Query 010341
Match_columns 512
No_of_seqs 225 out of 987
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 23:24:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010341.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010341hhsearch_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 4E-105 9E-110 816.0 32.0 421 35-511 12-437 (438)
2 COG5114 Histone acetyltransfer 100.0 2.7E-98 6E-103 734.3 28.7 420 35-511 3-429 (432)
3 COG5259 RSC8 RSC chromatin rem 99.7 2.8E-17 6.1E-22 170.4 6.2 111 32-146 219-329 (531)
4 PF04433 SWIRM: SWIRM domain; 99.5 3.3E-14 7.1E-19 119.4 7.1 78 434-511 3-85 (86)
5 cd02335 ZZ_ADA2 Zinc finger, Z 99.5 3.9E-14 8.3E-19 106.7 4.1 49 38-86 1-49 (49)
6 KOG1279 Chromatin remodeling f 99.3 2.4E-12 5.1E-17 138.5 8.5 81 60-146 223-303 (506)
7 cd02343 ZZ_EF Zinc finger, ZZ 99.3 2.1E-12 4.6E-17 95.9 3.3 46 38-84 1-46 (48)
8 cd02338 ZZ_PCMF_like Zinc fing 99.2 4.4E-12 9.6E-17 95.4 3.7 48 38-86 1-49 (49)
9 cd02334 ZZ_dystrophin Zinc fin 99.2 4.6E-12 1E-16 95.1 3.6 46 38-84 1-47 (49)
10 cd02345 ZZ_dah Zinc finger, ZZ 99.2 7E-12 1.5E-16 94.4 3.3 46 39-85 2-48 (49)
11 PF00249 Myb_DNA-binding: Myb- 99.1 7.1E-11 1.5E-15 88.3 5.0 45 96-140 2-47 (48)
12 cd02249 ZZ Zinc finger, ZZ typ 99.1 6.7E-11 1.4E-15 87.9 3.8 46 38-86 1-46 (46)
13 cd02336 ZZ_RSC8 Zinc finger, Z 99.0 2.1E-10 4.7E-15 84.5 3.2 42 38-80 1-42 (45)
14 cd02340 ZZ_NBR1_like Zinc fing 99.0 2.7E-10 5.8E-15 83.4 3.5 43 38-86 1-43 (43)
15 cd02341 ZZ_ZZZ3 Zinc finger, Z 99.0 2.8E-10 6.1E-15 85.1 3.5 45 38-86 1-48 (48)
16 cd02344 ZZ_HERC2 Zinc finger, 98.9 8.6E-10 1.9E-14 81.2 3.5 44 38-86 1-45 (45)
17 cd02339 ZZ_Mind_bomb Zinc fing 98.9 1.8E-09 3.9E-14 79.7 3.4 43 38-85 1-44 (45)
18 smart00291 ZnF_ZZ Zinc-binding 98.9 1.9E-09 4.1E-14 79.4 3.5 41 36-77 3-43 (44)
19 PF00569 ZZ: Zinc finger, ZZ t 98.8 2.6E-09 5.7E-14 79.4 2.1 42 36-78 3-45 (46)
20 smart00717 SANT SANT SWI3, AD 98.7 2.9E-08 6.4E-13 72.6 5.8 46 96-141 2-47 (49)
21 cd00167 SANT 'SWI3, ADA2, N-Co 98.7 4.4E-08 9.4E-13 70.6 5.5 44 97-140 1-44 (45)
22 PF13921 Myb_DNA-bind_6: Myb-l 98.6 7.8E-08 1.7E-12 74.9 5.9 41 98-139 1-41 (60)
23 TIGR01557 myb_SHAQKYF myb-like 98.6 8.6E-08 1.9E-12 74.4 5.6 48 96-143 4-56 (57)
24 cd02337 ZZ_CBP Zinc finger, ZZ 98.5 7.7E-08 1.7E-12 69.7 2.2 33 38-72 1-33 (41)
25 cd02342 ZZ_UBA_plant Zinc fing 98.4 1.5E-07 3.3E-12 68.1 2.4 33 38-71 1-34 (43)
26 PLN03212 Transcription repress 98.2 1.2E-06 2.7E-11 86.2 5.2 49 93-141 23-72 (249)
27 KOG4286 Dystrophin-like protei 98.1 3.7E-07 8.1E-12 100.2 -2.0 71 15-86 581-652 (966)
28 PLN03091 hypothetical protein; 98.0 6.7E-06 1.4E-10 86.8 5.2 49 93-141 12-61 (459)
29 KOG1280 Uncharacterized conser 98.0 3.9E-06 8.5E-11 85.5 2.8 52 35-87 6-58 (381)
30 KOG4582 Uncharacterized conser 97.9 6.6E-06 1.4E-10 83.7 3.5 46 38-88 153-199 (278)
31 KOG0048 Transcription factor, 97.9 1.3E-05 2.8E-10 79.8 4.4 46 95-140 9-55 (238)
32 PLN03212 Transcription repress 97.7 4E-05 8.7E-10 75.6 5.4 47 93-140 76-122 (249)
33 PLN03091 hypothetical protein; 97.4 0.00023 5E-09 75.4 5.7 48 92-140 64-111 (459)
34 KOG4301 Beta-dystrobrevin [Cyt 97.3 2E-05 4.3E-10 80.3 -2.6 67 17-84 220-287 (434)
35 KOG0048 Transcription factor, 97.0 0.00077 1.7E-08 67.2 5.2 46 93-139 60-105 (238)
36 KOG0049 Transcription factor, 96.5 0.004 8.7E-08 68.5 5.7 52 92-143 357-408 (939)
37 KOG0049 Transcription factor, 95.8 0.0086 1.9E-07 65.9 4.2 49 91-139 408-459 (939)
38 KOG0051 RNA polymerase I termi 94.3 0.041 8.9E-07 61.0 4.0 49 94-144 383-431 (607)
39 PF13837 Myb_DNA-bind_4: Myb/S 93.9 0.042 9E-07 45.7 2.4 45 96-140 2-63 (90)
40 PF07649 C1_3: C1-like domain; 92.3 0.083 1.8E-06 35.4 1.6 29 38-67 1-29 (30)
41 PF03107 C1_2: C1 domain; Int 91.0 0.18 4E-06 33.9 2.1 28 38-67 1-29 (30)
42 KOG0050 mRNA splicing protein 90.2 0.3 6.5E-06 53.1 4.0 48 95-143 7-54 (617)
43 KOG0051 RNA polymerase I termi 87.8 0.53 1.2E-05 52.5 4.0 52 94-145 435-511 (607)
44 COG5147 REB1 Myb superfamily p 86.0 0.56 1.2E-05 51.7 2.9 45 95-139 20-64 (512)
45 PF09111 SLIDE: SLIDE; InterP 85.1 1.1 2.3E-05 40.1 3.8 43 95-137 49-106 (118)
46 TIGR02894 DNA_bind_RsfA transc 83.7 0.83 1.8E-05 42.8 2.6 44 96-140 5-54 (161)
47 PF02207 zf-UBR: Putative zinc 83.3 0.95 2.1E-05 36.5 2.5 42 43-89 3-48 (71)
48 KOG4167 Predicted DNA-binding 83.1 1.5 3.3E-05 49.6 4.7 44 95-139 619-662 (907)
49 KOG0050 mRNA splicing protein 82.7 1.1 2.5E-05 48.7 3.4 46 93-140 57-102 (617)
50 COG5118 BDP1 Transcription ini 82.4 2.2 4.7E-05 44.9 5.2 44 95-139 365-408 (507)
51 PLN03000 amine oxidase 79.2 3.5 7.7E-05 48.5 6.1 72 439-511 90-167 (881)
52 KOG4282 Transcription factor G 79.2 2.5 5.4E-05 44.3 4.6 48 95-142 54-114 (345)
53 COG5147 REB1 Myb superfamily p 79.0 2 4.3E-05 47.5 3.8 50 93-143 70-119 (512)
54 KOG4468 Polycomb-group transcr 77.2 2.6 5.7E-05 46.8 4.0 45 95-140 88-142 (782)
55 PF13873 Myb_DNA-bind_5: Myb/S 72.4 4.8 0.00011 32.5 3.6 45 96-140 3-68 (78)
56 KOG0384 Chromodomain-helicase 72.0 2.5 5.4E-05 50.7 2.5 28 94-121 1132-1159(1373)
57 smart00396 ZnF_UBR1 Putative z 72.0 5.3 0.00011 32.4 3.7 42 42-88 2-47 (71)
58 PHA00442 host recBCD nuclease 72.0 4.4 9.5E-05 31.1 2.9 26 100-125 25-50 (59)
59 smart00420 HTH_DEOR helix_turn 71.5 9.9 0.00021 27.4 4.9 36 476-511 10-45 (53)
60 PF13412 HTH_24: Winged helix- 70.9 12 0.00026 27.3 5.1 44 468-511 5-48 (48)
61 KOG1778 CREB binding protein/P 69.6 2.5 5.5E-05 44.1 1.7 54 14-72 149-202 (319)
62 PF09862 DUF2089: Protein of u 68.7 10 0.00023 33.6 5.1 60 40-126 1-60 (113)
63 PF09012 FeoC: FeoC like trans 67.4 6.9 0.00015 31.1 3.4 40 472-511 5-45 (69)
64 PF00643 zf-B_box: B-box zinc 64.0 8.6 0.00019 27.3 3.1 39 37-85 3-41 (42)
65 PF08914 Myb_DNA-bind_2: Rap1 62.8 12 0.00025 30.0 3.9 47 96-142 3-58 (65)
66 PLN03142 Probable chromatin-re 62.3 9.6 0.00021 45.9 4.8 58 96-155 825-882 (1033)
67 KOG4329 DNA-binding protein [G 62.2 9.6 0.00021 40.2 4.1 43 96-139 278-321 (445)
68 PF07975 C1_4: TFIIH C1-like d 58.9 6.1 0.00013 30.1 1.6 29 39-68 1-36 (51)
69 PLN03142 Probable chromatin-re 57.5 13 0.00029 44.7 4.8 45 95-139 926-982 (1033)
70 PLN02328 lysine-specific histo 56.8 20 0.00043 42.2 6.0 69 443-511 144-218 (808)
71 PF01047 MarR: MarR family; I 56.3 12 0.00026 28.2 2.9 35 477-511 14-48 (59)
72 PF04504 DUF573: Protein of un 56.3 17 0.00036 31.4 4.0 33 94-126 3-42 (98)
73 PF08394 Arc_trans_TRASH: Arch 56.1 6.9 0.00015 27.9 1.3 31 40-70 1-32 (37)
74 PF12802 MarR_2: MarR family; 55.6 26 0.00056 26.5 4.7 50 457-511 1-52 (62)
75 COG3935 DnaD Putative primosom 55.0 13 0.00028 37.4 3.6 58 324-381 134-210 (246)
76 PF13404 HTH_AsnC-type: AsnC-t 54.8 36 0.00077 24.6 5.0 37 102-139 4-40 (42)
77 PF14569 zf-UDP: Zinc-binding 54.1 7 0.00015 32.3 1.3 33 37-70 9-45 (80)
78 PF10925 DUF2680: Protein of u 53.4 47 0.001 26.1 5.7 45 463-511 15-59 (59)
79 TIGR01889 Staph_reg_Sar staphy 53.2 51 0.0011 28.4 6.7 63 448-511 12-74 (109)
80 PF12776 Myb_DNA-bind_3: Myb/S 51.9 31 0.00067 28.7 5.0 44 97-140 1-61 (96)
81 TIGR02337 HpaR homoprotocatech 48.6 40 0.00087 29.3 5.4 61 446-511 13-73 (118)
82 PF08074 CHDCT2: CHDCT2 (NUC03 48.0 10 0.00022 35.8 1.5 29 97-125 5-33 (173)
83 KOG1194 Predicted DNA-binding 48.0 22 0.00048 38.6 4.1 46 93-139 185-230 (534)
84 smart00595 MADF subfamily of S 47.8 19 0.0004 29.7 2.9 23 117-140 29-51 (89)
85 PF03979 Sigma70_r1_1: Sigma-7 47.2 35 0.00077 28.1 4.5 41 469-509 10-53 (82)
86 KOG1356 Putative transcription 46.8 11 0.00023 43.9 1.7 35 35-71 227-261 (889)
87 PF04703 FaeA: FaeA-like prote 46.3 27 0.00058 27.7 3.4 43 468-511 2-46 (62)
88 KOG3554 Histone deacetylase co 46.0 22 0.00048 38.7 3.8 42 96-138 286-328 (693)
89 PF06461 DUF1086: Domain of Un 44.4 38 0.00083 31.4 4.6 55 96-151 39-95 (145)
90 PF09397 Ftsk_gamma: Ftsk gamm 44.3 45 0.00097 26.7 4.4 45 464-512 8-52 (65)
91 PF08513 LisH: LisH; InterPro 44.2 15 0.00033 24.0 1.4 12 499-510 6-17 (27)
92 COG5347 GTPase-activating prot 43.0 14 0.00031 38.6 1.9 56 38-106 21-76 (319)
93 PRK03573 transcriptional regul 42.8 72 0.0016 28.6 6.2 56 452-511 22-77 (144)
94 PF15614 WHIM3: WSTF, HB1, Itc 42.4 50 0.0011 24.7 4.1 28 331-358 4-36 (46)
95 PF05290 Baculo_IE-1: Baculovi 42.2 9.1 0.0002 34.9 0.2 53 35-90 78-130 (140)
96 PRK13923 putative spore coat p 40.1 30 0.00065 32.9 3.3 45 95-140 5-55 (170)
97 KOG1194 Predicted DNA-binding 40.0 18 0.00039 39.2 2.1 43 95-139 470-512 (534)
98 cd00090 HTH_ARSR Arsenical Res 39.5 62 0.0013 24.4 4.7 34 477-511 18-51 (78)
99 PF07261 DnaB_2: Replication i 39.2 6.6 0.00014 31.4 -1.1 23 354-376 54-76 (77)
100 PF13730 HTH_36: Helix-turn-he 38.4 90 0.0019 23.1 5.2 53 458-510 2-55 (55)
101 PF13463 HTH_27: Winged helix 38.3 64 0.0014 24.7 4.6 34 477-510 15-48 (68)
102 PF08784 RPA_C: Replication pr 38.0 29 0.00062 29.6 2.7 32 478-510 64-95 (102)
103 smart00345 HTH_GNTR helix_turn 37.8 51 0.0011 24.2 3.8 46 466-511 4-51 (60)
104 PF02954 HTH_8: Bacterial regu 36.5 49 0.0011 23.6 3.3 24 102-126 6-29 (42)
105 PLN02436 cellulose synthase A 35.7 23 0.00049 42.6 2.1 49 37-87 36-92 (1094)
106 PLN02189 cellulose synthase 35.6 23 0.00049 42.4 2.1 50 36-87 33-90 (1040)
107 PRK11512 DNA-binding transcrip 35.3 83 0.0018 28.3 5.4 52 455-511 34-85 (144)
108 PLN02915 cellulose synthase A 34.8 30 0.00066 41.5 3.0 50 36-87 14-71 (1044)
109 PF01388 ARID: ARID/BRIGHT DNA 34.6 83 0.0018 26.1 4.9 38 103-140 38-87 (92)
110 PF09107 SelB-wing_3: Elongati 34.1 82 0.0018 23.8 4.3 39 472-510 1-40 (50)
111 TIGR01446 DnaD_dom DnaD and ph 32.6 33 0.00071 27.3 2.0 18 355-372 55-72 (73)
112 smart00346 HTH_ICLR helix_turn 32.3 1E+02 0.0022 25.0 5.1 40 472-511 10-51 (91)
113 PLN02638 cellulose synthase A 31.8 28 0.00061 41.8 2.1 48 38-87 18-73 (1079)
114 COG4008 Predicted metal-bindin 31.8 1.1E+02 0.0024 27.8 5.3 24 455-478 87-110 (153)
115 COG1725 Predicted transcriptio 31.7 1.2E+02 0.0026 27.5 5.6 49 463-511 12-66 (125)
116 smart00843 Ftsk_gamma This dom 30.6 1.4E+02 0.003 23.8 5.2 45 464-512 7-51 (63)
117 PF01978 TrmB: Sugar-specific 30.4 51 0.0011 25.7 2.8 35 477-511 19-53 (68)
118 COG2956 Predicted N-acetylgluc 29.0 33 0.00072 36.1 1.8 26 35-61 352-377 (389)
119 KOG2807 RNA polymerase II tran 28.8 34 0.00074 35.7 1.9 32 36-68 329-360 (378)
120 TIGR02531 yecD_yerC TrpR-relat 28.5 1.1E+02 0.0023 26.0 4.5 49 323-372 7-58 (88)
121 PLN02400 cellulose synthase 28.2 36 0.00077 41.0 2.1 49 37-87 36-92 (1085)
122 PF09339 HTH_IclR: IclR helix- 28.2 79 0.0017 23.4 3.3 42 470-511 6-49 (52)
123 smart00550 Zalpha Z-DNA-bindin 27.8 1.6E+02 0.0035 23.3 5.3 44 468-511 8-53 (68)
124 PF13325 MCRS_N: N-terminal re 27.2 1E+02 0.0022 30.2 4.7 46 97-144 1-49 (199)
125 PF13076 DUF3940: Protein of u 26.9 75 0.0016 22.7 2.8 34 468-502 3-36 (38)
126 PRK08359 transcription factor; 26.1 48 0.001 31.7 2.3 40 38-77 7-48 (176)
127 PRK00420 hypothetical protein; 26.0 43 0.00093 29.7 1.8 28 38-65 24-53 (112)
128 PF00130 C1_1: Phorbol esters/ 25.8 59 0.0013 24.0 2.3 24 36-59 10-35 (53)
129 TIGR03277 methan_mark_9 putati 25.5 74 0.0016 27.9 3.1 23 455-477 86-108 (109)
130 PF14471 DUF4428: Domain of un 25.4 35 0.00076 25.9 1.0 30 39-71 1-30 (51)
131 smart00347 HTH_MARR helix_turn 25.1 1.5E+02 0.0031 24.0 4.8 51 456-511 5-55 (101)
132 KOG2789 Putative Zn-finger pro 25.1 39 0.00084 36.2 1.5 69 36-107 73-153 (482)
133 PF03374 ANT: Phage antirepres 24.6 1.2E+02 0.0026 26.0 4.4 36 472-510 15-51 (111)
134 PF10123 Mu-like_Pro: Mu-like 24.5 57 0.0012 34.0 2.6 25 441-465 301-325 (326)
135 PF07191 zinc-ribbons_6: zinc- 24.5 31 0.00067 28.1 0.5 22 36-59 16-37 (70)
136 PF12488 DUF3704: Protein of u 24.4 27 0.00058 23.1 0.1 9 239-247 7-15 (27)
137 PF05584 Sulfolobus_pRN: Sulfo 24.3 2E+02 0.0043 23.6 5.2 46 465-511 4-49 (72)
138 PRK14890 putative Zn-ribbon RN 24.2 77 0.0017 25.0 2.6 35 37-71 7-46 (59)
139 TIGR00622 ssl1 transcription f 24.2 67 0.0015 28.5 2.6 29 38-67 56-95 (112)
140 TIGR00270 conserved hypothetic 23.9 52 0.0011 30.8 2.0 39 39-77 2-40 (154)
141 PRK11179 DNA-binding transcrip 23.9 1.6E+02 0.0036 26.9 5.4 44 100-144 8-51 (153)
142 PF14319 Zn_Tnp_IS91: Transpos 23.9 38 0.00083 29.8 1.1 56 11-72 16-71 (111)
143 PF10545 MADF_DNA_bdg: Alcohol 23.8 75 0.0016 25.2 2.8 24 117-140 28-52 (85)
144 PRK10870 transcriptional repre 23.4 2E+02 0.0043 27.1 5.9 58 451-511 45-102 (176)
145 COG1813 Predicted transcriptio 23.0 89 0.0019 29.6 3.4 39 40-79 6-44 (165)
146 smart00418 HTH_ARSR helix_turn 22.7 1.6E+02 0.0035 21.3 4.3 34 478-511 8-41 (66)
147 cd00092 HTH_CRP helix_turn_hel 22.7 1.1E+02 0.0025 23.1 3.5 35 477-511 22-56 (67)
148 PRK11823 DNA repair protein Ra 22.3 56 0.0012 35.7 2.2 27 35-62 5-31 (446)
149 COG0068 HypF Hydrogenase matur 22.3 41 0.00089 38.7 1.1 58 16-73 79-163 (750)
150 KOG0818 GTPase-activating prot 22.1 56 0.0012 36.1 2.0 70 37-120 8-78 (669)
151 smart00501 BRIGHT BRIGHT, ARID 21.6 1.5E+02 0.0032 24.8 4.2 37 103-140 34-83 (93)
152 PF13842 Tnp_zf-ribbon_2: DDE_ 21.5 83 0.0018 21.5 2.1 27 39-66 2-29 (32)
153 PF00392 GntR: Bacterial regul 21.1 1.2E+02 0.0025 23.4 3.3 45 467-511 9-55 (64)
154 PLN02195 cellulose synthase A 21.1 59 0.0013 38.9 2.1 33 37-70 6-42 (977)
155 cd07377 WHTH_GntR Winged helix 20.9 1.7E+02 0.0038 21.7 4.2 48 464-511 7-56 (66)
156 PF07875 Coat_F: Coat F domain 20.8 83 0.0018 24.5 2.3 25 488-512 38-62 (64)
157 COG3877 Uncharacterized protei 20.6 3.1E+02 0.0068 24.2 5.9 64 36-126 5-68 (122)
158 cd04766 HTH_HspR Helix-Turn-He 20.1 4E+02 0.0087 22.0 6.6 60 300-359 22-86 (91)
No 1
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=4.2e-105 Score=815.96 Aligned_cols=421 Identities=50% Similarity=0.831 Sum_probs=371.5
Q ss_pred cCCcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHHHhC
Q 010341 35 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 114 (512)
Q Consensus 35 ~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~~~G 114 (512)
...|+|++|..+|++.+||+|++|++||||+.||+.|+|++.|+++|+|+||++++||+.+++|||+||++||+|+++||
T Consensus 12 g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G 91 (438)
T KOG0457|consen 12 GGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYG 91 (438)
T ss_pred CCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhC
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCCcccccCchHHHHHHhccCCCCCCCCCCCCCCCccCCCCCCCc
Q 010341 115 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKGPSKPGEATVKEESPFSPS 194 (512)
Q Consensus 115 ~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~~~~plp~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~p~ 194 (512)
||||++||+|||+||.+||++||.++|++++++|+|+++..+++++.+++++.+.+. .|+.|.
T Consensus 92 ~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~-----------------~~~~~~ 154 (438)
T KOG0457|consen 92 FGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRA-----------------EPFQPT 154 (438)
T ss_pred CCcHHHHHHHHcccchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhccccc-----------------ccCCCC
Confidence 999999999999999999999999999999999999999999999999998877531 234332
Q ss_pred hhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCCCHHH
Q 010341 195 RVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDADSEEE 274 (512)
Q Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFe~EydNdAE~li~dl~f~~~D~~~e 274 (512)
.. -|+.++.++|..++++||||+|.|||.||||+||++|+||+|+++|+|.+
T Consensus 155 ~~----------------------------~pr~p~~~~p~~~e~~gyMp~R~dFd~Eydn~AE~li~dm~f~e~D~~~d 206 (438)
T KOG0457|consen 155 DL----------------------------VPRKPGVSNPLRREISGYMPGRLDFDEEYDNEAEQLIRDMEFEEDDTEED 206 (438)
T ss_pred CC----------------------------CCCCCCCCCchHHHHhhhCccchhhhhhhcchhhhhHhhcccCCCCcHHH
Confidence 10 13444456789999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCC---CCCCCCCChhHHHHHHhhcccccCCChhHHHHHHHHHHHHHHHH
Q 010341 275 RDIKLRVLRIYSKRLDERKRRKDFILERNLLYP---NPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISEHRTL 351 (512)
Q Consensus 275 ~elKl~~l~iYn~rL~ER~rRK~~i~e~~Ll~~---~~~~k~~skeere~~~~l~~far~~~~~~~~~l~~~l~~E~~Lr 351 (512)
.+||+++|+|||+||+||.|||++|++|||+++ ++.++++|+|||++++++|+||||+|+.||++|+.++..|.+|+
T Consensus 207 ~elKla~ldiY~srl~eR~RRK~~I~d~nLl~~rk~q~~e~~~skEer~l~~s~k~fAR~~t~~d~~kfl~~~~eE~~L~ 286 (438)
T KOG0457|consen 207 HELKLAVLDIYNSRLKERKRRKRFIRDRNLLDYRKNQAMEKRLSKEERELYNSIKVFARFLTKSDHDKFLGSVAEEKELR 286 (438)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHhhccHHHHHHHHHHHHHhcccChHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999995 88899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCcchHHHHHHHHHHhhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCC--CCCCCCCCC
Q 010341 352 KRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSN--SRPSGQASS 429 (512)
Q Consensus 352 ~rI~~L~~~R~~Gittl~e~~~ye~~k~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~ 429 (512)
.||++||+||.+|+||++++.+|+.+|.++ .+.+......++...+ +. .+ .....++. +....+...
T Consensus 287 ~ri~~lqE~R~ag~tt~~e~~ky~~~k~~~-~~~s~~~~~~~~~~~~----i~-----~~-~~~~~~~~~~~~v~~~~~~ 355 (438)
T KOG0457|consen 287 KRISDLQEYRSAGLTTNAEPNKYERLKFKE-FRESTALLLSSGALRY----IK-----NS-NQEASGSASKRPVQQQSIY 355 (438)
T ss_pred HHHHHHHHHHHhcceeccccchhHHHHHHH-HHHHhhhccccchhhh----hh-----cc-ccccccccccCcccccccc
Confidence 999999999999999999999999999443 3333222222211100 00 00 00111111 122233456
Q ss_pred CCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCC
Q 010341 430 SHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGL 509 (512)
Q Consensus 430 ~~~~~l~i~~~pg~~lLs~~E~~LCs~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gw 509 (512)
++++++++.++++.++||++|+.||+.++|+|++||.+|++|.+|..++|.+++++|+.++|||++|+++|||||+++||
T Consensus 356 ~~~~~~~~~~~~~~q~Lse~E~~lc~~~~~~p~~yLe~~~vl~~e~~k~~~~kks~a~~l~Kid~~Kvd~vyd~~~~~~~ 435 (438)
T KOG0457|consen 356 KSATPLDISGAPDTQLLSEDEKRLCQELKILPKLYLELKEVLSREIKKGGTLKKSDAYRLFKIDPRKVDRVYDFLIAQGW 435 (438)
T ss_pred cCCCHHHHhcchhhhhhhhhHHHHHHHHHhccHHHHHHHHHHHHHHhccCcccchhHHHHhcCCcchHHHHHHHHHHhhh
Confidence 77899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CC
Q 010341 510 AP 511 (512)
Q Consensus 510 i~ 511 (512)
+.
T Consensus 436 ~~ 437 (438)
T KOG0457|consen 436 IG 437 (438)
T ss_pred cc
Confidence 96
No 2
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=2.7e-98 Score=734.30 Aligned_cols=420 Identities=31% Similarity=0.532 Sum_probs=363.1
Q ss_pred cCCcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHHHhC
Q 010341 35 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYG 114 (512)
Q Consensus 35 ~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~~~G 114 (512)
...++||+|..+||..++|+|++|++||||+.||.+|.+.+.|++.|+|++|+.+++||+.++|+++||++|+++++++|
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 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCCcccccCchHHHHHHhccCCCCCCCCCCCCCCCccCCCCCCCc
Q 010341 115 LGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHVVGKNRKELLAMAKGHIDDKKGPSKPGEATVKEESPFSPS 194 (512)
Q Consensus 115 ~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~~~~plp~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~p~ 194 (512)
+|||++||+|||+|+++||+.||.++|+++.++|||+....+...+++|++..+.+++.... +|..|
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 99999999999999999999999999999999999999888888899999887766543221 22222
Q ss_pred hhhhhhhhcCCCCCCCCCCCCccccccCCCCCCCCCCCCCCccccccccCCCCCCCcccCcchHhhhhccccCCCCCHHH
Q 010341 195 RVKIEEMHKVGPSGRGLNADPQTERSSKGKKPVTSGNDGPSLVELSGYNSKRQEFDPEYDNDAEQLLAEMEFKDADSEEE 274 (512)
Q Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kp~~~~~~~~~~~e~~GYmP~R~DFe~EydNdAE~li~dl~f~~~D~~~e 274 (512)
.||.. ++|.+|+++||||+|.|||+||+|+||..|+||.|++|+.+.+
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 13443 4799999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC---CCCCCCCCChhHHHHHHhhcccccCCChhHHHHHHHHHHHHHHHH
Q 010341 275 RDIKLRVLRIYSKRLDERKRRKDFILERNLLY---PNPFEKDLSPEERELCRRYDVFMRFHSKEDHEDLLQTVISEHRTL 351 (512)
Q Consensus 275 ~elKl~~l~iYn~rL~ER~rRK~~i~e~~Ll~---~~~~~k~~skeere~~~~l~~far~~~~~~~~~l~~~l~~E~~Lr 351 (512)
++||+++|+|||+||..|.+||+.|++++|+| -++.+|++||||+.++++++||||++|+.||+.|+++++.+.-++
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 478899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhCCcchHHHHHHHHHHhhhHHHHHHHHhhcCCCCCCCCCCCCcccccccccccCCCCCCCC---CCCCC
Q 010341 352 KRIQDLKEARAAGCRTSAEADRYLELKRGREAEEASRRAKEGGHAGASSQGGANVFMASESLRKDSNSNSRP---SGQAS 428 (512)
Q Consensus 352 ~rI~~L~~~R~~Gittl~e~~~ye~~k~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~ 428 (512)
+||++||+||.||+||++.|-+||++|-.+ .....+ .+...+.++.. +++.. .++..... ..-..
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-ASLSEGNSRYR-------SNSAH-RSNAEYSQMDVKNILP 345 (432)
T ss_pred HHHHHHHHHHhcCchhhhhhhhhhhhHHHh---hccchh-hhhcccchhhh-------ccccc-ccCcchhHHHHHhccC
Confidence 999999999999999999999999998331 000000 00000000000 00000 00000000 00013
Q ss_pred CCCCCcccccCCCccCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHh-CCCcCHHHHhhhhccCchhHHHHHHHHHHC
Q 010341 429 SSHVNDLYIMGFNETQLLSEAEKRLCCEIRLAPPLYLRMQEVMSREIFS-GNVNNKADAHHLFKIEPSKIDRVYDMLVKK 507 (512)
Q Consensus 429 ~~~~~~l~i~~~pg~~lLs~~E~~LCs~lrL~P~~YL~iK~~LirE~~~-~G~lk~~~A~~l~kiD~~K~~rIydFlv~~ 507 (512)
++...+.+|..+|++.|||++|++||++|+|.|++||.+|.++|+++++ +|.+++++|+.||+||.+|+.+|||||.+.
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 4556778899999999999999999999999999999999999999995 899999999999999999999999999999
Q ss_pred CCCC
Q 010341 508 GLAP 511 (512)
Q Consensus 508 Gwi~ 511 (512)
|||-
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=99.68 E-value=2.8e-17 Score=170.38 Aligned_cols=111 Identities=29% Similarity=0.603 Sum_probs=97.0
Q ss_pred CCCcCCcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHH
Q 010341 32 EGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIE 111 (512)
Q Consensus 32 ~~~~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~ 111 (512)
+...+..+|+.||..... .||+-..-.+|++|..||-+|.++....++ +|..++...+. ....|+.+|.++|||||+
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 334556899999999887 799998888999999999999999888766 68877664443 456899999999999999
Q ss_pred HhCCCChHHHHHHhCCCCHHHHHHHHHhhccCCCC
Q 010341 112 MYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNSPF 146 (512)
Q Consensus 112 ~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~~~ 146 (512)
+|| ++|..||.|||+||++||+.||.++++.+.+
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 9999999999999999999999999988764
No 4
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.50 E-value=3.3e-14 Score=119.40 Aligned_cols=78 Identities=33% Similarity=0.477 Sum_probs=68.9
Q ss_pred cccccCCCccCCCCHHHHHHHHHhCC--CchHHHHHHHHHHHHHH--hCCCcCHHHHhhhhc-cCchhHHHHHHHHHHCC
Q 010341 434 DLYIMGFNETQLLSEAEKRLCCEIRL--APPLYLRMQEVMSREIF--SGNVNNKADAHHLFK-IEPSKIDRVYDMLVKKG 508 (512)
Q Consensus 434 ~l~i~~~pg~~lLs~~E~~LCs~lrL--~P~~YL~iK~~LirE~~--~~G~lk~~~A~~l~k-iD~~K~~rIydFlv~~G 508 (512)
++++++.++.+.||+.|+++|..+++ .|..||.+|+.||++.. .++.+++++|+++++ +|++++.+||+||.+.|
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 578999999999999 99999999999999999
Q ss_pred CCC
Q 010341 509 LAP 511 (512)
Q Consensus 509 wi~ 511 (512)
||+
T Consensus 83 ~IN 85 (86)
T PF04433_consen 83 LIN 85 (86)
T ss_dssp SSS
T ss_pred ccC
Confidence 996
No 5
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.47 E-value=3.9e-14 Score=106.66 Aligned_cols=49 Identities=69% Similarity=1.499 Sum_probs=46.6
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeee
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
++||+|++++...+||+|++|+|||||..||+.|.+.+.|+++|+|++|
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 6
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=99.33 E-value=2.4e-12 Score=138.54 Aligned_cols=81 Identities=36% Similarity=0.862 Sum_probs=71.9
Q ss_pred CcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 60 DFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 60 d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
++.+|..||..|.+...++.+ +|.++.. .....||.+|+++||+||++|| .+|..||.|||+||.+||+.||.+
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-DFKVIGE----SARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred hhhhhHHHHhcCCccCccccc-cchhccc----cCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHh
Confidence 378999999999999999876 5755544 2467899999999999999999 999999999999999999999999
Q ss_pred hccCCCC
Q 010341 140 VYMNSPF 146 (512)
Q Consensus 140 ~y~~~~~ 146 (512)
.++.+++
T Consensus 297 LPieD~~ 303 (506)
T KOG1279|consen 297 LPIEDPY 303 (506)
T ss_pred cCccchh
Confidence 9998764
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=99.28 E-value=2.1e-12 Score=95.93 Aligned_cols=46 Identities=33% Similarity=0.717 Sum_probs=42.6
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCee
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 84 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~ 84 (512)
+.||+|.+.+.+ +||+|++|+|||||..||..|.+.+.|+++|+.+
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 369999998876 8999999999999999999999999999999764
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=99.25 E-value=4.4e-12 Score=95.43 Aligned_cols=48 Identities=38% Similarity=0.953 Sum_probs=44.6
Q ss_pred cccccCc-cCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeee
Q 010341 38 YHCNYCN-KDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 38 ~~C~~C~-~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
+.|++|+ .+|.+ .||+|..|+|||||..||+.|.+.+.|+++|+|+++
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=99.24 E-value=4.6e-12 Score=95.08 Aligned_cols=46 Identities=41% Similarity=0.977 Sum_probs=42.8
Q ss_pred cccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCee
Q 010341 38 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 84 (512)
Q Consensus 38 ~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~ 84 (512)
+.|++|++ +|.+ .||+|++|.|||||..||..|.+.+.|+++|+|+
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=99.22 E-value=7e-12 Score=94.35 Aligned_cols=46 Identities=43% Similarity=0.969 Sum_probs=43.5
Q ss_pred ccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeee
Q 010341 39 HCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 85 (512)
Q Consensus 39 ~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 85 (512)
.|++|.+ +|++ +||+|++|+|||||..||+.|.+.+.|+++|+|..
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 6999998 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=99.12 E-value=7.1e-11 Score=88.32 Aligned_cols=45 Identities=31% Similarity=0.716 Sum_probs=40.9
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 010341 96 PDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 140 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg-~rt~~ec~~hy~~~ 140 (512)
..||.+|+..|++||..||.+||..||.+|+ +||+.||+.||.++
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 5799999999999999999777999999999 99999999999865
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=99.10 E-value=6.7e-11 Score=87.88 Aligned_cols=46 Identities=41% Similarity=1.024 Sum_probs=42.5
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeee
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
|.|++|+++|.+ .||+|..|++||||..||+.|. +.|+++|.|..|
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 789999998754
No 13
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=99.01 E-value=2.1e-10 Score=84.51 Aligned_cols=42 Identities=31% Similarity=0.648 Sum_probs=40.0
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCC
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSN 80 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~ 80 (512)
|+|+.|+.|++. +||+|+.+.+++||..||.+|.++.+|.++
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 999999999999999999999999999877
No 14
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=99.00 E-value=2.7e-10 Score=83.41 Aligned_cols=43 Identities=42% Similarity=0.943 Sum_probs=39.0
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeee
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
+.||+|+.+|.+ .||+|..|++||||..||..+ .| ++|+|..|
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 899999999999999999998 68 89998754
No 15
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.00 E-value=2.8e-10 Score=85.12 Aligned_cols=45 Identities=36% Similarity=0.882 Sum_probs=40.9
Q ss_pred cccccCcc-CCCCCeeEEcCCCC--CcccchhhhcccccccCCCCCCCeeee
Q 010341 38 YHCNYCNK-DITGKIRIKCAVCP--DFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 38 ~~C~~C~~-~i~~~~ri~C~~C~--d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
|.||+|+. +|.+ +||+|.+|+ +||||..||..|. .|+.+|.+..|
T Consensus 1 y~Cd~C~~~pI~G-~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPG-TRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCcccc-ceEECCCCCCCCCccCHHHHhCcC---CCCCCCceeeC
Confidence 57999998 7887 999999999 9999999999997 79999988754
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=98.92 E-value=8.6e-10 Score=81.24 Aligned_cols=44 Identities=36% Similarity=0.906 Sum_probs=38.8
Q ss_pred cccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeee
Q 010341 38 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 38 ~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
+.||+|+. .|.+ .||+|++|.|||||..||..+ .|...|.|..|
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 46999996 6787 999999999999999999995 48889999765
No 17
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=98.86 E-value=1.8e-09 Score=79.72 Aligned_cols=43 Identities=42% Similarity=0.981 Sum_probs=37.2
Q ss_pred cccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeee
Q 010341 38 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 85 (512)
Q Consensus 38 ~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 85 (512)
+.||+|++ .|.+ +||+|++|+|||||..||.. +.|+.+|+|..
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 6666 99999999999999999996 45999999864
No 18
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=98.86 E-value=1.9e-09 Score=79.35 Aligned_cols=41 Identities=46% Similarity=1.093 Sum_probs=37.4
Q ss_pred CCcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCC
Q 010341 36 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPH 77 (512)
Q Consensus 36 ~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H 77 (512)
..+.|++|+.+|++ .||+|..|+|||||..||+.|.+.+.|
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 46789999999887 899999999999999999999987766
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=98.78 E-value=2.6e-09 Score=79.35 Aligned_cols=42 Identities=50% Similarity=1.118 Sum_probs=31.9
Q ss_pred CCcccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCC
Q 010341 36 ALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHK 78 (512)
Q Consensus 36 ~~~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~ 78 (512)
..+.|++|+. .|.+ .||+|..|+|||||..||..|.....|+
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 5688999998 6776 9999999999999999999999877775
No 20
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.71 E-value=2.9e-08 Score=72.64 Aligned_cols=46 Identities=33% Similarity=0.749 Sum_probs=43.0
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhc
Q 010341 96 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVY 141 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y 141 (512)
..||.+|+..|+.++..||.++|..||.++++||+.+|+.+|..+.
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=98.66 E-value=4.4e-08 Score=70.62 Aligned_cols=44 Identities=34% Similarity=0.791 Sum_probs=41.8
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 97 DWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 97 ~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
.||.+|+..|+.++..||.++|..||+.+++||+.+|+.||..+
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
>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=98.61 E-value=7.8e-08 Score=74.92 Aligned_cols=41 Identities=39% Similarity=0.920 Sum_probs=37.1
Q ss_pred CCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 98 WNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 98 Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
||.+|+..|++++..|| .+|..||+++|.||+.+|+.||..
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999 799999999998999999999998
No 23
>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=98.59 E-value=8.6e-08 Score=74.44 Aligned_cols=48 Identities=19% Similarity=0.339 Sum_probs=44.4
Q ss_pred CCCCchhHHHHHHHHHHhCCCCh---HHHHHHhC-CC-CHHHHHHHHHhhccC
Q 010341 96 PDWNADDEILLLEGIEMYGLGNW---AEIAEHVG-TK-TKELCIEHYTNVYMN 143 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~gnW---~~IA~~vg-~r-t~~ec~~hy~~~y~~ 143 (512)
..||++|...+|+||+.+|.||| ..|+++|+ ++ |+.||+.|+.++|+.
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 46999999999999999998899 99999998 57 999999999999863
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=98.46 E-value=7.7e-08 Score=69.70 Aligned_cols=33 Identities=42% Similarity=1.142 Sum_probs=29.3
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccc
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGV 72 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~ 72 (512)
|.||+|...+ + +||+|++|+|||||..||..+.
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 8999999999999999999965
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=98.40 E-value=1.5e-07 Score=68.07 Aligned_cols=33 Identities=45% Similarity=0.799 Sum_probs=29.8
Q ss_pred cccccCcc-CCCCCeeEEcCCCCCcccchhhhccc
Q 010341 38 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVG 71 (512)
Q Consensus 38 ~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G 71 (512)
+.||+|+. +|.+ .||+|..|.|||||..||...
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 7887 999999999999999999973
No 26
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.23 E-value=1.2e-06 Score=86.16 Aligned_cols=49 Identities=18% Similarity=0.472 Sum_probs=45.0
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 141 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg-~rt~~ec~~hy~~~y 141 (512)
+-+..||++|+..|+++|+.||.+||..||.+++ +||+.||++||.++.
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 4567899999999999999999889999999997 899999999998764
No 27
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=98.09 E-value=3.7e-07 Score=100.24 Aligned_cols=71 Identities=25% Similarity=0.479 Sum_probs=57.5
Q ss_pred CccceeehccCCCCCCCCCCcCCcccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeee
Q 010341 15 SPVTIQILQLQPGQGAGEGKRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVM 86 (512)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi 86 (512)
+|--+.|+.-.+...++|...+.-.|++|.. .|.+ +||+|..|.++|||..||..|...+.|+..|+..-.
T Consensus 581 epqsmVwL~vlhRv~~aE~~kH~~kCniCk~~pIvG-~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey 652 (966)
T KOG4286|consen 581 EPQSMVWLPVLHRVAAAETAKHQAKCNICKECPIIG-FRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEY 652 (966)
T ss_pred CcchhhHHHHHHHHHHHHHHHhhhhcchhhhCccce-eeeeehhhcChhHHhhHhhhcccccCCCCCCCceee
Confidence 3444555555555566777788889999996 6887 999999999999999999999999999999876544
No 28
>PLN03091 hypothetical protein; Provisional
Probab=97.99 E-value=6.7e-06 Score=86.76 Aligned_cols=49 Identities=24% Similarity=0.545 Sum_probs=44.7
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhhc
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNVY 141 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg-~rt~~ec~~hy~~~y 141 (512)
+-+..||.+||.+|+++|.+||.+||..||++++ +||+.||++||.++.
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 3456899999999999999999999999999998 899999999997764
No 29
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.97 E-value=3.9e-06 Score=85.52 Aligned_cols=52 Identities=33% Similarity=0.731 Sum_probs=46.1
Q ss_pred cCCcccccCccC-CCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeec
Q 010341 35 RALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMD 87 (512)
Q Consensus 35 ~~~~~C~~C~~~-i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~ 87 (512)
...+.|++|++. +++ .||+|..|.|||||..||-.|+.+..|.-+|+.+.|-
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 356789999986 565 8999999999999999999999999999999987663
No 30
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=97.92 E-value=6.6e-06 Score=83.67 Aligned_cols=46 Identities=39% Similarity=0.890 Sum_probs=39.2
Q ss_pred cccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecC
Q 010341 38 YHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDN 88 (512)
Q Consensus 38 ~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~ 88 (512)
..||.|++ .|.+ .||+|++|+|||||..|+..+ .|.-.|.+..+..
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 58999999 8998 999999999999999999986 3556787776543
No 31
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.86 E-value=1.3e-05 Score=79.80 Aligned_cols=46 Identities=17% Similarity=0.427 Sum_probs=44.3
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhC-CCCHHHHHHHHHhh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG-TKTKELCIEHYTNV 140 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg-~rt~~ec~~hy~~~ 140 (512)
.++||++||..|.+.|+.||-|+|..||++.| .|+...|+.+|.++
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~Ny 55 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNY 55 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcc
Confidence 58899999999999999999999999999999 99999999999876
No 32
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.73 E-value=4e-05 Score=75.64 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=44.1
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
+...+||.+|+.+|++++..|| ..|..||.+|.+||..+|+.||..+
T Consensus 76 I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~LpGRTDnqIKNRWns~ 122 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLG-NRWSLIAGRIPGRTDNEIKNYWNTH 122 (249)
T ss_pred cccCCCChHHHHHHHHHHHhcc-ccHHHHHhhcCCCCHHHHHHHHHHH
Confidence 5678999999999999999999 8999999999999999999999764
No 33
>PLN03091 hypothetical protein; Provisional
Probab=97.38 E-value=0.00023 Score=75.42 Aligned_cols=48 Identities=19% Similarity=0.351 Sum_probs=44.6
Q ss_pred CccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 92 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 92 p~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
.+.+..||.+|+.+|++.+..|| ..|..||.+|.+||..+|+.||..+
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=97.35 E-value=2e-05 Score=80.28 Aligned_cols=67 Identities=25% Similarity=0.576 Sum_probs=55.6
Q ss_pred cceeehccCCCCCCCCCCcCCcccccCcc-CCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCee
Q 010341 17 VTIQILQLQPGQGAGEGKRALYHCNYCNK-DITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYR 84 (512)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~-~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~ 84 (512)
--++|+.-.+..++.+...+.+.|++|.. .+.+ .||+|..|.+|.+|..||-.|...+.|.+.|.+.
T Consensus 220 ~cl~wlpLmhrla~v~nv~hpv~cs~c~srs~~g-fry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mk 287 (434)
T KOG4301|consen 220 QCLVWLPLMHRLATVENVFHPVECSYCRSRSMMG-FRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMK 287 (434)
T ss_pred hhHHHHHHHHHHHhhcccCCCccCcceecccccc-hhhhHhhcCCccccchhhccccCCCCcchHHHHH
Confidence 34556655556666777788899999986 5776 9999999999999999999999999999998665
No 35
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.05 E-value=0.00077 Score=67.15 Aligned_cols=46 Identities=20% Similarity=0.403 Sum_probs=42.7
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
+-++.||.+||..++++-..+| .-|..||.++++||..+++.||..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LPGRTDNeIKN~Wnt 105 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLPGRTDNEVKNHWNT 105 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCCCcCHHHHHHHHHH
Confidence 4578999999999999999999 679999999999999999999954
No 36
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.47 E-value=0.004 Score=68.46 Aligned_cols=52 Identities=27% Similarity=0.639 Sum_probs=47.3
Q ss_pred CccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 010341 92 PLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 143 (512)
Q Consensus 92 p~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~ 143 (512)
.+-.+.||.+|+.+|+.||+.||-.+|-.|-+.|.+|+..||+.+|.+..-.
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 3557899999999999999999988999999999999999999999986443
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.80 E-value=0.0086 Score=65.95 Aligned_cols=49 Identities=24% Similarity=0.348 Sum_probs=43.4
Q ss_pred CCccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCH---HHHHHHHHh
Q 010341 91 FPLICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTK---ELCIEHYTN 139 (512)
Q Consensus 91 ~p~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~---~ec~~hy~~ 139 (512)
+..-.+.|+-.||..|+++|++||.|+|..+|..+|.||. .-|+.++..
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 3445689999999999999999999999999999999998 678888764
No 38
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=94.29 E-value=0.041 Score=61.02 Aligned_cols=49 Identities=18% Similarity=0.384 Sum_probs=44.4
Q ss_pred cCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 010341 94 ICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 144 (512)
Q Consensus 94 ~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~ 144 (512)
..+.||.+|+..|...+.++| +.|..|++.|| |.|..|+.+|.++-..+
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 358899999999999999999 99999999998 79999999998876554
No 39
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=93.86 E-value=0.042 Score=45.72 Aligned_cols=45 Identities=29% Similarity=0.614 Sum_probs=33.3
Q ss_pred CCCCchhHHHHHHHHHH--hC--CC---------ChHHHHHHhC----CCCHHHHHHHHHhh
Q 010341 96 PDWNADDEILLLEGIEM--YG--LG---------NWAEIAEHVG----TKTKELCIEHYTNV 140 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~--~G--~g---------nW~~IA~~vg----~rt~~ec~~hy~~~ 140 (512)
..||.+|...||+++.. +. ++ -|..||+.|. .||+.||+.+|.++
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 46999999999999887 21 11 3999999985 69999999999875
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=92.28 E-value=0.083 Score=35.45 Aligned_cols=29 Identities=41% Similarity=0.992 Sum_probs=12.8
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhh
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIEC 67 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~C 67 (512)
..|+.|+..+.+...|+|..|. |+|...|
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 3699999998866899999995 9998877
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=90.97 E-value=0.18 Score=33.88 Aligned_cols=28 Identities=32% Similarity=0.999 Sum_probs=24.3
Q ss_pred cccccCccCCCCCe-eEEcCCCCCcccchhh
Q 010341 38 YHCNYCNKDITGKI-RIKCAVCPDFDLCIEC 67 (512)
Q Consensus 38 ~~C~~C~~~i~~~~-ri~C~~C~d~dLC~~C 67 (512)
+.|++|.+.+.+ . .|+|.+|. |++.+.|
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 9888777
No 42
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=90.15 E-value=0.3 Score=53.07 Aligned_cols=48 Identities=21% Similarity=0.524 Sum_probs=43.6
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 143 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~ 143 (512)
...|+..||..|--||..||-..|..||..+..+|+.+|..+|. -+++
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~-e~ld 54 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWE-EWLD 54 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHH-HHhC
Confidence 46799999999999999999888999999999999999999998 4444
No 43
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=87.77 E-value=0.53 Score=52.48 Aligned_cols=52 Identities=19% Similarity=0.373 Sum_probs=43.0
Q ss_pred cCCCCCchhHHHHHHHHH-------Hh------------------CCCChHHHHHHhCCCCHHHHHHHHHhhccCCC
Q 010341 94 ICPDWNADDEILLLEGIE-------MY------------------GLGNWAEIAEHVGTKTKELCIEHYTNVYMNSP 145 (512)
Q Consensus 94 ~~~~Wt~~Ee~~Lleai~-------~~------------------G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~~ 145 (512)
-...||-+|+..||.+|+ ++ ..=||..|++.+|||+..+|+.||.++-....
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 34 11279999999999999999999998865543
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=86.04 E-value=0.56 Score=51.66 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=42.2
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
.+.|+..|+..|+-+++.||..||..||..++.+++.+|..||..
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 458999999999999999999999999999999999999999944
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=85.11 E-value=1.1 Score=40.12 Aligned_cols=43 Identities=21% Similarity=0.441 Sum_probs=35.1
Q ss_pred CCCCCchhHHHHHHHHHHhCC---CChHHHHHHhC------------CCCHHHHHHHH
Q 010341 95 CPDWNADDEILLLEGIEMYGL---GNWAEIAEHVG------------TKTKELCIEHY 137 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~---gnW~~IA~~vg------------~rt~~ec~~hy 137 (512)
...||.+||.-||-.+..||+ |+|+.|-+.|- +||+.|+..|=
T Consensus 49 ~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~ 106 (118)
T PF09111_consen 49 KKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRC 106 (118)
T ss_dssp -SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHH
T ss_pred CCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHH
Confidence 478999999999999999999 99999998773 68888887654
No 46
>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=83.72 E-value=0.83 Score=42.76 Aligned_cols=44 Identities=20% Similarity=0.480 Sum_probs=36.8
Q ss_pred CCCCchhHHHHHHHHHHh---C---CCChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 96 PDWNADDEILLLEGIEMY---G---LGNWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~---G---~gnW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
..||.+|+++|-+.|-.| | +.-.++||+.++ ||+.-|..+|+.+
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~ 54 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY 54 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH
Confidence 579999999999999876 2 124788888886 9999999999775
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=83.31 E-value=0.95 Score=36.54 Aligned_cols=42 Identities=29% Similarity=0.587 Sum_probs=27.3
Q ss_pred CccCCC-CCeeEEcCCCCC---cccchhhhcccccccCCCCCCCeeeecCC
Q 010341 43 CNKDIT-GKIRIKCAVCPD---FDLCIECFSVGVEVHPHKSNHPYRVMDNL 89 (512)
Q Consensus 43 C~~~i~-~~~ri~C~~C~d---~dLC~~CF~~G~e~~~H~~~H~y~vi~~~ 89 (512)
|+..+. +.+.|+|..|.. ..+|..||..+. |. +|.|..+...
T Consensus 3 C~~~~~~~q~~y~C~tC~~~~~~~iC~~CF~~~~----H~-gH~~~~~~~~ 48 (71)
T PF02207_consen 3 CTYVWTSGQIFYRCLTCSLDESSGICEECFANSC----HE-GHRVVYYRSS 48 (71)
T ss_dssp S--B--TT-EEEEETTTBSSTT-BBEHHHHCTSG----GG-GSSEEEEE--
T ss_pred CCCCCcCCCEEEECccCCCCCCEEEchhhCCCCC----cC-CCcEEEEEeC
Confidence 555443 258899999964 679999999866 75 7899888654
No 48
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=83.12 E-value=1.5 Score=49.58 Aligned_cols=44 Identities=20% Similarity=0.423 Sum_probs=40.7
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
...||..|-.++-+|+-+|. .++..|++.|.+||..||.+.|+-
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 36799999999999999998 899999999999999999988863
No 49
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=82.67 E-value=1.1 Score=48.72 Aligned_cols=46 Identities=26% Similarity=0.633 Sum_probs=41.2
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
|-...|+.+||..||.+....- ..|-.||..|| ||..+|..||++.
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 4467899999999999999886 79999999997 8999999999873
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=82.37 E-value=2.2 Score=44.95 Aligned_cols=44 Identities=7% Similarity=0.314 Sum_probs=41.3
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
...|++.|..++..|++++| .++.-||...++|+..|++..|.+
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 799999999999999999998865
No 51
>PLN03000 amine oxidase
Probab=79.20 E-value=3.5 Score=48.53 Aligned_cols=72 Identities=18% Similarity=0.142 Sum_probs=56.1
Q ss_pred CCCccCCCCHHHHHHH--H-HhCCCchHHHHHHHHHHHHHHhCC--CcCHHHHhhhhccCc-hhHHHHHHHHHHCCCCC
Q 010341 439 GFNETQLLSEAEKRLC--C-EIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKIEP-SKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 439 ~~pg~~lLs~~E~~LC--s-~lrL~P~~YL~iK~~LirE~~~~G--~lk~~~A~~l~kiD~-~K~~rIydFlv~~Gwi~ 511 (512)
++| .+-||++|.+.- . .-++.+..||.|+..||+=..++- .+++++|...++.+- +-++.+|+||+.+|+|.
T Consensus 90 ~~p-~d~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r~G~in 167 (881)
T PLN03000 90 GFP-ADSLTEEEIEFGVVPIVGGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVTHGYIN 167 (881)
T ss_pred CCC-cccCCHHHHhccccCcccccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHHcCccc
Confidence 345 778999997751 1 124678999999999998887554 588889988886433 67889999999999985
No 52
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=79.20 E-value=2.5 Score=44.32 Aligned_cols=48 Identities=21% Similarity=0.500 Sum_probs=38.4
Q ss_pred CCCCCchhHHHHHHHHHHh----CCCC-----hHHHHHHhC----CCCHHHHHHHHHhhcc
Q 010341 95 CPDWNADDEILLLEGIEMY----GLGN-----WAEIAEHVG----TKTKELCIEHYTNVYM 142 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~----G~gn-----W~~IA~~vg----~rt~~ec~~hy~~~y~ 142 (512)
...|+.+|.+.||++-... +-++ |+.||..+. .||+.||+..|.+++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 3679999999999998633 3344 999999553 5999999999988754
No 53
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=79.04 E-value=2 Score=47.49 Aligned_cols=50 Identities=24% Similarity=0.548 Sum_probs=44.8
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccC
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMN 143 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~ 143 (512)
+-...|+.+|+-.|+++-..+| .-|..||..++++|..+|..+|....=.
T Consensus 70 lk~~~~~~eed~~li~l~~~~~-~~wstia~~~d~rt~~~~~ery~~~~~~ 119 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELG-TQWSTIADYKDRRTAQQCVERYVNTLED 119 (512)
T ss_pred cccccccHHHHHHHHHHHHhcC-chhhhhccccCccchHHHHHHHHHHhhh
Confidence 4467899999999999999999 5799999999999999999999976533
No 54
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=77.21 E-value=2.6 Score=46.76 Aligned_cols=45 Identities=18% Similarity=0.413 Sum_probs=38.7
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHH----------HhCCCCHHHHHHHHHhh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAE----------HVGTKTKELCIEHYTNV 140 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~----------~vg~rt~~ec~~hy~~~ 140 (512)
+..||-+|+..+.+||.++| .|++.|-+ .+..||..+++.||++.
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 89999933 33459999999999874
No 55
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=72.43 E-value=4.8 Score=32.53 Aligned_cols=45 Identities=22% Similarity=0.469 Sum_probs=37.4
Q ss_pred CCCCchhHHHHHHHHHHhC----------------CCChHHHHHHhC-----CCCHHHHHHHHHhh
Q 010341 96 PDWNADDEILLLEGIEMYG----------------LGNWAEIAEHVG-----TKTKELCIEHYTNV 140 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G----------------~gnW~~IA~~vg-----~rt~~ec~~hy~~~ 140 (512)
..||.+|...|++.|+.|- -.-|.+|+..+. .||..+++..|.++
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 5799999999999998872 125999999884 59999999999765
No 56
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=72.03 E-value=2.5 Score=50.67 Aligned_cols=28 Identities=39% Similarity=0.763 Sum_probs=26.9
Q ss_pred cCCCCCchhHHHHHHHHHHhCCCChHHH
Q 010341 94 ICPDWNADDEILLLEGIEMYGLGNWAEI 121 (512)
Q Consensus 94 ~~~~Wt~~Ee~~Lleai~~~G~gnW~~I 121 (512)
+..+|+.+++..||-||-.||+|+|+.|
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 57
>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=71.98 E-value=5.3 Score=32.36 Aligned_cols=42 Identities=29% Similarity=0.757 Sum_probs=29.2
Q ss_pred cCccCCC-CCeeEEcCCCC---CcccchhhhcccccccCCCCCCCeeeecC
Q 010341 42 YCNKDIT-GKIRIKCAVCP---DFDLCIECFSVGVEVHPHKSNHPYRVMDN 88 (512)
Q Consensus 42 ~C~~~i~-~~~ri~C~~C~---d~dLC~~CF~~G~e~~~H~~~H~y~vi~~ 88 (512)
.|+..++ +.+.|+|..|. ..-+|..||..+. | .+|+|.+...
T Consensus 2 ~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~----H-~gH~~~~~~~ 47 (71)
T smart00396 2 VCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNC----H-KGHDYSLKTS 47 (71)
T ss_pred CCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCC----C-CCCCEEEEEe
Confidence 4665543 33668899885 2458999999755 6 4688887765
No 58
>PHA00442 host recBCD nuclease inhibitor
Probab=71.95 E-value=4.4 Score=31.10 Aligned_cols=26 Identities=19% Similarity=0.489 Sum_probs=22.2
Q ss_pred chhHHHHHHHHHHhCCCChHHHHHHh
Q 010341 100 ADDEILLLEGIEMYGLGNWAEIAEHV 125 (512)
Q Consensus 100 ~~Ee~~Lleai~~~G~gnW~~IA~~v 125 (512)
-+-+..+|++++.+|..||+.+.+.+
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 35567899999999999999988765
No 59
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=71.46 E-value=9.9 Score=27.42 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=31.9
Q ss_pred HhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 476 FSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 476 ~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
..++.++..+....+.+....+.+..+.|.+.|||.
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 345679999999999999999999999999999984
No 60
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=70.87 E-value=12 Score=27.26 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=35.4
Q ss_pred HHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 468 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 468 K~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
+..++.....+|.++..+.-..+.+....+.+...-|+++|||.
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 34455556678889999999999999999999999999999983
No 61
>KOG1778 consensus CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription]
Probab=69.64 E-value=2.5 Score=44.06 Aligned_cols=54 Identities=28% Similarity=0.531 Sum_probs=39.4
Q ss_pred cCccceeehccCCCCCCCCCCcCCcccccCccCCCCCeeEEcCCCCCcccchhhhcccc
Q 010341 14 MSPVTIQILQLQPGQGAGEGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGV 72 (512)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~ 72 (512)
+.=.++.+....+. +++ +...+.|+.|+.+. ..+|+|.+|++|+.|..|+....
T Consensus 149 a~hss~~~~~~~H~--~t~-~~~~~~c~~c~~~~--~~~~~c~~~~d~d~~~~~~~k~~ 202 (319)
T KOG1778|consen 149 AKHSSIMLLFDLHL--QTE-KWFAYTCPICKLEV--LTAWHCEVCPDYDRCRACEEKPL 202 (319)
T ss_pred HHHHHHHHHHHHHh--ccc-CceeeecCcccccc--ccccccccCCchhhhhcccCCCC
Confidence 33334444444433 233 45788999999988 37899999999999999999865
No 62
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=68.68 E-value=10 Score=33.62 Aligned_cols=60 Identities=20% Similarity=0.423 Sum_probs=42.0
Q ss_pred cccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHHHhCCCChH
Q 010341 40 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLGNWA 119 (512)
Q Consensus 40 C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~~~G~gnW~ 119 (512)
|-+|+.++.- .+++|..|..- +.+ .|.+-.-.--..|++.+++..-... ||-.
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 78999998611 111 1111111123478899999888888 9999
Q ss_pred HHHHHhC
Q 010341 120 EIAEHVG 126 (512)
Q Consensus 120 ~IA~~vg 126 (512)
+|++.+|
T Consensus 54 e~e~~lg 60 (113)
T PF09862_consen 54 EMEKELG 60 (113)
T ss_pred HHHHHHC
Confidence 9999998
No 63
>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=67.45 E-value=6.9 Score=31.13 Aligned_cols=40 Identities=20% Similarity=0.384 Sum_probs=32.2
Q ss_pred HHHHH-hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 472 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 472 irE~~-~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
|++++ .+|..++.+.-.-|.+++.-+..+.++|+++|.|.
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 45555 78899999988889999999999999999999984
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=63.99 E-value=8.6 Score=27.25 Aligned_cols=39 Identities=28% Similarity=0.514 Sum_probs=27.8
Q ss_pred CcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeee
Q 010341 37 LYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRV 85 (512)
Q Consensus 37 ~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~v 85 (512)
...|..|.... ..+.|..|. ..+|..|+..+ |+. |.+..
T Consensus 3 ~~~C~~H~~~~---~~~~C~~C~-~~~C~~C~~~~-----H~~-H~~~~ 41 (42)
T PF00643_consen 3 EPKCPEHPEEP---LSLFCEDCN-EPLCSECTVSG-----HKG-HKIVP 41 (42)
T ss_dssp SSB-SSTTTSB---EEEEETTTT-EEEEHHHHHTS-----TTT-SEEEE
T ss_pred CccCccCCccc---eEEEecCCC-CccCccCCCCC-----CCC-CEEeE
Confidence 34688887642 568999998 57999999986 644 76654
No 65
>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=62.77 E-value=12 Score=29.97 Aligned_cols=47 Identities=23% Similarity=0.408 Sum_probs=32.3
Q ss_pred CCCCchhHHHHHHHHHHh---C---CCC--hHHHHHHhC-CCCHHHHHHHHHhhcc
Q 010341 96 PDWNADDEILLLEGIEMY---G---LGN--WAEIAEHVG-TKTKELCIEHYTNVYM 142 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~---G---~gn--W~~IA~~vg-~rt~~ec~~hy~~~y~ 142 (512)
..+|++||..|++.|..+ | -|| |.++++.-. .+|-.--++||.+...
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 3 356 999999877 7888888999988753
No 66
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=62.27 E-value=9.6 Score=45.87 Aligned_cols=58 Identities=24% Similarity=0.377 Sum_probs=46.3
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCCCccc
Q 010341 96 PDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPDMSHV 155 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~~~~plp~~~~~ 155 (512)
.+|+..+-..++.|+++||-.+-+.||..|++||++|++. |.+.|.... -.+.+....
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~-y~~~f~~~~-~~~~~~~~~ 882 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVER-YAKVFWERY-KELNDYDRI 882 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHH-HHHHHHHhh-hhhccHHHH
Confidence 4899999999999999999999999999999999999984 556655442 224444433
No 67
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=62.15 E-value=9.6 Score=40.22 Aligned_cols=43 Identities=28% Similarity=0.499 Sum_probs=37.9
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHH-HHHhCCCCHHHHHHHHHh
Q 010341 96 PDWNADDEILLLEGIEMYGLGNWAEI-AEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~gnW~~I-A~~vg~rt~~ec~~hy~~ 139 (512)
..|+.+|=+.+=++++.|| .|..-| +..|.||+..||+..|+.
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 788777 568899999999988764
No 68
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=58.91 E-value=6.1 Score=30.11 Aligned_cols=29 Identities=31% Similarity=0.774 Sum_probs=17.8
Q ss_pred ccccCccCCCCC-------eeEEcCCCCCcccchhhh
Q 010341 39 HCNYCNKDITGK-------IRIKCAVCPDFDLCIECF 68 (512)
Q Consensus 39 ~C~~C~~~i~~~-------~ri~C~~C~d~dLC~~CF 68 (512)
.|.+|.+.+... .+|+|..|. -..|..|=
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~-~~FC~dCD 36 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCK-NHFCIDCD 36 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT---B-HHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCC-CccccCcC
Confidence 478888877653 699999997 45788874
No 69
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=57.46 E-value=13 Score=44.71 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=37.8
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhC------------CCCHHHHHHHHHh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVG------------TKTKELCIEHYTN 139 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg------------~rt~~ec~~hy~~ 139 (512)
...||.+|+..||-.+..||+|+|+.|-..|. +||+.|+..+-..
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 70
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=56.81 E-value=20 Score=42.17 Aligned_cols=69 Identities=14% Similarity=0.156 Sum_probs=53.8
Q ss_pred cCCCCHHHHHH---HHHhCCCchHHHHHHHHHHHHHHhCC--CcCHHHHhhhhcc-CchhHHHHHHHHHHCCCCC
Q 010341 443 TQLLSEAEKRL---CCEIRLAPPLYLRMQEVMSREIFSGN--VNNKADAHHLFKI-EPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 443 ~~lLs~~E~~L---Cs~lrL~P~~YL~iK~~LirE~~~~G--~lk~~~A~~l~ki-D~~K~~rIydFlv~~Gwi~ 511 (512)
.+-||++|.+. =.-.+.-+..||.|+..||+=..++- .+++.+|...++. ..+-+..+|+||+..|+|+
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 56799988664 12234778999999999998887543 5888999888753 3467899999999999985
No 71
>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=56.28 E-value=12 Score=28.18 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=29.8
Q ss_pred hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 477 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 477 ~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
..|.++..+.-..+.++...+.++.+-|++.|||.
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 72
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=56.27 E-value=17 Score=31.37 Aligned_cols=33 Identities=24% Similarity=0.530 Sum_probs=25.4
Q ss_pred cCCCCCchhHHHHHHHHHHh----CCC---ChHHHHHHhC
Q 010341 94 ICPDWNADDEILLLEGIEMY----GLG---NWAEIAEHVG 126 (512)
Q Consensus 94 ~~~~Wt~~Ee~~Lleai~~~----G~g---nW~~IA~~vg 126 (512)
|..-||.++|+.||+|+-.| |.. +|...-++|.
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk 42 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVK 42 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHH
Confidence 56779999999999999888 643 5666666654
No 73
>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=56.15 E-value=6.9 Score=27.85 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=19.1
Q ss_pred cccCccCCCCCeeEEcCCCCCccc-chhhhcc
Q 010341 40 CNYCNKDITGKIRIKCAVCPDFDL-CIECFSV 70 (512)
Q Consensus 40 C~~C~~~i~~~~ri~C~~C~d~dL-C~~CF~~ 70 (512)
||+|+..|.+.+.+.=..=..|-+ |..|...
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 899999998765444332223434 5777654
No 74
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=55.60 E-value=26 Score=26.46 Aligned_cols=50 Identities=20% Similarity=0.297 Sum_probs=37.8
Q ss_pred hCCCchHHHHHHHHHHHHHHhCCC--cCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 457 IRLAPPLYLRMQEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 457 lrL~P~~YL~iK~~LirE~~~~G~--lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
++|.|..|..+--+. ..+. ++..+....+.+++.-+.++.+=|++.|||.
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 356677776554333 3333 8899999999999999999999999999983
No 75
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=55.04 E-value=13 Score=37.41 Aligned_cols=58 Identities=21% Similarity=0.182 Sum_probs=39.9
Q ss_pred hhcccccCCChhHHHHHHHHHHHH--------HHHHHHH-----------HHHHHHHHhCCcchHHHHHHHHHHhhh
Q 010341 324 RYDVFMRFHSKEDHEDLLQTVISE--------HRTLKRI-----------QDLKEARAAGCRTSAEADRYLELKRGR 381 (512)
Q Consensus 324 ~l~~far~~~~~~~~~l~~~l~~E--------~~Lr~rI-----------~~L~~~R~~Gittl~e~~~ye~~k~~R 381 (512)
-..-|.+++||-+.+.|..-|..= ..|+.-. .-|..|+.+||+|++++..|+++.+.|
T Consensus 134 F~~e~Gr~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~n~~YI~~IL~nW~k~gvkTv~dv~~~~~~~~~~ 210 (246)
T COG3935 134 FEEEFGRMLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKLNFKYIDAILRNWKKNGVKTVEDVRAREEERRTR 210 (246)
T ss_pred HHHHcCCcCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHH
Confidence 355677788888887776544321 1222222 238899999999999999998876654
No 76
>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=54.85 E-value=36 Score=24.61 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 102 DEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 102 Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
=+..+|..++.-|--.|.+||+.+|- |+..|..+...
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 36789999999888899999999984 88888887654
No 77
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=54.13 E-value=7 Score=32.32 Aligned_cols=33 Identities=27% Similarity=0.881 Sum_probs=16.0
Q ss_pred CcccccCccCC----CCCeeEEcCCCCCcccchhhhcc
Q 010341 37 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSV 70 (512)
Q Consensus 37 ~~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~ 70 (512)
...|.+|+.++ ++.+++-|.+|. |-+|-.||..
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC~-fPvCr~CyEY 45 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHECA-FPVCRPCYEY 45 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS------HHHHHH
T ss_pred CcccccccCccccCCCCCEEEEEcccC-CccchhHHHH
Confidence 44699998764 456899999997 8899999876
No 78
>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=53.41 E-value=47 Score=26.05 Aligned_cols=45 Identities=16% Similarity=0.322 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 463 LYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 463 ~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
.=|.+|..+|...+..|.|+.++|-.+. +.+..-+++..++|++.
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 3478999999999999999999998874 66778899999999863
No 79
>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=53.20 E-value=51 Score=28.43 Aligned_cols=63 Identities=16% Similarity=0.055 Sum_probs=48.8
Q ss_pred HHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 448 EAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 448 ~~E~~LCs~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
.-+..|=..++|.|..|..+..+-. -...+|.++..+....+.++...+.++.+=|++.|||.
T Consensus 12 ~~~~~l~~~~~ls~~q~~vL~~l~~-~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 12 SLKRYLKKEFNLSLEELLILYYLGK-LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHh-hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 3344555567999999987754432 11245789999999999999999999999999999984
No 80
>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=51.91 E-value=31 Score=28.65 Aligned_cols=44 Identities=23% Similarity=0.449 Sum_probs=33.4
Q ss_pred CCCchhHHHHHHHHHHh---C-------CC--ChHHHHHHhC-----CCCHHHHHHHHHhh
Q 010341 97 DWNADDEILLLEGIEMY---G-------LG--NWAEIAEHVG-----TKTKELCIEHYTNV 140 (512)
Q Consensus 97 ~Wt~~Ee~~Lleai~~~---G-------~g--nW~~IA~~vg-----~rt~~ec~~hy~~~ 140 (512)
.||.+.+..||+++... | |. .|+.|++.+. ..|..+|+.||..+
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 49999999999988433 1 11 3888998885 47899999998653
No 81
>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=48.56 E-value=40 Score=29.26 Aligned_cols=61 Identities=8% Similarity=0.025 Sum_probs=48.6
Q ss_pred CCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 446 LSEAEKRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 446 Ls~~E~~LCs~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
++..-......++|.|..|..+-.+ ..+|.++..+.-..+.++..-+.++.+=|.+.|||.
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 4444556677889999999765332 356778888888888999999999999999999984
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=48.02 E-value=10 Score=35.76 Aligned_cols=29 Identities=31% Similarity=0.678 Sum_probs=25.8
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHh
Q 010341 97 DWNADDEILLLEGIEMYGLGNWAEIAEHV 125 (512)
Q Consensus 97 ~Wt~~Ee~~Lleai~~~G~gnW~~IA~~v 125 (512)
-|...-+.-||.||-.||+|-|++|.+.-
T Consensus 5 iw~r~hdywll~gi~~hgy~rwqdi~nd~ 33 (173)
T PF08074_consen 5 IWHRRHDYWLLAGIVKHGYGRWQDIQNDP 33 (173)
T ss_pred hhhhhhhHHHHhHHhhccchhHHHHhcCC
Confidence 48888899999999999999999997743
No 83
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=48.01 E-value=22 Score=38.58 Aligned_cols=46 Identities=15% Similarity=0.440 Sum_probs=41.8
Q ss_pred ccCCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 93 LICPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 93 ~~~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
-|...||++|-.+|-.+.+.|| .+...|-..+.-|+-...+..|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHH
Confidence 3568999999999999999999 899999999999999999988865
No 84
>smart00595 MADF subfamily of SANT domain.
Probab=47.81 E-value=19 Score=29.67 Aligned_cols=23 Identities=39% Similarity=0.820 Sum_probs=20.9
Q ss_pred ChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 117 NWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 117 nW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
-|..||..+|. |.++|+.+|.++
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 85
>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=47.20 E-value=35 Score=28.15 Aligned_cols=41 Identities=17% Similarity=0.355 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCCcCHHHHhhhhc---cCchhHHHHHHHHHHCCC
Q 010341 469 EVMSREIFSGNVNNKADAHHLFK---IEPSKIDRVYDMLVKKGL 509 (512)
Q Consensus 469 ~~LirE~~~~G~lk~~~A~~l~k---iD~~K~~rIydFlv~~Gw 509 (512)
..||....+.|.|+-.+....++ +++..+..||++|...|.
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 34777777889999999888887 899999999999999885
No 86
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=46.81 E-value=11 Score=43.86 Aligned_cols=35 Identities=23% Similarity=0.754 Sum_probs=29.8
Q ss_pred cCCcccccCccCCCCCeeEEcCCCCCcccchhhhccc
Q 010341 35 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 71 (512)
Q Consensus 35 ~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G 71 (512)
.....|+.|.+.+.+ ++++|..|. |-+|+.|+-.-
T Consensus 227 g~~~mC~~C~~tlfn-~hw~C~~C~-~~~Cl~C~r~~ 261 (889)
T KOG1356|consen 227 GIREMCDRCETTLFN-IHWRCPRCG-FGVCLDCYRKW 261 (889)
T ss_pred Ccchhhhhhcccccc-eeEEccccC-Ceeeecchhhc
Confidence 455679999999887 899999998 66999999765
No 87
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=46.35 E-value=27 Score=27.67 Aligned_cols=43 Identities=12% Similarity=0.105 Sum_probs=32.7
Q ss_pred HHHHHHHHH-h-CCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 468 QEVMSREIF-S-GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 468 K~~LirE~~-~-~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
|+.++ +++ . ++.++-.+.-..+.|....++++..+|.+.|.|.
T Consensus 2 ke~Il-~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 2 KEKIL-EYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHCHH-HHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred cHHHH-HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 44444 344 3 6778888888889999999999999999999874
No 88
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=46.01 E-value=22 Score=38.65 Aligned_cols=42 Identities=26% Similarity=0.519 Sum_probs=33.8
Q ss_pred CCCCchhHHHHHHHHHHhCCCChHHHHH-HhCCCCHHHHHHHHH
Q 010341 96 PDWNADDEILLLEGIEMYGLGNWAEIAE-HVGTKTKELCIEHYT 138 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~gnW~~IA~-~vg~rt~~ec~~hy~ 138 (512)
+.|++.|-.++-||+++|| .++++|-. ++.=||-..+++.|+
T Consensus 286 EEWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHHHHH
Confidence 6899999999999999999 78888754 555677777776664
No 89
>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=44.37 E-value=38 Score=31.35 Aligned_cols=55 Identities=20% Similarity=0.403 Sum_probs=45.8
Q ss_pred CCCCchhHHHHHHHHHHhCCC--ChHHHHHHhCCCCHHHHHHHHHhhccCCCCCCCCC
Q 010341 96 PDWNADDEILLLEGIEMYGLG--NWAEIAEHVGTKTKELCIEHYTNVYMNSPFFPLPD 151 (512)
Q Consensus 96 ~~Wt~~Ee~~Lleai~~~G~g--nW~~IA~~vg~rt~~ec~~hy~~~y~~~~~~plp~ 151 (512)
-+++..+-..+|.+|..||+| +|......+-.||.+|++ .|..+|+...+.|.-+
T Consensus 39 lGFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~-aY~~LFm~HL~E~~~d 95 (145)
T PF06461_consen 39 LGFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIR-AYGSLFMRHLCEPGTD 95 (145)
T ss_pred eccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHH-HHHHHHHHHhcCCCcC
Confidence 378899999999999999998 799999999999998876 6778887776555433
No 90
>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=44.30 E-value=45 Score=26.68 Aligned_cols=45 Identities=20% Similarity=0.327 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCCC
Q 010341 464 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 512 (512)
Q Consensus 464 YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~~ 512 (512)
|-..++.++ ..|..+.+-...-|+|--|++.+|.|-|.+.|+|+|
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 467777777778899999999999999999999975
No 91
>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=44.16 E-value=15 Score=24.01 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=9.7
Q ss_pred HHHHHHHHCCCC
Q 010341 499 RVYDMLVKKGLA 510 (512)
Q Consensus 499 rIydFlv~~Gwi 510 (512)
-|||||+++|+.
T Consensus 6 lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 6 LIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHCT-H
T ss_pred HHHHHHHHCCcH
Confidence 589999999974
No 92
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=43.02 E-value=14 Score=38.56 Aligned_cols=56 Identities=21% Similarity=0.396 Sum_probs=32.8
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHH
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILL 106 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~L 106 (512)
-+|.=|+..- +.| |..--.+.||+.|-+..+..|.|.+- |.. +.-..||.+|-..|
T Consensus 21 k~CaDCga~~---P~W-~S~nlGvfiCi~CagvHRsLGvhiS~-----VKS----itLD~wt~~~l~~m 76 (319)
T COG5347 21 KKCADCGAPN---PTW-ASVNLGVFLCIDCAGVHRSLGVHISK-----VKS----LTLDNWTEEELRRM 76 (319)
T ss_pred CccccCCCCC---Cce-EecccCeEEEeecchhhhccccceee-----eee----eecccCCHHHHHHH
Confidence 3566688653 222 22223577999999988877766432 221 12245998774443
No 93
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=42.77 E-value=72 Score=28.62 Aligned_cols=56 Identities=16% Similarity=0.217 Sum_probs=44.7
Q ss_pred HHHHHhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 452 RLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 452 ~LCs~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
.....++|.|.+|..+-.+. ..++.++..+....+.+|..-+.++.+=|++.|||.
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 134557778888888999999999999999999985
No 94
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=42.45 E-value=50 Score=24.71 Aligned_cols=28 Identities=18% Similarity=0.431 Sum_probs=23.6
Q ss_pred CCChhHHHHHHHHH-----HHHHHHHHHHHHHH
Q 010341 331 FHSKEDHEDLLQTV-----ISEHRTLKRIQDLK 358 (512)
Q Consensus 331 ~~~~~~~~~l~~~l-----~~E~~Lr~rI~~L~ 358 (512)
+.+++++++|++.| ++|.+|++.+.+..
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
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=42.22 E-value=9.1 Score=34.90 Aligned_cols=53 Identities=21% Similarity=0.392 Sum_probs=38.4
Q ss_pred cCCcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCC
Q 010341 35 RALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLS 90 (512)
Q Consensus 35 ~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~ 90 (512)
+..|.||.|+..-++.-+.+=.+|-+|.+|..||+.-- .|-+.|+-=.+-..+
T Consensus 78 ~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LW---K~~~~ypvCPvCkTS 130 (140)
T PF05290_consen 78 PKLYECNICKETSAEERFLKPNECCGYSICNACYANLW---KFCNLYPVCPVCKTS 130 (140)
T ss_pred CCceeccCcccccchhhcCCcccccchHHHHHHHHHHH---HHcccCCCCCccccc
Confidence 37899999998766656677788999999999999855 354555544443333
No 96
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=40.12 E-value=30 Score=32.94 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=33.9
Q ss_pred CCCCCchhHHHHHHHHHHhCCC------ChHHHHHHhCCCCHHHHHHHHHhh
Q 010341 95 CPDWNADDEILLLEGIEMYGLG------NWAEIAEHVGTKTKELCIEHYTNV 140 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~g------nW~~IA~~vg~rt~~ec~~hy~~~ 140 (512)
...||.+++++|-+.|-.|+-. -.+.+++.+ .||+..|..+|+.+
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 3579999999998888877632 244555565 48999999999443
No 97
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=40.00 E-value=18 Score=39.22 Aligned_cols=43 Identities=26% Similarity=0.422 Sum_probs=36.3
Q ss_pred CCCCCchhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHh
Q 010341 95 CPDWNADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTN 139 (512)
Q Consensus 95 ~~~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~ 139 (512)
.-+||..|-- +...-..|| .+.+-||+.++++|++|+...|++
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 3689998755 777778999 899999999999999999977643
No 98
>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=39.54 E-value=62 Score=24.42 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=29.7
Q ss_pred hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 477 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 477 ~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
.++ ++..++...+.+....+.++.+-|++.|||.
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 99
>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=39.15 E-value=6.6 Score=31.41 Aligned_cols=23 Identities=22% Similarity=0.339 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCCcchHHHHHHHH
Q 010341 354 IQDLKEARAAGCRTSAEADRYLE 376 (512)
Q Consensus 354 I~~L~~~R~~Gittl~e~~~ye~ 376 (512)
..-|..|++.||+|++++..|++
T Consensus 54 ~~Il~~W~~~gi~t~e~~~~~~k 76 (77)
T PF07261_consen 54 EKILNNWKQKGIKTVEDAEEYEK 76 (77)
T ss_dssp HHHHHHHHHCT--SCCCCT----
T ss_pred HHHHHHHHHcCCCCHHHHHHHhh
Confidence 35688999999999999988764
No 100
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.37 E-value=90 Score=23.08 Aligned_cols=53 Identities=19% Similarity=0.209 Sum_probs=35.6
Q ss_pred CCCchHHHHHHHHHHHHHHhCC-CcCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 010341 458 RLAPPLYLRMQEVMSREIFSGN-VNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 510 (512)
Q Consensus 458 rL~P~~YL~iK~~LirE~~~~G-~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi 510 (512)
+|.|...+.+=-+.-.....++ ..+.+..-..+.+-.+.+.+..+-|++.|||
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 3555555544433322212333 2467777778889999999999999999997
No 101
>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=38.31 E-value=64 Score=24.68 Aligned_cols=34 Identities=26% Similarity=0.359 Sum_probs=28.4
Q ss_pred hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 010341 477 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 510 (512)
Q Consensus 477 ~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi 510 (512)
.++.++.++....+.++..-+.++.+=|++.|||
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 4788889999999999999999999999999998
No 102
>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=38.02 E-value=29 Score=29.58 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=24.1
Q ss_pred CCCcCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 010341 478 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 510 (512)
Q Consensus 478 ~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi 510 (512)
.|+-...-|.+| .++.++++.+.+||+..|+|
T Consensus 64 ~Gv~v~~I~~~l-~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 64 EGVHVDEIAQQL-GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TTEEHHHHHHHS-TS-HHHHHHHHHHHHHTTSE
T ss_pred CcccHHHHHHHh-CcCHHHHHHHHHHHHhCCeE
Confidence 354444444555 99999999999999999997
No 103
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=37.82 E-value=51 Score=24.20 Aligned_cols=46 Identities=13% Similarity=0.245 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHh-CCCc-CHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 466 RMQEVMSREIFS-GNVN-NKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 466 ~iK~~LirE~~~-~G~l-k~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
.++..++...+. +..+ +..+....+.+..+-+++.+.-|.+.|||.
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 345555444332 3455 777888888999999999999999999984
No 104
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=36.46 E-value=49 Score=23.61 Aligned_cols=24 Identities=29% Similarity=0.531 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHhCCCChHHHHHHhC
Q 010341 102 DEILLLEGIEMYGLGNWAEIAEHVG 126 (512)
Q Consensus 102 Ee~~Lleai~~~G~gnW~~IA~~vg 126 (512)
|-..+.++++.+| ||....|+.+|
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 105
>PLN02436 cellulose synthase A
Probab=35.65 E-value=23 Score=42.57 Aligned_cols=49 Identities=22% Similarity=0.663 Sum_probs=34.7
Q ss_pred CcccccCccCC----CCCeeEEcCCCCCcccchhhhccccc----ccCCCCCCCeeeec
Q 010341 37 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGVE----VHPHKSNHPYRVMD 87 (512)
Q Consensus 37 ~~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~e----~~~H~~~H~y~vi~ 87 (512)
...|.+|+.++ .+.+++-|.+|. |-+|-.||..-.. .-.|-+++ |+...
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~-fpvCr~Cyeyer~eg~~~Cpqckt~-Y~r~k 92 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECA-FPVCRPCYEYERREGNQACPQCKTR-YKRIK 92 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCC-CccccchhhhhhhcCCccCcccCCc-hhhcc
Confidence 34799999874 456999999997 9999999965333 22343443 76554
No 106
>PLN02189 cellulose synthase
Probab=35.57 E-value=23 Score=42.44 Aligned_cols=50 Identities=22% Similarity=0.644 Sum_probs=35.3
Q ss_pred CCcccccCccCC----CCCeeEEcCCCCCcccchhhhccccc----ccCCCCCCCeeeec
Q 010341 36 ALYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGVE----VHPHKSNHPYRVMD 87 (512)
Q Consensus 36 ~~~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~e----~~~H~~~H~y~vi~ 87 (512)
....|.+|+.++ .+.+++-|.+|. |-+|-.||..-.. .-.|-+++ |+...
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~-fpvCr~Cyeyer~eg~q~CpqCkt~-Y~r~k 90 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECG-FPVCRPCYEYERREGTQNCPQCKTR-YKRLK 90 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCC-CccccchhhhhhhcCCccCcccCCc-hhhcc
Confidence 344799999874 466999999997 9999999965333 22344453 77554
No 107
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.30 E-value=83 Score=28.32 Aligned_cols=52 Identities=12% Similarity=0.252 Sum_probs=43.5
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 455 CEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 455 s~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
..++|.|.+|..+..+ ...|.++.++....+.+|..-+.++.+=|++.|||.
T Consensus 34 ~~~glt~~q~~vL~~l-----~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 34 SPLDITAAQFKVLCSI-----RCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred cccCCCHHHHHHHHHH-----HHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5678999999877643 245678888888889999999999999999999984
No 108
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=34.78 E-value=30 Score=41.45 Aligned_cols=50 Identities=22% Similarity=0.657 Sum_probs=35.1
Q ss_pred CCcccccCccCC----CCCeeEEcCCCCCcccchhhhccccc----ccCCCCCCCeeeec
Q 010341 36 ALYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGVE----VHPHKSNHPYRVMD 87 (512)
Q Consensus 36 ~~~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~e----~~~H~~~H~y~vi~ 87 (512)
....|.+|+.++ .+.+++-|.+|. |-+|-.||.--.. .-.|-.+| |+...
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~-fpvCr~cyeye~~~g~~~cp~c~t~-y~~~~ 71 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCG-FPVCKPCYEYERSEGNQCCPQCNTR-YKRHK 71 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCC-CccccchhhhhhhcCCccCCccCCc-hhhhc
Confidence 455699999763 456999999997 9999999965332 23444454 76554
No 109
>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=34.59 E-value=83 Score=26.06 Aligned_cols=38 Identities=21% Similarity=0.354 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhCC-------CChHHHHHHhCCCC-----HHHHHHHHHhh
Q 010341 103 EILLLEGIEMYGL-------GNWAEIAEHVGTKT-----KELCIEHYTNV 140 (512)
Q Consensus 103 e~~Lleai~~~G~-------gnW~~IA~~vg~rt-----~~ec~~hy~~~ 140 (512)
-..|-.+|...|- +.|..||+.+|-.+ ..+.+.+|.++
T Consensus 38 L~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~ 87 (92)
T PF01388_consen 38 LYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKY 87 (92)
T ss_dssp HHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHH
Confidence 4667778887771 36999999998322 36778888765
No 110
>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=34.07 E-value=82 Score=23.78 Aligned_cols=39 Identities=15% Similarity=0.249 Sum_probs=32.1
Q ss_pred HHHHH-hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 010341 472 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 510 (512)
Q Consensus 472 irE~~-~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi 510 (512)
|++++ .+|.++.++++.++.+--.-+-.|.+||=..||.
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 6899999999999988877788999999999985
No 111
>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=32.55 E-value=33 Score=27.26 Aligned_cols=18 Identities=17% Similarity=0.287 Sum_probs=15.7
Q ss_pred HHHHHHHHhCCcchHHHH
Q 010341 355 QDLKEARAAGCRTSAEAD 372 (512)
Q Consensus 355 ~~L~~~R~~Gittl~e~~ 372 (512)
.-|..|++.||+|+++++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 458899999999999875
No 112
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=32.31 E-value=1e+02 Score=25.00 Aligned_cols=40 Identities=13% Similarity=0.108 Sum_probs=33.3
Q ss_pred HHHHH-hC-CCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 472 SREIF-SG-NVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 472 irE~~-~~-G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
|-+++ .. |.++..+.-..+.+...-+.++.+.|++.|||.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 44444 33 689999988888999999999999999999984
No 113
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=31.83 E-value=28 Score=41.84 Aligned_cols=48 Identities=23% Similarity=0.698 Sum_probs=34.2
Q ss_pred cccccCccCC----CCCeeEEcCCCCCcccchhhhcccc----cccCCCCCCCeeeec
Q 010341 38 YHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGV----EVHPHKSNHPYRVMD 87 (512)
Q Consensus 38 ~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~----e~~~H~~~H~y~vi~ 87 (512)
-.|.+|+.++ .+.+++-|.+|. |-+|-.||..-. -.-.|=+++ |+...
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC~-FPVCrpCYEYEr~eG~q~CPqCktr-Ykr~k 73 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVCA-FPVCRPCYEYERKDGNQSCPQCKTK-YKRHK 73 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccCC-CccccchhhhhhhcCCccCCccCCc-hhhhc
Confidence 3799999764 456999999997 999999996532 223444453 77664
No 114
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=31.79 E-value=1.1e+02 Score=27.80 Aligned_cols=24 Identities=17% Similarity=0.455 Sum_probs=20.5
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhC
Q 010341 455 CEIRLAPPLYLRMQEVMSREIFSG 478 (512)
Q Consensus 455 s~lrL~P~~YL~iK~~LirE~~~~ 478 (512)
+.++|.|..|+.+|..|-.+.+..
T Consensus 87 ~ri~mS~~EYM~lKkqLae~il~~ 110 (153)
T COG4008 87 NRINMSPEEYMELKKQLAEYILGH 110 (153)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhcc
Confidence 578999999999999998877643
No 115
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=31.71 E-value=1.2e+02 Score=27.49 Aligned_cols=49 Identities=16% Similarity=0.404 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHh----CC--CcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 463 LYLRMQEVMSREIFS----GN--VNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 463 ~YL~iK~~LirE~~~----~G--~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
-|.-|.+.+....++ .| .++..+.-..+.+.+|-+.|.|.-|.+.|+|.
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~ 66 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVE 66 (125)
T ss_pred HHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 577777777766663 33 45666666667899999999999999999874
No 116
>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=30.64 E-value=1.4e+02 Score=23.84 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCCC
Q 010341 464 YLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAPP 512 (512)
Q Consensus 464 YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~~ 512 (512)
|-..++.++ ..|..+.+-...=|+|--|++.+|.|-|.+.|.|+|
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 345556666667789999999999999999999975
No 117
>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=30.38 E-value=51 Score=25.73 Aligned_cols=35 Identities=20% Similarity=0.240 Sum_probs=31.5
Q ss_pred hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 477 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 477 ~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
..|..+..+.-..+.++...+.++.+-|.+.|||.
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 118
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=29.04 E-value=33 Score=36.09 Aligned_cols=26 Identities=19% Similarity=0.653 Sum_probs=21.2
Q ss_pred cCCcccccCccCCCCCeeEEcCCCCCc
Q 010341 35 RALYHCNYCNKDITGKIRIKCAVCPDF 61 (512)
Q Consensus 35 ~~~~~C~~C~~~i~~~~ri~C~~C~d~ 61 (512)
...|+|..|+-..-. .+|+|..|..+
T Consensus 352 ~~~YRC~~CGF~a~~-l~W~CPsC~~W 377 (389)
T COG2956 352 KPRYRCQNCGFTAHT-LYWHCPSCRAW 377 (389)
T ss_pred cCCceecccCCccee-eeeeCCCcccc
Confidence 578999999987654 89999999755
No 119
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=28.83 E-value=34 Score=35.72 Aligned_cols=32 Identities=22% Similarity=0.733 Sum_probs=24.5
Q ss_pred CCcccccCccCCCCCeeEEcCCCCCcccchhhh
Q 010341 36 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECF 68 (512)
Q Consensus 36 ~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF 68 (512)
....|.+|+.......+|+|..|..+ +|+.|=
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~-FCldCD 360 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNV-FCLDCD 360 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccce-eeccch
Confidence 44569999777666699999999843 777773
No 120
>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=28.49 E-value=1.1e+02 Score=26.00 Aligned_cols=49 Identities=10% Similarity=0.209 Sum_probs=36.6
Q ss_pred HhhcccccCCChhHHHHHHHHHHHHHHHH---HHHHHHHHHHHhCCcchHHHH
Q 010341 323 RRYDVFMRFHSKEDHEDLLQTVISEHRTL---KRIQDLKEARAAGCRTSAEAD 372 (512)
Q Consensus 323 ~~l~~far~~~~~~~~~l~~~l~~E~~Lr---~rI~~L~~~R~~Gittl~e~~ 372 (512)
..+..|..+.++++...|++.|....++. .| .++..|...|++.-+=++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~t~~e~~~Ls~R-~~I~~ll~~G~S~~eIA~ 58 (88)
T TIGR02531 7 ELFDAILTLKNREECYRFFDDIATINEIQSLAQR-LQVAKMLKQGKTYSDIEA 58 (88)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhCCHHHHHhhhHH-HHHHHHHHCCCCHHHHHH
Confidence 34567788999999999999998665544 46 788888889986544333
No 121
>PLN02400 cellulose synthase
Probab=28.20 E-value=36 Score=41.03 Aligned_cols=49 Identities=27% Similarity=0.701 Sum_probs=34.2
Q ss_pred CcccccCccCC----CCCeeEEcCCCCCcccchhhhccccc----ccCCCCCCCeeeec
Q 010341 37 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSVGVE----VHPHKSNHPYRVMD 87 (512)
Q Consensus 37 ~~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~G~e----~~~H~~~H~y~vi~ 87 (512)
.-.|.+|+.++ .+.+++-|.+|. |-+|-.||..-.. .-.|=+++ |+...
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCa-FPVCRpCYEYERkeGnq~CPQCkTr-YkR~K 92 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECA-FPVCRPCYEYERKDGTQCCPQCKTR-YRRHK 92 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCC-CccccchhheecccCCccCcccCCc-ccccc
Confidence 34799999874 456999999997 9999999965332 22333443 76654
No 122
>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=28.15 E-value=79 Score=23.40 Aligned_cols=42 Identities=19% Similarity=0.291 Sum_probs=32.8
Q ss_pred HHHHHHH--hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 470 VMSREIF--SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 470 ~LirE~~--~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
+-|-|++ .++.++..+.-+-+.+....+.++..-|++.||+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 3344555 34557899988889999999999999999999984
No 123
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=27.79 E-value=1.6e+02 Score=23.27 Aligned_cols=44 Identities=16% Similarity=0.135 Sum_probs=34.7
Q ss_pred HHHHHHHHHhCCC--cCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 468 QEVMSREIFSGNV--NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 468 K~~LirE~~~~G~--lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
++.++.-....|. ++..+.-..+.|+...++++..=|.+.|+|.
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 4444444445555 8988888889999999999999999999984
No 124
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=27.17 E-value=1e+02 Score=30.21 Aligned_cols=46 Identities=17% Similarity=0.356 Sum_probs=39.2
Q ss_pred CCCchhHHHHHHHHHHhCCCChHHHHHHhC---CCCHHHHHHHHHhhccCC
Q 010341 97 DWNADDEILLLEGIEMYGLGNWAEIAEHVG---TKTKELCIEHYTNVYMNS 144 (512)
Q Consensus 97 ~Wt~~Ee~~Lleai~~~G~gnW~~IA~~vg---~rt~~ec~~hy~~~y~~~ 144 (512)
.|++.++++|+.||++- .+-..|+.-|. .-|-.|+..+|..+-.+.
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 49999999999999965 58999988876 479999999999876553
No 125
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=26.92 E-value=75 Score=22.74 Aligned_cols=34 Identities=15% Similarity=0.538 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHH
Q 010341 468 QEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYD 502 (512)
Q Consensus 468 K~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIyd 502 (512)
|+.||...+..|+.+..+ +.|..+...-..+.|.
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 126
>PRK08359 transcription factor; Validated
Probab=26.10 E-value=48 Score=31.74 Aligned_cols=40 Identities=18% Similarity=0.380 Sum_probs=26.1
Q ss_pred cccccCccCCCCCeeEEcCCCCCcccchhhh-cccc-cccCC
Q 010341 38 YHCNYCNKDITGKIRIKCAVCPDFDLCIECF-SVGV-EVHPH 77 (512)
Q Consensus 38 ~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF-~~G~-e~~~H 77 (512)
..|-.|+++|.+..+.-=.+=...++|..|+ --|. +++.+
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 4499999999875222212222367899999 6688 55544
No 127
>PRK00420 hypothetical protein; Validated
Probab=26.02 E-value=43 Score=29.74 Aligned_cols=28 Identities=18% Similarity=0.369 Sum_probs=20.4
Q ss_pred cccccCccCCCC--CeeEEcCCCCCcccch
Q 010341 38 YHCNYCNKDITG--KIRIKCAVCPDFDLCI 65 (512)
Q Consensus 38 ~~C~~C~~~i~~--~~ri~C~~C~d~dLC~ 65 (512)
.+|..|+.++.. ...+.|..|.....|.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeeec
Confidence 589999998763 4677888887665553
No 128
>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=25.82 E-value=59 Score=24.02 Aligned_cols=24 Identities=33% Similarity=0.665 Sum_probs=18.1
Q ss_pred CCcccccCccCC--CCCeeEEcCCCC
Q 010341 36 ALYHCNYCNKDI--TGKIRIKCAVCP 59 (512)
Q Consensus 36 ~~~~C~~C~~~i--~~~~ri~C~~C~ 59 (512)
....|++|++.| ....-++|..|.
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 456799999998 344789999986
No 129
>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=25.54 E-value=74 Score=27.94 Aligned_cols=23 Identities=17% Similarity=0.534 Sum_probs=20.2
Q ss_pred HHhCCCchHHHHHHHHHHHHHHh
Q 010341 455 CEIRLAPPLYLRMQEVMSREIFS 477 (512)
Q Consensus 455 s~lrL~P~~YL~iK~~LirE~~~ 477 (512)
.+++|.|+.|+.+|..|..|.++
T Consensus 86 ~~igls~~EYm~lKkelae~i~~ 108 (109)
T TIGR03277 86 QRIGMSPEEYMELKKKLAEELLK 108 (109)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhc
Confidence 46899999999999999988764
No 130
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=25.38 E-value=35 Score=25.87 Aligned_cols=30 Identities=27% Similarity=0.422 Sum_probs=20.7
Q ss_pred ccccCccCCCCCeeEEcCCCCCcccchhhhccc
Q 010341 39 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVG 71 (512)
Q Consensus 39 ~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G 71 (512)
.|+.|+..+.-..+ ..=.|..+|..||..-
T Consensus 1 ~C~iCg~kigl~~~---~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR---FKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc---eeccCccchHHHHHHh
Confidence 49999998764222 2234556999999874
No 131
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=25.12 E-value=1.5e+02 Score=24.05 Aligned_cols=51 Identities=25% Similarity=0.409 Sum_probs=37.3
Q ss_pred HhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 456 EIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 456 ~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
..+|.+..+..+.-+. .+|.++.++....+.+....+.++++=|++.|||.
T Consensus 5 ~~~l~~~~~~il~~l~-----~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 5 PLGLTPTQFLVLRILY-----EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred ccCCCHHHHHHHHHHH-----HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 3455555555444333 35567777887888899999999999999999984
No 132
>KOG2789 consensus Putative Zn-finger protein [General function prediction only]
Probab=25.08 E-value=39 Score=36.19 Aligned_cols=69 Identities=22% Similarity=0.307 Sum_probs=44.9
Q ss_pred CCcccccCccC-CCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCc-----------cCCCCCchhH
Q 010341 36 ALYHCNYCNKD-ITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPL-----------ICPDWNADDE 103 (512)
Q Consensus 36 ~~~~C~~C~~~-i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~-----------~~~~Wt~~Ee 103 (512)
....|-+|... -...-+.+|.. --+|..||..=.-...|+.+-++.++.+..|+. +...|++.|=
T Consensus 73 r~~ecpicflyyps~~n~~rcC~---~~Ic~ecf~~~~~~~~~~pt~~a~v~~~~~f~~~s~p~~~~cp~c~t~~~~vey 149 (482)
T KOG2789|consen 73 RKTECPICFLYYPSAKNLVRCCS---ETICGECFAPFGCYSFEKPTYDATVVKNLIFKRKSAPFYTPCPDCDTSWTRVEY 149 (482)
T ss_pred ccccCceeeeecccccchhhhhc---cchhhhheecccCCCcccCccccccccccccccccccccccCCccCCcccceee
Confidence 34568888753 22223444432 459999999966668899988888887766553 3467887764
Q ss_pred HHHH
Q 010341 104 ILLL 107 (512)
Q Consensus 104 ~~Ll 107 (512)
....
T Consensus 150 ~~i~ 153 (482)
T KOG2789|consen 150 IKIV 153 (482)
T ss_pred eccc
Confidence 4433
No 133
>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=24.63 E-value=1.2e+02 Score=25.95 Aligned_cols=36 Identities=19% Similarity=0.309 Sum_probs=27.8
Q ss_pred HHHHH-hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCC
Q 010341 472 SREIF-SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLA 510 (512)
Q Consensus 472 irE~~-~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi 510 (512)
.-.++ ..|.++..++-+++.|- ..++++||.+.|||
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 33444 56889999988887444 67899999999998
No 134
>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=24.49 E-value=57 Score=34.04 Aligned_cols=25 Identities=16% Similarity=0.446 Sum_probs=22.3
Q ss_pred CccCCCCHHHHHHHHHhCCCchHHH
Q 010341 441 NETQLLSEAEKRLCCEIRLAPPLYL 465 (512)
Q Consensus 441 pg~~lLs~~E~~LCs~lrL~P~~YL 465 (512)
.+..-||.+|+..|++|+|.|..|+
T Consensus 301 ~~~~~Lt~ee~av~~~lGis~edf~ 325 (326)
T PF10123_consen 301 DGSAALTAEELAVCRQLGISPEDFA 325 (326)
T ss_pred CCCCCCCHHHHHHHHHcCCCHHHhc
Confidence 3456799999999999999999996
No 135
>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=24.47 E-value=31 Score=28.08 Aligned_cols=22 Identities=36% Similarity=0.834 Sum_probs=10.6
Q ss_pred CCcccccCccCCCCCeeEEcCCCC
Q 010341 36 ALYHCNYCNKDITGKIRIKCAVCP 59 (512)
Q Consensus 36 ~~~~C~~C~~~i~~~~ri~C~~C~ 59 (512)
..|+|..|..+.. ..-.|.+|.
T Consensus 16 ~~~~C~~C~~~~~--~~a~CPdC~ 37 (70)
T PF07191_consen 16 GHYHCEACQKDYK--KEAFCPDCG 37 (70)
T ss_dssp TEEEETTT--EEE--EEEE-TTT-
T ss_pred CEEECccccccce--ecccCCCcc
Confidence 4566777766654 345666664
No 136
>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=24.43 E-value=27 Score=23.14 Aligned_cols=9 Identities=22% Similarity=0.342 Sum_probs=7.3
Q ss_pred cccccCCCC
Q 010341 239 LSGYNSKRQ 247 (512)
Q Consensus 239 ~~GYmP~R~ 247 (512)
-.||||.|+
T Consensus 7 S~gyMp~s~ 15 (27)
T PF12488_consen 7 SFGYMPRSG 15 (27)
T ss_pred ccceeeecc
Confidence 479999885
No 137
>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=24.33 E-value=2e+02 Score=23.58 Aligned_cols=46 Identities=13% Similarity=0.109 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 465 LRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 465 L~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
|++++.++-- +.++..++++...-..|+.+++.....-|.+.|+|.
T Consensus 4 lt~~~~IL~~-ls~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 4 LTVTQKILII-LSKRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred hhHHHHHHHH-HHhccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 4455555533 344499999999999999999999999999999985
No 138
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=24.24 E-value=77 Score=24.97 Aligned_cols=35 Identities=20% Similarity=0.577 Sum_probs=19.3
Q ss_pred CcccccCccCCC--C-CeeEEcCCCCCc--ccchhhhccc
Q 010341 37 LYHCNYCNKDIT--G-KIRIKCAVCPDF--DLCIECFSVG 71 (512)
Q Consensus 37 ~~~C~~C~~~i~--~-~~ri~C~~C~d~--dLC~~CF~~G 71 (512)
...|..|+..|. + .+.+.|..|... --|..|-..+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~~ 46 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQS 46 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHhcC
Confidence 345777776654 1 356666666543 1266665543
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=24.21 E-value=67 Score=28.54 Aligned_cols=29 Identities=31% Similarity=0.760 Sum_probs=22.0
Q ss_pred cccccCccCCCC-----------CeeEEcCCCCCcccchhh
Q 010341 38 YHCNYCNKDITG-----------KIRIKCAVCPDFDLCIEC 67 (512)
Q Consensus 38 ~~C~~C~~~i~~-----------~~ri~C~~C~d~dLC~~C 67 (512)
..|.+|...+.. +.||+|..|. -+.|.+|
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~-~~FC~dC 95 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCK-NVFCVDC 95 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCC-Ccccccc
Confidence 469999986542 3689999997 5577777
No 140
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=23.94 E-value=52 Score=30.77 Aligned_cols=39 Identities=26% Similarity=0.516 Sum_probs=25.5
Q ss_pred ccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCC
Q 010341 39 HCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPH 77 (512)
Q Consensus 39 ~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H 77 (512)
.|-.|++.|.+..+.-=.+=....+|..|+--|.++..+
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 399999999875222112222367899999778865544
No 141
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.91 E-value=1.6e+02 Score=26.87 Aligned_cols=44 Identities=14% Similarity=0.105 Sum_probs=37.0
Q ss_pred chhHHHHHHHHHHhCCCChHHHHHHhCCCCHHHHHHHHHhhccCC
Q 010341 100 ADDEILLLEGIEMYGLGNWAEIAEHVGTKTKELCIEHYTNVYMNS 144 (512)
Q Consensus 100 ~~Ee~~Lleai~~~G~gnW~~IA~~vg~rt~~ec~~hy~~~y~~~ 144 (512)
.+-+..+|++++.-|--.|.+||+.+| -|+..|..++..+-=++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg-lS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG-VSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC-cCHHHHHHHHHHHHHCC
Confidence 356899999999999889999999998 48889999998764444
No 142
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.90 E-value=38 Score=29.80 Aligned_cols=56 Identities=18% Similarity=0.316 Sum_probs=40.2
Q ss_pred ccccCccceeehccCCCCCCCCCCcCCcccccCccCCCCCeeEEcCCCCCcccchhhhcccc
Q 010341 11 ERRMSPVTIQILQLQPGQGAGEGKRALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGV 72 (512)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~ 72 (512)
+....|+...++.++-.=++...+...+.|..|+. .++.+..|.+- .|+.|-..-.
T Consensus 16 ~~~l~~~~~k~~~~il~Crt~~~G~~~~~C~~Cg~-----~~~~~~SCk~R-~CP~C~~~~~ 71 (111)
T PF14319_consen 16 GGRLSPYQRKAVEAILACRTEALGFHRYRCEDCGH-----EKIVYNSCKNR-HCPSCQAKAT 71 (111)
T ss_pred cCCCCHHHHHHHHHHHhcCCccCCcceeecCCCCc-----eEEecCcccCc-CCCCCCChHH
Confidence 34577888888888877566666678889998774 34566677655 8888876644
No 143
>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=23.82 E-value=75 Score=25.23 Aligned_cols=24 Identities=29% Similarity=0.684 Sum_probs=20.4
Q ss_pred ChHHHHHHhCC-CCHHHHHHHHHhh
Q 010341 117 NWAEIAEHVGT-KTKELCIEHYTNV 140 (512)
Q Consensus 117 nW~~IA~~vg~-rt~~ec~~hy~~~ 140 (512)
-|..||..+|. -+.++|+.+|.++
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHH
Confidence 49999999984 5788999999775
No 144
>PRK10870 transcriptional repressor MprA; Provisional
Probab=23.42 E-value=2e+02 Score=27.12 Aligned_cols=58 Identities=10% Similarity=0.160 Sum_probs=46.0
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHHHHhCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 451 KRLCCEIRLAPPLYLRMQEVMSREIFSGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 451 ~~LCs~lrL~P~~YL~iK~~LirE~~~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
...-..++|.|..|..+..+. ...++.++..+....+.++..-+.++.+=|++.|||.
T Consensus 45 ~~~l~~~gLt~~q~~iL~~L~---~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 45 NKMLKAQGINETLFMALITLE---SQENHSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred HHHHHHCCCCHHHHHHHHHHh---cCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 445578999999998875543 1235677777878888899999999999999999984
No 145
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=23.02 E-value=89 Score=29.63 Aligned_cols=39 Identities=15% Similarity=0.436 Sum_probs=25.6
Q ss_pred cccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCC
Q 010341 40 CNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKS 79 (512)
Q Consensus 40 C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~ 79 (512)
|-.|++.+.. ...--.+=...+.|..|+--|.....|..
T Consensus 6 CEiCG~~i~~-~~~v~vegsel~VC~~Cak~G~~~~~~~~ 44 (165)
T COG1813 6 CELCGREIDK-PIKVKVEGAELTVCDDCAKFGTAAKTASG 44 (165)
T ss_pred eeccccccCC-CeeEEeecceeehhHHHHHhccCccccCC
Confidence 9999998874 22222222347799999977866555543
No 146
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=22.73 E-value=1.6e+02 Score=21.30 Aligned_cols=34 Identities=12% Similarity=0.158 Sum_probs=26.9
Q ss_pred CCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 478 GNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 478 ~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
.+.++..+....+.+....+.++.+-|++.|||.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 5667777777777788888888888888888874
No 147
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=22.68 E-value=1.1e+02 Score=23.08 Aligned_cols=35 Identities=11% Similarity=0.185 Sum_probs=30.7
Q ss_pred hCCCcCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 477 SGNVNNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 477 ~~G~lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
..+.++..+.-..+.+....+.+++.-|.+.|||.
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 34568888889999999999999999999999984
No 148
>PRK11823 DNA repair protein RadA; Provisional
Probab=22.35 E-value=56 Score=35.71 Aligned_cols=27 Identities=19% Similarity=0.597 Sum_probs=21.8
Q ss_pred cCCcccccCccCCCCCeeEEcCCCCCcc
Q 010341 35 RALYHCNYCNKDITGKIRIKCAVCPDFD 62 (512)
Q Consensus 35 ~~~~~C~~C~~~i~~~~ri~C~~C~d~d 62 (512)
...|.|..|+-.-.. .+++|..|..++
T Consensus 5 ~~~y~C~~Cg~~~~~-~~g~Cp~C~~w~ 31 (446)
T PRK11823 5 KTAYVCQECGAESPK-WLGRCPECGAWN 31 (446)
T ss_pred CCeEECCcCCCCCcc-cCeeCcCCCCcc
Confidence 467999999988665 788999998664
No 149
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=22.29 E-value=41 Score=38.69 Aligned_cols=58 Identities=22% Similarity=0.351 Sum_probs=39.0
Q ss_pred ccceeehccCC-CCCCCCCCcCCcccccCccCCCCC-------eeEEcCCCC-------------------Ccccchhhh
Q 010341 16 PVTIQILQLQP-GQGAGEGKRALYHCNYCNKDITGK-------IRIKCAVCP-------------------DFDLCIECF 68 (512)
Q Consensus 16 ~~~~~~~~~~~-~~~~~~~~~~~~~C~~C~~~i~~~-------~ri~C~~C~-------------------d~dLC~~CF 68 (512)
|....|.++.. +...++.++-.-.|.-|.+++... +++-|+.|. +|-||..|-
T Consensus 79 f~~F~I~~S~~~~~~~~~I~pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~ 158 (750)
T COG0068 79 FTDFRIRKSEGKGNKNTQIPPDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCD 158 (750)
T ss_pred CCceEEEecCCCCCcccccCCchhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHH
Confidence 55556666633 223356667777899999876532 455688882 478999999
Q ss_pred ccccc
Q 010341 69 SVGVE 73 (512)
Q Consensus 69 ~~G~e 73 (512)
..-.-
T Consensus 159 ~EY~d 163 (750)
T COG0068 159 KEYKD 163 (750)
T ss_pred HHhcC
Confidence 86443
No 150
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=22.13 E-value=56 Score=36.13 Aligned_cols=70 Identities=21% Similarity=0.352 Sum_probs=43.4
Q ss_pred CcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHHHhCCC
Q 010341 37 LYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGLG 116 (512)
Q Consensus 37 ~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~~~G~g 116 (512)
.-.|+-|+..=.+ |-... ....||.+||+-..+.|.|-+. +.- +-...|- .+-+.+.+++...|-.
T Consensus 8 ~evC~DC~~~dp~---WASvn-rGt~lC~eCcsvHrsLGrhIS~-----vrh----LR~s~W~-pt~l~~V~tLn~~gaN 73 (669)
T KOG0818|consen 8 SEVCADCSGPDPS---WASVN-RGTFLCDECCSVHRSLGRHISQ-----VRH----LRHTPWP-PTLLQMVETLNNNGAN 73 (669)
T ss_pred hhhhcccCCCCCc---ceeec-CceEehHhhhHHHhhhcchHHH-----HHH----hccCCCC-HHHHHHHHHHHhcCcc
Confidence 3468888865322 22222 3567999999998888887431 111 2345784 4567888888888832
Q ss_pred C-hHH
Q 010341 117 N-WAE 120 (512)
Q Consensus 117 n-W~~ 120 (512)
. |+.
T Consensus 74 sIWEh 78 (669)
T KOG0818|consen 74 SIWEH 78 (669)
T ss_pred hhhhh
Confidence 2 653
No 151
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=21.61 E-value=1.5e+02 Score=24.82 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCC--------ChHHHHHHhCCCC-----HHHHHHHHHhh
Q 010341 103 EILLLEGIEMYGLG--------NWAEIAEHVGTKT-----KELCIEHYTNV 140 (512)
Q Consensus 103 e~~Lleai~~~G~g--------nW~~IA~~vg~rt-----~~ec~~hy~~~ 140 (512)
-..|-.+|...| | .|..||+.+|-.. ..+.+.+|.++
T Consensus 34 L~~Ly~~V~~~G-G~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~ 83 (93)
T smart00501 34 LYRLYRLVQERG-GYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERY 83 (93)
T ss_pred HHHHHHHHHHcc-CHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHH
Confidence 456777888877 4 7999999999432 45566777654
No 152
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.46 E-value=83 Score=21.48 Aligned_cols=27 Identities=33% Similarity=0.864 Sum_probs=18.4
Q ss_pred ccccCccC-CCCCeeEEcCCCCCcccchh
Q 010341 39 HCNYCNKD-ITGKIRIKCAVCPDFDLCIE 66 (512)
Q Consensus 39 ~C~~C~~~-i~~~~ri~C~~C~d~dLC~~ 66 (512)
.|.+|... +....+|.|..|+ .-||..
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 47777653 3223789999995 778864
No 153
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=21.14 E-value=1.2e+02 Score=23.39 Aligned_cols=45 Identities=7% Similarity=0.159 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhCC-Cc-CHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 467 MQEVMSREIFSGN-VN-NKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 467 iK~~LirE~~~~G-~l-k~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
|++.|...-...| .| +..+..+.+.+-.+-+++.++.|.+.|||.
T Consensus 9 l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 9 LRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp HHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 3333333333334 55 777777778888888999999999999974
No 154
>PLN02195 cellulose synthase A
Probab=21.13 E-value=59 Score=38.88 Aligned_cols=33 Identities=24% Similarity=0.806 Sum_probs=26.6
Q ss_pred CcccccCccCC----CCCeeEEcCCCCCcccchhhhcc
Q 010341 37 LYHCNYCNKDI----TGKIRIKCAVCPDFDLCIECFSV 70 (512)
Q Consensus 37 ~~~C~~C~~~i----~~~~ri~C~~C~d~dLC~~CF~~ 70 (512)
.-.|.+|+.++ .+.+++-|.+|. |-+|-.||..
T Consensus 6 ~~~c~~cgd~~~~~~~g~~fvaC~eC~-~pvCrpCyey 42 (977)
T PLN02195 6 APICATCGEEVGVDSNGEAFVACHECS-YPLCKACLEY 42 (977)
T ss_pred CccceecccccCcCCCCCeEEEeccCC-Cccccchhhh
Confidence 34699998753 456999999997 9999999965
No 155
>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=20.90 E-value=1.7e+02 Score=21.70 Aligned_cols=48 Identities=8% Similarity=0.119 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHhCC-C-cCHHHHhhhhccCchhHHHHHHHHHHCCCCC
Q 010341 464 YLRMQEVMSREIFSGN-V-NNKADAHHLFKIEPSKIDRVYDMLVKKGLAP 511 (512)
Q Consensus 464 YL~iK~~LirE~~~~G-~-lk~~~A~~l~kiD~~K~~rIydFlv~~Gwi~ 511 (512)
|-.|+..++......| . .+..+....+.+..+.+++.+.=|.+.|||.
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 3344444443323222 2 3367777778899999999999999999984
No 156
>PF07875 Coat_F: Coat F domain; InterPro: IPR012851 The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination []. Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus [].
Probab=20.85 E-value=83 Score=24.49 Aligned_cols=25 Identities=12% Similarity=0.278 Sum_probs=18.7
Q ss_pred hhhccCchhHHHHHHHHHHCCCCCC
Q 010341 488 HLFKIEPSKIDRVYDMLVKKGLAPP 512 (512)
Q Consensus 488 ~l~kiD~~K~~rIydFlv~~Gwi~~ 512 (512)
.++.-...-...||+++.++||-++
T Consensus 38 ~~~~~~~~~~~~l~~~m~~kGwY~~ 62 (64)
T PF07875_consen 38 QILNECQQMQYELFNYMNQKGWYQP 62 (64)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCcCC
Confidence 3444455667799999999999764
No 157
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.56 E-value=3.1e+02 Score=24.23 Aligned_cols=64 Identities=19% Similarity=0.463 Sum_probs=43.1
Q ss_pred CCcccccCccCCCCCeeEEcCCCCCcccchhhhcccccccCCCCCCCeeeecCCCCCccCCCCCchhHHHHHHHHHHhCC
Q 010341 36 ALYHCNYCNKDITGKIRIKCAVCPDFDLCIECFSVGVEVHPHKSNHPYRVMDNLSFPLICPDWNADDEILLLEGIEMYGL 115 (512)
Q Consensus 36 ~~~~C~~C~~~i~~~~ri~C~~C~d~dLC~~CF~~G~e~~~H~~~H~y~vi~~~~~p~~~~~Wt~~Ee~~Lleai~~~G~ 115 (512)
....|-.|++.+.- ...+|..|..- ..|. |+ +..-++-..+++.+++..-...
T Consensus 5 ~~~~cPvcg~~~iV-TeL~c~~~etT-------Vrg~----------F~--------~s~F~~Lt~d~LeFv~lf~r~R- 57 (122)
T COG3877 5 VINRCPVCGRKLIV-TELKCSNCETT-------VRGN----------FK--------MSKFEYLTSDQLEFVELFLRCR- 57 (122)
T ss_pred CCCCCCccccccee-EEEecCCCCce-------Eecc----------ee--------cccccccCHhHhHHHHHHHHHc-
Confidence 45579999987553 57898888621 0111 22 1122355567788888888887
Q ss_pred CChHHHHHHhC
Q 010341 116 GNWAEIAEHVG 126 (512)
Q Consensus 116 gnW~~IA~~vg 126 (512)
||-.+|-...|
T Consensus 58 GnlKEvEr~lg 68 (122)
T COG3877 58 GNLKEVERELG 68 (122)
T ss_pred cCHHHHHHHHC
Confidence 89999999998
No 158
>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=20.12 E-value=4e+02 Score=22.00 Aligned_cols=60 Identities=15% Similarity=0.109 Sum_probs=44.5
Q ss_pred HhhccCCCCC---CCCCCChhHHHHHHhhccccc--CCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 010341 300 LERNLLYPNP---FEKDLSPEERELCRRYDVFMR--FHSKEDHEDLLQTVISEHRTLKRIQDLKE 359 (512)
Q Consensus 300 ~e~~Ll~~~~---~~k~~skeere~~~~l~~far--~~~~~~~~~l~~~l~~E~~Lr~rI~~L~~ 359 (512)
.+.|||.+.. ..+.++.++-.....++.+.+ -++-.+...++..+-+-..|+.+|.+|++
T Consensus 22 e~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~~l~~l~~ 86 (91)
T cd04766 22 ERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRA 86 (91)
T ss_pred HHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678987422 345678777666677777665 67888888888888888888888888874
Done!