Query 010514
Match_columns 508
No_of_seqs 199 out of 730
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 01:25:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010514.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010514hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0457 Histone acetyltransfer 100.0 7E-102 1E-106 793.9 31.9 408 1-507 27-437 (438)
2 COG5114 Histone acetyltransfer 100.0 4E-95 9E-100 714.3 30.3 407 1-507 18-429 (432)
3 COG5259 RSC8 RSC chromatin rem 99.5 8.1E-15 1.8E-19 152.7 6.9 84 11-97 246-329 (531)
4 PF04433 SWIRM: SWIRM domain; 99.4 1.8E-13 3.9E-18 115.1 6.5 78 430-507 3-85 (86)
5 KOG1279 Chromatin remodeling f 99.4 6.6E-13 1.4E-17 142.9 7.4 89 3-97 205-303 (506)
6 PF00249 Myb_DNA-binding: Myb- 99.2 4.2E-11 9.1E-16 89.8 5.5 45 47-91 2-47 (48)
7 cd02335 ZZ_ADA2 Zinc finger, Z 99.1 4.7E-11 1E-15 90.2 3.6 36 2-37 14-49 (49)
8 cd02334 ZZ_dystrophin Zinc fin 98.9 1.7E-09 3.8E-14 81.6 3.5 34 2-35 14-47 (49)
9 cd02343 ZZ_EF Zinc finger, ZZ 98.8 2.2E-09 4.7E-14 80.4 3.1 34 2-35 13-46 (48)
10 cd02338 ZZ_PCMF_like Zinc fing 98.8 3.1E-09 6.6E-14 80.3 3.8 36 2-37 14-49 (49)
11 smart00717 SANT SANT SWI3, AD 98.8 1.4E-08 3.1E-13 74.3 6.4 46 47-92 2-47 (49)
12 cd02345 ZZ_dah Zinc finger, ZZ 98.8 4.8E-09 1E-13 79.3 3.5 36 2-37 14-49 (49)
13 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 2E-08 4.3E-13 72.5 6.1 44 48-91 1-44 (45)
14 PF13921 Myb_DNA-bind_6: Myb-l 98.7 4.2E-08 9.1E-13 76.6 6.6 41 49-90 1-41 (60)
15 TIGR01557 myb_SHAQKYF myb-like 98.6 8.3E-08 1.8E-12 74.8 6.2 49 46-94 3-56 (57)
16 PLN03212 Transcription repress 98.4 4.9E-07 1.1E-11 89.2 5.7 50 43-92 22-72 (249)
17 cd02249 ZZ Zinc finger, ZZ typ 98.3 4.6E-07 9.9E-12 67.5 3.3 34 2-37 13-46 (46)
18 PLN03091 hypothetical protein; 98.1 2.8E-06 6.1E-11 89.7 5.7 50 43-92 11-61 (459)
19 KOG0048 Transcription factor, 98.1 3.7E-06 7.9E-11 83.7 4.6 47 46-92 9-56 (238)
20 cd02340 ZZ_NBR1_like Zinc fing 98.1 3.1E-06 6.8E-11 62.2 2.9 30 2-36 13-42 (43)
21 cd02339 ZZ_Mind_bomb Zinc fing 98.0 3.5E-06 7.7E-11 62.6 3.0 30 2-35 14-43 (45)
22 cd02341 ZZ_ZZZ3 Zinc finger, Z 98.0 4.2E-06 9.1E-11 63.0 3.4 32 2-36 14-47 (48)
23 cd02344 ZZ_HERC2 Zinc finger, 97.9 7.3E-06 1.6E-10 60.8 3.0 32 2-37 14-45 (45)
24 smart00291 ZnF_ZZ Zinc-binding 97.9 7.4E-06 1.6E-10 60.5 2.9 28 2-29 17-44 (44)
25 cd02336 ZZ_RSC8 Zinc finger, Z 97.9 1.1E-05 2.4E-10 59.9 3.3 32 1-32 12-43 (45)
26 PF00569 ZZ: Zinc finger, ZZ t 97.8 9.7E-06 2.1E-10 60.4 1.5 28 2-29 18-45 (46)
27 PLN03212 Transcription repress 97.8 3.9E-05 8.4E-10 76.0 5.8 48 43-91 75-122 (249)
28 PLN03091 hypothetical protein; 97.5 0.00021 4.6E-09 75.8 6.6 50 41-91 62-111 (459)
29 cd02337 ZZ_CBP Zinc finger, ZZ 97.4 6.4E-05 1.4E-09 54.8 1.7 22 2-23 12-33 (41)
30 KOG0048 Transcription factor, 97.0 0.0012 2.6E-08 65.9 6.1 49 41-90 57-105 (238)
31 KOG0049 Transcription factor, 96.8 0.0017 3.6E-08 71.5 5.6 53 42-94 356-408 (939)
32 KOG1280 Uncharacterized conser 96.5 0.0015 3.3E-08 67.3 2.6 35 3-37 23-57 (381)
33 cd02342 ZZ_UBA_plant Zinc fing 96.4 0.0021 4.5E-08 47.1 2.0 22 2-23 14-35 (43)
34 KOG0049 Transcription factor, 96.2 0.0036 7.8E-08 69.0 3.4 51 41-91 407-460 (939)
35 KOG4286 Dystrophin-like protei 95.8 0.0039 8.4E-08 69.7 1.7 36 2-37 617-652 (966)
36 KOG0051 RNA polymerase I termi 95.2 0.018 3.9E-07 63.9 3.9 89 3-95 340-431 (607)
37 KOG4582 Uncharacterized conser 94.8 0.022 4.7E-07 58.3 3.3 32 2-37 166-197 (278)
38 PF13837 Myb_DNA-bind_4: Myb/S 94.5 0.03 6.4E-07 46.6 2.9 46 47-92 2-64 (90)
39 KOG0051 RNA polymerase I termi 92.8 0.11 2.5E-06 57.7 4.4 53 44-96 434-511 (607)
40 KOG4301 Beta-dystrobrevin [Cyt 90.5 0.054 1.2E-06 56.1 -1.2 34 2-35 254-287 (434)
41 KOG0050 mRNA splicing protein 90.2 0.27 5.9E-06 53.5 3.8 49 45-94 6-54 (617)
42 PF09111 SLIDE: SLIDE; InterP 88.8 0.71 1.5E-05 41.4 4.8 44 46-89 49-107 (118)
43 KOG0050 mRNA splicing protein 88.0 0.34 7.5E-06 52.7 2.6 47 43-91 56-102 (617)
44 COG5147 REB1 Myb superfamily p 87.4 0.37 8.1E-06 53.1 2.5 45 46-90 20-64 (512)
45 COG5118 BDP1 Transcription ini 84.0 1.9 4.2E-05 45.4 5.6 44 46-90 365-408 (507)
46 KOG4282 Transcription factor G 83.7 1.7 3.7E-05 45.5 5.3 47 47-93 55-114 (345)
47 KOG4167 Predicted DNA-binding 82.7 1.9 4E-05 49.1 5.1 44 46-90 619-662 (907)
48 COG5347 GTPase-activating prot 81.5 0.81 1.8E-05 47.8 1.8 46 5-59 22-78 (319)
49 KOG4329 DNA-binding protein [G 78.3 3.1 6.8E-05 43.8 4.8 43 47-90 278-321 (445)
50 COG5147 REB1 Myb superfamily p 78.1 2.5 5.3E-05 46.8 4.2 49 44-93 70-118 (512)
51 PF13873 Myb_DNA-bind_5: Myb/S 77.9 3.5 7.6E-05 33.4 4.2 45 47-91 3-68 (78)
52 PF08914 Myb_DNA-bind_2: Rap1 77.0 4.6 0.0001 32.4 4.4 47 47-93 3-58 (65)
53 PHA00442 host recBCD nuclease 76.9 2.6 5.7E-05 32.5 2.8 28 50-77 24-51 (59)
54 TIGR02894 DNA_bind_RsfA transc 76.6 2 4.4E-05 40.4 2.6 44 47-91 5-54 (161)
55 KOG0384 Chromodomain-helicase 75.4 1.9 4.1E-05 51.8 2.5 29 45-73 1132-1160(1373)
56 KOG4468 Polycomb-group transcr 75.4 3.3 7.1E-05 46.2 4.2 45 46-91 88-142 (782)
57 PF02207 zf-UBR: Putative zinc 72.6 2.3 5E-05 34.4 1.7 34 2-40 12-48 (71)
58 smart00420 HTH_DEOR helix_turn 72.1 8.1 0.00018 27.9 4.5 39 469-507 7-45 (53)
59 PF13412 HTH_24: Winged helix- 71.6 9.7 0.00021 27.8 4.8 44 464-507 5-48 (48)
60 PLN03000 amine oxidase 70.6 7.2 0.00016 46.1 5.8 72 435-507 90-167 (881)
61 PLN03142 Probable chromatin-re 70.3 6.5 0.00014 47.3 5.4 48 47-95 825-872 (1033)
62 PLN03142 Probable chromatin-re 67.7 8.5 0.00019 46.3 5.7 44 46-89 926-981 (1033)
63 KOG0706 Predicted GTPase-activ 65.9 3.3 7.2E-05 44.7 1.7 70 5-90 25-107 (454)
64 smart00105 ArfGap Putative GTP 65.0 8.1 0.00018 34.0 3.7 45 5-59 5-60 (112)
65 PF09012 FeoC: FeoC like trans 63.4 7.4 0.00016 31.0 2.9 40 468-507 5-45 (69)
66 PF12802 MarR_2: MarR family; 63.3 14 0.00031 28.0 4.4 50 453-507 1-52 (62)
67 PF13404 HTH_AsnC-type: AsnC-t 62.6 23 0.0005 25.8 5.1 37 53-90 4-40 (42)
68 KOG0703 Predicted GTPase-activ 62.1 4.5 9.8E-05 41.5 1.8 71 5-90 27-115 (287)
69 PF08074 CHDCT2: CHDCT2 (NUC03 62.0 4.6 0.0001 38.1 1.6 30 47-76 4-33 (173)
70 PF01412 ArfGap: Putative GTPa 60.9 2.2 4.8E-05 37.8 -0.6 44 5-57 15-69 (116)
71 KOG3554 Histone deacetylase co 60.6 9.2 0.0002 41.6 3.8 43 47-90 286-329 (693)
72 PF00643 zf-B_box: B-box zinc 59.6 8.3 0.00018 27.4 2.3 27 2-35 14-40 (42)
73 PF09397 Ftsk_gamma: Ftsk gamm 59.6 16 0.00034 29.4 4.1 45 460-508 8-52 (65)
74 TIGR02337 HpaR homoprotocatech 58.2 33 0.00071 29.9 6.4 61 442-507 13-73 (118)
75 KOG0818 GTPase-activating prot 55.3 7.1 0.00015 42.8 1.9 56 5-71 10-78 (669)
76 TIGR01889 Staph_reg_Sar staphy 54.9 33 0.00071 29.7 5.7 64 443-507 11-74 (109)
77 PF04504 DUF573: Protein of un 54.4 18 0.0004 31.2 4.0 33 45-77 3-42 (98)
78 PRK03573 transcriptional regul 54.1 36 0.00079 30.6 6.2 56 448-507 22-77 (144)
79 PF06461 DUF1086: Domain of Un 53.5 28 0.0006 32.4 5.1 54 48-102 40-95 (145)
80 PLN03114 ADP-ribosylation fact 51.7 14 0.00031 39.1 3.4 25 5-29 24-59 (395)
81 PF12776 Myb_DNA-bind_3: Myb/S 51.5 36 0.00079 28.2 5.4 43 48-90 1-60 (96)
82 PF01047 MarR: MarR family; I 51.3 16 0.00035 27.5 2.9 35 473-507 14-48 (59)
83 smart00595 MADF subfamily of S 50.8 16 0.00035 30.1 3.0 23 68-91 29-51 (89)
84 smart00843 Ftsk_gamma This dom 50.1 40 0.00086 27.0 4.9 35 474-508 17-51 (63)
85 COG3935 DnaD Putative primosom 49.2 19 0.00042 36.3 3.8 58 311-368 134-210 (246)
86 PLN02328 lysine-specific histo 49.1 26 0.00057 41.2 5.4 69 439-507 144-218 (808)
87 PF13730 HTH_36: Helix-turn-he 47.8 43 0.00094 24.9 4.7 53 454-506 2-55 (55)
88 PRK13923 putative spore coat p 47.5 18 0.00038 34.6 3.0 44 46-90 5-54 (170)
89 KOG1194 Predicted DNA-binding 46.9 29 0.00063 37.8 4.8 47 43-90 184-230 (534)
90 PF03979 Sigma70_r1_1: Sigma-7 45.7 32 0.00069 28.5 4.0 41 465-505 10-53 (82)
91 PF10925 DUF2680: Protein of u 45.2 58 0.0013 25.7 5.1 45 459-507 15-59 (59)
92 PLN03119 putative ADP-ribosyla 44.4 22 0.00048 39.9 3.6 42 5-59 25-77 (648)
93 PF04703 FaeA: FaeA-like prote 44.1 26 0.00056 27.9 3.0 45 463-507 1-46 (62)
94 PF15614 WHIM3: WSTF, HB1, Itc 43.2 47 0.001 25.0 4.1 28 318-345 4-36 (46)
95 PF02954 HTH_8: Bacterial regu 43.0 36 0.00077 24.5 3.4 26 52-78 5-30 (42)
96 KOG1194 Predicted DNA-binding 41.9 14 0.00029 40.3 1.5 43 46-90 470-512 (534)
97 PRK11512 DNA-binding transcrip 41.8 52 0.0011 29.7 5.2 52 451-507 34-85 (144)
98 PLN03131 hypothetical protein; 39.9 33 0.00071 38.9 4.1 42 5-59 25-77 (705)
99 smart00396 ZnF_UBR1 Putative z 38.8 26 0.00057 28.4 2.4 34 2-40 12-48 (71)
100 cd00090 HTH_ARSR Arsenical Res 38.7 59 0.0013 24.6 4.4 34 473-507 18-51 (78)
101 PF13463 HTH_27: Winged helix 38.1 54 0.0012 25.2 4.1 34 473-506 15-48 (68)
102 COG4008 Predicted metal-bindin 37.0 81 0.0018 28.7 5.4 27 451-477 87-113 (153)
103 PF07261 DnaB_2: Replication i 35.3 9.1 0.0002 30.6 -0.8 23 341-363 54-76 (77)
104 TIGR03277 methan_mark_9 putati 33.7 44 0.00095 29.5 3.1 24 451-474 86-109 (109)
105 PF08513 LisH: LisH; InterPro 33.5 28 0.0006 22.9 1.4 12 495-506 6-17 (27)
106 smart00345 HTH_GNTR helix_turn 31.9 60 0.0013 23.8 3.3 46 462-507 4-51 (60)
107 PF01388 ARID: ARID/BRIGHT DNA 30.8 1E+02 0.0022 25.5 4.9 38 55-92 39-88 (92)
108 smart00550 Zalpha Z-DNA-bindin 30.0 1.2E+02 0.0026 24.1 4.9 44 464-507 8-53 (68)
109 PF01978 TrmB: Sugar-specific 29.7 43 0.00094 26.2 2.3 36 472-507 18-53 (68)
110 PF10123 Mu-like_Pro: Mu-like 29.0 37 0.0008 35.5 2.2 25 438-462 302-326 (326)
111 KOG0704 ADP-ribosylation facto 28.4 23 0.00049 37.4 0.6 26 5-30 21-57 (386)
112 PF08784 RPA_C: Replication pr 28.3 44 0.00095 28.5 2.2 31 476-506 65-95 (102)
113 PF13325 MCRS_N: N-terminal re 28.2 95 0.0021 30.5 4.7 46 48-95 1-49 (199)
114 PRK11179 DNA-binding transcrip 28.1 1.2E+02 0.0026 27.8 5.3 43 52-95 9-51 (153)
115 PRK10870 transcriptional repre 28.0 1.3E+02 0.0027 28.5 5.5 58 447-507 45-102 (176)
116 smart00347 HTH_MARR helix_turn 27.8 1.1E+02 0.0025 24.7 4.6 52 451-507 4-55 (101)
117 smart00346 HTH_ICLR helix_turn 27.3 1.1E+02 0.0023 24.9 4.3 40 468-507 10-51 (91)
118 PF13076 DUF3940: Protein of u 27.2 62 0.0013 23.3 2.4 34 464-498 3-36 (38)
119 TIGR01446 DnaD_dom DnaD and ph 26.8 46 0.00099 26.5 2.0 18 342-359 55-72 (73)
120 PF10545 MADF_DNA_bdg: Alcohol 26.6 63 0.0014 25.7 2.8 24 68-91 28-52 (85)
121 smart00418 HTH_ARSR helix_turn 24.7 1.2E+02 0.0027 22.0 4.0 34 474-507 8-41 (66)
122 COG1725 Predicted transcriptio 23.7 1.8E+02 0.0038 26.5 5.3 49 459-507 12-66 (125)
123 PRK13777 transcriptional regul 23.6 1.7E+02 0.0036 28.2 5.5 52 451-507 39-90 (185)
124 smart00290 ZnF_UBP Ubiquitin C 22.6 13 0.00028 27.5 -1.9 19 5-23 1-22 (50)
125 PF14569 zf-UDP: Zinc-binding 22.5 38 0.00082 28.3 0.7 19 2-21 27-45 (80)
126 PF05584 Sulfolobus_pRN: Sulfo 22.3 1.9E+02 0.0042 23.8 4.7 46 461-507 4-49 (72)
127 TIGR02531 yecD_yerC TrpR-relat 22.1 2.4E+02 0.0052 23.9 5.5 50 310-360 7-59 (88)
128 smart00344 HTH_ASNC helix_turn 21.8 2.1E+02 0.0045 24.1 5.3 40 51-91 2-41 (108)
129 PF12488 DUF3704: Protein of u 20.8 35 0.00075 22.8 0.1 9 226-234 7-15 (27)
130 cd04766 HTH_HspR Helix-Turn-He 20.7 4.9E+02 0.011 21.5 7.4 60 287-346 22-86 (91)
131 KOG3820 Aromatic amino acid hy 20.1 2.1E+02 0.0045 31.1 5.7 77 278-365 160-243 (461)
132 COG5340 Predicted transcriptio 20.1 1.1E+02 0.0025 30.6 3.5 50 458-507 11-61 (269)
133 cd00092 HTH_CRP helix_turn_hel 20.0 1.2E+02 0.0025 23.1 3.0 34 474-507 23-56 (67)
No 1
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=6.9e-102 Score=793.93 Aligned_cols=408 Identities=50% Similarity=0.810 Sum_probs=353.6
Q ss_pred CcEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCC
Q 010514 1 MVRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKS 80 (508)
Q Consensus 1 ~~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt 80 (508)
+|||+|++|+|||||++||+.|+|++.|+++|+|+||++++||+..++|||+||++||+|+++||||||++||+|||+||
T Consensus 27 ~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKt 106 (438)
T KOG0457|consen 27 LIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKT 106 (438)
T ss_pred ceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhcCCCCCCCCCccccccCCHHHHHHHHHHhHhhhhcchhHHhhhhccCCCCcccCCCCCccccccccCC
Q 010514 81 KSQCIDHYNAIYMNSPCFPLPDLSHVMGKNREELLAMAKEHQQVKKELPTVAELALKEDAPFSTRMKPETRKEDTTRQSS 160 (508)
Q Consensus 81 ~~ec~~hy~~~yi~~~~~plp~~~~~~~~~~~e~l~~~k~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~d~~~~~~~~~~ 160 (508)
.+||++||.++|++++++|+|++++.+|+.+.+++++++.+ ..||++
T Consensus 107 keeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~-----------------~~~~~~---------------- 153 (438)
T KOG0457|consen 107 KEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNR-----------------AEPFQP---------------- 153 (438)
T ss_pred hHHHHHHHHHHHhcCccccccccccccCcchHHHhhhcccc-----------------cccCCC----------------
Confidence 99999999999999999999999999999999988776521 012210
Q ss_pred CCCccccccCCCCCCCCccchhccccccccccchhhhhhcCCCCcccccccccCCCCCCCCCccccccccCCCcCCCccc
Q 010514 161 SGLTTVEVNSIDPSNGNAFSFKKASNMTQVKESVKVEVLAEPQSDRSIGEKKLRTSGDERPSMKELSGYNFKRQEFEIEY 240 (508)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~e~~GYmP~R~DFE~Ey 240 (508)
++ -.|+.++.++|..++++||||+|.|||.||
T Consensus 154 ----------------------------------------~~--------~~pr~p~~~~p~~~e~~gyMp~R~dFd~Ey 185 (438)
T KOG0457|consen 154 ----------------------------------------TD--------LVPRKPGVSNPLRREISGYMPGRLDFDEEY 185 (438)
T ss_pred ----------------------------------------CC--------CCCCCCCCCCchHHHHhhhCccchhhhhhh
Confidence 00 013444446889999999999999999999
Q ss_pred CCchhhhhcccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhcccCCC---CCcCcCCChHHHHHHHhhhhhhc
Q 010514 241 DNDAEHLLADMEFNKNDTDAERELKLRVLRIYGKRLDERKRRKDFILERNLLFP---DPFERNLSPEEREIYQQYKVFMR 317 (508)
Q Consensus 241 DNdAE~lladmeF~~~D~~~e~elKl~~l~~Yn~rL~eR~rRK~~i~e~~Ll~~---~~~~k~~tkeerel~~~l~~far 317 (508)
||+||++|+||+|.++|+|.+.+||+++|+||++||++|.|||++|++|||+++ |++++++|+|+|+|++++|+|||
T Consensus 186 dn~AE~li~dm~f~e~D~~~d~elKla~ldiY~srl~eR~RRK~~I~d~nLl~~rk~q~~e~~~skEer~l~~s~k~fAR 265 (438)
T KOG0457|consen 186 DNEAEQLIRDMEFEEDDTEEDHELKLAVLDIYNSRLKERKRRKRFIRDRNLLDYRKNQAMEKRLSKEERELYNSIKVFAR 265 (438)
T ss_pred cchhhhhHhhcccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccchhhhhHHHhhccHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999996 77899999999999999999999
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHhhhhccccCCCCCCccccccCCCcc
Q 010514 318 FHSKEDHEELLKSVIEEHRIVKRIQELQEAQAAGCRTSSEAHRFLEQKRKKEAEENGQRVKESGQAGPSGKVLQRPNSLK 397 (508)
Q Consensus 318 f~~~~d~~~l~~~l~~e~~Lr~rI~~Lq~~R~~Gi~tl~e~~~Ye~~k~~Re~e~~~~~~~~~~~~~~~~~~~~~~n~~~ 397 (508)
|+|+.||++|+.++..|.+|+.||.+||+||.+|+||++++.+|+++|.++. +.+....... +......++..
T Consensus 266 ~~t~~d~~kfl~~~~eE~~L~~ri~~lqE~R~ag~tt~~e~~ky~~~k~~~~-~~s~~~~~~~------~~~~~i~~~~~ 338 (438)
T KOG0457|consen 266 FLTKSDHDKFLGSVAEEKELRKRISDLQEYRSAGLTTNAEPNKYERLKFKEF-RESTALLLSS------GALRYIKNSNQ 338 (438)
T ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcceeccccchhHHHHHHHH-HHHhhhcccc------chhhhhhcccc
Confidence 9999999999999999999999999999999999999999999999984433 3222111111 11111111110
Q ss_pred ccccCCCCccCCCCccCCCCCCCcccccCCCCccccCCCcCCCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCC
Q 010514 398 EVEVSPRGVVRGSTSLQPFGNDSYSTIASSLEDWDISGFVGADLLSETEKRLCGEIKILPAHYLKMLEILSVEIYKGNVS 477 (508)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ldi~~~pg~~lLs~~Ek~LCs~lrL~P~~YL~iK~~LirE~~k~g~l 477 (508)
. ..++. .....+...+.++++++++.++|+.++||++|+.||+.++|+|++||.+|++|++|..|+|.+
T Consensus 339 ~--------~~~~~---~~~~v~~~~~~~~~~~~~~~~~~~~q~Lse~E~~lc~~~~~~p~~yLe~~~vl~~e~~k~~~~ 407 (438)
T KOG0457|consen 339 E--------ASGSA---SKRPVQQQSIYKSATPLDISGAPDTQLLSEDEKRLCQELKILPKLYLELKEVLSREIKKGGTL 407 (438)
T ss_pred c--------ccccc---ccCcccccccccCCCHHHHhcchhhhhhhhhHHHHHHHHHhccHHHHHHHHHHHHHHhccCcc
Confidence 0 00000 011112223677889999999999999999999999999999999999999999999998899
Q ss_pred CHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 478 KKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 478 ~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
++.+|..++|||++|+++|||||++.||+.
T Consensus 408 kks~a~~l~Kid~~Kvd~vyd~~~~~~~~~ 437 (438)
T KOG0457|consen 408 KKSDAYRLFKIDPRKVDRVYDFLIAQGWIG 437 (438)
T ss_pred cchhHHHHhcCCcchHHHHHHHHHHhhhcc
Confidence 999999999999999999999999999986
No 2
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=100.00 E-value=4e-95 Score=714.28 Aligned_cols=407 Identities=30% Similarity=0.503 Sum_probs=349.5
Q ss_pred CcEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCC
Q 010514 1 MVRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKS 80 (508)
Q Consensus 1 ~~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt 80 (508)
.++|+|++|++||||+.||++|.+.+.|..+|+|+||+.+++||+..+|+++||++|+++++.+|+|||++||+|||+|+
T Consensus 18 ~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~ 97 (432)
T COG5114 18 LTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRA 97 (432)
T ss_pred ceeeeeecccccceehhhhhccccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhh
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhcCCCCCCCCCccccccCCHHHHHHHHHHhHhhhhcchhHHhhhhccCCCCcccCCCCCccccccccCC
Q 010514 81 KSQCIDHYNAIYMNSPCFPLPDLSHVMGKNREELLAMAKEHQQVKKELPTVAELALKEDAPFSTRMKPETRKEDTTRQSS 160 (508)
Q Consensus 81 ~~ec~~hy~~~yi~~~~~plp~~~~~~~~~~~e~l~~~k~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~d~~~~~~~~~~ 160 (508)
.+||++||.++|+.|.++|||++...+-..+.+|++..+.+.+...
T Consensus 98 kee~k~HylK~y~es~~ypl~~i~~~~~v~q~~f~~qrr~rie~f~---------------------------------- 143 (432)
T COG5114 98 KEEIKSHYLKMYDESKYYPLPDITQNIHVPQDEFLEQRRHRIETFE---------------------------------- 143 (432)
T ss_pred hHHHHHHHHHHHhhcccccccccccCCCCchHHHHHHHHhhhhhcc----------------------------------
Confidence 9999999999999999999999999999999999876554322110
Q ss_pred CCCccccccCCCCCCCCccchhccccccccccchhhhhhcCCCCcccccccccCCCCCCCCCccccccccCCCcCCCccc
Q 010514 161 SGLTTVEVNSIDPSNGNAFSFKKASNMTQVKESVKVEVLAEPQSDRSIGEKKLRTSGDERPSMKELSGYNFKRQEFEIEY 240 (508)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~e~~GYmP~R~DFE~Ey 240 (508)
.|+ +.++||.. ++|.+++++||||+|.|||+||
T Consensus 144 ----------------------------------------~pp----i~prkP~a---S~P~cheiqgyMPgRleFd~Ey 176 (432)
T COG5114 144 ----------------------------------------LPP----INPRKPKA---SNPYCHEIQGYMPGRLEFDVEY 176 (432)
T ss_pred ----------------------------------------CCC----CCCCCCCC---CCCchhhhhccCCCccccchhh
Confidence 111 12234554 4799999999999999999999
Q ss_pred CCchhhhhcccccCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhcccCCC---CCcCcCCChHHHHHHHhhhhhhc
Q 010514 241 DNDAEHLLADMEFNKNDTDAERELKLRVLRIYGKRLDERKRRKDFILERNLLFP---DPFERNLSPEEREIYQQYKVFMR 317 (508)
Q Consensus 241 DNdAE~lladmeF~~~D~~~e~elKl~~l~~Yn~rL~eR~rRK~~i~e~~Ll~~---~~~~k~~tkeerel~~~l~~far 317 (508)
.|+||.+|+||.|++++.+.+++||+++|+|||+||..|.+||+.|++++|+|. |+.+|++||||+.|++++|||||
T Consensus 177 mnEaE~pikDm~fd~d~~el~~~lk~a~LdiYnsrlt~Ra~rK~~if~~nLmDyr~Lqa~dkk~skEe~~l~N~iK~fAr 256 (432)
T COG5114 177 MNEAEVPIKDMSFDGDKEELKKKLKNATLDIYNSRLTFRARRKHAIFGKNLMDYRNLQAKDKKRSKEECGLVNSIKWFAR 256 (432)
T ss_pred hhcccccccccccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhhhccHHHHhHHHhhhHHHH
Confidence 999999999999999999999999999999999999999999999999999994 67899999999999999999999
Q ss_pred cCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHhhhhccccCCCCCCccccccCCCcc
Q 010514 318 FHSKEDHEELLKSVIEEHRIVKRIQELQEAQAAGCRTSSEAHRFLEQKRKKEAEENGQRVKESGQAGPSGKVLQRPNSLK 397 (508)
Q Consensus 318 f~~~~d~~~l~~~l~~e~~Lr~rI~~Lq~~R~~Gi~tl~e~~~Ye~~k~~Re~e~~~~~~~~~~~~~~~~~~~~~~n~~~ 397 (508)
++|+.||+.|+++++.+.-+++||++||+||.||+|||+.|-+|+++|-.+ .....+. ....+....+.|..
T Consensus 257 ~lT~~Df~~F~~~~~e~v~~~kri~~LqewR~~glttle~g~kyeRDk~ek---f~~s~aa----s~~e~~~r~~~n~~- 328 (432)
T COG5114 257 YLTKSDFNVFFRDILEGVYIEKRIHELQEWRNNGLTTLEAGLKYERDKFEK---FGASTAA----SLSEGNSRYRSNSA- 328 (432)
T ss_pred hhcchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCchhhhhhhhhhhhHHHh---hccchhh----hhcccchhhhcccc-
Confidence 999999999999999999999999999999999999999999999988321 1100000 00111111111111
Q ss_pred ccccCCCCccCCCCccCCCCCCC-cccccCCCCccccCCCcCCCCCCHHHHHHHHHhCCCchHHHHHHHHHHHHHHh-CC
Q 010514 398 EVEVSPRGVVRGSTSLQPFGNDS-YSTIASSLEDWDISGFVGADLLSETEKRLCGEIKILPAHYLKMLEILSVEIYK-GN 475 (508)
Q Consensus 398 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ldi~~~pg~~lLs~~Ek~LCs~lrL~P~~YL~iK~~LirE~~k-~g 475 (508)
+.+++. -+..++ ....++.+.+.+|...|++.|||++|++||++|+|.|++||.+|.++|+++++ +|
T Consensus 329 --~~sna~---------~s~~d~~ni~p~K~~t~s~~q~a~d~~llS~dEq~LC~~l~i~PkpyL~LK~~~is~~l~t~g 397 (432)
T COG5114 329 --HRSNAE---------YSQMDVKNILPSKNMTISDIQHAPDYALLSDDEQRLCETLNISPKPYLELKKEVISCFLRTRG 397 (432)
T ss_pred --cccCcc---------hhHHHHHhccCCCCCChhhhhccchhhhhcchHHHHHHHhCCCCccHHHHHHHHHHHHHHhCC
Confidence 000000 000111 01256778889999999999999999999999999999999999999999999 78
Q ss_pred CCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 476 VSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 476 ~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.++++++..||+||.+|+.+|||||.+.|||.
T Consensus 398 ~f~K~d~~~Lf~id~~ka~~~YdfF~~~~Wi~ 429 (432)
T COG5114 398 EFTKEDFNRLFGIDLGKADGLYDFFLERGWIH 429 (432)
T ss_pred CccHHHHHHHhCcCcchhhHHHHHHHhccccC
Confidence 99999999999999999999999999999996
No 3
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=99.53 E-value=8.1e-15 Score=152.65 Aligned_cols=84 Identities=35% Similarity=0.691 Sum_probs=72.5
Q ss_pred CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 11 DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 11 ~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
+|++|..||-.|.++....++. |.-++...+. ....|+++|+++|||||++|| ++|..||.|||+||++||+.||.+
T Consensus 246 ~~n~C~~C~~qg~f~s~~~ssD-f~~v~~~~~~-~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 246 KYNSCSECYDQGRFPSEFTSSD-FKPVTISLLI-RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred hcccchHHHhcCcCCCcccccc-chhhhhhccc-ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCCCCHHHHHHHHHc
Confidence 4678999999999988887776 5544443333 556899999999999999999 899999999999999999999999
Q ss_pred hhcCCCC
Q 010514 91 IYMNSPC 97 (508)
Q Consensus 91 ~yi~~~~ 97 (508)
+++.+++
T Consensus 323 LPieD~~ 329 (531)
T COG5259 323 LPIEDNY 329 (531)
T ss_pred CCcchhh
Confidence 9998864
No 4
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=99.43 E-value=1.8e-13 Score=115.06 Aligned_cols=78 Identities=37% Similarity=0.538 Sum_probs=67.7
Q ss_pred ccccCCCcCCCCCCHHHHHHHHHhCC--CchHHHHHHHHHHHHHH--hCCCCCHHHhhhhhc-cCcccHHHHHHHHHHCC
Q 010514 430 DWDISGFVGADLLSETEKRLCGEIKI--LPAHYLKMLEILSVEIY--KGNVSKKSDAHNLFK-VEPNKVDRVYDMLVRKG 504 (508)
Q Consensus 430 ~ldi~~~pg~~lLs~~Ek~LCs~lrL--~P~~YL~iK~~LirE~~--k~g~l~~~~a~~l~k-iD~~K~~rIydfl~~~G 504 (508)
++++++.++.+.||+.|+++|..+++ .|..||.+|+.||.+.. .++.+++++|+++++ +|++++.+||+||.+.|
T Consensus 3 ~~~~~~~~~~~~l~~~E~~~~~e~~~~~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G 82 (86)
T PF04433_consen 3 IPAHSSWFDPDKLSEIEKQLCPEFFIGKTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWG 82 (86)
T ss_dssp CHCCHTTTTTTSS-HHHHHHCHHCTTSCHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTT
T ss_pred CccccCCCCcccCCHHHHHHhHHHhccCChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcC
Confidence 34566778899999999999999999 99999999999999944 367899999999999 99999999999999999
Q ss_pred CCC
Q 010514 505 IAQ 507 (508)
Q Consensus 505 wi~ 507 (508)
||.
T Consensus 83 ~IN 85 (86)
T PF04433_consen 83 LIN 85 (86)
T ss_dssp SSS
T ss_pred ccC
Confidence 995
No 5
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=99.37 E-value=6.6e-13 Score=142.93 Aligned_cols=89 Identities=36% Similarity=0.780 Sum_probs=78.3
Q ss_pred EEEeccCCC----------CcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHH
Q 010514 3 RIKCAMCSD----------FDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGNWGEV 72 (508)
Q Consensus 3 ri~C~~C~~----------~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~I 72 (508)
-++|..|.+ +.+|..||..|.....++.+.+ .++.. .....||.+|+++||+||++|| .+|..|
T Consensus 205 ~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df-~~~~~----~~~~~WT~qE~lLLLE~ie~y~-ddW~kV 278 (506)
T KOG1279|consen 205 AIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDF-KVIGE----SARPNWTEQETLLLLEAIEMYG-DDWNKV 278 (506)
T ss_pred ccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccc-hhccc----cCCCCccHHHHHHHHHHHHHhc-ccHHHH
Confidence 467888877 7899999999999999988775 44443 3468999999999999999999 899999
Q ss_pred HHHhCCCCHHHHHHHHHhhhcCCCC
Q 010514 73 SEHVGTKSKSQCIDHYNAIYMNSPC 97 (508)
Q Consensus 73 A~~v~~kt~~ec~~hy~~~yi~~~~ 97 (508)
|.|||+||.+||+.||.+.++.+++
T Consensus 279 a~hVg~ks~eqCI~kFL~LPieD~~ 303 (506)
T KOG1279|consen 279 ADHVGTKSQEQCILKFLRLPIEDPY 303 (506)
T ss_pred HhccCCCCHHHHHHHHHhcCccchh
Confidence 9999999999999999999998874
No 6
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.17 E-value=4.2e-11 Score=89.76 Aligned_cols=45 Identities=27% Similarity=0.694 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHHHhC-CCCHHHHHHHHHhh
Q 010514 47 PDWNADEEILLLEGIEMYGFGNWGEVSEHVG-TKSKSQCIDHYNAI 91 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~-~kt~~ec~~hy~~~ 91 (508)
..||.+|+.+|++||.+||.+||..||.+|+ +||+.||+.||.++
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 5799999999999999999877999999999 99999999999875
No 7
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=99.11 E-value=4.7e-11 Score=90.22 Aligned_cols=36 Identities=64% Similarity=1.286 Sum_probs=35.0
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
+||+|++|.|||||.+||+.|.+.+.|+++|+|+||
T Consensus 14 ~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~~~~~ 49 (49)
T cd02335 14 IRIKCAECPDFDLCLECFSAGAEIGKHRNDHNYRVV 49 (49)
T ss_pred cEEECCCCCCcchhHHhhhCcCCCCCCCCCCCeEeC
Confidence 799999999999999999999999999999999986
No 8
>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=98.86 E-value=1.7e-09 Score=81.56 Aligned_cols=34 Identities=35% Similarity=0.910 Sum_probs=33.0
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCee
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYR 35 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~ 35 (508)
+|++|++|.|||||..||..|.+.+.|+++|+|+
T Consensus 14 ~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~ 47 (49)
T cd02334 14 FRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMK 47 (49)
T ss_pred eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCee
Confidence 6999999999999999999999999999999987
No 9
>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=98.83 E-value=2.2e-09 Score=80.36 Aligned_cols=34 Identities=38% Similarity=0.801 Sum_probs=32.6
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCee
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYR 35 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~ 35 (508)
+|++|++|.|||||.+||+.|.+.+.|+.+|+.+
T Consensus 13 ~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~ 46 (48)
T cd02343 13 HRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMV 46 (48)
T ss_pred ceEECCCCCCchhHHHHHhCCccCCCCCCCCCcc
Confidence 7999999999999999999999999999999875
No 10
>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=98.82 E-value=3.1e-09 Score=80.34 Aligned_cols=36 Identities=36% Similarity=0.916 Sum_probs=34.3
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
+|++|+.|.|||||.+||+.|.+.+.|+++|+|+++
T Consensus 14 ~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~~ 49 (49)
T cd02338 14 RRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQCI 49 (49)
T ss_pred eeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEEC
Confidence 689999999999999999999999999999999874
No 11
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.79 E-value=1.4e-08 Score=74.30 Aligned_cols=46 Identities=26% Similarity=0.720 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhhh
Q 010514 47 PDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAIY 92 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~y 92 (508)
..||.+|+.+|+.++..||.++|..||.++++||+.+|+.+|..+.
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 5799999999999999999889999999999999999999998653
No 12
>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=98.78 E-value=4.8e-09 Score=79.27 Aligned_cols=36 Identities=31% Similarity=0.815 Sum_probs=33.6
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
+|++|++|.|||||++||+.|++.+.|+++|++..+
T Consensus 14 ~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~~ 49 (49)
T cd02345 14 IRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYEL 49 (49)
T ss_pred eeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcccC
Confidence 689999999999999999999999999999998743
No 13
>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=98.76 E-value=2e-08 Score=72.47 Aligned_cols=44 Identities=27% Similarity=0.756 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 48 DWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 48 ~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
.||.+|+..|+.++..||.++|..||..+++||..+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 49999999999999999988999999999999999999999764
No 14
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.69 E-value=4.2e-08 Score=76.55 Aligned_cols=41 Identities=34% Similarity=0.903 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 49 WNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 49 Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
||.+|+.+|++++..|| .+|..||++||+||+.+|+.||.+
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~ 41 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRN 41 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHH
Confidence 99999999999999999 799999999988999999999999
No 15
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.62 E-value=8.3e-08 Score=74.81 Aligned_cols=49 Identities=16% Similarity=0.312 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCH---HHHHHHhC-CC-CHHHHHHHHHhhhcC
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNW---GEVSEHVG-TK-SKSQCIDHYNAIYMN 94 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW---~~IA~~v~-~k-t~~ec~~hy~~~yi~ 94 (508)
+..||++|...+|+||+.+|.||| ..|+++|+ ++ |+.+|+.|+.++|+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 346999999999999999999899 99999987 46 999999999999863
No 16
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.37 E-value=4.9e-07 Score=89.22 Aligned_cols=50 Identities=18% Similarity=0.411 Sum_probs=45.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhC-CCCHHHHHHHHHhhh
Q 010514 43 PLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVG-TKSKSQCIDHYNAIY 92 (508)
Q Consensus 43 ~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~-~kt~~ec~~hy~~~y 92 (508)
.+.+..||++|+.+|+++|..||.+||..||.+++ +||+.||+++|.++.
T Consensus 22 glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 22 GMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 45577899999999999999999999999999997 799999999998875
No 17
>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=98.32 E-value=4.6e-07 Score=67.51 Aligned_cols=34 Identities=38% Similarity=0.991 Sum_probs=31.2
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
+|++|++|.|||||..||+.|. +.|..+|.|..|
T Consensus 13 ~r~~C~~C~d~dLC~~Cf~~~~--~~H~~~H~~~~~ 46 (46)
T cd02249 13 VRYHCLVCEDFDLCSSCYAKGK--KGHPPDHSFTEI 46 (46)
T ss_pred CEEECCCCCCCcCHHHHHCcCc--CCCCCCCCEeEC
Confidence 6899999999999999999998 899999998754
No 18
>PLN03091 hypothetical protein; Provisional
Probab=98.13 E-value=2.8e-06 Score=89.71 Aligned_cols=50 Identities=26% Similarity=0.511 Sum_probs=45.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhC-CCCHHHHHHHHHhhh
Q 010514 43 PLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVG-TKSKSQCIDHYNAIY 92 (508)
Q Consensus 43 ~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~-~kt~~ec~~hy~~~y 92 (508)
.+....||.+||.+|+++|.+||.+||..||.+++ +||+.+|++||.++.
T Consensus 11 klrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 11 KLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 34467899999999999999999999999999997 799999999998765
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.06 E-value=3.7e-06 Score=83.74 Aligned_cols=47 Identities=15% Similarity=0.361 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhC-CCCHHHHHHHHHhhh
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSEHVG-TKSKSQCIDHYNAIY 92 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~-~kt~~ec~~hy~~~y 92 (508)
.+.||++||.+|++.|.+||-|||..||++.| .|+.+.|+.+|.++-
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyL 56 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYL 56 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhccc
Confidence 57899999999999999999999999999999 899999999998864
No 20
>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=98.05 E-value=3.1e-06 Score=62.25 Aligned_cols=30 Identities=43% Similarity=0.933 Sum_probs=27.3
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeec
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRV 36 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~v 36 (508)
+|++|++|.|||||..||..| .| .+|+|.-
T Consensus 13 ~ry~C~~C~d~dLC~~C~~~~----~H-~~H~f~~ 42 (43)
T cd02340 13 VRYKCLVCPDYDLCESCEAKG----VH-PEHAMLK 42 (43)
T ss_pred CeEECCCCCCccchHHhhCcC----CC-CCCCEEe
Confidence 589999999999999999998 79 8898864
No 21
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=98.04 E-value=3.5e-06 Score=62.56 Aligned_cols=30 Identities=37% Similarity=0.955 Sum_probs=27.1
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCee
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYR 35 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~ 35 (508)
+|++|++|.|||||.+||+. +.|..+|+|.
T Consensus 14 ~RykC~~C~dyDLC~~C~~~----~~H~~~H~f~ 43 (45)
T cd02339 14 IRWKCAECPNYDLCTTCYHG----DKHDLEHRFY 43 (45)
T ss_pred CeEECCCCCCccchHHHhCC----CCCCCCCCEE
Confidence 69999999999999999996 5699999885
No 22
>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=98.03 E-value=4.2e-06 Score=63.01 Aligned_cols=32 Identities=38% Similarity=0.870 Sum_probs=29.3
Q ss_pred cEEEeccCC--CCcccHHHhhcCCCCCCCCCCCCeec
Q 010514 2 VRIKCAMCS--DFDLCVECFSVGAQIYPHESNHPYRV 36 (508)
Q Consensus 2 ~ri~C~~C~--~~~lC~~Cfs~G~e~~~H~~~H~y~v 36 (508)
+|++|.+|+ |||||..||..|. .|+.+|.+.-
T Consensus 14 ~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~ 47 (48)
T cd02341 14 TRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVK 47 (48)
T ss_pred ceEECCCCCCCCCccCHHHHhCcC---CCCCCCceee
Confidence 699999999 9999999999997 8999998754
No 23
>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=97.93 E-value=7.3e-06 Score=60.82 Aligned_cols=32 Identities=38% Similarity=0.969 Sum_probs=27.8
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
.|++|++|.|||||..||..+ .|...|.|.-|
T Consensus 14 ~RykC~~C~dyDLC~~Cf~~~----~H~~~H~F~ri 45 (45)
T cd02344 14 PRFKCRNCDDFDFCENCFKTR----KHNTRHTFGRI 45 (45)
T ss_pred CeEECCCCCCccchHHhhCCC----CcCCCCceeeC
Confidence 589999999999999999995 58888987643
No 24
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=97.92 E-value=7.4e-06 Score=60.47 Aligned_cols=28 Identities=46% Similarity=1.029 Sum_probs=25.6
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCC
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHE 29 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~ 29 (508)
+|++|..|+|||||.+||+.|.+.++|.
T Consensus 17 ~ry~C~~C~d~dlC~~Cf~~~~~~~~h~ 44 (44)
T smart00291 17 VRYHCLVCPDYDLCQSCFAKGSAGGEHE 44 (44)
T ss_pred CEEECCCCCCccchHHHHhCcCcCCCCC
Confidence 6899999999999999999999887773
No 25
>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=97.89 E-value=1.1e-05 Score=59.93 Aligned_cols=32 Identities=25% Similarity=0.467 Sum_probs=30.1
Q ss_pred CcEEEeccCCCCcccHHHhhcCCCCCCCCCCC
Q 010514 1 MVRIKCAMCSDFDLCVECFSVGAQIYPHESNH 32 (508)
Q Consensus 1 ~~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H 32 (508)
+||++|+.+.+++||..||..|..+.+|.+.+
T Consensus 12 ~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~D 43 (45)
T cd02336 12 RVRYHNLKAKKYDLCPSCYQEGRFPSNFQSSD 43 (45)
T ss_pred ceEEEecCCCccccChHHHhCcCCCCCCcccc
Confidence 58999999999999999999999999998876
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=97.78 E-value=9.7e-06 Score=60.43 Aligned_cols=28 Identities=46% Similarity=1.083 Sum_probs=22.1
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCC
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHE 29 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~ 29 (508)
+|++|..|+|||||..||..|.....|+
T Consensus 18 ~Ry~C~~C~d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 18 VRYHCLVCPDYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SEEEESSSSS-EEEHHHHHH--H-SSSS
T ss_pred CeEECCCCCCCchhhHHHhCcCCCCCcC
Confidence 6999999999999999999999877775
No 27
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.76 E-value=3.9e-05 Score=75.97 Aligned_cols=48 Identities=17% Similarity=0.321 Sum_probs=44.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 43 PLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 43 ~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
.+....||.+|+.+||+.+..|| ..|..||.+|.+||..+|+.||..+
T Consensus 75 ~I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~LpGRTDnqIKNRWns~ 122 (249)
T PLN03212 75 SVKRGGITSDEEDLILRLHRLLG-NRWSLIAGRIPGRTDNEIKNYWNTH 122 (249)
T ss_pred hcccCCCChHHHHHHHHHHHhcc-ccHHHHHhhcCCCCHHHHHHHHHHH
Confidence 46688999999999999999999 7999999999999999999999754
No 28
>PLN03091 hypothetical protein; Provisional
Probab=97.46 E-value=0.00021 Score=75.81 Aligned_cols=50 Identities=16% Similarity=0.345 Sum_probs=45.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 41 SFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 41 ~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
...+..+.||.+||.+||+.+..|| ..|..||.+|.+||..+|+.||..+
T Consensus 62 dP~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~LPGRTDnqIKNRWnsl 111 (459)
T PLN03091 62 RPDLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQLPGRTDNEIKNLWNSC 111 (459)
T ss_pred CCcccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhcCCCCHHHHHHHHHHH
Confidence 3457789999999999999999999 7999999999999999999999864
No 29
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=97.44 E-value=6.4e-05 Score=54.78 Aligned_cols=22 Identities=36% Similarity=1.180 Sum_probs=20.5
Q ss_pred cEEEeccCCCCcccHHHhhcCC
Q 010514 2 VRIKCAMCSDFDLCVECFSVGA 23 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~ 23 (508)
+|++|++|+|||||.+||++++
T Consensus 12 ~r~~C~~C~dfDLC~~C~~~~~ 33 (41)
T cd02337 12 TRWHCTVCEDYDLCITCYNTKN 33 (41)
T ss_pred CceECCCCcchhhHHHHhCCCC
Confidence 6899999999999999999965
No 30
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.01 E-value=0.0012 Score=65.87 Aligned_cols=49 Identities=16% Similarity=0.389 Sum_probs=44.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 41 SFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 41 ~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
.+.+.++.||.+||.+++++-..+| .-|..||.++++||..+++.||..
T Consensus 57 rP~ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LPGRTDNeIKN~Wnt 105 (238)
T KOG0048|consen 57 RPDLKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLPGRTDNEVKNHWNT 105 (238)
T ss_pred CCCccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCCCcCHHHHHHHHHH
Confidence 4456789999999999999999999 679999999999999999999954
No 31
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.81 E-value=0.0017 Score=71.48 Aligned_cols=53 Identities=26% Similarity=0.592 Sum_probs=48.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhhhcC
Q 010514 42 FPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAIYMN 94 (508)
Q Consensus 42 ~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~yi~ 94 (508)
..+..+.||.+|+.+|+.||+.||--+|-.|-+.|++||..||+++|.+..-.
T Consensus 356 Psikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 356 PSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred ccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 35678899999999999999999988999999999999999999999996543
No 32
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=96.50 E-value=0.0015 Score=67.26 Aligned_cols=35 Identities=43% Similarity=1.005 Sum_probs=33.3
Q ss_pred EEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 3 RIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 3 ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
|+||..|.|||||..||-+|+-+.-|.-+|+.+-|
T Consensus 23 rYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqci 57 (381)
T KOG1280|consen 23 RYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCI 57 (381)
T ss_pred eeEeeeecchhHHHHHhhcCCCCcccCCCCceeEE
Confidence 78999999999999999999999999999999865
No 33
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=96.38 E-value=0.0021 Score=47.09 Aligned_cols=22 Identities=41% Similarity=0.714 Sum_probs=19.9
Q ss_pred cEEEeccCCCCcccHHHhhcCC
Q 010514 2 VRIKCAMCSDFDLCVECFSVGA 23 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~ 23 (508)
.|++|..|.|||||-.||....
T Consensus 14 ~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 14 PRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred cceEeCCCCCCccHHHHhhhhc
Confidence 4899999999999999998754
No 34
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.18 E-value=0.0036 Score=68.98 Aligned_cols=51 Identities=22% Similarity=0.329 Sum_probs=45.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCH---HHHHHHHHhh
Q 010514 41 SFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSK---SQCIDHYNAI 91 (508)
Q Consensus 41 ~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~---~ec~~hy~~~ 91 (508)
.+....+.|+-.||..||++|++||.|+|..+|..+|.||. --|+.+++-.
T Consensus 407 ~~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~ 460 (939)
T KOG0049|consen 407 NRSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAA 460 (939)
T ss_pred HHhhccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHH
Confidence 45566789999999999999999999999999999999998 6788888763
No 35
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=95.83 E-value=0.0039 Score=69.74 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=33.0
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
+|+||..|-++|||..||.+|.-.++|+..|+..-.
T Consensus 617 ~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey 652 (966)
T KOG4286|consen 617 FRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEY 652 (966)
T ss_pred eeeeehhhcChhHHhhHhhhcccccCCCCCCCceee
Confidence 699999999999999999999999999999877644
No 36
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=95.15 E-value=0.018 Score=63.88 Aligned_cols=89 Identities=16% Similarity=0.225 Sum_probs=60.5
Q ss_pred EEEeccC-CCCcccHHHhhcCCCCCCCCCCCCeeccCC--CCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 010514 3 RIKCAMC-SDFDLCVECFSVGAQIYPHESNHPYRVMDN--LSFPLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTK 79 (508)
Q Consensus 3 ri~C~~C-~~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~--~~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~k 79 (508)
||.|..| ....-|..|...---. -...-.|+-+.. +-|...++.||++|+..|-..+.++| +.|..|++.|| |
T Consensus 340 ~i~s~~~~~~~~~l~n~~~~~Lp~--R~~~siy~~~rR~y~~FE~~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg-r 415 (607)
T KOG0051|consen 340 RIWSKDWKTIIRNLYNNLYKLLPY--RDRKSIYHHLRRAYTPFENKRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG-R 415 (607)
T ss_pred heeccCcchHHHHHHHhhhhhcCc--ccchhHHHHHHhcCCccccccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc-c
Confidence 4566666 3345666666653321 111222332221 11222468999999999999999999 99999999996 7
Q ss_pred CHHHHHHHHHhhhcCC
Q 010514 80 SKSQCIDHYNAIYMNS 95 (508)
Q Consensus 80 t~~ec~~hy~~~yi~~ 95 (508)
.|..|++||.++-..+
T Consensus 416 ~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 416 MPMDCRDRWRQYVKCG 431 (607)
T ss_pred CcHHHHHHHHHhhccc
Confidence 9999999999876554
No 37
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=94.83 E-value=0.022 Score=58.25 Aligned_cols=32 Identities=34% Similarity=0.818 Sum_probs=25.2
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCeecc
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYRVM 37 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~vi 37 (508)
.|++|++|.|||||-.|...+ .|.-.|.+.-+
T Consensus 166 ~RyKC~~C~dYDLCe~Ce~~~----~~h~~H~~lR~ 197 (278)
T KOG4582|consen 166 ARYKCTVCPDYDLCERCEAGN----EHHAAHAMLRL 197 (278)
T ss_pred ceeeecCCCccchhHHhhcCC----CCCcccceeec
Confidence 589999999999999999987 34455655543
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.54 E-value=0.03 Score=46.62 Aligned_cols=46 Identities=24% Similarity=0.598 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHH--hC--CC---------CHHHHHHHhC----CCCHHHHHHHHHhhh
Q 010514 47 PDWNADEEILLLEGIEM--YG--FG---------NWGEVSEHVG----TKSKSQCIDHYNAIY 92 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~--~G--~g---------nW~~IA~~v~----~kt~~ec~~hy~~~y 92 (508)
..||.+|...||+++.. +. ++ -|..||+.|. .||+.||+.+|.++.
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 11 11 3999999875 499999999998753
No 39
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=92.82 E-value=0.11 Score=57.72 Aligned_cols=53 Identities=28% Similarity=0.391 Sum_probs=44.4
Q ss_pred CCCCCCCHHHHHHHHHHHH-------Hh------------------CCCCHHHHHHHhCCCCHHHHHHHHHhhhcCCC
Q 010514 44 LICPDWNADEEILLLEGIE-------MY------------------GFGNWGEVSEHVGTKSKSQCIDHYNAIYMNSP 96 (508)
Q Consensus 44 ~~~~~Wta~Eel~LLe~i~-------~~------------------G~gnW~~IA~~v~~kt~~ec~~hy~~~yi~~~ 96 (508)
.....||-+|+.+||.+|+ ++ -.-||..|++.+|||+..+|+.||.++-....
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s 511 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHH
Confidence 4567899999999999995 44 12389999999999999999999999766543
No 40
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=90.50 E-value=0.054 Score=56.09 Aligned_cols=34 Identities=29% Similarity=0.775 Sum_probs=31.3
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCee
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYR 35 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~ 35 (508)
.|++|..|.+|-+|.+||-.|.-.+.|.+.|.++
T Consensus 254 fry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mk 287 (434)
T KOG4301|consen 254 FRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMK 287 (434)
T ss_pred hhhhHhhcCCccccchhhccccCCCCcchHHHHH
Confidence 4789999999999999999999999999999766
No 41
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=90.24 E-value=0.27 Score=53.51 Aligned_cols=49 Identities=18% Similarity=0.514 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhhhcC
Q 010514 45 ICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAIYMN 94 (508)
Q Consensus 45 ~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~yi~ 94 (508)
...-|+..||..|--+|..||-..|..||..+..+|+.+|..+|.. +++
T Consensus 6 kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e-~ld 54 (617)
T KOG0050|consen 6 KGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEE-WLD 54 (617)
T ss_pred ecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHH-HhC
Confidence 3567999999999999999998889999999999999999999984 443
No 42
>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=88.76 E-value=0.71 Score=41.37 Aligned_cols=44 Identities=20% Similarity=0.505 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCC---CCHHHHHHHhC------------CCCHHHHHHHHH
Q 010514 46 CPDWNADEEILLLEGIEMYGF---GNWGEVSEHVG------------TKSKSQCIDHYN 89 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~---gnW~~IA~~v~------------~kt~~ec~~hy~ 89 (508)
...||.+||.-||-.+..||+ |+|+.|-..|- +||+.|+..|-.
T Consensus 49 ~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 49 KKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp -SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 578999999999999999999 99999988763 677777665543
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=88.03 E-value=0.34 Score=52.75 Aligned_cols=47 Identities=21% Similarity=0.618 Sum_probs=41.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 43 PLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 43 ~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
.|....|+.+||..||.+.-.+- .-|-.||..|| ||..+|.+||++.
T Consensus 56 ~i~~tews~eederlLhlakl~p-~qwrtIa~i~g-r~~~qc~eRy~~l 102 (617)
T KOG0050|consen 56 AIKKTEWSREEDERLLHLAKLEP-TQWRTIADIMG-RTSQQCLERYNNL 102 (617)
T ss_pred HHhhhhhhhhHHHHHHHHHHhcC-CccchHHHHhh-hhHHHHHHHHHHH
Confidence 45567899999999999998776 78999999996 8999999999983
No 44
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=87.39 E-value=0.37 Score=53.06 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
.+.|+..||..|+-++..||..||..||..++.+++++|+.||.+
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~ 64 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNN 64 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhh
Confidence 468999999999999999999999999999999999999999944
No 45
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=83.98 E-value=1.9 Score=45.45 Aligned_cols=44 Identities=11% Similarity=0.315 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
...|++.|..++..|+.++| .++.-||...++|+..|++..|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCchhHHHHHHHHHH
Confidence 35899999999999999999 699999999999999999999976
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=83.68 E-value=1.7 Score=45.52 Aligned_cols=47 Identities=28% Similarity=0.572 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHHHh----CCCC-----HHHHHHHh---C-CCCHHHHHHHHHhhhc
Q 010514 47 PDWNADEEILLLEGIEMY----GFGN-----WGEVSEHV---G-TKSKSQCIDHYNAIYM 93 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~----G~gn-----W~~IA~~v---~-~kt~~ec~~hy~~~yi 93 (508)
..|+.+|.+.||++-... +-|+ |..||..+ | .||+.+|+..|.+++.
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 689999999999988533 3355 99999943 3 3999999999999764
No 47
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=82.66 E-value=1.9 Score=49.07 Aligned_cols=44 Identities=23% Similarity=0.438 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
..-||..|-.++-+||-+|. .++..|+..|.+||..||.+.|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 35799999999999999998 799999999999999999999865
No 48
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=81.49 E-value=0.81 Score=47.77 Aligned_cols=46 Identities=30% Similarity=0.558 Sum_probs=31.1
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHH
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLE 59 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe 59 (508)
+|++|. ++.||++|-..-...|.|.+ .|- .+.-..||.+|-..|..
T Consensus 22 ~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS----~VK-----SitLD~wt~~~l~~m~~ 78 (319)
T COG5347 22 KCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHIS----KVK-----SLTLDNWTEEELRRMEV 78 (319)
T ss_pred ccccCCCCCCceEecccCeEEEeecchhhhcccccee----eee-----eeecccCCHHHHHHHHH
Confidence 699996 57899999998888886643 222 12224699886555443
No 49
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=78.28 E-value=3.1 Score=43.83 Aligned_cols=43 Identities=26% Similarity=0.545 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHH-HHHhCCCCHHHHHHHHHh
Q 010514 47 PDWNADEEILLLEGIEMYGFGNWGEV-SEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G~gnW~~I-A~~v~~kt~~ec~~hy~~ 90 (508)
..|+.+|=+.+=++++.|| .|..-| |..|.+|+..||+..|+.
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHHH
Confidence 5899999999999999999 799999 778999999999988865
No 50
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=78.13 E-value=2.5 Score=46.83 Aligned_cols=49 Identities=18% Similarity=0.490 Sum_probs=44.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhhhc
Q 010514 44 LICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAIYM 93 (508)
Q Consensus 44 ~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~yi 93 (508)
+....|+.+|+-.|++.-..+| .-|..||..|+++|..+|..+|.+..=
T Consensus 70 lk~~~~~~eed~~li~l~~~~~-~~wstia~~~d~rt~~~~~ery~~~~~ 118 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELG-TQWSTIADYKDRRTAQQCVERYVNTLE 118 (512)
T ss_pred cccccccHHHHHHHHHHHHhcC-chhhhhccccCccchHHHHHHHHHHhh
Confidence 4568999999999999999999 469999999999999999999997653
No 51
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=77.87 E-value=3.5 Score=33.41 Aligned_cols=45 Identities=22% Similarity=0.452 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHhC----------------CCCHHHHHHHhC-----CCCHHHHHHHHHhh
Q 010514 47 PDWNADEEILLLEGIEMYG----------------FGNWGEVSEHVG-----TKSKSQCIDHYNAI 91 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G----------------~gnW~~IA~~v~-----~kt~~ec~~hy~~~ 91 (508)
..||.+|...|++.|+.|- -.-|++|+..+. .||..+++..|.++
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nl 68 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNL 68 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 5799999999999998872 124999999873 48999999999765
No 52
>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=76.96 E-value=4.6 Score=32.38 Aligned_cols=47 Identities=21% Similarity=0.369 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHHHHHh---C---CCC--HHHHHHHhC-CCCHHHHHHHHHhhhc
Q 010514 47 PDWNADEEILLLEGIEMY---G---FGN--WGEVSEHVG-TKSKSQCIDHYNAIYM 93 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~---G---~gn--W~~IA~~v~-~kt~~ec~~hy~~~yi 93 (508)
..+|++||..|++.|..+ | -|| |.++++.-. .+|-.--++||.+...
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~ 58 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLR 58 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence 468999999999999543 3 367 999999877 5788888999988754
No 53
>PHA00442 host recBCD nuclease inhibitor
Probab=76.86 E-value=2.6 Score=32.50 Aligned_cols=28 Identities=18% Similarity=0.436 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 010514 50 NADEEILLLEGIEMYGFGNWGEVSEHVG 77 (508)
Q Consensus 50 ta~Eel~LLe~i~~~G~gnW~~IA~~v~ 77 (508)
+-+-+..+|++++.+|..||+.+.+.+.
T Consensus 24 sLek~~~~L~~Lea~GVDNW~Gy~eA~e 51 (59)
T PHA00442 24 SLEKDNEFLKALRACGVDNWDGYMDAVE 51 (59)
T ss_pred HHHHhhHHHHHHHHcCCcchhhHHHHHH
Confidence 3466788999999999999999987663
No 54
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=76.56 E-value=2 Score=40.41 Aligned_cols=44 Identities=25% Similarity=0.520 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHh---C---CCCHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 47 PDWNADEEILLLEGIEMY---G---FGNWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~---G---~gnW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
..||.+||++|-+.|-.| | +.-.++|++.+ +||+.-|--+|+.+
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~ 54 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAY 54 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHH
Confidence 579999999999999776 2 22478899999 59999999999764
No 55
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=75.41 E-value=1.9 Score=51.75 Aligned_cols=29 Identities=31% Similarity=0.751 Sum_probs=27.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHH
Q 010514 45 ICPDWNADEEILLLEGIEMYGFGNWGEVS 73 (508)
Q Consensus 45 ~~~~Wta~Eel~LLe~i~~~G~gnW~~IA 73 (508)
+..+|+.+++-.||=||-.||+|+|+.|-
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhc
Confidence 67899999999999999999999999984
No 56
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=75.39 E-value=3.3 Score=46.19 Aligned_cols=45 Identities=22% Similarity=0.421 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHH----------HhCCCCHHHHHHHHHhh
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSE----------HVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~----------~v~~kt~~ec~~hy~~~ 91 (508)
...||-+|+.-+.+||.++| .|++.|-+ .+..||..+++.||++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 35899999999999999999 79999933 34569999999999884
No 57
>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=72.61 E-value=2.3 Score=34.42 Aligned_cols=34 Identities=29% Similarity=0.609 Sum_probs=25.5
Q ss_pred cEEEeccCCC---CcccHHHhhcCCCCCCCCCCCCeeccCCC
Q 010514 2 VRIKCAMCSD---FDLCVECFSVGAQIYPHESNHPYRVMDNL 40 (508)
Q Consensus 2 ~ri~C~~C~~---~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~ 40 (508)
+.++|..|.. ..+|..||..+. |. +|.|.+....
T Consensus 12 ~~y~C~tC~~~~~~~iC~~CF~~~~----H~-gH~~~~~~~~ 48 (71)
T PF02207_consen 12 IFYRCLTCSLDESSGICEECFANSC----HE-GHRVVYYRSS 48 (71)
T ss_dssp EEEEETTTBSSTT-BBEHHHHCTSG----GG-GSSEEEEE--
T ss_pred EEEECccCCCCCCEEEchhhCCCCC----cC-CCcEEEEEeC
Confidence 5789999964 779999999865 75 7888887653
No 58
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=72.08 E-value=8.1 Score=27.94 Aligned_cols=39 Identities=13% Similarity=0.154 Sum_probs=32.9
Q ss_pred HHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 469 VEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 469 rE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.....++.++..+....+.+....+.+..+.|.+.|||.
T Consensus 7 ~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 7 ELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 333445679999988899999999999999999999984
No 59
>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=71.64 E-value=9.7 Score=27.80 Aligned_cols=44 Identities=11% Similarity=0.155 Sum_probs=35.5
Q ss_pred HHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 464 LEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 464 K~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
+..++.....+|.++..+.-+.+.+....+.+.+.-|++.|||.
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 34556666678889999988889999999999999999999983
No 60
>PLN03000 amine oxidase
Probab=70.63 E-value=7.2 Score=46.10 Aligned_cols=72 Identities=21% Similarity=0.189 Sum_probs=55.6
Q ss_pred CCcCCCCCCHHHHHHH--H-HhCCCchHHHHHHHHHHHHHHhCC--CCCHHHhhhhhccCc-ccHHHHHHHHHHCCCCC
Q 010514 435 GFVGADLLSETEKRLC--G-EIKILPAHYLKMLEILSVEIYKGN--VSKKSDAHNLFKVEP-NKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 435 ~~pg~~lLs~~Ek~LC--s-~lrL~P~~YL~iK~~LirE~~k~g--~l~~~~a~~l~kiD~-~K~~rIydfl~~~Gwi~ 507 (508)
++| .+-||++|.+.- . .-++.+..||.|...+|+=-.++. .++++.|...++.+- +-+..+|+||+.+|+|.
T Consensus 90 ~~p-~d~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r~G~in 167 (881)
T PLN03000 90 GFP-ADSLTEEEIEFGVVPIVGGIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVTHGYIN 167 (881)
T ss_pred CCC-cccCCHHHHhccccCcccccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHHcCccc
Confidence 455 788999997651 1 124678999999999998777765 488999888876433 45669999999999985
No 61
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=70.26 E-value=6.5 Score=47.32 Aligned_cols=48 Identities=13% Similarity=0.360 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhhhcCC
Q 010514 47 PDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAIYMNS 95 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~yi~~ 95 (508)
.+|+..+=..++.|+++||-.+-+.||..|++||++|++. |.+.|...
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~-y~~~f~~~ 872 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVER-YAKVFWER 872 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHH-HHHHHHHh
Confidence 4799999999999999999999999999999999999764 55655543
No 62
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=67.74 E-value=8.5 Score=46.33 Aligned_cols=44 Identities=16% Similarity=0.400 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhC------------CCCHHHHHHHHH
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSEHVG------------TKSKSQCIDHYN 89 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~------------~kt~~ec~~hy~ 89 (508)
...||.+|+..||-.+..||+|+|+.|-..|. +||+.|+..+..
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 45799999999999999999999999987663 667776665554
No 63
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=65.89 E-value=3.3 Score=44.67 Aligned_cols=70 Identities=23% Similarity=0.386 Sum_probs=42.2
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCCHHH--
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGNWGE-- 71 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gnW~~-- 71 (508)
.|+.|. ++.||++|-+.-...|.|.+ |. .. ..+.. ||..+-.. .++| ||=..
T Consensus 25 vCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiS---FV--RS--TnLDs--Ws~~qLR~-----M~~G-GN~nA~~ 89 (454)
T KOG0706|consen 25 VCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHIS---FV--RS--TNLDS--WSWEQLRR-----MQVG-GNANARV 89 (454)
T ss_pred eecccCCCCCCceeecceEEEEEecchhhhccccceE---EE--ee--ccccc--CCHHHHhH-----hhhc-CchhHHH
Confidence 699995 57899999999999999976 22 21 12223 99875332 3566 65322
Q ss_pred HHHHhCCCCHHHHHHHHHh
Q 010514 72 VSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 72 IA~~v~~kt~~ec~~hy~~ 90 (508)
.=..=|.++. +|...|..
T Consensus 90 FFkqhg~~t~-d~~aKY~S 107 (454)
T KOG0706|consen 90 FFKQHGCVTL-DANAKYNS 107 (454)
T ss_pred HHHHcCCcch-hhhhhhcc
Confidence 2222223333 66776654
No 64
>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=64.97 E-value=8.1 Score=33.99 Aligned_cols=45 Identities=31% Similarity=0.649 Sum_probs=28.5
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHH
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLE 59 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe 59 (508)
.|++|. +..+|+.|-..-..++.|.+- |.. +.-..|+.+| +.+|+
T Consensus 5 ~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~-----VkS----l~md~w~~~~-i~~~~ 60 (112)
T smart00105 5 KCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISK-----VRS----LTLDTWTEEE-LRLLQ 60 (112)
T ss_pred cccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCe-----eee----cccCCCCHHH-HHHHH
Confidence 589995 356999999987777766422 221 2234799765 44444
No 65
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=63.40 E-value=7.4 Score=31.04 Aligned_cols=40 Identities=18% Similarity=0.341 Sum_probs=31.4
Q ss_pred HHHHH-hCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 468 SVEIY-KGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 468 irE~~-k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
|++++ .+|..+..+.-.-|++++.-+..+.++|+++|.|.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 34555 58899999888889999999999999999999983
No 66
>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=63.31 E-value=14 Score=28.00 Aligned_cols=50 Identities=14% Similarity=0.347 Sum_probs=38.0
Q ss_pred hCCCchHHHHHHHHHHHHHHhCCC--CCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 453 IKILPAHYLKMLEILSVEIYKGNV--SKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 453 lrL~P~~YL~iK~~LirE~~k~g~--l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
++|.|.+|..+-.+ ...+. ++..+....+.+++.-+.++.+=|++.|||.
T Consensus 1 ~glt~~q~~vL~~l-----~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 1 LGLTPSQFRVLMAL-----ARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp TTSTHHHHHHHHHH-----HHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CccCHHHHHHHHHH-----HHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 35677777655433 33343 8999988999999999999999999999984
No 67
>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=62.59 E-value=23 Score=25.76 Aligned_cols=37 Identities=19% Similarity=0.235 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 53 EEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 53 Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
=+..+|..++.-|--.|.+||+.+|- |+..|..++..
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 46789999999988899999999985 88999888754
No 68
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=62.06 E-value=4.5 Score=41.54 Aligned_cols=71 Identities=14% Similarity=0.444 Sum_probs=40.8
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCC-----
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGN----- 68 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gn----- 68 (508)
.||+|. ++.||+.|-..-..++.|- -+|. .+.-..||.++-..+.+ +| |
T Consensus 27 ~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hi----SkVk-----Sv~LD~W~~eqv~~m~~----~G--N~~an~ 91 (287)
T KOG0703|consen 27 VCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHI----SKVK-----SVTLDEWTDEQVDFMIS----MG--NAKANS 91 (287)
T ss_pred cccccCCCCCCeEEeecCeEEEeecccccccccchh----heee-----eeeccccCHHHHHHHHH----Hc--chhhhh
Confidence 699996 5789999977666555543 3332 12235699987554443 33 2
Q ss_pred -HHH-HHHHhCCCCHHHHHHHHHh
Q 010514 69 -WGE-VSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 69 -W~~-IA~~v~~kt~~ec~~hy~~ 90 (508)
|+. |......-+++..+++|+.
T Consensus 92 ~~ea~~p~~~~~p~~d~~~e~FIR 115 (287)
T KOG0703|consen 92 YYEAKLPDPFRRPGPDDLVEQFIR 115 (287)
T ss_pred hccccCCccccCCChHHHHHHHHH
Confidence 332 2333333455556666665
No 69
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=62.00 E-value=4.6 Score=38.14 Aligned_cols=30 Identities=27% Similarity=0.692 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHHHHh
Q 010514 47 PDWNADEEILLLEGIEMYGFGNWGEVSEHV 76 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v 76 (508)
.-|-..-+..||-||-.+|+|-|++|.+.-
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~ 33 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDP 33 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCC
Confidence 358889999999999999999999998753
No 70
>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=60.89 E-value=2.2 Score=37.78 Aligned_cols=44 Identities=27% Similarity=0.582 Sum_probs=22.8
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHH
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILL 57 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~L 57 (508)
.|++|. ++.+|+.|.+.-...+.|. .+|- . +.-..|+.+|-..|
T Consensus 15 ~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~i----s~Vk-S----i~~d~w~~~ev~~~ 69 (116)
T PF01412_consen 15 VCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHI----SRVK-S----ITMDNWSPEEVQRM 69 (116)
T ss_dssp B-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT------EE-E----TTTS---HHHHHHH
T ss_pred cCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccc----hhcc-c----cccCCCCHHHHHHH
Confidence 599995 4679999998877766653 2222 1 22235998865544
No 71
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=60.55 E-value=9.2 Score=41.57 Aligned_cols=43 Identities=26% Similarity=0.553 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHH-HHHhCCCCHHHHHHHHHh
Q 010514 47 PDWNADEEILLLEGIEMYGFGNWGEV-SEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 47 ~~Wta~Eel~LLe~i~~~G~gnW~~I-A~~v~~kt~~ec~~hy~~ 90 (508)
+.|++.|-.++-||+++|| .++.+| ++++.=||-..+++.|.-
T Consensus 286 EEWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIveyYYm 329 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVEYYYM 329 (693)
T ss_pred hhccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHHHHHH
Confidence 4899999999999999999 799999 567777888888877753
No 72
>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=59.57 E-value=8.3 Score=27.42 Aligned_cols=27 Identities=33% Similarity=0.737 Sum_probs=21.6
Q ss_pred cEEEeccCCCCcccHHHhhcCCCCCCCCCCCCee
Q 010514 2 VRIKCAMCSDFDLCVECFSVGAQIYPHESNHPYR 35 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~G~e~~~H~~~H~y~ 35 (508)
+.+-|..|. ..+|..|+..+ |+. |.+.
T Consensus 14 ~~~~C~~C~-~~~C~~C~~~~-----H~~-H~~~ 40 (42)
T PF00643_consen 14 LSLFCEDCN-EPLCSECTVSG-----HKG-HKIV 40 (42)
T ss_dssp EEEEETTTT-EEEEHHHHHTS-----TTT-SEEE
T ss_pred eEEEecCCC-CccCccCCCCC-----CCC-CEEe
Confidence 568899998 58999999987 655 7654
No 73
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=59.57 E-value=16 Score=29.41 Aligned_cols=45 Identities=22% Similarity=0.352 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCCC
Q 010514 460 YLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQA 508 (508)
Q Consensus 460 YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~~ 508 (508)
|-..++.++ ..+..+.+-.+.-|+|.-|++.+|.|-|.+.|+|+|
T Consensus 8 y~~a~~~V~----~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 8 YEEAVEFVI----EEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp HHHHHHHHH----HCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred HHHHHHHHH----HcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 444444443 467788888888899999999999999999999974
No 74
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=58.25 E-value=33 Score=29.88 Aligned_cols=61 Identities=7% Similarity=0.028 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 442 LSETEKRLCGEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 442 Ls~~Ek~LCs~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
++..-......++|.|..|..+-. ...+|.++..+....+.++..-+.++.+=|.+.|||.
T Consensus 13 ~~~~~~~~l~~~~lt~~q~~iL~~-----l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~ 73 (118)
T TIGR02337 13 AMSFFRPILAQHGLTEQQWRILRI-----LAEQGSMEFTQLANQACILRPSLTGILARLERDGLVT 73 (118)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH-----HHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence 344445666788999999976533 2356778888888888999999999999999999984
No 75
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=55.25 E-value=7.1 Score=42.84 Aligned_cols=56 Identities=32% Similarity=0.552 Sum_probs=40.2
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHHHHHHhCCCC--HHH
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLEGIEMYGFGN--WGE 71 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe~i~~~G~gn--W~~ 71 (508)
.|+.|. +..||-+|||.-...|.|-+ ++. .+-...|-. +-+.+++++...| .| |+.
T Consensus 10 vC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS-----~vr----hLR~s~W~p-t~l~~V~tLn~~g-aNsIWEh 78 (669)
T KOG0818|consen 10 VCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHIS-----QVR----HLRHTPWPP-TLLQMVETLNNNG-ANSIWEH 78 (669)
T ss_pred hhcccCCCCCcceeecCceEehHhhhHHHhhhcchHH-----HHH----HhccCCCCH-HHHHHHHHHHhcC-cchhhhh
Confidence 499995 45799999999999999854 111 134567954 4788888888888 34 764
No 76
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=54.89 E-value=33 Score=29.70 Aligned_cols=64 Identities=9% Similarity=0.064 Sum_probs=48.9
Q ss_pred CHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 443 SETEKRLCGEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 443 s~~Ek~LCs~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
..-+..+=..++|.|..|..+..+-. -...+|.++..+....+.++...+.++.+=|+++|||.
T Consensus 11 ~~~~~~l~~~~~ls~~q~~vL~~l~~-~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 11 KSLKRYLKKEFNLSLEELLILYYLGK-LENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh-hhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 33445555567999999987744332 11235789999988899999999999999999999984
No 77
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=54.40 E-value=18 Score=31.18 Aligned_cols=33 Identities=21% Similarity=0.499 Sum_probs=24.9
Q ss_pred CCCCCCHHHHHHHHHHHHHh----CCC---CHHHHHHHhC
Q 010514 45 ICPDWNADEEILLLEGIEMY----GFG---NWGEVSEHVG 77 (508)
Q Consensus 45 ~~~~Wta~Eel~LLe~i~~~----G~g---nW~~IA~~v~ 77 (508)
+..-||.++|+.||+|+-.| |.. +|...-++|.
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk 42 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVK 42 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHH
Confidence 45779999999999999888 632 5666655553
No 78
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=54.09 E-value=36 Score=30.60 Aligned_cols=56 Identities=14% Similarity=0.209 Sum_probs=44.7
Q ss_pred HHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 448 RLCGEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 448 ~LCs~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.....++|.|.+|..+-.+. ..++..+..+....+.++..-+.++.+=|++.|||.
T Consensus 22 ~~l~~~glt~~q~~vL~~l~----~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 22 HRLKPLELTQTHWVTLHNIH----QLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHhcCCCHHHHHHHHHHH----HcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 45578999999998764432 224457778878889999999999999999999985
No 79
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=53.46 E-value=28 Score=32.40 Aligned_cols=54 Identities=26% Similarity=0.567 Sum_probs=45.0
Q ss_pred CCCHHHHHHHHHHHHHhCCC--CHHHHHHHhCCCCHHHHHHHHHhhhcCCCCCCCCC
Q 010514 48 DWNADEEILLLEGIEMYGFG--NWGEVSEHVGTKSKSQCIDHYNAIYMNSPCFPLPD 102 (508)
Q Consensus 48 ~Wta~Eel~LLe~i~~~G~g--nW~~IA~~v~~kt~~ec~~hy~~~yi~~~~~plp~ 102 (508)
+++..+=..+|.+|..||+| +|......+..||.+| ...|..+|+..-+.|--|
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~e-i~aY~~LFm~HL~E~~~d 95 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKE-IRAYGSLFMRHLCEPGTD 95 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHH-HHHHHHHHHHHhcCCCcC
Confidence 79999999999999999998 7999999999999888 456788887665554444
No 80
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=51.74 E-value=14 Score=39.13 Aligned_cols=25 Identities=28% Similarity=0.615 Sum_probs=19.9
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCC
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHE 29 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~ 29 (508)
.|++|. +..||+.|-..-..++.|-
T Consensus 24 ~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHI 59 (395)
T PLN03114 24 ICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHI 59 (395)
T ss_pred cCccCCCCCCCceeeccceeehhhhhHhhccCCCCC
Confidence 599995 4679999998877777764
No 81
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=51.49 E-value=36 Score=28.24 Aligned_cols=43 Identities=21% Similarity=0.495 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----CHHHHHHHhC-----CCCHHHHHHHHHh
Q 010514 48 DWNADEEILLLEGIEMY---GF----G-----NWGEVSEHVG-----TKSKSQCIDHYNA 90 (508)
Q Consensus 48 ~Wta~Eel~LLe~i~~~---G~----g-----nW~~IA~~v~-----~kt~~ec~~hy~~ 90 (508)
.||.+.+..||+++... |. + .|..|+..+. ..|..+|+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 49999999999998433 11 1 3888888764 3678899888754
No 82
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=51.32 E-value=16 Score=27.55 Aligned_cols=35 Identities=17% Similarity=0.307 Sum_probs=29.9
Q ss_pred hCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 473 KGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 473 k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
..|.++..+.-..+.++...+.++.+-|++.|||.
T Consensus 14 ~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 14 ENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 45668888888889999999999999999999984
No 83
>smart00595 MADF subfamily of SANT domain.
Probab=50.80 E-value=16 Score=30.06 Aligned_cols=23 Identities=26% Similarity=0.758 Sum_probs=20.8
Q ss_pred CHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 68 NWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 68 nW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
-|..||..+|. |.++|+.+|.++
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 49999999987 999999999875
No 84
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=50.05 E-value=40 Score=27.00 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=30.8
Q ss_pred CCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCCC
Q 010514 474 GNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQA 508 (508)
Q Consensus 474 ~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~~ 508 (508)
.+..+-+-.+.-|+|--|++.+|.|-|.+.|.|+|
T Consensus 17 ~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 17 TQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred hCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 56667777778899999999999999999999975
No 85
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=49.19 E-value=19 Score=36.33 Aligned_cols=58 Identities=21% Similarity=0.234 Sum_probs=38.8
Q ss_pred hhhhhhccCChHHHHHHHHHHHHH--------HHHHHHH-----------HHHHHHHHhcCcchHHHHHHHHHHHHH
Q 010514 311 QYKVFMRFHSKEDHEELLKSVIEE--------HRIVKRI-----------QELQEAQAAGCRTSSEAHRFLEQKRKK 368 (508)
Q Consensus 311 ~l~~farf~~~~d~~~l~~~l~~e--------~~Lr~rI-----------~~Lq~~R~~Gi~tl~e~~~Ye~~k~~R 368 (508)
-..-|.+++||.+.+.|..-|..- ..|+.-. .-|..|+.+||+|++++..|+.+.+.|
T Consensus 134 F~~e~Gr~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~n~~YI~~IL~nW~k~gvkTv~dv~~~~~~~~~~ 210 (246)
T COG3935 134 FEEEFGRMLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKLNFKYIDAILRNWKKNGVKTVEDVRAREEERRTR 210 (246)
T ss_pred HHHHcCCcCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHH
Confidence 345667788888877776544321 1222221 248899999999999999998876644
No 86
>PLN02328 lysine-specific histone demethylase 1 homolog
Probab=49.12 E-value=26 Score=41.22 Aligned_cols=69 Identities=19% Similarity=0.204 Sum_probs=54.0
Q ss_pred CCCCCHHHHHH---HHHhCCCchHHHHHHHHHHHHHHhCC--CCCHHHhhhhhcc-CcccHHHHHHHHHHCCCCC
Q 010514 439 ADLLSETEKRL---CGEIKILPAHYLKMLEILSVEIYKGN--VSKKSDAHNLFKV-EPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 439 ~~lLs~~Ek~L---Cs~lrL~P~~YL~iK~~LirE~~k~g--~l~~~~a~~l~ki-D~~K~~rIydfl~~~Gwi~ 507 (508)
.+-||++|.+. =...+.-+..||.|...+|+=-.++. .+++..|...++. ..+-+..+|+||+..|+|.
T Consensus 144 ~~~l~~~e~~~~~~~~~~~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~~g~in 218 (808)
T PLN02328 144 VDSLTEEEIEANVVSTIGGTEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLEHGYIN 218 (808)
T ss_pred CccCCHHHHhhcCcchhcccceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhccCcee
Confidence 67799988664 23334788999999999998777765 4889999887653 3356789999999999985
No 87
>PF13730 HTH_36: Helix-turn-helix domain
Probab=47.75 E-value=43 Score=24.90 Aligned_cols=53 Identities=21% Similarity=0.241 Sum_probs=36.8
Q ss_pred CCCchHHHHHHHHHHHHHHhCCC-CCHHHhhhhhccCcccHHHHHHHHHHCCCC
Q 010514 454 KILPAHYLKMLEILSVEIYKGNV-SKKSDAHNLFKVEPNKVDRVYDMLVRKGIA 506 (508)
Q Consensus 454 rL~P~~YL~iK~~LirE~~k~g~-l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi 506 (508)
+|.|...+.+=.+.-...-.++. .+.+...+.+.+-.+.+.+..+-|++.|||
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 45666665554433222122333 477777788899999999999999999997
No 88
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=47.47 E-value=18 Score=34.58 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------CCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 46 CPDWNADEEILLLEGIEMYGF------GNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~------gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
...||.+++++|-+.|-.|+- .-.+.+++.+ .||+..|..+|+.
T Consensus 5 qdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs 54 (170)
T PRK13923 5 QDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNS 54 (170)
T ss_pred hhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHH
Confidence 357999999999888877752 2355666777 5899999999943
No 89
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=46.89 E-value=29 Score=37.82 Aligned_cols=47 Identities=13% Similarity=0.438 Sum_probs=41.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 43 PLICPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 43 ~~~~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
.-+-..||++|-.+|-.+.+.|| .+...|-..+..|+-.+.+..|..
T Consensus 184 ~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 184 TEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPHRSLASLVQYYYS 230 (534)
T ss_pred CCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHccCccHHHHHHHHHH
Confidence 33457899999999999999999 899999999999999998888754
No 90
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=45.68 E-value=32 Score=28.49 Aligned_cols=41 Identities=22% Similarity=0.396 Sum_probs=29.9
Q ss_pred HHHHHHHHhCCCCCHHHhhhhhc---cCcccHHHHHHHHHHCCC
Q 010514 465 EILSVEIYKGNVSKKSDAHNLFK---VEPNKVDRVYDMLVRKGI 505 (508)
Q Consensus 465 ~~LirE~~k~g~l~~~~a~~l~k---iD~~K~~rIydfl~~~Gw 505 (508)
..||....++|.++-.+....++ +++..+..||++|...|+
T Consensus 10 ~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 10 KKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 34777777789999999888887 888999999999999885
No 91
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=45.19 E-value=58 Score=25.66 Aligned_cols=45 Identities=11% Similarity=0.244 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 459 HYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 459 ~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.=|.+|..+|...++.|.|+.++|..+. ..+..-+++..++|++.
T Consensus 15 qm~e~kK~~idk~Ve~G~iTqeqAd~ik----~~id~~~~~~~qnGf~p 59 (59)
T PF10925_consen 15 QMLELKKQIIDKYVEAGVITQEQADAIK----KHIDQRQEYMQQNGFVP 59 (59)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHH----HHHHHHHHHHHHcCCCC
Confidence 4478999999999999999999998763 45668889999998863
No 92
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=44.44 E-value=22 Score=39.85 Aligned_cols=42 Identities=19% Similarity=0.544 Sum_probs=25.8
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHH
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLE 59 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe 59 (508)
+|++|. +..+|+.|-..-..++ | + |.. +.-..|+.+| +.+|+
T Consensus 25 ~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG-----h--R-VKS----LSLDkWT~EE-Ve~Mk 77 (648)
T PLN03119 25 RCINCNSLGPQYVCTTFWTFVCMACSGIHREFT-----H--R-VKS----VSMSKFTSKE-VEVLQ 77 (648)
T ss_pred ccccCCCCCCCceeeccceEEeccchhhhccCC-----c--e-eec----cccCCCCHHH-HHHHH
Confidence 699995 3568999987766553 3 2 222 2235799865 44444
No 93
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=44.12 E-value=26 Score=27.87 Aligned_cols=45 Identities=13% Similarity=0.120 Sum_probs=32.8
Q ss_pred HHHHHHHHHHh-CCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 463 MLEILSVEIYK-GNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 463 iK~~LirE~~k-~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
+|+.++.=+.. ++.++-.+.-+.|.+....++++...|.+.|.|.
T Consensus 1 ~ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 1 MKEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp -HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CcHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 35555543334 5778777777789999999999999999999884
No 94
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=43.24 E-value=47 Score=24.98 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=23.2
Q ss_pred cCChHHHHHHHHHH-----HHHHHHHHHHHHHH
Q 010514 318 FHSKEDHEELLKSV-----IEEHRIVKRIQELQ 345 (508)
Q Consensus 318 f~~~~d~~~l~~~l-----~~e~~Lr~rI~~Lq 345 (508)
+.+++++++|+..| ++|.+|++.+....
T Consensus 4 ~~~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~ 36 (46)
T PF15614_consen 4 YDDPEELDELLKALENPRGKRESKLKKELDKHR 36 (46)
T ss_pred ccCHHHHHHHHHHHcCcccHhHHHHHHHHHHHh
Confidence 56899999999999 79999998766553
No 95
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=43.01 E-value=36 Score=24.46 Aligned_cols=26 Identities=27% Similarity=0.423 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 010514 52 DEEILLLEGIEMYGFGNWGEVSEHVGT 78 (508)
Q Consensus 52 ~Eel~LLe~i~~~G~gnW~~IA~~v~~ 78 (508)
-|-..+.++++.+| ||...+|..+|-
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~~Lgi 30 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAARLLGI 30 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHHHHTS
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHCC
Confidence 36678899999999 999999999984
No 96
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=41.94 E-value=14 Score=40.27 Aligned_cols=43 Identities=21% Similarity=0.368 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHh
Q 010514 46 CPDWNADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNA 90 (508)
Q Consensus 46 ~~~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~ 90 (508)
.-+||..|-- ++..-..|| .|.+.||+.++++|++|....|++
T Consensus 470 ~~~wSp~e~s-~ircf~~y~-~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 470 NYGWSPEEKS-AIRCFHWYK-DNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred cCCCCCcccc-cccCchhhc-cchHHHHHHhcCCCHHHHHHHhcC
Confidence 3589988655 888888999 899999999999999998877753
No 97
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=41.78 E-value=52 Score=29.71 Aligned_cols=52 Identities=19% Similarity=0.294 Sum_probs=43.5
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 451 GEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 451 s~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
..++|.|.+|..+..+ ...|.++..+....+.++..-+.++.+=|++.|||.
T Consensus 34 ~~~glt~~q~~vL~~l-----~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 34 SPLDITAAQFKVLCSI-----RCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred cccCCCHHHHHHHHHH-----HHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4578999999877643 245678888888889999999999999999999984
No 98
>PLN03131 hypothetical protein; Provisional
Probab=39.91 E-value=33 Score=38.92 Aligned_cols=42 Identities=19% Similarity=0.537 Sum_probs=26.3
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCCCCCeeccCCCCCCCCCCCCCHHHHHHHHH
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHESNHPYRVMDNLSFPLICPDWNADEEILLLE 59 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~~~~~~~~~Wta~Eel~LLe 59 (508)
+|++|. ++.+|+.|-..-..++ | +| .. +.-..|+.+| +.+|+
T Consensus 25 ~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-----h--RV-KS----VTLD~WtdeE-V~~Mk 77 (705)
T PLN03131 25 RCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-----H--RV-KS----VSMSKFTSQD-VEALQ 77 (705)
T ss_pred ccccCCCCCCCeeEeccceEEchhchhhhcccC-----c--cc-cc----ccCCCCCHHH-HHHHH
Confidence 699995 4569999987766653 3 22 21 2235799875 44444
No 99
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=38.84 E-value=26 Score=28.39 Aligned_cols=34 Identities=29% Similarity=0.741 Sum_probs=24.9
Q ss_pred cEEEeccCC---CCcccHHHhhcCCCCCCCCCCCCeeccCCC
Q 010514 2 VRIKCAMCS---DFDLCVECFSVGAQIYPHESNHPYRVMDNL 40 (508)
Q Consensus 2 ~ri~C~~C~---~~~lC~~Cfs~G~e~~~H~~~H~y~vi~~~ 40 (508)
+.++|..|. ..-+|..||-.+. | .+|.|.+....
T Consensus 12 ~~y~C~tC~~~~~~~iC~~Cf~~~~----H-~gH~~~~~~~~ 48 (71)
T smart00396 12 VIYRCKTCGLDPTCVLCSDCFRSNC----H-KGHDYSLKTSR 48 (71)
T ss_pred EEEECcCCCCCCCEeEChHHCCCCC----C-CCCCEEEEEec
Confidence 347899995 2459999998754 6 46888887653
No 100
>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=38.66 E-value=59 Score=24.55 Aligned_cols=34 Identities=18% Similarity=0.271 Sum_probs=29.3
Q ss_pred hCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 473 KGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 473 k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.++ ++..++...+.+....+.++.+-|++.|||.
T Consensus 18 ~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~ 51 (78)
T cd00090 18 EGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVE 51 (78)
T ss_pred HCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeE
Confidence 344 8888888888999999999999999999984
No 101
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=38.06 E-value=54 Score=25.15 Aligned_cols=34 Identities=21% Similarity=0.320 Sum_probs=28.0
Q ss_pred hCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCC
Q 010514 473 KGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIA 506 (508)
Q Consensus 473 k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi 506 (508)
.++..+..+....+.++..-+.++.+=|++.|||
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 3677888999999999999999999999999998
No 102
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=37.05 E-value=81 Score=28.74 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=22.1
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCC
Q 010514 451 GEIKILPAHYLKMLEILSVEIYKGNVS 477 (508)
Q Consensus 451 s~lrL~P~~YL~iK~~LirE~~k~g~l 477 (508)
+.++|+|..|+.+|..|-.+.+-...+
T Consensus 87 ~ri~mS~~EYM~lKkqLae~il~~s~~ 113 (153)
T COG4008 87 NRINMSPEEYMELKKQLAEYILGHSEP 113 (153)
T ss_pred HhcCCCHHHHHHHHHHHHHHHhccCCC
Confidence 578999999999999998887754433
No 103
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=35.30 E-value=9.1 Score=30.60 Aligned_cols=23 Identities=17% Similarity=0.267 Sum_probs=14.7
Q ss_pred HHHHHHHHHhcCcchHHHHHHHH
Q 010514 341 IQELQEAQAAGCRTSSEAHRFLE 363 (508)
Q Consensus 341 I~~Lq~~R~~Gi~tl~e~~~Ye~ 363 (508)
..-|..|+..||+|++++..|++
T Consensus 54 ~~Il~~W~~~gi~t~e~~~~~~k 76 (77)
T PF07261_consen 54 EKILNNWKQKGIKTVEDAEEYEK 76 (77)
T ss_dssp HHHHHHHHHCT--SCCCCT----
T ss_pred HHHHHHHHHcCCCCHHHHHHHhh
Confidence 34688999999999999987764
No 104
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=33.71 E-value=44 Score=29.46 Aligned_cols=24 Identities=25% Similarity=0.473 Sum_probs=20.9
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhC
Q 010514 451 GEIKILPAHYLKMLEILSVEIYKG 474 (508)
Q Consensus 451 s~lrL~P~~YL~iK~~LirE~~k~ 474 (508)
.+++|.|+.|+.+|..|..|++++
T Consensus 86 ~~igls~~EYm~lKkelae~i~~~ 109 (109)
T TIGR03277 86 QRIGMSPEEYMELKKKLAEELLKK 109 (109)
T ss_pred HHcCCCHHHHHHHHHHHHHHHhcC
Confidence 468999999999999999988753
No 105
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=33.47 E-value=28 Score=22.88 Aligned_cols=12 Identities=42% Similarity=0.758 Sum_probs=9.7
Q ss_pred HHHHHHHHCCCC
Q 010514 495 RVYDMLVRKGIA 506 (508)
Q Consensus 495 rIydfl~~~Gwi 506 (508)
-|||||+++|+.
T Consensus 6 lI~~YL~~~Gy~ 17 (27)
T PF08513_consen 6 LIYDYLVENGYK 17 (27)
T ss_dssp HHHHHHHHCT-H
T ss_pred HHHHHHHHCCcH
Confidence 589999999974
No 106
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.87 E-value=60 Score=23.84 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHh-CCCC-CHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 462 KMLEILSVEIYK-GNVS-KKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 462 ~iK~~LirE~~k-~g~l-~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.++..++...+. +..+ +..+..+.+.+...-+.+.+.-|.+.|||.
T Consensus 4 ~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 344555444333 3345 777777788888889999999999999984
No 107
>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=30.82 E-value=1e+02 Score=25.53 Aligned_cols=38 Identities=24% Similarity=0.381 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCC-------CCHHHHHHHhCCCC-----HHHHHHHHHhhh
Q 010514 55 ILLLEGIEMYGF-------GNWGEVSEHVGTKS-----KSQCIDHYNAIY 92 (508)
Q Consensus 55 l~LLe~i~~~G~-------gnW~~IA~~v~~kt-----~~ec~~hy~~~y 92 (508)
..|-.+|...|= +.|..||..+|-.+ ..+.+.+|.++.
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L 88 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYL 88 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHh
Confidence 567777877761 36999999998422 356778887653
No 108
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=29.97 E-value=1.2e+02 Score=24.05 Aligned_cols=44 Identities=18% Similarity=0.095 Sum_probs=34.6
Q ss_pred HHHHHHHHHhCCC--CCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 464 LEILSVEIYKGNV--SKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 464 K~~LirE~~k~g~--l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
++.++.-....|. ++..+.-+.+.++...+.++..=|.+.|+|.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4444444445555 9998888889999999999999999999983
No 109
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=29.69 E-value=43 Score=26.20 Aligned_cols=36 Identities=17% Similarity=0.262 Sum_probs=31.9
Q ss_pred HhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 472 YKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 472 ~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
++.|..+..+.-..+.+....+.++.+-|.+.|||.
T Consensus 18 l~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 18 LKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 467888888888889999999999999999999984
No 110
>PF10123 Mu-like_Pro: Mu-like prophage I protein; InterPro: IPR012106 This entry is represented by the Bacteriophage Mu, Gp32. The characteristics of the protein distribution suggest prophage matches.
Probab=28.99 E-value=37 Score=35.45 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=22.4
Q ss_pred CCCCCCHHHHHHHHHhCCCchHHHH
Q 010514 438 GADLLSETEKRLCGEIKILPAHYLK 462 (508)
Q Consensus 438 g~~lLs~~Ek~LCs~lrL~P~~YL~ 462 (508)
+..-||.+|+..|.+|+|.|..|++
T Consensus 302 ~~~~Lt~ee~av~~~lGis~edf~K 326 (326)
T PF10123_consen 302 GSAALTAEELAVCRQLGISPEDFAK 326 (326)
T ss_pred CCCCCCHHHHHHHHHcCCCHHHhcC
Confidence 4668999999999999999999973
No 111
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=28.45 E-value=23 Score=37.41 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=20.0
Q ss_pred EeccCC-----------CCcccHHHhhcCCCCCCCCC
Q 010514 5 KCAMCS-----------DFDLCVECFSVGAQIYPHES 30 (508)
Q Consensus 5 ~C~~C~-----------~~~lC~~Cfs~G~e~~~H~~ 30 (508)
+|.+|. +..|||+|-..-.-++.|.+
T Consensus 21 ~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiS 57 (386)
T KOG0704|consen 21 KCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHIS 57 (386)
T ss_pred ceeecCCCCCCeEeecccEEEEEecCCcccccceeeE
Confidence 688995 45799999877777777753
No 112
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=28.33 E-value=44 Score=28.49 Aligned_cols=31 Identities=16% Similarity=0.247 Sum_probs=24.7
Q ss_pred CCCHHHhhhhhccCcccHHHHHHHHHHCCCC
Q 010514 476 VSKKSDAHNLFKVEPNKVDRVYDMLVRKGIA 506 (508)
Q Consensus 476 ~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi 506 (508)
.+...+..+-+.++.++++.+.+||+..|+|
T Consensus 65 Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 65 GVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred cccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 4666665555599999999999999999998
No 113
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=28.16 E-value=95 Score=30.45 Aligned_cols=46 Identities=15% Similarity=0.381 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHHHHhC---CCCHHHHHHHHHhhhcCC
Q 010514 48 DWNADEEILLLEGIEMYGFGNWGEVSEHVG---TKSKSQCIDHYNAIYMNS 95 (508)
Q Consensus 48 ~Wta~Eel~LLe~i~~~G~gnW~~IA~~v~---~kt~~ec~~hy~~~yi~~ 95 (508)
.|++.+|++|+.||++- .+-..|+.-|. .-|..|..++|..+..+.
T Consensus 1 rW~~~DDl~Li~av~~~--~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQT--NDLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHHh--cCHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 49999999999999875 48999988876 358999999999876443
No 114
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.05 E-value=1.2e+02 Score=27.79 Aligned_cols=43 Identities=12% Similarity=0.114 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhhhcCC
Q 010514 52 DEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAIYMNS 95 (508)
Q Consensus 52 ~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~yi~~ 95 (508)
+-|..+|++++.-|--.|.+||+.+|- |+..|..++..+-=.+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKMKQAG 51 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHHHHCC
Confidence 568999999999998899999999975 9999999998765443
No 115
>PRK10870 transcriptional repressor MprA; Provisional
Probab=27.97 E-value=1.3e+02 Score=28.51 Aligned_cols=58 Identities=10% Similarity=0.191 Sum_probs=46.0
Q ss_pred HHHHHHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 447 KRLCGEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 447 k~LCs~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
...-..++|.|.+|..+..+- ...++.++-.+....+.++..-+.++.+=|+++|||.
T Consensus 45 ~~~l~~~gLt~~q~~iL~~L~---~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 45 NKMLKAQGINETLFMALITLE---SQENHSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred HHHHHHCCCCHHHHHHHHHHh---cCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 445578999999999875543 1224568877877788999999999999999999984
No 116
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=27.80 E-value=1.1e+02 Score=24.71 Aligned_cols=52 Identities=23% Similarity=0.396 Sum_probs=37.8
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 451 GEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 451 s~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
...+|.+..+..+.-+. ..|.++..+....+.+....+.++++-|++.|||.
T Consensus 4 ~~~~l~~~~~~il~~l~-----~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 4 KPLGLTPTQFLVLRILY-----EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred cccCCCHHHHHHHHHHH-----HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 34455566555544333 35567787777788899999999999999999984
No 117
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=27.28 E-value=1.1e+02 Score=24.93 Aligned_cols=40 Identities=8% Similarity=0.125 Sum_probs=32.6
Q ss_pred HHHHH-hC-CCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 468 SVEIY-KG-NVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 468 irE~~-k~-g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
|-+.+ .. +.++..+.-..+.+...-+.++.+.|++.|||.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 34444 34 679998888888999999999999999999984
No 118
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=27.24 E-value=62 Score=23.31 Aligned_cols=34 Identities=18% Similarity=0.480 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHH
Q 010514 464 LEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYD 498 (508)
Q Consensus 464 K~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIyd 498 (508)
|+.||...+..|.++..+ ++|......-+.+.|.
T Consensus 3 K~~lI~~Li~~Giyk~~d-rqL~Eltl~ELe~ey~ 36 (38)
T PF13076_consen 3 KDFLIEKLIQSGIYKKED-RQLYELTLSELEKEYE 36 (38)
T ss_pred HHHHHHHHHHcCCcCccc-hHHHHcCHHHHHHHHH
Confidence 678898999999999988 8787776666656553
No 119
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=26.79 E-value=46 Score=26.46 Aligned_cols=18 Identities=17% Similarity=0.244 Sum_probs=15.5
Q ss_pred HHHHHHHHhcCcchHHHH
Q 010514 342 QELQEAQAAGCRTSSEAH 359 (508)
Q Consensus 342 ~~Lq~~R~~Gi~tl~e~~ 359 (508)
.-|..|++.||+|+++++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 358899999999999875
No 120
>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=26.60 E-value=63 Score=25.72 Aligned_cols=24 Identities=21% Similarity=0.646 Sum_probs=20.4
Q ss_pred CHHHHHHHhCC-CCHHHHHHHHHhh
Q 010514 68 NWGEVSEHVGT-KSKSQCIDHYNAI 91 (508)
Q Consensus 68 nW~~IA~~v~~-kt~~ec~~hy~~~ 91 (508)
-|..||..+|. -+.++|+.+|.++
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHH
Confidence 49999999986 4789999999764
No 121
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=24.67 E-value=1.2e+02 Score=22.02 Aligned_cols=34 Identities=9% Similarity=0.140 Sum_probs=26.5
Q ss_pred CCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 474 GNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 474 ~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.+.++..+....+.+....+.++.+-|.+.|||.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 5667777777777777778888888888888874
No 122
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=23.67 E-value=1.8e+02 Score=26.48 Aligned_cols=49 Identities=27% Similarity=0.457 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHhC----C--CCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 459 HYLKMLEILSVEIYKG----N--VSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 459 ~YL~iK~~LirE~~k~----g--~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
-|.-|.+.+...++++ | ..+..+.-..+.+.+|-+.|.|.-|.+.|+|.
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~ 66 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVE 66 (125)
T ss_pred HHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 5788888877776653 3 34655555568999999999999999999973
No 123
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=23.58 E-value=1.7e+02 Score=28.24 Aligned_cols=52 Identities=8% Similarity=-0.049 Sum_probs=41.4
Q ss_pred HHhCCCchHHHHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 451 GEIKILPAHYLKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 451 s~lrL~P~~YL~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
..++|.|.+|..+--+ ..++.++.++..+.+.++...+.++.+=|.+.|||.
T Consensus 39 ~~~gLt~~q~~iL~~L-----~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~ 90 (185)
T PRK13777 39 KPYDLNINEHHILWIA-----YHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLT 90 (185)
T ss_pred HHCCCCHHHHHHHHHH-----HhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEE
Confidence 4689999999766321 345667877777788899999999999999999984
No 124
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=22.56 E-value=13 Score=27.45 Aligned_cols=19 Identities=37% Similarity=1.087 Sum_probs=14.1
Q ss_pred EeccCC---CCcccHHHhhcCC
Q 010514 5 KCAMCS---DFDLCVECFSVGA 23 (508)
Q Consensus 5 ~C~~C~---~~~lC~~Cfs~G~ 23 (508)
+|..|. +..+|+.|+-.|.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 577785 4679999996554
No 125
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.45 E-value=38 Score=28.27 Aligned_cols=19 Identities=32% Similarity=0.999 Sum_probs=9.0
Q ss_pred cEEEeccCCCCcccHHHhhc
Q 010514 2 VRIKCAMCSDFDLCVECFSV 21 (508)
Q Consensus 2 ~ri~C~~C~~~~lC~~Cfs~ 21 (508)
+.+.|.+|. |-+|-.||.-
T Consensus 27 ~FVAC~eC~-fPvCr~CyEY 45 (80)
T PF14569_consen 27 VFVACHECA-FPVCRPCYEY 45 (80)
T ss_dssp B--S-SSS------HHHHHH
T ss_pred EEEEEcccC-CccchhHHHH
Confidence 568899998 8899999863
No 126
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=22.33 E-value=1.9e+02 Score=23.81 Aligned_cols=46 Identities=13% Similarity=0.183 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhCCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 461 LKMLEILSVEIYKGNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 461 L~iK~~LirE~~k~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
|++.+.++.-..++ ..+.++.....+++.+.+.....-|.+.|+|.
T Consensus 4 lt~~~~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 4 LTVTQKILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred hhHHHHHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 44555555444444 88999999999999999999999999999985
No 127
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=22.12 E-value=2.4e+02 Score=23.94 Aligned_cols=50 Identities=8% Similarity=0.230 Sum_probs=36.7
Q ss_pred HhhhhhhccCChHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCcchHHHHH
Q 010514 310 QQYKVFMRFHSKEDHEELLKSVIEEH---RIVKRIQELQEAQAAGCRTSSEAHR 360 (508)
Q Consensus 310 ~~l~~farf~~~~d~~~l~~~l~~e~---~Lr~rI~~Lq~~R~~Gi~tl~e~~~ 360 (508)
..+..|..+.++++...|++.|.-.. .|-.| .+...|...|++.-+=++.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~l~t~~e~~~Ls~R-~~I~~ll~~G~S~~eIA~~ 59 (88)
T TIGR02531 7 ELFDAILTLKNREECYRFFDDIATINEIQSLAQR-LQVAKMLKQGKTYSDIEAE 59 (88)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhCCHHHHHhhhHH-HHHHHHHHCCCCHHHHHHH
Confidence 34567889999999999999998554 45566 7777888889764444433
No 128
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.80 E-value=2.1e+02 Score=24.14 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCCCHHHHHHHHHhh
Q 010514 51 ADEEILLLEGIEMYGFGNWGEVSEHVGTKSKSQCIDHYNAI 91 (508)
Q Consensus 51 a~Eel~LLe~i~~~G~gnW~~IA~~v~~kt~~ec~~hy~~~ 91 (508)
.+.|..+|.++...|--.|.+||+.+|. ++..|..+...+
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~~L 41 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVKRL 41 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHHHH
No 129
>PF12488 DUF3704: Protein of unknown function (DUF3704) ; InterPro: IPR022173 This domain family is found in eukaryotes, and is approximately 30 amino acids in length.
Probab=20.81 E-value=35 Score=22.79 Aligned_cols=9 Identities=22% Similarity=0.187 Sum_probs=7.4
Q ss_pred cccccCCCc
Q 010514 226 LSGYNFKRQ 234 (508)
Q Consensus 226 ~~GYmP~R~ 234 (508)
..||||.|+
T Consensus 7 S~gyMp~s~ 15 (27)
T PF12488_consen 7 SFGYMPRSG 15 (27)
T ss_pred ccceeeecc
Confidence 479999886
No 130
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.75 E-value=4.9e+02 Score=21.53 Aligned_cols=60 Identities=17% Similarity=0.129 Sum_probs=45.3
Q ss_pred HhcccCCCCC---cCcCCChHHHHHHHhhhhhhc--cCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 010514 287 LERNLLFPDP---FERNLSPEEREIYQQYKVFMR--FHSKEDHEELLKSVIEEHRIVKRIQELQE 346 (508)
Q Consensus 287 ~e~~Ll~~~~---~~k~~tkeerel~~~l~~far--f~~~~d~~~l~~~l~~e~~Lr~rI~~Lq~ 346 (508)
.+.|||.+.. ..+.++.++-.....++.+.+ -++-.+...++..+-+-..|+++|.+|++
T Consensus 22 e~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~~l~~l~~ 86 (91)
T cd04766 22 ERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAELRAELDELRA 86 (91)
T ss_pred HHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568887532 345678777777777777766 67888898999888888889988888864
No 131
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=20.11 E-value=2.1e+02 Score=31.10 Aligned_cols=77 Identities=16% Similarity=0.149 Sum_probs=53.8
Q ss_pred HHHHhhhhH---HhcccCCCCCcCcCCChHHHH----HHHhhhhhhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 010514 278 ERKRRKDFI---LERNLLFPDPFERNLSPEERE----IYQQYKVFMRFHSKEDHEELLKSVIEEHRIVKRIQELQEAQAA 350 (508)
Q Consensus 278 eR~rRK~~i---~e~~Ll~~~~~~k~~tkeere----l~~~l~~farf~~~~d~~~l~~~l~~e~~Lr~rI~~Lq~~R~~ 350 (508)
-|+|||-|. +++--=|+- ..-.+|.||.. ++..|+.+..-|..-+|...+..|.++ +-||..
T Consensus 160 YR~RRk~fadiA~nyKhGdpI-P~veYT~eEikTWg~Vf~~L~~Ly~~HAC~ey~~~f~lLe~~----------cg~~ed 228 (461)
T KOG3820|consen 160 YRQRRKFFADIAFNYKHGDPI-PRVEYTEEEIKTWGTVFRTLTDLYPTHACAEYLDNFPLLEKY----------CGYRED 228 (461)
T ss_pred HHHHHHHHHHHHHhcccCCCC-CccccCHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh----------cCcCCC
Confidence 488898665 332221221 23467888854 788899998888888888877766544 556778
Q ss_pred cCcchHHHHHHHHHH
Q 010514 351 GCRTSSEAHRFLEQK 365 (508)
Q Consensus 351 Gi~tl~e~~~Ye~~k 365 (508)
.|-.|+++..|.+.+
T Consensus 229 nIPQLeDVs~FLk~~ 243 (461)
T KOG3820|consen 229 NIPQLEDVSKFLKKK 243 (461)
T ss_pred CcchHHHHHHHHHhc
Confidence 888889999998754
No 132
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=20.05 E-value=1.1e+02 Score=30.65 Aligned_cols=50 Identities=20% Similarity=0.254 Sum_probs=40.8
Q ss_pred hHHHHHHHHHHHHHHh-CCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 458 AHYLKMLEILSVEIYK-GNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 458 ~~YL~iK~~LirE~~k-~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
..|+..=++|+.-.++ .++++..|+..+..+++|-++.+..=|.++||+.
T Consensus 11 ~~~m~~~e~l~~laae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~Le 61 (269)
T COG5340 11 GLSMRESELLSHLAAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLE 61 (269)
T ss_pred hhhHHHHHHHHHHHHHhCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhh
Confidence 3466666666655556 4689999999999999999999999999999984
No 133
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=20.03 E-value=1.2e+02 Score=23.05 Aligned_cols=34 Identities=12% Similarity=0.205 Sum_probs=29.9
Q ss_pred CCCCCHHHhhhhhccCcccHHHHHHHHHHCCCCC
Q 010514 474 GNVSKKSDAHNLFKVEPNKVDRVYDMLVRKGIAQ 507 (508)
Q Consensus 474 ~g~l~~~~a~~l~kiD~~K~~rIydfl~~~Gwi~ 507 (508)
.+.++..+.-+.+.+....+.+++.-|.+.|||.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4568888888889999999999999999999984
Done!