Query 008658
Match_columns 558
No_of_seqs 246 out of 683
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 14:57:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008658hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5259 RSC8 RSC chromatin rem 100.0 4.5E-96 1E-100 760.6 28.5 415 11-546 46-468 (531)
2 KOG1279 Chromatin remodeling f 100.0 4.5E-86 9.7E-91 711.1 26.0 443 10-546 40-503 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 3.5E-27 7.6E-32 200.9 6.0 85 17-105 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 3.9E-22 8.6E-27 208.7 8.6 110 194-304 13-126 (438)
5 COG5114 Histone acetyltransfer 99.7 9.8E-19 2.1E-23 176.0 5.7 110 194-304 4-117 (432)
6 PF00249 Myb_DNA-binding: Myb- 99.0 2.3E-10 4.9E-15 87.0 4.9 44 252-295 2-47 (48)
7 cd02336 ZZ_RSC8 Zinc finger, Z 99.0 3.3E-10 7.1E-15 85.1 3.6 44 196-239 1-45 (45)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.8 5.7E-09 1.2E-13 82.6 5.5 41 254-294 1-41 (60)
9 PLN03000 amine oxidase 98.8 7E-09 1.5E-13 120.3 6.7 84 22-110 87-173 (881)
10 smart00717 SANT SANT SWI3, AD 98.8 1.6E-08 3.5E-13 75.0 5.8 44 252-295 2-46 (49)
11 PLN02328 lysine-specific histo 98.7 2.1E-08 4.5E-13 116.1 6.9 84 23-110 139-224 (808)
12 cd00167 SANT 'SWI3, ADA2, N-Co 98.7 4E-08 8.6E-13 71.8 5.6 43 253-295 1-44 (45)
13 PLN02529 lysine-specific histo 98.2 2.2E-06 4.7E-11 99.0 7.2 84 22-110 63-149 (738)
14 PLN03212 Transcription repress 98.2 2.2E-06 4.7E-11 85.8 5.4 45 250-294 24-70 (249)
15 TIGR01557 myb_SHAQKYF myb-like 98.1 5E-06 1.1E-10 65.8 5.7 44 251-294 3-52 (57)
16 cd02335 ZZ_ADA2 Zinc finger, Z 97.9 1E-05 2.2E-10 62.0 4.0 46 196-241 1-49 (49)
17 PLN03091 hypothetical protein; 97.9 9.3E-06 2E-10 87.0 5.2 45 250-294 13-59 (459)
18 cd02249 ZZ Zinc finger, ZZ typ 97.8 2.3E-05 5E-10 59.2 3.7 45 196-241 1-46 (46)
19 KOG0048 Transcription factor, 97.7 2.9E-05 6.3E-10 78.4 4.6 44 251-294 9-54 (238)
20 smart00291 ZnF_ZZ Zinc-binding 97.6 6.9E-05 1.5E-09 56.1 3.5 38 195-232 4-42 (44)
21 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.6 7.3E-05 1.6E-09 57.1 3.6 44 196-241 1-48 (48)
22 PLN03212 Transcription repress 97.6 9.1E-05 2E-09 74.4 5.1 46 249-294 76-121 (249)
23 cd02340 ZZ_NBR1_like Zinc fing 97.5 9.5E-05 2.1E-09 55.2 3.4 41 197-241 2-43 (43)
24 cd02345 ZZ_dah Zinc finger, ZZ 97.5 9.7E-05 2.1E-09 56.7 3.4 43 197-239 2-47 (49)
25 cd02343 ZZ_EF Zinc finger, ZZ 97.4 0.00016 3.4E-09 55.2 3.6 41 197-237 2-44 (48)
26 cd02338 ZZ_PCMF_like Zinc fing 97.4 0.00017 3.7E-09 55.3 3.6 44 197-240 2-48 (49)
27 cd02334 ZZ_dystrophin Zinc fin 97.3 0.00021 4.5E-09 54.9 3.5 43 197-239 2-47 (49)
28 PF00569 ZZ: Zinc finger, ZZ t 97.3 0.00014 3.1E-09 54.9 1.9 39 194-232 3-43 (46)
29 PLN03091 hypothetical protein; 97.2 0.00043 9.4E-09 74.5 5.8 46 249-294 65-110 (459)
30 cd02344 ZZ_HERC2 Zinc finger, 97.0 0.00069 1.5E-08 51.1 3.5 42 197-241 2-45 (45)
31 cd02339 ZZ_Mind_bomb Zinc fing 96.8 0.0015 3.1E-08 49.4 3.5 41 197-240 2-44 (45)
32 KOG0049 Transcription factor, 96.7 0.0016 3.5E-08 72.5 5.1 46 249-294 358-404 (939)
33 PLN02976 amine oxidase 96.3 0.0032 6.9E-08 76.9 4.4 83 25-110 454-542 (1713)
34 cd02337 ZZ_CBP Zinc finger, ZZ 96.2 0.0042 9.1E-08 45.9 2.7 34 196-230 1-35 (41)
35 cd02342 ZZ_UBA_plant Zinc fing 95.9 0.0065 1.4E-07 45.2 2.5 31 197-227 2-34 (43)
36 KOG0048 Transcription factor, 95.8 0.014 3.1E-07 58.9 5.8 43 250-292 61-103 (238)
37 KOG0049 Transcription factor, 95.8 0.0084 1.8E-07 67.0 3.9 52 250-304 411-466 (939)
38 PF13837 Myb_DNA-bind_4: Myb/S 94.9 0.013 2.7E-07 49.6 1.6 43 252-294 2-62 (90)
39 KOG0051 RNA polymerase I termi 93.2 0.095 2.1E-06 59.1 4.5 44 250-294 383-426 (607)
40 KOG0051 RNA polymerase I termi 92.5 0.11 2.4E-06 58.6 3.8 54 250-303 435-514 (607)
41 KOG4582 Uncharacterized conser 92.0 0.11 2.3E-06 54.0 2.8 32 196-227 153-186 (278)
42 KOG1280 Uncharacterized conser 90.6 0.18 4E-06 53.0 2.8 36 193-228 6-43 (381)
43 KOG0050 mRNA splicing protein 89.9 0.24 5.3E-06 54.6 3.1 45 250-295 58-102 (617)
44 KOG0050 mRNA splicing protein 89.9 0.27 5.9E-06 54.2 3.4 43 251-293 7-50 (617)
45 KOG4167 Predicted DNA-binding 89.1 0.59 1.3E-05 53.6 5.5 55 250-304 618-676 (907)
46 PF13873 Myb_DNA-bind_5: Myb/S 88.3 0.77 1.7E-05 37.9 4.4 44 252-295 3-68 (78)
47 KOG4286 Dystrophin-like protei 86.8 0.34 7.3E-06 55.6 1.8 39 196-234 604-644 (966)
48 PF15324 TALPID3: Hedgehog sig 85.7 2.7 5.9E-05 50.2 8.3 95 457-553 54-167 (1252)
49 KOG4329 DNA-binding protein [G 85.6 1.1 2.4E-05 47.7 4.7 51 251-301 277-328 (445)
50 COG5118 BDP1 Transcription ini 85.4 1.2 2.5E-05 47.6 4.8 45 250-294 364-408 (507)
51 TIGR02894 DNA_bind_RsfA transc 85.4 0.75 1.6E-05 43.8 3.1 42 251-293 4-52 (161)
52 KOG4468 Polycomb-group transcr 84.5 0.84 1.8E-05 51.2 3.4 44 251-294 88-141 (782)
53 KOG4282 Transcription factor G 82.3 1.6 3.5E-05 46.4 4.5 46 251-296 54-113 (345)
54 PRK00409 recombination and DNA 82.2 8.3 0.00018 45.8 10.6 81 468-549 491-572 (782)
55 TIGR01069 mutS2 MutS2 family p 81.8 9.3 0.0002 45.3 10.8 81 468-549 486-567 (771)
56 COG5147 REB1 Myb superfamily p 81.3 1.5 3.2E-05 49.2 3.8 45 250-294 71-115 (512)
57 COG5147 REB1 Myb superfamily p 77.5 1.4 2.9E-05 49.5 2.1 43 250-292 19-62 (512)
58 KOG4301 Beta-dystrobrevin [Cyt 70.6 2.1 4.5E-05 45.4 1.3 40 194-233 239-280 (434)
59 PF09111 SLIDE: SLIDE; InterP 67.3 6.9 0.00015 35.6 3.8 45 249-293 47-107 (118)
60 KOG0703 Predicted GTPase-activ 64.6 7.5 0.00016 40.5 3.9 97 195-303 25-125 (287)
61 PF04504 DUF573: Protein of un 64.2 8.8 0.00019 33.7 3.8 45 250-294 3-60 (98)
62 KOG3647 Predicted coiled-coil 62.4 33 0.0007 35.6 7.8 64 473-538 90-157 (338)
63 KOG1279 Chromatin remodeling f 62.4 4.8 0.00011 45.2 2.2 91 20-110 187-285 (506)
64 PF03107 C1_2: C1 domain; Int 62.4 7.7 0.00017 26.5 2.4 28 196-223 1-29 (30)
65 PF07649 C1_3: C1-like domain; 60.7 5.8 0.00013 27.0 1.6 27 197-223 2-29 (30)
66 smart00307 ILWEQ I/LWEQ domain 60.2 57 0.0012 32.5 9.0 64 474-538 133-197 (200)
67 PF12674 Zn_ribbon_2: Putative 59.7 4.8 0.0001 34.2 1.3 35 197-231 2-40 (81)
68 smart00345 HTH_GNTR helix_turn 59.5 14 0.00031 27.8 3.8 51 54-105 1-52 (60)
69 KOG3554 Histone deacetylase co 58.0 7.9 0.00017 42.6 2.8 52 252-303 286-338 (693)
70 PLN03142 Probable chromatin-re 56.8 14 0.00031 45.1 5.0 41 252-292 825-866 (1033)
71 PF00392 GntR: Bacterial regul 55.6 21 0.00045 28.2 4.3 54 52-106 3-57 (64)
72 PF05928 Zea_mays_MuDR: Zea ma 55.1 1.3E+02 0.0028 29.0 9.9 72 466-537 11-89 (207)
73 PF13404 HTH_AsnC-type: AsnC-t 54.7 24 0.00051 26.1 4.1 37 257-294 3-40 (42)
74 PF12776 Myb_DNA-bind_3: Myb/S 54.5 16 0.00035 30.9 3.7 42 253-294 1-60 (96)
75 KOG1194 Predicted DNA-binding 53.4 24 0.00053 38.9 5.5 46 249-294 185-230 (534)
76 PF12802 MarR_2: MarR family; 53.1 32 0.0007 26.4 4.9 44 66-109 14-57 (62)
77 PF06034 DUF919: Nucleopolyhed 52.9 42 0.00091 27.3 5.5 46 502-548 13-58 (62)
78 PF01022 HTH_5: Bacterial regu 51.7 38 0.00083 25.1 4.9 45 58-105 3-47 (47)
79 PRK13923 putative spore coat p 51.6 14 0.0003 35.8 3.1 41 251-292 5-52 (170)
80 cd00090 HTH_ARSR Arsenical Res 49.3 36 0.00079 26.2 4.8 44 61-107 11-54 (78)
81 PF09339 HTH_IclR: IclR helix- 48.9 28 0.0006 26.4 3.8 43 62-105 8-50 (52)
82 COG2916 Hns DNA-binding protei 48.7 1.5E+02 0.0033 27.5 9.1 49 493-545 4-52 (128)
83 PLN03119 putative ADP-ribosyla 48.1 22 0.00047 40.4 4.3 94 196-303 24-123 (648)
84 PF01475 FUR: Ferric uptake re 48.1 29 0.00063 30.8 4.5 51 55-106 6-61 (120)
85 COG1725 Predicted transcriptio 46.5 47 0.001 30.6 5.5 53 53-105 11-67 (125)
86 PF09862 DUF2089: Protein of u 45.4 33 0.00072 31.1 4.3 74 198-295 1-79 (113)
87 PLN03131 hypothetical protein; 45.2 34 0.00073 39.4 5.2 93 196-303 24-123 (705)
88 cd04779 HTH_MerR-like_sg4 Heli 43.9 1.3E+02 0.0027 28.0 8.1 52 493-547 78-129 (134)
89 PF02954 HTH_8: Bacterial regu 43.4 29 0.00063 25.3 3.1 24 258-281 6-29 (42)
90 PF01412 ArfGap: Putative GTPa 42.1 22 0.00047 31.9 2.6 58 196-265 14-72 (116)
91 PF13412 HTH_24: Winged helix- 41.6 78 0.0017 23.3 5.2 44 58-103 4-47 (48)
92 smart00595 MADF subfamily of S 39.6 22 0.00048 29.7 2.2 28 272-302 29-56 (89)
93 KOG4479 Transcription factor e 39.5 55 0.0012 28.0 4.4 44 53-100 36-89 (92)
94 KOG1194 Predicted DNA-binding 38.9 16 0.00034 40.4 1.4 44 250-294 469-512 (534)
95 KOG3859 Septins (P-loop GTPase 38.6 2.5E+02 0.0055 29.8 9.9 49 503-551 354-403 (406)
96 PF14471 DUF4428: Domain of un 38.3 20 0.00044 27.7 1.6 30 197-227 1-30 (51)
97 PLN03142 Probable chromatin-re 38.1 44 0.00094 41.1 5.1 45 249-293 924-981 (1033)
98 PF02841 GBP_C: Guanylate-bind 37.8 4.5E+02 0.0098 27.3 12.1 51 503-553 228-282 (297)
99 PRK09462 fur ferric uptake reg 37.3 51 0.0011 30.6 4.4 48 58-105 18-70 (148)
100 cd07153 Fur_like Ferric uptake 36.2 59 0.0013 28.4 4.5 46 59-105 3-53 (116)
101 PF06689 zf-C4_ClpX: ClpX C4-t 35.1 27 0.00059 25.7 1.7 31 196-226 2-33 (41)
102 smart00550 Zalpha Z-DNA-bindin 34.6 98 0.0021 25.0 5.2 50 58-107 7-56 (68)
103 KOG0384 Chromodomain-helicase 34.0 28 0.0006 43.0 2.5 28 249-276 1131-1159(1373)
104 COG5347 GTPase-activating prot 34.0 44 0.00096 35.6 3.8 98 195-304 20-125 (319)
105 PF04111 APG6: Autophagy prote 33.9 5.4E+02 0.012 27.2 12.0 48 500-547 74-121 (314)
106 KOG3915 Transcription regulato 33.5 3.6E+02 0.0077 30.3 10.4 50 482-541 514-569 (641)
107 COG5114 Histone acetyltransfer 33.5 52 0.0011 34.9 4.1 53 51-104 377-429 (432)
108 PHA00442 host recBCD nuclease 33.4 44 0.00095 26.4 2.7 25 256-280 25-50 (59)
109 COG4942 Membrane-bound metallo 32.8 2.9E+02 0.0064 30.6 9.9 63 485-555 67-131 (420)
110 TIGR02449 conserved hypothetic 32.6 1.9E+02 0.0041 23.8 6.3 42 506-547 2-43 (65)
111 PRK11546 zraP zinc resistance 32.2 4.4E+02 0.0096 24.9 12.7 69 486-555 44-123 (143)
112 PF03444 HrcA_DNA-bdg: Winged 32.0 1.2E+02 0.0027 25.7 5.4 55 53-108 4-58 (78)
113 TIGR01069 mutS2 MutS2 family p 31.5 5E+02 0.011 31.1 12.3 39 502-540 527-565 (771)
114 smart00105 ArfGap Putative GTP 31.4 74 0.0016 28.3 4.3 83 196-294 4-96 (112)
115 KOG1510 RNA polymerase II holo 31.3 4.5E+02 0.0097 24.7 9.5 54 492-549 70-129 (139)
116 smart00346 HTH_ICLR helix_turn 31.3 82 0.0018 26.0 4.4 43 62-105 10-52 (91)
117 PF01608 I_LWEQ: I/LWEQ domain 31.2 4.1E+02 0.0088 25.4 9.4 22 518-539 129-150 (152)
118 PF01047 MarR: MarR family; I 31.0 75 0.0016 24.2 3.8 37 74-110 18-54 (59)
119 PRK06474 hypothetical protein; 28.7 1E+02 0.0022 29.8 5.1 50 58-108 12-62 (178)
120 PF07956 DUF1690: Protein of U 28.1 1.3E+02 0.0028 28.3 5.4 57 483-539 61-118 (142)
121 KOG3564 GTPase-activating prot 27.3 2.9E+02 0.0062 31.2 8.5 63 492-556 52-114 (604)
122 COG0735 Fur Fe2+/Zn2+ uptake r 27.1 93 0.002 29.0 4.4 52 57-109 21-77 (145)
123 PRK11179 DNA-binding transcrip 26.9 87 0.0019 29.2 4.2 39 256-295 8-47 (153)
124 PF13463 HTH_27: Winged helix 26.9 1.4E+02 0.0031 23.1 4.9 42 69-110 14-55 (68)
125 PF15346 ARGLU: Arginine and g 26.4 5.7E+02 0.012 24.4 12.8 83 467-549 19-111 (149)
126 PF10820 DUF2543: Protein of u 26.2 48 0.001 27.6 1.9 31 71-101 46-79 (81)
127 PF08394 Arc_trans_TRASH: Arch 26.1 49 0.0011 24.1 1.7 11 198-208 1-11 (37)
128 TIGR00270 conserved hypothetic 25.6 2.8E+02 0.0061 26.4 7.3 32 197-228 2-35 (154)
129 PF12958 DUF3847: Protein of u 25.2 4.2E+02 0.0092 22.9 7.6 49 502-550 6-58 (86)
130 PRK00409 recombination and DNA 25.1 7.1E+02 0.015 29.9 12.1 39 502-540 532-570 (782)
131 cd07671 F-BAR_PSTPIP1 The F-BA 24.9 4.9E+02 0.011 26.5 9.4 53 497-549 146-216 (242)
132 PF08100 Dimerisation: Dimeris 24.8 1.2E+02 0.0027 23.4 3.9 27 71-97 20-50 (51)
133 smart00420 HTH_DEOR helix_turn 24.4 1.8E+02 0.0038 21.0 4.7 35 72-106 13-47 (53)
134 PTZ00007 (NAP-L) nucleosome as 24.4 1.4E+02 0.003 32.1 5.5 32 516-547 53-88 (337)
135 PRK14139 heat shock protein Gr 24.1 1.3E+02 0.0029 29.5 5.0 15 516-530 62-76 (185)
136 PHA03082 DNA-dependent RNA pol 24.0 17 0.00037 29.0 -1.0 18 196-213 5-22 (63)
137 PF09286 Pro-kuma_activ: Pro-k 23.7 72 0.0016 29.3 2.9 38 71-108 45-82 (143)
138 PF05864 Chordopox_RPO7: Chord 23.6 21 0.00046 28.4 -0.6 18 196-213 5-22 (63)
139 cd07377 WHTH_GntR Winged helix 23.5 1.2E+02 0.0026 23.1 3.7 52 53-105 5-57 (66)
140 PF09986 DUF2225: Uncharacteri 22.7 1.3E+02 0.0029 29.9 4.8 77 194-293 4-101 (214)
141 PF00643 zf-B_box: B-box zinc 22.6 1.1E+02 0.0024 21.9 3.1 31 196-228 4-34 (42)
142 cd08310 Death_NFkB-like Death 22.4 69 0.0015 26.5 2.3 23 256-282 2-24 (72)
143 COG1813 Predicted transcriptio 22.0 81 0.0018 30.5 2.9 32 197-228 5-37 (165)
144 cd07672 F-BAR_PSTPIP2 The F-BA 22.0 5.8E+02 0.013 25.9 9.3 48 502-549 152-217 (240)
145 cd08311 Death_p75NR Death doma 21.5 86 0.0019 26.3 2.6 26 256-282 2-27 (77)
146 KOG0706 Predicted GTPase-activ 21.4 1.4E+02 0.0031 33.1 4.9 55 196-262 24-79 (454)
147 PRK11169 leucine-responsive tr 21.2 1.2E+02 0.0027 28.6 4.0 39 256-295 13-52 (164)
148 PRK14161 heat shock protein Gr 20.9 7.1E+02 0.015 24.3 9.2 17 514-530 47-63 (178)
149 PF08914 Myb_DNA-bind_2: Rap1 20.5 1.8E+02 0.0039 23.6 4.3 43 252-294 3-55 (65)
150 PRK06800 fliH flagellar assemb 20.5 4.3E+02 0.0094 26.2 7.5 14 523-536 89-102 (228)
151 PLN02806 complex I subunit 20.4 1.8E+02 0.004 24.7 4.3 26 504-531 47-72 (81)
152 PRK13729 conjugal transfer pil 20.4 3.6E+02 0.0078 30.4 7.8 39 472-514 67-107 (475)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=4.5e-96 Score=760.65 Aligned_cols=415 Identities=28% Similarity=0.493 Sum_probs=336.8
Q ss_pred CCCcceeecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHH
Q 008658 11 KPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLL 90 (558)
Q Consensus 11 ~~~~~~iiIPs~~~wF~~~~ih~iE~~~~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~i 90 (558)
-++.++|+||||+.||++.+||+||+++.||||+|++++|||++|+.||||||+.||+||.+|||+|+||||++||||+|
T Consensus 46 ~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvagDV~ai 125 (531)
T COG5259 46 MEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAGDVAAI 125 (531)
T ss_pred hccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccchhHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhcccccccCCCCCCCCCCCCCCCCccccccceeecCCCCccccccCCCCCCCCCCCCCCCCCCCCCccccc
Q 008658 91 HKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVA 170 (558)
Q Consensus 91 ~rvh~FLe~wGlIN~~~~~~~~~~~~~~~~~~~p~~tg~f~v~~dtP~gl~~~~~p~~~kp~~~~~~~~~~~~~~~~~~~ 170 (558)
.|||+||++|||||||++| .+||+.+|| |+||||++++|||+||.|+.+++.... ...+++.. .+...
T Consensus 126 vrvHrFLekWGLINYqvdp-----~trPs~IgP-plt~h~q~l~dtP~gl~p~l~~~~~~~---~~~~a~~~---e~~~~ 193 (531)
T COG5259 126 VRVHRFLEKWGLINYQVDP-----GTRPSTIGP-PLTSHFQDLHDTPRGLSPFLPWGPINQ---RVLGAKEI---EYETH 193 (531)
T ss_pred HHHHHHHHHhcceeeccCC-----CCCccccCC-CcchhhHHHhhCccccccccCCCCccc---cccccchh---hhhhh
Confidence 9999999999999999999 578888887 588999999999999999865543311 11111110 00000
Q ss_pred CCCCCCCCCcccch----hhccccc---ccCCccCCCCCCCCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCceecc
Q 008658 171 GETGVKLPPLASYL----DVFGDLV---KLKGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFSD 242 (558)
Q Consensus 171 ~~~~~~~~~~~~~~----~~~~~~~---~~~~~~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~~~~ 242 (558)
.+..+ .|++.... ..+.++. ......|..||..|...||+..+ ..+++|..||.+|+||+...+.||..++
T Consensus 194 k~~~~-sps~~~~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~ 272 (531)
T COG5259 194 KEENY-SPSLKSPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVT 272 (531)
T ss_pred ccCCC-CchhhhhhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhh
Confidence 11111 11111110 0112222 12348899999999999999998 8899999999999999999999999998
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCCccccCCCCCCCCCCCccc
Q 008658 243 LGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLK 322 (558)
Q Consensus 243 ~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~LPIeD~~l~~~~~~~~~~~~~~~~~~~k 322 (558)
...+ ..+..||.+|+++|||||++||++|++||.|||+||++|||+|||||||+|.||...++...
T Consensus 273 ~~~~--~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~~~~------------ 338 (531)
T COG5259 273 ISLL--IRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDGKGD------------ 338 (531)
T ss_pred hhcc--cccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccCcCC------------
Confidence 8764 25679999999999999999999999999999999999999999999999999987653110
Q ss_pred cccccccccccchhhhhhhhhhcccccccCCCCcCCCcccccCCCCCCCCCCcHHHHHHHHHhccChHHHHHHHHHHHHH
Q 008658 323 EGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAA 402 (558)
Q Consensus 323 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~p~lk~~~~~PFs~a~NPVms~vAFLas~V~P~VAaaAA~aAl~~ 402 (558)
.+ .+..||..++||||++|+||+++|.|+|++-.+++.++.
T Consensus 339 ----------------------------------~~-----~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k~ 379 (531)
T COG5259 339 ----------------------------------NS-----KGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIKS 379 (531)
T ss_pred ----------------------------------CC-----CCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhhc
Confidence 01 134799999999999999999999999988776655321
Q ss_pred HhccCCCCccccCCCchhhccCCCCCCCCCChhhhhhhhhhhhccccccccccCCCCCCCchhhHHHHHHHHHHHHHHHH
Q 008658 403 LCNESSCPREIFDGDEDYLANGLSSPTMVSDPERALQVDASKMEENQSETQDASSEKNDVPLNLRIRTATATALGAAAAN 482 (558)
Q Consensus 403 l~~e~~~~~~~~~~~ed~~~~~~~~~~~~~~~e~~~~~~d~~~~~~~~~~~~~~~~~~~~ps~~~v~~Aaa~AL~aAA~k 482 (558)
.+.. . .+--+...+...+--||.+++.+
T Consensus 380 -g~~~-------------------------~--------------------------~n~e~~~~~~~~~~~al~s~~ek 407 (531)
T COG5259 380 -GKIS-------------------------H--------------------------INRESQEHIEEVIEYALDSGKEK 407 (531)
T ss_pred -ccee-------------------------c--------------------------CccchhhHHHHHHHHHHHHHHHH
Confidence 0000 0 00001234556677899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 483 AKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 546 (558)
Q Consensus 483 Ak~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~ 546 (558)
||++|+.|||+|.+|+..+|+.||+||++||.||.+||+.+++||..|+. .|+..|+.+-+
T Consensus 408 a~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L~~~~~L~rqeLd~---nlll~rl~~~e 468 (531)
T COG5259 408 AKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKSTSLERQELDA---NLLLRRLNAEE 468 (531)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhHHH
Confidence 99999999999999999999999999999999999999999999999999 55555554433
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=4.5e-86 Score=711.06 Aligned_cols=443 Identities=31% Similarity=0.526 Sum_probs=334.3
Q ss_pred CCCCcceeecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHH
Q 008658 10 TKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSL 89 (558)
Q Consensus 10 ~~~~~~~iiIPs~~~wF~~~~ih~iE~~~~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~ 89 (558)
...+.|.|+||||++||+|++||.||++++||||+|++++|||++|++||||||++||+||.+|||+|+|||+++||||+
T Consensus 40 ~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp~~ylt~ta~rrnl~gDv~a 119 (506)
T KOG1279|consen 40 VSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNPQEYLTFTACRRNLAGDVCA 119 (506)
T ss_pred cccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCcccchhHHHHHhcccchHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhcccccccCCCCCCCCCCCCCCCCccccccceeecCCCCccccccCCCCCCCCCCCCCCCCCCCCCcccc
Q 008658 90 LHKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAV 169 (558)
Q Consensus 90 i~rvh~FLe~wGlIN~~~~~~~~~~~~~~~~~~~p~~tg~f~v~~dtP~gl~~~~~p~~~kp~~~~~~~~~~~~~~~~~~ 169 (558)
|+|||+|||+||||||++++ +++|..++|| .++||+++.++|+|+.++.++... .....+.+..+
T Consensus 120 i~Rvh~FlE~WGLINy~~d~-----e~rp~~~~p~-~t~h~~~~~~tp~~~~~~~~~~~~---~~~~~~~~~~~------ 184 (506)
T KOG1279|consen 120 IARVHAFLEQWGLINYQVDA-----ESRPHPIEPP-ETSHFQVLADTPRGLAPLTPEDPQ---SQPDLGNPRME------ 184 (506)
T ss_pred HHHHHhhHHhhcccccccCh-----hhCCcccCCC-cccccccccCCCcccccCCCCCcc---ccccccccccc------
Confidence 99999999999999999999 5677777775 569999999999999887543222 11111111000
Q ss_pred cCCCCCCCCCcccchhhcccccc----cCCccCCCCCCCCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCceeccCC
Q 008658 170 AGETGVKLPPLASYLDVFGDLVK----LKGFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFSDLG 244 (558)
Q Consensus 170 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~~~~~~ 244 (558)
. +....+..+.... ....+|..|+.. ||+..+ ..+.+|.+||..|+|+..+...||+.+.
T Consensus 185 -------~--~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~-- 249 (506)
T KOG1279|consen 185 -------T--LSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIG-- 249 (506)
T ss_pred -------c--ccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccchhcc--
Confidence 0 1111111111111 233556555544 444444 7789999999999999999999993322
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCCccccCCCCCCCCCCCccccc
Q 008658 245 GNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLKEG 324 (558)
Q Consensus 245 ~~~~~~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~LPIeD~~l~~~~~~~~~~~~~~~~~~~k~~ 324 (558)
...+..||++|+++|||||++||+||.+||.|||+||++|||.|||+|||+|+|+....+.
T Consensus 250 ---~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l~~~~~~---------------- 310 (506)
T KOG1279|consen 250 ---ESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYLAKSEAS---------------- 310 (506)
T ss_pred ---ccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhhhhcccc----------------
Confidence 2457899999999999999999999999999999999999999999999999999774321
Q ss_pred cccccccccchhhhhhhhhhcccccccCCCCcCCCcccccCCCCCCCCCCcHHHHHHHHHhccChHHHHHHHHHHHHHHh
Q 008658 325 QSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALC 404 (558)
Q Consensus 325 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~p~lk~~~~~PFs~a~NPVms~vAFLas~V~P~VAaaAA~aAl~~l~ 404 (558)
.+|. ++ +..+|+.-+||||++++||+++|+|+|+..+++.+...+.
T Consensus 311 --------------------------------~~~~-~~-~~~~~sq~gnpv~s~~~~l~~~vdP~~~~~~~k~~~~~~~ 356 (506)
T KOG1279|consen 311 --------------------------------LGPL-SY-GPVPFSQDGNPVMSTVAFLASVVDPVVKSVAAKSAEEKFS 356 (506)
T ss_pred --------------------------------cCcc-cc-CCCccccCCCccccHHHHHHhccCchhhhhhhcccchhhh
Confidence 1222 44 3468888889999999999999999999999999998876
Q ss_pred ccC---CCCc--cccCCCchhh-c-cCCC-------CCCCCCCh--hhhhhhhhhhhccccccccccCCCCCCCchhhHH
Q 008658 405 NES---SCPR--EIFDGDEDYL-A-NGLS-------SPTMVSDP--ERALQVDASKMEENQSETQDASSEKNDVPLNLRI 468 (558)
Q Consensus 405 ~e~---~~~~--~~~~~~ed~~-~-~~~~-------~~~~~~~~--e~~~~~~d~~~~~~~~~~~~~~~~~~~~ps~~~v 468 (558)
+.. +.+. ......+... . .+.+ +...+.-+ +..... .++.. .+ ....+.+.. . +
T Consensus 357 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~e~~k~~~---~~~~~--~n---~~~~k~~e~-~-~ 426 (506)
T KOG1279|consen 357 KVNEESPLAKIEVSAKGVEEAASKLGGTDKSKFLALSDIACTLPDEEEKLQS---KLKAK--LN---PNKEKTIEL-G-L 426 (506)
T ss_pred hhhhcccchhhhHHhhhhHHhhhhhccchhhhhhhhhhhhhcccchHHHHHH---Hhhcc--cc---cchhhhhHH-H-H
Confidence 432 2110 0000000000 0 0000 00000000 000000 01100 00 000111111 2 7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 469 RTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 546 (558)
Q Consensus 469 ~~Aaa~AL~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~ 546 (558)
..|+..+|++||+|||+||.+|| +++++++.++++||+|+|.||++|+++|+++.+|+++++..|+.++.+|+.++-
T Consensus 427 ~~a~~~~ls~aa~k~k~la~~ee-~~~s~~~~~~~~q~~k~E~~l~~~~e~e~~~~~e~e~~~~~~~~~~~~~~~~~~ 503 (506)
T KOG1279|consen 427 STAANAALSAAAVKAKLLAAQEE-RIKSLVALLEETQLKKLEAKLRHFEEAETLLMREREQLERVRQRLKAERQQFHM 503 (506)
T ss_pred HHHHHHHHHHHHHhhhhhhhHHH-HHHHHhhhhhhhhhhhhhHHHHHHHHHHhhhhhhhhhHHHHHHHHHhcchhhhh
Confidence 89999999999999999999999 999999999999999999999999999999999999999999999999998873
No 3
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.94 E-value=3.5e-27 Score=200.88 Aligned_cols=85 Identities=41% Similarity=0.829 Sum_probs=78.2
Q ss_pred eecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccc-hHHHHHHHHH
Q 008658 17 YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFR 95 (558)
Q Consensus 17 iiIPs~~~wF~~~~ih~iE~~~~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~g-D~~~i~rvh~ 95 (558)
+++|.+++||+++.+|++|++.|||||.| ++|+.|+.|||.||..|+.||.+|||+++||+.+.| |++.+.|||+
T Consensus 1 ~~~~~~~~~~~~~~l~~~E~~~~~e~~~~----~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~ 76 (86)
T PF04433_consen 1 VVIPAHSSWFDPDKLSEIEKQLCPEFFIG----KTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYD 76 (86)
T ss_dssp -HCHCCHTTTTTTSS-HHHHHHCHHCTTS----CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHH
T ss_pred CCCccccCCCCcccCCHHHHHHhHHHhcc----CChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHH
Confidence 47899999999999999999999999998 799999999999999999999999999999999996 9999999999
Q ss_pred hhhhhccccc
Q 008658 96 LLDEWGLINF 105 (558)
Q Consensus 96 FLe~wGlIN~ 105 (558)
||++||+|||
T Consensus 77 FL~~~G~INf 86 (86)
T PF04433_consen 77 FLERWGLINF 86 (86)
T ss_dssp HHHHTTSSSS
T ss_pred HHHHcCccCC
Confidence 9999999998
No 4
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.86 E-value=3.9e-22 Score=208.67 Aligned_cols=110 Identities=23% Similarity=0.484 Sum_probs=100.5
Q ss_pred CCccCCCCCCCCCCc-eeeecC-CCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 008658 194 KGFKCGSCGEQCNSG-CYEYSK-GSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 270 (558)
Q Consensus 194 ~~~~C~~C~~~~~~~-~y~~~k-~~~~lC~~Cf~~G~-~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g 270 (558)
..+.|++|..+|+.. +++|.. ++|+||..||+.|. ++.|.+.|+|.+|+...++ .....||++||.+||+|++.||
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~-i~~~~WtadEEilLLea~~t~G 91 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFP-ILDPSWTADEEILLLEAAETYG 91 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCC-CCCCCCChHHHHHHHHHHHHhC
Confidence 469999999999986 599999 78999999999996 6899999999999997665 4578999999999999999999
Q ss_pred -CCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCC
Q 008658 271 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGS 304 (558)
Q Consensus 271 -~~W~~Ia~~vg~kt~~eC~~~fl~LPIeD~~l~~ 304 (558)
|||++||+|||+||+++|..||+..+++.++...
T Consensus 92 ~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~ 126 (438)
T KOG0457|consen 92 FGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPL 126 (438)
T ss_pred CCcHHHHHHHHcccchHHHHHHHHHHHhcCccccc
Confidence 9999999999999999999999998888888644
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.74 E-value=9.8e-19 Score=176.02 Aligned_cols=110 Identities=20% Similarity=0.350 Sum_probs=100.3
Q ss_pred CCccCCCCCCCCCC-ceeeecC-CCcccchhhhhcCCC-CCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 008658 194 KGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 270 (558)
Q Consensus 194 ~~~~C~~C~~~~~~-~~y~~~k-~~~~lC~~Cf~~G~~-~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g 270 (558)
..++|+.|..+|+. .++.|.. +.++||..||++|.+ +.|...|+|.+++.+..+ ....+|++.||++|+++++..|
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsyp-I~~e~WgadEEllli~~~~TlG 82 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYP-IGEEGWGADEELLLIECLDTLG 82 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCcc-ccCCCcCchHHHHHHHHHHhcC
Confidence 46899999999986 4899998 799999999999975 678889999999987765 4678999999999999999999
Q ss_pred -CCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCC
Q 008658 271 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGS 304 (558)
Q Consensus 271 -~~W~~Ia~~vg~kt~~eC~~~fl~LPIeD~~l~~ 304 (558)
|||++||+|||.|++++|..||+.+++|..|..-
T Consensus 83 lGNW~dIadyiGsr~kee~k~HylK~y~es~~ypl 117 (432)
T COG5114 83 LGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYPL 117 (432)
T ss_pred CCcHHHHHHHHhhhhhHHHHHHHHHHHhhcccccc
Confidence 9999999999999999999999999999999654
No 6
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.05 E-value=2.3e-10 Score=86.95 Aligned_cols=44 Identities=34% Similarity=0.700 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCC-HHHHHHHcC-CCCHHHHHHHHHcC
Q 008658 252 ATWTEAETLLLLESVMRHGDN-WELVAQNVP-TKSKLDCISKLIEL 295 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~~g~~-W~~Ia~~vg-~kt~~eC~~~fl~L 295 (558)
..||.+|+.+|+++|.+||.+ |..||++|+ +||..||..||.++
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 479999999999999999966 999999999 99999999999763
No 7
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=98.99 E-value=3.3e-10 Score=85.10 Aligned_cols=44 Identities=25% Similarity=0.767 Sum_probs=41.6
Q ss_pred ccCCCCCCCCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCce
Q 008658 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFR 239 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~ 239 (558)
++|+.||.||+.+||||++ .+++||+.||.+|+||.++++.||+
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~Dfv 45 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQSSDFI 45 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhCcCCCCCCcccccC
Confidence 5799999999999999999 7899999999999999999999985
No 8
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.82 E-value=5.7e-09 Score=82.58 Aligned_cols=41 Identities=29% Similarity=0.659 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 254 WTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 254 Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
||.+|+.+|++++..||.+|..||+++|+||+.+|..||..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999999999999999999999999988
No 9
>PLN03000 amine oxidase
Probab=98.78 E-value=7e-09 Score=120.26 Aligned_cols=84 Identities=27% Similarity=0.332 Sum_probs=73.3
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccch-HHHHHHHHHhhh
Q 008658 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGD-VSLLHKVFRLLD 98 (558)
Q Consensus 22 ~~~wF~~~~ih~iE~~~--~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~gD-~~~i~rvh~FLe 98 (558)
++.-|+.|.+++.|..+ || ...+ ..+..|+.|||.||.+|+.||..|||+++|...+..+ ...+.++|+||.
T Consensus 87 ~~~~~p~d~l~~~e~~~~~~~-~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~ 161 (881)
T PLN03000 87 LTAGFPADSLTEEEIEFGVVP-IVGG----IEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLV 161 (881)
T ss_pred HHcCCCcccCCHHHHhccccC-cccc----cchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHH
Confidence 35789999999999777 88 3333 4789999999999999999999999999999888653 489999999999
Q ss_pred hhcccccccCCC
Q 008658 99 EWGLINFGAVSR 110 (558)
Q Consensus 99 ~wGlIN~~~~~~ 110 (558)
++|+|||++...
T Consensus 162 r~G~in~g~~~~ 173 (881)
T PLN03000 162 THGYINFGIAQA 173 (881)
T ss_pred HcCcccHHHHHH
Confidence 999999999853
No 10
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.76 E-value=1.6e-08 Score=75.03 Aligned_cols=44 Identities=36% Similarity=0.728 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008658 252 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl~L 295 (558)
..||.+|+.+|+.++..|| .+|..||.++++||+.+|..+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5799999999999999999 9999999999999999999999764
No 11
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.69 E-value=2.1e-08 Score=116.14 Aligned_cols=84 Identities=26% Similarity=0.368 Sum_probs=75.4
Q ss_pred CCCCCCCCCCHHHHhh-cccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhcc-chHHHHHHHHHhhhhh
Q 008658 23 SSWFRWDDIHETERTA-LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLV-GDVSLLHKVFRLLDEW 100 (558)
Q Consensus 23 ~~wF~~~~ih~iE~~~-~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~-gD~~~i~rvh~FLe~w 100 (558)
+.-|+.+.+|+.|..+ |++...+ ..+..|+.|||.||.+|+.||..|||+++|+..+- -....+.++|.||.+.
T Consensus 139 ~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~~ 214 (808)
T PLN02328 139 SVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLEH 214 (808)
T ss_pred HcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhcc
Confidence 4689999999999888 8877765 57899999999999999999999999999998874 3568999999999999
Q ss_pred cccccccCCC
Q 008658 101 GLINFGAVSR 110 (558)
Q Consensus 101 GlIN~~~~~~ 110 (558)
|.|||+|.+.
T Consensus 215 g~in~gv~~~ 224 (808)
T PLN02328 215 GYINFGVAPV 224 (808)
T ss_pred Cceeeecccc
Confidence 9999999986
No 12
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.67 E-value=4e-08 Score=71.80 Aligned_cols=43 Identities=40% Similarity=0.784 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008658 253 TWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (558)
Q Consensus 253 ~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl~L 295 (558)
.||.+|+.+|+.++.+|| ++|..||+.+++||..+|..||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 499999999999999999 9999999999999999999999753
No 13
>PLN02529 lysine-specific histone demethylase 1
Probab=98.20 E-value=2.2e-06 Score=99.02 Aligned_cols=84 Identities=23% Similarity=0.350 Sum_probs=71.9
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchH-HHHHHHHHhhh
Q 008658 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDV-SLLHKVFRLLD 98 (558)
Q Consensus 22 ~~~wF~~~~ih~iE~~~--~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~-~~i~rvh~FLe 98 (558)
.+-=|+.+.+++.|+++ +|.. .++.+..|+.|||.|+.+|+.||..|||+++++..+.-++ .+|...|+||.
T Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l~ 137 (738)
T PLN02529 63 LSVGFPIDALLEEEIRAGVVREL-----GGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLL 137 (738)
T ss_pred HHcCCCccccCHHHHhccccCcc-----ccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHHH
Confidence 34679999999999855 5543 3568999999999999999999999999999998876543 57779999999
Q ss_pred hhcccccccCCC
Q 008658 99 EWGLINFGAVSR 110 (558)
Q Consensus 99 ~wGlIN~~~~~~ 110 (558)
+.|.|||++.|.
T Consensus 138 ~~~~inc~vnp~ 149 (738)
T PLN02529 138 YNGYINFGVSPS 149 (738)
T ss_pred hCCCcceeeccc
Confidence 999999999986
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.17 E-value=2.2e-06 Score=85.82 Aligned_cols=45 Identities=16% Similarity=0.443 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcC-CCCHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg-~kt~~eC~~~fl~ 294 (558)
....||.+|+.+|+++|++|| .+|..||+++| +||..||+.||.+
T Consensus 24 KRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N 70 (249)
T PLN03212 24 KRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMN 70 (249)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHH
Confidence 357899999999999999999 79999999997 7999999999985
No 15
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.13 E-value=5e-06 Score=65.78 Aligned_cols=44 Identities=20% Similarity=0.371 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCH---HHHHHHcC-CC-CHHHHHHHHHc
Q 008658 251 GATWTEAETLLLLESVMRHG-DNW---ELVAQNVP-TK-SKLDCISKLIE 294 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g-~~W---~~Ia~~vg-~k-t~~eC~~~fl~ 294 (558)
+..||++|..++|+||+.|| ||| ..|+++++ ++ |+.||..|+-.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QK 52 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQK 52 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHH
Confidence 45799999999999999999 599 99999987 67 99999999853
No 16
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.94 E-value=1e-05 Score=62.04 Aligned_cols=46 Identities=20% Similarity=0.625 Sum_probs=40.2
Q ss_pred ccCCCCCCCCCC-ceeeecC-CCcccchhhhhcCCC-CCCCCCCCceec
Q 008658 196 FKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRFS 241 (558)
Q Consensus 196 ~~C~~C~~~~~~-~~y~~~k-~~~~lC~~Cf~~G~~-~~~~s~~df~~~ 241 (558)
+.|++|+.++.. .||+|.. .+++||..||..|.. +.|...|.|+.+
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 469999999887 7999999 899999999999975 678888998764
No 17
>PLN03091 hypothetical protein; Provisional
Probab=97.94 E-value=9.3e-06 Score=87.00 Aligned_cols=45 Identities=20% Similarity=0.441 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcC-CCCHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg-~kt~~eC~~~fl~ 294 (558)
....||.+|+.+|+++|++|| .+|..||+++| +||..||+.||++
T Consensus 13 rKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~N 59 (459)
T PLN03091 13 RKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWIN 59 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHh
Confidence 356899999999999999999 79999999998 7999999999985
No 18
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=97.79 E-value=2.3e-05 Score=59.15 Aligned_cols=45 Identities=18% Similarity=0.478 Sum_probs=39.1
Q ss_pred ccCCCCCCCCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 008658 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~~~ 241 (558)
+.|+.|+.++...+|+|.. .+++||..||..|. +.|...|.|..+
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~-~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK-KGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc-CCCCCCCCEeEC
Confidence 4699999999999999999 88999999999998 667667887653
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.73 E-value=2.9e-05 Score=78.40 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcC-CCCHHHHHHHHHc
Q 008658 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 294 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg-~kt~~eC~~~fl~ 294 (558)
.+.||.+|+.+|.+.|++|| ++|..|+++.| .|+...|+++|+.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~N 54 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTN 54 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhc
Confidence 47899999999999999999 99999999999 8999999999985
No 20
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=97.57 E-value=6.9e-05 Score=56.10 Aligned_cols=38 Identities=24% Similarity=0.730 Sum_probs=34.0
Q ss_pred CccCCCCCCCCCCceeeecC-CCcccchhhhhcCCCCCC
Q 008658 195 GFKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGED 232 (558)
Q Consensus 195 ~~~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~ 232 (558)
.+.|+.|+..+...+|+|.. .+++||.+||..|.++..
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~ 42 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGE 42 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCC
Confidence 47899999999999999999 899999999999987643
No 21
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.57 E-value=7.3e-05 Score=57.13 Aligned_cols=44 Identities=27% Similarity=0.589 Sum_probs=37.1
Q ss_pred ccCCCCCC-CCCCceeeecC-C--CcccchhhhhcCCCCCCCCCCCceec
Q 008658 196 FKCGSCGE-QCNSGCYEYSK-G--SFVICEKCFKNGNYGEDKSKDDFRFS 241 (558)
Q Consensus 196 ~~C~~C~~-~~~~~~y~~~k-~--~~~lC~~Cf~~G~~~~~~s~~df~~~ 241 (558)
+.|++|+. .+...||+|.. . +|+||..||..|. .|...|.|.++
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~--~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE--SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC--CCCCCCceeeC
Confidence 46999998 88889999998 6 8999999999997 56666776653
No 22
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.56 E-value=9.1e-05 Score=74.36 Aligned_cols=46 Identities=20% Similarity=0.282 Sum_probs=42.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
.....||.+|+.+||+.+..||..|..||.++.+||..+|..||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999964
No 23
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=97.51 E-value=9.5e-05 Score=55.20 Aligned_cols=41 Identities=17% Similarity=0.358 Sum_probs=36.0
Q ss_pred cCCCCCCCCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 008658 197 KCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (558)
Q Consensus 197 ~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~~~ 241 (558)
.|+.|+..+...||+|.. .+++||..||..| .| ..|.|.++
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~---~H-~~H~f~~~ 43 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG---VH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC---CC-CCCCEEeC
Confidence 699999999999999999 7999999999998 45 77888754
No 24
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=97.49 E-value=9.7e-05 Score=56.66 Aligned_cols=43 Identities=14% Similarity=0.424 Sum_probs=36.8
Q ss_pred cCCCCCC-CCCCceeeecC-CCcccchhhhhcCCC-CCCCCCCCce
Q 008658 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFR 239 (558)
Q Consensus 197 ~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G~~-~~~~s~~df~ 239 (558)
.|+.|.. ++...||+|.. .+++||..||..|.. ..|...|.|.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~ 47 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMY 47 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcc
Confidence 5999998 99999999999 999999999999974 4566667664
No 25
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.41 E-value=0.00016 Score=55.19 Aligned_cols=41 Identities=20% Similarity=0.499 Sum_probs=34.3
Q ss_pred cCCCCCCCCCCceeeecC-CCcccchhhhhcCCCC-CCCCCCC
Q 008658 197 KCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYG-EDKSKDD 237 (558)
Q Consensus 197 ~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~-~~~s~~d 237 (558)
.|++|...+...||+|.+ .+++||..||..|... .|...|+
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hp 44 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHE 44 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCCCCCC
Confidence 599999988888999999 9999999999999865 4444443
No 26
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=97.39 E-value=0.00017 Score=55.29 Aligned_cols=44 Identities=16% Similarity=0.485 Sum_probs=37.0
Q ss_pred cCCCCC-CCCCCceeeecC-CCcccchhhhhcCCC-CCCCCCCCcee
Q 008658 197 KCGSCG-EQCNSGCYEYSK-GSFVICEKCFKNGNY-GEDKSKDDFRF 240 (558)
Q Consensus 197 ~C~~C~-~~~~~~~y~~~k-~~~~lC~~Cf~~G~~-~~~~s~~df~~ 240 (558)
.|+.|+ .++...+|+|.. .+|+||..||..|.. +.|...|.|..
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEE
Confidence 699999 788888999999 999999999999965 45666777754
No 27
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=97.34 E-value=0.00021 Score=54.86 Aligned_cols=43 Identities=26% Similarity=0.563 Sum_probs=35.7
Q ss_pred cCCCCCC-CCCCceeeecC-CCcccchhhhhcCCCC-CCCCCCCce
Q 008658 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYG-EDKSKDDFR 239 (558)
Q Consensus 197 ~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G~~~-~~~s~~df~ 239 (558)
.|+.|+. .+...||+|.. .+++||..||..|... .|...|+++
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 5999996 58889999999 9999999999999754 566666654
No 28
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=97.26 E-value=0.00014 Score=54.93 Aligned_cols=39 Identities=26% Similarity=0.715 Sum_probs=28.2
Q ss_pred CCccCCCCCC-CCCCceeeecC-CCcccchhhhhcCCCCCC
Q 008658 194 KGFKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGED 232 (558)
Q Consensus 194 ~~~~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~ 232 (558)
..+.|+.|+. .+...+|+|.. .+|+||..||..|.+...
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~ 43 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKGRHSHN 43 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH--H-SS
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCcCCCCC
Confidence 3578999999 66788999998 999999999999986543
No 29
>PLN03091 hypothetical protein; Provisional
Probab=97.23 E-value=0.00043 Score=74.50 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
...+.||.+|+.+||+.+..||..|.+||.++.+||..+|..||..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 3467899999999999999999999999999999999999888864
No 30
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=97.02 E-value=0.00069 Score=51.07 Aligned_cols=42 Identities=24% Similarity=0.608 Sum_probs=34.7
Q ss_pred cCCCCCC-CCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCceec
Q 008658 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRFS 241 (558)
Q Consensus 197 ~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~~~ 241 (558)
.|+.|+. .+...||+|.. .+|+||..||..+. |...|.|.+|
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~---H~~~H~F~ri 45 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRK---HNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCCC---cCCCCceeeC
Confidence 6999986 57778999999 99999999999954 4457778764
No 31
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=96.78 E-value=0.0015 Score=49.36 Aligned_cols=41 Identities=12% Similarity=0.455 Sum_probs=33.1
Q ss_pred cCCCCC-CCCCCceeeecC-CCcccchhhhhcCCCCCCCCCCCcee
Q 008658 197 KCGSCG-EQCNSGCYEYSK-GSFVICEKCFKNGNYGEDKSKDDFRF 240 (558)
Q Consensus 197 ~C~~C~-~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s~~df~~ 240 (558)
.|+.|+ ..+...||+|.. .+++||..||..+ .|...|.|.+
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~---~H~~~H~f~r 44 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGD---KHDLEHRFYR 44 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCC---CCCCCCCEEe
Confidence 699999 567788999999 7999999999964 3445677764
No 32
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.75 E-value=0.0016 Score=72.45 Aligned_cols=46 Identities=33% Similarity=0.660 Sum_probs=43.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
...+.||++|+.+|+.||++|| -+|-+|-+.|.+||-.||+.+|++
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~n 404 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTN 404 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHH
Confidence 4567899999999999999999 699999999999999999999986
No 33
>PLN02976 amine oxidase
Probab=96.34 E-value=0.0032 Score=76.94 Aligned_cols=83 Identities=23% Similarity=0.351 Sum_probs=71.1
Q ss_pred CCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhh------hccchHHHHHHHHHhhh
Q 008658 25 WFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRK------SLVGDVSLLHKVFRLLD 98 (558)
Q Consensus 25 wF~~~~ih~iE~~~~peff~~~~~~ktp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~------~l~gD~~~i~rvh~FLe 98 (558)
-+....+.+|||-.|.|...-+ ..-+-|+.+||.|+-.|-+|=.+-|.+++|-= .-.+-..+|.-|+.||+
T Consensus 454 gl~a~~~~~~e~~~~k~~lkr~---~~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~~~fld 530 (1713)
T PLN02976 454 GLKARAVGPIEKIKFKEVLKRK---GGLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREVYLFLD 530 (1713)
T ss_pred cccccccChHHHHHHHHHHHhc---cchHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHHHHHhh
Confidence 4456789999999999998754 36789999999999999999999999999942 22356789999999999
Q ss_pred hhcccccccCCC
Q 008658 99 EWGLINFGAVSR 110 (558)
Q Consensus 99 ~wGlIN~~~~~~ 110 (558)
+.|.||-++...
T Consensus 531 ~~gyin~g~~s~ 542 (1713)
T PLN02976 531 QRGYINAGIASE 542 (1713)
T ss_pred ccCceecccccc
Confidence 999999999875
No 34
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=96.18 E-value=0.0042 Score=45.93 Aligned_cols=34 Identities=15% Similarity=0.599 Sum_probs=28.7
Q ss_pred ccCCCCCCCCCCceeeecC-CCcccchhhhhcCCCC
Q 008658 196 FKCGSCGEQCNSGCYEYSK-GSFVICEKCFKNGNYG 230 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k-~~~~lC~~Cf~~G~~~ 230 (558)
+.|+.|....+ .+|+|.. .+|+||..||..+.-|
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~~~H~ 35 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNTKNHP 35 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCCCCCC
Confidence 46999988654 9999999 8999999999886544
No 35
>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=95.87 E-value=0.0065 Score=45.22 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=27.5
Q ss_pred cCCCCCC-CCCCceeeecC-CCcccchhhhhcC
Q 008658 197 KCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNG 227 (558)
Q Consensus 197 ~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G 227 (558)
.|+.|+. .+...||+|.. .+|+||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 6999996 68888999998 9999999999765
No 36
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.84 E-value=0.014 Score=58.92 Aligned_cols=43 Identities=16% Similarity=0.416 Sum_probs=40.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHH
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKL 292 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~f 292 (558)
..+.||.+||.+|+++-..||..|..||.++.+||..+.--||
T Consensus 61 krg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W 103 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW 103 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH
Confidence 3678999999999999999999999999999999999987776
No 37
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.75 E-value=0.0084 Score=67.02 Aligned_cols=52 Identities=27% Similarity=0.360 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCH---HHHHHHHHcCCcCCCCCCC
Q 008658 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSK---LDCISKLIELPFGEFMMGS 304 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~---~eC~~~fl~LPIeD~~l~~ 304 (558)
..+.||-+|+..||++|++|| |+|-++|-.+|.||. .-|+.+|+.. ..||+.
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~---k~rl~~ 466 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAA---KLRLAA 466 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHH---HHHHhc
Confidence 467899999999999999999 999999999999999 7799999862 345544
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.93 E-value=0.013 Score=49.60 Aligned_cols=43 Identities=26% Similarity=0.530 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHHHHHH------cC------C--CHHHHHHHcC----CCCHHHHHHHHHc
Q 008658 252 ATWTEAETLLLLESVMR------HG------D--NWELVAQNVP----TKSKLDCISKLIE 294 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~------~g------~--~W~~Ia~~vg----~kt~~eC~~~fl~ 294 (558)
..||++|+..||+.+.. ++ . -|..||+.+. .||+.||..+|-+
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~ 62 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKN 62 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 46999999999999877 21 1 5999998875 6999999999966
No 39
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.22 E-value=0.095 Score=59.11 Aligned_cols=44 Identities=23% Similarity=0.564 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
..+.||.+|+..|-..+.++|++|..|++.+| |.|..|+.+|-+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~ 426 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQ 426 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHH
Confidence 56889999999999999999999999999998 799999999975
No 40
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=92.54 E-value=0.11 Score=58.63 Aligned_cols=54 Identities=26% Similarity=0.427 Sum_probs=45.9
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc------------------C-CCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCC
Q 008658 250 HGATWTEAETLLLLESVM-------RH------------------G-DNWELVAQNVPTKSKLDCISKLIELPFGEFMMG 303 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie-------~~------------------g-~~W~~Ia~~vg~kt~~eC~~~fl~LPIeD~~l~ 303 (558)
....||-+|+.+||..|+ +| . =+|..|++.+|||+..||+.||-.|=+...+-.
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~ 514 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNK 514 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhc
Confidence 467899999999999995 44 1 289999999999999999999998877766643
No 41
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=91.99 E-value=0.11 Score=53.97 Aligned_cols=32 Identities=22% Similarity=0.664 Sum_probs=29.9
Q ss_pred ccCCCCCC-CCCCceeeecC-CCcccchhhhhcC
Q 008658 196 FKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNG 227 (558)
Q Consensus 196 ~~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G 227 (558)
..|+.|+. .+...||+|+. .+|+||..|+..+
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 68999999 88889999998 8999999999887
No 42
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=90.58 E-value=0.18 Score=53.03 Aligned_cols=36 Identities=25% Similarity=0.775 Sum_probs=30.3
Q ss_pred cCCccCCCCCCCCCC-ceeeecC-CCcccchhhhhcCC
Q 008658 193 LKGFKCGSCGEQCNS-GCYEYSK-GSFVICEKCFKNGN 228 (558)
Q Consensus 193 ~~~~~C~~C~~~~~~-~~y~~~k-~~~~lC~~Cf~~G~ 228 (558)
...+.|+.|++.--. .+|+|.. .+|+||..||.+|.
T Consensus 6 He~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~ 43 (381)
T KOG1280|consen 6 HEGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGA 43 (381)
T ss_pred cCCceeccccccceeeeeeEeeeecchhHHHHHhhcCC
Confidence 345789999988544 4799998 89999999999995
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=89.93 E-value=0.24 Score=54.57 Aligned_cols=45 Identities=18% Similarity=0.422 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcC
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIEL 295 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~L 295 (558)
....|+.+|+.+||.+-.....-|..|+.-|| ||..+|..||..|
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 45789999999999999999999999999998 8999999999874
No 44
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=89.88 E-value=0.27 Score=54.21 Aligned_cols=43 Identities=26% Similarity=0.577 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHH
Q 008658 251 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLI 293 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl 293 (558)
+..|+..|+..|=-+|.+|| ..|..|+..+..||+.||..+|.
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~ 50 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWE 50 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHH
Confidence 57899999999999999999 89999999999999999999995
No 45
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=89.14 E-value=0.59 Score=53.57 Aligned_cols=55 Identities=16% Similarity=0.366 Sum_probs=46.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc----CCcCCCCCCC
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE----LPFGEFMMGS 304 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~----LPIeD~~l~~ 304 (558)
...-||..|..++-.||-.|..|+..|++.|.+||..||+..|.- +|++-..|.+
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK~~~~~~~~~~d 676 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKKIMRLGRKIIDD 676 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHHhccchhhhHhh
Confidence 356799999999999999999999999999999999999999864 5555444443
No 46
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=88.27 E-value=0.77 Score=37.91 Aligned_cols=44 Identities=27% Similarity=0.424 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHcC-----------------CCHHHHHHHcC-----CCCHHHHHHHHHcC
Q 008658 252 ATWTEAETLLLLESVMRHG-----------------DNWELVAQNVP-----TKSKLDCISKLIEL 295 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~~g-----------------~~W~~Ia~~vg-----~kt~~eC~~~fl~L 295 (558)
..||.+|...|++.|+.|. .-|..|++.+. .||..++..+|-+|
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 5799999999999999984 15999998774 59999999998653
No 47
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=86.80 E-value=0.34 Score=55.56 Aligned_cols=39 Identities=28% Similarity=0.512 Sum_probs=31.7
Q ss_pred ccCCCCCC-CCCCceeeecC-CCcccchhhhhcCCCCCCCC
Q 008658 196 FKCGSCGE-QCNSGCYEYSK-GSFVICEKCFKNGNYGEDKS 234 (558)
Q Consensus 196 ~~C~~C~~-~~~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~s 234 (558)
..|+.|.. .+...+|+|.+ -+++||..||..|+.+.++.
T Consensus 604 ~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk 644 (966)
T KOG4286|consen 604 AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHK 644 (966)
T ss_pred hhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCC
Confidence 56999965 35667999999 89999999999998765443
No 48
>PF15324 TALPID3: Hedgehog signalling target
Probab=85.72 E-value=2.7 Score=50.18 Aligned_cols=95 Identities=21% Similarity=0.356 Sum_probs=61.7
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHH---HH---hhHH
Q 008658 457 SEKNDVPLNLRIRTATATALGAAAANAKLLADQEDREIEHLVAII-------------IETQMKKLHS---KI---NYFD 517 (558)
Q Consensus 457 ~~~~~~ps~~~v~~Aaa~AL~aAA~kAk~LA~~EEreI~~Lv~~l-------------Ie~QlkKLEl---KL---k~fe 517 (558)
....++.++..|..|+|+|+|+||-=-|...+.| -++.+....| .+.|.+ ++- |+ .|=.
T Consensus 54 ~sp~~iDSAtTVAAATAAAIATaAPLiKvQSdLE-AKVnsVselL~KLQEtDkqLqrvteqQt~-i~~~~ek~~ch~~Ek 131 (1252)
T PF15324_consen 54 TSPSGIDSATTVAAATAAAIATAAPLIKVQSDLE-AKVNSVSELLNKLQETDKQLQRVTEQQTS-IQNQHEKLHCHDHEK 131 (1252)
T ss_pred CCCCCCchHHHHHHHHHHHHHhhhhhhhhcchHH-HHHHHHHHHHHHhhhhhcchhhhhhhhcc-ccccccccchhhHHH
Confidence 3445666777888888999998886666665555 3333322221 222221 111 11 1122
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 008658 518 DLELIMEKEYNEMMQLKECLVEERIDVLERALKTGV 553 (558)
Q Consensus 518 eLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~~~g~ 553 (558)
.|..+|+.-.++||+.+||.+.=+--|+..|+++|-
T Consensus 132 Qmn~fmeQ~l~HLEKLQqQQi~iQshfIsSAl~~~s 167 (1252)
T PF15324_consen 132 QMNVFMEQHLRHLEKLQQQQIDIQSHFISSALKTGS 167 (1252)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 355678899999999999999999999999999764
No 49
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=85.57 E-value=1.1 Score=47.67 Aligned_cols=51 Identities=20% Similarity=0.207 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHH-HHcCCCCHHHHHHHHHcCCcCCCC
Q 008658 251 GATWTEAETLLLLESVMRHGDNWELVA-QNVPTKSKLDCISKLIELPFGEFM 301 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia-~~vg~kt~~eC~~~fl~LPIeD~~ 301 (558)
-..|+.+|=..+-+||+.||.|+..|- ..|.|||--||+..|..--....|
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKkSery 328 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKKSERY 328 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhcCcch
Confidence 357999999999999999999999995 789999999999998764444433
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=85.43 E-value=1.2 Score=47.63 Aligned_cols=45 Identities=16% Similarity=0.392 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
....||..|..++..|+.++|.|+..|+....+|...|.-.+|++
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 356899999999999999999999999999999999999999987
No 51
>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=85.35 E-value=0.75 Score=43.83 Aligned_cols=42 Identities=31% Similarity=0.510 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHcCCCCHHHHHHHHH
Q 008658 251 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKLI 293 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g--~-----~W~~Ia~~vg~kt~~eC~~~fl 293 (558)
.+.||.+|+++|-|.|-+|- | -.+.|++.++ ||+.-|-.+|.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWN 52 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWN 52 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHH
Confidence 46799999999999999996 2 5677777775 99999999995
No 52
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=84.46 E-value=0.84 Score=51.24 Aligned_cols=44 Identities=20% Similarity=0.353 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHH----------HHHcCCCCHHHHHHHHHc
Q 008658 251 GATWTEAETLLLLESVMRHGDNWELV----------AQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g~~W~~I----------a~~vg~kt~~eC~~~fl~ 294 (558)
...||.+|+.-+.+||..||.|+++| -..+..||+.|.+.||.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~ 141 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYR 141 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHH
Confidence 67899999999999999999999999 334557999999999977
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=82.34 E-value=1.6 Score=46.38 Aligned_cols=46 Identities=33% Similarity=0.519 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHHcC-----C-----CHHHHHH---HcC-CCCHHHHHHHHHcCC
Q 008658 251 GATWTEAETLLLLESVMRHG-----D-----NWELVAQ---NVP-TKSKLDCISKLIELP 296 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g-----~-----~W~~Ia~---~vg-~kt~~eC~~~fl~LP 296 (558)
...|+.+|++.||++....- + .|..||. .+| .||+.||..+|-+|.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 36899999999999885431 3 5999997 445 599999999997644
No 54
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=82.16 E-value=8.3 Score=45.80 Aligned_cols=81 Identities=27% Similarity=0.254 Sum_probs=58.3
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 468 IRTATATAL-GAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 546 (558)
Q Consensus 468 v~~Aaa~AL-~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~ 546 (558)
+..|.-.+| ...-.+|+.+...++.++++|+..|.+ +.+++|.+....+++..-+++.+++|++.+++|-.+|..+++
T Consensus 491 ~~iA~~~Glp~~ii~~A~~~~~~~~~~~~~li~~l~~-~~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~ 569 (782)
T PRK00409 491 FEIAKRLGLPENIIEEAKKLIGEDKEKLNELIASLEE-LERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLE 569 (782)
T ss_pred HHHHHHhCcCHHHHHHHHHHHhhhhhHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444 345589999999999999999999865 445577777777777777777777777777777777666655
Q ss_pred HHH
Q 008658 547 RAL 549 (558)
Q Consensus 547 ~~~ 549 (558)
.+.
T Consensus 570 ~~~ 572 (782)
T PRK00409 570 EAE 572 (782)
T ss_pred HHH
Confidence 543
No 55
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=81.76 E-value=9.3 Score=45.31 Aligned_cols=81 Identities=21% Similarity=0.096 Sum_probs=58.0
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 468 IRTATATAL-GAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 546 (558)
Q Consensus 468 v~~Aaa~AL-~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~ 546 (558)
+..|.-.+| ...-.+|+.+...++.++++|+..|.+. .+++|.++...+.+...+++.++.|++.+++|-.+|..+++
T Consensus 486 ~~iA~~~Glp~~ii~~A~~~~~~~~~~~~~li~~L~~~-~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~ 564 (771)
T TIGR01069 486 FEIAQRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSAL-EKELEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKL 564 (771)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444 3455799999999999999999998654 45577777777777777777777777777777777666655
Q ss_pred HHH
Q 008658 547 RAL 549 (558)
Q Consensus 547 ~~~ 549 (558)
.|.
T Consensus 565 ~a~ 567 (771)
T TIGR01069 565 ELE 567 (771)
T ss_pred HHH
Confidence 443
No 56
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=81.30 E-value=1.5 Score=49.18 Aligned_cols=45 Identities=18% Similarity=0.498 Sum_probs=42.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
....|+.+|+..|++.=..+|.-|..||.+++.+|..+|..+|+.
T Consensus 71 k~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~ 115 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVN 115 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHH
Confidence 457899999999999999999999999999999999999999985
No 57
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=77.53 E-value=1.4 Score=49.47 Aligned_cols=43 Identities=23% Similarity=0.412 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHH
Q 008658 250 HGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKL 292 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~f 292 (558)
..+.|+..|+..|+-+++.|| .+|..||..++.+|+.+|..|+
T Consensus 19 k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw 62 (512)
T COG5147 19 KGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW 62 (512)
T ss_pred cCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchh
Confidence 356899999999999999999 8999999999999999999999
No 58
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=70.60 E-value=2.1 Score=45.35 Aligned_cols=40 Identities=20% Similarity=0.594 Sum_probs=32.2
Q ss_pred CCccCCCCCCCC-CCceeeecC-CCcccchhhhhcCCCCCCC
Q 008658 194 KGFKCGSCGEQC-NSGCYEYSK-GSFVICEKCFKNGNYGEDK 233 (558)
Q Consensus 194 ~~~~C~~C~~~~-~~~~y~~~k-~~~~lC~~Cf~~G~~~~~~ 233 (558)
....|++|.... ...+|.|.. .++.+|.+||-.|+-|..+
T Consensus 239 hpv~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~h 280 (434)
T KOG4301|consen 239 HPVECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSH 280 (434)
T ss_pred CCccCcceecccccchhhhHhhcCCccccchhhccccCCCCc
Confidence 457799997764 455899998 8999999999999976443
No 59
>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=67.27 E-value=6.9 Score=35.60 Aligned_cols=45 Identities=20% Similarity=0.398 Sum_probs=34.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC----CCHHHHHHHcC------------CCCHHHHHHHHH
Q 008658 249 THGATWTEAETLLLLESVMRHG----DNWELVAQNVP------------TKSKLDCISKLI 293 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g----~~W~~Ia~~vg------------~kt~~eC~~~fl 293 (558)
..+..||.+|+.-||-.+.+|| |+|+.|-+.+- +||+.+...|.-
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 4578899999999999999999 59999977543 899988876653
No 60
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=64.59 E-value=7.5 Score=40.54 Aligned_cols=97 Identities=12% Similarity=0.180 Sum_probs=57.8
Q ss_pred CccCCCCCCCCCCceeeecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CC
Q 008658 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DN 272 (558)
Q Consensus 195 ~~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~-~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g-~~ 272 (558)
-.+|.-||.. .++.-.-.-++.||.+|-.--+ +|.|. .++... .-+.||+++...|.+.=..-. .-
T Consensus 25 N~~CADC~a~--~P~WaSwnlGvFiC~~C~giHR~lg~hi-----SkVkSv-----~LD~W~~eqv~~m~~~GN~~an~~ 92 (287)
T KOG0703|consen 25 NKVCADCGAK--GPRWASWNLGVFICLRCAGIHRSLGVHI-----SKVKSV-----TLDEWTDEQVDFMISMGNAKANSY 92 (287)
T ss_pred cCcccccCCC--CCCeEEeecCeEEEeecccccccccchh-----heeeee-----eccccCHHHHHHHHHHcchhhhhh
Confidence 4679988887 4555555678999999974443 34333 333332 236799999887765321111 24
Q ss_pred HHHH-HHHcCCCCHHHHHHHHHc-CCcCCCCCC
Q 008658 273 WELV-AQNVPTKSKLDCISKLIE-LPFGEFMMG 303 (558)
Q Consensus 273 W~~I-a~~vg~kt~~eC~~~fl~-LPIeD~~l~ 303 (558)
|+.- ....-..++++-+.+||+ =|..-.|+.
T Consensus 93 ~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~ 125 (287)
T KOG0703|consen 93 YEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLD 125 (287)
T ss_pred ccccCCccccCCChHHHHHHHHHHHHhhhhhcc
Confidence 5432 334445677888999988 233334444
No 61
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=64.23 E-value=8.8 Score=33.67 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=33.8
Q ss_pred CCCCCCHHHHHHHHHHHHHc----C----CCHHHHHHHcCCC-----CHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRH----G----DNWELVAQNVPTK-----SKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~----g----~~W~~Ia~~vg~k-----t~~eC~~~fl~ 294 (558)
+.+.||+++|..||+|+-.| | .||...-++|... |..|-..+.-+
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr 60 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR 60 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 35789999999999999888 4 4888888777532 56666555544
No 62
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=62.42 E-value=33 Score=35.56 Aligned_cols=64 Identities=17% Similarity=0.188 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----HHHHHHHHHHHHHHHHHHHHHHH
Q 008658 473 ATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINY----FDDLELIMEKEYNEMMQLKECLV 538 (558)
Q Consensus 473 a~AL~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~----feeLE~~me~Er~~LE~~Rq~L~ 538 (558)
.-.+..||.|+-.|+..| + +=+..-+-|.+|++++..+|+- -.+|+.-++|-+.+|||.|+.|-
T Consensus 90 ~~~~~~aa~Rplel~e~E-k-vlk~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle 157 (338)
T KOG3647|consen 90 KESLMSAAQRPLELLEVE-K-VLKSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLE 157 (338)
T ss_pred HHHHHHHHcCCccHHHHH-H-HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677888888888776 3 3344455678899999999986 46889999999999999999873
No 63
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=62.39 E-value=4.8 Score=45.18 Aligned_cols=91 Identities=9% Similarity=-0.032 Sum_probs=71.4
Q ss_pred CCCCCCCCCCCCCHHHHhhcccccCCCC-CCCChhhHHHHHHHHHHHHHhCCCceee-----HHHHhhhcc--chHHHHH
Q 008658 20 PSHSSWFRWDDIHETERTALKEFFDGSS-ISRTPKIYKEYRDFMINKYREEPSRRLT-----FTQVRKSLV--GDVSLLH 91 (558)
Q Consensus 20 Ps~~~wF~~~~ih~iE~~~~peff~~~~-~~ktp~~Y~~~Rn~ii~~y~~np~~~lt-----~t~~r~~l~--gD~~~i~ 91 (558)
+..++-++...=+.-....+++|+.+++ ....+..|+.+|+.++..++-.-..+.+ -+..+++.+ +.+-++-
T Consensus 187 ~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLLLE 266 (506)
T KOG1279|consen 187 SLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLLLE 266 (506)
T ss_pred cccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHHHH
Confidence 3455666666667788889999999872 2457788999999999999965444544 556677774 7899999
Q ss_pred HHHHhhhhhcccccccCCC
Q 008658 92 KVFRLLDEWGLINFGAVSR 110 (558)
Q Consensus 92 rvh~FLe~wGlIN~~~~~~ 110 (558)
+|+.|.+.|+-|+.+|..+
T Consensus 267 ~ie~y~ddW~kVa~hVg~k 285 (506)
T KOG1279|consen 267 AIEMYGDDWNKVADHVGTK 285 (506)
T ss_pred HHHHhcccHHHHHhccCCC
Confidence 9999999999999999864
No 64
>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=62.38 E-value=7.7 Score=26.51 Aligned_cols=28 Identities=25% Similarity=0.619 Sum_probs=23.6
Q ss_pred ccCCCCCCCCCCc-eeeecCCCcccchhh
Q 008658 196 FKCGSCGEQCNSG-CYEYSKGSFVICEKC 223 (558)
Q Consensus 196 ~~C~~C~~~~~~~-~y~~~k~~~~lC~~C 223 (558)
+.|..|++..... .|+|.+-.+.+.+.|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCCCeEcCcc
Confidence 3699999999998 999977778887776
No 65
>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=60.72 E-value=5.8 Score=26.97 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=12.5
Q ss_pred cCCCCCCCCCC-ceeeecCCCcccchhh
Q 008658 197 KCGSCGEQCNS-GCYEYSKGSFVICEKC 223 (558)
Q Consensus 197 ~C~~C~~~~~~-~~y~~~k~~~~lC~~C 223 (558)
.|+.|+..... ..|+|..-+|.|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 59999999988 7899998899988877
No 66
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=60.18 E-value=57 Score=32.47 Aligned_cols=64 Identities=17% Similarity=0.237 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 474 TALGAAAANAKLLADQEDR-EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLV 538 (558)
Q Consensus 474 ~AL~aAA~kAk~LA~~EEr-eI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~ 538 (558)
++--.+++|...-.+.|+. .+.----.+++...+.||...+.| +||+-|+.+|+.|-..|..-|
T Consensus 133 t~~LVaaak~~~~~~~e~~~~~d~s~l~~~~~k~~emE~Qv~IL-~lE~~L~~ar~~L~~lRk~~Y 197 (200)
T smart00307 133 TANLVAAVKSGMIFDEEQEEEEDFSKLSLHEGKTQEMEQQVEIL-KLENELEAARKKLAEIRKQHY 197 (200)
T ss_pred HHHHHHHHHHHHHHHHhhhhhcchhccchHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence 3333455555554432322 222222245555566666677777 789999999999888887654
No 67
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=59.70 E-value=4.8 Score=34.19 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=26.4
Q ss_pred cCCCCCCCCCCceeeecC----CCcccchhhhhcCCCCC
Q 008658 197 KCGSCGEQCNSGCYEYSK----GSFVICEKCFKNGNYGE 231 (558)
Q Consensus 197 ~C~~C~~~~~~~~y~~~k----~~~~lC~~Cf~~G~~~~ 231 (558)
.|.+||..+......-+. .+-+-|.-||.+|.|-.
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft~ 40 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFTQ 40 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCceee
Confidence 699999999877633332 45668999999998743
No 68
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=59.50 E-value=14 Score=27.82 Aligned_cols=51 Identities=14% Similarity=0.223 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHHHHhCCCcee-eHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008658 54 IYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 54 ~Y~~~Rn~ii~~y~~np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (558)
+|-.+|+.|+.... .|...| |..+....+.-....+.|...-|+.-|+|-.
T Consensus 1 i~~~l~~~i~~~~~-~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 1 VAERLREDIVSGEL-RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred CHHHHHHHHHcCCC-CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 36678888877533 467778 8999888887788999999999999999963
No 69
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=57.98 E-value=7.9 Score=42.62 Aligned_cols=52 Identities=15% Similarity=0.241 Sum_probs=43.9
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHH-HHcCCCCHHHHHHHHHcCCcCCCCCC
Q 008658 252 ATWTEAETLLLLESVMRHGDNWELVA-QNVPTKSKLDCISKLIELPFGEFMMG 303 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~~g~~W~~Ia-~~vg~kt~~eC~~~fl~LPIeD~~l~ 303 (558)
..|+.-|-.++-|++++||.|+++|- +++.=||-...++.|.-.--.|.|..
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYvq 338 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQ 338 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHHH
Confidence 57999999999999999999999996 66777888888888877766776654
No 70
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=56.81 E-value=14 Score=45.05 Aligned_cols=41 Identities=12% Similarity=0.284 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHH
Q 008658 252 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKL 292 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~f 292 (558)
..||..+-..++.|.++|| +|-..||..|++||++|...+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~ 866 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYA 866 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHH
Confidence 4699999999999999999 9999999999999999987543
No 71
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=55.57 E-value=21 Score=28.20 Aligned_cols=54 Identities=20% Similarity=0.314 Sum_probs=42.1
Q ss_pred hhhHHHHHHHHHHHHHhCCCcee-eHHHHhhhccchHHHHHHHHHhhhhhcccccc
Q 008658 52 PKIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (558)
Q Consensus 52 p~~Y~~~Rn~ii~~y~~np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~ 106 (558)
-++|-.+|+.|...-. -|...| +..+..+.+.--...+.+....|+.+|+|--.
T Consensus 3 ~~i~~~l~~~I~~g~~-~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRL-PPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHHHHHTTSS--TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHcCCC-CCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 3678888888887433 577899 99998888877789999999999999999643
No 72
>PF05928 Zea_mays_MuDR: Zea mays MURB-like protein (MuDR); InterPro: IPR009227 This family consists of several Zea mays (Maize) specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar [].
Probab=55.09 E-value=1.3e+02 Score=29.02 Aligned_cols=72 Identities=15% Similarity=0.165 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 008658 466 LRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKK-------LHSKINYFDDLELIMEKEYNEMMQLKECL 537 (558)
Q Consensus 466 ~~v~~Aaa~AL~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkK-------LElKLk~feeLE~~me~Er~~LE~~Rq~L 537 (558)
+.|..|-|+|.+|+-+|.-.|-...|.+--.-.+.|+--|..- +-.-||||-.+-+.+-+--+++-||.++|
T Consensus 11 ~~v~aaraaavaa~earc~~~vaekea~a~v~fa~IaaekvEavk~ss~Vd~vD~KYhv~IknslryaIQEmRRQs~~l 89 (207)
T PF05928_consen 11 DVVDAARAAAVAASEARCVVFVAEKEARAGVRFADIAAEKVEAVKISSKVDTVDMKYHVQIKNSLRYAIQEMRRQSQQL 89 (207)
T ss_pred HHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHHHhHHHHHHHhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4455666777777766665554444433333334444333332 23457888888887777777776666655
No 73
>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=54.74 E-value=24 Score=26.09 Aligned_cols=37 Identities=11% Similarity=0.146 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 257 AETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 257 ~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
+=+..||+.++.-+ -.|..||+.||- |+..|..+.-+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 44678999999999 799999999996 88888887654
No 74
>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=54.47 E-value=16 Score=30.87 Aligned_cols=42 Identities=21% Similarity=0.425 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHc-------C------CCHHHHHHHcC-----CCCHHHHHHHHHc
Q 008658 253 TWTEAETLLLLESVMRH-------G------DNWELVAQNVP-----TKSKLDCISKLIE 294 (558)
Q Consensus 253 ~Wt~~E~~~LLe~Ie~~-------g------~~W~~Ia~~vg-----~kt~~eC~~~fl~ 294 (558)
.||++.+..||+.+... + ..|..|++.+. ..|+.||..||-.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 49999999999988444 1 15888887665 4789999999854
No 75
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=53.37 E-value=24 Score=38.93 Aligned_cols=46 Identities=15% Similarity=0.340 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 249 THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
.+...||++|..+|-.+.+.||.++.+|-+.+.-||-..-+..|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHH
Confidence 3567899999999999999999999999999999999999998864
No 76
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=53.13 E-value=32 Score=26.39 Aligned_cols=44 Identities=18% Similarity=0.260 Sum_probs=36.3
Q ss_pred HHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccCC
Q 008658 66 YREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVS 109 (558)
Q Consensus 66 y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~~ 109 (558)
-..+|...+|+++..+.+.-+..++.|+..=|+.+|||--..++
T Consensus 14 l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 14 LARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 33466667999999999999999999999999999999876665
No 77
>PF06034 DUF919: Nucleopolyhedrovirus protein of unknown function (DUF919); InterPro: IPR009265 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several short baculovirus proteins of unknown function.
Probab=52.92 E-value=42 Score=27.25 Aligned_cols=46 Identities=22% Similarity=0.311 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 502 IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERA 548 (558)
Q Consensus 502 Ie~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~ 548 (558)
|...-++++.|+.|||.|-+ +++--.+|+...++|..-|..|+.-.
T Consensus 13 I~~~K~~l~ik~~H~Ekl~k-itK~p~El~~i~~kl~~~R~~FLn~~ 58 (62)
T PF06034_consen 13 INQMKRQLTIKSQHWEKLKK-ITKNPKELQEIEKKLQELRQNFLNFG 58 (62)
T ss_pred HHHHHHHHHHHHHHHHHHHh-ccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455679999999999955 56777788888899999999888543
No 78
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=51.66 E-value=38 Score=25.12 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008658 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 58 ~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (558)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+.|...|||++
T Consensus 3 ~R~~Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 3 TRLRILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 57888887665 5699999999999899999999999999999974
No 79
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=51.61 E-value=14 Score=35.75 Aligned_cols=41 Identities=27% Similarity=0.445 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHcCCCCHHHHHHHH
Q 008658 251 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKL 292 (558)
Q Consensus 251 ~~~Wt~~E~~~LLe~Ie~~g--~-----~W~~Ia~~vg~kt~~eC~~~f 292 (558)
...||.+++++|-+.|-.|+ | -...+++.+ .||...|..+|
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRw 52 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRW 52 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHH
Confidence 46799999999999999888 2 234445555 58999999999
No 80
>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=49.32 E-value=36 Score=26.18 Aligned_cols=44 Identities=23% Similarity=0.293 Sum_probs=34.9
Q ss_pred HHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccccc
Q 008658 61 FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (558)
Q Consensus 61 ~ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~ 107 (558)
.|+......+ +++.+..+.+.-....+.|+..-|...|+|+...
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3444433344 8999998888778999999999999999999643
No 81
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=48.95 E-value=28 Score=26.40 Aligned_cols=43 Identities=21% Similarity=0.316 Sum_probs=35.1
Q ss_pred HHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008658 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 62 ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (558)
|++.+...+ ..+|+++..+.+.-....+.|+..-|+.+|+|..
T Consensus 8 iL~~l~~~~-~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 8 ILEALAESG-GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHCHHCTB-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 566555554 4489999999999899999999999999999864
No 82
>COG2916 Hns DNA-binding protein H-NS [General function prediction only]
Probab=48.73 E-value=1.5e+02 Score=27.49 Aligned_cols=49 Identities=22% Similarity=0.187 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 493 EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVL 545 (558)
Q Consensus 493 eI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~ 545 (558)
-|..|...+-+++++-||-.++.|+.+.. ||+.-+..+...+.+|+.-+
T Consensus 4 n~r~l~~~~~e~~~e~lee~~ek~eq~~~----~r~~e~~~~~~~i~e~~~~~ 52 (128)
T COG2916 4 NIRTLRAMARETYLELLEEMLEKEEQVVQ----ERQEEEAAAIAEIEERQEKY 52 (128)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
Confidence 37788899999999999999988887764 45555555555555554443
No 83
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=48.11 E-value=22 Score=40.42 Aligned_cols=94 Identities=16% Similarity=0.188 Sum_probs=53.0
Q ss_pred ccCCCCCCCCCCceeeecCCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH-----HHcC
Q 008658 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV-----MRHG 270 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~I-----e~~g 270 (558)
..|.-|+.. ...+.|..-++.||..|-.--+- -.. ++... .-..||.+|...|..+= +.|-
T Consensus 24 k~CADCgs~--~P~WASiNlGIFICi~CSGIHRs-----LGh--RVKSL-----SLDkWT~EEVe~Mk~gGN~~AN~iye 89 (648)
T PLN03119 24 RRCINCNSL--GPQYVCTTFWTFVCMACSGIHRE-----FTH--RVKSV-----SMSKFTSKEVEVLQNGGNQRAREIYL 89 (648)
T ss_pred CccccCCCC--CCCceeeccceEEeccchhhhcc-----CCc--eeecc-----ccCCCCHHHHHHHHHhchHHHHHHHH
Confidence 568888875 36778888899999999644431 111 33322 23689998875443211 1222
Q ss_pred CCHHHHHHHcCCCCHHHHHHHHHc-CCcCCCCCC
Q 008658 271 DNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMG 303 (558)
Q Consensus 271 ~~W~~Ia~~vg~kt~~eC~~~fl~-LPIeD~~l~ 303 (558)
.+|..-...+...+..+-+..||+ -+++-.|..
T Consensus 90 anw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~ 123 (648)
T PLN03119 90 KNWDHQRQRLPENSNAERVREFIKNVYVQKKYAG 123 (648)
T ss_pred hhcccccCCCCCCccHHHHHHHHHHHHhhhhccC
Confidence 356543223333344555677887 344444443
No 84
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=48.08 E-value=29 Score=30.78 Aligned_cols=51 Identities=24% Similarity=0.292 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHhCCCceeeHHHHhhhcc-----chHHHHHHHHHhhhhhcccccc
Q 008658 55 YKEYRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINFG 106 (558)
Q Consensus 55 Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~-----gD~~~i~rvh~FLe~wGlIN~~ 106 (558)
.-.-|..|++....++. .+|+.+.-..|. -+..+|.|...+|+.-|||.=-
T Consensus 6 ~T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~ 61 (120)
T PF01475_consen 6 LTPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKI 61 (120)
T ss_dssp HHHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEE
Confidence 34578999998888877 999999877763 3678999999999999999843
No 85
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=46.54 E-value=47 Score=30.62 Aligned_cols=53 Identities=15% Similarity=0.370 Sum_probs=42.1
Q ss_pred hhHHHHHHHHHHHHHh---CCCcee-eHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008658 53 KIYKEYRDFMINKYRE---EPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 53 ~~Y~~~Rn~ii~~y~~---np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (558)
.+|.+|.|.|...-.. .|...| |+.+--..+.-..+.+.|.+.-||+-|+|.-
T Consensus 11 PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t 67 (125)
T COG1725 11 PIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVET 67 (125)
T ss_pred CHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 5999999999887654 666665 4555555565688999999999999999983
No 86
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=45.43 E-value=33 Score=31.08 Aligned_cols=74 Identities=15% Similarity=0.251 Sum_probs=49.0
Q ss_pred CCCCCCCCCCceeeecCCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHH
Q 008658 198 CGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVA 277 (558)
Q Consensus 198 C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia 277 (558)
|..||..+.-.+++|...+..+ .|+|... .-.--..|++.++...-+..||-++|+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i------~G~F~l~------------------~~~~L~~E~~~Fi~~Fi~~rGnlKe~e 56 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI------EGEFELP------------------WFARLSPEQLEFIKLFIKNRGNLKEME 56 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE------Eeeeccc------------------hhhcCCHHHHHHHHHHHHhcCCHHHHH
Confidence 8889999888888875533222 3433210 111235788899999999999999999
Q ss_pred HHcCC-----CCHHHHHHHHHcC
Q 008658 278 QNVPT-----KSKLDCISKLIEL 295 (558)
Q Consensus 278 ~~vg~-----kt~~eC~~~fl~L 295 (558)
+.+|- |++-+=+..=|.+
T Consensus 57 ~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 57 KELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHCCCcHHHHHHHHHHHHHhCC
Confidence 99992 5555555554443
No 87
>PLN03131 hypothetical protein; Provisional
Probab=45.24 E-value=34 Score=39.36 Aligned_cols=93 Identities=17% Similarity=0.198 Sum_probs=53.1
Q ss_pred ccCCCCCCCCCCceeeecCCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH------HHc
Q 008658 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV------MRH 269 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~I------e~~ 269 (558)
..|.-|+.. ...+.|..-++.||..|-.--+-- .. ++... .-..||++|...|- .+ +.|
T Consensus 24 k~CADCga~--~P~WASiNlGIFICi~CSGIHRsL-----gh--RVKSV-----TLD~WtdeEV~~Mk-~gGN~~AN~iy 88 (705)
T PLN03131 24 RRCINCNSL--GPQFVCTNFWTFICMTCSGIHREF-----TH--RVKSV-----SMSKFTSQDVEALQ-NGGNQRAREIY 88 (705)
T ss_pred CccccCCCC--CCCeeEeccceEEchhchhhhccc-----Cc--ccccc-----cCCCCCHHHHHHHH-HhccHHHHHHH
Confidence 468888764 367778888999999997544311 11 23222 23689998875443 22 223
Q ss_pred CCCHHHHHHHcCCCCHHHHHHHHHc-CCcCCCCCC
Q 008658 270 GDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMG 303 (558)
Q Consensus 270 g~~W~~Ia~~vg~kt~~eC~~~fl~-LPIeD~~l~ 303 (558)
-.+|..--..+...+..+-+..||+ -+++-.|+.
T Consensus 89 eanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~ 123 (705)
T PLN03131 89 LKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAG 123 (705)
T ss_pred HhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhc
Confidence 3456533333444455556677877 344444543
No 88
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=43.93 E-value=1.3e+02 Score=27.96 Aligned_cols=52 Identities=12% Similarity=0.310 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 493 EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 547 (558)
Q Consensus 493 eI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~ 547 (558)
++..-+ ..++.|+++||.+++.+.++-..|++ .+=+.++.+|..+-+.+++.
T Consensus 78 ~~~~~~-~~l~~~i~~Le~~l~~L~~~~~~l~~--~~~~~~~~~~~~~~~~~~~~ 129 (134)
T cd04779 78 EVAQEV-QLVCDQIDGLEHRLKQLKPIASQTDR--AQRMKMTKELSQQVLTLIQS 129 (134)
T ss_pred HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhcCHHhHHHHHH
Confidence 344433 45899999999999999999988877 56678888998888888764
No 89
>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=43.42 E-value=29 Score=25.32 Aligned_cols=24 Identities=25% Similarity=0.278 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHcC
Q 008658 258 ETLLLLESVMRHGDNWELVAQNVP 281 (558)
Q Consensus 258 E~~~LLe~Ie~~g~~W~~Ia~~vg 281 (558)
|-..|.++++.++||....|+.+|
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHC
Confidence 667889999999999999999999
No 90
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=42.07 E-value=22 Score=31.94 Aligned_cols=58 Identities=17% Similarity=0.264 Sum_probs=31.4
Q ss_pred ccCCCCCCCCCCceeeecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHH
Q 008658 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLES 265 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~-~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~ 265 (558)
..|.-|+.. .+.+.+..-++.||..|..--+ ++.|.+ +++ .. .-+.||.+|...|.++
T Consensus 14 ~~CaDCg~~--~p~w~s~~~GiflC~~Cag~HR~lg~~is---~Vk--Si-----~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 14 KVCADCGAP--NPTWASLNYGIFLCLECAGIHRSLGVHIS---RVK--SI-----TMDNWSPEEVQRMREG 72 (116)
T ss_dssp TB-TTT-SB--S--EEETTTTEEE-HHHHHHHHHHTTTT-----EE--ET-----TTS---HHHHHHHHHS
T ss_pred CcCCCCCCC--CCCEEEeecChhhhHHHHHHHHHhcccch---hcc--cc-----ccCCCCHHHHHHHHHH
Confidence 568888744 3477888888999999986553 444322 222 21 1246999998887654
No 91
>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=41.57 E-value=78 Score=23.28 Aligned_cols=44 Identities=27% Similarity=0.386 Sum_probs=35.6
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccc
Q 008658 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLI 103 (558)
Q Consensus 58 ~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlI 103 (558)
.+-.|++.-+.||. +|.++..+.+.-....+.|....|..-|+|
T Consensus 4 ~~~~Il~~l~~~~~--~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKILNYLRENPR--ITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHCTT--S-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 34567777777776 999999999988899999999999999997
No 92
>smart00595 MADF subfamily of SANT domain.
Probab=39.58 E-value=22 Score=29.71 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=23.1
Q ss_pred CHHHHHHHcCCCCHHHHHHHHHcCCcCCCCC
Q 008658 272 NWELVAQNVPTKSKLDCISKLIELPFGEFMM 302 (558)
Q Consensus 272 ~W~~Ia~~vg~kt~~eC~~~fl~LPIeD~~l 302 (558)
-|..||..+|. |.++|..+|-.| -+.|.
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L--R~~y~ 56 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL--RDRYR 56 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH--HHHHH
Confidence 69999999997 999999999773 34553
No 93
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=39.47 E-value=55 Score=27.97 Aligned_cols=44 Identities=30% Similarity=0.450 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHHHHHhCCCceeeHHHHh-------hhccchH---HHHHHHHHhhhhh
Q 008658 53 KIYKEYRDFMINKYREEPSRRLTFTQVR-------KSLVGDV---SLLHKVFRLLDEW 100 (558)
Q Consensus 53 ~~Y~~~Rn~ii~~y~~np~~~lt~t~~r-------~~l~gD~---~~i~rvh~FLe~w 100 (558)
++-..+||-|+.+=-.| +|+.+.. |-|+-|+ ..++|||.||.++
T Consensus 36 ~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 36 DIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKH 89 (92)
T ss_pred HHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHH
Confidence 56778999998865544 7777753 4455565 6899999999876
No 94
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=38.94 E-value=16 Score=40.37 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=39.4
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008658 250 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 294 (558)
Q Consensus 250 ~~~~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl~ 294 (558)
..-+||..|-. ++.-...|+.+...||+-+++||++|....||+
T Consensus 469 ~~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 469 INYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred ecCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 45689998887 778889999999999999999999999999986
No 95
>KOG3859 consensus Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]
Probab=38.60 E-value=2.5e+02 Score=29.76 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=41.1
Q ss_pred HHHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 008658 503 ETQMKKLHSKI-NYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKT 551 (558)
Q Consensus 503 e~QlkKLElKL-k~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~~~ 551 (558)
|..||+.|--| ..|+.|-..-..|+..||..|.+|=.|++.|.++...+
T Consensus 354 E~elke~Ekel~~kf~~lkr~h~eEk~kle~~rr~Leee~~~f~~rk~~~ 403 (406)
T KOG3859|consen 354 EAELKEAEKELHEKFDRLKRLHQEEKKKLEEKRKQLEEEVNAFQRRKTAA 403 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777666 36999999999999999999999999999998876654
No 96
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=38.28 E-value=20 Score=27.74 Aligned_cols=30 Identities=30% Similarity=0.520 Sum_probs=20.2
Q ss_pred cCCCCCCCCCCceeeecCCCcccchhhhhcC
Q 008658 197 KCGSCGEQCNSGCYEYSKGSFVICEKCFKNG 227 (558)
Q Consensus 197 ~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G 227 (558)
.|..||..++...-.-.+.+ .+|.+|+..-
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 49999999876431112233 6999999765
No 97
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=38.07 E-value=44 Score=41.08 Aligned_cols=45 Identities=16% Similarity=0.316 Sum_probs=37.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHc------------CCCCHHHHHHHHH
Q 008658 249 THGATWTEAETLLLLESVMRHG-DNWELVAQNV------------PTKSKLDCISKLI 293 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g-~~W~~Ia~~v------------g~kt~~eC~~~fl 293 (558)
..+..||.+|+..||-.+.+|| ++|+.|-+.+ .+||+.++..|..
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 4567899999999999999999 9999996644 3899998877663
No 98
>PF02841 GBP_C: Guanylate-binding protein, C-terminal domain; InterPro: IPR003191 Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) []. Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function (IPR015894 from INTERPRO), and an alpha-helical finger-like C-terminal domain. Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1DG3_A 2D4H_A 2B8W_B 2B92_A 2BC9_A 1F5N_A.
Probab=37.85 E-value=4.5e+02 Score=27.30 Aligned_cols=51 Identities=27% Similarity=0.439 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhhHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 008658 503 ETQMKKLHSKINYFDD----LELIMEKEYNEMMQLKECLVEERIDVLERALKTGV 553 (558)
Q Consensus 503 e~QlkKLElKLk~fee----LE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~~~g~ 553 (558)
..+.+.++.+-+.+++ |..-|+.||+.+.+..++++..++..-...++.|.
T Consensus 228 ~~~~~~le~~~~~~ee~~~~L~ekme~e~~~~~~e~e~~l~~k~~eq~~~l~e~~ 282 (297)
T PF02841_consen 228 KEQEQMLEQQERSYEEHIKQLKEKMEEEREQLLQEQERLLEQKLQEQEELLKEGF 282 (297)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555666655555 66668888888888888888777776666555553
No 99
>PRK09462 fur ferric uptake regulator; Provisional
Probab=37.33 E-value=51 Score=30.60 Aligned_cols=48 Identities=15% Similarity=0.251 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhcc-----chHHHHHHHHHhhhhhccccc
Q 008658 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 58 ~Rn~ii~~y~~np~~~lt~t~~r~~l~-----gD~~~i~rvh~FLe~wGlIN~ 105 (558)
-|-.|++.....+...+|+.+.-..|. -+..+|.|...+|+.-|||.=
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence 477788877766678999999876663 268999999999999999973
No 100
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=36.24 E-value=59 Score=28.41 Aligned_cols=46 Identities=22% Similarity=0.275 Sum_probs=38.2
Q ss_pred HHHHHHHHHhCCCceeeHHHHhhhcc-----chHHHHHHHHHhhhhhccccc
Q 008658 59 RDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 59 Rn~ii~~y~~np~~~lt~t~~r~~l~-----gD~~~i~rvh~FLe~wGlIN~ 105 (558)
|-.|++..... ...+|+.+.-..|. -+..++.|...+|..-|||.-
T Consensus 3 R~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 3 RLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 67788877665 58899999877773 378999999999999999984
No 101
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=35.11 E-value=27 Score=25.70 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=18.8
Q ss_pred ccCCCCCCCCCCc-eeeecCCCcccchhhhhc
Q 008658 196 FKCGSCGEQCNSG-CYEYSKGSFVICEKCFKN 226 (558)
Q Consensus 196 ~~C~~C~~~~~~~-~y~~~k~~~~lC~~Cf~~ 226 (558)
..|++||+.-+.+ .+.....+..+|..|...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 5799999998776 344334478899999653
No 102
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=34.63 E-value=98 Score=24.98 Aligned_cols=50 Identities=14% Similarity=0.088 Sum_probs=44.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccccc
Q 008658 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (558)
Q Consensus 58 ~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~ 107 (558)
.++.|+.....++..-+|..+.-+.|.-+...+.|+..=|+.-|+|.+..
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 57889998888876679999999999889999999999999999998754
No 103
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=33.97 E-value=28 Score=42.96 Aligned_cols=28 Identities=25% Similarity=0.767 Sum_probs=26.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHH
Q 008658 249 THGATWTEAETLLLLESVMRHG-DNWELV 276 (558)
Q Consensus 249 ~~~~~Wt~~E~~~LLe~Ie~~g-~~W~~I 276 (558)
..+..|..+++..||-||-+|| |+|+.|
T Consensus 1131 ~~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1131 SWDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred CcccCCCchhhhhHhhhhhhcccccHHHh
Confidence 3678999999999999999999 999998
No 104
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=33.97 E-value=44 Score=35.56 Aligned_cols=98 Identities=16% Similarity=0.127 Sum_probs=54.4
Q ss_pred CccCCCCCCCCCCceeeecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCH
Q 008658 195 GFKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNW 273 (558)
Q Consensus 195 ~~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~-~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g~~W 273 (558)
-..|.-||..- -.| -...-++.||.+|-.--+ .|.|.+ |++ .. .-+.||.+|..+|.-+=...-..|
T Consensus 20 Nk~CaDCga~~-P~W-~S~nlGvfiCi~CagvHRsLGvhiS---~VK--Si-----tLD~wt~~~l~~m~~gGN~~a~~~ 87 (319)
T COG5347 20 NKKCADCGAPN-PTW-ASVNLGVFLCIDCAGVHRSLGVHIS---KVK--SL-----TLDNWTEEELRRMEVGGNSNANRF 87 (319)
T ss_pred cCccccCCCCC-Cce-EecccCeEEEeecchhhhcccccee---eee--ee-----ecccCCHHHHHHHHHhcchhhhhH
Confidence 35798888875 334 333467899999976554 343332 222 21 235799999887765211111233
Q ss_pred HHHHH---H-cC--CCCHHHHHHHHHc-CCcCCCCCCC
Q 008658 274 ELVAQ---N-VP--TKSKLDCISKLIE-LPFGEFMMGS 304 (558)
Q Consensus 274 ~~Ia~---~-vg--~kt~~eC~~~fl~-LPIeD~~l~~ 304 (558)
.+--- + +. .+.-...+.+|++ ++..-.|...
T Consensus 88 ~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 88 YEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 32211 1 12 3566678888876 5555555543
No 105
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=33.94 E-value=5.4e+02 Score=27.22 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 500 IIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 547 (558)
Q Consensus 500 ~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~ 547 (558)
.-++.|+++++..++.+++.|..+.+++..+.....++..+|.++..+
T Consensus 74 ~~l~~el~~le~e~~~l~~eE~~~~~~~n~~~~~l~~~~~e~~sl~~q 121 (314)
T PF04111_consen 74 EELDQELEELEEELEELDEEEEEYWREYNELQLELIEFQEERDSLKNQ 121 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999999999999999999999888888777644
No 106
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=33.53 E-value=3.6e+02 Score=30.33 Aligned_cols=50 Identities=22% Similarity=0.286 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH------HHHHHHHHHHHHHHHHHHHHHHH
Q 008658 482 NAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDD------LELIMEKEYNEMMQLKECLVEER 541 (558)
Q Consensus 482 kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~fee------LE~~me~Er~~LE~~Rq~L~~eR 541 (558)
.|--.|.+.|++| |+.|-||||..+.| ||++|.-||+.-...+.+|-.||
T Consensus 514 va~dnar~qekQi----------q~Ek~ELkmd~lrerelreslekql~~ErklR~~~qkr~kkEk 569 (641)
T KOG3915|consen 514 VAIDNARAQEKQI----------QLEKTELKMDFLRERELRESLEKQLAMERKLRAIVQKRLKKEK 569 (641)
T ss_pred HHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334445555554 57888888888765 55555555555444444454454
No 107
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=33.49 E-value=52 Score=34.91 Aligned_cols=53 Identities=19% Similarity=0.281 Sum_probs=47.2
Q ss_pred ChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccc
Q 008658 51 TPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLIN 104 (558)
Q Consensus 51 tp~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN 104 (558)
.|..|+.+.--||..+.. ....+|.++|++.+.-|..-.-+|+.|.-.-|.|-
T Consensus 377 ~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 377 SPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred CCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 689999999999999885 45789999999998889999999999998888874
No 108
>PHA00442 host recBCD nuclease inhibitor
Probab=33.38 E-value=44 Score=26.39 Aligned_cols=25 Identities=24% Similarity=0.387 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHc
Q 008658 256 EAETLLLLESVMRHG-DNWELVAQNV 280 (558)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~~W~~Ia~~v 280 (558)
-+-....|++++..| +||..+.+.+
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 345668899999999 9999987654
No 109
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=32.82 E-value=2.9e+02 Score=30.59 Aligned_cols=63 Identities=27% Similarity=0.315 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 008658 485 LLADQEDREIEHLVAIIIETQ--MKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSK 555 (558)
Q Consensus 485 ~LA~~EEreI~~Lv~~lIe~Q--lkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~~~g~~~ 555 (558)
.|+++| .+|.++-..|++++ ++|++-+|...+.-...++.++ +.|..++.+-++.+ .++|..+
T Consensus 67 ~lk~~e-~~i~~~~~ql~~s~~~l~~~~~~I~~~~~~l~~l~~q~----r~qr~~La~~L~A~---~r~g~~p 131 (420)
T COG4942 67 QLKSLE-TEIASLEAQLIETADDLKKLRKQIADLNARLNALEVQE----REQRRRLAEQLAAL---QRSGRNP 131 (420)
T ss_pred HHHHHH-HHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH---HhccCCC
Confidence 344444 78999998888876 4666666655444433333333 55566666655544 5566544
No 110
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=32.60 E-value=1.9e+02 Score=23.75 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=32.9
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 506 MKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 547 (558)
Q Consensus 506 lkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~ 547 (558)
|+.|+.|+.++=.+=.-+..|-..|-.+-..+-.||..++..
T Consensus 2 L~~Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ek 43 (65)
T TIGR02449 2 LQALAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEK 43 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567778887777777777788888888888888888777654
No 111
>PRK11546 zraP zinc resistance protein; Provisional
Probab=32.24 E-value=4.4e+02 Score=24.92 Aligned_cols=69 Identities=13% Similarity=0.199 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HhhHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 008658 486 LADQEDREIEHLVAIIIETQMKKLHSK-INYFDDLELI----------MEKEYNEMMQLKECLVEERIDVLERALKTGVS 554 (558)
Q Consensus 486 LA~~EEreI~~Lv~~lIe~QlkKLElK-Lk~feeLE~~----------me~Er~~LE~~Rq~L~~eR~~~~~~~~~~g~~ 554 (558)
|-...-.+++.|...-... +..|..+ ...=.||..+ +..-.+++...|++|+.+|+.+-.+..+.||+
T Consensus 44 LT~EQQa~~q~I~~~f~~~-t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~~~~~~~~k~Gv~ 122 (143)
T PRK11546 44 LTTEQQAAWQKIHNDFYAQ-TSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRVKRDIAMAEAGIP 122 (143)
T ss_pred CCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 4444445555555544332 3323222 2333455544 45567889999999999999999999999998
Q ss_pred C
Q 008658 555 K 555 (558)
Q Consensus 555 ~ 555 (558)
.
T Consensus 123 ~ 123 (143)
T PRK11546 123 R 123 (143)
T ss_pred c
Confidence 4
No 112
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=32.03 E-value=1.2e+02 Score=25.67 Aligned_cols=55 Identities=15% Similarity=0.186 Sum_probs=45.1
Q ss_pred hhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccC
Q 008658 53 KIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (558)
Q Consensus 53 ~~Y~~~Rn~ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~ 108 (558)
++-.+|=..||+.|... .+.+.-.+.-+.|.-+.+.|..+..-|+..|||-=+.-
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~ 58 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPH 58 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCC
Confidence 45677888999999976 67888888777776688999999999999999974433
No 113
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=31.46 E-value=5e+02 Score=31.10 Aligned_cols=39 Identities=18% Similarity=0.218 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 502 IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEE 540 (558)
Q Consensus 502 Ie~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~e 540 (558)
++.+...++..++..+++..-++.+++.|+..|.+++.+
T Consensus 527 ~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~~ 565 (771)
T TIGR01069 527 LEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLE 565 (771)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555666667777777777777777777777766644
No 114
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=31.41 E-value=74 Score=28.33 Aligned_cols=83 Identities=22% Similarity=0.257 Sum_probs=46.9
Q ss_pred ccCCCCCCCCCCceeeecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CCH
Q 008658 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DNW 273 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~-~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~LLe~Ie~~g-~~W 273 (558)
..|.-|+.. .+.+.+..-+..||..|-.--+ ++.|.+ +++ .. .-..||.+|...| +..| ..+
T Consensus 4 ~~CaDC~~~--~p~w~s~~~GifvC~~CsgiHR~lg~his---~Vk--Sl-----~md~w~~~~i~~~----~~~GN~~~ 67 (112)
T smart00105 4 KKCFDCGAP--NPTWASVNLGVFLCIECSGIHRSLGVHIS---KVR--SL-----TLDTWTEEELRLL----QKGGNENA 67 (112)
T ss_pred CcccCCCCC--CCCcEEeccceeEhHHhHHHHHhcCCCcC---eee--ec-----ccCCCCHHHHHHH----HHhhhHHH
Confidence 358888773 4667777788999999976554 343321 222 21 2347999886433 3334 233
Q ss_pred HHHHHHcC--------CCCHHHHHHHHHc
Q 008658 274 ELVAQNVP--------TKSKLDCISKLIE 294 (558)
Q Consensus 274 ~~Ia~~vg--------~kt~~eC~~~fl~ 294 (558)
+.+=+.-+ ..+..+-...||+
T Consensus 68 n~~~e~~~~~~~~~~~~~~~~~~~~~fI~ 96 (112)
T smart00105 68 NSIWESNLDDFSLKPPDSDDQQKYESFIA 96 (112)
T ss_pred HHHHHhhCCccccCCCCCchHHHHHHHHH
Confidence 33322111 1224678888877
No 115
>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]
Probab=31.31 E-value=4.5e+02 Score=24.71 Aligned_cols=54 Identities=24% Similarity=0.356 Sum_probs=33.7
Q ss_pred HHHHHHHHHH------HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 492 REIEHLVAII------IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERAL 549 (558)
Q Consensus 492 reI~~Lv~~l------Ie~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~ 549 (558)
++|..||..| .+.|++| |+.+++=-.....|++.+....+.|+..=+..+....
T Consensus 70 kqId~LIdsLP~~~~~~e~Ql~~----i~kLq~en~e~~~el~~~v~~~e~Ll~~vq~~le~~a 129 (139)
T KOG1510|consen 70 KQIDTLIDSLPGEEGSAEAQLEK----IKKLQEENEEVALELEELVSKGEKLLEQVQSLLEDIA 129 (139)
T ss_pred HHHHHHHHhCCCcccCHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7888888876 6778777 2333333334556677777777777666555554443
No 116
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=31.31 E-value=82 Score=26.03 Aligned_cols=43 Identities=26% Similarity=0.401 Sum_probs=34.5
Q ss_pred HHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008658 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 62 ii~~y~~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (558)
|++....++ ..+|+++.-+.+.-....+.|....|+.+|+|-.
T Consensus 10 Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 10 VLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeee
Confidence 344333332 4799999999998899999999999999999965
No 117
>PF01608 I_LWEQ: I/LWEQ domain; InterPro: IPR002558 I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin P26039 from SWISSPROT and yeast Sla2p P33338 from SWISSPROT interact with F-actin []. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks []. I/LWEQ domains can be placed into four major groups based on sequence similarity: Metazoan talin. Dictyostelium discoideum (Slime mould) TalA/TalB P54633 from SWISSPROT and SLA110. Metazoan Hip1p O00291 from SWISSPROT. Saccharomyces cerevisiae Sla2p P33338 from SWISSPROT. ; GO: 0003779 actin binding; PDB: 2QDQ_A 2JSW_A 1R0D_B.
Probab=31.16 E-value=4.1e+02 Score=25.38 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 008658 518 DLELIMEKEYNEMMQLKECLVE 539 (558)
Q Consensus 518 eLE~~me~Er~~LE~~Rq~L~~ 539 (558)
+||+-|+.+|+.|-..|..-|.
T Consensus 129 ~lE~eLe~ar~kL~~lRk~~Y~ 150 (152)
T PF01608_consen 129 KLEKELEKARKKLAELRKAHYH 150 (152)
T ss_dssp HHHHHHHHHHHHHHHHHHH---
T ss_pred HHHHHHHHHHHHHHHHHHHHcC
Confidence 5788888888888888876543
No 118
>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=31.01 E-value=75 Score=24.18 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=33.6
Q ss_pred eeHHHHhhhccchHHHHHHHHHhhhhhcccccccCCC
Q 008658 74 LTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (558)
Q Consensus 74 lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~~~ 110 (558)
+|.++.-+.+.-+...+.|+..-|++.|||.-..++.
T Consensus 18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 9999999999999999999999999999999888874
No 119
>PRK06474 hypothetical protein; Provisional
Probab=28.65 E-value=1e+02 Score=29.81 Aligned_cols=50 Identities=14% Similarity=0.083 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccc-hHHHHHHHHHhhhhhcccccccC
Q 008658 58 YRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFRLLDEWGLINFGAV 108 (558)
Q Consensus 58 ~Rn~ii~~y~~np~~~lt~t~~r~~l~g-D~~~i~rvh~FLe~wGlIN~~~~ 108 (558)
.|-.|+..-..++. .+|++++...+.+ ....+.|....|+..|||.--..
T Consensus 12 ~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 12 VRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred HHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 68889987777654 4999999888743 56899999999999999995433
No 120
>PF07956 DUF1690: Protein of Unknown function (DUF1690) ; InterPro: IPR012471 Family of uncharacterised fungal proteins.
Probab=28.10 E-value=1.3e+02 Score=28.32 Aligned_cols=57 Identities=19% Similarity=0.307 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH-HHHHHHHHHHHHH
Q 008658 483 AKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKE-YNEMMQLKECLVE 539 (558)
Q Consensus 483 Ak~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~E-r~~LE~~Rq~L~~ 539 (558)
+..+++.+..+-..|....++..+.+|.-||..|..|+..-... ...++..|..|..
T Consensus 61 ~~~~~ed~~~~~~~lSs~~v~~~i~~L~~kLe~~~kl~~~~~~~~~~~v~~aR~~vv~ 118 (142)
T PF07956_consen 61 KSLLSEDEKDQDPGLSSKSVNEEIEKLREKLEERKKLRELKEEKNSEEVEKARSAVVR 118 (142)
T ss_pred HhhcccccccccccccHHHHHHHHHHHHHHHHHHHHHHhccccccchhhHHHHHHHHH
Confidence 33455455666788999999999999999999887776554432 4466778877754
No 121
>KOG3564 consensus GTPase-activating protein [General function prediction only]
Probab=27.27 E-value=2.9e+02 Score=31.23 Aligned_cols=63 Identities=21% Similarity=0.131 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 008658 492 REIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKW 556 (558)
Q Consensus 492 reI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~~~g~~~~ 556 (558)
++++.+++. -++.+--|+.||+|=...=...-++|+++|--++. +..|+++++.+++-|+..+
T Consensus 52 ~~~~~~L~K-a~tk~~~ldvklkha~~~vda~ik~rr~ae~d~~~-~E~~i~~i~d~l~~~~~~s 114 (604)
T KOG3564|consen 52 GKYKDLLAK-AETKRSALDVKLKHARNQVDAEIKRRRRAEADCEK-LETQIQLIKDMLKCDISGS 114 (604)
T ss_pred HHHHHHHHH-HHHhhhhccchHHHHHHHHHHHHHHHHHHhhhHHH-HHHHHHHHHHHHhcccccc
Confidence 344444433 24667778999999877666666777777777654 4668889999999888654
No 122
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=27.11 E-value=93 Score=29.04 Aligned_cols=52 Identities=17% Similarity=0.232 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhCCCceeeHHHHhhhccc-----hHHHHHHHHHhhhhhcccccccCC
Q 008658 57 EYRDFMINKYREEPSRRLTFTQVRKSLVG-----DVSLLHKVFRLLDEWGLINFGAVS 109 (558)
Q Consensus 57 ~~Rn~ii~~y~~np~~~lt~t~~r~~l~g-----D~~~i~rvh~FLe~wGlIN~~~~~ 109 (558)
.=|-.|++.....+. ++|+.+.-+.|.. ....+.|+..||+.-|||+-....
T Consensus 21 ~qR~~vl~~L~~~~~-~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~ 77 (145)
T COG0735 21 PQRLAVLELLLEADG-HLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFE 77 (145)
T ss_pred HHHHHHHHHHHhcCC-CCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeC
Confidence 347788886665544 4999998766642 379999999999999999966664
No 123
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=26.93 E-value=87 Score=29.19 Aligned_cols=39 Identities=13% Similarity=0.145 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008658 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (558)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl~L 295 (558)
++-+..||+.+++-| -.|..||+.+|. |+..|..++-+|
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL 47 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKM 47 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 456889999999999 799999999995 999999998664
No 124
>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=26.90 E-value=1.4e+02 Score=23.10 Aligned_cols=42 Identities=17% Similarity=0.211 Sum_probs=33.9
Q ss_pred CCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccCCC
Q 008658 69 EPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (558)
Q Consensus 69 np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~~~ 110 (558)
+....+|.++..+.+.-|...+.|+..=|...|||.-..++.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 478899999999999999999999999999999998777763
No 125
>PF15346 ARGLU: Arginine and glutamate-rich 1
Probab=26.38 E-value=5.7e+02 Score=24.35 Aligned_cols=83 Identities=19% Similarity=0.260 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 008658 467 RIRTATATALGAAAANAKLLADQEDR----------EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKEC 536 (558)
Q Consensus 467 ~v~~Aaa~AL~aAA~kAk~LA~~EEr----------eI~~Lv~~lIe~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~ 536 (558)
-|+.-+...|++-.+.+.+..-.++- +|.+=-...++-.=.|-+-.-+.-++||.+|+.-++.++..++.
T Consensus 19 ~V~krVee~l~~eei~~ei~rRvee~r~~me~~v~~ele~ek~~~l~e~r~keEeer~~~eELe~ileen~rkvEEAQrk 98 (149)
T PF15346_consen 19 AVRKRVEEELNSEEIEKEIQRRVEEERKKMEKQVAEELEREKEEALEEARRKEEEERKKREELEKILEENRRKVEEAQRK 98 (149)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666555555555544432 22222333344444556677788899999999999999999999
Q ss_pred HHHHHHHHHHHHH
Q 008658 537 LVEERIDVLERAL 549 (558)
Q Consensus 537 L~~eR~~~~~~~~ 549 (558)
+-.+|++.+-.-.
T Consensus 99 ~aeEr~~~~Eer~ 111 (149)
T PF15346_consen 99 LAEERLRMEEERR 111 (149)
T ss_pred HHHHHHHHHHHHH
Confidence 9999988865443
No 126
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=26.17 E-value=48 Score=27.56 Aligned_cols=31 Identities=16% Similarity=0.468 Sum_probs=21.3
Q ss_pred CceeeHHHHhhhc--cc-hHHHHHHHHHhhhhhc
Q 008658 71 SRRLTFTQVRKSL--VG-DVSLLHKVFRLLDEWG 101 (558)
Q Consensus 71 ~~~lt~t~~r~~l--~g-D~~~i~rvh~FLe~wG 101 (558)
++.++-.+-+..- +| |..-|--|-.||.+||
T Consensus 46 neeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 46 NEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred cHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 4555544433222 35 8888899999999999
No 127
>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=26.08 E-value=49 Score=24.13 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=8.6
Q ss_pred CCCCCCCCCCc
Q 008658 198 CGSCGEQCNSG 208 (558)
Q Consensus 198 C~~C~~~~~~~ 208 (558)
|+.||..+...
T Consensus 1 Cd~CG~~I~~e 11 (37)
T PF08394_consen 1 CDYCGGEITGE 11 (37)
T ss_pred CCccCCcccCC
Confidence 78899888753
No 128
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=25.57 E-value=2.8e+02 Score=26.36 Aligned_cols=32 Identities=22% Similarity=0.671 Sum_probs=23.4
Q ss_pred cCCCCCCCCCCceeee--cCCCcccchhhhhcCC
Q 008658 197 KCGSCGEQCNSGCYEY--SKGSFVICEKCFKNGN 228 (558)
Q Consensus 197 ~C~~C~~~~~~~~y~~--~k~~~~lC~~Cf~~G~ 228 (558)
.|-.||..+...-|.- ......+|..|+.=|.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECRKFGK 35 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHHhcCC
Confidence 4999999987663222 2256789999997776
No 129
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=25.24 E-value=4.2e+02 Score=22.90 Aligned_cols=49 Identities=14% Similarity=0.206 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHh
Q 008658 502 IETQMKKLHSKINYFDDLELIMEKEYNEMM----QLKECLVEERIDVLERALK 550 (558)
Q Consensus 502 Ie~QlkKLElKLk~feeLE~~me~Er~~LE----~~Rq~L~~eR~~~~~~~~~ 550 (558)
++.++++.+.||.+.++=+++++.-...|+ +.|-.-|..|-.++...+.
T Consensus 6 l~~e~e~~~~kl~q~e~~~k~L~nr~k~l~k~eRK~RtHRLi~rGa~lEsi~~ 58 (86)
T PF12958_consen 6 LQAEIEKAEKKLEQAEHKIKQLENRKKKLEKKERKERTHRLIERGAILESIFP 58 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHhh
Confidence 467788888888888888888888888774 6677777777777665543
No 130
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=25.12 E-value=7.1e+02 Score=29.89 Aligned_cols=39 Identities=15% Similarity=0.283 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 502 IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEE 540 (558)
Q Consensus 502 Ie~QlkKLElKLk~feeLE~~me~Er~~LE~~Rq~L~~e 540 (558)
++....+++..++..+++..-++++++.|++.|+.++.+
T Consensus 532 ~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~~ 570 (782)
T PRK00409 532 LEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEE 570 (782)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566666666666666777776666666665544
No 131
>cd07671 F-BAR_PSTPIP1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 1. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proline-Serine-Threonine Phosphatase-Interacting Protein 1 (PSTPIP1), also known as CD2 Binding Protein 1 (CD2BP1), is mainly expressed in hematopoietic cells. It is a binding partner of the cell surface receptor CD2 and PTP-PEST, a tyrosine phosphatase which functions in cell motility and Rac1 regulation. It also plays a role in the activation of the Wiskott-Aldrich syndrome protein (WASP), which couples actin rearrangement and T cell activation. Mutations in the gene encoding PSTPIP1 cause the autoinflammatory disorder known as PAPA (pyogenic sterile arthritis, pyoderma gangrenosum, and acne) syndrome. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain. F-BAR
Probab=24.86 E-value=4.9e+02 Score=26.47 Aligned_cols=53 Identities=21% Similarity=0.137 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHHhh------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 497 LVAIIIETQMKKLHSKINY------------------FDDLELIMEKEYNEMMQLKECLVEERIDVLERAL 549 (558)
Q Consensus 497 Lv~~lIe~QlkKLElKLk~------------------feeLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~ 549 (558)
.....-..|++|++.|++. +++.=...+++-...=..=|+|=.+|+.|+|.++
T Consensus 146 ~~~~~t~keleK~~~K~~k~~~~~~~a~~~Y~~~v~~l~~~~~~w~~~~~~~~~~~Q~lEeeRi~f~K~~l 216 (242)
T cd07671 146 SSSTGNPKQSEKSQNKAKQCRDAATEAERVYKQNIEQLDKARTEWETEHILTCEVFQLQEDDRITILRNAL 216 (242)
T ss_pred HhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334455678888888877 3344444445555555556777788999998765
No 132
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=24.78 E-value=1.2e+02 Score=23.41 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=23.2
Q ss_pred CceeeHHHHhhhcc----chHHHHHHHHHhh
Q 008658 71 SRRLTFTQVRKSLV----GDVSLLHKVFRLL 97 (558)
Q Consensus 71 ~~~lt~t~~r~~l~----gD~~~i~rvh~FL 97 (558)
..++|..+....|. .+...+.||.+||
T Consensus 20 ~~~ls~~eia~~l~~~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 20 GGPLSLSEIAARLPTSNPSAPPMLDRIMRLL 50 (51)
T ss_dssp TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence 58999999988887 7889999999998
No 133
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=24.38 E-value=1.8e+02 Score=20.95 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=30.9
Q ss_pred ceeeHHHHhhhccchHHHHHHHHHhhhhhcccccc
Q 008658 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (558)
Q Consensus 72 ~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~ 106 (558)
..+|+.+..+.+.-....+.|....|+.-|+|-..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35899999999988999999999999999999743
No 134
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=24.35 E-value=1.4e+02 Score=32.11 Aligned_cols=32 Identities=28% Similarity=0.468 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Q 008658 516 FDDLELIMEKEYNEMM----QLKECLVEERIDVLER 547 (558)
Q Consensus 516 feeLE~~me~Er~~LE----~~Rq~L~~eR~~~~~~ 547 (558)
+..||.-+.+|..+|| ++++-||..|..++..
T Consensus 53 ~~~le~ef~~ev~~LE~kY~~~~~Ply~kR~eII~G 88 (337)
T PTZ00007 53 FDDLEVEYNAELRKLRSKYEDLYNPIYDKRKEALVQ 88 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHcC
Confidence 3455666667777777 5778899999999863
No 135
>PRK14139 heat shock protein GrpE; Provisional
Probab=24.14 E-value=1.3e+02 Score=29.47 Aligned_cols=15 Identities=0% Similarity=0.098 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHH
Q 008658 516 FDDLELIMEKEYNEM 530 (558)
Q Consensus 516 feeLE~~me~Er~~L 530 (558)
|+.+=+-+++|++.+
T Consensus 62 feN~rKR~~kE~e~~ 76 (185)
T PRK14139 62 TENVRRRAQEDVAKA 76 (185)
T ss_pred HHHHHHHHHHHHHHH
Confidence 333333444444443
No 136
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=24.02 E-value=17 Score=28.95 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.5
Q ss_pred ccCCCCCCCCCCceeeec
Q 008658 196 FKCGSCGEQCNSGCYEYS 213 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~ 213 (558)
..|+.||.|++..+|+..
T Consensus 5 lVCsTCGrDlSeeRy~Ll 22 (63)
T PHA03082 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCcchhHHHHHHH
Confidence 579999999999998754
No 137
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=23.71 E-value=72 Score=29.25 Aligned_cols=38 Identities=16% Similarity=0.072 Sum_probs=26.8
Q ss_pred CceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccC
Q 008658 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (558)
Q Consensus 71 ~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~ 108 (558)
.+|||..+......-+-..+.+|.+||...||=...+.
T Consensus 45 gk~Lt~~e~~~~~~p~~~~v~~V~~wL~~~G~~~~~~~ 82 (143)
T PF09286_consen 45 GKYLTPEEFAALFAPSPEDVAAVKSWLKSHGLTVVEVS 82 (143)
T ss_dssp T----HHHHHHHHS--HHHHHHHHHHHHHCT-EEEEEE
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCceeEEe
Confidence 68999999999999888999999999999998555533
No 138
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.56 E-value=21 Score=28.45 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.3
Q ss_pred ccCCCCCCCCCCceeeec
Q 008658 196 FKCGSCGEQCNSGCYEYS 213 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~ 213 (558)
..|+.||.|++..+|...
T Consensus 5 lvCSTCGrDlSeeRy~Ll 22 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCCcchHHHHHHH
Confidence 579999999999988653
No 139
>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=23.47 E-value=1.2e+02 Score=23.06 Aligned_cols=52 Identities=19% Similarity=0.307 Sum_probs=36.6
Q ss_pred hhHHHHHHHHHHHHHhCCCcee-eHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008658 53 KIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (558)
Q Consensus 53 ~~Y~~~Rn~ii~~y~~np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (558)
++|-.|++.|+..-. .+...+ |..+..+.+.-....+.++..=|+..|+|-.
T Consensus 5 ~~~~~i~~~i~~~~~-~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 5 QIADQLREAILSGEL-KPGDRLPSERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred HHHHHHHHHHHcCCC-CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 456666666655422 333344 4888777776678999999999999999854
No 140
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=22.68 E-value=1.3e+02 Score=29.91 Aligned_cols=77 Identities=16% Similarity=0.316 Sum_probs=47.4
Q ss_pred CCccCCCCCCCCCCceeeecC---------------------CCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCC
Q 008658 194 KGFKCGSCGEQCNSGCYEYSK---------------------GSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGA 252 (558)
Q Consensus 194 ~~~~C~~C~~~~~~~~y~~~k---------------------~~~~lC~~Cf~~G~~~~~~s~~df~~~~~~~~~~~~~~ 252 (558)
+...|..|++......++... -.+.+|++|.-... ..||.
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~------~~~F~------------- 64 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF------EEDFE------------- 64 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc------ccccc-------------
Confidence 467899999887765544432 12468888863332 12232
Q ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHH
Q 008658 253 TWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLI 293 (558)
Q Consensus 253 ~Wt~~E~~~LLe~Ie~~g~~W~~Ia~~vg~kt~~eC~~~fl 293 (558)
..+..+...|.+.|.. .|... ++-|.||.++-+..|.
T Consensus 65 ~l~~~~~~~i~~~i~~---~~~~~-~~~~~Rt~~~ai~~Yk 101 (214)
T PF09986_consen 65 KLSPEQKEKIKENISS---RWKPR-DFSGERTLEEAIESYK 101 (214)
T ss_pred cCCHHHHHHHHHHHHh---hcccC-CCCCCCCHHHHHHHHH
Confidence 3455666666666554 46555 6666789988888774
No 141
>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=22.63 E-value=1.1e+02 Score=21.85 Aligned_cols=31 Identities=19% Similarity=0.319 Sum_probs=22.7
Q ss_pred ccCCCCCCCCCCceeeecCCCcccchhhhhcCC
Q 008658 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN 228 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~ 228 (558)
..|..|... ...|.|..-+..+|..|+..+.
T Consensus 4 ~~C~~H~~~--~~~~~C~~C~~~~C~~C~~~~H 34 (42)
T PF00643_consen 4 PKCPEHPEE--PLSLFCEDCNEPLCSECTVSGH 34 (42)
T ss_dssp SB-SSTTTS--BEEEEETTTTEEEEHHHHHTST
T ss_pred ccCccCCcc--ceEEEecCCCCccCccCCCCCC
Confidence 457666643 2578888888899999999884
No 142
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=22.42 E-value=69 Score=26.47 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHcCC
Q 008658 256 EAETLLLLESVMRHGDNWELVAQNVPT 282 (558)
Q Consensus 256 ~~E~~~LLe~Ie~~g~~W~~Ia~~vg~ 282 (558)
-++..+||+. |.||..+|+++|-
T Consensus 2 r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 2 RERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred HHHHHHHhCC----CCCHHHHHHHcCc
Confidence 3566678887 9999999999985
No 143
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=22.02 E-value=81 Score=30.48 Aligned_cols=32 Identities=22% Similarity=0.638 Sum_probs=22.7
Q ss_pred cCCCCCCCCCCce-eeecCCCcccchhhhhcCC
Q 008658 197 KCGSCGEQCNSGC-YEYSKGSFVICEKCFKNGN 228 (558)
Q Consensus 197 ~C~~C~~~~~~~~-y~~~k~~~~lC~~Cf~~G~ 228 (558)
.|-.||..+.... +.-......+|..|+.-|.
T Consensus 5 ~CEiCG~~i~~~~~v~vegsel~VC~~Cak~G~ 37 (165)
T COG1813 5 GCELCGREIDKPIKVKVEGAELTVCDDCAKFGT 37 (165)
T ss_pred ceeccccccCCCeeEEeecceeehhHHHHHhcc
Confidence 3999999988432 2222367889999996664
No 144
>cd07672 F-BAR_PSTPIP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proline-Serine-Threonine Phosphatase-Interacting Protein 2 (PSTPIP2), also known as Macrophage Actin-associated tYrosine Phosphorylated protein (MAYP), is mostly expressed in hematopoietic cells but is also expressed in the brain. It is involved in regulating cell adhesion and motility. Mutations in the gene encoding murine PSTPIP2 can cause autoinflammatory disorders such as chronic multifocal osteomyelitis and macrophage autoinflammatory disease. PSTPIP2 contains an N-terminal F-BAR domain and lacks the PEST motifs and SH3 domain that are found in PSTPIP1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They ca
Probab=21.98 E-value=5.8e+02 Score=25.88 Aligned_cols=48 Identities=23% Similarity=0.170 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhhHH------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008658 502 IETQMKKLHSKINYFD------------------DLELIMEKEYNEMMQLKECLVEERIDVLERAL 549 (558)
Q Consensus 502 Ie~QlkKLElKLk~fe------------------eLE~~me~Er~~LE~~Rq~L~~eR~~~~~~~~ 549 (558)
-..|++|++.||++-. +.=...+++....-+.=|+|=.||+.|+|.++
T Consensus 152 ~~ke~~K~~~Kl~K~~~~~~k~~~~Y~~~v~~l~~~~~~w~~~~~~~c~~fq~lEeeRi~f~k~~l 217 (240)
T cd07672 152 NVKQQEKLFAKLAQSKQNAEDADRLYMQNISVLDKIREDWQKEHVKACEFFEKQECERINFFRNAV 217 (240)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567888888887322 22122333333444445677788999998875
No 145
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=21.46 E-value=86 Score=26.33 Aligned_cols=26 Identities=35% Similarity=0.487 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHcCC
Q 008658 256 EAETLLLLESVMRHGDNWELVAQNVPT 282 (558)
Q Consensus 256 ~~E~~~LLe~Ie~~g~~W~~Ia~~vg~ 282 (558)
.+|..+||..= .-|.||...|.++|-
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~LG~ 27 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGELGY 27 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHcCC
Confidence 46777888521 346899999999995
No 146
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=21.35 E-value=1.4e+02 Score=33.11 Aligned_cols=55 Identities=18% Similarity=0.299 Sum_probs=35.4
Q ss_pred ccCCCCCCCCCCceeeecCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHH
Q 008658 196 FKCGSCGEQCNSGCYEYSKGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLL 262 (558)
Q Consensus 196 ~~C~~C~~~~~~~~y~~~k~~~~lC~~Cf~~G~-~~~~~s~~df~~~~~~~~~~~~~~~Wt~~E~~~L 262 (558)
..|.-|+..- +-.-...-++.||.+|-..-+ .|-|.+ |++-.. .+. ||-.+...+
T Consensus 24 KvCFDCgAkn--PtWaSVTYGIFLCiDCSAvHRnLGVHiS---FVRSTn------LDs-Ws~~qLR~M 79 (454)
T KOG0706|consen 24 KVCFDCGAKN--PTWASVTYGIFLCIDCSAVHRNLGVHIS---FVRSTN------LDS-WSWEQLRRM 79 (454)
T ss_pred ceecccCCCC--CCceeecceEEEEEecchhhhccccceE---EEeecc------ccc-CCHHHHhHh
Confidence 5688888763 222223357899999988774 577765 666432 233 998876543
No 147
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=21.23 E-value=1.2e+02 Score=28.55 Aligned_cols=39 Identities=15% Similarity=0.234 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008658 256 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 295 (558)
Q Consensus 256 ~~E~~~LLe~Ie~~g-~~W~~Ia~~vg~kt~~eC~~~fl~L 295 (558)
++-+.++|..++.-| -.|.+||+.||- |+..|..++-+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 667889999999999 799999999995 888898888653
No 148
>PRK14161 heat shock protein GrpE; Provisional
Probab=20.88 E-value=7.1e+02 Score=24.27 Aligned_cols=17 Identities=24% Similarity=0.245 Sum_probs=7.5
Q ss_pred hhHHHHHHHHHHHHHHH
Q 008658 514 NYFDDLELIMEKEYNEM 530 (558)
Q Consensus 514 k~feeLE~~me~Er~~L 530 (558)
.-|+.+-+-+++|+++.
T Consensus 47 AefeN~rkR~~ke~~~~ 63 (178)
T PRK14161 47 AEIDNTRKRLEKARDEA 63 (178)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444444444444443
No 149
>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=20.52 E-value=1.8e+02 Score=23.62 Aligned_cols=43 Identities=16% Similarity=0.336 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHHHcC-------C--CHHHHHHHcC-CCCHHHHHHHHHc
Q 008658 252 ATWTEAETLLLLESVMRHG-------D--NWELVAQNVP-TKSKLDCISKLIE 294 (558)
Q Consensus 252 ~~Wt~~E~~~LLe~Ie~~g-------~--~W~~Ia~~vg-~kt~~eC~~~fl~ 294 (558)
...|.+|+..|++.|..+. | =|...++.-. ..|-+-=..||++
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 4689999999999996553 2 4999987665 6788888888875
No 150
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=20.45 E-value=4.3e+02 Score=26.17 Aligned_cols=14 Identities=7% Similarity=0.140 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHHHH
Q 008658 523 MEKEYNEMMQLKEC 536 (558)
Q Consensus 523 me~Er~~LE~~Rq~ 536 (558)
|+.+|.+-++.+|+
T Consensus 89 ~e~~r~~fekekqq 102 (228)
T PRK06800 89 IEAARQQFQKEQQE 102 (228)
T ss_pred HHHHHHHHHHHHHH
Confidence 33333333333333
No 151
>PLN02806 complex I subunit
Probab=20.44 E-value=1.8e+02 Score=24.71 Aligned_cols=26 Identities=23% Similarity=0.348 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 008658 504 TQMKKLHSKINYFDDLELIMEKEYNEMM 531 (558)
Q Consensus 504 ~QlkKLElKLk~feeLE~~me~Er~~LE 531 (558)
.|+-|.|.||+ ++||+.|.++|..-+
T Consensus 47 n~l~~we~kL~--edldk~L~~~r~an~ 72 (81)
T PLN02806 47 NQLVKWEVKLK--EDLDKMLAKARAANN 72 (81)
T ss_pred HHHHHHHHHHH--HHHHHHHHHHHHHHh
Confidence 35667777776 689998888887644
No 152
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=20.36 E-value=3.6e+02 Score=30.40 Aligned_cols=39 Identities=13% Similarity=0.165 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHh
Q 008658 472 TATALGAAAANAKLLADQEDREIEHLVA--IIIETQMKKLHSKIN 514 (558)
Q Consensus 472 aa~AL~aAA~kAk~LA~~EEreI~~Lv~--~lIe~QlkKLElKLk 514 (558)
.-+||.....|++.| |++|..|-. .++..+++++|-||+
T Consensus 67 nqSALteqQ~kasEL----EKqLaaLrqElq~~saq~~dle~KIk 107 (475)
T PRK13729 67 RQHATTEMQVTAAQM----QKQYEEIRRELDVLNKQRGDDQRRIE 107 (475)
T ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhhhhhhHHHHHH
Confidence 345677777777777 677777632 233466666666665
Done!