Query 013548
Match_columns 441
No_of_seqs 201 out of 560
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 04:58:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013548hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01557 myb_SHAQKYF myb-like 99.6 1.3E-15 2.9E-20 118.2 5.9 50 58-107 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.4 2.6E-13 5.6E-18 99.6 5.9 45 60-104 1-47 (48)
3 KOG0457 Histone acetyltransfer 99.2 2E-11 4.3E-16 125.8 6.8 71 38-108 43-121 (438)
4 smart00717 SANT SANT SWI3, AD 99.0 5.4E-10 1.2E-14 78.0 6.0 46 60-105 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 6E-10 1.3E-14 76.9 5.5 44 62-105 1-45 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 98.8 3.8E-09 8.3E-14 79.8 4.9 42 63-104 1-42 (60)
7 KOG0724 Zuotin and related mol 98.8 4.1E-10 8.8E-15 110.4 -2.9 132 42-184 34-166 (335)
8 COG5114 Histone acetyltransfer 98.5 2.7E-07 5.9E-12 93.5 8.2 70 38-107 34-111 (432)
9 PLN03212 Transcription repress 98.4 5.4E-07 1.2E-11 88.2 7.1 60 47-106 10-73 (249)
10 PLN03212 Transcription repress 98.3 1.4E-06 3.1E-11 85.3 8.1 53 58-110 76-128 (249)
11 PLN03091 hypothetical protein; 98.3 4.1E-06 9E-11 87.6 11.3 54 58-111 65-118 (459)
12 COG5259 RSC8 RSC chromatin rem 98.2 1.1E-06 2.3E-11 92.4 5.2 52 50-101 267-320 (531)
13 PLN03091 hypothetical protein; 98.2 1.1E-06 2.5E-11 91.7 5.0 51 56-106 10-62 (459)
14 KOG1279 Chromatin remodeling f 98.0 5.6E-06 1.2E-10 87.9 5.8 65 38-102 229-295 (506)
15 KOG0048 Transcription factor, 98.0 1.2E-05 2.5E-10 77.0 6.8 53 58-110 60-112 (238)
16 KOG0048 Transcription factor, 97.5 7.7E-05 1.7E-09 71.4 4.0 47 60-106 9-57 (238)
17 PLN03162 golden-2 like transcr 96.9 0.0027 5.8E-08 66.3 7.8 54 58-111 235-293 (526)
18 KOG0049 Transcription factor, 96.7 0.0026 5.5E-08 70.1 5.7 49 58-106 358-407 (939)
19 KOG0049 Transcription factor, 96.3 0.0051 1.1E-07 67.8 5.4 56 59-114 411-467 (939)
20 KOG4329 DNA-binding protein [G 95.3 0.18 3.8E-06 53.1 11.4 71 36-109 249-324 (445)
21 KOG4468 Polycomb-group transcr 94.7 0.048 1E-06 59.9 5.6 52 60-111 88-149 (782)
22 KOG0724 Zuotin and related mol 94.0 0.033 7.2E-07 55.2 2.5 53 58-110 162-221 (335)
23 PF13837 Myb_DNA-bind_4: Myb/S 94.0 0.083 1.8E-06 42.2 4.2 52 60-111 1-70 (90)
24 KOG0051 RNA polymerase I termi 93.9 0.064 1.4E-06 58.9 4.4 50 58-107 434-509 (607)
25 KOG0050 mRNA splicing protein 93.4 0.08 1.7E-06 57.4 4.1 52 56-107 3-55 (617)
26 KOG0051 RNA polymerase I termi 93.3 0.1 2.2E-06 57.3 4.8 54 52-106 375-429 (607)
27 KOG3554 Histone deacetylase co 93.1 0.12 2.6E-06 55.8 4.8 69 58-126 283-357 (693)
28 COG5118 BDP1 Transcription ini 92.8 0.18 4E-06 53.2 5.6 44 58-101 363-406 (507)
29 PLN03142 Probable chromatin-re 92.7 0.2 4.4E-06 58.0 6.3 48 61-108 825-873 (1033)
30 KOG4167 Predicted DNA-binding 92.3 0.23 5.1E-06 55.8 5.8 42 60-101 619-660 (907)
31 smart00426 TEA TEA domain. 91.7 0.15 3.3E-06 42.0 2.8 43 60-102 3-66 (68)
32 KOG3841 TEF-1 and related tran 91.7 0.28 6.2E-06 51.7 5.3 54 58-111 74-148 (455)
33 KOG1194 Predicted DNA-binding 90.9 0.44 9.6E-06 51.3 5.9 42 60-101 187-228 (534)
34 PF13873 Myb_DNA-bind_5: Myb/S 90.4 1.2 2.6E-05 35.3 6.7 51 61-111 3-75 (78)
35 PF01285 TEA: TEA/ATTS domain 89.7 0.31 6.8E-06 51.6 3.7 47 58-104 47-112 (431)
36 PF09111 SLIDE: SLIDE; InterP 89.5 1.1 2.3E-05 40.0 6.3 57 54-110 43-115 (118)
37 COG5147 REB1 Myb superfamily p 85.9 1 2.2E-05 48.9 4.8 53 58-110 70-122 (512)
38 COG5147 REB1 Myb superfamily p 83.5 0.68 1.5E-05 50.3 2.2 56 54-109 14-70 (512)
39 PF08914 Myb_DNA-bind_2: Rap1 78.5 3.3 7.1E-05 33.5 4.0 48 60-107 2-59 (65)
40 PF12776 Myb_DNA-bind_3: Myb/S 77.2 7 0.00015 31.6 5.6 42 62-103 1-60 (96)
41 KOG0050 mRNA splicing protein 76.8 5.3 0.00012 44.0 6.1 51 58-109 57-107 (617)
42 KOG4282 Transcription factor G 69.2 14 0.0003 37.2 6.7 55 60-114 54-122 (345)
43 TIGR02894 DNA_bind_RsfA transc 65.7 11 0.00024 35.8 4.8 50 60-110 4-60 (161)
44 PF06461 DUF1086: Domain of Un 62.0 21 0.00046 33.4 5.9 48 62-109 40-90 (145)
45 PRK13923 putative spore coat p 61.7 11 0.00024 35.9 4.1 49 59-107 4-58 (170)
46 PF11035 SnAPC_2_like: Small n 60.3 40 0.00086 35.5 8.0 53 60-112 21-77 (344)
47 KOG1194 Predicted DNA-binding 56.3 19 0.00042 39.3 5.2 52 57-108 366-417 (534)
48 PLN03142 Probable chromatin-re 55.4 50 0.0011 39.1 8.8 54 59-112 925-991 (1033)
49 PF04504 DUF573: Protein of un 51.2 37 0.00079 29.2 5.2 50 61-110 5-71 (98)
50 KOG0385 Chromatin remodeling c 48.1 30 0.00065 40.3 5.3 54 58-112 793-847 (971)
51 KOG2009 Transcription initiati 47.7 18 0.00039 40.3 3.5 50 59-111 408-457 (584)
52 PF01388 ARID: ARID/BRIGHT DNA 45.5 59 0.0013 26.5 5.4 27 81-107 59-90 (92)
53 PF12451 VPS11_C: Vacuolar pro 45.1 18 0.00038 27.8 2.1 28 64-91 17-44 (49)
54 PF08281 Sigma70_r4_2: Sigma-7 44.1 72 0.0016 23.3 5.2 39 68-107 15-53 (54)
55 TIGR02937 sigma70-ECF RNA poly 35.8 1.1E+02 0.0025 24.8 5.7 47 62-110 110-156 (158)
56 PF10561 UPF0565: Uncharacteri 35.4 29 0.00063 35.8 2.6 34 47-80 268-301 (303)
57 PF02954 HTH_8: Bacterial regu 34.6 54 0.0012 23.7 3.2 28 66-93 5-33 (42)
58 smart00501 BRIGHT BRIGHT, ARID 34.3 1.1E+02 0.0024 25.2 5.5 30 81-110 55-89 (93)
59 PF13404 HTH_AsnC-type: AsnC-t 33.7 1.4E+02 0.0029 22.1 5.2 37 66-103 3-40 (42)
60 PF13325 MCRS_N: N-terminal re 32.2 75 0.0016 31.1 4.7 46 58-103 71-124 (199)
61 PTZ00196 60S ribosomal protein 28.9 19 0.0004 31.9 0.0 12 413-424 46-57 (98)
62 cd08780 Death_TRADD Death Doma 26.7 87 0.0019 27.4 3.7 38 64-104 1-42 (90)
63 cd06171 Sigma70_r4 Sigma70, re 26.6 2.1E+02 0.0045 19.3 5.1 43 62-106 10-52 (55)
64 PF04545 Sigma70_r4: Sigma-70, 24.5 2.8E+02 0.0061 20.1 5.7 30 79-109 20-49 (50)
65 PF08074 CHDCT2: CHDCT2 (NUC03 24.2 44 0.00095 32.2 1.5 28 60-87 3-31 (173)
66 KOG0384 Chromodomain-helicase 24.1 45 0.00097 40.5 1.9 53 59-112 1132-1197(1373)
67 PRK11179 DNA-binding transcrip 23.9 1.4E+02 0.003 26.8 4.6 38 65-103 8-46 (153)
68 PF09420 Nop16: Ribosome bioge 23.8 1.7E+02 0.0036 27.0 5.2 44 61-104 115-162 (164)
No 1
>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=99.60 E-value=1.3e-15 Score=118.18 Aligned_cols=50 Identities=40% Similarity=0.648 Sum_probs=45.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-h---HHHHhhcC-CC-CHHHHHHHHHHHHHH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRA-W---RKIEEHVG-TK-TAVQIRSHAQKFFSK 107 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrg-W---kkIAe~Vg-TR-T~~QVrSHAQKYF~K 107 (441)
+.+..||+|||.+||+||+.||.+ | ++|+++++ ++ |+.||+|||||||.+
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 357789999999999999999995 9 99998765 78 999999999999986
No 2
>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=99.43 E-value=2.6e-13 Score=99.64 Aligned_cols=45 Identities=47% Similarity=0.795 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKF 104 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVrSHAQKY 104 (441)
++.||.||+++|++||.+||.+ |+.||.+|| +||..||++|+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 4789999999999999999999 999999999 99999999999987
No 3
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.20 E-value=2e-11 Score=125.83 Aligned_cols=71 Identities=32% Similarity=0.611 Sum_probs=65.8
Q ss_pred ccccCCCCC-CCCCCCCcccccC------CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 013548 38 DQFSCGNDF-APKPRKPYTITKQ------RERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKV 108 (441)
Q Consensus 38 e~~s~G~~~-~~K~rKPytitk~------rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~Kl 108 (441)
+||++|++. .|+..|||.+... ...||.+|+.+||+|++.||.| |+.||+||||||..+|+.|+.|+|+.-
T Consensus 43 ~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 43 QCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred HHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhcC
Confidence 789999999 5599999998766 5699999999999999999999 999999999999999999999999864
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.03 E-value=5.4e-10 Score=77.95 Aligned_cols=46 Identities=33% Similarity=0.640 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHhC-cchHHHHhhcCCCCHHHHHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLFG-RAWRKIEEHVGTKTAVQIRSHAQKFF 105 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yG-rgWkkIAe~VgTRT~~QVrSHAQKYF 105 (441)
+..||.+|+.+|+.++..|| .+|..||.++++||+.||+.++..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 35799999999999999999 78999999999999999999998764
No 5
>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=99.01 E-value=6e-10 Score=76.90 Aligned_cols=44 Identities=36% Similarity=0.673 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhC-cchHHHHhhcCCCCHHHHHHHHHHHH
Q 013548 62 RWTEEEHKKFLEALKLFG-RAWRKIEEHVGTKTAVQIRSHAQKFF 105 (441)
Q Consensus 62 ~WT~EEH~lFLeaLe~yG-rgWkkIAe~VgTRT~~QVrSHAQKYF 105 (441)
.||.+|+.+|+.++..|| ..|..||.++++||..||+.|+++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 67999999999999999999998763
No 6
>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=98.84 E-value=3.8e-09 Score=79.85 Aligned_cols=42 Identities=40% Similarity=0.797 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHH
Q 013548 63 WTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKF 104 (441)
Q Consensus 63 WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKY 104 (441)
||.+|+.+|++++..||.+|+.||+++|.||+.||+.|+..+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~ 42 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNH 42 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999874
No 7
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.78 E-value=4.1e-10 Score=110.43 Aligned_cols=132 Identities=30% Similarity=0.242 Sum_probs=101.3
Q ss_pred CCCCCCCCCCCCcccccCCCC-CCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhHhcCCCCCCCC
Q 013548 42 CGNDFAPKPRKPYTITKQRER-WTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRESNGCSTSPV 120 (441)
Q Consensus 42 ~G~~~~~K~rKPytitk~rg~-WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r~~~G~~~~~~ 120 (441)
.+.+..++.+++|++...+.+ ||.++|..|.++|..|++.|..|-+|++.++.+|++.|+|+||-++.+.. +...
T Consensus 34 ~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~~----~~~~ 109 (335)
T KOG0724|consen 34 WTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKSD----TSLA 109 (335)
T ss_pred hHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCccc----cccc
Confidence 345556799999999987654 99999999999999997779999999999999999999999999997653 2234
Q ss_pred ccccCCCCCCCCCCCCCcCCCCCCCCCcCCCCcccccCCCCCccccccccCCCCccchhhcccc
Q 013548 121 EPVEIPPPRPKRKPMHPYPRKLAHPPVKESLNPELSRTSLSPILSVSERENQSPTSVLFAIGSD 184 (441)
Q Consensus 121 ~~i~IPpprpKRkp~HpyPrk~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~sP~svls~~~s~ 184 (441)
..+.+|++++++++.|+||++........ ..+..+...... +....++.++...+++
T Consensus 110 ~~~~~~~~~~~~k~~~~y~~~~~~~~~~~------~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 166 (335)
T KOG0724|consen 110 EVEEFYNFWPKFKSWRQYPQKDEPDEEDS------ENRSQSRYSGGT-QRGKSNAEELRRKGTP 166 (335)
T ss_pred cccccCCccccccccccCCCCCCcccccc------cchhhhhhcccc-cccccchhhhhhccch
Confidence 57789999999999999999987642211 223333334444 5556666666655444
No 8
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.51 E-value=2.7e-07 Score=93.52 Aligned_cols=70 Identities=26% Similarity=0.545 Sum_probs=62.4
Q ss_pred ccccCCCCC-CCCCCCCccccc------CCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHH
Q 013548 38 DQFSCGNDF-APKPRKPYTITK------QRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSK 107 (441)
Q Consensus 38 e~~s~G~~~-~~K~rKPytitk------~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~K 107 (441)
-||+.|... .+.+.++|++.. ....|+.+|+.+|++|++..|-| |..||+|||+|+...|++|+-|||..
T Consensus 34 pCF~~g~~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~e 111 (432)
T COG5114 34 PCFVNGIETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYDE 111 (432)
T ss_pred hhhhccccccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHhh
Confidence 468889888 458889998763 25689999999999999999999 99999999999999999999999874
No 9
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.41 E-value=5.4e-07 Score=88.20 Aligned_cols=60 Identities=22% Similarity=0.444 Sum_probs=49.5
Q ss_pred CCCCCCCcc--cccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHHH
Q 013548 47 APKPRKPYT--ITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFFS 106 (441)
Q Consensus 47 ~~K~rKPyt--itk~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVrSHAQKYF~ 106 (441)
.++++-|.- ....+++||.||++++++++++||.. |+.||.+++ +||..|||.++.+|+.
T Consensus 10 ~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~ 73 (249)
T PLN03212 10 VSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLR 73 (249)
T ss_pred CCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhc
Confidence 444444443 33568899999999999999999975 999999885 8999999999998873
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.33 E-value=1.4e-06 Score=85.28 Aligned_cols=53 Identities=21% Similarity=0.328 Sum_probs=48.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r 110 (441)
.+++.||.||++++++.+..||..|..||.+++.||..||+.|+..++.+..+
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHH
Confidence 56889999999999999999999999999999999999999999887766543
No 11
>PLN03091 hypothetical protein; Provisional
Probab=98.31 E-value=4.1e-06 Score=87.63 Aligned_cols=54 Identities=19% Similarity=0.411 Sum_probs=49.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhHh
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r~ 111 (441)
.+++.||.||++++|+.+..||..|.+||.+|+.||..||+.|+...++|..+.
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999999999999999999999999999877776554
No 12
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.24 E-value=1.1e-06 Score=92.36 Aligned_cols=52 Identities=37% Similarity=0.628 Sum_probs=43.9
Q ss_pred CCCCcccccC--CCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHH
Q 013548 50 PRKPYTITKQ--RERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHA 101 (441)
Q Consensus 50 ~rKPytitk~--rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHA 101 (441)
.-++.++... ...||.+|..++|+||+.||.+|.+||.||||||..||.-|+
T Consensus 267 Df~~v~~~~~~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 267 DFKPVTISLLIRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred cchhhhhhcccccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 3344444333 348999999999999999999999999999999999999886
No 13
>PLN03091 hypothetical protein; Provisional
Probab=98.23 E-value=1.1e-06 Score=91.68 Aligned_cols=51 Identities=18% Similarity=0.491 Sum_probs=45.5
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHHH
Q 013548 56 ITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFFS 106 (441)
Q Consensus 56 itk~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVrSHAQKYF~ 106 (441)
...+++.||.||++++++++++||.. |+.||.+++ +||..|||.++.+|+.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLd 62 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLR 62 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccC
Confidence 44567899999999999999999986 999999886 8999999999987754
No 14
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.04 E-value=5.6e-06 Score=87.93 Aligned_cols=65 Identities=29% Similarity=0.468 Sum_probs=51.3
Q ss_pred ccccCCCCCCCCCCCC--cccccCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHH
Q 013548 38 DQFSCGNDFAPKPRKP--YTITKQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQ 102 (441)
Q Consensus 38 e~~s~G~~~~~K~rKP--ytitk~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQ 102 (441)
+||..|....++..-. ......+..||++|-.++|+||++||.+|.+||.|||+||..||..|+-
T Consensus 229 ~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL 295 (506)
T KOG1279|consen 229 DCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFL 295 (506)
T ss_pred HHHhcCCccCccccccchhccccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHH
Confidence 5666666554432221 1233557899999999999999999999999999999999999999873
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.01 E-value=1.2e-05 Score=76.95 Aligned_cols=53 Identities=19% Similarity=0.400 Sum_probs=47.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r 110 (441)
.+++.||+||+.+.+++..+||..|..||.++++||...|+.|+.-..+|..+
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~ 112 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKKKLL 112 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999999999999999999999999766655443
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.52 E-value=7.7e-05 Score=71.37 Aligned_cols=47 Identities=19% Similarity=0.405 Sum_probs=44.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFFS 106 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVrSHAQKYF~ 106 (441)
+|+||.||+.++++-|++||.+ |..|+...| .|+-.|||-++-.|+.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLr 57 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLR 57 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccC
Confidence 7999999999999999999999 999999999 9999999999988864
No 17
>PLN03162 golden-2 like transcription factor; Provisional
Probab=96.92 E-value=0.0027 Score=66.30 Aligned_cols=54 Identities=33% Similarity=0.415 Sum_probs=46.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc---hHHHHhh--cCCCCHHHHHHHHHHHHHHHhHh
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRA---WRKIEEH--VGTKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrg---WkkIAe~--VgTRT~~QVrSHAQKYF~Kl~r~ 111 (441)
|.|-.||.|=|++|++||++.|-+ =|+|-++ |..=|..+|+||-|||...+++.
T Consensus 235 KpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l 293 (526)
T PLN03162 235 KAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHL 293 (526)
T ss_pred CCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccc
Confidence 567899999999999999999943 6778765 45789999999999999988754
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.66 E-value=0.0026 Score=70.08 Aligned_cols=49 Identities=22% Similarity=0.506 Sum_probs=44.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFS 106 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~ 106 (441)
.+.|+||++|+.+++.|+++||.. |-+|-+.|+.|+..|||.++-..+.
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~ 407 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLN 407 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHH
Confidence 568999999999999999999865 9999999999999999999877554
No 19
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.32 E-value=0.0051 Score=67.80 Aligned_cols=56 Identities=30% Similarity=0.566 Sum_probs=49.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHhHhcCC
Q 013548 59 QRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVVRESNG 114 (441)
Q Consensus 59 ~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~Kl~r~~~G 114 (441)
+.++||-.|+++++.++++||.| |.+||.++|.||..|.+++-..+.....+...|
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k~rl~~~ 467 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAKLRLAAG 467 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHHHHHHhcC
Confidence 47899999999999999999999 999999999999999888877666666666544
No 20
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=95.34 E-value=0.18 Score=53.06 Aligned_cols=71 Identities=21% Similarity=0.441 Sum_probs=52.4
Q ss_pred ccccccCCCCCCC-CCCCCcccc---cCCCCCCHHHHHHHHHHHHHhCcchHHHH-hhcCCCCHHHHHHHHHHHHHHHh
Q 013548 36 VKDQFSCGNDFAP-KPRKPYTIT---KQRERWTEEEHKKFLEALKLFGRAWRKIE-EHVGTKTAVQIRSHAQKFFSKVV 109 (441)
Q Consensus 36 ~~e~~s~G~~~~~-K~rKPytit---k~rg~WT~EEH~lFLeaLe~yGrgWkkIA-e~VgTRT~~QVrSHAQKYF~Kl~ 109 (441)
|.+.+-|+-+.-. ++|+++... ..-..|+++|-..|.+||+.||+++-.|. .-|.||+...|..+ ||.+.+
T Consensus 249 L~~LvkcnfDteeAlrr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVey---YYlWKk 324 (445)
T KOG4329|consen 249 LYELVKCNFDTEEALRRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEY---YYLWKK 324 (445)
T ss_pred HHHHHHcCCcHHHHHHhcCCcceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHH---HHHhhc
Confidence 4555666666533 455555433 33468999999999999999999999997 58999999998765 455543
No 21
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=94.73 E-value=0.048 Score=59.93 Aligned_cols=52 Identities=25% Similarity=0.530 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHH----------HhhcCCCCHHHHHHHHHHHHHHHhHh
Q 013548 60 RERWTEEEHKKFLEALKLFGRAWRKI----------EEHVGTKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrgWkkI----------Ae~VgTRT~~QVrSHAQKYF~Kl~r~ 111 (441)
+..||-.|...|..||++||+++.+| -.-+-.||-.|||.||-+-..++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~ 149 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKL 149 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhh
Confidence 67999999999999999999999988 23456789999999987655555443
No 22
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=94.04 E-value=0.033 Score=55.20 Aligned_cols=53 Identities=38% Similarity=0.452 Sum_probs=47.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-hHHHH-hhcCCCCHHHHHHHHH-----HHHHHHhH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRA-WRKIE-EHVGTKTAVQIRSHAQ-----KFFSKVVR 110 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrg-WkkIA-e~VgTRT~~QVrSHAQ-----KYF~Kl~r 110 (441)
+.+..|+..+|.+|+.++..||+. |..|. .++-.|++.|+.+|+| +|+.+...
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~ 221 (335)
T KOG0724|consen 162 RKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKS 221 (335)
T ss_pred hccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhh
Confidence 456799999999999999999998 99998 5788999999999999 88888743
No 23
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=93.98 E-value=0.083 Score=42.21 Aligned_cols=52 Identities=33% Similarity=0.587 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHHHHHH------hCc--------chHHHHhhc---C-CCCHHHHHHHHHHHHHHHhHh
Q 013548 60 RERWTEEEHKKFLEALKL------FGR--------AWRKIEEHV---G-TKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~------yGr--------gWkkIAe~V---g-TRT~~QVrSHAQKYF~Kl~r~ 111 (441)
|..||++|-..||+.+.. |+. -|+.||+.+ | .||+.||+........+-.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 357999999999999887 321 299999654 3 699999999998766555543
No 24
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.86 E-value=0.064 Score=58.86 Aligned_cols=50 Identities=28% Similarity=0.548 Sum_probs=42.2
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hh-------C----------cc--hHHHHhhcCCCCHHHHHHHHHHHHHH
Q 013548 58 KQRERWTEEEHKKFLEALK-------LF-------G----------RA--WRKIEEHVGTKTAVQIRSHAQKFFSK 107 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe-------~y-------G----------rg--WkkIAe~VgTRT~~QVrSHAQKYF~K 107 (441)
..+++||.||.+++|..++ +| | .+ |..|++.+|||+..|||.|++|...+
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~ 509 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTS 509 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhh
Confidence 4688999999999999996 44 1 22 99999999999999999999886543
No 25
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=93.41 E-value=0.08 Score=57.44 Aligned_cols=52 Identities=21% Similarity=0.452 Sum_probs=47.3
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHH
Q 013548 56 ITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSK 107 (441)
Q Consensus 56 itk~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~K 107 (441)
+....+.|+.-|++-+-.|+.+||.. |.+|+..+..+|+.||+.++.+|..-
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp 55 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDP 55 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCH
Confidence 44668899999999999999999998 99999999999999999999887654
No 26
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.28 E-value=0.1 Score=57.31 Aligned_cols=54 Identities=22% Similarity=0.569 Sum_probs=46.4
Q ss_pred CCccccc-CCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHH
Q 013548 52 KPYTITK-QRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFS 106 (441)
Q Consensus 52 KPytitk-~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~ 106 (441)
.-|++-. ++|.||++|.+.+..-..++|..|+.|+..+| |.|.-||.|+..|..
T Consensus 375 R~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~~~ 429 (607)
T KOG0051|consen 375 RAYTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQYVK 429 (607)
T ss_pred hcCCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHhhc
Confidence 3445555 89999999999999999999999999999985 678999999987643
No 27
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=93.11 E-value=0.12 Score=55.75 Aligned_cols=69 Identities=23% Similarity=0.349 Sum_probs=48.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHH-hhcCCCCHHHHHHHHHH-----HHHHHhHhcCCCCCCCCccccCC
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIE-EHVGTKTAVQIRSHAQK-----FFSKVVRESNGCSTSPVEPVEIP 126 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIA-e~VgTRT~~QVrSHAQK-----YF~Kl~r~~~G~~~~~~~~i~IP 126 (441)
..-+.|+..|-.+|.+||++||+++..|- +|++=|+..-|..++-- -|...+|......++-.+.+-||
T Consensus 283 DemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYYmwKttdRYvqqKrlKaaeadsKlkqvYIP 357 (693)
T KOG3554|consen 283 DEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQQKRLKAAEADSKLKQVYIP 357 (693)
T ss_pred hhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHHHHhhhhHHHHHHhhhhhhhhhhhheeecc
Confidence 44679999999999999999999999996 79999987777555411 12223333222233345677777
No 28
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.82 E-value=0.18 Score=53.21 Aligned_cols=44 Identities=27% Similarity=0.505 Sum_probs=40.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHA 101 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHA 101 (441)
+...+||.+|-++|-.||.++|.++..|+.++++|...||+.-+
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKf 406 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKF 406 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHH
Confidence 34569999999999999999999999999999999999998644
No 29
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=92.71 E-value=0.2 Score=58.03 Aligned_cols=48 Identities=21% Similarity=0.503 Sum_probs=44.7
Q ss_pred CCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 013548 61 ERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKV 108 (441)
Q Consensus 61 g~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~Kl 108 (441)
..||..+=..|+.|.++||++ ...||..|++||+.+|+.+++-|+.+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~ 873 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERY 873 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhh
Confidence 379999999999999999998 999999999999999999999888764
No 30
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=92.25 E-value=0.23 Score=55.83 Aligned_cols=42 Identities=26% Similarity=0.380 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHA 101 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHA 101 (441)
...||..|..+|-.||-.|-+++-.|+..|.+||..||--++
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyY 660 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYY 660 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHH
Confidence 468999999999999999999999999999999999996554
No 31
>smart00426 TEA TEA domain.
Probab=91.73 E-value=0.15 Score=41.98 Aligned_cols=43 Identities=30% Similarity=0.478 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hH---------------HHHhhcC-----CCCHHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLFGRA-WR---------------KIEEHVG-----TKTAVQIRSHAQ 102 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrg-Wk---------------kIAe~Vg-----TRT~~QVrSHAQ 102 (441)
.+.|.++=+..|++||+.|-.. ++ -|++||- .||..||-||-|
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQ 66 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQ 66 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhe
Confidence 4679999999999999999542 22 3455543 599999999987
No 32
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=91.68 E-value=0.28 Score=51.70 Aligned_cols=54 Identities=28% Similarity=0.436 Sum_probs=44.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHhC---c------------c-hHHHHhhcC-----CCCHHHHHHHHHHHHHHHhHh
Q 013548 58 KQRERWTEEEHKKFLEALKLFG---R------------A-WRKIEEHVG-----TKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yG---r------------g-WkkIAe~Vg-----TRT~~QVrSHAQKYF~Kl~r~ 111 (441)
...+.|+.+=++.|+|||..|. + | =..||.||. |||..||-||-|=+-.+..|+
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 4468999999999999999993 2 2 467898886 899999999999776666554
No 33
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=90.92 E-value=0.44 Score=51.27 Aligned_cols=42 Identities=21% Similarity=0.489 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHA 101 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHA 101 (441)
...||.||-.+|..|+..||+++.+|-..++-|+..-++-++
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY 228 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH
Confidence 458999999999999999999999999999999988777665
No 34
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=90.42 E-value=1.2 Score=35.25 Aligned_cols=51 Identities=22% Similarity=0.459 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHHHh-----C----------cc--hHHHHhhc-----CCCCHHHHHHHHHHHHHHHhHh
Q 013548 61 ERWTEEEHKKFLEALKLF-----G----------RA--WRKIEEHV-----GTKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 61 g~WT~EEH~lFLeaLe~y-----G----------rg--WkkIAe~V-----gTRT~~QVrSHAQKYF~Kl~r~ 111 (441)
..||.+|-..|++-++.| | +. |..|+..+ +.||..|++..++.+-...++.
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 479999999999999998 3 12 99998432 3799999999999887776553
No 35
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=89.71 E-value=0.31 Score=51.59 Aligned_cols=47 Identities=26% Similarity=0.412 Sum_probs=32.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCc---c-h----------HHHHhhcC-----CCCHHHHHHHHHHH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGR---A-W----------RKIEEHVG-----TKTAVQIRSHAQKF 104 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGr---g-W----------kkIAe~Vg-----TRT~~QVrSHAQKY 104 (441)
+..+.|+++=+..|++||+.|-. . + +-|++||- .||..||.||.|-.
T Consensus 47 ~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 47 DGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 56789999999999999999942 1 2 35677765 69999999999965
No 36
>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=89.50 E-value=1.1 Score=39.98 Aligned_cols=57 Identities=19% Similarity=0.471 Sum_probs=43.1
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCc---c-hHHHHh------------hcCCCCHHHHHHHHHHHHHHHhH
Q 013548 54 YTITKQRERWTEEEHKKFLEALKLFGR---A-WRKIEE------------HVGTKTAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 54 ytitk~rg~WT~EEH~lFLeaLe~yGr---g-WkkIAe------------~VgTRT~~QVrSHAQKYF~Kl~r 110 (441)
|....++..||++|+.-+|-.+.+||- + |..|-+ |+.+||+..|.-|+.-...-+.|
T Consensus 43 y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 43 YPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp STSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred cCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 444566778999999999999999999 6 998843 45599999999999866555554
No 37
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=85.93 E-value=1 Score=48.94 Aligned_cols=53 Identities=21% Similarity=0.414 Sum_probs=47.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r 110 (441)
.++..|+.+|+..++..-.++|..|..||.+|+.||..||...+..-+.....
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 56789999999999999999999999999999999999998888776665543
No 38
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=83.50 E-value=0.68 Score=50.26 Aligned_cols=56 Identities=14% Similarity=0.312 Sum_probs=47.6
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 013548 54 YTITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (441)
Q Consensus 54 ytitk~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~Kl~ 109 (441)
+......+.|+..|+..++-+++.||.. |..||..++.||..||+.|...|.....
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~l 70 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQL 70 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhc
Confidence 4455667899999999999999999987 9999987788999999999966655443
No 39
>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=78.53 E-value=3.3 Score=33.45 Aligned_cols=48 Identities=27% Similarity=0.407 Sum_probs=30.1
Q ss_pred CCCCCHHHHHHHHHHHHHh---C-----cc-hHHHHhhcC-CCCHHHHHHHHHHHHHH
Q 013548 60 RERWTEEEHKKFLEALKLF---G-----RA-WRKIEEHVG-TKTAVQIRSHAQKFFSK 107 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~y---G-----rg-WkkIAe~Vg-TRT~~QVrSHAQKYF~K 107 (441)
|.+.|.+|+..++.-|..+ | .. |+.+++.-. ..|-.-.|.|+-|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT--
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence 4578999999999999665 3 22 999997545 78878888887766544
No 40
>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=77.17 E-value=7 Score=31.60 Aligned_cols=42 Identities=29% Similarity=0.502 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHHh---C-----c-----chHHHHhh----cC-CCCHHHHHHHHHH
Q 013548 62 RWTEEEHKKFLEALKLF---G-----R-----AWRKIEEH----VG-TKTAVQIRSHAQK 103 (441)
Q Consensus 62 ~WT~EEH~lFLeaLe~y---G-----r-----gWkkIAe~----Vg-TRT~~QVrSHAQK 103 (441)
.||++++..||+.|... | . +|..|++. .| ..|..||++|.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999999665 1 1 38888742 33 4689999999865
No 41
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=76.75 E-value=5.3 Score=44.00 Aligned_cols=51 Identities=25% Similarity=0.500 Sum_probs=44.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~ 109 (441)
.++.-|+.||++++|.+...+..-|..|+..|| ||..||--|+++......
T Consensus 57 i~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll~~~~ 107 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLLDVYV 107 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHHHHHH
Confidence 457799999999999999999999999999884 899999999988554443
No 42
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=69.18 E-value=14 Score=37.20 Aligned_cols=55 Identities=20% Similarity=0.442 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC----------cchHHHHh---hcC-CCCHHHHHHHHHHHHHHHhHhcCC
Q 013548 60 RERWTEEEHKKFLEALKLFG----------RAWRKIEE---HVG-TKTAVQIRSHAQKFFSKVVRESNG 114 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yG----------rgWkkIAe---~Vg-TRT~~QVrSHAQKYF~Kl~r~~~G 114 (441)
...|+.+|=..||++..... ..|..||+ ..| -||+.||+....+...+.++...+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~ 122 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAK 122 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 47899999999999876541 23999985 344 699999999998777766665433
No 43
>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=65.66 E-value=11 Score=35.78 Aligned_cols=50 Identities=18% Similarity=0.285 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCc-c------hHHHHhhcCCCCHHHHHHHHHHHHHHHhH
Q 013548 60 RERWTEEEHKKFLEALKLFGR-A------WRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGr-g------WkkIAe~VgTRT~~QVrSHAQKYF~Kl~r 110 (441)
...||.||+.++-+.+-+|=+ | +..+++.+ +||+.-|..++..|..|.-.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~ 60 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYE 60 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHH
Confidence 458999999999999999943 2 44444443 79999999999998876543
No 44
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=61.96 E-value=21 Score=33.43 Aligned_cols=48 Identities=21% Similarity=0.453 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHHHhCcc---hHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 013548 62 RWTEEEHKKFLEALKLFGRA---WRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (441)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrg---WkkIAe~VgTRT~~QVrSHAQKYF~Kl~ 109 (441)
-.+..+...||.++-+||-+ |+-+-..+..||...|+.|+--|+.+|.
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~ 90 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRAYGSLFMRHLC 90 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHHHHHHHHHHhc
Confidence 57899999999999999975 9988888899999999999988888885
No 45
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=61.73 E-value=11 Score=35.95 Aligned_cols=49 Identities=22% Similarity=0.313 Sum_probs=37.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHH--hhcC---CCCHHHHHHHHHHHHHH
Q 013548 59 QRERWTEEEHKKFLEALKLFGRA-WRKIE--EHVG---TKTAVQIRSHAQKFFSK 107 (441)
Q Consensus 59 ~rg~WT~EEH~lFLeaLe~yGrg-WkkIA--e~Vg---TRT~~QVrSHAQKYF~K 107 (441)
....||.|++.++-+.+-.|++. =.+++ +.+| .||+.+|..+|..+..+
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVRK 58 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHHH
Confidence 35689999999999999999874 44444 2334 79999999999665553
No 46
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=60.26 E-value=40 Score=35.46 Aligned_cols=53 Identities=21% Similarity=0.448 Sum_probs=43.4
Q ss_pred CCCCCHHHHHHHHHHHHHh-Ccc---hHHHHhhcCCCCHHHHHHHHHHHHHHHhHhc
Q 013548 60 RERWTEEEHKKFLEALKLF-GRA---WRKIEEHVGTKTAVQIRSHAQKFFSKVVRES 112 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~y-Grg---WkkIAe~VgTRT~~QVrSHAQKYF~Kl~r~~ 112 (441)
-..||..|...+|.+|+.- |.. -..|+..|.+|+..+|+..-|+.-.++.|+.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvarea 77 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREA 77 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999999865 543 4456778999999999999998877776653
No 47
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=56.34 E-value=19 Score=39.32 Aligned_cols=52 Identities=4% Similarity=-0.019 Sum_probs=45.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 013548 57 TKQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKV 108 (441)
Q Consensus 57 tk~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl 108 (441)
-+....||.+|..+.+.+|++||++..-|+..||.++..|+......|-.+.
T Consensus 366 c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~ 417 (534)
T KOG1194|consen 366 CRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQ 417 (534)
T ss_pred hhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHH
Confidence 3445899999999999999999999999999999999999998877765554
No 48
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=55.43 E-value=50 Score=39.13 Aligned_cols=54 Identities=15% Similarity=0.367 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHHh------------hcCCCCHHHHHHHHHHHHHHHhHhc
Q 013548 59 QRERWTEEEHKKFLEALKLFGRA-WRKIEE------------HVGTKTAVQIRSHAQKFFSKVVRES 112 (441)
Q Consensus 59 ~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe------------~VgTRT~~QVrSHAQKYF~Kl~r~~ 112 (441)
++..||+||+..+|-.+-+||.+ |..|-. |+.+||+..+.-++.-.+.-+.|+.
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e~ 991 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKEN 991 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHHH
Confidence 34469999999999999999988 999932 4669999999999987777777764
No 49
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=51.16 E-value=37 Score=29.21 Aligned_cols=50 Identities=22% Similarity=0.381 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHHHh----Cc----chHHHHhhcCCC-----CHHHHHHHH----HHHHHHHhH
Q 013548 61 ERWTEEEHKKFLEALKLF----GR----AWRKIEEHVGTK-----TAVQIRSHA----QKFFSKVVR 110 (441)
Q Consensus 61 g~WT~EEH~lFLeaLe~y----Gr----gWkkIAe~VgTR-----T~~QVrSHA----QKYF~Kl~r 110 (441)
..||++++..+|+||..| |. +|....++|... |..|+..-. +||+..+.+
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k 71 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK 71 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh
Confidence 359999999999999999 74 366665655433 556665443 345544444
No 50
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=48.07 E-value=30 Score=40.25 Aligned_cols=54 Identities=22% Similarity=0.431 Sum_probs=47.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHhHhc
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVVRES 112 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQKYF~Kl~r~~ 112 (441)
..-..||..+-..|+.|-++||++ -..||.-|-. |+..|..+|.-||.++.+.+
T Consensus 793 ~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 793 QGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred ccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 334579999999999999999998 9999977766 99999999999999988764
No 51
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=47.67 E-value=18 Score=40.31 Aligned_cols=50 Identities=24% Similarity=0.410 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhHh
Q 013548 59 QRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRE 111 (441)
Q Consensus 59 ~rg~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r~ 111 (441)
..++||.+|=.+|-.||..+|-...-|+...+.|+..||+- ||-++-+|.
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~---K~~~eE~r~ 457 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKA---KFKKEEKRN 457 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHH---HHhhhhhcc
Confidence 46799999999999999999999999999999999999974 565555443
No 52
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=45.46 E-value=59 Score=26.46 Aligned_cols=27 Identities=33% Similarity=0.695 Sum_probs=20.7
Q ss_pred chHHHHhhcCCC---C--HHHHHHHHHHHHHH
Q 013548 81 AWRKIEEHVGTK---T--AVQIRSHAQKFFSK 107 (441)
Q Consensus 81 gWkkIAe~VgTR---T--~~QVrSHAQKYF~K 107 (441)
.|..||+.+|-- + ..+++.|+.+|+..
T Consensus 59 ~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 59 KWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp THHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred hHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 499999887732 2 47999999999764
No 53
>PF12451 VPS11_C: Vacuolar protein sorting protein 11 C terminal; InterPro: IPR024763 Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion. This entry represents the C-terminal domain of vps11.
Probab=45.07 E-value=18 Score=27.75 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHhCcchHHHHhhcCC
Q 013548 64 TEEEHKKFLEALKLFGRAWRKIEEHVGT 91 (441)
Q Consensus 64 T~EEH~lFLeaLe~yGrgWkkIAe~VgT 91 (441)
..+.|++|..+|+.-..+++-||+|+|-
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 3567999999998888889999999983
No 54
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=44.08 E-value=72 Score=23.31 Aligned_cols=39 Identities=13% Similarity=0.250 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHH
Q 013548 68 HKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSK 107 (441)
Q Consensus 68 H~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~K 107 (441)
+...+.-.-..|..|+.||+.+| .|...|+.|.++=..+
T Consensus 15 ~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 15 QREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRRARKK 53 (54)
T ss_dssp HHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHHHhh
Confidence 33444444555777999999886 7888888887654443
No 55
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=35.81 E-value=1.1e+02 Score=24.78 Aligned_cols=47 Identities=17% Similarity=0.288 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHhH
Q 013548 62 RWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~r 110 (441)
..++.|...|..- -..|..++.||+.+|. +...|+.+-++-..++++
T Consensus 110 ~L~~~~~~ii~~~-~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLR-YLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhH-HhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHh
Confidence 4556666555322 2347779999998886 777788777777777654
No 56
>PF10561 UPF0565: Uncharacterised protein family UPF0565; InterPro: IPR018881 This family of proteins has no known function.
Probab=35.42 E-value=29 Score=35.78 Aligned_cols=34 Identities=29% Similarity=0.567 Sum_probs=30.2
Q ss_pred CCCCCCCcccccCCCCCCHHHHHHHHHHHHHhCc
Q 013548 47 APKPRKPYTITKQRERWTEEEHKKFLEALKLFGR 80 (441)
Q Consensus 47 ~~K~rKPytitk~rg~WT~EEH~lFLeaLe~yGr 80 (441)
.+-.-.||++.....+|-..|+..|++-|+.+|-
T Consensus 268 i~vH~TPyQv~D~~RpwI~~E~~~F~~~L~~~~~ 301 (303)
T PF10561_consen 268 IHVHVTPYQVSDPMRPWIGKEEKKFVKLLKKLGA 301 (303)
T ss_pred EEEecCcccccCCCCcHHHHHHHHHHHHHHHhCC
Confidence 3456689999999999999999999999999985
No 57
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=34.56 E-value=54 Score=23.70 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhCcchHHHHhhcC-CCC
Q 013548 66 EEHKKFLEALKLFGRAWRKIEEHVG-TKT 93 (441)
Q Consensus 66 EEH~lFLeaLe~yGrgWkkIAe~Vg-TRT 93 (441)
=|...+.++|+.+|....+.|+.+| +|+
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgisr~ 33 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGISRR 33 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCCCHH
Confidence 3778899999999999999999887 444
No 58
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=34.27 E-value=1.1e+02 Score=25.22 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=23.4
Q ss_pred chHHHHhhcCCC-----CHHHHHHHHHHHHHHHhH
Q 013548 81 AWRKIEEHVGTK-----TAVQIRSHAQKFFSKVVR 110 (441)
Q Consensus 81 gWkkIAe~VgTR-----T~~QVrSHAQKYF~Kl~r 110 (441)
.|..||+.+|-. ...+++.|+++|....++
T Consensus 55 ~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE~ 89 (93)
T smart00501 55 KWKEIARELGIPDTSTSAASSLRKHYERYLLPFER 89 (93)
T ss_pred CHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHHH
Confidence 399999877643 468899999999877654
No 59
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=33.67 E-value=1.4e+02 Score=22.06 Aligned_cols=37 Identities=24% Similarity=0.460 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHH
Q 013548 66 EEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQK 103 (441)
Q Consensus 66 EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQK 103 (441)
+=+.+.|..|+.-|+. |..||+.+|- |+..|..+.++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl-S~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL-SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc-CHHHHHHHHHH
Confidence 3467899999999998 9999999874 55556555543
No 60
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=32.23 E-value=75 Score=31.10 Aligned_cols=46 Identities=11% Similarity=0.156 Sum_probs=36.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc---hHHHH-----hhcCCCCHHHHHHHHHH
Q 013548 58 KQRERWTEEEHKKFLEALKLFGRA---WRKIE-----EHVGTKTAVQIRSHAQK 103 (441)
Q Consensus 58 k~rg~WT~EEH~lFLeaLe~yGrg---WkkIA-----e~VgTRT~~QVrSHAQK 103 (441)
..+..||.+|++++........-. |++|= .|-.+||+.+...|++-
T Consensus 71 q~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~l 124 (199)
T PF13325_consen 71 QSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRL 124 (199)
T ss_pred cccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHH
Confidence 357899999999999977666432 88883 46779999999999984
No 61
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=28.92 E-value=19 Score=31.85 Aligned_cols=12 Identities=50% Similarity=1.193 Sum_probs=10.4
Q ss_pred cCcccccchhhh
Q 013548 413 KGFVPYKKRIVE 424 (441)
Q Consensus 413 KGFVPYKRclaE 424 (441)
-||-||.||+-|
T Consensus 46 ~GfaPYErr~mE 57 (98)
T PTZ00196 46 CGFSPYERRMIE 57 (98)
T ss_pred hcccHHHHHHHH
Confidence 499999998877
No 62
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into s
Probab=26.66 E-value=87 Score=27.45 Aligned_cols=38 Identities=16% Similarity=0.439 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHhCcchHHHHhhcCC----CCHHHHHHHHHHH
Q 013548 64 TEEEHKKFLEALKLFGRAWRKIEEHVGT----KTAVQIRSHAQKF 104 (441)
Q Consensus 64 T~EEH~lFLeaLe~yGrgWkkIAe~VgT----RT~~QVrSHAQKY 104 (441)
|.++.+.|-+. .|+.|++++..+|- =|..+|..=+.+|
T Consensus 1 ~~~~~q~~~~n---vGr~WK~laR~Lg~~cral~d~~ID~I~~~y 42 (90)
T cd08780 1 TPADQQHFAKS---VGKKWKPVGRSLQKNCRALRDPAIDNLAYEY 42 (90)
T ss_pred CHHHHHHHHHH---HhHHHHHHHHHHcccccccchhHHHHHHhhc
Confidence 45566666554 48899999999982 2445555444443
No 63
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.58 E-value=2.1e+02 Score=19.30 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHH
Q 013548 62 RWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFS 106 (441)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVrSHAQKYF~ 106 (441)
.++.++ ..++..+-..|..++.||+.+| -+..+|..+-++...
T Consensus 10 ~l~~~~-~~~~~~~~~~~~~~~~ia~~~~-~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPERE-REVILLRFGEGLSYEEIAEILG-ISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHH-HHHHHHHHhcCCCHHHHHHHHC-cCHHHHHHHHHHHHH
Confidence 345554 4444555456777999998766 455666555554433
No 64
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=24.47 E-value=2.8e+02 Score=20.10 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=21.7
Q ss_pred CcchHHHHhhcCCCCHHHHHHHHHHHHHHHh
Q 013548 79 GRAWRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (441)
Q Consensus 79 GrgWkkIAe~VgTRT~~QVrSHAQKYF~Kl~ 109 (441)
|..+..||+.+|- |...|+.+-.+-+.+++
T Consensus 20 ~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 20 GLTLEEIAERLGI-SRSTVRRILKRALKKLR 49 (50)
T ss_dssp T-SHHHHHHHHTS-CHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCC-cHHHHHHHHHHHHHHhc
Confidence 4559999998875 77777777766666664
No 65
>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=24.15 E-value=44 Score=32.22 Aligned_cols=28 Identities=21% Similarity=0.510 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hHHHHh
Q 013548 60 RERWTEEEHKKFLEALKLFGRA-WRKIEE 87 (441)
Q Consensus 60 rg~WT~EEH~lFLeaLe~yGrg-WkkIAe 87 (441)
...|-..-+-.||.|+..||.+ |..|..
T Consensus 3 ~~iw~r~hdywll~gi~~hgy~rwqdi~n 31 (173)
T PF08074_consen 3 YEIWHRRHDYWLLAGIVKHGYGRWQDIQN 31 (173)
T ss_pred hhhhhhhhhHHHHhHHhhccchhHHHHhc
Confidence 4578888889999999999998 999973
No 66
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=24.11 E-value=45 Score=40.46 Aligned_cols=53 Identities=17% Similarity=0.391 Sum_probs=40.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHH--------hhcC----CCCHHHHHHHHHHHHHHHhHhc
Q 013548 59 QRERWTEEEHKKFLEALKLFGRA-WRKIE--------EHVG----TKTAVQIRSHAQKFFSKVVRES 112 (441)
Q Consensus 59 ~rg~WT~EEH~lFLeaLe~yGrg-WkkIA--------e~Vg----TRT~~QVrSHAQKYF~Kl~r~~ 112 (441)
-...|..+++..||.|+-+||.| |..|- +-|. --+..|.+.++ .|..++.+..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~-~yLls~~~~~ 1197 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRA-DYLLSLLRKH 1197 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHH-HHHHHHHhhc
Confidence 45689999999999999999999 99993 2222 23456777777 4888877664
No 67
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.93 E-value=1.4e+02 Score=26.78 Aligned_cols=38 Identities=21% Similarity=0.358 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHH
Q 013548 65 EEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQK 103 (441)
Q Consensus 65 ~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVrSHAQK 103 (441)
++-+.++|.+|++-|+- |..||+.+|. ++..|+.+.++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~r 46 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEK 46 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHH
Confidence 46788999999999998 9999999874 55666655543
No 68
>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=23.80 E-value=1.7e+02 Score=27.04 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHHhCcchHHHHhhc----CCCCHHHHHHHHHHH
Q 013548 61 ERWTEEEHKKFLEALKLFGRAWRKIEEHV----GTKTAVQIRSHAQKF 104 (441)
Q Consensus 61 g~WT~EEH~lFLeaLe~yGrgWkkIAe~V----gTRT~~QVrSHAQKY 104 (441)
.+=|..|..-....|++||.+++.++.-. --.|+.||+--..+|
T Consensus 115 ~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 115 RRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 35567888888888999999999999432 358999999887776
Done!