Query 024102
Match_columns 272
No_of_seqs 284 out of 937
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:59:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024102.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024102hhsearch_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 5.9E-21 1.3E-25 149.1 9.0 71 115-185 2-78 (88)
2 smart00526 H15 Domain in histo 99.8 4.9E-21 1.1E-25 141.6 8.0 64 115-178 2-66 (66)
3 PF00538 Linker_histone: linke 99.8 4.8E-21 1E-25 145.8 7.7 69 116-184 1-77 (77)
4 KOG4012 Histone H1 [Chromatin 99.5 2.9E-14 6.3E-19 130.2 7.4 76 111-186 38-120 (243)
5 PF00249 Myb_DNA-binding: Myb- 99.4 5.8E-13 1.3E-17 92.5 3.6 47 5-57 1-48 (48)
6 PLN03212 Transcription repress 99.1 9.2E-11 2E-15 107.4 5.3 56 1-61 21-76 (249)
7 smart00717 SANT SANT SWI3, AD 99.1 2.1E-10 4.6E-15 76.7 5.3 48 5-58 1-48 (49)
8 PLN03091 hypothetical protein; 99.0 6.9E-10 1.5E-14 108.6 7.4 105 3-166 12-118 (459)
9 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 1E-09 2.2E-14 72.5 5.0 45 7-57 1-45 (45)
10 PF13921 Myb_DNA-bind_6: Myb-l 98.9 1E-09 2.3E-14 78.8 4.8 44 8-58 1-44 (60)
11 KOG0048 Transcription factor, 98.9 1.3E-09 2.7E-14 99.0 5.4 104 5-168 9-115 (238)
12 PLN03212 Transcription repress 98.6 3.9E-08 8.4E-13 90.3 4.9 51 3-60 76-126 (249)
13 PLN03091 hypothetical protein; 98.5 1.2E-07 2.7E-12 93.0 5.3 51 3-60 65-115 (459)
14 KOG0048 Transcription factor, 98.1 3.5E-06 7.5E-11 76.6 4.9 51 3-60 60-110 (238)
15 TIGR01557 myb_SHAQKYF myb-like 98.0 1.1E-05 2.4E-10 58.8 5.5 49 3-56 1-53 (57)
16 KOG0049 Transcription factor, 97.9 1.2E-05 2.6E-10 82.3 4.7 53 2-60 357-409 (939)
17 KOG0051 RNA polymerase I termi 97.6 4E-05 8.6E-10 78.2 3.7 50 4-61 383-432 (607)
18 KOG0457 Histone acetyltransfer 97.6 5.3E-05 1.1E-09 74.5 4.1 49 6-60 73-121 (438)
19 KOG0049 Transcription factor, 97.4 8.4E-05 1.8E-09 76.3 2.7 62 3-70 410-471 (939)
20 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00022 4.7E-09 54.3 1.6 55 5-61 1-68 (90)
21 PF09111 SLIDE: SLIDE; InterP 96.5 0.0013 2.8E-08 54.6 1.9 58 2-59 46-112 (118)
22 PF13873 Myb_DNA-bind_5: Myb/S 96.4 0.003 6.5E-08 47.4 3.0 53 5-59 2-71 (78)
23 KOG0050 mRNA splicing protein 96.0 0.0035 7.7E-08 63.2 2.2 50 6-61 8-57 (617)
24 KOG1279 Chromatin remodeling f 96.0 0.0088 1.9E-07 60.5 4.9 52 4-62 252-303 (506)
25 COG5147 REB1 Myb superfamily p 95.5 0.0042 9.1E-08 62.8 0.6 50 3-60 289-338 (512)
26 COG5114 Histone acetyltransfer 95.4 0.013 2.8E-07 56.4 3.2 48 7-60 65-112 (432)
27 COG5259 RSC8 RSC chromatin rem 95.3 0.018 3.8E-07 57.7 3.9 46 5-57 279-324 (531)
28 PF13325 MCRS_N: N-terminal re 95.2 0.027 5.8E-07 50.8 4.4 58 4-62 72-131 (199)
29 PLN03142 Probable chromatin-re 95.0 0.029 6.3E-07 61.2 5.0 58 3-60 924-987 (1033)
30 COG5147 REB1 Myb superfamily p 94.5 0.016 3.4E-07 58.8 1.4 51 3-59 18-68 (512)
31 PF08074 CHDCT2: CHDCT2 (NUC03 94.4 0.036 7.7E-07 48.7 3.1 48 6-53 4-58 (173)
32 PF08914 Myb_DNA-bind_2: Rap1 93.6 0.12 2.6E-06 38.7 4.2 50 5-59 2-59 (65)
33 PF10264 Stork_head: Winged he 93.3 0.39 8.4E-06 37.6 6.7 66 118-183 10-77 (80)
34 PF14338 Mrr_N: Mrr N-terminal 93.1 0.28 6E-06 38.2 5.8 66 119-184 1-82 (92)
35 PF00250 Fork_head: Fork head 92.5 0.23 5E-06 39.6 4.6 56 118-177 4-63 (96)
36 cd00059 FH Forkhead (FH), also 91.2 0.41 8.8E-06 36.9 4.6 33 117-150 3-35 (78)
37 KOG0051 RNA polymerase I termi 90.2 0.29 6.3E-06 50.6 3.8 53 3-61 434-511 (607)
38 KOG0384 Chromodomain-helicase 90.0 0.17 3.7E-06 55.9 2.1 52 6-57 1134-1191(1373)
39 KOG2656 DNA methyltransferase 89.4 0.39 8.4E-06 47.5 3.7 55 6-61 131-189 (445)
40 smart00339 FH FORKHEAD. FORKHE 89.3 0.46 1E-05 37.4 3.5 32 118-150 4-35 (89)
41 KOG4282 Transcription factor G 89.2 0.39 8.5E-06 45.7 3.7 55 5-61 54-117 (345)
42 KOG0050 mRNA splicing protein 87.8 0.44 9.5E-06 48.6 3.1 48 4-59 58-105 (617)
43 PF12776 Myb_DNA-bind_3: Myb/S 84.4 1.1 2.4E-05 34.3 3.1 52 7-60 1-65 (96)
44 PF09420 Nop16: Ribosome bioge 80.2 4.9 0.00011 34.7 5.9 50 4-56 113-162 (164)
45 PF04504 DUF573: Protein of un 75.6 3.2 7E-05 33.1 3.2 58 4-61 3-66 (98)
46 PF11839 DUF3359: Protein of u 75.5 22 0.00048 28.7 8.0 50 215-264 35-84 (96)
47 PF08672 APC2: Anaphase promot 74.2 3 6.5E-05 30.7 2.5 26 157-182 35-60 (60)
48 COG5118 BDP1 Transcription ini 69.9 7.2 0.00016 38.8 4.7 50 3-59 363-412 (507)
49 PRK13923 putative spore coat p 68.1 1.5 3.2E-05 38.8 -0.3 50 1-53 1-52 (170)
50 PF14947 HTH_45: Winged helix- 65.3 6.5 0.00014 29.6 2.8 56 121-184 5-60 (77)
51 PF05402 PqqD: Coenzyme PQQ sy 61.7 17 0.00037 26.0 4.3 39 135-173 28-67 (68)
52 PF11626 Rap1_C: TRF2-interact 55.9 11 0.00024 29.2 2.6 20 5-24 47-74 (87)
53 smart00550 Zalpha Z-DNA-bindin 51.8 64 0.0014 23.7 6.0 59 118-184 5-66 (68)
54 PF13325 MCRS_N: N-terminal re 50.8 29 0.00062 31.5 4.8 49 7-60 1-49 (199)
55 PF01726 LexA_DNA_bind: LexA D 48.2 53 0.0011 24.2 5.1 22 158-179 41-62 (65)
56 TIGR02894 DNA_bind_RsfA transc 47.6 7.3 0.00016 34.3 0.4 49 5-59 4-57 (161)
57 PF08784 RPA_C: Replication pr 47.1 37 0.0008 26.4 4.4 54 116-176 44-98 (102)
58 cd00092 HTH_CRP helix_turn_hel 46.1 90 0.0019 21.6 5.9 28 157-184 39-67 (67)
59 PF05066 HARE-HTH: HB1, ASXL, 44.8 62 0.0013 23.7 5.1 62 119-182 2-69 (72)
60 COG4742 Predicted transcriptio 44.6 25 0.00054 33.2 3.5 48 129-184 20-67 (260)
61 PF05928 Zea_mays_MuDR: Zea ma 42.1 72 0.0016 28.5 5.7 27 217-243 12-38 (207)
62 PF05732 RepL: Firmicute plasm 41.3 82 0.0018 27.4 6.0 63 120-186 42-119 (165)
63 PF06969 HemN_C: HemN C-termin 40.5 53 0.0012 23.2 4.0 51 128-184 12-62 (66)
64 PF11839 DUF3359: Protein of u 39.3 2E+02 0.0042 23.4 7.4 34 222-255 49-82 (96)
65 smart00595 MADF subfamily of S 39.1 18 0.0004 27.1 1.5 27 27-60 29-55 (89)
66 PF13463 HTH_27: Winged helix 37.8 54 0.0012 22.9 3.7 47 122-177 6-52 (68)
67 cd01392 HTH_LacI Helix-turn-he 34.5 37 0.00081 22.7 2.3 36 131-166 3-38 (52)
68 PF08220 HTH_DeoR: DeoR-like h 32.8 58 0.0013 23.0 3.1 27 158-184 29-55 (57)
69 KOG4329 DNA-binding protein [G 32.6 74 0.0016 31.8 4.7 43 6-54 278-320 (445)
70 PF08343 RNR_N: Ribonucleotide 31.8 39 0.00085 26.3 2.3 50 124-175 3-59 (82)
71 PF01325 Fe_dep_repress: Iron 31.7 1.9E+02 0.004 20.8 5.7 46 125-177 10-56 (60)
72 PF00356 LacI: Bacterial regul 30.4 40 0.00087 23.3 1.9 39 128-166 2-40 (46)
73 smart00419 HTH_CRP helix_turn_ 29.9 65 0.0014 20.8 2.9 26 157-182 22-47 (48)
74 KOG4468 Polycomb-group transcr 29.6 62 0.0013 34.3 3.8 26 5-31 88-113 (782)
75 KOG1194 Predicted DNA-binding 29.3 68 0.0015 32.8 4.0 51 5-62 187-237 (534)
76 KOG3614 Ca2+/Mg2+-permeable ca 29.3 1.1E+02 0.0025 35.0 6.0 34 237-270 603-636 (1381)
77 PF13412 HTH_24: Winged helix- 29.1 1.4E+02 0.003 19.8 4.5 39 128-173 9-47 (48)
78 smart00354 HTH_LACI helix_turn 29.1 50 0.0011 24.2 2.3 39 128-166 3-41 (70)
79 CHL00137 rps13 ribosomal prote 28.4 91 0.002 26.0 4.0 49 135-183 49-97 (122)
80 smart00420 HTH_DEOR helix_turn 28.1 1.5E+02 0.0032 19.1 4.4 40 134-180 12-51 (53)
81 smart00346 HTH_ICLR helix_turn 27.9 1.4E+02 0.003 22.0 4.7 52 124-184 10-63 (91)
82 PF12363 DUF3647: Phage protei 27.3 1.8E+02 0.0038 23.6 5.5 53 120-174 53-105 (113)
83 PF03234 CDC37_N: Cdc37 N term 27.0 1.2E+02 0.0027 26.9 4.8 41 110-150 99-140 (177)
84 PF01047 MarR: MarR family; I 26.4 76 0.0016 21.7 2.8 41 130-177 11-51 (59)
85 smart00347 HTH_MARR helix_turn 26.0 1.1E+02 0.0024 22.4 3.8 48 120-177 11-58 (101)
86 PF07106 TBPIP: Tat binding pr 24.3 68 0.0015 27.4 2.6 36 140-175 4-50 (169)
87 PF08944 p47_phox_C: NADPH oxi 23.7 36 0.00079 25.2 0.7 8 263-270 38-45 (58)
88 KOG2009 Transcription initiati 23.2 99 0.0021 32.4 4.0 48 4-58 408-455 (584)
89 PF13309 HTH_22: HTH domain 22.4 31 0.00067 25.3 0.1 23 124-146 41-63 (64)
90 PRK05179 rpsM 30S ribosomal pr 21.5 1.2E+02 0.0027 25.1 3.6 52 132-183 46-97 (122)
91 PF08671 SinI: Anti-repressor 21.3 1.8E+02 0.004 18.6 3.5 25 120-149 5-29 (30)
92 PF07037 DUF1323: Putative tra 21.3 51 0.0011 27.8 1.2 23 130-152 5-27 (122)
93 PF12029 DUF3516: Domain of un 21.2 2.3E+02 0.005 29.0 5.9 61 121-185 61-130 (461)
94 PF14412 AHH: A nuclease famil 21.0 1.3E+02 0.0028 23.6 3.5 24 110-133 61-85 (109)
95 PF02796 HTH_7: Helix-turn-hel 20.9 32 0.00068 23.2 -0.1 22 128-149 24-45 (45)
96 COG3432 Predicted transcriptio 20.6 75 0.0016 25.7 2.0 56 121-184 17-76 (95)
97 PRK15431 ferrous iron transpor 20.5 1E+02 0.0022 24.0 2.7 40 138-177 3-50 (78)
98 PF12840 HTH_20: Helix-turn-he 20.2 1.9E+02 0.0041 20.3 3.9 39 132-177 20-58 (61)
99 PF10929 DUF2811: Protein of u 20.1 1.4E+02 0.003 22.1 3.1 28 140-171 12-42 (57)
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=5.9e-21 Score=149.13 Aligned_cols=71 Identities=37% Similarity=0.653 Sum_probs=67.1
Q ss_pred CCCCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCC-cchHHHHHHHHHhhhhcCceeeec-----cccccCCC
Q 024102 115 KNGPKYNAMIFEAISTLKDANGSDISAIANFIEERQEAP-PNFRRLLSSRLRRLVSQGKLEKVR-----NCYKIRKE 185 (272)
Q Consensus 115 ~~hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~-~n~~~~L~~~LKrlV~~GkLvkvK-----~sykl~~~ 185 (272)
.+||+|.+||+|||.+|+|++|||+++|++||+++|.+. ++|+.+|+.+|+++|++|.|++++ |+|+|++.
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 579999999999999999999999999999999999765 899999999999999999999999 89999743
No 2
>smart00526 H15 Domain in histone families 1 and 5.
Probab=99.84 E-value=4.9e-21 Score=141.58 Aligned_cols=64 Identities=45% Similarity=0.733 Sum_probs=61.4
Q ss_pred CCCCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCC-CcchHHHHHHHHHhhhhcCceeeecc
Q 024102 115 KNGPKYNAMIFEAISTLKDANGSDISAIANFIEERQEA-PPNFRRLLSSRLRRLVSQGKLEKVRN 178 (272)
Q Consensus 115 ~~hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v-~~n~~~~L~~~LKrlV~~GkLvkvK~ 178 (272)
.+||+|.+||+|||.+|+||+|||+++|++||+++|++ +++|+.+|+.+|+++|++|.|+|++|
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 57999999999999999999999999999999999986 78999999999999999999999986
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=99.84 E-value=4.8e-21 Score=145.84 Aligned_cols=69 Identities=39% Similarity=0.694 Sum_probs=64.2
Q ss_pred CCCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcC--CCc-chHHHHHHHHHhhhhcCceeeec-----cccccCC
Q 024102 116 NGPKYNAMIFEAISTLKDANGSDISAIANFIEERQE--APP-NFRRLLSSRLRRLVSQGKLEKVR-----NCYKIRK 184 (272)
Q Consensus 116 ~hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~--v~~-n~~~~L~~~LKrlV~~GkLvkvK-----~sykl~~ 184 (272)
+||+|.+||+|||.+|+||+|||+++|.+||+++|+ +++ +|+.+|+.+|+++|++|.|+|++ |+|||+.
T Consensus 1 shP~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~k 77 (77)
T PF00538_consen 1 SHPPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLSK 77 (77)
T ss_dssp -SSCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEESS
T ss_pred CCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecCC
Confidence 599999999999999999999999999999999996 444 79999999999999999999999 8999963
No 4
>KOG4012 consensus Histone H1 [Chromatin structure and dynamics]
Probab=99.51 E-value=2.9e-14 Score=130.23 Aligned_cols=76 Identities=30% Similarity=0.444 Sum_probs=68.0
Q ss_pred CCCCCCCCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcC-C-CcchHHHHHHHHHhhhhcCceeeecc-----ccccC
Q 024102 111 ALDGKNGPKYNAMIFEAISTLKDANGSDISAIANFIEERQE-A-PPNFRRLLSSRLRRLVSQGKLEKVRN-----CYKIR 183 (272)
Q Consensus 111 ~~~~~~hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~-v-~~n~~~~L~~~LKrlV~~GkLvkvK~-----sykl~ 183 (272)
......||+|.+||.|||..|+||+|+|+.+|++||.++|- . -++|+.+|+..|+++|.+|.|+|++| +|+|.
T Consensus 38 ~k~~a~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k~n~~lk~alK~~v~~g~l~QtkG~GAsGsFk~~ 117 (243)
T KOG4012|consen 38 VKKKAAHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEKNNSRLKLALKKGVSKGVLVQTKGTGASGSFKLA 117 (243)
T ss_pred cccccCCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhhhhHHHHHHHHhhhccCceeeeccCCcccccccc
Confidence 34567899999999999999999999999999999999991 1 34789999999999999999999985 99998
Q ss_pred CCC
Q 024102 184 KET 186 (272)
Q Consensus 184 ~~~ 186 (272)
...
T Consensus 118 KK~ 120 (243)
T KOG4012|consen 118 KKA 120 (243)
T ss_pred ccc
Confidence 755
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=99.35 E-value=5.8e-13 Score=92.50 Aligned_cols=47 Identities=34% Similarity=0.681 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCC-CCCHHHHHHHHHHhc
Q 024102 5 KQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLT-QRSNIDLKDKWRNLS 57 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~-~RT~vdLkdKWRnl~ 57 (272)
|++||+||++.|+++|.+||.++|..|+.. ++ +||..||+++|++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~------~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKR------MPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHH------HSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHH------cCCCCCHHHHHHHHHhhC
Confidence 689999999999999999999889999995 45 999999999999874
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.09 E-value=9.2e-11 Score=107.42 Aligned_cols=56 Identities=27% Similarity=0.551 Sum_probs=50.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccccc
Q 024102 1 MGNQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNA 61 (272)
Q Consensus 1 mg~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~ 61 (272)
+|.+|++||+|||+.|+..|++||.++|..|++. + ..+||+.||++||.|.+.+..
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 4778999999999999999999999999999884 1 258999999999999997764
No 7
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.08 E-value=2.1e-10 Score=76.71 Aligned_cols=48 Identities=35% Similarity=0.713 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcc
Q 024102 5 KQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSV 58 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~ 58 (272)
+..||++|+..|+.+|..||.++|..|... +++||..+|+++|+++.+
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 468999999999999999997799999995 569999999999999864
No 8
>PLN03091 hypothetical protein; Provisional
Probab=99.00 E-value=6.9e-10 Score=108.60 Aligned_cols=105 Identities=26% Similarity=0.411 Sum_probs=78.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccccccCCCCccCCCCCCCCCCCCC
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNAQQGSKDKIRGPKLKTTVVAPL 82 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~~~~~~~k~r~~~~~~~~~~~~ 82 (272)
.+|++||+|||+.|+..|.+||.++|..|++. ...+||+.||++||.|.+.+.. ++++-+
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~-----~g~gRT~KQCRERW~NyLdP~I------------kKgpWT--- 71 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQ-----AGLQRCGKSCRLRWINYLRPDL------------KRGTFS--- 71 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhh-----hccCcCcchHhHHHHhccCCcc------------cCCCCC---
Confidence 36789999999999999999999999999974 1258999999999999997764 222222
Q ss_pred CCCCCCCCcccccccccCCCccCCCCccCCCCCCCCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcC--CCcchHHHH
Q 024102 83 SNTPNSAPAASLTRNVSSGAVMNDTSTSALDGKNGPKYNAMIFEAISTLKDANGSDISAIANFIEERQE--APPNFRRLL 160 (272)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~--v~~n~~~~L 160 (272)
+-=+.+|++.+..+ |.....|++|+..+-. +...|..+|
T Consensus 72 -----------------------------------~EED~lLLeL~k~~----GnKWskIAk~LPGRTDnqIKNRWnslL 112 (459)
T PLN03091 72 -----------------------------------QQEENLIIELHAVL----GNRWSQIAAQLPGRTDNEIKNLWNSCL 112 (459)
T ss_pred -----------------------------------HHHHHHHHHHHHHh----CcchHHHHHhcCCCCHHHHHHHHHHHH
Confidence 00166777777664 6789999999977752 334455666
Q ss_pred HHHHHh
Q 024102 161 SSRLRR 166 (272)
Q Consensus 161 ~~~LKr 166 (272)
+..|++
T Consensus 113 KKklr~ 118 (459)
T PLN03091 113 KKKLRQ 118 (459)
T ss_pred HHHHHH
Confidence 666654
No 9
>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=98.97 E-value=1e-09 Score=72.46 Aligned_cols=45 Identities=40% Similarity=0.821 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhc
Q 024102 7 KWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLS 57 (272)
Q Consensus 7 ~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~ 57 (272)
+||.+|+..|+.++.+||.++|..|+.. +++||..||+++|.++.
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 5999999999999999998899999995 56899999999998863
No 10
>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=98.95 E-value=1e-09 Score=78.78 Aligned_cols=44 Identities=41% Similarity=0.718 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcc
Q 024102 8 WTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSV 58 (272)
Q Consensus 8 WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~ 58 (272)
||.|||+.|+.+|.+||. +|+.|+.. |++||..+|++||++++.
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~------l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEH------LGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHH------STTS-HHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHH------HCcCCHHHHHHHHHHHCc
Confidence 999999999999999995 99999994 557999999999999543
No 11
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.92 E-value=1.3e-09 Score=99.02 Aligned_cols=104 Identities=17% Similarity=0.259 Sum_probs=78.3
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCC-CCCHHHHHHHHHHhcccccccCCCCccCCCCCCCCCCCCCC
Q 024102 5 KQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLT-QRSNIDLKDKWRNLSVSNAQQGSKDKIRGPKLKTTVVAPLS 83 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~-~RT~vdLkdKWRnl~~~~~~~~~~~k~r~~~~~~~~~~~~~ 83 (272)
|++||+|||+.|+..|++||.|+|..|.++ +. +|++.+|+-||.|.+++.. +|+..+ +
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~------~gl~R~GKSCRlRW~NyLrP~i------------krg~fT-~-- 67 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKL------AGLRRCGKSCRLRWTNYLRPDL------------KRGNFS-D-- 67 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhh------cCCCccchHHHHHhhcccCCCc------------cCCCCC-H--
Confidence 499999999999999999999999999997 23 9999999999999999876 345443 0
Q ss_pred CCCCCCCcccccccccCCCccCCCCccCCCCCCCCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhc--CCCcchHHHHH
Q 024102 84 NTPNSAPAASLTRNVSSGAVMNDTSTSALDGKNGPKYNAMIFEAISTLKDANGSDISAIANFIEERQ--EAPPNFRRLLS 161 (272)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y--~v~~n~~~~L~ 161 (272)
-=+.+|+++=..+..+ ...|++++-.+- .+..-+...|+
T Consensus 68 -----------------------------------eEe~~Ii~lH~~~GNr----Ws~IA~~LPGRTDNeIKN~Wnt~lk 108 (238)
T KOG0048|consen 68 -----------------------------------EEEDLIIKLHALLGNR----WSLIAGRLPGRTDNEVKNHWNTHLK 108 (238)
T ss_pred -----------------------------------HHHHHHHHHHHHHCcH----HHHHHhhCCCcCHHHHHHHHHHHHH
Confidence 0167888777776555 888888876653 22222466666
Q ss_pred HHHHhhh
Q 024102 162 SRLRRLV 168 (272)
Q Consensus 162 ~~LKrlV 168 (272)
++|..+-
T Consensus 109 kkl~~~~ 115 (238)
T KOG0048|consen 109 KKLLKMG 115 (238)
T ss_pred HHHHHcC
Confidence 6665553
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.61 E-value=3.9e-08 Score=90.32 Aligned_cols=51 Identities=20% Similarity=0.365 Sum_probs=46.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
-.+.+||.|||+.|+..+..||. +|..|++. |++||..+||+||.++++..
T Consensus 76 I~kgpWT~EED~lLlel~~~~Gn-KWs~IAk~------LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGN-RWSLIAGR------IPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccc-cHHHHHhh------cCCCCHHHHHHHHHHHHhHH
Confidence 46889999999999999999996 99999993 78999999999999887664
No 13
>PLN03091 hypothetical protein; Provisional
Probab=98.50 E-value=1.2e-07 Score=93.01 Aligned_cols=51 Identities=20% Similarity=0.433 Sum_probs=46.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
-.+++||.|||+.|+..+.+||. +|..|.. +|+|||..+||+||..+++..
T Consensus 65 IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk------~LPGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGN-RWSQIAA------QLPGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCc-chHHHHH------hcCCCCHHHHHHHHHHHHHHH
Confidence 46899999999999999999997 9999998 378999999999999887653
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.10 E-value=3.5e-06 Score=76.64 Aligned_cols=51 Identities=22% Similarity=0.432 Sum_probs=45.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
-+|+.||+|||..|+.+...||. +|..|++. |+|||...+|..|...++..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GN-rWs~IA~~------LPGRTDNeIKN~Wnt~lkkk 110 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGN-RWSLIAGR------LPGRTDNEVKNHWNTHLKKK 110 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCc-HHHHHHhh------CCCcCHHHHHHHHHHHHHHH
Confidence 36899999999999999999998 99999994 89999999999997765443
No 15
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.03 E-value=1.1e-05 Score=58.84 Aligned_cols=49 Identities=20% Similarity=0.398 Sum_probs=40.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCCh---hhhhcCCCCCCCCCCC-CHHHHHHHHHHh
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKW---KNILRDPQFAPSLTQR-SNIDLKDKWRNL 56 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW---~~I~~~~~F~~~l~~R-T~vdLkdKWRnl 56 (272)
++|..||+||...++.||+.||.|+| +.|+... -..| |..|++.+....
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~-----~~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELM-----VVDGLTRDQVASHLQKY 53 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHc-----CCCCCCHHHHHHHHHHH
Confidence 47889999999999999999999999 9998842 1245 999999876543
No 16
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.89 E-value=1.2e-05 Score=82.30 Aligned_cols=53 Identities=19% Similarity=0.513 Sum_probs=47.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 2 GNQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 2 g~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
|-+.++||++||..|+.+|.+||...|.+|... +++|+..||++||.|.+...
T Consensus 357 sikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~------vPnRSdsQcR~RY~nvL~~s 409 (939)
T KOG0049|consen 357 SVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQA------VPNRSDSQCRERYTNVLNRS 409 (939)
T ss_pred cccCCCCCCHHHHHHHHHHHHhCccchhhHHHh------cCCccHHHHHHHHHHHHHHh
Confidence 457899999999999999999999999999984 68999999999998876543
No 17
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.62 E-value=4e-05 Score=78.17 Aligned_cols=50 Identities=38% Similarity=0.704 Sum_probs=46.2
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccccc
Q 024102 4 QKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNA 61 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~ 61 (272)
.|+.||+||++.|...|..||. .|..|.+ +-+|.+.+|+|+||++.+.+.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~-------~lgr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGK-------ALGRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHH-------HHccCcHHHHHHHHHhhcccc
Confidence 6899999999999999999996 9999998 359999999999999988764
No 18
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.61 E-value=5.3e-05 Score=74.45 Aligned_cols=49 Identities=27% Similarity=0.527 Sum_probs=44.5
Q ss_pred CCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 6 QKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 6 ~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
--||.+||-.|+++++.||-|||..|+.. ...||..+|++.|.++...+
T Consensus 73 ~~WtadEEilLLea~~t~G~GNW~dIA~h------IGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 73 PSWTADEEILLLEAAETYGFGNWQDIADH------IGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred CCCChHHHHHHHHHHHHhCCCcHHHHHHH------HcccchHHHHHHHHHHHhcC
Confidence 46999999999999999999999999995 55899999999999987654
No 19
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.40 E-value=8.4e-05 Score=76.35 Aligned_cols=62 Identities=21% Similarity=0.335 Sum_probs=49.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccccccCCCCccC
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNAQQGSKDKIR 70 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~~~~~~~k~r 70 (272)
.++..||-.||+.|+..|.+||.|+|.+|+. +|++||..|+..+-+.+......|.+.+-..
T Consensus 410 ~K~~rW~l~edeqL~~~V~~YG~g~WakcA~------~Lp~~t~~q~~rrR~R~~~~k~rl~~~~~~~ 471 (939)
T KOG0049|consen 410 AKVERWTLVEDEQLLYAVKVYGKGNWAKCAM------LLPKKTSRQLRRRRLRLIAAKLRLAAGFCNA 471 (939)
T ss_pred hccCceeecchHHHHHHHHHHccchHHHHHH------HccccchhHHHHHHHHHHHHHHHHhcCCccc
Confidence 5788999999999999999999999999999 4899999888877766655544444444433
No 20
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.12 E-value=0.00022 Score=54.34 Aligned_cols=55 Identities=25% Similarity=0.464 Sum_probs=35.9
Q ss_pred CCCCCHHHHHHHHHHHHh------hCC-----C--ChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccccc
Q 024102 5 KQKWTAEEEEALLAGVAK------HGP-----G--KWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNA 61 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k------~G~-----G--kW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~ 61 (272)
|..||.+|+..|+..+.. ++. + -|..|+..- ...=..||+.||++||.||.+...
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l--~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEEL--AEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHH--HHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHH--HHcCCCCCHHHHHHHHHHHHHHHH
Confidence 578999999999999887 221 2 599997742 111127999999999999987654
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=96.53 E-value=0.0013 Score=54.56 Aligned_cols=58 Identities=28% Similarity=0.445 Sum_probs=45.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCC---CChhhhh----cCCC--CCCCCCCCCHHHHHHHHHHhccc
Q 024102 2 GNQKQKWTAEEEEALLAGVAKHGP---GKWKNIL----RDPQ--FAPSLTQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 2 g~~r~~WT~eEd~~L~~GV~k~G~---GkW~~I~----~~~~--F~~~l~~RT~vdLkdKWRnl~~~ 59 (272)
+..++.||.+||..|+..+.+||- |.|..|. .+|. |+-||.+||+.+|..|-..|+..
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 9998875 4554 45567899999999999888764
No 22
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.38 E-value=0.003 Score=47.39 Aligned_cols=53 Identities=34% Similarity=0.550 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHhh-----CC-----------CChhhhhcCCCCCCCC-CCCCHHHHHHHHHHhccc
Q 024102 5 KQKWTAEEEEALLAGVAKH-----GP-----------GKWKNILRDPQFAPSL-TQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~-----G~-----------GkW~~I~~~~~F~~~l-~~RT~vdLkdKWRnl~~~ 59 (272)
+..||.+|.+.|+..|.+| |. .-|..|... |+... ..||..+|+.+|.||...
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 4689999999999999997 31 469999986 43322 379999999999999754
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.01 E-value=0.0035 Score=63.21 Aligned_cols=50 Identities=26% Similarity=0.482 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccccc
Q 024102 6 QKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNA 61 (272)
Q Consensus 6 ~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~ 61 (272)
.-|+.-||+.|..+|.+||...|+.|.+. |+..|..||+.||...+.+..
T Consensus 8 gvwrntEdeilkaav~kyg~nqws~i~sl------l~~kt~rqC~~rw~e~ldp~i 57 (617)
T KOG0050|consen 8 GVWRNTEDEVLKAAVMKYGKNQWSRIASL------LNRKTARQCKARWEEWLDPAI 57 (617)
T ss_pred ceecccHHHHHHHHHHHcchHHHHHHHHH------HhhcchhHHHHHHHHHhCHHH
Confidence 57999999999999999999999999994 678999999999987776654
No 24
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=95.99 E-value=0.0088 Score=60.51 Aligned_cols=52 Identities=19% Similarity=0.408 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccccc
Q 024102 4 QKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNAQ 62 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~~ 62 (272)
.+..||.+|.-.|+.||++||. .|.+|..+ ..+||..||-.|+..|=....+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~h------Vg~ks~eqCI~kFL~LPieD~~ 303 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD-DWNKVADH------VGTKSQEQCILKFLRLPIEDPY 303 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc-cHHHHHhc------cCCCCHHHHHHHHHhcCccchh
Confidence 4678999999999999999998 99999996 5699999999999887544443
No 25
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.55 E-value=0.0042 Score=62.83 Aligned_cols=50 Identities=36% Similarity=0.628 Sum_probs=45.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
..+++||.+|+..|...+.++|. .|..|-.. .+|-+.+|+|+||+..+.+
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~-------~~rmp~~crd~wr~~~~~g 338 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHGG-SWTEIGKL-------LGRMPNDCRDRWRDYVKCG 338 (512)
T ss_pred hhhccCccccccccccccccccc-hhhHhhhh-------hccCcHHHHHHHhhhcccc
Confidence 35789999999999999999995 99999884 4899999999999999886
No 26
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.39 E-value=0.013 Score=56.44 Aligned_cols=48 Identities=23% Similarity=0.495 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 7 KWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 7 ~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
.|+.+||-.|+++.+..|-|+|..|+.. ...|+..+||+.|-.+....
T Consensus 65 ~WgadEEllli~~~~TlGlGNW~dIady------iGsr~kee~k~HylK~y~es 112 (432)
T COG5114 65 GWGADEELLLIECLDTLGLGNWEDIADY------IGSRAKEEIKSHYLKMYDES 112 (432)
T ss_pred CcCchHHHHHHHHHHhcCCCcHHHHHHH------HhhhhhHHHHHHHHHHHhhc
Confidence 6999999999999999999999999984 56899999999998776543
No 27
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=95.27 E-value=0.018 Score=57.69 Aligned_cols=46 Identities=20% Similarity=0.456 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhc
Q 024102 5 KQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLS 57 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~ 57 (272)
...||.+|.-.|++||+.||. .|.+|+.+ ..++|..||--||-+|=
T Consensus 279 dk~WS~qE~~LLLEGIe~ygD-dW~kVA~H------VgtKt~EqCIl~FL~LP 324 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGD-DWDKVARH------VGTKTKEQCILHFLQLP 324 (531)
T ss_pred cccccHHHHHHHHHHHHHhhh-hHHHHHHH------hCCCCHHHHHHHHHcCC
Confidence 358999999999999999998 99999996 56999999999997663
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=95.16 E-value=0.027 Score=50.82 Aligned_cols=58 Identities=19% Similarity=0.280 Sum_probs=47.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhC--CCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccccc
Q 024102 4 QKQKWTAEEEEALLAGVAKHG--PGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNAQ 62 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~G--~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~~ 62 (272)
.|-+||.+||+.|........ ..++.+|+.++. ..|..+||+.+|.+.|+.|..+..-
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~-~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKNR-SVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhCh-hhhccccCHHHHHHHHHHHHHhchh
Confidence 578999999999999877764 368999999764 2235689999999999999877653
No 29
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.02 E-value=0.029 Score=61.19 Aligned_cols=58 Identities=22% Similarity=0.354 Sum_probs=48.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhh----hcCC--CCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNI----LRDP--QFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I----~~~~--~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
.+++.||.|||..|+-.+.+||-|+|..| ...| .|.-||.+||+..|..|-.+|+...
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~ 987 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLI 987 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHH
Confidence 34567999999999999999999999997 3344 4567789999999999998887654
No 30
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=94.53 E-value=0.016 Score=58.76 Aligned_cols=51 Identities=25% Similarity=0.491 Sum_probs=44.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~ 59 (272)
+..+.|+..||+.|..+|++||+.+|..|... |..|+..||+.||-+...+
T Consensus 18 ~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~------~~~~~~kq~~~rw~~~lnp 68 (512)
T COG5147 18 RKGGSWKRTEDEDLKALVKKLGPNNWSKVASL------LISSTGKQSSNRWNNHLNP 68 (512)
T ss_pred ecCCCCCCcchhHHHHHHhhcccccHHHHHHH------hcccccccccchhhhhhch
Confidence 45578999999999999999999999999995 4569999999999665544
No 31
>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=94.42 E-value=0.036 Score=48.73 Aligned_cols=48 Identities=35% Similarity=0.771 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCC---CCC----CCHHHHHHHH
Q 024102 6 QKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPS---LTQ----RSNIDLKDKW 53 (272)
Q Consensus 6 ~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~---l~~----RT~vdLkdKW 53 (272)
.-|-..-|-.|+.||.+||-|+|..|..||.|.-+ |.+ =+.-++|.||
T Consensus 4 ~iw~r~hdywll~gi~~hgy~rwqdi~nd~~f~IiNEPFk~e~~kgnfle~KNkF 58 (173)
T PF08074_consen 4 EIWHRRHDYWLLAGIVKHGYGRWQDIQNDPRFAIINEPFKTESQKGNFLEMKNKF 58 (173)
T ss_pred hhhhhhhhHHHHhHHhhccchhHHHHhcCCceeeecccccccccccchHHHHHHH
Confidence 45888999999999999999999999999998611 211 1335888887
No 32
>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=93.63 E-value=0.12 Score=38.69 Aligned_cols=50 Identities=22% Similarity=0.367 Sum_probs=30.7
Q ss_pred CCCCCHHHHHHHHHHHHhhCC------C--ChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccc
Q 024102 5 KQKWTAEEEEALLAGVAKHGP------G--KWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~------G--kW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~ 59 (272)
|.+||.+||++|++-|..+.. | =|+.+.... ...+|-..++|||+..+..
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 678999999999999965422 2 388887752 3489999999999766554
No 33
>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=93.26 E-value=0.39 Score=37.58 Aligned_cols=66 Identities=14% Similarity=0.153 Sum_probs=55.7
Q ss_pred CCHHHHHHHHHHhcCc-CCCCCHHHHHHHHHHhc-CCCcchHHHHHHHHHhhhhcCceeeeccccccC
Q 024102 118 PKYNAMIFEAISTLKD-ANGSDISAIANFIEERQ-EAPPNFRRLLSSRLRRLVSQGKLEKVRNCYKIR 183 (272)
Q Consensus 118 p~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y-~v~~n~~~~L~~~LKrlV~~GkLvkvK~sykl~ 183 (272)
-++.+.|..+|..|+- ....+..+|..++..+| ++...-...|..+|-.|+..|+|..+.+-|.|-
T Consensus 10 iPL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfiv 77 (80)
T PF10264_consen 10 IPLPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIV 77 (80)
T ss_pred eeHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeCCCceEee
Confidence 3589999999999976 45579999999999999 453334788999999999999999998777764
No 34
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=93.13 E-value=0.28 Score=38.17 Aligned_cols=66 Identities=18% Similarity=0.324 Sum_probs=55.6
Q ss_pred CHHHHHHHHHHhcCc-CCCCCHHHHHHHHHHhcCCC--------------cchHHHHHHHHHhhhhcCceeeec-ccccc
Q 024102 119 KYNAMIFEAISTLKD-ANGSDISAIANFIEERQEAP--------------PNFRRLLSSRLRRLVSQGKLEKVR-NCYKI 182 (272)
Q Consensus 119 ~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y~v~--------------~n~~~~L~~~LKrlV~~GkLvkvK-~sykl 182 (272)
+|++|+.-.|..|++ .+..++..|...|.+++++. ..|+..+.=++..|+..|-|..++ |.|+|
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 589999999999999 66789999999999987532 147788888999999999999975 78999
Q ss_pred CC
Q 024102 183 RK 184 (272)
Q Consensus 183 ~~ 184 (272)
++
T Consensus 81 T~ 82 (92)
T PF14338_consen 81 TE 82 (92)
T ss_pred CH
Confidence 75
No 35
>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=92.51 E-value=0.23 Score=39.60 Aligned_cols=56 Identities=23% Similarity=0.264 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcC----CCcchHHHHHHHHHhhhhcCceeeec
Q 024102 118 PKYNAMIFEAISTLKDANGSDISAIANFIEERQE----APPNFRRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 118 p~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----v~~n~~~~L~~~LKrlV~~GkLvkvK 177 (272)
-+|..||..||.+ -..++.+.+-|.+||+.+|. .+..++..|+..|- .+.-|+++.
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 4799999999998 34456899999999999983 34566777777763 445677665
No 36
>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=91.21 E-value=0.41 Score=36.94 Aligned_cols=33 Identities=24% Similarity=0.283 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhc
Q 024102 117 GPKYNAMIFEAISTLKDANGSDISAIANFIEERQ 150 (272)
Q Consensus 117 hp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y 150 (272)
.-+|..||..||.... .++.+..-|.+||+++|
T Consensus 3 ~~sY~~LI~~Ai~~sp-~~~lTL~eIy~~I~~~~ 35 (78)
T cd00059 3 PYSYSALIAMAIQSSP-EKRLTLSEIYKWISDNF 35 (78)
T ss_pred CCCHHHHHHHHHHhCC-CCCeeHHHHHHHHHHhC
Confidence 3479999999999955 56689999999999998
No 37
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=90.22 E-value=0.29 Score=50.62 Aligned_cols=53 Identities=32% Similarity=0.531 Sum_probs=44.0
Q ss_pred CCCCCCCHHHHHHHHHHHH-------hh------------------CCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhc
Q 024102 3 NQKQKWTAEEEEALLAGVA-------KH------------------GPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLS 57 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~-------k~------------------G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~ 57 (272)
+.+..||-||++.|++.|+ .| -.-+|..|..+ +..|+..||+-||-.|+
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 4789999999999999996 23 22489999884 67999999999999988
Q ss_pred cccc
Q 024102 58 VSNA 61 (272)
Q Consensus 58 ~~~~ 61 (272)
....
T Consensus 508 ~~~s 511 (607)
T KOG0051|consen 508 TSPS 511 (607)
T ss_pred hhHH
Confidence 7654
No 38
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=90.02 E-value=0.17 Score=55.92 Aligned_cols=52 Identities=31% Similarity=0.562 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCC---CCC---CCCCHHHHHHHHHHhc
Q 024102 6 QKWTAEEEEALLAGVAKHGPGKWKNILRDPQFA---PSL---TQRSNIDLKDKWRNLS 57 (272)
Q Consensus 6 ~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~---~~l---~~RT~vdLkdKWRnl~ 57 (272)
--|..++|..|+-||-+||-|+|-.|..||.++ -+| ..=+..+|.-|=.-++
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~~yLl 1191 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRADYLL 1191 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHHHHHH
Confidence 359999999999999999999999999999754 011 1335677777755444
No 39
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=89.36 E-value=0.39 Score=47.48 Aligned_cols=55 Identities=22% Similarity=0.309 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHH----HHhccccc
Q 024102 6 QKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKW----RNLSVSNA 61 (272)
Q Consensus 6 ~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKW----Rnl~~~~~ 61 (272)
..||.+|.+.|.+...+|-- +|=.|...|.-..|-.+||-.|||||| |++.+...
T Consensus 131 n~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred ccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 46999999999999999998 999999987433233579999999998 55555444
No 40
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=89.34 E-value=0.46 Score=37.40 Aligned_cols=32 Identities=28% Similarity=0.278 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhc
Q 024102 118 PKYNAMIFEAISTLKDANGSDISAIANFIEERQ 150 (272)
Q Consensus 118 p~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y 150 (272)
-+|..||..||..- ..++.+...|.+||+++|
T Consensus 4 ~sY~~lI~~ai~~s-p~~~ltl~~Iy~~I~~~~ 35 (89)
T smart00339 4 YSYIALIAMAILSS-PDKRLTLSEIYKWIEDNF 35 (89)
T ss_pred CCHHHHHHHHHHhC-CCCCeeHHHHHHHHHHhC
Confidence 36999999999995 456789999999999998
No 41
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=89.24 E-value=0.39 Score=45.69 Aligned_cols=55 Identities=27% Similarity=0.384 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHh----hCCCC-----hhhhhcCCCCCCCCCCCCHHHHHHHHHHhccccc
Q 024102 5 KQKWTAEEEEALLAGVAK----HGPGK-----WKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNA 61 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k----~G~Gk-----W~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~ 61 (272)
...|+.+|...|+..-.+ ++.|+ |..|... +...=..||+.+|+.||.||.+...
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k--~~~~g~~rs~~qck~K~~nl~k~Yk 117 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARK--MAELGYPRSPKQCKAKIENLKKKYK 117 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHH--HHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 378999999999987664 34455 9999872 2212247999999999999988764
No 42
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=87.82 E-value=0.44 Score=48.62 Aligned_cols=48 Identities=25% Similarity=0.486 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccc
Q 024102 4 QKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~ 59 (272)
++--|+.|||+.|+....-+-+ .|+.|.. +-+||+.+|-.||-+++-.
T Consensus 58 ~~tews~eederlLhlakl~p~-qwrtIa~-------i~gr~~~qc~eRy~~ll~~ 105 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPT-QWRTIAD-------IMGRTSQQCLERYNNLLDV 105 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCC-ccchHHH-------HhhhhHHHHHHHHHHHHHH
Confidence 3557999999999999988877 9999988 4699999999999988643
No 43
>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=84.36 E-value=1.1 Score=34.25 Aligned_cols=52 Identities=31% Similarity=0.606 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhh---C----CC-----ChhhhhcCCCCCCCC-CCCCHHHHHHHHHHhcccc
Q 024102 7 KWTAEEEEALLAGVAKH---G----PG-----KWKNILRDPQFAPSL-TQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 7 ~WT~eEd~~L~~GV~k~---G----~G-----kW~~I~~~~~F~~~l-~~RT~vdLkdKWRnl~~~~ 60 (272)
.||+++++.|++.+... | .| .|..|... |...+ ...|..||++||..|.+.-
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~--~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEE--FNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHH--HHHHhCCcccHHHHHHHHHHHHHHH
Confidence 59999999999998654 2 22 36777664 43222 3568899999998876543
No 44
>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=80.18 E-value=4.9 Score=34.69 Aligned_cols=50 Identities=24% Similarity=0.339 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHh
Q 024102 4 QKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNL 56 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl 56 (272)
+.+.-|..|...|..+|++||. .+..+..|..++. .-.|..||+.+.+.+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~--~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNY--MQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCc--ccCCHHHHHHHHHHh
Confidence 5677899999999999999997 9999999987663 368999999987765
No 45
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=75.64 E-value=3.2 Score=33.13 Aligned_cols=58 Identities=26% Similarity=0.319 Sum_probs=38.7
Q ss_pred CCCCCCHHHHHHHHHHHHhh----CCCChhhhhcCCCC-CCCC-CCCCHHHHHHHHHHhccccc
Q 024102 4 QKQKWTAEEEEALLAGVAKH----GPGKWKNILRDPQF-APSL-TQRSNIDLKDKWRNLSVSNA 61 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~----G~GkW~~I~~~~~F-~~~l-~~RT~vdLkdKWRnl~~~~~ 61 (272)
..|.||+++|-.|+.|+--| |.+....+..-++| .+.+ ..=|..||.||-|.|.+...
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 45789999999999999877 76444433222211 0111 23588999999999976654
No 46
>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=75.47 E-value=22 Score=28.73 Aligned_cols=50 Identities=26% Similarity=0.171 Sum_probs=32.3
Q ss_pred chHHHHHHHHHHHHHHHhhHhhhhHHHHHHHHHHHHhHHhHHHHHHHHHH
Q 024102 215 EIVEEASITAAYRIAEAENKSFLAAEAFKEAERVSKMAEDTDAMLQLVKE 264 (272)
Q Consensus 215 ~t~~eAa~aAA~~VAEAE~~~~~A~eA~~eae~~~~~ae~a~~~~~la~e 264 (272)
.|++++-..+.-+-..|+.+...|.+|...|+.+.+.|+.++--++=|.|
T Consensus 35 ~~a~~a~~~a~~a~~~A~~A~~~AdeA~~kA~~A~aaA~~Aqq~A~eAne 84 (96)
T PF11839_consen 35 STAEQAQATAASAQSAAASAQQRADEAASKADAALAAAEAAQQTADEANE 84 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555666666667777777777777777777766665554
No 47
>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=74.20 E-value=3 Score=30.66 Aligned_cols=26 Identities=42% Similarity=0.529 Sum_probs=21.8
Q ss_pred HHHHHHHHHhhhhcCceeeecccccc
Q 024102 157 RRLLSSRLRRLVSQGKLEKVRNCYKI 182 (272)
Q Consensus 157 ~~~L~~~LKrlV~~GkLvkvK~sykl 182 (272)
...|..-|-++|+.|+|+.+.|+|||
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 36789999999999999999999997
No 48
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=69.93 E-value=7.2 Score=38.85 Aligned_cols=50 Identities=16% Similarity=0.276 Sum_probs=43.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhccc
Q 024102 3 NQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 3 ~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~ 59 (272)
...-+||.+|-+.+..++..+|+ .+..|... |++|+-.|+|-||.+--+.
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~l------fP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGT-DFSLISSL------FPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcc-hHHHHHHh------cCchhHHHHHHHHHHHhhh
Confidence 34568999999999999999998 99999985 6899999999999765443
No 49
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=68.13 E-value=1.5 Score=38.81 Aligned_cols=50 Identities=20% Similarity=0.321 Sum_probs=35.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCC--CCCCCCCHHHHHHHH
Q 024102 1 MGNQKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFA--PSLTQRSNIDLKDKW 53 (272)
Q Consensus 1 mg~~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~--~~l~~RT~vdLkdKW 53 (272)
|--....||.|+|..|-.-|-+|+.--=..+.. |. ...-+||...|.+||
T Consensus 1 mk~rqdawt~e~d~llae~vl~~i~eg~tql~a---fe~~g~~L~rt~aac~fRw 52 (170)
T PRK13923 1 MKTRQDAWTQERDGLLAEVVLRHIREGGTQLKA---FEEVGDALKRTAAACGFRW 52 (170)
T ss_pred CcchhhhhhhHHHHHHHHHHHHHHhccchHHHH---HHHHHHHHhhhHHHHHhHH
Confidence 455677899999999999999887621122222 21 112489999999999
No 50
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=65.31 E-value=6.5 Score=29.62 Aligned_cols=56 Identities=20% Similarity=0.326 Sum_probs=38.0
Q ss_pred HHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeeccccccCC
Q 024102 121 NAMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRNCYKIRK 184 (272)
Q Consensus 121 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~sykl~~ 184 (272)
.++|.+=+..|. .+|.+.+-|.... +++ -..+...|+.|++.|-+...++.|+|.+
T Consensus 5 ~~Ii~~IL~~l~-~~~~~~t~i~~~~----~L~---~~~~~~yL~~L~~~gLI~~~~~~Y~lTe 60 (77)
T PF14947_consen 5 LEIIFDILKILS-KGGAKKTEIMYKA----NLN---YSTLKKYLKELEEKGLIKKKDGKYRLTE 60 (77)
T ss_dssp THHHHHHHHHH--TT-B-HHHHHTTS----T-----HHHHHHHHHHHHHTTSEEEETTEEEE-H
T ss_pred HHHHHHHHHHHH-cCCCCHHHHHHHh----CcC---HHHHHHHHHHHHHCcCeeCCCCEEEECc
Confidence 467777777776 6777777776222 221 2568889999999999988889999975
No 51
>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=61.75 E-value=17 Score=25.96 Aligned_cols=39 Identities=15% Similarity=0.275 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHhcCCCc-chHHHHHHHHHhhhhcCce
Q 024102 135 NGSDISAIANFIEERQEAPP-NFRRLLSSRLRRLVSQGKL 173 (272)
Q Consensus 135 ~GSS~~AI~kyIe~~y~v~~-n~~~~L~~~LKrlV~~GkL 173 (272)
++.|...|.+.+.++|++++ ....-+..-|..|.+.|-|
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 46899999999999999866 4778888899999998865
No 52
>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=55.92 E-value=11 Score=29.20 Aligned_cols=20 Identities=40% Similarity=0.665 Sum_probs=11.8
Q ss_pred CCCCCHHHHHHH--------HHHHHhhC
Q 024102 5 KQKWTAEEEEAL--------LAGVAKHG 24 (272)
Q Consensus 5 r~~WT~eEd~~L--------~~GV~k~G 24 (272)
.+-||+|+|+.| ...++|||
T Consensus 47 ~GiWT~eDD~~L~~~~~~~~~~L~~khG 74 (87)
T PF11626_consen 47 PGIWTPEDDEMLRSGDKDDIERLIKKHG 74 (87)
T ss_dssp TT---HHHHHHHTS--HHHHHHHHHHH-
T ss_pred CCCcCHHHHHHHHcCCHHHHHHHHHHhC
Confidence 678999999999 34445666
No 53
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=51.76 E-value=64 Score=23.66 Aligned_cols=59 Identities=20% Similarity=0.265 Sum_probs=41.5
Q ss_pred CCHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeec---cccccCC
Q 024102 118 PKYNAMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVR---NCYKIRK 184 (272)
Q Consensus 118 p~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK---~sykl~~ 184 (272)
..+.+-|++.|..-.++ |.+..-|++-+ +++ +.-++..|.+|...|.+++.. +.|+|..
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 34667788888765333 57777776655 444 357899999999999999853 5677753
No 54
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=50.84 E-value=29 Score=31.51 Aligned_cols=49 Identities=14% Similarity=0.424 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 7 KWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 7 ~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
+|+++.|-.|+.+|..-. .=..|...=.|+ ..-|-..+.+||..|+--.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS---~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFS---CKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcC---CcCcHHHHHHHHHHHHcCh
Confidence 699999999999998642 556665554464 5678999999999998654
No 55
>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=48.22 E-value=53 Score=24.25 Aligned_cols=22 Identities=14% Similarity=0.223 Sum_probs=18.9
Q ss_pred HHHHHHHHhhhhcCceeeeccc
Q 024102 158 RLLSSRLRRLVSQGKLEKVRNC 179 (272)
Q Consensus 158 ~~L~~~LKrlV~~GkLvkvK~s 179 (272)
..+..+|+.|...|-|.+..|.
T Consensus 41 ~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 41 STVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHCcCccCCCCC
Confidence 4578899999999999988764
No 56
>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=47.56 E-value=7.3 Score=34.26 Aligned_cols=49 Identities=22% Similarity=0.407 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHHhh---CCCChhhhhcCCCCCCC--CCCCCHHHHHHHHHHhccc
Q 024102 5 KQKWTAEEEEALLAGVAKH---GPGKWKNILRDPQFAPS--LTQRSNIDLKDKWRNLSVS 59 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~---G~GkW~~I~~~~~F~~~--l~~RT~vdLkdKWRnl~~~ 59 (272)
...||.|||..|-.-|-+| |. ..+.- |..+ --+||+.-|.=||-..++.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~---TQL~A---FeEvg~~L~RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGS---TQLSA---FEEVGRALNRTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcch---HHHHH---HHHHHHHHcccHHHhcchHHHHHHH
Confidence 4579999999999999998 33 12221 3211 2389999999999777763
No 57
>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=47.14 E-value=37 Score=26.45 Aligned_cols=54 Identities=13% Similarity=0.192 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHh-cCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeee
Q 024102 116 NGPKYNAMIFEAIST-LKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKV 176 (272)
Q Consensus 116 ~hp~y~~MI~EAI~~-Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkv 176 (272)
...+..++|++.|.. .....|.++.-|.+-+ .++ ..-|+.+|..|+..|.|.-+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l----~~~---~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL----GMS---ENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS----TS----HHHHHHHHHHHHHTTSEEES
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh----CcC---HHHHHHHHHHHHhCCeEecc
Confidence 345679999999999 7788999999999877 333 45799999999999998743
No 58
>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=46.07 E-value=90 Score=21.58 Aligned_cols=28 Identities=21% Similarity=0.437 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhhcCceeeec-cccccCC
Q 024102 157 RRLLSSRLRRLVSQGKLEKVR-NCYKIRK 184 (272)
Q Consensus 157 ~~~L~~~LKrlV~~GkLvkvK-~sykl~~ 184 (272)
...++..|+.|...|.|.... |.|.|.+
T Consensus 39 ~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 39 RETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred HHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 467888999999999999887 8888753
No 59
>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=44.81 E-value=62 Score=23.66 Aligned_cols=62 Identities=13% Similarity=0.153 Sum_probs=35.2
Q ss_pred CHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCC---cchHHHHHHHHHhh--hhcCceeee-cccccc
Q 024102 119 KYNAMIFEAISTLKDANGSDISAIANFIEERQEAP---PNFRRLLSSRLRRL--VSQGKLEKV-RNCYKI 182 (272)
Q Consensus 119 ~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~---~n~~~~L~~~LKrl--V~~GkLvkv-K~sykl 182 (272)
+|.+.+.+.+...+ ...+..-|.+.|.++.... .+....|...|-.- -..|.|+++ .|.|-|
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 35556666666555 5689999999999876332 23334455444333 488899999 577765
No 60
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=44.61 E-value=25 Score=33.15 Aligned_cols=48 Identities=17% Similarity=0.292 Sum_probs=34.5
Q ss_pred HhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeeccccccCC
Q 024102 129 STLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRNCYKIRK 184 (272)
Q Consensus 129 ~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~sykl~~ 184 (272)
--|++ +.-+..-|+.++.-. ...+..+||+|.+.|-++|..+.|+|++
T Consensus 20 llL~e-gPkti~EI~~~l~vs-------~~ai~pqiKkL~~~~LV~~~~~~Y~LS~ 67 (260)
T COG4742 20 LLLKE-GPKTIEEIKNELNVS-------SSAILPQIKKLKDKGLVVQEGDRYSLSS 67 (260)
T ss_pred HHHHh-CCCCHHHHHHHhCCC-------cHHHHHHHHHHhhCCCEEecCCEEEecc
Confidence 34444 334556666555422 3568889999999999999999999975
No 61
>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=42.07 E-value=72 Score=28.52 Aligned_cols=27 Identities=30% Similarity=0.298 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHhhHhhhhHHHHH
Q 024102 217 VEEASITAAYRIAEAENKSFLAAEAFK 243 (272)
Q Consensus 217 ~~eAa~aAA~~VAEAE~~~~~A~eA~~ 243 (272)
+.|||.+||.+-+||....+.||--+|
T Consensus 12 ~v~aaraaavaa~earc~~~vaekea~ 38 (207)
T PF05928_consen 12 VVDAARAAAVAASEARCVVFVAEKEAR 38 (207)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhHHHH
Confidence 578899999999999888887764333
No 62
>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=41.32 E-value=82 Score=27.40 Aligned_cols=63 Identities=17% Similarity=0.308 Sum_probs=45.7
Q ss_pred HHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcC----C-------Ccc---hHHHHHHHHHhhhhcCceeeec-cccccCC
Q 024102 120 YNAMIFEAISTLKDANGSDISAIANFIEERQE----A-------PPN---FRRLLSSRLRRLVSQGKLEKVR-NCYKIRK 184 (272)
Q Consensus 120 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~----v-------~~n---~~~~L~~~LKrlV~~GkLvkvK-~sykl~~ 184 (272)
|.+.|...+. --|.....|..||-++.. + -.. -..-++..|+.|.+.|-|.+++ |.|.|.|
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 YLENIIKVLD----LIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMINP 117 (165)
T ss_pred HHHHHHHHhh----hhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEECc
Confidence 4445555444 346678999999998752 1 000 1355889999999999999997 8999999
Q ss_pred CC
Q 024102 185 ET 186 (272)
Q Consensus 185 ~~ 186 (272)
..
T Consensus 118 ~~ 119 (165)
T PF05732_consen 118 NF 119 (165)
T ss_pred HH
Confidence 76
No 63
>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=40.50 E-value=53 Score=23.25 Aligned_cols=51 Identities=22% Similarity=0.305 Sum_probs=34.3
Q ss_pred HHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeeccccccCC
Q 024102 128 ISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRNCYKIRK 184 (272)
Q Consensus 128 I~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~sykl~~ 184 (272)
|..|.=..|.|...+.. +|. .+|...+...|..+++.|-|+...+++++++
T Consensus 12 ~~~LR~~~Gi~~~~~~~----~~g--~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~ 62 (66)
T PF06969_consen 12 MLGLRCNEGIDLSEFEQ----RFG--IDFAEEFQKELEELQEDGLLEIDGGRLRLTE 62 (66)
T ss_dssp HHHHHHHSEEEHHHHHH----HTT----THHH-HHHHHHHHHTTSEEE-SSEEEE-T
T ss_pred HHHHHhHCCcCHHHHHH----HHC--cCHHHHHHHHHHHHHHCCCEEEeCCEEEECc
Confidence 34444466777766543 443 2367777888999999999999999999975
No 64
>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=39.33 E-value=2e+02 Score=23.35 Aligned_cols=34 Identities=24% Similarity=0.220 Sum_probs=17.5
Q ss_pred HHHHHHHHHHhhHhhhhHHHHHHHHHHHHhHHhH
Q 024102 222 ITAAYRIAEAENKSFLAAEAFKEAERVSKMAEDT 255 (272)
Q Consensus 222 ~aAA~~VAEAE~~~~~A~eA~~eae~~~~~ae~a 255 (272)
.+|..+-..|+.+...|.+|.-.|+++.+.|+++
T Consensus 49 ~~A~~A~~~AdeA~~kA~~A~aaA~~Aqq~A~eA 82 (96)
T PF11839_consen 49 SAAASAQQRADEAASKADAALAAAEAAQQTADEA 82 (96)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444445555555555555555555555544
No 65
>smart00595 MADF subfamily of SANT domain.
Probab=39.07 E-value=18 Score=27.10 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=20.9
Q ss_pred ChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccc
Q 024102 27 KWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSN 60 (272)
Q Consensus 27 kW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~ 60 (272)
-|..|... + +-|..+|+.||++|....
T Consensus 29 aW~~Ia~~--l-----~~~~~~~~~kw~~LR~~y 55 (89)
T smart00595 29 AWEEIAEE--L-----GLSVEECKKRWKNLRDRY 55 (89)
T ss_pred HHHHHHHH--H-----CcCHHHHHHHHHHHHHHH
Confidence 58888885 2 339999999999996443
No 66
>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=37.82 E-value=54 Score=22.94 Aligned_cols=47 Identities=19% Similarity=0.270 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeec
Q 024102 122 AMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 122 ~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK 177 (272)
..|+..|. .+..+.+...|..+..-. +..++..|++|++.|-|.+..
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 345556666666655422 457889999999999998764
No 67
>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=34.49 E-value=37 Score=22.70 Aligned_cols=36 Identities=8% Similarity=0.251 Sum_probs=26.2
Q ss_pred cCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHh
Q 024102 131 LKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRR 166 (272)
Q Consensus 131 Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKr 166 (272)
|.++-|.|.++|..++..+..+.+.....+...++.
T Consensus 3 lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~ 38 (52)
T cd01392 3 IARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEE 38 (52)
T ss_pred HHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 456679999999999998877766666655555544
No 68
>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=32.78 E-value=58 Score=23.04 Aligned_cols=27 Identities=15% Similarity=0.260 Sum_probs=22.7
Q ss_pred HHHHHHHHhhhhcCceeeeccccccCC
Q 024102 158 RLLSSRLRRLVSQGKLEKVRNCYKIRK 184 (272)
Q Consensus 158 ~~L~~~LKrlV~~GkLvkvK~sykl~~ 184 (272)
.-++.-|..|...|.|.++.|.+.+..
T Consensus 29 ~TiRRDl~~L~~~g~i~r~~GG~~~~~ 55 (57)
T PF08220_consen 29 MTIRRDLNKLEKQGLIKRTHGGAVLND 55 (57)
T ss_pred HHHHHHHHHHHHCCCEEEEcCEEEeCC
Confidence 457778889999999999999887764
No 69
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=32.64 E-value=74 Score=31.81 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHH
Q 024102 6 QKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWR 54 (272)
Q Consensus 6 ~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWR 54 (272)
--||.+|=..+-.|++.||. ....|... -++.|+-..|-.=|.
T Consensus 278 ~~wsEeEcr~FEegl~~yGK-DF~lIr~n-----kvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGK-DFHLIRAN-----KVRTRSVGELVEYYY 320 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcc-cHHHHHhc-----ccccchHHHHHHHHH
Confidence 36999999999999999998 99999885 378999999876543
No 70
>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=31.85 E-value=39 Score=26.34 Aligned_cols=50 Identities=28% Similarity=0.373 Sum_probs=33.3
Q ss_pred HHHHHHhcCcCCCC-----CHHHHHHHHHHhcCCCcchH--HHHHHHHHhhhhcCceee
Q 024102 124 IFEAISTLKDANGS-----DISAIANFIEERQEAPPNFR--RLLSSRLRRLVSQGKLEK 175 (272)
Q Consensus 124 I~EAI~~Lker~GS-----S~~AI~kyIe~~y~v~~n~~--~~L~~~LKrlV~~GkLvk 175 (272)
.+.|...+.+.+|. ++.|+..|++++- -+|.. ..+..+|.-||++|-...
T Consensus 3 ~LNn~~~~~~~~G~~~l~kD~eA~~~y~~~~V--~pnt~~F~S~~Erl~yLv~~~YYe~ 59 (82)
T PF08343_consen 3 ELNNELNIYDEDGKIQLEKDKEAVRAYFKEHV--NPNTVKFNSLKERLDYLVENDYYEK 59 (82)
T ss_dssp HHHHGGG---TTS---THHHHHHHHHHHHHTT--GGGB---SSHHHHHHHHHHTTSB-H
T ss_pred HHHHHHcCCCCCCCcCchhHHHHHHHHHHHhc--ccceeecCCHHHHHHHHHHcCcHHH
Confidence 34566677778886 7899999999864 33434 448889999999987654
No 71
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=31.70 E-value=1.9e+02 Score=20.84 Aligned_cols=46 Identities=22% Similarity=0.266 Sum_probs=32.1
Q ss_pred HHHHHhcC-cCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeec
Q 024102 125 FEAISTLK-DANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 125 ~EAI~~Lk-er~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK 177 (272)
+++|-.|. +....+...|++++.=. ...++..|++|...|-+...+
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~vs-------~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLGVS-------PPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHTS--------HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHcCCCCccHHHHHHHHCCC-------hHHHHHHHHHHHHCCCEEecC
Confidence 34444443 45567888888877533 457889999999999988654
No 72
>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=30.41 E-value=40 Score=23.31 Aligned_cols=39 Identities=10% Similarity=0.181 Sum_probs=30.1
Q ss_pred HHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHh
Q 024102 128 ISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRR 166 (272)
Q Consensus 128 I~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKr 166 (272)
|..+-+.-|.|..++.++|.....+.+.-+..+...++.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEE 40 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHH
Confidence 445566789999999999998877877777777666654
No 73
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=29.95 E-value=65 Score=20.75 Aligned_cols=26 Identities=27% Similarity=0.383 Sum_probs=21.0
Q ss_pred HHHHHHHHHhhhhcCceeeecccccc
Q 024102 157 RRLLSSRLRRLVSQGKLEKVRNCYKI 182 (272)
Q Consensus 157 ~~~L~~~LKrlV~~GkLvkvK~sykl 182 (272)
...++..|+.|.+.|.|...++.|.|
T Consensus 22 ~~tv~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 22 RETVSRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHHHHHHHCCCEEEeCCEEEE
Confidence 34578889999999999988777765
No 74
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=29.60 E-value=62 Score=34.26 Aligned_cols=26 Identities=27% Similarity=0.672 Sum_probs=24.1
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCChhhh
Q 024102 5 KQKWTAEEEEALLAGVAKHGPGKWKNI 31 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~GkW~~I 31 (272)
|.-||-.|++.+.+|++.||. ....|
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 678999999999999999997 88877
No 75
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=29.29 E-value=68 Score=32.82 Aligned_cols=51 Identities=20% Similarity=0.280 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcccccc
Q 024102 5 KQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSVSNAQ 62 (272)
Q Consensus 5 r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~~~~~ 62 (272)
.-.||.||--.|-....-||. +..+|.+. |++|+-..|..=|.++.+...+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~------LP~rsLaSlvqyYy~~KK~~~~ 237 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGK-DFHKIRQA------LPHRSLASLVQYYYSWKKTREY 237 (534)
T ss_pred cccchHHHHHHHHHHHHHhcc-cHHHHHHH------ccCccHHHHHHHHHHHHHHhhH
Confidence 357999999999999999998 99999985 8899999888777666655543
No 76
>KOG3614 consensus Ca2+/Mg2+-permeable cation channels (LTRPC family) [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=29.26 E-value=1.1e+02 Score=35.00 Aligned_cols=34 Identities=26% Similarity=0.395 Sum_probs=27.0
Q ss_pred hhHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHhh
Q 024102 237 LAAEAFKEAERVSKMAEDTDAMLQLVKEIYERCS 270 (272)
Q Consensus 237 ~A~eA~~eae~~~~~ae~a~~~~~la~ei~~~c~ 270 (272)
.|.||..+.|.++.+-+-++.|=++|.|+|++|-
T Consensus 603 lA~ea~d~~~~s~el~~~s~~f~~lAveLfd~cy 636 (1381)
T KOG3614|consen 603 LAHEAHDWHEAAKELKTLSDEFEGLAVELFDECY 636 (1381)
T ss_pred HhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4444444777777788889999999999999993
No 77
>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=29.15 E-value=1.4e+02 Score=19.75 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=25.2
Q ss_pred HHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCce
Q 024102 128 ISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKL 173 (272)
Q Consensus 128 I~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkL 173 (272)
|..|.+..|.|..-|++-+.=. ...++..|++|+..|.|
T Consensus 9 l~~l~~~~~~t~~ela~~~~is-------~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 9 LNYLRENPRITQKELAEKLGIS-------RSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHCTTS-HHHHHHHHTS--------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHcCCCCHHHHHHHhCCC-------HHHHHHHHHHHHHCcCc
Confidence 3344445557777776655311 46788999999999976
No 78
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=29.14 E-value=50 Score=24.15 Aligned_cols=39 Identities=8% Similarity=0.191 Sum_probs=27.5
Q ss_pred HHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHh
Q 024102 128 ISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRR 166 (272)
Q Consensus 128 I~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKr 166 (272)
|..|.+.-|.|+.+|..++..+..+.+..+..+...++.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~ 41 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEE 41 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Confidence 345566679999999999988777766656666555543
No 79
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=28.36 E-value=91 Score=26.00 Aligned_cols=49 Identities=24% Similarity=0.346 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeeccccccC
Q 024102 135 NGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRNCYKIR 183 (272)
Q Consensus 135 ~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~sykl~ 183 (272)
+-.....|.+||+++|.+..+++..+..-|++++.-|..--..+...|+
T Consensus 49 t~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLP 97 (122)
T CHL00137 49 TDEQISALREIIEENYQVEGDLRRFESLNIKRLMEINCYRGRRHRLGLP 97 (122)
T ss_pred CHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHHHhCchhcccccCCCC
Confidence 3345788999999899999999999999999999988876666666664
No 80
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=28.10 E-value=1.5e+02 Score=19.09 Aligned_cols=40 Identities=18% Similarity=0.296 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeecccc
Q 024102 134 ANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRNCY 180 (272)
Q Consensus 134 r~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~sy 180 (272)
..+.+...|..++ +++ ...+...|+.|...|.|.+..+-+
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 4567777777775 332 456788889999999998876543
No 81
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=27.91 E-value=1.4e+02 Score=22.01 Aligned_cols=52 Identities=15% Similarity=0.280 Sum_probs=37.0
Q ss_pred HHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeee--ccccccCC
Q 024102 124 IFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKV--RNCYKIRK 184 (272)
Q Consensus 124 I~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkv--K~sykl~~ 184 (272)
|++.|..- +.+.+...|...+ +++ +..+...|+.|++.|-|.+. .+.|.+.+
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 45555432 2578899998887 333 46788889999999999986 35677754
No 82
>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=27.30 E-value=1.8e+02 Score=23.65 Aligned_cols=53 Identities=19% Similarity=0.312 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCcee
Q 024102 120 YNAMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLE 174 (272)
Q Consensus 120 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLv 174 (272)
+.++|.-|....+++- |...|-.||++-+.....+..++...|+.|..+|-+.
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 9999999999855444557888888888888777543
No 83
>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=27.01 E-value=1.2e+02 Score=26.88 Aligned_cols=41 Identities=17% Similarity=0.261 Sum_probs=31.9
Q ss_pred cCCCCCCCCCHHHHHHHHHHhcCc-CCCCCHHHHHHHHHHhc
Q 024102 110 SALDGKNGPKYNAMIFEAISTLKD-ANGSDISAIANFIEERQ 150 (272)
Q Consensus 110 ~~~~~~~hp~y~~MI~EAI~~Lke-r~GSS~~AI~kyIe~~y 150 (272)
.....+.+|+|+.||..-+..+++ +.+.+..++..+|..+.
T Consensus 99 ~~~~~~~~p~y~~Mi~~L~~qvk~~~de~~~~~~~~~l~~H~ 140 (177)
T PF03234_consen 99 VENKDPEQPTYDEMIEDLLDQVKKEPDEKSGKAELEELQEHR 140 (177)
T ss_pred cccCCCCCCCHHHHHHHHHHHHhcccCcccHHHHHHHHHHHH
Confidence 345567789999999999888875 55556888888888775
No 84
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=26.38 E-value=76 Score=21.73 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=31.2
Q ss_pred hcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeec
Q 024102 130 TLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 130 ~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK 177 (272)
.|.+..|.+...|+.++.-. +..++..+++|+..|-|++..
T Consensus 11 ~l~~~~~~~~~~la~~~~~~-------~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 11 ILYENGGITQSELAEKLGIS-------RSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHSSEEHHHHHHHHTS--------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHcCCCCHHHHHHHHCCC-------hhHHHHHHHHHHHCCCEEecc
Confidence 34456668888888877533 567899999999999999765
No 85
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=25.98 E-value=1.1e+02 Score=22.38 Aligned_cols=48 Identities=13% Similarity=0.223 Sum_probs=34.6
Q ss_pred HHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeec
Q 024102 120 YNAMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 120 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK 177 (272)
..-.|+..|... .+.+...|..++. ++ ...++..|++|++.|-|...+
T Consensus 11 ~~~~il~~l~~~---~~~~~~~la~~~~----~s---~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 11 TQFLVLRILYEE---GPLSVSELAKRLG----VS---PSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHC----CC---chhHHHHHHHHHHCCCeEecC
Confidence 456677777663 3677888877652 32 346889999999999998765
No 86
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=24.26 E-value=68 Score=27.40 Aligned_cols=36 Identities=25% Similarity=0.460 Sum_probs=26.5
Q ss_pred HHHHHHHHHhcC------CCcch-----HHHHHHHHHhhhhcCceee
Q 024102 140 SAIANFIEERQE------APPNF-----RRLLSSRLRRLVSQGKLEK 175 (272)
Q Consensus 140 ~AI~kyIe~~y~------v~~n~-----~~~L~~~LKrlV~~GkLvk 175 (272)
.+|..|+...|. |-.|+ +..+..+|..||++|+|+.
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~ 50 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE 50 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee
Confidence 578888888763 22333 3568899999999999983
No 87
>PF08944 p47_phox_C: NADPH oxidase subunit p47Phox, C terminal domain; InterPro: IPR015039 The C-terminal domain of the phagocyte NADPH oxidase subunit p47Phox contains conserved PxxP motifs that allow binding to SH3 domains, with subsequent activation of the NADPH oxidase, and generation of superoxide, which plays a crucial role in host defence against microbial infection []. ; PDB: 1K4U_P 1UEC_A.
Probab=23.68 E-value=36 Score=25.18 Aligned_cols=8 Identities=50% Similarity=0.937 Sum_probs=3.2
Q ss_pred HHHHHHhh
Q 024102 263 KEIYERCS 270 (272)
Q Consensus 263 ~ei~~~c~ 270 (272)
.+||+||+
T Consensus 38 ~~IL~RCs 45 (58)
T PF08944_consen 38 ELILQRCS 45 (58)
T ss_dssp HHHHHSS-
T ss_pred HHHHHHhh
Confidence 34444443
No 88
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=23.18 E-value=99 Score=32.45 Aligned_cols=48 Identities=21% Similarity=0.406 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCChhhhhcCCCCCCCCCCCCHHHHHHHHHHhcc
Q 024102 4 QKQKWTAEEEEALLAGVAKHGPGKWKNILRDPQFAPSLTQRSNIDLKDKWRNLSV 58 (272)
Q Consensus 4 ~r~~WT~eEd~~L~~GV~k~G~GkW~~I~~~~~F~~~l~~RT~vdLkdKWRnl~~ 58 (272)
-..+||.+|-+....+...+|. +-+.|... |++|+..++|-|+++--+
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs-~~slis~l------~p~R~rk~iK~K~~~eE~ 455 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGS-DFSLISNL------FPLRDRKQIKAKFKKEEK 455 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcc-cccccccc------cccccHHHHHHHHhhhhh
Confidence 3568999999999999999998 99999885 579999999999976443
No 89
>PF13309 HTH_22: HTH domain
Probab=22.36 E-value=31 Score=25.28 Aligned_cols=23 Identities=9% Similarity=0.247 Sum_probs=19.3
Q ss_pred HHHHHHhcCcCCCCCHHHHHHHH
Q 024102 124 IFEAISTLKDANGSDISAIANFI 146 (272)
Q Consensus 124 I~EAI~~Lker~GSS~~AI~kyI 146 (272)
|..|+..+.+.=|.|+.||.+||
T Consensus 41 lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 41 LKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred cCcHHHHHHHHHCCCHHHHHHHc
Confidence 56677777788899999999997
No 90
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=21.52 E-value=1.2e+02 Score=25.14 Aligned_cols=52 Identities=21% Similarity=0.353 Sum_probs=42.5
Q ss_pred CcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeeccccccC
Q 024102 132 KDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRNCYKIR 183 (272)
Q Consensus 132 ker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~sykl~ 183 (272)
++-+-.....|.++|+++|.+..+++..+..-|++|+.-+..--..+...|+
T Consensus 46 ~~L~~~qi~~l~~~i~~~~~i~~dL~~~~~~dI~rl~~I~sYRG~RH~~gLP 97 (122)
T PRK05179 46 KDLTDEELDKIREEIDKNYKVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLP 97 (122)
T ss_pred ccCCHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHhcceeeeecccCCC
Confidence 4444556788999999889999999999999999999998877766666664
No 91
>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=21.29 E-value=1.8e+02 Score=18.62 Aligned_cols=25 Identities=28% Similarity=0.377 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhcCcCCCCCHHHHHHHHHHh
Q 024102 120 YNAMIFEAISTLKDANGSDISAIANFIEER 149 (272)
Q Consensus 120 y~~MI~EAI~~Lker~GSS~~AI~kyIe~~ 149 (272)
+-.+|.||+.. |.|..-|..|++-+
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 45788888864 99999999999854
No 92
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=21.27 E-value=51 Score=27.80 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=19.8
Q ss_pred hcCcCCCCCHHHHHHHHHHhcCC
Q 024102 130 TLKDANGSDISAIANFIEERQEA 152 (272)
Q Consensus 130 ~Lker~GSS~~AI~kyIe~~y~v 152 (272)
.|.+-.|.|+|+|-+||.+..|.
T Consensus 5 ELA~~tG~srQTINrWvRkegW~ 27 (122)
T PF07037_consen 5 ELAELTGYSRQTINRWVRKEGWK 27 (122)
T ss_pred HHHHHhCccHHHHHHHHHhcCce
Confidence 56778999999999999998753
No 93
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=21.17 E-value=2.3e+02 Score=28.97 Aligned_cols=61 Identities=21% Similarity=0.516 Sum_probs=48.8
Q ss_pred HHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHH---HhhhhcCceeeec------cccccCCC
Q 024102 121 NAMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRL---RRLVSQGKLEKVR------NCYKIRKE 185 (272)
Q Consensus 121 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~L---KrlV~~GkLvkvK------~sykl~~~ 185 (272)
..||+.-| .|.|-...++...|.+||+.+..-++++..++ +.|+..|.++++. ..|+|...
T Consensus 61 haMlLnvl----~r~gd~~~~~~~Ll~~nhe~~~~~~~~~~ra~~i~r~L~~agvve~~~~~~~~G~~~~ltvd 130 (461)
T PF12029_consen 61 HAMLLNVL----ARPGDAFAAMRHLLRDNHEPRARQRRLIRRAIEIYRSLLDAGVVERLPEPDEGGRRYRLTVD 130 (461)
T ss_pred HHHHHHHH----cCCCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCCEEEeccCCCCCceEEEecc
Confidence 56877766 78888999999999999988776677777776 8999999999864 26666543
No 94
>PF14412 AHH: A nuclease family of the HNH/ENDO VII superfamily with conserved AHH
Probab=21.01 E-value=1.3e+02 Score=23.58 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=20.1
Q ss_pred cCCCCCCCCC-HHHHHHHHHHhcCc
Q 024102 110 SALDGKNGPK-YNAMIFEAISTLKD 133 (272)
Q Consensus 110 ~~~~~~~hp~-y~~MI~EAI~~Lke 133 (272)
.+.....||. |.+.|.+.|..+..
T Consensus 61 ~~~H~g~H~~~Y~~~V~~~L~~~~~ 85 (109)
T PF14412_consen 61 RPPHRGRHPNEYNKYVRERLDKIEN 85 (109)
T ss_pred cCCcCCCCcHHHHHHHHHHHHHHHH
Confidence 3456688999 99999999999877
No 95
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=20.87 E-value=32 Score=23.21 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=14.5
Q ss_pred HHhcCcCCCCCHHHHHHHHHHh
Q 024102 128 ISTLKDANGSDISAIANFIEER 149 (272)
Q Consensus 128 I~~Lker~GSS~~AI~kyIe~~ 149 (272)
|..+-+.-|.|+++|.+|+.+|
T Consensus 24 i~~IA~~~gvsr~TvyR~l~~~ 45 (45)
T PF02796_consen 24 IAEIAKQFGVSRSTVYRYLNKN 45 (45)
T ss_dssp HHHHHHHTTS-HHHHHHHHCC-
T ss_pred HHHHHHHHCcCHHHHHHHHhcC
Confidence 3455557888888888887643
No 96
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=20.56 E-value=75 Score=25.65 Aligned_cols=56 Identities=23% Similarity=0.384 Sum_probs=36.9
Q ss_pred HHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeecc----ccccCC
Q 024102 121 NAMIFEAISTLKDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVRN----CYKIRK 184 (272)
Q Consensus 121 ~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK~----sykl~~ 184 (272)
.++|++.+.. ...+|.-.+-|. |.+--|| ......|+-|+++|.+++.++ .|.|.+
T Consensus 17 ~eIi~dIL~~-~~~~~~~~Tri~------y~aNlny-~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~ 76 (95)
T COG3432 17 LEIIFDILKA-ISEGGIGITRII------YGANLNY-KRAQKYIEMLVEKGLIIKQDNGRRKVYELTE 76 (95)
T ss_pred HHHHHHHHHH-hcCCCCCceeee------eecCcCH-HHHHHHHHHHHhCCCEEeccCCccceEEECh
Confidence 7888988887 566666666554 3222222 346677899999995555554 388864
No 97
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=20.51 E-value=1e+02 Score=24.03 Aligned_cols=40 Identities=15% Similarity=0.368 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHhcCCC-----cch---HHHHHHHHHhhhhcCceeeec
Q 024102 138 DISAIANFIEERQEAP-----PNF---RRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 138 S~~AI~kyIe~~y~v~-----~n~---~~~L~~~LKrlV~~GkLvkvK 177 (272)
|...|..||..+-.+. ..| -..+..-|.+++..|++.++.
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 5677888888775321 112 246888899999999999985
No 98
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=20.15 E-value=1.9e+02 Score=20.28 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=27.2
Q ss_pred CcCCCCCHHHHHHHHHHhcCCCcchHHHHHHHHHhhhhcCceeeec
Q 024102 132 KDANGSDISAIANFIEERQEAPPNFRRLLSSRLRRLVSQGKLEKVR 177 (272)
Q Consensus 132 ker~GSS~~AI~kyIe~~y~v~~n~~~~L~~~LKrlV~~GkLvkvK 177 (272)
....+.+...|+.-+ +++ ...++.+|+.|...|-|..++
T Consensus 20 ~~~~~~t~~ela~~l----~~~---~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 20 ASNGPMTVSELAEEL----GIS---QSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHCSTBEHHHHHHHH----TS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred hcCCCCCHHHHHHHH----CCC---HHHHHHHHHHHHHCCCeEEec
Confidence 445566666666555 333 345899999999999988765
No 99
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=20.13 E-value=1.4e+02 Score=22.09 Aligned_cols=28 Identities=39% Similarity=0.715 Sum_probs=19.4
Q ss_pred HHHHHHHHHhcCCCcch--HHHHHHHHH-hhhhcC
Q 024102 140 SAIANFIEERQEAPPNF--RRLLSSRLR-RLVSQG 171 (272)
Q Consensus 140 ~AI~kyIe~~y~v~~n~--~~~L~~~LK-rlV~~G 171 (272)
++++.||+.+ |++ .+++..+|. -|+.+|
T Consensus 12 ~~m~~fie~h----P~WDQ~Rl~~aALa~FL~QnG 42 (57)
T PF10929_consen 12 QAMKDFIETH----PNWDQYRLFQAALAGFLLQNG 42 (57)
T ss_pred HHHHHHHHcC----CCchHHHHHHHHHHHHHHHcC
Confidence 5788999988 444 477888883 455555
Done!