Query 022048
Match_columns 303
No_of_seqs 296 out of 879
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 07:37:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022048.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022048hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00073 H15 linker histone 1 a 99.8 8.5E-21 1.8E-25 150.6 9.5 71 122-192 2-78 (88)
2 smart00526 H15 Domain in histo 99.8 9.1E-21 2E-25 142.3 8.0 64 122-185 2-66 (66)
3 PF00538 Linker_histone: linke 99.8 8.7E-21 1.9E-25 146.7 7.3 68 123-190 1-76 (77)
4 KOG4012 Histone H1 [Chromatin 99.5 2.9E-14 6.3E-19 132.4 6.6 74 119-192 39-119 (243)
5 PF00249 Myb_DNA-binding: Myb- 99.3 1.9E-12 4E-17 91.4 4.1 48 5-57 1-48 (48)
6 smart00717 SANT SANT SWI3, AD 99.0 5.9E-10 1.3E-14 75.6 5.4 48 5-58 1-48 (49)
7 PLN03212 Transcription repress 99.0 5E-10 1.1E-14 104.4 5.0 56 1-61 21-76 (249)
8 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 2.1E-09 4.5E-14 72.0 5.1 45 7-57 1-45 (45)
9 PF13921 Myb_DNA-bind_6: Myb-l 98.8 5.8E-09 1.3E-13 76.1 5.4 43 8-57 1-43 (60)
10 KOG0048 Transcription factor, 98.8 5.6E-09 1.2E-13 96.3 5.4 52 5-61 9-60 (238)
11 PLN03091 hypothetical protein; 98.7 9.7E-09 2.1E-13 102.3 4.9 54 3-61 12-65 (459)
12 PLN03212 Transcription repress 98.5 1.1E-07 2.5E-12 88.8 4.9 52 3-61 76-127 (249)
13 PLN03091 hypothetical protein; 98.4 3.2E-07 6.9E-12 91.7 5.0 50 3-59 65-114 (459)
14 TIGR01557 myb_SHAQKYF myb-like 97.8 4.6E-05 1E-09 56.6 5.4 50 3-56 1-53 (57)
15 KOG0048 Transcription factor, 97.8 2.7E-05 5.9E-10 71.9 4.8 52 3-61 60-111 (238)
16 KOG0049 Transcription factor, 97.7 3.3E-05 7.2E-10 80.5 4.5 54 2-61 357-410 (939)
17 KOG0051 RNA polymerase I termi 97.5 8.7E-05 1.9E-09 77.0 3.6 49 4-60 383-431 (607)
18 KOG0457 Histone acetyltransfer 97.3 0.00023 4.9E-09 71.3 4.1 50 6-61 73-122 (438)
19 PF13837 Myb_DNA-bind_4: Myb/S 97.2 0.00024 5.1E-09 55.0 2.5 54 5-60 1-67 (90)
20 KOG0049 Transcription factor, 96.6 0.0014 3.1E-08 68.7 3.0 49 3-57 410-458 (939)
21 PF09111 SLIDE: SLIDE; InterP 96.4 0.003 6.6E-08 53.3 3.3 58 2-59 46-112 (118)
22 PF13873 Myb_DNA-bind_5: Myb/S 96.0 0.0065 1.4E-07 46.3 3.1 53 5-59 2-71 (78)
23 PF13325 MCRS_N: N-terminal re 95.9 0.011 2.4E-07 54.3 4.6 56 4-61 72-130 (199)
24 PF08074 CHDCT2: CHDCT2 (NUC03 95.7 0.0082 1.8E-07 53.7 2.8 47 6-53 4-58 (173)
25 KOG0050 mRNA splicing protein 95.5 0.0077 1.7E-07 61.9 2.3 46 6-57 8-53 (617)
26 PLN03142 Probable chromatin-re 94.7 0.041 8.9E-07 61.0 5.1 57 4-60 925-987 (1033)
27 KOG1279 Chromatin remodeling f 94.6 0.067 1.5E-06 55.2 6.2 49 4-59 252-300 (506)
28 COG5147 REB1 Myb superfamily p 94.6 0.0097 2.1E-07 61.3 0.1 49 4-60 290-338 (512)
29 COG5114 Histone acetyltransfer 94.5 0.03 6.5E-07 54.9 3.1 46 7-58 65-110 (432)
30 PF08914 Myb_DNA-bind_2: Rap1 94.3 0.07 1.5E-06 40.7 4.3 50 5-59 2-59 (65)
31 PF10264 Stork_head: Winged he 93.4 0.4 8.7E-06 38.2 7.0 65 124-190 9-77 (80)
32 PF14338 Mrr_N: Mrr N-terminal 93.3 0.28 6.1E-06 38.8 6.1 66 126-191 1-82 (92)
33 COG5147 REB1 Myb superfamily p 93.1 0.043 9.2E-07 56.7 1.5 47 5-57 20-66 (512)
34 COG5259 RSC8 RSC chromatin rem 92.6 0.12 2.7E-06 52.8 4.0 45 5-56 279-323 (531)
35 KOG2656 DNA methyltransferase 91.6 0.18 4E-06 50.6 3.7 59 6-65 131-193 (445)
36 KOG0384 Chromodomain-helicase 91.4 0.11 2.4E-06 58.3 2.2 53 7-59 1135-1193(1373)
37 PF00250 Fork_head: Fork head 91.3 0.32 6.9E-06 39.5 4.3 56 125-184 4-63 (96)
38 cd00059 FH Forkhead (FH), also 91.1 0.42 9.2E-06 37.6 4.6 33 125-158 4-36 (78)
39 KOG4282 Transcription factor G 89.6 0.36 7.7E-06 46.7 3.7 52 6-59 55-115 (345)
40 KOG0051 RNA polymerase I termi 86.9 0.6 1.3E-05 49.2 3.6 54 3-62 434-512 (607)
41 smart00339 FH FORKHEAD. FORKHE 86.4 1.4 2.9E-05 35.4 4.6 32 126-158 5-36 (89)
42 PF12776 Myb_DNA-bind_3: Myb/S 82.6 1.4 3E-05 34.2 3.1 51 7-59 1-64 (96)
43 KOG0050 mRNA splicing protein 81.2 1.2 2.6E-05 46.4 2.9 47 5-59 59-105 (617)
44 PF11839 DUF3359: Protein of u 76.6 18 0.00038 29.9 7.8 52 239-290 35-86 (96)
45 PF14947 HTH_45: Winged helix- 75.9 2.7 5.9E-05 32.3 2.8 56 128-191 5-60 (77)
46 PF08672 APC2: Anaphase promot 75.4 3 6.6E-05 31.3 2.8 26 164-189 35-60 (60)
47 PF04504 DUF573: Protein of un 72.0 2.8 6E-05 34.2 2.0 58 4-61 3-66 (98)
48 PF09420 Nop16: Ribosome bioge 70.8 12 0.00026 32.8 5.9 51 4-57 113-163 (164)
49 PRK13923 putative spore coat p 67.6 1.9 4.1E-05 38.9 0.2 60 1-61 1-60 (170)
50 PF05402 PqqD: Coenzyme PQQ sy 63.1 12 0.00026 27.3 3.8 39 142-180 28-67 (68)
51 COG5118 BDP1 Transcription ini 59.1 15 0.00033 37.3 4.7 48 5-59 365-412 (507)
52 PF05732 RepL: Firmicute plasm 58.1 21 0.00045 31.7 5.0 71 127-201 42-127 (165)
53 PF05928 Zea_mays_MuDR: Zea ma 54.6 25 0.00054 32.0 4.9 26 241-266 12-37 (207)
54 smart00550 Zalpha Z-DNA-bindin 51.6 74 0.0016 23.8 6.5 59 125-191 5-66 (68)
55 PF08784 RPA_C: Replication pr 51.3 30 0.00066 27.4 4.6 52 124-182 45-97 (102)
56 PF11626 Rap1_C: TRF2-interact 50.1 15 0.00032 29.0 2.6 13 5-17 47-59 (87)
57 PF06969 HemN_C: HemN C-termin 43.5 50 0.0011 23.9 4.4 48 138-191 15-62 (66)
58 PF05066 HARE-HTH: HB1, ASXL, 43.2 69 0.0015 23.9 5.2 62 126-189 2-69 (72)
59 cd00092 HTH_CRP helix_turn_hel 42.9 35 0.00075 24.2 3.4 42 143-191 25-67 (67)
60 COG4742 Predicted transcriptio 41.6 41 0.00089 32.3 4.5 48 136-191 20-67 (260)
61 COG3432 Predicted transcriptio 39.8 23 0.0005 29.2 2.2 56 128-191 17-76 (95)
62 smart00346 HTH_ICLR helix_turn 35.8 1.3E+02 0.0027 22.7 5.7 52 131-191 10-63 (91)
63 PF13325 MCRS_N: N-terminal re 33.4 75 0.0016 29.4 4.7 50 7-61 1-50 (199)
64 smart00419 HTH_CRP helix_turn_ 32.2 64 0.0014 21.2 3.2 25 165-189 23-47 (48)
65 smart00347 HTH_MARR helix_turn 31.6 87 0.0019 23.4 4.2 49 126-184 10-58 (101)
66 PF01726 LexA_DNA_bind: LexA D 31.3 1.2E+02 0.0027 22.7 4.9 23 165-187 41-63 (65)
67 smart00420 HTH_DEOR helix_turn 30.4 1.6E+02 0.0034 19.4 4.9 40 141-187 12-51 (53)
68 PF02295 z-alpha: Adenosine de 30.1 1.3E+02 0.0028 22.8 4.8 51 127-185 5-55 (66)
69 TIGR01932 hflC HflC protein. H 29.1 1.8E+02 0.0039 28.1 6.8 13 265-277 254-266 (317)
70 cd01392 HTH_LacI Helix-turn-he 28.2 52 0.0011 22.4 2.2 36 138-173 3-38 (52)
71 PF13463 HTH_27: Winged helix 28.1 88 0.0019 22.3 3.5 47 129-184 6-52 (68)
72 TIGR01933 hflK HflK protein. H 26.8 2.4E+02 0.0052 25.9 6.9 13 272-284 205-217 (261)
73 KOG4329 DNA-binding protein [G 25.3 1.1E+02 0.0024 31.2 4.7 46 7-58 279-324 (445)
74 PF08220 HTH_DeoR: DeoR-like h 24.8 1.6E+02 0.0034 21.2 4.3 27 165-191 29-55 (57)
75 PF08671 SinI: Anti-repressor 24.7 1.4E+02 0.003 19.7 3.5 25 127-156 5-29 (30)
76 PF12363 DUF3647: Phage protei 24.6 2.1E+02 0.0045 23.7 5.5 53 127-181 53-105 (113)
77 smart00595 MADF subfamily of S 24.5 46 0.001 25.3 1.5 26 27-59 29-54 (89)
78 PRK11029 FtsH protease regulat 24.2 2.5E+02 0.0055 27.7 6.9 15 271-285 272-286 (334)
79 smart00354 HTH_LACI helix_turn 23.7 63 0.0014 24.1 2.1 39 136-174 4-42 (70)
80 TIGR02894 DNA_bind_RsfA transc 23.4 28 0.0006 31.3 0.1 53 6-61 5-59 (161)
81 PF00356 LacI: Bacterial regul 23.4 49 0.0011 23.4 1.3 39 136-174 3-41 (46)
82 PF08343 RNR_N: Ribonucleotide 23.1 68 0.0015 25.6 2.2 49 132-182 4-59 (82)
83 PF13412 HTH_24: Winged helix- 22.2 1.4E+02 0.0031 20.1 3.5 38 136-180 10-47 (48)
84 PF11839 DUF3359: Protein of u 21.2 4.8E+02 0.01 21.6 7.5 23 256-278 59-81 (96)
85 PF09012 FeoC: FeoC like trans 21.1 1.4E+02 0.003 22.1 3.5 38 147-184 3-48 (69)
86 KOG2009 Transcription initiati 20.7 1.1E+02 0.0024 32.7 3.8 49 5-60 409-457 (584)
87 KOG4468 Polycomb-group transcr 20.7 51 0.0011 35.5 1.4 26 5-31 88-113 (782)
88 KOG2668 Flotillins [Intracellu 20.3 3.2E+02 0.0069 27.9 6.6 25 265-289 331-355 (428)
89 cd03404 Band_7_HflK Band_7_Hfl 20.2 3.7E+02 0.0081 24.7 6.9 16 264-279 222-237 (266)
90 PF03234 CDC37_N: Cdc37 N term 20.1 1.8E+02 0.0039 26.4 4.6 39 119-157 101-140 (177)
91 PRK15431 ferrous iron transpor 20.0 2.1E+02 0.0047 22.8 4.4 40 145-184 3-50 (78)
No 1
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=99.84 E-value=8.5e-21 Score=150.56 Aligned_cols=71 Identities=35% Similarity=0.525 Sum_probs=67.3
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCC-ccHHHHHHHHHHhhhhCCceeeeC-----cceecCCC
Q 022048 122 RSIVRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAP-PDFKRLLSAKLKYLAGTGKLVKIK-----RKYRIAPT 192 (303)
Q Consensus 122 ~~hP~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp-~nf~~lL~~~LKrlV~~GkLvkvK-----~syKl~~~ 192 (303)
.+||+|.+||+|||.+|+||+|||+++|++||+++|++. ++|+.+|+.+|+++|++|.|++++ |+|+|++.
T Consensus 2 ~~hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~~~ 78 (88)
T cd00073 2 PSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSKK 78 (88)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCCCCccceEeCCC
Confidence 579999999999999999999999999999999999965 999999999999999999999999 89999743
No 2
>smart00526 H15 Domain in histone families 1 and 5.
Probab=99.83 E-value=9.1e-21 Score=142.29 Aligned_cols=64 Identities=42% Similarity=0.610 Sum_probs=61.7
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCC-CccHHHHHHHHHHhhhhCCceeeeCc
Q 022048 122 RSIVRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWA-PPDFKRLLSAKLKYLAGTGKLVKIKR 185 (303)
Q Consensus 122 ~~hP~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v-p~nf~~lL~~~LKrlV~~GkLvkvK~ 185 (303)
.+||+|.+||+|||.+|+||+|||+++|++||+++|++ |++|+.+|+.+|+++|++|.|+|++|
T Consensus 2 ~~hP~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 2 PSHPPYSEMITEAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQVKG 66 (66)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeecCC
Confidence 57999999999999999999999999999999999995 88999999999999999999999987
No 3
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=99.83 E-value=8.7e-21 Score=146.67 Aligned_cols=68 Identities=38% Similarity=0.575 Sum_probs=63.9
Q ss_pred CCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCC--Cc-cHHHHHHHHHHhhhhCCceeeeC-----cceecC
Q 022048 123 SIVRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWA--PP-DFKRLLSAKLKYLAGTGKLVKIK-----RKYRIA 190 (303)
Q Consensus 123 ~hP~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v--p~-nf~~lL~~~LKrlV~~GkLvkvK-----~syKl~ 190 (303)
+||+|.+||+|||.+|+||+|||+++|++||+++|++ ++ +|+.+|+.+|+++|++|.|+|++ |+|||+
T Consensus 1 shP~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~ 76 (77)
T PF00538_consen 1 SHPPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLS 76 (77)
T ss_dssp -SSCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEES
T ss_pred CCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecC
Confidence 5999999999999999999999999999999999973 44 89999999999999999999999 899996
No 4
>KOG4012 consensus Histone H1 [Chromatin structure and dynamics]
Probab=99.49 E-value=2.9e-14 Score=132.42 Aligned_cols=74 Identities=30% Similarity=0.359 Sum_probs=67.0
Q ss_pred CCCCCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCC--CccHHHHHHHHHHhhhhCCceeeeCc-----ceecCC
Q 022048 119 APKRSIVRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWA--PPDFKRLLSAKLKYLAGTGKLVKIKR-----KYRIAP 191 (303)
Q Consensus 119 ~~~~~hP~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v--p~nf~~lL~~~LKrlV~~GkLvkvK~-----syKl~~ 191 (303)
-....||+|.+||.|||.+|+||+|+|+.+|++||.++|.. -++|+.+|+..|+++|.+|.|+|++| +|+|..
T Consensus 39 k~~a~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k~n~~lk~alK~~v~~g~l~QtkG~GAsGsFk~~K 118 (243)
T KOG4012|consen 39 KKKAAHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEKNNSRLKLALKKGVSKGVLVQTKGTGASGSFKLAK 118 (243)
T ss_pred ccccCCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhhhhHHHHHHHHhhhccCceeeeccCCccccccccc
Confidence 35678999999999999999999999999999999999942 46789999999999999999999985 999875
Q ss_pred C
Q 022048 192 T 192 (303)
Q Consensus 192 ~ 192 (303)
-
T Consensus 119 K 119 (243)
T KOG4012|consen 119 K 119 (243)
T ss_pred c
Confidence 3
No 5
>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=99.31 E-value=1.9e-12 Score=91.40 Aligned_cols=48 Identities=27% Similarity=0.533 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
|++||+||++.|+++|.+||.++|..|+.. |. .+||..||+++|++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~--~~---~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKR--MP---GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHH--HS---SSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHH--cC---CCCCHHHHHHHHHhhC
Confidence 689999999999999999999889999982 22 3899999999999974
No 6
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.01 E-value=5.9e-10 Score=75.57 Aligned_cols=48 Identities=33% Similarity=0.601 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcc
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSV 58 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k 58 (303)
+..||++|+..|+.+|..||.++|..|... |.+||..+|+++|+++.+
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~------~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKE------LPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHH------cCCCCHHHHHHHHHHHcC
Confidence 468999999999999999997799999882 458999999999999864
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.97 E-value=5e-10 Score=104.37 Aligned_cols=56 Identities=32% Similarity=0.526 Sum_probs=48.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 1 MGAPKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 1 Mg~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
+|.+|++||+|||+.|+..|++||.++|..|.+. + ..+||+.||++||.|++.-..
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~--~---g~gRT~KQCReRW~N~L~P~I 76 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKR--A---GLLRCGKSCRLRWMNYLRPSV 76 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHh--h---hcCCCcchHHHHHHHhhchhc
Confidence 4788999999999999999999999999999872 2 148999999999999985543
No 8
>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=98.91 E-value=2.1e-09 Score=71.95 Aligned_cols=45 Identities=36% Similarity=0.689 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 7 KWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 7 ~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
+||.||+..|+.++.+||.++|..|... +.+||..+|+++|.++.
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~------~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKE------LPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhH------cCCCCHHHHHHHHHHhC
Confidence 5999999999999999998899999982 45799999999999863
No 9
>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=98.83 E-value=5.8e-09 Score=76.06 Aligned_cols=43 Identities=35% Similarity=0.616 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 8 WTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 8 WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
||.|||+.|+.+|.+||. +|..|.. .|..||..+|++||++.+
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~------~l~~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAE------HLGNRTPKQCRNRWRNHL 43 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHH------HSTTS-HHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHH------HHCcCCHHHHHHHHHHHC
Confidence 999999999999999996 9999988 244699999999999944
No 10
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.80 E-value=5.6e-09 Score=96.28 Aligned_cols=52 Identities=23% Similarity=0.284 Sum_probs=46.2
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
|++||+|||+.|++.|++||.|+|..|.++- + | +|++.+|+-||.|+++-..
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~--g--l-~R~GKSCRlRW~NyLrP~i 60 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLA--G--L-RRCGKSCRLRWTNYLRPDL 60 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhc--C--C-CccchHHHHHhhcccCCCc
Confidence 4999999999999999999999999999842 2 2 8999999999999987633
No 11
>PLN03091 hypothetical protein; Provisional
Probab=98.73 E-value=9.7e-09 Score=102.34 Aligned_cols=54 Identities=24% Similarity=0.362 Sum_probs=46.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 3 APKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
.+|++||+|||+.|+..|++||.++|..|.+. + ..+||+.||++||.|++.-..
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~--~---g~gRT~KQCRERW~NyLdP~I 65 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQ--A---GLQRCGKSCRLRWINYLRPDL 65 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhh--h---ccCcCcchHhHHHHhccCCcc
Confidence 36789999999999999999999999999872 1 148999999999999876544
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.50 E-value=1.1e-07 Score=88.80 Aligned_cols=52 Identities=17% Similarity=0.218 Sum_probs=46.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 3 APKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
..+.+||.|||+.|+..+..||. +|..|.. .|++||..+||.||.++++...
T Consensus 76 I~kgpWT~EED~lLlel~~~~Gn-KWs~IAk------~LpGRTDnqIKNRWns~LrK~l 127 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGN-RWSLIAG------RIPGRTDNEIKNYWNTHLRKKL 127 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccc-cHHHHHh------hcCCCCHHHHHHHHHHHHhHHH
Confidence 46789999999999999999997 9999988 3679999999999998877643
No 13
>PLN03091 hypothetical protein; Provisional
Probab=98.38 E-value=3.2e-07 Score=91.70 Aligned_cols=50 Identities=20% Similarity=0.333 Sum_probs=45.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 3 APKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
..+.+||.|||+.|++.+.+||. +|..|.. .|+|||..+||+||..+++.
T Consensus 65 IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk------~LPGRTDnqIKNRWnslLKK 114 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGN-RWSQIAA------QLPGRTDNEIKNLWNSCLKK 114 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCc-chHHHHH------hcCCCCHHHHHHHHHHHHHH
Confidence 46889999999999999999998 9999997 36799999999999987765
No 14
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.80 E-value=4.6e-05 Score=56.60 Aligned_cols=50 Identities=18% Similarity=0.349 Sum_probs=40.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCch---hhhccCCCccccCCCCChHHHHHHHHhh
Q 022048 3 APKQKWTQEEEAALKAGVIKHGAGKW---RTILKDPEFSGVLYLRSNVDLKDKWRNM 56 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~k~G~G~W---~~I~~~~~f~~~l~~RT~vdLKDKWRnl 56 (303)
++|..||+||...++.||+.||.|+| +.|+.. +. ..+.|..+++-....+
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~--~~--~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILEL--MV--VDGLTRDQVASHLQKY 53 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHH--cC--CCCCCHHHHHHHHHHH
Confidence 57889999999999999999999999 999873 22 1233999998765443
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.78 E-value=2.7e-05 Score=71.94 Aligned_cols=52 Identities=19% Similarity=0.292 Sum_probs=45.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 3 APKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
-+|+.||+|||+.|+..-..||. +|+.|++ .|+|||.-.+|.-|...++...
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GN-rWs~IA~------~LPGRTDNeIKN~Wnt~lkkkl 111 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGN-RWSLIAG------RLPGRTDNEVKNHWNTHLKKKL 111 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCc-HHHHHHh------hCCCcCHHHHHHHHHHHHHHHH
Confidence 46899999999999999999998 8999998 4789999999999976654433
No 16
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.70 E-value=3.3e-05 Score=80.55 Aligned_cols=54 Identities=22% Similarity=0.453 Sum_probs=47.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 2 GAPKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 2 g~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
|.++.+||++||..|+.+|.+||..-|.+|.. .|++|+..||++||.|.+-..+
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~------~vPnRSdsQcR~RY~nvL~~s~ 410 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQ------AVPNRSDSQCRERYTNVLNRSA 410 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHH------hcCCccHHHHHHHHHHHHHHhh
Confidence 56788999999999999999999999999987 2569999999999988775544
No 17
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.45 E-value=8.7e-05 Score=77.02 Aligned_cols=49 Identities=39% Similarity=0.694 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccC
Q 022048 4 PKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMS 60 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~ 60 (303)
.|+.||+||++.|...|..||. .|+.|-+ +-+|.+.+|+|+||++.+..
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~-------~lgr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGK-------ALGRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHH-------HHccCcHHHHHHHHHhhccc
Confidence 6889999999999999999997 9999987 34899999999999998774
No 18
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.29 E-value=0.00023 Score=71.32 Aligned_cols=50 Identities=24% Similarity=0.418 Sum_probs=43.8
Q ss_pred CCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 6 QKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 6 ~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
--||.+||=.|++++++||-|||..|.+. ...||.-+||+.|.++....-
T Consensus 73 ~~WtadEEilLLea~~t~G~GNW~dIA~h------IGtKtkeeck~hy~k~fv~s~ 122 (438)
T KOG0457|consen 73 PSWTADEEILLLEAAETYGFGNWQDIADH------IGTKTKEECKEHYLKHFVNSP 122 (438)
T ss_pred CCCChHHHHHHHHHHHHhCCCcHHHHHHH------HcccchHHHHHHHHHHHhcCc
Confidence 36999999999999999999999999982 347999999999999876543
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.19 E-value=0.00024 Score=54.98 Aligned_cols=54 Identities=22% Similarity=0.459 Sum_probs=35.1
Q ss_pred CCCCCHHHHHHHHHHHHh------hCC-----C--chhhhccCCCccccCCCCChHHHHHHHHhhcccC
Q 022048 5 KQKWTQEEEAALKAGVIK------HGA-----G--KWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMS 60 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k------~G~-----G--~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~ 60 (303)
|..||.+|+..|++.+.. ++. + -|..|... +...=..||+.||++||.||.+.-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~--l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEE--LAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHH--HHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHH--HHHcCCCCCHHHHHHHHHHHHHHH
Confidence 578999999999998887 221 1 59999773 211112799999999999998763
No 20
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.58 E-value=0.0014 Score=68.72 Aligned_cols=49 Identities=22% Similarity=0.384 Sum_probs=41.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 3 APKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
.++..||-.||+.|+..|++||.|+|.+|.. +|.+||..|+..|-+.+.
T Consensus 410 ~K~~rW~l~edeqL~~~V~~YG~g~WakcA~------~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 410 AKVERWTLVEDEQLLYAVKVYGKGNWAKCAM------LLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred hccCceeecchHHHHHHHHHHccchHHHHHH------HccccchhHHHHHHHHHH
Confidence 4678999999999999999999999999987 367899977766554444
No 21
>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=96.37 E-value=0.003 Score=53.31 Aligned_cols=58 Identities=22% Similarity=0.403 Sum_probs=44.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCC---Cchhhhcc----CCCcc--ccCCCCChHHHHHHHHhhccc
Q 022048 2 GAPKQKWTQEEEAALKAGVIKHGA---GKWRTILK----DPEFS--GVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 2 g~~r~~WT~EE~~~L~~GV~k~G~---G~W~~I~~----~~~f~--~~l~~RT~vdLKDKWRnl~k~ 59 (303)
+..++.||.|||..|+-.+.+||. |.|..|.. .|.|. =+|.+||+.+|..|-..|.+.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 356789999999999999999999 99988754 45543 345799999999999887653
No 22
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.99 E-value=0.0065 Score=46.32 Aligned_cols=53 Identities=30% Similarity=0.473 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHhh-----CC-----------CchhhhccCCCccccC-CCCChHHHHHHHHhhccc
Q 022048 5 KQKWTQEEEAALKAGVIKH-----GA-----------GKWRTILKDPEFSGVL-YLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~-----G~-----------G~W~~I~~~~~f~~~l-~~RT~vdLKDKWRnl~k~ 59 (303)
+..||.+|...|++.|++| |. .-|..|... |..+. ..||..+|+.+|.||...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~--lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEE--LNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHH--HHhcCCCCCCHHHHHHHHHHHHHH
Confidence 4589999999999999998 31 269999884 33222 389999999999999754
No 23
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=95.89 E-value=0.011 Score=54.25 Aligned_cols=56 Identities=23% Similarity=0.344 Sum_probs=46.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhCC--CchhhhccCCCccccC-CCCChHHHHHHHHhhcccCC
Q 022048 4 PKQKWTQEEEAALKAGVIKHGA--GKWRTILKDPEFSGVL-YLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~G~--G~W~~I~~~~~f~~~l-~~RT~vdLKDKWRnl~k~~~ 61 (303)
.|.+||.+||+.|..+.....+ ..+..|+.++ .++| .+||+.+|.+.|+.|.++..
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n--~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKN--RSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhC--hhhhccccCHHHHHHHHHHHHHhch
Confidence 5679999999999998877754 5799999964 4455 47999999999999998866
No 24
>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=95.67 E-value=0.0082 Score=53.66 Aligned_cols=47 Identities=32% Similarity=0.843 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCC--CC------ChHHHHHHH
Q 022048 6 QKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLY--LR------SNVDLKDKW 53 (303)
Q Consensus 6 ~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~--~R------T~vdLKDKW 53 (303)
.-|-..-|-+|+.||.+||.|.|.+|..||.|. +++ -+ +.-+.|.||
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~~f~-IiNEPFk~e~~kgnfle~KNkF 58 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDPRFA-IINEPFKTESQKGNFLEMKNKF 58 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCCcee-eecccccccccccchHHHHHHH
Confidence 468889999999999999999999999999986 221 12 235888887
No 25
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=95.49 E-value=0.0077 Score=61.91 Aligned_cols=46 Identities=28% Similarity=0.592 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 6 QKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 6 ~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
.-|+.-||+.|..+|.+||...|+.|.. .|+.-|..||+.||..+.
T Consensus 8 gvwrntEdeilkaav~kyg~nqws~i~s------ll~~kt~rqC~~rw~e~l 53 (617)
T KOG0050|consen 8 GVWRNTEDEVLKAAVMKYGKNQWSRIAS------LLNRKTARQCKARWEEWL 53 (617)
T ss_pred ceecccHHHHHHHHHHHcchHHHHHHHH------HHhhcchhHHHHHHHHHh
Confidence 4699999999999999999999999987 356789999999997554
No 26
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.67 E-value=0.041 Score=61.04 Aligned_cols=57 Identities=18% Similarity=0.286 Sum_probs=47.2
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCchhhhcc----CCC--ccccCCCCChHHHHHHHHhhcccC
Q 022048 4 PKQKWTQEEEAALKAGVIKHGAGKWRTILK----DPE--FSGVLYLRSNVDLKDKWRNMSVMS 60 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~----~~~--f~~~l~~RT~vdLKDKWRnl~k~~ 60 (303)
+++.||.|||..|+-.+.+||.|+|..|.. .|. |.-+|.+||+..|+.|...|.+.-
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~ 987 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLI 987 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHH
Confidence 456699999999999999999999999833 343 445578999999999998887653
No 27
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=94.62 E-value=0.067 Score=55.23 Aligned_cols=49 Identities=16% Similarity=0.348 Sum_probs=42.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 4 PKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
.+..||.+|+-.|+.||++||. .|.+|... ...||.-||=.|+..+=..
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~h------Vg~ks~eqCI~kFL~LPie 300 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD-DWNKVADH------VGTKSQEQCILKFLRLPIE 300 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc-cHHHHHhc------cCCCCHHHHHHHHHhcCcc
Confidence 3568999999999999999998 99999872 3589999999999888443
No 28
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=94.61 E-value=0.0097 Score=61.32 Aligned_cols=49 Identities=37% Similarity=0.631 Sum_probs=44.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccC
Q 022048 4 PKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMS 60 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~ 60 (303)
.++.||.||+..|..-|.++|. .|+.|-.. .+|-+-+|.|+||++.+..
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~-------~~rmp~~crd~wr~~~~~g 338 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHGG-SWTEIGKL-------LGRMPNDCRDRWRDYVKCG 338 (512)
T ss_pred hhccCccccccccccccccccc-hhhHhhhh-------hccCcHHHHHHHhhhcccc
Confidence 5789999999999999999996 99999773 3799999999999998873
No 29
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.49 E-value=0.03 Score=54.95 Aligned_cols=46 Identities=24% Similarity=0.412 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcc
Q 022048 7 KWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSV 58 (303)
Q Consensus 7 ~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k 58 (303)
-|+.+||-.|+++.+..|.|||..|... ...|+..+||+.|-.+.-
T Consensus 65 ~WgadEEllli~~~~TlGlGNW~dIady------iGsr~kee~k~HylK~y~ 110 (432)
T COG5114 65 GWGADEELLLIECLDTLGLGNWEDIADY------IGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CcCchHHHHHHHHHHhcCCCcHHHHHHH------HhhhhhHHHHHHHHHHHh
Confidence 5999999999999999999999999872 347999999999977754
No 30
>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=94.34 E-value=0.07 Score=40.67 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=31.3
Q ss_pred CCCCCHHHHHHHHHHHHhh---C---CCc--hhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 5 KQKWTQEEEAALKAGVIKH---G---AGK--WRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~---G---~G~--W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
|.++|.|||.+|++-|..+ | .|| |+.+.... +..+|-..++|||+..+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~-----~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKH-----PTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS------SSS--SHHHHHHHHHHT--
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHc-----CCCCCHHHHHHHHHHHHhc
Confidence 6789999999999999654 4 244 88887742 2489999999999766543
No 31
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=93.38 E-value=0.4 Score=38.24 Aligned_cols=65 Identities=18% Similarity=0.273 Sum_probs=55.9
Q ss_pred CCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHHHhCC-C--CccHHHHHHHHHHhhhhCCceeeeCcceecC
Q 022048 124 IVRLDNLIMEAITTLKE-PGGSNKTTIAAYIEEKYW-A--PPDFKRLLSAKLKYLAGTGKLVKIKRKYRIA 190 (303)
Q Consensus 124 hP~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y~-v--p~nf~~lL~~~LKrlV~~GkLvkvK~syKl~ 190 (303)
.-++.+.|..+|..|+- ....+..+|..++..+|+ + |+ ...|...|-.|+..|||....+-|.|-
T Consensus 9 fiPL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps--~e~l~~~L~~Li~erkIY~tg~GYfiv 77 (80)
T PF10264_consen 9 FIPLPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPS--QEVLYNTLGTLIKERKIYHTGEGYFIV 77 (80)
T ss_pred ceeHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCC--HHHHHHHHHHHHHcCceeeCCCceEee
Confidence 34689999999999994 667899999999999997 3 44 588999999999999999998777663
No 32
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=93.28 E-value=0.28 Score=38.81 Aligned_cols=66 Identities=23% Similarity=0.382 Sum_probs=56.2
Q ss_pred CHHHHHHHHHHhcCC-CCCCCHHHHHHHHHHhCCCC--------------ccHHHHHHHHHHhhhhCCceeeeC-cceec
Q 022048 126 RLDNLIMEAITTLKE-PGGSNKTTIAAYIEEKYWAP--------------PDFKRLLSAKLKYLAGTGKLVKIK-RKYRI 189 (303)
Q Consensus 126 ~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y~vp--------------~nf~~lL~~~LKrlV~~GkLvkvK-~syKl 189 (303)
+|++|+.-.|..|++ ....++..|...|.+++.++ +.|...++=++..|+..|-|..++ |.|+|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~rG~~~i 80 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKRGIWRI 80 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCCCceEE
Confidence 489999999999999 66789999999999987632 147888899999999999999974 78999
Q ss_pred CC
Q 022048 190 AP 191 (303)
Q Consensus 190 ~~ 191 (303)
.+
T Consensus 81 T~ 82 (92)
T PF14338_consen 81 TE 82 (92)
T ss_pred CH
Confidence 76
No 33
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=93.10 E-value=0.043 Score=56.69 Aligned_cols=47 Identities=23% Similarity=0.466 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
...|+..||+.|..+|++||+.+|..|... | ..|++.||+-||-|..
T Consensus 20 ~gsw~~~EDe~l~~~vk~l~~nnws~vas~--~----~~~~~kq~~~rw~~~l 66 (512)
T COG5147 20 GGSWKRTEDEDLKALVKKLGPNNWSKVASL--L----ISSTGKQSSNRWNNHL 66 (512)
T ss_pred CCCCCCcchhHHHHHHhhcccccHHHHHHH--h----cccccccccchhhhhh
Confidence 457999999999999999999999999883 3 4599999999995544
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=92.63 E-value=0.12 Score=52.76 Aligned_cols=45 Identities=13% Similarity=0.369 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhh
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNM 56 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl 56 (303)
...||.+|.-.|++||+.||. .|.+|... ...+|.-||=-++-+|
T Consensus 279 dk~WS~qE~~LLLEGIe~ygD-dW~kVA~H------VgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGD-DWDKVARH------VGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhh-hHHHHHHH------hCCCCHHHHHHHHHcC
Confidence 358999999999999999998 99999982 4589999999999766
No 35
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=91.58 E-value=0.18 Score=50.56 Aligned_cols=59 Identities=19% Similarity=0.210 Sum_probs=46.3
Q ss_pred CCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHH----HhhcccCCCCCC
Q 022048 6 QKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKW----RNMSVMSNGWGS 65 (303)
Q Consensus 6 ~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKW----Rnl~k~~~~~gs 65 (303)
.-||.||.+.|.+..++|.- .|-.|..-|.-..+-.+||--|||||| |++.+..+..++
T Consensus 131 n~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s~s 193 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPSNS 193 (445)
T ss_pred ccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCCch
Confidence 35999999999999999998 999998865211112469999999999 666666666655
No 36
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=91.45 E-value=0.11 Score=58.31 Aligned_cols=53 Identities=25% Similarity=0.594 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHhhCCCchhhhccCCCcc---ccC---CCCChHHHHHHHHhhccc
Q 022048 7 KWTQEEEAALKAGVIKHGAGKWRTILKDPEFS---GVL---YLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 7 ~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~---~~l---~~RT~vdLKDKWRnl~k~ 59 (303)
-|..++|..|+-||-+||.|+|..|..||.+. -+| ..=+.++|.-|-.-++..
T Consensus 1135 ~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~~yLls~ 1193 (1373)
T KOG0384|consen 1135 DWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRADYLLSL 1193 (1373)
T ss_pred CCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHHHHHHHH
Confidence 59999999999999999999999999999754 111 134567777776555443
No 37
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=91.34 E-value=0.32 Score=39.51 Aligned_cols=56 Identities=23% Similarity=0.243 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCC----CCccHHHHHHHHHHhhhhCCceeeeC
Q 022048 125 VRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYW----APPDFKRLLSAKLKYLAGTGKLVKIK 184 (303)
Q Consensus 125 P~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----vp~nf~~lL~~~LKrlV~~GkLvkvK 184 (303)
-+|..||..||.+ -..++.++.-|.+||+.+|+ .+..++.-|+..|. .+.-|++|.
T Consensus 4 ~sY~~LI~~Ai~~-sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS---~~~~F~kv~ 63 (96)
T PF00250_consen 4 YSYATLIAMAILS-SPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLS---LNKCFVKVP 63 (96)
T ss_dssp S-HHHHHHHHHHT-STTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHH---HSTTEEEES
T ss_pred CcHHHHHHHHHHh-CCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhcc---ccceeeecC
Confidence 4699999999998 34456899999999999997 25566777777663 445677764
No 38
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=91.07 E-value=0.42 Score=37.55 Aligned_cols=33 Identities=18% Similarity=0.182 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCC
Q 022048 125 VRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYW 158 (303)
Q Consensus 125 P~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~ 158 (303)
-+|..||..||.... .++.++.-|.+||+++|+
T Consensus 4 ~sY~~LI~~Ai~~sp-~~~lTL~eIy~~I~~~~p 36 (78)
T cd00059 4 YSYSALIAMAIQSSP-EKRLTLSEIYKWISDNFP 36 (78)
T ss_pred CCHHHHHHHHHHhCC-CCCeeHHHHHHHHHHhCC
Confidence 479999999999955 567899999999999997
No 39
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=89.58 E-value=0.36 Score=46.70 Aligned_cols=52 Identities=25% Similarity=0.394 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHHh----hCCCc-----hhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 6 QKWTQEEEAALKAGVIK----HGAGK-----WRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 6 ~~WT~EE~~~L~~GV~k----~G~G~-----W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
..||.+|+..|+....+ ++.|+ |..|... +...=.-||+.+|+.||.||.++
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k--~~~~g~~rs~~qck~K~~nl~k~ 115 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARK--MAELGYPRSPKQCKAKIENLKKK 115 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHH--HHHhCCCCCHHHHHHHHHHHHHH
Confidence 68999999999987653 34454 9999872 21111369999999999999887
No 40
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=86.94 E-value=0.6 Score=49.24 Aligned_cols=54 Identities=22% Similarity=0.354 Sum_probs=43.8
Q ss_pred CCCCCCCHHHHHHHHHHHH-------hh------------------CCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 3 APKQKWTQEEEAALKAGVI-------KH------------------GAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 3 ~~r~~WT~EE~~~L~~GV~-------k~------------------G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
+.|..||-||++.|++.|+ .| -.-+|..|.++ +..|+.++|+-||-.|.
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~------~~TR~~~qCr~Kw~kl~ 507 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEM------LGTRSRIQCRYKWYKLT 507 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHh------hcCCCcchHHHHHHHHH
Confidence 4788999999999999996 33 12379998773 56899999999999998
Q ss_pred ccCCC
Q 022048 58 VMSNG 62 (303)
Q Consensus 58 k~~~~ 62 (303)
.....
T Consensus 508 ~~~s~ 512 (607)
T KOG0051|consen 508 TSPSF 512 (607)
T ss_pred hhHHh
Confidence 77653
No 41
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=86.41 E-value=1.4 Score=35.43 Aligned_cols=32 Identities=22% Similarity=0.175 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCC
Q 022048 126 RLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYW 158 (303)
Q Consensus 126 ~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~ 158 (303)
+|..||..||... ..++.+...|.+||+++|.
T Consensus 5 sY~~lI~~ai~~s-p~~~ltl~~Iy~~I~~~~p 36 (89)
T smart00339 5 SYIALIAMAILSS-PDKRLTLSEIYKWIEDNFP 36 (89)
T ss_pred CHHHHHHHHHHhC-CCCCeeHHHHHHHHHHhCc
Confidence 5999999999995 4567899999999999986
No 42
>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=82.64 E-value=1.4 Score=34.24 Aligned_cols=51 Identities=27% Similarity=0.500 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhh-------CCC-----chhhhccCCCccccC-CCCChHHHHHHHHhhccc
Q 022048 7 KWTQEEEAALKAGVIKH-------GAG-----KWRTILKDPEFSGVL-YLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 7 ~WT~EE~~~L~~GV~k~-------G~G-----~W~~I~~~~~f~~~l-~~RT~vdLKDKWRnl~k~ 59 (303)
.||+++++.|++.+... +.| .|..|.. .|...+ ..-|..+|+.||..|.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~--~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAE--EFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHH--HHHHHhCCcccHHHHHHHHHHHHHH
Confidence 59999999999988644 222 4777876 343322 256788999999888765
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=81.21 E-value=1.2 Score=46.38 Aligned_cols=47 Identities=23% Similarity=0.449 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
+--||.|||+.|+....-+-+ .|.+|.. +-+||..+|-.||-|++-.
T Consensus 59 ~tews~eederlLhlakl~p~-qwrtIa~-------i~gr~~~qc~eRy~~ll~~ 105 (617)
T KOG0050|consen 59 KTEWSREEDERLLHLAKLEPT-QWRTIAD-------IMGRTSQQCLERYNNLLDV 105 (617)
T ss_pred hhhhhhhHHHHHHHHHHhcCC-ccchHHH-------HhhhhHHHHHHHHHHHHHH
Confidence 456999999999999988877 9999986 3489999999999988644
No 44
>PF11839 DUF3359: Protein of unknown function (DUF3359); InterPro: IPR021793 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=76.63 E-value=18 Score=29.93 Aligned_cols=52 Identities=42% Similarity=0.359 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022048 239 MTPQEAAAAAARAVAEAEAAVAEAEEAAREADVAEADAEVAQAFAAAAMKTL 290 (303)
Q Consensus 239 ~t~~EAA~aAA~aVAEAE~~~~~AeeA~~Eae~~e~~aE~a~~f~~~a~~~~ 290 (303)
.|++++-..+.-+-..|+.+...|.+|...|+.+.+.|+.||.-++.|.+-+
T Consensus 35 ~~a~~a~~~a~~a~~~A~~A~~~AdeA~~kA~~A~aaA~~Aqq~A~eAnek~ 86 (96)
T PF11839_consen 35 STAEQAQATAASAQSAAASAQQRADEAASKADAALAAAEAAQQTADEANEKA 86 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666777778888888888888888888888888887775543
No 45
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=75.90 E-value=2.7 Score=32.29 Aligned_cols=56 Identities=29% Similarity=0.366 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeCcceecCC
Q 022048 128 DNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIKRKYRIAP 191 (303)
Q Consensus 128 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK~syKl~~ 191 (303)
.++|.+-+..+. .+|.+.+-|....- ++ -..+...|+.|++.|-|...++.|+|.+
T Consensus 5 ~~Ii~~IL~~l~-~~~~~~t~i~~~~~----L~---~~~~~~yL~~L~~~gLI~~~~~~Y~lTe 60 (77)
T PF14947_consen 5 LEIIFDILKILS-KGGAKKTEIMYKAN----LN---YSTLKKYLKELEEKGLIKKKDGKYRLTE 60 (77)
T ss_dssp THHHHHHHHHH--TT-B-HHHHHTTST---------HHHHHHHHHHHHHTTSEEEETTEEEE-H
T ss_pred HHHHHHHHHHHH-cCCCCHHHHHHHhC----cC---HHHHHHHHHHHHHCcCeeCCCCEEEECc
Confidence 567888888887 67777777763332 21 2557889999999999988889999965
No 46
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=75.42 E-value=3 Score=31.27 Aligned_cols=26 Identities=27% Similarity=0.270 Sum_probs=21.5
Q ss_pred HHHHHHHHHhhhhCCceeeeCcceec
Q 022048 164 KRLLSAKLKYLAGTGKLVKIKRKYRI 189 (303)
Q Consensus 164 ~~lL~~~LKrlV~~GkLvkvK~syKl 189 (303)
...|...|-++|+.|+|+.+.|+|||
T Consensus 35 ~~eL~~fL~~lv~e~~L~~~~G~YkL 60 (60)
T PF08672_consen 35 LEELQEFLDRLVEEGKLECSGGSYKL 60 (60)
T ss_dssp HHHHHHHHHHHHHTTSEE--TTEEEE
T ss_pred HHHHHHHHHHHHHCCcEEecCCEEeC
Confidence 36688899999999999999999997
No 47
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=72.04 E-value=2.8 Score=34.19 Aligned_cols=58 Identities=24% Similarity=0.319 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHHHHHhh----CCCchhhhccCCCc-cccCC-CCChHHHHHHHHhhcccCC
Q 022048 4 PKQKWTQEEEAALKAGVIKH----GAGKWRTILKDPEF-SGVLY-LRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~----G~G~W~~I~~~~~f-~~~l~-~RT~vdLKDKWRnl~k~~~ 61 (303)
..+-||+|+|=.|++|+-.| |.+....+..-++| .+.|. .=|..||.||-|.|.+...
T Consensus 3 ~qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~ 66 (98)
T PF04504_consen 3 FQRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR 66 (98)
T ss_pred CcCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 35679999999999999877 75433332211111 11121 3477899999999977633
No 48
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=70.77 E-value=12 Score=32.85 Aligned_cols=51 Identities=16% Similarity=0.289 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhc
Q 022048 4 PKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMS 57 (303)
Q Consensus 4 ~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~ 57 (303)
....=|..|...|...|++||. .+..+..|..... -..|..||+.+.+.+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~--~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNY--MQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCc--ccCCHHHHHHHHHHhc
Confidence 4567799999999999999996 9999999876553 3689999999988764
No 49
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=67.60 E-value=1.9 Score=38.92 Aligned_cols=60 Identities=20% Similarity=0.238 Sum_probs=39.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 1 MGAPKQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 1 Mg~~r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
|......||.|||..|-.-|-+|+.--=..+.. ++..+..-+||...|.+||-..++..+
T Consensus 1 mk~rqdawt~e~d~llae~vl~~i~eg~tql~a-fe~~g~~L~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 1 MKTRQDAWTQERDGLLAEVVLRHIREGGTQLKA-FEEVGDALKRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred CcchhhhhhhHHHHHHHHHHHHHHhccchHHHH-HHHHHHHHhhhHHHHHhHHHHHHHHHH
Confidence 445567899999999999999887622223322 111112237999999999966655444
No 50
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=63.08 E-value=12 Score=27.29 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHhCCCCc-cHHHHHHHHHHhhhhCCce
Q 022048 142 GGSNKTTIAAYIEEKYWAPP-DFKRLLSAKLKYLAGTGKL 180 (303)
Q Consensus 142 ~GSS~~AI~kyIe~~y~vp~-nf~~lL~~~LKrlV~~GkL 180 (303)
++.|...|.+.+.++|.+++ ....-+..-|..|.+.|-|
T Consensus 28 g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT--
T ss_pred CCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 46899999999999999854 4778899999999998876
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=59.14 E-value=15 Score=37.35 Aligned_cols=48 Identities=15% Similarity=0.277 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
--+||.+|.+.+..++..+|+ .+..|.. .|+.|.-.|+|-||.+=.+.
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGt-dF~LIs~------lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGT-DFSLISS------LFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcc-hHHHHHH------hcCchhHHHHHHHHHHHhhh
Confidence 348999999999999999999 8999987 35689999999999876554
No 52
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=58.07 E-value=21 Score=31.72 Aligned_cols=71 Identities=23% Similarity=0.272 Sum_probs=51.2
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCC----CCccH----------HHHHHHHHHhhhhCCceeeeC-cceecCC
Q 022048 127 LDNLIMEAITTLKEPGGSNKTTIAAYIEEKYW----APPDF----------KRLLSAKLKYLAGTGKLVKIK-RKYRIAP 191 (303)
Q Consensus 127 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----vp~nf----------~~lL~~~LKrlV~~GkLvkvK-~syKl~~ 191 (303)
|.+.|...+.- -|.....|..||-++.. +-... ..-++..|+.|.+.|-|.+++ |.|.|.|
T Consensus 42 ~~~ni~~~l~l----~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP 117 (165)
T PF05732_consen 42 YLENIIKVLDL----IGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMINP 117 (165)
T ss_pred HHHHHHHHhhh----hchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEECc
Confidence 45555555544 36668999999998753 11111 255889999999999999997 8999999
Q ss_pred CCCCCcccCC
Q 022048 192 TLPFQDRRRN 201 (303)
Q Consensus 192 ~~~~~~~r~~ 201 (303)
..+..|.+..
T Consensus 118 ~~~~kG~~~~ 127 (165)
T PF05732_consen 118 NFFFKGDRDK 127 (165)
T ss_pred HHheeCcHHH
Confidence 8776665553
No 53
>PF05928 Zea_mays_MuDR: Zea mays MURB-like protein (MuDR); InterPro: IPR009227 This family consists of several Zea mays (Maize) specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar [].
Probab=54.57 E-value=25 Score=32.00 Aligned_cols=26 Identities=46% Similarity=0.363 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022048 241 PQEAAAAAARAVAEAEAAVAEAEEAA 266 (303)
Q Consensus 241 ~~EAA~aAA~aVAEAE~~~~~AeeA~ 266 (303)
+.|||.+||.+-+||.-..+.||--+
T Consensus 12 ~v~aaraaavaa~earc~~~vaekea 37 (207)
T PF05928_consen 12 VVDAARAAAVAASEARCVVFVAEKEA 37 (207)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhHHH
Confidence 56788888888888887777765433
No 54
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=51.65 E-value=74 Score=23.79 Aligned_cols=59 Identities=20% Similarity=0.262 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeC---cceecCC
Q 022048 125 VRLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIK---RKYRIAP 191 (303)
Q Consensus 125 P~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK---~syKl~~ 191 (303)
..+.+-|++.|..-.++ |.+..-|++-+ .++ ++-++.+|.+|...|.|++.. +.|+|..
T Consensus 5 ~~~~~~IL~~L~~~g~~-~~ta~eLa~~l----gl~---~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 5 DSLEEKILEFLENSGDE-TSTALQLAKNL----GLP---KKEVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred hHHHHHHHHHHHHCCCC-CcCHHHHHHHH----CCC---HHHHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 34567788888765433 68888887776 444 357899999999999999853 5677753
No 55
>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=51.33 E-value=30 Score=27.45 Aligned_cols=52 Identities=15% Similarity=0.302 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHh-cCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceee
Q 022048 124 IVRLDNLIMEAITT-LKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVK 182 (303)
Q Consensus 124 hP~y~~MI~EAI~~-Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvk 182 (303)
..+..++|++.|.. .....|.++..|.+-+ .+ + ..-|+.+|..|+..|.|.-
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~--~---~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GM--S---ENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS------HHHHHHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--Cc--C---HHHHHHHHHHHHhCCeEec
Confidence 45679999999999 7778999999999887 33 3 3578999999999999864
No 56
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=50.11 E-value=15 Score=28.99 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=8.5
Q ss_pred CCCCCHHHHHHHH
Q 022048 5 KQKWTQEEEAALK 17 (303)
Q Consensus 5 r~~WT~EE~~~L~ 17 (303)
.+-||+|+|+.|.
T Consensus 47 ~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 47 PGIWTPEDDEMLR 59 (87)
T ss_dssp TT---HHHHHHHT
T ss_pred CCCcCHHHHHHHH
Confidence 6679999999993
No 57
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=43.55 E-value=50 Score=23.86 Aligned_cols=48 Identities=19% Similarity=0.268 Sum_probs=32.3
Q ss_pred cCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeCcceecCC
Q 022048 138 LKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIKRKYRIAP 191 (303)
Q Consensus 138 Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK~syKl~~ 191 (303)
|.=..|.|...+.. +|.. +|...+...|..+++.|-|+...+++++++
T Consensus 15 LR~~~Gi~~~~~~~----~~g~--~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~ 62 (66)
T PF06969_consen 15 LRCNEGIDLSEFEQ----RFGI--DFAEEFQKELEELQEDGLLEIDGGRLRLTE 62 (66)
T ss_dssp HHHHSEEEHHHHHH----HTT----THHH-HHHHHHHHHTTSEEE-SSEEEE-T
T ss_pred HHhHCCcCHHHHHH----HHCc--CHHHHHHHHHHHHHHCCCEEEeCCEEEECc
Confidence 33356777665544 3432 366777888999999999999999999976
No 58
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=43.18 E-value=69 Score=23.88 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=35.1
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCC---ccHHHHHHHHHHhh--hhCCceeee-Ccceec
Q 022048 126 RLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAP---PDFKRLLSAKLKYL--AGTGKLVKI-KRKYRI 189 (303)
Q Consensus 126 ~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp---~nf~~lL~~~LKrl--V~~GkLvkv-K~syKl 189 (303)
+|.+.+.+.+...+ ...+..-|.+.|.++.... .+....|+..|-.- -..|.|+++ .|.|-|
T Consensus 2 t~~eaa~~vL~~~~--~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg~~~~~L 69 (72)
T PF05066_consen 2 TFKEAAYEVLEEAG--RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIKNEDSRFVKVGPGRWGL 69 (72)
T ss_dssp -HHHHHHHHHHHH---S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH-T-SS-EESSSSEEE-
T ss_pred CHHHHHHHHHHhcC--CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcccCCCCEEEeCCCcEEe
Confidence 35566666666655 6689999999999875432 23334444444333 478899998 577755
No 59
>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=42.86 E-value=35 Score=24.19 Aligned_cols=42 Identities=29% Similarity=0.459 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeC-cceecCC
Q 022048 143 GSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIK-RKYRIAP 191 (303)
Q Consensus 143 GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK-~syKl~~ 191 (303)
..+...|+..+. ++ ...++..|+.|...|-|.... |.|.|.|
T Consensus 25 ~~s~~ela~~~g----~s---~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 25 PLTRQEIADYLG----LT---RETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CcCHHHHHHHHC----CC---HHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 356666665553 21 356788999999999999887 8898854
No 60
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=41.60 E-value=41 Score=32.32 Aligned_cols=48 Identities=21% Similarity=0.327 Sum_probs=36.3
Q ss_pred HhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeCcceecCC
Q 022048 136 TTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIKRKYRIAP 191 (303)
Q Consensus 136 ~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK~syKl~~ 191 (303)
-.|++ +.-+..-|+.++. ++ ...+..+||+|.+.|-++|..+.|+|++
T Consensus 20 llL~e-gPkti~EI~~~l~----vs---~~ai~pqiKkL~~~~LV~~~~~~Y~LS~ 67 (260)
T COG4742 20 LLLKE-GPKTIEEIKNELN----VS---SSAILPQIKKLKDKGLVVQEGDRYSLSS 67 (260)
T ss_pred HHHHh-CCCCHHHHHHHhC----CC---cHHHHHHHHHHhhCCCEEecCCEEEecc
Confidence 34555 3456777777764 32 2567889999999999999999999975
No 61
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=39.83 E-value=23 Score=29.15 Aligned_cols=56 Identities=18% Similarity=0.299 Sum_probs=37.5
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeCcc----eecCC
Q 022048 128 DNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIKRK----YRIAP 191 (303)
Q Consensus 128 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK~s----yKl~~ 191 (303)
.++|++.|.. ...+|.-.+-|.-..-=+| +.....|+-|+++|-+++.++. |.|.+
T Consensus 17 ~eIi~dIL~~-~~~~~~~~Tri~y~aNlny-------~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~ 76 (95)
T COG3432 17 LEIIFDILKA-ISEGGIGITRIIYGANLNY-------KRAQKYIEMLVEKGLIIKQDNGRRKVYELTE 76 (95)
T ss_pred HHHHHHHHHH-hcCCCCCceeeeeecCcCH-------HHHHHHHHHHHhCCCEEeccCCccceEEECh
Confidence 8899999987 5666666655543222222 3457788999999955555543 88865
No 62
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=35.76 E-value=1.3e+02 Score=22.68 Aligned_cols=52 Identities=23% Similarity=0.376 Sum_probs=37.4
Q ss_pred HHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeee--CcceecCC
Q 022048 131 IMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKI--KRKYRIAP 191 (303)
Q Consensus 131 I~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkv--K~syKl~~ 191 (303)
|++.|..- +.+.+...|.+.+ .+| +.-+...|+.|++.|-|.+. .+.|.+.+
T Consensus 10 Il~~l~~~--~~~~t~~~ia~~l----~i~---~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~ 63 (91)
T smart00346 10 VLRALAEE--PGGLTLAELAERL----GLS---KSTAHRLLNTLQELGYVEQDGQNGRYRLGP 63 (91)
T ss_pred HHHHHHhC--CCCcCHHHHHHHh----CCC---HHHHHHHHHHHHHCCCeeecCCCCceeecH
Confidence 55555442 2578999999888 333 36678899999999999986 35677754
No 63
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=33.44 E-value=75 Score=29.42 Aligned_cols=50 Identities=14% Similarity=0.318 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccCC
Q 022048 7 KWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 7 ~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~~ 61 (303)
+|+++.|=.|+.+|..-. .=..|...=.|+ ..-|-..+.+||..|+--..
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS---~~fT~~Ei~~RW~~llyd~~ 50 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFS---CKFTLQEIEERWYALLYDPV 50 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcC---CcCcHHHHHHHHHHHHcChh
Confidence 699999999999998543 566665544565 46788999999999976533
No 64
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=32.22 E-value=64 Score=21.22 Aligned_cols=25 Identities=24% Similarity=0.255 Sum_probs=20.8
Q ss_pred HHHHHHHHhhhhCCceeeeCcceec
Q 022048 165 RLLSAKLKYLAGTGKLVKIKRKYRI 189 (303)
Q Consensus 165 ~lL~~~LKrlV~~GkLvkvK~syKl 189 (303)
..++..|+.|.+.|-|...++.|.|
T Consensus 23 ~tv~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 23 ETVSRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHHHHHHCCCEEEeCCEEEE
Confidence 4567888899999999988887765
No 65
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=31.55 E-value=87 Score=23.37 Aligned_cols=49 Identities=10% Similarity=0.133 Sum_probs=35.4
Q ss_pred CHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeC
Q 022048 126 RLDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIK 184 (303)
Q Consensus 126 ~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK 184 (303)
...-.|+..|.... +.+...|..++. ++ ...++..|++|++.|-|...+
T Consensus 10 ~~~~~il~~l~~~~---~~~~~~la~~~~----~s---~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 10 PTQFLVLRILYEEG---PLSVSELAKRLG----VS---PSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHHcC---CcCHHHHHHHHC----CC---chhHHHHHHHHHHCCCeEecC
Confidence 34566777777633 678888887763 22 355889999999999998764
No 66
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=31.25 E-value=1.2e+02 Score=22.72 Aligned_cols=23 Identities=22% Similarity=0.179 Sum_probs=19.1
Q ss_pred HHHHHHHHhhhhCCceeeeCcce
Q 022048 165 RLLSAKLKYLAGTGKLVKIKRKY 187 (303)
Q Consensus 165 ~lL~~~LKrlV~~GkLvkvK~sy 187 (303)
..+..+|+.|...|-|.+..|.-
T Consensus 41 ~tv~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 41 STVQRHLKALERKGYIRRDPGKA 63 (65)
T ss_dssp HHHHHHHHHHHHTTSEEEGCCSC
T ss_pred HHHHHHHHHHHHCcCccCCCCCC
Confidence 55788999999999999887653
No 67
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=30.36 E-value=1.6e+02 Score=19.40 Aligned_cols=40 Identities=15% Similarity=0.210 Sum_probs=29.0
Q ss_pred CCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeCcce
Q 022048 141 PGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIKRKY 187 (303)
Q Consensus 141 r~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK~sy 187 (303)
..+.+...|..++ .++ ..-+...|+.|...|.|.+..+-+
T Consensus 12 ~~~~s~~~l~~~l----~~s---~~tv~~~l~~L~~~g~i~~~~~~~ 51 (53)
T smart00420 12 QGKVSVEELAELL----GVS---EMTIRRDLNKLEEQGLLTRVHGGA 51 (53)
T ss_pred cCCcCHHHHHHHH----CCC---HHHHHHHHHHHHHCCCEEEeecCc
Confidence 3567888887776 332 355688889999999998876543
No 68
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=30.14 E-value=1.3e+02 Score=22.78 Aligned_cols=51 Identities=29% Similarity=0.378 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeCc
Q 022048 127 LDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIKR 185 (303)
Q Consensus 127 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK~ 185 (303)
..+.|++.|..+. |++..+|.+.+.=+ +| ++-++..|-+|-.+|.|.+..+
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~--~~---kk~VN~~LY~L~k~g~v~k~~~ 55 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLS--VP---KKEVNRVLYRLEKQGKVCKEGG 55 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHT--S----HHHHHHHHHHHHHTTSEEEECS
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcc--hh---HHHHHHHHHHHHHCCCEeeCCC
Confidence 4578888888887 66777777766533 12 5789999999999999987654
No 69
>TIGR01932 hflC HflC protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described.//Regulation of FtsH protease appears to be negative (PubMed:8947034, PubMed:96367)
Probab=29.06 E-value=1.8e+02 Score=28.09 Aligned_cols=13 Identities=23% Similarity=0.432 Sum_probs=5.4
Q ss_pred HHHHHHHHHHHHH
Q 022048 265 AAREADVAEADAE 277 (303)
Q Consensus 265 A~~Eae~~e~~aE 277 (303)
|-+++..+.+++|
T Consensus 254 A~a~a~~~~Aege 266 (317)
T TIGR01932 254 AYRTARIIKGEGD 266 (317)
T ss_pred HHHHHHHHHhhHH
Confidence 3344444444333
No 70
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.19 E-value=52 Score=22.39 Aligned_cols=36 Identities=11% Similarity=0.148 Sum_probs=25.2
Q ss_pred cCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHh
Q 022048 138 LKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKY 173 (303)
Q Consensus 138 Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKr 173 (303)
|.++-|.|..+|..++..+..+.+.....+...++.
T Consensus 3 lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~ 38 (52)
T cd01392 3 IARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEE 38 (52)
T ss_pred HHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 445678999999999988877765555555555544
No 71
>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=28.07 E-value=88 Score=22.25 Aligned_cols=47 Identities=19% Similarity=0.248 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCceeeeC
Q 022048 129 NLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLVKIK 184 (303)
Q Consensus 129 ~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLvkvK 184 (303)
..|+.+|. .+..+.+...|..+..-. +..++..|++|++.|-|.+..
T Consensus 6 ~~vL~~l~--~~~~~~t~~~l~~~~~~~-------~~~vs~~i~~L~~~glv~~~~ 52 (68)
T PF13463_consen 6 WQVLRALA--HSDGPMTQSDLAERLGIS-------KSTVSRIIKKLEEKGLVEKER 52 (68)
T ss_dssp HHHHHHHT----TS-BEHHHHHHHTT---------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHH--ccCCCcCHHHHHHHHCcC-------HHHHHHHHHHHHHCCCEEecC
Confidence 34555555 355566777776665422 356789999999999998763
No 72
>TIGR01933 hflK HflK protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described.//Regulation of FtsH by HflKC appears to be negative (PubMed:8947034,PubMed:96367)
Probab=26.79 E-value=2.4e+02 Score=25.92 Aligned_cols=13 Identities=23% Similarity=0.192 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHH
Q 022048 272 AEADAEVAQAFAA 284 (303)
Q Consensus 272 ~e~~aE~a~~f~~ 284 (303)
++++|++...+++
T Consensus 205 a~g~a~~~~~~~~ 217 (261)
T TIGR01933 205 AKGDVARFTKLLA 217 (261)
T ss_pred hhhhHHHHHHHHH
Confidence 3444444444444
No 73
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=25.30 E-value=1.1e+02 Score=31.18 Aligned_cols=46 Identities=20% Similarity=0.278 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcc
Q 022048 7 KWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSV 58 (303)
Q Consensus 7 ~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k 58 (303)
-||++|=..+-.|++.||. ....|... -++.|+--.|=.=|.-.+|
T Consensus 279 ~wsEeEcr~FEegl~~yGK-DF~lIr~n-----kvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGK-DFHLIRAN-----KVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred cCCHHHHHHHHHHHHHhcc-cHHHHHhc-----ccccchHHHHHHHHHHhhc
Confidence 4999999999999999998 89999774 2567888887765544433
No 74
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=24.77 E-value=1.6e+02 Score=21.20 Aligned_cols=27 Identities=11% Similarity=0.112 Sum_probs=22.5
Q ss_pred HHHHHHHHhhhhCCceeeeCcceecCC
Q 022048 165 RLLSAKLKYLAGTGKLVKIKRKYRIAP 191 (303)
Q Consensus 165 ~lL~~~LKrlV~~GkLvkvK~syKl~~ 191 (303)
.-++.-|..|...|.|.++.|.+.+..
T Consensus 29 ~TiRRDl~~L~~~g~i~r~~GG~~~~~ 55 (57)
T PF08220_consen 29 MTIRRDLNKLEKQGLIKRTHGGAVLND 55 (57)
T ss_pred HHHHHHHHHHHHCCCEEEEcCEEEeCC
Confidence 346777889999999999999888765
No 75
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=24.71 E-value=1.4e+02 Score=19.68 Aligned_cols=25 Identities=32% Similarity=0.393 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHHh
Q 022048 127 LDNLIMEAITTLKEPGGSNKTTIAAYIEEK 156 (303)
Q Consensus 127 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~ 156 (303)
+-.+|.||+.. |.|..-|..|++.+
T Consensus 5 W~~Li~eA~~~-----Gls~eeir~FL~~~ 29 (30)
T PF08671_consen 5 WVELIKEAKES-----GLSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHHHHHT-----T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHc-----CCCHHHHHHHHHhC
Confidence 56789999875 99999999999753
No 76
>PF12363 DUF3647: Phage protein ; InterPro: IPR024410 Proteins in this entry are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.
Probab=24.61 E-value=2.1e+02 Score=23.70 Aligned_cols=53 Identities=25% Similarity=0.305 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCcee
Q 022048 127 LDNLIMEAITTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKLV 181 (303)
Q Consensus 127 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkLv 181 (303)
..++|.-|....+.+- |...|-.||++-+.....+..++..-|+.|..+|.+.
T Consensus 53 l~d~i~~a~~~~~~~~--s~~eIe~~ie~~~e~~~~~~~l~~~vl~el~~s~~~k 105 (113)
T PF12363_consen 53 LADIIYAATAHEKKRP--SREEIEDYIEDIIEDEDDIEELFDEVLKELKKSNFFK 105 (113)
T ss_pred HHHHHHHHhcccCCCC--CHHHHHHHHHHHHhcchhHHHHHHHHHHHHHhChhHH
Confidence 4566666666666654 9999999999855444557888888888888887653
No 77
>smart00595 MADF subfamily of SANT domain.
Probab=24.48 E-value=46 Score=25.34 Aligned_cols=26 Identities=23% Similarity=0.521 Sum_probs=20.0
Q ss_pred chhhhccCCCccccCCCCChHHHHHHHHhhccc
Q 022048 27 KWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVM 59 (303)
Q Consensus 27 ~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~ 59 (303)
-|..|... + +-|..+|+.||.||...
T Consensus 29 aW~~Ia~~--l-----~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 29 AWEEIAEE--L-----GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHH--H-----CcCHHHHHHHHHHHHHH
Confidence 58888773 2 23999999999999644
No 78
>PRK11029 FtsH protease regulator HflC; Provisional
Probab=24.25 E-value=2.5e+02 Score=27.67 Aligned_cols=15 Identities=53% Similarity=0.614 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHH
Q 022048 271 VAEADAEVAQAFAAA 285 (303)
Q Consensus 271 ~~e~~aE~a~~f~~~ 285 (303)
+++.+|++.+.++++
T Consensus 272 ~aegeA~a~~~~~~a 286 (334)
T PRK11029 272 RGEGDAEAAKLFADA 286 (334)
T ss_pred HhhhHHHHHHHHHHH
Confidence 456677777777544
No 79
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=23.75 E-value=63 Score=24.06 Aligned_cols=39 Identities=13% Similarity=0.190 Sum_probs=26.3
Q ss_pred HhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhh
Q 022048 136 TTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYL 174 (303)
Q Consensus 136 ~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrl 174 (303)
..|...-|.|+.+|..++..+..+.+..+..+...++.+
T Consensus 4 ~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 4 KDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEEL 42 (70)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHh
Confidence 344556689999999988887777555555555555443
No 80
>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=23.42 E-value=28 Score=31.32 Aligned_cols=53 Identities=21% Similarity=0.306 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHhhCCCchhhhccCCCcccc--CCCCChHHHHHHHHhhcccCC
Q 022048 6 QKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGV--LYLRSNVDLKDKWRNMSVMSN 61 (303)
Q Consensus 6 ~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~--l~~RT~vdLKDKWRnl~k~~~ 61 (303)
-.||.|||-.|-.-|-+|=---=+.+.. |..+ --+||+--|-=||-..++.-+
T Consensus 5 DAWT~eeDlLLAEtVLrhIReG~TQL~A---FeEvg~~L~RTsAACGFRWNs~VRkqY 59 (161)
T TIGR02894 5 DAWTHEEDLLLAETVLRHIREGSTQLSA---FEEVGRALNRTAAACGFRWNAYVRKQY 59 (161)
T ss_pred cccccHHHHHHHHHHHHHHhcchHHHHH---HHHHHHHHcccHHHhcchHHHHHHHHH
Confidence 4799999999999999882100022221 3211 127999999999999988655
No 81
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=23.38 E-value=49 Score=23.41 Aligned_cols=39 Identities=10% Similarity=0.170 Sum_probs=28.7
Q ss_pred HhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhh
Q 022048 136 TTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYL 174 (303)
Q Consensus 136 ~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrl 174 (303)
..+-+.-|.|..++..+|.....+.+..+..+...++.+
T Consensus 3 ~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 3 KDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEEL 41 (46)
T ss_dssp HHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence 344456799999999999988778776676666665543
No 82
>PF08343 RNR_N: Ribonucleotide reductase N-terminal; InterPro: IPR013554 This domain is found at the N terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyse the formation of deoxyribonucleotides []. It occurs together with the RNR all-alpha domain (IPR013509 from INTERPRO) and the RNR barrel domain (IPR000788 from INTERPRO). ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0006260 DNA replication, 0055114 oxidation-reduction process, 0005971 ribonucleoside-diphosphate reductase complex; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A.
Probab=23.08 E-value=68 Score=25.55 Aligned_cols=49 Identities=22% Similarity=0.428 Sum_probs=31.3
Q ss_pred HHHHHhcCCCCCC-----CHHHHHHHHHHhCCCCccHHHH--HHHHHHhhhhCCceee
Q 022048 132 MEAITTLKEPGGS-----NKTTIAAYIEEKYWAPPDFKRL--LSAKLKYLAGTGKLVK 182 (303)
Q Consensus 132 ~EAI~~Lker~GS-----S~~AI~kyIe~~y~vp~nf~~l--L~~~LKrlV~~GkLvk 182 (303)
+.|...+.+.+|. ++.|+..|++++-. +|.... +..+|+-||++|-...
T Consensus 4 LNn~~~~~~~~G~~~l~kD~eA~~~y~~~~V~--pnt~~F~S~~Erl~yLv~~~YYe~ 59 (82)
T PF08343_consen 4 LNNELNIYDEDGKIQLEKDKEAVRAYFKEHVN--PNTVKFNSLKERLDYLVENDYYEK 59 (82)
T ss_dssp HHHGGG---TTS---THHHHHHHHHHHHHTTG--GGB---SSHHHHHHHHHHTTSB-H
T ss_pred HHHHHcCCCCCCCcCchhHHHHHHHHHHHhcc--cceeecCCHHHHHHHHHHcCcHHH
Confidence 4566677778886 78999999998543 333333 7888999999986653
No 83
>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=22.20 E-value=1.4e+02 Score=20.12 Aligned_cols=38 Identities=18% Similarity=0.221 Sum_probs=25.8
Q ss_pred HhcCCCCCCCHHHHHHHHHHhCCCCccHHHHHHHHHHhhhhCCce
Q 022048 136 TTLKEPGGSNKTTIAAYIEEKYWAPPDFKRLLSAKLKYLAGTGKL 180 (303)
Q Consensus 136 ~~Lker~GSS~~AI~kyIe~~y~vp~nf~~lL~~~LKrlV~~GkL 180 (303)
..|.+..|.|..-|++-+.=. ...++.+|++|++.|.|
T Consensus 10 ~~l~~~~~~t~~ela~~~~is-------~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 10 NYLRENPRITQKELAEKLGIS-------RSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHCTTS-HHHHHHHHTS--------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHcCCCCHHHHHHHhCCC-------HHHHHHHHHHHHHCcCc
Confidence 334445567888777776421 36689999999999976
No 84
>PF11839 DUF3359: Protein of unknown function (DUF3359); InterPro: IPR021793 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=21.24 E-value=4.8e+02 Score=21.60 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 022048 256 EAAVAEAEEAAREADVAEADAEV 278 (303)
Q Consensus 256 E~~~~~AeeA~~Eae~~e~~aE~ 278 (303)
+.+...|++|.-.|+++.+.|++
T Consensus 59 deA~~kA~~A~aaA~~Aqq~A~e 81 (96)
T PF11839_consen 59 DEAASKADAALAAAEAAQQTADE 81 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333333333333333
No 85
>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=21.07 E-value=1.4e+02 Score=22.15 Aligned_cols=38 Identities=24% Similarity=0.383 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCCC-----ccH---HHHHHHHHHhhhhCCceeeeC
Q 022048 147 TTIAAYIEEKYWAP-----PDF---KRLLSAKLKYLAGTGKLVKIK 184 (303)
Q Consensus 147 ~AI~kyIe~~y~vp-----~nf---~~lL~~~LKrlV~~GkLvkvK 184 (303)
..|..||.++..+. ..| ...|..-|..++..|.|.++.
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence 45666666654321 011 256788899999999999874
No 86
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=20.74 E-value=1.1e+02 Score=32.69 Aligned_cols=49 Identities=18% Similarity=0.347 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhhccCCCccccCCCCChHHHHHHHHhhcccC
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTILKDPEFSGVLYLRSNVDLKDKWRNMSVMS 60 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I~~~~~f~~~l~~RT~vdLKDKWRnl~k~~ 60 (303)
..+||.+|.+....+...+|. +-+.|... |+.|+..++|.|+++=.+..
T Consensus 409 ~~~w~~se~e~fyka~~~~gs-~~slis~l------~p~R~rk~iK~K~~~eE~r~ 457 (584)
T KOG2009|consen 409 TDKWDASETELFYKALSERGS-DFSLISNL------FPLRDRKQIKAKFKKEEKRN 457 (584)
T ss_pred cCcccchhhHHhhhHHhhhcc-cccccccc------cccccHHHHHHHHhhhhhcc
Confidence 458999999999999999998 88888773 56899999999997765553
No 87
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=20.68 E-value=51 Score=35.47 Aligned_cols=26 Identities=23% Similarity=0.544 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCchhhh
Q 022048 5 KQKWTQEEEAALKAGVIKHGAGKWRTI 31 (303)
Q Consensus 5 r~~WT~EE~~~L~~GV~k~G~G~W~~I 31 (303)
|.-||..|++.+.+|++.||. .+..|
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~V 113 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKV 113 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHH
Confidence 678999999999999999998 77777
No 88
>KOG2668 consensus Flotillins [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=20.31 E-value=3.2e+02 Score=27.95 Aligned_cols=25 Identities=48% Similarity=0.437 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 022048 265 AAREADVAEADAEVAQAFAAAAMKT 289 (303)
Q Consensus 265 A~~Eae~~e~~aE~a~~f~~~a~~~ 289 (303)
|.-|+|++.+.||+.+.+.++|...
T Consensus 331 akaeaeqm~~ka~v~~~y~~aa~l~ 355 (428)
T KOG2668|consen 331 AKAEAEQMAAKAEVYQAYAQAAYLR 355 (428)
T ss_pred hhhHHHHHHHHHHHHHHhhhhHHHH
Confidence 4457888888888888888887643
No 89
>cd03404 Band_7_HflK Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this band 7 domain family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflK is an integral membrane protein which may localize to the plasma membrane. HflK associates with another band 7 family member (HflC) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during la
Probab=20.22 E-value=3.7e+02 Score=24.67 Aligned_cols=16 Identities=50% Similarity=0.547 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 022048 264 EAAREADVAEADAEVA 279 (303)
Q Consensus 264 eA~~Eae~~e~~aE~a 279 (303)
+|-+++..+.+++|+.
T Consensus 222 ~a~~~~~~~~ae~~a~ 237 (266)
T cd03404 222 EAYKEEVIAEAQGEAA 237 (266)
T ss_pred HHHHHhHHHHHHHHHH
Confidence 3444444444444433
No 90
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=20.09 E-value=1.8e+02 Score=26.37 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=30.8
Q ss_pred CCCCCCCCHHHHHHHHHHhcCC-CCCCCHHHHHHHHHHhC
Q 022048 119 APKRSIVRLDNLIMEAITTLKE-PGGSNKTTIAAYIEEKY 157 (303)
Q Consensus 119 ~~~~~hP~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y 157 (303)
...+.+|+|+.||..-+..+++ ..+.+..++..+|..+.
T Consensus 101 ~~~~~~p~y~~Mi~~L~~qvk~~~de~~~~~~~~~l~~H~ 140 (177)
T PF03234_consen 101 NKDPEQPTYDEMIEDLLDQVKKEPDEKSGKAELEELQEHR 140 (177)
T ss_pred cCCCCCCCHHHHHHHHHHHHhcccCcccHHHHHHHHHHHH
Confidence 5577789999999999988874 55556888888887764
No 91
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=20.01 E-value=2.1e+02 Score=22.77 Aligned_cols=40 Identities=18% Similarity=0.289 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHhCCCCc-----cH---HHHHHHHHHhhhhCCceeeeC
Q 022048 145 NKTTIAAYIEEKYWAPP-----DF---KRLLSAKLKYLAGTGKLVKIK 184 (303)
Q Consensus 145 S~~AI~kyIe~~y~vp~-----nf---~~lL~~~LKrlV~~GkLvkvK 184 (303)
|...|..||..+-.+.. .| -..+..=|.+++..|+|.++-
T Consensus 3 ~L~qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 3 SLIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred cHHHHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 56677778877754311 11 245777889999999999884
Done!