Query 012625
Match_columns 459
No_of_seqs 201 out of 554
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 04:36:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012625.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012625hhsearch_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 1.6E-15 3.4E-20 118.4 5.9 50 58-107 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.4 3E-13 6.4E-18 99.8 6.0 46 60-105 1-48 (48)
3 KOG0457 Histone acetyltransfer 99.1 6E-11 1.3E-15 122.9 6.8 71 38-108 43-121 (438)
4 smart00717 SANT SANT SWI3, AD 99.0 5.4E-10 1.2E-14 78.4 5.9 46 60-105 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 6.1E-10 1.3E-14 77.3 5.5 44 62-105 1-45 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 98.8 3.9E-09 8.5E-14 80.2 4.8 43 63-105 1-43 (60)
7 KOG0724 Zuotin and related mol 98.8 4.7E-10 1E-14 110.6 -1.2 134 43-187 35-169 (335)
8 COG5114 Histone acetyltransfer 98.5 3.4E-07 7.3E-12 93.2 8.1 70 38-107 34-111 (432)
9 PLN03212 Transcription repress 98.4 6.5E-07 1.4E-11 88.1 7.2 66 41-106 3-73 (249)
10 PLN03212 Transcription repress 98.3 1.8E-06 3.9E-11 85.0 6.7 53 58-110 76-128 (249)
11 PLN03091 hypothetical protein; 98.2 1.3E-06 2.7E-11 91.8 5.1 51 56-106 10-62 (459)
12 PLN03091 hypothetical protein; 98.2 6E-06 1.3E-10 86.8 9.5 54 58-111 65-118 (459)
13 COG5259 RSC8 RSC chromatin rem 98.2 1.7E-06 3.7E-11 91.3 5.2 43 60-102 279-321 (531)
14 KOG1279 Chromatin remodeling f 97.9 1.4E-05 3.1E-10 85.3 5.9 65 38-102 229-295 (506)
15 KOG0048 Transcription factor, 97.9 3.3E-05 7.2E-10 74.3 6.9 52 58-109 60-111 (238)
16 KOG0048 Transcription factor, 97.5 7.2E-05 1.6E-09 71.9 4.0 47 60-106 9-57 (238)
17 PLN03162 golden-2 like transcr 96.9 0.0024 5.1E-08 66.9 7.8 54 58-111 235-293 (526)
18 KOG0049 Transcription factor, 96.5 0.0035 7.6E-08 69.3 5.7 50 58-107 358-408 (939)
19 KOG0049 Transcription factor, 96.2 0.0071 1.5E-07 67.0 5.5 56 59-114 411-467 (939)
20 KOG4468 Polycomb-group transcr 94.8 0.043 9.3E-07 60.5 5.6 52 60-111 88-149 (782)
21 PF13837 Myb_DNA-bind_4: Myb/S 94.2 0.072 1.6E-06 42.8 4.3 52 60-111 1-70 (90)
22 KOG4329 DNA-binding protein [G 94.1 0.07 1.5E-06 56.2 4.9 64 38-101 251-319 (445)
23 COG5118 BDP1 Transcription ini 93.7 0.11 2.5E-06 54.9 5.6 44 58-101 363-406 (507)
24 KOG0724 Zuotin and related mol 93.6 0.047 1E-06 54.5 2.6 53 58-110 162-221 (335)
25 PLN03142 Probable chromatin-re 93.4 0.14 3.1E-06 59.5 6.4 49 61-109 825-874 (1033)
26 KOG0051 RNA polymerase I termi 93.2 0.11 2.4E-06 57.4 4.8 53 52-105 375-428 (607)
27 KOG0051 RNA polymerase I termi 93.0 0.11 2.4E-06 57.3 4.5 50 58-107 434-509 (607)
28 KOG0050 mRNA splicing protein 92.9 0.097 2.1E-06 57.1 3.7 53 56-108 3-56 (617)
29 KOG3554 Histone deacetylase co 92.5 0.15 3.3E-06 55.3 4.5 68 57-127 282-358 (693)
30 KOG1194 Predicted DNA-binding 92.4 0.24 5.2E-06 53.4 5.9 47 60-108 187-233 (534)
31 KOG4167 Predicted DNA-binding 91.7 0.28 6.1E-06 55.5 5.6 43 59-101 618-660 (907)
32 KOG3841 TEF-1 and related tran 91.4 0.35 7.6E-06 51.3 5.7 54 58-111 74-148 (455)
33 PF13873 Myb_DNA-bind_5: Myb/S 89.9 1.3 2.9E-05 35.2 6.6 51 61-111 3-75 (78)
34 smart00426 TEA TEA domain. 89.8 0.34 7.4E-06 40.2 3.1 43 60-102 3-66 (68)
35 PF01285 TEA: TEA/ATTS domain 88.9 0.41 9E-06 51.0 3.9 48 57-104 46-112 (431)
36 PF09111 SLIDE: SLIDE; InterP 88.4 1.3 2.9E-05 39.6 6.2 57 54-110 43-115 (118)
37 COG5147 REB1 Myb superfamily p 85.6 1.1 2.4E-05 49.0 4.8 53 58-110 70-122 (512)
38 COG5147 REB1 Myb superfamily p 82.0 0.85 1.8E-05 49.8 2.2 56 54-109 14-70 (512)
39 KOG0050 mRNA splicing protein 78.2 4.6 0.0001 44.7 6.2 52 59-111 58-109 (617)
40 PF08914 Myb_DNA-bind_2: Rap1 75.6 4.7 0.0001 32.7 4.1 49 60-108 2-60 (65)
41 PF12776 Myb_DNA-bind_3: Myb/S 75.3 8.3 0.00018 31.4 5.6 43 62-104 1-61 (96)
42 KOG4282 Transcription factor G 72.1 11 0.00024 38.1 6.8 55 60-114 54-122 (345)
43 TIGR02894 DNA_bind_RsfA transc 67.3 10 0.00022 36.2 4.9 50 60-110 4-60 (161)
44 PF11035 SnAPC_2_like: Small n 66.5 25 0.00055 37.0 8.0 53 60-112 21-77 (344)
45 PF06461 DUF1086: Domain of Un 61.8 21 0.00046 33.6 5.9 48 62-109 40-90 (145)
46 PRK13923 putative spore coat p 56.1 15 0.00033 35.2 4.0 48 59-106 4-57 (170)
47 KOG1194 Predicted DNA-binding 55.8 20 0.00043 39.4 5.3 54 56-109 365-418 (534)
48 PLN03142 Probable chromatin-re 55.6 52 0.0011 39.2 9.0 55 58-112 924-991 (1033)
49 KOG2009 Transcription initiati 55.0 9.4 0.0002 42.6 2.8 50 59-111 408-457 (584)
50 KOG0385 Chromatin remodeling c 53.1 23 0.0005 41.3 5.4 56 56-112 791-847 (971)
51 PF04504 DUF573: Protein of un 51.8 13 0.00028 32.1 2.6 54 61-114 5-75 (98)
52 PF01388 ARID: ARID/BRIGHT DNA 51.6 41 0.00089 27.6 5.4 27 81-107 59-90 (92)
53 PF08281 Sigma70_r4_2: Sigma-7 46.8 61 0.0013 23.8 5.2 35 72-107 19-53 (54)
54 PF12451 VPS11_C: Vacuolar pro 46.6 16 0.00035 28.1 2.2 28 64-91 17-44 (49)
55 KOG0384 Chromodomain-helicase 44.6 76 0.0016 38.8 8.0 54 59-113 1132-1198(1373)
56 smart00501 BRIGHT BRIGHT, ARID 40.9 77 0.0017 26.3 5.5 30 81-110 55-89 (93)
57 cd08780 Death_TRADD Death Doma 40.5 39 0.00084 29.7 3.7 38 64-104 1-42 (90)
58 PF02954 HTH_8: Bacterial regu 39.3 43 0.00093 24.4 3.3 28 66-93 5-33 (42)
59 PF10561 UPF0565: Uncharacteri 38.5 24 0.00053 36.5 2.6 34 47-80 268-301 (303)
60 TIGR02937 sigma70-ECF RNA poly 38.2 1E+02 0.0022 25.3 5.8 47 62-110 110-156 (158)
61 PF13325 MCRS_N: N-terminal re 32.5 73 0.0016 31.4 4.7 46 58-103 71-124 (199)
62 PF13404 HTH_AsnC-type: AsnC-t 32.2 1.5E+02 0.0032 22.0 5.2 37 66-103 3-40 (42)
63 smart00595 MADF subfamily of S 31.6 90 0.002 25.1 4.4 22 81-103 29-50 (89)
64 PF04545 Sigma70_r4: Sigma-70, 29.2 2.2E+02 0.0047 20.8 5.8 43 65-109 7-49 (50)
65 PTZ00196 60S ribosomal protein 27.0 21 0.00045 31.7 -0.0 12 431-442 46-57 (98)
66 cd06171 Sigma70_r4 Sigma70, re 24.8 1.9E+02 0.0042 19.6 4.6 43 62-106 10-52 (55)
67 PF08074 CHDCT2: CHDCT2 (NUC03 23.6 46 0.001 32.3 1.6 28 60-87 3-31 (173)
68 PRK11179 DNA-binding transcrip 23.5 1.5E+02 0.0033 26.7 4.8 39 65-104 8-47 (153)
69 PF09420 Nop16: Ribosome bioge 22.2 1.8E+02 0.0039 27.0 5.1 45 60-104 114-162 (164)
70 PF07750 GcrA: GcrA cell cycle 21.8 1.1E+02 0.0024 28.7 3.7 34 62-96 2-37 (162)
71 KOG1019 Retinoblastoma pathway 20.2 68 0.0015 37.5 2.3 64 38-101 22-86 (837)
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=99.59 E-value=1.6e-15 Score=118.36 Aligned_cols=50 Identities=40% Similarity=0.648 Sum_probs=45.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-h---HHHHhhcC-CC-CHHHHHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRA-W---RKIEEHVG-TK-TAVQIRSHAQKFFSK 107 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrg-W---kkIAe~Vg-TR-T~~QVRSHAQKYF~K 107 (459)
|.+..||+|||.+||+||+.||.+ | +.|+++++ ++ |..||+|||||||.+
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 356799999999999999999995 9 99998765 77 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=99.42 E-value=3e-13 Score=99.82 Aligned_cols=46 Identities=46% Similarity=0.793 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFF 105 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVRSHAQKYF 105 (459)
++.||+||+++|++|+.+||.+ |+.||.+|| +||..||++|+++|.
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 4789999999999999999999 999999999 999999999999883
No 3
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=99.14 E-value=6e-11 Score=122.90 Aligned_cols=71 Identities=32% Similarity=0.615 Sum_probs=65.9
Q ss_pred ccccCCCCCC-CCCCCCcccccC------CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 012625 38 DQFSCGNDFA-PKPRKPYTITKQ------RERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKV 108 (459)
Q Consensus 38 e~~s~G~~~~-~k~rKPytitk~------r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~Kl 108 (459)
+||++|++.+ |+..|||.+... ...||.+|..+||+|++.||.| |..||+||||||..+|+.|+-|+|..-
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 7899999995 599999998876 4699999999999999999999 999999999999999999999999763
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.03 E-value=5.4e-10 Score=78.38 Aligned_cols=46 Identities=33% Similarity=0.640 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC-cchHHHHhhcCCCCHHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFG-RAWRKIEEHVGTKTAVQIRSHAQKFF 105 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yG-rgWkkIAe~VgTRT~~QVRSHAQKYF 105 (459)
+..||++|+.+|+.++..|| .+|..||.++++||+.||+.|+..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 35799999999999999999 78999999999999999999998765
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=6.1e-10 Score=77.29 Aligned_cols=44 Identities=36% Similarity=0.673 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhC-cchHHHHhhcCCCCHHHHHHHHHHHH
Q 012625 62 RWTEEEHKKFLEALKLFG-RAWRKIEEHVGTKTAVQIRSHAQKFF 105 (459)
Q Consensus 62 ~WT~EEH~lFLeaLe~yG-rgWkkIAe~VgTRT~~QVRSHAQKYF 105 (459)
.||.+|+.+|+.++..|| ..|..||+++++||..||+.|+++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 77999999999999999999998763
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=3.9e-09 Score=80.22 Aligned_cols=43 Identities=40% Similarity=0.794 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHH
Q 012625 63 WTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFF 105 (459)
Q Consensus 63 WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF 105 (459)
||+||++++++++..||.+|+.||+++|+||+.||+.|+..++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHL 43 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999998743
No 7
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.82 E-value=4.7e-10 Score=110.60 Aligned_cols=134 Identities=29% Similarity=0.234 Sum_probs=104.0
Q ss_pred CCCCCCCCCCCcccccCCCC-CCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCCC
Q 012625 43 GNDFAPKPRKPYTITKQRER-WTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRESNGCSTSPVE 121 (459)
Q Consensus 43 G~~~~~k~rKPytitk~r~~-WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~~~G~~~~~~~ 121 (459)
+.+..++.+++|++.+.+.+ ||.++|..|.++|..|++.|..|-+|++.++.+|++.|+|+||-++.+.. .+..+
T Consensus 35 ~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~~----~~~~~ 110 (335)
T KOG0724|consen 35 TEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKSD----TSLAE 110 (335)
T ss_pred HHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCccc----ccccc
Confidence 44556789999999987554 99999999999999997779999999999999999999999999997653 22346
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCCCcCCCCcccccCCCCCccccccccCCCCccceeccccccCC
Q 012625 122 PVEIPPPRPKRKPMHPYPRKLAHPPVKESLNPELSRTSLSPILSVSERENQSPTSVLFAIGSDAFG 187 (459)
Q Consensus 122 ~i~iPpprpKRkp~HpyPrk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sp~svls~~~~~~~g 187 (459)
.+.||++++++++.|+||++........ ..+..+...... +....++.+++..+++..-
T Consensus 111 ~~~~~~~~~~~k~~~~y~~~~~~~~~~~------~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 169 (335)
T KOG0724|consen 111 VEEFYNFWPKFKSWRQYPQKDEPDEEDS------ENRSQSRYSGGT-QRGKSNAEELRRKGTPVTE 169 (335)
T ss_pred ccccCCccccccccccCCCCCCcccccc------cchhhhhhcccc-cccccchhhhhhccchhHH
Confidence 7789999999999999999987753322 222233333344 6667777777766655433
No 8
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.49 E-value=3.4e-07 Score=93.25 Aligned_cols=70 Identities=26% Similarity=0.552 Sum_probs=62.5
Q ss_pred ccccCCCCCC-CCCCCCcccccC------CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHH
Q 012625 38 DQFSCGNDFA-PKPRKPYTITKQ------RERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSK 107 (459)
Q Consensus 38 e~~s~G~~~~-~k~rKPytitk~------r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~K 107 (459)
-||..|...+ +.+.++|.|... ...|+.+|+.+|++|++-.|-| |..||.|||+|+...|++|+-|||..
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 4688898885 588999987643 4689999999999999999999 99999999999999999999999973
No 9
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.39 E-value=6.5e-07 Score=88.08 Aligned_cols=66 Identities=24% Similarity=0.478 Sum_probs=52.0
Q ss_pred cCCCCC-CCCCCCCccc--ccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHHH
Q 012625 41 SCGNDF-APKPRKPYTI--TKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFFS 106 (459)
Q Consensus 41 s~G~~~-~~k~rKPyti--tk~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVRSHAQKYF~ 106 (459)
+||-+. .++++.|.-. ...+++||+||++++++++++||.. |+.||.+++ +||..|||.++.+|+.
T Consensus 3 ~~~~~~~~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~ 73 (249)
T PLN03212 3 SCGGKKPVSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLR 73 (249)
T ss_pred CCCCCCCCCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhc
Confidence 444333 4445555432 3458899999999999999999965 999999886 8999999999999873
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.25 E-value=1.8e-06 Score=85.04 Aligned_cols=53 Identities=21% Similarity=0.328 Sum_probs=48.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r 110 (459)
.+++.||.||.+++++.+..||..|..||.+++.||..||+.|+..++.+..+
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 45789999999999999999999999999999999999999999887766543
No 11
>PLN03091 hypothetical protein; Provisional
Probab=98.22 E-value=1.3e-06 Score=91.81 Aligned_cols=51 Identities=18% Similarity=0.491 Sum_probs=45.6
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHHH
Q 012625 56 ITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFFS 106 (459)
Q Consensus 56 itk~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVRSHAQKYF~ 106 (459)
....++.||.||++++++++++||.. |+.||.+++ +||..|||.++.+|+.
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 999999887 8999999999998764
No 12
>PLN03091 hypothetical protein; Provisional
Probab=98.19 E-value=6e-06 Score=86.82 Aligned_cols=54 Identities=19% Similarity=0.411 Sum_probs=49.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHHh
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~ 111 (459)
.+++.||.||++++++.+..||..|..||.+|+.||..||+.|+...++|..+.
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999999999999999999999999999999877776554
No 13
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.18 E-value=1.7e-06 Score=91.31 Aligned_cols=43 Identities=35% Similarity=0.669 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQ 102 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQ 102 (459)
...||.+|..++|+||++||.+|.+||.||||||..||--|+-
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL 321 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFL 321 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHH
Confidence 3489999999999999999999999999999999999999863
No 14
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.91 E-value=1.4e-05 Score=85.31 Aligned_cols=65 Identities=29% Similarity=0.499 Sum_probs=50.8
Q ss_pred ccccCCCCCCCCCCCCc--ccccCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHH
Q 012625 38 DQFSCGNDFAPKPRKPY--TITKQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQ 102 (459)
Q Consensus 38 e~~s~G~~~~~k~rKPy--titk~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQ 102 (459)
+||..|....+...-.+ .....+..||++|-.++|+||++||-+|.+||.|||+||..||-.|.-
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 55665655444322211 133567899999999999999999999999999999999999999864
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.86 E-value=3.3e-05 Score=74.28 Aligned_cols=52 Identities=19% Similarity=0.422 Sum_probs=46.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~ 109 (459)
-+++.||+||+++.+++...||..|..||.++++||...|+.|+.-.++|..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkkkl 111 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKKKL 111 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHHHH
Confidence 3489999999999999999999999999999999999999999966654443
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.54 E-value=7.2e-05 Score=71.95 Aligned_cols=47 Identities=19% Similarity=0.405 Sum_probs=45.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcC-CCCHHHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFGRA-WRKIEEHVG-TKTAVQIRSHAQKFFS 106 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~Vg-TRT~~QVRSHAQKYF~ 106 (459)
+|+||.||+.++++-|+.||.+ |..|++.+| .|+-.|||-++-.|+.
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 7999999999999999999998 999999999 9999999999998865
No 17
>PLN03162 golden-2 like transcription factor; Provisional
Probab=96.95 E-value=0.0024 Score=66.95 Aligned_cols=54 Identities=31% Similarity=0.404 Sum_probs=46.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc---hHHHHhhc--CCCCHHHHHHHHHHHHHHHHHh
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRA---WRKIEEHV--GTKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrg---WkkIAe~V--gTRT~~QVRSHAQKYF~Kl~r~ 111 (459)
|.|-.||.|=|++|++|+++.|-+ =|+|-+++ ..=|..+|+||-|||...+++.
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 57787654 4789999999999999988754
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.53 E-value=0.0035 Score=69.35 Aligned_cols=50 Identities=22% Similarity=0.515 Sum_probs=44.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCc-chHHHHhhcCCCCHHHHHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGR-AWRKIEEHVGTKTAVQIRSHAQKFFSK 107 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGr-gWkkIAe~VgTRT~~QVRSHAQKYF~K 107 (459)
-+.++||++|+.+++.|+.+||- +|-+|-+.|++|+..|||.+|-..+..
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 46789999999999999999985 499999999999999999998776543
No 19
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.16 E-value=0.0071 Score=67.01 Aligned_cols=56 Identities=30% Similarity=0.566 Sum_probs=49.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHHHhhCC
Q 012625 59 QRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVVRESNG 114 (459)
Q Consensus 59 ~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~~~G 114 (459)
+.++||-.|+++++.++++||.+ |-+||.++|.||..|.+..-..+.....+...|
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 46899999999999999999999 999999999999999988877776666666544
No 20
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=94.84 E-value=0.043 Score=60.55 Aligned_cols=52 Identities=25% Similarity=0.530 Sum_probs=43.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHH----------HhhcCCCCHHHHHHHHHHHHHHHHHh
Q 012625 60 RERWTEEEHKKFLEALKLFGRAWRKI----------EEHVGTKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrgWkkI----------Ae~VgTRT~~QVRSHAQKYF~Kl~r~ 111 (459)
+..||-.|.+-|..||++||+++.+| -.-+-.||-.|||.||-+...++.+.
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 33566789999999987655555544
No 21
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.19 E-value=0.072 Score=42.82 Aligned_cols=52 Identities=31% Similarity=0.548 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHH------hCc--------chHHHHhhcC----CCCHHHHHHHHHHHHHHHHHh
Q 012625 60 RERWTEEEHKKFLEALKL------FGR--------AWRKIEEHVG----TKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~------yGr--------gWkkIAe~Vg----TRT~~QVRSHAQKYF~Kl~r~ 111 (459)
|..||++|...||+.+.. ++. -|+.||+.+. .||+.||+........+-.+.
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 457999999999999887 221 2999996543 699999999998766655544
No 22
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=94.06 E-value=0.07 Score=56.19 Aligned_cols=64 Identities=23% Similarity=0.471 Sum_probs=47.2
Q ss_pred ccccCCCCCCC-CCCCCcc---cccCCCCCCHHHHHHHHHHHHHhCcchHHHH-hhcCCCCHHHHHHHH
Q 012625 38 DQFSCGNDFAP-KPRKPYT---ITKQRERWTEEEHKKFLEALKLFGRAWRKIE-EHVGTKTAVQIRSHA 101 (459)
Q Consensus 38 e~~s~G~~~~~-k~rKPyt---itk~r~~WT~EEH~lFLeaLe~yGrgWkkIA-e~VgTRT~~QVRSHA 101 (459)
+.+-|+-+.-. ++|++.. ++.....|+++|...|.+||+.||+++..|- .-|.||+.-.|-.+|
T Consensus 251 ~LvkcnfDteeAlrr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyY 319 (445)
T KOG4329|consen 251 ELVKCNFDTEEALRRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYY 319 (445)
T ss_pred HHHHcCCcHHHHHHhcCCcceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHH
Confidence 33445544422 3444433 3345579999999999999999999999996 589999998887664
No 23
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=93.65 E-value=0.11 Score=54.92 Aligned_cols=44 Identities=27% Similarity=0.505 Sum_probs=40.1
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHA 101 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHA 101 (459)
+...+||.+|-++|..||.++|-++..|+..+++|...||+.-+
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKf 406 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKF 406 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHH
Confidence 33569999999999999999999999999999999999998643
No 24
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=93.59 E-value=0.047 Score=54.47 Aligned_cols=53 Identities=38% Similarity=0.457 Sum_probs=47.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-hHHHHh-hcCCCCHHHHHHHHH-----HHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRA-WRKIEE-HVGTKTAVQIRSHAQ-----KFFSKVVR 110 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe-~VgTRT~~QVRSHAQ-----KYF~Kl~r 110 (459)
+.+..|+..+|.+|+.++..||+. |..|.+ ++-.|++.|+.+|+| +||.+...
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~ 221 (335)
T KOG0724|consen 162 RKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKS 221 (335)
T ss_pred hccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhh
Confidence 456799999999999999999998 999985 788999999999999 88887743
No 25
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.41 E-value=0.14 Score=59.53 Aligned_cols=49 Identities=20% Similarity=0.481 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 012625 61 ERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (459)
Q Consensus 61 ~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~Kl~ 109 (459)
..||..+-..|+.|.++||++ ...||..|++||+.+|+.+++-|+.+..
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~ 874 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYK 874 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhh
Confidence 379999999999999999998 9999999999999999999998887743
No 26
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=93.18 E-value=0.11 Score=57.36 Aligned_cols=53 Identities=23% Similarity=0.579 Sum_probs=46.2
Q ss_pred CCccccc-CCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHH
Q 012625 52 KPYTITK-QRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFF 105 (459)
Q Consensus 52 KPytitk-~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF 105 (459)
.-|++-. .++.||+||.+.+..-..++|..|+.|++.+| |.|.-||.|+..|.
T Consensus 375 R~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~~ 428 (607)
T KOG0051|consen 375 RAYTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQYV 428 (607)
T ss_pred hcCCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHhh
Confidence 3445555 89999999999999999999999999999985 67899999998774
No 27
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=92.95 E-value=0.11 Score=57.30 Aligned_cols=50 Identities=28% Similarity=0.548 Sum_probs=42.4
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hh-------C----------cc--hHHHHhhcCCCCHHHHHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALK-------LF-------G----------RA--WRKIEEHVGTKTAVQIRSHAQKFFSK 107 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe-------~y-------G----------rg--WkkIAe~VgTRT~~QVRSHAQKYF~K 107 (459)
.++++||.||.+++|..++ +| | .+ |..|++-+|||+..|||.|++|...+
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 99999999999999999999987544
No 28
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=92.86 E-value=0.097 Score=57.08 Aligned_cols=53 Identities=21% Similarity=0.444 Sum_probs=47.7
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 012625 56 ITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKV 108 (459)
Q Consensus 56 itk~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~Kl 108 (459)
+....+-|+.-|++.+-.|+.+||.. |.+|+..+..+|+.||+.+|.+|..-.
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~ 56 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPA 56 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHH
Confidence 34567899999999999999999998 999999999999999999999887643
No 29
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=92.46 E-value=0.15 Score=55.25 Aligned_cols=68 Identities=24% Similarity=0.358 Sum_probs=48.2
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCcchHHHH-hhcCCCCHHHHHHHHHHHHHH--------HHHhhCCCCCCCCCcccCCC
Q 012625 57 TKQRERWTEEEHKKFLEALKLFGRAWRKIE-EHVGTKTAVQIRSHAQKFFSK--------VVRESNGCSTSPVEPVEIPP 127 (459)
Q Consensus 57 tk~r~~WT~EEH~lFLeaLe~yGrgWkkIA-e~VgTRT~~QVRSHAQKYF~K--------l~r~~~G~~~~~~~~i~iPp 127 (459)
....+-|+..|-.+|.+||++||+++..|- +|++=|+..-|-.++ |+. .+|...-..++-.+.|-||+
T Consensus 282 RDemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyY---YmwKttdRYvqqKrlKaaeadsKlkqvYIP~ 358 (693)
T KOG3554|consen 282 RDEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYY---YMWKTTDRYVQQKRLKAAEADSKLKQVYIPT 358 (693)
T ss_pred hhhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHH---HHHhhhhHHHHHHhhhhhhhhhhhheeeccC
Confidence 345679999999999999999999999996 799999876665544 332 22222222234457777873
No 30
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=92.40 E-value=0.24 Score=53.41 Aligned_cols=47 Identities=21% Similarity=0.441 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKV 108 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl 108 (459)
...||.||-.+|..|++.||+++.+|-..++-|+..-++-++ ||.|.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY--y~~KK 233 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY--YSWKK 233 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH--HHHHH
Confidence 358999999999999999999999999999999988887766 44443
No 31
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=91.68 E-value=0.28 Score=55.47 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=39.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHH
Q 012625 59 QRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHA 101 (459)
Q Consensus 59 ~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHA 101 (459)
....||..|..+|-.||-.|-+|+..|+..|.+||..||--+|
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyY 660 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYY 660 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHH
Confidence 3568999999999999999999999999999999999997765
No 32
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=91.41 E-value=0.35 Score=51.28 Aligned_cols=54 Identities=28% Similarity=0.436 Sum_probs=44.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHhC---c------------c-hHHHHhhcC-----CCCHHHHHHHHHHHHHHHHHh
Q 012625 58 KQRERWTEEEHKKFLEALKLFG---R------------A-WRKIEEHVG-----TKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yG---r------------g-WkkIAe~Vg-----TRT~~QVRSHAQKYF~Kl~r~ 111 (459)
...+.|+++=++.|+|||.+|. + | =..||.||. |||..||-||-|=+-.+..|.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999993 2 2 467899886 899999999999666655554
No 33
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=89.90 E-value=1.3 Score=35.24 Aligned_cols=51 Identities=24% Similarity=0.479 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHHHh-----C----------c--chHHHHhhc-----CCCCHHHHHHHHHHHHHHHHHh
Q 012625 61 ERWTEEEHKKFLEALKLF-----G----------R--AWRKIEEHV-----GTKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 61 ~~WT~EEH~lFLeaLe~y-----G----------r--gWkkIAe~V-----gTRT~~QVRSHAQKYF~Kl~r~ 111 (459)
..||.+|-..|++-++.| | + -|..|+..+ +.||..|++..++.+-...++.
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 579999999999999998 3 1 299998533 3799999999999887776653
No 34
>smart00426 TEA TEA domain.
Probab=89.76 E-value=0.34 Score=40.18 Aligned_cols=43 Identities=28% Similarity=0.444 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-h---------------HHHHhhcC-----CCCHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFGRA-W---------------RKIEEHVG-----TKTAVQIRSHAQ 102 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrg-W---------------kkIAe~Vg-----TRT~~QVRSHAQ 102 (459)
...|.++=+..|++||+.|-.. + .-|++||- .||..||-||-|
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 4679999999999999999532 2 23566553 599999999987
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=88.89 E-value=0.41 Score=50.96 Aligned_cols=48 Identities=25% Similarity=0.372 Sum_probs=32.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCc-----------c-h--HHHHhhcC-----CCCHHHHHHHHHHH
Q 012625 57 TKQRERWTEEEHKKFLEALKLFGR-----------A-W--RKIEEHVG-----TKTAVQIRSHAQKF 104 (459)
Q Consensus 57 tk~r~~WT~EEH~lFLeaLe~yGr-----------g-W--kkIAe~Vg-----TRT~~QVRSHAQKY 104 (459)
.+..+.|+++=+..|++||++|-. - | +.|++||- .||..||.||.|-.
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 356789999999999999999932 1 2 45777765 69999999999966
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=88.44 E-value=1.3 Score=39.58 Aligned_cols=57 Identities=19% Similarity=0.471 Sum_probs=42.8
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCc---c-hHHHHh------------hcCCCCHHHHHHHHHHHHHHHHH
Q 012625 54 YTITKQRERWTEEEHKKFLEALKLFGR---A-WRKIEE------------HVGTKTAVQIRSHAQKFFSKVVR 110 (459)
Q Consensus 54 ytitk~r~~WT~EEH~lFLeaLe~yGr---g-WkkIAe------------~VgTRT~~QVRSHAQKYF~Kl~r 110 (459)
|....++..||++|+.-+|-.+.+||. + |..|-. |+.+||+..|.-++.-...-+.|
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 444566789999999999999999999 5 988843 46699999999999855554444
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=85.55 E-value=1.1 Score=49.00 Aligned_cols=53 Identities=21% Similarity=0.414 Sum_probs=47.9
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r 110 (459)
.++..|+.+|...++..-..+|.-|..||.+++.||..||...|..-+.....
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 45679999999999999999999999999999999999999988887776654
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=81.96 E-value=0.85 Score=49.80 Aligned_cols=56 Identities=14% Similarity=0.312 Sum_probs=47.6
Q ss_pred cccccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 012625 54 YTITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (459)
Q Consensus 54 ytitk~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~Kl~ 109 (459)
+......+.|+..|++.++-+++.||.. |..||..++.||..||+.|.-.|.....
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 5555677899999999999999999987 9999987778999999999966655443
No 39
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=78.22 E-value=4.6 Score=44.66 Aligned_cols=52 Identities=25% Similarity=0.486 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHHh
Q 012625 59 QRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 59 ~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~ 111 (459)
++.-|+.||++++|.+...+..-|..|+..|| ||..||--|+++.+......
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll~~~~s~ 109 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLLDVYVSY 109 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999999999999999884 89999999999876655443
No 40
>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=75.59 E-value=4.7 Score=32.73 Aligned_cols=49 Identities=27% Similarity=0.386 Sum_probs=30.6
Q ss_pred CCCCCHHHHHHHHHHHHHh---C-----cc-hHHHHhhcC-CCCHHHHHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLF---G-----RA-WRKIEEHVG-TKTAVQIRSHAQKFFSKV 108 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~y---G-----rg-WkkIAe~Vg-TRT~~QVRSHAQKYF~Kl 108 (459)
|.+.|.+|+..++.-|..+ | .. |+.+++.-+ ..|-.=.|.|+-|.+...
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 4678999999999999665 3 22 999997555 788888888887765543
No 41
>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=75.34 E-value=8.3 Score=31.35 Aligned_cols=43 Identities=30% Similarity=0.552 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHHh---C-c---------chHHHHh----hcC-CCCHHHHHHHHHHH
Q 012625 62 RWTEEEHKKFLEALKLF---G-R---------AWRKIEE----HVG-TKTAVQIRSHAQKF 104 (459)
Q Consensus 62 ~WT~EEH~lFLeaLe~y---G-r---------gWkkIAe----~Vg-TRT~~QVRSHAQKY 104 (459)
.||++++..||+.|... | + +|..|++ ..| ..|..||++|...+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999999665 1 1 3888874 233 56899999998643
No 42
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=72.13 E-value=11 Score=38.10 Aligned_cols=55 Identities=20% Similarity=0.442 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHhC----------cchHHHHh---hcC-CCCHHHHHHHHHHHHHHHHHhhCC
Q 012625 60 RERWTEEEHKKFLEALKLFG----------RAWRKIEE---HVG-TKTAVQIRSHAQKFFSKVVRESNG 114 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yG----------rgWkkIAe---~Vg-TRT~~QVRSHAQKYF~Kl~r~~~G 114 (459)
...|+.+|-..||++..... ..|..||+ ..| -||+.||+.-......+.++...+
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 47899999999999876542 23999986 344 699999999998777776666543
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=67.25 E-value=10 Score=36.23 Aligned_cols=50 Identities=20% Similarity=0.339 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHh---Cc----chHHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLF---GR----AWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~y---Gr----gWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r 110 (459)
...||.||+.++-+.+-.| |. .+..++..+ +||+.-|..++..|..|.-.
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 4689999999999999999 32 266666555 79999999999998876543
No 44
>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=66.51 E-value=25 Score=37.02 Aligned_cols=53 Identities=21% Similarity=0.448 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHh-Ccc---hHHHHhhcCCCCHHHHHHHHHHHHHHHHHhh
Q 012625 60 RERWTEEEHKKFLEALKLF-GRA---WRKIEEHVGTKTAVQIRSHAQKFFSKVVRES 112 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~y-Grg---WkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~~ 112 (459)
-..||..|...+|.+|+.. |.. -..|++.|.+|+..+|+.+-|+.-.++.|+.
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 4699999999999999876 543 4567788999999999999998888877763
No 45
>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=61.82 E-value=21 Score=33.63 Aligned_cols=48 Identities=21% Similarity=0.453 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHHHHHHhCcc---hHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 012625 62 RWTEEEHKKFLEALKLFGRA---WRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (459)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrg---WkkIAe~VgTRT~~QVRSHAQKYF~Kl~ 109 (459)
-.+..+...||.++-.||-+ |+-+-..+..||...|+.|+--|+.+|.
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 9999888899999999999987777774
No 46
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=56.14 E-value=15 Score=35.24 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=36.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHHh--hcC---CCCHHHHHHHHHHHHH
Q 012625 59 QRERWTEEEHKKFLEALKLFGRA-WRKIEE--HVG---TKTAVQIRSHAQKFFS 106 (459)
Q Consensus 59 ~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe--~Vg---TRT~~QVRSHAQKYF~ 106 (459)
....||.|++.++-+.+-.|++. =.+++. .+| .||+.+|..+|..+..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHH
Confidence 45689999999999999999864 334432 233 7999999999955554
No 47
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=55.77 E-value=20 Score=39.40 Aligned_cols=54 Identities=4% Similarity=-0.012 Sum_probs=46.4
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 012625 56 ITKQRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (459)
Q Consensus 56 itk~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~ 109 (459)
+-+.+..||.+|..+.+.+|+.||++..-|+-.||.++..|+....-.|-.+..
T Consensus 365 ~c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~m 418 (534)
T KOG1194|consen 365 TCRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQM 418 (534)
T ss_pred hhhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHH
Confidence 335568999999999999999999999999999999999999987766655543
No 48
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=55.61 E-value=52 Score=39.21 Aligned_cols=55 Identities=15% Similarity=0.366 Sum_probs=45.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc-hHHHHh------------hcCCCCHHHHHHHHHHHHHHHHHhh
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRA-WRKIEE------------HVGTKTAVQIRSHAQKFFSKVVRES 112 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe------------~VgTRT~~QVRSHAQKYF~Kl~r~~ 112 (459)
.++..+|+||+..+|-.+.+||.+ |..|-. |+.+||+..+.-++.-.+.-+.|+.
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e~ 991 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKEN 991 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHHH
Confidence 344569999999999999999988 999832 5669999999999987777776663
No 49
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=55.03 E-value=9.4 Score=42.64 Aligned_cols=50 Identities=24% Similarity=0.410 Sum_probs=44.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHHh
Q 012625 59 QRERWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVRE 111 (459)
Q Consensus 59 ~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~ 111 (459)
...+||.+|-++|-.||..+|-+..-|+...+.|+..||+- ||-++-+|.
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 35799999999999999999999999999999999999984 666665554
No 50
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=53.14 E-value=23 Score=41.32 Aligned_cols=56 Identities=21% Similarity=0.442 Sum_probs=48.8
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHHHHHHHHhh
Q 012625 56 ITKQRERWTEEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKFFSKVVRES 112 (459)
Q Consensus 56 itk~r~~WT~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKYF~Kl~r~~ 112 (459)
....-..||..+-..|+.|-++||++ -..||.-|-. |+..|..+|.-||.++.+..
T Consensus 791 l~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 791 LSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred hhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 34445689999999999999999998 9999987766 99999999999999988764
No 51
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=51.81 E-value=13 Score=32.09 Aligned_cols=54 Identities=24% Similarity=0.421 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHHh----Cc----chHHHHhhcCCC-----CHHHHHHH----HHHHHHHHHHhhCC
Q 012625 61 ERWTEEEHKKFLEALKLF----GR----AWRKIEEHVGTK-----TAVQIRSH----AQKFFSKVVRESNG 114 (459)
Q Consensus 61 ~~WT~EEH~lFLeaLe~y----Gr----gWkkIAe~VgTR-----T~~QVRSH----AQKYF~Kl~r~~~G 114 (459)
..||++++..+|+||..| |. +|...-++|... |..|+..- =+||+..+.+...|
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k~~~g 75 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKKSKNG 75 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhhcccC
Confidence 469999999999999999 74 366655555432 55665433 34455555553334
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=51.57 E-value=41 Score=27.56 Aligned_cols=27 Identities=33% Similarity=0.695 Sum_probs=20.8
Q ss_pred chHHHHhhcCCC---C--HHHHHHHHHHHHHH
Q 012625 81 AWRKIEEHVGTK---T--AVQIRSHAQKFFSK 107 (459)
Q Consensus 81 gWkkIAe~VgTR---T--~~QVRSHAQKYF~K 107 (459)
.|..||+.+|-- + ..+++.|+.+|+..
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
>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=46.78 E-value=61 Score=23.84 Aligned_cols=35 Identities=14% Similarity=0.221 Sum_probs=22.0
Q ss_pred HHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHH
Q 012625 72 LEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSK 107 (459)
Q Consensus 72 LeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~K 107 (459)
+.-.-..|..|+.||+.+| .|...|+.|.++=..+
T Consensus 19 ~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 19 FLLRYFQGMSYAEIAEILG-ISESTVKRRLRRARKK 53 (54)
T ss_dssp HHHHHTS---HHHHHHHCT-S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHHHhh
Confidence 3333456778999999886 7888888887765444
No 54
>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=46.63 E-value=16 Score=28.09 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHhCcchHHHHhhcCC
Q 012625 64 TEEEHKKFLEALKLFGRAWRKIEEHVGT 91 (459)
Q Consensus 64 T~EEH~lFLeaLe~yGrgWkkIAe~VgT 91 (459)
..+.|++|..+|+.-.-+++-||+|+|-
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 3567999999997777779999999983
No 55
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=44.58 E-value=76 Score=38.85 Aligned_cols=54 Identities=17% Similarity=0.397 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCcc-hHHHH--------hhcC----CCCHHHHHHHHHHHHHHHHHhhC
Q 012625 59 QRERWTEEEHKKFLEALKLFGRA-WRKIE--------EHVG----TKTAVQIRSHAQKFFSKVVRESN 113 (459)
Q Consensus 59 ~r~~WT~EEH~lFLeaLe~yGrg-WkkIA--------e~Vg----TRT~~QVRSHAQKYF~Kl~r~~~ 113 (459)
-...|..+++..||.|+-+||.+ |..|- +-|. --++.|.+.++ .|+.++.+...
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dKi~~~e~~P~a~~L~~R~-~yLls~~~~~~ 1198 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDKIFLVETVPQAKHLQRRA-DYLLSLLRKHD 1198 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhhhcccccCCchHHHHHHH-HHHHHHHhhcc
Confidence 45689999999999999999999 99993 2222 23467788888 48888877653
No 56
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=40.85 E-value=77 Score=26.33 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=23.7
Q ss_pred chHHHHhhcCCC-----CHHHHHHHHHHHHHHHHH
Q 012625 81 AWRKIEEHVGTK-----TAVQIRSHAQKFFSKVVR 110 (459)
Q Consensus 81 gWkkIAe~VgTR-----T~~QVRSHAQKYF~Kl~r 110 (459)
.|..|++.+|-. ...+++.|+++|+...++
T Consensus 55 ~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE~ 89 (93)
T smart00501 55 KWKEIARELGIPDTSTSAASSLRKHYERYLLPFER 89 (93)
T ss_pred CHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHHH
Confidence 399999877633 468999999999877654
No 57
>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=40.50 E-value=39 Score=29.72 Aligned_cols=38 Identities=16% Similarity=0.454 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHHHhCcchHHHHhhcCC----CCHHHHHHHHHHH
Q 012625 64 TEEEHKKFLEALKLFGRAWRKIEEHVGT----KTAVQIRSHAQKF 104 (459)
Q Consensus 64 T~EEH~lFLeaLe~yGrgWkkIAe~VgT----RT~~QVRSHAQKY 104 (459)
|+++.+.|-+.| |++|+.+++.+|- =|..+|..=+.+|
T Consensus 1 ~~~~~q~~~~nv---Gr~WK~laR~Lg~~cral~d~~ID~I~~~y 42 (90)
T cd08780 1 TPADQQHFAKSV---GKKWKPVGRSLQKNCRALRDPAIDNLAYEY 42 (90)
T ss_pred CHHHHHHHHHHH---hHHHHHHHHHHcccccccchhHHHHHHhhc
Confidence 566777777655 8899999999982 2445555544443
No 58
>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=39.29 E-value=43 Score=24.36 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHhCcchHHHHhhcC-CCC
Q 012625 66 EEHKKFLEALKLFGRAWRKIEEHVG-TKT 93 (459)
Q Consensus 66 EEH~lFLeaLe~yGrgWkkIAe~Vg-TRT 93 (459)
=|...+.++|+.+|......|+.+| +|+
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 3788899999999999999999888 454
No 59
>PF10561 UPF0565: Uncharacterised protein family UPF0565; InterPro: IPR018881 This family of proteins has no known function.
Probab=38.49 E-value=24 Score=36.50 Aligned_cols=34 Identities=29% Similarity=0.567 Sum_probs=30.3
Q ss_pred CCCCCCCcccccCCCCCCHHHHHHHHHHHHHhCc
Q 012625 47 APKPRKPYTITKQRERWTEEEHKKFLEALKLFGR 80 (459)
Q Consensus 47 ~~k~rKPytitk~r~~WT~EEH~lFLeaLe~yGr 80 (459)
.+-.--||++.....+|-..|+..|++-|+.+|-
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 60
>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=38.18 E-value=1e+02 Score=25.26 Aligned_cols=47 Identities=17% Similarity=0.303 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 012625 62 RWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVVR 110 (459)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~r 110 (459)
..++.|...|..-+ ..|..+..||+.+|. |...|+.+-++-..++++
T Consensus 110 ~L~~~~~~ii~~~~-~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRY-LEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHH-hcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHh
Confidence 55666666654322 347779999999886 788888888887777754
No 61
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=32.54 E-value=73 Score=31.36 Aligned_cols=46 Identities=11% Similarity=0.156 Sum_probs=36.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCcc---hHHHH-----hhcCCCCHHHHHHHHHH
Q 012625 58 KQRERWTEEEHKKFLEALKLFGRA---WRKIE-----EHVGTKTAVQIRSHAQK 103 (459)
Q Consensus 58 k~r~~WT~EEH~lFLeaLe~yGrg---WkkIA-----e~VgTRT~~QVRSHAQK 103 (459)
..+..||.+|.+++........-. |.+|= -|-.+||+.+...|++-
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 357899999999999976665432 88873 47789999999999994
No 62
>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=32.17 E-value=1.5e+02 Score=22.00 Aligned_cols=37 Identities=24% Similarity=0.460 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHH
Q 012625 66 EEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQK 103 (459)
Q Consensus 66 EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQK 103 (459)
+=+.++|..|+.-|+. |..||+.+|- |+..|..+.++
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 4467889999999987 9999999874 55556555543
No 63
>smart00595 MADF subfamily of SANT domain.
Probab=31.59 E-value=90 Score=25.09 Aligned_cols=22 Identities=23% Similarity=0.542 Sum_probs=18.7
Q ss_pred chHHHHhhcCCCCHHHHHHHHHH
Q 012625 81 AWRKIEEHVGTKTAVQIRSHAQK 103 (459)
Q Consensus 81 gWkkIAe~VgTRT~~QVRSHAQK 103 (459)
.|..||.-+|. |..+|+.++..
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~ 50 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKN 50 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHH
Confidence 39999999988 99999887754
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=29.21 E-value=2.2e+02 Score=20.80 Aligned_cols=43 Identities=16% Similarity=0.235 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 012625 65 EEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFSKVV 109 (459)
Q Consensus 65 ~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~Kl~ 109 (459)
++|.+.|..-+ ..|..+..||+.+|- |...|+.+-.+-+.+|+
T Consensus 7 ~~er~vi~~~y-~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 7 PREREVIRLRY-FEGLTLEEIAERLGI-SRSTVRRILKRALKKLR 49 (50)
T ss_dssp HHHHHHHHHHH-TST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh-cCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhc
Confidence 44444443333 335569999998875 77788888777777765
No 65
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=27.00 E-value=21 Score=31.72 Aligned_cols=12 Identities=50% Similarity=1.193 Sum_probs=10.4
Q ss_pred cCcccccchhhh
Q 012625 431 KGFVPYKKRIVE 442 (459)
Q Consensus 431 kGFVPYKr~laE 442 (459)
-||-||.||+-|
T Consensus 46 ~GfaPYErr~mE 57 (98)
T PTZ00196 46 CGFSPYERRMIE 57 (98)
T ss_pred hcccHHHHHHHH
Confidence 499999999877
No 66
>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=24.80 E-value=1.9e+02 Score=19.56 Aligned_cols=43 Identities=16% Similarity=0.238 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHHhCcchHHHHhhcCCCCHHHHHHHHHHHHH
Q 012625 62 RWTEEEHKKFLEALKLFGRAWRKIEEHVGTKTAVQIRSHAQKFFS 106 (459)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrgWkkIAe~VgTRT~~QVRSHAQKYF~ 106 (459)
.+++++.. ++..+-..|..++.||+.+| -+..+|..+-++...
T Consensus 10 ~l~~~~~~-~~~~~~~~~~~~~~ia~~~~-~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPERERE-VILLRFGEGLSYEEIAEILG-ISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHH-HHHHHHhcCCCHHHHHHHHC-cCHHHHHHHHHHHHH
Confidence 45555544 44444456777999998776 455566555554433
No 67
>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=23.59 E-value=46 Score=32.25 Aligned_cols=28 Identities=21% Similarity=0.510 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-hHHHHh
Q 012625 60 RERWTEEEHKKFLEALKLFGRA-WRKIEE 87 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrg-WkkIAe 87 (459)
...|-.+-+..||.|+..||.+ |..|..
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 999963
No 68
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.53 E-value=1.5e+02 Score=26.70 Aligned_cols=39 Identities=21% Similarity=0.362 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHhCcc-hHHHHhhcCCCCHHHHHHHHHHH
Q 012625 65 EEEHKKFLEALKLFGRA-WRKIEEHVGTKTAVQIRSHAQKF 104 (459)
Q Consensus 65 ~EEH~lFLeaLe~yGrg-WkkIAe~VgTRT~~QVRSHAQKY 104 (459)
++-+.++|.+|+.-|+- |..||+-+|. ++..|+.+.++.
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~rL 47 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEKM 47 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHHH
Confidence 46788999999999998 9999999874 556666665544
No 69
>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=22.18 E-value=1.8e+02 Score=26.96 Aligned_cols=45 Identities=18% Similarity=0.282 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCcchHHHHhhcC----CCCHHHHHHHHHHH
Q 012625 60 RERWTEEEHKKFLEALKLFGRAWRKIEEHVG----TKTAVQIRSHAQKF 104 (459)
Q Consensus 60 r~~WT~EEH~lFLeaLe~yGrgWkkIAe~Vg----TRT~~QVRSHAQKY 104 (459)
..+=|..|..-....|++||.|++.|+.-.. -.|+.||+--..+|
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 3456788888888889999999999996443 58999999888777
No 70
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=21.76 E-value=1.1e+02 Score=28.72 Aligned_cols=34 Identities=26% Similarity=0.475 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHHHHhCcchHHHHhhcC--CCCHHH
Q 012625 62 RWTEEEHKKFLEALKLFGRAWRKIEEHVG--TKTAVQ 96 (459)
Q Consensus 62 ~WT~EEH~lFLeaLe~yGrgWkkIAe~Vg--TRT~~Q 96 (459)
.||+|+-+++ ..|-.=|..-.+||+-+| ||+.+.
T Consensus 2 ~Wtde~~~~L-~~lw~~G~SasqIA~~lg~vsRnAVi 37 (162)
T PF07750_consen 2 SWTDERVERL-RKLWAEGLSASQIARQLGGVSRNAVI 37 (162)
T ss_pred CCCHHHHHHH-HHHHHcCCCHHHHHHHhCCcchhhhh
Confidence 5998887754 444466777999999999 555443
No 71
>KOG1019 consensus Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=20.23 E-value=68 Score=37.55 Aligned_cols=64 Identities=23% Similarity=0.415 Sum_probs=48.8
Q ss_pred ccccCCCCCCCCCCCCcccccCCCCCCHHHHHHHHHHHHHhCcchHHHHhhcC-CCCHHHHHHHH
Q 012625 38 DQFSCGNDFAPKPRKPYTITKQRERWTEEEHKKFLEALKLFGRAWRKIEEHVG-TKTAVQIRSHA 101 (459)
Q Consensus 38 e~~s~G~~~~~k~rKPytitk~r~~WT~EEH~lFLeaLe~yGrgWkkIAe~Vg-TRT~~QVRSHA 101 (459)
...++|.....+-|++..--+-.--|+..|-.+|.++...||++|+..+..+- +|...+|..-.
T Consensus 22 p~~~~~~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vell~ 86 (837)
T KOG1019|consen 22 PRYDSGSTSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVELLK 86 (837)
T ss_pred ccccccccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHHHH
Confidence 33455666666677776666667799999999999999999999999987654 58877776443
Done!