Query 010085
Match_columns 518
No_of_seqs 265 out of 724
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 20:52:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010085.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010085hhsearch_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 2.2E-79 4.8E-84 636.0 13.8 303 172-517 40-362 (531)
2 KOG1279 Chromatin remodeling f 100.0 2.8E-74 6E-79 614.8 20.5 313 154-517 22-337 (506)
3 PF04433 SWIRM: SWIRM domain; 99.9 2.4E-27 5.2E-32 200.0 5.4 86 181-270 1-86 (86)
4 KOG0457 Histone acetyltransfer 99.9 7.7E-25 1.7E-29 228.5 9.1 111 344-456 13-126 (438)
5 COG5114 Histone acetyltransfer 99.8 3.5E-21 7.6E-26 194.4 6.0 110 344-455 4-116 (432)
6 cd02336 ZZ_RSC8 Zinc finger, Z 99.2 2.7E-11 5.8E-16 91.8 3.8 45 346-390 1-45 (45)
7 PF00249 Myb_DNA-binding: Myb- 99.1 8.6E-11 1.9E-15 89.0 5.5 44 404-447 2-47 (48)
8 PF13921 Myb_DNA-bind_6: Myb-l 98.9 2.9E-09 6.3E-14 83.6 5.7 41 406-446 1-41 (60)
9 smart00717 SANT SANT SWI3, AD 98.9 4.8E-09 1E-13 76.7 6.0 44 404-447 2-46 (49)
10 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 1.1E-08 2.5E-13 73.7 5.8 43 405-447 1-44 (45)
11 PLN03000 amine oxidase 98.8 8.3E-09 1.8E-13 118.6 6.3 84 186-274 87-172 (881)
12 PLN02328 lysine-specific histo 98.7 1.7E-08 3.6E-13 115.6 6.2 88 186-277 138-226 (808)
13 cd02335 ZZ_ADA2 Zinc finger, Z 98.5 1.4E-07 3.1E-12 72.4 4.3 47 346-392 1-49 (49)
14 TIGR01557 myb_SHAQKYF myb-like 98.2 1.5E-06 3.3E-11 69.1 4.9 45 404-448 4-54 (57)
15 cd02345 ZZ_dah Zinc finger, ZZ 98.2 9.8E-07 2.1E-11 68.0 3.6 44 347-390 2-47 (49)
16 PLN03212 Transcription repress 98.2 1.6E-06 3.5E-11 86.8 5.1 45 403-447 25-71 (249)
17 PLN02529 lysine-specific histo 98.2 1.6E-06 3.4E-11 99.0 5.6 87 186-277 63-151 (738)
18 cd02343 ZZ_EF Zinc finger, ZZ 98.2 1.9E-06 4.1E-11 66.4 3.6 40 347-386 2-41 (48)
19 cd02338 ZZ_PCMF_like Zinc fing 98.1 2.4E-06 5.1E-11 65.8 4.1 45 347-391 2-48 (49)
20 smart00291 ZnF_ZZ Zinc-binding 98.1 2.2E-06 4.8E-11 64.4 3.7 40 345-384 4-43 (44)
21 cd02334 ZZ_dystrophin Zinc fin 98.1 2.5E-06 5.3E-11 66.0 3.9 44 347-390 2-47 (49)
22 cd02249 ZZ Zinc finger, ZZ typ 98.1 2.7E-06 5.9E-11 64.4 3.9 45 346-392 1-46 (46)
23 cd02340 ZZ_NBR1_like Zinc fing 98.1 3.5E-06 7.5E-11 63.3 3.7 42 347-392 2-43 (43)
24 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.0 6.3E-06 1.4E-10 63.5 3.9 44 346-392 1-48 (48)
25 PLN03091 hypothetical protein; 98.0 8.2E-06 1.8E-10 87.3 5.2 45 403-447 14-60 (459)
26 PF00569 ZZ: Zinc finger, ZZ t 97.9 5.3E-06 1.1E-10 63.0 1.4 41 345-385 4-45 (46)
27 KOG0048 Transcription factor, 97.7 2.9E-05 6.3E-10 77.4 4.5 45 403-447 9-55 (238)
28 PLN03212 Transcription repress 97.7 5.3E-05 1.1E-09 76.1 5.3 46 401-446 76-121 (249)
29 cd02344 ZZ_HERC2 Zinc finger, 97.7 5E-05 1.1E-09 57.8 3.7 42 347-392 2-45 (45)
30 cd02339 ZZ_Mind_bomb Zinc fing 97.4 0.00019 4.2E-09 54.6 3.8 41 347-391 2-44 (45)
31 PLN03091 hypothetical protein; 97.3 0.0003 6.4E-09 75.7 5.9 46 401-446 65-110 (459)
32 cd02337 ZZ_CBP Zinc finger, ZZ 96.8 0.00094 2E-08 49.9 2.8 33 346-379 1-33 (41)
33 KOG0048 Transcription factor, 96.6 0.0032 7E-08 62.9 5.9 43 402-444 61-103 (238)
34 KOG0049 Transcription factor, 96.5 0.0032 6.8E-08 70.4 5.2 46 402-447 359-405 (939)
35 PLN02976 amine oxidase 96.4 0.0051 1.1E-07 74.9 6.6 86 187-275 452-542 (1713)
36 cd02342 ZZ_UBA_plant Zinc fing 96.3 0.0026 5.7E-08 48.1 2.3 32 347-378 2-34 (43)
37 PF13837 Myb_DNA-bind_4: Myb/S 96.0 0.0042 9.2E-08 51.8 2.3 45 404-448 2-64 (90)
38 KOG0049 Transcription factor, 95.9 0.007 1.5E-07 67.8 4.1 46 403-448 412-461 (939)
39 KOG4286 Dystrophin-like protei 95.6 0.0054 1.2E-07 69.6 1.8 42 346-387 604-646 (966)
40 KOG4582 Uncharacterized conser 95.4 0.01 2.3E-07 60.9 2.9 44 346-392 153-197 (278)
41 KOG1280 Uncharacterized conser 94.0 0.04 8.7E-07 58.0 3.0 41 345-385 8-49 (381)
42 KOG0051 RNA polymerase I termi 93.0 0.12 2.6E-06 58.2 4.8 46 402-448 383-428 (607)
43 KOG4301 Beta-dystrobrevin [Cyt 92.2 0.064 1.4E-06 56.6 1.4 95 346-452 241-340 (434)
44 KOG0051 RNA polymerase I termi 91.9 0.15 3.2E-06 57.5 3.8 49 402-450 435-509 (607)
45 KOG0050 mRNA splicing protein 91.1 0.2 4.3E-06 55.4 3.7 44 403-446 7-51 (617)
46 PF13873 Myb_DNA-bind_5: Myb/S 90.5 0.61 1.3E-05 38.3 5.3 44 404-447 3-68 (78)
47 KOG4167 Predicted DNA-binding 90.1 0.47 1E-05 54.4 5.5 45 402-446 618-662 (907)
48 COG5118 BDP1 Transcription ini 89.8 0.65 1.4E-05 49.8 6.0 45 403-447 365-409 (507)
49 KOG0050 mRNA splicing protein 88.9 0.36 7.7E-06 53.5 3.5 44 403-447 59-102 (617)
50 KOG4282 Transcription factor G 88.5 0.6 1.3E-05 48.9 4.8 46 404-449 55-114 (345)
51 TIGR02894 DNA_bind_RsfA transc 83.4 1.1 2.4E-05 43.0 3.2 44 403-447 4-54 (161)
52 COG5147 REB1 Myb superfamily p 82.4 0.79 1.7E-05 51.1 2.2 42 403-444 20-62 (512)
53 KOG4468 Polycomb-group transcr 82.0 1.3 2.7E-05 50.1 3.5 45 403-447 88-142 (782)
54 KOG4329 DNA-binding protein [G 78.9 2.9 6.3E-05 44.9 4.9 44 404-447 278-322 (445)
55 COG5147 REB1 Myb superfamily p 78.1 2 4.4E-05 48.0 3.6 46 402-447 71-116 (512)
56 PF04504 DUF573: Protein of un 75.4 4.6 0.0001 35.5 4.4 45 403-447 4-61 (98)
57 PLN03142 Probable chromatin-re 68.9 7 0.00015 47.3 5.3 40 404-443 825-865 (1033)
58 KOG1279 Chromatin remodeling f 68.6 6.3 0.00014 44.1 4.6 96 182-277 185-287 (506)
59 KOG0847 Transcription factor, 67.1 3.4 7.3E-05 41.7 1.9 17 11-27 218-235 (288)
60 PF09111 SLIDE: SLIDE; InterP 64.3 11 0.00024 34.3 4.6 43 402-444 48-106 (118)
61 PF12776 Myb_DNA-bind_3: Myb/S 63.3 8.1 0.00017 32.5 3.3 43 405-447 1-61 (96)
62 COG1725 Predicted transcriptio 60.7 14 0.0003 34.2 4.5 56 216-271 10-68 (125)
63 PF07649 C1_3: C1-like domain; 60.0 6 0.00013 27.2 1.6 27 347-374 2-29 (30)
64 PLN03119 putative ADP-ribosyla 58.9 13 0.00029 42.1 4.8 96 346-457 24-125 (648)
65 KOG1194 Predicted DNA-binding 58.0 17 0.00037 40.3 5.2 45 403-447 187-231 (534)
66 PF13404 HTH_AsnC-type: AsnC-t 57.3 26 0.00057 26.1 4.7 37 409-446 3-40 (42)
67 PF02954 HTH_8: Bacterial regu 56.1 17 0.00037 26.8 3.5 26 409-434 5-30 (42)
68 KOG3554 Histone deacetylase co 54.8 11 0.00024 41.8 3.2 44 404-447 286-330 (693)
69 PF03107 C1_2: C1 domain; Int 54.0 12 0.00026 25.8 2.3 27 347-374 2-29 (30)
70 KOG0703 Predicted GTPase-activ 53.1 15 0.00033 38.4 3.8 105 337-456 14-126 (287)
71 smart00595 MADF subfamily of S 52.9 12 0.00026 31.1 2.6 24 424-448 29-52 (89)
72 PLN03131 hypothetical protein; 51.2 22 0.00048 40.8 5.0 95 346-457 24-125 (705)
73 PF01475 FUR: Ferric uptake re 50.0 12 0.00027 32.9 2.3 50 220-270 7-60 (120)
74 PRK13923 putative spore coat p 49.6 22 0.00047 34.6 4.0 41 403-444 5-52 (170)
75 KOG1194 Predicted DNA-binding 48.8 9.4 0.0002 42.2 1.6 44 403-447 470-513 (534)
76 smart00345 HTH_GNTR helix_turn 46.2 21 0.00045 26.6 2.8 50 219-270 2-52 (60)
77 PF00643 zf-B_box: B-box zinc 45.3 26 0.00057 25.3 3.1 38 346-391 4-41 (42)
78 PF10446 DUF2457: Protein of u 44.7 13 0.00028 40.9 1.9 29 155-185 191-227 (458)
79 PHA00442 host recBCD nuclease 44.5 23 0.00051 28.4 2.8 26 407-432 24-50 (59)
80 PF00392 GntR: Bacterial regul 44.5 28 0.00061 27.4 3.3 54 216-271 3-57 (64)
81 COG5347 GTPase-activating prot 44.4 27 0.00058 37.1 4.1 99 345-456 20-125 (319)
82 PF08914 Myb_DNA-bind_2: Rap1 43.7 40 0.00086 27.7 4.1 43 404-446 3-55 (65)
83 PRK09462 fur ferric uptake reg 43.3 24 0.00052 32.5 3.2 49 222-270 18-70 (148)
84 PRK06474 hypothetical protein; 42.7 38 0.00082 32.7 4.5 49 222-271 12-60 (178)
85 PLN03142 Probable chromatin-re 42.1 41 0.00089 41.0 5.6 46 402-447 925-983 (1033)
86 PF12674 Zn_ribbon_2: Putative 40.9 15 0.00033 31.3 1.4 35 347-381 2-39 (81)
87 COG5114 Histone acetyltransfer 40.0 27 0.00058 37.2 3.3 69 193-269 361-429 (432)
88 PF02207 zf-UBR: Putative zinc 39.7 20 0.00044 29.4 1.9 34 357-394 11-47 (71)
89 KOG0384 Chromodomain-helicase 39.0 21 0.00045 43.9 2.5 27 402-428 1132-1159(1373)
90 PF09862 DUF2089: Protein of u 39.0 59 0.0013 29.7 4.9 74 348-447 1-79 (113)
91 PF10820 DUF2543: Protein of u 38.0 26 0.00056 29.7 2.2 55 194-266 23-79 (81)
92 cd07153 Fur_like Ferric uptake 37.2 45 0.00097 28.9 3.8 48 222-270 2-53 (116)
93 PF01022 HTH_5: Bacterial regu 36.8 62 0.0013 24.1 4.0 45 222-270 3-47 (47)
94 KOG4479 Transcription factor e 35.9 37 0.00081 29.5 2.9 46 216-265 35-89 (92)
95 PF12802 MarR_2: MarR family; 35.6 61 0.0013 24.7 4.0 42 232-274 16-57 (62)
96 PF09026 CENP-B_dimeris: Centr 33.8 7 0.00015 34.8 -1.8 17 80-96 43-59 (101)
97 PRK11179 DNA-binding transcrip 33.7 67 0.0015 29.8 4.6 39 408-447 8-47 (153)
98 KOG0706 Predicted GTPase-activ 31.5 42 0.00092 37.1 3.2 61 338-414 16-79 (454)
99 PF09339 HTH_IclR: IclR helix- 31.0 58 0.0013 24.7 3.1 44 225-270 7-50 (52)
100 PF06689 zf-C4_ClpX: ClpX C4-t 29.3 23 0.0005 26.3 0.6 31 346-377 2-33 (41)
101 cd00090 HTH_ARSR Arsenical Res 28.7 1E+02 0.0022 23.3 4.2 44 225-272 11-54 (78)
102 COG0735 Fur Fe2+/Zn2+ uptake r 28.3 59 0.0013 30.3 3.2 51 222-273 22-76 (145)
103 PF01412 ArfGap: Putative GTPa 28.1 54 0.0012 29.3 2.8 60 345-417 13-72 (116)
104 cd08310 Death_NFkB-like Death 27.1 51 0.0011 27.4 2.3 24 407-434 1-24 (72)
105 PF14569 zf-UDP: Zinc-binding 27.1 36 0.00077 29.3 1.4 50 345-395 9-67 (80)
106 smart00344 HTH_ASNC helix_turn 26.3 1.1E+02 0.0025 26.0 4.5 38 409-447 3-41 (108)
107 cd08783 Death_MALT1 Death doma 26.0 66 0.0014 28.7 2.9 33 414-446 12-54 (97)
108 PF13412 HTH_24: Winged helix- 25.7 1.3E+02 0.0029 22.0 4.2 44 222-268 4-47 (48)
109 smart00550 Zalpha Z-DNA-bindin 25.5 1.4E+02 0.003 24.2 4.5 49 222-271 7-55 (68)
110 PRK11639 zinc uptake transcrip 25.1 57 0.0012 31.1 2.5 52 213-270 23-78 (169)
111 KOG4752 Ribosomal protein L41 24.5 34 0.00074 23.1 0.6 6 12-17 2-8 (26)
112 PRK11169 leucine-responsive tr 24.4 1.1E+02 0.0025 28.6 4.4 39 408-447 13-52 (164)
113 PF14471 DUF4428: Domain of un 23.4 43 0.00094 26.2 1.1 30 347-378 1-30 (51)
114 smart00105 ArfGap Putative GTP 23.1 1E+02 0.0023 27.3 3.7 92 347-455 5-106 (112)
115 PF03444 HrcA_DNA-bdg: Winged 22.2 1.9E+02 0.0042 24.8 4.9 53 217-271 4-56 (78)
116 PF10545 MADF_DNA_bdg: Alcohol 22.1 74 0.0016 25.5 2.4 25 423-447 27-52 (85)
117 PRK00430 fis global DNA-bindin 21.7 1.1E+02 0.0024 26.7 3.5 26 409-434 55-80 (95)
118 PRK01905 DNA-binding protein F 21.1 1.2E+02 0.0027 25.1 3.5 28 407-434 35-62 (77)
119 KOG0477 DNA replication licens 21.1 76 0.0017 37.1 2.9 77 344-421 291-372 (854)
120 KOG0486 Transcription factor P 20.9 34 0.00074 36.4 0.1 13 10-22 162-175 (351)
121 PF01388 ARID: ARID/BRIGHT DNA 20.9 1.5E+02 0.0032 24.9 4.0 36 411-446 38-86 (92)
122 COG1499 NMD3 NMD protein affec 20.8 1.1E+02 0.0024 33.0 4.0 66 346-420 7-73 (355)
123 PF08114 PMP1_2: ATPase proteo 20.7 41 0.00088 25.7 0.5 11 12-22 31-41 (43)
124 PLN02638 cellulose synthase A 20.4 85 0.0018 38.5 3.3 49 346-395 18-75 (1079)
125 cd08781 Death_UNC5-like Death 20.2 78 0.0017 26.9 2.2 26 409-434 7-32 (83)
126 PLN02436 cellulose synthase A 20.2 1.5E+02 0.0032 36.6 5.1 49 345-394 36-93 (1094)
No 1
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=100.00 E-value=2.2e-79 Score=636.01 Aligned_cols=303 Identities=31% Similarity=0.566 Sum_probs=251.8
Q ss_pred ccccc---CCceeeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccCC
Q 010085 172 VVKRF---GSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVD 248 (518)
Q Consensus 172 ~~k~~---qth~iiIPSyS~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~ 248 (518)
.+++| |+|+||||||+.||++.+||+||+++.||||+||+++|||++|+.||||||++||+||.+|||+|+|||||+
T Consensus 40 e~~~Fl~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNva 119 (531)
T COG5259 40 EAETFLMEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVA 119 (531)
T ss_pred hhhhhhhccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccc
Confidence 34455 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHhhhhhcccccccCCCCCCCCCCCCccccCCCCceecCCccccccccccccCCCCccccccccccC---
Q 010085 249 GVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSS--- 325 (518)
Q Consensus 249 g~Dv~~i~RIh~FLe~wGLINy~~~p~~~p~~~~~~~l~~~~~G~~~~~~~~l~~~~~l~~fd~pk~~~~~~~i~~~--- 325 (518)
| |||+|.|||+|||+|||||||++|.++| +.|.++.+|+++..+++ +++|++|..+.++.+.......
T Consensus 120 g-DV~aivrvHrFLekWGLINYqvdp~trP-----s~IgPplt~h~q~l~dt---P~gl~p~l~~~~~~~~~~~a~~~e~ 190 (531)
T COG5259 120 G-DVAAIVRVHRFLEKWGLINYQVDPGTRP-----STIGPPLTSHFQDLHDT---PRGLSPFLPWGPINQRVLGAKEIEY 190 (531)
T ss_pred h-hHHHHHHHHHHHHHhcceeeccCCCCCc-----cccCCCcchhhHHHhhC---ccccccccCCCCccccccccchhhh
Confidence 9 9999999999999999999999999998 45778889999887765 4678888776654332111111
Q ss_pred -----CCCCCCCcCc-------hhHHHhhcc--CCcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCcee
Q 010085 326 -----SCGGADFFDL-------DNTIRERLS--ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIR 391 (518)
Q Consensus 326 -----~~~~~~~~~l-------~~~~~e~~~--~~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~k 391 (518)
.+.+.....+ ...+..+.. ...|+.||+.+...+|+.++..++.+|..||.+|+|+.+..++||.+
T Consensus 191 ~~~k~~~~sps~~~~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~ 270 (531)
T COG5259 191 ETHKEENYSPSLKSPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKP 270 (531)
T ss_pred hhhccCCCCchhhhhhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchh
Confidence 0000000000 011222222 27899999999999999999889999999999999999999999999
Q ss_pred eCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCCCCCCcCccccCCCCCccCCCCCC
Q 010085 392 VDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSR 471 (518)
Q Consensus 392 vd~~k~~~~~~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqLPIED~fLe~~~~~~~~~~~~~~~~ 471 (518)
++.... .....||+||+++|||||++||++|++||.|||+||+||||+|||||||+|.||.+..-
T Consensus 271 v~~~~~---~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~------------ 335 (531)
T COG5259 271 VTISLL---IRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDG------------ 335 (531)
T ss_pred hhhhcc---cccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccC------------
Confidence 986532 24579999999999999999999999999999999999999999999999999986420
Q ss_pred CCCCCccccCCCCCCCCCcccccccCCCCCCCCCCchhhhhhhhcc
Q 010085 472 DDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALDELREC 517 (518)
Q Consensus 472 ~~~g~~~~~~~g~~~g~~~~~~~~~~~~PFs~a~NPVMS~vAFLa~ 517 (518)
.|+ ...+.+||..++|||||+|+||+.
T Consensus 336 --------------~~~-----~~~G~~~f~~seNPVlstis~L~~ 362 (531)
T COG5259 336 --------------KGD-----NSKGRLPFDGSENPVLSTISFLAG 362 (531)
T ss_pred --------------cCC-----CCCCccccccCCCchhhHHHHHHH
Confidence 011 013568999999999999999985
No 2
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=100.00 E-value=2.8e-74 Score=614.80 Aligned_cols=313 Identities=32% Similarity=0.573 Sum_probs=256.8
Q ss_pred CCCCcccccCCcccccCccccccCCceeeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhC
Q 010085 154 RSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDN 233 (518)
Q Consensus 154 ~~~~~~v~~~p~~~~~~~~~k~~qth~iiIPSyS~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~n 233 (518)
...+.+++ |.++.......++|+|+|+||||++||+|++||+||++++||||+|++++|||++||+||||||++||+|
T Consensus 22 ~~~~~~~~--~~~~~~~~~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrln 99 (506)
T KOG1279|consen 22 ESQETLGG--PAAHDAAKTVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLN 99 (506)
T ss_pred cCcccccc--cchhhhcccccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccC
Confidence 45556666 6677777888999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccccccCCCCCCCCCCCCccccCCCCceecCCccccccccccccCCC
Q 010085 234 PEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKP 313 (518)
Q Consensus 234 p~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~~~p~~~p~~~~~~~l~~~~~G~~~~~~~~l~~~~~l~~fd~p 313 (518)
|.+|||+|+||||++| |||+|+|||+|||+||||||+++++++|. .+.++.+|++++..++ +++++++..+
T Consensus 100 p~~ylt~ta~rrnl~g-Dv~ai~Rvh~FlE~WGLINy~~d~e~rp~-----~~~p~~t~h~~~~~~t---p~~~~~~~~~ 170 (506)
T KOG1279|consen 100 PQEYLTFTACRRNLAG-DVCAIARVHAFLEQWGLINYQVDAESRPH-----PIEPPETSHFQVLADT---PRGLAPLTPE 170 (506)
T ss_pred cccchhHHHHHhcccc-hHHHHHHHHhhHHhhcccccccChhhCCc-----ccCCCcccccccccCC---CcccccCCCC
Confidence 9999999999999999 99999999999999999999999999984 3666778888776554 4566666554
Q ss_pred CccccccccccC---CCCCCCCcCchhHHHhhccCCcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCce
Q 010085 314 KCSLKVADVYSS---SCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYI 390 (518)
Q Consensus 314 k~~~~~~~i~~~---~~~~~~~~~l~~~~~e~~~~~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~ 390 (518)
....+....... .........+.....+.+...+|..|+.+ +|+..+..++.+|.+||..|+++..++..||.
T Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~ 246 (506)
T KOG1279|consen 171 DPQSQPDLGNPRMETLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSDFK 246 (506)
T ss_pred CccccccccccccccccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCccccccch
Confidence 433221111110 01111222333344455666778877765 67777777899999999999999999999992
Q ss_pred eeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCCCCCCcCccccCCCCCccCCCCC
Q 010085 391 RVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSS 470 (518)
Q Consensus 391 kvd~~k~~~~~~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqLPIED~fLe~~~~~~~~~~~~~~~ 470 (518)
.+ +...+..||++|+++|||||++||++|++||.|||+||++|||+|||+|||+|+||.+.+
T Consensus 247 ~~------~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LPieD~~l~~~~------------ 308 (506)
T KOG1279|consen 247 VI------GESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLPIEDPYLAKSE------------ 308 (506)
T ss_pred hc------cccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcCccchhhhhcc------------
Confidence 22 334578999999999999999999999999999999999999999999999999998742
Q ss_pred CCCCCCccccCCCCCCCCCcccccccCCCCCCCCCCchhhhhhhhcc
Q 010085 471 RDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALDELREC 517 (518)
Q Consensus 471 ~~~~g~~~~~~~g~~~g~~~~~~~~~~~~PFs~a~NPVMS~vAFLa~ 517 (518)
|+ +||+. +++.||++.+|||||+++||++
T Consensus 309 ------------~~-~~~~~-----~~~~~~sq~gnpv~s~~~~l~~ 337 (506)
T KOG1279|consen 309 ------------AS-LGPLS-----YGPVPFSQDGNPVMSTVAFLAS 337 (506)
T ss_pred ------------cc-cCccc-----cCCCccccCCCccccHHHHHHh
Confidence 22 56654 6889999999999999999986
No 3
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.94 E-value=2.4e-27 Score=199.99 Aligned_cols=86 Identities=43% Similarity=0.962 Sum_probs=78.7
Q ss_pred eeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHH
Q 010085 181 HVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR 260 (518)
Q Consensus 181 iiIPSyS~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~ 260 (518)
+++|.+++||+++.+|++|++.+||||.| ++|+.||.|||.||..|+.||.+|||+++||+.+.|.|++.+.|||+
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 46899999999999999999999999998 79999999999999999999999999999999998679999999999
Q ss_pred hhhhhccccc
Q 010085 261 FLNHWGIINY 270 (518)
Q Consensus 261 FLe~wGLINy 270 (518)
||++||+|||
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=99.91 E-value=7.7e-25 Score=228.47 Aligned_cols=111 Identities=31% Similarity=0.590 Sum_probs=100.9
Q ss_pred cCCcCCCCCCCCCc-ceeeecCCCCcccChhhhhcCCCCCCCC-CCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHHHHc
Q 010085 344 SENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY 421 (518)
Q Consensus 344 ~~~~C~~C~~~~~~-v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~kvd~~k~~~~~~~~~WT~eEellLLEaIe~y 421 (518)
.++.|++|..+|+. ++++|.+|.+++||..||+.|.+.+.|+ +|.|.+|++..++ ....+||++||++||||+++|
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 GKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFP--ILDPSWTADEEILLLEAAETY 90 (438)
T ss_pred CCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCC--CCCCCCChHHHHHHHHHHHHh
Confidence 36899999999998 5799999999999999999999999998 6999999986543 356899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhhCCCCCCcCcc
Q 010085 422 N-DNWNEIAEHVSTKSKAQCILHFVRLPMEDGILEN 456 (518)
Q Consensus 422 G-gNW~~IAehVGtKT~eECi~HFlqLPIED~fLe~ 456 (518)
| |||.+||+|||+||++||+.||++.+|+.++..-
T Consensus 91 G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s~~~~~ 126 (438)
T KOG0457|consen 91 GFGNWQDIADHIGTKTKEECKEHYLKHFVNSPIFPL 126 (438)
T ss_pred CCCcHHHHHHHHcccchHHHHHHHHHHHhcCccccc
Confidence 9 9999999999999999999999999998777543
No 5
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.83 E-value=3.5e-21 Score=194.38 Aligned_cols=110 Identities=24% Similarity=0.472 Sum_probs=100.8
Q ss_pred cCCcCCCCCCCCCc-ceeeecCCCCcccChhhhhcCCCCCCCC-CCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHHHHc
Q 010085 344 SENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY 421 (518)
Q Consensus 344 ~~~~C~~C~~~~~~-v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~kvd~~k~~~~~~~~~WT~eEellLLEaIe~y 421 (518)
.+++|++|..+|+. +++.|.+|.+++||..||.+|.+.+.|+ .|+|.+|+.+.+. ....+|++.||++|+++++..
T Consensus 4 ~k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsyp--I~~e~WgadEEllli~~~~Tl 81 (432)
T COG5114 4 VKIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYP--IGEEGWGADEELLLIECLDTL 81 (432)
T ss_pred ceeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCcc--ccCCCcCchHHHHHHHHHHhc
Confidence 45799999999997 6999999999999999999999999998 7999999877643 456899999999999999999
Q ss_pred C-CCHHHHHHHhCCCCHHHHHHHHhhCCCCCCcCc
Q 010085 422 N-DNWNEIAEHVSTKSKAQCILHFVRLPMEDGILE 455 (518)
Q Consensus 422 G-gNW~~IAehVGtKT~eECi~HFlqLPIED~fLe 455 (518)
| |||++||.|||.|+++||..||+.+++|..|..
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 999999999999999999999999999987744
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=99.15 E-value=2.7e-11 Score=91.81 Aligned_cols=45 Identities=38% Similarity=0.780 Sum_probs=43.1
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCce
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYI 390 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~ 390 (518)
+.|+.|+++++.+||||+++.+++||+.||.+|+||.+|++.||+
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=99.12 E-value=8.6e-11 Score=88.97 Aligned_cols=44 Identities=27% Similarity=0.681 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHcCCC-HHHHHHHhC-CCCHHHHHHHHhhC
Q 010085 404 ETWSDQETFLLLEGIEMYNDN-WNEIAEHVS-TKSKAQCILHFVRL 447 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yGgN-W~~IAehVG-tKT~eECi~HFlqL 447 (518)
..||.+|+.+|++||.+||.+ |..||++|+ +||..||..||.++
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 479999999999999999955 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=98.88 E-value=2.9e-09 Score=83.57 Aligned_cols=41 Identities=34% Similarity=0.762 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 010085 406 WSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (518)
Q Consensus 406 WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlq 446 (518)
||.+|+.+|++++..||.+|.+||+++|+||+.+|..||..
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=98.87 E-value=4.8e-09 Score=76.71 Aligned_cols=44 Identities=30% Similarity=0.686 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 404 ETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlqL 447 (518)
..||.+|+.+|++++..|| .+|..||+++++||+.+|..+|..+
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=98.79 E-value=1.1e-08 Score=73.75 Aligned_cols=43 Identities=33% Similarity=0.753 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 405 TWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 405 ~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlqL 447 (518)
.||.+|+.+|+.++++|| ++|..||+.+++||..+|..||.++
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
>PLN03000 amine oxidase
Probab=98.76 E-value=8.3e-09 Score=118.58 Aligned_cols=84 Identities=23% Similarity=0.325 Sum_probs=72.2
Q ss_pred CCCCCCCCCCCHHHHhh--cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhh
Q 010085 186 HSDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (518)
Q Consensus 186 yS~WF~~~~Ih~iEk~~--lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe 263 (518)
++.-|+.+++++.|..+ || .- ..+.+..||.|||.||.+|+.||..+||+++|...+..--...+.++|.||.
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 46789999999999776 67 22 2367899999999999999999999999999998875423478999999999
Q ss_pred hhcccccccCC
Q 010085 264 HWGIINYCAAV 274 (518)
Q Consensus 264 ~wGLINy~~~p 274 (518)
+.|+|||++..
T Consensus 162 r~G~in~g~~~ 172 (881)
T PLN03000 162 THGYINFGIAQ 172 (881)
T ss_pred HcCcccHHHHH
Confidence 99999999874
No 12
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=98.69 E-value=1.7e-08 Score=115.64 Aligned_cols=88 Identities=23% Similarity=0.288 Sum_probs=76.9
Q ss_pred CCCCCCCCCCCHHHHhh-cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhh
Q 010085 186 HSDWFSPDTVHRLERQV-VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH 264 (518)
Q Consensus 186 yS~WF~~~~Ih~iEk~~-lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~ 264 (518)
++.-|..+++|+.|..+ |+..-.+ +.+..||.|||.||.+|+.||..+||+++|+..+-.-....+.++|.||.+
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 47889999999988777 6666554 689999999999999999999999999999988754456789999999999
Q ss_pred hcccccccCCCCC
Q 010085 265 WGIINYCAAVQSP 277 (518)
Q Consensus 265 wGLINy~~~p~~~ 277 (518)
.|.|||+|.|...
T Consensus 214 ~g~in~gv~~~~~ 226 (808)
T PLN02328 214 HGYINFGVAPVIK 226 (808)
T ss_pred cCceeeecccccc
Confidence 9999999998653
No 13
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.49 E-value=1.4e-07 Score=72.42 Aligned_cols=47 Identities=34% Similarity=0.680 Sum_probs=42.5
Q ss_pred CcCCCCCCCCCc-ceeeecCCCCcccChhhhhcCCCCCCCC-CCCceee
Q 010085 346 NHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (518)
Q Consensus 346 ~~C~~C~~~~~~-v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~kv 392 (518)
+.|++|.+++.. .+|+|.+|.+++||.+||..|.+...|+ +|.|+.|
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 369999998887 8999999999999999999999999997 6888764
No 14
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.24 E-value=1.5e-06 Score=69.09 Aligned_cols=45 Identities=16% Similarity=0.390 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCH---HHHHHHhC-CC-CHHHHHHHHhhCC
Q 010085 404 ETWSDQETFLLLEGIEMYN-DNW---NEIAEHVS-TK-SKAQCILHFVRLP 448 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yG-gNW---~~IAehVG-tK-T~eECi~HFlqLP 448 (518)
..||++|..++|+||+.|| |+| .+|+++++ ++ |+.||..|+-.+.
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4799999999999999999 699 99999987 67 9999999976543
No 15
>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=98.23 E-value=9.8e-07 Score=67.98 Aligned_cols=44 Identities=25% Similarity=0.496 Sum_probs=40.0
Q ss_pred cCCCCCC-CCCcceeeecCCCCcccChhhhhcCCCCCCCC-CCCce
Q 010085 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYI 390 (518)
Q Consensus 347 ~C~~C~~-~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~ 390 (518)
.|++|.+ ++..++|+|..|.+++||.+||..|++..+|+ .|.|.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~ 47 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMY 47 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcc
Confidence 5999998 99999999999999999999999999999997 56664
No 16
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.19 E-value=1.6e-06 Score=86.79 Aligned_cols=45 Identities=16% Similarity=0.427 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC-CCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG-gNW~~IAehVG-tKT~eECi~HFlqL 447 (518)
...||.+|+.+|+++|++|| .+|..||+++| +||..||+.+|.++
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 89999999997 89999999999875
No 17
>PLN02529 lysine-specific histone demethylase 1
Probab=98.19 E-value=1.6e-06 Score=98.98 Aligned_cols=87 Identities=22% Similarity=0.245 Sum_probs=72.7
Q ss_pred CCCCCCCCCCCHHHHhh--cCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhh
Q 010085 186 HSDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLN 263 (518)
Q Consensus 186 yS~WF~~~~Ih~iEk~~--lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe 263 (518)
++.=|+.+++++-|+++ +|+. ..+.+..|+.|||.||.+|+.||..+||+++++..+..--...|...|.||.
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 35679999999999854 5543 4679999999999999999999999999999988765412345778999999
Q ss_pred hhcccccccCCCCC
Q 010085 264 HWGIINYCAAVQSP 277 (518)
Q Consensus 264 ~wGLINy~~~p~~~ 277 (518)
+.|.|||.|.|...
T Consensus 138 ~~~~inc~vnp~~~ 151 (738)
T PLN02529 138 YNGYINFGVSPSFA 151 (738)
T ss_pred hCCCcceeeccccc
Confidence 99999999998653
No 18
>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=98.15 E-value=1.9e-06 Score=66.39 Aligned_cols=40 Identities=30% Similarity=0.600 Sum_probs=37.5
Q ss_pred cCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCC
Q 010085 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS 386 (518)
Q Consensus 347 ~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss 386 (518)
.|++|...+..++|+|.+|.+++||..||..|++..+|+.
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 19
>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=98.15 E-value=2.4e-06 Score=65.83 Aligned_cols=45 Identities=20% Similarity=0.403 Sum_probs=40.9
Q ss_pred cCCCCC-CCCCcceeeecCCCCcccChhhhhcCCCCCCCC-CCCcee
Q 010085 347 HCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (518)
Q Consensus 347 ~C~~C~-~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~k 391 (518)
.|+.|+ .++...+|+|..|.+++||.+||..|.....|+ +|.|+.
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 599999 789889999999999999999999999999998 677754
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=98.14 E-value=2.2e-06 Score=64.40 Aligned_cols=40 Identities=33% Similarity=0.630 Sum_probs=36.9
Q ss_pred CCcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCC
Q 010085 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGH 384 (518)
Q Consensus 345 ~~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~h 384 (518)
...|+.|+.++...+|+|..|.+++||.+||..|+++..|
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 3579999999999999999999999999999999988776
No 21
>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=98.13 E-value=2.5e-06 Score=65.98 Aligned_cols=44 Identities=34% Similarity=0.684 Sum_probs=39.3
Q ss_pred cCCCCCC-CCCcceeeecCCCCcccChhhhhcCCCCCCCC-CCCce
Q 010085 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYI 390 (518)
Q Consensus 347 ~C~~C~~-~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~ 390 (518)
.|+.|++ ++...+|+|.+|.+++||..||..|++...|+ .|.++
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 68889999999999999999999999999998 46654
No 22
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=98.12 E-value=2.7e-06 Score=64.37 Aligned_cols=45 Identities=29% Similarity=0.705 Sum_probs=39.4
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCC-CCCceee
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~kv 392 (518)
+.|+.|++++...+|+|..|.+++||..||+.|. ..|. .|.|+++
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 6666 6877653
No 23
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=98.08 E-value=3.5e-06 Score=63.34 Aligned_cols=42 Identities=29% Similarity=0.558 Sum_probs=38.3
Q ss_pred cCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceee
Q 010085 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRV 392 (518)
Q Consensus 347 ~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kv 392 (518)
.|+.|+.++...+|+|..|.+++||..||..| +|..|.|+++
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 6777888864
No 24
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=98.00 E-value=6.3e-06 Score=63.47 Aligned_cols=44 Identities=27% Similarity=0.662 Sum_probs=38.0
Q ss_pred CcCCCCCC-CCCcceeeecCCC--CcccChhhhhcCCCCCCCC-CCCceee
Q 010085 346 NHCNYCSQ-PIPAVYYQSQKEV--DVLLCPECFHEGRFVTGHS-SLDYIRV 392 (518)
Q Consensus 346 ~~C~~C~~-~~~~v~y~c~k~~--d~~LC~~CFs~G~~p~~hs-s~DF~kv 392 (518)
+.|+.|+. ++..++|+|..|. +++||..||..|. .|+ .|.|.++
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 8999999999999 9999999999997 675 5766653
No 25
>PLN03091 hypothetical protein; Provisional
Probab=97.96 E-value=8.2e-06 Score=87.34 Aligned_cols=45 Identities=22% Similarity=0.531 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC-CCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG-gNW~~IAehVG-tKT~eECi~HFlqL 447 (518)
...||.+|+.+|+++|++|| .+|..||+++| +||..||+.||+++
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 45799999999999999999 89999999998 79999999999875
No 26
>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=97.87 E-value=5.3e-06 Score=62.97 Aligned_cols=41 Identities=34% Similarity=0.686 Sum_probs=31.2
Q ss_pred CCcCCCCCC-CCCcceeeecCCCCcccChhhhhcCCCCCCCC
Q 010085 345 ENHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS 385 (518)
Q Consensus 345 ~~~C~~C~~-~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs 385 (518)
.+.|+.|+. ++...+|+|..|.+++||..||..|++...|+
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 77789999999999999999999999887775
No 27
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.73 E-value=2.9e-05 Score=77.41 Aligned_cols=45 Identities=13% Similarity=0.406 Sum_probs=43.1
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC-CCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVS-TKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG-gNW~~IAehVG-tKT~eECi~HFlqL 447 (518)
...||.+|+.+|.+-|++|| ++|..|+++.| .|+-.+|+++|+.+
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 47899999999999999999 99999999999 99999999999986
No 28
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.67 E-value=5.3e-05 Score=76.09 Aligned_cols=46 Identities=13% Similarity=0.229 Sum_probs=42.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 010085 401 IDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (518)
Q Consensus 401 ~~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlq 446 (518)
.....||.+|+.+||+.+..||..|..||++|.+||..+|..||..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns 121 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNT 121 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHH
Confidence 3467899999999999999999999999999999999999999964
No 29
>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=97.65 E-value=5e-05 Score=57.84 Aligned_cols=42 Identities=24% Similarity=0.600 Sum_probs=35.9
Q ss_pred cCCCCCC-CCCcceeeecCCCCcccChhhhhcCCCCCCCC-CCCceee
Q 010085 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIRV 392 (518)
Q Consensus 347 ~C~~C~~-~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~kv 392 (518)
.|++|+. ++...+|+|..|.+++||..||..+ .|+ .|.|.+|
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 6888775
No 30
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=97.38 E-value=0.00019 Score=54.59 Aligned_cols=41 Identities=24% Similarity=0.603 Sum_probs=34.3
Q ss_pred cCCCCC-CCCCcceeeecCCCCcccChhhhhcCCCCCCCC-CCCcee
Q 010085 347 HCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHS-SLDYIR 391 (518)
Q Consensus 347 ~C~~C~-~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hs-s~DF~k 391 (518)
.|+.|+ .++..++|+|..|.+++||..||..+ .|+ .|.|++
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 599999 67778999999999999999999964 454 677765
No 31
>PLN03091 hypothetical protein; Provisional
Probab=97.34 E-value=0.0003 Score=75.71 Aligned_cols=46 Identities=20% Similarity=0.361 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 010085 401 IDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (518)
Q Consensus 401 ~~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlq 446 (518)
.....||.+|+.+||+.+..||..|.+||++|.+||..+|..||..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWns 110 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNS 110 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHH
Confidence 3457899999999999999999999999999999999999988865
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=96.84 E-value=0.00094 Score=49.86 Aligned_cols=33 Identities=21% Similarity=0.526 Sum_probs=28.7
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCC
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGR 379 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~ 379 (518)
+.|+.|.+.+ ..+|+|+.|.+|+||..||..+.
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 4699998855 49999999999999999998854
No 33
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.63 E-value=0.0032 Score=62.89 Aligned_cols=43 Identities=19% Similarity=0.393 Sum_probs=40.1
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHH
Q 010085 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHF 444 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HF 444 (518)
....||.+||.+|+++-..+|.-|..||.++.+||-.++..||
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 4578999999999999999999999999999999999998776
No 34
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.50 E-value=0.0032 Score=70.43 Aligned_cols=46 Identities=26% Similarity=0.658 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlqL 447 (518)
....||.+|+.+|+.||++|| -+|-+|-+.|.+||-.||+.+|++.
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 356899999999999999999 8999999999999999999999874
No 35
>PLN02976 amine oxidase
Probab=96.41 E-value=0.0051 Score=74.88 Aligned_cols=86 Identities=22% Similarity=0.379 Sum_probs=71.1
Q ss_pred CCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhcc---CCC--CCHHHHHHHHHh
Q 010085 187 SDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL---VDG--VSPEDLTRIFRF 261 (518)
Q Consensus 187 S~WF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~---l~g--~Dv~~i~RIh~F 261 (518)
++=+....+.+|||-.|.|...-|. .-+.||++||.|+-+|-++=.+-|.+++|-=- +.. .-...|.-|+.|
T Consensus 452 ~~gl~a~~~~~~e~~~~k~~lkr~~---~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~~~f 528 (1713)
T PLN02976 452 SAGLKARAVGPIEKIKFKEVLKRKG---GLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREVYLF 528 (1713)
T ss_pred hccccccccChHHHHHHHHHHHhcc---chHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHHHHH
Confidence 4456677899999999999987653 67899999999999999999999999999411 111 245688999999
Q ss_pred hhhhcccccccCCC
Q 010085 262 LNHWGIINYCAAVQ 275 (518)
Q Consensus 262 Le~wGLINy~~~p~ 275 (518)
|++.|.||-++...
T Consensus 529 ld~~gyin~g~~s~ 542 (1713)
T PLN02976 529 LDQRGYINAGIASE 542 (1713)
T ss_pred hhccCceecccccc
Confidence 99999999998764
No 36
>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=96.32 E-value=0.0026 Score=48.07 Aligned_cols=32 Identities=34% Similarity=0.710 Sum_probs=28.6
Q ss_pred cCCCCCC-CCCcceeeecCCCCcccChhhhhcC
Q 010085 347 HCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEG 378 (518)
Q Consensus 347 ~C~~C~~-~~~~v~y~c~k~~d~~LC~~CFs~G 378 (518)
.|+.|+. ++...+|+|..|.+++||..||...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 5999995 8888999999999999999999753
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.00 E-value=0.0042 Score=51.84 Aligned_cols=45 Identities=33% Similarity=0.678 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHH------cC------C--CHHHHHHHhC----CCCHHHHHHHHhhCC
Q 010085 404 ETWSDQETFLLLEGIEM------YN------D--NWNEIAEHVS----TKSKAQCILHFVRLP 448 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~------yG------g--NW~~IAehVG----tKT~eECi~HFlqLP 448 (518)
..||.+|+..||+.+.. |+ + -|..||+.+. .||+.||..+|-+|-
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 46999999999999977 21 1 4999999984 599999999998873
No 38
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.91 E-value=0.007 Score=67.80 Aligned_cols=46 Identities=24% Similarity=0.403 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCH---HHHHHHHhhCC
Q 010085 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSK---AQCILHFVRLP 448 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~---eECi~HFlqLP 448 (518)
.+.||-+|+..||++|++|| |+|-++|-.+|.||. .-|+.+|+..-
T Consensus 412 ~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 412 VERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred cCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 46899999999999999999 999999999999998 66999998753
No 39
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=95.62 E-value=0.0054 Score=69.56 Aligned_cols=42 Identities=36% Similarity=0.747 Sum_probs=37.4
Q ss_pred CcCCCCC-CCCCcceeeecCCCCcccChhhhhcCCCCCCCCCC
Q 010085 346 NHCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSL 387 (518)
Q Consensus 346 ~~C~~C~-~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~ 387 (518)
.+|+.|. .+|..++|+|++|-+++||..||..|+-..+|+-|
T Consensus 604 ~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~ 646 (966)
T KOG4286|consen 604 AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMH 646 (966)
T ss_pred hhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCC
Confidence 5799997 56678999999999999999999999999998754
No 40
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=95.41 E-value=0.01 Score=60.93 Aligned_cols=44 Identities=23% Similarity=0.453 Sum_probs=36.8
Q ss_pred CcCCCCCC-CCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceee
Q 010085 346 NHCNYCSQ-PIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRV 392 (518)
Q Consensus 346 ~~C~~C~~-~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kv 392 (518)
..|+.|+. .+...+|+|..|.+++||.+|+..+ ..|-.|-|.++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~---~~h~~H~~lR~ 197 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN---EHHAAHAMLRL 197 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC---CCCcccceeec
Confidence 57999999 8889999999999999999999876 34445666663
No 41
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=93.99 E-value=0.04 Score=58.04 Aligned_cols=41 Identities=22% Similarity=0.440 Sum_probs=33.8
Q ss_pred CCcCCCCCCCCCc-ceeeecCCCCcccChhhhhcCCCCCCCC
Q 010085 345 ENHCNYCSQPIPA-VYYQSQKEVDVLLCPECFHEGRFVTGHS 385 (518)
Q Consensus 345 ~~~C~~C~~~~~~-v~y~c~k~~d~~LC~~CFs~G~~p~~hs 385 (518)
...|+.|++.--. -+|+|..|.||+||..||.+|.-...|.
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 4579999975444 4899999999999999999997766664
No 42
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=92.96 E-value=0.12 Score=58.18 Aligned_cols=46 Identities=15% Similarity=0.338 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCC
Q 010085 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLP 448 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqLP 448 (518)
....||.+|+..|-.-+.++|++|..|++.|| |.|..|..+|-|+=
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~~ 428 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQYV 428 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHhh
Confidence 56789999999999999999999999999997 79999999999863
No 43
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=92.21 E-value=0.064 Score=56.57 Aligned_cols=95 Identities=19% Similarity=0.363 Sum_probs=60.3
Q ss_pred CcCCCCC-CCCCcceeeecCCCCcccChhhhhcCCCCCCCCC-CCceeeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcC-
Q 010085 346 NHCNYCS-QPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS-LDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYN- 422 (518)
Q Consensus 346 ~~C~~C~-~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss-~DF~kvd~~k~~~~~~~~~WT~eEellLLEaIe~yG- 422 (518)
..|++|. ..++..+|.|+.|.++.+|.+||-.|+-...|+. |.|..-. .|-.- ..+|..||.+--
T Consensus 241 v~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mke~S-----------s~ksp-~k~Lv~aisksl~ 308 (434)
T KOG4301|consen 241 VECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMKEYS-----------SWKSP-AKKLVHAISKSLT 308 (434)
T ss_pred ccCcceecccccchhhhHhhcCCccccchhhccccCCCCcchHHHHHHhh-----------cccCh-HHHHHHHhhhccc
Confidence 5799996 5566789999999999999999999999888874 4433221 12211 236677776542
Q ss_pred --CCHHHHHHHhCCCCHHHHHHHHhhCCCCCC
Q 010085 423 --DNWNEIAEHVSTKSKAQCILHFVRLPMEDG 452 (518)
Q Consensus 423 --gNW~~IAehVGtKT~eECi~HFlqLPIED~ 452 (518)
.-=+.+--.|+.++..---+-|+.-+.++.
T Consensus 309 c~s~~~~l~~~v~sqpekpldl~~iv~~~p~~ 340 (434)
T KOG4301|consen 309 CSSLREPLHPEVPSQPEKPLDLAHIVPQFPDT 340 (434)
T ss_pred ccccccccCCCCCCCCCCCcchhhccCCCCCC
Confidence 122334444555555545555555555443
No 44
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=91.92 E-value=0.15 Score=57.52 Aligned_cols=49 Identities=27% Similarity=0.506 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHH-------Hc------------------C-CCHHHHHHHhCCCCHHHHHHHHhhCCCC
Q 010085 402 DGETWSDQETFLLLEGIE-------MY------------------N-DNWNEIAEHVSTKSKAQCILHFVRLPME 450 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe-------~y------------------G-gNW~~IAehVGtKT~eECi~HFlqLPIE 450 (518)
....||-+|+.+||..|+ .| . =+|..|++.+|||+..||+.||-+|=+.
T Consensus 435 ~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~ 509 (607)
T KOG0051|consen 435 NRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTS 509 (607)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhh
Confidence 356899999999999995 33 1 2799999999999999999999998554
No 45
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.11 E-value=0.2 Score=55.36 Aligned_cols=44 Identities=25% Similarity=0.582 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhh
Q 010085 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVR 446 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlq 446 (518)
+..|+..|+..|=-|+.+|| ..|.+|+..+..||+.||..+|..
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 46799999999999999999 789999999999999999999874
No 46
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=90.49 E-value=0.61 Score=38.27 Aligned_cols=44 Identities=30% Similarity=0.445 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHcC-----------------CCHHHHHHHhC-----CCCHHHHHHHHhhC
Q 010085 404 ETWSDQETFLLLEGIEMYN-----------------DNWNEIAEHVS-----TKSKAQCILHFVRL 447 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yG-----------------gNW~~IAehVG-----tKT~eECi~HFlqL 447 (518)
..||.+|...||+-|+.|. .-|..|++.+. .||..|+..+|-+|
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 4799999999999999882 25999999993 69999999998764
No 47
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=90.07 E-value=0.47 Score=54.44 Aligned_cols=45 Identities=20% Similarity=0.435 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhh
Q 010085 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVR 446 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlq 446 (518)
...-||-.|..++-.||-.|..|+..|++.|.+||-.||+..|.-
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 346799999999999999999999999999999999999998863
No 48
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.77 E-value=0.65 Score=49.79 Aligned_cols=45 Identities=13% Similarity=0.364 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqL 447 (518)
...||..|..++..|+.++|.++.-||....+|...|+..+|++=
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~E 409 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKE 409 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999999974
No 49
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=88.91 E-value=0.36 Score=53.48 Aligned_cols=44 Identities=25% Similarity=0.514 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqL 447 (518)
...|+.+|+.+||.+...+-..|-.||.-|| ||..||..+|..|
T Consensus 59 ~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 59 KTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred hhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHH
Confidence 4689999999999999999999999999997 7999999999886
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=88.53 E-value=0.6 Score=48.88 Aligned_cols=46 Identities=28% Similarity=0.500 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHc----C-C-----CHHHHHHHh---C-CCCHHHHHHHHhhCCC
Q 010085 404 ETWSDQETFLLLEGIEMY----N-D-----NWNEIAEHV---S-TKSKAQCILHFVRLPM 449 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~y----G-g-----NW~~IAehV---G-tKT~eECi~HFlqLPI 449 (518)
..|+.+|++.||++.... . + .|..||..+ | .||+.||..+|-+|..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 679999999999998643 2 4 499999944 3 5999999999988843
No 51
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=83.39 E-value=1.1 Score=42.99 Aligned_cols=44 Identities=18% Similarity=0.443 Sum_probs=37.3
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYN--D-----NWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG--g-----NW~~IAehVGtKT~eECi~HFlqL 447 (518)
.+.||.+|+++|-|.|-.|- | -.++|++.+ +||+.-|-.+|-..
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~ 54 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAY 54 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHH
Confidence 35799999999999999983 3 488899999 48999999998653
No 52
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=82.43 E-value=0.79 Score=51.11 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHH
Q 010085 403 GETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHF 444 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HF 444 (518)
...|+..|+..|+-+++.|| .||..||..++.||+++|..|+
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 9999999999999999999999
No 53
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=82.00 E-value=1.3 Score=50.10 Aligned_cols=45 Identities=20% Similarity=0.427 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHH----------HHhCCCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYNDNWNEIA----------EHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yGgNW~~IA----------ehVGtKT~eECi~HFlqL 447 (518)
...||-+|+.-+.+||..||-|+++|- ..+..||+.|...||.++
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 468999999999999999999999993 334469999999999886
No 54
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=78.94 E-value=2.9 Score=44.89 Aligned_cols=44 Identities=25% Similarity=0.471 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHH-HHhCCCCHHHHHHHHhhC
Q 010085 404 ETWSDQETFLLLEGIEMYNDNWNEIA-EHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yGgNW~~IA-ehVGtKT~eECi~HFlqL 447 (518)
..|+.+|=..+=+||+.||.|+..|- ..|.|||--||+..|.+-
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 57999999999999999999999995 589999999999887754
No 55
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=78.10 E-value=2 Score=47.98 Aligned_cols=46 Identities=22% Similarity=0.496 Sum_probs=42.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 402 DGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqL 447 (518)
....|+.+|+-.|++.-..+|--|..||..++.+|..+|..+|+.+
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 56
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=75.44 E-value=4.6 Score=35.46 Aligned_cols=45 Identities=24% Similarity=0.446 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHHc----C----CCHHHHHHHhCCC-----CHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMY----N----DNWNEIAEHVSTK-----SKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~y----G----gNW~~IAehVGtK-----T~eECi~HFlqL 447 (518)
..-||.++|+.||+||-.| | .||...-++|... |..|-..+.-+|
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 4679999999999999888 4 4899988888532 667776665554
No 57
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=68.94 E-value=7 Score=47.31 Aligned_cols=40 Identities=20% Similarity=0.362 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHH
Q 010085 404 ETWSDQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILH 443 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~H 443 (518)
..||..+-..++.|.++|| +|-..||..|++||++|...+
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 999999999999999998754
No 58
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=68.64 E-value=6.3 Score=44.13 Aligned_cols=96 Identities=9% Similarity=-0.049 Sum_probs=76.8
Q ss_pred eCCCCCCCCCCCCCCHHHHhhcCcccCCCC-CCCChHHHHHHHHHHHHHHHhCCCceEe-----HHHhhccCCC-CCHHH
Q 010085 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKS-PDHTPEKYMECRNHIVAKYMDNPEKRLI-----VSDCQGLVDG-VSPED 254 (518)
Q Consensus 182 iIPSyS~WF~~~~Ih~iEk~~lPEfF~g~~-~~ktpe~Y~~~RN~iI~~yr~np~~yLT-----~t~crr~l~g-~Dv~~ 254 (518)
..+.+++-++...=+.-.....++|+.+++ ....+..|+.+|+.+++.++---..+.+ -+..+++.+. ..+-.
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 566678888888888999999999998873 3677888999999999999765444543 5556777654 57888
Q ss_pred HHHHHHhhhhhcccccccCCCCC
Q 010085 255 LTRIFRFLNHWGIINYCAAVQSP 277 (518)
Q Consensus 255 i~RIh~FLe~wGLINy~~~p~~~ 277 (518)
+-+|+.|.+.|+-|+.+|-..++
T Consensus 265 LE~ie~y~ddW~kVa~hVg~ks~ 287 (506)
T KOG1279|consen 265 LEAIEMYGDDWNKVADHVGTKSQ 287 (506)
T ss_pred HHHHHHhcccHHHHHhccCCCCH
Confidence 99999999999999999996553
No 59
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=67.11 E-value=3.4 Score=41.67 Aligned_cols=17 Identities=24% Similarity=0.597 Sum_probs=10.7
Q ss_pred hh-HHHhhhcCcccccCC
Q 010085 11 TR-KWKRRKREPRKQLNK 27 (518)
Q Consensus 11 ~~-~~~~~~~~~~~~~~~ 27 (518)
.| |||||--..-++-++
T Consensus 218 RRTKWRKkhAaEmasakk 235 (288)
T KOG0847|consen 218 RRTKWRKKHAAEMASAKK 235 (288)
T ss_pred chhhhhhhhccchhhccc
Confidence 45 999998744444333
No 60
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=64.35 E-value=11 Score=34.32 Aligned_cols=43 Identities=19% Similarity=0.402 Sum_probs=34.6
Q ss_pred CCCCCCHHHHHHHHHHHHHcC----CCHHHHHHHhC------------CCCHHHHHHHH
Q 010085 402 DGETWSDQETFLLLEGIEMYN----DNWNEIAEHVS------------TKSKAQCILHF 444 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yG----gNW~~IAehVG------------tKT~eECi~HF 444 (518)
.+..||.+|+-.||-.+.+|| |+|+.|-+.|- +||+.++..+-
T Consensus 48 ~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~ 106 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRC 106 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHH
Confidence 357899999999999999998 58999999883 79998887664
No 61
>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=63.32 E-value=8.1 Score=32.48 Aligned_cols=43 Identities=28% Similarity=0.459 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHc---C----------CCHHHHHHHhC-----CCCHHHHHHHHhhC
Q 010085 405 TWSDQETFLLLEGIEMY---N----------DNWNEIAEHVS-----TKSKAQCILHFVRL 447 (518)
Q Consensus 405 ~WT~eEellLLEaIe~y---G----------gNW~~IAehVG-----tKT~eECi~HFlqL 447 (518)
.||.+++..||+.+... | ..|+.|++.+. ..|+.||..||-.|
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 24899999885 47899999998765
No 62
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=60.73 E-value=14 Score=34.24 Aligned_cols=56 Identities=21% Similarity=0.250 Sum_probs=44.1
Q ss_pred hHHHHHHHHHHHHHHH---hCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccccc
Q 010085 216 PEKYMECRNHIVAKYM---DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (518)
Q Consensus 216 pe~Y~~~RN~iI~~yr---~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~ 271 (518)
-.+|.+|.|.|...=. +.|...|--+--.....|+..+.+.|.+.-||+-|+|.-.
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4599999999988765 5777777554433333568999999999999999999764
No 63
>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=59.96 E-value=6 Score=27.18 Aligned_cols=27 Identities=33% Similarity=0.806 Sum_probs=12.3
Q ss_pred cCCCCCCCCCc-ceeeecCCCCcccChhh
Q 010085 347 HCNYCSQPIPA-VYYQSQKEVDVLLCPEC 374 (518)
Q Consensus 347 ~C~~C~~~~~~-v~y~c~k~~d~~LC~~C 374 (518)
.|+.|+..+.. ..|+|..| ++.|...|
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 89999988 78887777
No 64
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=58.94 E-value=13 Score=42.15 Aligned_cols=96 Identities=20% Similarity=0.341 Sum_probs=53.1
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHH-----HH
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGI-----EM 420 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellLLEaI-----e~ 420 (518)
..|.-|+... ..+.|.. ..+.+|..|-.--|... .+|+. ..-+.||.+|...|..+= +.
T Consensus 24 k~CADCgs~~--P~WASiN-lGIFICi~CSGIHRsLG-------hRVKS------LSLDkWT~EEVe~Mk~gGN~~AN~i 87 (648)
T PLN03119 24 RRCINCNSLG--PQYVCTT-FWTFVCMACSGIHREFT-------HRVKS------VSMSKFTSKEVEVLQNGGNQRAREI 87 (648)
T ss_pred CccccCCCCC--CCceeec-cceEEeccchhhhccCC-------ceeec------cccCCCCHHHHHHHHHhchHHHHHH
Confidence 4788887633 4444443 46789999954433321 14443 223689998875443221 12
Q ss_pred cCCCHHHHHHHhCCCCHHHHHHHHhhC-CCCCCcCccc
Q 010085 421 YNDNWNEIAEHVSTKSKAQCILHFVRL-PMEDGILENV 457 (518)
Q Consensus 421 yGgNW~~IAehVGtKT~eECi~HFlqL-PIED~fLe~~ 457 (518)
|..+|..--..+...+..+=+..||+. |++-.|....
T Consensus 88 yeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~ 125 (648)
T PLN03119 88 YLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGAN 125 (648)
T ss_pred HHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcC
Confidence 334565432233333345556678884 7777777664
No 65
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=57.97 E-value=17 Score=40.27 Aligned_cols=45 Identities=11% Similarity=0.421 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqL 447 (518)
-+.||++|..||=.|.+.||.+..+|-+.+.-||-...+..|...
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999888654
No 66
>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=57.35 E-value=26 Score=26.12 Aligned_cols=37 Identities=16% Similarity=0.171 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhh
Q 010085 409 QETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVR 446 (518)
Q Consensus 409 eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlq 446 (518)
+=+..||+.++.-+ -.|.+||+.||- |+.+|..+.-+
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 34678999999888 899999999996 88888877644
No 67
>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=56.10 E-value=17 Score=26.78 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Q 010085 409 QETFLLLEGIEMYNDNWNEIAEHVST 434 (518)
Q Consensus 409 eEellLLEaIe~yGgNW~~IAehVGt 434 (518)
-|-..|.++++.++||..+.|+.+|-
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 36778999999999999999999993
No 68
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=54.76 E-value=11 Score=41.82 Aligned_cols=44 Identities=27% Similarity=0.460 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHHH-HhCCCCHHHHHHHHhhC
Q 010085 404 ETWSDQETFLLLEGIEMYNDNWNEIAE-HVSTKSKAQCILHFVRL 447 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~yGgNW~~IAe-hVGtKT~eECi~HFlqL 447 (518)
..|++-|-.++=||+++||.|+++|-. ++.=||-..++..|.-.
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmw 330 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMW 330 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHH
Confidence 589999999999999999999998865 44446666666555433
No 69
>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=54.00 E-value=12 Score=25.84 Aligned_cols=27 Identities=22% Similarity=0.643 Sum_probs=22.0
Q ss_pred cCCCCCCCCCcc-eeeecCCCCcccChhh
Q 010085 347 HCNYCSQPIPAV-YYQSQKEVDVLLCPEC 374 (518)
Q Consensus 347 ~C~~C~~~~~~v-~y~c~k~~d~~LC~~C 374 (518)
.|..|++.+... .|+|.+|. +.+.+.|
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 599999999888 99997764 7777666
No 70
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=53.06 E-value=15 Score=38.39 Aligned_cols=105 Identities=18% Similarity=0.363 Sum_probs=59.6
Q ss_pred hHHHhhccC---CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCC--CCceeeCCCCCCCCCCCCCCCHHHH
Q 010085 337 NTIRERLSE---NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSS--LDYIRVDPAREYGDIDGETWSDQET 411 (518)
Q Consensus 337 ~~~~e~~~~---~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss--~DF~kvd~~k~~~~~~~~~WT~eEe 411 (518)
..+++++.. ..|.-|+..-+ +..+- ...+.||.+|-. -|.+ .++.+|... .-+.||+++.
T Consensus 14 ~~l~~Ll~~~~N~~CADC~a~~P--~WaSw-nlGvFiC~~C~g------iHR~lg~hiSkVkSv------~LD~W~~eqv 78 (287)
T KOG0703|consen 14 RRLRELLREPDNKVCADCGAKGP--RWASW-NLGVFICLRCAG------IHRSLGVHISKVKSV------TLDEWTDEQV 78 (287)
T ss_pred HHHHHHHcCcccCcccccCCCCC--CeEEe-ecCeEEEeeccc------ccccccchhheeeee------eccccCHHHH
Confidence 344554443 47888876532 22221 246889999943 3443 245555432 2368999998
Q ss_pred HHHHHHHHHcC-CCHHH-HHHHhCCCCHHHHHHHHhhC-CCCCCcCcc
Q 010085 412 FLLLEGIEMYN-DNWNE-IAEHVSTKSKAQCILHFVRL-PMEDGILEN 456 (518)
Q Consensus 412 llLLEaIe~yG-gNW~~-IAehVGtKT~eECi~HFlqL-PIED~fLe~ 456 (518)
..|.+-=..-. -=|+. |.......++++-+.+||+- |..-+||..
T Consensus 79 ~~m~~~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~ 126 (287)
T KOG0703|consen 79 DFMISMGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDP 126 (287)
T ss_pred HHHHHHcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccc
Confidence 77664221000 12443 34444456678889999984 666777775
No 71
>smart00595 MADF subfamily of SANT domain.
Probab=52.91 E-value=12 Score=31.10 Aligned_cols=24 Identities=33% Similarity=0.627 Sum_probs=21.7
Q ss_pred CHHHHHHHhCCCCHHHHHHHHhhCC
Q 010085 424 NWNEIAEHVSTKSKAQCILHFVRLP 448 (518)
Q Consensus 424 NW~~IAehVGtKT~eECi~HFlqLP 448 (518)
-|..||..+|. |.++|..+|-.|=
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~LR 52 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHHH
Confidence 69999999997 9999999998873
No 72
>PLN03131 hypothetical protein; Provisional
Probab=51.19 E-value=22 Score=40.81 Aligned_cols=95 Identities=17% Similarity=0.332 Sum_probs=53.4
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHH------H
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGI------E 419 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellLLEaI------e 419 (518)
..|.-|+... ..+.|.. ..+.+|..|-.--|.. + | +|+. ..-+.||++|...| +.+ +
T Consensus 24 k~CADCga~~--P~WASiN-lGIFICi~CSGIHRsL-g---h---RVKS------VTLD~WtdeEV~~M-k~gGN~~AN~ 86 (705)
T PLN03131 24 RRCINCNSLG--PQFVCTN-FWTFICMTCSGIHREF-T---H---RVKS------VSMSKFTSQDVEAL-QNGGNQRARE 86 (705)
T ss_pred CccccCCCCC--CCeeEec-cceEEchhchhhhccc-C---c---cccc------ccCCCCCHHHHHHH-HHhccHHHHH
Confidence 4788887533 4444433 4688999996543332 1 1 3432 12368999886543 322 2
Q ss_pred HcCCCHHHHHHHhCCCCHHHHHHHHhh-CCCCCCcCccc
Q 010085 420 MYNDNWNEIAEHVSTKSKAQCILHFVR-LPMEDGILENV 457 (518)
Q Consensus 420 ~yGgNW~~IAehVGtKT~eECi~HFlq-LPIED~fLe~~ 457 (518)
.|..+|..--..+...+..+=+..||+ -|++-.|+...
T Consensus 87 iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~ 125 (705)
T PLN03131 87 IYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGK 125 (705)
T ss_pred HHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCC
Confidence 233456533333444445556677887 47777777654
No 73
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=49.99 E-value=12 Score=32.91 Aligned_cols=50 Identities=20% Similarity=0.274 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHhCCCceEeHHHhhccC----CCCCHHHHHHHHHhhhhhccccc
Q 010085 220 MECRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 220 ~~~RN~iI~~yr~np~~yLT~t~crr~l----~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
-.-|..|++....++. .+|+.+.-..| ..++...|.|...+|+.-|||.=
T Consensus 7 T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~ 60 (120)
T PF01475_consen 7 TPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK 60 (120)
T ss_dssp HHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred CHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence 4568899999988876 99999975544 23788999999999999999964
No 74
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=49.61 E-value=22 Score=34.60 Aligned_cols=41 Identities=17% Similarity=0.416 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHcC--C-----CHHHHHHHhCCCCHHHHHHHH
Q 010085 403 GETWSDQETFLLLEGIEMYN--D-----NWNEIAEHVSTKSKAQCILHF 444 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yG--g-----NW~~IAehVGtKT~eECi~HF 444 (518)
.+.||.+|+++|-+.|-.|+ | -...+++.+ .||...|-.+|
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 35799999999999888886 3 255566667 58999999999
No 75
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=48.76 E-value=9.4 Score=42.16 Aligned_cols=44 Identities=27% Similarity=0.397 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 403 GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 403 ~~~WT~eEellLLEaIe~yGgNW~~IAehVGtKT~eECi~HFlqL 447 (518)
.-+||-.|-- |+....+|+.+...||+-++|||++|....||+-
T Consensus 470 ~~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~n 513 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMDN 513 (534)
T ss_pred cCCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcCc
Confidence 4589988877 7788889999999999999999999999999873
No 76
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=46.23 E-value=21 Score=26.65 Aligned_cols=50 Identities=20% Similarity=0.240 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhCCCceE-eHHHhhccCCCCCHHHHHHHHHhhhhhccccc
Q 010085 219 YMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 219 Y~~~RN~iI~~yr~np~~yL-T~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
|-.+|+.|+... ..|...| |..+.-..+ |+....+.|...-|+.-|+|-.
T Consensus 2 ~~~l~~~i~~~~-~~~~~~l~s~~~la~~~-~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 2 AERLREDIVSGE-LRPGDKLPSERELAAQL-GVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHHHcCC-CCCCCcCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEE
Confidence 556777777764 3466778 787765554 5688899999999999999964
No 77
>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=45.31 E-value=26 Score=25.26 Aligned_cols=38 Identities=18% Similarity=0.340 Sum_probs=26.4
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCcee
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIR 391 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~k 391 (518)
..|..|... ...|.|..|. ..+|..|+..+ |+.|+++.
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 457777642 3678888874 57999999876 66676654
No 78
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=44.70 E-value=13 Score=40.95 Aligned_cols=29 Identities=17% Similarity=0.178 Sum_probs=16.2
Q ss_pred CCCcccccCCcccccCc--------cccccCCceeeCCC
Q 010085 155 SDTSCVITPPQIMEGKG--------VVKRFGSRVHVLPM 185 (518)
Q Consensus 155 ~~~~~v~~~p~~~~~~~--------~~k~~qth~iiIPS 185 (518)
.+|.+||- +|=|-.- +.-|...++|+||.
T Consensus 191 DSTDFVCG--TLDEDRPLE~AY~Scle~Rr~~K~~~iPQ 227 (458)
T PF10446_consen 191 DSTDFVCG--TLDEDRPLEAAYISCLEARRREKHIPIPQ 227 (458)
T ss_pred CcccccCC--CcCCcchHHHHHHHHHHHHHHcCCCCCCC
Confidence 55889984 2222221 12355677788875
No 79
>PHA00442 host recBCD nuclease inhibitor
Probab=44.51 E-value=23 Score=28.44 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=21.3
Q ss_pred CHHHHHHHHHHHHHcC-CCHHHHHHHh
Q 010085 407 SDQETFLLLEGIEMYN-DNWNEIAEHV 432 (518)
Q Consensus 407 T~eEellLLEaIe~yG-gNW~~IAehV 432 (518)
+-+-....|++++.+| +||+-+.+.+
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 3455677899999999 9999988765
No 80
>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=44.48 E-value=28 Score=27.44 Aligned_cols=54 Identities=24% Similarity=0.266 Sum_probs=39.8
Q ss_pred hHHHHHHHHHHHHHHHhCCCceE-eHHHhhccCCCCCHHHHHHHHHhhhhhcccccc
Q 010085 216 PEKYMECRNHIVAKYMDNPEKRL-IVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (518)
Q Consensus 216 pe~Y~~~RN~iI~~yr~np~~yL-T~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~ 271 (518)
-++|-.+++.|.+-- .-|...| |..+--+.+ |+-...+.+....|+.+|+|--.
T Consensus 3 ~~i~~~l~~~I~~g~-~~~g~~lps~~~la~~~-~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 3 EQIYDQLRQAILSGR-LPPGDRLPSERELAERY-GVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHHHHHTTS-S-TTSBE--HHHHHHHH-TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHcCC-CCCCCEeCCHHHHHHHh-ccCCcHHHHHHHHHHHCCcEEEE
Confidence 367888888888754 4577899 888865444 56788999999999999999543
No 81
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=44.36 E-value=27 Score=37.07 Aligned_cols=99 Identities=16% Similarity=0.341 Sum_probs=52.8
Q ss_pred CCcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCC
Q 010085 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDN 424 (518)
Q Consensus 345 ~~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellLLEaIe~yGgN 424 (518)
...|.-|+..- ..|.-| .-.+.||.+|-..=|--+.| ..+|.. ..-+.||.+|..+|..+=...-..
T Consensus 20 Nk~CaDCga~~-P~W~S~--nlGvfiCi~CagvHRsLGvh----iS~VKS------itLD~wt~~~l~~m~~gGN~~a~~ 86 (319)
T COG5347 20 NKKCADCGAPN-PTWASV--NLGVFLCIDCAGVHRSLGVH----ISKVKS------LTLDNWTEEELRRMEVGGNSNANR 86 (319)
T ss_pred cCccccCCCCC-CceEec--ccCeEEEeecchhhhccccc----eeeeee------eecccCCHHHHHHHHHhcchhhhh
Confidence 45799898765 223322 24789999996543333222 223332 123689999988877621111122
Q ss_pred HHHHHH------HhCCCCHHHHHHHHhh-CCCCCCcCcc
Q 010085 425 WNEIAE------HVSTKSKAQCILHFVR-LPMEDGILEN 456 (518)
Q Consensus 425 W~~IAe------hVGtKT~eECi~HFlq-LPIED~fLe~ 456 (518)
|.+--- .+..+.-...+.+|++ ++.+-+|.+.
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 222111 1113445677777776 6666555554
No 82
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=43.69 E-value=40 Score=27.69 Aligned_cols=43 Identities=14% Similarity=0.360 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHHHc-------CCC--HHHHHHHhC-CCCHHHHHHHHhh
Q 010085 404 ETWSDQETFLLLEGIEMY-------NDN--WNEIAEHVS-TKSKAQCILHFVR 446 (518)
Q Consensus 404 ~~WT~eEellLLEaIe~y-------GgN--W~~IAehVG-tKT~eECi~HFlq 446 (518)
...|.+|+..||+-|..+ +|| |.+.++.-. .+|-+--..||++
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K 55 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLK 55 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 368999999999999654 255 999999766 6888888899987
No 83
>PRK09462 fur ferric uptake regulator; Provisional
Probab=43.28 E-value=24 Score=32.55 Aligned_cols=49 Identities=12% Similarity=0.204 Sum_probs=38.7
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccC----CCCCHHHHHHHHHhhhhhccccc
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l----~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
-|-.|++.....+...+|+.+.-..| .+++...|.|...+|+.-|||.=
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence 36677777766667899999975444 33789999999999999999963
No 84
>PRK06474 hypothetical protein; Provisional
Probab=42.70 E-value=38 Score=32.66 Aligned_cols=49 Identities=22% Similarity=0.267 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccccc
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~ 271 (518)
.|-.|++.-..++. .+|++++-..+.++....+.|..+.|+..|||.--
T Consensus 12 ~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~ 60 (178)
T PRK06474 12 VRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVV 60 (178)
T ss_pred HHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence 68889988777654 49999987776556778999999999999999854
No 85
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=42.08 E-value=41 Score=41.02 Aligned_cols=46 Identities=13% Similarity=0.314 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHHHHHhC------------CCCHHHHHHHHhhC
Q 010085 402 DGETWSDQETFLLLEGIEMYN-DNWNEIAEHVS------------TKSKAQCILHFVRL 447 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yG-gNW~~IAehVG------------tKT~eECi~HFlqL 447 (518)
.+..||.+|+-.||-.+.+|| |+|++|-+.|. +||+.|+..+-..|
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 356899999999999999999 99999988773 79999988775443
No 86
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=40.89 E-value=15 Score=31.33 Aligned_cols=35 Identities=20% Similarity=0.544 Sum_probs=24.4
Q ss_pred cCCCCCCCCCcceeeecC---CCCcccChhhhhcCCCC
Q 010085 347 HCNYCSQPIPAVYYQSQK---EVDVLLCPECFHEGRFV 381 (518)
Q Consensus 347 ~C~~C~~~~~~v~y~c~k---~~d~~LC~~CFs~G~~p 381 (518)
.|-.||.++......-.+ ..+-+-|.-||.+|.|.
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 599999999865422111 23456899999999774
No 87
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=40.05 E-value=27 Score=37.25 Aligned_cols=69 Identities=13% Similarity=0.351 Sum_probs=54.2
Q ss_pred CCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccc
Q 010085 193 DTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIIN 269 (518)
Q Consensus 193 ~~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLIN 269 (518)
.=+++-|.+.+--+ .-.|.-||.+.-.||..+.. ....+|.++|++++. .|+.-.-+|+.|.-.-|+|-
T Consensus 361 ~llS~dEq~LC~~l------~i~PkpyL~LK~~~is~~l~-t~g~f~K~d~~~Lf~-id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 361 ALLSDDEQRLCETL------NISPKPYLELKKEVISCFLR-TRGEFTKEDFNRLFG-IDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred hhhcchHHHHHHHh------CCCCccHHHHHHHHHHHHHH-hCCCccHHHHHHHhC-cCcchhhHHHHHHHhccccC
Confidence 34556666644222 34699999999999999965 467899999999875 79999999999998888873
No 88
>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=39.71 E-value=20 Score=29.39 Aligned_cols=34 Identities=18% Similarity=0.442 Sum_probs=23.3
Q ss_pred cceeeecCCC---CcccChhhhhcCCCCCCCCCCCceeeCC
Q 010085 357 AVYYQSQKEV---DVLLCPECFHEGRFVTGHSSLDYIRVDP 394 (518)
Q Consensus 357 ~v~y~c~k~~---d~~LC~~CFs~G~~p~~hss~DF~kvd~ 394 (518)
.+.|+|..|. ...+|..||..+ .|..|+|+.+..
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~----~H~gH~~~~~~~ 47 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANS----CHEGHRVVYYRS 47 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTS----GGGGSSEEEEE-
T ss_pred CEEEECccCCCCCCEEEchhhCCCC----CcCCCcEEEEEe
Confidence 4577777764 378999999876 566788876654
No 89
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=39.04 E-value=21 Score=43.92 Aligned_cols=27 Identities=26% Similarity=0.499 Sum_probs=25.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-CCHHHH
Q 010085 402 DGETWSDQETFLLLEGIEMYN-DNWNEI 428 (518)
Q Consensus 402 ~~~~WT~eEellLLEaIe~yG-gNW~~I 428 (518)
...+|..+++-.||=||-+|| |+|+.|
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHh
Confidence 567999999999999999999 999986
No 90
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=39.02 E-value=59 Score=29.67 Aligned_cols=74 Identities=12% Similarity=0.146 Sum_probs=46.7
Q ss_pred CCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHH
Q 010085 348 CNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNE 427 (518)
Q Consensus 348 C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellLLEaIe~yGgNW~~ 427 (518)
|-.|+..+.-.+++|..|.-. -.|.| ..- .-.--..|++.+++..-+..||-.+
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 CPVCGGELVVTRLKCPSCGTE-------IEGEF---------ELP----------WFARLSPEQLEFIKLFIKNRGNLKE 54 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE-------EEeee---------ccc----------hhhcCCHHHHHHHHHHHHhcCCHHH
Confidence 778888887778887776321 01222 110 0012346888888888888999999
Q ss_pred HHHHhCC-----CCHHHHHHHHhhC
Q 010085 428 IAEHVST-----KSKAQCILHFVRL 447 (518)
Q Consensus 428 IAehVGt-----KT~eECi~HFlqL 447 (518)
|++.+|- |.+-+=+..=|.+
T Consensus 55 ~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 55 MEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 9999992 5554444444444
No 91
>PF10820 DUF2543: Protein of unknown function (DUF2543); InterPro: IPR020251 This entry contains proteins with no known function.
Probab=37.95 E-value=26 Score=29.67 Aligned_cols=55 Identities=24% Similarity=0.468 Sum_probs=35.1
Q ss_pred CCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceEeHHHhhcc--CCCCCHHHHHHHHHhhhhhc
Q 010085 194 TVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL--VDGVSPEDLTRIFRFLNHWG 266 (518)
Q Consensus 194 ~Ih~iEk~~lPEfF~g~~~~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~--l~g~Dv~~i~RIh~FLe~wG 266 (518)
-|++-||..|-.+|.- +| -|+--++.++-.+-+.. -+|+|..-|--|-.||.+||
T Consensus 23 pVse~erd~LAhYFQl----------------Li--tRLmnneeIsEeaQ~EMA~eAgi~~~rID~IA~fLNqWG 79 (81)
T PF10820_consen 23 PVSEAERDALAHYFQL----------------LI--TRLMNNEEISEEAQQEMASEAGIDEQRIDDIANFLNQWG 79 (81)
T ss_pred CcchhhhhHHHHHHHH----------------HH--HHHhccHhhhHHHHHHHHHHcCCcHHHHHHHHHHHHHhc
Confidence 4667777777666631 12 22222456655443221 26789999999999999999
No 92
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=37.17 E-value=45 Score=28.93 Aligned_cols=48 Identities=15% Similarity=0.255 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccC----CCCCHHHHHHHHHhhhhhccccc
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l----~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
-|-.|++..... .+.+|+.+.-..| .+++...+.|...+|+.-|||.-
T Consensus 2 qR~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~ 53 (116)
T cd07153 2 QRLAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE 53 (116)
T ss_pred HHHHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence 367788877665 5889999975554 23789999999999999999974
No 93
>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=36.81 E-value=62 Score=24.11 Aligned_cols=45 Identities=20% Similarity=0.288 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhccccc
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
.|-.||..-.. ..+++.+..+.+ |++-..+.+=.+-|+..|||.+
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 57788887755 558999988776 5688999999999999999975
No 94
>KOG4479 consensus Transcription factor e(y)2 [Transcription]
Probab=35.92 E-value=37 Score=29.48 Aligned_cols=46 Identities=35% Similarity=0.400 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHHHHhCCCceEeHHHh--------hccCCC-CCHHHHHHHHHhhhhh
Q 010085 216 PEKYMECRNHIVAKYMDNPEKRLIVSDC--------QGLVDG-VSPEDLTRIFRFLNHW 265 (518)
Q Consensus 216 pe~Y~~~RN~iI~~yr~np~~yLT~t~c--------rr~l~g-~Dv~~i~RIh~FLe~w 265 (518)
-++-..+||-|+.+=-.| +|+.+- |.++.. +--..++|||.||.++
T Consensus 35 d~ik~mcrniimEkG~~n----~tvdqL~AeitPkaRaLVPd~VKkEll~rirt~L~~~ 89 (92)
T KOG4479|consen 35 DDIKEMCRNIIMEKGVDN----ITVDQLAAEITPKARALVPDVVKKELLLRIRTALDKH 89 (92)
T ss_pred HHHHHHHHHHHHHhcccc----ccHHHHHHHhCchhhhhchHHHHHHHHHHHHHHHHHH
Confidence 456678999998876544 777653 333322 4447899999999876
No 95
>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=35.65 E-value=61 Score=24.69 Aligned_cols=42 Identities=21% Similarity=0.352 Sum_probs=33.0
Q ss_pred hCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccccccCC
Q 010085 232 DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAV 274 (518)
Q Consensus 232 ~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~~~p 274 (518)
.+|...+|+++.-+.+ +++-.++.|+.+=|++.|||--..++
T Consensus 16 ~~~~~~~t~~~la~~l-~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 16 RHPGEELTQSELAERL-GISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HSTTSGEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HCCCCCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 5666679999987665 46899999999999999999766554
No 96
>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=33.84 E-value=7 Score=34.76 Aligned_cols=17 Identities=12% Similarity=0.149 Sum_probs=10.5
Q ss_pred eccCCccccCCchhhHh
Q 010085 80 LIDGGTRICEFPTAVQR 96 (518)
Q Consensus 80 ~~~~~~~~~~f~~~~~~ 96 (518)
+...|++.++|-+|.|-
T Consensus 43 ~p~fgea~~~~~~v~rY 59 (101)
T PF09026_consen 43 VPEFGEAMAYFTMVKRY 59 (101)
T ss_dssp ---HHHHHHHHHHHHHH
T ss_pred chhHHHHHhhcchHhhh
Confidence 34478888888776665
No 97
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=33.67 E-value=67 Score=29.77 Aligned_cols=39 Identities=15% Similarity=0.194 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 408 DQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 408 ~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlqL 447 (518)
++-+..||+.++.-| -.|.+||+.+|. |+..|..++-+|
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL 47 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKM 47 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 457889999999988 899999999985 899999998887
No 98
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=31.47 E-value=42 Score=37.10 Aligned_cols=61 Identities=25% Similarity=0.536 Sum_probs=37.9
Q ss_pred HHHhhccCCcCCCCCCCCCc---ceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHH
Q 010085 338 TIRERLSENHCNYCSQPIPA---VYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLL 414 (518)
Q Consensus 338 ~~~e~~~~~~C~~C~~~~~~---v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellL 414 (518)
+++.....-.|.-|+..-+. +.| .+.||.+|-..-|.-+-|-+ |+|-.+ + +.||..|...+
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 44443334579999876543 444 68999999766555555544 766432 2 23998876654
No 99
>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=30.98 E-value=58 Score=24.66 Aligned_cols=44 Identities=16% Similarity=0.292 Sum_probs=33.7
Q ss_pred HHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhccccc
Q 010085 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 225 ~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
.|++.....+ ..+|+++.-+.+ |..-..+.|+..-|+++|+|..
T Consensus 7 ~iL~~l~~~~-~~~t~~eia~~~-gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESG-GPLTLSEIARAL-GLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHCHHCTB-SCEEHHHHHHHH-TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcCC-CCCCHHHHHHHH-CcCHHHHHHHHHHHHHCcCeec
Confidence 3566665554 448999987765 5789999999999999999864
No 100
>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=29.34 E-value=23 Score=26.34 Aligned_cols=31 Identities=23% Similarity=0.697 Sum_probs=17.1
Q ss_pred CcCCCCCCCCCcc-eeeecCCCCcccChhhhhc
Q 010085 346 NHCNYCSQPIPAV-YYQSQKEVDVLLCPECFHE 377 (518)
Q Consensus 346 ~~C~~C~~~~~~v-~y~c~k~~d~~LC~~CFs~ 377 (518)
..|++|++.-..+ .+. .-..+..+|..|...
T Consensus 2 ~~CSFCgr~~~~v~~li-~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLI-SGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEE-EES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhcee-cCCCCcEECHHHHHH
Confidence 4799999887764 333 222358899999643
No 101
>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=28.72 E-value=1e+02 Score=23.26 Aligned_cols=44 Identities=23% Similarity=0.412 Sum_probs=33.1
Q ss_pred HHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhccccccc
Q 010085 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCA 272 (518)
Q Consensus 225 ~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~~ 272 (518)
.|+......+ +++.+..+.+ |+....+.|+..-|++.|+|+...
T Consensus 11 ~il~~l~~~~---~~~~ei~~~~-~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 11 RILRLLLEGP---LTVSELAERL-GLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHCC---cCHHHHHHHH-CcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3444433444 8888877665 568899999999999999998753
No 102
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=28.29 E-value=59 Score=30.29 Aligned_cols=51 Identities=14% Similarity=0.232 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccC----CCCCHHHHHHHHHhhhhhcccccccC
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINYCAA 273 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l----~g~Dv~~i~RIh~FLe~wGLINy~~~ 273 (518)
-|-.|++.-...+.. +|+.+.-+.| .++.+..+.|...+|+.-|||+-...
T Consensus 22 qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~ 76 (145)
T COG0735 22 QRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF 76 (145)
T ss_pred HHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEe
Confidence 467788877666544 9999874444 33778999999999999999987544
No 103
>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=28.05 E-value=54 Score=29.29 Aligned_cols=60 Identities=30% Similarity=0.533 Sum_probs=29.1
Q ss_pred CCcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHHHHH
Q 010085 345 ENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEG 417 (518)
Q Consensus 345 ~~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellLLEa 417 (518)
...|.-|+.. ...+.+.. -.+.||..|...=+..+.| ..+|.. ..-+.||.+|..+|.++
T Consensus 13 N~~CaDCg~~--~p~w~s~~-~GiflC~~Cag~HR~lg~~----is~VkS------i~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 13 NKVCADCGAP--NPTWASLN-YGIFLCLECAGIHRSLGVH----ISRVKS------ITMDNWSPEEVQRMREG 72 (116)
T ss_dssp CTB-TTT-SB--S--EEETT-TTEEE-HHHHHHHHHHTTT----T--EEE------TTTS---HHHHHHHHHS
T ss_pred cCcCCCCCCC--CCCEEEee-cChhhhHHHHHHHHHhccc----chhccc------cccCCCCHHHHHHHHHH
Confidence 3579888753 33555554 4688999998653332222 223322 12246999998887654
No 104
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=27.11 E-value=51 Score=27.43 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=20.0
Q ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHhCC
Q 010085 407 SDQETFLLLEGIEMYNDNWNEIAEHVST 434 (518)
Q Consensus 407 T~eEellLLEaIe~yGgNW~~IAehVGt 434 (518)
|-++..+||+. |.+|..+|+++|-
T Consensus 1 ~r~~L~~lLd~----~~dWr~LA~~L~~ 24 (72)
T cd08310 1 TRERLCKLLDD----GCDWRELAQLLDL 24 (72)
T ss_pred CHHHHHHHhCC----CCCHHHHHHHcCc
Confidence 34667788887 9999999999985
No 105
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=27.07 E-value=36 Score=29.30 Aligned_cols=50 Identities=20% Similarity=0.490 Sum_probs=16.6
Q ss_pred CCcCCCCCCCCC-----cceeeecCCCCcccChhhhh----cCCCCCCCCCCCceeeCCC
Q 010085 345 ENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFH----EGRFVTGHSSLDYIRVDPA 395 (518)
Q Consensus 345 ~~~C~~C~~~~~-----~v~y~c~k~~d~~LC~~CFs----~G~~p~~hss~DF~kvd~~ 395 (518)
...|..||.++. .++..|.+| .|-+|..||. +|+-....-...|.+....
T Consensus 9 ~qiCqiCGD~VGl~~~Ge~FVAC~eC-~fPvCr~CyEYErkeg~q~CpqCkt~ykr~kgs 67 (80)
T PF14569_consen 9 GQICQICGDDVGLTENGEVFVACHEC-AFPVCRPCYEYERKEGNQVCPQCKTRYKRHKGS 67 (80)
T ss_dssp S-B-SSS--B--B-SSSSB--S-SSS------HHHHHHHHHTS-SB-TTT--B----TT-
T ss_pred CcccccccCccccCCCCCEEEEEccc-CCccchhHHHHHhhcCcccccccCCCcccccCC
Confidence 357999987764 367888887 5888888886 2322222224566665543
No 106
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.32 E-value=1.1e+02 Score=25.99 Aligned_cols=38 Identities=21% Similarity=0.157 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 409 QETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 409 eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlqL 447 (518)
+.+..+|..++..+ -.|.+||+.+|. ++..|..+..+|
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L 41 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL 41 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 56789999999888 789999999985 777777776665
No 107
>cd08783 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins
Probab=25.97 E-value=66 Score=28.68 Aligned_cols=33 Identities=27% Similarity=0.499 Sum_probs=23.5
Q ss_pred HHHHHHHcC--CCHHHHHHHhCCC-----CH---HHHHHHHhh
Q 010085 414 LLEGIEMYN--DNWNEIAEHVSTK-----SK---AQCILHFVR 446 (518)
Q Consensus 414 LLEaIe~yG--gNW~~IAehVGtK-----T~---eECi~HFlq 446 (518)
|=+.++.-. .+|.+.|+.+|.+ |+ ++|+++++.
T Consensus 12 L~~lLD~~~~~~gWr~LAe~lg~~~~fr~S~~el~~cslkvl~ 54 (97)
T cd08783 12 LSELLDRAADGKGWRKLAELAGSRGRFRLSCLDLEQCSLKVLE 54 (97)
T ss_pred HHHHHhCCCccCCHHHHHHHHccCCccccCHHHHHHHHHHHhc
Confidence 334444432 7899999999973 44 789999875
No 108
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=25.73 E-value=1.3e+02 Score=22.04 Aligned_cols=44 Identities=20% Similarity=0.402 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhccc
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGII 268 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLI 268 (518)
.+-.|++.-+.||. +|.++.-+.+ |+....+.|...-|+.-|+|
T Consensus 4 ~~~~Il~~l~~~~~--~t~~ela~~~-~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 4 TQRKILNYLRENPR--ITQKELAEKL-GISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHCTT--S-HHHHHHHH-TS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHcCC--CCHHHHHHHh-CCCHHHHHHHHHHHHHCcCc
Confidence 34567777677765 9999987775 57889999999999999997
No 109
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=25.47 E-value=1.4e+02 Score=24.23 Aligned_cols=49 Identities=10% Similarity=0.146 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccccc
Q 010085 222 CRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (518)
Q Consensus 222 ~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~ 271 (518)
.++.|+.....++..-+|..+.-+.| |++-..+.|+..=|+.-|+|-..
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l-gl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL-GLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH-CCCHHHHHHHHHHHHHCCCEEec
Confidence 57889999988876669999987776 67889999999999999999775
No 110
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=25.10 E-value=57 Score=31.10 Aligned_cols=52 Identities=19% Similarity=0.259 Sum_probs=39.4
Q ss_pred CCChHHHHHHHHHHHHHHHhCCCceEeHHHhhccC----CCCCHHHHHHHHHhhhhhccccc
Q 010085 213 DHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHWGIINY 270 (518)
Q Consensus 213 ~ktpe~Y~~~RN~iI~~yr~np~~yLT~t~crr~l----~g~Dv~~i~RIh~FLe~wGLINy 270 (518)
-.|++ |-.|++..... .+.+|..+.-..| ..++...|.|...+|+.-|||+=
T Consensus 23 R~T~q-----R~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~ 78 (169)
T PRK11639 23 RLTPQ-----RLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHK 78 (169)
T ss_pred CCCHH-----HHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEE
Confidence 45664 55677777655 5799999975444 23788999999999999999964
No 111
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=24.46 E-value=34 Score=23.08 Aligned_cols=6 Identities=50% Similarity=1.675 Sum_probs=4.3
Q ss_pred h-HHHhh
Q 010085 12 R-KWKRR 17 (518)
Q Consensus 12 ~-~~~~~ 17 (518)
| ||||+
T Consensus 2 r~kwrkk 8 (26)
T KOG4752|consen 2 RAKWRKK 8 (26)
T ss_pred chHHHHH
Confidence 5 88864
No 112
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=24.38 E-value=1.1e+02 Score=28.60 Aligned_cols=39 Identities=21% Similarity=0.249 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHcC-CCHHHHHHHhCCCCHHHHHHHHhhC
Q 010085 408 DQETFLLLEGIEMYN-DNWNEIAEHVSTKSKAQCILHFVRL 447 (518)
Q Consensus 408 ~eEellLLEaIe~yG-gNW~~IAehVGtKT~eECi~HFlqL 447 (518)
++-+.+||.+++.-+ -.|.+||+.||- |+.-|..+.-+|
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~rL 52 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 667889999999988 899999999985 888888888776
No 113
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.37 E-value=43 Score=26.17 Aligned_cols=30 Identities=23% Similarity=0.514 Sum_probs=20.5
Q ss_pred cCCCCCCCCCcceeeecCCCCcccChhhhhcC
Q 010085 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEG 378 (518)
Q Consensus 347 ~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G 378 (518)
.|..|++.++-..- .+-.|-.+|.+||..-
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 48999998875431 2234557999999764
No 114
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=23.10 E-value=1e+02 Score=27.33 Aligned_cols=92 Identities=26% Similarity=0.357 Sum_probs=47.8
Q ss_pred cCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcC-CCH
Q 010085 347 HCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYN-DNW 425 (518)
Q Consensus 347 ~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~eEellLLEaIe~yG-gNW 425 (518)
.|.-|+.. ...+.+.. ..+.+|..|-.--+....| ..+|.. ..-+.||.+|... |+ .-| ...
T Consensus 5 ~CaDC~~~--~p~w~s~~-~GifvC~~CsgiHR~lg~h----is~VkS------l~md~w~~~~i~~-~~---~~GN~~~ 67 (112)
T smart00105 5 KCFDCGAP--NPTWASVN-LGVFLCIECSGIHRSLGVH----ISKVRS------LTLDTWTEEELRL-LQ---KGGNENA 67 (112)
T ss_pred cccCCCCC--CCCcEEec-cceeEhHHhHHHHHhcCCC----cCeeee------cccCCCCHHHHHH-HH---HhhhHHH
Confidence 68888863 33444442 4688999997654433322 222322 1225799977643 33 333 223
Q ss_pred HHHHHHhC--------CCCHHHHHHHHhh-CCCCCCcCc
Q 010085 426 NEIAEHVS--------TKSKAQCILHFVR-LPMEDGILE 455 (518)
Q Consensus 426 ~~IAehVG--------tKT~eECi~HFlq-LPIED~fLe 455 (518)
+++=+.-+ ..+..+-...|++ -|++-.|..
T Consensus 68 n~~~e~~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 106 (112)
T smart00105 68 NSIWESNLDDFSLKPPDSDDQQKYESFIAAKYEEKLFVP 106 (112)
T ss_pred HHHHHhhCCccccCCCCCchHHHHHHHHHHHHHhhhccc
Confidence 33322221 1124677788887 355555543
No 115
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.18 E-value=1.9e+02 Score=24.84 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHhCCCceEeHHHhhccCCCCCHHHHHHHHHhhhhhcccccc
Q 010085 217 EKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYC 271 (518)
Q Consensus 217 e~Y~~~RN~iI~~yr~np~~yLT~t~crr~l~g~Dv~~i~RIh~FLe~wGLINy~ 271 (518)
++-.+|=..||+.|... .+.+.-.+.-+.| +.+-..|..+.+-||..|||-=+
T Consensus 4 ~rq~~IL~alV~~Y~~~-~~PVgSk~ia~~l-~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 4 ERQREILKALVELYIET-GEPVGSKTIAEEL-GRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHHhc-CCCcCHHHHHHHH-CCChHHHHHHHHHHHHCCCccCC
Confidence 45567888999999876 6777766665555 45778999999999999999654
No 116
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=22.06 E-value=74 Score=25.46 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCC-CCHHHHHHHHhhC
Q 010085 423 DNWNEIAEHVST-KSKAQCILHFVRL 447 (518)
Q Consensus 423 gNW~~IAehVGt-KT~eECi~HFlqL 447 (518)
.-|..||..+|. -+.++|..++-+|
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHH
Confidence 469999999985 4678999999885
No 117
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=21.74 E-value=1.1e+02 Score=26.69 Aligned_cols=26 Identities=19% Similarity=0.018 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Q 010085 409 QETFLLLEGIEMYNDNWNEIAEHVST 434 (518)
Q Consensus 409 eEellLLEaIe~yGgNW~~IAehVGt 434 (518)
-|...|.++++.++||+.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 47778999999999999999999994
No 118
>PRK01905 DNA-binding protein Fis; Provisional
Probab=21.13 E-value=1.2e+02 Score=25.13 Aligned_cols=28 Identities=29% Similarity=0.057 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHhCC
Q 010085 407 SDQETFLLLEGIEMYNDNWNEIAEHVST 434 (518)
Q Consensus 407 T~eEellLLEaIe~yGgNW~~IAehVGt 434 (518)
..-|...+.++++.++||+.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 4457778999999999999999999993
No 119
>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]
Probab=21.07 E-value=76 Score=37.05 Aligned_cols=77 Identities=25% Similarity=0.396 Sum_probs=46.5
Q ss_pred cCCcCCCCCCCCCcceeeec-CCCCcccChhhhhcCCCCCCCC---CCCceeeCCCCCCCC-CCCCCCCHHHHHHHHHHH
Q 010085 344 SENHCNYCSQPIPAVYYQSQ-KEVDVLLCPECFHEGRFVTGHS---SLDYIRVDPAREYGD-IDGETWSDQETFLLLEGI 418 (518)
Q Consensus 344 ~~~~C~~C~~~~~~v~y~c~-k~~d~~LC~~CFs~G~~p~~hs---s~DF~kvd~~k~~~~-~~~~~WT~eEellLLEaI 418 (518)
+++.|.-|+..+ ..+++.+ .......|+.|-+.|-|..+.. -.+|+++......+. ..+.-=-..|..+|-+.|
T Consensus 291 vky~C~KC~~vl-gPF~qs~n~evkp~~C~~cqSkGpf~vn~e~TvyrnYQritiQEspg~v~~GrlPRsk~vILl~DLv 369 (854)
T KOG0477|consen 291 VKYDCLKCGFVL-GPFVQSSNSEVKPGSCPECQSKGPFEVNVEETVYRNYQRITIQESPGTVPAGRLPRSKEVILLADLV 369 (854)
T ss_pred HhhhHHhhCCcc-CceeeccCceeCCCCCccccCCCCCccchhhhhhcccceeeeccCCCcCCCCccccchhheehhhhh
Confidence 357899998544 3444433 3456789999999998865543 356998875543221 122333445666666666
Q ss_pred HHc
Q 010085 419 EMY 421 (518)
Q Consensus 419 e~y 421 (518)
...
T Consensus 370 D~~ 372 (854)
T KOG0477|consen 370 DSC 372 (854)
T ss_pred hhc
Confidence 443
No 120
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=20.94 E-value=34 Score=36.40 Aligned_cols=13 Identities=38% Similarity=1.084 Sum_probs=9.8
Q ss_pred chh-HHHhhhcCcc
Q 010085 10 DTR-KWKRRKREPR 22 (518)
Q Consensus 10 ~~~-~~~~~~~~~~ 22 (518)
+.| |||||-|+.+
T Consensus 162 nrrakwrkrErN~~ 175 (351)
T KOG0486|consen 162 NRRAKWRKRERNQQ 175 (351)
T ss_pred cchhhhhhhhhhHH
Confidence 456 8998888765
No 121
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=20.91 E-value=1.5e+02 Score=24.86 Aligned_cols=36 Identities=17% Similarity=0.382 Sum_probs=25.4
Q ss_pred HHHHHHHHHHcCC--------CHHHHHHHhCCC---CH--HHHHHHHhh
Q 010085 411 TFLLLEGIEMYND--------NWNEIAEHVSTK---SK--AQCILHFVR 446 (518)
Q Consensus 411 ellLLEaIe~yGg--------NW~~IAehVGtK---T~--eECi~HFlq 446 (518)
...|-.+|..+|| .|..||+.+|-. +. .+...+|.+
T Consensus 38 L~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~ 86 (92)
T PF01388_consen 38 LYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEK 86 (92)
T ss_dssp HHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHH
Confidence 4678888888874 699999999832 22 455566654
No 122
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=20.78 E-value=1.1e+02 Score=33.01 Aligned_cols=66 Identities=18% Similarity=0.158 Sum_probs=35.5
Q ss_pred CcCCCCCCCCCcceeeecCCCCcccChhhhhcCCCCCCCCCCCceeeCCCCCCCCCCCCCCCH-HHHHHHHHHHHH
Q 010085 346 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSD-QETFLLLEGIEM 420 (518)
Q Consensus 346 ~~C~~C~~~~~~v~y~c~k~~d~~LC~~CFs~G~~p~~hss~DF~kvd~~k~~~~~~~~~WT~-eEellLLEaIe~ 420 (518)
..|..||..+.. .--.+|.+||.. .++.---.+.+...-...--....+..|-+ .....+|++++.
T Consensus 7 ~~C~~CGr~~~~--------~~~~lC~dC~~~-~~~~~~ip~~~~v~~C~~Cga~~~~~~W~~~~~~~~~l~~~~~ 73 (355)
T COG1499 7 ILCVRCGRSVDP--------LIDGLCGDCYVE-TTPLIEIPDEVNVEVCRHCGAYRIRGRWVDEEGANRLLEALED 73 (355)
T ss_pred cEeccCCCcCch--------hhccccHHHHhc-cCccccCCCceEEEECCcCCCccCCCcceeccccchHHHHHHH
Confidence 469899987631 124599999987 333222222222211111101224578988 547777777764
No 123
>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].
Probab=20.71 E-value=41 Score=25.67 Aligned_cols=11 Identities=55% Similarity=1.054 Sum_probs=9.1
Q ss_pred hHHHhhhcCcc
Q 010085 12 RKWKRRKREPR 22 (518)
Q Consensus 12 ~~~~~~~~~~~ 22 (518)
|||..|||..+
T Consensus 31 RKw~aRkr~l~ 41 (43)
T PF08114_consen 31 RKWQARKRALQ 41 (43)
T ss_pred HHHHHHHHHHh
Confidence 79999999643
No 124
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=20.44 E-value=85 Score=38.46 Aligned_cols=49 Identities=14% Similarity=0.381 Sum_probs=34.2
Q ss_pred CcCCCCCCCCC-----cceeeecCCCCcccChhhhhc----CCCCCCCCCCCceeeCCC
Q 010085 346 NHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFHE----GRFVTGHSSLDYIRVDPA 395 (518)
Q Consensus 346 ~~C~~C~~~~~-----~v~y~c~k~~d~~LC~~CFs~----G~~p~~hss~DF~kvd~~ 395 (518)
..|..||.++. .+++.|.+| .|-+|..||.= |+-...+-...|.+.+..
T Consensus 18 qiCqICGD~vg~~~~Ge~FVAC~eC-~FPVCrpCYEYEr~eG~q~CPqCktrYkr~kgs 75 (1079)
T PLN02638 18 QVCQICGDNVGKTVDGEPFVACDVC-AFPVCRPCYEYERKDGNQSCPQCKTKYKRHKGS 75 (1079)
T ss_pred ceeeecccccCcCCCCCEEEEeccC-CCccccchhhhhhhcCCccCCccCCchhhhcCC
Confidence 47999998874 378899998 58899999963 332333445777766543
No 125
>cd08781 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit
Probab=20.20 E-value=78 Score=26.90 Aligned_cols=26 Identities=19% Similarity=0.313 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Q 010085 409 QETFLLLEGIEMYNDNWNEIAEHVST 434 (518)
Q Consensus 409 eEellLLEaIe~yGgNW~~IAehVGt 434 (518)
++.-.||+.-...|.||...|+++|-
T Consensus 7 ~~Lc~~LD~~~~~g~dWr~LA~~Lgl 32 (83)
T cd08781 7 QKLCSSLDPPNPRGNDWRLLAKKLSV 32 (83)
T ss_pred HHHHHHcCCCCCCCCCHHHHHHHhCc
Confidence 45556666666678899999999994
No 126
>PLN02436 cellulose synthase A
Probab=20.20 E-value=1.5e+02 Score=36.56 Aligned_cols=49 Identities=16% Similarity=0.413 Sum_probs=33.8
Q ss_pred CCcCCCCCCCCC-----cceeeecCCCCcccChhhhhcCCCC----CCCCCCCceeeCC
Q 010085 345 ENHCNYCSQPIP-----AVYYQSQKEVDVLLCPECFHEGRFV----TGHSSLDYIRVDP 394 (518)
Q Consensus 345 ~~~C~~C~~~~~-----~v~y~c~k~~d~~LC~~CFs~G~~p----~~hss~DF~kvd~ 394 (518)
...|..||.++. .+++.|.+| .|-+|..||.--+.- ..+-...|.+...
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C-~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~kg 93 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNEC-AFPVCRPCYEYERREGNQACPQCKTRYKRIKG 93 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccC-CCccccchhhhhhhcCCccCcccCCchhhccC
Confidence 347999998874 378899998 588999999644332 2233566776553
Done!