Query 008612
Match_columns 559
No_of_seqs 242 out of 681
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 14:21:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008612.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008612hhsearch_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 4.3E-96 9E-101 761.8 28.6 415 11-546 46-467 (531)
2 KOG1279 Chromatin remodeling f 100.0 3.7E-86 8.1E-91 712.2 27.1 444 10-547 40-503 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 4.4E-27 9.6E-32 200.4 6.0 85 17-105 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 1.9E-23 4.1E-28 218.8 8.8 112 194-306 13-127 (438)
5 COG5114 Histone acetyltransfer 99.8 8.7E-20 1.9E-24 183.9 5.8 111 194-305 4-117 (432)
6 cd02336 ZZ_RSC8 Zinc finger, Z 99.1 6.3E-11 1.4E-15 89.2 3.8 45 196-240 1-45 (45)
7 PF00249 Myb_DNA-binding: Myb- 99.0 2.5E-10 5.4E-15 86.9 4.9 44 253-296 2-47 (48)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.8 5.7E-09 1.2E-13 82.6 5.5 41 255-295 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 1.5E-08 3.4E-13 75.1 5.8 44 253-296 2-46 (49)
11 PLN02328 lysine-specific histo 98.7 2.2E-08 4.7E-13 116.0 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 43 254-296 1-44 (45)
13 cd02335 ZZ_ADA2 Zinc finger, Z 98.3 7.8E-07 1.7E-11 68.3 4.2 47 196-242 1-49 (49)
14 PLN02529 lysine-specific histo 98.2 2.3E-06 5E-11 98.8 7.2 84 22-110 63-149 (738)
15 PLN03212 Transcription repress 98.2 1.6E-06 3.5E-11 86.8 5.0 45 251-295 24-70 (249)
16 cd02249 ZZ Zinc finger, ZZ typ 98.1 2.2E-06 4.9E-11 64.8 3.9 46 196-242 1-46 (46)
17 TIGR01557 myb_SHAQKYF myb-like 98.1 6.7E-06 1.4E-10 65.2 5.7 44 252-295 3-52 (57)
18 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.0 7.2E-06 1.6E-10 62.8 3.8 45 196-242 1-48 (48)
19 PLN03091 hypothetical protein; 98.0 7.2E-06 1.6E-10 88.0 5.0 44 252-295 14-59 (459)
20 smart00291 ZnF_ZZ Zinc-binding 97.9 8.5E-06 1.8E-10 61.1 3.7 39 195-233 4-42 (44)
21 cd02345 ZZ_dah Zinc finger, ZZ 97.9 8.7E-06 1.9E-10 62.6 3.6 45 197-241 2-48 (49)
22 cd02340 ZZ_NBR1_like Zinc fing 97.9 9.2E-06 2E-10 60.8 3.6 42 197-242 2-43 (43)
23 cd02343 ZZ_EF Zinc finger, ZZ 97.9 1.1E-05 2.3E-10 61.7 3.8 43 197-239 2-45 (48)
24 cd02338 ZZ_PCMF_like Zinc fing 97.9 1.2E-05 2.7E-10 61.7 3.9 45 197-241 2-48 (49)
25 cd02334 ZZ_dystrophin Zinc fin 97.8 1.8E-05 3.9E-10 60.8 3.8 44 197-240 2-47 (49)
26 KOG0048 Transcription factor, 97.8 1.9E-05 4.1E-10 79.7 4.5 44 252-295 9-54 (238)
27 PF00569 ZZ: Zinc finger, ZZ t 97.7 1.8E-05 3.9E-10 59.9 2.1 40 194-233 3-43 (46)
28 cd02344 ZZ_HERC2 Zinc finger, 97.6 8.5E-05 1.8E-09 56.1 3.7 43 197-242 2-45 (45)
29 PLN03212 Transcription repress 97.5 0.00011 2.3E-09 74.0 5.1 45 251-295 77-121 (249)
30 cd02339 ZZ_Mind_bomb Zinc fing 97.5 0.00014 3E-09 55.0 3.7 42 197-241 2-44 (45)
31 PLN03091 hypothetical protein; 97.2 0.00047 1E-08 74.3 5.8 45 251-295 66-110 (459)
32 cd02337 ZZ_CBP Zinc finger, ZZ 97.2 0.0003 6.5E-09 52.1 2.9 38 196-234 1-38 (41)
33 cd02342 ZZ_UBA_plant Zinc fing 96.8 0.00092 2E-08 49.8 2.7 32 197-228 2-34 (43)
34 KOG0049 Transcription factor, 96.8 0.0012 2.6E-08 73.5 4.7 45 251-295 359-404 (939)
35 PLN02976 amine oxidase 96.3 0.0035 7.7E-08 76.6 4.6 83 25-110 454-542 (1713)
36 KOG0049 Transcription factor, 95.9 0.0063 1.4E-07 68.1 3.9 45 251-295 411-459 (939)
37 KOG0048 Transcription factor, 95.8 0.016 3.5E-07 58.6 5.8 42 252-293 62-103 (238)
38 KOG4582 Uncharacterized conser 95.5 0.0088 1.9E-07 62.0 3.0 44 196-242 153-197 (278)
39 KOG1280 Uncharacterized conser 95.2 0.013 2.9E-07 61.4 2.9 46 193-238 6-53 (381)
40 PF13837 Myb_DNA-bind_4: Myb/S 95.0 0.012 2.6E-07 49.8 1.6 43 253-295 2-62 (90)
41 KOG4286 Dystrophin-like protei 93.8 0.03 6.5E-07 63.8 1.9 41 195-235 603-644 (966)
42 KOG0051 RNA polymerase I termi 93.2 0.095 2.1E-06 59.2 4.6 44 251-295 383-426 (607)
43 KOG0050 mRNA splicing protein 92.1 0.12 2.7E-06 56.9 3.4 43 252-294 7-50 (617)
44 KOG0051 RNA polymerase I termi 91.7 0.15 3.3E-06 57.5 3.8 54 251-304 435-514 (607)
45 KOG0050 mRNA splicing protein 89.7 0.27 5.8E-06 54.3 3.2 44 252-296 59-102 (617)
46 PF13873 Myb_DNA-bind_5: Myb/S 89.2 0.61 1.3E-05 38.5 4.4 44 253-296 3-68 (78)
47 KOG4167 Predicted DNA-binding 88.5 0.69 1.5E-05 53.1 5.5 54 252-305 619-676 (907)
48 KOG4301 Beta-dystrobrevin [Cyt 88.0 0.23 5E-06 52.3 1.3 41 194-234 239-280 (434)
49 KOG4329 DNA-binding protein [G 85.2 1.2 2.5E-05 47.6 4.7 51 252-302 277-328 (445)
50 TIGR02894 DNA_bind_RsfA transc 85.2 0.77 1.7E-05 43.9 3.1 42 252-294 4-52 (161)
51 PF15324 TALPID3: Hedgehog sig 84.9 3.1 6.7E-05 49.8 8.3 94 458-553 54-166 (1252)
52 COG5118 BDP1 Transcription ini 84.7 1.3 2.9E-05 47.3 4.8 45 251-295 364-408 (507)
53 KOG4468 Polycomb-group transcr 83.7 0.95 2.1E-05 50.9 3.4 45 252-296 88-142 (782)
54 COG5147 REB1 Myb superfamily p 82.5 1.3 2.7E-05 49.8 3.8 44 252-295 72-115 (512)
55 PRK00409 recombination and DNA 82.2 8.3 0.00018 45.8 10.6 81 469-550 491-572 (782)
56 TIGR01069 mutS2 MutS2 family p 81.7 9.4 0.0002 45.3 10.8 81 469-550 486-567 (771)
57 KOG4282 Transcription factor G 80.6 1.7 3.6E-05 46.2 3.9 45 253-297 55-113 (345)
58 COG5147 REB1 Myb superfamily p 80.1 1 2.2E-05 50.5 2.1 42 252-293 20-62 (512)
59 PF03107 C1_2: C1 domain; Int 69.0 4.5 9.8E-05 27.7 2.3 28 196-224 1-29 (30)
60 PF09111 SLIDE: SLIDE; InterP 67.4 6.9 0.00015 35.7 3.8 44 250-293 47-106 (118)
61 PF07649 C1_3: C1-like domain; 67.3 3.8 8.3E-05 27.9 1.7 27 197-224 2-29 (30)
62 KOG1279 Chromatin remodeling f 62.8 4.7 0.0001 45.3 2.2 91 20-110 187-285 (506)
63 PF04504 DUF573: Protein of un 60.6 11 0.00024 33.1 3.8 44 252-295 4-60 (98)
64 smart00307 ILWEQ I/LWEQ domain 59.8 58 0.0013 32.5 9.0 63 476-539 134-197 (200)
65 PLN03142 Probable chromatin-re 58.8 13 0.00028 45.5 5.0 41 253-293 825-866 (1033)
66 smart00345 HTH_GNTR helix_turn 58.5 15 0.00033 27.7 3.8 51 54-105 1-52 (60)
67 KOG3647 Predicted coiled-coil 57.1 45 0.00098 34.6 7.8 64 474-539 90-157 (338)
68 PF12674 Zn_ribbon_2: Putative 56.9 6.3 0.00014 33.6 1.5 35 197-231 2-39 (81)
69 PF13404 HTH_AsnC-type: AsnC-t 56.3 21 0.00046 26.4 4.1 37 258-295 3-40 (42)
70 KOG3554 Histone deacetylase co 56.0 8.9 0.00019 42.3 2.8 52 253-304 286-338 (693)
71 KOG0703 Predicted GTPase-activ 54.7 14 0.00029 38.8 3.8 88 195-295 25-115 (287)
72 PF12776 Myb_DNA-bind_3: Myb/S 54.0 17 0.00036 30.8 3.7 42 254-295 1-60 (96)
73 PF00392 GntR: Bacterial regul 53.5 24 0.00051 27.9 4.3 54 52-106 3-57 (64)
74 PF06034 DUF919: Nucleopolyhed 51.6 45 0.00097 27.2 5.5 45 503-548 13-57 (62)
75 PF12802 MarR_2: MarR family; 51.6 35 0.00077 26.2 4.9 43 67-109 15-57 (62)
76 PF05928 Zea_mays_MuDR: Zea ma 51.5 1.6E+02 0.0034 28.5 9.9 72 467-538 11-89 (207)
77 KOG1194 Predicted DNA-binding 50.7 25 0.00055 38.9 5.1 45 251-295 186-230 (534)
78 PF09862 DUF2089: Protein of u 50.7 26 0.00056 31.8 4.4 74 198-296 1-79 (113)
79 PF01022 HTH_5: Bacterial regu 49.0 48 0.001 24.7 5.1 45 58-105 3-47 (47)
80 cd00090 HTH_ARSR Arsenical Res 48.9 37 0.00081 26.1 4.8 44 61-107 11-54 (78)
81 PF09339 HTH_IclR: IclR helix- 48.2 29 0.00063 26.4 3.8 44 61-105 7-50 (52)
82 COG2916 Hns DNA-binding protei 47.2 1.6E+02 0.0036 27.3 9.1 49 494-546 4-52 (128)
83 PRK13923 putative spore coat p 47.2 17 0.00037 35.3 2.9 41 252-293 5-52 (170)
84 PF01475 FUR: Ferric uptake re 46.8 32 0.00068 30.6 4.5 51 55-106 6-61 (120)
85 cd04779 HTH_MerR-like_sg4 Heli 44.4 1.2E+02 0.0026 28.1 8.1 52 494-548 78-129 (134)
86 COG1725 Predicted transcriptio 43.7 55 0.0012 30.2 5.5 55 52-106 10-68 (125)
87 PF02954 HTH_8: Bacterial regu 43.5 29 0.00063 25.4 3.1 25 258-282 5-29 (42)
88 KOG3859 Septins (P-loop GTPase 41.1 2.2E+02 0.0047 30.3 9.9 72 481-552 326-403 (406)
89 COG5347 GTPase-activating prot 40.2 26 0.00057 37.3 3.3 98 195-305 20-125 (319)
90 smart00595 MADF subfamily of S 39.8 22 0.00047 29.8 2.2 28 273-303 29-56 (89)
91 PF13412 HTH_24: Winged helix- 39.1 90 0.0019 23.0 5.2 44 58-103 4-47 (48)
92 PF02841 GBP_C: Guanylate-bind 37.9 4.5E+02 0.0098 27.3 12.1 51 504-554 228-282 (297)
93 PLN03142 Probable chromatin-re 37.3 46 0.00099 41.0 5.1 45 250-294 924-981 (1033)
94 PRK11546 zraP zinc resistance 36.0 3.9E+02 0.0084 25.4 12.2 70 487-556 44-123 (143)
95 PRK09462 fur ferric uptake reg 35.6 56 0.0012 30.3 4.5 48 58-105 18-70 (148)
96 PF01608 I_LWEQ: I/LWEQ domain 35.0 3.2E+02 0.007 26.1 9.4 22 519-540 129-150 (152)
97 PLN03119 putative ADP-ribosyla 35.0 48 0.001 37.9 4.4 94 195-304 23-123 (648)
98 KOG3915 Transcription regulato 34.7 3.3E+02 0.0071 30.6 10.4 37 506-542 527-569 (641)
99 cd07153 Fur_like Ferric uptake 34.6 65 0.0014 28.2 4.5 46 59-105 3-53 (116)
100 PF04111 APG6: Autophagy prote 34.5 5.8E+02 0.013 27.0 12.3 48 501-548 74-121 (314)
101 PF06689 zf-C4_ClpX: ClpX C4-t 34.2 25 0.00054 26.0 1.4 31 196-227 2-33 (41)
102 PHA00442 host recBCD nuclease 34.0 42 0.00091 26.6 2.7 24 258-281 26-50 (59)
103 smart00550 Zalpha Z-DNA-bindin 34.0 1E+02 0.0022 24.9 5.2 50 58-107 7-56 (68)
104 PF03444 HrcA_DNA-bdg: Winged 33.6 1.1E+02 0.0024 26.0 5.4 54 53-107 4-57 (78)
105 COG5114 Histone acetyltransfer 32.8 54 0.0012 34.8 4.1 68 30-104 362-429 (432)
106 smart00105 ArfGap Putative GTP 32.6 72 0.0016 28.5 4.4 83 196-295 4-96 (112)
107 KOG4479 Transcription factor e 32.4 84 0.0018 27.0 4.4 44 53-100 36-89 (92)
108 KOG1194 Predicted DNA-binding 32.3 23 0.0005 39.2 1.4 44 251-295 469-512 (534)
109 KOG0384 Chromodomain-helicase 32.1 31 0.00067 42.6 2.5 27 251-277 1132-1159(1373)
110 TIGR01069 mutS2 MutS2 family p 32.0 4.8E+02 0.01 31.2 12.3 39 503-541 527-565 (771)
111 PF01412 ArfGap: Putative GTPa 32.0 24 0.00052 31.7 1.3 59 195-266 13-72 (116)
112 TIGR02449 conserved hypothetic 31.8 2E+02 0.0042 23.7 6.3 42 507-548 2-43 (65)
113 PLN03131 hypothetical protein; 31.4 81 0.0017 36.5 5.4 93 195-304 23-123 (705)
114 COG1813 Predicted transcriptio 31.3 47 0.001 32.1 3.1 33 197-229 5-37 (165)
115 smart00346 HTH_ICLR helix_turn 30.6 86 0.0019 25.9 4.4 43 62-105 10-52 (91)
116 PF01047 MarR: MarR family; I 30.2 79 0.0017 24.1 3.8 37 74-110 18-54 (59)
117 KOG3564 GTPase-activating prot 30.2 2.4E+02 0.0051 31.9 8.5 64 492-557 51-114 (604)
118 PF14471 DUF4428: Domain of un 29.8 30 0.00066 26.8 1.3 30 197-228 1-30 (51)
119 PRK11179 DNA-binding transcrip 28.4 79 0.0017 29.5 4.2 39 257-296 8-47 (153)
120 PF07956 DUF1690: Protein of U 28.3 1.3E+02 0.0027 28.4 5.4 57 484-540 61-118 (142)
121 PTZ00007 (NAP-L) nucleosome as 27.5 1.1E+02 0.0025 32.8 5.5 31 517-547 53-87 (337)
122 PRK06474 hypothetical protein; 27.0 1.1E+02 0.0025 29.5 5.1 50 58-108 12-62 (178)
123 PF10820 DUF2543: Protein of u 26.7 46 0.001 27.7 1.9 31 71-101 46-79 (81)
124 PF13463 HTH_27: Winged helix 26.5 1.5E+02 0.0032 23.1 4.9 50 61-110 6-55 (68)
125 PRK00409 recombination and DNA 25.5 6.9E+02 0.015 30.0 12.1 39 503-541 532-570 (782)
126 COG0735 Fur Fe2+/Zn2+ uptake r 25.1 1.1E+02 0.0023 28.7 4.4 52 57-109 21-77 (145)
127 PRK14139 heat shock protein Gr 25.0 1.6E+02 0.0034 29.1 5.6 16 517-532 62-77 (185)
128 PF00412 LIM: LIM domain; Int 24.9 53 0.0011 24.9 1.9 33 193-227 24-56 (58)
129 PHA03082 DNA-dependent RNA pol 24.8 16 0.00034 29.3 -1.1 18 196-213 5-22 (63)
130 PF05864 Chordopox_RPO7: Chord 24.8 19 0.00041 28.8 -0.6 18 196-213 5-22 (63)
131 PF15346 ARGLU: Arginine and g 24.7 6.2E+02 0.013 24.2 13.0 82 468-549 19-110 (149)
132 cd07671 F-BAR_PSTPIP1 The F-BA 24.5 5E+02 0.011 26.4 9.4 53 498-550 146-216 (242)
133 TIGR00270 conserved hypothetic 24.1 3.2E+02 0.007 26.0 7.4 33 197-229 2-35 (154)
134 PF12958 DUF3847: Protein of u 24.0 4.6E+02 0.0099 22.7 7.6 49 503-551 6-58 (86)
135 KOG1988 Uncharacterized conser 23.7 2.1E+02 0.0045 34.5 7.1 60 497-557 563-622 (970)
136 PF09286 Pro-kuma_activ: Pro-k 23.6 73 0.0016 29.3 2.9 38 71-108 45-82 (143)
137 smart00420 HTH_DEOR helix_turn 23.4 1.9E+02 0.0041 20.8 4.7 35 72-106 13-47 (53)
138 PF14569 zf-UDP: Zinc-binding 23.0 52 0.0011 28.0 1.6 49 195-244 9-66 (80)
139 PRK11169 leucine-responsive tr 22.5 1.1E+02 0.0024 28.9 4.0 39 257-296 13-52 (164)
140 PRK14161 heat shock protein Gr 22.4 6.3E+02 0.014 24.7 9.2 18 514-531 46-63 (178)
141 PF08100 Dimerisation: Dimeris 22.2 1.5E+02 0.0032 23.0 3.9 27 71-97 20-50 (51)
142 cd07377 WHTH_GntR Winged helix 22.1 1.3E+02 0.0029 22.8 3.7 52 53-105 5-57 (66)
143 cd07672 F-BAR_PSTPIP2 The F-BA 21.9 5.9E+02 0.013 25.9 9.3 48 503-550 152-217 (240)
144 PRK06800 fliH flagellar assemb 21.7 3.6E+02 0.0077 26.8 7.2 14 529-542 62-75 (228)
145 cd08310 Death_NFkB-like Death 21.0 77 0.0017 26.3 2.3 23 257-283 2-24 (72)
146 PF09420 Nop16: Ribosome bioge 20.8 1.5E+02 0.0033 28.2 4.6 43 252-294 114-160 (164)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=4.3e-96 Score=761.79 Aligned_cols=415 Identities=27% Similarity=0.484 Sum_probs=337.1
Q ss_pred CCCcceeecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHH
Q 008612 11 KPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLL 90 (559)
Q Consensus 11 ~~~~~~iiIPs~~~wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i 90 (559)
-++.++||||||+.||++.+||+||+++.||||+|++++|||++|+.||||||++||+||.+|||+|+||||++||||+|
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 008612 91 HKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVA 170 (559)
Q Consensus 91 ~rvh~FLe~wGlIN~~~~~~~~~~~~~~~~~~~p~~tg~f~v~~dtP~gl~~~~~p~~~kp~~~~~~~~~~s~~~~~~~~ 170 (559)
.|||+||++|||||||++| .+||+.+|| |+||||++++|||+||+|+.+++... ....+++. .+....
T Consensus 126 vrvHrFLekWGLINYqvdp-----~trPs~IgP-plt~h~q~l~dtP~gl~p~l~~~~~~---~~~~~a~~---~e~~~~ 193 (531)
T COG5259 126 VRVHRFLEKWGLINYQVDP-----GTRPSTIGP-PLTSHFQDLHDTPRGLSPFLPWGPIN---QRVLGAKE---IEYETH 193 (531)
T ss_pred HHHHHHHHHhcceeeccCC-----CCCccccCC-CcchhhHHHhhCccccccccCCCCcc---ccccccch---hhhhhh
Confidence 9999999999999999999 578888887 58899999999999999986544331 11111110 110000
Q ss_pred CCCCCCCCCcccch----hhhcccc---ccCCccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceecc
Q 008612 171 GETGVKLPPLASYL----DVFGDLV---KLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSD 243 (559)
Q Consensus 171 ~~~~~~~~~~~~~~----~~~~~~~---~~~~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~~ 243 (559)
.+..+ .|++.... ..+.++. ......|..||+.|..+||+..+...+++|..||.+|+||+..++.||..++
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 11111100 0111222 1234899999999999999999988999999999999999999999999998
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCCccccCCCCCCCCCCCccc
Q 008612 244 LGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLK 323 (559)
Q Consensus 244 ~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l~~~~~~~~~~~~~~~~~~~~ 323 (559)
...+. .+..||.+|+++|||||++||++|++||.|||+||++|||+|||||||+|.||...++..
T Consensus 273 ~~~~~--~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~~~------------- 337 (531)
T COG5259 273 ISLLI--RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDGKG------------- 337 (531)
T ss_pred hhccc--ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccCcC-------------
Confidence 87642 567999999999999999999999999999999999999999999999999998765310
Q ss_pred cccccccccccchhhhhhhhhhcccccccCCCCcCCCcccccCCCCCCCCCCcHHHHHHHHHhccChHHHHHHHHHHHHH
Q 008612 324 EGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAA 403 (559)
Q Consensus 324 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~p~lk~~~~~Pfs~a~NPVms~vAFLas~V~P~VAaaAA~aAl~~ 403 (559)
+. ..+..||..++||||++|+||+++|.|+|++-.+++.++.
T Consensus 338 ------------------------------------~~--~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k~ 379 (531)
T COG5259 338 ------------------------------------DN--SKGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIKS 379 (531)
T ss_pred ------------------------------------CC--CCCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhhc
Confidence 00 0134799999999999999999999999988777665321
Q ss_pred HhccCCCCccccCCCchhhccCCCCCCCCCChhhhhhhhhhhhccccccccccCCCCCCCchhhHHHHHHHHHHHHHHHH
Q 008612 404 LCNESSCPREIFDGDEDYLANGLSSPTMVSDPERALQVDASKMEENQSETQDASSEKNDVPLNLRIRTATATALGAAAAN 483 (559)
Q Consensus 404 l~~e~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~Aaa~AL~aAA~k 483 (559)
.+. . . .+.-+...+...+-.||.+++.+
T Consensus 380 -g~~-~------------------------~--------------------------~n~e~~~~~~~~~~~al~s~~ek 407 (531)
T COG5259 380 -GKI-S------------------------H--------------------------INRESQEHIEEVIEYALDSGKEK 407 (531)
T ss_pred -cce-e------------------------c--------------------------CccchhhHHHHHHHHHHHHHHHH
Confidence 000 0 0 00001123556677899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 484 AKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVL 546 (559)
Q Consensus 484 Ak~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~ 546 (559)
||+.|+.|||+|.+|+..+|+.||+||++||.||.+||+.+..||+.|+. .|+..|+.+-
T Consensus 408 a~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L~~~~~L~rqeLd~---nlll~rl~~~ 467 (531)
T COG5259 408 AKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKSTSLERQELDA---NLLLRRLNAE 467 (531)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhHH
Confidence 99999999999999999999999999999999999999999999999999 4555554443
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=3.7e-86 Score=712.19 Aligned_cols=444 Identities=31% Similarity=0.525 Sum_probs=336.9
Q ss_pred CCCCcceeecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHH
Q 008612 10 TKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSL 89 (559)
Q Consensus 10 ~~~~~~~iiIPs~~~wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~ 89 (559)
...+.|.|+||||++||+|++||+||++++||||+|++++|||++|++||||||++||+||.+|||+|+|||+++||||+
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 008612 90 LHKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAV 169 (559)
Q Consensus 90 i~rvh~FLe~wGlIN~~~~~~~~~~~~~~~~~~~p~~tg~f~v~~dtP~gl~~~~~p~~~kp~~~~~~~~~~s~~~~~~~ 169 (559)
|+|||+|||+||||||++++ +.+|..++|| .++||+++.++|+|+.++..+... .....+.+.- +
T Consensus 120 i~Rvh~FlE~WGLINy~~d~-----e~rp~~~~p~-~t~h~~~~~~tp~~~~~~~~~~~~---~~~~~~~~~~------~ 184 (506)
T KOG1279|consen 120 IARVHAFLEQWGLINYQVDA-----ESRPHPIEPP-ETSHFQVLADTPRGLAPLTPEDPQ---SQPDLGNPRM------E 184 (506)
T ss_pred HHHHHhhHHhhcccccccCh-----hhCCcccCCC-cccccccccCCCcccccCCCCCcc---cccccccccc------c
Confidence 99999999999999999999 5777778875 569999999999999887543222 1111111100 0
Q ss_pred cCCCCCCCCCcccchhhhccccc----cCCccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceeccCC
Q 008612 170 AGETGVKLPPLASYLDVFGDLVK----LKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLG 245 (559)
Q Consensus 170 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~~~~ 245 (559)
.+..+++..+.... ....+|..|+.. ||+..+...+.+|.+||.+|+|+..+...||+.+..
T Consensus 185 ---------~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~- 250 (506)
T KOG1279|consen 185 ---------TLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGE- 250 (506)
T ss_pred ---------cccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccchhccc-
Confidence 01111111111111 233556665554 566666567999999999999999999999933322
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCCccccCCCCCCCCCCCccccc
Q 008612 246 GNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLKEG 325 (559)
Q Consensus 246 ~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l~~~~~~~~~~~~~~~~~~~~~~ 325 (559)
..+..||++|+++|||+|++||+||++||.|||+||++|||.|||+|||+|+|+....+.
T Consensus 251 ----~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l~~~~~~---------------- 310 (506)
T KOG1279|consen 251 ----SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYLAKSEAS---------------- 310 (506)
T ss_pred ----cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhhhhcccc----------------
Confidence 357899999999999999999999999999999999999999999999999999774321
Q ss_pred cccccccccchhhhhhhhhhcccccccCCCCcCCCcccccCCCCCCCCCCcHHHHHHHHHhccChHHHHHHHHHHHHHHh
Q 008612 326 QSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALC 405 (559)
Q Consensus 326 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~p~lk~~~~~Pfs~a~NPVms~vAFLas~V~P~VAaaAA~aAl~~l~ 405 (559)
.+|. ++ +..+|+.-+||||++++||+++|+|+|+..+++.+...+.
T Consensus 311 --------------------------------~~~~-~~-~~~~~sq~gnpv~s~~~~l~~~vdP~~~~~~~k~~~~~~~ 356 (506)
T KOG1279|consen 311 --------------------------------LGPL-SY-GPVPFSQDGNPVMSTVAFLASVVDPVVKSVAAKSAEEKFS 356 (506)
T ss_pred --------------------------------cCcc-cc-CCCccccCCCccccHHHHHHhccCchhhhhhhcccchhhh
Confidence 1332 44 3477888889999999999999999999999999998876
Q ss_pred ccC---CCCc--cccCCCchhh-c-cCCC-------CCCCCCCh--hhhhhhhhhhhccccccccccCCCCCCCchhhHH
Q 008612 406 NES---SCPR--EIFDGDEDYL-A-NGLS-------SPTMVSDP--ERALQVDASKMEENQSETQDASSEKNDVPLNLRI 469 (559)
Q Consensus 406 ~e~---~~~~--~~~~~~ed~~-~-~~~~-------~~~~~~~~--~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v 469 (559)
+.. +.+. ......+... . .+.. +...+.-+ +..... .++. .......+.+.. . +
T Consensus 357 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~e~~k~~~---~~~~-----~~n~~~~k~~e~-~-~ 426 (506)
T KOG1279|consen 357 KVNEESPLAKIEVSAKGVEEAASKLGGTDKSKFLALSDIACTLPDEEEKLQS---KLKA-----KLNPNKEKTIEL-G-L 426 (506)
T ss_pred hhhhcccchhhhHHhhhhHHhhhhhccchhhhhhhhhhhhhcccchHHHHHH---Hhhc-----ccccchhhhhHH-H-H
Confidence 532 2111 0000000000 0 0000 00000000 000000 0000 000001111111 2 7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 470 RTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 547 (559)
Q Consensus 470 ~~Aaa~AL~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~ 547 (559)
..|+..+|++||++||+||.+|| +++++++.++++||+|+|.||++|+++|+++.+|++++++.|+.++.+|+.++-
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=99.93 E-value=4.4e-27 Score=200.43 Aligned_cols=85 Identities=41% Similarity=0.829 Sum_probs=78.1
Q ss_pred eecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccc-hHHHHHHHHH
Q 008612 17 YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFR 95 (559)
Q Consensus 17 iiIPs~~~wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~g-D~~~i~rvh~ 95 (559)
+++|.+++||+++.+|++|++.|||||.| ++|+.|+.|||.||..|+.||.+|||+++||+.+.| |++.+.|||+
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 008612 96 LLDEWGLINF 105 (559)
Q Consensus 96 FLe~wGlIN~ 105 (559)
||++||+|||
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=99.89 E-value=1.9e-23 Score=218.80 Aligned_cols=112 Identities=22% Similarity=0.483 Sum_probs=102.9
Q ss_pred CCccCCCCCCCCCCc-eeEeccCCCcccchhhhhcC-CCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 008612 194 KGFKCGSCGEQCNSG-CYEYSKQGSFVICEKCFKNG-NYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 271 (559)
Q Consensus 194 ~~~~C~~Cg~~~~~~-~y~~~k~~~~~lC~~Cf~~G-~~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g 271 (559)
..+.|.+|..+|+.. |++|..|.+|+||..||+.| .++.|.+.|+|.+|+...+++ ....||++||.+||+|+++||
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 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPI-LDPSWTADEEILLLEAAETYG 91 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCC-CCCCCChHHHHHHHHHHHHhC
Confidence 469999999999875 69999999999999999999 589999999999999977665 478999999999999999999
Q ss_pred -CCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCCc
Q 008612 272 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSA 306 (559)
Q Consensus 272 -~nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l~~~ 306 (559)
|||.+||+|||+||+++|..||+..+++.++..-.
T Consensus 92 ~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~~ 127 (438)
T KOG0457|consen 92 FGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPLP 127 (438)
T ss_pred CCcHHHHHHHHcccchHHHHHHHHHHHhcCcccccc
Confidence 99999999999999999999999999888886543
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.78 E-value=8.7e-20 Score=183.89 Aligned_cols=111 Identities=20% Similarity=0.353 Sum_probs=102.7
Q ss_pred CCccCCCCCCCCCC-ceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC
Q 008612 194 KGFKCGSCGEQCNS-GCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG 271 (559)
Q Consensus 194 ~~~~C~~Cg~~~~~-~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g 271 (559)
..++|+.|..+|+. +++.|..|.+++||..||.+|. .+.|...|+|.+++.+..++ ....|++.||++|+++++..|
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsypI-~~e~WgadEEllli~~~~TlG 82 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYPI-GEEGWGADEELLLIECLDTLG 82 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCccc-cCCCcCchHHHHHHHHHHhcC
Confidence 45899999999985 6999999999999999999996 68888999999999887776 478999999999999999999
Q ss_pred -CCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCC
Q 008612 272 -DNWELVAQNVPTKSKLDCISKLIELPFGEFMMGS 305 (559)
Q Consensus 272 -~nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l~~ 305 (559)
|||++||+|||.|++++|..||+.+++|..|..-
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
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=99.10 E-value=6.3e-11 Score=89.16 Aligned_cols=45 Identities=24% Similarity=0.749 Sum_probs=43.1
Q ss_pred ccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCce
Q 008612 196 FKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFR 240 (559)
Q Consensus 196 ~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~ 240 (559)
+.|..||.||+.+||||.++.+++||+.||.+|+||.++++.||+
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 579999999999999999999999999999999999999999985
No 7
>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=99.04 E-value=2.5e-10 Score=86.86 Aligned_cols=44 Identities=34% Similarity=0.700 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHcCCC-HHHHHHHcC-CCCHHHHHHHHHcC
Q 008612 253 ATWTEAETLLLLESVMRHGDN-WELVAQNVP-TKSKLDCISKLIEL 296 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~~g~n-W~~Ia~~vg-~kT~~eC~~~flqL 296 (559)
..||.+|+.+|+++|.+||.+ |..||++|+ +||+.||..||.++
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 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=82.64 Aligned_cols=41 Identities=29% Similarity=0.659 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 255 WTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 255 WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
||.+|+.+|++++..||.+|..||+++|+||+.+|..||..
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=120.32 Aligned_cols=84 Identities=27% Similarity=0.332 Sum_probs=73.3
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccch-HHHHHHHHHhhh
Q 008612 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGD-VSLLHKVFRLLD 98 (559)
Q Consensus 22 ~~~wF~~~~i~~iE~~~--~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD-~~~i~rvh~FLe 98 (559)
++.-|+.+.+++.|..+ || ...+ ..+..|+.|||.||.+|+.||..|||+++|...+..+ ...+.++|+||.
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 4689999999999999999999999999999887653 489999999999
Q ss_pred hhcccccccCCC
Q 008612 99 EWGLINFGAVSR 110 (559)
Q Consensus 99 ~wGlIN~~~~~~ 110 (559)
++|+|||++...
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=1.5e-08 Score=75.14 Aligned_cols=44 Identities=36% Similarity=0.728 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008612 253 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 296 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~flqL 296 (559)
..||.+|+.+|+.++.+|| .+|..||.++++||+.+|..+|..+
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=2.2e-08 Score=116.02 Aligned_cols=84 Identities=26% Similarity=0.368 Sum_probs=75.5
Q ss_pred CCCCCCCCCCHHHHhh-cccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhcc-chHHHHHHHHHhhhhh
Q 008612 23 SSWFRWDDIHETERTA-LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLV-GDVSLLHKVFRLLDEW 100 (559)
Q Consensus 23 ~~wF~~~~i~~iE~~~-~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~-gD~~~i~rvh~FLe~w 100 (559)
+.-|+.+.+|+.|..+ |++...+ ..+..|+.|||.||.+|+.||..|||+++|+..+- -....+.++|.||.+.
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 4789999999999888 8877766 47899999999999999999999999999998774 3567999999999999
Q ss_pred cccccccCCC
Q 008612 101 GLINFGAVSR 110 (559)
Q Consensus 101 GlIN~~~~~~ 110 (559)
|.|||+|.+.
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=71.84 Aligned_cols=43 Identities=40% Similarity=0.784 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008612 254 TWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 296 (559)
Q Consensus 254 ~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~flqL 296 (559)
.||.+|+.+|+.++.+|| ++|..||+.+++||..+|..||.++
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
>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=98.29 E-value=7.8e-07 Score=68.28 Aligned_cols=47 Identities=19% Similarity=0.609 Sum_probs=42.0
Q ss_pred ccCCCCCCCCCC-ceeEeccCCCcccchhhhhcCC-CCCCCCCCCceec
Q 008612 196 FKCGSCGEQCNS-GCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFS 242 (559)
Q Consensus 196 ~~C~~Cg~~~~~-~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~ 242 (559)
+.|++|+.++.. .||+|..|.+|+||..||..|. .+.|...|.|+.+
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 469999998887 7999999999999999999996 5788899999864
No 14
>PLN02529 lysine-specific histone demethylase 1
Probab=98.19 E-value=2.3e-06 Score=98.83 Aligned_cols=84 Identities=23% Similarity=0.350 Sum_probs=71.4
Q ss_pred CCCCCCCCCCCHHHHhh--cccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchH-HHHHHHHHhhh
Q 008612 22 HSSWFRWDDIHETERTA--LKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDV-SLLHKVFRLLD 98 (559)
Q Consensus 22 ~~~wF~~~~i~~iE~~~--~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~-~~i~rvh~FLe 98 (559)
.+-=|+.+.+++-|+++ +|.. ..+.+..|+.|||.|+.+|+.||..|||+++++..+.-++ .+|...|+||.
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 34579999999999855 4433 3568999999999999999999999999999998876543 56779999999
Q ss_pred hhcccccccCCC
Q 008612 99 EWGLINFGAVSR 110 (559)
Q Consensus 99 ~wGlIN~~~~~~ 110 (559)
+.|.|||.|.|.
T Consensus 138 ~~~~inc~vnp~ 149 (738)
T PLN02529 138 YNGYINFGVSPS 149 (738)
T ss_pred hCCCcceeeccc
Confidence 999999999986
No 15
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.19 E-value=1.6e-06 Score=86.85 Aligned_cols=45 Identities=16% Similarity=0.443 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcC-CCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg-~kT~~eC~~~flq 295 (559)
....||.+|+.+|+++|++|| .+|..||+++| +||+.||+.||.+
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 356899999999999999999 79999999997 8999999999985
No 16
>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=98.15 E-value=2.2e-06 Score=64.80 Aligned_cols=46 Identities=17% Similarity=0.450 Sum_probs=41.0
Q ss_pred ccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceec
Q 008612 196 FKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFS 242 (559)
Q Consensus 196 ~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~ 242 (559)
+.|+.|+.++...||+|..|.+++||..||..|. +.|...|.|..+
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 4699999999999999999999999999999998 777778888753
No 17
>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=98.09 E-value=6.7e-06 Score=65.20 Aligned_cols=44 Identities=20% Similarity=0.371 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCH---HHHHHHcC-CC-CHHHHHHHHHc
Q 008612 252 GATWTEAETLLLLESVMRHG-DNW---ELVAQNVP-TK-SKLDCISKLIE 295 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g-~nW---~~Ia~~vg-~k-T~~eC~~~flq 295 (559)
+..||++|..++|+||+.|| ||| ..|+++++ ++ |+.||..|+-.
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 18
>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=97.98 E-value=7.2e-06 Score=62.78 Aligned_cols=45 Identities=27% Similarity=0.558 Sum_probs=39.3
Q ss_pred ccCCCCCC-CCCCceeEeccCC--CcccchhhhhcCCCCCCCCCCCceec
Q 008612 196 FKCGSCGE-QCNSGCYEYSKQG--SFVICEKCFKNGNYGEDKSKDDFRFS 242 (559)
Q Consensus 196 ~~C~~Cg~-~~~~~~y~~~k~~--~~~lC~~Cf~~G~~~~~~ss~df~~~ 242 (559)
+.|++|+. ++...||+|..|. +|+||..||..|. .|...|.|.++
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 8888999999999 9999999999997 67777777654
No 19
>PLN03091 hypothetical protein; Provisional
Probab=97.97 E-value=7.2e-06 Score=87.97 Aligned_cols=44 Identities=20% Similarity=0.447 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcC-CCCHHHHHHHHHc
Q 008612 252 GATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 295 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg-~kT~~eC~~~flq 295 (559)
.+.||.+|+.+|+++|++|| .+|..||+++| +||+.||+.||++
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~N 59 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWIN 59 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHh
Confidence 56799999999999999999 79999999998 7999999999985
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=97.95 E-value=8.5e-06 Score=61.12 Aligned_cols=39 Identities=23% Similarity=0.691 Sum_probs=35.3
Q ss_pred CccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCC
Q 008612 195 GFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGED 233 (559)
Q Consensus 195 ~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~ 233 (559)
.+.|+.|+..+...||+|..|.+++||.+||..|.++..
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 478999999999999999999999999999999987643
No 21
>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=97.93 E-value=8.7e-06 Score=62.56 Aligned_cols=45 Identities=13% Similarity=0.364 Sum_probs=39.0
Q ss_pred cCCCCCC-CCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCcee
Q 008612 197 KCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRF 241 (559)
Q Consensus 197 ~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~ 241 (559)
.|+.|+. ++...||+|..|.+|+||..||..|. ...|...|.|..
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYE 48 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCccc
Confidence 6999998 99989999999999999999999996 456667777653
No 22
>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=97.93 E-value=9.2e-06 Score=60.77 Aligned_cols=42 Identities=17% Similarity=0.331 Sum_probs=37.6
Q ss_pred cCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceec
Q 008612 197 KCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFS 242 (559)
Q Consensus 197 ~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~ 242 (559)
.|+.|+..+...||+|..|.+|+||..||..| .| ..|.|.++
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 69999999999999999999999999999998 45 77888764
No 23
>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=97.92 E-value=1.1e-05 Score=61.65 Aligned_cols=43 Identities=19% Similarity=0.476 Sum_probs=36.2
Q ss_pred cCCCCCCCCCCceeEeccCCCcccchhhhhcCCC-CCCCCCCCc
Q 008612 197 KCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNY-GEDKSKDDF 239 (559)
Q Consensus 197 ~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~-~~~~ss~df 239 (559)
.|++|...+...||+|++|.+++||..||..|.. ..|...|+.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm 45 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEM 45 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCCCCCCc
Confidence 5999999888889999999999999999999974 455555543
No 24
>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=97.90 E-value=1.2e-05 Score=61.71 Aligned_cols=45 Identities=16% Similarity=0.457 Sum_probs=38.9
Q ss_pred cCCCCC-CCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCcee
Q 008612 197 KCGSCG-EQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRF 241 (559)
Q Consensus 197 ~C~~Cg-~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~ 241 (559)
.|+.|+ .++...||+|..|.+|+||..||..|. .+.|...|+|..
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 788888999999999999999999996 456666888764
No 25
>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=97.83 E-value=1.8e-05 Score=60.83 Aligned_cols=44 Identities=25% Similarity=0.521 Sum_probs=37.5
Q ss_pred cCCCCCC-CCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCce
Q 008612 197 KCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFR 240 (559)
Q Consensus 197 ~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~ 240 (559)
.|+.|+. ++...||+|..|.+|+||..||..|. .+.|...|++.
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 6999996 58889999999999999999999996 45666777764
No 26
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.80 E-value=1.9e-05 Score=79.74 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcC-CCCHHHHHHHHHc
Q 008612 252 GATWTEAETLLLLESVMRHG-DNWELVAQNVP-TKSKLDCISKLIE 295 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg-~kT~~eC~~~flq 295 (559)
.+.||.+|+.+|.+.|++|| ++|..|+++.| .|+.+.|++||+.
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 8999999999984
No 27
>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=97.72 E-value=1.8e-05 Score=59.95 Aligned_cols=40 Identities=25% Similarity=0.678 Sum_probs=29.4
Q ss_pred CCccCCCCCC-CCCCceeEeccCCCcccchhhhhcCCCCCC
Q 008612 194 KGFKCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNGNYGED 233 (559)
Q Consensus 194 ~~~~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~ 233 (559)
..+.|+.|+. .+...||+|..|.+|+||..||..|.++..
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 3578999998 667889999999999999999999986543
No 28
>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=97.55 E-value=8.5e-05 Score=56.13 Aligned_cols=43 Identities=23% Similarity=0.575 Sum_probs=36.2
Q ss_pred cCCCCCC-CCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceec
Q 008612 197 KCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFS 242 (559)
Q Consensus 197 ~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~ 242 (559)
.|+.|+. .+...||+|..|.+|+||..||..+. |...|.|.+|
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 6999996 67778999999999999999999954 5567888764
No 29
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.53 E-value=0.00011 Score=74.03 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
..+.||.+|+.+||+.+..||..|..||+++.+||..+|..||..
T Consensus 77 ~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 77 KRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred ccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 367899999999999999999999999999999999999999964
No 30
>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=97.45 E-value=0.00014 Score=55.00 Aligned_cols=42 Identities=12% Similarity=0.426 Sum_probs=34.9
Q ss_pred cCCCCC-CCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCcee
Q 008612 197 KCGSCG-EQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRF 241 (559)
Q Consensus 197 ~C~~Cg-~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~ 241 (559)
.|+.|+ ..+...||+|..|.+++||..||..+ .|...|.|.+
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 56778899999999999999999964 3555677764
No 31
>PLN03091 hypothetical protein; Provisional
Probab=97.21 E-value=0.00047 Score=74.34 Aligned_cols=45 Identities=18% Similarity=0.350 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
..+.||.+|+.+||+.+..||..|.+||+++.+||..+|..||..
T Consensus 66 kKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 66 KRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred cCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 357899999999999999999999999999999999999988864
No 32
>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=97.19 E-value=0.0003 Score=52.14 Aligned_cols=38 Identities=13% Similarity=0.511 Sum_probs=31.6
Q ss_pred ccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCC
Q 008612 196 FKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDK 234 (559)
Q Consensus 196 ~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ 234 (559)
+.|+.|+...+ .||+|..|.+|+||..||..+.-|.++
T Consensus 1 y~C~~C~~~~~-~r~~C~~C~dfDLC~~C~~~~~H~H~~ 38 (41)
T cd02337 1 YTCNECKHHVE-TRWHCTVCEDYDLCITCYNTKNHPHKM 38 (41)
T ss_pred CcCCCCCCcCC-CceECCCCcchhhHHHHhCCCCCCccc
Confidence 46999998654 999999999999999999987655443
No 33
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=96.83 E-value=0.00092 Score=49.81 Aligned_cols=32 Identities=22% Similarity=0.645 Sum_probs=28.8
Q ss_pred cCCCCCC-CCCCceeEeccCCCcccchhhhhcC
Q 008612 197 KCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNG 228 (559)
Q Consensus 197 ~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G 228 (559)
.|+.|+. ++...||+|..|.+|+||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 6999996 7888899999999999999999765
No 34
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.81 E-value=0.0012 Score=73.53 Aligned_cols=45 Identities=33% Similarity=0.675 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
.-+.||.+|+.+|+.+|++|| .+|.+|-+.|.+||-.||+.+|++
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~n 404 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTN 404 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHH
Confidence 467899999999999999999 799999999999999999999986
No 35
>PLN02976 amine oxidase
Probab=96.31 E-value=0.0035 Score=76.63 Aligned_cols=83 Identities=23% Similarity=0.351 Sum_probs=71.3
Q ss_pred CCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhh------hccchHHHHHHHHHhhh
Q 008612 25 WFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRK------SLVGDVSLLHKVFRLLD 98 (559)
Q Consensus 25 wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~------~l~gD~~~i~rvh~FLe 98 (559)
=+....+.+|||-.|.|...-+ ..-+-|+.+||.|+-.|-+|=.+-|.+++|-= .-.+-..+|.-|+.||+
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 4556789999999999999744 35789999999999999999999999999942 22356889999999999
Q ss_pred hhcccccccCCC
Q 008612 99 EWGLINFGAVSR 110 (559)
Q Consensus 99 ~wGlIN~~~~~~ 110 (559)
+.|.||-++...
T Consensus 531 ~~gyin~g~~s~ 542 (1713)
T PLN02976 531 QRGYINAGIASE 542 (1713)
T ss_pred ccCceecccccc
Confidence 999999999875
No 36
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.94 E-value=0.0063 Score=68.07 Aligned_cols=45 Identities=31% Similarity=0.381 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCH---HHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSK---LDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~---~eC~~~flq 295 (559)
..+.||-+|+..||++|++|| |+|.++|-.+|.||. .-|+.+|+.
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHH
Confidence 457899999999999999999 999999999999999 779999986
No 37
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.77 E-value=0.016 Score=58.61 Aligned_cols=42 Identities=17% Similarity=0.421 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHH
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKL 293 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~f 293 (559)
.+.||.+||.+|+++=..||..|..||.++++||..+..-||
T Consensus 62 rg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W 103 (238)
T KOG0048|consen 62 RGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW 103 (238)
T ss_pred CCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH
Confidence 678999999999999999999999999999999999987776
No 38
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=95.54 E-value=0.0088 Score=62.00 Aligned_cols=44 Identities=18% Similarity=0.462 Sum_probs=35.6
Q ss_pred ccCCCCCC-CCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceec
Q 008612 196 FKCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFS 242 (559)
Q Consensus 196 ~~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~ 242 (559)
..|+.|+. .+...||+|..|.+|+||.+|+..+ .++-.|.|.++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~---~~h~~H~~lR~ 197 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN---EHHAAHAMLRL 197 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC---CCCcccceeec
Confidence 68999999 8888899999999999999999887 23334555553
No 39
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=95.21 E-value=0.013 Score=61.44 Aligned_cols=46 Identities=20% Similarity=0.523 Sum_probs=36.0
Q ss_pred cCCccCCCCCCCCC-CceeEeccCCCcccchhhhhcCC-CCCCCCCCC
Q 008612 193 LKGFKCGSCGEQCN-SGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDD 238 (559)
Q Consensus 193 ~~~~~C~~Cg~~~~-~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~d 238 (559)
.....|..|++.-- .-+|+|..|.+|+||..||.+|. .+.|...|.
T Consensus 6 He~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHP 53 (381)
T KOG1280|consen 6 HEGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHP 53 (381)
T ss_pred cCCceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCc
Confidence 34578999997654 45899999999999999999994 455544443
No 40
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.99 E-value=0.012 Score=49.79 Aligned_cols=43 Identities=26% Similarity=0.530 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHHHHHHH------cC------C--CHHHHHHHcC----CCCHHHHHHHHHc
Q 008612 253 ATWTEAETLLLLESVMR------HG------D--NWELVAQNVP----TKSKLDCISKLIE 295 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~------~g------~--nW~~Ia~~vg----~kT~~eC~~~flq 295 (559)
..||++|+..||+.+.. ++ + -|..||+.+. .||+.||..+|-+
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 46999999999999977 21 1 5999998875 6999999999966
No 41
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=93.84 E-value=0.03 Score=63.83 Aligned_cols=41 Identities=27% Similarity=0.489 Sum_probs=34.1
Q ss_pred CccCCCCCC-CCCCceeEeccCCCcccchhhhhcCCCCCCCC
Q 008612 195 GFKCGSCGE-QCNSGCYEYSKQGSFVICEKCFKNGNYGEDKS 235 (559)
Q Consensus 195 ~~~C~~Cg~-~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~s 235 (559)
-..|+.|.. .+...||+|.+|-+++||..||..|+.+.++.
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk 644 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHK 644 (966)
T ss_pred hhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCC
Confidence 357999974 56678999999999999999999998765443
No 42
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.24 E-value=0.095 Score=59.17 Aligned_cols=44 Identities=23% Similarity=0.564 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
..+.||.+|+..|-..+.++|++|..|++.+| |.|..|+.+|-+
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 47889999999999999999999999999998 799999999975
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=92.10 E-value=0.12 Score=56.86 Aligned_cols=43 Identities=26% Similarity=0.577 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHH
Q 008612 252 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLI 294 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~fl 294 (559)
+..|+..|+..|=-++.+|| ..|..|+..+..||+.||..+|-
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 67899999999999999999 89999999999999999999995
No 44
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=91.74 E-value=0.15 Score=57.54 Aligned_cols=54 Identities=26% Similarity=0.427 Sum_probs=45.7
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc------------------C-CCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCC
Q 008612 251 HGATWTEAETLLLLESVM-------RH------------------G-DNWELVAQNVPTKSKLDCISKLIELPFGEFMMG 304 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie-------~~------------------g-~nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l~ 304 (559)
....||-+|+.+||..|+ +| . =+|..|++-+|||+..||+.||-+|=+...+-.
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 189999999999999999999998877766643
No 45
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=89.70 E-value=0.27 Score=54.34 Aligned_cols=44 Identities=18% Similarity=0.427 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcC
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIEL 296 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flqL 296 (559)
...|+.+|+.+||.+-.....-|..|+.-|| ||..+|..||..|
T Consensus 59 ~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 59 KTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 5679999999999999999999999999998 8999999999774
No 46
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=89.16 E-value=0.61 Score=38.54 Aligned_cols=44 Identities=27% Similarity=0.424 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHcC-----------------CCHHHHHHHcC-----CCCHHHHHHHHHcC
Q 008612 253 ATWTEAETLLLLESVMRHG-----------------DNWELVAQNVP-----TKSKLDCISKLIEL 296 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~~g-----------------~nW~~Ia~~vg-----~kT~~eC~~~flqL 296 (559)
..||.+|...|++.|++|. .-|..|++.+. .||..++..+|-+|
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 69999999998653
No 47
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=88.50 E-value=0.69 Score=53.11 Aligned_cols=54 Identities=17% Similarity=0.381 Sum_probs=46.3
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc----CCcCCCCCCC
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE----LPFGEFMMGS 305 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq----LPIeD~~l~~ 305 (559)
..-||..|..++-.+|-.|..|+..|++.|.+||-.||++.|.- ++++-..|.+
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK~~~~~~~~~~d 676 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKKIMRLGRKIIDD 676 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHHhccchhhhHhh
Confidence 56799999999999999999999999999999999999999863 5554444443
No 48
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=88.02 E-value=0.23 Score=52.30 Aligned_cols=41 Identities=20% Similarity=0.560 Sum_probs=33.9
Q ss_pred CCccCCCCCCCC-CCceeEeccCCCcccchhhhhcCCCCCCC
Q 008612 194 KGFKCGSCGEQC-NSGCYEYSKQGSFVICEKCFKNGNYGEDK 234 (559)
Q Consensus 194 ~~~~C~~Cg~~~-~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ 234 (559)
-...|++|.... ...+|.|..|.++.+|..||-.|+.|..+
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 457899998665 45699999999999999999999876443
No 49
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=85.24 E-value=1.2 Score=47.65 Aligned_cols=51 Identities=20% Similarity=0.207 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHH-HHcCCCCHHHHHHHHHcCCcCCCC
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELVA-QNVPTKSKLDCISKLIELPFGEFM 302 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia-~~vg~kT~~eC~~~flqLPIeD~~ 302 (559)
-..|+.+|=..+=+||+.||.|+..|- ..|.|||--+|+..|..--....|
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKkSery 328 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKKSERY 328 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhcCcch
Confidence 357999999999999999999999995 789999999999999765444444
No 50
>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=85.21 E-value=0.77 Score=43.85 Aligned_cols=42 Identities=31% Similarity=0.510 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHcCCCCHHHHHHHHH
Q 008612 252 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKLI 294 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g--~-----nW~~Ia~~vg~kT~~eC~~~fl 294 (559)
...||.+|+++|-|.|.+|- | -.+.|++.++ ||+.-|-.||.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWN 52 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWN 52 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHH
Confidence 46799999999999999995 2 5777777775 99999999994
No 51
>PF15324 TALPID3: Hedgehog signalling target
Probab=84.95 E-value=3.1 Score=49.79 Aligned_cols=94 Identities=21% Similarity=0.346 Sum_probs=59.4
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHH---HH---hhHH
Q 008612 458 SEKNDVPLNLRIRTATATALGAAAANAKLLADQEDREIEHLV-------------AIIIETQMKKLHS---KI---NYFD 518 (559)
Q Consensus 458 ~~~~~~~~~~~v~~Aaa~AL~aAA~kAk~LA~~EEreI~~Lv-------------~~lIe~QlkKLEl---KL---k~fe 518 (559)
....++.++..|-+|+|+|+|+||--=|...+.|- ++.+.. ..+.+.|.+ ++- |+ .|=.
T Consensus 54 ~sp~~iDSAtTVAAATAAAIATaAPLiKvQSdLEA-KVnsVselL~KLQEtDkqLqrvteqQt~-i~~~~ek~~ch~~Ek 131 (1252)
T PF15324_consen 54 TSPSGIDSATTVAAATAAAIATAAPLIKVQSDLEA-KVNSVSELLNKLQETDKQLQRVTEQQTS-IQNQHEKLHCHDHEK 131 (1252)
T ss_pred CCCCCCchHHHHHHHHHHHHHhhhhhhhhcchHHH-HHHHHHHHHHHhhhhhcchhhhhhhhcc-ccccccccchhhHHH
Confidence 34556667778888888888888865555555442 222211 112222221 110 11 0122
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 008612 519 DLELIMEKEYNEMMQLKECLVEERIDVLERALKTG 553 (559)
Q Consensus 519 eLE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~~~g 553 (559)
.|..+|+.--++||+.+||.+.=+--|+..|++.|
T Consensus 132 Qmn~fmeQ~l~HLEKLQqQQi~iQshfIsSAl~~~ 166 (1252)
T PF15324_consen 132 QMNVFMEQHLRHLEKLQQQQIDIQSHFISSALKTG 166 (1252)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 35567889999999999999999999999999976
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=84.69 E-value=1.3 Score=47.33 Aligned_cols=45 Identities=16% Similarity=0.392 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
....||..|..++.-|+.++|.|+.-|++...+|...|...+|++
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 53
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=83.69 E-value=0.95 Score=50.93 Aligned_cols=45 Identities=22% Similarity=0.375 Sum_probs=39.5
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHH----------HHHcCCCCHHHHHHHHHcC
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELV----------AQNVPTKSKLDCISKLIEL 296 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~I----------a~~vg~kT~~eC~~~flqL 296 (559)
.+.||.+|+.-+.+||.+||.|+++| -..+..||+.|.+.||.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 56899999999999999999999999 3345579999999999773
No 54
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=82.46 E-value=1.3 Score=49.76 Aligned_cols=44 Identities=18% Similarity=0.505 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
...|+.+|+..|++.=..+|.-|..||.+++.+|..+|..+|+.
T Consensus 72 ~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~ 115 (512)
T COG5147 72 KKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVN 115 (512)
T ss_pred cccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHH
Confidence 57899999999999999999999999999999999999999985
No 55
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=82.16 E-value=8.3 Score=45.83 Aligned_cols=81 Identities=27% Similarity=0.254 Sum_probs=57.9
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 469 IRTATATAL-GAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 547 (559)
Q Consensus 469 v~~Aaa~AL-~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~ 547 (559)
+..|.-.+| ...-.+|+.+...++.++++|+..|.+ +.+++|.+....+.+...+++.+++|++.+++|-.+|..+++
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 345689999999999999999999865 445577777777777777777777777777777777666655
Q ss_pred HHH
Q 008612 548 RAL 550 (559)
Q Consensus 548 ~~~ 550 (559)
.+-
T Consensus 570 ~~~ 572 (782)
T PRK00409 570 EAE 572 (782)
T ss_pred HHH
Confidence 543
No 56
>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=81.69 E-value=9.4 Score=45.31 Aligned_cols=81 Identities=21% Similarity=0.096 Sum_probs=57.6
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 469 IRTATATAL-GAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLE 547 (559)
Q Consensus 469 v~~Aaa~AL-~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~ 547 (559)
+..|.-.+| ...-.+|+.+...++.++++|+..|.+. .+++|.++...+.+...+++.++.|++.+++|-.+|..+++
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 334443344 3456799999999999999999998654 45577777777777777777777777777777777666655
Q ss_pred HHH
Q 008612 548 RAL 550 (559)
Q Consensus 548 ~~~ 550 (559)
.|-
T Consensus 565 ~a~ 567 (771)
T TIGR01069 565 ELE 567 (771)
T ss_pred HHH
Confidence 443
No 57
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=80.59 E-value=1.7 Score=46.24 Aligned_cols=45 Identities=33% Similarity=0.530 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHHcC----------CCHHHHHH---HcC-CCCHHHHHHHHHcCC
Q 008612 253 ATWTEAETLLLLESVMRHG----------DNWELVAQ---NVP-TKSKLDCISKLIELP 297 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~~g----------~nW~~Ia~---~vg-~kT~~eC~~~flqLP 297 (559)
..|+.+|++.||++....- ..|..||. ..| .||+.||..+|=+|.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 6799999999999985431 35999997 344 599999999997654
No 58
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=80.06 E-value=1 Score=50.48 Aligned_cols=42 Identities=24% Similarity=0.417 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHH
Q 008612 252 GATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKL 293 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~f 293 (559)
.+.|+..|+..|+-+++.|| .+|..||..++.+|+++|..|+
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw 62 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW 62 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchh
Confidence 56899999999999999999 8999999999999999999999
No 59
>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=69.03 E-value=4.5 Score=27.72 Aligned_cols=28 Identities=25% Similarity=0.590 Sum_probs=23.2
Q ss_pred ccCCCCCCCCCCc-eeEeccCCCcccchhh
Q 008612 196 FKCGSCGEQCNSG-CYEYSKQGSFVICEKC 224 (559)
Q Consensus 196 ~~C~~Cg~~~~~~-~y~~~k~~~~~lC~~C 224 (559)
+.|..|++..... .|+|.+|. +.+.+.|
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCC-CeEcCcc
Confidence 3699999999988 99998764 8887776
No 60
>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=67.38 E-value=6.9 Score=35.69 Aligned_cols=44 Identities=20% Similarity=0.428 Sum_probs=34.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC----CCHHHHHHHcC------------CCCHHHHHHHH
Q 008612 250 THGATWTEAETLLLLESVMRHG----DNWELVAQNVP------------TKSKLDCISKL 293 (559)
Q Consensus 250 ~~~~~WT~~E~~~LLe~Ie~~g----~nW~~Ia~~vg------------~kT~~eC~~~f 293 (559)
..+..||.+|+.-||-.+.+|| |+|+.|-+.+- +||+.+.-.|.
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~ 106 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRC 106 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHH
Confidence 3478899999999999999999 59999977553 78998877665
No 61
>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=67.28 E-value=3.8 Score=27.95 Aligned_cols=27 Identities=30% Similarity=0.769 Sum_probs=12.3
Q ss_pred cCCCCCCCCCC-ceeEeccCCCcccchhh
Q 008612 197 KCGSCGEQCNS-GCYEYSKQGSFVICEKC 224 (559)
Q Consensus 197 ~C~~Cg~~~~~-~~y~~~k~~~~~lC~~C 224 (559)
.|+.|+..... ..|+|..| +|.|...|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~C-df~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSEC-DFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT------HHH
T ss_pred cCCcCCCcCCCCceEECccC-CCccChhc
Confidence 69999999988 78999986 78888877
No 62
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=62.81 E-value=4.7 Score=45.32 Aligned_cols=91 Identities=9% Similarity=-0.032 Sum_probs=71.3
Q ss_pred CCCCCCCCCCCCCHHHHhhcccccCCCC-CCCChhhHHHHHHHHHHHHHhCCCceee-----HHHHhhhcc--chHHHHH
Q 008612 20 PSHSSWFRWDDIHETERTALKEFFDGSS-ISRTPKIYKEYRDFMINKYREEPSRRLT-----FTQVRKSLV--GDVSLLH 91 (559)
Q Consensus 20 Ps~~~wF~~~~i~~iE~~~~peff~~~~-~~ktp~~Y~~~RN~ii~~yr~np~~~lt-----~t~~r~~l~--gD~~~i~ 91 (559)
+..+.-++...=+.-....+++|+.+++ ....+..|+.+|+.+++.++-.-..+.+ -+..+++.. +++-++-
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 3455666666777788889999998872 2457788999999999999964444443 556677774 7899999
Q ss_pred HHHHhhhhhcccccccCCC
Q 008612 92 KVFRLLDEWGLINFGAVSR 110 (559)
Q Consensus 92 rvh~FLe~wGlIN~~~~~~ 110 (559)
+|+.|.+.|+-|+.+|..+
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 63
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=60.57 E-value=11 Score=33.07 Aligned_cols=44 Identities=18% Similarity=0.339 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHHHHHc----C----CCHHHHHHHcCC-----CCHHHHHHHHHc
Q 008612 252 GATWTEAETLLLLESVMRH----G----DNWELVAQNVPT-----KSKLDCISKLIE 295 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~----g----~nW~~Ia~~vg~-----kT~~eC~~~flq 295 (559)
.+.||+++|..||+||-.| | .||...-++|.. =|..|-..+.-+
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr 60 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR 60 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence 5779999999999999888 5 488888877753 266666666544
No 64
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=59.79 E-value=58 Score=32.46 Aligned_cols=63 Identities=16% Similarity=0.228 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 476 ALGAAAANAKLLADQEDR-EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLV 539 (559)
Q Consensus 476 AL~aAA~kAk~LA~~EEr-eI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~ 539 (559)
+--.+++|...-.+.|+. ++.----.+++...+.+|...+.| +||+-|+.+|+.|-..|..-|
T Consensus 134 ~~LVaaak~~~~~~~e~~~~~d~s~l~~~~~k~~emE~Qv~IL-~lE~~L~~ar~~L~~lRk~~Y 197 (200)
T smart00307 134 ANLVAAVKSGMIFDEEQEEEEDFSKLSLHEGKTQEMEQQVEIL-KLENELEAARKKLAEIRKQHY 197 (200)
T ss_pred HHHHHHHHHHHHHHHhhhhhcchhccchHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence 333455555554332322 222222245555556666677777 789999999999888887654
No 65
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=58.79 E-value=13 Score=45.53 Aligned_cols=41 Identities=12% Similarity=0.284 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHH
Q 008612 253 ATWTEAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKL 293 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~f 293 (559)
..||..+-..++.+.++|| +|-..||..|++||++|...+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~ 866 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYA 866 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHH
Confidence 4799999999999999999 9999999999999999987544
No 66
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=58.51 E-value=15 Score=27.69 Aligned_cols=51 Identities=14% Similarity=0.223 Sum_probs=40.9
Q ss_pred hHHHHHHHHHHHHHhCCCcee-eHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008612 54 IYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 54 ~Y~~~RN~ii~~yr~np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (559)
+|-.+|+.|+.... .|...| |..+....+.-....+.|...-|+.-|+|-.
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 36677888777533 466778 8999888887778999999999999999963
No 67
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=57.15 E-value=45 Score=34.63 Aligned_cols=64 Identities=17% Similarity=0.181 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----HHHHHHHHHHHHHHHHHHHHHHH
Q 008612 474 ATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINY----FDDLELIMEKEYNEMMQLKECLV 539 (559)
Q Consensus 474 a~AL~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~----feeLE~~~e~Er~~LE~~rq~L~ 539 (559)
.-.+-.||.|+-.|+..| ++-+..-.-|.+|++++..+|+- -.+|+.-+++-+.+||+.|+.|-
T Consensus 90 ~~~~~~aa~Rplel~e~E--kvlk~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle 157 (338)
T KOG3647|consen 90 KESLMSAAQRPLELLEVE--KVLKSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLE 157 (338)
T ss_pred HHHHHHHHcCCccHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445677888888887665 34444556678899999999986 46888999999999999999873
No 68
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=56.94 E-value=6.3 Score=33.56 Aligned_cols=35 Identities=26% Similarity=0.484 Sum_probs=25.3
Q ss_pred cCCCCCCCCCCceeEecc---CCCcccchhhhhcCCCC
Q 008612 197 KCGSCGEQCNSGCYEYSK---QGSFVICEKCFKNGNYG 231 (559)
Q Consensus 197 ~C~~Cg~~~~~~~y~~~k---~~~~~lC~~Cf~~G~~~ 231 (559)
.|.+||.++......-.. ..+-+-|.-||.+|.|-
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~G~Ft 39 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQNGEFT 39 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcCCcee
Confidence 699999999866532222 24556899999999864
No 69
>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=56.29 E-value=21 Score=26.39 Aligned_cols=37 Identities=11% Similarity=0.146 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 258 AETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 258 ~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
+=+..||..++.-+ --|..||+.||- |+..|..+.-+
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 88889887654
No 70
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=56.01 E-value=8.9 Score=42.32 Aligned_cols=52 Identities=15% Similarity=0.241 Sum_probs=44.0
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHH-HHcCCCCHHHHHHHHHcCCcCCCCCC
Q 008612 253 ATWTEAETLLLLESVMRHGDNWELVA-QNVPTKSKLDCISKLIELPFGEFMMG 304 (559)
Q Consensus 253 ~~WT~~E~~~LLe~Ie~~g~nW~~Ia-~~vg~kT~~eC~~~flqLPIeD~~l~ 304 (559)
..|++-|-.++-|++++||.|+++|- +++.=||-...++.|.-.--.|.|..
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYvq 338 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQ 338 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHHH
Confidence 57999999999999999999999996 66777888888888877766776654
No 71
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=54.72 E-value=14 Score=38.76 Aligned_cols=88 Identities=14% Similarity=0.224 Sum_probs=52.1
Q ss_pred CccCCCCCCCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-C
Q 008612 195 GFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-D 272 (559)
Q Consensus 195 ~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~ 272 (559)
-..|.-||.. ..+.-.-. -++.||.+|-.--+ +|.|. .++.... -..||+++...|.+.=..-. .
T Consensus 25 N~~CADC~a~--~P~WaSwn-lGvFiC~~C~giHR~lg~hi-----SkVkSv~-----LD~W~~eqv~~m~~~GN~~an~ 91 (287)
T KOG0703|consen 25 NKVCADCGAK--GPRWASWN-LGVFICLRCAGIHRSLGVHI-----SKVKSVT-----LDEWTDEQVDFMISMGNAKANS 91 (287)
T ss_pred cCcccccCCC--CCCeEEee-cCeEEEeecccccccccchh-----heeeeee-----ccccCHHHHHHHHHHcchhhhh
Confidence 4679999887 33333333 57889999954442 55443 3333322 35799999877765321100 2
Q ss_pred CHHHH-HHHcCCCCHHHHHHHHHc
Q 008612 273 NWELV-AQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 273 nW~~I-a~~vg~kT~~eC~~~flq 295 (559)
-|+.- ....-..++++-+++||+
T Consensus 92 ~~ea~~p~~~~~p~~d~~~e~FIR 115 (287)
T KOG0703|consen 92 YYEAKLPDPFRRPGPDDLVEQFIR 115 (287)
T ss_pred hccccCCccccCCChHHHHHHHHH
Confidence 35432 333435678888999988
No 72
>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=54.03 E-value=17 Score=30.83 Aligned_cols=42 Identities=21% Similarity=0.425 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHHc-------C------CCHHHHHHHcC-----CCCHHHHHHHHHc
Q 008612 254 TWTEAETLLLLESVMRH-------G------DNWELVAQNVP-----TKSKLDCISKLIE 295 (559)
Q Consensus 254 ~WT~~E~~~LLe~Ie~~-------g------~nW~~Ia~~vg-----~kT~~eC~~~flq 295 (559)
.||.+.+..||+.+... + ..|+.|++.+. ..|..||..||-.
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 49999999999998444 1 15888987775 4789999999854
No 73
>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=53.54 E-value=24 Score=27.94 Aligned_cols=54 Identities=20% Similarity=0.310 Sum_probs=41.9
Q ss_pred hhhHHHHHHHHHHHHHhCCCcee-eHHHHhhhccchHHHHHHHHHhhhhhcccccc
Q 008612 52 PKIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (559)
Q Consensus 52 p~~Y~~~RN~ii~~yr~np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~ 106 (559)
-++|-.+|+.|...- .-|..+| +..+..+.+.--...+.+....|+.+|+|--.
T Consensus 3 ~~i~~~l~~~I~~g~-~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 3 EQIYDQLRQAILSGR-LPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHHHHHTTS-S-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHcCC-CCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 367888888888743 3578899 99998888877789999999999999999643
No 74
>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=51.61 E-value=45 Score=27.15 Aligned_cols=45 Identities=22% Similarity=0.314 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 503 IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 548 (559)
Q Consensus 503 Ie~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~ 548 (559)
|...-++|+.|+.|||.|-+ +++--.+|+...++|..-|..|+.-
T Consensus 13 I~~~K~~l~ik~~H~Ekl~k-itK~p~El~~i~~kl~~~R~~FLn~ 57 (62)
T PF06034_consen 13 INQMKRQLTIKSQHWEKLKK-ITKNPKELQEIEKKLQELRQNFLNF 57 (62)
T ss_pred HHHHHHHHHHHHHHHHHHHh-ccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34455679999999999954 5677778888889999999988854
No 75
>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=51.56 E-value=35 Score=26.20 Aligned_cols=43 Identities=19% Similarity=0.266 Sum_probs=35.8
Q ss_pred HhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccCC
Q 008612 67 REEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVS 109 (559)
Q Consensus 67 r~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~~ 109 (559)
..+|...+|+++..+.+.-+..++.|+..=|+.+|||--..++
T Consensus 15 ~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 15 ARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 3466667999999999999999999999999999999876665
No 76
>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=51.51 E-value=1.6e+02 Score=28.51 Aligned_cols=72 Identities=15% Similarity=0.165 Sum_probs=40.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 008612 467 LRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKK-------LHSKINYFDDLELIMEKEYNEMMQLKECL 538 (559)
Q Consensus 467 ~~v~~Aaa~AL~aAA~kAk~LA~~EEreI~~Lv~~lIe~QlkK-------LElKLk~feeLE~~~e~Er~~LE~~rq~L 538 (559)
+.|..|-|+|.+|+-+|--.|-...|.+--.-.+.|+--|... +-.-||+|-.+-+.+-+--+++-||.++|
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 4456666677777666655544333333333333343333332 23357888888877777776666666554
No 77
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=50.73 E-value=25 Score=38.86 Aligned_cols=45 Identities=16% Similarity=0.348 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
....||++|..+|-.+.+.||.++.+|-+.+..||-..-+..|..
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHH
Confidence 467899999999999999999999999999999999999998864
No 78
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=50.70 E-value=26 Score=31.83 Aligned_cols=74 Identities=15% Similarity=0.277 Sum_probs=49.9
Q ss_pred CCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHH
Q 008612 198 CGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELV 277 (559)
Q Consensus 198 C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~I 277 (559)
|..||..+.-.+++|..|...+ .|+|.. .. -.--..|++.++...-+..||-.+|
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i-------~G~F~l------------~~------~~~L~~E~~~Fi~~Fi~~rGnlKe~ 55 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI-------EGEFEL------------PW------FARLSPEQLEFIKLFIKNRGNLKEM 55 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE-------Eeeecc------------ch------hhcCCHHHHHHHHHHHHhcCCHHHH
Confidence 8899999988888888864222 333311 00 1123578889999999999999999
Q ss_pred HHHcCC-----CCHHHHHHHHHcC
Q 008612 278 AQNVPT-----KSKLDCISKLIEL 296 (559)
Q Consensus 278 a~~vg~-----kT~~eC~~~flqL 296 (559)
++.+|- |..-+=+..=|.+
T Consensus 56 e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 56 EKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHCCCcHHHHHHHHHHHHHhCC
Confidence 999992 5554444444443
No 79
>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=48.99 E-value=48 Score=24.66 Aligned_cols=45 Identities=22% Similarity=0.206 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008612 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 58 ~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (559)
.|-.||..-.. ..+++.+..+.+.-+-..+.+=.+.|...|||++
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 5599999999999899999999999999999974
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=48.86 E-value=37 Score=26.11 Aligned_cols=44 Identities=23% Similarity=0.293 Sum_probs=34.9
Q ss_pred HHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccccc
Q 008612 61 FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (559)
Q Consensus 61 ~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~ 107 (559)
.|+......+ +++.+..+.+.-....+.|+..-|...|+|+...
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 8999999888878999999999999999999643
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=48.24 E-value=29 Score=26.36 Aligned_cols=44 Identities=20% Similarity=0.285 Sum_probs=35.7
Q ss_pred HHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008612 61 FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 61 ~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (559)
.|++.+...+ ..+|+++..+.+.-....+.|+..-|+.+|+|..
T Consensus 7 ~iL~~l~~~~-~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESG-GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCTB-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 3566566554 4589999999999899999999999999999864
No 82
>COG2916 Hns DNA-binding protein H-NS [General function prediction only]
Probab=47.21 E-value=1.6e+02 Score=27.33 Aligned_cols=49 Identities=22% Similarity=0.208 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 494 EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVL 546 (559)
Q Consensus 494 eI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~ 546 (559)
-|..|...+-+++++-||-.++.|+.+. .||+.-+..+.+.+.+|+.-+
T Consensus 4 n~r~l~~~~~e~~~e~lee~~ek~eq~~----~~r~~e~~~~~~~i~e~~~~~ 52 (128)
T COG2916 4 NIRTLRAMARETYLELLEEMLEKEEQVV----QERQEEEAAAIAEIEERQEKY 52 (128)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Confidence 3778889999999999999998887776 455555555555555554433
No 83
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=47.15 E-value=17 Score=35.26 Aligned_cols=41 Identities=27% Similarity=0.445 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHcCCCCHHHHHHHH
Q 008612 252 GATWTEAETLLLLESVMRHG--D-----NWELVAQNVPTKSKLDCISKL 293 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g--~-----nW~~Ia~~vg~kT~~eC~~~f 293 (559)
...||.+++++|-+.|-.|+ | -...+++.+ .||...|..+|
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 45799999999999998887 2 344455555 48999999999
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=46.80 E-value=32 Score=30.60 Aligned_cols=51 Identities=24% Similarity=0.292 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHhCCCceeeHHHHhhhcc-----chHHHHHHHHHhhhhhcccccc
Q 008612 55 YKEYRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINFG 106 (559)
Q Consensus 55 Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~-----gD~~~i~rvh~FLe~wGlIN~~ 106 (559)
.-.-|..|++....++. .+|+.+.-..|. -+..+|.|...+|+.-|||.=-
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 34578999998888876 999999877763 3678999999999999999843
No 85
>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=44.37 E-value=1.2e+02 Score=28.08 Aligned_cols=52 Identities=12% Similarity=0.310 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 494 EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 548 (559)
Q Consensus 494 eI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~ 548 (559)
++..-+ ..++.|+++||.+++.+.++-..|++ .+=+.++.+|..+-+.+++.
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 56678889999888888764
No 86
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=43.73 E-value=55 Score=30.23 Aligned_cols=55 Identities=15% Similarity=0.347 Sum_probs=43.1
Q ss_pred hhhHHHHHHHHHHHHHh---CCCcee-eHHHHhhhccchHHHHHHHHHhhhhhcccccc
Q 008612 52 PKIYKEYRDFMINKYRE---EPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (559)
Q Consensus 52 p~~Y~~~RN~ii~~yr~---np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~ 106 (559)
-.+|.+|.|.|...-.. .|...| |+.+-...+.-..+.+.|.+.-||+-|+|.-.
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 36999999999887763 677766 44455555556899999999999999999843
No 87
>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=43.45 E-value=29 Score=25.39 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHcC
Q 008612 258 AETLLLLESVMRHGDNWELVAQNVP 282 (559)
Q Consensus 258 ~E~~~LLe~Ie~~g~nW~~Ia~~vg 282 (559)
-|-..|.++++.++||....|+.+|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHC
Confidence 3667899999999999999999999
No 88
>KOG3859 consensus Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]
Probab=41.05 E-value=2.2e+02 Score=30.28 Aligned_cols=72 Identities=18% Similarity=0.317 Sum_probs=50.4
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHH---HHHHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 008612 481 AANAKLLAD--QEDREIEHLVAII---IETQMKKLHSKI-NYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKT 552 (559)
Q Consensus 481 A~kAk~LA~--~EEreI~~Lv~~l---Ie~QlkKLElKL-k~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~~~ 552 (559)
|.|...|+. ..|.+|+..--.- -|..||+.|--| ..|+.|-..-..|+..||..|.+|=.|++.|.++...+
T Consensus 326 aKr~e~~~e~qrkEee~rqmFvqrvkekE~elke~Ekel~~kf~~lkr~h~eEk~kle~~rr~Leee~~~f~~rk~~~ 403 (406)
T KOG3859|consen 326 AKRNEFLGELQRKEEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKRLHQEEKKKLEEKRKQLEEEVNAFQRRKTAA 403 (406)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444443 2344444433222 355677777666 36999999999999999999999999999998876654
No 89
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=40.20 E-value=26 Score=37.31 Aligned_cols=98 Identities=16% Similarity=0.127 Sum_probs=55.1
Q ss_pred CccCCCCCCCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcCCC
Q 008612 195 GFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDN 273 (559)
Q Consensus 195 ~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~n 273 (559)
-..|.-||..- -.|.-|. -++.||.+|-.--+ .|.|.+ |++ .. .=..||.+|..+|.-+=...-..
T Consensus 20 Nk~CaDCga~~-P~W~S~n--lGvfiCi~CagvHRsLGvhiS---~VK--Si-----tLD~wt~~~l~~m~~gGN~~a~~ 86 (319)
T COG5347 20 NKKCADCGAPN-PTWASVN--LGVFLCIDCAGVHRSLGVHIS---KVK--SL-----TLDNWTEEELRRMEVGGNSNANR 86 (319)
T ss_pred cCccccCCCCC-CceEecc--cCeEEEeecchhhhcccccee---eee--ee-----ecccCCHHHHHHHHHhcchhhhh
Confidence 46799998876 4454444 58999999965553 554432 222 21 13579999887766521110023
Q ss_pred HHHHHH---H-cC--CCCHHHHHHHHHc-CCcCCCCCCC
Q 008612 274 WELVAQ---N-VP--TKSKLDCISKLIE-LPFGEFMMGS 305 (559)
Q Consensus 274 W~~Ia~---~-vg--~kT~~eC~~~flq-LPIeD~~l~~ 305 (559)
|.+--- + +. .+.-...+.+|++ ++..-.|...
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 332211 1 12 4566778888876 5555555443
No 90
>smart00595 MADF subfamily of SANT domain.
Probab=39.78 E-value=22 Score=29.78 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=23.2
Q ss_pred CHHHHHHHcCCCCHHHHHHHHHcCCcCCCCC
Q 008612 273 NWELVAQNVPTKSKLDCISKLIELPFGEFMM 303 (559)
Q Consensus 273 nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l 303 (559)
-|..||..+|. |.++|..+|-.| -+.|.
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 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=39.06 E-value=90 Score=22.98 Aligned_cols=44 Identities=27% Similarity=0.386 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccc
Q 008612 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLI 103 (559)
Q Consensus 58 ~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlI 103 (559)
.+-.|++.-+.||. +|.++..+.+.-....+.|....|+.-|+|
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 34567777777775 999999999988899999999999999997
No 92
>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=37.86 E-value=4.5e+02 Score=27.33 Aligned_cols=51 Identities=27% Similarity=0.439 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhhHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 008612 504 ETQMKKLHSKINYFDD----LELIMEKEYNEMMQLKECLVEERIDVLERALKTGV 554 (559)
Q Consensus 504 e~QlkKLElKLk~fee----LE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~~~g~ 554 (559)
..+.+.++.+-+.+++ |..-|+.||+.+.+..++++..++..-...++.|.
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 3444555555555555 66668888888888888888777776666665553
No 93
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=37.30 E-value=46 Score=40.96 Aligned_cols=45 Identities=16% Similarity=0.316 Sum_probs=37.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHc------------CCCCHHHHHHHHH
Q 008612 250 THGATWTEAETLLLLESVMRHG-DNWELVAQNV------------PTKSKLDCISKLI 294 (559)
Q Consensus 250 ~~~~~WT~~E~~~LLe~Ie~~g-~nW~~Ia~~v------------g~kT~~eC~~~fl 294 (559)
..+..||.+|+..||-.+.+|| ++|+.|-+.+ .+||+.++-.|.-
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 3467899999999999999999 9999996654 3799999877653
No 94
>PRK11546 zraP zinc resistance protein; Provisional
Probab=35.99 E-value=3.9e+02 Score=25.36 Aligned_cols=70 Identities=11% Similarity=0.138 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 008612 487 LADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELI----------MEKEYNEMMQLKECLVEERIDVLERALKTGVSK 556 (559)
Q Consensus 487 LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~----------~e~Er~~LE~~rq~L~~eR~~~~~~~~~~g~~~ 556 (559)
|-...-.+++.|...-......--+.....=.||..+ +..-.+++...|++|+.+|+.+-.+..+.|||.
T Consensus 44 LT~EQQa~~q~I~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~~~~~~~~k~Gv~~ 123 (143)
T PRK11546 44 LTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRVKRDIAMAEAGIPR 123 (143)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 4444455555555544433222222222333455544 455678899999999999999999999999994
No 95
>PRK09462 fur ferric uptake regulator; Provisional
Probab=35.57 E-value=56 Score=30.32 Aligned_cols=48 Identities=15% Similarity=0.251 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhcc-----chHHHHHHHHHhhhhhccccc
Q 008612 58 YRDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 58 ~RN~ii~~yr~np~~~lt~t~~r~~l~-----gD~~~i~rvh~FLe~wGlIN~ 105 (559)
-|-.|++.....+...+|+.+.-..|. -+...|.|...+|+.-|||.=
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 477788877665678999999876663 268999999999999999973
No 96
>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=35.03 E-value=3.2e+02 Score=26.13 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 008612 519 DLELIMEKEYNEMMQLKECLVE 540 (559)
Q Consensus 519 eLE~~~e~Er~~LE~~rq~L~~ 540 (559)
+||+.|+.+|+.|-..|..-|.
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 5788888888888888876554
No 97
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=35.02 E-value=48 Score=37.89 Aligned_cols=94 Identities=16% Similarity=0.217 Sum_probs=50.6
Q ss_pred CccCCCCCCCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH-----H
Q 008612 195 GFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV-----M 268 (559)
Q Consensus 195 ~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~I-----e 268 (559)
-..|.-|+... ..+.|.. -++.||..|-.--+ ++ . ++... .-..||.+|...|..+= +
T Consensus 23 Nk~CADCgs~~--P~WASiN-lGIFICi~CSGIHRsLG------h--RVKSL-----SLDkWT~EEVe~Mk~gGN~~AN~ 86 (648)
T PLN03119 23 NRRCINCNSLG--PQYVCTT-FWTFVCMACSGIHREFT------H--RVKSV-----SMSKFTSKEVEVLQNGGNQRARE 86 (648)
T ss_pred CCccccCCCCC--CCceeec-cceEEeccchhhhccCC------c--eeecc-----ccCCCCHHHHHHHHHhchHHHHH
Confidence 35788898753 5566665 57889999954332 22 1 33332 23679998875443211 1
Q ss_pred HcCCCHHHHHHHcCCCCHHHHHHHHHc-CCcCCCCCC
Q 008612 269 RHGDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMG 304 (559)
Q Consensus 269 ~~g~nW~~Ia~~vg~kT~~eC~~~flq-LPIeD~~l~ 304 (559)
.|-.+|..-...++..+..+-+..||+ -|++-.|..
T Consensus 87 iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~ 123 (648)
T PLN03119 87 IYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAG 123 (648)
T ss_pred HHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccC
Confidence 122356543223343344555667887 344444443
No 98
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=34.71 E-value=3.3e+02 Score=30.64 Aligned_cols=37 Identities=22% Similarity=0.334 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhHHH------HHHHHHHHHHHHHHHHHHHHHHH
Q 008612 506 QMKKLHSKINYFDD------LELIMEKEYNEMMQLKECLVEER 542 (559)
Q Consensus 506 QlkKLElKLk~fee------LE~~~e~Er~~LE~~rq~L~~eR 542 (559)
|+.|-||||..+.| ||++|.-||+.-...+.+|-.||
T Consensus 527 q~Ek~ELkmd~lrerelreslekql~~ErklR~~~qkr~kkEk 569 (641)
T KOG3915|consen 527 QLEKTELKMDFLRERELRESLEKQLAMERKLRAIVQKRLKKEK 569 (641)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57888888888765 56666666665555555555554
No 99
>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=34.62 E-value=65 Score=28.16 Aligned_cols=46 Identities=22% Similarity=0.275 Sum_probs=38.2
Q ss_pred HHHHHHHHHhCCCceeeHHHHhhhcc-----chHHHHHHHHHhhhhhccccc
Q 008612 59 RDFMINKYREEPSRRLTFTQVRKSLV-----GDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 59 RN~ii~~yr~np~~~lt~t~~r~~l~-----gD~~~i~rvh~FLe~wGlIN~ 105 (559)
|-.|++..... ...+|+.+.-..|. -+..++.|...+|..-|||.-
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 100
>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=34.51 E-value=5.8e+02 Score=27.02 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 501 IIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 548 (559)
Q Consensus 501 ~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~ 548 (559)
.-++.|+++++..+..+++.|..+.+++..++....++..+|.++..+
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 456788999999999999999999999999999999888888776644
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=34.15 E-value=25 Score=25.97 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=18.0
Q ss_pred ccCCCCCCCCCCc-eeEeccCCCcccchhhhhc
Q 008612 196 FKCGSCGEQCNSG-CYEYSKQGSFVICEKCFKN 227 (559)
Q Consensus 196 ~~C~~Cg~~~~~~-~y~~~k~~~~~lC~~Cf~~ 227 (559)
..|++||+.-+.+ ++.... .+..||..|...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~-~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGP-NGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES--SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCC-CCcEECHHHHHH
Confidence 5799999988766 333332 368899999643
No 102
>PHA00442 host recBCD nuclease inhibitor
Probab=34.02 E-value=42 Score=26.58 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHc
Q 008612 258 AETLLLLESVMRHG-DNWELVAQNV 281 (559)
Q Consensus 258 ~E~~~LLe~Ie~~g-~nW~~Ia~~v 281 (559)
+-....|++++.+| +||+.+.+.+
T Consensus 26 ek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 26 EKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHhhHHHHHHHHcCCcchhhHHHHH
Confidence 44567899999999 9999987654
No 103
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=34.01 E-value=1e+02 Score=24.94 Aligned_cols=50 Identities=14% Similarity=0.088 Sum_probs=44.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccccc
Q 008612 58 YRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (559)
Q Consensus 58 ~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~ 107 (559)
.++.|+.....++..-+|..+..+.|.-+...+.|+..=|+.-|+|.+..
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 104
>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=33.61 E-value=1.1e+02 Score=26.00 Aligned_cols=54 Identities=15% Similarity=0.201 Sum_probs=44.9
Q ss_pred hhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccccc
Q 008612 53 KIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGA 107 (559)
Q Consensus 53 ~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~ 107 (559)
++-.+|=..||+.|... .+.+...+.-+.|.-+...|..+.+-|+..|||-=+.
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p 57 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQP 57 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCC
Confidence 45677888999999976 6888888877777768899999999999999997433
No 105
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=32.76 E-value=54 Score=34.84 Aligned_cols=68 Identities=16% Similarity=0.243 Sum_probs=53.5
Q ss_pred CCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccc
Q 008612 30 DIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLIN 104 (559)
Q Consensus 30 ~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN 104 (559)
=+++-|.+-+--+ .-.|..|+.+.--||..+... ...+|.++|++.+.-|..-.-+|++|.-.-|.|-
T Consensus 362 llS~dEq~LC~~l------~i~PkpyL~LK~~~is~~l~t-~g~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 362 LLSDDEQRLCETL------NISPKPYLELKKEVISCFLRT-RGEFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred hhcchHHHHHHHh------CCCCccHHHHHHHHHHHHHHh-CCCccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 3445555544322 236899999999999998853 5789999999998889999999999998888874
No 106
>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=32.57 E-value=72 Score=28.45 Aligned_cols=83 Identities=22% Similarity=0.261 Sum_probs=45.3
Q ss_pred ccCCCCCCCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CC
Q 008612 196 FKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHG-DN 273 (559)
Q Consensus 196 ~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~Ie~~g-~n 273 (559)
..|.-|+.. .+.+-+.. -+..+|..|-.--+ ++.|. .+++ .. . -..||.+|...| +..| ..
T Consensus 4 ~~CaDC~~~--~p~w~s~~-~GifvC~~CsgiHR~lg~hi---s~Vk--Sl----~-md~w~~~~i~~~----~~~GN~~ 66 (112)
T smart00105 4 KKCFDCGAP--NPTWASVN-LGVFLCIECSGIHRSLGVHI---SKVR--SL----T-LDTWTEEELRLL----QKGGNEN 66 (112)
T ss_pred CcccCCCCC--CCCcEEec-cceeEhHHhHHHHHhcCCCc---Ceee--ec----c-cCCCCHHHHHHH----HHhhhHH
Confidence 368888874 34455554 58899999976553 44432 1222 21 1 247999886433 3444 23
Q ss_pred HHHHHHHcC--------CCCHHHHHHHHHc
Q 008612 274 WELVAQNVP--------TKSKLDCISKLIE 295 (559)
Q Consensus 274 W~~Ia~~vg--------~kT~~eC~~~flq 295 (559)
++.+=+.-+ ..+..+-+..||+
T Consensus 67 ~n~~~e~~~~~~~~~~~~~~~~~~~~~fI~ 96 (112)
T smart00105 67 ANSIWESNLDDFSLKPPDSDDQQKYESFIA 96 (112)
T ss_pred HHHHHHhhCCccccCCCCCchHHHHHHHHH
Confidence 333322111 1224678888877
No 107
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=32.41 E-value=84 Score=26.99 Aligned_cols=44 Identities=30% Similarity=0.450 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHHHHhCCCceeeHHHHh-------hhccchH---HHHHHHHHhhhhh
Q 008612 53 KIYKEYRDFMINKYREEPSRRLTFTQVR-------KSLVGDV---SLLHKVFRLLDEW 100 (559)
Q Consensus 53 ~~Y~~~RN~ii~~yr~np~~~lt~t~~r-------~~l~gD~---~~i~rvh~FLe~w 100 (559)
++-..+||-|+.+=-.| +|+.+.. |-|+-|+ ..++|||.||.++
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 56678999998865544 7777753 4455565 6899999999876
No 108
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=32.26 E-value=23 Score=39.17 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=38.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHc
Q 008612 251 HGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIE 295 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flq 295 (559)
..-.||..|-. ++.--..|+.+...||+.+++|||+|.-..||+
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 34679998877 777778999999999999999999999999976
No 109
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=32.10 E-value=31 Score=42.62 Aligned_cols=27 Identities=26% Similarity=0.777 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHH
Q 008612 251 HGATWTEAETLLLLESVMRHG-DNWELV 277 (559)
Q Consensus 251 ~~~~WT~~E~~~LLe~Ie~~g-~nW~~I 277 (559)
.+..|..+++..||=||-+|| |+|+.|
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHh
Confidence 578899999999999999999 999998
No 110
>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=31.98 E-value=4.8e+02 Score=31.24 Aligned_cols=39 Identities=18% Similarity=0.218 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 503 IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEE 541 (559)
Q Consensus 503 Ie~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~e 541 (559)
++.+...++..++..+++..-++.+++.|+..|.+++.+
T Consensus 527 ~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~~ 565 (771)
T TIGR01069 527 LEQKNEHLEKLLKEQEKLKKELEQEMEELKERERNKKLE 565 (771)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555666666777777777777777777777766644
No 111
>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=31.97 E-value=24 Score=31.70 Aligned_cols=59 Identities=17% Similarity=0.262 Sum_probs=31.0
Q ss_pred CccCCCCCCCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHH
Q 008612 195 GFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLES 266 (559)
Q Consensus 195 ~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~ 266 (559)
-..|.-||.. ...+.+.. -++.+|..|..--+ ++.|.+ +++ .. .-..||.+|...|.++
T Consensus 13 N~~CaDCg~~--~p~w~s~~-~GiflC~~Cag~HR~lg~~is---~Vk--Si-----~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 13 NKVCADCGAP--NPTWASLN-YGIFLCLECAGIHRSLGVHIS---RVK--SI-----TMDNWSPEEVQRMREG 72 (116)
T ss_dssp CTB-TTT-SB--S--EEETT-TTEEE-HHHHHHHHHHTTTT-----EE--ET-----TTS---HHHHHHHHHS
T ss_pred cCcCCCCCCC--CCCEEEee-cChhhhHHHHHHHHHhcccch---hcc--cc-----ccCCCCHHHHHHHHHH
Confidence 3679989854 33666666 68999999986553 554332 222 21 1235999998877654
No 112
>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=31.78 E-value=2e+02 Score=23.71 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=32.0
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 507 MKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLER 548 (559)
Q Consensus 507 lkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~ 548 (559)
|+.|+.|+.++=.+=.-+..|-..|-.+...+-.||..++..
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 567777777777777777788888888888888888777654
No 113
>PLN03131 hypothetical protein; Provisional
Probab=31.38 E-value=81 Score=36.49 Aligned_cols=93 Identities=17% Similarity=0.245 Sum_probs=51.0
Q ss_pred CccCCCCCCCCCCceeEeccCCCcccchhhhhcCC-CCCCCCCCCceeccCCCCCCCCCCCCCHHHHHHHHHHH------
Q 008612 195 GFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN-YGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESV------ 267 (559)
Q Consensus 195 ~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~-~~~~~ss~df~~~~~~~~~~~~~~~WT~~E~~~LLe~I------ 267 (559)
-..|.-|+... ..+.|.. -++.||..|-.--+ ++ . ++... .-..||.+|...| +.+
T Consensus 23 Nk~CADCga~~--P~WASiN-lGIFICi~CSGIHRsLg------h--RVKSV-----TLD~WtdeEV~~M-k~gGN~~AN 85 (705)
T PLN03131 23 NRRCINCNSLG--PQFVCTN-FWTFICMTCSGIHREFT------H--RVKSV-----SMSKFTSQDVEAL-QNGGNQRAR 85 (705)
T ss_pred CCccccCCCCC--CCeeEec-cceEEchhchhhhcccC------c--ccccc-----cCCCCCHHHHHHH-HHhccHHHH
Confidence 35788888653 4555555 68889999954433 32 1 33322 2357999887533 222
Q ss_pred HHcCCCHHHHHHHcCCCCHHHHHHHHHc-CCcCCCCCC
Q 008612 268 MRHGDNWELVAQNVPTKSKLDCISKLIE-LPFGEFMMG 304 (559)
Q Consensus 268 e~~g~nW~~Ia~~vg~kT~~eC~~~flq-LPIeD~~l~ 304 (559)
+.|-.+|..--..++..+..+-+..||+ -|++-.|+.
T Consensus 86 ~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~ 123 (705)
T PLN03131 86 EIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAG 123 (705)
T ss_pred HHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhc
Confidence 1222356533333444455566677877 344444543
No 114
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=31.26 E-value=47 Score=32.13 Aligned_cols=33 Identities=21% Similarity=0.568 Sum_probs=24.1
Q ss_pred cCCCCCCCCCCceeEeccCCCcccchhhhhcCC
Q 008612 197 KCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGN 229 (559)
Q Consensus 197 ~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~ 229 (559)
.|-.||..+......-.......+|..|+.-|.
T Consensus 5 ~CEiCG~~i~~~~~v~vegsel~VC~~Cak~G~ 37 (165)
T COG1813 5 GCELCGREIDKPIKVKVEGAELTVCDDCAKFGT 37 (165)
T ss_pred ceeccccccCCCeeEEeecceeehhHHHHHhcc
Confidence 399999998854434444467899999996663
No 115
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.58 E-value=86 Score=25.94 Aligned_cols=43 Identities=26% Similarity=0.401 Sum_probs=34.6
Q ss_pred HHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008612 62 MINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 62 ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (559)
|++....++ ..+|+++.-+.+.-....+.|....|+.+|+|-.
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 116
>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=30.21 E-value=79 Score=24.09 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=33.6
Q ss_pred eeHHHHhhhccchHHHHHHHHHhhhhhcccccccCCC
Q 008612 74 LTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (559)
Q Consensus 74 lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~~~ 110 (559)
+|.++.-+.+.-+...+.|+..-|++.|||.-..++.
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 117
>KOG3564 consensus GTPase-activating protein [General function prediction only]
Probab=30.15 E-value=2.4e+02 Score=31.91 Aligned_cols=64 Identities=20% Similarity=0.108 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 008612 492 DREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKW 557 (559)
Q Consensus 492 EreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~~~g~~~~ 557 (559)
-++++.+++. -++.+--|+.||+|=...=...-++|+++|--++. +.-|+++++.+++-|+..+
T Consensus 51 ~~~~~~~L~K-a~tk~~~ldvklkha~~~vda~ik~rr~ae~d~~~-~E~~i~~i~d~l~~~~~~s 114 (604)
T KOG3564|consen 51 LGKYKDLLAK-AETKRSALDVKLKHARNQVDAEIKRRRRAEADCEK-LETQIQLIKDMLKCDISGS 114 (604)
T ss_pred HHHHHHHHHH-HHHhhhhccchHHHHHHHHHHHHHHHHHHhhhHHH-HHHHHHHHHHHHhcccccc
Confidence 3344444433 24567778999999877766667778888777764 4668899999999888754
No 118
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.83 E-value=30 Score=26.84 Aligned_cols=30 Identities=30% Similarity=0.484 Sum_probs=20.1
Q ss_pred cCCCCCCCCCCceeEeccCCCcccchhhhhcC
Q 008612 197 KCGSCGEQCNSGCYEYSKQGSFVICEKCFKNG 228 (559)
Q Consensus 197 ~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G 228 (559)
.|..||..++...- .+-.+..+|.+||..-
T Consensus 1 ~C~iCg~kigl~~~--~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR--FKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc--eeccCccchHHHHHHh
Confidence 49999999875421 2222336999999764
No 119
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.40 E-value=79 Score=29.50 Aligned_cols=39 Identities=13% Similarity=0.145 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008612 257 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 296 (559)
Q Consensus 257 ~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~flqL 296 (559)
++-+.+||+.+++-| -.|.+||+.+|. |+..|..++-+|
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 899999999985 999999999664
No 120
>PF07956 DUF1690: Protein of Unknown function (DUF1690) ; InterPro: IPR012471 Family of uncharacterised fungal proteins.
Probab=28.32 E-value=1.3e+02 Score=28.42 Aligned_cols=57 Identities=19% Similarity=0.307 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH-HHHHHHHHHHHHH
Q 008612 484 AKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKE-YNEMMQLKECLVE 540 (559)
Q Consensus 484 Ak~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~E-r~~LE~~rq~L~~ 540 (559)
+..+++.+..+-..|....++..+.+|.-||..|..|+..-... ...++..|..|..
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 4466788877764
No 121
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=27.46 E-value=1.1e+02 Score=32.84 Aligned_cols=31 Identities=29% Similarity=0.467 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHH
Q 008612 517 FDDLELIMEKEYNEMM----QLKECLVEERIDVLE 547 (559)
Q Consensus 517 feeLE~~~e~Er~~LE----~~rq~L~~eR~~~~~ 547 (559)
+..||.-+.+|..+|| ++++-||..|..++.
T Consensus 53 ~~~le~ef~~ev~~LE~kY~~~~~Ply~kR~eII~ 87 (337)
T PTZ00007 53 FDDLEVEYNAELRKLRSKYEDLYNPIYDKRKEALV 87 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHc
Confidence 3455666667777777 577889999999986
No 122
>PRK06474 hypothetical protein; Provisional
Probab=27.00 E-value=1.1e+02 Score=29.52 Aligned_cols=50 Identities=14% Similarity=0.083 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhhccc-hHHHHHHHHHhhhhhcccccccC
Q 008612 58 YRDFMINKYREEPSRRLTFTQVRKSLVG-DVSLLHKVFRLLDEWGLINFGAV 108 (559)
Q Consensus 58 ~RN~ii~~yr~np~~~lt~t~~r~~l~g-D~~~i~rvh~FLe~wGlIN~~~~ 108 (559)
.|-.|+..-..++. .+|++++...+.+ ....|.|....|+..|||.--..
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 56799999999999999995433
No 123
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=26.69 E-value=46 Score=27.73 Aligned_cols=31 Identities=16% Similarity=0.468 Sum_probs=21.4
Q ss_pred CceeeHHHHhhhc--cc-hHHHHHHHHHhhhhhc
Q 008612 71 SRRLTFTQVRKSL--VG-DVSLLHKVFRLLDEWG 101 (559)
Q Consensus 71 ~~~lt~t~~r~~l--~g-D~~~i~rvh~FLe~wG 101 (559)
++.++-.+-+..- +| |..-|--|-.||.+||
T Consensus 46 neeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 46 NEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred cHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 4556544433222 35 8888999999999999
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=26.52 E-value=1.5e+02 Score=23.06 Aligned_cols=50 Identities=14% Similarity=0.185 Sum_probs=36.6
Q ss_pred HHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccCCC
Q 008612 61 FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110 (559)
Q Consensus 61 ~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~~~ 110 (559)
+.|=.+-.+....+|.++..+.+.-|...+.|+..=|...|||.-..++.
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 33432333478899999999999999999999999999999998777763
No 125
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=25.46 E-value=6.9e+02 Score=30.00 Aligned_cols=39 Identities=15% Similarity=0.283 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 503 IETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEE 541 (559)
Q Consensus 503 Ie~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~e 541 (559)
++....+++..++..+++..-++++++.|++.|+.++.+
T Consensus 532 ~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~~~~~~~ 570 (782)
T PRK00409 532 LEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEE 570 (782)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566666666666666666666666666665544
No 126
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=25.14 E-value=1.1e+02 Score=28.69 Aligned_cols=52 Identities=17% Similarity=0.223 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhCCCceeeHHHHhhhccc-----hHHHHHHHHHhhhhhcccccccCC
Q 008612 57 EYRDFMINKYREEPSRRLTFTQVRKSLVG-----DVSLLHKVFRLLDEWGLINFGAVS 109 (559)
Q Consensus 57 ~~RN~ii~~yr~np~~~lt~t~~r~~l~g-----D~~~i~rvh~FLe~wGlIN~~~~~ 109 (559)
.=|-.|++.....+ .++|+.+.-+.|.. -...+.|+..||+.-|||+-....
T Consensus 21 ~qR~~vl~~L~~~~-~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~ 77 (145)
T COG0735 21 PQRLAVLELLLEAD-GHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFE 77 (145)
T ss_pred HHHHHHHHHHHhcC-CCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeC
Confidence 34778888666554 44999998766642 389999999999999999966664
No 127
>PRK14139 heat shock protein GrpE; Provisional
Probab=24.99 E-value=1.6e+02 Score=29.06 Aligned_cols=16 Identities=0% Similarity=0.065 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 008612 517 FDDLELIMEKEYNEMM 532 (559)
Q Consensus 517 feeLE~~~e~Er~~LE 532 (559)
|+.+=+-+++|++.+.
T Consensus 62 feN~rKR~~kE~e~~~ 77 (185)
T PRK14139 62 TENVRRRAQEDVAKAH 77 (185)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444444455554443
No 128
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=24.87 E-value=53 Score=24.93 Aligned_cols=33 Identities=27% Similarity=0.717 Sum_probs=24.7
Q ss_pred cCCccCCCCCCCCCCceeEeccCCCcccchhhhhc
Q 008612 193 LKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKN 227 (559)
Q Consensus 193 ~~~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~ 227 (559)
..=+.|..|+..+....+.-. .+...|..||.+
T Consensus 24 ~~Cf~C~~C~~~l~~~~~~~~--~~~~~C~~c~~~ 56 (58)
T PF00412_consen 24 PECFKCSKCGKPLNDGDFYEK--DGKPYCKDCYQK 56 (58)
T ss_dssp TTTSBETTTTCBTTTSSEEEE--TTEEEEHHHHHH
T ss_pred ccccccCCCCCccCCCeeEeE--CCEEECHHHHhh
Confidence 456889999999987754443 357899999864
No 129
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=24.84 E-value=16 Score=29.27 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.5
Q ss_pred ccCCCCCCCCCCceeEec
Q 008612 196 FKCGSCGEQCNSGCYEYS 213 (559)
Q Consensus 196 ~~C~~Cg~~~~~~~y~~~ 213 (559)
..|+.||.|++..||+..
T Consensus 5 lVCsTCGrDlSeeRy~Ll 22 (63)
T PHA03082 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCcchhHHHHHHH
Confidence 579999999999998753
No 130
>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=24.76 E-value=19 Score=28.78 Aligned_cols=18 Identities=22% Similarity=0.663 Sum_probs=15.3
Q ss_pred ccCCCCCCCCCCceeEec
Q 008612 196 FKCGSCGEQCNSGCYEYS 213 (559)
Q Consensus 196 ~~C~~Cg~~~~~~~y~~~ 213 (559)
..|+.||.|++..||...
T Consensus 5 lvCSTCGrDlSeeRy~Ll 22 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRLL 22 (63)
T ss_pred eeecccCCcchHHHHHHH
Confidence 579999999999988643
No 131
>PF15346 ARGLU: Arginine and glutamate-rich 1
Probab=24.73 E-value=6.2e+02 Score=24.18 Aligned_cols=82 Identities=20% Similarity=0.272 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 008612 468 RIRTATATALGAAAANAKLLADQEDR----------EIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKEC 537 (559)
Q Consensus 468 ~v~~Aaa~AL~aAA~kAk~LA~~EEr----------eI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~ 537 (559)
.|+.-+...|++-.+.+.+..-.++- +|.+=-...++-.=.|-+-.-+.-++||.+|+.-++.++..++.
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 34555556666655555555544432 22222233344444556677788899999999999999999999
Q ss_pred HHHHHHHHHHHH
Q 008612 538 LVEERIDVLERA 549 (559)
Q Consensus 538 L~~eR~~~~~~~ 549 (559)
+-.+|++.+-..
T Consensus 99 ~aeEr~~~~Eer 110 (149)
T PF15346_consen 99 LAEERLRMEEER 110 (149)
T ss_pred HHHHHHHHHHHH
Confidence 999998886543
No 132
>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=24.48 E-value=5e+02 Score=26.42 Aligned_cols=53 Identities=21% Similarity=0.137 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHhh------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 498 LVAIIIETQMKKLHSKINY------------------FDDLELIMEKEYNEMMQLKECLVEERIDVLERAL 550 (559)
Q Consensus 498 Lv~~lIe~QlkKLElKLk~------------------feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~ 550 (559)
.....-..|++|++.|++. +++.-...+++-...=..=|+|=.+|+.|+|.++
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 3334445678888888876 3333334444444555555777788999998775
No 133
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=24.09 E-value=3.2e+02 Score=25.97 Aligned_cols=33 Identities=21% Similarity=0.540 Sum_probs=24.0
Q ss_pred cCCCCCCCCCCc-eeEeccCCCcccchhhhhcCC
Q 008612 197 KCGSCGEQCNSG-CYEYSKQGSFVICEKCFKNGN 229 (559)
Q Consensus 197 ~C~~Cg~~~~~~-~y~~~k~~~~~lC~~Cf~~G~ 229 (559)
.|-.||..+... +..-.......+|..|+.-|.
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 499999998755 333334456889999997776
No 134
>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=24.00 E-value=4.6e+02 Score=22.74 Aligned_cols=49 Identities=14% Similarity=0.206 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHh
Q 008612 503 IETQMKKLHSKINYFDDLELIMEKEYNEMM----QLKECLVEERIDVLERALK 551 (559)
Q Consensus 503 Ie~QlkKLElKLk~feeLE~~~e~Er~~LE----~~rq~L~~eR~~~~~~~~~ 551 (559)
++.++++.+.||.+.++=+++++.-...|+ +.|-.-+.+|-.++...+.
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 466788888888888888888888777774 6677777777777665543
No 135
>KOG1988 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.73 E-value=2.1e+02 Score=34.52 Aligned_cols=60 Identities=8% Similarity=-0.005 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 008612 497 HLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKW 557 (559)
Q Consensus 497 ~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~~~g~~~~ 557 (559)
+|...+.---..+...+|+++.+.|-++..|+.+++. .+.-|.+++.+.+.|+.+|=+.+
T Consensus 563 sL~~~v~sd~~~~wl~sL~eIs~ae~ll~le~d~y~~-~~~~la~~L~~~q~al~sl~a~s 622 (970)
T KOG1988|consen 563 SLKTNVQSDHNCCWLKSLTEISHAECLLGLENDNYLD-ALSELAHCLANYQSALASLGAIS 622 (970)
T ss_pred HHhhcccchhHHHHHHHHHHHHHHHHHHccCccchhh-hHHHHHHHHHHHHHHHHhccccC
Confidence 4444444555678999999999999889999999984 45567899999999998765443
No 136
>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=23.63 E-value=73 Score=29.26 Aligned_cols=38 Identities=16% Similarity=0.072 Sum_probs=26.9
Q ss_pred CceeeHHHHhhhccchHHHHHHHHHhhhhhcccccccC
Q 008612 71 SRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV 108 (559)
Q Consensus 71 ~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~~~ 108 (559)
.+|||..+......-+-..+.+|.+||...||=...+.
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 137
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=23.37 E-value=1.9e+02 Score=20.81 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=30.9
Q ss_pred ceeeHHHHhhhccchHHHHHHHHHhhhhhcccccc
Q 008612 72 RRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFG 106 (559)
Q Consensus 72 ~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~~ 106 (559)
..+|..+..+.+.-....+.|....|+.-|+|-..
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 138
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.96 E-value=52 Score=28.00 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=16.0
Q ss_pred CccCCCCCCCCC-----CceeEeccCCCcccchhhhhc----CCCCCCCCCCCceeccC
Q 008612 195 GFKCGSCGEQCN-----SGCYEYSKQGSFVICEKCFKN----GNYGEDKSKDDFRFSDL 244 (559)
Q Consensus 195 ~~~C~~Cg~~~~-----~~~y~~~k~~~~~lC~~Cf~~----G~~~~~~ss~df~~~~~ 244 (559)
...|.+||.+.+ .+++.|..| .|-+|-.||.- |+---..-...|.+...
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC-~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kg 66 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHEC-AFPVCRPCYEYERKEGNQVCPQCKTRYKRHKG 66 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS------HHHHHHHHHTS-SB-TTT--B----TT
T ss_pred CcccccccCccccCCCCCEEEEEccc-CCccchhHHHHHhhcCcccccccCCCcccccC
Confidence 467999998764 346678875 68888888853 33222233455665443
No 139
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=22.53 E-value=1.1e+02 Score=28.88 Aligned_cols=39 Identities=15% Similarity=0.234 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHcCCCCHHHHHHHHHcC
Q 008612 257 EAETLLLLESVMRHG-DNWELVAQNVPTKSKLDCISKLIEL 296 (559)
Q Consensus 257 ~~E~~~LLe~Ie~~g-~nW~~Ia~~vg~kT~~eC~~~flqL 296 (559)
++-+.++|..+++-| -.|.+||+.||- |+..|..|+-+|
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 799999999985 888899988653
No 140
>PRK14161 heat shock protein GrpE; Provisional
Probab=22.38 E-value=6.3e+02 Score=24.67 Aligned_cols=18 Identities=22% Similarity=0.220 Sum_probs=8.7
Q ss_pred HhhHHHHHHHHHHHHHHH
Q 008612 514 INYFDDLELIMEKEYNEM 531 (559)
Q Consensus 514 Lk~feeLE~~~e~Er~~L 531 (559)
..-|+.+-+-+++|+++.
T Consensus 46 ~AefeN~rkR~~ke~~~~ 63 (178)
T PRK14161 46 TAEIDNTRKRLEKARDEA 63 (178)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334444445555555544
No 141
>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=22.18 E-value=1.5e+02 Score=23.02 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=23.2
Q ss_pred CceeeHHHHhhhcc----chHHHHHHHHHhh
Q 008612 71 SRRLTFTQVRKSLV----GDVSLLHKVFRLL 97 (559)
Q Consensus 71 ~~~lt~t~~r~~l~----gD~~~i~rvh~FL 97 (559)
..++|..+....|. .+...+.||.+||
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 48999999988887 7899999999998
No 142
>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=22.10 E-value=1.3e+02 Score=22.83 Aligned_cols=52 Identities=19% Similarity=0.307 Sum_probs=36.7
Q ss_pred hhHHHHHHHHHHHHHhCCCcee-eHHHHhhhccchHHHHHHHHHhhhhhccccc
Q 008612 53 KIYKEYRDFMINKYREEPSRRL-TFTQVRKSLVGDVSLLHKVFRLLDEWGLINF 105 (559)
Q Consensus 53 ~~Y~~~RN~ii~~yr~np~~~l-t~t~~r~~l~gD~~~i~rvh~FLe~wGlIN~ 105 (559)
++|-.+++.|+..-. .+...+ |..+..+.+.-....+.++..=|+..|+|-.
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 556666666665422 333344 4888777777678999999999999999854
No 143
>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=21.89 E-value=5.9e+02 Score=25.90 Aligned_cols=48 Identities=23% Similarity=0.170 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhhHH------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612 503 IETQMKKLHSKINYFD------------------DLELIMEKEYNEMMQLKECLVEERIDVLERAL 550 (559)
Q Consensus 503 Ie~QlkKLElKLk~fe------------------eLE~~~e~Er~~LE~~rq~L~~eR~~~~~~~~ 550 (559)
-..|++|++.||+.-. +.-...+++-..--+.-|+|=.||++|+|.++
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 22122233333334445567788999998875
No 144
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=21.66 E-value=3.6e+02 Score=26.81 Aligned_cols=14 Identities=14% Similarity=0.397 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHHH
Q 008612 529 NEMMQLKECLVEER 542 (559)
Q Consensus 529 ~~LE~~rq~L~~eR 542 (559)
+.|++.|++|+.||
T Consensus 62 Q~l~~er~~l~~er 75 (228)
T PRK06800 62 QKLERERQQLLADR 75 (228)
T ss_pred HHHHHHHHHHHHHH
Confidence 33333333333333
No 145
>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=21.04 E-value=77 Score=26.26 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHcCC
Q 008612 257 EAETLLLLESVMRHGDNWELVAQNVPT 283 (559)
Q Consensus 257 ~~E~~~LLe~Ie~~g~nW~~Ia~~vg~ 283 (559)
-++..+||+. |.||..+|+++|-
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 146
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=20.75 E-value=1.5e+02 Score=28.21 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHcC----CCCHHHHHHHHH
Q 008612 252 GATWTEAETLLLLESVMRHGDNWELVAQNVP----TKSKLDCISKLI 294 (559)
Q Consensus 252 ~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg----~kT~~eC~~~fl 294 (559)
...-|..|...+-..|++||+|+...+.-.. ..|+.|+...+-
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHH
Confidence 4568899999999999999999999995444 479999987764
Done!