HHHHHHHHcCCcCCCCCCCc
Q 013569 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSK---LDCISKLIELPFGEFMMGSA 305 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~---~eCi~~flqLPIeD~fL~~~ 305 (440)
...+.||-+|+..||++|++|| |+|-++|-.+|.||. .-|+.+|+.. ..+|+..
T Consensus 410 ~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~---k~rl~~~ 467 (939)
T KOG0049|consen 410 AKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAA---KLRLAAG 467 (939)
T ss_pred hccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHH---HHHHhcC
Confidence 3467899999999999999999 999999999999999 7799999853 3555544
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.88 E-value=0.0039 Score=51.00 Aligned_cols=44 Identities=27% Similarity=0.548 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHHHHHHH------cC------C--CHHHHHhHCC----CCCHHHHHHHHHcC
Q 013569 252 ATWTEAETLLLLESVMR------HG------D--NWELVAQNVP----TKSKLDCISKLIEL 295 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~------~g------~--nW~~Ia~~Vg----tKT~~eCi~~flqL 295 (440)
..||.+|+..||+.+.. ++ + -|..||+.+. .||+.||..+|-.|
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 46999999999999877 21 1 5999999885 69999999999763
No 39
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.68 E-value=0.034 Score=60.91 Aligned_cols=44 Identities=23% Similarity=0.564 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
..+.||.+|+..|-..+.++|++|..|++.+| |.|..|+.||-+
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 57889999999999999999999999999998 799999999976
No 40
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=93.68 E-value=0.055 Score=58.07 Aligned_cols=43 Identities=26% Similarity=0.577 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHH
Q 013569 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLI 293 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~fl 293 (440)
+..|+..|+..|--+|.+|| ..|.+|+..+..||+.||..+|-
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 78999999999999999999995
No 41
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.39 E-value=0.07 Score=58.54 Aligned_cols=54 Identities=26% Similarity=0.427 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc------------------C-CCHHHHHhHCCCCCHHHHHHHHHcCCcCCCCCC
Q 013569 250 HGATWTEAETLLLLESVM-------RH------------------G-DNWELVAQNVPTKSKLDCISKLIELPFGEFMMG 303 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie-------~~------------------g-~nW~~Ia~~VgtKT~~eCi~~flqLPIeD~fL~ 303 (440)
....||-+|+.+||..|+ +| . =+|..|++.+|||+..||+.||-+|=+...+-.
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~ 514 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNK 514 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhc
Confidence 467899999999999995 44 1 289999999999999999999998766655543
No 42
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=92.91 E-value=0.074 Score=53.49 Aligned_cols=43 Identities=19% Similarity=0.491 Sum_probs=34.5
Q ss_pred ccCCCCCC-CCCCceeEecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 013569 196 FKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (440)
Q Consensus 196 ~~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s~~df~~i 241 (440)
..|+.|+. .+...||+|+. .+|+||..|+..+ .++-.|.+.++
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 8999999999876 22334555553
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.89 E-value=0.13 Score=55.33 Aligned_cols=45 Identities=18% Similarity=0.422 Sum_probs=41.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
....|+.+|+.+||.+-......|..|+..|| ||..||.+||..|
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 35689999999999999999999999999998 8999999999863
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=91.51 E-value=0.3 Score=39.08 Aligned_cols=44 Identities=27% Similarity=0.424 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHHcC-----------------CCHHHHHhHCC-----CCCHHHHHHHHHcC
Q 013569 252 ATWTEAETLLLLESVMRHG-----------------DNWELVAQNVP-----TKSKLDCISKLIEL 295 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-----------------~nW~~Ia~~Vg-----tKT~~eCi~~flqL 295 (440)
..||.+|...||+.|++|. .-|+.|++.+. .||..|+..+|-.|
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 15999998873 69999999998654
No 45
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=91.09 E-value=0.32 Score=54.36 Aligned_cols=44 Identities=18% Similarity=0.358 Sum_probs=41.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHH
Q 013569 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~fl 293 (440)
....||..|..++-.||-.|..|+..|++.|.+||-.||++.|.
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 46
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=89.55 E-value=0.25 Score=50.91 Aligned_cols=36 Identities=25% Similarity=0.775 Sum_probs=30.5
Q ss_pred cCCccCCCCCCCCCC-ceeEecC-CCcccchhhhhcCC
Q 013569 193 LKGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGN 228 (440)
Q Consensus 193 ~~~~~C~~Cg~dc~~-~~y~~~k-~~~~LC~~CF~~G~ 228 (440)
...+.|+.|++.--. -+|+|+. .+|+||..||.+|.
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 445789999987544 6899998 89999999999994
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.07 E-value=0.56 Score=48.88 Aligned_cols=45 Identities=16% Similarity=0.392 Sum_probs=42.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
....||..|..++..|+.++|.++..|++..++|...|...+|++
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
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=88.90 E-value=0.4 Score=52.07 Aligned_cols=45 Identities=18% Similarity=0.498 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
....|+.+|+..|++.=..+|.-|..||..++.||..+|..+|+.
T Consensus 71 k~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~ 115 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVN 115 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHH
Confidence 467899999999999999999999999999999999999999985
No 49
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=88.55 E-value=0.4 Score=44.58 Aligned_cols=42 Identities=31% Similarity=0.510 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHhHCCCCCHHHHHHHHH
Q 013569 251 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKLI 293 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g--~-----nW~~Ia~~VgtKT~~eCi~~fl 293 (440)
.+.||.+|+++|-|.|.+|- | -.+.|++.++ ||+.-|-.||.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWN 52 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWN 52 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHH
Confidence 46799999999999999986 2 5778888885 99999999996
No 50
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=87.96 E-value=0.73 Score=47.95 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHH-HhHCCCCCHHHHHHHHHc
Q 013569 251 GATWTEAETLLLLESVMRHGDNWELV-AQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~I-a~~VgtKT~~eCi~~flq 294 (440)
-..|+.+|=+.+-+||+.||.|+..| +..|.|||--||+..|.+
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 35799999999999999999999999 678999999999998863
No 51
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=87.33 E-value=0.32 Score=54.48 Aligned_cols=40 Identities=28% Similarity=0.491 Sum_probs=32.3
Q ss_pred CccCCCCCC-CCCCceeEecC-CCcccchhhhhcCCCCCCCC
Q 013569 195 GFKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKS 234 (440)
Q Consensus 195 ~~~C~~Cg~-dc~~~~y~~~k-~~~~LC~~CF~~G~~~~~~s 234 (440)
...|+.|.. .+...||+|.+ -+++||..||-.|+.+.++.
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 356999965 35667999999 79999999999998765544
No 52
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=86.56 E-value=0.7 Score=47.44 Aligned_cols=44 Identities=34% Similarity=0.552 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHHcC-----C-----CHHHHHhH---CC-CCCHHHHHHHHHcC
Q 013569 252 ATWTEAETLLLLESVMRHG-----D-----NWELVAQN---VP-TKSKLDCISKLIEL 295 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-----~-----nW~~Ia~~---Vg-tKT~~eCi~~flqL 295 (440)
..|+.+|++.||++....- + .|+.||.. +| .||+.||..+|-.|
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 3 59999983 34 59999999998644
No 53
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=86.15 E-value=0.65 Score=50.92 Aligned_cols=44 Identities=20% Similarity=0.353 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHH----------HhHCCCCCHHHHHHHHHc
Q 013569 251 GATWTEAETLLLLESVMRHGDNWELV----------AQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~I----------a~~VgtKT~~eCi~~flq 294 (440)
...||.+|+.-+.+||.++|.|+++| -..+..||+.|.+.||.|
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 66899999999999999999999999 344557999999999975
No 54
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=85.41 E-value=0.48 Score=51.50 Aligned_cols=42 Identities=24% Similarity=0.417 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHH
Q 013569 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKL 292 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~f 292 (440)
.+.|+..|+..|+-+++.|| .+|..||..++.||+++|..|+
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 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=78.89 E-value=2.5 Score=37.44 Aligned_cols=45 Identities=20% Similarity=0.400 Sum_probs=35.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC----CCHHHHHhHC------------CCCCHHHHHHHHH
Q 013569 249 THGATWTEAETLLLLESVMRHG----DNWELVAQNV------------PTKSKLDCISKLI 293 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g----~nW~~Ia~~V------------gtKT~~eCi~~fl 293 (440)
..+..||.+|+..||-.+.+|| |.|+.|-+.+ .+||+.+...|.-
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 4578899999999999999999 5999997765 3899999877654
No 56
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=74.23 E-value=3.1 Score=42.19 Aligned_cols=98 Identities=12% Similarity=0.190 Sum_probs=58.9
Q ss_pred CccCCCCCCCCCCceeEecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CC
Q 013569 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DN 272 (440)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~n 272 (440)
-.+|.-||.. .++...-.-++.||.+|-.--+ +|.| +.++... .-+.||+++...|.+.=..-. .-
T Consensus 25 N~~CADC~a~--~P~WaSwnlGvFiC~~C~giHR~lg~h-----iSkVkSv-----~LD~W~~eqv~~m~~~GN~~an~~ 92 (287)
T KOG0703|consen 25 NKVCADCGAK--GPRWASWNLGVFICLRCAGIHRSLGVH-----ISKVKSV-----TLDEWTDEQVDFMISMGNAKANSY 92 (287)
T ss_pred cCcccccCCC--CCCeEEeecCeEEEeecccccccccch-----hheeeee-----eccccCHHHHHHHHHHcchhhhhh
Confidence 4679988877 4455555678999999964332 3433 3344332 236799999887765321111 23
Q ss_pred HHHH-HhHCCCCCHHHHHHHHHc-CCcCCCCCCC
Q 013569 273 WELV-AQNVPTKSKLDCISKLIE-LPFGEFMMGS 304 (440)
Q Consensus 273 W~~I-a~~VgtKT~~eCi~~flq-LPIeD~fL~~ 304 (440)
|+.- ....-..++++-+++||+ =+....|+..
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 333335688889999997 3333455554
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=71.72 E-value=5.1 Score=32.86 Aligned_cols=42 Identities=21% Similarity=0.425 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHc-------C------CCHHHHHhHCC-----CCCHHHHHHHHHc
Q 013569 253 TWTEAETLLLLESVMRH-------G------DNWELVAQNVP-----TKSKLDCISKLIE 294 (440)
Q Consensus 253 ~WT~~E~~~LLe~Ie~~-------g------~nW~~Ia~~Vg-----tKT~~eCi~~flq 294 (440)
.||.+++..||+.+... + ..|+.|++.+. ..|+.||..||-.
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 49999999999998543 1 16899988775 5799999999864
No 58
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=70.25 E-value=3.2 Score=44.59 Aligned_cols=52 Identities=15% Similarity=0.243 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHH-HhHCCCCCHHHHHHHHHcCCcCCCCCC
Q 013569 252 ATWTEAETLLLLESVMRHGDNWELV-AQNVPTKSKLDCISKLIELPFGEFMMG 303 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g~nW~~I-a~~VgtKT~~eCi~~flqLPIeD~fL~ 303 (440)
..|+.-|-.++-|++++||.|+++| ++++.=||-...++.|.-.--.|.|..
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYvq 338 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQ 338 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHHH
Confidence 4799999999999999999999999 467777888888888875555565543
No 59
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=68.89 E-value=6.7 Score=33.47 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=35.2
Q ss_pred CCCCCCHHHHHHHHHHHHHc----C----CCHHHHHhHCCC-----CCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRH----G----DNWELVAQNVPT-----KSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~----g----~nW~~Ia~~Vgt-----KT~~eCi~~flq 294 (440)
...-||+++|..||+|+-.| | .||...-++|.. =|..|-..+.-+
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 488888777753 277787777665
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=68.75 E-value=9.4 Score=27.53 Aligned_cols=38 Identities=13% Similarity=0.177 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 257 AETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 257 ~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
+=+.+||+.++.-+ -.|.+||+.||- |+..|..+.-+|
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHHh
Confidence 44678999999998 799999999995 889998887543
No 61
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=68.42 E-value=2.5 Score=43.84 Aligned_cols=41 Identities=22% Similarity=0.583 Sum_probs=32.9
Q ss_pred CCccCCCCCCCCCC-ceeEecC-CCcccchhhhhcCCCCCCCC
Q 013569 194 KGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNYGEDKS 234 (440)
Q Consensus 194 ~~~~C~~Cg~dc~~-~~y~~~k-~~~~LC~~CF~~G~~~~~~s 234 (440)
-...|++|.....- .+|.|.. ..+.+|..||-.|+-+..++
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hs 281 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHS 281 (434)
T ss_pred CCccCcceecccccchhhhHhhcCCccccchhhccccCCCCcc
Confidence 45679999777544 6899998 88999999999999875443
No 62
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=65.81 E-value=8.4 Score=45.63 Aligned_cols=40 Identities=13% Similarity=0.301 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHH
Q 013569 252 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISK 291 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~ 291 (440)
..||..+-..++.|.++|| ++-..||..|++||++|....
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 4799999999999999999 899999999999999998754
No 63
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=63.29 E-value=6 Score=37.25 Aligned_cols=41 Identities=27% Similarity=0.445 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHhHCCCCCHHHHHHHH
Q 013569 251 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKL 292 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g--~-----nW~~Ia~~VgtKT~~eCi~~f 292 (440)
...||.+++++|-+.|-.|+ | -.+.+++.+ .||...|..+|
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 46799999999999998888 2 345556666 48999999999
No 64
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.13 E-value=10 Score=27.64 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHhCCCcee-eHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 55 YKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 55 Y~~~RN~ii~~yr~np~~~L-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
|-.+|+.|+.... .|...| |..+..+.+.-....+.|...-|+.-|+|-.
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 5667787777533 467788 8998888887778999999999999999863
No 65
>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=62.47 E-value=20 Score=26.70 Aligned_cols=43 Identities=19% Similarity=0.266 Sum_probs=35.7
Q ss_pred HhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCCC
Q 013569 67 REEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVS 109 (440)
Q Consensus 67 r~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~~ 109 (440)
..+|...+|+++..+.+.-+-.++.|+..=|+.+|||--..++
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 3466667999999999999999999999999999999766554
No 66
>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=61.23 E-value=6 Score=26.24 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=12.5
Q ss_pred cCCCCCCCCCC-ceeEecCCCcccchhh
Q 013569 197 KCGSCGEQCNS-GCYEYSKGSFVICEKC 223 (440)
Q Consensus 197 ~C~~Cg~dc~~-~~y~~~k~~~~LC~~C 223 (440)
.|+.|+..... ..|+|..-++.|...|
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 69999999988 8999998888888877
No 67
>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=59.84 E-value=9 Score=25.54 Aligned_cols=27 Identities=22% Similarity=0.556 Sum_probs=22.8
Q ss_pred cCCCCCCCCCCc-eeEecCCCcccchhh
Q 013569 197 KCGSCGEQCNSG-CYEYSKGSFVICEKC 223 (440)
Q Consensus 197 ~C~~Cg~dc~~~-~y~~~k~~~~LC~~C 223 (440)
.|+.|++..... .|+|.+-.+.+..+|
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 699999999888 999977678877766
No 68
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=59.36 E-value=17 Score=39.19 Aligned_cols=46 Identities=15% Similarity=0.340 Sum_probs=42.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
.....||++|..+|-.+.+.||.+..+|-+.+.-||-...+..|..
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
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=58.16 E-value=6.2 Score=43.11 Aligned_cols=92 Identities=9% Similarity=-0.021 Sum_probs=71.9
Q ss_pred cCCCCCCCCCCCCCHHHHhhcccccCCCC-CCCChhHHHHHHHHHHHHHHhCCCceee-----HHHHHhhcc--chHHHH
Q 013569 19 IPSHSSWFRWDDIHETERTALKEFFDGSS-ISRTPKIYKEYRDFMINKYREEPSRRLT-----FTQVRKSLV--GDVSLL 90 (440)
Q Consensus 19 IPsy~~WF~~~~ih~iEk~~lpefF~g~~-~~ktp~~Y~~~RN~ii~~yr~np~~~LT-----~t~~r~~l~--gDv~~i 90 (440)
.+.+++-++...=+.-....+++|+.+++ ....+..|+.+|+.+++.++.--..+.+ -+..+++.. +.+-++
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 44566677777777888899999999873 2457788999999999999954334443 455666664 688999
Q ss_pred HHHHHHhhhhccccccCCCC
Q 013569 91 HKVFRLLDEWGLINFGAVSR 110 (440)
Q Consensus 91 ~Rih~FLe~wGlINy~~~~~ 110 (440)
-+|+.|.+.|+-|+.+|-.+
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 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=57.50 E-value=18 Score=31.02 Aligned_cols=50 Identities=24% Similarity=0.297 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhcccccc
Q 013569 56 KEYRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINFG 106 (440)
Q Consensus 56 ~~~RN~ii~~yr~np~~~LT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlINy~ 106 (440)
-.-|..|++....++. .+|+.+.-..|. -+...|.|...+|+.-|||.=-
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 999999887773 3678999999999999999843
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=55.69 E-value=23 Score=27.15 Aligned_cols=53 Identities=21% Similarity=0.326 Sum_probs=41.3
Q ss_pred hhHHHHHHHHHHHHHHhCCCcee-eHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 52 PKIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 52 p~~Y~~~RN~ii~~yr~np~~~L-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
-++|-.+|+.|.+--. -|...| +..+..+.+.--...+.+.+..|+.+|+|--
T Consensus 3 ~~i~~~l~~~I~~g~~-~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRL-PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHHTTSS--TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHcCCC-CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEE
Confidence 3678888888887433 577899 9999888887778999999999999999953
No 72
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=54.05 E-value=31 Score=25.58 Aligned_cols=44 Identities=23% Similarity=0.293 Sum_probs=34.6
Q ss_pred HHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 013569 61 FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (440)
Q Consensus 61 ~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~ 107 (440)
.|+......+ +++.+..+.+.-....+.|+..-|...|+|+...
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 8999998888878999999999999999998643
No 73
>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=53.65 E-value=37 Score=24.50 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+-|...|||.+
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 57788886665 5699999999999899999999999999999974
No 74
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=53.53 E-value=19 Score=39.96 Aligned_cols=96 Identities=16% Similarity=0.223 Sum_probs=54.6
Q ss_pred CccCCCCCCCCCCceeEecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH-----HH
Q 013569 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV-----MR 268 (440)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~I-----e~ 268 (440)
-..|.-|+.. ...+-|..-++.+|..|-.--+ ++ + ++... .-..||.+|...|..+= +.
T Consensus 23 Nk~CADCgs~--~P~WASiNlGIFICi~CSGIHRsLG-----h---RVKSL-----SLDkWT~EEVe~Mk~gGN~~AN~i 87 (648)
T PLN03119 23 NRRCINCNSL--GPQYVCTTFWTFVCMACSGIHREFT-----H---RVKSV-----SMSKFTSKEVEVLQNGGNQRAREI 87 (648)
T ss_pred CCccccCCCC--CCCceeeccceEEeccchhhhccCC-----c---eeecc-----ccCCCCHHHHHHHHHhchHHHHHH
Confidence 3568888864 3677788889999999964332 21 1 33332 23679998875443221 11
Q ss_pred cCCCHHHHHhHCCCCCHHHHHHHHHc-CCcCCCCCCCc
Q 013569 269 HGDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMGSA 305 (440)
Q Consensus 269 ~g~nW~~Ia~~VgtKT~~eCi~~flq-LPIeD~fL~~~ 305 (440)
|-.+|..-...++..+..+-+..||+ -+++.+|....
T Consensus 88 yeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~ 125 (648)
T PLN03119 88 YLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGAN 125 (648)
T ss_pred HHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcC
Confidence 22356543333444444566678887 34444554443
No 75
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=53.31 E-value=7.3 Score=32.23 Aligned_cols=34 Identities=26% Similarity=0.496 Sum_probs=25.0
Q ss_pred cCCCCCCCCCCceeEecC----CCcccchhhhhcCCCC
Q 013569 197 KCGSCGEQCNSGCYEYSK----GSFVICEKCFKNGNYG 230 (440)
Q Consensus 197 ~C~~Cg~dc~~~~y~~~k----~~~~LC~~CF~~G~~~ 230 (440)
.|.+||..+......=+. ..-+-|.-||.+|.|-
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft 39 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFT 39 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCcee
Confidence 699999998876522222 3456799999999874
No 76
>PLN03131 hypothetical protein; Provisional
Probab=53.11 E-value=20 Score=40.03 Aligned_cols=94 Identities=17% Similarity=0.240 Sum_probs=54.5
Q ss_pred CccCCCCCCCCCCceeEecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH------H
Q 013569 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV------M 267 (440)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~I------e 267 (440)
-..|.-|+.. ...+-|..-++.+|..|-.--+ ++ + ++... .-..||.+|...|- .+ +
T Consensus 23 Nk~CADCga~--~P~WASiNlGIFICi~CSGIHRsLg-----h---RVKSV-----TLD~WtdeEV~~Mk-~gGN~~AN~ 86 (705)
T PLN03131 23 NRRCINCNSL--GPQFVCTNFWTFICMTCSGIHREFT-----H---RVKSV-----SMSKFTSQDVEALQ-NGGNQRARE 86 (705)
T ss_pred CCccccCCCC--CCCeeEeccceEEchhchhhhcccC-----c---ccccc-----cCCCCCHHHHHHHH-HhccHHHHH
Confidence 3568888864 3667788888999999965433 21 1 33322 23579998875442 21 1
Q ss_pred HcCCCHHHHHhHCCCCCHHHHHHHHHc-CCcCCCCCCC
Q 013569 268 RHGDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMGS 304 (440)
Q Consensus 268 ~~g~nW~~Ia~~VgtKT~~eCi~~flq-LPIeD~fL~~ 304 (440)
.|-.+|..--..++..+..+-+..||+ -+++.+|+..
T Consensus 87 iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~ 124 (705)
T PLN03131 87 IYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGG 124 (705)
T ss_pred HHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcC
Confidence 222356543334444555666778886 3444555544
No 77
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=52.01 E-value=20 Score=42.54 Aligned_cols=46 Identities=15% Similarity=0.308 Sum_probs=38.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHhHC------------CCCCHHHHHHHHHc
Q 013569 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNV------------PTKSKLDCISKLIE 294 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~V------------gtKT~~eCi~~flq 294 (440)
..+..||.+|+..||-.+.+|| ++|++|-+.+ .+||+.++-.|...
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~ 982 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDT 982 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHH
Confidence 4467899999999999999999 9999996655 38999998877643
No 78
>smart00595 MADF subfamily of SANT domain.
Probab=51.79 E-value=11 Score=30.50 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=23.2
Q ss_pred CHHHHHhHCCCCCHHHHHHHHHcCCcCCCCC
Q 013569 272 NWELVAQNVPTKSKLDCISKLIELPFGEFMM 302 (440)
Q Consensus 272 nW~~Ia~~VgtKT~~eCi~~flqLPIeD~fL 302 (440)
-|..||+.+|. |.++|..+|..| -+.|.
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 999999999864 34453
No 79
>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=49.39 E-value=21 Score=25.42 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHcCCCHHHHHhHCC
Q 013569 257 AETLLLLESVMRHGDNWELVAQNVP 281 (440)
Q Consensus 257 ~E~~~LLe~Ie~~g~nW~~Ia~~Vg 281 (440)
-|-..|.++++.++||..+.|+.+|
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 80
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=49.33 E-value=56 Score=23.34 Aligned_cols=44 Identities=27% Similarity=0.386 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccc
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLI 103 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlI 103 (440)
.+-.|++.-+.||. +|.++..+.+.-....+.|...-|+.-|+|
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 81
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=49.16 E-value=29 Score=25.51 Aligned_cols=43 Identities=21% Similarity=0.316 Sum_probs=35.0
Q ss_pred HHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 62 ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
|++.....+ ..+|+++.-+.+.-....+.|+..=|+.+|+|..
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 4589999999999899999999999999999864
No 82
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=47.50 E-value=34 Score=28.97 Aligned_cols=47 Identities=21% Similarity=0.258 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhccccc
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlINy 105 (440)
-|-.|++..... .+.+|+.+.-..|. -+...+.|...+|..-|||.-
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 58899999887773 378999999999999999984
No 83
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=46.98 E-value=41 Score=30.19 Aligned_cols=54 Identities=15% Similarity=0.330 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHHHHH---hCCCceee-HHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 013569 53 KIYKEYRDFMINKYR---EEPSRRLT-FTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (440)
Q Consensus 53 ~~Y~~~RN~ii~~yr---~np~~~LT-~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 106 (440)
-+|.+|.|.|...-. +.|...|- +.+--..+.-..+.+.|.+.-||+-|+|.-.
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 4444444555889999999999999999843
No 84
>PRK09462 fur ferric uptake regulator; Provisional
Probab=46.38 E-value=33 Score=30.83 Aligned_cols=48 Identities=15% Similarity=0.251 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhccccc
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlINy 105 (440)
-|-.|++.....+.+.+|+.+.-..|. -+...|.|...+|+.-|||.=
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 467788876655678999999877763 268999999999999999973
No 85
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=46.24 E-value=10 Score=40.77 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=39.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
..-+||..|-. ++.--..|+.+.+.||+.+++||++|....|++
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 34589998877 777778899999999999999999999999986
No 86
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=45.50 E-value=56 Score=25.68 Aligned_cols=50 Identities=14% Similarity=0.088 Sum_probs=44.2
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~ 107 (440)
.++.|+.....++..-+|..+.-+.|.-+...+.|+..=|+.-|+|-...
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
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=43.75 E-value=33 Score=30.98 Aligned_cols=39 Identities=13% Similarity=0.145 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
++-+.+||+.+++-| -.|.+||+.+|. |+..|..|+-+|
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 467889999999999 799999999985 999999999775
No 88
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=43.36 E-value=48 Score=27.77 Aligned_cols=44 Identities=30% Similarity=0.450 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHHHhCCCceeeHHHHH-------hhccchH---HHHHHHHHHhhhh
Q 013569 53 KIYKEYRDFMINKYREEPSRRLTFTQVR-------KSLVGDV---SLLHKVFRLLDEW 100 (440)
Q Consensus 53 ~~Y~~~RN~ii~~yr~np~~~LT~t~~r-------~~l~gDv---~~i~Rih~FLe~w 100 (440)
++-..+||-|+.+=-.| +|+.+.. |-|+-|+ ..++||+.||.++
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 67778999998865544 7777754 3344465 7899999999976
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=42.49 E-value=73 Score=23.99 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=33.8
Q ss_pred CCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCCCC
Q 013569 69 EPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (440)
Q Consensus 69 np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~~~ 110 (440)
+....+|.++..+.+.-|...+.|+..=|...|||.-..++.
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
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=41.73 E-value=34 Score=35.46 Aligned_cols=68 Identities=16% Similarity=0.244 Sum_probs=54.1
Q ss_pred CCCHHHHhhcccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccc
Q 013569 30 DIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLIN 104 (440)
Q Consensus 30 ~ih~iEk~~lpefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlIN 104 (440)
-+++-|++..--+ .-.|..||.+.--||..+.. ....+|.++|++.+.-|+.-.-+|+.|.-.-|.|-
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 4455565554333 23689999999999999885 45789999999999889999999999998888773
No 91
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=39.92 E-value=20 Score=43.00 Aligned_cols=27 Identities=26% Similarity=0.777 Sum_probs=25.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHH
Q 013569 250 HGATWTEAETLLLLESVMRHG-DNWELV 276 (440)
Q Consensus 250 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~I 276 (440)
....|..+++..||=||-+|| |+|+.|
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 92
>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=39.53 E-value=54 Score=28.34 Aligned_cols=83 Identities=22% Similarity=0.290 Sum_probs=46.9
Q ss_pred ccCCCCCCCCCCceeEecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CCH
Q 013569 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DNW 273 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~nW 273 (440)
..|.-|+.. .+.+-+..-+..+|..|-.--+ ++.|. .+++ .. .-..||.+|.+.| +..| ...
T Consensus 4 ~~CaDC~~~--~p~w~s~~~GifvC~~CsgiHR~lg~hi---s~Vk--Sl-----~md~w~~~~i~~~----~~~GN~~~ 67 (112)
T smart00105 4 KKCFDCGAP--NPTWASVNLGVFLCIECSGIHRSLGVHI---SKVR--SL-----TLDTWTEEELRLL----QKGGNENA 67 (112)
T ss_pred CcccCCCCC--CCCcEEeccceeEhHHhHHHHHhcCCCc---Ceee--ec-----ccCCCCHHHHHHH----HHhhhHHH
Confidence 358778863 4566777788999999986443 34332 1222 21 1247999886433 3444 233
Q ss_pred HHHHhHC--------CCCCHHHHHHHHHc
Q 013569 274 ELVAQNV--------PTKSKLDCISKLIE 294 (440)
Q Consensus 274 ~~Ia~~V--------gtKT~~eCi~~flq 294 (440)
+++=+.- +..+..+-++.|++
T Consensus 68 n~~~e~~~~~~~~~~~~~~~~~~~~~fI~ 96 (112)
T smart00105 68 NSIWESNLDDFSLKPPDSDDQQKYESFIA 96 (112)
T ss_pred HHHHHhhCCccccCCCCCchHHHHHHHHH
Confidence 3332111 12235688888886
No 93
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=39.30 E-value=49 Score=29.21 Aligned_cols=74 Identities=16% Similarity=0.288 Sum_probs=48.5
Q ss_pred CCCCCCCCCCceeEecCCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHH
Q 013569 198 CGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVA 277 (440)
Q Consensus 198 C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia 277 (440)
|-.||..+.-.+++|...+..+ +|+|.. ..| .--..|++.+++..-+..||-.+|+
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 7889988888888875433222 343321 111 1225788899999999999999999
Q ss_pred hHCCC-----CCHHHHHHHHHcC
Q 013569 278 QNVPT-----KSKLDCISKLIEL 295 (440)
Q Consensus 278 ~~Vgt-----KT~~eCi~~flqL 295 (440)
+.+|- |.+-+=+..=|.+
T Consensus 57 ~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 57 KELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHCCCcHHHHHHHHHHHHHhCC
Confidence 99992 5555555544443
No 94
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.90 E-value=91 Score=25.84 Aligned_cols=54 Identities=15% Similarity=0.201 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 013569 53 KIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (440)
Q Consensus 53 ~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~ 107 (440)
++-.+|=..||+.|... .+.+...+.-+.|.-+-..|..+..-|+..|||-=+.
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p 57 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQP 57 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCC
Confidence 45667778999999976 6888888887778778899999999999999997433
No 95
>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=38.77 E-value=58 Score=25.81 Aligned_cols=43 Identities=19% Similarity=0.387 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHHHcC-------CC--HHHHHhHCC-CCCHHHHHHHHHc
Q 013569 252 ATWTEAETLLLLESVMRHG-------DN--WELVAQNVP-TKSKLDCISKLIE 294 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-------~n--W~~Ia~~Vg-tKT~~eCi~~flq 294 (440)
...|.+|+..|++-|..+. || |++.++.-. ..|-+-=..||++
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 6888888999985
No 96
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=35.18 E-value=51 Score=30.19 Aligned_cols=39 Identities=15% Similarity=0.234 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
++-+.+||..+++-| -.|.+||+.||- |+..|..|+-+|
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 888999998765
No 97
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=34.41 E-value=74 Score=25.40 Aligned_cols=34 Identities=24% Similarity=0.326 Sum_probs=31.0
Q ss_pred ceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 72 ~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
..+|+++.-+.+.-....+.|+...|+.+|+|-.
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 4799999999998889999999999999999964
No 98
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=33.35 E-value=69 Score=29.01 Aligned_cols=51 Identities=18% Similarity=0.230 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccc-----hHHHHHHHHHHhhhhccccccCCC
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLVG-----DVSLLHKVFRLLDEWGLINFGAVS 109 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~g-----Dv~~i~Rih~FLe~wGlINy~~~~ 109 (440)
-|-.|++.-...+ .++|+.+.-+.|.. .+..+.|...+|+.-|||+-....
T Consensus 22 qR~~vl~~L~~~~-~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~ 77 (145)
T COG0735 22 QRLAVLELLLEAD-GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFE 77 (145)
T ss_pred HHHHHHHHHHhcC-CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeC
Confidence 4778888666555 44999998777642 479999999999999999966664
No 99
>PHA00442 host recBCD nuclease inhibitor
Probab=33.34 E-value=43 Score=25.93 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHhHC
Q 013569 257 AETLLLLESVMRHG-DNWELVAQNV 280 (440)
Q Consensus 257 ~E~~~LLe~Ie~~g-~nW~~Ia~~V 280 (440)
+-....|++++..| +||+.+.+.+
T Consensus 26 ek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 26 EKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHhhHHHHHHHHcCCcchhhHHHHH
Confidence 44567899999999 9999987654
No 100
>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=32.98 E-value=75 Score=23.42 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=33.4
Q ss_pred eeHHHHHhhccchHHHHHHHHHHhhhhccccccCCCC
Q 013569 74 LTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (440)
Q Consensus 74 LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~~~ 110 (440)
+|.++.-+.+..+...+.|+..-|++.|||.-..++.
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 101
>PRK06474 hypothetical protein; Provisional
Probab=32.67 E-value=86 Score=29.37 Aligned_cols=50 Identities=14% Similarity=0.060 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-chHHHHHHHHHHhhhhccccccCC
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLV-GDVSLLHKVFRLLDEWGLINFGAV 108 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~-gDv~~i~Rih~FLe~wGlINy~~~ 108 (440)
.|-.|+..-..++. .+|++++...+. -....+.|..+.|+..|||.--..
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 499999988874 356789999999999999995433
No 102
>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=32.26 E-value=34 Score=29.73 Aligned_cols=84 Identities=17% Similarity=0.249 Sum_probs=42.6
Q ss_pred CccCCCCCCCCCCceeEecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CC
Q 013569 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DN 272 (440)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~n 272 (440)
-..|.-||.. .+.+.+..-++.+|..|..--+ ++.+.+ +++ .. .-+.|+.+|..+|.++ | ..
T Consensus 13 N~~CaDCg~~--~p~w~s~~~GiflC~~Cag~HR~lg~~is---~Vk--Si-----~~d~w~~~ev~~~~~~----GN~~ 76 (116)
T PF01412_consen 13 NKVCADCGAP--NPTWASLNYGIFLCLECAGIHRSLGVHIS---RVK--SI-----TMDNWSPEEVQRMREG----GNKR 76 (116)
T ss_dssp CTB-TTT-SB--S--EEETTTTEEE-HHHHHHHHHHTTTT-----EE--ET-----TTS---HHHHHHHHHS----HHHH
T ss_pred cCcCCCCCCC--CCCEEEeecChhhhHHHHHHHHHhcccch---hcc--cc-----ccCCCCHHHHHHHHHH----ChHH
Confidence 3578888744 3577888889999999986443 443322 222 21 1235999998887654 3 22
Q ss_pred HHHHHhH-------CCCCCHHHHHHHHHc
Q 013569 273 WELVAQN-------VPTKSKLDCISKLIE 294 (440)
Q Consensus 273 W~~Ia~~-------VgtKT~~eCi~~flq 294 (440)
.+.+=++ ....+..+=+..||+
T Consensus 77 ~n~~~e~~~~~~~~~~~~~~~~~~~~fI~ 105 (116)
T PF01412_consen 77 ANSIWEANSPPPKKPPPSSDQEKREQFIR 105 (116)
T ss_dssp HHHHHTTTSTTTTTHCTTSHHHHHHHHHH
T ss_pred HHHHHHcCCCCCCCCCCCCcHHHHHHHHH
Confidence 3333221 123456666667765
No 103
>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=31.15 E-value=71 Score=22.20 Aligned_cols=31 Identities=19% Similarity=0.319 Sum_probs=22.4
Q ss_pred ccCCCCCCCCCCceeEecCCCcccchhhhhcCC
Q 013569 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN 228 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~ 228 (440)
..|..|... ...|.|......+|..|+..+.
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 2678888888899999999873
No 104
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=31.00 E-value=10 Score=29.58 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.8
Q ss_pred ccCCCCCCCCCCceeEec
Q 013569 196 FKCGSCGEQCNSGCYEYS 213 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~ 213 (440)
..|+.||.|++..+|+..
T Consensus 5 lVCsTCGrDlSeeRy~Ll 22 (63)
T PHA03082 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCcchhHHHHHHH
Confidence 579999999999998754
No 105
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=30.72 E-value=32 Score=25.94 Aligned_cols=29 Identities=31% Similarity=0.712 Sum_probs=20.1
Q ss_pred cCCCCCCCCCCce-eEecCCCcccchhhhhcC
Q 013569 197 KCGSCGEQCNSGC-YEYSKGSFVICEKCFKNG 227 (440)
Q Consensus 197 ~C~~Cg~dc~~~~-y~~~k~~~~LC~~CF~~G 227 (440)
.|..||..++... ++- +++ .+|..|+..-
T Consensus 1 ~C~iCg~kigl~~~~k~-~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI-KDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec-cCc-cchHHHHHHh
Confidence 4899999987642 222 234 5999999764
No 106
>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=30.58 E-value=13 Score=29.04 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.5
Q ss_pred ccCCCCCCCCCCceeEec
Q 013569 196 FKCGSCGEQCNSGCYEYS 213 (440)
Q Consensus 196 ~~C~~Cg~dc~~~~y~~~ 213 (440)
..|+.||.|++..+|...
T Consensus 5 lvCSTCGrDlSeeRy~Ll 22 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCCcchHHHHHHH
Confidence 579999999999988754
No 107
>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=30.46 E-value=49 Score=29.36 Aligned_cols=38 Identities=16% Similarity=0.072 Sum_probs=26.8
Q ss_pred CceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 013569 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (440)
Q Consensus 71 ~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 108 (440)
.+|||..+......-+-..+.+|.+||...||=...+.
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 68999999999999888999999999999998555533
No 108
>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=29.89 E-value=31 Score=24.78 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=18.6
Q ss_pred ccCCCCCCCCCCc-eeEecCCCcccchhhhhc
Q 013569 196 FKCGSCGEQCNSG-CYEYSKGSFVICEKCFKN 226 (440)
Q Consensus 196 ~~C~~Cg~dc~~~-~y~~~k~~~~LC~~CF~~ 226 (440)
..|++||+.-+.+ .+.....+..+|..|...
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 344334478899999753
No 109
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=29.51 E-value=1.4e+02 Score=20.78 Aligned_cols=34 Identities=15% Similarity=0.218 Sum_probs=30.4
Q ss_pred ceeeHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 72 ~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
..+|+.+..+.+.-....+.|....|+.-|+|-.
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 110
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=28.23 E-value=84 Score=30.37 Aligned_cols=77 Identities=16% Similarity=0.329 Sum_probs=47.4
Q ss_pred CCccCCCCCCCCCCceeEecC-----C----------------CcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCC
Q 013569 194 KGFKCGSCGEQCNSGCYEYSK-----G----------------SFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGA 252 (440)
Q Consensus 194 ~~~~C~~Cg~dc~~~~y~~~k-----~----------------~~~LC~~CF~~G~~~~~~s~~df~~i~~~~~~~~~~~ 252 (440)
++..|..|+..-....++... . .+.+|+.|.-... ..||.
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 567899999887655444322 1 2457888853321 12332
Q ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHH
Q 013569 253 TWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (440)
Q Consensus 253 ~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~fl 293 (440)
..+..+..+|.+.|.. .|... +.-+.||.++-+..|.
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 3446666666666654 56655 6666789988888875
No 111
>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=28.19 E-value=96 Score=28.62 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHhHCC----CCCHHHHHHHHH
Q 013569 251 GATWTEAETLLLLESVMRHGDNWELVAQNVP----TKSKLDCISKLI 293 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~Vg----tKT~~eCi~~fl 293 (440)
...-|..|...+-..|++||+|+...|.-.. -.|+.|+..++-
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 4567899999999999999999999987554 479999987764
No 112
>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=27.86 E-value=96 Score=22.78 Aligned_cols=52 Identities=19% Similarity=0.307 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHHHHHhCCCcee-eHHHHHhhccchHHHHHHHHHHhhhhccccc
Q 013569 53 KIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (440)
Q Consensus 53 ~~Y~~~RN~ii~~yr~np~~~L-T~t~~r~~l~gDv~~i~Rih~FLe~wGlINy 105 (440)
++|-.+++.|+..-. .+...+ |..+..+.+.-....+.+...=|+..|+|-.
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 113
>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=27.80 E-value=49 Score=26.65 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHhHCCC
Q 013569 256 EAETLLLLESVMRHGDNWELVAQNVPT 282 (440)
Q Consensus 256 ~~E~~~LLe~Ie~~g~nW~~Ia~~Vgt 282 (440)
-++..+||+. |.+|...|+++|-
T Consensus 2 r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 2 RERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred HHHHHHHhCC----CCCHHHHHHHcCc
Confidence 4566688887 8999999999985
No 114
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=27.78 E-value=92 Score=25.90 Aligned_cols=39 Identities=15% Similarity=0.141 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHhHCCCCCHHHHHHHHHcC
Q 013569 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (440)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~nW~~Ia~~VgtKT~~eCi~~flqL 295 (440)
++.+.++|..++..+ -.|.+||+.+|. ++..|..+..+|
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L 41 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL 41 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 356789999999988 699999999984 888888888664
No 115
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=27.18 E-value=1.1e+02 Score=23.07 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=23.1
Q ss_pred CceeeHHHHHhhcc----chHHHHHHHHHHh
Q 013569 71 SRRLTFTQVRKSLV----GDVSLLHKVFRLL 97 (440)
Q Consensus 71 ~~~LT~t~~r~~l~----gDv~~i~Rih~FL 97 (440)
...+|..+....+. .+...+.||.+||
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 116
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=26.87 E-value=82 Score=29.20 Aligned_cols=46 Identities=11% Similarity=0.105 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhcc-----chHHHHHHHHHHhhhhcccc
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLIN 104 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~-----gDv~~i~Rih~FLe~wGlIN 104 (440)
-|-.|++..... .+.+|+.+.-..|. -+...|.|...+|+.-|||+
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 26899999999999999997
No 117
>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=26.50 E-value=74 Score=25.44 Aligned_cols=43 Identities=26% Similarity=0.224 Sum_probs=32.0
Q ss_pred HHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 013569 63 INKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (440)
Q Consensus 63 i~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 108 (440)
|...|.+. ++..+-.+.+..|...+..+...|+..|||==+..
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 118
>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=26.12 E-value=61 Score=26.50 Aligned_cols=26 Identities=35% Similarity=0.487 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHhHCCC
Q 013569 256 EAETLLLLESVMRHGDNWELVAQNVPT 282 (440)
Q Consensus 256 ~~E~~~LLe~Ie~~g~nW~~Ia~~Vgt 282 (440)
.+|..+||.+= .-|.||...|.++|-
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 345799999999995
No 119
>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=25.38 E-value=1.2e+02 Score=28.63 Aligned_cols=49 Identities=16% Similarity=0.244 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccCC
Q 013569 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (440)
Q Consensus 58 ~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~~ 108 (440)
.|+.||..-..++ .+|+++..+.+.-+..++.|...-|++-|||-....
T Consensus 2 tr~~IL~~L~~~~--~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~ 50 (203)
T TIGR02702 2 TKEDILSYLLKQG--QATAAALAEALAISPQAVRRHLKDLETEGLIEYEAV 50 (203)
T ss_pred HHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeec
Confidence 4778888665543 399999999998899999999999999999976543
No 120
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=25.25 E-value=53 Score=26.79 Aligned_cols=30 Identities=17% Similarity=0.565 Sum_probs=20.9
Q ss_pred CceeeHHHHHhhc---cc-hHHHHHHHHHHhhhhc
Q 013569 71 SRRLTFTQVRKSL---VG-DVSLLHKVFRLLDEWG 101 (440)
Q Consensus 71 ~~~LT~t~~r~~l---~g-Dv~~i~Rih~FLe~wG 101 (440)
++.++-.+ ++-+ +| |..-|--|-.||.+||
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 7888899999999999
No 121
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=25.10 E-value=70 Score=33.12 Aligned_cols=98 Identities=16% Similarity=0.127 Sum_probs=55.4
Q ss_pred CccCCCCCCCCCCceeEecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCH
Q 013569 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNW 273 (440)
Q Consensus 195 ~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~G~-~~~~~s~~df~~i~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW 273 (440)
-..|.-||..- -.| -...-++.||.+|-.--| .|.|.+ |+| .. .=+.||.+|..+|.-+=...-..|
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 35788888775 233 333467899999976443 343321 222 21 235799999877765211111233
Q ss_pred HHHHhH----CC--CCCHHHHHHHHHc-CCcCCCCCCC
Q 013569 274 ELVAQN----VP--TKSKLDCISKLIE-LPFGEFMMGS 304 (440)
Q Consensus 274 ~~Ia~~----Vg--tKT~~eCi~~flq-LPIeD~fL~~ 304 (440)
-+---- +. .+.-...+.+|++ ++.+-+|...
T Consensus 88 ~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 88 YEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 322111 22 4677888999985 6666666654
No 122
>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=24.99 E-value=46 Score=24.43 Aligned_cols=33 Identities=30% Similarity=0.748 Sum_probs=24.4
Q ss_pred cCCccCCCCCCCCCCceeEecCCCcccchhhhhc
Q 013569 193 LKGFKCGSCGEQCNSGCYEYSKGSFVICEKCFKN 226 (440)
Q Consensus 193 ~~~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF~~ 226 (440)
..=+.|..|+..+....+.- ..+...|..||.+
T Consensus 24 ~~Cf~C~~C~~~l~~~~~~~-~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGDFYE-KDGKPYCKDCYQK 56 (58)
T ss_dssp TTTSBETTTTCBTTTSSEEE-ETTEEEEHHHHHH
T ss_pred ccccccCCCCCccCCCeeEe-ECCEEECHHHHhh
Confidence 45688999999998865332 3557899999864
No 123
>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=24.83 E-value=1.3e+02 Score=23.50 Aligned_cols=46 Identities=15% Similarity=0.238 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 013569 56 KEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (440)
Q Consensus 56 ~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~ 107 (440)
+++|++|-+ ...+|+.+..+.+.-+...+.-+.++|++.|.|.=..
T Consensus 3 ~~i~~~l~~------~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 3 QEIRDYLRE------RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHH------S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHH------cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence 456666654 4678999999999999999999999999999998433
No 124
>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=23.36 E-value=1.1e+02 Score=23.55 Aligned_cols=36 Identities=19% Similarity=0.201 Sum_probs=32.2
Q ss_pred CceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 013569 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (440)
Q Consensus 71 ~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 106 (440)
...+|+.+..+.+.-+-..+.|+..-|++.|||.-.
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 457999999999998999999999999999999743
No 125
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=23.27 E-value=3.1e+02 Score=25.28 Aligned_cols=32 Identities=22% Similarity=0.671 Sum_probs=23.0
Q ss_pred cCCCCCCCCCCceeEe--cCCCcccchhhhhcCC
Q 013569 197 KCGSCGEQCNSGCYEY--SKGSFVICEKCFKNGN 228 (440)
Q Consensus 197 ~C~~Cg~dc~~~~y~~--~k~~~~LC~~CF~~G~ 228 (440)
.|-.||..+...-|.- ......+|..|+.=|.
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 4999999987652322 2256789999997776
No 126
>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=22.68 E-value=61 Score=25.28 Aligned_cols=25 Identities=24% Similarity=0.480 Sum_probs=20.9
Q ss_pred CCHHHHHhHCCC-CCHHHHHHHHHcC
Q 013569 271 DNWELVAQNVPT-KSKLDCISKLIEL 295 (440)
Q Consensus 271 ~nW~~Ia~~Vgt-KT~~eCi~~flqL 295 (440)
.-|..||..+|. -+.++|..+|.+|
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHH
Confidence 369999999995 4789999999873
No 127
>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=22.06 E-value=2.3e+02 Score=20.93 Aligned_cols=36 Identities=22% Similarity=0.189 Sum_probs=31.3
Q ss_pred ceeeHHHHHhhccchHHHHHHHHHHhhhhccccccC
Q 013569 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (440)
Q Consensus 72 ~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~~ 107 (440)
..+|..+....+.-....+.|+..-|+..|+|=...
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 468999988888889999999999999999997543
No 128
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.89 E-value=44 Score=29.17 Aligned_cols=26 Identities=35% Similarity=0.830 Sum_probs=19.2
Q ss_pred CCccCCCCCCCCCCceeEecCCCcccchhhh
Q 013569 194 KGFKCGSCGEQCNSGCYEYSKGSFVICEKCF 224 (440)
Q Consensus 194 ~~~~C~~Cg~dc~~~~y~~~k~~~~LC~~CF 224 (440)
.+..|.+||.. +|=..| .-++|+.|=
T Consensus 8 tKR~Cp~CG~k----FYDLnk-~PivCP~CG 33 (108)
T PF09538_consen 8 TKRTCPSCGAK----FYDLNK-DPIVCPKCG 33 (108)
T ss_pred CcccCCCCcch----hccCCC-CCccCCCCC
Confidence 45789999887 666666 567899983
No 129
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=21.85 E-value=55 Score=27.20 Aligned_cols=50 Identities=20% Similarity=0.488 Sum_probs=17.8
Q ss_pred CCccCCCCCCCCC-----CceeEecCCCcccchhhhh----cCCCCCCCCCCCceeccC
Q 013569 194 KGFKCGSCGEQCN-----SGCYEYSKGSFVICEKCFK----NGNYGEDKSKDDFRFSDL 243 (440)
Q Consensus 194 ~~~~C~~Cg~dc~-----~~~y~~~k~~~~LC~~CF~----~G~~~~~~s~~df~~i~~ 243 (440)
....|.+||.+.. .+++.|..-.|-+|-.||. +|+----.-...|++...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kg 66 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRYKRHKG 66 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B----TT
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCcccccC
Confidence 3467999998875 3567888888999999997 343222223466766544
No 130
>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=21.73 E-value=56 Score=30.81 Aligned_cols=29 Identities=21% Similarity=0.661 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHhHC
Q 013569 252 ATWTEAETLLLLESVMRHG-DNWELVAQNV 280 (440)
Q Consensus 252 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~V 280 (440)
..|-..-+..||-||-+|| +.|++|....
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~ 33 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDP 33 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCC
Confidence 4699999999999999999 9999997643
No 131
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=21.43 E-value=58 Score=34.63 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=38.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHhH-----CCC-CCHHHHHHHHH
Q 013569 249 THGATWTEAETLLLLESVMRHGDNWELVAQN-----VPT-KSKLDCISKLI 293 (440)
Q Consensus 249 ~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~-----Vgt-KT~~eCi~~fl 293 (440)
..+..||.+|+..|.+.-+.|.=.|--||+- .++ ||-++-.++|.
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 454 99999999996
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=21.35 E-value=1.7e+02 Score=23.42 Aligned_cols=45 Identities=20% Similarity=0.271 Sum_probs=33.9
Q ss_pred HHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 013569 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (440)
Q Consensus 62 ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 106 (440)
|+.....+..+.+|..+....+.--...+.+|..-|.+-|||.-.
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
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=21.30 E-value=1.3e+02 Score=28.37 Aligned_cols=66 Identities=12% Similarity=0.074 Sum_probs=47.5
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHHHHHhCCCceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 013569 40 KEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (440)
Q Consensus 40 pefF~g~~~~ktp~~Y~~~RN~ii~~yr~np~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 106 (440)
|.|=.-...+.+..+|-.+|..|+. -+..|...|+-.+....+.-=-..+..-..-|+..|||-..
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 4443333345567899999999997 45689999998776666643446677777789999999753
No 134
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=20.52 E-value=1.9e+02 Score=23.55 Aligned_cols=37 Identities=19% Similarity=0.341 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHcCC--------CHHHHHhHCCCC---CH--HHHHHHHHc
Q 013569 258 ETLLLLESVMRHGD--------NWELVAQNVPTK---SK--LDCISKLIE 294 (440)
Q Consensus 258 E~~~LLe~Ie~~g~--------nW~~Ia~~VgtK---T~--~eCi~~flq 294 (440)
+..+|-.+|.+.|| .|..||+.+|-. +. .+...+|.+
T Consensus 37 DL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~ 86 (92)
T PF01388_consen 37 DLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEK 86 (92)
T ss_dssp SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHH
T ss_pred cHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHH
Confidence 34688899999884 799999999832 22 455566643
No 135
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=20.52 E-value=42 Score=34.16 Aligned_cols=44 Identities=5% Similarity=-0.146 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHhHCCCCCHHHHHHHHHc
Q 013569 251 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (440)
Q Consensus 251 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~VgtKT~~eCi~~flq 294 (440)
...||.++...++++|..|+..|+.|-++++.++..+-+.|...
T Consensus 53 ~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~ 96 (335)
T KOG0724|consen 53 EPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQK 96 (335)
T ss_pred ccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCC
Confidence 44599999999999999999999999999999999999999754
No 136
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.40 E-value=1.8e+02 Score=20.73 Aligned_cols=36 Identities=19% Similarity=0.173 Sum_probs=30.7
Q ss_pred CceeeHHHHHhhccchHHHHHHHHHHhhhhcccccc
Q 013569 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (440)
Q Consensus 71 ~~~LT~t~~r~~l~gDv~~i~Rih~FLe~wGlINy~ 106 (440)
...+|++++.+.+.-....+.|+.+=|.++|+|...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 467899999988876778899999999999999744
No 137
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=20.21 E-value=1.6e+02 Score=20.28 Aligned_cols=27 Identities=19% Similarity=0.300 Sum_probs=19.4
Q ss_pred HHHHhhccchHHHHHHHHHHhhhhccc
Q 013569 77 TQVRKSLVGDVSLLHKVFRLLDEWGLI 103 (440)
Q Consensus 77 t~~r~~l~gDv~~i~Rih~FLe~wGlI 103 (440)
.+.-..+.--...+.|++..|++-|||
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 333333434578899999999999998
Done!