Query 020749
Match_columns 322
No_of_seqs 227 out of 786
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:50:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020749.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020749hhsearch_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 2.7E-15 5.8E-20 112.4 6.1 50 77-126 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.5 1.9E-14 4.2E-19 101.9 6.0 46 79-124 1-48 (48)
3 KOG0724 Zuotin and related mol 99.5 1.1E-15 2.4E-20 144.4 -4.8 235 62-310 35-296 (335)
4 smart00717 SANT SANT SWI3, AD 99.2 2.1E-11 4.6E-16 82.2 5.3 46 79-124 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4.9E-11 1.1E-15 79.6 5.5 43 81-123 1-44 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.1 8.1E-11 1.8E-15 85.9 4.9 43 82-124 1-43 (60)
7 KOG0457 Histone acetyltransfer 98.9 2.4E-09 5.1E-14 107.1 7.3 64 63-126 50-120 (438)
8 PLN03212 Transcription repress 98.8 4.3E-09 9.3E-14 99.1 5.8 51 77-127 23-75 (249)
9 PLN03091 hypothetical protein; 98.8 7.7E-09 1.7E-13 103.9 5.2 52 75-126 10-63 (459)
10 PLN03212 Transcription repress 98.7 3.2E-08 7E-13 93.3 8.6 53 77-129 76-128 (249)
11 PLN03091 hypothetical protein; 98.6 6.2E-08 1.4E-12 97.5 7.3 53 77-129 65-117 (459)
12 KOG0048 Transcription factor, 98.5 7.1E-08 1.5E-12 88.8 4.1 51 79-129 9-61 (238)
13 KOG0048 Transcription factor, 98.5 2.6E-07 5.5E-12 85.2 7.3 53 77-129 60-112 (238)
14 COG5259 RSC8 RSC chromatin rem 98.4 2.3E-07 5E-12 94.1 5.2 41 80-120 280-320 (531)
15 KOG1279 Chromatin remodeling f 98.3 7.7E-07 1.7E-11 91.1 5.5 44 77-120 251-294 (506)
16 COG5114 Histone acetyltransfer 98.3 2.3E-06 4.9E-11 84.1 8.3 64 63-126 41-111 (432)
17 PLN03162 golden-2 like transcr 97.9 5.8E-05 1.3E-09 75.6 10.1 76 76-151 234-327 (526)
18 KOG0049 Transcription factor, 97.7 5.1E-05 1.1E-09 80.1 6.0 53 77-129 358-411 (939)
19 KOG4468 Polycomb-group transcr 97.0 0.0025 5.5E-08 67.1 8.2 53 78-130 87-149 (782)
20 KOG0051 RNA polymerase I termi 96.8 0.0014 3E-08 68.9 4.9 55 71-126 375-430 (607)
21 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0024 5.3E-08 49.2 4.9 51 79-129 1-69 (90)
22 KOG0049 Transcription factor, 96.5 0.0037 8E-08 66.6 5.3 52 78-129 411-463 (939)
23 KOG0050 mRNA splicing protein 96.3 0.0043 9.4E-08 64.5 4.8 55 75-129 3-58 (617)
24 KOG0051 RNA polymerase I termi 96.3 0.0049 1.1E-07 64.9 4.6 51 77-127 434-510 (607)
25 COG5118 BDP1 Transcription ini 95.7 0.021 4.6E-07 57.8 6.2 42 77-118 363-404 (507)
26 KOG4329 DNA-binding protein [G 95.5 0.019 4.1E-07 57.9 4.9 57 68-127 263-323 (445)
27 COG5147 REB1 Myb superfamily p 95.5 0.0086 1.9E-07 62.1 2.7 58 72-129 13-71 (512)
28 KOG4167 Predicted DNA-binding 95.2 0.034 7.3E-07 60.1 5.8 42 79-120 619-660 (907)
29 PF13873 Myb_DNA-bind_5: Myb/S 95.1 0.097 2.1E-06 39.9 6.7 51 79-129 2-74 (78)
30 KOG1194 Predicted DNA-binding 93.9 0.11 2.5E-06 53.6 5.9 41 80-120 188-228 (534)
31 KOG3841 TEF-1 and related tran 93.8 0.55 1.2E-05 47.9 10.4 54 77-130 74-148 (455)
32 PF11035 SnAPC_2_like: Small n 93.7 2.3 5E-05 42.5 14.4 53 78-130 20-76 (344)
33 COG5147 REB1 Myb superfamily p 92.9 0.13 2.8E-06 53.6 4.6 53 77-129 70-122 (512)
34 KOG0724 Zuotin and related mol 92.4 0.086 1.9E-06 50.5 2.5 70 77-153 162-238 (335)
35 PF09111 SLIDE: SLIDE; InterP 92.2 0.54 1.2E-05 40.2 6.8 59 71-129 41-115 (118)
36 PLN03142 Probable chromatin-re 91.6 0.38 8.3E-06 53.9 6.6 47 80-126 825-872 (1033)
37 KOG0050 mRNA splicing protein 91.4 0.21 4.6E-06 52.4 4.0 48 78-126 58-105 (617)
38 smart00426 TEA TEA domain. 91.2 0.25 5.3E-06 39.2 3.3 43 79-121 3-66 (68)
39 PF12776 Myb_DNA-bind_3: Myb/S 91.1 0.7 1.5E-05 36.0 5.8 43 81-123 1-61 (96)
40 KOG4282 Transcription factor G 91.0 2.8 6E-05 40.6 11.1 52 79-130 54-119 (345)
41 KOG3554 Histone deacetylase co 90.2 0.26 5.6E-06 51.5 3.4 45 76-120 282-327 (693)
42 TIGR02894 DNA_bind_RsfA transc 89.3 0.75 1.6E-05 41.7 5.2 48 79-127 4-58 (161)
43 PF08914 Myb_DNA-bind_2: Rap1 88.4 0.74 1.6E-05 35.6 4.0 48 79-126 2-59 (65)
44 PF01285 TEA: TEA/ATTS domain 86.5 0.69 1.5E-05 47.3 3.7 48 76-123 46-112 (431)
45 PRK13923 putative spore coat p 83.3 1.6 3.6E-05 39.8 4.2 49 78-126 4-58 (170)
46 PF04504 DUF573: Protein of un 80.2 6.6 0.00014 32.3 6.3 42 79-120 4-58 (98)
47 KOG2009 Transcription initiati 79.6 1.6 3.6E-05 46.4 3.3 50 78-130 408-457 (584)
48 PF13404 HTH_AsnC-type: AsnC-t 79.1 7.4 0.00016 27.4 5.5 37 85-122 3-40 (42)
49 KOG0493 Transcription factor E 72.8 39 0.00085 33.6 10.3 73 58-131 222-305 (342)
50 KOG1194 Predicted DNA-binding 72.7 7.5 0.00016 40.8 5.7 58 72-129 362-419 (534)
51 PF08281 Sigma70_r4_2: Sigma-7 72.6 14 0.00031 25.9 5.6 39 85-124 13-51 (54)
52 PF02954 HTH_8: Bacterial regu 70.4 11 0.00025 26.0 4.6 32 86-118 6-37 (42)
53 PF01388 ARID: ARID/BRIGHT DNA 66.8 13 0.00027 29.1 4.7 38 89-126 40-90 (92)
54 PRK11179 DNA-binding transcrip 66.6 12 0.00025 32.3 4.9 44 84-132 8-52 (153)
55 PLN03142 Probable chromatin-re 66.0 16 0.00035 41.4 7.0 54 77-130 924-990 (1033)
56 KOG1878 Nuclear receptor coreg 63.5 2.4 5.1E-05 49.4 0.1 47 85-131 360-406 (1672)
57 PRK11169 leucine-responsive tr 63.1 17 0.00037 31.7 5.3 44 84-132 13-57 (164)
58 smart00501 BRIGHT BRIGHT, ARID 62.2 25 0.00053 27.9 5.6 39 90-128 37-88 (93)
59 PF04545 Sigma70_r4: Sigma-70, 62.2 41 0.00088 23.5 6.2 41 87-128 9-49 (50)
60 TIGR02937 sigma70-ECF RNA poly 61.2 30 0.00065 27.1 5.9 47 81-129 110-156 (158)
61 PF10141 ssDNA-exonuc_C: Singl 58.8 9.7 0.00021 34.4 3.1 46 256-301 90-138 (195)
62 PF11626 Rap1_C: TRF2-interact 58.5 6 0.00013 31.6 1.6 18 76-93 44-61 (87)
63 PF06461 DUF1086: Domain of Un 55.8 33 0.00071 30.9 5.8 49 81-129 40-91 (145)
64 PF09420 Nop16: Ribosome bioge 55.7 22 0.00048 31.4 4.8 46 78-123 113-162 (164)
65 cd06171 Sigma70_r4 Sigma70, re 53.6 54 0.0012 21.3 5.4 43 81-125 10-52 (55)
66 smart00344 HTH_ASNC helix_turn 52.4 34 0.00073 27.1 4.9 44 84-132 2-46 (108)
67 KOG0385 Chromatin remodeling c 50.8 21 0.00045 40.0 4.5 60 71-131 787-847 (971)
68 smart00595 MADF subfamily of S 47.4 35 0.00075 26.2 4.2 23 100-123 29-51 (89)
69 KOG0384 Chromodomain-helicase 46.4 53 0.0011 38.5 6.9 54 78-132 1132-1198(1373)
70 KOG2656 DNA methyltransferase 45.9 18 0.00038 37.5 2.9 50 80-129 131-186 (445)
71 PF07750 GcrA: GcrA cell cycle 45.9 33 0.00072 30.7 4.4 37 81-118 2-38 (162)
72 KOG1019 Retinoblastoma pathway 45.3 12 0.00026 41.6 1.7 57 62-118 27-84 (837)
73 PF10561 UPF0565: Uncharacteri 44.2 19 0.00041 35.7 2.7 29 71-99 273-301 (303)
74 PF13325 MCRS_N: N-terminal re 42.5 57 0.0012 30.6 5.5 46 78-123 72-125 (199)
75 PRK01905 DNA-binding protein F 42.2 73 0.0016 24.8 5.3 28 83-110 35-62 (77)
76 PRK00430 fis global DNA-bindin 41.9 68 0.0015 26.3 5.2 26 85-110 55-80 (95)
77 PHA00442 host recBCD nuclease 40.6 18 0.00039 28.0 1.5 33 75-107 8-49 (59)
78 PRK11924 RNA polymerase sigma 39.3 1E+02 0.0022 25.5 6.1 32 97-129 140-171 (179)
79 PF10440 WIYLD: Ubiquitin-bind 38.4 19 0.00042 28.3 1.5 19 88-106 30-48 (65)
80 PF06628 Catalase-rel: Catalas 37.8 1.2E+02 0.0025 23.2 5.7 39 81-129 19-57 (68)
81 KOG0487 Transcription factor A 37.3 24 0.00053 35.1 2.3 59 64-131 233-294 (308)
82 TIGR02985 Sig70_bacteroi1 RNA 34.6 1.5E+02 0.0034 23.9 6.3 31 97-128 128-158 (161)
83 PRK09643 RNA polymerase sigma 33.8 1.2E+02 0.0025 26.6 5.9 33 96-129 148-180 (192)
84 PF10545 MADF_DNA_bdg: Alcohol 33.3 75 0.0016 23.4 4.0 26 100-125 28-54 (85)
85 PF11593 Med3: Mediator comple 32.9 74 0.0016 32.7 4.9 13 65-77 190-202 (379)
86 cd08780 Death_TRADD Death Doma 32.5 80 0.0017 26.5 4.3 24 83-109 1-24 (90)
87 cd08311 Death_p75NR Death doma 31.7 38 0.00082 26.9 2.2 32 84-118 2-34 (77)
88 PF12088 DUF3565: Protein of u 30.8 21 0.00045 28.0 0.5 11 305-315 13-23 (61)
89 PRK09652 RNA polymerase sigma 30.6 1.8E+02 0.0039 24.1 6.2 30 97-127 143-172 (182)
90 COG3604 FhlA Transcriptional r 29.1 62 0.0014 34.6 3.8 45 80-125 501-545 (550)
91 PF13384 HTH_23: Homeodomain-l 28.0 1.1E+02 0.0023 21.1 3.7 34 83-118 3-36 (50)
92 KOG0850 Transcription factor D 27.7 3.6E+02 0.0078 26.4 8.3 66 63-129 109-179 (245)
93 PF01527 HTH_Tnp_1: Transposas 27.6 2E+02 0.0043 21.2 5.4 46 78-125 3-48 (76)
94 KOG1878 Nuclear receptor coreg 27.6 22 0.00048 41.9 0.3 50 70-119 216-265 (1672)
95 PF12451 VPS11_C: Vacuolar pro 27.3 60 0.0013 23.8 2.4 28 83-110 17-44 (49)
96 cd08317 Death_ank Death domain 25.9 57 0.0012 25.6 2.3 23 88-110 5-27 (84)
97 smart00005 DEATH DEATH domain, 25.5 68 0.0015 24.5 2.6 24 87-110 5-29 (88)
98 TIGR02950 SigM_subfam RNA poly 25.1 75 0.0016 26.0 2.9 31 98-129 121-151 (154)
99 PF09862 DUF2089: Protein of u 24.7 2.2E+02 0.0048 24.6 5.8 44 84-128 35-78 (113)
100 TIGR02915 PEP_resp_reg putativ 24.7 96 0.0021 30.4 4.1 29 84-112 404-433 (445)
101 TIGR02939 RpoE_Sigma70 RNA pol 24.5 1.7E+02 0.0037 24.8 5.1 30 98-128 154-183 (190)
102 COG1522 Lrp Transcriptional re 24.2 2.1E+02 0.0046 23.7 5.5 44 84-132 7-51 (154)
103 PF01410 COLFI: Fibrillar coll 24.1 40 0.00088 31.1 1.3 16 4-19 21-36 (214)
104 PRK12515 RNA polymerase sigma 23.4 2E+02 0.0043 24.8 5.4 32 97-129 146-177 (189)
105 PRK09641 RNA polymerase sigma 23.1 2.3E+02 0.005 24.0 5.6 32 97-129 151-182 (187)
106 PF00191 Annexin: Annexin; In 22.5 1.1E+02 0.0025 22.0 3.2 39 88-126 4-42 (66)
107 PF01726 LexA_DNA_bind: LexA D 22.2 2.7E+02 0.0057 21.3 5.2 39 94-136 19-59 (65)
108 PRK12546 RNA polymerase sigma 22.1 2.2E+02 0.0049 25.0 5.5 32 97-129 128-159 (188)
109 PRK10365 transcriptional regul 22.1 96 0.0021 30.2 3.5 29 84-112 404-433 (441)
110 TIGR02983 SigE-fam_strep RNA p 22.0 2.5E+02 0.0054 23.3 5.6 32 97-129 125-156 (162)
111 PRK11923 algU RNA polymerase s 21.9 2.4E+02 0.0053 24.2 5.6 31 98-129 154-184 (193)
112 PF07638 Sigma70_ECF: ECF sigm 21.9 2.6E+02 0.0057 24.5 5.9 41 86-127 139-179 (185)
113 PRK11608 pspF phage shock prot 21.7 1.2E+02 0.0026 29.4 4.0 38 85-131 286-324 (326)
114 TIGR02954 Sig70_famx3 RNA poly 21.0 2.7E+02 0.0059 23.4 5.7 30 98-128 135-164 (169)
115 TIGR02984 Sig-70_plancto1 RNA 20.7 3.6E+02 0.0077 22.8 6.3 31 97-128 155-185 (189)
116 PRK09648 RNA polymerase sigma 20.5 3E+02 0.0066 23.6 5.9 30 98-128 155-184 (189)
117 PRK10100 DNA-binding transcrip 20.5 2.7E+02 0.0058 25.5 5.8 46 81-129 155-200 (216)
118 PRK13919 putative RNA polymera 20.3 3.6E+02 0.0078 22.9 6.3 31 98-129 151-181 (186)
119 cd08803 Death_ank3 Death domai 20.3 1E+02 0.0022 24.8 2.8 24 87-110 4-27 (84)
120 KOG0527 HMG-box transcription 20.3 4.2E+02 0.0092 26.7 7.6 29 80-108 71-108 (331)
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=99.58 E-value=2.7e-15 Score=112.39 Aligned_cols=50 Identities=48% Similarity=0.727 Sum_probs=46.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCc-hH---HHHHHHhC-CC-CHHHHHHHHHHHHHH
Q 020749 77 KSRESWTEQEHDKFLEALQLFDR-DW---KKIEAFIG-SK-TVIQIRSHAQKYFLK 126 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGr-dW---kkIA~~Vg-TR-T~~QcRSHaQKYf~k 126 (322)
|.|..||+|||++||+||+.||+ +| ++|+++++ ++ |..||+||+||||.+
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 46789999999999999999997 99 99998765 67 999999999999976
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=99.52 E-value=1.9e-14 Score=101.91 Aligned_cols=46 Identities=41% Similarity=0.724 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHcCch-HHHHHHHhC-CCCHHHHHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLFDRD-WKKIEAFIG-SKTVIQIRSHAQKYF 124 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~yGrd-WkkIA~~Vg-TRT~~QcRSHaQKYf 124 (322)
++.||+||+++|+++|++||.+ |+.||++|+ +||..||++||++|.
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 5789999999999999999986 999999999 999999999999873
No 3
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=99.47 E-value=1.1e-15 Score=144.37 Aligned_cols=235 Identities=22% Similarity=0.146 Sum_probs=162.4
Q ss_pred cCCCCCcCCCCcccccCCCC-CCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc-CCC---CCC
Q 020749 62 AEDPSKKIRKPYTITKSRES-WTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN-GTS---EHV 136 (322)
Q Consensus 62 ~ed~~kKirKPyti~k~r~~-WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~-g~~---e~i 136 (322)
.++..++++|+|++.+.+.+ ||.+|+++|.++|..|++.|+.|-++++.++..|++.|+|+||-++.+. +.. +.+
T Consensus 35 ~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~~~~~~~~~~~ 114 (335)
T KOG0724|consen 35 TEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKSDTSLAEVEEF 114 (335)
T ss_pred HHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCcccccccccccc
Confidence 56677999999999987554 9999999999999999889999999999999999999999999998874 222 348
Q ss_pred CCCCCCCCCCCCcCCCCCCCcccccccccCcCCccccCCCccccCCCCCCccCCCCCCccCCCCCCCCCCCccccccccc
Q 020749 137 PPPRPKRKAAHPYPQKAPKTVHGVSQFGGQVQSSAALLEPGYIYRPDSSSVLGNPVPVAALSSWSYDSVPPVNVSQVTKD 216 (322)
Q Consensus 137 P~prpkRk~~h~yp~~~~~~~~~~~~~~~~~qss~~~~~~g~~~~~dsssv~~~~~~~~~~~sw~~~~~~~~~~~~~~~~ 216 (322)
|++++++++.|+|+++...+.... ..........+. +++....+..+..++.+.......|....- .
T Consensus 115 ~~~~~~~k~~~~y~~~~~~~~~~~--~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~ 181 (335)
T KOG0724|consen 115 YNFWPKFKSWRQYPQKDEPDEEDS--ENRSQSRYSGGT-QRGKSNAEELRRKGTPVTERERKLVLLALK----------K 181 (335)
T ss_pred CCccccccccccCCCCCCcccccc--cchhhhhhcccc-cccccchhhhhhccchhHHHHHHHHHhhhc----------c
Confidence 999999999999999987654322 111111122233 445555555555555555443333332110 1
Q ss_pred CCCCCCCCCCCcc----cccCCCCCCC------CccccccccCCCCCCCCcccCCChHHHHh--hhhccc-----C----
Q 020749 217 DVGLPGSSNAQNF----CYSSSNDSTL------RTWPVGETIDRGDHGKPRRVMPDFAQVYS--FLGSVF-----D---- 275 (322)
Q Consensus 217 d~~~~g~~~~~n~----c~sss~es~s------~~~~~~~~~~~~~~~~~l~~~PdFaqVY~--FiGsvF-----d---- 275 (322)
++.........++ +.. .-++-. +........+.....+.++.++++.+++. |+++++ +
T Consensus 182 ~~~~~~~~~~~~~~~~r~~~-~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 260 (335)
T KOG0724|consen 182 DGKIDWRKISQNVEKERTPE-QVASHAQEKAFEKALARQKSGEEEKRRKSIEDITTASEAEDRKKEDEAAKEAKKKPRDT 260 (335)
T ss_pred cccccceechhhhhhhhcch-hhhhhhhhhhhHHHHHHHhhhccccccchhhhhhccchhhhhhcchhhhhhhhcccccc
Confidence 1110000111110 100 011110 11112223445667888899999999988 999999 8
Q ss_pred CCchhHHHhhccCCcchHHHHHHHHh-hcccccccC
Q 020749 276 PNSTGHIQRLKQMDPINFETVCYYDF-LIPLSICCG 310 (322)
Q Consensus 276 p~~~~hlqkLk~MdpI~~eTvlLlMR-NL~~~~~~~ 310 (322)
|...+|.++++.|++++.++.++.|. |+..+||++
T Consensus 261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 296 (335)
T KOG0724|consen 261 PSLKSRNKRLKSFDGIAEESSETEDSLELVAALSAP 296 (335)
T ss_pred ccccchhhhcccCCccCCCchhHHHhHHHHHhhhcc
Confidence 88999999999999999999999999 799999875
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.21 E-value=2.1e-11 Score=82.21 Aligned_cols=46 Identities=24% Similarity=0.539 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYF 124 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~yG-rdWkkIA~~VgTRT~~QcRSHaQKYf 124 (322)
+..||.||+++|++++.+|| .+|+.|++++++||..||+.||..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 46899999999999999999 89999999999999999999887654
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=99.18 E-value=4.9e-11 Score=79.58 Aligned_cols=43 Identities=30% Similarity=0.581 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHH
Q 020749 81 SWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKY 123 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yG-rdWkkIA~~VgTRT~~QcRSHaQKY 123 (322)
.||.||+.+|++++.+|| .+|..|++.+++||..||+.||+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999998765
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=99.12 E-value=8.1e-11 Score=85.91 Aligned_cols=43 Identities=33% Similarity=0.670 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHH
Q 020749 82 WTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (322)
Q Consensus 82 WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf 124 (322)
||.||+++|++++++||.+|++||+++|.||..||+.||.+++
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 9999999999999999999999999999999999999987643
No 7
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.91 E-value=2.4e-09 Score=107.09 Aligned_cols=64 Identities=31% Similarity=0.555 Sum_probs=59.2
Q ss_pred CCCCCcCCCCcccccC------CCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 63 EDPSKKIRKPYTITKS------RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 63 ed~~kKirKPyti~k~------r~~WT~EEhelFLeaLk~yG-rdWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
|-..++..+||.+-+. ...||.+|+.+||+|++.|| ++|..||++||+||..+|+.|+.|+|..
T Consensus 50 E~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 50 ETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVN 120 (438)
T ss_pred ccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhc
Confidence 6677899999998876 57999999999999999999 8999999999999999999999999876
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.83 E-value=4.3e-09 Score=99.15 Aligned_cols=51 Identities=16% Similarity=0.287 Sum_probs=46.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHcC-chHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Q 020749 77 KSRESWTEQEHDKFLEALQLFD-RDWKKIEAFIG-SKTVIQIRSHAQKYFLKV 127 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yG-rdWkkIA~~Vg-TRT~~QcRSHaQKYf~kl 127 (322)
.+++.||.|||++|++++++|| .+|+.||+.++ .||..|||.||.+|+..-
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~ 75 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPS 75 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchh
Confidence 4688999999999999999999 59999999886 899999999999998653
No 9
>PLN03091 hypothetical protein; Provisional
Probab=98.76 E-value=7.7e-09 Score=103.95 Aligned_cols=52 Identities=15% Similarity=0.340 Sum_probs=46.0
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhC-CCCHHHHHHHHHHHHHH
Q 020749 75 ITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIG-SKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 75 i~k~r~~WT~EEhelFLeaLk~yGr-dWkkIA~~Vg-TRT~~QcRSHaQKYf~k 126 (322)
...+++.||.|||++|+++|++||. +|+.||+.++ .||..|||.||.+|+..
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP 63 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRP 63 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCC
Confidence 3456789999999999999999995 8999999887 89999999999987643
No 10
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.74 E-value=3.2e-08 Score=93.30 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=48.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.+++.||.||++++++++++||..|..||++|+.||..|||+||..++++..+
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 35889999999999999999999999999999999999999999888777544
No 11
>PLN03091 hypothetical protein; Provisional
Probab=98.63 E-value=6.2e-08 Score=97.54 Aligned_cols=53 Identities=19% Similarity=0.330 Sum_probs=48.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.+++.||.||+++|++.+++||.+|.+||++|+.||..|||+||...++|..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999999999999999999999999887776544
No 12
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.52 E-value=7.1e-08 Score=88.81 Aligned_cols=51 Identities=16% Similarity=0.286 Sum_probs=47.0
Q ss_pred CCCCCHHHHHHHHHHHHHcC-chHHHHHHHhC-CCCHHHHHHHHHHHHHHHhh
Q 020749 79 RESWTEQEHDKFLEALQLFD-RDWKKIEAFIG-SKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~yG-rdWkkIA~~Vg-TRT~~QcRSHaQKYf~kl~k 129 (322)
++.||.|||++|++.|++|| ++|..|++..| .|+..|||-||-.|++.--|
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 79999999999999999999 58999999999 99999999999999776444
No 13
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.51 E-value=2.6e-07 Score=85.15 Aligned_cols=53 Identities=17% Similarity=0.306 Sum_probs=48.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.+++.||+||+++++++..+||.+|..||+++++||...||+||.-.++|..+
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 35899999999999999999999999999999999999999999887665443
No 14
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.43 E-value=2.3e-07 Score=94.06 Aligned_cols=41 Identities=32% Similarity=0.627 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 020749 80 ESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (322)
Q Consensus 80 ~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHa 120 (322)
..||.+|..+|||||+.||.+|.+||.|||+||.+||.-|+
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 48999999999999999999999999999999999999875
No 15
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.30 E-value=7.7e-07 Score=91.12 Aligned_cols=44 Identities=34% Similarity=0.632 Sum_probs=41.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 020749 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHa 120 (322)
..+..||++|..+||++|++||.+|.+|+.|||+||..||..|.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kF 294 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKF 294 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHH
Confidence 45789999999999999999999999999999999999999974
No 16
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.29 E-value=2.3e-06 Score=84.14 Aligned_cols=64 Identities=27% Similarity=0.504 Sum_probs=56.3
Q ss_pred CCCCCcCCCCcccccC------CCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 63 EDPSKKIRKPYTITKS------RESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 63 ed~~kKirKPyti~k~------r~~WT~EEhelFLeaLk~yG-rdWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
+.+.+..-++|+|-.. .+.|+.+|+.+|+++++-.| ++|..||.|||+|+.+.||+|+-||+..
T Consensus 41 ~tg~H~pyH~YRiietnsypI~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~e 111 (432)
T COG5114 41 ETGVHSPYHGYRIIETNSYPIGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYDE 111 (432)
T ss_pred cccccCCCCCeeEeeccCccccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHhh
Confidence 4556677788887643 57999999999999999999 7999999999999999999999999874
No 17
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.92 E-value=5.8e-05 Score=75.62 Aligned_cols=76 Identities=26% Similarity=0.392 Sum_probs=57.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcCc---hHHHHHHHh--CCCCHHHHHHHHHHHHHHHhhcCCC-------------CCCC
Q 020749 76 TKSRESWTEQEHDKFLEALQLFDR---DWKKIEAFI--GSKTVIQIRSHAQKYFLKVQKNGTS-------------EHVP 137 (322)
Q Consensus 76 ~k~r~~WT~EEhelFLeaLk~yGr---dWkkIA~~V--gTRT~~QcRSHaQKYf~kl~k~g~~-------------e~iP 137 (322)
+|.|-.||.|-|++|+++|++.|- .-|+|-+++ ..-|..+|+||.|||...+++.... ...|
T Consensus 234 KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~~~~~P 313 (526)
T PLN03162 234 KKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRAYTQAP 313 (526)
T ss_pred CCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhhhccCC
Confidence 467889999999999999999993 688888775 4689999999999999998754322 1233
Q ss_pred CCCCCCCCCCCcCC
Q 020749 138 PPRPKRKAAHPYPQ 151 (322)
Q Consensus 138 ~prpkRk~~h~yp~ 151 (322)
..+-+|+..+|+..
T Consensus 314 ~~rs~~~~g~p~~~ 327 (526)
T PLN03162 314 WPRSSRRDGLPYLV 327 (526)
T ss_pred cccCCCCCCCcccc
Confidence 34556666666543
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=97.71 E-value=5.1e-05 Score=80.15 Aligned_cols=53 Identities=21% Similarity=0.397 Sum_probs=46.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 77 KSRESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yG-rdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.+.+.||.+||.+|+.|+.+|| ++|-+|-+.|++|+..|||.|+.+.+..-.|
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K 411 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAK 411 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhc
Confidence 3689999999999999999999 5999999999999999999987766555433
No 19
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=96.97 E-value=0.0025 Score=67.15 Aligned_cols=53 Identities=28% Similarity=0.506 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHH----------HHHhCCCCHHHHHHHHHHHHHHHhhc
Q 020749 78 SRESWTEQEHDKFLEALQLFDRDWKKI----------EAFIGSKTVIQIRSHAQKYFLKVQKN 130 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yGrdWkkI----------A~~VgTRT~~QcRSHaQKYf~kl~k~ 130 (322)
.+..||..|++-|..||++||+|+.+| -.-+..||..|||.||-+...++.|.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~ 149 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKL 149 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhh
Confidence 378999999999999999999999998 23356789999999876655555443
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.81 E-value=0.0014 Score=68.89 Aligned_cols=55 Identities=24% Similarity=0.476 Sum_probs=47.4
Q ss_pred CCccccc-CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 71 KPYTITK-SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 71 KPyti~k-~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
.-|++=. .++.||+||++.|...+.++|.+|+.|++.+|. .+.-||.||..|...
T Consensus 375 R~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lgr-~P~~crd~wr~~~~~ 430 (607)
T KOG0051|consen 375 RAYTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALGR-MPMDCRDRWRQYVKC 430 (607)
T ss_pred hcCCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHcc-CcHHHHHHHHHhhcc
Confidence 3444545 899999999999999999999999999999985 789999999887544
No 21
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.79 E-value=0.0024 Score=49.18 Aligned_cols=51 Identities=29% Similarity=0.504 Sum_probs=35.1
Q ss_pred CCCCCHHHHHHHHHHHHH------cC--------chHHHHHHHhC----CCCHHHHHHHHHHHHHHHhh
Q 020749 79 RESWTEQEHDKFLEALQL------FD--------RDWKKIEAFIG----SKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~------yG--------rdWkkIA~~Vg----TRT~~QcRSHaQKYf~kl~k 129 (322)
|..||.+|...||+.+.. |+ .-|+.||+.+. .||+.||+..|.....+-++
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 468999999999998866 31 16999997653 59999999999776555543
No 22
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.48 E-value=0.0037 Score=66.63 Aligned_cols=52 Identities=23% Similarity=0.450 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-chHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 78 SRESWTEQEHDKFLEALQLFD-RDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yG-rdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
+.++||-.|+++|+++|++|| +.|-+||.++|.||..|.+++=..+.....+
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k~r 463 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAKLR 463 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHHHHH
Confidence 468999999999999999999 5999999999999998877765554443333
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.34 E-value=0.0043 Score=64.50 Aligned_cols=55 Identities=18% Similarity=0.410 Sum_probs=48.8
Q ss_pred cccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 75 ITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 75 i~k~r~~WT~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
+-+.++.|+..|++.+..++.+||. .|.+|+..+..+|..||+.+|.+|....-+
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~ 58 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIK 58 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHh
Confidence 3457899999999999999999996 899999999999999999999998765433
No 24
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.25 E-value=0.0049 Score=64.93 Aligned_cols=51 Identities=22% Similarity=0.458 Sum_probs=43.3
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hc-------C------------chHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 020749 77 KSRESWTEQEHDKFLEALQ-------LF-------D------------RDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk-------~y-------G------------rdWkkIA~~VgTRT~~QcRSHaQKYf~kl 127 (322)
..++.||.||+++||+.++ +| | =.|..|++.+|||+..|||.||++....-
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~ 510 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSP 510 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhH
Confidence 4689999999999999995 44 1 17999999999999999999998865554
No 25
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.70 E-value=0.021 Score=57.84 Aligned_cols=42 Identities=26% Similarity=0.554 Sum_probs=39.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 020749 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRS 118 (322)
+...+|+.+|.++|..||.++|-++.-|+.++++|...||+-
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKa 404 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKA 404 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHH
Confidence 345799999999999999999999999999999999999998
No 26
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=95.51 E-value=0.019 Score=57.94 Aligned_cols=57 Identities=23% Similarity=0.478 Sum_probs=45.2
Q ss_pred cCCCCcccc---cCCCCCCHHHHHHHHHHHHHcCchHHHHH-HHhCCCCHHHHHHHHHHHHHHH
Q 020749 68 KIRKPYTIT---KSRESWTEQEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHAQKYFLKV 127 (322)
Q Consensus 68 KirKPyti~---k~r~~WT~EEhelFLeaLk~yGrdWkkIA-~~VgTRT~~QcRSHaQKYf~kl 127 (322)
++|+++..+ ..-..|+++|=..|.++|+.||+|+..|. .-|.+|++-.|-.+ ||+..
T Consensus 263 lrr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVey---YYlWK 323 (445)
T KOG4329|consen 263 LRRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEY---YYLWK 323 (445)
T ss_pred HHhcCCcceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHH---HHHhh
Confidence 444444433 33468999999999999999999999997 57999999999984 56654
No 27
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=95.50 E-value=0.0086 Score=62.10 Aligned_cols=58 Identities=16% Similarity=0.250 Sum_probs=50.3
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 72 PYTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 72 Pyti~k~r~~WT~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.+......+.|+..||+.++-+++.||. +|.+||..+..|+..||+.||..|.....+
T Consensus 13 ~~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk 71 (512)
T COG5147 13 LMQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLK 71 (512)
T ss_pred cccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcc
Confidence 3555567889999999999999999994 999999999999999999999888766544
No 28
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=95.16 E-value=0.034 Score=60.10 Aligned_cols=42 Identities=29% Similarity=0.426 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHa 120 (322)
...||..|..+|-+||-.|.+|+..|+++|.+||+.||-.++
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 458999999999999999999999999999999999999864
No 29
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.08 E-value=0.097 Score=39.93 Aligned_cols=51 Identities=18% Similarity=0.434 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHc-----C------------chHHHHHHHh-----CCCCHHHHHHHHHHHHHHHhh
Q 020749 79 RESWTEQEHDKFLEALQLF-----D------------RDWKKIEAFI-----GSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~y-----G------------rdWkkIA~~V-----gTRT~~QcRSHaQKYf~kl~k 129 (322)
...||.+|.+.|++.+++| | +-|..|++.+ +.||..|+|..|+.+....++
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3579999999999999887 2 2699998643 369999999999988777654
No 30
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=93.85 E-value=0.11 Score=53.60 Aligned_cols=41 Identities=22% Similarity=0.477 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHH
Q 020749 80 ESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHA 120 (322)
Q Consensus 80 ~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHa 120 (322)
..||.||-.+|-++++.||+++.+|.+.++.|+...++-++
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY 228 (534)
T ss_pred ccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH
Confidence 48999999999999999999999999999999988887654
No 31
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=93.77 E-value=0.55 Score=47.88 Aligned_cols=54 Identities=24% Similarity=0.395 Sum_probs=43.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcC---c-------------hHHHHHHHhC-----CCCHHHHHHHHHHHHHHHhhc
Q 020749 77 KSRESWTEQEHDKFLEALQLFD---R-------------DWKKIEAFIG-----SKTVIQIRSHAQKYFLKVQKN 130 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yG---r-------------dWkkIA~~Vg-----TRT~~QcRSHaQKYf~kl~k~ 130 (322)
...+.|+++=++.|.|||..|. | +=.-||.||. +||.+||-+|-|-.-+++.|.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999998872 1 3356898875 799999999999877666554
No 32
>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=93.75 E-value=2.3 Score=42.54 Aligned_cols=53 Identities=19% Similarity=0.325 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHc-Cc---hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 020749 78 SRESWTEQEHDKFLEALQLF-DR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~y-Gr---dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~ 130 (322)
....||..|...+|.+|+-- |. |-..|++.+.+|+..||+...|+.-.++.+.
T Consensus 20 gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvare 76 (344)
T PF11035_consen 20 GPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVARE 76 (344)
T ss_pred CcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHH
Confidence 35699999999999999866 43 6667888999999999999888876665553
No 33
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=92.87 E-value=0.13 Score=53.60 Aligned_cols=53 Identities=13% Similarity=0.364 Sum_probs=47.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 77 KSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.++..|+.||++.++..-.++|-.|..|+.+++.||..||..+|..-+....+
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 46789999999999999999999999999999999999999988876655443
No 34
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=92.44 E-value=0.086 Score=50.46 Aligned_cols=70 Identities=27% Similarity=0.354 Sum_probs=56.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHcCc-hHHHHH-HHhCCCCHHHHHHHHH-----HHHHHHhhcCCCCCCCCCCCCCCCCCCc
Q 020749 77 KSRESWTEQEHDKFLEALQLFDR-DWKKIE-AFIGSKTVIQIRSHAQ-----KYFLKVQKNGTSEHVPPPRPKRKAAHPY 149 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yGr-dWkkIA-~~VgTRT~~QcRSHaQ-----KYf~kl~k~g~~e~iP~prpkRk~~h~y 149 (322)
+.+..|+..++.+++.++.++|+ +|..|+ .++..|+..|+.+|+| +|+.+....+. ...|+++|++
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~-------~~~~~s~~~~ 234 (335)
T KOG0724|consen 162 RKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEE-------EKRRKSIEDI 234 (335)
T ss_pred hccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhcc-------ccccchhhhh
Confidence 46789999999999999999996 999988 5678899999999999 88888744332 3556677776
Q ss_pred CCCC
Q 020749 150 PQKA 153 (322)
Q Consensus 150 p~~~ 153 (322)
+-..
T Consensus 235 ~~~~ 238 (335)
T KOG0724|consen 235 TTAS 238 (335)
T ss_pred hccc
Confidence 6543
No 35
>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=92.24 E-value=0.54 Score=40.23 Aligned_cols=59 Identities=20% Similarity=0.412 Sum_probs=45.1
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCc----hHHHHHH------------HhCCCCHHHHHHHHHHHHHHHhh
Q 020749 71 KPYTITKSRESWTEQEHDKFLEALQLFDR----DWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 71 KPyti~k~r~~WT~EEhelFLeaLk~yGr----dWkkIA~------------~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
-.|.....+..||+|||.-+|-.+.+||- .|..|-+ ++.+||+..+.-|+.-...-+.|
T Consensus 41 i~y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 41 INYPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp -SSTSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred eccCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 34666677899999999999999999995 8999854 35699999999999776666554
No 36
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=91.62 E-value=0.38 Score=53.87 Aligned_cols=47 Identities=21% Similarity=0.487 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 80 ESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 80 ~~WT~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
..|+..+=..|+.|.++||| +...||..|++||..+|+.+++-|+.+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~ 872 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWER 872 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 47999999999999999997 899999999999999999988777655
No 37
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=91.36 E-value=0.21 Score=52.44 Aligned_cols=48 Identities=19% Similarity=0.450 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
++..|+.||++++|.+.+.+..-|.-|+..|| ||..||-.|+++.+-.
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ll~~ 105 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNNLLDV 105 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999987 6999999999885433
No 38
>smart00426 TEA TEA domain.
Probab=91.20 E-value=0.25 Score=39.16 Aligned_cols=43 Identities=28% Similarity=0.488 Sum_probs=31.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCc--hH------------H--HHHHHhC-----CCCHHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLFDR--DW------------K--KIEAFIG-----SKTVIQIRSHAQ 121 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~yGr--dW------------k--kIA~~Vg-----TRT~~QcRSHaQ 121 (322)
...|.++=+..|++||+.|-. .+ + -|++|+- .||..||-||-|
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 468999999999999999852 12 1 1555543 488888888865
No 39
>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=91.06 E-value=0.7 Score=35.98 Aligned_cols=43 Identities=23% Similarity=0.371 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHc---C----------chHHHHHHHh----C-CCCHHHHHHHHHHH
Q 020749 81 SWTEQEHDKFLEALQLF---D----------RDWKKIEAFI----G-SKTVIQIRSHAQKY 123 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~y---G----------rdWkkIA~~V----g-TRT~~QcRSHaQKY 123 (322)
.||+++++.||+.+... | ..|+.|++.+ | ..|..||++|+...
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 59999999999988554 1 1599987433 3 36899999998654
No 40
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.02 E-value=2.8 Score=40.56 Aligned_cols=52 Identities=17% Similarity=0.346 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHHc----------CchHHHHHH---HhC-CCCHHHHHHHHHHHHHHHhhc
Q 020749 79 RESWTEQEHDKFLEALQLF----------DRDWKKIEA---FIG-SKTVIQIRSHAQKYFLKVQKN 130 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~y----------GrdWkkIA~---~Vg-TRT~~QcRSHaQKYf~kl~k~ 130 (322)
...|+.+|-..||++.... +..|..||+ ..| -||..|||..+.+...+-++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 5899999999999977433 126999996 234 599999999987765555443
No 41
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=90.23 E-value=0.26 Score=51.48 Aligned_cols=45 Identities=27% Similarity=0.487 Sum_probs=38.3
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcCchHHHHH-HHhCCCCHHHHHHHH
Q 020749 76 TKSRESWTEQEHDKFLEALQLFDRDWKKIE-AFIGSKTVIQIRSHA 120 (322)
Q Consensus 76 ~k~r~~WT~EEhelFLeaLk~yGrdWkkIA-~~VgTRT~~QcRSHa 120 (322)
+..-+.|+..|-.+|.|+|++||+|+..|- +|++=|+...|..++
T Consensus 282 RDemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyY 327 (693)
T KOG3554|consen 282 RDEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYY 327 (693)
T ss_pred hhhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHH
Confidence 345679999999999999999999999997 788888877777643
No 42
>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=89.32 E-value=0.75 Score=41.74 Aligned_cols=48 Identities=15% Similarity=0.263 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHHc---Cc----hHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLF---DR----DWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~y---Gr----dWkkIA~~VgTRT~~QcRSHaQKYf~kl 127 (322)
...||.|||.+|-+.+-+| |+ -+..+++-+ +||..-|.-||+.|.++.
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHH
Confidence 4689999999999999888 42 455555443 589999999999998864
No 43
>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=88.40 E-value=0.74 Score=35.63 Aligned_cols=48 Identities=21% Similarity=0.284 Sum_probs=30.7
Q ss_pred CCCCCHHHHHHHHHHHHHcC---------chHHHHHHHhC-CCCHHHHHHHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLFD---------RDWKKIEAFIG-SKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~yG---------rdWkkIA~~Vg-TRT~~QcRSHaQKYf~k 126 (322)
|..+|.|||..+++.|+.+. .=|+.+++.-. ..|-.-.|+||.|.+..
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 56789999999999997652 15999997655 78999999987666544
No 44
>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=86.55 E-value=0.69 Score=47.27 Aligned_cols=48 Identities=25% Similarity=0.398 Sum_probs=32.1
Q ss_pred ccCCCCCCHHHHHHHHHHHHHcC-----------c-hH--HHHHHHhC-----CCCHHHHHHHHHHH
Q 020749 76 TKSRESWTEQEHDKFLEALQLFD-----------R-DW--KKIEAFIG-----SKTVIQIRSHAQKY 123 (322)
Q Consensus 76 ~k~r~~WT~EEhelFLeaLk~yG-----------r-dW--kkIA~~Vg-----TRT~~QcRSHaQKY 123 (322)
.+..+.|+++=+..|+|||+.|- | .| +-|+.||. .||.+||-+|.|-.
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 45679999999999999999983 1 12 23787764 59999999999977
No 45
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=83.32 E-value=1.6 Score=39.82 Aligned_cols=49 Identities=18% Similarity=0.310 Sum_probs=37.0
Q ss_pred CCCCCCHHHHHHHHHHHHHcCc-hHHHHHHH--hC---CCCHHHHHHHHHHHHHH
Q 020749 78 SRESWTEQEHDKFLEALQLFDR-DWKKIEAF--IG---SKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yGr-dWkkIA~~--Vg---TRT~~QcRSHaQKYf~k 126 (322)
....||.||+.+|-+.+-.|++ .=.+++.| +| .||..+|.-||+.+.++
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 3578999999999999988885 33334422 23 58999999999877665
No 46
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=80.17 E-value=6.6 Score=32.34 Aligned_cols=42 Identities=19% Similarity=0.339 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHHHHHc----C----chHHHHHHHhCCC-----CHHHHHHHH
Q 020749 79 RESWTEQEHDKFLEALQLF----D----RDWKKIEAFIGSK-----TVIQIRSHA 120 (322)
Q Consensus 79 r~~WT~EEhelFLeaLk~y----G----rdWkkIA~~VgTR-----T~~QcRSHa 120 (322)
...||+|++..+|+||..| | .+|...-++|... |..|+..-.
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Ki 58 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKI 58 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHH
Confidence 4679999999999999888 6 3787776665432 667776644
No 47
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=79.62 E-value=1.6 Score=46.37 Aligned_cols=50 Identities=22% Similarity=0.392 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhc
Q 020749 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKN 130 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~ 130 (322)
....|+.+|-++|..++..+|-+..-|+.....|+..|||- ||-++-++.
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 35899999999999999999999999999999999999997 776665444
No 48
>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=79.13 E-value=7.4 Score=27.44 Aligned_cols=37 Identities=19% Similarity=0.286 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHH
Q 020749 85 QEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQK 122 (322)
Q Consensus 85 EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQK 122 (322)
+-|.++|..|+.-|+ .|..||+.+|- |...|..+.++
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 567899999999996 99999999997 78888888765
No 49
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=72.77 E-value=39 Score=33.58 Aligned_cols=73 Identities=18% Similarity=0.206 Sum_probs=49.1
Q ss_pred cccccCCCCCcCCCCcccc-------cCCCCCCHHHHHHHHHHHHHcC----chHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 58 TMSFAEDPSKKIRKPYTIT-------KSRESWTEQEHDKFLEALQLFD----RDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 58 ~~~~~ed~~kKirKPyti~-------k~r~~WT~EEhelFLeaLk~yG----rdWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
-||+--..+.+-||+++.. +.|..+|.|.-++|..-++.-- ++-..++.-++- +..|||.-+|+-..|
T Consensus 222 RYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgL-NEsQIKIWFQNKRAK 300 (342)
T KOG0493|consen 222 RYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGL-NESQIKIWFQNKRAK 300 (342)
T ss_pred cccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCc-CHHHhhHHhhhhhhh
Confidence 3554444455555555433 2478899999888887665433 355667766664 899999988888888
Q ss_pred HhhcC
Q 020749 127 VQKNG 131 (322)
Q Consensus 127 l~k~g 131 (322)
|+|..
T Consensus 301 iKKsT 305 (342)
T KOG0493|consen 301 IKKST 305 (342)
T ss_pred hhhcc
Confidence 87753
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=72.74 E-value=7.5 Score=40.77 Aligned_cols=58 Identities=2% Similarity=-0.038 Sum_probs=49.2
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 72 PYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 72 Pyti~k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
|...-+...+||.+|..+++.+|++||++...|+-.||.++..|+++-...|-++..-
T Consensus 362 pes~c~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~mf 419 (534)
T KOG1194|consen 362 PESTCRMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQMF 419 (534)
T ss_pred CchhhhhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHHH
Confidence 3333345689999999999999999999999999999999999999988887666543
No 51
>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=72.58 E-value=14 Score=25.91 Aligned_cols=39 Identities=5% Similarity=0.142 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHH
Q 020749 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYF 124 (322)
Q Consensus 85 EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf 124 (322)
+++...+......|..|++||+.+| .|...|+.|.++=.
T Consensus 13 ~~~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 13 ERQREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRRAR 51 (54)
T ss_dssp HHHHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHHHH
Confidence 4555566666777889999999997 58899998765543
No 52
>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=70.36 E-value=11 Score=26.03 Aligned_cols=32 Identities=16% Similarity=0.176 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 020749 86 EHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (322)
Q Consensus 86 EhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRS 118 (322)
|.+.+.++|+.+|++..+.|+.+|- +...+..
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgi-sr~tL~~ 37 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGI-SRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS--HHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCC-CHHHHHH
Confidence 7788899999999999999999985 3334443
No 53
>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=66.77 E-value=13 Score=29.14 Aligned_cols=38 Identities=26% Similarity=0.540 Sum_probs=26.4
Q ss_pred HHHHHHHHcC--------chHHHHHHHhCCCC-----HHHHHHHHHHHHHH
Q 020749 89 KFLEALQLFD--------RDWKKIEAFIGSKT-----VIQIRSHAQKYFLK 126 (322)
Q Consensus 89 lFLeaLk~yG--------rdWkkIA~~VgTRT-----~~QcRSHaQKYf~k 126 (322)
+|-.++.++| +.|..|++.+|--. ..++|.++.+|+..
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 3444555665 27999999887422 47899999988754
No 54
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=66.64 E-value=12 Score=32.25 Aligned_cols=44 Identities=20% Similarity=0.285 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 020749 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (322)
Q Consensus 84 ~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g~ 132 (322)
++.|.++|+.|++-|| .|..||+.+|- +...|+.|.++ +...|-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl-S~~tV~~Ri~r----L~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV-SPGTIHVRVEK----MKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc-CHHHHHHHHHH----HHHCCC
Confidence 4678999999999997 99999999986 88889887654 555654
No 55
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=65.98 E-value=16 Score=41.45 Aligned_cols=54 Identities=15% Similarity=0.342 Sum_probs=45.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHcC-chHHHHHH------------HhCCCCHHHHHHHHHHHHHHHhhc
Q 020749 77 KSRESWTEQEHDKFLEALQLFD-RDWKKIEA------------FIGSKTVIQIRSHAQKYFLKVQKN 130 (322)
Q Consensus 77 k~r~~WT~EEhelFLeaLk~yG-rdWkkIA~------------~VgTRT~~QcRSHaQKYf~kl~k~ 130 (322)
.++..||+|||..+|-.+.+|| .+|..|-+ |+.+||+..+..|+.-.+..+.|.
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e 990 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKE 990 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHH
Confidence 4566799999999999999999 68999843 356999999999998877777664
No 56
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=63.46 E-value=2.4 Score=49.37 Aligned_cols=47 Identities=21% Similarity=0.220 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcC
Q 020749 85 QEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 131 (322)
Q Consensus 85 EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g 131 (322)
||.+.-..||..+||+|.+|+..|+++|..||++.+-||-.+...++
T Consensus 360 ee~ev~k~Glveh~R~~aai~p~vvt~tes~c~na~a~~~~r~N~d~ 406 (1672)
T KOG1878|consen 360 EEMEVAKSGLVEHGREWAAILPKVVTKTESQCKNAYAKYKNRHNLDE 406 (1672)
T ss_pred hhhhhhhccchhhhhhHHHhcCccceecccchhhHHHhhhhhhcchh
Confidence 45667778999999999999999999999999985545554444443
No 57
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=63.05 E-value=17 Score=31.70 Aligned_cols=44 Identities=14% Similarity=0.219 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 020749 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (322)
Q Consensus 84 ~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g~ 132 (322)
++-|.++|.+|++-|| .|..||+-+|- +...|+.|.++ +.+.|-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl-S~~tv~~Ri~r----L~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL-SPTPCLERVRR----LERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc-CHHHHHHHHHH----HHHCCC
Confidence 6789999999999998 99999999986 77888887654 555553
No 58
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=62.22 E-value=25 Score=27.91 Aligned_cols=39 Identities=23% Similarity=0.465 Sum_probs=28.6
Q ss_pred HHHHHHHcCc--------hHHHHHHHhCCC-----CHHHHHHHHHHHHHHHh
Q 020749 90 FLEALQLFDR--------DWKKIEAFIGSK-----TVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 90 FLeaLk~yGr--------dWkkIA~~VgTR-----T~~QcRSHaQKYf~kl~ 128 (322)
|-.++.+.|+ .|..|++.+|-. ...++|.++++|+....
T Consensus 37 Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE 88 (93)
T smart00501 37 LYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPFE 88 (93)
T ss_pred HHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHH
Confidence 3445777663 799999988754 36789999999876653
No 59
>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=62.20 E-value=41 Score=23.48 Aligned_cols=41 Identities=10% Similarity=0.131 Sum_probs=27.1
Q ss_pred HHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 87 HDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 87 helFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
+...+...-..|..+..||+.+|- |...|+.+-.+-+.+++
T Consensus 9 er~vi~~~y~~~~t~~eIa~~lg~-s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 9 EREVIRLRYFEGLTLEEIAERLGI-SRSTVRRILKRALKKLR 49 (50)
T ss_dssp HHHHHHHHHTST-SHHHHHHHHTS-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCHHHHHHHHCC-cHHHHHHHHHHHHHHhc
Confidence 333444433446799999999986 77777777666666664
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=61.20 E-value=30 Score=27.08 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
..++.|...|. ..-..|..+..||+.+|- +...|+.+.++-+.++++
T Consensus 110 ~L~~~~~~ii~-~~~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLV-LRYLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHh-hHHhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHh
Confidence 45555555543 222357899999999987 788888887777777654
No 61
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=58.82 E-value=9.7 Score=34.42 Aligned_cols=46 Identities=22% Similarity=0.226 Sum_probs=33.5
Q ss_pred CcccCCC---hHHHHhhhhcccCCCchhHHHhhccCCcchHHHHHHHHh
Q 020749 256 PRRVMPD---FAQVYSFLGSVFDPNSTGHIQRLKQMDPINFETVCYYDF 301 (322)
Q Consensus 256 ~l~~~Pd---FaqVY~FiGsvFdp~~~~hlqkLk~MdpI~~eTvlLlMR 301 (322)
.+..||+ |+++|+||-..=.=+...|++.|-.-==|+.+++.++++
T Consensus 90 y~~~~P~Re~F~~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~ 138 (195)
T PF10141_consen 90 YFEGMPTREQFKKLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLK 138 (195)
T ss_pred hhcCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHH
Confidence 4677886 999999998752223477888886666677777777664
No 62
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=58.50 E-value=6 Score=31.56 Aligned_cols=18 Identities=11% Similarity=0.348 Sum_probs=10.0
Q ss_pred ccCCCCCCHHHHHHHHHH
Q 020749 76 TKSRESWTEQEHDKFLEA 93 (322)
Q Consensus 76 ~k~r~~WT~EEhelFLea 93 (322)
....+.||+|+|+.|+.+
T Consensus 44 ~n~~GiWT~eDD~~L~~~ 61 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSG 61 (87)
T ss_dssp TT-TT---HHHHHHHTS-
T ss_pred CCCCCCcCHHHHHHHHcC
Confidence 345799999999998543
No 63
>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=55.76 E-value=33 Score=30.93 Aligned_cols=49 Identities=18% Similarity=0.380 Sum_probs=43.3
Q ss_pred CCCHHHHHHHHHHHHHcCc---hHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 81 SWTEQEHDKFLEALQLFDR---DWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yGr---dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
-++..+...||.+|-+||- +|+-+-..+..||..+++.+.--|+.+|--
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~E 91 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRAYGSLFMRHLCE 91 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHHHHHHHHHHhcC
Confidence 6789999999999999994 899998889999999999999777777743
No 64
>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=55.74 E-value=22 Score=31.42 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=36.2
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhC----CCCHHHHHHHHHHH
Q 020749 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIG----SKTVIQIRSHAQKY 123 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yGrdWkkIA~~Vg----TRT~~QcRSHaQKY 123 (322)
....=|.+|.+-+...|++||.|+++++.-.. -.|..||+....+|
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 44566788888888899999999999994333 47999999876665
No 65
>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=53.65 E-value=54 Score=21.30 Aligned_cols=43 Identities=12% Similarity=0.150 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHH
Q 020749 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~ 125 (322)
.+++++ ..+++.+-..|..++.||+.+|- +..+|+.+.++...
T Consensus 10 ~l~~~~-~~~~~~~~~~~~~~~~ia~~~~~-s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPERE-REVILLRFGEGLSYEEIAEILGI-SRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHH-HHHHHHHHhcCCCHHHHHHHHCc-CHHHHHHHHHHHHH
Confidence 455554 44445555567899999998874 66777766555433
No 66
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=52.40 E-value=34 Score=27.07 Aligned_cols=44 Identities=18% Similarity=0.342 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 020749 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (322)
Q Consensus 84 ~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g~ 132 (322)
++.|.++|+.|++.|+ .|+.|++.+|- +...|+.+.+ ++.+.|.
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l~~-s~~tv~~~l~----~L~~~g~ 46 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKVGL-SPSTVHNRVK----RLEEEGV 46 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHHCc-CHHHHHHHHH----HHHHCCC
Confidence 3678899999999986 99999999976 7788887654 4555554
No 67
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=50.85 E-value=21 Score=40.01 Aligned_cols=60 Identities=18% Similarity=0.395 Sum_probs=50.3
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcC
Q 020749 71 KPYTITKSRESWTEQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 131 (322)
Q Consensus 71 KPyti~k~r~~WT~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g 131 (322)
|+.-....-..||..+=..|+.+.++||+ +-..|++-|-. |++.|..++.-+|.++.+..
T Consensus 787 k~~ll~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 787 KEELLSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred hhhhhhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 34444555678999999999999999997 89999988877 99999999998888887653
No 68
>smart00595 MADF subfamily of SANT domain.
Probab=47.43 E-value=35 Score=26.22 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=20.5
Q ss_pred hHHHHHHHhCCCCHHHHHHHHHHH
Q 020749 100 DWKKIEAFIGSKTVIQIRSHAQKY 123 (322)
Q Consensus 100 dWkkIA~~VgTRT~~QcRSHaQKY 123 (322)
-|..|+.-++. |..+|+.+|...
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 69999999988 999999999763
No 69
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=46.41 E-value=53 Score=38.47 Aligned_cols=54 Identities=15% Similarity=0.301 Sum_probs=38.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcC-chHHHHH--------HHhC----CCCHHHHHHHHHHHHHHHhhcCC
Q 020749 78 SRESWTEQEHDKFLEALQLFD-RDWKKIE--------AFIG----SKTVIQIRSHAQKYFLKVQKNGT 132 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yG-rdWkkIA--------~~Vg----TRT~~QcRSHaQKYf~kl~k~g~ 132 (322)
-...|..||+..||.||-+|| +.|.+|- +-+. --...|...++ .|+..+.+...
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 356899999999999999999 6999994 1111 12355666665 67777766543
No 70
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=45.92 E-value=18 Score=37.47 Aligned_cols=50 Identities=22% Similarity=0.330 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHcCchHHHHHHH-----hCC-CCHHHHHHHHHHHHHHHhh
Q 020749 80 ESWTEQEHDKFLEALQLFDRDWKKIEAF-----IGS-KTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 80 ~~WT~EEhelFLeaLk~yGrdWkkIA~~-----VgT-RT~~QcRSHaQKYf~kl~k 129 (322)
..||.||.+-|.+..+.|.-+|--|+.- .+. ||.+..|.++=...+++.+
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~k 186 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLK 186 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHH
Confidence 4699999999999999999989888843 555 9999999976444444443
No 71
>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=45.91 E-value=33 Score=30.69 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 020749 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRS 118 (322)
.||+|+.++|.+.. .-|..-.+||+-+|..|...|.-
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViG 38 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIG 38 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhh
Confidence 59999888665554 66889999999999555555554
No 72
>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=45.30 E-value=12 Score=41.58 Aligned_cols=57 Identities=19% Similarity=0.359 Sum_probs=44.9
Q ss_pred cCCCCCcCCCCcccccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhC-CCCHHHHHH
Q 020749 62 AEDPSKKIRKPYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIG-SKTVIQIRS 118 (322)
Q Consensus 62 ~ed~~kKirKPyti~k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~Vg-TRT~~QcRS 118 (322)
.....-+.|++..-.+-...|+..|-++|+++..++|+.|+..+..+- +|...++.-
T Consensus 27 ~~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vel 84 (837)
T KOG1019|consen 27 GSTSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVEL 84 (837)
T ss_pred cccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHH
Confidence 333334566666666778899999999999999999999999997764 488777764
No 73
>PF10561 UPF0565: Uncharacterised protein family UPF0565; InterPro: IPR018881 This family of proteins has no known function.
Probab=44.23 E-value=19 Score=35.68 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=27.6
Q ss_pred CCcccccCCCCCCHHHHHHHHHHHHHcCc
Q 020749 71 KPYTITKSRESWTEQEHDKFLEALQLFDR 99 (322)
Q Consensus 71 KPyti~k~r~~WT~EEhelFLeaLk~yGr 99 (322)
.||.+....+.|=.+|++.|++.|+++|-
T Consensus 273 TPyQv~D~~RpwI~~E~~~F~~~L~~~~~ 301 (303)
T PF10561_consen 273 TPYQVSDPMRPWIGKEEKKFVKLLKKLGA 301 (303)
T ss_pred CcccccCCCCcHHHHHHHHHHHHHHHhCC
Confidence 79999999999999999999999999984
No 74
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=42.54 E-value=57 Score=30.61 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=36.3
Q ss_pred CCCCCCHHHHHHHHHHHHHcC---chHHHHH-----HHhCCCCHHHHHHHHHHH
Q 020749 78 SRESWTEQEHDKFLEALQLFD---RDWKKIE-----AFIGSKTVIQIRSHAQKY 123 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yG---rdWkkIA-----~~VgTRT~~QcRSHaQKY 123 (322)
.+..||.+|+++|........ ..+++|= -|-.+||+.+...||+-.
T Consensus 72 ~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lm 125 (199)
T PF13325_consen 72 SKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLM 125 (199)
T ss_pred ccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHH
Confidence 578999999999999765554 3788873 355789999999999843
No 75
>PRK01905 DNA-binding protein Fis; Provisional
Probab=42.23 E-value=73 Score=24.82 Aligned_cols=28 Identities=7% Similarity=0.061 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhCC
Q 020749 83 TEQEHDKFLEALQLFDRDWKKIEAFIGS 110 (322)
Q Consensus 83 T~EEhelFLeaLk~yGrdWkkIA~~VgT 110 (322)
..-|.+.+.++|+.+|.++.+.|+.+|-
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGI 62 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGI 62 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC
Confidence 3457788999999999999999999885
No 76
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=41.86 E-value=68 Score=26.33 Aligned_cols=26 Identities=12% Similarity=0.081 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCC
Q 020749 85 QEHDKFLEALQLFDRDWKKIEAFIGS 110 (322)
Q Consensus 85 EEhelFLeaLk~yGrdWkkIA~~VgT 110 (322)
-|...+.++++.+|+++.+.|+.+|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGI 80 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGI 80 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 47778999999999999999999995
No 77
>PHA00442 host recBCD nuclease inhibitor
Probab=40.61 E-value=18 Score=28.02 Aligned_cols=33 Identities=24% Similarity=0.622 Sum_probs=26.1
Q ss_pred cccCCCCC--------CHHHHHHHHHHHHHcC-chHHHHHHH
Q 020749 75 ITKSRESW--------TEQEHDKFLEALQLFD-RDWKKIEAF 107 (322)
Q Consensus 75 i~k~r~~W--------T~EEhelFLeaLk~yG-rdWkkIA~~ 107 (322)
++..|..| +-|.+..||++|+..| .+|..+.+.
T Consensus 8 VtitRd~wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy~eA 49 (59)
T PHA00442 8 VTITRDAWNDMQGYIDSLEKDNEFLKALRACGVDNWDGYMDA 49 (59)
T ss_pred eeecHHHHHHHHHHHHHHHHhhHHHHHHHHcCCcchhhHHHH
Confidence 34556777 5677889999999999 599998754
No 78
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.28 E-value=1e+02 Score=25.55 Aligned_cols=32 Identities=13% Similarity=0.230 Sum_probs=23.3
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.|..++.||+.+|- +...|+.+..+-..++++
T Consensus 140 ~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 140 EGLSYREIAEILGV-PVGTVKSRLRRARQLLRE 171 (179)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 46789999999885 567777776666666544
No 79
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=38.45 E-value=19 Score=28.32 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=15.5
Q ss_pred HHHHHHHHHcCchHHHHHH
Q 020749 88 DKFLEALQLFDRDWKKIEA 106 (322)
Q Consensus 88 elFLeaLk~yGrdWkkIA~ 106 (322)
.-+.+.|+.||++|.-|.+
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3466688999999999984
No 80
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=37.76 E-value=1.2e+02 Score=23.24 Aligned_cols=39 Identities=18% Similarity=0.425 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.++++|.+.|+ +.|+..++.=+..+|+.++-.||.++..
T Consensus 19 ~l~~~er~~lv----------~nia~~l~~v~~~~i~~r~l~~f~~vd~ 57 (68)
T PF06628_consen 19 VLSDEERERLV----------ENIAGHLSGVSDEEIQERVLAYFYKVDP 57 (68)
T ss_dssp HSSHHHHHHHH----------HHHHHHHTTSSHHHHHHHHHHHHHHH-H
T ss_pred HCCHHHHHHHH----------HHHHHHHccCChhhHHHHHHHHHHHhCH
Confidence 56888888888 4578888887777799999999988754
No 81
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=37.33 E-value=24 Score=35.07 Aligned_cols=59 Identities=22% Similarity=0.308 Sum_probs=36.0
Q ss_pred CCCCcCCCCcccccCCCCCCHHHHHHHHHHHHHc---CchHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcC
Q 020749 64 DPSKKIRKPYTITKSRESWTEQEHDKFLEALQLF---DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNG 131 (322)
Q Consensus 64 d~~kKirKPyti~k~r~~WT~EEhelFLeaLk~y---GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g 131 (322)
..++|.|+|||. .=|.|-|+-|| +.+| .|+|+ |++.+- -|..|||.-+|+=..|.+|..
T Consensus 233 ~~~RKKRcPYTK-----~QtlELEkEFl--fN~YitkeKR~E-lSr~lN-LTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 233 RRGRKKRCPYTK-----HQTLELEKEFL--FNMYITKEKRLE-LSRTLN-LTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccCCchH-----HHHHHHHHHHH--HHHHHhHHHHHH-HHHhcc-cchhheeeeehhhhhHHhhhh
Confidence 455788888871 12333333333 3333 24555 887764 489999998887777766653
No 82
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=34.63 E-value=1.5e+02 Score=23.90 Aligned_cols=31 Identities=19% Similarity=0.333 Sum_probs=23.5
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
.|..++.||+.+|- +...|+++...-..+++
T Consensus 128 ~~~~~~eIA~~lgi-s~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 128 EGKSYKEIAEELGI-SVKTVEYHISKALKELR 158 (161)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 46799999998886 88888887766555554
No 83
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=33.85 E-value=1.2e+02 Score=26.57 Aligned_cols=33 Identities=6% Similarity=0.083 Sum_probs=23.3
Q ss_pred HcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 96 LFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 96 ~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
..|..++.||+.+|. +...|++|...=..++++
T Consensus 148 ~~g~s~~EIA~~lg~-s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 148 MQGYSVADAARMLGV-AEGTVKSRCARGRARLAE 180 (192)
T ss_pred HcCCCHHHHHHHHCc-CHHHHHHHHHHHHHHHHH
Confidence 346789999998885 778888876554444433
No 84
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=33.30 E-value=75 Score=23.44 Aligned_cols=26 Identities=15% Similarity=0.234 Sum_probs=20.9
Q ss_pred hHHHHHHHhCC-CCHHHHHHHHHHHHH
Q 020749 100 DWKKIEAFIGS-KTVIQIRSHAQKYFL 125 (322)
Q Consensus 100 dWkkIA~~VgT-RT~~QcRSHaQKYf~ 125 (322)
-|..|+..++. -+..+|+.+|+....
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 69999998885 578899999987433
No 85
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=32.86 E-value=74 Score=32.67 Aligned_cols=13 Identities=46% Similarity=0.549 Sum_probs=9.2
Q ss_pred CCCcCCCCccccc
Q 020749 65 PSKKIRKPYTITK 77 (322)
Q Consensus 65 ~~kKirKPyti~k 77 (322)
..||-|||...+|
T Consensus 190 t~KKpRKPRqtKK 202 (379)
T PF11593_consen 190 TAKKPRKPRQTKK 202 (379)
T ss_pred ccCCCCCCCCccc
Confidence 3478888887555
No 86
>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=32.50 E-value=80 Score=26.47 Aligned_cols=24 Identities=17% Similarity=0.459 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhC
Q 020749 83 TEQEHDKFLEALQLFDRDWKKIEAFIG 109 (322)
Q Consensus 83 T~EEhelFLeaLk~yGrdWkkIA~~Vg 109 (322)
|+++.+.|-+ ..|++|++++..+|
T Consensus 1 ~~~~~q~~~~---nvGr~WK~laR~Lg 24 (90)
T cd08780 1 TPADQQHFAK---SVGKKWKPVGRSLQ 24 (90)
T ss_pred CHHHHHHHHH---HHhHHHHHHHHHHc
Confidence 4555555554 34899999999998
No 87
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. 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 adaptor
Probab=31.74 E-value=38 Score=26.93 Aligned_cols=32 Identities=28% Similarity=0.498 Sum_probs=22.7
Q ss_pred HHHHHHHHH-HHHHcCchHHHHHHHhCCCCHHHHHH
Q 020749 84 EQEHDKFLE-ALQLFDRDWKKIEAFIGSKTVIQIRS 118 (322)
Q Consensus 84 ~EEhelFLe-aLk~yGrdWkkIA~~VgTRT~~QcRS 118 (322)
.||-+++|. + ..|+||+..|..+|- +...|+.
T Consensus 2 ~~~v~~ll~~~--nlG~dW~~LA~~LG~-~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG--RPGRDWRSLAGELGY-EDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC--CCccCHHHHHHHcCC-CHHHHHH
Confidence 467777775 3 568899999999886 3444544
No 88
>PF12088 DUF3565: Protein of unknown function (DUF3565); InterPro: IPR021948 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
Probab=30.75 E-value=21 Score=28.00 Aligned_cols=11 Identities=45% Similarity=1.138 Sum_probs=9.9
Q ss_pred cccccCCCCcc
Q 020749 305 LSICCGHSNHV 315 (322)
Q Consensus 305 ~~~~~~~~~~~ 315 (322)
|.|.|||.-||
T Consensus 13 A~L~CGH~QHv 23 (61)
T PF12088_consen 13 AELSCGHTQHV 23 (61)
T ss_pred EEecccccccc
Confidence 67999999998
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.62 E-value=1.8e+02 Score=24.11 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=20.0
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl 127 (322)
.|..++.||+.+|- +...|+.+..+-..++
T Consensus 143 ~~~s~~eIA~~lgi-s~~tV~~~l~ra~~~L 172 (182)
T PRK09652 143 EGLSYEEIAEIMGC-PIGTVRSRIFRAREAL 172 (182)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHH
Confidence 46799999999885 5666665544444444
No 90
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=29.13 E-value=62 Score=34.65 Aligned_cols=45 Identities=18% Similarity=0.219 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHH
Q 020749 80 ESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (322)
Q Consensus 80 ~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~ 125 (322)
..--+.|.++++++|++.|.+|.+-|+.+|. ++.|+-+++++|=+
T Consensus 501 ~~~~~~eR~~I~~aL~~~~~~~a~AAr~LGl-~~~~L~~~~kRlGI 545 (550)
T COG3604 501 EATEEFERQLIIAALEETNGNWAGAARRLGL-TRRTLLYRMKRLGI 545 (550)
T ss_pred hhhHHHHHHHHHHHHHHhCCcHHHHHHHhCC-CHHHHHHHHHHcCC
Confidence 3334678888999999999999998889887 78888887766533
No 91
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.99 E-value=1.1e+02 Score=21.08 Aligned_cols=34 Identities=12% Similarity=0.231 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHH
Q 020749 83 TEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRS 118 (322)
Q Consensus 83 T~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRS 118 (322)
+.++....+..+.. |...++||+.+|- +...|..
T Consensus 3 ~~~~R~~ii~l~~~-G~s~~~ia~~lgv-s~~Tv~~ 36 (50)
T PF13384_consen 3 SEERRAQIIRLLRE-GWSIREIAKRLGV-SRSTVYR 36 (50)
T ss_dssp -------HHHHHHH-T--HHHHHHHHTS--HHHHHH
T ss_pred chhHHHHHHHHHHC-CCCHHHHHHHHCc-CHHHHHH
Confidence 34555667777777 9999999999984 5555554
No 92
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=27.70 E-value=3.6e+02 Score=26.39 Aligned_cols=66 Identities=18% Similarity=0.202 Sum_probs=38.5
Q ss_pred CCCCCcCC-CCcccccCCCCCCHHHHHHHHHHHHHcC----chHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 63 EDPSKKIR-KPYTITKSRESWTEQEHDKFLEALQLFD----RDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 63 ed~~kKir-KPyti~k~r~~WT~EEhelFLeaLk~yG----rdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
|+...+++ |+++++|.|+.++.-.-..|-.-+++-- -+=.++|.-+|- |..|||.-+|+=.-|++|
T Consensus 109 E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGL-TQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 109 EPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGL-TQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred CcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCC-chhHhhhhhhhhHHHHHH
Confidence 44444444 6667777777777655444444333322 133456666664 899999988775444433
No 93
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=27.60 E-value=2e+02 Score=21.18 Aligned_cols=46 Identities=7% Similarity=0.026 Sum_probs=32.7
Q ss_pred CCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHH
Q 020749 78 SRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFL 125 (322)
Q Consensus 78 ~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~ 125 (322)
.+..||+|+-..+++.+..-|.....|+.-.|= +..++.. |.+-|.
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi-~~~~l~~-W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGI-SPSTLYN-WRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS--HHHHHH-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccccc-ccccccH-HHHHHh
Confidence 567899999999999998888999999988787 6666665 555444
No 94
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=27.59 E-value=22 Score=41.94 Aligned_cols=50 Identities=16% Similarity=0.262 Sum_probs=42.3
Q ss_pred CCCcccccCCCCCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHH
Q 020749 70 RKPYTITKSRESWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSH 119 (322)
Q Consensus 70 rKPyti~k~r~~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSH 119 (322)
.|.|+-......|+++|++.|.+-+-++-++...|+.|+-.||..+|--+
T Consensus 216 nkv~k~~~~~n~Ws~~Ek~~fk~rf~~H~knf~~~as~~erkSv~d~vlf 265 (1672)
T KOG1878|consen 216 NKVHKDRQRMNEWSPEEKELFKSRFAQHVKNFGLIASFFERKSVSDCVLF 265 (1672)
T ss_pred ccccchHHHhhhccccccccccchhhhcCcchhhhhhhhcccchhhceee
Confidence 34444444678999999999999999999999999999999999998654
No 95
>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=27.26 E-value=60 Score=23.75 Aligned_cols=28 Identities=21% Similarity=0.517 Sum_probs=23.9
Q ss_pred CHHHHHHHHHHHHHcCchHHHHHHHhCC
Q 020749 83 TEQEHDKFLEALQLFDRDWKKIEAFIGS 110 (322)
Q Consensus 83 T~EEhelFLeaLk~yGrdWkkIA~~VgT 110 (322)
..+.|++|...|+.-....+-||+|+|.
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 4567999999998777899999999984
No 96
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=25.89 E-value=57 Score=25.58 Aligned_cols=23 Identities=17% Similarity=0.473 Sum_probs=18.1
Q ss_pred HHHHHHHHHcCchHHHHHHHhCC
Q 020749 88 DKFLEALQLFDRDWKKIEAFIGS 110 (322)
Q Consensus 88 elFLeaLk~yGrdWkkIA~~VgT 110 (322)
..|...-+..|.+|+++|..+|-
T Consensus 5 ~~l~~ia~~lG~dW~~LAr~Lg~ 27 (84)
T cd08317 5 IRLADISNLLGSDWPQLARELGV 27 (84)
T ss_pred chHHHHHHHHhhHHHHHHHHcCC
Confidence 34556667779999999999884
No 97
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=25.50 E-value=68 Score=24.46 Aligned_cols=24 Identities=21% Similarity=0.545 Sum_probs=18.2
Q ss_pred HHHHHHHHHH-cCchHHHHHHHhCC
Q 020749 87 HDKFLEALQL-FDRDWKKIEAFIGS 110 (322)
Q Consensus 87 helFLeaLk~-yGrdWkkIA~~VgT 110 (322)
.+.|...++. .|.+|+++|..+|-
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~Lg~ 29 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKLGL 29 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHcCC
Confidence 3455555555 79999999999985
No 98
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=25.07 E-value=75 Score=26.04 Aligned_cols=31 Identities=13% Similarity=0.301 Sum_probs=24.1
Q ss_pred CchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 98 DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 98 GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
|..++.||+.+|. +...|+++..+-..++++
T Consensus 121 g~s~~eIA~~lgi-s~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 121 EFSYKEIAELLNL-SLAKVKSNLFRARKELKK 151 (154)
T ss_pred cCcHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 4589999999886 688888887777666654
No 99
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.74 E-value=2.2e+02 Score=24.55 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 84 EQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 84 ~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
.+|+..|++.+-+..++-|.|++.+|- +.--||++..+...++.
T Consensus 35 ~~E~~~Fi~~Fi~~rGnlKe~e~~lgi-SYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 35 SPEQLEFIKLFIKNRGNLKEMEKELGI-SYPTVRNRLDKIIEKLG 78 (113)
T ss_pred CHHHHHHHHHHHHhcCCHHHHHHHHCC-CcHHHHHHHHHHHHHhC
Confidence 578999999999999999999999886 78889998887766653
No 100
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=24.74 E-value=96 Score=30.42 Aligned_cols=29 Identities=14% Similarity=0.308 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHcCchHHHHHHHhCC-CC
Q 020749 84 EQEHDKFLEALQLFDRDWKKIEAFIGS-KT 112 (322)
Q Consensus 84 ~EEhelFLeaLk~yGrdWkkIA~~VgT-RT 112 (322)
+-|.+.+.++|+++|++..+.|+.+|= |+
T Consensus 404 ~~E~~~i~~al~~~~gn~~~aA~~Lgisr~ 433 (445)
T TIGR02915 404 RAEREAVRKAIARVDGNIARAAELLGITRP 433 (445)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence 347788999999999999999999984 54
No 101
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=24.48 E-value=1.7e+02 Score=24.82 Aligned_cols=30 Identities=13% Similarity=0.163 Sum_probs=21.4
Q ss_pred CchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 98 DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 98 GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
|..++.||+.+|- |...|+++...-..+++
T Consensus 154 ~~s~~EIA~~lgi-s~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 154 GLSYEDIARIMDC-PVGTVRSRIFRAREAIA 183 (190)
T ss_pred CCCHHHHHHHHCc-CHHHHHHHHHHHHHHHH
Confidence 5688889988886 57888887655555553
No 102
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=24.25 E-value=2.1e+02 Score=23.73 Aligned_cols=44 Identities=14% Similarity=0.212 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHcCc-hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCC
Q 020749 84 EQEHDKFLEALQLFDR-DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGT 132 (322)
Q Consensus 84 ~EEhelFLeaLk~yGr-dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g~ 132 (322)
++-+.++|+.|+.-|+ .++.||+.+| -+..-|+.|- .++.+.|.
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg-lS~~~v~~Ri----~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG-LSPSTVLRRI----KRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC-CCHHHHHHHH----HHHHHCCc
Confidence 4678899999999997 8999999999 4788888764 45666664
No 103
>PF01410 COLFI: Fibrillar collagen C-terminal domain; InterPro: IPR000885 Collagens contain a large number of globular domains in between the regions of triple helical repeats IPR008160 from INTERPRO. These domains are involved in binding diverse substrates. One of these domains is found at the C terminus of fibrillar collagens. The exact function of this domain is unknown.; GO: 0005201 extracellular matrix structural constituent, 0005581 collagen
Probab=24.08 E-value=40 Score=31.13 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=14.3
Q ss_pred CCCCCCCCccccCCCC
Q 020749 4 VNPNPAQGFFFFDPMN 19 (322)
Q Consensus 4 ~~p~~~~~~~~~dp~~ 19 (322)
.+|+.+.|.|++||.+
T Consensus 21 ~~p~~~dG~YwIDPN~ 36 (214)
T PF01410_consen 21 CHPELPDGEYWIDPNG 36 (214)
T ss_pred hCcccCCCcEeECCCC
Confidence 5799999999999984
No 104
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.42 E-value=2e+02 Score=24.82 Aligned_cols=32 Identities=6% Similarity=0.150 Sum_probs=22.6
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.|.+.+.||+.+|- |...|+++..+=..++++
T Consensus 146 ~~~s~~eIA~~lgi-s~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 146 HEKSVEEVGEIVGI-PESTVKTRMFYARKKLAE 177 (189)
T ss_pred cCCCHHHHHHHHCc-CHHHHHHHHHHHHHHHHH
Confidence 36689999998886 777777776555555544
No 105
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=23.13 E-value=2.3e+02 Score=23.97 Aligned_cols=32 Identities=16% Similarity=0.157 Sum_probs=22.3
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.|..++.||+.+|- |...|+++..+-..++++
T Consensus 151 ~~~s~~eIA~~lgi-s~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 151 EDLSLKEISEILDL-PVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 46689999998885 577777776555555543
No 106
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=22.46 E-value=1.1e+02 Score=22.04 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=31.1
Q ss_pred HHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHH
Q 020749 88 DKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLK 126 (322)
Q Consensus 88 elFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~k 126 (322)
++|.++++..|.+=..|-+.+.+|+..|.+.=.+.|...
T Consensus 4 ~~l~~a~~~~g~de~~li~Il~~rs~~ql~~i~~~Y~~~ 42 (66)
T PF00191_consen 4 ELLHAALKGWGTDEDVLIEILCTRSPAQLRAIKQAYKKK 42 (66)
T ss_dssp HHHHHHHSSSSSTHHHHHHHHHHSTHHHHHHHHHHHHHH
T ss_pred HHHHHHccCCCCChhHhhhHHhhhcccccceeehhhhhh
Confidence 377788888887766777788899999999877777555
No 107
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.25 E-value=2.7e+02 Score=21.31 Aligned_cols=39 Identities=10% Similarity=0.171 Sum_probs=27.5
Q ss_pred HHHcCc--hHHHHHHHhCCCCHHHHHHHHHHHHHHHhhcCCCCCC
Q 020749 94 LQLFDR--DWKKIEAFIGSKTVIQIRSHAQKYFLKVQKNGTSEHV 136 (322)
Q Consensus 94 Lk~yGr--dWkkIA~~VgTRT~~QcRSHaQKYf~kl~k~g~~e~i 136 (322)
++++|. .-..|++.+|-++..-|.. |+..|.+.|.....
T Consensus 19 ~~~~G~~Pt~rEIa~~~g~~S~~tv~~----~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 19 IEENGYPPTVREIAEALGLKSTSTVQR----HLKALERKGYIRRD 59 (65)
T ss_dssp HHHHSS---HHHHHHHHTSSSHHHHHH----HHHHHHHTTSEEEG
T ss_pred HHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHHCcCccCC
Confidence 355574 7888999999999887776 46667777764433
No 108
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.14 E-value=2.2e+02 Score=25.04 Aligned_cols=32 Identities=13% Similarity=0.202 Sum_probs=24.9
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.|..++.||+.+|- +...|++|.++=..++++
T Consensus 128 ~g~s~~EIA~~Lgi-S~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 128 SGFSYEEAAEMCGV-AVGTVKSRANRARARLAE 159 (188)
T ss_pred cCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 46789999999885 688888887776666655
No 109
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=22.11 E-value=96 Score=30.15 Aligned_cols=29 Identities=21% Similarity=0.250 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHcCchHHHHHHHhCC-CC
Q 020749 84 EQEHDKFLEALQLFDRDWKKIEAFIGS-KT 112 (322)
Q Consensus 84 ~EEhelFLeaLk~yGrdWkkIA~~VgT-RT 112 (322)
+-|.+.+.++|+++|++..+.|+.+|- |+
T Consensus 404 ~~e~~~i~~~l~~~~gn~~~aa~~Lgisr~ 433 (441)
T PRK10365 404 EVEKEVILAALEKTGGNKTEAARQLGITRK 433 (441)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence 457778999999999999999999984 44
No 110
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=22.03 E-value=2.5e+02 Score=23.27 Aligned_cols=32 Identities=13% Similarity=0.219 Sum_probs=24.0
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.|..-+.||+.+|- +...|++|..+-..++++
T Consensus 125 ~g~s~~eIA~~lgi-s~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 125 EDLSEAQVAEALGI-SVGTVKSRLSRALARLRE 156 (162)
T ss_pred hcCCHHHHHHHhCC-CHHHHHHHHHHHHHHHHH
Confidence 35678888888875 688888887777777655
No 111
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=21.92 E-value=2.4e+02 Score=24.21 Aligned_cols=31 Identities=16% Similarity=0.201 Sum_probs=20.9
Q ss_pred CchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 98 DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 98 GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
|...+.||+.+|- |...|++|.++-..++++
T Consensus 154 g~s~~eIA~~lgi-s~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 154 GLSYEDIASVMQC-PVGTVRSRIFRAREAIDK 184 (193)
T ss_pred CCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHH
Confidence 4578888888876 577777776655555543
No 112
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=21.91 E-value=2.6e+02 Score=24.52 Aligned_cols=41 Identities=10% Similarity=0.070 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 020749 86 EHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKV 127 (322)
Q Consensus 86 EhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl 127 (322)
+..+.++.....|-.|+.||+.+|- +..-|+.+++.-..++
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~lgi-S~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERLGI-SERTVRRRLRRARAWL 179 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCc-CHHHHHHHHHHHHHHH
Confidence 3344444444456799999999875 6666777666554444
No 113
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=21.72 E-value=1.2e+02 Score=29.40 Aligned_cols=38 Identities=18% Similarity=0.201 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHcCchHHHHHHHhCC-CCHHHHHHHHHHHHHHHhhcC
Q 020749 85 QEHDKFLEALQLFDRDWKKIEAFIGS-KTVIQIRSHAQKYFLKVQKNG 131 (322)
Q Consensus 85 EEhelFLeaLk~yGrdWkkIA~~VgT-RT~~QcRSHaQKYf~kl~k~g 131 (322)
-|.+.+.++|+.++++-.+.|+.+|= |+ ..++|+++.|
T Consensus 286 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~---------tLyrklk~~g 324 (326)
T PRK11608 286 QEKELLQRSLQQAKFNQKRAAELLGLTYH---------QLRALLKKHQ 324 (326)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHH---------HHHHHHHHcC
Confidence 37788999999999999999999984 44 2456666654
No 114
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=21.02 E-value=2.7e+02 Score=23.36 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=20.4
Q ss_pred CchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 98 DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 98 GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
|...+.||+.+|- |...|+++..+-..+++
T Consensus 135 g~s~~eiA~~lgi-s~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 135 DLTIKEIAEVMNK-PEGTVKTYLHRALKKLK 164 (169)
T ss_pred CCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 4577788888775 77777776655555554
No 115
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=20.66 E-value=3.6e+02 Score=22.76 Aligned_cols=31 Identities=0% Similarity=-0.039 Sum_probs=19.7
Q ss_pred cCchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 97 FDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 97 yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
.|...+.||+.+|- |...|+.+..+-..+++
T Consensus 155 ~g~s~~eIA~~lgi-s~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 155 EGLSFAEVAERMDR-SEGAVSMLWVRGLARLR 185 (189)
T ss_pred cCCCHHHHHHHHCc-CHHHHHHHHHHHHHHHH
Confidence 45677888887775 56666666555555554
No 116
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.53 E-value=3e+02 Score=23.60 Aligned_cols=30 Identities=13% Similarity=0.185 Sum_probs=19.0
Q ss_pred CchHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Q 020749 98 DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQ 128 (322)
Q Consensus 98 GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~ 128 (322)
|..++.||+.+|- +...|+++..+-..+++
T Consensus 155 g~s~~EIA~~lgi-s~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 155 GLSAEETAEAVGS-TPGAVRVAQHRALARLR 184 (189)
T ss_pred CCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 5678888888775 45666665544444443
No 117
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.51 E-value=2.7e+02 Score=25.48 Aligned_cols=46 Identities=13% Similarity=0.097 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHcCchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 81 SWTEQEHDKFLEALQLFDRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 81 ~WT~EEhelFLeaLk~yGrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
.-|+.|.+-|....+ |...+.||+.++ -+...|+.|...-|.|+.-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L~-iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSLF-ISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHhC-CCHHHHHHHHHHHHHHhCC
Confidence 367777666554444 999999998877 4888999999888888743
No 118
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.28 E-value=3.6e+02 Score=22.95 Aligned_cols=31 Identities=6% Similarity=0.283 Sum_probs=23.2
Q ss_pred CchHHHHHHHhCCCCHHHHHHHHHHHHHHHhh
Q 020749 98 DRDWKKIEAFIGSKTVIQIRSHAQKYFLKVQK 129 (322)
Q Consensus 98 GrdWkkIA~~VgTRT~~QcRSHaQKYf~kl~k 129 (322)
|..-+.||+.+|- |...|+++..+-..++++
T Consensus 151 ~~s~~eIA~~lgi-s~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 151 GYTHREAAQLLGL-PLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCCHHHHHHHHCc-CHHHHHHHHHHHHHHHHH
Confidence 5577888888876 678888887777776654
No 119
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=20.28 E-value=1e+02 Score=24.80 Aligned_cols=24 Identities=4% Similarity=0.134 Sum_probs=18.4
Q ss_pred HHHHHHHHHHcCchHHHHHHHhCC
Q 020749 87 HDKFLEALQLFDRDWKKIEAFIGS 110 (322)
Q Consensus 87 helFLeaLk~yGrdWkkIA~~VgT 110 (322)
+.++...-...|.+|+++|..+|-
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eLg~ 27 (84)
T cd08803 4 DIRMAIVADHLGLSWTELARELNF 27 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHcCC
Confidence 344555567889999999998884
No 120
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=20.25 E-value=4.2e+02 Score=26.67 Aligned_cols=29 Identities=14% Similarity=0.386 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHHH---------HHHcCchHHHHHHHh
Q 020749 80 ESWTEQEHDKFLEA---------LQLFDRDWKKIEAFI 108 (322)
Q Consensus 80 ~~WT~EEhelFLea---------Lk~yGrdWkkIA~~V 108 (322)
-.|+..|+.++.+- =|+.|+.||.+.+.-
T Consensus 71 MVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~E 108 (331)
T KOG0527|consen 71 MVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEE 108 (331)
T ss_pred hhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhh
Confidence 48999999999873 377899999987653
Done!