Query 008553
Match_columns 561
No_of_seqs 246 out of 942
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 13:36:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0457 Histone acetyltransfer 100.0 5E-107 1E-111 842.8 32.6 420 81-560 13-437 (438)
2 COG5114 Histone acetyltransfer 100.0 9.2E-99 2E-103 749.7 27.8 420 80-560 3-429 (432)
3 COG5259 RSC8 RSC chromatin rem 99.7 2E-17 4.3E-22 174.2 6.1 108 80-191 222-329 (531)
4 PF04433 SWIRM: SWIRM domain; 99.5 6.3E-14 1.4E-18 119.5 6.7 78 483-560 3-85 (86)
5 cd02335 ZZ_ADA2 Zinc finger, Z 99.5 3.4E-14 7.3E-19 108.9 3.8 49 83-131 1-49 (49)
6 KOG1279 Chromatin remodeling f 99.4 2.5E-13 5.5E-18 148.1 7.1 80 106-191 224-303 (506)
7 cd02343 ZZ_EF Zinc finger, ZZ 99.3 1E-12 2.3E-17 99.6 3.6 46 83-129 1-46 (48)
8 cd02338 ZZ_PCMF_like Zinc fing 99.3 2.6E-12 5.7E-17 98.5 3.4 48 83-131 1-49 (49)
9 cd02334 ZZ_dystrophin Zinc fin 99.3 3.1E-12 6.8E-17 97.9 3.4 46 83-129 1-47 (49)
10 cd02345 ZZ_dah Zinc finger, ZZ 99.2 5.5E-12 1.2E-16 96.7 3.7 47 84-131 2-49 (49)
11 cd02249 ZZ Zinc finger, ZZ typ 99.1 4.9E-11 1.1E-15 90.2 3.4 46 83-131 1-46 (46)
12 PF00249 Myb_DNA-binding: Myb- 99.1 1.6E-10 3.6E-15 87.8 5.1 45 141-185 2-47 (48)
13 cd02340 ZZ_NBR1_like Zinc fing 99.0 1.7E-10 3.6E-15 86.2 3.2 43 83-131 1-43 (43)
14 cd02341 ZZ_ZZZ3 Zinc finger, Z 99.0 1.8E-10 3.9E-15 87.9 3.3 45 83-131 1-48 (48)
15 cd02336 ZZ_RSC8 Zinc finger, Z 99.0 4.3E-10 9.2E-15 84.6 3.5 43 83-126 1-43 (45)
16 cd02344 ZZ_HERC2 Zinc finger, 98.9 8E-10 1.7E-14 83.1 3.2 44 83-131 1-45 (45)
17 cd02339 ZZ_Mind_bomb Zinc fing 98.9 1.1E-09 2.5E-14 82.4 3.1 42 83-129 1-43 (45)
18 smart00291 ZnF_ZZ Zinc-binding 98.9 1.5E-09 3.2E-14 81.4 3.4 41 81-122 3-43 (44)
19 PF00569 ZZ: Zinc finger, ZZ t 98.8 1.7E-09 3.8E-14 81.8 2.4 42 81-123 3-45 (46)
20 smart00717 SANT SANT SWI3, AD 98.6 5.5E-08 1.2E-12 72.2 5.7 45 141-185 2-46 (49)
21 cd00167 SANT 'SWI3, ADA2, N-Co 98.6 7.7E-08 1.7E-12 70.3 5.5 44 142-185 1-44 (45)
22 TIGR01557 myb_SHAQKYF myb-like 98.6 1.1E-07 2.3E-12 75.4 5.6 49 140-188 3-56 (57)
23 cd02337 ZZ_CBP Zinc finger, ZZ 98.6 2.9E-08 6.4E-13 73.4 2.2 33 83-117 1-33 (41)
24 PF13921 Myb_DNA-bind_6: Myb-l 98.5 1.8E-07 3.9E-12 74.0 5.9 41 143-184 1-41 (60)
25 cd02342 ZZ_UBA_plant Zinc fing 98.4 9.1E-08 2E-12 70.8 2.1 33 83-116 1-34 (43)
26 PLN03212 Transcription repress 98.1 2.7E-06 5.8E-11 85.3 5.2 49 138-186 23-72 (249)
27 KOG1280 Uncharacterized conser 98.1 1.4E-06 3E-11 90.3 2.7 51 81-132 7-58 (381)
28 KOG4582 Uncharacterized conser 98.0 2.5E-06 5.4E-11 88.0 3.3 45 83-132 153-198 (278)
29 KOG4286 Dystrophin-like protei 98.0 1.7E-06 3.7E-11 96.7 0.1 69 63-132 577-653 (966)
30 PLN03091 hypothetical protein; 97.9 1.4E-05 3.1E-10 85.7 5.2 49 138-186 12-61 (459)
31 KOG0048 Transcription factor, 97.8 1.7E-05 3.7E-10 80.2 4.3 46 140-185 9-55 (238)
32 PLN03212 Transcription repress 97.5 0.00016 3.5E-09 72.7 5.4 48 137-185 75-122 (249)
33 KOG4301 Beta-dystrobrevin [Cyt 97.2 6.2E-05 1.3E-09 78.1 -0.5 51 79-130 237-288 (434)
34 PLN03091 hypothetical protein; 97.0 0.00092 2E-08 72.1 6.0 48 137-185 64-111 (459)
35 KOG0048 Transcription factor, 96.4 0.0045 9.8E-08 62.6 5.6 46 138-184 60-105 (238)
36 KOG0049 Transcription factor, 95.8 0.014 3E-07 65.4 5.7 51 137-187 357-407 (939)
37 KOG0049 Transcription factor, 95.5 0.014 3E-07 65.4 4.3 49 136-184 408-459 (939)
38 KOG0051 RNA polymerase I termi 94.1 0.051 1.1E-06 61.3 4.4 89 96-189 339-431 (607)
39 PF13837 Myb_DNA-bind_4: Myb/S 92.6 0.087 1.9E-06 44.4 2.4 45 141-185 2-63 (90)
40 PF07649 C1_3: C1-like domain; 92.1 0.091 2E-06 36.0 1.6 28 84-112 2-29 (30)
41 PF03107 C1_2: C1 domain; Int 91.6 0.14 3.1E-06 35.2 2.1 28 83-112 1-29 (30)
42 KOG0051 RNA polymerase I termi 89.1 0.38 8.3E-06 54.5 4.0 51 139-189 435-510 (607)
43 KOG0050 mRNA splicing protein 87.9 0.52 1.1E-05 52.1 4.0 48 140-188 7-54 (617)
44 COG5147 REB1 Myb superfamily p 84.1 0.77 1.7E-05 51.4 2.9 45 140-184 20-64 (512)
45 PF02207 zf-UBR: Putative zinc 81.8 0.87 1.9E-05 37.5 1.8 43 87-134 2-48 (71)
46 PF09862 DUF2089: Protein of u 79.5 3.7 8E-05 37.2 5.0 60 85-171 1-60 (113)
47 KOG0050 mRNA splicing protein 79.3 1.7 3.8E-05 48.2 3.5 45 138-184 57-101 (617)
48 PF09111 SLIDE: SLIDE; InterP 78.7 2.5 5.5E-05 38.5 3.8 44 140-183 49-107 (118)
49 COG5118 BDP1 Transcription ini 78.4 3.3 7.2E-05 44.4 5.1 44 140-184 365-408 (507)
50 KOG4282 Transcription factor G 77.7 2.9 6.2E-05 44.5 4.5 47 141-187 55-114 (345)
51 KOG4468 Polycomb-group transcr 77.1 2.5 5.4E-05 47.7 3.9 45 140-185 88-142 (782)
52 KOG1778 CREB binding protein/P 76.3 1.3 2.8E-05 47.0 1.4 46 79-132 166-211 (319)
53 COG3935 DnaD Putative primosom 73.1 8 0.00017 39.6 6.1 58 373-430 134-210 (246)
54 KOG4167 Predicted DNA-binding 71.9 5.1 0.00011 46.4 4.7 44 140-184 619-662 (907)
55 smart00420 HTH_DEOR helix_turn 70.3 11 0.00023 27.8 4.8 36 525-560 10-45 (53)
56 PF13412 HTH_24: Winged helix- 70.1 11 0.00023 28.1 4.8 44 517-560 5-48 (48)
57 PLN03000 amine oxidase 69.6 8.4 0.00018 46.2 6.1 72 488-560 90-167 (881)
58 smart00396 ZnF_UBR1 Putative z 69.0 4.9 0.00011 33.2 2.9 42 87-133 2-47 (71)
59 PHA00442 host recBCD nuclease 68.2 5.9 0.00013 31.2 3.0 27 145-171 25-51 (59)
60 KOG0384 Chromodomain-helicase 67.3 3.6 7.8E-05 50.2 2.5 28 139-166 1132-1159(1373)
61 TIGR02894 DNA_bind_RsfA transc 65.6 4.6 0.0001 38.6 2.4 44 141-185 5-54 (161)
62 COG5147 REB1 Myb superfamily p 64.9 6.4 0.00014 44.3 3.7 48 138-186 70-117 (512)
63 PF13873 Myb_DNA-bind_5: Myb/S 63.0 9.6 0.00021 31.3 3.6 45 141-185 3-68 (78)
64 PF09012 FeoC: FeoC like trans 62.8 9.1 0.0002 31.0 3.4 40 521-560 5-45 (69)
65 PLN03142 Probable chromatin-re 58.9 12 0.00025 45.9 4.7 59 141-201 825-883 (1033)
66 KOG4329 DNA-binding protein [G 58.6 12 0.00027 40.2 4.3 43 141-184 278-321 (445)
67 PF07975 C1_4: TFIIH C1-like d 58.5 6.6 0.00014 30.6 1.7 30 84-114 1-37 (51)
68 PF08914 Myb_DNA-bind_2: Rap1 58.4 15 0.00032 30.0 3.8 47 141-187 3-58 (65)
69 PF14569 zf-UDP: Zinc-binding 56.8 5.8 0.00013 33.5 1.2 33 82-115 9-45 (80)
70 PF01047 MarR: MarR family; I 55.8 12 0.00026 28.7 2.9 35 526-560 14-48 (59)
71 PF08394 Arc_trans_TRASH: Arch 55.7 7.6 0.00016 28.3 1.5 31 85-115 1-32 (37)
72 PF12802 MarR_2: MarR family; 53.5 28 0.00061 26.8 4.7 50 506-560 1-52 (62)
73 PLN02638 cellulose synthase A 51.3 13 0.00027 45.4 3.3 33 84-117 19-55 (1079)
74 PF04504 DUF573: Protein of un 51.2 22 0.00047 31.3 4.0 33 139-171 3-42 (98)
75 PLN03142 Probable chromatin-re 50.0 23 0.0005 43.4 5.2 45 140-184 926-982 (1033)
76 KOG1356 Putative transcription 49.8 8.8 0.00019 45.2 1.7 36 79-116 226-261 (889)
77 TIGR01889 Staph_reg_Sar staphy 49.8 49 0.0011 29.1 6.1 63 497-560 12-74 (109)
78 PF13404 HTH_AsnC-type: AsnC-t 48.8 50 0.0011 24.4 5.0 37 147-184 4-40 (42)
79 PF00643 zf-B_box: B-box zinc 47.8 15 0.00033 26.5 2.1 39 82-130 3-41 (42)
80 TIGR02337 HpaR homoprotocatech 47.2 64 0.0014 28.5 6.5 61 495-560 13-73 (118)
81 PF08074 CHDCT2: CHDCT2 (NUC03 46.9 11 0.00023 36.3 1.5 29 141-169 4-32 (173)
82 KOG2789 Putative Zn-finger pro 46.5 11 0.00024 40.9 1.6 87 63-152 55-153 (482)
83 PLN02328 lysine-specific histo 46.1 35 0.00075 40.8 5.8 69 492-560 144-218 (808)
84 PF05290 Baculo_IE-1: Baculovi 44.5 9.1 0.0002 35.6 0.6 53 81-136 79-131 (140)
85 PF06461 DUF1086: Domain of Un 44.0 39 0.00085 31.9 4.7 55 141-196 39-95 (145)
86 PF04703 FaeA: FaeA-like prote 43.6 30 0.00065 28.0 3.4 45 516-560 1-46 (62)
87 PF07261 DnaB_2: Replication i 43.0 5.2 0.00011 32.6 -1.1 23 403-425 54-76 (77)
88 PF03979 Sigma70_r1_1: Sigma-7 42.6 45 0.00097 28.1 4.5 41 518-558 10-53 (82)
89 PRK03573 transcriptional regul 42.2 72 0.0016 29.1 6.2 56 501-560 22-77 (144)
90 smart00595 MADF subfamily of S 41.8 26 0.00057 29.3 3.0 23 162-185 29-51 (89)
91 PF15614 WHIM3: WSTF, HB1, Itc 41.4 50 0.0011 25.3 4.0 28 380-407 4-36 (46)
92 KOG3554 Histone deacetylase co 40.0 34 0.00073 38.0 4.1 42 141-183 286-328 (693)
93 PF12776 Myb_DNA-bind_3: Myb/S 38.9 62 0.0013 27.3 4.9 43 142-184 1-60 (96)
94 PF09397 Ftsk_gamma: Ftsk gamm 38.2 60 0.0013 26.6 4.4 45 513-561 8-52 (65)
95 COG5347 GTPase-activating prot 37.9 18 0.00039 38.5 1.7 57 84-154 22-78 (319)
96 PF08513 LisH: LisH; InterPro 37.7 21 0.00047 23.9 1.4 12 548-559 6-17 (27)
97 COG4008 Predicted metal-bindin 37.6 71 0.0015 29.6 5.1 53 504-557 87-152 (153)
98 PLN02436 cellulose synthase A 37.5 21 0.00045 43.6 2.2 34 83-117 37-74 (1094)
99 TIGR00270 conserved hypothetic 37.3 1.3E+02 0.0028 28.7 7.2 40 84-123 2-41 (154)
100 KOG1194 Predicted DNA-binding 37.1 22 0.00047 39.4 2.1 43 140-184 470-512 (534)
101 PLN02915 cellulose synthase A 35.7 22 0.00048 43.3 2.1 35 82-117 15-53 (1044)
102 PF13730 HTH_36: Helix-turn-he 35.6 1E+02 0.0022 23.2 5.2 53 507-559 2-55 (55)
103 PRK11512 DNA-binding transcrip 35.4 81 0.0018 28.9 5.4 52 504-560 34-85 (144)
104 PF02954 HTH_8: Bacterial regu 35.1 52 0.0011 24.0 3.3 25 147-172 6-30 (42)
105 PF13463 HTH_27: Winged helix 35.0 75 0.0016 24.8 4.5 34 526-559 15-48 (68)
106 KOG1194 Predicted DNA-binding 34.2 51 0.0011 36.6 4.3 48 136-184 183-230 (534)
107 TIGR01446 DnaD_dom DnaD and ph 33.3 31 0.00066 28.0 2.0 18 404-421 55-72 (73)
108 smart00345 HTH_GNTR helix_turn 33.1 66 0.0014 24.0 3.8 46 515-560 4-51 (60)
109 cd00090 HTH_ARSR Arsenical Res 33.1 1.1E+02 0.0024 23.4 5.2 34 526-560 18-51 (78)
110 PF10925 DUF2680: Protein of u 32.6 1.3E+02 0.0029 24.1 5.4 44 512-559 15-58 (59)
111 PRK13923 putative spore coat p 32.1 37 0.0008 33.0 2.6 44 140-184 5-54 (170)
112 COG1725 Predicted transcriptio 31.6 1.2E+02 0.0025 28.1 5.6 50 511-560 11-66 (125)
113 PLN02400 cellulose synthase 31.4 28 0.00061 42.5 2.1 34 83-117 37-74 (1085)
114 PLN02189 cellulose synthase 31.4 30 0.00065 42.2 2.2 34 83-117 35-72 (1040)
115 smart00347 HTH_MARR helix_turn 30.1 85 0.0018 25.9 4.3 52 504-560 4-55 (101)
116 PF13076 DUF3940: Protein of u 29.7 60 0.0013 23.8 2.8 34 517-551 3-36 (38)
117 PRK08359 transcription factor; 29.6 41 0.0009 32.8 2.5 40 83-122 7-48 (176)
118 smart00843 Ftsk_gamma This dom 28.9 1.5E+02 0.0032 24.2 5.1 45 513-561 7-51 (63)
119 PLN03158 methionine aminopepti 28.7 14 0.00029 40.5 -1.1 41 81-127 8-56 (396)
120 PF09107 SelB-wing_3: Elongati 28.5 1.1E+02 0.0024 23.6 4.2 39 521-559 1-40 (50)
121 PF00130 C1_1: Phorbol esters/ 28.0 51 0.0011 24.9 2.3 24 81-104 10-35 (53)
122 TIGR03277 methan_mark_9 putati 27.6 63 0.0014 29.0 3.1 23 504-526 86-108 (109)
123 PF08784 RPA_C: Replication pr 27.5 53 0.0011 28.5 2.6 32 527-559 64-95 (102)
124 COG3058 FdhE Uncharacterized p 27.0 12 0.00026 39.0 -1.8 28 76-104 205-232 (308)
125 PLN02195 cellulose synthase A 26.9 38 0.00082 41.1 2.0 34 83-117 7-44 (977)
126 PF01978 TrmB: Sugar-specific 26.4 63 0.0014 25.7 2.7 35 526-560 19-53 (68)
127 KOG2807 RNA polymerase II tran 26.1 40 0.00087 35.9 1.8 32 81-113 329-360 (378)
128 smart00346 HTH_ICLR helix_turn 26.0 1.5E+02 0.0032 24.4 5.1 40 521-560 10-51 (91)
129 PF07191 zinc-ribbons_6: zinc- 26.0 29 0.00062 28.9 0.6 31 84-114 3-38 (70)
130 TIGR02531 yecD_yerC TrpR-relat 25.2 1.5E+02 0.0033 25.6 5.0 49 372-421 7-58 (88)
131 COG2956 Predicted N-acetylgluc 24.6 44 0.00096 35.9 1.8 26 80-106 352-377 (389)
132 KOG3579 Predicted E3 ubiquitin 24.4 57 0.0012 34.2 2.5 42 74-115 260-301 (352)
133 PRK04023 DNA polymerase II lar 24.2 47 0.001 40.4 2.1 44 498-553 1078-1121(1121)
134 PRK10870 transcriptional repre 23.3 1.9E+02 0.0042 27.7 5.9 58 500-560 45-102 (176)
135 PF01388 ARID: ARID/BRIGHT DNA 22.9 1.6E+02 0.0035 24.8 4.7 37 149-185 39-87 (92)
136 TIGR00622 ssl1 transcription f 22.8 55 0.0012 29.7 1.8 30 83-113 56-96 (112)
137 PF03811 Zn_Tnp_IS1: InsA N-te 22.5 67 0.0014 23.2 1.9 23 81-103 4-35 (36)
138 smart00550 Zalpha Z-DNA-bindin 22.4 2.2E+02 0.0049 22.9 5.2 44 517-560 8-53 (68)
139 PF10123 Mu-like_Pro: Mu-like 22.2 58 0.0013 34.5 2.2 26 490-515 301-326 (326)
140 cd04766 HTH_HspR Helix-Turn-He 22.1 4.1E+02 0.009 22.4 7.1 61 349-409 22-87 (91)
141 KOG3993 Transcription factor ( 21.8 26 0.00056 38.5 -0.5 46 78-130 263-322 (500)
142 PF03705 CheR_N: CheR methyltr 21.5 3.1E+02 0.0068 20.7 5.7 40 382-423 1-50 (57)
143 smart00418 HTH_ARSR helix_turn 21.1 1.8E+02 0.0039 21.4 4.3 34 527-560 8-41 (66)
144 PF09339 HTH_IclR: IclR helix- 20.8 1.3E+02 0.0027 22.8 3.3 42 519-560 6-49 (52)
145 PRK11179 DNA-binding transcrip 20.5 2.1E+02 0.0045 26.7 5.4 42 146-188 9-50 (153)
146 PRK00420 hypothetical protein; 20.4 62 0.0014 29.3 1.7 29 82-110 23-53 (112)
147 PF07875 Coat_F: Coat F domain 20.3 82 0.0018 25.1 2.2 25 537-561 38-62 (64)
148 PRK11823 DNA repair protein Ra 20.3 66 0.0014 35.7 2.2 27 80-107 5-31 (446)
149 PF12488 DUF3704: Protein of u 20.1 37 0.0008 23.1 0.1 9 288-296 7-15 (27)
No 1
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=5.2e-107 Score=842.79 Aligned_cols=420 Identities=51% Similarity=0.860 Sum_probs=370.6
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCCCcCCCCCCchhHHHHHHHHHHcCC
Q 008553 81 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGL 160 (561)
Q Consensus 81 ~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~~~~~Wta~Eel~LLeaie~~G~ 160 (561)
..|+|++|..+|++.+||+|++|+|||||+.||+.|+|++.|+++|+|+||++++||+.+++|||+||++||+|++.|||
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~ 92 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGF 92 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCcccccccchHHHHHHhccCcccccccccCCCCCCCCCccCCCCC
Q 008553 161 GNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKVAVAGPSKPGEATVKEESPF 240 (561)
Q Consensus 161 gnW~~Ia~~vgtkt~~ec~~hy~~~yl~~~~~plp~~~~~~~~~~~e~~~~~k~~~~~k~~~~~~~~~~~~~~~~~~~p~ 240 (561)
|||++||+||||||++||++||.++|++++++|+|+++..+++++.+++++++.+. .||
T Consensus 93 GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~---------------------~~~ 151 (438)
T KOG0457|consen 93 GNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRA---------------------EPF 151 (438)
T ss_pred CcHHHHHHHHcccchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhccccc---------------------ccC
Confidence 99999999999999999999999999999999999999999999999998876432 233
Q ss_pred CCchhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCCC
Q 008553 241 SPSRVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDADS 320 (561)
Q Consensus 241 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFE~EydNdAE~li~dmeF~~~D~ 320 (561)
.|... .|+.++..+|..++++||||+|.|||.||||+||++|+||+|+++|+
T Consensus 152 ~~~~~----------------------------~pr~p~~~~p~~~e~~gyMp~R~dFd~Eydn~AE~li~dm~f~e~D~ 203 (438)
T KOG0457|consen 152 QPTDL----------------------------VPRKPGVSNPLRREISGYMPGRLDFDEEYDNEAEQLIRDMEFEEDDT 203 (438)
T ss_pred CCCCC----------------------------CCCCCCCCCchHHHHhhhCccchhhhhhhcchhhhhHhhcccCCCCc
Confidence 33210 12333445788999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC---CCCCCCCChHHHHHHHhhchhcccCChhHHHHHHHHHHHHH
Q 008553 321 EEERDIKLRVLRIYSKRLDERKRRKDFILERNLLYP---NPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISEH 397 (561)
Q Consensus 321 ~~e~elKL~~l~iYn~rL~ER~rRK~~i~er~Ll~~---~~~~k~~skeErel~~rlk~farf~s~ed~e~l~~~l~~E~ 397 (561)
|.+.+||+++|+|||+||+||.|||++|++|||+++ |+.++++|+|||++++++|+||||+|+.||++|+.+++.|.
T Consensus 204 ~~d~elKla~ldiY~srl~eR~RRK~~I~d~nLl~~rk~q~~e~~~skEer~l~~s~k~fAR~~t~~d~~kfl~~~~eE~ 283 (438)
T KOG0457|consen 204 EEDHELKLAVLDIYNSRLKERKRRKRFIRDRNLLDYRKNQAMEKRLSKEERELYNSIKVFARFLTKSDHDKFLGSVAEEK 283 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHhhccHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999995 78899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCC-CCCC-CCC
Q 008553 398 RTLKRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNS-NSRP-SGQ 475 (561)
Q Consensus 398 ~Lr~RI~eLqeyR~~Gi~tl~e~~~Ye~~k~~Re~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~ 475 (561)
+|+.||++|||||.+|+||++++.+|+.+|.++ .+.+......+++.. .+.. +.....++ +.++ ..+
T Consensus 284 ~L~~ri~~lqE~R~ag~tt~~e~~ky~~~k~~~-~~~s~~~~~~~~~~~---------~i~~-~~~~~~~~~~~~~v~~~ 352 (438)
T KOG0457|consen 284 ELRKRISDLQEYRSAGLTTNAEPNKYERLKFKE-FRESTALLLSSGALR---------YIKN-SNQEASGSASKRPVQQQ 352 (438)
T ss_pred HHHHHHHHHHHHHHhcceeccccchhHHHHHHH-HHHHhhhccccchhh---------hhhc-cccccccccccCccccc
Confidence 999999999999999999999999999999443 333322222211100 0000 01111122 1122 223
Q ss_pred CCCCCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHH
Q 008553 476 ASSSHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVK 555 (561)
Q Consensus 476 ~~~~~~~~ldi~~~pg~~LLS~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~ 555 (561)
...++++++++.++++.++||+.|++||+.++|+|.+||.+|++|++|..++|.+++++|+.+||||++|+++|||||++
T Consensus 353 ~~~~~~~~~~~~~~~~~q~Lse~E~~lc~~~~~~p~~yLe~~~vl~~e~~k~~~~kks~a~~l~Kid~~Kvd~vyd~~~~ 432 (438)
T KOG0457|consen 353 SIYKSATPLDISGAPDTQLLSEDEKRLCQELKILPKLYLELKEVLSREIKKGGTLKKSDAYRLFKIDPRKVDRVYDFLIA 432 (438)
T ss_pred ccccCCCHHHHhcchhhhhhhhhHHHHHHHHHhccHHHHHHHHHHHHHHhccCcccchhHHHHhcCCcchHHHHHHHHHH
Confidence 34667899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCC
Q 008553 556 KGLAP 560 (561)
Q Consensus 556 ~Gwi~ 560 (561)
+||+.
T Consensus 433 ~~~~~ 437 (438)
T KOG0457|consen 433 QGWIG 437 (438)
T ss_pred hhhcc
Confidence 99986
No 2
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=9.2e-99 Score=749.68 Aligned_cols=420 Identities=32% Similarity=0.540 Sum_probs=362.5
Q ss_pred cCCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCCCcCCCCCCchhHHHHHHHHHHcC
Q 008553 80 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 159 (561)
Q Consensus 80 ~~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~~~~~Wta~Eel~LLeaie~~G 159 (561)
...++||+|..+||..++|+|++|++||||+.||.+|.+.+.|++.|+|+||+.+++||++++|+++||++|+++++..|
T Consensus 3 ~~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlG 82 (432)
T COG5114 3 GVKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLG 82 (432)
T ss_pred CceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcC
Confidence 36799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCcccccccchHHHHHHhccCcccccccccCCCCCCCCCccCCCC
Q 008553 160 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKVAVAGPSKPGEATVKEESP 239 (561)
Q Consensus 160 ~gnW~~Ia~~vgtkt~~ec~~hy~~~yl~~~~~plp~~~~~~~~~~~e~~~~~k~~~~~k~~~~~~~~~~~~~~~~~~~p 239 (561)
+|||++||+|||+|+++||+.||.++|+++.++|||++...+...+.+|++..+.+++... ++|
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~ypl~~i~~~~~v~q~~f~~qrr~rie~f~----------------~pp 146 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYPLPDITQNIHVPQDEFLEQRRHRIETFE----------------LPP 146 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccccccccccCCCCchHHHHHHHHhhhhhcc----------------CCC
Confidence 9999999999999999999999999999999999999998888899999987655443211 122
Q ss_pred CCCchhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCC
Q 008553 240 FSPSRVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDAD 319 (561)
Q Consensus 240 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFE~EydNdAE~li~dmeF~~~D 319 (561)
..| .||..| +|.+++++||||+|.|||+||+|+||..|+||.|++|+
T Consensus 147 i~p------------------------------rkP~aS---~P~cheiqgyMPgRleFd~EymnEaE~pikDm~fd~d~ 193 (432)
T COG5114 147 INP------------------------------RKPKAS---NPYCHEIQGYMPGRLEFDVEYMNEAEVPIKDMSFDGDK 193 (432)
T ss_pred CCC------------------------------CCCCCC---CCchhhhhccCCCccccchhhhhcccccccccccCCch
Confidence 322 145544 69999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC---CCCCCCCCChHHHHHHHhhchhcccCChhHHHHHHHHHHHH
Q 008553 320 SEEERDIKLRVLRIYSKRLDERKRRKDFILERNLLY---PNPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISE 396 (561)
Q Consensus 320 ~~~e~elKL~~l~iYn~rL~ER~rRK~~i~er~Ll~---~~~~~k~~skeErel~~rlk~farf~s~ed~e~l~~~l~~E 396 (561)
.+.+++||+++|+|||+||.-|.+||+.|+++||+| -++.+|++||||+.+++++|||||++|+.||+.|+++++++
T Consensus 194 ~el~~~lk~a~LdiYnsrlt~Ra~rK~~if~~nLmDyr~Lqa~dkk~skEe~~l~N~iK~fAr~lT~~Df~~F~~~~~e~ 273 (432)
T COG5114 194 EELKKKLKNATLDIYNSRLTFRARRKHAIFGKNLMDYRNLQAKDKKRSKEECGLVNSIKWFARYLTKSDFNVFFRDILEG 273 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhhhccHHHHhHHHhhhHHHHhhcchhHHHHHHHHhhh
Confidence 999999999999999999999999999999999999 47889999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCCCCC-C--
Q 008553 397 HRTLKRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSNSRP-S-- 473 (561)
Q Consensus 397 ~~Lr~RI~eLqeyR~~Gi~tl~e~~~Ye~~k~~Re~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-- 473 (561)
.-+++||++||+||.||+||++.|-+|+++|-.+ -..+..+.. ..+ |....+++.+.. +..... .
T Consensus 274 v~~~kri~~LqewR~~glttle~g~kyeRDk~ek--------f~~s~aas~-~e~--~~r~~~n~~~~s-na~~s~~d~~ 341 (432)
T COG5114 274 VYIEKRIHELQEWRNNGLTTLEAGLKYERDKFEK--------FGASTAASL-SEG--NSRYRSNSAHRS-NAEYSQMDVK 341 (432)
T ss_pred hhHHHHHHHHHHHHhcCchhhhhhhhhhhhHHHh--------hccchhhhh-ccc--chhhhccccccc-CcchhHHHHH
Confidence 9999999999999999999999999999998321 111100000 000 000111111100 000000 0
Q ss_pred CCCCCCCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHh-CCCCCHHHhhhhhcCCchhHHHHHHH
Q 008553 474 GQASSSHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDM 552 (561)
Q Consensus 474 ~~~~~~~~~~ldi~~~pg~~LLS~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~-~g~lkk~dA~~l~kiD~~K~~rIydF 552 (561)
....++...+-+|..+|++.|||++|++||.+|+|.|++||.+|.+||+++++ +|.++|+|++.||+||.+|+.+||||
T Consensus 342 ni~p~K~~t~s~~q~a~d~~llS~dEq~LC~~l~i~PkpyL~LK~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~Ydf 421 (432)
T COG5114 342 NILPSKNMTISDIQHAPDYALLSDDEQRLCETLNISPKPYLELKKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDF 421 (432)
T ss_pred hccCCCCCChhhhhccchhhhhcchHHHHHHHhCCCCccHHHHHHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHH
Confidence 00124445677899999999999999999999999999999999999999995 89999999999999999999999999
Q ss_pred HHHCCCCC
Q 008553 553 LVKKGLAP 560 (561)
Q Consensus 553 lv~~Gwi~ 560 (561)
|.+.|||.
T Consensus 422 F~~~~Wi~ 429 (432)
T COG5114 422 FLERGWIH 429 (432)
T ss_pred HHhccccC
Confidence 99999995
No 3
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=99.69 E-value=2e-17 Score=174.21 Aligned_cols=108 Identities=30% Similarity=0.613 Sum_probs=95.1
Q ss_pred cCCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCCCcCCCCCCchhHHHHHHHHHHcC
Q 008553 80 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 159 (561)
Q Consensus 80 ~~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~~~~~Wta~Eel~LLeaie~~G 159 (561)
.+..+|+.||..+.. .||+-..-.+|++|..||.+|.++....++ +|..+....+. ....|+.+|+++|||||++||
T Consensus 222 ~~~~~C~~cG~~~~~-t~y~nlra~~~n~C~~C~~qg~f~s~~~ss-Df~~v~~~~~~-~dk~WS~qE~~LLLEGIe~yg 298 (531)
T COG5259 222 KHPSSCSCCGNKSFN-TRYHNLRAEKYNSCSECYDQGRFPSEFTSS-DFKPVTISLLI-RDKNWSRQELLLLLEGIEMYG 298 (531)
T ss_pred cCCceeeccCccccc-hhhhhhhhhhcccchHHHhcCcCCCccccc-cchhhhhhccc-ccccccHHHHHHHHHHHHHhh
Confidence 346899999999887 899988878999999999999999888777 67776654433 456899999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCC
Q 008553 160 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPF 191 (561)
Q Consensus 160 ~gnW~~Ia~~vgtkt~~ec~~hy~~~yl~~~~ 191 (561)
++|..||.|||+||++||+.||.++++.+++
T Consensus 299 -DdW~kVA~HVgtKt~EqCIl~FL~LPieD~~ 329 (531)
T COG5259 299 -DDWDKVARHVGTKTKEQCILHFLQLPIEDNY 329 (531)
T ss_pred -hhHHHHHHHhCCCCHHHHHHHHHcCCcchhh
Confidence 9999999999999999999999999998764
No 4
>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=99.48 E-value=6.3e-14 Score=119.53 Aligned_cols=78 Identities=33% Similarity=0.477 Sum_probs=68.9
Q ss_pred cccccCCCccCCCCHHHHHHHHHhCC--CchHHHHHHHHHHHHHH--hCCCCCHHHhhhhhc-CCchhHHHHHHHHHHCC
Q 008553 483 DLYIMGFNETQLLSEAEKRLCCEIRL--APPLYLRMQEVMSREIF--SGNVNNKADAHHLFK-IEPSKIDRVYDMLVKKG 557 (561)
Q Consensus 483 ~ldi~~~pg~~LLS~~Ek~LC~~lrL--~P~~YL~iK~~LirE~~--~~g~lkk~dA~~l~k-iD~~K~~rIydFlv~~G 557 (561)
++++++.++.+.||+.|+++|..+++ .|..||.+|..||.+.. .++.+++++|+.+++ +|++++.+||+||.+.|
T Consensus 3 ~~~~~~~~~~~~l~~~E~~~~~e~~~~~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G 82 (86)
T PF04433_consen 3 IPAHSSWFDPDKLSEIEKQLCPEFFIGKTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWG 82 (86)
T ss_dssp CHCCHTTTTTTSS-HHHHHHCHHCTTSCHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTT
T ss_pred CccccCCCCcccCCHHHHHHhHHHhccCChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcC
Confidence 45677788999999999999999999 99999999999999954 678999999999999 99999999999999999
Q ss_pred CCC
Q 008553 558 LAP 560 (561)
Q Consensus 558 wi~ 560 (561)
||+
T Consensus 83 ~IN 85 (86)
T PF04433_consen 83 LIN 85 (86)
T ss_dssp SSS
T ss_pred ccC
Confidence 996
No 5
>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=99.46 E-value=3.4e-14 Score=108.95 Aligned_cols=49 Identities=69% Similarity=1.499 Sum_probs=46.5
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccc
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
++||+|.+++.+..||+|++|+|||||..||+.|.+.+.|+++|+|++|
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 5799999998877999999999999999999999999999999999986
No 6
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=99.41 E-value=2.5e-13 Score=148.12 Aligned_cols=80 Identities=35% Similarity=0.853 Sum_probs=71.8
Q ss_pred cccchhhhhcccccCCCCCCCCcccccCCCCCcCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 106 FDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 106 fdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
+.+|..||..|.+..+++.+ +|.++... ....||.+|+++||+||++|| .+|..||.|||+||++||+.||.+.
T Consensus 224 ~~~c~~c~~~g~~~~~~~~~-Df~~~~~~----~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 224 VNLCADCYDQGEFPSEFKKS-DFKVIGES----ARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred hhhhHHHHhcCCccCccccc-cchhcccc----CCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHhc
Confidence 78999999999999999877 56555442 368999999999999999999 9999999999999999999999999
Q ss_pred ccCCCC
Q 008553 186 YMNSPF 191 (561)
Q Consensus 186 yl~~~~ 191 (561)
++.+++
T Consensus 298 PieD~~ 303 (506)
T KOG1279|consen 298 PIEDPY 303 (506)
T ss_pred Cccchh
Confidence 998864
No 7
>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=99.32 E-value=1e-12 Score=99.59 Aligned_cols=46 Identities=33% Similarity=0.717 Sum_probs=43.0
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcc
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 129 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~ 129 (561)
+.||+|.+.+.+ .||+|++|+|||||..||..|.+.+.|+++|+++
T Consensus 1 i~CdgC~~~~~~-~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~ 46 (48)
T cd02343 1 ISCDGCDEIAPW-HRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMV 46 (48)
T ss_pred CCCCCCCCcCCC-ceEECCCCCCchhHHHHHhCCccCCCCCCCCCcc
Confidence 469999998877 9999999999999999999999999999999875
No 8
>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=99.27 E-value=2.6e-12 Score=98.53 Aligned_cols=48 Identities=38% Similarity=0.953 Sum_probs=44.7
Q ss_pred ccccccc-cccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccc
Q 008553 83 YHCNYCN-KDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 83 ~~Cd~C~-~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
+.|++|+ .+|.+ .||+|.+|+|||||..||..|.+.+.|+++|+|+++
T Consensus 1 i~C~~C~~~~i~g-~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~~ 49 (49)
T cd02338 1 VSCDGCGKSNFTG-RRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQCI 49 (49)
T ss_pred CCCCCCcCCCcEE-eeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEEC
Confidence 4699999 68997 999999999999999999999999999999999874
No 9
>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=99.26 E-value=3.1e-12 Score=97.92 Aligned_cols=46 Identities=41% Similarity=0.977 Sum_probs=43.0
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcc
Q 008553 83 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 129 (561)
Q Consensus 83 ~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~ 129 (561)
+.||+|++ +|.+ .||+|++|+|||||..||..|.+.+.|+++|+|+
T Consensus 1 ~~Cd~C~~~pi~g-~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 1 AKCNICKEFPITG-FRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCCcee-eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 36999997 5888 9999999999999999999999999999999986
No 10
>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=99.24 E-value=5.5e-12 Score=96.74 Aligned_cols=47 Identities=43% Similarity=0.968 Sum_probs=44.0
Q ss_pred ccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccc
Q 008553 84 HCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 84 ~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
.|++|.+ +|++ +||+|++|+|||||..||+.|.+.+.|+++|+|..+
T Consensus 2 ~C~~C~~~~i~g-~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~~ 49 (49)
T cd02345 2 SCSACRKQDISG-IRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYEL 49 (49)
T ss_pred cCCCCCCCCceE-eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcccC
Confidence 6999998 9997 999999999999999999999999999999988653
No 11
>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=99.11 E-value=4.9e-11 Score=90.22 Aligned_cols=46 Identities=41% Similarity=1.024 Sum_probs=42.4
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccc
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
|.|++|+++|.+ .||+|.+|+|||||..||+.+. +.|+++|+|..|
T Consensus 1 ~~C~~C~~~i~g-~r~~C~~C~d~dLC~~Cf~~~~--~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLKPIVG-VRYHCLVCEDFDLCSSCYAKGK--KGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCCCCcC-CEEECCCCCCCcCHHHHHCcCc--CCCCCCCCEeEC
Confidence 579999999998 9999999999999999999987 889999998754
No 12
>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=99.07 E-value=1.6e-10 Score=87.83 Aligned_cols=45 Identities=31% Similarity=0.716 Sum_probs=41.0
Q ss_pred CCCCchhHHHHHHHHHHcCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 008553 141 PDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 185 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~ 185 (561)
..||.+|+.+|++||.+||.+||..||.+|+ +||+.||+.||.++
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 5799999999999999999877999999999 99999999999864
No 13
>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=99.02 E-value=1.7e-10 Score=86.16 Aligned_cols=43 Identities=42% Similarity=0.943 Sum_probs=38.9
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccc
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
+.||+|+.+|.+ .||+|.+|+|||||..||..+ .| +.|+|..|
T Consensus 1 v~Cd~C~~~i~G-~ry~C~~C~d~dLC~~C~~~~----~H-~~H~f~~~ 43 (43)
T cd02340 1 VICDGCQGPIVG-VRYKCLVCPDYDLCESCEAKG----VH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCCcCcC-CeEECCCCCCccchHHhhCcC----CC-CCCCEEeC
Confidence 469999999998 999999999999999999987 68 89988753
No 14
>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=99.02 E-value=1.8e-10 Score=87.90 Aligned_cols=45 Identities=36% Similarity=0.882 Sum_probs=40.9
Q ss_pred cccccccc-ccCCceeEEcCCCC--CcccchhhhhcccccCCCCCCCCcccc
Q 008553 83 YHCNYCNK-DITGKIRIKCAVCP--DFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 83 ~~Cd~C~~-~i~~~~ri~C~~C~--dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
|.||+|+. +|.+ +||+|.+|+ +||||..||..|. .|+.+|.+..|
T Consensus 1 y~Cd~C~~~pI~G-~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPG-TRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCcccc-ceEECCCCCCCCCccCHHHHhCcC---CCCCCCceeeC
Confidence 57999998 8998 999999999 9999999999997 79999987654
No 15
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.97 E-value=4.3e-10 Score=84.65 Aligned_cols=43 Identities=30% Similarity=0.636 Sum_probs=40.5
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCC
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNH 126 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H 126 (561)
|+|+.|+.|++. +||+|+.+.++|||+.||.+|.++.+|.+..
T Consensus 1 y~C~~Cg~D~t~-vryh~~~~~~~dLC~~CF~~G~f~~~~~s~D 43 (45)
T cd02336 1 YHCFTCGNDCTR-VRYHNLKAKKYDLCPSCYQEGRFPSNFQSSD 43 (45)
T ss_pred CcccCCCCccCc-eEEEecCCCccccChHHHhCcCCCCCCcccc
Confidence 689999999996 9999999999999999999999999998773
No 16
>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=98.91 E-value=8e-10 Score=83.10 Aligned_cols=44 Identities=36% Similarity=0.906 Sum_probs=38.7
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccc
Q 008553 83 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 131 (561)
Q Consensus 83 ~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi 131 (561)
+.||+|+. .|.| .||+|.+|+|||||..||..+ .|...|.|..|
T Consensus 1 V~Cd~C~~~pI~G-~RykC~~C~dyDLC~~Cf~~~----~H~~~H~F~ri 45 (45)
T cd02344 1 VTCDGCQMFPING-PRFKCRNCDDFDFCENCFKTR----KHNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCCcc-CeEECCCCCCccchHHhhCCC----CcCCCCceeeC
Confidence 47999996 6888 999999999999999999995 59889988654
No 17
>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=98.88 E-value=1.1e-09 Score=82.42 Aligned_cols=42 Identities=43% Similarity=1.020 Sum_probs=36.9
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcc
Q 008553 83 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 129 (561)
Q Consensus 83 ~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~ 129 (561)
+.||+|++ .|.+ .||+|++|+|||||..||.. +.|+.+|+|.
T Consensus 1 i~Cd~C~~~~i~G-~RykC~~C~dyDLC~~C~~~----~~H~~~H~f~ 43 (45)
T cd02339 1 IICDTCRKQGIIG-IRWKCAECPNYDLCTTCYHG----DKHDLEHRFY 43 (45)
T ss_pred CCCCCCCCCCccc-CeEECCCCCCccchHHHhCC----CCCCCCCCEE
Confidence 36999995 6777 99999999999999999996 4699999885
No 18
>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=98.87 E-value=1.5e-09 Score=81.42 Aligned_cols=41 Identities=46% Similarity=1.093 Sum_probs=37.4
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCC
Q 008553 81 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPH 122 (561)
Q Consensus 81 ~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~H 122 (561)
..+.|++|+++|++ .||+|.+|+|||||..||..|.+.+.|
T Consensus 3 ~~~~C~~C~~~i~g-~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 3 HSYSCDTCGKPIVG-VRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CCcCCCCCCCCCcC-CEEECCCCCCccchHHHHhCcCcCCCC
Confidence 46789999999998 899999999999999999999877666
No 19
>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=98.82 E-value=1.7e-09 Score=81.82 Aligned_cols=42 Identities=50% Similarity=1.118 Sum_probs=32.0
Q ss_pred CCcccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCC
Q 008553 81 ALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 123 (561)
Q Consensus 81 ~~~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk 123 (561)
..+.|++|+. .|.+ .||+|.+|+|||||..||..|.....|+
T Consensus 3 ~~~~C~~C~~~~i~g-~Ry~C~~C~d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIG-VRYHCLVCPDYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SSCE-SSS-SSSEES-SEEEESSSSS-EEEHHHHHH--H-SSSS
T ss_pred CCeECcCCCCCcCcC-CeEECCCCCCCchhhHHHhCcCCCCCcC
Confidence 4689999998 6787 9999999999999999999998777774
No 20
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.65 E-value=5.5e-08 Score=72.20 Aligned_cols=45 Identities=33% Similarity=0.766 Sum_probs=42.7
Q ss_pred CCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 141 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
..||.+|+..|+.++..||.++|..||.++++||+.+|+.+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 579999999999999999988999999999999999999999865
No 21
>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=98.61 E-value=7.7e-08 Score=70.34 Aligned_cols=44 Identities=34% Similarity=0.791 Sum_probs=41.8
Q ss_pred CCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 142 DWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 142 ~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
.||.+|+..|+.++..||.++|..||..+++||+.+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 49999999999999999988999999999999999999999764
No 22
>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=98.57 E-value=1.1e-07 Score=75.36 Aligned_cols=49 Identities=18% Similarity=0.317 Sum_probs=44.8
Q ss_pred CCCCCchhHHHHHHHHHHcCCCCh---HHHHHHhC-CC-CHHHHHHHHHhhccC
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNW---AEIAEHVG-TK-TKELCIEHYTNVYMN 188 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW---~~Ia~~vg-tk-t~~ec~~hy~~~yl~ 188 (561)
+..||++|...+|+||+.+|.||| ..|+++++ ++ |+.||+.|+.++|+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 356999999999999999999999 99999988 57 999999999999863
No 23
>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=98.56 E-value=2.9e-08 Score=73.36 Aligned_cols=33 Identities=42% Similarity=1.111 Sum_probs=29.3
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhhhccc
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
|+||+|.+. .+ +||+|++|+|||||..||..+.
T Consensus 1 y~C~~C~~~-~~-~r~~C~~C~dfDLC~~C~~~~~ 33 (41)
T cd02337 1 YTCNECKHH-VE-TRWHCTVCEDYDLCITCYNTKN 33 (41)
T ss_pred CcCCCCCCc-CC-CceECCCCcchhhHHHHhCCCC
Confidence 579999984 45 9999999999999999999854
No 24
>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=98.52 E-value=1.8e-07 Score=74.04 Aligned_cols=41 Identities=39% Similarity=0.920 Sum_probs=37.0
Q ss_pred CCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 143 WNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 143 Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
||.+|+.+|++++..|| .+|..||+++|+||+.+|+.||..
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999 799999999998999999999998
No 25
>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=98.44 E-value=9.1e-08 Score=70.76 Aligned_cols=33 Identities=45% Similarity=0.799 Sum_probs=30.1
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcc
Q 008553 83 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVG 116 (561)
Q Consensus 83 ~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G 116 (561)
+.||+|+. +|.+ .||+|.+|+|||||..||...
T Consensus 1 I~CDgCg~~PI~G-~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITG-PRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccc-cceEeCCCCCCccHHHHhhhh
Confidence 46999997 7998 999999999999999999874
No 26
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.13 E-value=2.7e-06 Score=85.27 Aligned_cols=49 Identities=18% Similarity=0.472 Sum_probs=44.9
Q ss_pred cCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 008553 138 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 186 (561)
Q Consensus 138 ~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~y 186 (561)
+-+..||.+|+.+|+++|+.||.+||..||.++| +||+.||+++|.++.
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 4467899999999999999999999999999997 799999999998763
No 27
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.11 E-value=1.4e-06 Score=90.26 Aligned_cols=51 Identities=33% Similarity=0.741 Sum_probs=46.1
Q ss_pred CCccccccccc-cCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccccc
Q 008553 81 ALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 132 (561)
Q Consensus 81 ~~~~Cd~C~~~-i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~ 132 (561)
..+.||+|++. +++ .||||..|.|||||..||..|+-++.|.-+|+.+.|-
T Consensus 7 e~v~CdgC~k~~~t~-rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil 58 (381)
T KOG1280|consen 7 EGVSCDGCGKTAFTF-RRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCIL 58 (381)
T ss_pred CCceeccccccceee-eeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEe
Confidence 46889999986 565 9999999999999999999999999999999987663
No 28
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=98.05 E-value=2.5e-06 Score=88.05 Aligned_cols=45 Identities=40% Similarity=0.906 Sum_probs=38.8
Q ss_pred cccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccccc
Q 008553 83 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 132 (561)
Q Consensus 83 ~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~ 132 (561)
..||.|++ .|.| .||+|++|+|||||..|+..+ .|+-.|.+.-|.
T Consensus 153 v~CD~C~~~~IvG-~RyKC~~C~dYDLCe~Ce~~~----~~h~~H~~lR~~ 198 (278)
T KOG4582|consen 153 VPCDNCGKPGIVG-ARYKCTVCPDYDLCERCEAGN----EHHAAHAMLRLH 198 (278)
T ss_pred ccCCCccCCcccc-ceeeecCCCccchhHHhhcCC----CCCcccceeecc
Confidence 68999999 8998 999999999999999999975 466777776543
No 29
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=97.96 E-value=1.7e-06 Score=96.72 Aligned_cols=69 Identities=23% Similarity=0.380 Sum_probs=57.5
Q ss_pred CCCCCCCCCCC-------CCCCCCcCCcccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccccc
Q 008553 63 SDNSDTAAPGQ-------GAGEGKRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 132 (561)
Q Consensus 63 ~~~~~~~~~~~-------~~~~~~~~~~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~ 132 (561)
+-+.|+.++++ .++|.-.+.-.|++|.+ .|.| +||+|.+|.++|||..||..|..-+.|+..|++.-..
T Consensus 577 w~~~epqsmVwL~vlhRv~~aE~~kH~~kCniCk~~pIvG-~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~ 653 (966)
T KOG4286|consen 577 WMRLEPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIG-FRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYC 653 (966)
T ss_pred HhccCcchhhHHHHHHHHHHHHHHHhhhhcchhhhCccce-eeeeehhhcChhHHhhHhhhcccccCCCCCCCceeee
Confidence 55667777772 44556678889999997 6888 9999999999999999999999999999998776543
No 30
>PLN03091 hypothetical protein; Provisional
Probab=97.87 E-value=1.4e-05 Score=85.69 Aligned_cols=49 Identities=24% Similarity=0.545 Sum_probs=44.4
Q ss_pred cCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 008553 138 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 186 (561)
Q Consensus 138 ~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~y 186 (561)
+-...||.+|+.+|+++|++||.+||..||.++| +||+.||++||.++.
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 3456899999999999999999999999999998 799999999998653
No 31
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.81 E-value=1.7e-05 Score=80.15 Aligned_cols=46 Identities=17% Similarity=0.427 Sum_probs=44.1
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 185 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~ 185 (561)
.+.||.+|+..|.+.|++||-|||..||++.| .|+.+.|+.+|.+|
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~Ny 55 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNY 55 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcc
Confidence 58899999999999999999999999999999 89999999999865
No 32
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.45 E-value=0.00016 Score=72.71 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=44.3
Q ss_pred CcCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 137 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 137 p~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
.+....||.+|+.+|++.+..|| ..|..||.++.+||..+|+.||..+
T Consensus 75 ~I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~LpGRTDnqIKNRWns~ 122 (249)
T PLN03212 75 SVKRGGITSDEEDLILRLHRLLG-NRWSLIAGRIPGRTDNEIKNYWNTH 122 (249)
T ss_pred hcccCCCChHHHHHHHHHHHhcc-ccHHHHHhhcCCCCHHHHHHHHHHH
Confidence 35678999999999999999999 7899999999999999999999753
No 33
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=97.23 E-value=6.2e-05 Score=78.11 Aligned_cols=51 Identities=27% Similarity=0.728 Sum_probs=45.2
Q ss_pred CcCCcccccccc-ccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccc
Q 008553 79 KRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 130 (561)
Q Consensus 79 ~~~~~~Cd~C~~-~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~v 130 (561)
-...+.|++|.. .+++ .||+|..|.+|.+|.+||-.|.--+.|.+.|.+.-
T Consensus 237 v~hpv~cs~c~srs~~g-fry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mke 288 (434)
T KOG4301|consen 237 VFHPVECSYCRSRSMMG-FRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMKE 288 (434)
T ss_pred cCCCccCcceecccccc-hhhhHhhcCCccccchhhccccCCCCcchHHHHHH
Confidence 357789999985 6887 99999999999999999999999999999996653
No 34
>PLN03091 hypothetical protein; Provisional
Probab=97.05 E-value=0.00092 Score=72.15 Aligned_cols=48 Identities=19% Similarity=0.351 Sum_probs=44.4
Q ss_pred CcCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 137 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 137 p~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
.+....||.+|+.+||+.+..|| ..|..||.++.+||..+|+.||..+
T Consensus 64 ~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~LPGRTDnqIKNRWnsl 111 (459)
T PLN03091 64 DLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQLPGRTDNEIKNLWNSC 111 (459)
T ss_pred cccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhcCCCCHHHHHHHHHHH
Confidence 35678999999999999999999 7999999999999999999999864
No 35
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.44 E-value=0.0045 Score=62.61 Aligned_cols=46 Identities=20% Similarity=0.403 Sum_probs=42.4
Q ss_pred cCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 138 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 138 ~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
+-++.||.+||.+++++-..+| .-|..||.++.+||..+++.||..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LPGRTDNeIKN~Wnt 105 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLPGRTDNEVKNHWNT 105 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCCCcCHHHHHHHHHH
Confidence 4578999999999999999999 569999999999999999999954
No 36
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.78 E-value=0.014 Score=65.41 Aligned_cols=51 Identities=27% Similarity=0.649 Sum_probs=46.8
Q ss_pred CcCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhhcc
Q 008553 137 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYM 187 (561)
Q Consensus 137 p~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yl 187 (561)
.+-.+.||.+|+.+|+.||+.||-.+|-.|-+.|.+||..||+.+|.+.--
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~ 407 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLN 407 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHH
Confidence 455789999999999999999998899999999999999999999998643
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.45 E-value=0.014 Score=65.40 Aligned_cols=49 Identities=24% Similarity=0.348 Sum_probs=43.7
Q ss_pred CCcCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCH---HHHHHHHHh
Q 008553 136 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTK---ELCIEHYTN 184 (561)
Q Consensus 136 ~p~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~---~ec~~hy~~ 184 (561)
+..-.+.|+-.||..|+++|++||.|+|..+|..+|.||. .-|+.+++.
T Consensus 408 ~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 408 RSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred HhhccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHH
Confidence 4445689999999999999999999999999999999998 678888876
No 38
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.11 E-value=0.051 Score=61.26 Aligned_cols=89 Identities=13% Similarity=0.198 Sum_probs=61.8
Q ss_pred eeEEcCCC-CCcccchhhhhcccccCCCCCCCCcccccCCCCCc---CCCCCCchhHHHHHHHHHHcCCCChHHHHHHhC
Q 008553 96 IRIKCAVC-PDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPL---ICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG 171 (561)
Q Consensus 96 ~ri~C~~C-~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~---~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vg 171 (561)
.|+.|..| +..+-|-.|...-.-. -+..-.|+-+.. .|.+ ..+-||.+|+..|-..+.++| +.|.+|++.+|
T Consensus 339 ~~i~s~~~~~~~~~l~n~~~~~Lp~--R~~~siy~~~rR-~y~~FE~~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg 414 (607)
T KOG0051|consen 339 QRIWSKDWKTIIRNLYNNLYKLLPY--RDRKSIYHHLRR-AYTPFENKRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG 414 (607)
T ss_pred hheeccCcchHHHHHHHhhhhhcCc--ccchhHHHHHHh-cCCccccccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc
Confidence 45666666 4456677776653311 111112332221 2222 358899999999999999999 99999999998
Q ss_pred CCCHHHHHHHHHhhccCC
Q 008553 172 TKTKELCIEHYTNVYMNS 189 (561)
Q Consensus 172 tkt~~ec~~hy~~~yl~~ 189 (561)
|.|..|+.||.++-..+
T Consensus 415 -r~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 415 -RMPMDCRDRWRQYVKCG 431 (607)
T ss_pred -cCcHHHHHHHHHhhccc
Confidence 79999999999876554
No 39
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=92.55 E-value=0.087 Score=44.45 Aligned_cols=45 Identities=29% Similarity=0.614 Sum_probs=32.8
Q ss_pred CCCCchhHHHHHHHHHH--cC--CC---------ChHHHHHHhC----CCCHHHHHHHHHhh
Q 008553 141 PDWNADDEILLLEGIEM--YG--LG---------NWAEIAEHVG----TKTKELCIEHYTNV 185 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~--~G--~g---------nW~~Ia~~vg----tkt~~ec~~hy~~~ 185 (561)
..||.+|...||+.+.. +. ++ -|..||+.+. .||+.||+.+|.++
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 47999999999998876 11 11 3999999885 49999999999875
No 40
>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=92.10 E-value=0.091 Score=36.02 Aligned_cols=28 Identities=46% Similarity=1.031 Sum_probs=12.9
Q ss_pred cccccccccCCceeEEcCCCCCcccchhh
Q 008553 84 HCNYCNKDITGKIRIKCAVCPDFDLCIEC 112 (561)
Q Consensus 84 ~Cd~C~~~i~~~~ri~C~~C~dfdLC~~C 112 (561)
.|+.|++.+.+...|+|.+| ||+|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C-df~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC-DFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT------HHH
T ss_pred cCCcCCCcCCCCceEECccC-CCccChhc
Confidence 69999999886689999999 59998887
No 41
>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=91.56 E-value=0.14 Score=35.21 Aligned_cols=28 Identities=32% Similarity=0.999 Sum_probs=24.6
Q ss_pred ccccccccccCCce-eEEcCCCCCcccchhh
Q 008553 83 YHCNYCNKDITGKI-RIKCAVCPDFDLCIEC 112 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~-ri~C~~C~dfdLC~~C 112 (561)
+.|+.|.+.+.+ . .|+|.+|. |++.+.|
T Consensus 1 ~~C~~C~~~~~~-~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 1 FWCDVCRRKIDG-FYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCCcCC-CEeEEeCCCC-CeEcCcc
Confidence 479999999988 5 99999997 9888877
No 42
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=89.07 E-value=0.38 Score=54.46 Aligned_cols=51 Identities=20% Similarity=0.378 Sum_probs=42.7
Q ss_pred CCCCCCchhHHHHHHHHH-------Hc------------------CCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 008553 139 ICPDWNADDEILLLEGIE-------MY------------------GLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 189 (561)
Q Consensus 139 ~~~~Wta~Eel~LLeaie-------~~------------------G~gnW~~Ia~~vgtkt~~ec~~hy~~~yl~~ 189 (561)
....||-+||.+||..|+ ++ ..=||..|++.+|||+..+|+.||.++-...
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~ 510 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSP 510 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhH
Confidence 467899999999999995 44 1128999999999999999999999875543
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=87.92 E-value=0.52 Score=52.14 Aligned_cols=48 Identities=21% Similarity=0.524 Sum_probs=43.6
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 188 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yl~ 188 (561)
...|+..||..|=-|+..||-..|..||..+..||+.+|..+|. -+|+
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~-e~ld 54 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWE-EWLD 54 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHH-HHhC
Confidence 46799999999999999999888999999999999999999998 4454
No 44
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=84.07 E-value=0.77 Score=51.44 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=42.3
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
.+.|+..|+..|+-+++.||..||..||..++.+++++|+.||..
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~ 64 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNN 64 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhh
Confidence 468999999999999999999999999999999999999999943
No 45
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=81.80 E-value=0.87 Score=37.48 Aligned_cols=43 Identities=28% Similarity=0.557 Sum_probs=28.1
Q ss_pred ccccccC-CceeEEcCCCCC---cccchhhhhcccccCCCCCCCCcccccCC
Q 008553 87 YCNKDIT-GKIRIKCAVCPD---FDLCIECFSVGVEVHPHKSNHPYRVMDNL 134 (561)
Q Consensus 87 ~C~~~i~-~~~ri~C~~C~d---fdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~ 134 (561)
.|+..+. +.+.|+|..|.. ..+|..||..+. |. +|.|..+...
T Consensus 2 ~C~~~~~~~q~~y~C~tC~~~~~~~iC~~CF~~~~----H~-gH~~~~~~~~ 48 (71)
T PF02207_consen 2 KCTYVWTSGQIFYRCLTCSLDESSGICEECFANSC----HE-GHRVVYYRSS 48 (71)
T ss_dssp SS--B--TT-EEEEETTTBSSTT-BBEHHHHCTSG----GG-GSSEEEEE--
T ss_pred cCCCCCcCCCEEEECccCCCCCCEEEchhhCCCCC----cC-CCcEEEEEeC
Confidence 3666553 368999999964 679999999864 75 8888887654
No 46
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=79.47 E-value=3.7 Score=37.20 Aligned_cols=60 Identities=18% Similarity=0.448 Sum_probs=42.0
Q ss_pred ccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCCCcCCCCCCchhHHHHHHHHHHcCCCChH
Q 008553 85 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWA 164 (561)
Q Consensus 85 Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~~~~~Wta~Eel~LLeaie~~G~gnW~ 164 (561)
|-.|+..+.- .+++|..|.. .+.++ |.+ ..-.--.+|++.+++..-... ||-.
T Consensus 1 CPvCg~~l~v-t~l~C~~C~t------------~i~G~-----F~l--------~~~~~L~~E~~~Fi~~Fi~~r-GnlK 53 (113)
T PF09862_consen 1 CPVCGGELVV-TRLKCPSCGT------------EIEGE-----FEL--------PWFARLSPEQLEFIKLFIKNR-GNLK 53 (113)
T ss_pred CCCCCCceEE-EEEEcCCCCC------------EEEee-----ecc--------chhhcCCHHHHHHHHHHHHhc-CCHH
Confidence 8899999885 8999999851 11111 111 011122378899999888887 8999
Q ss_pred HHHHHhC
Q 008553 165 EIAEHVG 171 (561)
Q Consensus 165 ~Ia~~vg 171 (561)
+|++.+|
T Consensus 54 e~e~~lg 60 (113)
T PF09862_consen 54 EMEKELG 60 (113)
T ss_pred HHHHHHC
Confidence 9999998
No 47
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=79.26 E-value=1.7 Score=48.20 Aligned_cols=45 Identities=27% Similarity=0.634 Sum_probs=40.9
Q ss_pred cCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 138 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 138 ~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
|-...|+.+||..||.+....- ..|-.||..|| +|..+|.+||.+
T Consensus 57 i~~tews~eederlLhlakl~p-~qwrtIa~i~g-r~~~qc~eRy~~ 101 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEP-TQWRTIADIMG-RTSQQCLERYNN 101 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcC-CccchHHHHhh-hhHHHHHHHHHH
Confidence 4567999999999999998887 78999999998 799999999987
No 48
>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=78.67 E-value=2.5 Score=38.50 Aligned_cols=44 Identities=20% Similarity=0.434 Sum_probs=35.2
Q ss_pred CCCCCchhHHHHHHHHHHcCC---CChHHHHHHhC------------CCCHHHHHHHHH
Q 008553 140 CPDWNADDEILLLEGIEMYGL---GNWAEIAEHVG------------TKTKELCIEHYT 183 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~---gnW~~Ia~~vg------------tkt~~ec~~hy~ 183 (561)
...||.+|+.-||-.+..||+ |+|+.|-..|- +||+.|+..|-.
T Consensus 49 ~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 49 KKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp -SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 478999999999999999999 99999988763 788877776654
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=78.39 E-value=3.3 Score=44.40 Aligned_cols=44 Identities=7% Similarity=0.314 Sum_probs=41.4
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
...|++.|..++..|++++| -++.-||....+|+..|++..|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCchhHHHHHHHHHH
Confidence 46899999999999999999 799999999999999999999875
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=77.71 E-value=2.9 Score=44.53 Aligned_cols=47 Identities=23% Similarity=0.577 Sum_probs=37.4
Q ss_pred CCCCchhHHHHHHHHHH----cCCCC-----hHHHHHHh---C-CCCHHHHHHHHHhhcc
Q 008553 141 PDWNADDEILLLEGIEM----YGLGN-----WAEIAEHV---G-TKTKELCIEHYTNVYM 187 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~----~G~gn-----W~~Ia~~v---g-tkt~~ec~~hy~~~yl 187 (561)
..|+.+|.+.||++... ++-|+ |.+||..+ | .||+.+|+..|.+++-
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 67999999999998752 23344 99999944 3 4999999999998654
No 51
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=77.11 E-value=2.5 Score=47.71 Aligned_cols=45 Identities=18% Similarity=0.418 Sum_probs=39.5
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHH----------HHHhCCCCHHHHHHHHHhh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEI----------AEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~I----------a~~vgtkt~~ec~~hy~~~ 185 (561)
...||.+|+.-+.+||.++| .|++.| -..+..||.++++.||++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 56899999999999999999 899999 3344579999999999884
No 52
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=76.31 E-value=1.3 Score=47.00 Aligned_cols=46 Identities=35% Similarity=0.817 Sum_probs=37.6
Q ss_pred CcCCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccccc
Q 008553 79 KRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 132 (561)
Q Consensus 79 ~~~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~ 132 (561)
+...+.|..|..+. ..+|+|.+|++||.|..|+.... | .|.|..+.
T Consensus 166 ~~~~~~c~~c~~~~--~~~~~c~~~~d~d~~~~~~~k~~----h--~h~~~~~~ 211 (319)
T KOG1778|consen 166 KWFAYTCPICKLEV--LTAWHCEVCPDYDRCRACEEKPL----H--PHLYEAME 211 (319)
T ss_pred CceeeecCcccccc--ccccccccCCchhhhhcccCCCC----C--Ccchhccc
Confidence 56788999999988 37999999999999999999865 3 35565554
No 53
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=73.10 E-value=8 Score=39.61 Aligned_cols=58 Identities=21% Similarity=0.182 Sum_probs=40.2
Q ss_pred hhchhcccCChhHHHHHHHHHHHH--------HHHHHHH-----------HHHHHHHHhCCCchHHHHHHHHHHHhh
Q 008553 373 RYDVFMRFHSKEDHEDLLQTVISE--------HRTLKRI-----------QDLKEARAAGCRTSAEADRYLELKRGR 430 (561)
Q Consensus 373 rlk~farf~s~ed~e~l~~~l~~E--------~~Lr~RI-----------~eLqeyR~~Gi~tl~e~~~Ye~~k~~R 430 (561)
-..-|.|++||-+.|.|..-|..= ..|+.-. .-|..|+.+|++|++++..|+++.+.|
T Consensus 134 F~~e~Gr~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~n~~YI~~IL~nW~k~gvkTv~dv~~~~~~~~~~ 210 (246)
T COG3935 134 FEEEFGRMLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKLNFKYIDAILRNWKKNGVKTVEDVRAREEERRTR 210 (246)
T ss_pred HHHHcCCcCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHH
Confidence 445677788888888876554321 1222222 238899999999999999998776654
No 54
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=71.87 E-value=5.1 Score=46.41 Aligned_cols=44 Identities=20% Similarity=0.423 Sum_probs=40.5
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
...||..|-.++-+|+-.|. .++..|+..|.+||..||.+.|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 36799999999999999998 799999999999999999988764
No 55
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=70.26 E-value=11 Score=27.76 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=31.9
Q ss_pred HhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 525 FSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 525 ~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
..++.++..+....+.+....+.+..+.|.+.|||.
T Consensus 10 ~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 10 AQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 345678999999999999999999999999999984
No 56
>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=70.09 E-value=11 Score=28.10 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=35.5
Q ss_pred HHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 517 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 517 K~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
+..++.....+|.++..+.-..+.+....+.+...-|+++|||.
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 34455666678889999999999999999999999999999984
No 57
>PLN03000 amine oxidase
Probab=69.65 E-value=8.4 Score=46.23 Aligned_cols=72 Identities=18% Similarity=0.142 Sum_probs=55.5
Q ss_pred CCCccCCCCHHHHHHH--H-HhCCCchHHHHHHHHHHHHHHhCC--CCCHHHhhhhhcCCc-hhHHHHHHHHHHCCCCC
Q 008553 488 GFNETQLLSEAEKRLC--C-EIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKIEP-SKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 488 ~~pg~~LLS~~Ek~LC--~-~lrL~P~~YL~iK~~LirE~~~~g--~lkk~dA~~l~kiD~-~K~~rIydFlv~~Gwi~ 560 (561)
++| .+-||++|...- . .-++.+..||.|...+|+=...+- .+++++|...++.+- +-+..+|+||+.+|+|+
T Consensus 90 ~~p-~d~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r~G~in 167 (881)
T PLN03000 90 GFP-ADSLTEEEIEFGVVPIVGGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVTHGYIN 167 (881)
T ss_pred CCC-cccCCHHHHhccccCcccccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHHcCccc
Confidence 445 678999887651 1 124678999999999998777553 578888988877433 67889999999999985
No 58
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=69.04 E-value=4.9 Score=33.25 Aligned_cols=42 Identities=29% Similarity=0.757 Sum_probs=30.2
Q ss_pred ccccccC-CceeEEcCCCC---CcccchhhhhcccccCCCCCCCCcccccC
Q 008553 87 YCNKDIT-GKIRIKCAVCP---DFDLCIECFSVGVEVHPHKSNHPYRVMDN 133 (561)
Q Consensus 87 ~C~~~i~-~~~ri~C~~C~---dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~ 133 (561)
.|+..++ +...|+|..|. ..-+|..||..+. | .+|.|.+...
T Consensus 2 ~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~----H-~gH~~~~~~~ 47 (71)
T smart00396 2 VCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNC----H-KGHDYSLKTS 47 (71)
T ss_pred CCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCC----C-CCCCEEEEEe
Confidence 4776653 44779999995 2458999999754 7 4788887754
No 59
>PHA00442 host recBCD nuclease inhibitor
Probab=68.23 E-value=5.9 Score=31.18 Aligned_cols=27 Identities=19% Similarity=0.462 Sum_probs=22.4
Q ss_pred chhHHHHHHHHHHcCCCChHHHHHHhC
Q 008553 145 ADDEILLLEGIEMYGLGNWAEIAEHVG 171 (561)
Q Consensus 145 a~Eel~LLeaie~~G~gnW~~Ia~~vg 171 (561)
-+-+..+|++++.+|.+||+.+.+.+.
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~e 51 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAVE 51 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHHH
Confidence 355677999999999999999987653
No 60
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=67.34 E-value=3.6 Score=50.19 Aligned_cols=28 Identities=39% Similarity=0.763 Sum_probs=26.8
Q ss_pred CCCCCCchhHHHHHHHHHHcCCCChHHH
Q 008553 139 ICPDWNADDEILLLEGIEMYGLGNWAEI 166 (561)
Q Consensus 139 ~~~~Wta~Eel~LLeaie~~G~gnW~~I 166 (561)
+..+|+.+++-.||=||-.||+|+|+.|
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHh
Confidence 6789999999999999999999999998
No 61
>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=65.61 E-value=4.6 Score=38.64 Aligned_cols=44 Identities=20% Similarity=0.480 Sum_probs=36.3
Q ss_pred CCCCchhHHHHHHHHHHc---C---CCChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 141 PDWNADDEILLLEGIEMY---G---LGNWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~---G---~gnW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
..||.+|+++|-+.|..| | +--.++|++.++ ||+.-|--+|+.+
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~ 54 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY 54 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH
Confidence 579999999999998765 2 224788999885 8999999999865
No 62
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=64.85 E-value=6.4 Score=44.29 Aligned_cols=48 Identities=25% Similarity=0.569 Sum_probs=43.6
Q ss_pred cCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhhc
Q 008553 138 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVY 186 (561)
Q Consensus 138 ~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~y 186 (561)
+-...|+.+|+-.|++.-..+| --|..||..++.+|..+|..+|....
T Consensus 70 lk~~~~~~eed~~li~l~~~~~-~~wstia~~~d~rt~~~~~ery~~~~ 117 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELG-TQWSTIADYKDRRTAQQCVERYVNTL 117 (512)
T ss_pred cccccccHHHHHHHHHHHHhcC-chhhhhccccCccchHHHHHHHHHHh
Confidence 3467999999999999999999 46999999999999999999999764
No 63
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=63.00 E-value=9.6 Score=31.33 Aligned_cols=45 Identities=22% Similarity=0.469 Sum_probs=36.9
Q ss_pred CCCCchhHHHHHHHHHHcC----------------CCChHHHHHHhC-----CCCHHHHHHHHHhh
Q 008553 141 PDWNADDEILLLEGIEMYG----------------LGNWAEIAEHVG-----TKTKELCIEHYTNV 185 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G----------------~gnW~~Ia~~vg-----tkt~~ec~~hy~~~ 185 (561)
..||.+|...|++.|+.|. -.-|.+|+..+. .||..+++..|.++
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 5799999999999988762 125999999883 59999999999764
No 64
>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=62.76 E-value=9.1 Score=31.03 Aligned_cols=40 Identities=20% Similarity=0.384 Sum_probs=31.8
Q ss_pred HHHHH-hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 521 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 521 irE~~-~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
|++++ .+|..+..+.-.-|++++.-+..+.++|+++|.|.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 34545 78899999888889999999999999999999983
No 65
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=58.88 E-value=12 Score=45.86 Aligned_cols=59 Identities=24% Similarity=0.434 Sum_probs=47.2
Q ss_pred CCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCccccc
Q 008553 141 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVV 201 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yl~~~~~plp~~~~~~ 201 (561)
.+|+..+=..++.|+++||-.+-+.||..|++||++|++. |.+.|... +-.+.+....+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~-y~~~f~~~-~~~~~~~~~~~ 883 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVER-YAKVFWER-YKELNDYDRII 883 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHH-HHHHHHHh-hhhhccHHHHH
Confidence 5899999999999999999999999999999999999984 55666543 23355554443
No 66
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=58.62 E-value=12 Score=40.16 Aligned_cols=43 Identities=28% Similarity=0.499 Sum_probs=37.7
Q ss_pred CCCCchhHHHHHHHHHHcCCCChHHH-HHHhCCCCHHHHHHHHHh
Q 008553 141 PDWNADDEILLLEGIEMYGLGNWAEI-AEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~gnW~~I-a~~vgtkt~~ec~~hy~~ 184 (561)
.+|+.+|=+.+=+|++.|| .|+.-| +..|.||+..||...|+.
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHHH
Confidence 6899999999999999999 677777 558999999999987764
No 67
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=58.46 E-value=6.6 Score=30.62 Aligned_cols=30 Identities=30% Similarity=0.738 Sum_probs=18.8
Q ss_pred cccccccccCCc-------eeEEcCCCCCcccchhhhh
Q 008553 84 HCNYCNKDITGK-------IRIKCAVCPDFDLCIECFS 114 (561)
Q Consensus 84 ~Cd~C~~~i~~~-------~ri~C~~C~dfdLC~~CF~ 114 (561)
.|.+|.+.+... .+|+|..|. -.+|.+|=.
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~-~~FC~dCD~ 37 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCK-NHFCIDCDV 37 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT---B-HHHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCC-CccccCcCh
Confidence 488899887653 799999997 568888844
No 68
>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=58.39 E-value=15 Score=29.98 Aligned_cols=47 Identities=23% Similarity=0.408 Sum_probs=32.2
Q ss_pred CCCCchhHHHHHHHHHHc---C---CCC--hHHHHHHhC-CCCHHHHHHHHHhhcc
Q 008553 141 PDWNADDEILLLEGIEMY---G---LGN--WAEIAEHVG-TKTKELCIEHYTNVYM 187 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~---G---~gn--W~~Ia~~vg-tkt~~ec~~hy~~~yl 187 (561)
..+|++|+..|++.|..+ | -|| |.++++.-. ..|-.--++||.+...
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~ 58 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLR 58 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence 468999999999999433 3 367 999999877 5888888999987643
No 69
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=56.82 E-value=5.8 Score=33.54 Aligned_cols=33 Identities=27% Similarity=0.881 Sum_probs=16.6
Q ss_pred Ccccccccccc----CCceeEEcCCCCCcccchhhhhc
Q 008553 82 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSV 115 (561)
Q Consensus 82 ~~~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~ 115 (561)
...|.+|+.++ .+.+++-|.+|. |-+|-.||..
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~-fPvCr~CyEY 45 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECA-FPVCRPCYEY 45 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS------HHHHHH
T ss_pred CcccccccCccccCCCCCEEEEEcccC-CccchhHHHH
Confidence 34699999764 466999999996 9999999986
No 70
>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=55.76 E-value=12 Score=28.74 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=29.4
Q ss_pred hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 526 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 526 ~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
..|.++..+--..+.++...+.++.+-|+++|||.
T Consensus 14 ~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 14 ENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 44557778888889999999999999999999984
No 71
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=55.72 E-value=7.6 Score=28.33 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=19.2
Q ss_pred ccccccccCCceeEEcCCCCCccc-chhhhhc
Q 008553 85 CNYCNKDITGKIRIKCAVCPDFDL-CIECFSV 115 (561)
Q Consensus 85 Cd~C~~~i~~~~ri~C~~C~dfdL-C~~CF~~ 115 (561)
||+|++.|.+.+.+.=..=..|-+ |..|...
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 899999998765443332223444 4777654
No 72
>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=53.55 E-value=28 Score=26.78 Aligned_cols=50 Identities=20% Similarity=0.297 Sum_probs=37.9
Q ss_pred hCCCchHHHHHHHHHHHHHHhCCC--CCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 506 IRLAPPLYLRMQEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 506 lrL~P~~YL~iK~~LirE~~~~g~--lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
++|.|.+|..+-.+. ..+. ++..+....+.+++.-+.++.+=|+++|||.
T Consensus 1 ~glt~~q~~vL~~l~-----~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 1 LGLTPSQFRVLMALA-----RHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp TTSTHHHHHHHHHHH-----HSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CccCHHHHHHHHHHH-----HCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 356777776554333 3333 8888989999999999999999999999983
No 73
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=51.31 E-value=13 Score=45.39 Aligned_cols=33 Identities=27% Similarity=0.887 Sum_probs=27.7
Q ss_pred ccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 008553 84 HCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 84 ~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
.|.+|+.++ .+.+++-|.+|. |-+|-.||..-+
T Consensus 19 iCqICGD~vg~~~~Ge~FVAC~eC~-FPVCrpCYEYEr 55 (1079)
T PLN02638 19 VCQICGDNVGKTVDGEPFVACDVCA-FPVCRPCYEYER 55 (1079)
T ss_pred eeeecccccCcCCCCCEEEEeccCC-Cccccchhhhhh
Confidence 699999774 466999999996 999999997633
No 74
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=51.17 E-value=22 Score=31.29 Aligned_cols=33 Identities=24% Similarity=0.530 Sum_probs=24.8
Q ss_pred CCCCCCchhHHHHHHHHHHc----CCC---ChHHHHHHhC
Q 008553 139 ICPDWNADDEILLLEGIEMY----GLG---NWAEIAEHVG 171 (561)
Q Consensus 139 ~~~~Wta~Eel~LLeaie~~----G~g---nW~~Ia~~vg 171 (561)
+..-||.++|+.||+|+-.| |.. +|...-++|.
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk 42 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVK 42 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHH
Confidence 45789999999999999777 633 5666655553
No 75
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=49.98 E-value=23 Score=43.43 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=37.8
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHh------------CCCCHHHHHHHHHh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHV------------GTKTKELCIEHYTN 184 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~v------------gtkt~~ec~~hy~~ 184 (561)
...||.+|+.-||-.+..||+|+|+.|-..| .+||+.|+..+...
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~ 982 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDT 982 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHH
Confidence 3579999999999999999999999997766 37888888776654
No 76
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=49.82 E-value=8.8 Score=45.21 Aligned_cols=36 Identities=25% Similarity=0.763 Sum_probs=31.0
Q ss_pred CcCCccccccccccCCceeEEcCCCCCcccchhhhhcc
Q 008553 79 KRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 116 (561)
Q Consensus 79 ~~~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G 116 (561)
+.....|+.|.+.+.+ +.|+|..|. |-.|+.|+-.-
T Consensus 226 ~g~~~mC~~C~~tlfn-~hw~C~~C~-~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 226 KGIREMCDRCETTLFN-IHWRCPRCG-FGVCLDCYRKW 261 (889)
T ss_pred cCcchhhhhhcccccc-eeEEccccC-Ceeeecchhhc
Confidence 3456789999999987 999999997 77999999865
No 77
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=49.78 E-value=49 Score=29.09 Aligned_cols=63 Identities=16% Similarity=0.055 Sum_probs=48.4
Q ss_pred HHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 497 EAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 497 ~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
.-+..|=..++|.|..|..+..+-. -...+|.++..+....+.++...+.++.+=|+++|||.
T Consensus 12 ~~~~~l~~~~~ls~~q~~vL~~l~~-~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 12 SLKRYLKKEFNLSLEELLILYYLGK-LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHh-hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 3344555567999999987754432 11245788888999999999999999999999999984
No 78
>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=48.80 E-value=50 Score=24.40 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 147 DEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 147 Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
=+..+|..++.-|--.|.+||+.+|- |+.+|..++..
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 36789999999888889999999995 88888887654
No 79
>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=47.79 E-value=15 Score=26.52 Aligned_cols=39 Identities=28% Similarity=0.531 Sum_probs=27.4
Q ss_pred CccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccc
Q 008553 82 LYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 130 (561)
Q Consensus 82 ~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~v 130 (561)
...|..|... ...+-|..|. .-+|..|+..+ |+. |.+..
T Consensus 3 ~~~C~~H~~~---~~~~~C~~C~-~~~C~~C~~~~-----H~~-H~~~~ 41 (42)
T PF00643_consen 3 EPKCPEHPEE---PLSLFCEDCN-EPLCSECTVSG-----HKG-HKIVP 41 (42)
T ss_dssp SSB-SSTTTS---BEEEEETTTT-EEEEHHHHHTS-----TTT-SEEEE
T ss_pred CccCccCCcc---ceEEEecCCC-CccCccCCCCC-----CCC-CEEeE
Confidence 3467777753 2678999997 57999999985 654 76543
No 80
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=47.22 E-value=64 Score=28.48 Aligned_cols=61 Identities=8% Similarity=0.025 Sum_probs=47.7
Q ss_pred CCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 495 LSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 495 LS~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
++..-......++|.|..|..+..+ ..+|.++.++.-..+.++..-+.++.+=|.++|||.
T Consensus 13 ~~~~~~~~l~~~~lt~~q~~iL~~l-----~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~ 73 (118)
T TIGR02337 13 AMSFFRPILAQHGLTEQQWRILRIL-----AEQGSMEFTQLANQACILRPSLTGILARLERDGLVT 73 (118)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH-----HHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence 3444455667889999999765332 356678888888888999999999999999999984
No 81
>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=46.92 E-value=11 Score=36.31 Aligned_cols=29 Identities=31% Similarity=0.693 Sum_probs=25.4
Q ss_pred CCCCchhHHHHHHHHHHcCCCChHHHHHH
Q 008553 141 PDWNADDEILLLEGIEMYGLGNWAEIAEH 169 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~gnW~~Ia~~ 169 (561)
.-|-..-+.-||.||-.+|+|-|++|...
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd 32 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQND 32 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcC
Confidence 35888888999999999999999999764
No 82
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=46.50 E-value=11 Score=40.92 Aligned_cols=87 Identities=20% Similarity=0.254 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCCCCCCCcCCccccccccc-cCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCCCc---
Q 008553 63 SDNSDTAAPGQGAGEGKRALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPL--- 138 (561)
Q Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~Cd~C~~~-i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~--- 138 (561)
++|-+-...+.+..........|-.|... -+..-+.+|.. --+|..||..-.-...|+.+-++.+..++.|+.
T Consensus 55 ~G~d~~~~ts~Hlls~~rr~~ecpicflyyps~~n~~rcC~---~~Ic~ecf~~~~~~~~~~pt~~a~v~~~~~f~~~s~ 131 (482)
T KOG2789|consen 55 NGNDARTKTSSHLLSTSRRKTECPICFLYYPSAKNLVRCCS---ETICGECFAPFGCYSFEKPTYDATVVKNLIFKRKSA 131 (482)
T ss_pred CCcccccccccchhhhccccccCceeeeecccccchhhhhc---cchhhhheecccCCCcccCccccccccccccccccc
Confidence 34444445566666666677889999854 23335556543 449999999977778899988888877766653
Q ss_pred --------CCCCCCchhHHHHH
Q 008553 139 --------ICPDWNADDEILLL 152 (561)
Q Consensus 139 --------~~~~Wta~Eel~LL 152 (561)
+...|++.|=....
T Consensus 132 p~~~~cp~c~t~~~~vey~~i~ 153 (482)
T KOG2789|consen 132 PFYTPCPDCDTSWTRVEYIKIV 153 (482)
T ss_pred cccccCCccCCcccceeeeccc
Confidence 34678876644433
No 83
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=46.11 E-value=35 Score=40.85 Aligned_cols=69 Identities=14% Similarity=0.156 Sum_probs=53.2
Q ss_pred cCCCCHHHHHH---HHHhCCCchHHHHHHHHHHHHHHhCC--CCCHHHhhhhhcC-CchhHHHHHHHHHHCCCCC
Q 008553 492 TQLLSEAEKRL---CCEIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKI-EPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 492 ~~LLS~~Ek~L---C~~lrL~P~~YL~iK~~LirE~~~~g--~lkk~dA~~l~ki-D~~K~~rIydFlv~~Gwi~ 560 (561)
.+-||++|.+. =.-.+.-+..||.|+..+|+=...+- .+++.+|...++. ..+-++.+|+||+..|+|+
T Consensus 144 ~~~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~~g~in 218 (808)
T PLN02328 144 VDSLTEEEIEANVVSTIGGTEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLEHGYIN 218 (808)
T ss_pred CccCCHHHHhhcCcchhcccceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhccCcee
Confidence 56688887653 22234788999999999998777543 5788899888762 3468999999999999985
No 84
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=44.51 E-value=9.1 Score=35.65 Aligned_cols=53 Identities=23% Similarity=0.442 Sum_probs=40.7
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCC
Q 008553 81 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSF 136 (561)
Q Consensus 81 ~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~ 136 (561)
..|.||.|...-++..+.+=.+|-+|.+|.-||+.-. .|-+.|+-=.+...+|
T Consensus 79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LW---K~~~~ypvCPvCkTSF 131 (140)
T PF05290_consen 79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLW---KFCNLYPVCPVCKTSF 131 (140)
T ss_pred CceeccCcccccchhhcCCcccccchHHHHHHHHHHH---HHcccCCCCCcccccc
Confidence 6899999998877767888889999999999999865 3555666555544444
No 85
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=43.97 E-value=39 Score=31.92 Aligned_cols=55 Identities=20% Similarity=0.403 Sum_probs=46.3
Q ss_pred CCCCchhHHHHHHHHHHcCCC--ChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCC
Q 008553 141 PDWNADDEILLLEGIEMYGLG--NWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPD 196 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~g--nW~~Ia~~vgtkt~~ec~~hy~~~yl~~~~~plp~ 196 (561)
-+++..+-..+|.+|..||+| +|......+-.||.+|.+ .|..+|+.+-+-|.-|
T Consensus 39 lGFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~-aY~~LFm~HL~E~~~d 95 (145)
T PF06461_consen 39 LGFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIR-AYGSLFMRHLCEPGTD 95 (145)
T ss_pred eccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHH-HHHHHHHHHhcCCCcC
Confidence 478899999999999999998 799999999999998887 5788888776555443
No 86
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=43.58 E-value=30 Score=28.01 Aligned_cols=45 Identities=13% Similarity=0.092 Sum_probs=33.0
Q ss_pred HHHHHHHHHHh-CCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 516 MQEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 516 iK~~LirE~~~-~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
+|+.++.=+.. ++.++-.|.-+.+.|....++++...|.+.|.|.
T Consensus 1 ~ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 1 MKEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp -HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CcHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 35555533333 6778878888889999999999999999999874
No 87
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=42.98 E-value=5.2 Score=32.58 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCCCchHHHHHHHH
Q 008553 403 IQDLKEARAAGCRTSAEADRYLE 425 (561)
Q Consensus 403 I~eLqeyR~~Gi~tl~e~~~Ye~ 425 (561)
..-|..|+..||+|++++..|++
T Consensus 54 ~~Il~~W~~~gi~t~e~~~~~~k 76 (77)
T PF07261_consen 54 EKILNNWKQKGIKTVEDAEEYEK 76 (77)
T ss_dssp HHHHHHHHHCT--SCCCCT----
T ss_pred HHHHHHHHHcCCCCHHHHHHHhh
Confidence 35688999999999999988764
No 88
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=42.55 E-value=45 Score=28.10 Aligned_cols=41 Identities=17% Similarity=0.355 Sum_probs=29.9
Q ss_pred HHHHHHHHhCCCCCHHHhhhhhc---CCchhHHHHHHHHHHCCC
Q 008553 518 EVMSREIFSGNVNNKADAHHLFK---IEPSKIDRVYDMLVKKGL 558 (561)
Q Consensus 518 ~~LirE~~~~g~lkk~dA~~l~k---iD~~K~~rIydFlv~~Gw 558 (561)
..||....+.|.++-.+....|+ +++..+..||++|...|+
T Consensus 10 ~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 10 KKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 33676667889999998888887 899999999999999986
No 89
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=42.25 E-value=72 Score=29.12 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=44.4
Q ss_pred HHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 501 RLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 501 ~LC~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
.....++|.|.+|..+-.+. ..++.++..+.-..+.++..-+.++.+=|++.|||.
T Consensus 22 ~~l~~~glt~~q~~vL~~l~----~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 22 HRLKPLELTQTHWVTLHNIH----QLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHhcCCCHHHHHHHHHHH----HcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 45578999999998764442 134456777878888999999999999999999984
No 90
>smart00595 MADF subfamily of SANT domain.
Probab=41.75 E-value=26 Score=29.28 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=20.8
Q ss_pred ChHHHHHHhCCCCHHHHHHHHHhh
Q 008553 162 NWAEIAEHVGTKTKELCIEHYTNV 185 (561)
Q Consensus 162 nW~~Ia~~vgtkt~~ec~~hy~~~ 185 (561)
-|..||..+|. |.++|+.+|.++
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 49999999998 999999999874
No 91
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=41.43 E-value=50 Score=25.29 Aligned_cols=28 Identities=18% Similarity=0.431 Sum_probs=23.7
Q ss_pred cCChhHHHHHHHHH-----HHHHHHHHHHHHHH
Q 008553 380 FHSKEDHEDLLQTV-----ISEHRTLKRIQDLK 407 (561)
Q Consensus 380 f~s~ed~e~l~~~l-----~~E~~Lr~RI~eLq 407 (561)
+.+++++++|++.| ++|.+|++.+....
T Consensus 4 ~~~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~ 36 (46)
T PF15614_consen 4 YDDPEELDELLKALENPRGKRESKLKKELDKHR 36 (46)
T ss_pred ccCHHHHHHHHHHHcCcccHhHHHHHHHHHHHh
Confidence 56799999999999 79999988877654
No 92
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=39.98 E-value=34 Score=38.00 Aligned_cols=42 Identities=26% Similarity=0.519 Sum_probs=33.9
Q ss_pred CCCCchhHHHHHHHHHHcCCCChHHHHH-HhCCCCHHHHHHHHH
Q 008553 141 PDWNADDEILLLEGIEMYGLGNWAEIAE-HVGTKTKELCIEHYT 183 (561)
Q Consensus 141 ~~Wta~Eel~LLeaie~~G~gnW~~Ia~-~vgtkt~~ec~~hy~ 183 (561)
+.|++.|-.++-||+++|| .++++|-. ++.=||-..+++.|.
T Consensus 286 EEWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHHHHH
Confidence 6899999999999999999 78888855 444577777776664
No 93
>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=38.86 E-value=62 Score=27.27 Aligned_cols=43 Identities=26% Similarity=0.466 Sum_probs=31.7
Q ss_pred CCCchhHHHHHHHHHHc---CC----C-----ChHHHHHHhC-----CCCHHHHHHHHHh
Q 008553 142 DWNADDEILLLEGIEMY---GL----G-----NWAEIAEHVG-----TKTKELCIEHYTN 184 (561)
Q Consensus 142 ~Wta~Eel~LLeaie~~---G~----g-----nW~~Ia~~vg-----tkt~~ec~~hy~~ 184 (561)
.||.+.+..||+.+... |. + .|+.|+..+. ..|..+|+.||..
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 49999999999987322 11 1 3888888774 4789999999865
No 94
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=38.22 E-value=60 Score=26.57 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCCC
Q 008553 513 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 561 (561)
Q Consensus 513 YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~~ 561 (561)
|-..++.++ ..|..+.+-...-|+|.-++..+|.|-|.+.|+|+|
T Consensus 8 y~~a~~~V~----~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 8 YEEAVEFVI----EEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp HHHHHHHHH----HCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred HHHHHHHHH----HcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 445555544 467777777778899999999999999999999965
No 95
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=37.95 E-value=18 Score=38.51 Aligned_cols=57 Identities=21% Similarity=0.406 Sum_probs=33.6
Q ss_pred cccccccccCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCcccccCCCCCcCCCCCCchhHHHHHHH
Q 008553 84 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEG 154 (561)
Q Consensus 84 ~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~vi~~~~~p~~~~~Wta~Eel~LLea 154 (561)
.|.-|+..-. .+.-|. ..+.||+.|-...+..|.|.+-= .. +.-..|+.+| +..|+-
T Consensus 22 ~CaDCga~~P--~W~S~n--lGvfiCi~CagvHRsLGvhiS~V-----KS----itLD~wt~~~-l~~m~~ 78 (319)
T COG5347 22 KCADCGAPNP--TWASVN--LGVFLCIDCAGVHRSLGVHISKV-----KS----LTLDNWTEEE-LRRMEV 78 (319)
T ss_pred ccccCCCCCC--ceEecc--cCeEEEeecchhhhccccceeee-----ee----eecccCCHHH-HHHHHH
Confidence 4665886542 222222 36789999999988888775321 11 2235699655 554444
No 96
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=37.72 E-value=21 Score=23.86 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=9.7
Q ss_pred HHHHHHHHCCCC
Q 008553 548 RVYDMLVKKGLA 559 (561)
Q Consensus 548 rIydFlv~~Gwi 559 (561)
-|||||+++|+.
T Consensus 6 lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 6 LIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHCT-H
T ss_pred HHHHHHHHCCcH
Confidence 589999999974
No 97
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=37.60 E-value=71 Score=29.60 Aligned_cols=53 Identities=15% Similarity=0.327 Sum_probs=34.4
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCC-------------CCHHHhhhhhcCCchhHHHHHHHHHHCC
Q 008553 504 CEIRLAPPLYLRMQEVMSREIFSGNV-------------NNKADAHHLFKIEPSKIDRVYDMLVKKG 557 (561)
Q Consensus 504 ~~lrL~P~~YL~iK~~LirE~~~~g~-------------lkk~dA~~l~kiD~~K~~rIydFlv~~G 557 (561)
+.++|+|..|+.+|..|-.+++.... ++.+.|+.-+- +.+..++-|.+|..++
T Consensus 87 ~ri~mS~~EYM~lKkqLae~il~~s~~~~e~v~v~a~a~v~~eeAr~ale-eagDl~~A~k~l~~~~ 152 (153)
T COG4008 87 NRINMSPEEYMELKKQLAEYILGHSEPPVEEVEVLADAFVTPEEAREALE-EAGDLRTAMKILRMKS 152 (153)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhccCCCcHHHHHHHHHhcCCHHHHHHHHH-HcCCHHHHHHHHHHhc
Confidence 57899999999999999988774333 44445554332 3344555566665543
No 98
>PLN02436 cellulose synthase A
Probab=37.54 E-value=21 Score=43.59 Aligned_cols=34 Identities=26% Similarity=0.823 Sum_probs=28.4
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 008553 83 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 83 ~~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
..|.+|+-++ .+.+++-|.+|. |-+|..||..-.
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~-fpvCr~Cyeyer 74 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECA-FPVCRPCYEYER 74 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCC-Cccccchhhhhh
Confidence 3699999775 466999999996 999999997644
No 99
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=37.30 E-value=1.3e+02 Score=28.68 Aligned_cols=40 Identities=25% Similarity=0.498 Sum_probs=26.1
Q ss_pred cccccccccCCceeEEcCCCCCcccchhhhhcccccCCCC
Q 008553 84 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 123 (561)
Q Consensus 84 ~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk 123 (561)
.|-.|++.|.+..+.-=.+=....+|..|+.-|.++..+.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~G~~~~~~~ 41 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKFGKEIIKKP 41 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhcCCccccCC
Confidence 3999999998752221122123678999998888765543
No 100
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=37.13 E-value=22 Score=39.38 Aligned_cols=43 Identities=26% Similarity=0.422 Sum_probs=36.4
Q ss_pred CCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 140 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
.-+||..|-- +...-..|| .|.+-||+-++|||++|+...|++
T Consensus 470 ~~~wSp~e~s-~ircf~~y~-~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYK-DNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred cCCCCCcccc-cccCchhhc-cchHHHHHHhcCCCHHHHHHHhcC
Confidence 3689986654 777788999 899999999999999999987754
No 101
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=35.69 E-value=22 Score=43.25 Aligned_cols=35 Identities=26% Similarity=0.802 Sum_probs=28.3
Q ss_pred Ccccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 008553 82 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 82 ~~~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
...|..|+.++ .+.+++-|.+|. |-+|-.||....
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~-fpvCr~cyeye~ 53 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCG-FPVCKPCYEYER 53 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCC-Cccccchhhhhh
Confidence 34599999764 466999999996 999999996533
No 102
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.55 E-value=1e+02 Score=23.25 Aligned_cols=53 Identities=19% Similarity=0.209 Sum_probs=35.4
Q ss_pred CCCchHHHHHHHHHHHHHHhCC-CCCHHHhhhhhcCCchhHHHHHHHHHHCCCC
Q 008553 507 RLAPPLYLRMQEVMSREIFSGN-VNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 559 (561)
Q Consensus 507 rL~P~~YL~iK~~LirE~~~~g-~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 559 (561)
+|.|...+.+-.+.-.-.-.++ ..+.+..-..+.+-.+.+.+..+-|++.|||
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 4555555555443322222333 2466777777889999999999999999997
No 103
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.40 E-value=81 Score=28.91 Aligned_cols=52 Identities=12% Similarity=0.252 Sum_probs=43.2
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 504 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 504 ~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
..++|.|.+|..+..+ ...|.++.++.-..+.+|..-+.++.+=|+++|||.
T Consensus 34 ~~~glt~~q~~vL~~l-----~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 34 SPLDITAAQFKVLCSI-----RCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred cccCCCHHHHHHHHHH-----HHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5678999999877643 235668888888889999999999999999999984
No 104
>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=35.11 E-value=52 Score=24.03 Aligned_cols=25 Identities=28% Similarity=0.502 Sum_probs=20.9
Q ss_pred hHHHHHHHHHHcCCCChHHHHHHhCC
Q 008553 147 DEILLLEGIEMYGLGNWAEIAEHVGT 172 (561)
Q Consensus 147 Eel~LLeaie~~G~gnW~~Ia~~vgt 172 (561)
|-..+.++++.+| ||....|+.+|-
T Consensus 6 E~~~i~~aL~~~~-gn~~~aA~~Lgi 30 (42)
T PF02954_consen 6 EKQLIRQALERCG-GNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHTT-T-HHHHHHHHTS
T ss_pred HHHHHHHHHHHhC-CCHHHHHHHHCC
Confidence 5567888999999 999999999983
No 105
>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=35.03 E-value=75 Score=24.78 Aligned_cols=34 Identities=26% Similarity=0.359 Sum_probs=28.3
Q ss_pred hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCC
Q 008553 526 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 559 (561)
Q Consensus 526 ~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 559 (561)
.++..+.++....+.++..-+.++.+=|++.|||
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 4778888999999999999999999999999998
No 106
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=34.16 E-value=51 Score=36.56 Aligned_cols=48 Identities=15% Similarity=0.400 Sum_probs=41.9
Q ss_pred CCcCCCCCCchhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHh
Q 008553 136 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 136 ~p~~~~~Wta~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
+.-+...||++|-.+|-.+.+.|| .+...|-..+.-|+-...+..|..
T Consensus 183 r~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 183 RTEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred cCCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHH
Confidence 344568999999888999999999 899999999999999999887754
No 107
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=33.35 E-value=31 Score=27.95 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=15.8
Q ss_pred HHHHHHHHhCCCchHHHH
Q 008553 404 QDLKEARAAGCRTSAEAD 421 (561)
Q Consensus 404 ~eLqeyR~~Gi~tl~e~~ 421 (561)
.-|..|+..||+|+++++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 458899999999999875
No 108
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.12 E-value=66 Score=24.03 Aligned_cols=46 Identities=13% Similarity=0.250 Sum_probs=33.2
Q ss_pred HHHHHHHHHHH-hCCCC-CHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 515 RMQEVMSREIF-SGNVN-NKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 515 ~iK~~LirE~~-~~g~l-kk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
.++..++...+ .+..+ +..+.-..+.+..+-+++.+.-|.+.|||.
T Consensus 4 ~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34444444433 23445 677778888999999999999999999983
No 109
>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=33.05 E-value=1.1e+02 Score=23.37 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=29.7
Q ss_pred hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 526 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 526 ~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
.++ ++..+....+.+....+.++.+-|++.|||.
T Consensus 18 ~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 18 EGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred HCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 444 8888888888999999999999999999984
No 110
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=32.60 E-value=1.3e+02 Score=24.07 Aligned_cols=44 Identities=14% Similarity=0.272 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCC
Q 008553 512 LYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 559 (561)
Q Consensus 512 ~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 559 (561)
.=|.+|..+|...+..|.|+.++|-.+. +.+..-+++..++|++
T Consensus 15 qm~e~kK~~idk~Ve~G~iTqeqAd~ik----~~id~~~~~~~qnGf~ 58 (59)
T PF10925_consen 15 QMLELKKQIIDKYVEAGVITQEQADAIK----KHIDQRQEYMQQNGFV 58 (59)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHH----HHHHHHHHHHHHcCCC
Confidence 3478899999999999999999998763 5667888999999986
No 111
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=32.05 E-value=37 Score=32.98 Aligned_cols=44 Identities=16% Similarity=0.263 Sum_probs=32.5
Q ss_pred CCCCCchhHHHHHHHHHHcCC------CChHHHHHHhCCCCHHHHHHHHHh
Q 008553 140 CPDWNADDEILLLEGIEMYGL------GNWAEIAEHVGTKTKELCIEHYTN 184 (561)
Q Consensus 140 ~~~Wta~Eel~LLeaie~~G~------gnW~~Ia~~vgtkt~~ec~~hy~~ 184 (561)
...||.+++++|-+.+-.|+- .-.+.++..+ .||+..|..+|+.
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs 54 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNS 54 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHH
Confidence 357999999999887776652 1245555665 4899999999953
No 112
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=31.65 E-value=1.2e+02 Score=28.14 Aligned_cols=50 Identities=20% Similarity=0.501 Sum_probs=38.3
Q ss_pred hHHHHHHHHHHHHHHhC----C--CCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 511 PLYLRMQEVMSREIFSG----N--VNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 511 ~~YL~iK~~LirE~~~~----g--~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
.-|.-|.+.+...+++| | .++..+.-..+.+.+|-+.|.|.-|.+.|+|.
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~ 66 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVE 66 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 45888888887777643 3 35555555567899999999999999999974
No 113
>PLN02400 cellulose synthase
Probab=31.45 E-value=28 Score=42.52 Aligned_cols=34 Identities=29% Similarity=0.889 Sum_probs=28.1
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 008553 83 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 83 ~~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
-.|.+|+.++ .+.+++-|.+|. |-.|-.||..-.
T Consensus 37 qiCqICGD~VG~t~dGe~FVAC~eCa-FPVCRpCYEYER 74 (1085)
T PLN02400 37 QICQICGDDVGVTETGDVFVACNECA-FPVCRPCYEYER 74 (1085)
T ss_pred ceeeecccccCcCCCCCEEEEEccCC-Cccccchhheec
Confidence 3699999774 466999999996 999999997633
No 114
>PLN02189 cellulose synthase
Probab=31.38 E-value=30 Score=42.16 Aligned_cols=34 Identities=26% Similarity=0.836 Sum_probs=28.3
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 008553 83 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 83 ~~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
..|..|+.++ .+.+++-|.+|. |-+|-.||..-.
T Consensus 35 ~~C~iCgd~vg~~~~g~~fvaC~~C~-fpvCr~Cyeyer 72 (1040)
T PLN02189 35 QVCEICGDEIGLTVDGDLFVACNECG-FPVCRPCYEYER 72 (1040)
T ss_pred ccccccccccCcCCCCCEEEeeccCC-Cccccchhhhhh
Confidence 4699999774 466999999996 999999997644
No 115
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=30.10 E-value=85 Score=25.91 Aligned_cols=52 Identities=25% Similarity=0.383 Sum_probs=38.2
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 504 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 504 ~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
...+|.+..+..+.-+. .+|.++.++....+.+....+.++++=|++.|||.
T Consensus 4 ~~~~l~~~~~~il~~l~-----~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 4 KPLGLTPTQFLVLRILY-----EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred cccCCCHHHHHHHHHHH-----HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 34556666555554433 34567777777788899999999999999999984
No 116
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=29.75 E-value=60 Score=23.81 Aligned_cols=34 Identities=15% Similarity=0.538 Sum_probs=28.8
Q ss_pred HHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHH
Q 008553 517 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYD 551 (561)
Q Consensus 517 K~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIyd 551 (561)
|+.||...+..|+.+..| ++|..+...-..+.|.
T Consensus 3 K~~lI~~Li~~Giyk~~d-rqL~Eltl~ELe~ey~ 36 (38)
T PF13076_consen 3 KDFLIEKLIQSGIYKKED-RQLYELTLSELEKEYE 36 (38)
T ss_pred HHHHHHHHHHcCCcCccc-hHHHHcCHHHHHHHHH
Confidence 677888888999999998 9898888888777774
No 117
>PRK08359 transcription factor; Validated
Probab=29.60 E-value=41 Score=32.82 Aligned_cols=40 Identities=18% Similarity=0.380 Sum_probs=26.3
Q ss_pred ccccccccccCCceeEEcCCCCCcccchhhh-hccc-ccCCC
Q 008553 83 YHCNYCNKDITGKIRIKCAVCPDFDLCIECF-SVGV-EVHPH 122 (561)
Q Consensus 83 ~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF-~~G~-e~~~H 122 (561)
..|-.|+++|.+..+.-=.+=...++|..|+ --|. +++.+
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k~G~~~~~~~ 48 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGAELLVCDRCYEKYGRKKPGTF 48 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCeEEehHHHHHHHhCCCccCCc
Confidence 4599999999875222112222367899999 7788 56554
No 118
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=28.86 E-value=1.5e+02 Score=24.24 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCCC
Q 008553 513 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 561 (561)
Q Consensus 513 YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~~ 561 (561)
|-..++.++ ..+..+.+-...-|+|--|+..+|.|-|.+.|+|.|
T Consensus 7 y~~a~~~V~----~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 7 YDEAVELVI----ETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred HHHHHHHHH----HhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 444444443 345566666677799999999999999999999975
No 119
>PLN03158 methionine aminopeptidase; Provisional
Probab=28.73 E-value=14 Score=40.55 Aligned_cols=41 Identities=29% Similarity=0.783 Sum_probs=29.3
Q ss_pred CCccccccccccCCceeEEcCCCCCcc-------cc-hhhhhcccccCCCCCCCC
Q 008553 81 ALYHCNYCNKDITGKIRIKCAVCPDFD-------LC-IECFSVGVEVHPHKSNHP 127 (561)
Q Consensus 81 ~~~~Cd~C~~~i~~~~ri~C~~C~dfd-------LC-~~CF~~G~e~~~Hk~~H~ 127 (561)
....|.+|++.-+ .+|..|-... .| ..||.... ..|+.-|.
T Consensus 8 ~~~~c~~c~~~a~----l~Cp~C~k~~~~~~~s~fCsq~CFk~~w--~~Hk~~h~ 56 (396)
T PLN03158 8 SPLACARCSKPAH----LQCPKCLELKLPREGASFCSQDCFKAAW--SSHKSVHT 56 (396)
T ss_pred CcccccCCCCccc----ccCccchhcCCCCCCceeECHHHHHHHH--HHHHHHHH
Confidence 4455889998643 7898885432 46 78999876 56887783
No 120
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=28.53 E-value=1.1e+02 Score=23.62 Aligned_cols=39 Identities=15% Similarity=0.249 Sum_probs=32.2
Q ss_pred HHHHH-hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCC
Q 008553 521 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 559 (561)
Q Consensus 521 irE~~-~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 559 (561)
|++++ .+|.++..+++.++.+--.-+-.|.+||-..||.
T Consensus 1 i~~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T 40 (50)
T PF09107_consen 1 IRELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREGIT 40 (50)
T ss_dssp HHHHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred ChHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCE
Confidence 34555 6899999999999998888888999999999984
No 121
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=27.96 E-value=51 Score=24.88 Aligned_cols=24 Identities=33% Similarity=0.665 Sum_probs=18.5
Q ss_pred CCcccccccccc--CCceeEEcCCCC
Q 008553 81 ALYHCNYCNKDI--TGKIRIKCAVCP 104 (561)
Q Consensus 81 ~~~~Cd~C~~~i--~~~~ri~C~~C~ 104 (561)
....|++|++.| ....-++|..|.
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~ 35 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCG 35 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT
T ss_pred CCCCCcccCcccCCCCCCeEEECCCC
Confidence 456899999999 445889999996
No 122
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=27.57 E-value=63 Score=28.99 Aligned_cols=23 Identities=17% Similarity=0.534 Sum_probs=20.5
Q ss_pred HHhCCCchHHHHHHHHHHHHHHh
Q 008553 504 CEIRLAPPLYLRMQEVMSREIFS 526 (561)
Q Consensus 504 ~~lrL~P~~YL~iK~~LirE~~~ 526 (561)
.+++|.|..|+.+|..|..|+++
T Consensus 86 ~~igls~~EYm~lKkelae~i~~ 108 (109)
T TIGR03277 86 QRIGMSPEEYMELKKKLAEELLK 108 (109)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhc
Confidence 46899999999999999998875
No 123
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=27.55 E-value=53 Score=28.46 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=24.7
Q ss_pred CCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCC
Q 008553 527 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 559 (561)
Q Consensus 527 ~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi 559 (561)
.|+-...-|.+| .++.++++.+.+||+..|+|
T Consensus 64 ~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 64 EGVHVDEIAQQL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TTEEHHHHHHHS-TS-HHHHHHHHHHHHHTTSE
T ss_pred CcccHHHHHHHh-CcCHHHHHHHHHHHHhCCeE
Confidence 354444555555 99999999999999999997
No 124
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=27.00 E-value=12 Score=38.98 Aligned_cols=28 Identities=29% Similarity=0.721 Sum_probs=20.1
Q ss_pred CCCCcCCccccccccccCCceeEEcCCCC
Q 008553 76 GEGKRALYHCNYCNKDITGKIRIKCAVCP 104 (561)
Q Consensus 76 ~~~~~~~~~Cd~C~~~i~~~~ri~C~~C~ 104 (561)
++......+|+.|..+-.. +|++|+.|.
T Consensus 205 ~~~GlRYL~CslC~teW~~-VR~KC~nC~ 232 (308)
T COG3058 205 TEQGLRYLHCSLCETEWHY-VRVKCSNCE 232 (308)
T ss_pred ccccchhhhhhhHHHHHHH-HHHHhcccc
Confidence 3334456688888888775 888888885
No 125
>PLN02195 cellulose synthase A
Probab=26.86 E-value=38 Score=41.06 Aligned_cols=34 Identities=24% Similarity=0.816 Sum_probs=27.7
Q ss_pred cccccccccc----CCceeEEcCCCCCcccchhhhhccc
Q 008553 83 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 117 (561)
Q Consensus 83 ~~Cd~C~~~i----~~~~ri~C~~C~dfdLC~~CF~~G~ 117 (561)
..|..|+.++ .+.+++-|.+|. |-+|-.||...+
T Consensus 7 ~~c~~cgd~~~~~~~g~~fvaC~eC~-~pvCrpCyeyer 44 (977)
T PLN02195 7 PICATCGEEVGVDSNGEAFVACHECS-YPLCKACLEYEI 44 (977)
T ss_pred ccceecccccCcCCCCCeEEEeccCC-Cccccchhhhhh
Confidence 4699999754 466999999996 999999997643
No 126
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=26.35 E-value=63 Score=25.68 Aligned_cols=35 Identities=20% Similarity=0.240 Sum_probs=31.0
Q ss_pred hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 526 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 526 ~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
..|..+..+.-..+.++.+.+.++.+-|.+.|||.
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 67778878888888999999999999999999984
No 127
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=26.08 E-value=40 Score=35.91 Aligned_cols=32 Identities=22% Similarity=0.702 Sum_probs=24.7
Q ss_pred CCccccccccccCCceeEEcCCCCCcccchhhh
Q 008553 81 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECF 113 (561)
Q Consensus 81 ~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF 113 (561)
...+|.+|+.......+|+|..|.. -+|+.|=
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~-~FCldCD 360 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKN-VFCLDCD 360 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccc-eeeccch
Confidence 4456999977766669999999974 4788874
No 128
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=26.03 E-value=1.5e+02 Score=24.45 Aligned_cols=40 Identities=13% Similarity=0.108 Sum_probs=33.0
Q ss_pred HHHHH-hC-CCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 521 SREIF-SG-NVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 521 irE~~-~~-g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
|-+.+ .. +.++..+.-..+.+...-+.++.+.|++.|||.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 44444 33 678888888888999999999999999999984
No 129
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=25.97 E-value=29 Score=28.90 Aligned_cols=31 Identities=23% Similarity=0.796 Sum_probs=12.9
Q ss_pred cccccccccCCc-eeEEcCCCC-Ccc---cchhhhh
Q 008553 84 HCNYCNKDITGK-IRIKCAVCP-DFD---LCIECFS 114 (561)
Q Consensus 84 ~Cd~C~~~i~~~-~ri~C~~C~-dfd---LC~~CF~ 114 (561)
.|-.|...+... ..|+|..|. +|. +|++|-.
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~ 38 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQ 38 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-S
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCccc
Confidence 456666555321 356666664 232 4555543
No 130
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=25.18 E-value=1.5e+02 Score=25.57 Aligned_cols=49 Identities=10% Similarity=0.207 Sum_probs=36.7
Q ss_pred HhhchhcccCChhHHHHHHHHHHHHHH---HHHHHHHHHHHHHhCCCchHHHH
Q 008553 372 RRYDVFMRFHSKEDHEDLLQTVISEHR---TLKRIQDLKEARAAGCRTSAEAD 421 (561)
Q Consensus 372 ~rlk~farf~s~ed~e~l~~~l~~E~~---Lr~RI~eLqeyR~~Gi~tl~e~~ 421 (561)
..+..|..+.++++...|++.|....+ |-.| .+..+|...|++.-+=++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~t~~e~~~Ls~R-~~I~~ll~~G~S~~eIA~ 58 (88)
T TIGR02531 7 ELFDAILTLKNREECYRFFDDIATINEIQSLAQR-LQVAKMLKQGKTYSDIEA 58 (88)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhCCHHHHHhhhHH-HHHHHHHHCCCCHHHHHH
Confidence 356678899999999999999985544 4456 778888889986544333
No 131
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=24.57 E-value=44 Score=35.86 Aligned_cols=26 Identities=19% Similarity=0.653 Sum_probs=21.7
Q ss_pred cCCccccccccccCCceeEEcCCCCCc
Q 008553 80 RALYHCNYCNKDITGKIRIKCAVCPDF 106 (561)
Q Consensus 80 ~~~~~Cd~C~~~i~~~~ri~C~~C~df 106 (561)
...|.|..|+-.... .+|+|..|..+
T Consensus 352 ~~~YRC~~CGF~a~~-l~W~CPsC~~W 377 (389)
T COG2956 352 KPRYRCQNCGFTAHT-LYWHCPSCRAW 377 (389)
T ss_pred cCCceecccCCccee-eeeeCCCcccc
Confidence 478999999988764 89999999755
No 132
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.41 E-value=57 Score=34.18 Aligned_cols=42 Identities=19% Similarity=0.587 Sum_probs=33.2
Q ss_pred CCCCCCcCCccccccccccCCceeEEcCCCCCcccchhhhhc
Q 008553 74 GAGEGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSV 115 (561)
Q Consensus 74 ~~~~~~~~~~~Cd~C~~~i~~~~ri~C~~C~dfdLC~~CF~~ 115 (561)
+++.+.....+|..|..-+..+.+++|..-+--.+|-.|--.
T Consensus 260 ~s~~A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 260 DSGAAPSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred ccccCCCCceeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 445556778999999999998899999887777778777544
No 133
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.20 E-value=47 Score=40.40 Aligned_cols=44 Identities=20% Similarity=0.310 Sum_probs=29.2
Q ss_pred HHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHH
Q 008553 498 AEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDML 553 (561)
Q Consensus 498 ~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFl 553 (561)
-=+.||...++.. |+.-.=.||.. +...+|.-|.+|...|-|||
T Consensus 1078 ~s~~la~~Y~v~~--Y~kQRi~~l~~----------~I~slF~~~~~kq~~l~dF~ 1121 (1121)
T PRK04023 1078 VSKKLAEEYGVSD--YTKQRLELLER----------GIKSLFENDKSKQSGLSDFF 1121 (1121)
T ss_pred HHHHHHHHcCChH--HHHHHHHHHHH----------HHHHhhccccccccchhhhC
Confidence 3467888887765 66555444433 34457777888888888875
No 134
>PRK10870 transcriptional repressor MprA; Provisional
Probab=23.34 E-value=1.9e+02 Score=27.69 Aligned_cols=58 Identities=10% Similarity=0.160 Sum_probs=45.7
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 500 KRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 500 k~LC~~lrL~P~~YL~iK~~LirE~~~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
...-..++|.|..|..+..+- ...++.++..+.-..+.++..-+.++.+=|+++|||.
T Consensus 45 ~~~l~~~gLt~~q~~iL~~L~---~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 45 NKMLKAQGINETLFMALITLE---SQENHSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred HHHHHHCCCCHHHHHHHHHHh---cCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 445578999999998875543 1234567777777788899999999999999999984
No 135
>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=22.94 E-value=1.6e+02 Score=24.76 Aligned_cols=37 Identities=22% Similarity=0.389 Sum_probs=25.3
Q ss_pred HHHHHHHHHcCC-------CChHHHHHHhCCCC-----HHHHHHHHHhh
Q 008553 149 ILLLEGIEMYGL-------GNWAEIAEHVGTKT-----KELCIEHYTNV 185 (561)
Q Consensus 149 l~LLeaie~~G~-------gnW~~Ia~~vgtkt-----~~ec~~hy~~~ 185 (561)
..|-.+|...|- +.|..||+.+|-.+ ..+.+.+|.++
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~ 87 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKY 87 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHH
Confidence 456667776661 36999999998422 35677888765
No 136
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.82 E-value=55 Score=29.72 Aligned_cols=30 Identities=30% Similarity=0.685 Sum_probs=22.1
Q ss_pred ccccccccccCC-----------ceeEEcCCCCCcccchhhh
Q 008553 83 YHCNYCNKDITG-----------KIRIKCAVCPDFDLCIECF 113 (561)
Q Consensus 83 ~~Cd~C~~~i~~-----------~~ri~C~~C~dfdLC~~CF 113 (561)
..|.+|+..+.. ..||+|..|. -+.|.+|=
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~-~~FC~dCD 96 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCK-NVFCVDCD 96 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCC-Cccccccc
Confidence 359999886542 3689999996 66788773
No 137
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=22.53 E-value=67 Score=23.21 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=16.3
Q ss_pred CCcccccccccc---------CCceeEEcCCC
Q 008553 81 ALYHCNYCNKDI---------TGKIRIKCAVC 103 (561)
Q Consensus 81 ~~~~Cd~C~~~i---------~~~~ri~C~~C 103 (561)
+.++|-.|+.+- .+..||+|..|
T Consensus 4 i~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred EeeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 567888887543 34578888877
No 138
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=22.44 E-value=2.2e+02 Score=22.92 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=33.9
Q ss_pred HHHHHHHHHhCCC--CCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 517 QEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 517 K~~LirE~~~~g~--lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
++.++.=....|. ++..+.-..+.|+...++++..=|.+.|+|.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444433344455 8888888888999999999999999999983
No 139
>PF10123 Mu-like_Pro: Mu-like prophage I protein; InterPro: IPR012106 This entry is represented by the Bacteriophage Mu, Gp32. The characteristics of the protein distribution suggest prophage matches.
Probab=22.21 E-value=58 Score=34.52 Aligned_cols=26 Identities=15% Similarity=0.464 Sum_probs=22.7
Q ss_pred CccCCCCHHHHHHHHHhCCCchHHHH
Q 008553 490 NETQLLSEAEKRLCCEIRLAPPLYLR 515 (561)
Q Consensus 490 pg~~LLS~~Ek~LC~~lrL~P~~YL~ 515 (561)
.+..-||.+|+..|.+|+|.|.-|++
T Consensus 301 ~~~~~Lt~ee~av~~~lGis~edf~K 326 (326)
T PF10123_consen 301 DGSAALTAEELAVCRQLGISPEDFAK 326 (326)
T ss_pred CCCCCCCHHHHHHHHHcCCCHHHhcC
Confidence 34567999999999999999999973
No 140
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.13 E-value=4.1e+02 Score=22.38 Aligned_cols=61 Identities=15% Similarity=0.100 Sum_probs=45.9
Q ss_pred HhhccCCCC---CCCCCCChHHHHHHHhhchhcc--cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008553 349 LERNLLYPN---PFEKDLSPEERELCRRYDVFMR--FHSKEDHEDLLQTVISEHRTLKRIQDLKEA 409 (561)
Q Consensus 349 ~er~Ll~~~---~~~k~~skeErel~~rlk~far--f~s~ed~e~l~~~l~~E~~Lr~RI~eLqey 409 (561)
.+.||+.+. ...+.++.++-.....++.+.+ -++-.+...++..+-+-..|+.+|.+|++.
T Consensus 22 e~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~~l~~l~~~ 87 (91)
T cd04766 22 ERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRAR 87 (91)
T ss_pred HHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457899752 2345678888777777777766 678888888888888888888888888743
No 141
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=21.82 E-value=26 Score=38.53 Aligned_cols=46 Identities=22% Similarity=0.494 Sum_probs=31.6
Q ss_pred CCcCCccccccccc--------------cCCceeEEcCCCCCcccchhhhhcccccCCCCCCCCccc
Q 008553 78 GKRALYHCNYCNKD--------------ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 130 (561)
Q Consensus 78 ~~~~~~~Cd~C~~~--------------i~~~~ri~C~~C~dfdLC~~CF~~G~e~~~Hk~~H~Y~v 130 (561)
.....|.|.-|... |.. +-|+|.+|....-|..-.+ .|+.||.=+.
T Consensus 263 n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~-vEYrCPEC~KVFsCPANLA------SHRRWHKPR~ 322 (500)
T KOG3993|consen 263 NVIGDYICQLCKEKYEDAFALAQHRCPRIVH-VEYRCPECDKVFSCPANLA------SHRRWHKPRP 322 (500)
T ss_pred ccHHHHHHHHHHHhhhhHHHHhhccCCeeEE-eeecCCcccccccCchhhh------hhhcccCCch
Confidence 35678999999742 222 5578888887766665444 5999997654
No 142
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=21.51 E-value=3.1e+02 Score=20.71 Aligned_cols=40 Identities=20% Similarity=0.187 Sum_probs=24.3
Q ss_pred ChhHHHHHHHHHH----------HHHHHHHHHHHHHHHHHhCCCchHHHHHH
Q 008553 382 SKEDHEDLLQTVI----------SEHRTLKRIQDLKEARAAGCRTSAEADRY 423 (561)
Q Consensus 382 s~ed~e~l~~~l~----------~E~~Lr~RI~eLqeyR~~Gi~tl~e~~~Y 423 (561)
|..+|+.|.+-|. +...|..||..+ .++.|+.++++--.+
T Consensus 1 sd~~f~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~r--m~~~~~~~~~~y~~~ 50 (57)
T PF03705_consen 1 SDAEFERFRELIYRRTGIDLSEYKRSLLERRLARR--MRALGLPSFAEYYEL 50 (57)
T ss_dssp -HHHHHHHHHHHHHHH-----GGGHHHHHHHHHHH--HHHHT---HHHHHHH
T ss_pred CHHHHHHHHHHHHHHHCCCCchhhHHHHHHHHHHH--HHHcCCCCHHHHHHH
Confidence 3456666666554 456788888855 478999999876444
No 143
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=21.07 E-value=1.8e+02 Score=21.45 Aligned_cols=34 Identities=12% Similarity=0.158 Sum_probs=26.6
Q ss_pred CCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 527 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 527 ~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
++..+..+....+.+....+.++.+-|.+.|||.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 5666777777777788888888888888888874
No 144
>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=20.78 E-value=1.3e+02 Score=22.75 Aligned_cols=42 Identities=19% Similarity=0.291 Sum_probs=32.5
Q ss_pred HHHHHHH--hCCCCCHHHhhhhhcCCchhHHHHHHHHHHCCCCC
Q 008553 519 VMSREIF--SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 560 (561)
Q Consensus 519 ~LirE~~--~~g~lkk~dA~~l~kiD~~K~~rIydFlv~~Gwi~ 560 (561)
+-|-|++ .++.++..+.-.-+.+....+.++..-|++.||+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 3344555 34457888888888999999999999999999984
No 145
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=20.49 E-value=2.1e+02 Score=26.68 Aligned_cols=42 Identities=14% Similarity=0.122 Sum_probs=36.1
Q ss_pred hhHHHHHHHHHHcCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 008553 146 DDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 188 (561)
Q Consensus 146 ~Eel~LLeaie~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yl~ 188 (561)
+-+..+|++++.-|--.|.+||+.+|. |+..|..++.++-=+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHHHHC
Confidence 568899999999998899999999985 888999999876433
No 146
>PRK00420 hypothetical protein; Validated
Probab=20.41 E-value=62 Score=29.33 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=20.9
Q ss_pred CccccccccccCC--ceeEEcCCCCCcccch
Q 008553 82 LYHCNYCNKDITG--KIRIKCAVCPDFDLCI 110 (561)
Q Consensus 82 ~~~Cd~C~~~i~~--~~ri~C~~C~dfdLC~ 110 (561)
..+|..|+.++.. ...+.|..|.....|.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCeeeec
Confidence 3689999998763 4677788877655554
No 147
>PF07875 Coat_F: Coat F domain; InterPro: IPR012851 The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination []. Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus [].
Probab=20.34 E-value=82 Score=25.06 Aligned_cols=25 Identities=12% Similarity=0.278 Sum_probs=18.9
Q ss_pred hhhcCCchhHHHHHHHHHHCCCCCC
Q 008553 537 HLFKIEPSKIDRVYDMLVKKGLAPP 561 (561)
Q Consensus 537 ~l~kiD~~K~~rIydFlv~~Gwi~~ 561 (561)
.++.-...-...||+++.++||-++
T Consensus 38 ~~~~~~~~~~~~l~~~m~~kGwY~~ 62 (64)
T PF07875_consen 38 QILNECQQMQYELFNYMNQKGWYQP 62 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcCC
Confidence 3444455667799999999999764
No 148
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.25 E-value=66 Score=35.72 Aligned_cols=27 Identities=19% Similarity=0.597 Sum_probs=21.9
Q ss_pred cCCccccccccccCCceeEEcCCCCCcc
Q 008553 80 RALYHCNYCNKDITGKIRIKCAVCPDFD 107 (561)
Q Consensus 80 ~~~~~Cd~C~~~i~~~~ri~C~~C~dfd 107 (561)
...|.|..|+..-.. .+++|..|..++
T Consensus 5 ~~~y~C~~Cg~~~~~-~~g~Cp~C~~w~ 31 (446)
T PRK11823 5 KTAYVCQECGAESPK-WLGRCPECGAWN 31 (446)
T ss_pred CCeEECCcCCCCCcc-cCeeCcCCCCcc
Confidence 457899999988665 889999998664
No 149
>PF12488 DUF3704: Protein of unknown function (DUF3704) ; InterPro: IPR022173 This domain family is found in eukaryotes, and is approximately 30 amino acids in length.
Probab=20.13 E-value=37 Score=23.12 Aligned_cols=9 Identities=22% Similarity=0.342 Sum_probs=7.3
Q ss_pred cccccCCCC
Q 008553 288 LSGYNSKRQ 296 (561)
Q Consensus 288 ~~GYmP~R~ 296 (561)
-.||||.|+
T Consensus 7 S~gyMp~s~ 15 (27)
T PF12488_consen 7 SFGYMPRSG 15 (27)
T ss_pred ccceeeecc
Confidence 479999885
Done!