Query 004116
Match_columns 773
No_of_seqs 244 out of 716
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 17:50:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004116.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004116hhsearch_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 1.1E-96 2E-101 795.5 28.5 406 177-661 48-475 (531)
2 KOG1279 Chromatin remodeling f 100.0 2.4E-90 5.2E-95 771.6 27.9 457 153-663 21-506 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 8.6E-27 1.9E-31 206.5 5.7 86 181-270 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 3.9E-24 8.5E-29 232.8 8.9 110 344-455 13-125 (438)
5 COG5114 Histone acetyltransfer 99.8 1E-20 2.2E-25 198.5 5.9 110 344-455 4-116 (432)
6 cd02336 ZZ_RSC8 Zinc finger, Z 99.0 1.9E-10 4.1E-15 91.2 3.4 45 346-390 1-45 (45)
7 PF00249 Myb_DNA-binding: Myb- 99.0 9.3E-10 2E-14 87.5 5.7 44 404-447 2-47 (48)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.7 2.5E-08 5.4E-13 82.4 5.6 41 406-446 1-41 (60)
9 smart00717 SANT SANT SWI3, AD 98.7 4.2E-08 9.1E-13 75.6 5.9 44 404-447 2-46 (49)
10 cd00167 SANT 'SWI3, ADA2, N-Co 98.6 9.1E-08 2E-12 72.7 5.7 43 405-447 1-44 (45)
11 cd02335 ZZ_ADA2 Zinc finger, Z 98.4 3.5E-07 7.7E-12 73.7 4.2 47 346-392 1-49 (49)
12 PLN03000 amine oxidase 98.3 7.6E-07 1.7E-11 107.6 6.8 84 186-274 87-172 (881)
13 PLN02328 lysine-specific histo 98.2 2.5E-06 5.5E-11 102.9 6.7 88 186-277 138-226 (808)
14 cd02345 ZZ_dah Zinc finger, ZZ 98.1 2.1E-06 4.6E-11 69.4 3.4 45 347-391 2-48 (49)
15 cd02338 ZZ_PCMF_like Zinc fing 98.0 4.3E-06 9.2E-11 67.6 3.8 45 347-391 2-48 (49)
16 cd02343 ZZ_EF Zinc finger, ZZ 98.0 3.9E-06 8.5E-11 67.6 3.4 40 347-386 2-41 (48)
17 cd02334 ZZ_dystrophin Zinc fin 98.0 4.7E-06 1E-10 67.5 3.6 44 347-390 2-47 (49)
18 cd02249 ZZ Zinc finger, ZZ typ 98.0 7.6E-06 1.7E-10 65.0 3.8 45 346-392 1-46 (46)
19 cd02340 ZZ_NBR1_like Zinc fing 98.0 7.4E-06 1.6E-10 64.5 3.7 42 347-392 2-43 (43)
20 smart00291 ZnF_ZZ Zinc-binding 98.0 6.9E-06 1.5E-10 64.8 3.5 40 345-384 4-43 (44)
21 TIGR01557 myb_SHAQKYF myb-like 98.0 1.2E-05 2.5E-10 67.1 5.0 47 403-449 3-55 (57)
22 PLN03212 Transcription repress 97.8 1.9E-05 4.1E-10 82.9 5.1 45 403-447 25-71 (249)
23 cd02341 ZZ_ZZZ3 Zinc finger, Z 97.8 1.9E-05 4.1E-10 63.7 3.8 44 346-392 1-48 (48)
24 PF00569 ZZ: Zinc finger, ZZ t 97.7 1.5E-05 3.2E-10 63.6 0.8 41 345-385 4-45 (46)
25 PLN03091 hypothetical protein; 97.6 8.1E-05 1.8E-09 83.5 5.2 45 403-447 14-60 (459)
26 cd02344 ZZ_HERC2 Zinc finger, 97.5 0.0001 2.2E-09 58.8 3.6 42 347-392 2-45 (45)
27 PLN02529 lysine-specific histo 97.5 0.0001 2.3E-09 88.6 5.4 86 186-276 63-150 (738)
28 cd02339 ZZ_Mind_bomb Zinc fing 97.2 0.0003 6.5E-09 56.1 3.6 41 347-391 2-44 (45)
29 PLN03212 Transcription repress 97.1 0.00056 1.2E-08 72.1 5.3 47 401-447 76-122 (249)
30 KOG0048 Transcription factor, 97.1 0.00047 1E-08 72.5 4.4 45 403-447 9-55 (238)
31 PLN03091 hypothetical protein; 96.6 0.0027 5.8E-08 71.7 5.9 47 401-447 65-111 (459)
32 cd02337 ZZ_CBP Zinc finger, ZZ 96.4 0.0017 3.7E-08 50.8 2.0 33 346-379 1-33 (41)
33 cd02342 ZZ_UBA_plant Zinc fing 96.1 0.0037 8.1E-08 49.4 2.1 31 347-377 2-33 (43)
34 KOG0049 Transcription factor, 95.3 0.02 4.3E-07 67.0 5.1 46 402-447 359-405 (939)
35 KOG4582 Uncharacterized conser 95.1 0.013 2.8E-07 63.4 2.7 45 346-393 153-198 (278)
36 PF13837 Myb_DNA-bind_4: Myb/S 94.9 0.017 3.8E-07 50.9 2.5 44 404-447 2-63 (90)
37 KOG4286 Dystrophin-like protei 94.7 0.014 3E-07 69.1 1.6 43 345-387 603-646 (966)
38 KOG0049 Transcription factor, 94.7 0.027 5.9E-07 65.9 3.9 45 403-447 412-460 (939)
39 PLN02976 amine oxidase 94.6 0.029 6.4E-07 71.7 4.3 81 190-275 455-542 (1713)
40 KOG0048 Transcription factor, 94.1 0.079 1.7E-06 55.9 5.7 43 402-444 61-103 (238)
41 KOG1280 Uncharacterized conser 93.2 0.053 1.2E-06 59.7 2.5 41 345-385 8-49 (381)
42 KOG0051 RNA polymerase I termi 90.9 0.21 4.7E-06 58.9 4.0 51 402-452 435-511 (607)
43 KOG4301 Beta-dystrobrevin [Cyt 90.3 0.13 2.8E-06 56.7 1.4 41 346-386 241-282 (434)
44 KOG0051 RNA polymerase I termi 90.3 0.33 7.1E-06 57.4 4.8 45 402-447 383-427 (607)
45 KOG4167 Predicted DNA-binding 88.5 0.66 1.4E-05 55.6 5.5 45 402-446 618-662 (907)
46 COG5118 BDP1 Transcription ini 86.0 1.4 3E-05 49.5 5.8 45 402-446 364-408 (507)
47 PF13873 Myb_DNA-bind_5: Myb/S 85.7 1.7 3.7E-05 37.6 5.3 44 404-447 3-68 (78)
48 KOG4282 Transcription factor G 84.6 1 2.3E-05 49.8 4.3 47 403-449 54-114 (345)
49 KOG0050 mRNA splicing protein 81.5 1.3 2.9E-05 51.3 3.6 45 402-447 58-102 (617)
50 KOG0050 mRNA splicing protein 80.7 1.5 3.3E-05 50.9 3.7 44 403-446 7-51 (617)
51 PRK00409 recombination and DNA 79.4 12 0.00026 46.3 11.1 75 580-655 489-564 (782)
52 TIGR01069 mutS2 MutS2 family p 79.1 13 0.00029 45.9 11.3 75 580-655 484-559 (771)
53 COG5180 PBP1 Protein interacti 77.3 3.6 7.9E-05 47.4 5.3 53 666-723 506-558 (654)
54 TIGR02894 DNA_bind_RsfA transc 76.7 2.3 4.9E-05 42.9 3.1 44 403-447 4-54 (161)
55 KOG4468 Polycomb-group transcr 74.4 2.7 5.8E-05 49.7 3.3 45 403-447 88-142 (782)
56 KOG4329 DNA-binding protein [G 72.9 5 0.00011 45.1 4.8 48 403-450 277-325 (445)
57 PF15324 TALPID3: Hedgehog sig 72.4 51 0.0011 41.9 13.4 91 578-669 61-169 (1252)
58 PLN03119 putative ADP-ribosyla 69.1 6 0.00013 46.9 4.6 96 346-457 24-125 (648)
59 PF00392 GntR: Bacterial regul 67.9 8.3 0.00018 32.2 4.1 53 216-270 3-56 (64)
60 PF04504 DUF573: Protein of un 66.9 8.9 0.00019 35.5 4.5 45 403-447 4-61 (98)
61 KOG1832 HIV-1 Vpr-binding prot 65.1 5.5 0.00012 49.3 3.4 20 24-43 1398-1417(1516)
62 PLN03131 hypothetical protein; 64.1 8.8 0.00019 45.9 4.7 95 346-457 24-125 (705)
63 COG5147 REB1 Myb superfamily p 62.5 7 0.00015 46.0 3.6 46 402-447 71-116 (512)
64 PF10446 DUF2457: Protein of u 62.3 3 6.5E-05 47.9 0.6 11 175-185 217-227 (458)
65 COG5147 REB1 Myb superfamily p 59.7 5.6 0.00012 46.8 2.2 42 403-444 20-62 (512)
66 KOG1924 RhoA GTPase effector D 59.3 62 0.0014 40.1 10.5 14 368-381 212-225 (1102)
67 PLN03142 Probable chromatin-re 59.2 13 0.00027 47.5 5.2 40 404-443 825-865 (1033)
68 PF07649 C1_3: C1-like domain; 58.4 6.1 0.00013 28.6 1.4 27 347-374 2-29 (30)
69 smart00307 ILWEQ I/LWEQ domain 56.0 65 0.0014 33.8 8.9 38 614-652 160-197 (200)
70 PF03276 Gag_spuma: Spumavirus 52.6 2.8E+02 0.0061 33.3 14.1 9 761-769 268-276 (582)
71 PF12776 Myb_DNA-bind_3: Myb/S 51.5 16 0.00035 32.5 3.3 43 405-447 1-61 (96)
72 PRK00846 hypothetical protein; 50.7 1.4E+02 0.0031 26.8 9.0 54 611-665 6-59 (77)
73 PF09111 SLIDE: SLIDE; InterP 48.7 23 0.00051 34.0 4.1 44 402-445 48-107 (118)
74 PF15219 TEX12: Testis-express 47.7 1.4E+02 0.0031 27.8 8.6 58 605-663 38-98 (100)
75 PF03107 C1_2: C1 domain; Int 47.1 16 0.00035 26.6 2.1 27 347-374 2-29 (30)
76 PF05928 Zea_mays_MuDR: Zea ma 45.6 2.2E+02 0.0047 29.2 10.3 72 580-651 11-89 (207)
77 KOG0847 Transcription factor, 45.6 14 0.0003 39.1 2.2 19 10-28 217-237 (288)
78 KOG3647 Predicted coiled-coil 45.5 1.1E+02 0.0024 33.6 8.8 63 589-653 92-158 (338)
79 PF04111 APG6: Autophagy prote 43.6 2.9E+02 0.0064 30.7 12.2 48 614-661 74-121 (314)
80 KOG1832 HIV-1 Vpr-binding prot 43.1 17 0.00037 45.3 2.7 14 30-43 1409-1422(1516)
81 KOG3915 Transcription regulato 43.0 90 0.0019 36.6 8.1 36 619-654 527-568 (641)
82 KOG3859 Septins (P-loop GTPase 42.5 1.6E+02 0.0035 32.9 9.6 60 605-664 339-402 (406)
83 KOG1194 Predicted DNA-binding 42.2 39 0.00084 39.3 5.1 46 402-447 186-231 (534)
84 PF09862 DUF2089: Protein of u 41.7 41 0.0009 32.3 4.5 61 348-434 1-61 (113)
85 cd04779 HTH_MerR-like_sg4 Heli 41.4 1.6E+02 0.0036 28.7 8.7 52 607-661 78-129 (134)
86 PF02954 HTH_8: Bacterial regu 41.0 37 0.0008 26.4 3.4 26 409-434 5-30 (42)
87 KOG1194 Predicted DNA-binding 40.4 15 0.00032 42.6 1.5 43 403-446 470-512 (534)
88 PF01608 I_LWEQ: I/LWEQ domain 39.7 2.3E+02 0.0049 28.7 9.5 21 632-652 129-149 (152)
89 smart00345 HTH_GNTR helix_turn 39.6 32 0.0007 27.2 3.1 51 218-270 1-52 (60)
90 KOG0706 Predicted GTPase-activ 39.4 24 0.00052 40.8 3.0 61 338-414 16-79 (454)
91 PF00643 zf-B_box: B-box zinc 38.3 30 0.00066 26.4 2.6 38 346-391 4-41 (42)
92 KOG3554 Histone deacetylase co 38.1 28 0.0006 40.5 3.2 51 404-454 286-337 (693)
93 smart00595 MADF subfamily of S 37.8 28 0.00061 30.6 2.6 24 423-447 28-51 (89)
94 PF12674 Zn_ribbon_2: Putative 37.7 17 0.00038 32.7 1.3 35 347-381 2-39 (81)
95 PF02207 zf-UBR: Putative zinc 37.0 22 0.00048 30.8 1.8 35 357-395 11-48 (71)
96 PRK02793 phi X174 lysis protei 36.8 2.8E+02 0.0061 24.4 8.6 47 616-665 6-54 (72)
97 COG3074 Uncharacterized protei 36.3 1.5E+02 0.0033 26.4 6.6 60 602-661 7-74 (79)
98 PF13404 HTH_AsnC-type: AsnC-t 36.1 88 0.0019 24.6 4.8 37 409-446 3-40 (42)
99 PRK13729 conjugal transfer pil 36.1 4.1E+02 0.009 31.5 12.2 40 585-628 66-107 (475)
100 PRK13923 putative spore coat p 34.1 37 0.0008 34.8 3.1 41 403-444 5-52 (170)
101 COG5347 GTPase-activating prot 33.8 45 0.00098 37.3 4.0 99 344-455 19-124 (319)
102 PF10820 DUF2543: Protein of u 33.7 31 0.00067 30.6 2.1 55 194-266 23-79 (81)
103 PF06034 DUF919: Nucleopolyhed 33.3 1.2E+02 0.0025 26.4 5.4 44 616-660 13-56 (62)
104 KOG4849 mRNA cleavage factor I 32.5 2.5E+02 0.0053 32.1 9.2 16 405-422 90-105 (498)
105 PF04931 DNA_pol_phi: DNA poly 31.9 28 0.0006 43.2 2.1 7 132-138 729-735 (784)
106 PF01412 ArfGap: Putative GTPa 31.8 26 0.00055 33.2 1.5 62 343-417 11-72 (116)
107 PHA00442 host recBCD nuclease 31.7 47 0.001 28.0 2.8 25 408-432 25-50 (59)
108 TIGR01069 mutS2 MutS2 family p 31.5 5.1E+02 0.011 32.5 12.8 19 519-537 415-433 (771)
109 PF15346 ARGLU: Arginine and g 31.3 5.7E+02 0.012 25.9 13.3 50 614-663 62-111 (149)
110 PRK06474 hypothetical protein; 31.3 73 0.0016 32.4 4.8 48 222-270 12-59 (178)
111 PRK04406 hypothetical protein; 31.2 3.8E+02 0.0083 23.9 8.6 48 615-665 8-57 (75)
112 PF01022 HTH_5: Bacterial regu 30.9 1.1E+02 0.0024 24.0 4.8 45 222-270 3-47 (47)
113 KOG0703 Predicted GTPase-activ 30.8 47 0.001 36.6 3.4 99 345-456 25-126 (287)
114 PRK06800 fliH flagellar assemb 30.6 1.3E+02 0.0028 31.5 6.2 27 634-660 86-112 (228)
115 KOG2129 Uncharacterized conser 30.4 9.6E+02 0.021 28.3 17.5 42 605-647 259-300 (552)
116 smart00105 ArfGap Putative GTP 29.5 55 0.0012 30.8 3.3 93 346-455 4-106 (112)
117 PF09339 HTH_IclR: IclR helix- 28.3 74 0.0016 25.5 3.4 43 226-270 8-50 (52)
118 PF12958 DUF3847: Protein of u 28.1 2.6E+02 0.0056 25.8 7.1 49 616-664 6-58 (86)
119 PF07956 DUF1690: Protein of U 28.0 1.3E+02 0.0029 29.8 5.8 56 597-652 61-117 (142)
120 KOG1924 RhoA GTPase effector D 27.8 1.4E+03 0.03 29.3 16.2 13 745-757 589-601 (1102)
121 PRK06800 fliH flagellar assemb 27.7 1.9E+02 0.0041 30.3 6.8 20 639-658 59-78 (228)
122 PF12802 MarR_2: MarR family; 27.1 1.1E+02 0.0024 24.6 4.4 43 231-274 15-57 (62)
123 PF14569 zf-UDP: Zinc-binding 26.9 36 0.00078 30.7 1.4 51 343-394 7-66 (80)
124 PRK02119 hypothetical protein; 26.9 4.5E+02 0.0097 23.3 8.6 47 616-665 7-55 (73)
125 PF06689 zf-C4_ClpX: ClpX C4-t 26.5 27 0.00058 27.4 0.5 30 346-376 2-32 (41)
126 PF07271 Cytadhesin_P30: Cytad 26.4 3.3E+02 0.0071 30.1 8.7 16 643-658 156-171 (279)
127 KOG0384 Chromodomain-helicase 26.0 45 0.00097 43.1 2.5 28 402-429 1132-1160(1373)
128 KOG2072 Translation initiation 25.5 9E+02 0.02 30.8 12.9 28 633-661 664-691 (988)
129 KOG4661 Hsp27-ERE-TATA-binding 24.9 3E+02 0.0065 33.3 8.6 17 438-454 461-477 (940)
130 PRK00106 hypothetical protein; 24.8 8.7E+02 0.019 29.4 12.6 14 506-519 3-16 (535)
131 PRK00409 recombination and DNA 24.7 7.4E+02 0.016 31.2 12.6 20 519-538 420-439 (782)
132 COG1725 Predicted transcriptio 24.5 1.3E+02 0.0028 29.4 4.9 58 213-271 8-68 (125)
133 PF09026 CENP-B_dimeris: Centr 24.5 25 0.00054 32.9 0.0 8 83-90 46-53 (101)
134 COG3883 Uncharacterized protei 24.2 4.3E+02 0.0093 29.1 9.2 58 605-664 51-108 (265)
135 COG2916 Hns DNA-binding protei 23.8 6.2E+02 0.013 25.0 9.3 50 607-660 4-53 (128)
136 PF08112 ATP-synt_E_2: ATP syn 23.7 3.2E+02 0.007 23.1 6.1 23 631-653 33-55 (56)
137 PLN03142 Probable chromatin-re 23.2 1.2E+02 0.0027 39.0 5.7 46 402-447 925-983 (1033)
138 PRK11414 colanic acid/biofilm 23.1 1.1E+02 0.0025 31.3 4.5 65 204-270 2-66 (221)
139 PLN02436 cellulose synthase A 22.7 1.1E+02 0.0023 39.5 4.8 49 344-393 35-92 (1094)
140 PF14471 DUF4428: Domain of un 22.5 46 0.00099 27.5 1.2 30 347-378 1-30 (51)
141 PTZ00009 heat shock 70 kDa pro 22.3 1.5E+03 0.032 27.7 14.3 14 417-430 322-335 (653)
142 PLN02638 cellulose synthase A 22.1 63 0.0014 41.5 2.7 49 344-393 16-73 (1079)
143 KOG1279 Chromatin remodeling f 21.8 55 0.0012 38.8 2.1 95 182-276 185-286 (506)
144 cd00090 HTH_ARSR Arsenical Res 21.7 1.6E+02 0.0034 23.6 4.3 33 238-271 21-53 (78)
145 PF03286 Pox_Ag35: Pox virus A 20.8 52 0.0011 34.6 1.4 27 85-111 136-162 (200)
146 KOG4739 Uncharacterized protei 20.6 1.1E+03 0.024 25.6 11.5 29 346-375 4-32 (233)
147 TIGR02449 conserved hypothetic 20.6 3.9E+02 0.0085 23.4 6.5 17 648-664 43-59 (65)
148 PRK15422 septal ring assembly 20.5 4E+02 0.0086 24.3 6.6 30 601-630 6-35 (79)
149 TIGR02812 fadR_gamma fatty aci 20.3 1.1E+02 0.0023 31.7 3.7 57 213-271 6-63 (235)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=1.1e-96 Score=795.54 Aligned_cols=406 Identities=32% Similarity=0.551 Sum_probs=333.0
Q ss_pred CCceeeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHH
Q 004116 177 GSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLT 256 (773)
Q Consensus 177 ~~~~ivIPsyS~WFd~~~IH~IEKr~lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~ 256 (773)
|+|+||||+|+.|||+.+||+|||++.||||+|++++|||++||+|||||||+||+||++|||||+|||||+| |||+|+
T Consensus 48 Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvag-DV~aiv 126 (531)
T COG5259 48 QTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAG-DVAAIV 126 (531)
T ss_pred cCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccch-hHHHHH
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999 599999
Q ss_pred HHHHhhhhhcccccccCCCCCCCCCCCCccccCCCCccccCCcccccccccccccCCccCcccc-------------ccc
Q 004116 257 RIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVA-------------DVY 323 (773)
Q Consensus 257 RVH~FLE~WGLINYqvdp~~~P~~~~~~~i~~~~~G~~~~~s~~l~~~~~l~~fd~~k~~~~~~-------------~i~ 323 (773)
|||+|||+||||||||||.++| +.|+++.+||++..+++ +.|+.+|..+....+.. ..+
T Consensus 127 rvHrFLekWGLINYqvdp~trP-----s~IgPplt~h~q~l~dt---P~gl~p~l~~~~~~~~~~~a~~~e~~~~k~~~~ 198 (531)
T COG5259 127 RVHRFLEKWGLINYQVDPGTRP-----STIGPPLTSHFQDLHDT---PRGLSPFLPWGPINQRVLGAKEIEYETHKEENY 198 (531)
T ss_pred HHHHHHHHhcceeeccCCCCCc-----cccCCCcchhhHHHhhC---ccccccccCCCCccccccccchhhhhhhccCCC
Confidence 9999999999999999999998 45677889999887665 57888887665432211 222
Q ss_pred CCCC------CCCCCcCchhHHHhhccCCCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCC
Q 004116 324 SSSC------GGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPARE 397 (773)
Q Consensus 324 s~~~------~~~d~~~l~~~~~e~~~~~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~ 397 (773)
++.. ..+++.++.... ......|..||+.+...+|+.++..++.+|..||..|+|+.+..+.||..++....
T Consensus 199 sps~~~~~k~s~~k~~el~~~~--~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~~~~~ 276 (531)
T COG5259 199 SPSLKSPKKESQGKVDELKDHS--EKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVTISLL 276 (531)
T ss_pred CchhhhhhhhcCCCcccccccc--ccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhhhhcc
Confidence 2211 011122211111 01236899999999999999998889999999999999999999999999987542
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhCCCCCCCcccCCCCCCCCcCCCCCCCCCCCc
Q 004116 398 YGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSRDDRGGL 477 (773)
Q Consensus 398 ~~~~~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqLPIED~fLe~~~~~~~s~~~~~~~~~d~~~~ 477 (773)
..+..||++|+++|||||++||++|++||.||||||+||||+|||+|||+|.||.+... .
T Consensus 277 ---~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~----------------~- 336 (531)
T COG5259 277 ---IRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDG----------------K- 336 (531)
T ss_pred ---cccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccC----------------c-
Confidence 25679999999999999999999999999999999999999999999999999976421 0
Q ss_pred ccCCCCCCCCCCcccccccCCcccCCCCCchHHHHHHHHhhcChHHHHHHHHHHHHHHHhhcccCCCCCCCCcccccccc
Q 004116 478 HSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGNRMNSENVHNRE 557 (773)
Q Consensus 478 ~~dsng~~~G~~~~~~~~~~~~PFs~a~NPVMS~VAFLas~V~P~VAaAAA~AAl~~l~~~~~~~~~d~~~~sE~~~~~~ 557 (773)
|.. ..+.+||+.++|||||+|+||+++|.|+|+...+.+.++. .+. .
T Consensus 337 ---------~~~-----~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k~-g~~----~-------------- 383 (531)
T COG5259 337 ---------GDN-----SKGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIKS-GKI----S-------------- 383 (531)
T ss_pred ---------CCC-----CCCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhhc-cce----e--------------
Confidence 000 0135799999999999999999999999988777765211 000 0
Q ss_pred ccCCCCCCCCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 558 EENSGVHGPWGQNGAEAALLSAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLL 637 (773)
Q Consensus 558 ~~~d~~~~~~~~n~~~~~~~s~~~vk~Aa~~aLaaAA~KAk~LA~~EEREI~rLv~~IIe~QLKKLElKLk~feELE~~l 637 (773)
.. ..-+.+.+...+..||.+++.|||++|+.|||+|++|+..+|+.||+||++||.+|++||+.+
T Consensus 384 ----------~~-----n~e~~~~~~~~~~~al~s~~eka~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L~~~~ 448 (531)
T COG5259 384 ----------HI-----NRESQEHIEEVIEYALDSGKEKAKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKST 448 (531)
T ss_pred ----------cC-----ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 00 011234566777789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHH---HHHHHHHHHHHHHHH
Q 004116 638 MRECEQVEK---ARQRFATERTRIVST 661 (773)
Q Consensus 638 e~Ere~LE~---~Rq~L~~eR~~~~~~ 661 (773)
.+||..|+. .|+-.+.+-+-.+..
T Consensus 449 ~L~rqeLd~nlll~rl~~~e~l~~~~e 475 (531)
T COG5259 449 SLERQELDANLLLRRLNAEEKLFAIDE 475 (531)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 999999999 444444444433333
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=2.4e-90 Score=771.56 Aligned_cols=457 Identities=34% Similarity=0.544 Sum_probs=354.5
Q ss_pred CCCCCcccccCCccccccccccccCCceeeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHh
Q 004116 153 ERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMD 232 (773)
Q Consensus 153 ~~~~~~~v~~~p~~~~~~~~~k~~~~~~ivIPsyS~WFd~~~IH~IEKr~lPEFF~gk~~~ktPeiYk~yRNfMIntYR~ 232 (773)
+++-+.+++ |.++.......++|+|.|+||||++||||++||+||||++||||+|++++|||++||+||||||++||+
T Consensus 21 ~~~~~~~~~--~~~~~~~~~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrl 98 (506)
T KOG1279|consen 21 DESQETLGG--PAAHDAAKTVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRL 98 (506)
T ss_pred CcCcccccc--cchhhhcccccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhcc
Confidence 344555555 345566667778999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceeeHHHHhhccCCCChhHHHHHHHhhhhhcccccccCCCCCCCCCCCCccccCCCCccccCCcccccccccccccC
Q 004116 233 NPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDK 312 (773)
Q Consensus 233 NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINYqvdp~~~P~~~~~~~i~~~~~G~~~~~s~~l~~~~~l~~fd~ 312 (773)
||.+|||+|+|||||+| |||+|+|||+|||+|||||||+|++.+|. .+.+..+||++++.++ ++++++++.
T Consensus 99 np~~ylt~ta~rrnl~g-Dv~ai~Rvh~FlE~WGLINy~~d~e~rp~-----~~~p~~t~h~~~~~~t---p~~~~~~~~ 169 (506)
T KOG1279|consen 99 NPQEYLTFTACRRNLAG-DVCAIARVHAFLEQWGLINYQVDAESRPH-----PIEPPETSHFQVLADT---PRGLAPLTP 169 (506)
T ss_pred CcccchhHHHHHhcccc-hHHHHHHHHhhHHhhcccccccChhhCCc-----ccCCCcccccccccCC---CcccccCCC
Confidence 99999999999999999 69999999999999999999999999983 3456678888887554 566766665
Q ss_pred CccCcccccccC---CCCCCCCCcCchhHHHhhccCCCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCc
Q 004116 313 PKCSLKVADVYS---SSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDY 389 (773)
Q Consensus 313 ~k~~~~~~~i~s---~~~~~~d~~~l~~~~~e~~~~~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF 389 (773)
.....+...... ......+...+..+..+.+...+|..|+.+ +|+..+..++.+|.+||..|+|+..++..||
T Consensus 170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df 245 (506)
T KOG1279|consen 170 EDPQSQPDLGNPRMETLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDF 245 (506)
T ss_pred CCccccccccccccccccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccc
Confidence 443221111110 001111223333334556667788888765 6777776789999999999999999999999
Q ss_pred eecCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhCCCCCCCcccCCCCCCCCcCCCC
Q 004116 390 IRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSS 469 (773)
Q Consensus 390 ~rvd~~~~~~~~~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqLPIED~fLe~~~~~~~s~~~~~~ 469 (773)
..+ ....+..||++|++||||||++||+||++||+|||+||++|||+|||+|||+|+||...+.
T Consensus 246 ~~~------~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l~~~~~---------- 309 (506)
T KOG1279|consen 246 KVI------GESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYLAKSEA---------- 309 (506)
T ss_pred hhc------cccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhhhhccc----------
Confidence 222 2346789999999999999999999999999999999999999999999999999976321
Q ss_pred CCCCCCCcccCCCCCCCCCCcccccccCCcccCCCCCchHHHHHHHHhhcChHHHHHHHHHHHHHHHhhcccCCCCC-C-
Q 004116 470 SRDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGN-R- 547 (773)
Q Consensus 470 ~~~d~~~~~~dsng~~~G~~~~~~~~~~~~PFs~a~NPVMS~VAFLas~V~P~VAaAAA~AAl~~l~~~~~~~~~d~-~- 547 (773)
+ .|++. .++.+|+..+|||||+++||+++|||+|+..+++.+...+.+.+....... +
T Consensus 310 --------------~-~~~~~-----~~~~~~sq~gnpv~s~~~~l~~~vdP~~~~~~~k~~~~~~~~~~~~~~~~~~~~ 369 (506)
T KOG1279|consen 310 --------------S-LGPLS-----YGPVPFSQDGNPVMSTVAFLASVVDPVVKSVAAKSAEEKFSKVNEESPLAKIEV 369 (506)
T ss_pred --------------c-cCccc-----cCCCccccCCCccccHHHHHHhccCchhhhhhhcccchhhhhhhhcccchhhhH
Confidence 1 23322 356889988899999999999999999999999999998876643210000 0
Q ss_pred --CCccccccccccCCC---------------------C-CCCCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHhHH
Q 004116 548 --MNSENVHNREEENSG---------------------V-HGPWGQNGAEAALLSAEKVKAAAKAGLAAAATKAKLFADH 603 (773)
Q Consensus 548 --~~sE~~~~~~~~~d~---------------------~-~~~~~~n~~~~~~~s~~~vk~Aa~~aLaaAA~KAk~LA~~ 603 (773)
...+..-..-.+.+. . .....+.. ....+-.. +..|+..+|++||.|||+||.+
T Consensus 370 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~e~~k~~~~~~~~~n~~-~~k~~e~~-~~~a~~~~ls~aa~k~k~la~~ 447 (506)
T KOG1279|consen 370 SAKGVEEAASKLGGTDKSKFLALSDIACTLPDEEEKLQSKLKAKLNPN-KEKTIELG-LSTAANAALSAAAVKAKLLAAQ 447 (506)
T ss_pred HhhhhHHhhhhhccchhhhhhhhhhhhhcccchHHHHHHHhhcccccc-hhhhhHHH-HHHHHHHHHHHHHHhhhhhhhH
Confidence 000000000000000 0 00000000 00111112 6788999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 004116 604 EEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRL 663 (773)
Q Consensus 604 EEREI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~rl 663 (773)
|| +++.+++.++++|++|+|.||++|+++|+++.+|++++++.|+.++.+|..++..||
T Consensus 448 ee-~~~s~~~~~~~~q~~k~E~~l~~~~e~e~~~~~e~e~~~~~~~~~~~~~~~~~~~~l 506 (506)
T KOG1279|consen 448 EE-RIKSLVALLEETQLKKLEAKLRHFEEAETLLMREREQLERVRQRLKAERQQFHMARL 506 (506)
T ss_pred HH-HHHHHhhhhhhhhhhhhhHHHHHHHHHHhhhhhhhhhHHHHHHHHHhcchhhhhhcC
Confidence 99 999999999999999999999999999999999999999999999999999998875
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=8.6e-27 Score=206.47 Aligned_cols=86 Identities=43% Similarity=0.962 Sum_probs=78.6
Q ss_pred eeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHH
Q 004116 181 HVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR 260 (773)
Q Consensus 181 ivIPsyS~WFd~~~IH~IEKr~lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~ 260 (773)
+++|.+++||+++.+|++||+.+||||.| ++|+.|+.+||.||..||.||.+|||+|+||+++.|.|+..+.|||+
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 89999999999999999999999999999999998767999999999
Q ss_pred hhhhhccccc
Q 004116 261 FLNHWGIINY 270 (773)
Q Consensus 261 FLE~WGLINY 270 (773)
||++||+|||
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=99.90 E-value=3.9e-24 Score=232.78 Aligned_cols=110 Identities=31% Similarity=0.612 Sum_probs=100.8
Q ss_pred cCCCCCCCCCCCCc-ceeecccCcCcccChhhhccCCCCCCCC-CCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHhc
Q 004116 344 SENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY 421 (773)
Q Consensus 344 ~~~~C~~C~~~~~~-~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~rvd~~~~~~~~~~~~WT~qEellLLEaIe~y 421 (773)
..+.|++|..+|+. ++++|.+|.+|+||+.||+.|.+.+.|+ +|+|.+|++... .....+||++||++||||+++|
T Consensus 13 ~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~--~i~~~~WtadEEilLLea~~t~ 90 (438)
T KOG0457|consen 13 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSF--PILDPSWTADEEILLLEAAETY 90 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCC--CCCCCCCChHHHHHHHHHHHHh
Confidence 46899999999998 5699999999999999999999999996 799999998654 2467899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHHhCCCCCCCcc
Q 004116 422 N-DNWNEIAEHVSTKSKAQCILHFVRLPMEDGILE 455 (773)
Q Consensus 422 g-gNW~~IAehVGtKT~eECi~hFlqLPIED~fLe 455 (773)
| |||.+||+||||||++||..||++.+|+.++..
T Consensus 91 G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~ 125 (438)
T KOG0457|consen 91 GFGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFP 125 (438)
T ss_pred CCCcHHHHHHHHcccchHHHHHHHHHHHhcCcccc
Confidence 9 999999999999999999999999999888653
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.81 E-value=1e-20 Score=198.51 Aligned_cols=110 Identities=24% Similarity=0.479 Sum_probs=101.3
Q ss_pred cCCCCCCCCCCCCc-ceeecccCcCcccChhhhccCCCCCCCC-CCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHhc
Q 004116 344 SENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY 421 (773)
Q Consensus 344 ~~~~C~~C~~~~~~-~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~rvd~~~~~~~~~~~~WT~qEellLLEaIe~y 421 (773)
.+++|++|..+|+. +++.|.+|.+++||..||.+|.+.+.|+ .|+|.+|+.... .....+|++.||++|+++++..
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsy--pI~~e~WgadEEllli~~~~Tl 81 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSY--PIGEEGWGADEELLLIECLDTL 81 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCc--cccCCCcCchHHHHHHHHHHhc
Confidence 46799999999997 7999999999999999999999999987 799999987654 3567899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHHhCCCCCCCcc
Q 004116 422 N-DNWNEIAEHVSTKSKAQCILHFVRLPMEDGILE 455 (773)
Q Consensus 422 g-gNW~~IAehVGtKT~eECi~hFlqLPIED~fLe 455 (773)
| |||.+||+|||.|+++||..||+++++|..|..
T Consensus 82 GlGNW~dIadyiGsr~kee~k~HylK~y~es~~yp 116 (432)
T COG5114 82 GLGNWEDIADYIGSRAKEEIKSHYLKMYDESKYYP 116 (432)
T ss_pred CCCcHHHHHHHHhhhhhHHHHHHHHHHHhhccccc
Confidence 9 999999999999999999999999999988753
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=99.02 E-value=1.9e-10 Score=91.16 Aligned_cols=45 Identities=38% Similarity=0.780 Sum_probs=43.1
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCce
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYI 390 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~ 390 (773)
++|+.|+++|+.+||+|+++.+++||..||.+|+||.+|++.||+
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 479999999999999999999999999999999999999999995
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=98.97 E-value=9.3e-10 Score=87.53 Aligned_cols=44 Identities=27% Similarity=0.681 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCC-HHHHHHHhC-CCCHHHHHHHHHhC
Q 004116 404 ETWSDQETFLLLEGIEMYNDN-WNEIAEHVS-TKSKAQCILHFVRL 447 (773)
Q Consensus 404 ~~WT~qEellLLEaIe~yggN-W~~IAehVG-tKT~eECi~hFlqL 447 (773)
..||.+|+.+|++||.+||.+ |..||++|+ +||..||..||.+|
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 99999999999864
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=98.69 E-value=2.5e-08 Score=82.36 Aligned_cols=41 Identities=34% Similarity=0.762 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHh
Q 004116 406 WSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (773)
Q Consensus 406 WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlq 446 (773)
||.+|+.+|++++..||.+|..||+++|+||+.+|..||..
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 99999999999999999999999999999999999999999
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.67 E-value=4.2e-08 Score=75.63 Aligned_cols=44 Identities=30% Similarity=0.686 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 404 ETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 404 ~~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~hFlqL 447 (773)
..||.+|+.+|+.++..|| .+|..||+++++||+.+|..+|..+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 4799999999999999999 9999999999999999999999875
No 10
>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=98.59 E-value=9.1e-08 Score=72.74 Aligned_cols=43 Identities=33% Similarity=0.753 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 405 TWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 405 ~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~hFlqL 447 (773)
.||.+|+.+|+.++.+|| ++|..||+.+++||..+|..||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 499999999999999999 9999999999999999999999764
No 11
>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=98.38 E-value=3.5e-07 Score=73.69 Aligned_cols=47 Identities=34% Similarity=0.680 Sum_probs=42.8
Q ss_pred CCCCCCCCCCCc-ceeecccCcCcccChhhhccCCCCCCCC-CCCceec
Q 004116 346 NHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (773)
Q Consensus 346 ~~C~~C~~~~~~-~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~rv 392 (773)
+.|++|.+++.. .+|+|.+|.+++||.+||..|.+...|+ +|.|+.|
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 369999999887 9999999999999999999999999997 6899865
No 12
>PLN03000 amine oxidase
Probab=98.31 E-value=7.6e-07 Score=107.64 Aligned_cols=84 Identities=23% Similarity=0.325 Sum_probs=72.2
Q ss_pred CCCCCCCCCCCHHHHhh--cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhh
Q 004116 186 HSDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (773)
Q Consensus 186 yS~WFd~~~IH~IEKr~--lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE 263 (773)
++.=|..+++++.|..+ || .- .++.+..|+.+||-|+.+|+.||..|||+.+|...+-..-...+.++|.||.
T Consensus 87 ~~~~~p~d~l~~~e~~~~~~~-~~----~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~ 161 (881)
T PLN03000 87 LTAGFPADSLTEEEIEFGVVP-IV----GGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLV 161 (881)
T ss_pred HHcCCCcccCCHHHHhccccC-cc----cccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHH
Confidence 56789999999999777 67 22 2467899999999999999999999999999998875533577899999999
Q ss_pred hhcccccccCC
Q 004116 264 HWGIINYCAAV 274 (773)
Q Consensus 264 ~WGLINYqvdp 274 (773)
+.|+|||++..
T Consensus 162 r~G~in~g~~~ 172 (881)
T PLN03000 162 THGYINFGIAQ 172 (881)
T ss_pred HcCcccHHHHH
Confidence 99999999863
No 13
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.15 E-value=2.5e-06 Score=102.90 Aligned_cols=88 Identities=23% Similarity=0.288 Sum_probs=75.9
Q ss_pred CCCCCCCCCCCHHHHhh-cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhhh
Q 004116 186 HSDWFSPDTVHRLERQV-VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH 264 (773)
Q Consensus 186 yS~WFd~~~IH~IEKr~-lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~ 264 (773)
.+.-|..+++|+-|-.+ |+..-.+ +.+..|+.+||-|+.+||.||..|||+.+|+..+-......+.++|.||.+
T Consensus 138 ~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~ 213 (808)
T PLN02328 138 ISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLE 213 (808)
T ss_pred HHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhc
Confidence 67889999999988776 6666554 789999999999999999999999999999987644335689999999999
Q ss_pred hcccccccCCCCC
Q 004116 265 WGIINYCAAVQSP 277 (773)
Q Consensus 265 WGLINYqvdp~~~ 277 (773)
-|.|||.|.|...
T Consensus 214 ~g~in~gv~~~~~ 226 (808)
T PLN02328 214 HGYINFGVAPVIK 226 (808)
T ss_pred cCceeeecccccc
Confidence 9999999998654
No 14
>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=98.12 E-value=2.1e-06 Score=69.35 Aligned_cols=45 Identities=24% Similarity=0.488 Sum_probs=40.6
Q ss_pred CCCCCCC-CCCcceeecccCcCcccChhhhccCCCCCCCC-CCCcee
Q 004116 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (773)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~r 391 (773)
.|++|.+ ++..++|+|..|.+++||.+||..|++..+|+ +|.|..
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 99999999999999999999999999988886 566653
No 15
>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=98.04 E-value=4.3e-06 Score=67.57 Aligned_cols=45 Identities=20% Similarity=0.403 Sum_probs=41.4
Q ss_pred CCCCCC-CCCCcceeecccCcCcccChhhhccCCCCCCCC-CCCcee
Q 004116 347 HCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (773)
Q Consensus 347 ~C~~C~-~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~r 391 (773)
.|++|+ .++...+|+|..|.+++||.+||..|.....|+ +|.|+.
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 789999999999999999999999999999997 788765
No 16
>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=98.04 E-value=3.9e-06 Score=67.59 Aligned_cols=40 Identities=30% Similarity=0.600 Sum_probs=37.5
Q ss_pred CCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCC
Q 004116 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS 386 (773)
Q Consensus 347 ~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss 386 (773)
.|++|...+..++|+|.+|.+++||..||..|++..+|+.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~ 41 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHED 41 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCCC
Confidence 5999999888899999999999999999999999999974
No 17
>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=98.02 E-value=4.7e-06 Score=67.49 Aligned_cols=44 Identities=34% Similarity=0.684 Sum_probs=39.6
Q ss_pred CCCCCCC-CCCcceeecccCcCcccChhhhccCCCCCCCC-CCCce
Q 004116 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYI 390 (773)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~ 390 (773)
.|++|++ ++...+|+|.+|.+++||..||..|++...|+ .|+++
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 5999996 68899999999999999999999999999997 56664
No 18
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=97.96 E-value=7.6e-06 Score=65.03 Aligned_cols=45 Identities=29% Similarity=0.705 Sum_probs=39.5
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCC-CCCceec
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~rv 392 (773)
+.|+.|+.++...+|+|..|.+++||..||+.|. ..|. .|.|..+
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 3699999999999999999999999999999998 5665 6888754
No 19
>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=97.96 E-value=7.4e-06 Score=64.53 Aligned_cols=42 Identities=29% Similarity=0.558 Sum_probs=38.5
Q ss_pred CCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceec
Q 004116 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRV 392 (773)
Q Consensus 347 ~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rv 392 (773)
.|++|+.++...+|+|..|.+++||.+||..| +|..|.|+++
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~----~H~~H~f~~~ 43 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG----VHPEHAMLKI 43 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC----CCCCCCEEeC
Confidence 69999999999999999999999999999988 6778888864
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=97.96 E-value=6.9e-06 Score=64.76 Aligned_cols=40 Identities=33% Similarity=0.630 Sum_probs=36.9
Q ss_pred CCCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCC
Q 004116 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGH 384 (773)
Q Consensus 345 ~~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~h 384 (773)
...|+.|+.++...+|+|..|.+++||.+||..|+++..|
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcCcCCCC
Confidence 4679999999999999999999999999999999988766
No 21
>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=97.95 E-value=1.2e-05 Score=67.14 Aligned_cols=47 Identities=15% Similarity=0.386 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCH---HHHHHHhC-CC-CHHHHHHHHHhCCC
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNW---NEIAEHVS-TK-SKAQCILHFVRLPM 449 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW---~~IAehVG-tK-T~eECi~hFlqLPI 449 (773)
...||++|..++|+||+.|| ||| .+|+++++ ++ |+.||..|+-.+.+
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 35799999999999999999 599 99999987 57 99999999877654
No 22
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.83 E-value=1.9e-05 Score=82.91 Aligned_cols=45 Identities=16% Similarity=0.427 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhC-CCCHHHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW~~IAehVG-tKT~eECi~hFlqL 447 (773)
...||.+|+.+|+++|++|| .+|..||+++| +||..||..+|.++
T Consensus 25 Rg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~ 71 (249)
T PLN03212 25 RGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNY 71 (249)
T ss_pred CCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHh
Confidence 46799999999999999999 79999999997 79999999999976
No 23
>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=97.81 E-value=1.9e-05 Score=63.70 Aligned_cols=44 Identities=27% Similarity=0.662 Sum_probs=38.0
Q ss_pred CCCCCCCC-CCCcceeecccCc--CcccChhhhccCCCCCCCC-CCCceec
Q 004116 346 NHCNYCSQ-PIPAVYYQSQKEV--DVLLCPECFHEGRFVTGHS-SLDYIRV 392 (773)
Q Consensus 346 ~~C~~C~~-~~~~~~y~c~kc~--d~~LC~~CFs~G~~~~~hs-s~dF~rv 392 (773)
+.|++|+. ++..++|+|..|. +++||.+||..|. .|+ +|.|.++
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 9999999999999 9999999999997 665 5766653
No 24
>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=97.65 E-value=1.5e-05 Score=63.55 Aligned_cols=41 Identities=34% Similarity=0.686 Sum_probs=31.2
Q ss_pred CCCCCCCCC-CCCcceeecccCcCcccChhhhccCCCCCCCC
Q 004116 345 ENHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS 385 (773)
Q Consensus 345 ~~~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs 385 (773)
...|+.|+. ++...+|+|..|.+++||..||..|++...|+
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH--H-SSSS
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCcCCCCCcC
Confidence 467999998 77889999999999999999999999887774
No 25
>PLN03091 hypothetical protein; Provisional
Probab=97.55 E-value=8.1e-05 Score=83.49 Aligned_cols=45 Identities=22% Similarity=0.531 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhC-CCCHHHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW~~IAehVG-tKT~eECi~hFlqL 447 (773)
...||.+|+.+|+++|++|| .+|..||+++| +||..||+.+|+++
T Consensus 14 Kg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~Ny 60 (459)
T PLN03091 14 KGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINY 60 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhc
Confidence 35799999999999999999 79999999998 79999999999875
No 26
>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=97.49 E-value=0.0001 Score=58.79 Aligned_cols=42 Identities=24% Similarity=0.600 Sum_probs=36.2
Q ss_pred CCCCCCC-CCCcceeecccCcCcccChhhhccCCCCCCCC-CCCceec
Q 004116 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (773)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~rv 392 (773)
.|++|+. ++...+|+|..|.+++||..||..+ .|+ .|.|.+|
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~----~H~~~H~F~ri 45 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTR----KHNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCC----CcCCCCceeeC
Confidence 6999985 7888999999999999999999985 464 6888875
No 27
>PLN02529 lysine-specific histone demethylase 1
Probab=97.49 E-value=0.0001 Score=88.62 Aligned_cols=86 Identities=22% Similarity=0.246 Sum_probs=71.5
Q ss_pred CCCCCCCCCCCHHHHhh--cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhh
Q 004116 186 HSDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (773)
Q Consensus 186 yS~WFd~~~IH~IEKr~--lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE 263 (773)
++-=|..+++.+-|+++ +|+. .++.++.|+.+||-|+.+||.||..|||+.+++..+...-...|...|.||.
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 56678999999988854 5543 3789999999999999999999999999999887764422334668999999
Q ss_pred hhcccccccCCCC
Q 004116 264 HWGIINYCAAVQS 276 (773)
Q Consensus 264 ~WGLINYqvdp~~ 276 (773)
+-|.|||.|.|..
T Consensus 138 ~~~~inc~vnp~~ 150 (738)
T PLN02529 138 YNGYINFGVSPSF 150 (738)
T ss_pred hCCCcceeecccc
Confidence 9999999999864
No 28
>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=97.25 E-value=0.0003 Score=56.13 Aligned_cols=41 Identities=24% Similarity=0.603 Sum_probs=34.6
Q ss_pred CCCCCC-CCCCcceeecccCcCcccChhhhccCCCCCCCC-CCCcee
Q 004116 347 HCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (773)
Q Consensus 347 ~C~~C~-~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hs-s~dF~r 391 (773)
.|++|+ .++..++|+|..|.+++||.+||..+ .|+ .|.|.+
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 67788999999999999999999963 353 677765
No 29
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.13 E-value=0.00056 Score=72.07 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=43.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 401 IDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 401 ~~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqL 447 (773)
.....||.+|+.+||+.+..||..|..||.+|.+||..+|..+|..+
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~ 122 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTH 122 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHH
Confidence 34579999999999999999999999999999999999999999653
No 30
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.09 E-value=0.00047 Score=72.51 Aligned_cols=45 Identities=13% Similarity=0.406 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhC-CCCHHHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW~~IAehVG-tKT~eECi~hFlqL 447 (773)
...||.+|+.+|.+.|++|| ++|..|+++.| .|+-..|+++++.+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~Ny 55 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNY 55 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcc
Confidence 36899999999999999999 99999999999 89999999999964
No 31
>PLN03091 hypothetical protein; Provisional
Probab=96.64 E-value=0.0027 Score=71.66 Aligned_cols=47 Identities=19% Similarity=0.343 Sum_probs=43.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 401 IDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 401 ~~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqL 447 (773)
.....||.+|+.+||+.+..||..|.+||+++..||..+|..||..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnsl 111 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSC 111 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHH
Confidence 34578999999999999999999999999999999999999888753
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=96.45 E-value=0.0017 Score=50.84 Aligned_cols=33 Identities=21% Similarity=0.526 Sum_probs=28.7
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCC
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGR 379 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~ 379 (773)
+.|+.|.+.+ ..+|+|+.|.+|+||..||..+.
T Consensus 1 y~C~~C~~~~-~~r~~C~~C~dfDLC~~C~~~~~ 33 (41)
T cd02337 1 YTCNECKHHV-ETRWHCTVCEDYDLCITCYNTKN 33 (41)
T ss_pred CcCCCCCCcC-CCceECCCCcchhhHHHHhCCCC
Confidence 4699999855 49999999999999999998754
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=96.07 E-value=0.0037 Score=49.43 Aligned_cols=31 Identities=35% Similarity=0.771 Sum_probs=28.5
Q ss_pred CCCCCCC-CCCcceeecccCcCcccChhhhcc
Q 004116 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHE 377 (773)
Q Consensus 347 ~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~ 377 (773)
.|+.|+. ++...+|+|..|.+++||..||..
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 6999996 888899999999999999999975
No 34
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.34 E-value=0.02 Score=66.99 Aligned_cols=46 Identities=26% Similarity=0.658 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~hFlqL 447 (773)
....||.+|+.+|+-||++|| -+|-+|-+.|.+||-.||..+|++.
T Consensus 359 khg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 359 KHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 346899999999999999999 6999999999999999999999874
No 35
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=95.14 E-value=0.013 Score=63.41 Aligned_cols=45 Identities=22% Similarity=0.446 Sum_probs=38.1
Q ss_pred CCCCCCCC-CCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecC
Q 004116 346 NHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVD 393 (773)
Q Consensus 346 ~~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd 393 (773)
..|+.|+. .|...+|+|..|.|++||.+|+..+ ..|-.|-|.++.
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~---~~h~~H~~lR~~ 198 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN---EHHAAHAMLRLH 198 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC---CCCcccceeecc
Confidence 57999999 9999999999999999999999876 345567777743
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.92 E-value=0.017 Score=50.88 Aligned_cols=44 Identities=34% Similarity=0.645 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHHh--c----C--------CCHHHHHHHhC----CCCHHHHHHHHHhC
Q 004116 404 ETWSDQETFLLLEGIEM--Y----N--------DNWNEIAEHVS----TKSKAQCILHFVRL 447 (773)
Q Consensus 404 ~~WT~qEellLLEaIe~--y----g--------gNW~~IAehVG----tKT~eECi~hFlqL 447 (773)
..||++|+..||+.+.. + + .-|..||+.+. .||+.||..+|-.|
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 47999999999999987 2 1 15999999985 59999999999876
No 37
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=94.68 E-value=0.014 Score=69.14 Aligned_cols=43 Identities=35% Similarity=0.774 Sum_probs=36.9
Q ss_pred CCCCCCCCC-CCCcceeecccCcCcccChhhhccCCCCCCCCCC
Q 004116 345 ENHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSL 387 (773)
Q Consensus 345 ~~~C~~C~~-~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~ 387 (773)
...|+.|.+ +|..++|+|++|-+++||..||..|+-..+|+-|
T Consensus 603 ~~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~ 646 (966)
T KOG4286|consen 603 QAKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMH 646 (966)
T ss_pred hhhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCC
Confidence 357999954 5567899999999999999999999999999754
No 38
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=94.67 E-value=0.027 Score=65.89 Aligned_cols=45 Identities=24% Similarity=0.416 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCH---HHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSK---AQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~---eECi~hFlqL 447 (773)
.+.||-+|+..||++|++|| |+|-+||-.+|.||. .-|..+|+..
T Consensus 412 ~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~ 460 (939)
T KOG0049|consen 412 VERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAA 460 (939)
T ss_pred cCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHH
Confidence 46899999999999999999 999999999999998 6699999875
No 39
>PLN02976 amine oxidase
Probab=94.63 E-value=0.029 Score=71.70 Aligned_cols=81 Identities=23% Similarity=0.432 Sum_probs=66.9
Q ss_pred CCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCC---CC----hhHHHHHHHhh
Q 004116 190 FSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDG---VS----PEDLTRIFRFL 262 (773)
Q Consensus 190 Fd~~~IH~IEKr~lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G---~d----v~sI~RVH~FL 262 (773)
..-..|.+|||-.|.|....| -.-+-|+++||-|+-.|-.|=.+-|-+|+|= +++ .| ...|.-|+.||
T Consensus 455 l~a~~~~~~e~~~~k~~lkr~---~~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~--v~~~~~~~e~~~~~l~r~~~~fl 529 (1713)
T PLN02976 455 LKARAVGPIEKIKFKEVLKRK---GGLQEYLECRNMILGLWSKDVSRILPLADCG--VTDTPSEDESPRASLIREVYLFL 529 (1713)
T ss_pred ccccccChHHHHHHHHHHHhc---cchHHHHHHHHHHHHHhhhhhhhcccHhhcc--ccCCcccccCchhhHHHHHHHHh
Confidence 344678999999999998754 3578999999999999999999999999995 211 11 46688899999
Q ss_pred hhhcccccccCCC
Q 004116 263 NHWGIINYCAAVQ 275 (773)
Q Consensus 263 E~WGLINYqvdp~ 275 (773)
+|-|.||-.+..+
T Consensus 530 d~~gyin~g~~s~ 542 (1713)
T PLN02976 530 DQRGYINAGIASE 542 (1713)
T ss_pred hccCceecccccc
Confidence 9999999998764
No 40
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=94.14 E-value=0.079 Score=55.89 Aligned_cols=43 Identities=19% Similarity=0.393 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHH
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHF 444 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hF 444 (773)
....||.+||.+|+++=..||.-|..||.++.+||-.+...|+
T Consensus 61 krg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W 103 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW 103 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH
Confidence 3578999999999999999999999999999999998887766
No 41
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=93.23 E-value=0.053 Score=59.69 Aligned_cols=41 Identities=22% Similarity=0.440 Sum_probs=33.8
Q ss_pred CCCCCCCCCCCCc-ceeecccCcCcccChhhhccCCCCCCCC
Q 004116 345 ENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS 385 (773)
Q Consensus 345 ~~~C~~C~~~~~~-~~y~c~kc~d~~LC~~CFs~G~~~~~hs 385 (773)
...|+.|++.--. -+|+|..|.||+||..||.+|.-...|.
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~ 49 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHD 49 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccC
Confidence 3579999876533 5799999999999999999997766664
No 42
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=90.87 E-value=0.21 Score=58.87 Aligned_cols=51 Identities=25% Similarity=0.484 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHH-------hc------------------C-CCHHHHHHHhCCCCHHHHHHHHHhCCCCCC
Q 004116 402 DGETWSDQETFLLLEGIE-------MY------------------N-DNWNEIAEHVSTKSKAQCILHFVRLPMEDG 452 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe-------~y------------------g-gNW~~IAehVGtKT~eECi~hFlqLPIED~ 452 (773)
....||-+|+.+||..|+ .| . =+|..|++.+|||+..||..||-+|=+...
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s 511 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHH
Confidence 356899999999999995 33 1 389999999999999999999999866544
No 43
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=90.30 E-value=0.13 Score=56.74 Aligned_cols=41 Identities=29% Similarity=0.681 Sum_probs=34.9
Q ss_pred CCCCCCC-CCCCcceeecccCcCcccChhhhccCCCCCCCCC
Q 004116 346 NHCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS 386 (773)
Q Consensus 346 ~~C~~C~-~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss 386 (773)
..|++|. ..++..+|.|+.|.++.+|.+||-.|+-...|+.
T Consensus 241 v~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsn 282 (434)
T KOG4301|consen 241 VECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSN 282 (434)
T ss_pred ccCcceecccccchhhhHhhcCCccccchhhccccCCCCcch
Confidence 4699995 4556789999999999999999999998877763
No 44
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=90.26 E-value=0.33 Score=57.39 Aligned_cols=45 Identities=16% Similarity=0.358 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqL 447 (773)
....||.+|+..|-.-+.++|++|..|++.|| |.|..|..+|-++
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~ 427 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQY 427 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHh
Confidence 46789999999999999999999999999998 6999999999886
No 45
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=88.46 E-value=0.66 Score=55.57 Aligned_cols=45 Identities=20% Similarity=0.435 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHh
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlq 446 (773)
..+-||..|..++-+||-.|.-|+..|++.|.+||..||+..|.-
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 457899999999999999999999999999999999999998863
No 46
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=86.00 E-value=1.4 Score=49.48 Aligned_cols=45 Identities=13% Similarity=0.386 Sum_probs=42.5
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHh
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlq 446 (773)
....||..|+.++..|+.++|-|+.-|+....+|+..|+..+|++
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 346899999999999999999999999999999999999999985
No 47
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=85.71 E-value=1.7 Score=37.60 Aligned_cols=44 Identities=30% Similarity=0.445 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHhcC-----------------CCHHHHHHHhC-----CCCHHHHHHHHHhC
Q 004116 404 ETWSDQETFLLLEGIEMYN-----------------DNWNEIAEHVS-----TKSKAQCILHFVRL 447 (773)
Q Consensus 404 ~~WT~qEellLLEaIe~yg-----------------gNW~~IAehVG-----tKT~eECi~hFlqL 447 (773)
..||.+|...||+-|+.|. .-|..|++.+. .||..||..+|-.|
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 5799999999999999883 35999999983 58999999988654
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=84.62 E-value=1 Score=49.79 Aligned_cols=47 Identities=28% Similarity=0.479 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHhc----------CCCHHHHHHHh---C-CCCHHHHHHHHHhCCC
Q 004116 403 GETWSDQETFLLLEGIEMY----------NDNWNEIAEHV---S-TKSKAQCILHFVRLPM 449 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~y----------ggNW~~IAehV---G-tKT~eECi~hFlqLPI 449 (773)
...|+.+|++.||++.... +-.|..||... | .||+.||..+|-.|..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 3689999999999999743 14499999944 3 4999999999988855
No 49
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=81.49 E-value=1.3 Score=51.32 Aligned_cols=45 Identities=24% Similarity=0.506 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqL 447 (773)
....|+.+|+..||.+......-|-.||.-|| +|..+|..+|..|
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 34689999999999999999999999999998 7999999999886
No 50
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=80.73 E-value=1.5 Score=50.89 Aligned_cols=44 Identities=25% Similarity=0.582 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHHHHh
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVR 446 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~hFlq 446 (773)
+.-|+..|+..|=-|+.+|| ..|.+|+..+..||+.||..+|..
T Consensus 7 ggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e 51 (617)
T KOG0050|consen 7 GGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEE 51 (617)
T ss_pred cceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHH
Confidence 45799999999999999999 899999999999999999999974
No 51
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=79.38 E-value=12 Score=46.33 Aligned_cols=75 Identities=17% Similarity=0.256 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 580 EKVKAAAKAGLA-AAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATER 655 (773)
Q Consensus 580 ~~vk~Aa~~aLa-aAA~KAk~LA~~EEREI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR 655 (773)
..+..|...+|- ..-.+|+.+...++.++++|+..|.+. .+++|.+...++++..-+++.+++||+.++.|-.+|
T Consensus 489 ~a~~iA~~~Glp~~ii~~A~~~~~~~~~~~~~li~~l~~~-~~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~ 564 (782)
T PRK00409 489 NAFEIAKRLGLPENIIEEAKKLIGEDKEKLNELIASLEEL-ERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEE 564 (782)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhhhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346666666664 456889999999999999999987653 233455544444444444444444444444443333
No 52
>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=79.14 E-value=13 Score=45.94 Aligned_cols=75 Identities=17% Similarity=0.189 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 580 EKVKAAAKAGLA-AAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATER 655 (773)
Q Consensus 580 ~~vk~Aa~~aLa-aAA~KAk~LA~~EEREI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR 655 (773)
..+..|...+|- ..-.+|+.+...++.++++|+..|.+.+ +++|.++..++.+..-+++++++||+.+++|-.+|
T Consensus 484 ~a~~iA~~~Glp~~ii~~A~~~~~~~~~~~~~li~~L~~~~-~~~e~~~~~~~~~~~e~~~~~~~l~~~~~~l~~~~ 559 (771)
T TIGR01069 484 YAFEIAQRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALE-KELEQKNEHLEKLLKEQEKLKKELEQEMEELKERE 559 (771)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHHhhHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346666666664 4568899999999999999999875433 33555555444444444444444444444443333
No 53
>COG5180 PBP1 Protein interacting with poly(A)-binding protein [RNA processing and modification]
Probab=77.33 E-value=3.6 Score=47.40 Aligned_cols=53 Identities=28% Similarity=0.432 Sum_probs=29.5
Q ss_pred CCCCCCCCCCcccCCccCCCCCCCCCCccCCCCCCCCCCcccCCCCCCCCCCCCCcCC
Q 004116 666 GGVPSQMNLPVVAPSMVNNNIGNNRPQVMSASSSQPSIPGYSANQPVHPHMQFRPQQM 723 (773)
Q Consensus 666 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 723 (773)
|..-|.|+.+ |+.+|.+. .+ -|.++|..|+-|.|+||+.- .+---|.|+||+|
T Consensus 506 GNa~~~~~~A-~~~~M~~~-m~--~P~~~PSA~P~P~M~~~~~G-~~~~Y~P~~PQ~~ 558 (654)
T COG5180 506 GNAVPGMNPA-MGMNMGGM-MG--FPMGGPSASPNPMMNGFAAG-SMGMYMPFQPQPM 558 (654)
T ss_pred cccccccChh-hcCCccce-ee--ccCCCCCCCCCCCcCCcccC-CcccccCCCCCcc
Confidence 5555555543 55555443 22 45778888888888886543 2222344444433
No 54
>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=76.70 E-value=2.3 Score=42.86 Aligned_cols=44 Identities=18% Similarity=0.474 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHhc---C----CCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMY---N----DNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~y---g----gNW~~IAehVGtKT~eECi~hFlqL 447 (773)
.+.||.+|+++|-|.|..| | .-.++|++.++ ||+.-|-.+|..+
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~-RTsAACGFRWNs~ 54 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN-RTAAACGFRWNAY 54 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc-ccHHHhcchHHHH
Confidence 3679999999999999999 3 46888999995 8999999998754
No 55
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=74.36 E-value=2.7 Score=49.68 Aligned_cols=45 Identities=20% Similarity=0.437 Sum_probs=39.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHH----------HHHhCCCCHHHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMYNDNWNEI----------AEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yggNW~~I----------AehVGtKT~eECi~hFlqL 447 (773)
...||.+|+.-+.+||..||-|+++| -..+..||+.|...||.++
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 46899999999999999999999999 3345568999999999876
No 56
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=72.85 E-value=5 Score=45.11 Aligned_cols=48 Identities=23% Similarity=0.389 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHHH-HHhCCCCHHHHHHHHHhCCCC
Q 004116 403 GETWSDQETFLLLEGIEMYNDNWNEIA-EHVSTKSKAQCILHFVRLPME 450 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yggNW~~IA-ehVGtKT~eECi~hFlqLPIE 450 (773)
-..|+.+|=..+=+||+.||-|+..|- ..|.|||--||+..|..--..
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKkS 325 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKKS 325 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhcC
Confidence 368999999999999999999999995 589999999999988765443
No 57
>PF15324 TALPID3: Hedgehog signalling target
Probab=72.37 E-value=51 Score=41.90 Aligned_cols=91 Identities=24% Similarity=0.332 Sum_probs=56.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH-----HHHHHHH-------HHH--HHHH----HHHHHHHHH
Q 004116 578 SAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANII-----NHQLKRL-------ELK--LKQF----AEVETLLMR 639 (773)
Q Consensus 578 s~~~vk~Aa~~aLaaAA~KAk~LA~~EEREI~rLv~~II-----e~QLKKL-------ElK--Lk~f----eELE~~le~ 639 (773)
+...|.+|+++|+++||---|...+.| -++......|= +.||+.+ +.| --|. ..|-.+|+.
T Consensus 61 SAtTVAAATAAAIATaAPLiKvQSdLE-AKVnsVselL~KLQEtDkqLqrvteqQt~i~~~~ek~~ch~~EkQmn~fmeQ 139 (1252)
T PF15324_consen 61 SATTVAAATAAAIATAAPLIKVQSDLE-AKVNSVSELLNKLQETDKQLQRVTEQQTSIQNQHEKLHCHDHEKQMNVFMEQ 139 (1252)
T ss_pred hHHHHHHHHHHHHHhhhhhhhhcchHH-HHHHHHHHHHHHhhhhhcchhhhhhhhccccccccccchhhHHHHHHHHHHH
Confidence 456788888999988886666555443 33332222210 1111111 110 0112 234456778
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCC
Q 004116 640 ECEQVEKARQRFATERTRIVSTRLGPGGVP 669 (773)
Q Consensus 640 Ere~LE~~Rq~L~~eR~~~~~~rl~~~~~~ 669 (773)
-.+.||+.+||.+.-+-.|+...|.+|+.-
T Consensus 140 ~l~HLEKLQqQQi~iQshfIsSAl~~~s~q 169 (1252)
T PF15324_consen 140 HLRHLEKLQQQQIDIQSHFISSALKTGSLQ 169 (1252)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 888999999999999999999999987755
No 58
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=69.12 E-value=6 Score=46.87 Aligned_cols=96 Identities=19% Similarity=0.332 Sum_probs=54.7
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHH-----Hh
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGI-----EM 420 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEaI-----e~ 420 (773)
..|.-|+... ..+.|.. ..+.+|..|-.--|.. . .+|+. ..-+.||++|...|..+= +.
T Consensus 24 k~CADCgs~~--P~WASiN-lGIFICi~CSGIHRsL------G-hRVKS------LSLDkWT~EEVe~Mk~gGN~~AN~i 87 (648)
T PLN03119 24 RRCINCNSLG--PQYVCTT-FWTFVCMACSGIHREF------T-HRVKS------VSMSKFTSKEVEVLQNGGNQRAREI 87 (648)
T ss_pred CccccCCCCC--CCceeec-cceEEeccchhhhccC------C-ceeec------cccCCCCHHHHHHHHHhchHHHHHH
Confidence 4688888643 5555554 3678999996543332 1 14443 233689998865443211 22
Q ss_pred cCCCHHHHHHHhCCCCHHHHHHHHHhC-CCCCCCcccC
Q 004116 421 YNDNWNEIAEHVSTKSKAQCILHFVRL-PMEDGILENV 457 (773)
Q Consensus 421 yggNW~~IAehVGtKT~eECi~hFlqL-PIED~fLe~~ 457 (773)
|..+|..--..+...+-.+-+..||+. |++..|....
T Consensus 88 yeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~ 125 (648)
T PLN03119 88 YLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGAN 125 (648)
T ss_pred HHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcC
Confidence 335676432233333445566788884 7777777543
No 59
>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=67.89 E-value=8.3 Score=32.24 Aligned_cols=53 Identities=25% Similarity=0.285 Sum_probs=40.2
Q ss_pred hHHHHHHHHHHHHHHHhCCCcee-eHHHHhhccCCCChhHHHHHHHhhhhhccccc
Q 004116 216 PEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (773)
Q Consensus 216 PeiYk~yRNfMIntYR~NP~eYL-TvTacRRnL~G~dv~sI~RVH~FLE~WGLINY 270 (773)
-++|..+++.|.+- +.-|.++| |..+--+.+ |.....+.+....|+.+|||--
T Consensus 3 ~~i~~~l~~~I~~g-~~~~g~~lps~~~la~~~-~vsr~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 3 EQIYDQLRQAILSG-RLPPGDRLPSERELAERY-GVSRTTVREALRRLEAEGLIER 56 (64)
T ss_dssp HHHHHHHHHHHHTT-SS-TTSBE--HHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHcC-CCCCCCEeCCHHHHHHHh-ccCCcHHHHHHHHHHHCCcEEE
Confidence 36899999998886 57789999 888854333 3447889999999999999954
No 60
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=66.85 E-value=8.9 Score=35.51 Aligned_cols=45 Identities=24% Similarity=0.446 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHHhc----C----CCHHHHHHHhCCC-----CHHHHHHHHHhC
Q 004116 403 GETWSDQETFLLLEGIEMY----N----DNWNEIAEHVSTK-----SKAQCILHFVRL 447 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~y----g----gNW~~IAehVGtK-----T~eECi~hFlqL 447 (773)
..-||+++|+.||+||-.| | .||...-++|... |..|-..+.-+|
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrL 61 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRL 61 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence 4679999999999999988 4 5999988888643 666666665554
No 61
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=65.10 E-value=5.5 Score=49.26 Aligned_cols=20 Identities=30% Similarity=0.526 Sum_probs=8.4
Q ss_pred hhccCCcCcccccchhhhcc
Q 004116 24 QLNKLDEDDVVEDEDEEQDN 43 (773)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~ 43 (773)
-|+...+||..||||+|+|+
T Consensus 1398 GR~r~~~dd~DeeeD~e~Ed 1417 (1516)
T KOG1832|consen 1398 GRRRPTDDDSDEEEDDETED 1417 (1516)
T ss_pred cccCCCccccCccccchhhc
Confidence 34444334444444444444
No 62
>PLN03131 hypothetical protein; Provisional
Probab=64.05 E-value=8.8 Score=45.90 Aligned_cols=95 Identities=18% Similarity=0.336 Sum_probs=55.2
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHH------H
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGI------E 419 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEaI------e 419 (773)
..|.-|+... ..+.|.. ..+.+|+.|-.--|.. +| +|.. ..-+.||++|...| +.+ +
T Consensus 24 k~CADCga~~--P~WASiN-lGIFICi~CSGIHRsL-gh------RVKS------VTLD~WtdeEV~~M-k~gGN~~AN~ 86 (705)
T PLN03131 24 RRCINCNSLG--PQFVCTN-FWTFICMTCSGIHREF-TH------RVKS------VSMSKFTSQDVEAL-QNGGNQRARE 86 (705)
T ss_pred CccccCCCCC--CCeeEec-cceEEchhchhhhccc-Cc------cccc------ccCCCCCHHHHHHH-HHhccHHHHH
Confidence 4688888643 4555544 4688999997544433 11 4443 22368999886543 332 2
Q ss_pred hcCCCHHHHHHHhCCCCHHHHHHHHHhC-CCCCCCcccC
Q 004116 420 MYNDNWNEIAEHVSTKSKAQCILHFVRL-PMEDGILENV 457 (773)
Q Consensus 420 ~yggNW~~IAehVGtKT~eECi~hFlqL-PIED~fLe~~ 457 (773)
.|..+|..--..+...+..+-+..||+. |++..|+...
T Consensus 87 iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~ 125 (705)
T PLN03131 87 IYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGK 125 (705)
T ss_pred HHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCC
Confidence 3345676433334444555667788884 7777777543
No 63
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=62.49 E-value=7 Score=46.04 Aligned_cols=46 Identities=22% Similarity=0.496 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqL 447 (773)
....|+.+|.-.|++.=..++--|..||..|+.+|..+|..+|+.+
T Consensus 71 k~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~ 116 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNT 116 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHH
Confidence 3468999999999999999999999999999999999999999954
No 64
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=62.28 E-value=3 Score=47.85 Aligned_cols=11 Identities=18% Similarity=0.208 Sum_probs=7.5
Q ss_pred ccCCceeeCCC
Q 004116 175 RFGSRVHVLPM 185 (773)
Q Consensus 175 ~~~~~~ivIPs 185 (773)
|...++++||-
T Consensus 217 Rr~~K~~~iPQ 227 (458)
T PF10446_consen 217 RRREKHIPIPQ 227 (458)
T ss_pred HHHcCCCCCCC
Confidence 44577888874
No 65
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=59.71 E-value=5.6 Score=46.81 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHHH
Q 004116 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHF 444 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~hF 444 (773)
...|+..|+..|+-+++.|| .||..||...+.+++++|..|.
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 45899999999999999999 8999999999999999999998
No 66
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=59.35 E-value=62 Score=40.09 Aligned_cols=14 Identities=21% Similarity=0.667 Sum_probs=7.8
Q ss_pred cccChhhhccCCCC
Q 004116 368 VLLCPECFHEGRFV 381 (773)
Q Consensus 368 ~~LC~~CFs~G~~~ 381 (773)
++-|...|.+..+.
T Consensus 212 iIrClka~mNn~~G 225 (1102)
T KOG1924|consen 212 IIRCLKAFMNNKFG 225 (1102)
T ss_pred HHHHHHHHhccccc
Confidence 45566666555543
No 67
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=59.18 E-value=13 Score=47.53 Aligned_cols=40 Identities=20% Similarity=0.362 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHH
Q 004116 404 ETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILH 443 (773)
Q Consensus 404 ~~WT~qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~h 443 (773)
.+||..+-..++.|.++|| +|-..||..|++||++|...+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 4799999999999999999 999999999999999998753
No 68
>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=58.36 E-value=6.1 Score=28.64 Aligned_cols=27 Identities=33% Similarity=0.806 Sum_probs=12.4
Q ss_pred CCCCCCCCCCc-ceeecccCcCcccChhh
Q 004116 347 HCNYCSQPIPA-VYYQSQKEVDVLLCPEC 374 (773)
Q Consensus 347 ~C~~C~~~~~~-~~y~c~kc~d~~LC~~C 374 (773)
.|+.|+.++.. ..|.|..| +|.|...|
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 59999999988 89999998 78887777
No 69
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=55.95 E-value=65 Score=33.84 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 614 NIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFA 652 (773)
Q Consensus 614 ~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~ 652 (773)
.+++...+-+|...+-| +||+-|+.+|+.|-..|+.-|
T Consensus 160 ~~~~~k~~emE~Qv~IL-~lE~~L~~ar~~L~~lRk~~Y 197 (200)
T smart00307 160 SLHEGKTQEMEQQVEIL-KLENELEAARKKLAEIRKQHY 197 (200)
T ss_pred chHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence 45555556666677777 788888888888888777654
No 70
>PF03276 Gag_spuma: Spumavirus gag protein; InterPro: IPR004957 The Spumavirus gag protein is a core viral polyprotein that undergoes specific enzymatic cleavages in vivo to yield the mature protein.; GO: 0019028 viral capsid
Probab=52.60 E-value=2.8e+02 Score=33.35 Aligned_cols=9 Identities=33% Similarity=0.549 Sum_probs=6.5
Q ss_pred ccccCCCCC
Q 004116 761 MIRSASGTS 769 (773)
Q Consensus 761 ~~~~~~~~~ 769 (773)
-+|.|.|+.
T Consensus 268 hIRaViGet 276 (582)
T PF03276_consen 268 HIRAVIGET 276 (582)
T ss_pred HHHhhhCCC
Confidence 378888864
No 71
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=51.51 E-value=16 Score=32.46 Aligned_cols=43 Identities=28% Similarity=0.459 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhc---C----------CCHHHHHHHhC-----CCCHHHHHHHHHhC
Q 004116 405 TWSDQETFLLLEGIEMY---N----------DNWNEIAEHVS-----TKSKAQCILHFVRL 447 (773)
Q Consensus 405 ~WT~qEellLLEaIe~y---g----------gNW~~IAehVG-----tKT~eECi~hFlqL 447 (773)
.||.+++..||+.+... | ..|+.|++.+. ..|+.||..||-.|
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 49999999999998543 1 35889999885 36889999998665
No 72
>PRK00846 hypothetical protein; Provisional
Probab=50.68 E-value=1.4e+02 Score=26.84 Aligned_cols=54 Identities=20% Similarity=0.180 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 004116 611 LSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLGP 665 (773)
Q Consensus 611 Lv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~rl~~ 665 (773)
|-..-++..|..||.||.|-+++=..|...--. .+..-..+..+++.+..||..
T Consensus 6 ~~~~~le~Ri~~LE~rlAfQe~tIe~LN~~v~~-qq~~I~~L~~ql~~L~~rL~~ 59 (77)
T PRK00846 6 LRDQALEARLVELETRLSFQEQALTELSEALAD-ARLTGARNAELIRHLLEDLGK 59 (77)
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
Confidence 445567788999999999977654444332211 111122344556777778874
No 73
>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=48.68 E-value=23 Score=34.01 Aligned_cols=44 Identities=18% Similarity=0.376 Sum_probs=34.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcC----CCHHHHHHHhC------------CCCHHHHHHHHH
Q 004116 402 DGETWSDQETFLLLEGIEMYN----DNWNEIAEHVS------------TKSKAQCILHFV 445 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yg----gNW~~IAehVG------------tKT~eECi~hFl 445 (773)
....||.+|+--||-.+.+|| |+|+.|-+.|- +||+.++-.+--
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 357899999999999999998 79999999874 788888766543
No 74
>PF15219 TEX12: Testis-expressed 12
Probab=47.68 E-value=1.4e+02 Score=27.77 Aligned_cols=58 Identities=19% Similarity=0.350 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhh
Q 004116 605 EREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVE---KARQRFATERTRIVSTRL 663 (773)
Q Consensus 605 EREI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE---~~Rq~L~~eR~~~~~~rl 663 (773)
-+||+-++.+--..--++-..-+.+.+|++-++ +|-..|| +++..++.+|++++.+.|
T Consensus 38 skEinlmls~yA~ilSEraavd~syi~eiD~lf-kEA~~lEnfLkqkre~LrQrlt~isntL 98 (100)
T PF15219_consen 38 SKEINLMLSTYAKILSERAAVDASYITEIDGLF-KEANALENFLKQKRECLRQRLTVISNTL 98 (100)
T ss_pred HHHHHHHHHHHHHHHhHHHHhhhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345555555444444444455556666666555 3444444 677788888999988765
No 75
>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=47.07 E-value=16 Score=26.59 Aligned_cols=27 Identities=22% Similarity=0.643 Sum_probs=22.2
Q ss_pred CCCCCCCCCCcc-eeecccCcCcccChhh
Q 004116 347 HCNYCSQPIPAV-YYQSQKEVDVLLCPEC 374 (773)
Q Consensus 347 ~C~~C~~~~~~~-~y~c~kc~d~~LC~~C 374 (773)
.|..|++.+... .|+|.+|. +.+.+.|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC-CeEcCcc
Confidence 699999999988 99997764 7776666
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=45.61 E-value=2.2e+02 Score=29.25 Aligned_cols=72 Identities=18% Similarity=0.271 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 580 EKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKR-------LELKLKQFAEVETLLMRECEQVEKARQRF 651 (773)
Q Consensus 580 ~~vk~Aa~~aLaaAA~KAk~LA~~EEREI~rLv~~IIe~QLKK-------LElKLk~feELE~~le~Ere~LE~~Rq~L 651 (773)
+.|.+|-++|++|+-+|.-.|-...|-+--.-.+.|+--|.+. +-.-||+|-.+-+.+.+-.++.-||.|+|
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 3444555556666656655554433333333344444444432 23457888888887766655555555444
No 77
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=45.56 E-value=14 Score=39.11 Aligned_cols=19 Identities=26% Similarity=0.580 Sum_probs=11.8
Q ss_pred cch-HHHhhhc-chhhhhccC
Q 004116 10 DTR-KWKRRKR-EPRKQLNKL 28 (773)
Q Consensus 10 ~~~-~~~~~~~-~~~~~~~~~ 28 (773)
.+| |||||-- +.....++|
T Consensus 217 NRRTKWRKkhAaEmasakkkq 237 (288)
T KOG0847|consen 217 NRRTKWRKKHAAEMASAKKKQ 237 (288)
T ss_pred cchhhhhhhhccchhhccccC
Confidence 445 9999877 444444444
No 78
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=45.54 E-value=1.1e+02 Score=33.62 Aligned_cols=63 Identities=19% Similarity=0.302 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 589 GLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQ----FAEVETLLMRECEQVEKARQRFAT 653 (773)
Q Consensus 589 aLaaAA~KAk~LA~~EEREI~rLv~~IIe~QLKKLElKLk~----feELE~~le~Ere~LE~~Rq~L~~ 653 (773)
.+-.||.|+-.|+.. |+=+ +..-.-|.+|++++..||+. ..+|+.-+++-+.+||+.|++|-+
T Consensus 92 ~~~~aa~Rplel~e~-Ekvl-k~aIq~i~~~~q~~~~~Lnnvasdea~L~~Kierrk~ElEr~rkRle~ 158 (338)
T KOG3647|consen 92 SLMSAAQRPLELLEV-EKVL-KSAIQAIQVRLQSSRAQLNNVASDEAALGSKIERRKAELERTRKRLEA 158 (338)
T ss_pred HHHHHHcCCccHHHH-HHHH-HHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567777777643 3333 34445567888888888875 467888888888999988888743
No 79
>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=43.64 E-value=2.9e+02 Score=30.73 Aligned_cols=48 Identities=23% Similarity=0.367 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 614 NIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVST 661 (773)
Q Consensus 614 ~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~ 661 (773)
.-++.++++|+.+++.+++.|..+.+++..++....++..+|..+-.+
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 456778899999999999999999999999988888877777666554
No 80
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=43.15 E-value=17 Score=45.28 Aligned_cols=14 Identities=43% Similarity=0.715 Sum_probs=5.7
Q ss_pred cCcccccchhhhcc
Q 004116 30 EDDVVEDEDEEQDN 43 (773)
Q Consensus 30 ~~~~~~~~~~~~~~ 43 (773)
+||.+|+||+|||+
T Consensus 1409 eeeD~e~Ed~dEdd 1422 (1516)
T KOG1832|consen 1409 EEEDDETEDEDEDD 1422 (1516)
T ss_pred ccccchhhcccccc
Confidence 33334444444443
No 81
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=43.04 E-value=90 Score=36.57 Aligned_cols=36 Identities=31% Similarity=0.384 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHH
Q 004116 619 QLKRLELKLKQFAE------VETLLMRECEQVEKARQRFATE 654 (773)
Q Consensus 619 QLKKLElKLk~feE------LE~~le~Ere~LE~~Rq~L~~e 654 (773)
|++|-||||.++.| ||++|..||+.--..+.+|-.|
T Consensus 527 q~Ek~ELkmd~lrerelreslekql~~ErklR~~~qkr~kkE 568 (641)
T KOG3915|consen 527 QLEKTELKMDFLRERELRESLEKQLAMERKLRAIVQKRLKKE 568 (641)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777777777754 5555555554444444444444
No 82
>KOG3859 consensus Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning]
Probab=42.55 E-value=1.6e+02 Score=32.86 Aligned_cols=60 Identities=20% Similarity=0.334 Sum_probs=45.9
Q ss_pred HHHHHHHHHH---HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 004116 605 EREIQRLSAN---IINHQLKRLELKL-KQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLG 664 (773)
Q Consensus 605 EREI~rLv~~---IIe~QLKKLElKL-k~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~rl~ 664 (773)
|.||+..--. --+..||+.|.-| ..|+.|-..-..|+..||..|.+|-.|+..|.+.+.+
T Consensus 339 Eee~rqmFvqrvkekE~elke~Ekel~~kf~~lkr~h~eEk~kle~~rr~Leee~~~f~~rk~~ 402 (406)
T KOG3859|consen 339 EEEMRQMFVQRVKEKEAELKEAEKELHEKFDRLKRLHQEEKKKLEEKRKQLEEEVNAFQRRKTA 402 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455443332 2355677777766 4799999999999999999999999999999887654
No 83
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=42.17 E-value=39 Score=39.34 Aligned_cols=46 Identities=11% Similarity=0.380 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlqL 447 (773)
.-+.||++|..||=.|.+.||-+..+|-+.+.-||-...+..|...
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH
Confidence 3478999999999999999999999999999999999998888654
No 84
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=41.66 E-value=41 Score=32.26 Aligned_cols=61 Identities=13% Similarity=0.213 Sum_probs=41.7
Q ss_pred CCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCHHH
Q 004116 348 CNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNE 427 (773)
Q Consensus 348 C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEaIe~yggNW~~ 427 (773)
|-.|+.++.-.+++|..|...+ .|.|... .| .--..|++.+++..-+..||-.+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i-------~G~F~l~----~~---------------~~L~~E~~~Fi~~Fi~~rGnlKe 54 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI-------EGEFELP----WF---------------ARLSPEQLEFIKLFIKNRGNLKE 54 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE-------Eeeeccc----hh---------------hcCCHHHHHHHHHHHHhcCCHHH
Confidence 8889988887888877763211 2322110 01 11235888889988899999999
Q ss_pred HHHHhCC
Q 004116 428 IAEHVST 434 (773)
Q Consensus 428 IAehVGt 434 (773)
|++.+|-
T Consensus 55 ~e~~lgi 61 (113)
T PF09862_consen 55 MEKELGI 61 (113)
T ss_pred HHHHHCC
Confidence 9999993
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=41.40 E-value=1.6e+02 Score=28.73 Aligned_cols=52 Identities=19% Similarity=0.316 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 607 EIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVST 661 (773)
Q Consensus 607 EI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~ 661 (773)
++..-+ ..++.|+++||.+++.+.++-..|++ .+=+.++.+|..+-+..++.
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 46899999999999999999888866 56678888888888777654
No 86
>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=41.02 E-value=37 Score=26.37 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHhCC
Q 004116 409 QETFLLLEGIEMYNDNWNEIAEHVST 434 (773)
Q Consensus 409 qEellLLEaIe~yggNW~~IAehVGt 434 (773)
-|-..|.++++.++||..+.|+.+|-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgi 30 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCC
Confidence 37788999999999999999999994
No 87
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=40.39 E-value=15 Score=42.58 Aligned_cols=43 Identities=28% Similarity=0.429 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCHHHHHHHHHh
Q 004116 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yggNW~~IAehVGtKT~eECi~hFlq 446 (773)
.-+||..|-. ++.....|+++...||+-++||||+|....||+
T Consensus 470 ~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred cCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 3589988777 777778999999999999999999999998885
No 88
>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=39.74 E-value=2.3e+02 Score=28.68 Aligned_cols=21 Identities=14% Similarity=0.227 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 004116 632 EVETLLMRECEQVEKARQRFA 652 (773)
Q Consensus 632 ELE~~le~Ere~LE~~Rq~L~ 652 (773)
+||+-|+.||+.|-..|+.=|
T Consensus 129 ~lE~eLe~ar~kL~~lRk~~Y 149 (152)
T PF01608_consen 129 KLEKELEKARKKLAELRKAHY 149 (152)
T ss_dssp HHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHc
Confidence 567777777777766666544
No 89
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=39.56 E-value=32 Score=27.15 Aligned_cols=51 Identities=20% Similarity=0.224 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHhCCCcee-eHHHHhhccCCCChhHHHHHHHhhhhhccccc
Q 004116 218 KYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (773)
Q Consensus 218 iYk~yRNfMIntYR~NP~eYL-TvTacRRnL~G~dv~sI~RVH~FLE~WGLINY 270 (773)
+|-.+|+.|+... ..|...| |..+.-..+ |....++.|...-|++-|+|-.
T Consensus 1 i~~~l~~~i~~~~-~~~~~~l~s~~~la~~~-~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 1 VAERLREDIVSGE-LRPGDKLPSERELAAQL-GVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred CHHHHHHHHHcCC-CCCCCcCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEE
Confidence 3666777777653 4578888 787754443 4457899999999999999964
No 90
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=39.44 E-value=24 Score=40.79 Aligned_cols=61 Identities=25% Similarity=0.499 Sum_probs=39.2
Q ss_pred HHHhhccCCCCCCCCCCCCc---ceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHH
Q 004116 338 TIRERLSENHCNYCSQPIPA---VYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLL 414 (773)
Q Consensus 338 ~~~e~~~~~~C~~C~~~~~~---~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellL 414 (773)
++|....--.|.-|+..-+. +.| .+.||++|-..-|.-+-|-+ |+|-.+ . +.||..+...+
T Consensus 16 kLRs~~~NKvCFDCgAknPtWaSVTY------GIFLCiDCSAvHRnLGVHiS--FVRSTn-------L-DsWs~~qLR~M 79 (454)
T KOG0706|consen 16 KLRSQSENKVCFDCGAKNPTWASVTY------GIFLCIDCSAVHRNLGVHIS--FVRSTN-------L-DSWSWEQLRRM 79 (454)
T ss_pred HHhcCCCCceecccCCCCCCceeecc------eEEEEEecchhhhccccceE--EEeecc-------c-ccCCHHHHhHh
Confidence 34444444579999887543 444 58999999877666555544 766432 1 34999876543
No 91
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=38.28 E-value=30 Score=26.38 Aligned_cols=38 Identities=18% Similarity=0.340 Sum_probs=26.6
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCcee
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIR 391 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~r 391 (773)
..|..|... .+.|.|..|. ..+|..|+..+ |+.|+++.
T Consensus 4 ~~C~~H~~~--~~~~~C~~C~-~~~C~~C~~~~-----H~~H~~~~ 41 (42)
T PF00643_consen 4 PKCPEHPEE--PLSLFCEDCN-EPLCSECTVSG-----HKGHKIVP 41 (42)
T ss_dssp SB-SSTTTS--BEEEEETTTT-EEEEHHHHHTS-----TTTSEEEE
T ss_pred ccCccCCcc--ceEEEecCCC-CccCccCCCCC-----CCCCEEeE
Confidence 467777653 3678888874 58999999875 77776654
No 92
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=38.11 E-value=28 Score=40.52 Aligned_cols=51 Identities=25% Similarity=0.420 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHHH-HhCCCCHHHHHHHHHhCCCCCCCc
Q 004116 404 ETWSDQETFLLLEGIEMYNDNWNEIAE-HVSTKSKAQCILHFVRLPMEDGIL 454 (773)
Q Consensus 404 ~~WT~qEellLLEaIe~yggNW~~IAe-hVGtKT~eECi~hFlqLPIED~fL 454 (773)
..|++-|-.++=||+++||-|+++|-. ++.=||-..++..|.-.--.|.|.
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYv 337 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYV 337 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHH
Confidence 579999999999999999999999965 555688888888776655555444
No 93
>smart00595 MADF subfamily of SANT domain.
Probab=37.78 E-value=28 Score=30.58 Aligned_cols=24 Identities=33% Similarity=0.646 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCCHHHHHHHHHhC
Q 004116 423 DNWNEIAEHVSTKSKAQCILHFVRL 447 (773)
Q Consensus 423 gNW~~IAehVGtKT~eECi~hFlqL 447 (773)
.-|..||..+|. |.++|..++-.|
T Consensus 28 ~aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 28 KAWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHHCc-CHHHHHHHHHHH
Confidence 369999999998 999999999876
No 94
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=37.73 E-value=17 Score=32.65 Aligned_cols=35 Identities=20% Similarity=0.544 Sum_probs=24.9
Q ss_pred CCCCCCCCCCcceeeccc---CcCcccChhhhccCCCC
Q 004116 347 HCNYCSQPIPAVYYQSQK---EVDVLLCPECFHEGRFV 381 (773)
Q Consensus 347 ~C~~C~~~~~~~~y~c~k---c~d~~LC~~CFs~G~~~ 381 (773)
.|-.||.++......-.+ ...-.-|.-||.+|.|.
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 699999999875532222 23456899999999874
No 95
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=37.03 E-value=22 Score=30.79 Aligned_cols=35 Identities=17% Similarity=0.440 Sum_probs=23.6
Q ss_pred cceeecccCc---CcccChhhhccCCCCCCCCCCCceecCCC
Q 004116 357 AVYYQSQKEV---DVLLCPECFHEGRFVTGHSSLDYIRVDPA 395 (773)
Q Consensus 357 ~~~y~c~kc~---d~~LC~~CFs~G~~~~~hss~dF~rvd~~ 395 (773)
.+.|+|..|. ...+|..||..+ .|..|+|..+...
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~----~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANS----CHEGHRVVYYRSS 48 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTS----GGGGSSEEEEE--
T ss_pred CEEEECccCCCCCCEEEchhhCCCC----CcCCCcEEEEEeC
Confidence 4677777764 378999999875 4778888776543
No 96
>PRK02793 phi X174 lysis protein; Provisional
Probab=36.83 E-value=2.8e+02 Score=24.38 Aligned_cols=47 Identities=17% Similarity=0.153 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHhhCC
Q 004116 616 INHQLKRLELKLKQFAEVETLLMRECEQVEKARQ--RFATERTRIVSTRLGP 665 (773)
Q Consensus 616 Ie~QLKKLElKLk~feELE~~le~Ere~LE~~Rq--~L~~eR~~~~~~rl~~ 665 (773)
++..|..||.||.|-+++=.-|.. .|-++++ ..+..+++.+..||+.
T Consensus 6 ~e~Ri~~LE~~lafQe~tIe~Ln~---~v~~Qq~~I~~L~~~l~~L~~rl~~ 54 (72)
T PRK02793 6 LEARLAELESRLAFQEITIEELNV---TVTAHEMEMAKLRDHLRLLTEKLKA 54 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 677899999999997765333322 2222222 2234557777778874
No 97
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.26 E-value=1.5e+02 Score=26.40 Aligned_cols=60 Identities=22% Similarity=0.223 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHH
Q 004116 602 DHEEREIQRLSANIINHQLKRLELKLKQ--FAEVETLLMRECEQVEKARQRF------ATERTRIVST 661 (773)
Q Consensus 602 ~~EEREI~rLv~~IIe~QLKKLElKLk~--feELE~~le~Ere~LE~~Rq~L------~~eR~~~~~~ 661 (773)
++=|.+|+..|.+|-=.||.-=|||=+. +..=..-...-|+.|++.-++| +.||++-+.-
T Consensus 7 ekLE~KiqqAvdTI~LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerlrsLLG 74 (79)
T COG3074 7 EKLEAKVQQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRALLG 74 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3447789999998888888777776543 3333333344455555444444 4555554443
No 98
>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=36.14 E-value=88 Score=24.62 Aligned_cols=37 Identities=16% Similarity=0.171 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhcC-CCHHHHHHHhCCCCHHHHHHHHHh
Q 004116 409 QETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVR 446 (773)
Q Consensus 409 qEellLLEaIe~yg-gNW~~IAehVGtKT~eECi~hFlq 446 (773)
+=+..||+.++.-+ --|.+||+.||- |+..|..+.-+
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 34578899999877 799999999996 88888877654
No 99
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=36.08 E-value=4.1e+02 Score=31.51 Aligned_cols=40 Identities=8% Similarity=0.206 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Q 004116 585 AAKAGLAAAATKAKLFADHEEREIQRLSA--NIINHQLKRLELKLK 628 (773)
Q Consensus 585 Aa~~aLaaAA~KAk~LA~~EEREI~rLv~--~IIe~QLKKLElKLk 628 (773)
....+|.....|++.| |++|..|-. .++..+++++|.||+
T Consensus 66 VnqSALteqQ~kasEL----EKqLaaLrqElq~~saq~~dle~KIk 107 (475)
T PRK13729 66 VRQHATTEMQVTAAQM----QKQYEEIRRELDVLNKQRGDDQRRIE 107 (475)
T ss_pred HHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHhhhhhhHHHHHH
Confidence 3345566666666655 667766622 233455666666655
No 100
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=34.08 E-value=37 Score=34.79 Aligned_cols=41 Identities=17% Similarity=0.419 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHHHhcC-------CCHHHHHHHhCCCCHHHHHHHH
Q 004116 403 GETWSDQETFLLLEGIEMYN-------DNWNEIAEHVSTKSKAQCILHF 444 (773)
Q Consensus 403 ~~~WT~qEellLLEaIe~yg-------gNW~~IAehVGtKT~eECi~hF 444 (773)
.+.||.+|+++|-+.|-.|+ .-...+++.+ .||...|-.+|
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 36799999999999888885 3456666777 48999999999
No 101
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=33.85 E-value=45 Score=37.28 Aligned_cols=99 Identities=17% Similarity=0.319 Sum_probs=53.0
Q ss_pred cCCCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCC
Q 004116 344 SENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYND 423 (773)
Q Consensus 344 ~~~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEaIe~ygg 423 (773)
.-..|.-|+..- -.|.-|. -.+.||++|-.--|--+.| ..+|.. ..-+.||.+|..+|.-+=...-.
T Consensus 19 ~Nk~CaDCga~~-P~W~S~n--lGvfiCi~CagvHRsLGvh----iS~VKS------itLD~wt~~~l~~m~~gGN~~a~ 85 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVN--LGVFLCIDCAGVHRSLGVH----ISKVKS------LTLDNWTEEELRRMEVGGNSNAN 85 (319)
T ss_pred ccCccccCCCCC-CceEecc--cCeEEEeecchhhhccccc----eeeeee------eecccCCHHHHHHHHHhcchhhh
Confidence 345799998875 2343332 4688999997554433333 223332 23368999888777652111112
Q ss_pred CHHHHHHHh----C--CCCHHHHHHHHHh-CCCCCCCcc
Q 004116 424 NWNEIAEHV----S--TKSKAQCILHFVR-LPMEDGILE 455 (773)
Q Consensus 424 NW~~IAehV----G--tKT~eECi~hFlq-LPIED~fLe 455 (773)
.|.+--.-. . .+.-...+.+|++ +|.+-.|.+
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccc
Confidence 333211111 1 2344667777776 555555544
No 102
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=33.74 E-value=31 Score=30.56 Aligned_cols=55 Identities=24% Similarity=0.407 Sum_probs=36.7
Q ss_pred CCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhh--ccCCCChhHHHHHHHhhhhhc
Q 004116 194 TVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQG--LVDGVSPEDLTRIFRFLNHWG 266 (773)
Q Consensus 194 ~IH~IEKr~lPEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRR--nL~G~dv~sI~RVH~FLE~WG 266 (773)
-|.+-||.+|-+||.- . .-|+--++-++-.+-+. .-+|.+..-|=-|-.||++||
T Consensus 23 pVse~erd~LAhYFQl----------------L--itRLmnneeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 23 PVSEAERDALAHYFQL----------------L--ITRLMNNEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred CcchhhhhHHHHHHHH----------------H--HHHHhccHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 4667777777777631 1 22444466666655443 346777777888999999999
No 103
>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=33.34 E-value=1.2e+02 Score=26.40 Aligned_cols=44 Identities=11% Similarity=0.382 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 616 INHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVS 660 (773)
Q Consensus 616 Ie~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~ 660 (773)
|+..-++|+.|+.|||.|-++ ++--.+|+...++|..-|..|+.
T Consensus 13 I~~~K~~l~ik~~H~Ekl~ki-tK~p~El~~i~~kl~~~R~~FLn 56 (62)
T PF06034_consen 13 INQMKRQLTIKSQHWEKLKKI-TKNPKELQEIEKKLQELRQNFLN 56 (62)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHHHHHHHH
Confidence 344456799999999998554 45556677777888888887774
No 104
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=32.49 E-value=2.5e+02 Score=32.09 Aligned_cols=16 Identities=13% Similarity=0.300 Sum_probs=11.9
Q ss_pred CCCHHHHHHHHHHHHhcC
Q 004116 405 TWSDQETFLLLEGIEMYN 422 (773)
Q Consensus 405 ~WT~qEellLLEaIe~yg 422 (773)
=||..|+ ||+||+..|
T Consensus 90 W~TTD~D--L~~A~~S~G 105 (498)
T KOG4849|consen 90 WYTTDAD--LLKALQSTG 105 (498)
T ss_pred EEeccHH--HHHHHHhhh
Confidence 4777765 579998876
No 105
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=31.87 E-value=28 Score=43.19 Aligned_cols=7 Identities=14% Similarity=0.107 Sum_probs=2.7
Q ss_pred cCcccch
Q 004116 132 ISFGQLQ 138 (773)
Q Consensus 132 is~gql~ 138 (773)
|.-.|+.
T Consensus 729 mdDe~m~ 735 (784)
T PF04931_consen 729 MDDEQMM 735 (784)
T ss_pred cCHHHHH
Confidence 3333333
No 106
>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=31.83 E-value=26 Score=33.15 Aligned_cols=62 Identities=29% Similarity=0.492 Sum_probs=30.4
Q ss_pred ccCCCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHH
Q 004116 343 LSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEG 417 (773)
Q Consensus 343 ~~~~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEa 417 (773)
..-..|.-|+..- +.+.+.. -.+.+|..|..--+..+.| ..+|.. ..-+.||.+|...|.++
T Consensus 11 ~~N~~CaDCg~~~--p~w~s~~-~GiflC~~Cag~HR~lg~~----is~VkS------i~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 11 PGNKVCADCGAPN--PTWASLN-YGIFLCLECAGIHRSLGVH----ISRVKS------ITMDNWSPEEVQRMREG 72 (116)
T ss_dssp TTCTB-TTT-SBS----EEETT-TTEEE-HHHHHHHHHHTTT----T--EEE------TTTS---HHHHHHHHHS
T ss_pred cCcCcCCCCCCCC--CCEEEee-cChhhhHHHHHHHHHhccc----chhccc------cccCCCCHHHHHHHHHH
Confidence 3445799998543 4566555 4688999998654433322 223322 12346999988777544
No 107
>PHA00442 host recBCD nuclease inhibitor
Probab=31.74 E-value=47 Score=28.04 Aligned_cols=25 Identities=20% Similarity=0.416 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHhcC-CCHHHHHHHh
Q 004116 408 DQETFLLLEGIEMYN-DNWNEIAEHV 432 (773)
Q Consensus 408 ~qEellLLEaIe~yg-gNW~~IAehV 432 (773)
-+-....|++++.+| +||+-+.+.+
T Consensus 25 Lek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 25 LEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 345677899999999 9999988766
No 108
>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=31.47 E-value=5.1e+02 Score=32.54 Aligned_cols=19 Identities=32% Similarity=0.254 Sum_probs=9.3
Q ss_pred cChHHHHHHHHHHHHHHHh
Q 004116 519 VGPRVAAACAHASLAALSK 537 (773)
Q Consensus 519 V~P~VAaAAA~AAl~~l~~ 537 (773)
.||.-..+.|.+-|+.+.+
T Consensus 415 tD~~eg~ala~aiLe~l~~ 433 (771)
T TIGR01069 415 TDPDEGSALAISILEYLLK 433 (771)
T ss_pred CCHHHHHHHHHHHHHHHHh
Confidence 3444445555555555543
No 109
>PF15346 ARGLU: Arginine and glutamate-rich 1
Probab=31.33 E-value=5.7e+02 Score=25.89 Aligned_cols=50 Identities=26% Similarity=0.375 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 004116 614 NIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRL 663 (773)
Q Consensus 614 ~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~rl 663 (773)
..++-.=.|-+-.-+.-++||.+|+.-+.-+|..++.+..+|+.++-.|.
T Consensus 62 ~~l~e~r~keEeer~~~eELe~ileen~rkvEEAQrk~aeEr~~~~Eer~ 111 (149)
T PF15346_consen 62 EALEEARRKEEEERKKREELEKILEENRRKVEEAQRKLAEERLRMEEERR 111 (149)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445567777888999999999999999888888888888865543
No 110
>PRK06474 hypothetical protein; Provisional
Probab=31.32 E-value=73 Score=32.42 Aligned_cols=48 Identities=23% Similarity=0.272 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhccccc
Q 004116 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (773)
Q Consensus 222 yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINY 270 (773)
.|-.|+..-..++.. +|++++-..+.+....+|.|..+.|+..|||.-
T Consensus 12 ~R~~Il~~L~~~~~~-~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~ 59 (178)
T PRK06474 12 VRMKICQVLMRNKEG-LTPLELVKILKDVPQATLYRHLQTMVDSGILHV 59 (178)
T ss_pred HHHHHHHHHHhCCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEE
Confidence 688888887777553 999998766655556789999999999999995
No 111
>PRK04406 hypothetical protein; Provisional
Probab=31.16 E-value=3.8e+02 Score=23.86 Aligned_cols=48 Identities=10% Similarity=0.134 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHhhCC
Q 004116 615 IINHQLKRLELKLKQFAEVETLLMRECEQVEKARQ--RFATERTRIVSTRLGP 665 (773)
Q Consensus 615 IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq--~L~~eR~~~~~~rl~~ 665 (773)
-++..+..||.||.|.+++=.-|... |-++++ ..+..+++.+.+||..
T Consensus 8 ~le~Ri~~LE~~lAfQE~tIe~LN~~---v~~Qq~~I~~L~~ql~~L~~rl~~ 57 (75)
T PRK04406 8 QLEERINDLECQLAFQEQTIEELNDA---LSQQQLLITKMQDQMKYVVGKVKN 57 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46678899999999877653333221 222222 2234557777778874
No 112
>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=30.88 E-value=1.1e+02 Score=24.01 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhccccc
Q 004116 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (773)
Q Consensus 222 yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINY 270 (773)
.|-.||..-.. ..+|+++..+.+ |.+-.++.+=.+.|+..|||.|
T Consensus 3 ~R~~Il~~L~~---~~~~~~el~~~l-~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 3 TRLRILKLLSE---GPLTVSELAEEL-GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHHHHTT---SSEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHh---CCCchhhHHHhc-cccchHHHHHHHHHHHCcCeeC
Confidence 47778877666 459999998876 5567899999999999999975
No 113
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=30.85 E-value=47 Score=36.64 Aligned_cols=99 Identities=14% Similarity=0.290 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHhc-CC
Q 004116 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY-ND 423 (773)
Q Consensus 345 ~~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEaIe~y-gg 423 (773)
-.+|.-|+..- ++..+-. ..+.||+.|-.--|-.+. ++.+|.. ..-+.||+++...|.+-=..- .-
T Consensus 25 N~~CADC~a~~--P~WaSwn-lGvFiC~~C~giHR~lg~----hiSkVkS------v~LD~W~~eqv~~m~~~GN~~an~ 91 (287)
T KOG0703|consen 25 NKVCADCGAKG--PRWASWN-LGVFICLRCAGIHRSLGV----HISKVKS------VTLDEWTDEQVDFMISMGNAKANS 91 (287)
T ss_pred cCcccccCCCC--CCeEEee-cCeEEEeecccccccccc----hhheeee------eeccccCHHHHHHHHHHcchhhhh
Confidence 35788888763 3332222 468899999543332222 4555553 234789999977665421000 02
Q ss_pred CHHH-HHHHhCCCCHHHHHHHHHhC-CCCCCCccc
Q 004116 424 NWNE-IAEHVSTKSKAQCILHFVRL-PMEDGILEN 456 (773)
Q Consensus 424 NW~~-IAehVGtKT~eECi~hFlqL-PIED~fLe~ 456 (773)
=|+. |......-++++-+.+||+- |....|+..
T Consensus 92 ~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~ 126 (287)
T KOG0703|consen 92 YYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDP 126 (287)
T ss_pred hccccCCccccCCChHHHHHHHHHHHHhhhhhccc
Confidence 2443 23333445678889999983 556667664
No 114
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=30.64 E-value=1.3e+02 Score=31.46 Aligned_cols=27 Identities=22% Similarity=0.148 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 634 ETLLMRECEQVEKARQRFATERTRIVS 660 (773)
Q Consensus 634 E~~le~Ere~LE~~Rq~L~~eR~~~~~ 660 (773)
+.-|+.+|.+.|+.+|+.+.+-..|+=
T Consensus 86 ~~~~e~~r~~fekekqq~~~~~t~~Lw 112 (228)
T PRK06800 86 MKEIEAARQQFQKEQQETAYEWTELLW 112 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555555555555554443
No 115
>KOG2129 consensus Uncharacterized conserved protein H4 [Function unknown]
Probab=30.41 E-value=9.6e+02 Score=28.26 Aligned_cols=42 Identities=24% Similarity=0.299 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 605 EREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKA 647 (773)
Q Consensus 605 EREI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~ 647 (773)
..||.||-..+--.|.. -..||.+|-+=|.-++.|-++|++.
T Consensus 259 ~~EveRlrt~l~~Aqk~-~~ek~~qy~~Ee~~~reen~rlQrk 300 (552)
T KOG2129|consen 259 QAEVERLRTYLSRAQKS-YQEKLMQYRAEEVDHREENERLQRK 300 (552)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 45566666665555533 3445555555555555554444443
No 116
>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=29.53 E-value=55 Score=30.77 Aligned_cols=93 Identities=26% Similarity=0.364 Sum_probs=48.3
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhhccCCCCCCCCCCCceecCCCCCCCCCCCCCCCHHHHHHHHHHHHhcC-CC
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYN-DN 424 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G~~~~~hss~dF~rvd~~~~~~~~~~~~WT~qEellLLEaIe~yg-gN 424 (773)
..|.-|+.. .+.+.+.. ..+.+|..|-.--+..+.| +.+|.. ..-+.||.+|.. +|+.+ | ..
T Consensus 4 ~~CaDC~~~--~p~w~s~~-~GifvC~~CsgiHR~lg~h----is~VkS------l~md~w~~~~i~-~~~~~---GN~~ 66 (112)
T smart00105 4 KKCFDCGAP--NPTWASVN-LGVFLCIECSGIHRSLGVH----ISKVRS------LTLDTWTEEELR-LLQKG---GNEN 66 (112)
T ss_pred CcccCCCCC--CCCcEEec-cceeEhHHhHHHHHhcCCC----cCeeee------cccCCCCHHHHH-HHHHh---hhHH
Confidence 368888874 34444443 4688999997654433322 222332 123589997754 33322 2 12
Q ss_pred HHHHHHHh--------CCCCHHHHHHHHHh-CCCCCCCcc
Q 004116 425 WNEIAEHV--------STKSKAQCILHFVR-LPMEDGILE 455 (773)
Q Consensus 425 W~~IAehV--------GtKT~eECi~hFlq-LPIED~fLe 455 (773)
++++=+.- ...+..+-...||+ -|++..|..
T Consensus 67 ~n~~~e~~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 106 (112)
T smart00105 67 ANSIWESNLDDFSLKPPDSDDQQKYESFIAAKYEEKLFVP 106 (112)
T ss_pred HHHHHHhhCCccccCCCCCchHHHHHHHHHHHHHhhhccc
Confidence 22222211 11124677788887 355555543
No 117
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=28.28 E-value=74 Score=25.53 Aligned_cols=43 Identities=16% Similarity=0.299 Sum_probs=32.7
Q ss_pred HHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhccccc
Q 004116 226 IVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (773)
Q Consensus 226 MIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINY 270 (773)
|++.....+.. +|+++.-+.+ |.+-.++.|+..-|+.+|+|-.
T Consensus 8 iL~~l~~~~~~-~t~~eia~~~-gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 8 ILEALAESGGP-LTLSEIARAL-GLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHCHHCTBSC-EEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHcCCCC-CCHHHHHHHH-CcCHHHHHHHHHHHHHCcCeec
Confidence 55555555444 8999987665 5568899999999999999865
No 118
>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=28.14 E-value=2.6e+02 Score=25.75 Aligned_cols=49 Identities=22% Similarity=0.262 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHhhC
Q 004116 616 INHQLKRLELKLKQFAEVETLLMRECEQVE----KARQRFATERTRIVSTRLG 664 (773)
Q Consensus 616 Ie~QLKKLElKLk~feELE~~le~Ere~LE----~~Rq~L~~eR~~~~~~rl~ 664 (773)
++.++++++.||.+.++=++.|+.-...|+ +.|-.-+..|-.++-.-+-
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 456677777777777777777777777774 6777788888877766554
No 119
>PF07956 DUF1690: Protein of Unknown function (DUF1690) ; InterPro: IPR012471 Family of uncharacterised fungal proteins.
Probab=27.96 E-value=1.3e+02 Score=29.81 Aligned_cols=56 Identities=27% Similarity=0.409 Sum_probs=39.2
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q 004116 597 AKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRE-CEQVEKARQRFA 652 (773)
Q Consensus 597 Ak~LA~~EEREI~rLv~~IIe~QLKKLElKLk~feELE~~le~E-re~LE~~Rq~L~ 652 (773)
+.++++.+..+-..|....++..+.+|..||..|..|+..-... ...++..|..|.
T Consensus 61 ~~~~~ed~~~~~~~lSs~~v~~~i~~L~~kLe~~~kl~~~~~~~~~~~v~~aR~~vv 117 (142)
T PF07956_consen 61 KSLLSEDEKDQDPGLSSKSVNEEIEKLREKLEERKKLRELKEEKNSEEVEKARSAVV 117 (142)
T ss_pred HhhcccccccccccccHHHHHHHHHHHHHHHHHHHHHHhccccccchhhHHHHHHHH
Confidence 33444445566678899999999999999999887776655432 345566666654
No 120
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=27.84 E-value=1.4e+03 Score=29.26 Aligned_cols=13 Identities=23% Similarity=0.163 Sum_probs=5.6
Q ss_pred ccccCCCCCCCCC
Q 004116 745 VMFNARGGPQPTL 757 (773)
Q Consensus 745 ~~~~~~~~~~~~~ 757 (773)
.||-.+.|..|.+
T Consensus 589 ~g~~Gg~ppPP~~ 601 (1102)
T KOG1924|consen 589 GGFLGGPPPPPPP 601 (1102)
T ss_pred CCCCCCCCCCCCC
Confidence 4444444444433
No 121
>PRK06800 fliH flagellar assembly protein H; Validated
Probab=27.67 E-value=1.9e+02 Score=30.31 Aligned_cols=20 Identities=25% Similarity=0.569 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 004116 639 RECEQVEKARQRFATERTRI 658 (773)
Q Consensus 639 ~Ere~LE~~Rq~L~~eR~~~ 658 (773)
.|+..|++.|++|+++|.+|
T Consensus 59 ~eqQ~l~~er~~l~~er~~~ 78 (228)
T PRK06800 59 QEQQKLERERQQLLADREQF 78 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444445555554444
No 122
>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=27.07 E-value=1.1e+02 Score=24.63 Aligned_cols=43 Identities=21% Similarity=0.339 Sum_probs=32.6
Q ss_pred HhCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhcccccccCC
Q 004116 231 MDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAV 274 (773)
Q Consensus 231 R~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINYqvdp 274 (773)
..+|..-+|+++.-+.+ |.+-.++.|+.+=|+++|||--..++
T Consensus 15 ~~~~~~~~t~~~la~~l-~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 15 ARHPGEELTQSELAERL-GISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHSTTSGEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHCCCCCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 35566679999976655 44578999999999999999776554
No 123
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=26.89 E-value=36 Score=30.71 Aligned_cols=51 Identities=22% Similarity=0.505 Sum_probs=18.1
Q ss_pred ccCCCCCCCCCCCC-----cceeecccCcCcccChhhhc----cCCCCCCCCCCCceecCC
Q 004116 343 LSENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFH----EGRFVTGHSSLDYIRVDP 394 (773)
Q Consensus 343 ~~~~~C~~C~~~~~-----~~~y~c~kc~d~~LC~~CFs----~G~~~~~hss~dF~rvd~ 394 (773)
+....|..||.++. .+++.|.+| .|-+|-.||. .|+-..-.-...|.+...
T Consensus 7 ~~~qiCqiCGD~VGl~~~Ge~FVAC~eC-~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kg 66 (80)
T PF14569_consen 7 LNGQICQICGDDVGLTENGEVFVACHEC-AFPVCRPCYEYERKEGNQVCPQCKTRYKRHKG 66 (80)
T ss_dssp -SS-B-SSS--B--B-SSSSB--S-SSS------HHHHHHHHHTS-SB-TTT--B----TT
T ss_pred cCCcccccccCccccCCCCCEEEEEccc-CCccchhHHHHHhhcCcccccccCCCcccccC
Confidence 34567999998885 478889888 5889999985 333222223456766554
No 124
>PRK02119 hypothetical protein; Provisional
Probab=26.86 E-value=4.5e+02 Score=23.25 Aligned_cols=47 Identities=13% Similarity=0.169 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHhhCC
Q 004116 616 INHQLKRLELKLKQFAEVETLLMRECEQVEKARQR--FATERTRIVSTRLGP 665 (773)
Q Consensus 616 Ie~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~--L~~eR~~~~~~rl~~ 665 (773)
++..+..||.||.|-+++=.-|.. .|-+++++ .+..+++.+..||+.
T Consensus 7 ~e~Ri~~LE~rla~QE~tie~LN~---~v~~Qq~~id~L~~ql~~L~~rl~~ 55 (73)
T PRK02119 7 LENRIAELEMKIAFQENLLEELNQ---ALIEQQFVIDKMQVQLRYMANKLKD 55 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 567889999999987664332322 22222222 233456677777764
No 125
>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=26.50 E-value=27 Score=27.42 Aligned_cols=30 Identities=23% Similarity=0.701 Sum_probs=16.6
Q ss_pred CCCCCCCCCCCcc-eeecccCcCcccChhhhc
Q 004116 346 NHCNYCSQPIPAV-YYQSQKEVDVLLCPECFH 376 (773)
Q Consensus 346 ~~C~~C~~~~~~~-~y~c~kc~d~~LC~~CFs 376 (773)
..|++|++.-..+ .+. ....+..+|.+|..
T Consensus 2 ~~CSFCgr~~~~v~~li-~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLI-SGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEE-EES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhcee-cCCCCcEECHHHHH
Confidence 4799999988764 222 22225789999864
No 126
>PF07271 Cytadhesin_P30: Cytadhesin P30/P32; InterPro: IPR009896 This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localised on the tip organelle. It is thought that it is important in cytadherence and virulence [].; GO: 0007157 heterophilic cell-cell adhesion, 0009405 pathogenesis, 0016021 integral to membrane
Probab=26.43 E-value=3.3e+02 Score=30.07 Aligned_cols=16 Identities=19% Similarity=0.135 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHH
Q 004116 643 QVEKARQRFATERTRI 658 (773)
Q Consensus 643 ~LE~~Rq~L~~eR~~~ 658 (773)
++...++-++..|+..
T Consensus 156 ~Vq~~~~~~fq~rI~~ 171 (279)
T PF07271_consen 156 QVQPSFRPLFQQRICP 171 (279)
T ss_pred ccccccCccccccccc
Confidence 4445566666555444
No 127
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=25.96 E-value=45 Score=43.14 Aligned_cols=28 Identities=25% Similarity=0.474 Sum_probs=25.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcC-CCHHHHH
Q 004116 402 DGETWSDQETFLLLEGIEMYN-DNWNEIA 429 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yg-gNW~~IA 429 (773)
.+.+|..++...||=||-+|| |+|+.|-
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhc
Confidence 568999999999999999999 9999973
No 128
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=25.45 E-value=9e+02 Score=30.82 Aligned_cols=28 Identities=21% Similarity=0.404 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 633 VETLLMRECEQVEKARQRFATERTRIVST 661 (773)
Q Consensus 633 LE~~le~Ere~LE~~Rq~L~~eR~~~~~~ 661 (773)
.++++.+..++|++.|+.| ..|++....
T Consensus 664 ~d~i~~~q~eel~Ke~kEl-q~rL~~q~K 691 (988)
T KOG2072|consen 664 ADQIKARQIEELEKERKEL-QSRLQYQEK 691 (988)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHHHh
Confidence 4678999999999999876 455555443
No 129
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=24.91 E-value=3e+02 Score=33.29 Aligned_cols=17 Identities=24% Similarity=0.614 Sum_probs=13.4
Q ss_pred HHHHHHHHhCCCCCCCc
Q 004116 438 AQCILHFVRLPMEDGIL 454 (773)
Q Consensus 438 eECi~hFlqLPIED~fL 454 (773)
--||.|..+.-+-..++
T Consensus 461 tkCI~hLHrTELHGrmI 477 (940)
T KOG4661|consen 461 TKCIEHLHRTELHGRMI 477 (940)
T ss_pred HHHHHHhhhhhhcceee
Confidence 56999999988776655
No 130
>PRK00106 hypothetical protein; Provisional
Probab=24.83 E-value=8.7e+02 Score=29.35 Aligned_cols=14 Identities=29% Similarity=0.368 Sum_probs=6.8
Q ss_pred CchHHHHHHHHhhc
Q 004116 506 NPVMALVAFLASAV 519 (773)
Q Consensus 506 NPVMS~VAFLas~V 519 (773)
|-++-+|+-|.++|
T Consensus 3 ~~~~~~~~~~~~~~ 16 (535)
T PRK00106 3 NIIILVVSALIGLV 16 (535)
T ss_pred chHHHHHHHHHHHH
Confidence 33444555555554
No 131
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=24.68 E-value=7.4e+02 Score=31.16 Aligned_cols=20 Identities=35% Similarity=0.320 Sum_probs=12.2
Q ss_pred cChHHHHHHHHHHHHHHHhh
Q 004116 519 VGPRVAAACAHASLAALSKQ 538 (773)
Q Consensus 519 V~P~VAaAAA~AAl~~l~~~ 538 (773)
.||.-.++.+.+.++.+.+.
T Consensus 420 tDp~eg~ala~aile~l~~~ 439 (782)
T PRK00409 420 TDPDEGAALAISILEYLRKR 439 (782)
T ss_pred CCHHHHHHHHHHHHHHHHHC
Confidence 45666666666666666543
No 132
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=24.47 E-value=1.3e+02 Score=29.39 Aligned_cols=58 Identities=22% Similarity=0.294 Sum_probs=43.7
Q ss_pred CCChHHHHHHHHHHHHHHH---hCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhcccccc
Q 004116 213 DHTPEKYMECRNHIVAKYM---DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (773)
Q Consensus 213 ~ktPeiYk~yRNfMIntYR---~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINYq 271 (773)
++.| +|..+.|.|...=. +.|.+.|--+=---...|++..++.|++.-||+=|+|.-.
T Consensus 8 s~~P-IY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 8 SSKP-IYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCCC-HHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3444 99999999977654 7888887543222233477899999999999999999863
No 133
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=24.47 E-value=25 Score=32.87 Aligned_cols=8 Identities=25% Similarity=0.335 Sum_probs=3.1
Q ss_pred CCccccCC
Q 004116 83 GGTRICEF 90 (773)
Q Consensus 83 ~~~~~~~~ 90 (773)
=|+.-..|
T Consensus 46 fgea~~~~ 53 (101)
T PF09026_consen 46 FGEAMAYF 53 (101)
T ss_dssp HHHHHHHH
T ss_pred HHHHHhhc
Confidence 33333333
No 134
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.21 E-value=4.3e+02 Score=29.09 Aligned_cols=58 Identities=14% Similarity=0.278 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 004116 605 EREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLG 664 (773)
Q Consensus 605 EREI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~~rl~ 664 (773)
+.+|++|.+.|=++ .+|++.+=+.+++++.-|.+=..+++..++++ .+|..+|..|++
T Consensus 51 q~ei~~L~~qi~~~-~~k~~~~~~~i~~~~~eik~l~~eI~~~~~~I-~~r~~~l~~raR 108 (265)
T COG3883 51 QNEIESLDNQIEEI-QSKIDELQKEIDQSKAEIKKLQKEIAELKENI-VERQELLKKRAR 108 (265)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 67788888776444 34455555555555555544444444333332 344555555544
No 135
>COG2916 Hns DNA-binding protein H-NS [General function prediction only]
Probab=23.82 E-value=6.2e+02 Score=25.03 Aligned_cols=50 Identities=24% Similarity=0.125 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 607 EIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVS 660 (773)
Q Consensus 607 EI~rLv~~IIe~QLKKLElKLk~feELE~~le~Ere~LE~~Rq~L~~eR~~~~~ 660 (773)
-|..|...+-+++++-||..++.|+.+...- ++-+..+...+.+|+.-+.
T Consensus 4 n~r~l~~~~~e~~~e~lee~~ek~eq~~~~r----~~e~~~~~~~i~e~~~~~~ 53 (128)
T COG2916 4 NIRTLRAMARETYLELLEEMLEKEEQVVQER----QEEEAAAIAEIEERQEKYG 53 (128)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHH
Confidence 3677888899999999999998887765544 4445555555555555554
No 136
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=23.66 E-value=3.2e+02 Score=23.11 Aligned_cols=23 Identities=17% Similarity=0.345 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 004116 631 AEVETLLMRECEQVEKARQRFAT 653 (773)
Q Consensus 631 eELE~~le~Ere~LE~~Rq~L~~ 653 (773)
.|.|++|..-+.+||..|...+.
T Consensus 33 ~EY~kiLk~r~~~lEevKrk~LK 55 (56)
T PF08112_consen 33 MEYEKILKQRRKELEEVKRKALK 55 (56)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 57888888888899888887654
No 137
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=23.25 E-value=1.2e+02 Score=39.00 Aligned_cols=46 Identities=13% Similarity=0.314 Sum_probs=38.8
Q ss_pred CCCCCCHHHHHHHHHHHHhcC-CCHHHHHHHhC------------CCCHHHHHHHHHhC
Q 004116 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVS------------TKSKAQCILHFVRL 447 (773)
Q Consensus 402 ~~~~WT~qEellLLEaIe~yg-gNW~~IAehVG------------tKT~eECi~hFlqL 447 (773)
....||.+|+-.||-.+.+|| |+|++|-+.|. +||+.|+-.+...|
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 456799999999999999999 99999988874 78998887765543
No 138
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=23.05 E-value=1.1e+02 Score=31.32 Aligned_cols=65 Identities=14% Similarity=0.100 Sum_probs=49.0
Q ss_pred CcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhccccc
Q 004116 204 PHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (773)
Q Consensus 204 PEFF~gk~~~ktPeiYk~yRNfMIntYR~NP~eYLTvTacRRnL~G~dv~sI~RVH~FLE~WGLINY 270 (773)
|-|=+-+..+.+-++|..+|+.|++- ++.|+..|+-.+--..+ |+.-..+.....-|+.-|||-+
T Consensus 2 ~~~~~~~~~~~~e~v~~~l~~~I~~g-~l~pG~~L~e~~La~~l-gVSRtpVREAL~~L~~eGLV~~ 66 (221)
T PRK11414 2 PGTEKTQHISLTLQVENDLKHQLSIG-ALKPGARLITKNLAEQL-GMSITPVREALLRLVSVNALSV 66 (221)
T ss_pred CCCcccCCCCHHHHHHHHHHHHHHhC-CCCCCCccCHHHHHHHH-CCCchhHHHHHHHHHHCCCEEe
Confidence 33433344567788999999999977 78999999876633333 4445678999999999999976
No 139
>PLN02436 cellulose synthase A
Probab=22.75 E-value=1.1e+02 Score=39.52 Aligned_cols=49 Identities=18% Similarity=0.456 Sum_probs=34.4
Q ss_pred cCCCCCCCCCCCC-----cceeecccCcCcccChhhhccCC----CCCCCCCCCceecC
Q 004116 344 SENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFHEGR----FVTGHSSLDYIRVD 393 (773)
Q Consensus 344 ~~~~C~~C~~~~~-----~~~y~c~kc~d~~LC~~CFs~G~----~~~~hss~dF~rvd 393 (773)
....|..||.+++ .+++.|.+| .|-+|..||.--+ -..-+....|.+..
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C-~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~k 92 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNEC-AFPVCRPCYEYERREGNQACPQCKTRYKRIK 92 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccC-CCccccchhhhhhhcCCccCcccCCchhhcc
Confidence 4458999999885 488999999 5889999996333 22333455676554
No 140
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=22.53 E-value=46 Score=27.46 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=21.0
Q ss_pred CCCCCCCCCCcceeecccCcCcccChhhhccC
Q 004116 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEG 378 (773)
Q Consensus 347 ~C~~C~~~~~~~~y~c~kc~d~~LC~~CFs~G 378 (773)
.|..|++.++...- .+-.|..+|.+||..-
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 49999999876431 2334557999999653
No 141
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=22.34 E-value=1.5e+03 Score=27.75 Aligned_cols=14 Identities=7% Similarity=-0.045 Sum_probs=8.3
Q ss_pred HHHhcCCCHHHHHH
Q 004116 417 GIEMYNDNWNEIAE 430 (773)
Q Consensus 417 aIe~yggNW~~IAe 430 (773)
+|+.-+-+|.+|..
T Consensus 322 ~L~~a~~~~~~i~~ 335 (653)
T PTZ00009 322 VLKDAGMDKRSVHE 335 (653)
T ss_pred HHHHcCCCHHHCcE
Confidence 44445567777754
No 142
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.08 E-value=63 Score=41.48 Aligned_cols=49 Identities=14% Similarity=0.418 Sum_probs=35.6
Q ss_pred cCCCCCCCCCCCC-----cceeecccCcCcccChhhhc----cCCCCCCCCCCCceecC
Q 004116 344 SENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFH----EGRFVTGHSSLDYIRVD 393 (773)
Q Consensus 344 ~~~~C~~C~~~~~-----~~~y~c~kc~d~~LC~~CFs----~G~~~~~hss~dF~rvd 393 (773)
....|..||.++. .+++.|.+| .|-+|-.||. +|+-..-+....|.+.+
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC-~FPVCrpCYEYEr~eG~q~CPqCktrYkr~k 73 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVC-AFPVCRPCYEYERKDGNQSCPQCKTKYKRHK 73 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccC-CCccccchhhhhhhcCCccCCccCCchhhhc
Confidence 4457999999885 488999999 5889999995 33333444566777655
No 143
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=21.82 E-value=55 Score=38.80 Aligned_cols=95 Identities=9% Similarity=-0.047 Sum_probs=70.3
Q ss_pred eCCCCCCCCCCCCCCHHHHhhcCcccCCCC-CCCChHHHHHHHHHHHHHHHhCCCceee-----HHHHhhccCCC-ChhH
Q 004116 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKS-PDHTPEKYMECRNHIVAKYMDNPEKRLI-----VSDCQGLVDGV-SPED 254 (773)
Q Consensus 182 vIPsyS~WFd~~~IH~IEKr~lPEFF~gk~-~~ktPeiYk~yRNfMIntYR~NP~eYLT-----vTacRRnL~G~-dv~s 254 (773)
..+.+++=++...=+.-....+++|+.+++ ....+..|+.+|..++...+---.-+.+ -+..+++.+.- .+-.
T Consensus 185 ~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLL 264 (506)
T KOG1279|consen 185 TLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLL 264 (506)
T ss_pred cccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHH
Confidence 567788888888888889999999998872 2567777888888888887653333333 34556655432 2556
Q ss_pred HHHHHHhhhhhcccccccCCCC
Q 004116 255 LTRIFRFLNHWGIINYCAAVQS 276 (773)
Q Consensus 255 I~RVH~FLE~WGLINYqvdp~~ 276 (773)
|=+|+.|.+.|+.|+.+|--.+
T Consensus 265 LE~ie~y~ddW~kVa~hVg~ks 286 (506)
T KOG1279|consen 265 LEAIEMYGDDWNKVADHVGTKS 286 (506)
T ss_pred HHHHHHhcccHHHHHhccCCCC
Confidence 7899999999999999998543
No 144
>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=21.66 E-value=1.6e+02 Score=23.63 Aligned_cols=33 Identities=24% Similarity=0.381 Sum_probs=27.6
Q ss_pred eeHHHHhhccCCCChhHHHHHHHhhhhhcccccc
Q 004116 238 LIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (773)
Q Consensus 238 LTvTacRRnL~G~dv~sI~RVH~FLE~WGLINYq 271 (773)
+++.+..+.+ |.+..++.|+..-|.++|+|+.-
T Consensus 21 ~~~~ei~~~~-~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 21 LTVSELAERL-GLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred cCHHHHHHHH-CcCHhHHHHHHHHHHHCCCeEEE
Confidence 8888877665 44578999999999999999974
No 145
>PF03286 Pox_Ag35: Pox virus Ag35 surface protein; InterPro: IPR004966 The Pox virus Ag35 surface protein is an evelope protein known as protein H5.; GO: 0019031 viral envelope
Probab=20.84 E-value=52 Score=34.56 Aligned_cols=27 Identities=15% Similarity=0.080 Sum_probs=17.3
Q ss_pred ccccCCcchhhhhccCCchhHHHHHHH
Q 004116 85 TRICEFPTAVQRVVNRPHVSVMDIVAI 111 (773)
Q Consensus 85 ~~~~~~~~~~~~~v~~ph~~v~a~~a~ 111 (773)
+.|....-.+..+|+.-+-++..|+|+
T Consensus 136 ~~I~kdlK~l~~rVsavstVLeDvQAa 162 (200)
T PF03286_consen 136 ANIIKDLKNLNARVSAVSTVLEDVQAA 162 (200)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence 345555566777777776666666554
No 146
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=20.64 E-value=1.1e+03 Score=25.56 Aligned_cols=29 Identities=21% Similarity=0.412 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCcceeecccCcCcccChhhh
Q 004116 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECF 375 (773)
Q Consensus 346 ~~C~~C~~~~~~~~y~c~kc~d~~LC~~CF 375 (773)
.+|+.|+.-+...-++-.-|. ..+|..|.
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~-HvfC~~C~ 32 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACR-HVFCEPCL 32 (233)
T ss_pred EEeccccccCCCCceeeeech-hhhhhhhc
Confidence 367777766654433334442 45677774
No 147
>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=20.60 E-value=3.9e+02 Score=23.40 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHhhC
Q 004116 648 RQRFATERTRIVSTRLG 664 (773)
Q Consensus 648 Rq~L~~eR~~~~~~rl~ 664 (773)
|..+...|+..+..||.
T Consensus 43 kne~Ar~rvEamI~RLk 59 (65)
T TIGR02449 43 KNEQARQKVEAMITRLK 59 (65)
T ss_pred HHHHHHHHHHHHHHhhh
Confidence 33444455555555554
No 148
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=20.49 E-value=4e+02 Score=24.31 Aligned_cols=30 Identities=27% Similarity=0.176 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 004116 601 ADHEEREIQRLSANIINHQLKRLELKLKQF 630 (773)
Q Consensus 601 A~~EEREI~rLv~~IIe~QLKKLElKLk~f 630 (773)
-++=|-+|+..|-+|-=.||+-=|+|-+.-
T Consensus 6 leqLE~KIqqAvdtI~LLqmEieELKekn~ 35 (79)
T PRK15422 6 FEKLEAKVQQAIDTITLLQMEIEELKEKNN 35 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345588999999999989988888887643
No 149
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=20.33 E-value=1.1e+02 Score=31.73 Aligned_cols=57 Identities=16% Similarity=0.088 Sum_probs=45.8
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCcee-eHHHHhhccCCCChhHHHHHHHhhhhhcccccc
Q 004116 213 DHTPEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (773)
Q Consensus 213 ~ktPeiYk~yRNfMIntYR~NP~eYL-TvTacRRnL~G~dv~sI~RVH~FLE~WGLINYq 271 (773)
+.+..+|..+|+.|++- ++.|++.| |-.+--..+ |+.-..+.....-|+..|||-..
T Consensus 6 ~~~~~v~~~l~~~I~~g-~l~pG~~LpsE~~La~~l-gVSRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 6 SPAGFAEEYIVESIWNN-RFPPGSILPAERELSELI-GVTRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred hhHHHHHHHHHHHHHcC-CCCCCCcCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCCEEEe
Confidence 45678999999999987 68899999 676643333 44467899999999999999863
Done!