Query 009958
Match_columns 521
No_of_seqs 217 out of 947
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 19:21:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009958hhsearch_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 6E-104 1E-108 810.6 32.5 420 45-520 13-437 (438)
2 COG5114 Histone acetyltransfer 100.0 2.5E-96 5E-101 723.8 27.9 420 44-520 3-429 (432)
3 COG5259 RSC8 RSC chromatin rem 99.7 4.1E-17 9E-22 169.9 6.2 111 41-155 219-329 (531)
4 cd02335 ZZ_ADA2 Zinc finger, Z 99.5 4.2E-14 9.2E-19 107.0 4.2 49 47-95 1-49 (49)
5 PF04433 SWIRM: SWIRM domain; 99.4 1.6E-13 3.6E-18 115.6 6.6 78 443-520 3-85 (86)
6 KOG1279 Chromatin remodeling f 99.3 1.3E-12 2.7E-17 141.1 7.1 81 69-155 223-303 (506)
7 cd02343 ZZ_EF Zinc finger, ZZ 99.3 2.7E-12 5.9E-17 95.9 3.5 46 47-93 1-46 (48)
8 cd02338 ZZ_PCMF_like Zinc fing 99.2 4.9E-12 1.1E-16 95.7 3.7 48 47-95 1-49 (49)
9 cd02334 ZZ_dystrophin Zinc fin 99.2 6.4E-12 1.4E-16 94.9 3.7 46 47-93 1-47 (49)
10 cd02345 ZZ_dah Zinc finger, ZZ 99.2 9E-12 1.9E-16 94.3 3.4 46 48-94 2-48 (49)
11 PF00249 Myb_DNA-binding: Myb- 99.1 6.9E-11 1.5E-15 88.8 5.0 45 105-149 2-47 (48)
12 cd02249 ZZ Zinc finger, ZZ typ 99.1 7.8E-11 1.7E-15 88.0 3.9 46 47-95 1-46 (46)
13 cd02340 ZZ_NBR1_like Zinc fing 99.0 3.9E-10 8.4E-15 83.0 3.6 43 47-95 1-43 (43)
14 cd02341 ZZ_ZZZ3 Zinc finger, Z 99.0 4.3E-10 9.3E-15 84.6 3.6 45 47-95 1-48 (48)
15 cd02336 ZZ_RSC8 Zinc finger, Z 99.0 4.5E-10 9.7E-15 83.3 3.4 42 47-89 1-42 (45)
16 cd02344 ZZ_HERC2 Zinc finger, 98.8 2.3E-09 5E-14 79.5 3.6 44 47-95 1-45 (45)
17 smart00291 ZnF_ZZ Zinc-binding 98.8 2.5E-09 5.5E-14 79.1 3.6 41 45-86 3-43 (44)
18 cd02339 ZZ_Mind_bomb Zinc fing 98.8 2.8E-09 6.1E-14 79.2 3.5 43 47-94 1-44 (45)
19 PF00569 ZZ: Zinc finger, ZZ t 98.7 4.2E-09 9E-14 78.7 2.2 42 45-87 3-45 (46)
20 smart00717 SANT SANT SWI3, AD 98.7 2.8E-08 6.1E-13 73.0 5.8 46 105-150 2-47 (49)
21 cd00167 SANT 'SWI3, ADA2, N-Co 98.7 4.1E-08 8.8E-13 71.0 5.5 44 106-149 1-44 (45)
22 TIGR01557 myb_SHAQKYF myb-like 98.6 6.6E-08 1.4E-12 75.5 5.6 49 104-152 3-56 (57)
23 PF13921 Myb_DNA-bind_6: Myb-l 98.6 9.1E-08 2E-12 74.9 6.0 41 107-148 1-41 (60)
24 cd02337 ZZ_CBP Zinc finger, ZZ 98.4 9.9E-08 2.2E-12 69.5 2.2 33 47-81 1-33 (41)
25 cd02342 ZZ_UBA_plant Zinc fing 98.3 2.7E-07 5.8E-12 67.3 2.4 33 47-80 1-34 (43)
26 PLN03212 Transcription repress 98.3 8.3E-07 1.8E-11 87.8 5.2 49 102-150 23-72 (249)
27 PLN03091 hypothetical protein; 98.0 4.8E-06 1E-10 88.2 5.2 49 102-150 12-61 (459)
28 KOG1280 Uncharacterized conser 97.9 4.4E-06 9.4E-11 85.6 2.8 52 44-96 6-58 (381)
29 KOG0048 Transcription factor, 97.9 1.1E-05 2.3E-10 80.7 4.3 46 104-149 9-55 (238)
30 KOG4582 Uncharacterized conser 97.8 1E-05 2.3E-10 82.5 3.6 46 47-97 153-199 (278)
31 KOG4286 Dystrophin-like protei 97.8 4.5E-06 9.8E-11 92.3 0.3 57 40-97 597-654 (966)
32 PLN03212 Transcription repress 97.6 7.3E-05 1.6E-09 74.2 5.4 48 101-149 75-122 (249)
33 PLN03091 hypothetical protein; 97.3 0.00039 8.4E-09 74.0 6.1 48 101-149 64-111 (459)
34 KOG4301 Beta-dystrobrevin [Cyt 97.0 0.00013 2.8E-09 74.9 -0.5 53 40-93 234-287 (434)
35 KOG0048 Transcription factor, 96.8 0.0021 4.6E-08 64.3 5.8 48 101-149 59-106 (238)
36 KOG0049 Transcription factor, 96.4 0.0042 9.2E-08 68.6 5.6 51 101-151 357-407 (939)
37 KOG0049 Transcription factor, 95.9 0.0076 1.6E-07 66.7 4.3 49 100-148 408-459 (939)
38 PF13837 Myb_DNA-bind_4: Myb/S 94.3 0.03 6.5E-07 46.7 2.4 45 105-149 2-63 (90)
39 KOG0051 RNA polymerase I termi 94.3 0.046 1E-06 60.9 4.4 49 103-153 383-431 (607)
40 PF07649 C1_3: C1-like domain; 92.5 0.078 1.7E-06 35.8 1.6 29 47-76 1-29 (30)
41 PF03107 C1_2: C1 domain; Int 90.4 0.22 4.7E-06 33.7 2.1 28 47-76 1-29 (30)
42 KOG0050 mRNA splicing protein 89.6 0.34 7.4E-06 52.9 3.9 48 104-152 7-54 (617)
43 KOG0051 RNA polymerase I termi 89.5 0.35 7.6E-06 54.1 4.0 52 103-154 435-511 (607)
44 COG5147 REB1 Myb superfamily p 87.0 0.46 9.9E-06 52.5 2.9 45 104-148 20-64 (512)
45 PF09111 SLIDE: SLIDE; InterP 86.1 0.91 2E-05 40.8 3.9 44 104-147 49-107 (118)
46 KOG0050 mRNA splicing protein 85.0 0.78 1.7E-05 50.2 3.4 46 102-149 57-102 (617)
47 PF02207 zf-UBR: Putative zinc 85.0 0.71 1.5E-05 37.5 2.4 43 51-98 2-48 (71)
48 TIGR02894 DNA_bind_RsfA transc 83.0 0.93 2E-05 42.7 2.6 44 105-149 5-54 (161)
49 KOG4282 Transcription factor G 82.8 1.6 3.4E-05 45.9 4.6 47 105-151 55-114 (345)
50 COG5118 BDP1 Transcription ini 81.3 2.5 5.4E-05 44.7 5.2 44 104-148 365-408 (507)
51 KOG4468 Polycomb-group transcr 77.6 2.5 5.4E-05 47.2 4.0 45 104-149 88-142 (782)
52 KOG1778 CREB binding protein/P 74.0 1.7 3.6E-05 45.6 1.5 45 44-96 167-211 (319)
53 PF13873 Myb_DNA-bind_5: Myb/S 74.0 4.3 9.2E-05 33.0 3.7 45 105-149 3-68 (78)
54 PLN03000 amine oxidase 73.9 5.9 0.00013 46.9 6.1 73 447-520 89-167 (881)
55 KOG4167 Predicted DNA-binding 73.4 4.5 9.8E-05 46.2 4.7 44 104-148 619-662 (907)
56 PF08914 Myb_DNA-bind_2: Rap1 73.0 5.2 0.00011 32.2 3.8 47 105-151 3-58 (65)
57 PHA00442 host recBCD nuclease 72.6 4.2 9E-05 31.4 2.9 28 108-135 24-51 (59)
58 COG5147 REB1 Myb superfamily p 72.5 3.6 7.8E-05 45.7 3.7 49 102-151 70-118 (512)
59 smart00396 ZnF_UBR1 Putative z 72.2 4.8 0.0001 32.8 3.5 43 51-98 2-48 (71)
60 KOG0384 Chromodomain-helicase 72.1 2.5 5.4E-05 50.9 2.5 28 103-130 1132-1159(1373)
61 PF09862 DUF2089: Protein of u 69.0 8.7 0.00019 34.3 4.7 60 49-135 1-60 (113)
62 PF13412 HTH_24: Winged helix- 68.6 14 0.0003 27.0 5.1 44 477-520 5-48 (48)
63 smart00420 HTH_DEOR helix_turn 67.4 13 0.00029 26.8 4.8 36 485-520 10-45 (53)
64 PF00643 zf-B_box: B-box zinc 66.9 5 0.00011 28.6 2.3 39 46-94 3-41 (42)
65 PF14569 zf-UDP: Zinc-binding 66.0 3.5 7.6E-05 34.3 1.5 35 45-80 8-46 (80)
66 PF08394 Arc_trans_TRASH: Arch 65.1 4.2 9E-05 29.2 1.5 31 49-79 1-32 (37)
67 PLN03142 Probable chromatin-re 62.6 9.5 0.00021 46.1 4.8 48 105-153 825-872 (1033)
68 PLN03142 Probable chromatin-re 61.4 10 0.00023 45.7 4.9 45 104-148 926-982 (1033)
69 PF12802 MarR_2: MarR family; 60.7 18 0.00039 27.5 4.6 50 466-520 1-52 (62)
70 PF07975 C1_4: TFIIH C1-like d 60.2 6.1 0.00013 30.3 1.8 30 48-78 1-37 (51)
71 PF13404 HTH_AsnC-type: AsnC-t 59.8 26 0.00057 25.5 5.0 37 111-148 4-40 (42)
72 PF09012 FeoC: FeoC like trans 58.8 12 0.00026 29.9 3.4 40 481-520 5-45 (69)
73 PF01047 MarR: MarR family; I 56.2 12 0.00026 28.4 2.8 35 486-520 14-48 (59)
74 KOG1356 Putative transcription 55.9 7.4 0.00016 45.3 2.3 38 41-80 224-261 (889)
75 TIGR01889 Staph_reg_Sar staphy 54.0 40 0.00087 29.2 6.2 64 456-520 11-74 (109)
76 PF09397 Ftsk_gamma: Ftsk gamm 53.1 26 0.00056 28.2 4.4 45 473-521 8-52 (65)
77 TIGR02337 HpaR homoprotocatech 52.5 48 0.001 28.9 6.5 61 455-520 13-73 (118)
78 PF12776 Myb_DNA-bind_3: Myb/S 52.1 30 0.00066 28.8 5.0 44 106-149 1-61 (96)
79 COG3935 DnaD Putative primosom 52.0 16 0.00034 37.1 3.6 57 334-390 135-210 (246)
80 PRK13923 putative spore coat p 50.0 13 0.00029 35.5 2.6 45 104-149 5-55 (170)
81 PLN02328 lysine-specific histo 48.9 32 0.0007 40.6 6.1 69 452-520 144-218 (808)
82 PF08074 CHDCT2: CHDCT2 (NUC03 48.8 9.8 0.00021 36.1 1.5 28 106-133 5-32 (173)
83 PRK03573 transcriptional regul 48.8 50 0.0011 29.8 6.2 56 461-520 22-77 (144)
84 PF10925 DUF2680: Protein of u 48.7 60 0.0013 25.6 5.7 45 472-520 15-59 (59)
85 PLN02638 cellulose synthase A 48.0 15 0.00032 44.3 3.1 34 47-81 18-55 (1079)
86 smart00595 MADF subfamily of S 47.8 19 0.0004 29.8 3.0 23 126-149 29-51 (89)
87 PF04504 DUF573: Protein of un 47.8 21 0.00045 31.0 3.3 32 103-134 3-41 (98)
88 KOG1194 Predicted DNA-binding 46.9 12 0.00027 40.6 2.1 43 104-148 470-512 (534)
89 KOG4329 DNA-binding protein [G 46.3 23 0.00049 37.7 3.8 43 105-148 278-321 (445)
90 PLN02915 cellulose synthase A 46.1 17 0.00036 43.7 3.2 36 45-81 14-53 (1044)
91 PLN02436 cellulose synthase A 45.8 12 0.00027 44.8 2.1 35 46-81 36-74 (1094)
92 TIGR00270 conserved hypothetic 44.9 79 0.0017 29.7 7.0 39 48-86 2-40 (154)
93 PF13730 HTH_36: Helix-turn-he 43.8 65 0.0014 24.0 5.2 53 467-519 2-55 (55)
94 PF15614 WHIM3: WSTF, HB1, Itc 43.6 46 0.001 25.1 4.1 28 340-367 4-36 (46)
95 PF06461 DUF1086: Domain of Un 42.5 42 0.00091 31.3 4.6 53 105-158 39-93 (145)
96 PF03979 Sigma70_r1_1: Sigma-7 42.2 47 0.001 27.6 4.5 41 478-518 10-53 (82)
97 smart00843 Ftsk_gamma This dom 41.2 72 0.0016 25.6 5.1 45 473-521 7-51 (63)
98 COG3058 FdhE Uncharacterized p 41.1 5.1 0.00011 41.0 -1.7 31 37-68 202-232 (308)
99 KOG1194 Predicted DNA-binding 40.5 37 0.0008 37.1 4.4 48 100-148 183-230 (534)
100 PF04703 FaeA: FaeA-like prote 39.4 38 0.00083 27.0 3.3 44 477-520 2-46 (62)
101 PRK11512 DNA-binding transcrip 39.1 66 0.0014 29.1 5.4 52 464-520 34-85 (144)
102 PF13463 HTH_27: Winged helix 39.0 60 0.0013 25.0 4.5 34 486-519 15-48 (68)
103 PF02954 HTH_8: Bacterial regu 38.3 45 0.00097 24.0 3.3 24 111-135 6-29 (42)
104 PLN02400 cellulose synthase 38.1 19 0.00042 43.4 2.1 35 46-81 36-74 (1085)
105 PLN02189 cellulose synthase 37.4 20 0.00044 43.0 2.1 36 45-81 33-72 (1040)
106 KOG2807 RNA polymerase II tran 37.3 21 0.00045 37.5 1.9 31 46-77 330-360 (378)
107 cd00090 HTH_ARSR Arsenical Res 36.9 72 0.0016 24.1 4.6 34 486-520 18-51 (78)
108 PF07261 DnaB_2: Replication i 36.6 7.4 0.00016 31.2 -1.1 23 363-385 54-76 (77)
109 KOG3554 Histone deacetylase co 35.5 40 0.00088 36.9 3.8 42 105-147 286-328 (693)
110 PF05290 Baculo_IE-1: Baculovi 34.1 15 0.00032 33.8 0.3 53 45-100 79-131 (140)
111 PRK08359 transcription factor; 34.1 31 0.00067 33.2 2.4 40 47-86 7-48 (176)
112 smart00345 HTH_GNTR helix_turn 33.1 67 0.0015 23.7 3.8 46 475-520 4-51 (60)
113 PLN02195 cellulose synthase A 32.9 29 0.00063 41.5 2.4 35 46-81 6-44 (977)
114 PF08513 LisH: LisH; InterPro 32.1 30 0.00066 22.7 1.4 13 507-519 5-17 (27)
115 PF14471 DUF4428: Domain of un 30.4 30 0.00066 26.4 1.4 30 48-80 1-30 (51)
116 COG3196 Uncharacterized protei 30.3 49 0.0011 30.9 3.0 98 30-134 15-130 (183)
117 PF09107 SelB-wing_3: Elongati 30.1 1E+02 0.0022 23.4 4.2 39 481-519 1-40 (50)
118 TIGR01446 DnaD_dom DnaD and ph 29.9 38 0.00082 27.0 2.0 18 364-381 55-72 (73)
119 TIGR03277 methan_mark_9 putati 29.6 56 0.0012 28.8 3.1 23 464-486 86-108 (109)
120 KOG3993 Transcription factor ( 29.5 14 0.0003 40.0 -0.8 50 38-94 259-322 (500)
121 PF01388 ARID: ARID/BRIGHT DNA 29.3 1.1E+02 0.0024 25.5 4.8 38 113-150 39-88 (92)
122 COG1725 Predicted transcriptio 29.2 1.4E+02 0.003 27.2 5.6 50 471-520 11-66 (125)
123 smart00347 HTH_MARR helix_turn 28.9 93 0.002 25.4 4.3 52 464-520 4-55 (101)
124 smart00346 HTH_ICLR helix_turn 28.8 1.3E+02 0.0027 24.6 5.1 40 481-520 10-51 (91)
125 PRK00420 hypothetical protein; 27.4 38 0.00083 30.2 1.7 30 46-75 23-54 (112)
126 PRK10870 transcriptional repre 26.9 1.5E+02 0.0033 28.0 5.9 58 460-520 45-102 (176)
127 COG1813 Predicted transcriptio 26.2 79 0.0017 30.2 3.7 38 49-87 6-43 (165)
128 PF13325 MCRS_N: N-terminal re 25.9 1.1E+02 0.0023 30.2 4.6 46 106-153 1-49 (199)
129 PF09339 HTH_IclR: IclR helix- 25.7 89 0.0019 23.2 3.3 43 478-520 5-49 (52)
130 PRK11179 DNA-binding transcrip 25.6 1.4E+02 0.0031 27.4 5.3 43 110-153 9-51 (153)
131 smart00550 Zalpha Z-DNA-bindin 25.4 1.8E+02 0.004 23.1 5.2 44 477-520 8-53 (68)
132 KOG3579 Predicted E3 ubiquitin 25.4 1.1E+02 0.0024 31.6 4.8 40 40-79 262-301 (352)
133 COG4008 Predicted metal-bindin 25.2 1.1E+02 0.0025 27.9 4.2 27 464-490 87-113 (153)
134 PF01978 TrmB: Sugar-specific 25.0 75 0.0016 24.9 2.9 35 486-520 19-53 (68)
135 PF00130 C1_1: Phorbol esters/ 24.8 68 0.0015 23.8 2.5 24 45-68 10-35 (53)
136 PF10123 Mu-like_Pro: Mu-like 24.6 56 0.0012 34.2 2.6 25 450-474 301-325 (326)
137 PF13076 DUF3940: Protein of u 24.5 87 0.0019 22.6 2.8 34 477-511 3-36 (38)
138 PF08784 RPA_C: Replication pr 23.9 68 0.0015 27.4 2.6 33 486-519 63-95 (102)
139 TIGR00622 ssl1 transcription f 23.8 52 0.0011 29.4 1.9 30 47-77 56-96 (112)
140 PF07191 zinc-ribbons_6: zinc- 23.7 30 0.00065 28.4 0.3 20 46-67 17-36 (70)
141 KOG0006 E3 ubiquitin-protein l 23.6 59 0.0013 34.1 2.4 24 45-68 133-156 (446)
142 PF10545 MADF_DNA_bdg: Alcohol 23.6 77 0.0017 25.3 2.8 24 126-149 28-52 (85)
143 PF05584 Sulfolobus_pRN: Sulfo 23.2 2.1E+02 0.0045 23.7 5.1 46 474-520 4-49 (72)
144 cd04766 HTH_HspR Helix-Turn-He 22.9 3.8E+02 0.0081 22.3 7.0 61 309-369 22-87 (91)
145 PF12488 DUF3704: Protein of u 22.3 31 0.00067 23.0 0.1 9 248-256 7-15 (27)
146 PF03374 ANT: Phage antirepres 22.1 1.6E+02 0.0034 25.4 4.6 36 481-519 15-51 (111)
147 smart00418 HTH_ARSR helix_turn 21.9 1.7E+02 0.0037 21.3 4.3 34 487-520 8-41 (66)
148 PRK13777 transcriptional regul 21.9 2E+02 0.0044 27.8 5.7 52 464-520 39-90 (185)
149 PF13842 Tnp_zf-ribbon_2: DDE_ 21.8 78 0.0017 21.8 2.0 27 48-75 2-29 (32)
150 cd00092 HTH_CRP helix_turn_hel 21.4 1.2E+02 0.0027 23.0 3.4 35 486-520 22-56 (67)
151 PF12674 Zn_ribbon_2: Putative 21.2 52 0.0011 27.6 1.3 35 48-83 2-39 (81)
152 smart00501 BRIGHT BRIGHT, ARID 20.7 1.6E+02 0.0034 24.7 4.2 37 113-149 35-83 (93)
153 COG2956 Predicted N-acetylgluc 20.6 60 0.0013 34.4 1.8 28 42-70 350-377 (389)
154 PRK14890 putative Zn-ribbon RN 20.5 1.1E+02 0.0023 24.4 2.7 35 46-80 7-46 (59)
155 PF00412 LIM: LIM domain; Int 20.5 41 0.00088 25.2 0.5 30 47-79 27-56 (58)
156 TIGR02531 yecD_yerC TrpR-relat 20.3 2.3E+02 0.005 24.1 5.0 48 333-381 8-58 (88)
157 cd07377 WHTH_GntR Winged helix 20.2 1.8E+02 0.0039 21.7 4.2 48 473-520 7-56 (66)
No 1
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=6.4e-104 Score=810.57 Aligned_cols=420 Identities=50% Similarity=0.833 Sum_probs=370.2
Q ss_pred CCcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhCC
Q 009958 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGL 124 (521)
Q Consensus 45 ~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLeai~~~G~ 124 (521)
..|+|++|..+|++.+||+|++|++||||+.||+.|+|++.|+++|+|+||++++||+..++|||+||++||+|++.|||
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 CChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCcccccccchHHHHHHhccCcCCCCCCCCCCCCCccCCCCCCCch
Q 009958 125 GNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKGPSKPGEATVKEESPFSPSR 204 (521)
Q Consensus 125 gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~plp~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~t~~~~~p~~p~~ 204 (521)
|||++||+|||+||.+||++||.++|++++++|+|+++..+|+++.+++++.+.+. .|+.|..
T Consensus 93 GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~-----------------~~~~~~~ 155 (438)
T KOG0457|consen 93 GNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRA-----------------EPFQPTD 155 (438)
T ss_pred CcHHHHHHHHcccchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhccccc-----------------ccCCCCC
Confidence 99999999999999999999999999999999999999999999999998876531 2333321
Q ss_pred hhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCCCHHHH
Q 009958 205 VKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDADSEEER 284 (521)
Q Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFE~EydNdAE~li~dmeF~~~D~~~e~ 284 (521)
. .|++++.++|..++++||||+|.|||.||||+||++|+||+|+++|+|.+.
T Consensus 156 ~----------------------------~pr~p~~~~p~~~e~~gyMp~R~dFd~Eydn~AE~li~dm~f~e~D~~~d~ 207 (438)
T KOG0457|consen 156 L----------------------------VPRKPGVSNPLRREISGYMPGRLDFDEEYDNEAEQLIRDMEFEEDDTEEDH 207 (438)
T ss_pred C----------------------------CCCCCCCCCchHHHHhhhCccchhhhhhhcchhhhhHhhcccCCCCcHHHH
Confidence 0 133444567889999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC---CCCCCCCChHHHHHHHhhchhcccCChhHHHHHHHHHHHHHHHHH
Q 009958 285 DIKLRVLRIYSKRLDERKRRKDFILERNLLYP---NPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISEHRTLK 361 (521)
Q Consensus 285 elKL~~l~iYn~rL~ER~rRK~~v~e~~Ll~~---~~~~k~~tkeer~~~~~l~~farf~~~~~~~~l~~~l~~e~~Lr~ 361 (521)
+||+++|+|||+||+||.|||++|++|+|+++ |+.++++|+|+|++++++|+||||+|+.||++|+.+++.|.+|+.
T Consensus 208 elKla~ldiY~srl~eR~RRK~~I~d~nLl~~rk~q~~e~~~skEer~l~~s~k~fAR~~t~~d~~kfl~~~~eE~~L~~ 287 (438)
T KOG0457|consen 208 ELKLAVLDIYNSRLKERKRRKRFIRDRNLLDYRKNQAMEKRLSKEERELYNSIKVFARFLTKSDHDKFLGSVAEEKELRK 287 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHhhccHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999994 888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhCccchHHHHHHHHHHHhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCC--CCCCCCCCCC
Q 009958 362 RIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSN--SRPSGQASSS 439 (521)
Q Consensus 362 rI~~L~~yR~~Gi~tl~e~~~ye~~k~~Re~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 439 (521)
||.+||+||.+|+||++++.+|+.+|.++. +........+++.. . +. .+ .....++. +....+...+
T Consensus 288 ri~~lqE~R~ag~tt~~e~~ky~~~k~~~~-~~s~~~~~~~~~~~---~-i~-----~~-~~~~~~~~~~~~v~~~~~~~ 356 (438)
T KOG0457|consen 288 RISDLQEYRSAGLTTNAEPNKYERLKFKEF-RESTALLLSSGALR---Y-IK-----NS-NQEASGSASKRPVQQQSIYK 356 (438)
T ss_pred HHHHHHHHHHhcceeccccchhHHHHHHHH-HHHhhhccccchhh---h-hh-----cc-ccccccccccCccccccccc
Confidence 999999999999999999999999994432 22222211111100 0 00 00 11111111 2223334566
Q ss_pred CCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCC
Q 009958 440 HVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 519 (521)
Q Consensus 440 ~~~~l~i~~~pg~~lLs~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi 519 (521)
+++++++.++|+.++||+.|+.||+.++|+|.+||.+|++|++|..++|.+++++|..++|||++|+++|||||+++||+
T Consensus 357 ~~~~~~~~~~~~~q~Lse~E~~lc~~~~~~p~~yLe~~~vl~~e~~k~~~~kks~a~~l~Kid~~Kvd~vyd~~~~~~~~ 436 (438)
T KOG0457|consen 357 SATPLDISGAPDTQLLSEDEKRLCQELKILPKLYLELKEVLSREIKKGGTLKKSDAYRLFKIDPRKVDRVYDFLIAQGWI 436 (438)
T ss_pred CCCHHHHhcchhhhhhhhhHHHHHHHHHhccHHHHHHHHHHHHHHhccCcccchhHHHHhcCCcchHHHHHHHHHHhhhc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C
Q 009958 520 P 520 (521)
Q Consensus 520 ~ 520 (521)
+
T Consensus 437 ~ 437 (438)
T KOG0457|consen 437 G 437 (438)
T ss_pred c
Confidence 6
No 2
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=2.5e-96 Score=723.82 Aligned_cols=420 Identities=31% Similarity=0.530 Sum_probs=361.0
Q ss_pred cCCcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhC
Q 009958 44 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 123 (521)
Q Consensus 44 ~~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLeai~~~G 123 (521)
...++||+|..+|+..++|+|++|++||||+.||++|.+.+.|.+.|+|+||..+++||+.++|+++||++|+++++.+|
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 37899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCcccccccchHHHHHHhccCcCCCCCCCCCCCCCccCCCCCCCc
Q 009958 124 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKGPSKPGEATVKEESPFSPS 203 (521)
Q Consensus 124 ~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~plp~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~t~~~~~p~~p~ 203 (521)
+|||++||+|||+|+.+||+.||.++|+++.++|||+....+...+.++++..+.+++.... +|..|
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~ypl~~i~~~~~v~q~~f~~qrr~rie~f~~------------ppi~p- 149 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYPLPDITQNIHVPQDEFLEQRRHRIETFEL------------PPINP- 149 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccccccccccCCCCchHHHHHHHHhhhhhccC------------CCCCC-
Confidence 99999999999999999999999999999999999999877777888998876655442221 12222
Q ss_pred hhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCCCHHH
Q 009958 204 RVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDADSEEE 283 (521)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFE~EydNdAE~li~dmeF~~~D~~~e 283 (521)
.||.. ++|.+++++||||+|.|||+||+|+||..|+||.|++|+.+.+
T Consensus 150 -----------------------------rkP~a---S~P~cheiqgyMPgRleFd~EymnEaE~pikDm~fd~d~~el~ 197 (432)
T COG5114 150 -----------------------------RKPKA---SNPYCHEIQGYMPGRLEFDVEYMNEAEVPIKDMSFDGDKEELK 197 (432)
T ss_pred -----------------------------CCCCC---CCCchhhhhccCCCccccchhhhhcccccccccccCCchHHHH
Confidence 13444 4699999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC---CCCCCCCCChHHHHHHHhhchhcccCChhHHHHHHHHHHHHHHHH
Q 009958 284 RDIKLRVLRIYSKRLDERKRRKDFILERNLLY---PNPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISEHRTL 360 (521)
Q Consensus 284 ~elKL~~l~iYn~rL~ER~rRK~~v~e~~Ll~---~~~~~k~~tkeer~~~~~l~~farf~~~~~~~~l~~~l~~e~~Lr 360 (521)
++||+++|+|||+||.-|.+||+.|++++|+| -|+.+|++||||+.++++++||||++|+.||+.|++.++.+.-++
T Consensus 198 ~~lk~a~LdiYnsrlt~Ra~rK~~if~~nLmDyr~Lqa~dkk~skEe~~l~N~iK~fAr~lT~~Df~~F~~~~~e~v~~~ 277 (432)
T COG5114 198 KKLKNATLDIYNSRLTFRARRKHAIFGKNLMDYRNLQAKDKKRSKEECGLVNSIKWFARYLTKSDFNVFFRDILEGVYIE 277 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhhhccHHHHhHHHhhhHHHHhhcchhHHHHHHHHhhhhhHH
Confidence 99999999999999999999999999999999 577899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhCccchHHHHHHHHHHHhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCCCCC-CC--CCC
Q 009958 361 KRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSNSRP-SG--QAS 437 (521)
Q Consensus 361 ~rI~~L~~yR~~Gi~tl~e~~~ye~~k~~Re~e~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~ 437 (521)
+||++||+||.||+|||+.|-+||++|-.+ .....+ .+...+.+.. .+++.. +++..... .. ...
T Consensus 278 kri~~LqewR~~glttle~g~kyeRDk~ek---f~~s~a-as~~e~~~r~-------~~n~~~-~sna~~s~~d~~ni~p 345 (432)
T COG5114 278 KRIHELQEWRNNGLTTLEAGLKYERDKFEK---FGASTA-ASLSEGNSRY-------RSNSAH-RSNAEYSQMDVKNILP 345 (432)
T ss_pred HHHHHHHHHHhcCchhhhhhhhhhhhHHHh---hccchh-hhhcccchhh-------hccccc-ccCcchhHHHHHhccC
Confidence 999999999999999999999999997321 000000 0000111111 001100 00000000 00 012
Q ss_pred CCCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHh-CCCCCHHHhhhhhccCchhHHHHHHHHHHC
Q 009958 438 SSHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDMLVKK 516 (521)
Q Consensus 438 ~~~~~~l~i~~~pg~~lLs~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~-~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~ 516 (521)
++...+-+|..+|.+.|||++|++||++|+|.|++||.+|.++|+++++ +|.++|++|..||+||.+|+.+|||||.+.
T Consensus 346 ~K~~t~s~~q~a~d~~llS~dEq~LC~~l~i~PkpyL~LK~~~is~~l~t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~ 425 (432)
T COG5114 346 SKNMTISDIQHAPDYALLSDDEQRLCETLNISPKPYLELKKEVISCFLRTRGEFTKEDFNRLFGIDLGKADGLYDFFLER 425 (432)
T ss_pred CCCCChhhhhccchhhhhcchHHHHHHHhCCCCccHHHHHHHHHHHHHHhCCCccHHHHHHHhCcCcchhhHHHHHHHhc
Confidence 3445677899999999999999999999999999999999999999995 899999999999999999999999999999
Q ss_pred CCCC
Q 009958 517 GLAP 520 (521)
Q Consensus 517 Gwi~ 520 (521)
|||-
T Consensus 426 ~Wi~ 429 (432)
T COG5114 426 GWIH 429 (432)
T ss_pred cccC
Confidence 9995
No 3
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=99.67 E-value=4.1e-17 Score=169.88 Aligned_cols=111 Identities=29% Similarity=0.603 Sum_probs=96.5
Q ss_pred CCCcCCcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHH
Q 009958 41 EGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIE 120 (521)
Q Consensus 41 ~~~~~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLeai~ 120 (521)
+...+..+|+.||..+.. .||+-..-.++++|..||-+|.++....++ +|..++...+. ....|+.+|.++||+||+
T Consensus 219 ~~~~~~~~C~~cG~~~~~-t~y~nlra~~~n~C~~C~~qg~f~s~~~ss-Df~~v~~~~~~-~dk~WS~qE~~LLLEGIe 295 (531)
T COG5259 219 HSEKHPSSCSCCGNKSFN-TRYHNLRAEKYNSCSECYDQGRFPSEFTSS-DFKPVTISLLI-RDKNWSRQELLLLLEGIE 295 (531)
T ss_pred ccccCCceeeccCccccc-hhhhhhhhhhcccchHHHhcCcCCCccccc-cchhhhhhccc-ccccccHHHHHHHHHHHH
Confidence 334456899999999887 899988888999999999999999888766 67777664443 456899999999999999
Q ss_pred HhCCCChHHHHHHhCCCCHHHHHHHHHhhccCCCC
Q 009958 121 MYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNSPF 155 (521)
Q Consensus 121 ~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~ 155 (521)
+|| .+|..||.|||+||++||+.||.++++.+++
T Consensus 296 ~yg-DdW~kVA~HVgtKt~EqCIl~FL~LPieD~~ 329 (531)
T COG5259 296 MYG-DDWDKVARHVGTKTKEQCILHFLQLPIEDNY 329 (531)
T ss_pred Hhh-hhHHHHHHHhCCCCHHHHHHHHHcCCcchhh
Confidence 999 8999999999999999999999999998864
No 4
>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=4.2e-14 Score=106.99 Aligned_cols=49 Identities=69% Similarity=1.499 Sum_probs=46.6
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeec
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 95 (521)
++|++|.+++...+||+|++|+|||||..||+.|.+.+.|+++|+|++|
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 5799999999877999999999999999999999999999999999986
No 5
>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=99.44 E-value=1.6e-13 Score=115.62 Aligned_cols=78 Identities=33% Similarity=0.477 Sum_probs=68.8
Q ss_pred cccccCCCccCCCCHHHHHHHHHhCC--CchHHHHHHHHHHHHHH--hCCCCCHHHhhhhhc-cCchhHHHHHHHHHHCC
Q 009958 443 DLYIMGFNETQLLSEAEKRLCCEIRL--APPLYLRMQEVMSREIF--SGNVNNKADAHHLFK-IEPSKIDRVYDMLVKKG 517 (521)
Q Consensus 443 ~l~i~~~pg~~lLs~~Ek~LC~~lrL--~P~~YL~iK~~LirE~~--~~G~lkk~~a~~l~k-iD~~k~~~Iydfl~~~G 517 (521)
++++++.++.+.||+.|+++|..+++ .|..||.+|..||.+.. .++.+++++|+++++ +|++++.+||+||.+.|
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 009958 518 LAP 520 (521)
Q Consensus 518 wi~ 520 (521)
||.
T Consensus 83 ~IN 85 (86)
T PF04433_consen 83 LIN 85 (86)
T ss_dssp SSS
T ss_pred ccC
Confidence 994
No 6
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=99.34 E-value=1.3e-12 Score=141.14 Aligned_cols=81 Identities=36% Similarity=0.862 Sum_probs=71.5
Q ss_pred CcccchhhhhccccccCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 69 DFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 69 d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
++.+|..||..|.+...++.+ +|.++... ....||.+|+++||+||++|| .+|..||.|||+||++||+.||.+
T Consensus 223 ~~~~c~~c~~~g~~~~~~~~~-Df~~~~~~----~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 223 DVNLCADCYDQGEFPSEFKKS-DFKVIGES----ARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred hhhhhHHHHhcCCccCccccc-cchhcccc----CCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHh
Confidence 378999999999999998776 56544432 367999999999999999999 899999999999999999999999
Q ss_pred hccCCCC
Q 009958 149 VYMNSPF 155 (521)
Q Consensus 149 ~yi~~~~ 155 (521)
.++.+++
T Consensus 297 LPieD~~ 303 (506)
T KOG1279|consen 297 LPIEDPY 303 (506)
T ss_pred cCccchh
Confidence 9998864
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=99.27 E-value=2.7e-12 Score=95.94 Aligned_cols=46 Identities=33% Similarity=0.717 Sum_probs=42.7
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCee
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 93 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~ 93 (521)
+.||+|.+.+.+ +||+|++|+|||||..||+.|.+.+.|+.+|+.+
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 469999998876 9999999999999999999999999999999865
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=99.24 E-value=4.9e-12 Score=95.72 Aligned_cols=48 Identities=38% Similarity=0.953 Sum_probs=44.6
Q ss_pred ccccccc-ccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeec
Q 009958 47 YHCNYCN-KDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (521)
Q Consensus 47 ~~Cd~C~-~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 95 (521)
+.|++|+ .+|.+ .||+|++|+|||||..||+.|.+.+.|+++|+|+++
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 68987 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=99.23 E-value=6.4e-12 Score=94.88 Aligned_cols=46 Identities=41% Similarity=0.977 Sum_probs=42.9
Q ss_pred cccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCee
Q 009958 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 93 (521)
Q Consensus 47 ~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~ 93 (521)
+.|++|++ +|.+ .||+|++|.|||||..||..|.+.+.|+++|+|+
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 5887 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=99.21 E-value=9e-12 Score=94.28 Aligned_cols=46 Identities=43% Similarity=0.969 Sum_probs=43.5
Q ss_pred ccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeee
Q 009958 48 HCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (521)
Q Consensus 48 ~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 94 (521)
.|++|.+ +|++ +||+|++|+|||||..||+.|.+.+.|+++|+|..
T Consensus 2 ~C~~C~~~~i~g-~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02345 2 SCSACRKQDISG-IRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48 (49)
T ss_pred cCCCCCCCCceE-eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCccc
Confidence 6999999 9997 99999999999999999999999999999998864
No 11
>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=99.13 E-value=6.9e-11 Score=88.77 Aligned_cols=45 Identities=31% Similarity=0.716 Sum_probs=41.2
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 009958 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 149 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~ 149 (521)
..||.+|+.+|++||.+||.+||..||.+|+ +||+.||+.||.++
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 5799999999999999999888999999999 99999999999875
No 12
>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=99.09 E-value=7.8e-11 Score=87.95 Aligned_cols=46 Identities=41% Similarity=1.024 Sum_probs=42.5
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeec
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 95 (521)
|.|++|+++|.+ +||+|.+|++||||..||+.+. +.|.++|+|..|
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 9999999999999999999998 789999998764
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=98.98 E-value=3.9e-10 Score=83.02 Aligned_cols=43 Identities=42% Similarity=0.943 Sum_probs=39.0
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeec
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 95 (521)
+.|++|+.+|.+ .||+|++|++||||..||..+ .| ++|+|..|
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 999999999999999999997 68 89998754
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=98.97 E-value=4.3e-10 Score=84.62 Aligned_cols=45 Identities=36% Similarity=0.882 Sum_probs=40.9
Q ss_pred cccccccc-cCCCCeeEEcCCCC--CcccchhhhhccccccCCCCCCCeeec
Q 009958 47 YHCNYCNK-DITGKIRIKCAVCP--DFDLCIECFSVGVEVHPHKSNHPYRVM 95 (521)
Q Consensus 47 ~~Cd~C~~-~i~~~~ri~C~~C~--d~dLC~~CF~~G~e~~~H~~~H~y~vi 95 (521)
|.|++|+. +|.+ +||+|++|+ +||||..||..|. .|+.+|.+..|
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 57999999 7887 999999999 9999999999997 79999988754
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=98.96 E-value=4.5e-10 Score=83.33 Aligned_cols=42 Identities=31% Similarity=0.648 Sum_probs=39.9
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCC
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSN 89 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~ 89 (521)
|+|+.|+.|++. +||+|+.+.+++||+.||.+|.++.+|.++
T Consensus 1 y~C~~Cg~D~t~-vryh~~~~~~~dLC~~CF~~G~f~~~~~s~ 42 (45)
T cd02336 1 YHCFTCGNDCTR-VRYHNLKAKKYDLCPSCYQEGRFPSNFQSS 42 (45)
T ss_pred CcccCCCCccCc-eEEEecCCCccccChHHHhCcCCCCCCccc
Confidence 689999999996 999999999999999999999999999876
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=98.84 E-value=2.3e-09 Score=79.47 Aligned_cols=44 Identities=36% Similarity=0.906 Sum_probs=38.7
Q ss_pred cccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeec
Q 009958 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 95 (521)
Q Consensus 47 ~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 95 (521)
+.||+|+. +|.+ .||+|++|.|||||..||..+ .|...|.|..|
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 47999997 6887 999999999999999999995 59889998764
No 17
>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=98.84 E-value=2.5e-09 Score=79.08 Aligned_cols=41 Identities=46% Similarity=1.093 Sum_probs=37.3
Q ss_pred CCcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCC
Q 009958 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPH 86 (521)
Q Consensus 45 ~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H 86 (521)
..+.|++|+.+|.+ .||+|+.|+|||||..||+.|.+.+.|
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 46789999999987 899999999999999999999877766
No 18
>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=98.82 E-value=2.8e-09 Score=79.18 Aligned_cols=43 Identities=42% Similarity=0.981 Sum_probs=37.2
Q ss_pred cccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeee
Q 009958 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (521)
Q Consensus 47 ~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 94 (521)
+.||+|++ .|.+ +||+|++|+|||||..||.. +.|+.+|+|..
T Consensus 1 i~Cd~C~~~~i~G-~RykC~~C~dyDLC~~C~~~----~~H~~~H~f~r 44 (45)
T cd02339 1 IICDTCRKQGIIG-IRWKCAECPNYDLCTTCYHG----DKHDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCCccc-CeEECCCCCCccchHHHhCC----CCCCCCCCEEe
Confidence 36999995 6766 99999999999999999996 46999999863
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=98.74 E-value=4.2e-09 Score=78.69 Aligned_cols=42 Identities=50% Similarity=1.118 Sum_probs=31.8
Q ss_pred CCcccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCC
Q 009958 45 ALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 87 (521)
Q Consensus 45 ~~~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~ 87 (521)
..+.|++|+. .|.+ +||+|..|+|||||..||..|.....|+
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 5689999999 6777 9999999999999999999998777764
No 20
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.71 E-value=2.8e-08 Score=72.96 Aligned_cols=46 Identities=33% Similarity=0.749 Sum_probs=43.1
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhc
Q 009958 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVY 150 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~y 150 (521)
..||.+|+..|+.++..||.++|..||.++++||+.+|+.+|..+.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 5799999999999999999889999999999999999999998653
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=98.67 E-value=4.1e-08 Score=71.03 Aligned_cols=44 Identities=34% Similarity=0.791 Sum_probs=41.9
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 106 DWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 106 ~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
.||.+|+..|+.++..||.++|..||..+++||+.+|+.||..+
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=98.62 E-value=6.6e-08 Score=75.48 Aligned_cols=49 Identities=18% Similarity=0.317 Sum_probs=44.9
Q ss_pred CCCCCchhHHHHHHHHHHhCCCCh---HHHHHHhC-CC-CHHHHHHHHHhhccC
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNW---AEIAEHVG-TK-TKELCIEHYTNVYMN 152 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW---~~Ia~~vg-tk-t~~ec~~hy~~~yi~ 152 (521)
+..||++|...+|+||+.+|.|+| ..|+++|+ ++ |+.||+.|+.++|+.
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 346999999999999999999999 99999998 67 999999999999864
No 23
>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=98.60 E-value=9.1e-08 Score=74.85 Aligned_cols=41 Identities=39% Similarity=0.920 Sum_probs=37.1
Q ss_pred CCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 107 WNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 107 Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
||.+|+.+|+.++..|| .+|..||.+||+||+.+|+.||..
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 699999999998999999999998
No 24
>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=98.44 E-value=9.9e-08 Score=69.54 Aligned_cols=33 Identities=42% Similarity=1.142 Sum_probs=29.2
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhccc
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
|.|++|...+ + +||+|++|+|||||..||..+.
T Consensus 1 y~C~~C~~~~-~-~r~~C~~C~dfDLC~~C~~~~~ 33 (41)
T cd02337 1 YTCNECKHHV-E-TRWHCTVCEDYDLCITCYNTKN 33 (41)
T ss_pred CcCCCCCCcC-C-CceECCCCcchhhHHHHhCCCC
Confidence 5799999844 4 9999999999999999999854
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=98.34 E-value=2.7e-07 Score=67.26 Aligned_cols=33 Identities=45% Similarity=0.799 Sum_probs=30.0
Q ss_pred cccccccc-cCCCCeeEEcCCCCCcccchhhhhcc
Q 009958 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVG 80 (521)
Q Consensus 47 ~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G 80 (521)
+.||+|+. +|.+ .||+|..|.|||||..||...
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 6888 999999999999999999974
No 26
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.28 E-value=8.3e-07 Score=87.78 Aligned_cols=49 Identities=18% Similarity=0.472 Sum_probs=45.2
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 009958 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 150 (521)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~y 150 (521)
+-+..||.+||.+|+++|+.||.+||..||.+++ +||+.||++||.++.
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 4567899999999999999999999999999997 899999999999764
No 27
>PLN03091 hypothetical protein; Provisional
Probab=98.04 E-value=4.8e-06 Score=88.21 Aligned_cols=49 Identities=24% Similarity=0.545 Sum_probs=44.8
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 009958 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 150 (521)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~y 150 (521)
+-+..||.+||.+|+++|.+||.+||..||.+++ +||+.||++||.++.
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 3457899999999999999999999999999998 899999999998764
No 28
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.95 E-value=4.4e-06 Score=85.62 Aligned_cols=52 Identities=33% Similarity=0.731 Sum_probs=46.3
Q ss_pred cCCccccccccc-CCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeecc
Q 009958 44 RALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 96 (521)
Q Consensus 44 ~~~~~Cd~C~~~-i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~ 96 (521)
.-.+.|++|++. +++ .||+|..|.|||||..||-.|+-...|.-+|+.+.|-
T Consensus 6 He~v~CdgC~k~~~t~-rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil 58 (381)
T KOG1280|consen 6 HEGVSCDGCGKTAFTF-RRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCIL 58 (381)
T ss_pred cCCceeccccccceee-eeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEe
Confidence 356789999996 565 9999999999999999999999999999999987663
No 29
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.89 E-value=1.1e-05 Score=80.73 Aligned_cols=46 Identities=17% Similarity=0.427 Sum_probs=44.4
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 149 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg-tkt~~ec~~hy~~~ 149 (521)
.++||++||..|.+.|+.||.|||..||++.| .|+...|+.+|.+|
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 58999999999999999999999999999999 99999999999976
No 30
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=97.85 E-value=1e-05 Score=82.55 Aligned_cols=46 Identities=39% Similarity=0.890 Sum_probs=39.0
Q ss_pred cccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccC
Q 009958 47 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDN 97 (521)
Q Consensus 47 ~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~ 97 (521)
..||.|++ .|.+ .||+|++|+|||||..|++.+ .|.-.|.+..|..
T Consensus 153 v~CD~C~~~~IvG-~RyKC~~C~dYDLCe~Ce~~~----~~h~~H~~lR~~t 199 (278)
T KOG4582|consen 153 VPCDNCGKPGIVG-ARYKCTVCPDYDLCERCEAGN----EHHAAHAMLRLHT 199 (278)
T ss_pred ccCCCccCCcccc-ceeeecCCCccchhHHhhcCC----CCCcccceeeccc
Confidence 68999999 8888 999999999999999999976 3556777766543
No 31
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=97.81 E-value=4.5e-06 Score=92.34 Aligned_cols=57 Identities=26% Similarity=0.521 Sum_probs=48.4
Q ss_pred CCCCcCCcccccccc-cCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccC
Q 009958 40 GEGKRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDN 97 (521)
Q Consensus 40 ~~~~~~~~~Cd~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~ 97 (521)
+|.-.+.-.|++|.+ +|.+ +||+|..|.++|||..||..|...+.|+..|+..-...
T Consensus 597 aE~~kH~~kCniCk~~pIvG-~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~ 654 (966)
T KOG4286|consen 597 AETAKHQAKCNICKECPIIG-FRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCT 654 (966)
T ss_pred HHHHHhhhhcchhhhCccce-eeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeC
Confidence 444567778999987 5887 99999999999999999999999999999887665433
No 32
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.62 E-value=7.3e-05 Score=74.20 Aligned_cols=48 Identities=19% Similarity=0.279 Sum_probs=44.5
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 101 ~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
.+....||.+|+.+|++++..|| ..|..||.+|.+||..+|+.||..+
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 7899999999999999999999864
No 33
>PLN03091 hypothetical protein; Provisional
Probab=97.28 E-value=0.00039 Score=74.05 Aligned_cols=48 Identities=19% Similarity=0.351 Sum_probs=44.5
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 101 ~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
.+....||.+||.+||+.+..|| ..|..||.+|.+||..+|+.||..+
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 34
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=97.03 E-value=0.00013 Score=74.88 Aligned_cols=53 Identities=28% Similarity=0.712 Sum_probs=46.1
Q ss_pred CCCCcCCccccccccc-CCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCee
Q 009958 40 GEGKRALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 93 (521)
Q Consensus 40 ~~~~~~~~~Cd~C~~~-i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~ 93 (521)
.+.....+.|++|... +.+ .||+|..|.+|.+|.+||-.|...+.|.+.|.+.
T Consensus 234 v~nv~hpv~cs~c~srs~~g-fry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mk 287 (434)
T KOG4301|consen 234 VENVFHPVECSYCRSRSMMG-FRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMK 287 (434)
T ss_pred hcccCCCccCcceecccccc-hhhhHhhcCCccccchhhccccCCCCcchHHHHH
Confidence 4444678899999875 776 9999999999999999999999999999998665
No 35
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.78 E-value=0.0021 Score=64.27 Aligned_cols=48 Identities=19% Similarity=0.368 Sum_probs=43.4
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 101 ~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
-+-++.||.+||.+|+++-..+| .-|..||.++++||..+++.||...
T Consensus 59 ~ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 59 DLKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred CccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCCCcCHHHHHHHHHHH
Confidence 34578999999999999999999 5699999999999999999999643
No 36
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.44 E-value=0.0042 Score=68.58 Aligned_cols=51 Identities=27% Similarity=0.649 Sum_probs=47.0
Q ss_pred CCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhcc
Q 009958 101 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYM 151 (521)
Q Consensus 101 ~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi 151 (521)
.+-.+.||.+||.+|+.||+.||--+|-.|-+.|.+|+..||+++|.+..-
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 455789999999999999999998899999999999999999999998644
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.91 E-value=0.0076 Score=66.67 Aligned_cols=49 Identities=24% Similarity=0.348 Sum_probs=43.6
Q ss_pred CCCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCH---HHHHHHHHh
Q 009958 100 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTK---ELCIEHYTN 148 (521)
Q Consensus 100 ~~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~---~ec~~hy~~ 148 (521)
+..-.+.|+..||..|+++|++||.|+|..+|..+|.||. .-|+.+++.
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 4455689999999999999999999999999999999998 668888765
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.32 E-value=0.03 Score=46.74 Aligned_cols=45 Identities=29% Similarity=0.614 Sum_probs=33.3
Q ss_pred CCCCchhHHHHHHHHHH--hC--CC---------ChHHHHHHhC----CCCHHHHHHHHHhh
Q 009958 105 PDWNADDEILLLEGIEM--YG--LG---------NWAEIAEHVG----TKTKELCIEHYTNV 149 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~--~G--~g---------nW~~Ia~~vg----tkt~~ec~~hy~~~ 149 (521)
..||.+|...||+++.. +. ++ -|..||..|. .||+.||+.+|.++
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 47999999999998877 21 21 3999999985 69999999999875
No 39
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.27 E-value=0.046 Score=60.88 Aligned_cols=49 Identities=18% Similarity=0.384 Sum_probs=44.7
Q ss_pred CCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 009958 103 ICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 153 (521)
Q Consensus 103 ~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~ 153 (521)
.++.||.+|+..|-..+.++| +.|.+|++.|| |.|..|+.||.++-..+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg-r~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG-RMPMDCRDRWRQYVKCG 431 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc-cCcHHHHHHHHHhhccc
Confidence 358999999999999999999 99999999997 79999999999886555
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=92.49 E-value=0.078 Score=35.80 Aligned_cols=29 Identities=41% Similarity=0.992 Sum_probs=12.8
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhh
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIEC 76 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~C 76 (521)
+.|+.|+..+.+...|+|.+|. |+|...|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cd-f~lH~~C 29 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECD-FDLHEEC 29 (30)
T ss_dssp ---TTTS----S--EEE-TTT------HHH
T ss_pred CcCCcCCCcCCCCceEECccCC-CccChhc
Confidence 3699999999766899999995 9998887
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=90.41 E-value=0.22 Score=33.72 Aligned_cols=28 Identities=32% Similarity=0.999 Sum_probs=24.4
Q ss_pred cccccccccCCCCe-eEEcCCCCCcccchhh
Q 009958 47 YHCNYCNKDITGKI-RIKCAVCPDFDLCIEC 76 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~-ri~C~~C~d~dLC~~C 76 (521)
+.|+.|.+.+.+ . .|+|.+|. |++.+.|
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 479999999987 5 99999998 9888877
No 42
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=89.61 E-value=0.34 Score=52.89 Aligned_cols=48 Identities=21% Similarity=0.524 Sum_probs=43.6
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 152 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~ 152 (521)
...|+.-||..|--||..||-..|..||..+..+|+.||..+|. -+|+
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 46799999999999999999888999999999999999999999 4444
No 43
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=89.46 E-value=0.35 Score=54.12 Aligned_cols=52 Identities=19% Similarity=0.373 Sum_probs=42.9
Q ss_pred CCCCCCchhHHHHHHHHH-------Hh------------------CCCChHHHHHHhCCCCHHHHHHHHHhhccCCC
Q 009958 103 ICPDWNADDEILLLEGIE-------MY------------------GLGNWAEIAEHVGTKTKELCIEHYTNVYMNSP 154 (521)
Q Consensus 103 ~~~~Wta~Eel~LLeai~-------~~------------------G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~~ 154 (521)
....||-+|+..||.+|+ ++ ..=||..|++.+|||+..+|+.||.++-....
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s 511 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHH
Confidence 357899999999999995 33 11289999999999999999999998765443
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=86.97 E-value=0.46 Score=52.52 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=42.4
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
.+.|+..||..|+-+++.||..||..||..++.+++.+|+.||..
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 468999999999999999999999999999999999999999954
No 45
>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=86.11 E-value=0.91 Score=40.79 Aligned_cols=44 Identities=20% Similarity=0.434 Sum_probs=35.4
Q ss_pred CCCCCchhHHHHHHHHHHhCC---CChHHHHHHhC------------CCCHHHHHHHHH
Q 009958 104 CPDWNADDEILLLEGIEMYGL---GNWAEIAEHVG------------TKTKELCIEHYT 147 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~---gnW~~Ia~~vg------------tkt~~ec~~hy~ 147 (521)
...||.+||.-||-.+..||+ |+|+.|-..|- +||+.|+..|=.
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 688888766543
No 46
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=85.01 E-value=0.78 Score=50.20 Aligned_cols=46 Identities=26% Similarity=0.633 Sum_probs=41.3
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
|-...|+.+||.+||.+....- ..|-.||..|| +|..+|.+||++.
T Consensus 57 i~~tews~eederlLhlakl~p-~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEP-TQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcC-CccchHHHHhh-hhHHHHHHHHHHH
Confidence 4467899999999999998887 78999999997 8999999999873
No 47
>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=84.98 E-value=0.71 Score=37.50 Aligned_cols=43 Identities=28% Similarity=0.557 Sum_probs=28.4
Q ss_pred cccccCC-CCeeEEcCCCCC---cccchhhhhccccccCCCCCCCeeeccCC
Q 009958 51 YCNKDIT-GKIRIKCAVCPD---FDLCIECFSVGVEVHPHKSNHPYRVMDNL 98 (521)
Q Consensus 51 ~C~~~i~-~~~ri~C~~C~d---~dLC~~CF~~G~e~~~H~~~H~y~vi~~~ 98 (521)
.|+..+. +.+.|+|..|.. ..+|..||..+. |. .|.|.++...
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 8999888654
No 48
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=82.99 E-value=0.93 Score=42.70 Aligned_cols=44 Identities=20% Similarity=0.480 Sum_probs=37.2
Q ss_pred CCCCchhHHHHHHHHHHh---C---CCChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 105 PDWNADDEILLLEGIEMY---G---LGNWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~---G---~gnW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
..||.+||++|-+.|-.| | +--.++|++.++ ||+.-|-.+|+.+
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~ 54 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY 54 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH
Confidence 579999999999999777 2 124788999985 9999999999975
No 49
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=82.84 E-value=1.6 Score=45.95 Aligned_cols=47 Identities=21% Similarity=0.532 Sum_probs=38.4
Q ss_pred CCCCchhHHHHHHHHHHh----CCCC-----hHHHHHHhC----CCCHHHHHHHHHhhcc
Q 009958 105 PDWNADDEILLLEGIEMY----GLGN-----WAEIAEHVG----TKTKELCIEHYTNVYM 151 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~----G~gn-----W~~Ia~~vg----tkt~~ec~~hy~~~yi 151 (521)
..|+.+|.+.||++.... +-|+ |++||..+. .||+.||+..|.+++.
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 689999999999988543 3345 999999553 5999999999998754
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=81.26 E-value=2.5 Score=44.74 Aligned_cols=44 Identities=7% Similarity=0.314 Sum_probs=41.3
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
...|++.|-.++..|++++| -++.-||....+|+..|++..|.+
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 47899999999999999999 699999999999999999998875
No 51
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=77.56 E-value=2.5 Score=47.15 Aligned_cols=45 Identities=18% Similarity=0.413 Sum_probs=38.9
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHH----------HhCCCCHHHHHHHHHhh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAE----------HVGTKTKELCIEHYTNV 149 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~----------~vgtkt~~ec~~hy~~~ 149 (521)
...||.+|+..+.+||.++| .|++.|-+ .+..||..|++.||++.
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 79999933 33469999999999874
No 52
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=74.03 E-value=1.7 Score=45.59 Aligned_cols=45 Identities=33% Similarity=0.812 Sum_probs=36.5
Q ss_pred cCCcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeecc
Q 009958 44 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 96 (521)
Q Consensus 44 ~~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~ 96 (521)
...+.|..|..+. ..+|.|.+|++|+.|..|+.... | .|.|..+.
T Consensus 167 ~~~~~c~~c~~~~--~~~~~c~~~~d~d~~~~~~~k~~----h--~h~~~~~~ 211 (319)
T KOG1778|consen 167 WFAYTCPICKLEV--LTAWHCEVCPDYDRCRACEEKPL----H--PHLYEAME 211 (319)
T ss_pred ceeeecCcccccc--ccccccccCCchhhhhcccCCCC----C--Ccchhccc
Confidence 4678999999998 37899999999999999999865 3 35565554
No 53
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=73.97 E-value=4.3 Score=33.01 Aligned_cols=45 Identities=22% Similarity=0.480 Sum_probs=37.5
Q ss_pred CCCCchhHHHHHHHHHHh-----C-----------CCChHHHHHHhC-----CCCHHHHHHHHHhh
Q 009958 105 PDWNADDEILLLEGIEMY-----G-----------LGNWAEIAEHVG-----TKTKELCIEHYTNV 149 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~-----G-----------~gnW~~Ia~~vg-----tkt~~ec~~hy~~~ 149 (521)
..||.+|...|++.|+.| | -.-|++|+..+. .||..+++..|.++
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 579999999999999887 2 125999999884 59999999999865
No 54
>PLN03000 amine oxidase
Probab=73.94 E-value=5.9 Score=46.92 Aligned_cols=73 Identities=18% Similarity=0.137 Sum_probs=56.5
Q ss_pred cCCCccCCCCHHHHHHH--H-HhCCCchHHHHHHHHHHHHHHhCC--CCCHHHhhhhhccCc-hhHHHHHHHHHHCCCCC
Q 009958 447 MGFNETQLLSEAEKRLC--C-EIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKIEP-SKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 447 ~~~pg~~lLs~~Ek~LC--~-~lrL~P~~YL~iK~~LirE~~~~G--~lkk~~a~~l~kiD~-~k~~~Iydfl~~~Gwi~ 520 (521)
.++| .+-||++|.+.- . .-++.+..||.|...||+=...+- .+++++|...++.+. +.+..+|+||+.+|+|.
T Consensus 89 ~~~p-~d~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r~G~in 167 (881)
T PLN03000 89 AGFP-ADSLTEEEIEFGVVPIVGGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVTHGYIN 167 (881)
T ss_pred cCCC-cccCCHHHHhccccCcccccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHHcCccc
Confidence 3455 678999997751 1 124678999999999998888654 588888888876433 77889999999999984
No 55
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=73.44 E-value=4.5 Score=46.21 Aligned_cols=44 Identities=20% Similarity=0.423 Sum_probs=40.5
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
..-||..|-.++-+||-.|. .++..|++.|.+||..||.+.|+.
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 46899999999999999998 799999999999999999988763
No 56
>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=73.00 E-value=5.2 Score=32.15 Aligned_cols=47 Identities=23% Similarity=0.408 Sum_probs=32.5
Q ss_pred CCCCchhHHHHHHHHHHh---C---CCC--hHHHHHHhC-CCCHHHHHHHHHhhcc
Q 009958 105 PDWNADDEILLLEGIEMY---G---LGN--WAEIAEHVG-TKTKELCIEHYTNVYM 151 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~---G---~gn--W~~Ia~~vg-tkt~~ec~~hy~~~yi 151 (521)
..+|++||..|++.|..+ | -|| |.++++.-. .+|-.--++||.+...
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 468999999999999543 3 467 999999877 6888888999988753
No 57
>PHA00442 host recBCD nuclease inhibitor
Probab=72.56 E-value=4.2 Score=31.45 Aligned_cols=28 Identities=18% Similarity=0.456 Sum_probs=23.5
Q ss_pred CchhHHHHHHHHHHhCCCChHHHHHHhC
Q 009958 108 NADDEILLLEGIEMYGLGNWAEIAEHVG 135 (521)
Q Consensus 108 ta~Eel~LLeai~~~G~gnW~~Ia~~vg 135 (521)
+-+-+..+|++++.+|..||+.+.+.+.
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~eA~e 51 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYMDAVE 51 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHHHHHH
Confidence 3466788999999999999999987663
No 58
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=72.48 E-value=3.6 Score=45.68 Aligned_cols=49 Identities=24% Similarity=0.543 Sum_probs=44.2
Q ss_pred CCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhcc
Q 009958 102 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYM 151 (521)
Q Consensus 102 ~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi 151 (521)
+-...|+.+|+-.|++.-..+|. -|..||..++++|..+|..+|....=
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~-~wstia~~~d~rt~~~~~ery~~~~~ 118 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGT-QWSTIADYKDRRTAQQCVERYVNTLE 118 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCc-hhhhhccccCccchHHHHHHHHHHhh
Confidence 34679999999999999999994 69999999999999999999997643
No 59
>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=72.22 E-value=4.8 Score=32.77 Aligned_cols=43 Identities=28% Similarity=0.698 Sum_probs=30.9
Q ss_pred cccccCC-CCeeEEcCCCC---CcccchhhhhccccccCCCCCCCeeeccCC
Q 009958 51 YCNKDIT-GKIRIKCAVCP---DFDLCIECFSVGVEVHPHKSNHPYRVMDNL 98 (521)
Q Consensus 51 ~C~~~i~-~~~ri~C~~C~---d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~ 98 (521)
.|+..++ +.+.|+|..|. ..-+|..||..+ .| ..|.|.+....
T Consensus 2 ~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~----~H-~gH~~~~~~~~ 48 (71)
T smart00396 2 VCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSN----CH-KGHDYSLKTSR 48 (71)
T ss_pred CCCCccCCCCEEEECcCCCCCCCEeEChHHCCCC----CC-CCCCEEEEEec
Confidence 5666653 44779999995 245999999975 47 57888887653
No 60
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=72.08 E-value=2.5 Score=50.88 Aligned_cols=28 Identities=39% Similarity=0.763 Sum_probs=26.8
Q ss_pred CCCCCCchhHHHHHHHHHHhCCCChHHH
Q 009958 103 ICPDWNADDEILLLEGIEMYGLGNWAEI 130 (521)
Q Consensus 103 ~~~~Wta~Eel~LLeai~~~G~gnW~~I 130 (521)
+..+|+.+++-.||-||=.||+|+|+.|
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
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=69.04 E-value=8.7 Score=34.33 Aligned_cols=60 Identities=20% Similarity=0.423 Sum_probs=41.6
Q ss_pred cccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccCCCCCCCCCCCCchhHHHHHHHHHHhCCCChH
Q 009958 49 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWA 128 (521)
Q Consensus 49 Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLeai~~~G~gnW~ 128 (521)
|-.|+.++.- .+++|..|..- +.+ .|.+-.-.--.+|++.++...-... ||-.
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-TRLKCPSCGTE------------IEG-------------EFELPWFARLSPEQLEFIKLFIKNR-GNLK 53 (113)
T ss_pred CCCCCCceEE-EEEEcCCCCCE------------EEe-------------eeccchhhcCCHHHHHHHHHHHHhc-CCHH
Confidence 8899999875 78999888621 111 1111111123468899998888887 9999
Q ss_pred HHHHHhC
Q 009958 129 EIAEHVG 135 (521)
Q Consensus 129 ~Ia~~vg 135 (521)
+|++.+|
T Consensus 54 e~e~~lg 60 (113)
T PF09862_consen 54 EMEKELG 60 (113)
T ss_pred HHHHHHC
Confidence 9999998
No 62
>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=68.65 E-value=14 Score=27.02 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=35.6
Q ss_pred HHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 477 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 477 K~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
+..++.....+|.++..+.-..+.+....+.+...-|++.|||.
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 63
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=67.36 E-value=13 Score=26.81 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=31.9
Q ss_pred HhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 485 FSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 485 ~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..++.++..+....+.+....+.+..+.|.+.|||.
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 64
>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=66.94 E-value=5 Score=28.64 Aligned_cols=39 Identities=28% Similarity=0.531 Sum_probs=28.0
Q ss_pred CcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeee
Q 009958 46 LYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (521)
Q Consensus 46 ~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 94 (521)
...|..|... ...+.|..|. .-+|..|+..+ |+. |.+..
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 3467777754 2678999997 57999999976 754 76654
No 65
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=66.03 E-value=3.5 Score=34.27 Aligned_cols=35 Identities=26% Similarity=0.821 Sum_probs=17.6
Q ss_pred CCcccccccccC----CCCeeEEcCCCCCcccchhhhhcc
Q 009958 45 ALYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVG 80 (521)
Q Consensus 45 ~~~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G 80 (521)
....|.+|+-++ .+.+++-|.+|. |-+|-.||...
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~-fPvCr~CyEYE 46 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECA-FPVCRPCYEYE 46 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS------HHHHHHH
T ss_pred CCcccccccCccccCCCCCEEEEEcccC-CccchhHHHHH
Confidence 345799999875 466999999997 99999999863
No 66
>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=65.11 E-value=4.2 Score=29.16 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=21.1
Q ss_pred cccccccCCCCeeEEcCCCCCccc-chhhhhc
Q 009958 49 CNYCNKDITGKIRIKCAVCPDFDL-CIECFSV 79 (521)
Q Consensus 49 Cd~C~~~i~~~~ri~C~~C~d~dL-C~~CF~~ 79 (521)
||+|+..|.+.+.+.=..-..|-+ |..|...
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 999999998766655444344555 4777764
No 67
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=62.64 E-value=9.5 Score=46.10 Aligned_cols=48 Identities=25% Similarity=0.421 Sum_probs=42.5
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 009958 105 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 153 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~ 153 (521)
.+|+..+=..++.|+++||-.+-+.||..|++||++|++. |.+.|...
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~-y~~~f~~~ 872 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVER-YAKVFWER 872 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHH-HHHHHHHh
Confidence 4899999999999999999999999999999999999984 55565544
No 68
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=61.37 E-value=10 Score=45.74 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=37.6
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhC------------CCCHHHHHHHHHh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG------------TKTKELCIEHYTN 148 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg------------tkt~~ec~~hy~~ 148 (521)
...||.+||..||-.+..||+|+|+.|-..|- +||+.|+..|-..
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~ 982 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDT 982 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHH
Confidence 35799999999999999999999999977663 6888888766543
No 69
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=60.72 E-value=18 Score=27.48 Aligned_cols=50 Identities=20% Similarity=0.297 Sum_probs=38.3
Q ss_pred hCCCchHHHHHHHHHHHHHHhCCC--CCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 466 IRLAPPLYLRMQEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 466 lrL~P~~YL~iK~~LirE~~~~G~--lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
++|.|.+|..+-.+. ..+. ++..+....+.+++.-+.++.+=|++.|||.
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 356777776554433 3333 8888999999999999999999999999983
No 70
>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=60.18 E-value=6.1 Score=30.31 Aligned_cols=30 Identities=30% Similarity=0.738 Sum_probs=18.8
Q ss_pred ccccccccCCCC-------eeEEcCCCCCcccchhhhh
Q 009958 48 HCNYCNKDITGK-------IRIKCAVCPDFDLCIECFS 78 (521)
Q Consensus 48 ~Cd~C~~~i~~~-------~ri~C~~C~d~dLC~~CF~ 78 (521)
.|.+|.+.+... .+|+|..|. -.+|.+|=.
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 488899888653 699999998 458888844
No 71
>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=59.75 E-value=26 Score=25.48 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 111 DEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 111 Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
=|..||..++.-|--.|.+||+.+|- |+..|..++..
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 46889999999998899999999984 88889887754
No 72
>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=58.81 E-value=12 Score=29.90 Aligned_cols=40 Identities=20% Similarity=0.384 Sum_probs=31.9
Q ss_pred HHHHH-hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 481 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 481 irE~~-~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
|++++ .+|..+..+.-.-|.+++.-+..+.++|++.|.|.
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 44555 78899999888889999999999999999999983
No 73
>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=56.18 E-value=12 Score=28.40 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=29.7
Q ss_pred hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 486 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 486 ~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..|.++..+.-..+.++...+.++.+-|++.|||.
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 45558888888889999999999999999999984
No 74
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=55.88 E-value=7.4 Score=45.27 Aligned_cols=38 Identities=24% Similarity=0.694 Sum_probs=31.7
Q ss_pred CCCcCCcccccccccCCCCeeEEcCCCCCcccchhhhhcc
Q 009958 41 EGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 80 (521)
Q Consensus 41 ~~~~~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G 80 (521)
.++-..-.|+.|.+.+.+ ++++|..|. |-+|+.|+-.-
T Consensus 224 a~~g~~~mC~~C~~tlfn-~hw~C~~C~-~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 224 AVKGIREMCDRCETTLFN-IHWRCPRCG-FGVCLDCYRKW 261 (889)
T ss_pred cccCcchhhhhhcccccc-eeEEccccC-Ceeeecchhhc
Confidence 344566789999999987 899999997 66999999765
No 75
>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=54.04 E-value=40 Score=29.23 Aligned_cols=64 Identities=16% Similarity=0.055 Sum_probs=49.3
Q ss_pred CHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 456 SEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 456 s~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..-+..|=..++|.|..|..+..+-. -...+|.++..+....+.++...+.++.+=|+++|||.
T Consensus 11 ~~~~~~l~~~~~ls~~q~~vL~~l~~-~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 11 KSLKRYLKKEFNLSLEELLILYYLGK-LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh-hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 33445555668999999987754432 11245788888899999999999999999999999984
No 76
>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=53.07 E-value=26 Score=28.21 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCCC
Q 009958 473 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 521 (521)
Q Consensus 473 YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~~ 521 (521)
|-..++.++ ..|..+.+-.+.-|+|..+++.+|.|-|...|+|++
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 445555554 467788888889999999999999999999999864
No 77
>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=52.51 E-value=48 Score=28.90 Aligned_cols=61 Identities=8% Similarity=0.025 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 455 LSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 455 Ls~~Ek~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
++..-..+...++|.|.+|..+-.+ ..+|.++..+....+.++..-+.++.+=|.+.|||.
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 3444456667889999999866332 356778888888888999999999999999999985
No 78
>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=52.12 E-value=30 Score=28.81 Aligned_cols=44 Identities=23% Similarity=0.449 Sum_probs=33.0
Q ss_pred CCCchhHHHHHHHHHHh---C-------CC--ChHHHHHHhC-----CCCHHHHHHHHHhh
Q 009958 106 DWNADDEILLLEGIEMY---G-------LG--NWAEIAEHVG-----TKTKELCIEHYTNV 149 (521)
Q Consensus 106 ~Wta~Eel~LLeai~~~---G-------~g--nW~~Ia~~vg-----tkt~~ec~~hy~~~ 149 (521)
.||.+.+..||+++... | |. .|+.|+..+. ..|..||+.||..+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999977333 1 11 3888988875 57899999998753
No 79
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=52.01 E-value=16 Score=37.06 Aligned_cols=57 Identities=21% Similarity=0.204 Sum_probs=38.7
Q ss_pred hchhcccCChhHHHHHHHHHHHH--------HHHHHHH-----------HHHHHHHHhCccchHHHHHHHHHHHhh
Q 009958 334 YDVFMRFHSKEDHEDLLQTVISE--------HRTLKRI-----------QDLKEARAAGCRTSAEADRYLELKRGR 390 (521)
Q Consensus 334 l~~farf~~~~~~~~l~~~l~~e--------~~Lr~rI-----------~~L~~yR~~Gi~tl~e~~~ye~~k~~R 390 (521)
..-|.++++|-+.+.|..-|..= ..|+.-. .-|..|+.+||+|++++..|++..+.|
T Consensus 135 ~~e~Gr~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~n~~YI~~IL~nW~k~gvkTv~dv~~~~~~~~~~ 210 (246)
T COG3935 135 EEEFGRMLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKLNFKYIDAILRNWKKNGVKTVEDVRAREEERRTR 210 (246)
T ss_pred HHHcCCcCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHH
Confidence 45677788888887775543211 1222211 238899999999999999998776544
No 80
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=50.02 E-value=13 Score=35.48 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=33.6
Q ss_pred CCCCCchhHHHHHHHHHHhCCC------ChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 104 CPDWNADDEILLLEGIEMYGLG------NWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~g------nW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
...||.+++++|-+.|-.|+-. -.+.++..+ .+|+..|..+|+.+
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~ 55 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSV 55 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHH
Confidence 4679999999998888777521 245555666 48999999999543
No 81
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=48.85 E-value=32 Score=40.64 Aligned_cols=69 Identities=14% Similarity=0.156 Sum_probs=54.0
Q ss_pred cCCCCHHHHHH---HHHhCCCchHHHHHHHHHHHHHHhCC--CCCHHHhhhhhcc-CchhHHHHHHHHHHCCCCC
Q 009958 452 TQLLSEAEKRL---CCEIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKI-EPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 452 ~~lLs~~Ek~L---C~~lrL~P~~YL~iK~~LirE~~~~G--~lkk~~a~~l~ki-D~~k~~~Iydfl~~~Gwi~ 520 (521)
.+-||++|.+. =...+.-+..||.|...||+=..++- .+++++|...++. ..+-+..+|+||+..|+|.
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 56799988764 22334788999999999998887654 5888899887652 3468999999999999984
No 82
>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=48.83 E-value=9.8 Score=36.07 Aligned_cols=28 Identities=32% Similarity=0.724 Sum_probs=25.2
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHH
Q 009958 106 DWNADDEILLLEGIEMYGLGNWAEIAEH 133 (521)
Q Consensus 106 ~Wta~Eel~LLeai~~~G~gnW~~Ia~~ 133 (521)
-|-..-|.-||.||-.+|+|-|++|...
T Consensus 5 iw~r~hdywll~gi~~hgy~rwqdi~nd 32 (173)
T PF08074_consen 5 IWHRRHDYWLLAGIVKHGYGRWQDIQND 32 (173)
T ss_pred hhhhhhhHHHHhHHhhccchhHHHHhcC
Confidence 4888889999999999999999999764
No 83
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=48.77 E-value=50 Score=29.77 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=44.6
Q ss_pred HHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 461 RLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 461 ~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
.....++|.|.+|..+-.+. ..++.++..+....+.++..-+.++.+=|++.|||.
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 134456777888888999999999999999999985
No 84
>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=48.69 E-value=60 Score=25.61 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 472 LYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 472 ~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
.=|.+|..+|...+..|.|++++|..+. +.+..-+++....|++.
T Consensus 15 qm~e~kK~~idk~Ve~G~iTqeqAd~ik----~~id~~~~~~~qnGf~p 59 (59)
T PF10925_consen 15 QMLELKKQIIDKYVEAGVITQEQADAIK----KHIDQRQEYMQQNGFVP 59 (59)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHH----HHHHHHHHHHHHcCCCC
Confidence 4478999999999999999999998864 66778899999999863
No 85
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=48.03 E-value=15 Score=44.30 Aligned_cols=34 Identities=26% Similarity=0.845 Sum_probs=28.3
Q ss_pred cccccccccC----CCCeeEEcCCCCCcccchhhhhccc
Q 009958 47 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 47 ~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
-.|.+|+-++ .+.+++-|.+|. |-+|-.||....
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~-FPVCrpCYEYEr 55 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCA-FPVCRPCYEYER 55 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCC-Cccccchhhhhh
Confidence 4799999875 466999999997 999999996533
No 86
>smart00595 MADF subfamily of SANT domain.
Probab=47.84 E-value=19 Score=29.78 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=20.9
Q ss_pred ChHHHHHHhCCCCHHHHHHHHHhh
Q 009958 126 NWAEIAEHVGTKTKELCIEHYTNV 149 (521)
Q Consensus 126 nW~~Ia~~vgtkt~~ec~~hy~~~ 149 (521)
-|..||..+|. |.++|+.+|.++
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 59999999997 999999999875
No 87
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=47.79 E-value=21 Score=30.96 Aligned_cols=32 Identities=25% Similarity=0.558 Sum_probs=24.0
Q ss_pred CCCCCCchhHHHHHHHHHHh----CCC---ChHHHHHHh
Q 009958 103 ICPDWNADDEILLLEGIEMY----GLG---NWAEIAEHV 134 (521)
Q Consensus 103 ~~~~Wta~Eel~LLeai~~~----G~g---nW~~Ia~~v 134 (521)
+..-||.++|+.||+|+-.| |.+ +|...-++|
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~v 41 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFV 41 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHH
Confidence 45779999999999999888 643 455555554
No 88
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=46.89 E-value=12 Score=40.62 Aligned_cols=43 Identities=26% Similarity=0.422 Sum_probs=37.1
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 104 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 104 ~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
.-+||..|-- +...-..|| .|.+.||+.++++||+|+...|++
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 3689987655 888889999 799999999999999999987764
No 89
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=46.28 E-value=23 Score=37.74 Aligned_cols=43 Identities=28% Similarity=0.499 Sum_probs=37.2
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHH-HHHhCCCCHHHHHHHHHh
Q 009958 105 PDWNADDEILLLEGIEMYGLGNWAEI-AEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~I-a~~vgtkt~~ec~~hy~~ 148 (521)
..|+.+|=+.+-++++.|| .++.-| +..|.||+..||...|..
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 5899999999999999999 576666 568899999999987764
No 90
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=46.08 E-value=17 Score=43.69 Aligned_cols=36 Identities=25% Similarity=0.777 Sum_probs=29.4
Q ss_pred CCcccccccccC----CCCeeEEcCCCCCcccchhhhhccc
Q 009958 45 ALYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 45 ~~~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
....|.+|+-++ .+.+++-|.+|. |-+|-.||....
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~-fpvCr~cyeye~ 53 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCG-FPVCKPCYEYER 53 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCC-Cccccchhhhhh
Confidence 455799999874 466999999997 999999996543
No 91
>PLN02436 cellulose synthase A
Probab=45.80 E-value=12 Score=44.82 Aligned_cols=35 Identities=26% Similarity=0.758 Sum_probs=29.0
Q ss_pred CcccccccccC----CCCeeEEcCCCCCcccchhhhhccc
Q 009958 46 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 46 ~~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
...|.+|+-++ .+.+++-|.+|. |-+|..||....
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~-fpvCr~Cyeyer 74 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECA-FPVCRPCYEYER 74 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCC-Cccccchhhhhh
Confidence 34799999875 466999999997 999999996544
No 92
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=44.90 E-value=79 Score=29.67 Aligned_cols=39 Identities=26% Similarity=0.516 Sum_probs=26.0
Q ss_pred ccccccccCCCCeeEEcCCCCCcccchhhhhccccccCC
Q 009958 48 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPH 86 (521)
Q Consensus 48 ~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H 86 (521)
.|-.|++.|.+..+.-=.+=....+|..|+--|.++..+
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~G~~~~~~ 40 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKFGKEIIKK 40 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhcCCccccC
Confidence 399999999874222222222367899999888865544
No 93
>PF13730 HTH_36: Helix-turn-helix domain
Probab=43.77 E-value=65 Score=23.99 Aligned_cols=53 Identities=19% Similarity=0.209 Sum_probs=36.6
Q ss_pred CCCchHHHHHHHHHHHHHHhCC-CCCHHHhhhhhccCchhHHHHHHHHHHCCCC
Q 009958 467 RLAPPLYLRMQEVMSREIFSGN-VNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 519 (521)
Q Consensus 467 rL~P~~YL~iK~~LirE~~~~G-~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi 519 (521)
+|.|...+.+=.++-.-...++ ..+.+.....+.+-.+.+.+..+-|++.|||
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 4555555555443332222333 2467777888899999999999999999997
No 94
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=43.61 E-value=46 Score=25.06 Aligned_cols=28 Identities=18% Similarity=0.431 Sum_probs=23.7
Q ss_pred cCChhHHHHHHHHH-----HHHHHHHHHHHHHH
Q 009958 340 FHSKEDHEDLLQTV-----ISEHRTLKRIQDLK 367 (521)
Q Consensus 340 f~~~~~~~~l~~~l-----~~e~~Lr~rI~~L~ 367 (521)
+.+++++++|++.| ++|.+|++.+.+..
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 95
>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=42.53 E-value=42 Score=31.29 Aligned_cols=53 Identities=19% Similarity=0.388 Sum_probs=44.6
Q ss_pred CCCCchhHHHHHHHHHHhCCC--ChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCC
Q 009958 105 PDWNADDEILLLEGIEMYGLG--NWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPL 158 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~g--nW~~Ia~~vgtkt~~ec~~hy~~~yi~~~~~pl 158 (521)
-+++..+-..+|.+|..||+| +|......+-.||.+|.+ .|-.+|+..-+-|.
T Consensus 39 lGFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~-aY~~LFm~HL~E~~ 93 (145)
T PF06461_consen 39 LGFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIR-AYGSLFMRHLCEPG 93 (145)
T ss_pred eccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHH-HHHHHHHHHhcCCC
Confidence 378999999999999999999 799999999999998887 57777776655443
No 96
>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=42.16 E-value=47 Score=27.58 Aligned_cols=41 Identities=17% Similarity=0.355 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCCCCHHHhhhhhc---cCchhHHHHHHHHHHCCC
Q 009958 478 EVMSREIFSGNVNNKADAHHLFK---IEPSKIDRVYDMLVKKGL 518 (521)
Q Consensus 478 ~~LirE~~~~G~lkk~~a~~l~k---iD~~k~~~Iydfl~~~Gw 518 (521)
..||....+.|.++-.+....++ +++..+..||++|...|.
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 34777777889999998888887 899999999999999885
No 97
>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=41.21 E-value=72 Score=25.59 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCCC
Q 009958 473 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 521 (521)
Q Consensus 473 YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~~ 521 (521)
|-..++.++ ..|..+-+-.+.-|+|-.|++.+|.|-|...|.|++
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 444444444 456667777788899999999999999999999975
No 98
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=41.15 E-value=5.1 Score=40.97 Aligned_cols=31 Identities=29% Similarity=0.702 Sum_probs=18.6
Q ss_pred CCCCCCCcCCcccccccccCCCCeeEEcCCCC
Q 009958 37 QGAGEGKRALYHCNYCNKDITGKIRIKCAVCP 68 (521)
Q Consensus 37 ~~~~~~~~~~~~Cd~C~~~i~~~~ri~C~~C~ 68 (521)
.|.++....-.+|+.|..+... ||++|+.|.
T Consensus 202 ~g~~~~GlRYL~CslC~teW~~-VR~KC~nC~ 232 (308)
T COG3058 202 IGETEQGLRYLHCSLCETEWHY-VRVKCSNCE 232 (308)
T ss_pred ecCccccchhhhhhhHHHHHHH-HHHHhcccc
Confidence 4444444455567777776654 777776664
No 99
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=40.46 E-value=37 Score=37.12 Aligned_cols=48 Identities=15% Similarity=0.400 Sum_probs=41.8
Q ss_pred CCCCCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 009958 100 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 148 (521)
Q Consensus 100 ~~~~~~~Wta~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~ 148 (521)
+.-+...||++|-.+|-.|.+.|| .+...|-..+.-|+-...+..|..
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 334567999998888889999999 799999999999999999988764
No 100
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=39.38 E-value=38 Score=26.96 Aligned_cols=44 Identities=11% Similarity=0.061 Sum_probs=32.7
Q ss_pred HHHHHHHHHh-CCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 477 QEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 477 K~~LirE~~~-~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
|+.++.=... ++.++-.|.-+.|.+....++++...|.+.|.|.
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 4444432223 6778888888889999999999999999999874
No 101
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.14 E-value=66 Score=29.12 Aligned_cols=52 Identities=12% Similarity=0.252 Sum_probs=43.3
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 464 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 464 ~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..++|.|.+|..+..+ ..+|.++..+....+.++..-+.++.+=|++.|||.
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 5578999999877643 245668888888888999999999999999999984
No 102
>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=39.00 E-value=60 Score=24.96 Aligned_cols=34 Identities=26% Similarity=0.359 Sum_probs=28.3
Q ss_pred hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCC
Q 009958 486 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 519 (521)
Q Consensus 486 ~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi 519 (521)
.++.++..+....+.++..-+.++.+=|++.|||
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 103
>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=38.26 E-value=45 Score=24.00 Aligned_cols=24 Identities=29% Similarity=0.531 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHhCCCChHHHHHHhC
Q 009958 111 DEILLLEGIEMYGLGNWAEIAEHVG 135 (521)
Q Consensus 111 Eel~LLeai~~~G~gnW~~Ia~~vg 135 (521)
|-..|.++++.+| ||....|+.+|
T Consensus 6 E~~~i~~aL~~~~-gn~~~aA~~Lg 29 (42)
T PF02954_consen 6 EKQLIRQALERCG-GNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHTT-T-HHHHHHHHT
T ss_pred HHHHHHHHHHHhC-CCHHHHHHHHC
Confidence 5567889999999 99999999998
No 104
>PLN02400 cellulose synthase
Probab=38.15 E-value=19 Score=43.36 Aligned_cols=35 Identities=29% Similarity=0.822 Sum_probs=28.8
Q ss_pred CcccccccccC----CCCeeEEcCCCCCcccchhhhhccc
Q 009958 46 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 46 ~~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
.-.|.+|+-++ .+.+++-|.+|. |-+|-.||....
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCa-FPVCRpCYEYER 74 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECA-FPVCRPCYEYER 74 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCC-Cccccchhheec
Confidence 34799999875 466999999997 999999996533
No 105
>PLN02189 cellulose synthase
Probab=37.44 E-value=20 Score=42.99 Aligned_cols=36 Identities=25% Similarity=0.746 Sum_probs=29.4
Q ss_pred CCcccccccccC----CCCeeEEcCCCCCcccchhhhhccc
Q 009958 45 ALYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 45 ~~~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
....|.+|+-++ .+.+++-|.+|. |-+|-.||....
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~-fpvCr~Cyeyer 72 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECG-FPVCRPCYEYER 72 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCC-Cccccchhhhhh
Confidence 344799999874 466999999997 999999996544
No 106
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=37.27 E-value=21 Score=37.46 Aligned_cols=31 Identities=23% Similarity=0.751 Sum_probs=24.2
Q ss_pred CcccccccccCCCCeeEEcCCCCCcccchhhh
Q 009958 46 LYHCNYCNKDITGKIRIKCAVCPDFDLCIECF 77 (521)
Q Consensus 46 ~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF 77 (521)
.-+|..|+.......+|+|..|... +|+.|=
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~-FCldCD 360 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNV-FCLDCD 360 (378)
T ss_pred CcceeeeccccCCCCcEEchhccce-eeccch
Confidence 3459999777666699999999854 788884
No 107
>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=36.86 E-value=72 Score=24.15 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=29.5
Q ss_pred hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 486 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 486 ~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
.++ ++..++...+.+....+.++.+-|++.|||.
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 108
>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=36.64 E-value=7.4 Score=31.23 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCccchHHHHHHHH
Q 009958 363 IQDLKEARAAGCRTSAEADRYLE 385 (521)
Q Consensus 363 I~~L~~yR~~Gi~tl~e~~~ye~ 385 (521)
..-|..|++.||+|++++..|++
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 35688999999999999988754
No 109
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=35.51 E-value=40 Score=36.93 Aligned_cols=42 Identities=26% Similarity=0.519 Sum_probs=31.8
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHH-HhCCCCHHHHHHHHH
Q 009958 105 PDWNADDEILLLEGIEMYGLGNWAEIAE-HVGTKTKELCIEHYT 147 (521)
Q Consensus 105 ~~Wta~Eel~LLeai~~~G~gnW~~Ia~-~vgtkt~~ec~~hy~ 147 (521)
+.|++.|-.++-||+++|| .++++|-. ++.=|+-..+.+.|.
T Consensus 286 EEWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHHHHH
Confidence 6899999999999999999 57777644 444566666665554
No 110
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=34.09 E-value=15 Score=33.76 Aligned_cols=53 Identities=23% Similarity=0.442 Sum_probs=38.7
Q ss_pred CCcccccccccCCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeeeccCCCC
Q 009958 45 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSF 100 (521)
Q Consensus 45 ~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~ 100 (521)
..|.|+.|...-++.-+.+=.+|-+|.+|--||+.-. .|-+.|+-=.+...+|
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 6899999998766656677778999999999999854 3555565444444333
No 111
>PRK08359 transcription factor; Validated
Probab=34.06 E-value=31 Score=33.24 Aligned_cols=40 Identities=18% Similarity=0.380 Sum_probs=26.7
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhh-hccc-cccCC
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECF-SVGV-EVHPH 86 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF-~~G~-e~~~H 86 (521)
..|-.|+.+|.+..+.-=.+=....+|..|+ --|. +++.+
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 4499999999875232222323367899999 6687 55544
No 112
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.06 E-value=67 Score=23.65 Aligned_cols=46 Identities=13% Similarity=0.245 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHh-CCCC-CHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 475 RMQEVMSREIFS-GNVN-NKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 475 ~iK~~LirE~~~-~G~l-kk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
.++..++...+. +..+ +..+....+.+...-+.+.+.-|.+.|||.
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 344555444333 3345 677778888899999999999999999984
No 113
>PLN02195 cellulose synthase A
Probab=32.92 E-value=29 Score=41.50 Aligned_cols=35 Identities=23% Similarity=0.782 Sum_probs=28.3
Q ss_pred CcccccccccC----CCCeeEEcCCCCCcccchhhhhccc
Q 009958 46 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV 81 (521)
Q Consensus 46 ~~~Cd~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~ 81 (521)
...|.+|+-++ .+.+++-|.+|. |-+|-.||....
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~-~pvCrpCyeyer 44 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECS-YPLCKACLEYEI 44 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCC-Cccccchhhhhh
Confidence 34799999854 456999999997 999999996543
No 114
>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=32.06 E-value=30 Score=22.73 Aligned_cols=13 Identities=38% Similarity=0.761 Sum_probs=10.0
Q ss_pred HHHHHHHHHCCCC
Q 009958 507 DRVYDMLVKKGLA 519 (521)
Q Consensus 507 ~~Iydfl~~~Gwi 519 (521)
.-|||||+++|+.
T Consensus 5 ~lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 5 QLIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHHCT-H
T ss_pred HHHHHHHHHCCcH
Confidence 3589999999974
No 115
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=30.36 E-value=30 Score=26.39 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=20.9
Q ss_pred ccccccccCCCCeeEEcCCCCCcccchhhhhcc
Q 009958 48 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 80 (521)
Q Consensus 48 ~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G 80 (521)
.|+.|+..+.-..+++ =.|..+|..||..-
T Consensus 1 ~C~iCg~kigl~~~~k---~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK---IKDGYICKDCLKKL 30 (51)
T ss_pred CCCcccccccccccee---ccCccchHHHHHHh
Confidence 4999999986433333 33456999999874
No 116
>COG3196 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.29 E-value=49 Score=30.94 Aligned_cols=98 Identities=14% Similarity=0.220 Sum_probs=57.4
Q ss_pred CCCCCCCCCCCCCCcCCcccccccccCCCCeeE----EcCCCCCcccchhhhhccccccCCCC--CCCeeeccCCCCCC-
Q 009958 30 SDTAAPGQGAGEGKRALYHCNYCNKDITGKIRI----KCAVCPDFDLCIECFSVGVEVHPHKS--NHPYRVMDNLSFPL- 102 (521)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~Cd~C~~~i~~~~ri----~C~~C~d~dLC~~CF~~G~e~~~H~~--~H~y~vi~~~~~~~- 102 (521)
++|..+|..++ ..+.|+.|.+.-. +.| .|..=-.-.||+.|.+.|..-..... +..|-.|++ .+|-
T Consensus 15 P~PL~tGsiEa----d~v~C~CCeq~r~--y~YtGp~Y~~~El~~~LCPWCIADGSAA~rf~aSF~D~~~~i~~-~vp~d 87 (183)
T COG3196 15 PDPLGTGSIEA----DEVSCVCCEQRRP--YTYTGPVYAEEELNEALCPWCIADGSAASRFDASFTDAMWAVPD-DVPED 87 (183)
T ss_pred CCcccCCceee----cceeeeeccccCc--eeecCCcccHhhcccccCCceecCCcHHHhhhcccchhhccCCC-CChHH
Confidence 55655664443 3678999988642 223 33321225699999999874332221 234655554 3331
Q ss_pred ----------CCCCCCchhHHHHH-HHHHHhCCCChHHHHHHh
Q 009958 103 ----------ICPDWNADDEILLL-EGIEMYGLGNWAEIAEHV 134 (521)
Q Consensus 103 ----------~~~~Wta~Eel~LL-eai~~~G~gnW~~Ia~~v 134 (521)
-=.+|..++.+.-. ++..-.|.--|++|++..
T Consensus 88 ~~~Ev~ERTPGYtgWQQE~WL~hCgDaCaF~G~vG~~eI~dl~ 130 (183)
T COG3196 88 VTEEVLERTPGYTGWQQEEWLHHCGDACAFLGPVGASEIADLP 130 (183)
T ss_pred HHHHHHhcCCCcchhHHHHHHHHhcchhhhcccccHHHHHHhH
Confidence 01468777776665 455556666799998764
No 117
>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=30.05 E-value=1e+02 Score=23.42 Aligned_cols=39 Identities=15% Similarity=0.249 Sum_probs=32.5
Q ss_pred HHHHH-hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCC
Q 009958 481 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 519 (521)
Q Consensus 481 irE~~-~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi 519 (521)
|++++ .+|.++..+++.++.+--.-+-.|.+||-..||.
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 6899999999999998888888999999999985
No 118
>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=29.86 E-value=38 Score=27.01 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=15.7
Q ss_pred HHHHHHHHhCccchHHHH
Q 009958 364 QDLKEARAAGCRTSAEAD 381 (521)
Q Consensus 364 ~~L~~yR~~Gi~tl~e~~ 381 (521)
.-|..|++.||+|+++++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 458899999999999875
No 119
>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=29.60 E-value=56 Score=28.85 Aligned_cols=23 Identities=17% Similarity=0.534 Sum_probs=20.4
Q ss_pred HHhCCCchHHHHHHHHHHHHHHh
Q 009958 464 CEIRLAPPLYLRMQEVMSREIFS 486 (521)
Q Consensus 464 ~~lrL~P~~YL~iK~~LirE~~~ 486 (521)
.+++|.|..|+.+|..|..|.++
T Consensus 86 ~~igls~~EYm~lKkelae~i~~ 108 (109)
T TIGR03277 86 QRIGMSPEEYMELKKKLAEELLK 108 (109)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhc
Confidence 46899999999999999988874
No 120
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=29.55 E-value=14 Score=40.01 Aligned_cols=50 Identities=20% Similarity=0.433 Sum_probs=33.1
Q ss_pred CCCCCCcCCccccccccc--------------CCCCeeEEcCCCCCcccchhhhhccccccCCCCCCCeee
Q 009958 38 GAGEGKRALYHCNYCNKD--------------ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 94 (521)
Q Consensus 38 ~~~~~~~~~~~Cd~C~~~--------------i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 94 (521)
++...+...|.|..|... |.. +-|+|.+|....-|. +..-.|+++|.=+.
T Consensus 259 ~~i~n~iGdyiCqLCK~kYeD~F~LAQHrC~RIV~-vEYrCPEC~KVFsCP------ANLASHRRWHKPR~ 322 (500)
T KOG3993|consen 259 AGIPNVIGDYICQLCKEKYEDAFALAQHRCPRIVH-VEYRCPECDKVFSCP------ANLASHRRWHKPRP 322 (500)
T ss_pred ccCcccHHHHHHHHHHHhhhhHHHHhhccCCeeEE-eeecCCcccccccCc------hhhhhhhcccCCch
Confidence 445567788999999753 222 556777777664454 34456999996553
No 121
>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=29.30 E-value=1.1e+02 Score=25.47 Aligned_cols=38 Identities=24% Similarity=0.399 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCC-------CChHHHHHHhCCC---C--HHHHHHHHHhhc
Q 009958 113 ILLLEGIEMYGL-------GNWAEIAEHVGTK---T--KELCIEHYTNVY 150 (521)
Q Consensus 113 l~LLeai~~~G~-------gnW~~Ia~~vgtk---t--~~ec~~hy~~~y 150 (521)
..|-.+|...|- +.|..||..+|-. + ..+.+.+|.++-
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L 88 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYL 88 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHh
Confidence 556677777761 3699999999832 2 367788887653
No 122
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=29.22 E-value=1.4e+02 Score=27.25 Aligned_cols=50 Identities=18% Similarity=0.446 Sum_probs=38.2
Q ss_pred hHHHHHHHHHHHHHHh----CC--CCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 471 PLYLRMQEVMSREIFS----GN--VNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 471 ~~YL~iK~~LirE~~~----~G--~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
.-|.-|.+.+....++ .| .++..+.-..+.+.+|-+.|.|.-|.+.|+|.
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 3577777777766663 34 46666666667899999999999999999874
No 123
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=28.92 E-value=93 Score=25.35 Aligned_cols=52 Identities=25% Similarity=0.383 Sum_probs=38.2
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 464 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 464 ~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
...+|.+..+..+.-+. .+|.++..+....+.+....+.++++-|++.|||.
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 34556666655554433 34567777777788899999999999999999984
No 124
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=28.79 E-value=1.3e+02 Score=24.55 Aligned_cols=40 Identities=13% Similarity=0.108 Sum_probs=33.3
Q ss_pred HHHHH-hC-CCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 481 SREIF-SG-NVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 481 irE~~-~~-G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
|-+.+ .. |.++..+.-..+.+...-+.++.+.|++.|||.
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 44454 33 689998888888999999999999999999984
No 125
>PRK00420 hypothetical protein; Validated
Probab=27.42 E-value=38 Score=30.23 Aligned_cols=30 Identities=17% Similarity=0.324 Sum_probs=21.7
Q ss_pred CcccccccccCCC--CeeEEcCCCCCcccchh
Q 009958 46 LYHCNYCNKDITG--KIRIKCAVCPDFDLCIE 75 (521)
Q Consensus 46 ~~~Cd~C~~~i~~--~~ri~C~~C~d~dLC~~ 75 (521)
..+|..|+.++.. ...+.|..|.....|..
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence 3689999998763 46778888876666543
No 126
>PRK10870 transcriptional repressor MprA; Provisional
Probab=26.92 E-value=1.5e+02 Score=28.00 Aligned_cols=58 Identities=10% Similarity=0.160 Sum_probs=45.8
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 460 KRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 460 k~LC~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
...-..++|.|.+|..+..+. ...++.++-.+....+.++..-+.++.+=|++.|||.
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 445578999999999875543 1234667777777788899999999999999999984
No 127
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=26.19 E-value=79 Score=30.16 Aligned_cols=38 Identities=16% Similarity=0.444 Sum_probs=25.1
Q ss_pred cccccccCCCCeeEEcCCCCCcccchhhhhccccccCCC
Q 009958 49 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 87 (521)
Q Consensus 49 Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~ 87 (521)
|-.|++.+.. ...--.+=.....|..|+--|.....|.
T Consensus 6 CEiCG~~i~~-~~~v~vegsel~VC~~Cak~G~~~~~~~ 43 (165)
T COG1813 6 CELCGREIDK-PIKVKVEGAELTVCDDCAKFGTAAKTAS 43 (165)
T ss_pred eeccccccCC-CeeEEeecceeehhHHHHHhccCccccC
Confidence 9999999874 2222222234779999997776555554
No 128
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=25.91 E-value=1.1e+02 Score=30.19 Aligned_cols=46 Identities=17% Similarity=0.356 Sum_probs=38.7
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHhC---CCCHHHHHHHHHhhccCC
Q 009958 106 DWNADDEILLLEGIEMYGLGNWAEIAEHVG---TKTKELCIEHYTNVYMNS 153 (521)
Q Consensus 106 ~Wta~Eel~LLeai~~~G~gnW~~Ia~~vg---tkt~~ec~~hy~~~yi~~ 153 (521)
.|++.+|++|+.||++- .+-+.|+.-|. .-|..|+..+|..+-.+.
T Consensus 1 rW~~~DDl~Li~av~~~--~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQT--NDLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHHh--cCHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 49999999999999996 48888888775 479999999999875443
No 129
>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=25.66 E-value=89 Score=23.23 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=33.3
Q ss_pred HHHHHHHH--hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 478 EVMSREIF--SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 478 ~~LirE~~--~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
.+-|-|++ .++.++..+.-..+.+....+.++..-|++.||+.
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 34444555 34457888888889999999999999999999984
No 130
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=25.58 E-value=1.4e+02 Score=27.36 Aligned_cols=43 Identities=14% Similarity=0.109 Sum_probs=37.2
Q ss_pred hhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 009958 110 DDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 153 (521)
Q Consensus 110 ~Eel~LLeai~~~G~gnW~~Ia~~vgtkt~~ec~~hy~~~yi~~ 153 (521)
+-|..||++++.-|--.|.+||+.+| -|+..|..++..+-=.+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg-lS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG-VSPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC-cCHHHHHHHHHHHHHCC
Confidence 56899999999999889999999998 48899999998875444
No 131
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=25.44 E-value=1.8e+02 Score=23.05 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=34.4
Q ss_pred HHHHHHHHHhCCC--CCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 477 QEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 477 K~~LirE~~~~G~--lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
++.++.=....|. ++..+.-+.+.++...+.++..=|.+.|+|.
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 3444444445555 8888888889999999999999999999984
No 132
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.41 E-value=1.1e+02 Score=31.65 Aligned_cols=40 Identities=20% Similarity=0.606 Sum_probs=31.7
Q ss_pred CCCCcCCcccccccccCCCCeeEEcCCCCCcccchhhhhc
Q 009958 40 GEGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSV 79 (521)
Q Consensus 40 ~~~~~~~~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~ 79 (521)
...+....+|..|..-+.++-+++|...+.-.+|-.|--.
T Consensus 262 ~~A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRe 301 (352)
T KOG3579|consen 262 GAAPSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRE 301 (352)
T ss_pred ccCCCCceeehhhhhhhccCceeecCCCcccceecccCHH
Confidence 4455667899999999999899999887777778777544
No 133
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=25.24 E-value=1.1e+02 Score=27.88 Aligned_cols=27 Identities=15% Similarity=0.381 Sum_probs=22.1
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCC
Q 009958 464 CEIRLAPPLYLRMQEVMSREIFSGNVN 490 (521)
Q Consensus 464 ~~lrL~P~~YL~iK~~LirE~~~~G~l 490 (521)
+.++|+|..|+.+|..|-.+.+....+
T Consensus 87 ~ri~mS~~EYM~lKkqLae~il~~s~~ 113 (153)
T COG4008 87 NRINMSPEEYMELKKQLAEYILGHSEP 113 (153)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhccCCC
Confidence 578999999999999998887754433
No 134
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=24.99 E-value=75 Score=24.89 Aligned_cols=35 Identities=20% Similarity=0.240 Sum_probs=31.4
Q ss_pred hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 486 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 486 ~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..|..+-.+....+.++...+.++.+-|.+.|||.
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 67888888888888999999999999999999984
No 135
>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=24.78 E-value=68 Score=23.82 Aligned_cols=24 Identities=33% Similarity=0.665 Sum_probs=18.5
Q ss_pred CCcccccccccC--CCCeeEEcCCCC
Q 009958 45 ALYHCNYCNKDI--TGKIRIKCAVCP 68 (521)
Q Consensus 45 ~~~~Cd~C~~~i--~~~~ri~C~~C~ 68 (521)
....|++|++.| ....-++|..|.
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 456899999998 445789999986
No 136
>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=24.61 E-value=56 Score=34.21 Aligned_cols=25 Identities=16% Similarity=0.446 Sum_probs=22.4
Q ss_pred CccCCCCHHHHHHHHHhCCCchHHH
Q 009958 450 NETQLLSEAEKRLCCEIRLAPPLYL 474 (521)
Q Consensus 450 pg~~lLs~~Ek~LC~~lrL~P~~YL 474 (521)
.+..-||.+|+..|.+|+|.|..|+
T Consensus 301 ~~~~~Lt~ee~av~~~lGis~edf~ 325 (326)
T PF10123_consen 301 DGSAALTAEELAVCRQLGISPEDFA 325 (326)
T ss_pred CCCCCCCHHHHHHHHHcCCCHHHhc
Confidence 3466899999999999999999996
No 137
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=24.46 E-value=87 Score=22.58 Aligned_cols=34 Identities=15% Similarity=0.538 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHH
Q 009958 477 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYD 511 (521)
Q Consensus 477 K~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iyd 511 (521)
|+.||...+..|+.+..+ +.|..+...-..+.|.
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 677888888999999988 8888888777777764
No 138
>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=23.87 E-value=68 Score=27.38 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=25.0
Q ss_pred hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCC
Q 009958 486 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 519 (521)
Q Consensus 486 ~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi 519 (521)
..|+-...-|.+| .++.++++.+.+||+..|+|
T Consensus 63 ~~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 63 EEGVHVDEIAQQL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TTTEEHHHHHHHS-TS-HHHHHHHHHHHHHTTSE
T ss_pred CCcccHHHHHHHh-CcCHHHHHHHHHHHHhCCeE
Confidence 3454444555555 99999999999999999997
No 139
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.81 E-value=52 Score=29.39 Aligned_cols=30 Identities=30% Similarity=0.685 Sum_probs=22.5
Q ss_pred cccccccccCCC-----------CeeEEcCCCCCcccchhhh
Q 009958 47 YHCNYCNKDITG-----------KIRIKCAVCPDFDLCIECF 77 (521)
Q Consensus 47 ~~Cd~C~~~i~~-----------~~ri~C~~C~d~dLC~~CF 77 (521)
..|.+|+..+.. ..+|+|..|. -++|.+|=
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 359999997642 3589999997 55788873
No 140
>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=23.73 E-value=30 Score=28.35 Aligned_cols=20 Identities=40% Similarity=0.936 Sum_probs=7.4
Q ss_pred CcccccccccCCCCeeEEcCCC
Q 009958 46 LYHCNYCNKDITGKIRIKCAVC 67 (521)
Q Consensus 46 ~~~Cd~C~~~i~~~~ri~C~~C 67 (521)
.++|..|.++.. ....|.+|
T Consensus 17 ~~~C~~C~~~~~--~~a~CPdC 36 (70)
T PF07191_consen 17 HYHCEACQKDYK--KEAFCPDC 36 (70)
T ss_dssp EEEETTT--EEE--EEEE-TTT
T ss_pred EEECccccccce--ecccCCCc
Confidence 445555554432 33444444
No 141
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=23.61 E-value=59 Score=34.11 Aligned_cols=24 Identities=29% Similarity=0.771 Sum_probs=19.7
Q ss_pred CCcccccccccCCCCeeEEcCCCC
Q 009958 45 ALYHCNYCNKDITGKIRIKCAVCP 68 (521)
Q Consensus 45 ~~~~Cd~C~~~i~~~~ri~C~~C~ 68 (521)
..++|..|.+-..+..|++|+.|.
T Consensus 133 FyV~Ck~Cd~v~~GKLRV~C~~C~ 156 (446)
T KOG0006|consen 133 FYVWCKNCDDVKRGKLRVYCQKCS 156 (446)
T ss_pred eEEEecchhhccCCceEEEeeccc
Confidence 446899999888888999998885
No 142
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=23.59 E-value=77 Score=25.27 Aligned_cols=24 Identities=29% Similarity=0.684 Sum_probs=20.3
Q ss_pred ChHHHHHHhCC-CCHHHHHHHHHhh
Q 009958 126 NWAEIAEHVGT-KTKELCIEHYTNV 149 (521)
Q Consensus 126 nW~~Ia~~vgt-kt~~ec~~hy~~~ 149 (521)
-|+.||..+|. -+.++|+.+|.++
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHH
Confidence 49999999984 5788999999874
No 143
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=23.17 E-value=2.1e+02 Score=23.67 Aligned_cols=46 Identities=15% Similarity=0.158 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 474 LRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 474 L~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
|++.+.++- .+.++..+.++......++.+.+.....-|.+.|+|.
T Consensus 4 lt~~~~IL~-~ls~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 4 LTVTQKILI-ILSKRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred hhHHHHHHH-HHHhccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 344555543 3344599999999999999999999999999999985
No 144
>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=22.91 E-value=3.8e+02 Score=22.30 Aligned_cols=61 Identities=15% Similarity=0.104 Sum_probs=44.4
Q ss_pred HhhccCCCCC---CCCCCChHHHHHHHhhchhcc--cCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 009958 309 LERNLLYPNP---FEKDLSPEERELCRRYDVFMR--FHSKEDHEDLLQTVISEHRTLKRIQDLKEA 369 (521)
Q Consensus 309 ~e~~Ll~~~~---~~k~~tkeer~~~~~l~~far--f~~~~~~~~l~~~l~~e~~Lr~rI~~L~~y 369 (521)
.+.|||.+.. ..+.++.++-.....++.+.+ -++-.+...++..+-+-..|+.+|.+|++.
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 3578987422 345678777776677777665 678888888888777777888888888743
No 145
>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=22.32 E-value=31 Score=23.03 Aligned_cols=9 Identities=22% Similarity=0.342 Sum_probs=7.2
Q ss_pred cccccCCCC
Q 009958 248 LSGYNSKRQ 256 (521)
Q Consensus 248 ~~GYmP~R~ 256 (521)
-.||||.|+
T Consensus 7 S~gyMp~s~ 15 (27)
T PF12488_consen 7 SFGYMPRSG 15 (27)
T ss_pred ccceeeecc
Confidence 379999885
No 146
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=22.12 E-value=1.6e+02 Score=25.37 Aligned_cols=36 Identities=19% Similarity=0.309 Sum_probs=27.7
Q ss_pred HHHHH-hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCC
Q 009958 481 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 519 (521)
Q Consensus 481 irE~~-~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi 519 (521)
.-.++ ..|.++..++-+++.|- ..++++||.+.|||
T Consensus 15 ~d~~~~~~~~~ti~~~AK~L~i~---~~~l~~~Lr~~g~l 51 (111)
T PF03374_consen 15 YDAFVDSDGLYTIREAAKLLGIG---RNKLFQWLREKGWL 51 (111)
T ss_pred HHHHHcCCCCccHHHHHHHhCCC---HHHHHHHHHhCCce
Confidence 33344 56888988888887554 67889999999998
No 147
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=21.93 E-value=1.7e+02 Score=21.28 Aligned_cols=34 Identities=12% Similarity=0.158 Sum_probs=26.7
Q ss_pred CCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 487 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 487 ~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
++.++..+....+.+....+.++.+-|.+.|||.
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 148
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=21.89 E-value=2e+02 Score=27.77 Aligned_cols=52 Identities=8% Similarity=-0.089 Sum_probs=40.8
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 464 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 464 ~~lrL~P~~YL~iK~~LirE~~~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..++|.|.+|..+-.+ ..++.++.++...++.++...+.++.+=|.+.|||.
T Consensus 39 ~~~gLt~~q~~iL~~L-----~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~ 90 (185)
T PRK13777 39 KPYDLNINEHHILWIA-----YHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLT 90 (185)
T ss_pred HHCCCCHHHHHHHHHH-----HhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEE
Confidence 4689999999766322 244566777777788899999999999999999984
No 149
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.85 E-value=78 Score=21.77 Aligned_cols=27 Identities=33% Similarity=0.864 Sum_probs=18.6
Q ss_pred cccccccc-CCCCeeEEcCCCCCcccchh
Q 009958 48 HCNYCNKD-ITGKIRIKCAVCPDFDLCIE 75 (521)
Q Consensus 48 ~Cd~C~~~-i~~~~ri~C~~C~d~dLC~~ 75 (521)
.|.+|.+. +....+|.|..|+ .-||..
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~-v~lC~~ 29 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCD-VPLCVE 29 (32)
T ss_pred CCeECCcCCccceeEEEccCCC-CcccCC
Confidence 47777664 3223889999995 778864
No 150
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=21.45 E-value=1.2e+02 Score=22.98 Aligned_cols=35 Identities=11% Similarity=0.185 Sum_probs=30.6
Q ss_pred hCCCCCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 486 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 486 ~~G~lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
..+.++..+.-..+.+....+.+++.-|.+.|||.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 34568888888999999999999999999999984
No 151
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=21.18 E-value=52 Score=27.58 Aligned_cols=35 Identities=17% Similarity=0.323 Sum_probs=24.7
Q ss_pred ccccccccCCCCeeEEcCC---CCCcccchhhhhccccc
Q 009958 48 HCNYCNKDITGKIRIKCAV---CPDFDLCIECFSVGVEV 83 (521)
Q Consensus 48 ~Cd~C~~~i~~~~ri~C~~---C~d~dLC~~CF~~G~e~ 83 (521)
.|-+|+.+++... ..-++ ...-+-|.-||..|.+.
T Consensus 2 ~CQSCGMPl~~~~-~~Gte~dGs~s~~YC~yCy~~G~Ft 39 (81)
T PF12674_consen 2 FCQSCGMPLSKDE-DFGTEADGSKSEDYCSYCYQNGEFT 39 (81)
T ss_pred cCCcCcCccCCcc-ccccccCCCCchhHHHHHhcCCcee
Confidence 5999999997633 33333 23457899999999764
No 152
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=20.65 E-value=1.6e+02 Score=24.74 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCC-------CChHHHHHHhCCC-----CHHHHHHHHHhh
Q 009958 113 ILLLEGIEMYGL-------GNWAEIAEHVGTK-----TKELCIEHYTNV 149 (521)
Q Consensus 113 l~LLeai~~~G~-------gnW~~Ia~~vgtk-----t~~ec~~hy~~~ 149 (521)
..|-.+|...|- ..|..||..+|-. ...+.+.+|.++
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~ 83 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHH
Confidence 456677877761 2699999999843 245667777665
No 153
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=20.56 E-value=60 Score=34.44 Aligned_cols=28 Identities=18% Similarity=0.641 Sum_probs=21.3
Q ss_pred CCcCCcccccccccCCCCeeEEcCCCCCc
Q 009958 42 GKRALYHCNYCNKDITGKIRIKCAVCPDF 70 (521)
Q Consensus 42 ~~~~~~~Cd~C~~~i~~~~ri~C~~C~d~ 70 (521)
...+.|+|..|+-... +.+|+|..|..+
T Consensus 350 ~~~~~YRC~~CGF~a~-~l~W~CPsC~~W 377 (389)
T COG2956 350 RRKPRYRCQNCGFTAH-TLYWHCPSCRAW 377 (389)
T ss_pred hhcCCceecccCCcce-eeeeeCCCcccc
Confidence 3457889999988865 488898888754
No 154
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=20.51 E-value=1.1e+02 Score=24.39 Aligned_cols=35 Identities=20% Similarity=0.577 Sum_probs=22.0
Q ss_pred CcccccccccCC--C-CeeEEcCCCCCc--ccchhhhhcc
Q 009958 46 LYHCNYCNKDIT--G-KIRIKCAVCPDF--DLCIECFSVG 80 (521)
Q Consensus 46 ~~~Cd~C~~~i~--~-~~ri~C~~C~d~--dLC~~CF~~G 80 (521)
...|.+|+..|. + .+.+.|..|... --|..|-..+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 446888887764 2 367777777643 2377776554
No 155
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=20.50 E-value=41 Score=25.22 Aligned_cols=30 Identities=17% Similarity=0.512 Sum_probs=16.7
Q ss_pred cccccccccCCCCeeEEcCCCCCcccchhhhhc
Q 009958 47 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSV 79 (521)
Q Consensus 47 ~~Cd~C~~~i~~~~ri~C~~C~d~dLC~~CF~~ 79 (521)
+.|..|++.|....++. =.+-.+|..||.+
T Consensus 27 f~C~~C~~~l~~~~~~~---~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 27 FKCSKCGKPLNDGDFYE---KDGKPYCKDCYQK 56 (58)
T ss_dssp SBETTTTCBTTTSSEEE---ETTEEEEHHHHHH
T ss_pred cccCCCCCccCCCeeEe---ECCEEECHHHHhh
Confidence 46777777776533222 1234567777753
No 156
>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=20.31 E-value=2.3e+02 Score=24.11 Aligned_cols=48 Identities=10% Similarity=0.205 Sum_probs=35.8
Q ss_pred hhchhcccCChhHHHHHHHHHHHHH---HHHHHHHHHHHHHHhCccchHHHH
Q 009958 333 RYDVFMRFHSKEDHEDLLQTVISEH---RTLKRIQDLKEARAAGCRTSAEAD 381 (521)
Q Consensus 333 ~l~~farf~~~~~~~~l~~~l~~e~---~Lr~rI~~L~~yR~~Gi~tl~e~~ 381 (521)
.+..|..+.++++...|++.|.-.. .|-.| .++..|...|++.-+=++
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~l~t~~e~~~Ls~R-~~I~~ll~~G~S~~eIA~ 58 (88)
T TIGR02531 8 LFDAILTLKNREECYRFFDDIATINEIQSLAQR-LQVAKMLKQGKTYSDIEA 58 (88)
T ss_pred HHHHHHhCCCHHHHHHHHHHhCCHHHHHhhhHH-HHHHHHHHCCCCHHHHHH
Confidence 4567888999999999999998544 35556 778888888986544333
No 157
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=20.23 E-value=1.8e+02 Score=21.70 Aligned_cols=48 Identities=8% Similarity=0.119 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhCC-C-CCHHHhhhhhccCchhHHHHHHHHHHCCCCC
Q 009958 473 YLRMQEVMSREIFSGN-V-NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 520 (521)
Q Consensus 473 YL~iK~~LirE~~~~G-~-lkk~~a~~l~kiD~~k~~~Iydfl~~~Gwi~ 520 (521)
|-.|+..++......| . .+..+....+.+..+.+.+.+.-|.+.|||.
T Consensus 7 ~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 7 ADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3344444444333322 2 3366777778899999999999999999984
Done!