Query 046075
Match_columns 328
No_of_seqs 290 out of 1377
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:29:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046075.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046075hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 7.1E-39 1.5E-43 316.5 12.5 132 1-142 1-132 (459)
2 PLN03212 Transcription repress 100.0 2.1E-38 4.5E-43 294.5 11.5 132 2-143 13-144 (249)
3 KOG0048 Transcription factor, 100.0 6.4E-36 1.4E-40 277.9 11.1 121 11-140 5-125 (238)
4 KOG0049 Transcription factor, 99.7 1.1E-18 2.3E-23 179.0 5.7 112 1-123 347-459 (939)
5 KOG0049 Transcription factor, 99.7 2.9E-18 6.3E-23 175.8 7.7 118 10-135 248-419 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 6.7E-17 1.5E-21 119.5 3.2 60 18-79 1-60 (60)
7 KOG0051 RNA polymerase I termi 99.6 2.1E-15 4.6E-20 155.3 6.5 114 14-130 383-515 (607)
8 COG5147 REB1 Myb superfamily p 99.5 3.5E-15 7.6E-20 152.1 5.7 107 11-127 16-122 (512)
9 KOG0050 mRNA splicing protein 99.5 3.3E-15 7.1E-20 150.6 5.3 108 13-131 5-112 (617)
10 PF00249 Myb_DNA-binding: Myb- 99.4 6.1E-14 1.3E-18 100.0 0.5 48 15-62 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.3 2.2E-12 4.7E-17 92.0 4.7 46 68-122 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.2 5.3E-12 1.1E-16 93.2 3.2 54 71-133 1-54 (60)
13 PLN03212 Transcription repress 99.2 8E-12 1.7E-16 117.2 4.3 78 48-141 12-91 (249)
14 KOG0048 Transcription factor, 99.1 3.3E-11 7.1E-16 112.5 3.7 85 64-157 5-91 (238)
15 smart00717 SANT SANT SWI3, AD 99.1 1.4E-10 3E-15 79.8 5.0 47 68-123 1-48 (49)
16 PLN03091 hypothetical protein; 99.0 8.7E-11 1.9E-15 117.7 3.0 66 63-137 9-76 (459)
17 smart00717 SANT SANT SWI3, AD 99.0 1.1E-10 2.4E-15 80.3 1.8 48 15-63 1-48 (49)
18 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 1.2E-09 2.6E-14 74.1 5.1 43 70-121 1-44 (45)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 7.4E-10 1.6E-14 75.2 1.5 44 17-61 1-44 (45)
20 KOG0051 RNA polymerase I termi 98.7 2.2E-08 4.7E-13 104.0 5.3 103 12-125 305-431 (607)
21 COG5147 REB1 Myb superfamily p 98.5 8.7E-09 1.9E-13 105.7 -2.4 107 13-123 289-397 (512)
22 TIGR01557 myb_SHAQKYF myb-like 97.8 7.7E-06 1.7E-10 61.2 1.8 49 14-62 2-54 (57)
23 KOG0457 Histone acetyltransfer 97.5 3.3E-05 7.2E-10 77.8 1.6 99 12-111 69-180 (438)
24 PF08914 Myb_DNA-bind_2: Rap1 97.2 0.00065 1.4E-08 52.1 5.0 60 68-127 2-62 (65)
25 KOG0050 mRNA splicing protein 97.2 0.00024 5.2E-09 73.1 3.2 60 66-134 5-65 (617)
26 TIGR01557 myb_SHAQKYF myb-like 97.2 0.001 2.2E-08 49.8 5.8 46 68-122 3-54 (57)
27 PF13325 MCRS_N: N-terminal re 97.1 0.0028 6.1E-08 58.5 9.2 109 17-128 1-132 (199)
28 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00061 1.3E-08 53.3 3.7 61 68-129 1-70 (90)
29 TIGR02894 DNA_bind_RsfA transc 97.0 0.00096 2.1E-08 59.6 4.4 59 66-128 2-61 (161)
30 KOG0457 Histone acetyltransfer 96.8 0.0021 4.6E-08 65.0 5.7 49 65-122 69-118 (438)
31 COG5259 RSC8 RSC chromatin rem 96.6 0.00072 1.6E-08 69.0 1.0 46 14-61 278-323 (531)
32 KOG1279 Chromatin remodeling f 96.4 0.0013 2.9E-08 68.1 1.5 47 12-60 250-296 (506)
33 COG5259 RSC8 RSC chromatin rem 96.1 0.0053 1.2E-07 62.8 4.2 45 68-121 279-323 (531)
34 PF13837 Myb_DNA-bind_4: Myb/S 96.1 0.0013 2.9E-08 51.4 -0.2 46 16-61 2-63 (90)
35 KOG1279 Chromatin remodeling f 96.0 0.0074 1.6E-07 62.7 4.8 46 67-121 252-297 (506)
36 PRK13923 putative spore coat p 96.0 0.0085 1.8E-07 54.2 4.1 59 66-127 3-61 (170)
37 PF08914 Myb_DNA-bind_2: Rap1 95.9 0.0028 6E-08 48.7 0.8 51 15-65 2-60 (65)
38 TIGR02894 DNA_bind_RsfA transc 95.7 0.0031 6.8E-08 56.4 0.4 50 13-64 2-57 (161)
39 COG5114 Histone acetyltransfer 94.3 0.013 2.8E-07 57.8 0.1 48 15-63 63-110 (432)
40 PF13873 Myb_DNA-bind_5: Myb/S 94.2 0.096 2.1E-06 40.3 4.9 57 68-124 2-71 (78)
41 PRK13923 putative spore coat p 94.2 0.011 2.4E-07 53.4 -0.5 50 12-63 2-57 (170)
42 PF13873 Myb_DNA-bind_5: Myb/S 94.0 0.014 3.1E-07 44.9 -0.1 49 14-62 1-69 (78)
43 PLN03142 Probable chromatin-re 93.0 0.2 4.4E-06 56.4 6.7 109 17-126 826-988 (1033)
44 COG5114 Histone acetyltransfer 91.9 0.17 3.7E-06 50.1 3.9 47 67-122 62-109 (432)
45 PF09111 SLIDE: SLIDE; InterP 91.2 0.33 7.2E-06 41.4 4.4 56 65-125 46-113 (118)
46 PF12776 Myb_DNA-bind_3: Myb/S 90.6 0.9 1.9E-05 35.8 6.2 54 70-123 1-63 (96)
47 KOG2656 DNA methyltransferase 89.9 0.35 7.7E-06 48.9 4.0 53 69-130 131-189 (445)
48 KOG4282 Transcription factor G 87.8 0.88 1.9E-05 44.6 5.1 60 68-129 54-119 (345)
49 COG5118 BDP1 Transcription ini 86.7 0.9 2E-05 46.1 4.5 46 70-124 367-412 (507)
50 KOG1194 Predicted DNA-binding 83.2 3 6.6E-05 43.2 6.5 48 67-123 186-233 (534)
51 PF09111 SLIDE: SLIDE; InterP 79.9 1.2 2.7E-05 38.0 2.0 35 11-45 45-82 (118)
52 PF11626 Rap1_C: TRF2-interact 75.6 2.7 5.8E-05 33.6 2.7 25 11-35 43-75 (87)
53 COG5118 BDP1 Transcription ini 75.2 1.7 3.8E-05 44.1 1.9 64 13-78 363-434 (507)
54 PF08281 Sigma70_r4_2: Sigma-7 75.2 6.6 0.00014 27.7 4.5 42 73-124 12-53 (54)
55 PF12776 Myb_DNA-bind_3: Myb/S 71.2 2.1 4.5E-05 33.7 1.1 44 17-60 1-60 (96)
56 KOG4282 Transcription factor G 71.1 1.7 3.7E-05 42.6 0.8 47 15-61 54-112 (345)
57 KOG4167 Predicted DNA-binding 69.1 8.5 0.00019 42.2 5.4 56 57-121 605-663 (907)
58 KOG4468 Polycomb-group transcr 59.0 16 0.00036 39.3 5.2 56 68-133 88-153 (782)
59 smart00595 MADF subfamily of S 59.0 10 0.00022 29.4 2.9 24 98-122 29-52 (89)
60 PF13404 HTH_AsnC-type: AsnC-t 56.3 3.5 7.7E-05 28.7 -0.1 38 21-60 3-40 (42)
61 PF04545 Sigma70_r4: Sigma-70, 52.9 30 0.00066 24.1 4.3 41 74-124 7-47 (50)
62 KOG0384 Chromodomain-helicase 52.0 18 0.00039 41.9 4.4 71 14-91 1132-1203(1373)
63 PF11626 Rap1_C: TRF2-interact 51.7 15 0.00032 29.3 2.8 17 64-80 43-59 (87)
64 PRK11179 DNA-binding transcrip 51.3 5.2 0.00011 34.7 0.1 46 20-67 8-53 (153)
65 PF07750 GcrA: GcrA cell cycle 48.5 17 0.00038 32.5 3.0 40 70-119 2-41 (162)
66 PRK11169 leucine-responsive tr 46.5 5.5 0.00012 35.0 -0.5 46 19-66 12-57 (164)
67 PF11035 SnAPC_2_like: Small n 45.4 96 0.0021 31.1 7.8 54 68-128 21-75 (344)
68 PF13325 MCRS_N: N-terminal re 45.1 35 0.00076 31.8 4.5 44 70-123 1-47 (199)
69 KOG4468 Polycomb-group transcr 43.3 22 0.00047 38.4 3.2 49 14-63 87-144 (782)
70 TIGR02985 Sig70_bacteroi1 RNA 42.2 48 0.001 27.4 4.7 25 101-127 134-158 (161)
71 PF10545 MADF_DNA_bdg: Alcohol 39.1 36 0.00077 25.5 3.1 25 99-123 29-54 (85)
72 KOG2009 Transcription initiati 36.5 32 0.0007 36.9 3.2 48 67-123 408-455 (584)
73 KOG2656 DNA methyltransferase 36.4 16 0.00035 37.4 0.9 50 12-62 127-181 (445)
74 KOG4167 Predicted DNA-binding 33.4 18 0.0004 39.7 0.9 44 15-60 619-662 (907)
75 PRK09645 RNA polymerase sigma 31.7 1E+02 0.0022 26.3 5.1 23 100-123 138-160 (173)
76 PF02954 HTH_8: Bacterial regu 30.4 23 0.0005 24.3 0.7 30 21-51 5-34 (42)
77 PRK12532 RNA polymerase sigma 30.3 1.2E+02 0.0025 26.7 5.4 31 100-131 156-189 (195)
78 PF01388 ARID: ARID/BRIGHT DNA 30.1 80 0.0017 24.7 3.9 46 77-123 39-89 (92)
79 PF09420 Nop16: Ribosome bioge 29.4 88 0.0019 27.7 4.4 46 67-121 113-162 (164)
80 COG2197 CitB Response regulato 28.8 77 0.0017 28.9 4.1 44 69-124 147-190 (211)
81 PRK09643 RNA polymerase sigma 28.0 1.2E+02 0.0026 26.8 5.0 23 100-123 154-176 (192)
82 PRK12523 RNA polymerase sigma 27.0 1.5E+02 0.0033 25.4 5.4 30 101-131 140-169 (172)
83 PLN03142 Probable chromatin-re 26.9 43 0.00094 38.3 2.4 33 13-45 924-956 (1033)
84 smart00351 PAX Paired Box doma 26.6 1.1E+02 0.0023 25.9 4.2 73 13-87 13-92 (125)
85 PRK11179 DNA-binding transcrip 26.0 82 0.0018 27.2 3.5 46 74-128 9-54 (153)
86 PRK09642 RNA polymerase sigma 25.0 1.6E+02 0.0034 24.8 5.1 24 99-123 125-148 (160)
87 TIGR02937 sigma70-ECF RNA poly 24.9 1.8E+02 0.0038 23.1 5.1 24 100-124 130-153 (158)
88 PRK12512 RNA polymerase sigma 23.8 1.8E+02 0.0039 25.1 5.3 28 100-128 151-178 (184)
89 PF09420 Nop16: Ribosome bioge 23.6 54 0.0012 29.1 2.0 47 13-60 112-161 (164)
90 PF04504 DUF573: Protein of un 23.5 1.3E+02 0.0028 24.7 4.0 50 69-123 5-63 (98)
91 PRK11924 RNA polymerase sigma 23.3 1.3E+02 0.0028 25.3 4.2 24 99-123 144-167 (179)
92 PRK09652 RNA polymerase sigma 23.1 1.6E+02 0.0035 24.8 4.8 23 100-123 148-170 (182)
93 cd08319 Death_RAIDD Death doma 22.7 99 0.0021 24.7 3.1 29 76-114 2-30 (83)
94 PF00196 GerE: Bacterial regul 22.5 92 0.002 22.3 2.7 43 70-124 3-45 (58)
95 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 22.4 1.2E+02 0.0027 22.2 3.3 35 74-118 7-41 (50)
96 smart00344 HTH_ASNC helix_turn 20.8 39 0.00084 27.0 0.4 43 21-65 3-45 (108)
97 PRK04217 hypothetical protein; 20.7 2.1E+02 0.0045 24.2 4.8 44 70-124 42-85 (110)
98 COG1522 Lrp Transcriptional re 20.5 33 0.00071 29.0 -0.1 45 20-66 7-51 (154)
99 PF07638 Sigma70_ECF: ECF sigm 20.2 2.3E+02 0.005 25.0 5.4 36 77-122 141-176 (185)
100 PRK09047 RNA polymerase factor 20.2 1.9E+02 0.0041 24.1 4.6 24 100-124 126-149 (161)
101 cd06171 Sigma70_r4 Sigma70, re 20.1 2.3E+02 0.005 18.3 4.2 36 76-121 15-50 (55)
102 smart00501 BRIGHT BRIGHT, ARID 20.1 1.8E+02 0.004 22.9 4.2 47 77-124 35-86 (93)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=7.1e-39 Score=316.53 Aligned_cols=132 Identities=61% Similarity=1.177 Sum_probs=128.5
Q ss_pred CCCCCcccCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHH
Q 046075 1 MGRSPCCDESRSLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIII 80 (328)
Q Consensus 1 mgR~~cc~k~~~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li 80 (328)
|||++||.| .+++||+||+|||++|+++|++||..+|..||+.++++|+++|||+||.+||+|.+++++||+|||++|+
T Consensus 1 mgr~~Cc~K-qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLL 79 (459)
T PLN03091 1 MGRHSCCYK-QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLII 79 (459)
T ss_pred CCCCccCcC-CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHH
Confidence 999999999 9999999999999999999999999999999999988999999999999999999999999999999999
Q ss_pred HHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCc
Q 046075 81 NLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMGIDPITHKPRVDL 142 (328)
Q Consensus 81 ~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~~p~~~~p~~~~ 142 (328)
++|++||++|. +||++|||||+++|||||+.+||+++++.+++|.+++|....
T Consensus 80 eL~k~~GnKWs---------kIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~ 132 (459)
T PLN03091 80 ELHAVLGNRWS---------QIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEV 132 (459)
T ss_pred HHHHHhCcchH---------HHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCcccc
Confidence 99999999999 999999999999999999999999999999999999987754
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=2.1e-38 Score=294.50 Aligned_cols=132 Identities=57% Similarity=1.118 Sum_probs=126.5
Q ss_pred CCCCcccCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHH
Q 046075 2 GRSPCCDESRSLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIIIN 81 (328)
Q Consensus 2 gR~~cc~k~~~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li~ 81 (328)
.|+|||+| ++++|++||+|||++|+++|++||..+|..||+.++++|+++|||+||.+||+|.+++++||+|||++|++
T Consensus 13 ~~~pcc~K-~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLle 91 (249)
T PLN03212 13 KTTPCCTK-MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILR 91 (249)
T ss_pred CCCCCccc-CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHH
Confidence 37899999 99999999999999999999999998999999999889999999999999999999999999999999999
Q ss_pred HHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCcc
Q 046075 82 LHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMGIDPITHKPRVDLS 143 (328)
Q Consensus 82 Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~~p~~~~p~~~~~ 143 (328)
+|.+||++|. .||++|||||+++|||||+.++++++++.+++|.+++|.....
T Consensus 92 l~~~~GnKWs---------~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~~~ 144 (249)
T PLN03212 92 LHRLLGNRWS---------LIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDANN 144 (249)
T ss_pred HHHhccccHH---------HHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCccc
Confidence 9999999999 9999999999999999999999999999999999998866543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=6.4e-36 Score=277.86 Aligned_cols=121 Identities=63% Similarity=1.114 Sum_probs=113.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCc
Q 046075 11 RSLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIIINLHSVLGNKY 90 (328)
Q Consensus 11 ~~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li~Lv~~~G~kW 90 (328)
+.+.||+||+|||++|+++|++||.++|..||+.+|++||+|+||+||.|||+|++++|.||+|||.+|++||..+|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 34558999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 046075 91 FSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMGIDPITHKPRV 140 (328)
Q Consensus 91 ~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~~p~~~~p~~ 140 (328)
+ .||++|||||+++|||+|+++||+|+.+++.++.+..+.+
T Consensus 85 s---------~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~~~~~~ 125 (238)
T KOG0048|consen 85 S---------LIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPSTHRPST 125 (238)
T ss_pred H---------HHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCcccccc
Confidence 9 9999999999999999999999999999987666655433
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.74 E-value=1.1e-18 Score=179.03 Aligned_cols=112 Identities=26% Similarity=0.417 Sum_probs=99.4
Q ss_pred CCCCCcccCCCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHH
Q 046075 1 MGRSPCCDESRSLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIII 80 (328)
Q Consensus 1 mgR~~cc~k~~~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li 80 (328)
+||...... |++|+|+||++||.+|+.+|.+||.++|.+|-+.+ |||+..|||+||.|+|+...|++.||-.||+.|+
T Consensus 347 I~R~~~~Ld-Psikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~v-PnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~ 424 (939)
T KOG0049|consen 347 ITRFSHTLD-PSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAV-PNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLL 424 (939)
T ss_pred hhhheeccC-ccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhc-CCccHHHHHHHHHHHHHHhhccCceeecchHHHH
Confidence 356666555 99999999999999999999999999999999999 8999999999999999999999999999999999
Q ss_pred HHHHHhCC-CccccccchhHHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 81 NLHSVLGN-KYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 81 ~Lv~~~G~-kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
.+|.+||. .|. +||..||.||..|.+.|=...+.
T Consensus 425 ~~V~~YG~g~Wa---------kcA~~Lp~~t~~q~~rrR~R~~~ 459 (939)
T KOG0049|consen 425 YAVKVYGKGNWA---------KCAMLLPKKTSRQLRRRRLRLIA 459 (939)
T ss_pred HHHHHHccchHH---------HHHHHccccchhHHHHHHHHHHH
Confidence 99999996 465 99999999999665544443343
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.74 E-value=2.9e-18 Score=175.85 Aligned_cols=118 Identities=20% Similarity=0.399 Sum_probs=108.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccc----------------------------------
Q 046075 10 SRSLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCR---------------------------------- 55 (328)
Q Consensus 10 ~~~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR---------------------------------- 55 (328)
.|+++|..|++|||++|..+...+|..+|..||..+|.+|+..||.
T Consensus 248 ~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nS 327 (939)
T KOG0049|consen 248 NPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINS 327 (939)
T ss_pred CCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccC
Confidence 4899999999999999999999999999999999999779999997
Q ss_pred --------------------cccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHH
Q 046075 56 --------------------LRWTNYLRPDIRRGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIK 115 (328)
Q Consensus 56 --------------------~RW~n~L~P~ikkg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcK 115 (328)
.||...|+|.+++|+||.+||.+|+.+|.+||.+.|. +|.+.+|||++.|||
T Consensus 328 hI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~--------k~R~~vPnRSdsQcR 399 (939)
T KOG0049|consen 328 HIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWA--------KVRQAVPNRSDSQCR 399 (939)
T ss_pred ccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchh--------hHHHhcCCccHHHHH
Confidence 6899999999999999999999999999999976443 999999999999999
Q ss_pred HHHHHHHHHHHHhcCCCCCC
Q 046075 116 NFWNTHIRKKFLQMGIDPIT 135 (328)
Q Consensus 116 nRW~~~Lkkkl~k~~~~p~~ 135 (328)
.||.+.|...++...|+-..
T Consensus 400 ~RY~nvL~~s~K~~rW~l~e 419 (939)
T KOG0049|consen 400 ERYTNVLNRSAKVERWTLVE 419 (939)
T ss_pred HHHHHHHHHhhccCceeecc
Confidence 99999999999998886543
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=99.65 E-value=6.7e-17 Score=119.49 Aligned_cols=60 Identities=42% Similarity=0.898 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHH
Q 046075 18 WTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERII 79 (328)
Q Consensus 18 WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~L 79 (328)
||+|||++|+.+|.+||. +|..||+.|| .|++.+|+.||.++|+|.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999995 9999999995 89999999999999999999999999999987
No 7
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.57 E-value=2.1e-15 Score=155.32 Aligned_cols=114 Identities=26% Similarity=0.456 Sum_probs=100.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCC--CCCCCCCHHHHHHHHHHHH-------
Q 046075 14 KKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPD--IRRGRFSEEEERIIINLHS------- 84 (328)
Q Consensus 14 kKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~--ikkg~WT~EED~~Li~Lv~------- 84 (328)
++|.||+||++.|..+|..||. .|..|++.|| |.+..||+||++|..+. .+++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 8999999999999999999995 9999999997 99999999999999987 4899999999999999996
Q ss_pred Hh-------CC---CccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcC
Q 046075 85 VL-------GN---KYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMG 130 (328)
Q Consensus 85 ~~-------G~---kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~ 130 (328)
++ |. .=.++...|+|+.|++.+..|+..|||.+|+.++........
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~ 515 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKR 515 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcc
Confidence 23 11 122455789999999999999999999999999987765543
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.55 E-value=3.5e-15 Score=152.08 Aligned_cols=107 Identities=25% Similarity=0.457 Sum_probs=102.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCc
Q 046075 11 RSLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIIINLHSVLGNKY 90 (328)
Q Consensus 11 ~~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li~Lv~~~G~kW 90 (328)
-.++.|.|+..||+.|..+|+++|..+|.+||..+. .|++++|+.||.++++|.++++.|+.|||..|+.+..++|..|
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 367899999999999999999999999999999996 6999999999999999999999999999999999999999999
Q ss_pred cccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHH
Q 046075 91 FSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFL 127 (328)
Q Consensus 91 ~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~ 127 (328)
. .||..+++||..+|.+||+..+.....
T Consensus 95 s---------tia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 S---------TIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred h---------hhccccCccchHHHHHHHHHHhhhhhc
Confidence 9 899999999999999999999887666
No 9
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.55 E-value=3.3e-15 Score=150.62 Aligned_cols=108 Identities=22% Similarity=0.461 Sum_probs=101.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCccc
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIIINLHSVLGNKYFS 92 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li~Lv~~~G~kW~~ 92 (328)
++-|-|+..||+.|..+|.+||...|.+|++.+ ..++++||+.||..+|+|.|++..|+.|||++|+++...+...|.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll-~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr- 82 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLL-NRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR- 82 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHH-hhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc-
Confidence 678999999999999999999998999999999 599999999999999999999999999999999999999999999
Q ss_pred cccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q 046075 93 FNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMGI 131 (328)
Q Consensus 93 i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~ 131 (328)
.||..| ||+.+||-.||+.++-.......-
T Consensus 83 --------tIa~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 83 --------TIADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred --------hHHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 899998 999999999999999887766543
No 10
>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=99.39 E-value=6.1e-14 Score=99.99 Aligned_cols=48 Identities=40% Similarity=0.820 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccccc
Q 046075 15 KGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYL 62 (328)
Q Consensus 15 Kg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 62 (328)
|++||+|||++|+++|.+||.++|..||..|+.+||+.||+.||+++|
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 689999999999999999998679999999955999999999999875
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.31 E-value=2.2e-12 Score=91.96 Aligned_cols=46 Identities=24% Similarity=0.526 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-ccccccchhHHHHHhhCC-CCCHHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLGNK-YFSFNMHIYSIEIIYHLP-GRTDNEIKNFWNTHI 122 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~k-W~~i~~~I~w~~IA~~lp-gRT~~qcKnRW~~~L 122 (328)
|++||.|||++|+++|.+||.+ |. .||..|| +||..||++||++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~---------~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWK---------KIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHH---------HHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHH---------HHHHHcCCCCCHHHHHHHHHhhC
Confidence 5899999999999999999999 88 9999999 999999999999864
No 12
>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=99.23 E-value=5.3e-12 Score=93.25 Aligned_cols=54 Identities=28% Similarity=0.517 Sum_probs=45.0
Q ss_pred CCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcCCCC
Q 046075 71 FSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMGIDP 133 (328)
Q Consensus 71 WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~~p 133 (328)
||+|||++|+++|..||.+|. .||++|+.||+.+|++||+.+|++++.+..+++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~---------~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~ 54 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWK---------KIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTK 54 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HH---------HHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSH
T ss_pred CCHHHHHHHHHHHHHHCcCHH---------HHHHHHCcCCHHHHHHHHHHHCcccccCCCcCH
Confidence 999999999999999999998 999999669999999999998877666655543
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.21 E-value=8e-12 Score=117.20 Aligned_cols=78 Identities=15% Similarity=0.298 Sum_probs=66.3
Q ss_pred cccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCC-CccccccchhHHHHHhhC-CCCCHHHHHHHHHHHHHHH
Q 046075 48 NRCGKSCRLRWTNYLRPDIRRGRFSEEEERIIINLHSVLGN-KYFSFNMHIYSIEIIYHL-PGRTDNEIKNFWNTHIRKK 125 (328)
Q Consensus 48 ~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li~Lv~~~G~-kW~~i~~~I~w~~IA~~l-pgRT~~qcKnRW~~~Lkkk 125 (328)
.|+..-|. ++.+++++||+|||++|+++|++||. +|. .||+.+ ++||+.|||.||.++|++.
T Consensus 12 ~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~---------~IAk~~g~gRT~KQCReRW~N~L~P~ 75 (249)
T PLN03212 12 KKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWR---------SLPKRAGLLRCGKSCRLRWMNYLRPS 75 (249)
T ss_pred CCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHH---------HHHHhhhcCCCcchHHHHHHHhhchh
Confidence 56555553 35789999999999999999999994 687 999998 6999999999999999999
Q ss_pred HHhcCCCCCCCCCCCC
Q 046075 126 FLQMGIDPITHKPRVD 141 (328)
Q Consensus 126 l~k~~~~p~~~~p~~~ 141 (328)
+.+..|++.++.-...
T Consensus 76 I~kgpWT~EED~lLle 91 (249)
T PLN03212 76 VKRGGITSDEEDLILR 91 (249)
T ss_pred cccCCCChHHHHHHHH
Confidence 9999998876664433
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.12 E-value=3.3e-11 Score=112.47 Aligned_cols=85 Identities=14% Similarity=0.217 Sum_probs=70.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCC-ccccccchhHHHHHhhCC-CCCHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCC
Q 046075 64 PDIRRGRFSEEEERIIINLHSVLGNK-YFSFNMHIYSIEIIYHLP-GRTDNEIKNFWNTHIRKKFLQMGIDPITHKPRVD 141 (328)
Q Consensus 64 P~ikkg~WT~EED~~Li~Lv~~~G~k-W~~i~~~I~w~~IA~~lp-gRT~~qcKnRW~~~Lkkkl~k~~~~p~~~~p~~~ 141 (328)
+.+.||+||.|||++|+++|.+||.. |. .||+.++ +|++.+||-||.++|++.++++.|++++..-...
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~---------~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~ 75 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGT---------ALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIK 75 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcc---------hhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHH
Confidence 44558999999999999999999976 87 9999999 9999999999999999999999999988877666
Q ss_pred ccccCCCcccccCCCC
Q 046075 142 LSQFLNLPQTLYSSPF 157 (328)
Q Consensus 142 ~~~~~~~~q~~~~~~~ 157 (328)
+......-....+.-+
T Consensus 76 lH~~~GNrWs~IA~~L 91 (238)
T KOG0048|consen 76 LHALLGNRWSLIAGRL 91 (238)
T ss_pred HHHHHCcHHHHHHhhC
Confidence 5554444444444333
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.10 E-value=1.4e-10 Score=79.84 Aligned_cols=47 Identities=34% Similarity=0.729 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLG-NKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G-~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
+++||++||.+|+.++..|| .+|. .||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~---------~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWE---------KIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHH---------HHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 8898 99999999999999999998764
No 16
>PLN03091 hypothetical protein; Provisional
Probab=99.04 E-value=8.7e-11 Score=117.66 Aligned_cols=66 Identities=14% Similarity=0.251 Sum_probs=59.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCC-CccccccchhHHHHHhhC-CCCCHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 046075 63 RPDIRRGRFSEEEERIIINLHSVLGN-KYFSFNMHIYSIEIIYHL-PGRTDNEIKNFWNTHIRKKFLQMGIDPITHK 137 (328)
Q Consensus 63 ~P~ikkg~WT~EED~~Li~Lv~~~G~-kW~~i~~~I~w~~IA~~l-pgRT~~qcKnRW~~~Lkkkl~k~~~~p~~~~ 137 (328)
++.+++++||+|||++|+++|.+||. +|. .||+.+ ++|++.|||.||.++|++.+++..|+++++.
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs---------~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~ 76 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWS---------SVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEEN 76 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHH---------HHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHH
Confidence 35789999999999999999999996 576 999988 4999999999999999999999999876653
No 17
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.01 E-value=1.1e-10 Score=80.31 Aligned_cols=48 Identities=38% Similarity=0.854 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccC
Q 046075 15 KGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLR 63 (328)
Q Consensus 15 Kg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 63 (328)
+++||++||.+|+.++..||..+|..||..++ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999669999999994 9999999999998764
No 18
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.96 E-value=1.2e-09 Score=74.14 Aligned_cols=43 Identities=28% Similarity=0.592 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHHhC-CCccccccchhHHHHHhhCCCCCHHHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVLG-NKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTH 121 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~G-~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~ 121 (328)
+||.+||..|+.++..|| .+|. .||..|++||..+|++||+.+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~---------~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWE---------KIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHH---------HHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8887 999999999999999999875
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.86 E-value=7.4e-10 Score=75.16 Aligned_cols=44 Identities=39% Similarity=0.835 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccc
Q 046075 17 PWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNY 61 (328)
Q Consensus 17 ~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 61 (328)
+||++||..|+.++.+||..+|..||+.++ +|++.+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHh
Confidence 599999999999999999779999999995 89999999999865
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.66 E-value=2.2e-08 Score=104.04 Aligned_cols=103 Identities=25% Similarity=0.332 Sum_probs=83.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----C-----------C--------cccccccccccccccccccccccccCCCC-C
Q 046075 12 SLKKGPWTPEEDQKLVDYIGRHGH----G-----------S--------WNALPKLAGLNRCGKSCRLRWTNYLRPDI-R 67 (328)
Q Consensus 12 ~lkKg~WT~EEDe~L~~lV~k~G~----~-----------n--------W~~IAk~lg~~Rt~kQCR~RW~n~L~P~i-k 67 (328)
.++-+.|+++||+.|...|..|-. . . |..|...+ |.|+.+..+.+-++.-.|-- +
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~L-p~R~~~siy~~~rR~y~~FE~~ 383 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLL-PYRDRKSIYHHLRRAYTPFENK 383 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhc-CcccchhHHHHHHhcCCccccc
Confidence 345589999999999999987621 1 1 56777778 67999998773333333322 9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKK 125 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkk 125 (328)
+|.||+||++.|..+|.++|+.|. .|+..| ||.+..|+.||+.+++..
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~---------~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWK---------EIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHH---------HHHHHH-ccCcHHHHHHHHHhhccc
Confidence 999999999999999999999998 999999 999999999999988765
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.51 E-value=8.7e-09 Score=105.72 Aligned_cols=107 Identities=28% Similarity=0.545 Sum_probs=89.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCC--CCCCCCCCHHHHHHHHHHHHHhCCCc
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRP--DIRRGRFSEEEERIIINLHSVLGNKY 90 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P--~ikkg~WT~EED~~Li~Lv~~~G~kW 90 (328)
-.+|.||+||++.|..++..+|. .|..|.+.++ |-+..||+||++|..+ .+++++|+.||+.+|...|.+.-..=
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred hhhccCccccccccccccccccc-hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 46899999999999999999995 9999999986 9999999999999998 67888999999999999987443211
Q ss_pred cccccchhHHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 91 FSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 91 ~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
.....|.|-.|+.+++.|....|+.++.....
T Consensus 366 -~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 366 -QQSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred -hhhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 12346777799999999999888887766544
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.84 E-value=7.7e-06 Score=61.21 Aligned_cols=49 Identities=12% Similarity=0.331 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---ccccccccccc-ccccccccccccc
Q 046075 14 KKGPWTPEEDQKLVDYIGRHGHGSW---NALPKLAGLNR-CGKSCRLRWTNYL 62 (328)
Q Consensus 14 kKg~WT~EEDe~L~~lV~k~G~~nW---~~IAk~lg~~R-t~kQCR~RW~n~L 62 (328)
++-.||+||..+++++|+.+|.++| +.|++.|+..| |..||+.+.+.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4668999999999999999998899 99999997667 9999999988764
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.53 E-value=3.3e-05 Score=77.77 Aligned_cols=99 Identities=17% Similarity=0.281 Sum_probs=66.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccccc-CCCCCCCCC-------CHHHHHHHHHH-
Q 046075 12 SLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYL-RPDIRRGRF-------SEEEERIIINL- 82 (328)
Q Consensus 12 ~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L-~P~ikkg~W-------T~EED~~Li~L- 82 (328)
.+-...||.+|+-.|++++..||.|||..||.++| .|++.+|+++|.+++ +..+-.-+| ...||.....-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~ 147 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNR 147 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhcccc
Confidence 45678899999999999999999999999999999 999999999999964 322222232 33454444433
Q ss_pred HHHhCCCc----cccccchhHHHHHhhCCCCCH
Q 046075 83 HSVLGNKY----FSFNMHIYSIEIIYHLPGRTD 111 (328)
Q Consensus 83 v~~~G~kW----~~i~~~I~w~~IA~~lpgRT~ 111 (328)
+..++.+- ......-.=++|+.+||+|.+
T Consensus 148 ~~~~~~~~~~pr~p~~~~p~~~e~~gyMp~R~d 180 (438)
T KOG0457|consen 148 AEPFQPTDLVPRKPGVSNPLRREISGYMPGRLD 180 (438)
T ss_pred cccCCCCCCCCCCCCCCCchHHHHhhhCccchh
Confidence 33333210 000011112388999999964
No 24
>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=97.21 E-value=0.00065 Score=52.15 Aligned_cols=60 Identities=17% Similarity=0.131 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCC-CCCHHHHHHHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLP-GRTDNEIKNFWNTHIRKKFL 127 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lp-gRT~~qcKnRW~~~Lkkkl~ 127 (328)
|.+||.|||..|++.|..+...-..+..+--|..++..-+ .+|-...|+||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 4689999999999999887655555677788889999988 99999999999998887654
No 25
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.19 E-value=0.00024 Score=73.12 Aligned_cols=60 Identities=17% Similarity=0.273 Sum_probs=54.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHhcCCCCC
Q 046075 66 IRRGRFSEEEERIIINLHSVLG-NKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQMGIDPI 134 (328)
Q Consensus 66 ikkg~WT~EED~~Li~Lv~~~G-~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~~p~ 134 (328)
++-|-|+.-||+.|-..|.+|| +.|+ +|++.++-.|+.||++||...|.+.+++..|...
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws---------~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~e 65 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWS---------RIASLLNRKTARQCKARWEEWLDPAIKKTEWSRE 65 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHH---------HHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhh
Confidence 5678999999999999999999 4677 9999999999999999999999999998887643
No 26
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.19 E-value=0.001 Score=49.79 Aligned_cols=46 Identities=13% Similarity=0.187 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Cc---cccccchhHHHHHhhCC-CC-CHHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLGN-KY---FSFNMHIYSIEIIYHLP-GR-TDNEIKNFWNTHI 122 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~-kW---~~i~~~I~w~~IA~~lp-gR-T~~qcKnRW~~~L 122 (328)
+-.||+||..+.++++..||. +| . .|++.|. .| |..||+.+...+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk---------~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPK---------RILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchH---------HHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999997 89 7 8999885 45 9999999887653
No 27
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.12 E-value=0.0028 Score=58.55 Aligned_cols=109 Identities=19% Similarity=0.320 Sum_probs=68.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccc--ccccccccccccccccc-CCCC--------------------CCCCCCH
Q 046075 17 PWTPEEDQKLVDYIGRHGHGSWNALPKLA--GLNRCGKSCRLRWTNYL-RPDI--------------------RRGRFSE 73 (328)
Q Consensus 17 ~WT~EEDe~L~~lV~k~G~~nW~~IAk~l--g~~Rt~kQCR~RW~n~L-~P~i--------------------kkg~WT~ 73 (328)
+|++++|-.|+.+|..-. +-..|+.-+ ...-|-.....||+..| +|.+ .+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999998765 455554433 22334455668888764 3332 3468999
Q ss_pred HHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Q 046075 74 EEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQ 128 (328)
Q Consensus 74 EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k 128 (328)
+||++|..........=.. ...|--..-+-+-++||+.++.++|..+.+..+..
T Consensus 79 ~EE~lL~~v~s~~~p~le~-Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL~ 132 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLET-FQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLLP 132 (199)
T ss_pred HHHHHHHhhhhccCCcHHH-HHHHHHhChhhhccccCHHHHHHHHHHHHHhchhh
Confidence 9999999976554332110 00000001112347899999999999766666554
No 28
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.05 E-value=0.00061 Score=53.35 Aligned_cols=61 Identities=23% Similarity=0.377 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHHH--hCCCc---cccccchhHHHHHhhC----CCCCHHHHHHHHHHHHHHHHHhc
Q 046075 68 RGRFSEEEERIIINLHSV--LGNKY---FSFNMHIYSIEIIYHL----PGRTDNEIKNFWNTHIRKKFLQM 129 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~--~G~kW---~~i~~~I~w~~IA~~l----pgRT~~qcKnRW~~~Lkkkl~k~ 129 (328)
|..||.+|...||+++.. +-... ........|..||..| ..||+.||++||.++ ++.+++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L-~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL-KKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH-HHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHHHHHH
Confidence 357999999999999987 21111 1223345678999998 469999999999885 5555554
No 29
>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=96.96 E-value=0.00096 Score=59.63 Aligned_cols=59 Identities=19% Similarity=0.209 Sum_probs=43.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCccc-cccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Q 046075 66 IRRGRFSEEEERIIINLHSVLGNKYFS-FNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQ 128 (328)
Q Consensus 66 ikkg~WT~EED~~Li~Lv~~~G~kW~~-i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k 128 (328)
.+...||.|||.+|.+.|-.|=..-++ ++ -...++..| +||+..|.-|||..+|+.+..
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~---AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLS---AFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHH---HHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 356789999999999999887432211 00 001667777 999999999999999988754
No 30
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.78 E-value=0.0021 Score=65.04 Aligned_cols=49 Identities=20% Similarity=0.402 Sum_probs=43.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CCccccccchhHHHHHhhCCCCCHHHHHHHHHHHH
Q 046075 65 DIRRGRFSEEEERIIINLHSVLG-NKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHI 122 (328)
Q Consensus 65 ~ikkg~WT~EED~~Li~Lv~~~G-~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~L 122 (328)
.+-...||.+||..|++++..|| .+|. .||.++..||..+||.+|.++.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~---------dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQ---------DIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHH---------HHHHHHcccchHHHHHHHHHHH
Confidence 44566899999999999999999 6677 9999999999999999997654
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.60 E-value=0.00072 Score=68.99 Aligned_cols=46 Identities=20% Similarity=0.510 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccc
Q 046075 14 KKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNY 61 (328)
Q Consensus 14 kKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 61 (328)
....||.+|..+|+++|+.||. +|.+||.++| +|+..||..|+.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 5679999999999999999996 9999999999 99999999999763
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.41 E-value=0.0013 Score=68.13 Aligned_cols=47 Identities=23% Similarity=0.539 Sum_probs=43.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccc
Q 046075 12 SLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTN 60 (328)
Q Consensus 12 ~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n 60 (328)
..-++.||.+|+-+|+++|++||. +|.+||.++| +|+..||..++.+
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLR 296 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHh
Confidence 346788999999999999999996 9999999998 9999999999876
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.14 E-value=0.0053 Score=62.83 Aligned_cols=45 Identities=11% Similarity=0.197 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTH 121 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~ 121 (328)
...||.+|..+|++.++.||..|. +||.|+..||..||--||-.+
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~---------kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWD---------KVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHH---------HHHHHhCCCCHHHHHHHHHcC
Confidence 358999999999999999999998 999999999999999999754
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.12 E-value=0.0013 Score=51.42 Aligned_cols=46 Identities=28% Similarity=0.663 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHHHHHHHh------C---C----CCcccccccc---cccccccccccccccc
Q 046075 16 GPWTPEEDQKLVDYIGRH------G---H----GSWNALPKLA---GLNRCGKSCRLRWTNY 61 (328)
Q Consensus 16 g~WT~EEDe~L~~lV~k~------G---~----~nW~~IAk~l---g~~Rt~kQCR~RW~n~ 61 (328)
-.||.+|...|++++... + . .-|..||..| |..|++.||+.||.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 479999999999998872 1 1 0399999876 6789999999999874
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.05 E-value=0.0074 Score=62.72 Aligned_cols=46 Identities=11% Similarity=0.255 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHH
Q 046075 67 RRGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTH 121 (328)
Q Consensus 67 kkg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~ 121 (328)
.++.||.+|..+|++.+..||.+|. +||.|+.+||..||--|+..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~---------kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWN---------KVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHH---------HHHhccCCCCHHHHHHHHHhc
Confidence 3568999999999999999999998 999999999999999988654
No 36
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.95 E-value=0.0085 Score=54.17 Aligned_cols=59 Identities=17% Similarity=0.150 Sum_probs=42.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHH
Q 046075 66 IRRGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFL 127 (328)
Q Consensus 66 ikkg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~ 127 (328)
.++..||.|||.+|.+.|-.|+..-..=-.. -..++..| +||..+|..|||..+++++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~a--fe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKA--FEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHH--HHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 4567899999999999998888654320000 01344445 89999999999999997653
No 37
>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=95.94 E-value=0.0028 Score=48.71 Aligned_cols=51 Identities=29% Similarity=0.530 Sum_probs=32.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------CC--cccccccccccccccccccccccccCCC
Q 046075 15 KGPWTPEEDQKLVDYIGRHGH------GS--WNALPKLAGLNRCGKSCRLRWTNYLRPD 65 (328)
Q Consensus 15 Kg~WT~EEDe~L~~lV~k~G~------~n--W~~IAk~lg~~Rt~kQCR~RW~n~L~P~ 65 (328)
+.++|.|||+.|+++|..+.. |+ |.++++.--..+|..+-|+||.+.|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 457999999999999966521 22 9999987623899999999999988764
No 38
>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=95.72 E-value=0.0031 Score=56.40 Aligned_cols=50 Identities=30% Similarity=0.676 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-C-----CcccccccccccccccccccccccccCC
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGH-G-----SWNALPKLAGLNRCGKSCRLRWTNYLRP 64 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~-~-----nW~~IAk~lg~~Rt~kQCR~RW~n~L~P 64 (328)
.+.-.||.|||.+|.+.|-+|=. | ...++++.++ ||+..|.-||..+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 46678999999999999999832 1 3888888885 9999999999988874
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.29 E-value=0.013 Score=57.80 Aligned_cols=48 Identities=17% Similarity=0.512 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccC
Q 046075 15 KGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLR 63 (328)
Q Consensus 15 Kg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 63 (328)
--.|+..|+-+|++.....|.|||.-||..+| .|+...|+.+|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 34599999999999999999999999999999 9999999999988665
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.23 E-value=0.096 Score=40.29 Aligned_cols=57 Identities=25% Similarity=0.227 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-----Ccc---ccccchhHHHHHhhC-----CCCCHHHHHHHHHHHHHH
Q 046075 68 RGRFSEEEERIIINLHSVLGN-----KYF---SFNMHIYSIEIIYHL-----PGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~-----kW~---~i~~~I~w~~IA~~l-----pgRT~~qcKnRW~~~Lkk 124 (328)
+..||.+|...|++++.+|.. .-. .....--|..|+..| +.||..++|.+|.++...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 457999999999999988731 110 001134466898886 369999999999887654
No 41
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.19 E-value=0.011 Score=53.40 Aligned_cols=50 Identities=24% Similarity=0.557 Sum_probs=39.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCC------cccccccccccccccccccccccccC
Q 046075 12 SLKKGPWTPEEDQKLVDYIGRHGHGS------WNALPKLAGLNRCGKSCRLRWTNYLR 63 (328)
Q Consensus 12 ~lkKg~WT~EEDe~L~~lV~k~G~~n------W~~IAk~lg~~Rt~kQCR~RW~n~L~ 63 (328)
..++..||.|||.+|.+.|-.|+... ...++..+ +|++.+|..||..+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 35778899999999999999987533 55555666 5999999999976655
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.02 E-value=0.014 Score=44.91 Aligned_cols=49 Identities=22% Similarity=0.463 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----ccccccccccccccccc
Q 046075 14 KKGPWTPEEDQKLVDYIGRHGH----------------GSWNALPKLA----GLNRCGKSCRLRWTNYL 62 (328)
Q Consensus 14 kKg~WT~EEDe~L~~lV~k~G~----------------~nW~~IAk~l----g~~Rt~kQCR~RW~n~L 62 (328)
++..||.+|.+.|+++|.+|.. .-|..|+..+ +..|+..+|+.+|.+..
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4678999999999999998821 1299999765 23799999999998754
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.05 E-value=0.2 Score=56.36 Aligned_cols=109 Identities=13% Similarity=0.244 Sum_probs=73.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcccccccccccccccccc-----------------------------------------
Q 046075 17 PWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCR----------------------------------------- 55 (328)
Q Consensus 17 ~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR----------------------------------------- 55 (328)
.|+..+=..++.+..+||..+-..||..|+ +++...++
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488888888899999999888889998885 66666554
Q ss_pred -------cccccc-c-CCCCCCCCCCHHHHHHHHHHHHHhC-CCccccccchhHHH---HHhhCCCCCHHHHHHHHHHHH
Q 046075 56 -------LRWTNY-L-RPDIRRGRFSEEEERIIINLHSVLG-NKYFSFNMHIYSIE---IIYHLPGRTDNEIKNFWNTHI 122 (328)
Q Consensus 56 -------~RW~n~-L-~P~ikkg~WT~EED~~Li~Lv~~~G-~kW~~i~~~I~w~~---IA~~lpgRT~~qcKnRW~~~L 122 (328)
.-|... + -+..++..+|.|||..|+-++.+|| ..|..|...|.-.- .-=++..||+.+|..|.+++|
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 112110 1 1233345699999999999999999 55762211110000 000146899999999999998
Q ss_pred HHHH
Q 046075 123 RKKF 126 (328)
Q Consensus 123 kkkl 126 (328)
+-..
T Consensus 985 ~~~~ 988 (1033)
T PLN03142 985 RLIE 988 (1033)
T ss_pred HHHH
Confidence 7643
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=91.93 E-value=0.17 Score=50.12 Aligned_cols=47 Identities=21% Similarity=0.348 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhC-CCccccccchhHHHHHhhCCCCCHHHHHHHHHHHH
Q 046075 67 RRGRFSEEEERIIINLHSVLG-NKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHI 122 (328)
Q Consensus 67 kkg~WT~EED~~Li~Lv~~~G-~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~L 122 (328)
--..|+.+|+.+|++....+| .+|. .||.+++.|+..+||.+|..+.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~---------dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWE---------DIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHH---------HHHHHHhhhhhHHHHHHHHHHH
Confidence 345799999999999999999 5677 9999999999999999997654
No 45
>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=91.15 E-value=0.33 Score=41.41 Aligned_cols=56 Identities=25% Similarity=0.350 Sum_probs=39.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----CccccccchhHHHHHhh--------CCCCCHHHHHHHHHHHHHHH
Q 046075 65 DIRRGRFSEEEERIIINLHSVLGN----KYFSFNMHIYSIEIIYH--------LPGRTDNEIKNFWNTHIRKK 125 (328)
Q Consensus 65 ~ikkg~WT~EED~~Li~Lv~~~G~----kW~~i~~~I~w~~IA~~--------lpgRT~~qcKnRW~~~Lkkk 125 (328)
..++..||++||..|+-++.+||- .|..|.. .|... +..||+.++..|-+++|+--
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~-----~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQ-----EIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHH-----HHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHH-----HHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 456778999999999999999997 5652221 22221 35899999999999998753
No 46
>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=90.57 E-value=0.9 Score=35.80 Aligned_cols=54 Identities=20% Similarity=0.202 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHHh---CCC-ccccccchhHHHHHhhCC-----CCCHHHHHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVL---GNK-YFSFNMHIYSIEIIYHLP-----GRTDNEIKNFWNTHIR 123 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~---G~k-W~~i~~~I~w~~IA~~lp-----gRT~~qcKnRW~~~Lk 123 (328)
.||+++++.|++++.+. |+. =...-..+-|..|+..|. ..|..||++||..+-+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 49999999999998554 332 011122567789999872 3578999999966543
No 47
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=89.89 E-value=0.35 Score=48.93 Aligned_cols=53 Identities=21% Similarity=0.306 Sum_probs=45.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhh-----CCC-CCHHHHHHHHHHHHHHHHHhcC
Q 046075 69 GRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYH-----LPG-RTDNEIKNFWNTHIRKKFLQMG 130 (328)
Q Consensus 69 g~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~-----lpg-RT~~qcKnRW~~~Lkkkl~k~~ 130 (328)
..||.+|-+.|++|++.|.=+|- .||.. ++. ||-.++|+||+...++-++...
T Consensus 131 n~WskeETD~LF~lck~fDLRf~---------VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFF---------VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEE---------EEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 56999999999999999999997 67776 555 9999999999999988776654
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=87.77 E-value=0.88 Score=44.61 Aligned_cols=60 Identities=17% Similarity=0.157 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCcc--ccccchhHHHHHhhC----CCCCHHHHHHHHHHHHHHHHHhc
Q 046075 68 RGRFSEEEERIIINLHSVLGNKYF--SFNMHIYSIEIIYHL----PGRTDNEIKNFWNTHIRKKFLQM 129 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~kW~--~i~~~I~w~~IA~~l----pgRT~~qcKnRW~~~Lkkkl~k~ 129 (328)
...|+.+|-..||++..++-.... .. ..=.|..||..| .-||+.|||+||.++.++ +++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~-k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~-Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKL-KGPLWEEVARKMAELGYPRSPKQCKAKIENLKKK-YKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhh-cccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH-HHHH
Confidence 368999999999998864311000 00 011244899865 359999999999886654 4443
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=86.72 E-value=0.9 Score=46.06 Aligned_cols=46 Identities=22% Similarity=0.293 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
+||.+|-++..++...+|..+. .||..+|.|...|||-+|..--|+
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~---------LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFS---------LISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHH---------HHHHhcCchhHHHHHHHHHHHhhh
Confidence 7999999999999999999998 999999999999999999765554
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=83.25 E-value=3 Score=43.20 Aligned_cols=48 Identities=13% Similarity=0.295 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 67 RRGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 67 kkg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
....||.||-.++-+++..||..+. +|.+.||.|+-..+..+|+..-|
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~---------kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFH---------KIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHH---------HHHHHccCccHHHHHHHHHHHHH
Confidence 3457999999999999999999998 99999999999999988876543
No 51
>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=79.86 E-value=1.2 Score=37.97 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=29.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 046075 11 RSLKKGPWTPEEDQKLVDYIGRHGH---GSWNALPKLA 45 (328)
Q Consensus 11 ~~lkKg~WT~EEDe~L~~lV~k~G~---~nW~~IAk~l 45 (328)
+.-++..||.+||.-|+-.+.+||. +.|..|...+
T Consensus 45 ~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 45 PNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp STSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 3677899999999999999999999 8999998765
No 52
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=75.59 E-value=2.7 Score=33.60 Aligned_cols=25 Identities=40% Similarity=0.728 Sum_probs=14.8
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCC
Q 046075 11 RSLKKGPWTPEEDQKL--------VDYIGRHGH 35 (328)
Q Consensus 11 ~~lkKg~WT~EEDe~L--------~~lV~k~G~ 35 (328)
|.--.|-||+|+|+.| .+++++||.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 3445889999999999 556778873
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=75.19 E-value=1.7 Score=44.07 Aligned_cols=64 Identities=17% Similarity=0.308 Sum_probs=50.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccc--cCCC-----C-CCCCCCHHHHHH
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNY--LRPD-----I-RRGRFSEEEERI 78 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~--L~P~-----i-kkg~WT~EED~~ 78 (328)
..--+||.+|-++..++....|. ++..|+.++ |+|..+|+...|.+- .+|. + .+.++..+|-.+
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lf-P~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k 434 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGT-DFSLISSLF-PNRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNK 434 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcc-hHHHHHHhc-CchhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhh
Confidence 34457999999999999999997 999999999 899999999998763 2331 1 245777777643
No 54
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=75.16 E-value=6.6 Score=27.74 Aligned_cols=42 Identities=29% Similarity=0.327 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 73 EEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 73 ~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
++++..++.++...|-.+. +||..+ |.|...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~---------eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYA---------EIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HH---------HHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHH---------HHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4677888999888898888 999999 99999999988766543
No 55
>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=71.17 E-value=2.1 Score=33.70 Aligned_cols=44 Identities=32% Similarity=0.675 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Ccccccccc----ccccccccccccccc
Q 046075 17 PWTPEEDQKLVDYIGRH---GHG---------SWNALPKLA----GLNRCGKSCRLRWTN 60 (328)
Q Consensus 17 ~WT~EEDe~L~~lV~k~---G~~---------nW~~IAk~l----g~~Rt~kQCR~RW~n 60 (328)
.||+++++.|++++... |.. .|..|++.+ |...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988544 221 288888655 345667788888754
No 56
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=71.09 E-value=1.7 Score=42.59 Aligned_cols=47 Identities=23% Similarity=0.532 Sum_probs=36.8
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC-----CCcccccccc---cccccccccccccccc
Q 046075 15 KGPWTPEEDQKLVDYIGRH----GH-----GSWNALPKLA---GLNRCGKSCRLRWTNY 61 (328)
Q Consensus 15 Kg~WT~EEDe~L~~lV~k~----G~-----~nW~~IAk~l---g~~Rt~kQCR~RW~n~ 61 (328)
-..|+.+|-..|+++..+- .. ..|..||+.+ |..|++.||+.+|.+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl 112 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENL 112 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 3789999999999987542 11 2499999843 6689999999999773
No 57
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=69.13 E-value=8.5 Score=42.18 Aligned_cols=56 Identities=7% Similarity=0.124 Sum_probs=45.0
Q ss_pred ccccccCCCCC---CCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHH
Q 046075 57 RWTNYLRPDIR---RGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTH 121 (328)
Q Consensus 57 RW~n~L~P~ik---kg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~ 121 (328)
||+.|+--+.. ...||+.|-.+.-++...|..++- +|++.++++|-.||-.+|++.
T Consensus 605 ~~~~h~la~Y~Y~gSd~WTp~E~~lF~kA~y~~~KDF~---------~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 605 RLKCHPLANYHYAGSDKWTPLERKLFNKALYTYSKDFI---------FVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred CccccccceeeecCcccccHHHHHHHHHHHHHhcccHH---------HHHHHhccccHHHHHHHHHHH
Confidence 45554433322 458999999999999999999987 999999999999998887654
No 58
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=59.02 E-value=16 Score=39.27 Aligned_cols=56 Identities=13% Similarity=0.409 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhh----------CCCCCHHHHHHHHHHHHHHHHHhcCCCC
Q 046075 68 RGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYH----------LPGRTDNEIKNFWNTHIRKKFLQMGIDP 133 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~----------lpgRT~~qcKnRW~~~Lkkkl~k~~~~p 133 (328)
|..||.+|+.-...+.+++|.++. +|-.. ..-+|..|+|.+|+..+++..+-. |.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe---------~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~-F~~ 153 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFE---------KVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLL-FGP 153 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHH---------HHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhh-ccc
Confidence 568999999999999999999997 55222 234688899999999888765544 544
No 59
>smart00595 MADF subfamily of SANT domain.
Probab=58.96 E-value=10 Score=29.44 Aligned_cols=24 Identities=25% Similarity=0.117 Sum_probs=20.1
Q ss_pred hHHHHHhhCCCCCHHHHHHHHHHHH
Q 046075 98 YSIEIIYHLPGRTDNEIKNFWNTHI 122 (328)
Q Consensus 98 ~w~~IA~~lpgRT~~qcKnRW~~~L 122 (328)
-|..||..|.. |..+|+.+|+++-
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~LR 52 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHHH
Confidence 46699999955 9999999998764
No 60
>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=56.26 E-value=3.5 Score=28.75 Aligned_cols=38 Identities=24% Similarity=0.366 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCccccccccccccccccccccccc
Q 046075 21 EEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTN 60 (328)
Q Consensus 21 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n 60 (328)
+=|.+|+.+.+..|...|.+||+.+| =+...|+.|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 45889999999999999999999997 777888888753
No 61
>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=52.92 E-value=30 Score=24.08 Aligned_cols=41 Identities=24% Similarity=0.347 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 74 EEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 74 EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
+++..++.++-..|-.+. .||..| |-|...|+.+-...+++
T Consensus 7 ~~er~vi~~~y~~~~t~~---------eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLE---------EIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHH---------HHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHH---------HHHHHH-CCcHHHHHHHHHHHHHH
Confidence 456667777665555666 999999 88999999988877754
No 62
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=52.05 E-value=18 Score=41.90 Aligned_cols=71 Identities=21% Similarity=0.303 Sum_probs=47.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHh-CCCcc
Q 046075 14 KKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIRRGRFSEEEERIIINLHSVL-GNKYF 91 (328)
Q Consensus 14 kKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ikkg~WT~EED~~Li~Lv~~~-G~kW~ 91 (328)
.-.-|..+||..|+-.|-+||.++|..|-.--.++=+.+ ..+...+-.+.+=..+-..|+.+...+ +.+|.
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~ 1203 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTP 1203 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCCCc
Confidence 556799999999999999999999999953111111111 111111345566677777788777776 56665
No 63
>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=51.72 E-value=15 Score=29.32 Aligned_cols=17 Identities=24% Similarity=0.550 Sum_probs=10.2
Q ss_pred CCCCCCCCCHHHHHHHH
Q 046075 64 PDIRRGRFSEEEERIII 80 (328)
Q Consensus 64 P~ikkg~WT~EED~~Li 80 (328)
|....|-||+|+|..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 66678899999999994
No 64
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=51.25 E-value=5.2 Score=34.69 Aligned_cols=46 Identities=13% Similarity=0.184 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCC
Q 046075 20 PEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDIR 67 (328)
Q Consensus 20 ~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ik 67 (328)
.+-|.+|+.+.++.|.-.|.+||+.+| -+...|+.|+.+....++-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 357999999999999999999999997 8999999999876655443
No 65
>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=48.52 E-value=17 Score=32.46 Aligned_cols=40 Identities=18% Similarity=0.185 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWN 119 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~ 119 (328)
.||+|+.++|.+|..+ |-.-+ +||..|.|.|.+.|.-+-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~Sas---------qIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSAS---------QIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHH---------HHHHHhCCcchhhhhhhhh
Confidence 5999999999999754 55445 9999998899988865443
No 66
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=46.48 E-value=5.5 Score=35.00 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=39.1
Q ss_pred CHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCC
Q 046075 19 TPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDI 66 (328)
Q Consensus 19 T~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~i 66 (328)
-.+-|.+|+.+.++.|.-.|.+||+.+| -+...|+.|+.+..+.++
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 3567999999999999999999999997 888899999987665544
No 67
>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=45.36 E-value=96 Score=31.13 Aligned_cols=54 Identities=24% Similarity=0.470 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Q 046075 68 RGRFSEEEERIIINLHSVL-GNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQ 128 (328)
Q Consensus 68 kg~WT~EED~~Li~Lv~~~-G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k 128 (328)
-..||.-|...|+.+.... |... +--..|++.++||+..+|++.- ..||.++.+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~e------pd~ael~~~l~~Rs~aEI~~fl-~~LK~rvar 75 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPE------PDAAELAKELPGRSEAEIRDFL-QQLKGRVAR 75 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCC------cCHHHHHhhccCcCHHHHHHHH-HHHHHHHHH
Confidence 3479999999888887654 4433 3334899999999999999865 445555544
No 68
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=45.11 E-value=35 Score=31.81 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhC---CCCCHHHHHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHL---PGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~l---pgRT~~qcKnRW~~~Lk 123 (328)
.|++++|-.|+.+|.. |+.-. .|+..+ -.-|-.+|..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~---------~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLE---------SVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHH---------HHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999999865 33332 344433 24688999999999884
No 69
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=43.29 E-value=22 Score=38.37 Aligned_cols=49 Identities=16% Similarity=0.343 Sum_probs=36.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccc---------ccccccccccccccccC
Q 046075 14 KKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAG---------LNRCGKSCRLRWTNYLR 63 (328)
Q Consensus 14 kKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg---------~~Rt~kQCR~RW~n~L~ 63 (328)
+|..||..|.+-...+++.+|. +..+|-..+- --++..|.|.+|++.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 3678999999999999999995 9998833221 13566678888776543
No 70
>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=42.25 E-value=48 Score=27.36 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=20.4
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHHHH
Q 046075 101 EIIYHLPGRTDNEIKNFWNTHIRKKFL 127 (328)
Q Consensus 101 ~IA~~lpgRT~~qcKnRW~~~Lkkkl~ 127 (328)
.||..+ |.+...|+.+....+ ++++
T Consensus 134 eIA~~l-gis~~tv~~~~~ra~-~~Lr 158 (161)
T TIGR02985 134 EIAEEL-GISVKTVEYHISKAL-KELR 158 (161)
T ss_pred HHHHHH-CCCHHHHHHHHHHHH-HHHH
Confidence 999998 899999999998754 4444
No 71
>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=39.13 E-value=36 Score=25.47 Aligned_cols=25 Identities=20% Similarity=0.167 Sum_probs=19.5
Q ss_pred HHHHHhhCCC-CCHHHHHHHHHHHHH
Q 046075 99 SIEIIYHLPG-RTDNEIKNFWNTHIR 123 (328)
Q Consensus 99 w~~IA~~lpg-RT~~qcKnRW~~~Lk 123 (328)
|..||..|.. -+..+|+.||.++..
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHH
Confidence 4599999953 578899999987554
No 72
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=36.47 E-value=32 Score=36.87 Aligned_cols=48 Identities=17% Similarity=0.259 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 67 RRGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 67 kkg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
..++|+.+|-++-.....+.|.+.+ .|+..+|+|+..|||-++..--+
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~s---------lis~l~p~R~rk~iK~K~~~eE~ 455 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFS---------LISNLFPLRDRKQIKAKFKKEEK 455 (584)
T ss_pred ccCcccchhhHHhhhHHhhhccccc---------ccccccccccHHHHHHHHhhhhh
Confidence 4568999999999999999999998 89999999999999998855433
No 73
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=36.42 E-value=16 Score=37.43 Aligned_cols=50 Identities=18% Similarity=0.268 Sum_probs=42.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccc-----cccccccccccccccccc
Q 046075 12 SLKKGPWTPEEDQKLVDYIGRHGHGSWNALPKL-----AGLNRCGKSCRLRWTNYL 62 (328)
Q Consensus 12 ~lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~-----lg~~Rt~kQCR~RW~n~L 62 (328)
.+.-..||++|-+.|.+++++|-- .|-.||.. .+..||-....+||..+.
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 355578999999999999999996 99999976 654599999999997653
No 74
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=33.43 E-value=18 Score=39.72 Aligned_cols=44 Identities=14% Similarity=0.237 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccc
Q 046075 15 KGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTN 60 (328)
Q Consensus 15 Kg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n 60 (328)
...||+.|-.+..+++-.|.. ++..|++.+ ++++.+||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~km~-~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQKMV-KSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHHHHh-ccccHHHHHHHHHH
Confidence 346999999999999999995 999999999 69999999887754
No 75
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=31.66 E-value=1e+02 Score=26.31 Aligned_cols=23 Identities=22% Similarity=0.333 Sum_probs=18.9
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 100 IEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
..||..| |.+...|+.|....++
T Consensus 138 ~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 138 AQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred HHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3899999 9999999999875553
No 76
>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=30.41 E-value=23 Score=24.28 Aligned_cols=30 Identities=27% Similarity=0.379 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccc
Q 046075 21 EEDQKLVDYIGRHGHGSWNALPKLAGLNRCG 51 (328)
Q Consensus 21 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~ 51 (328)
-|.+.|.++...++ ++..+.|+.+|..|+.
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~~Lgisr~t 34 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAARLLGISRRT 34 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHCCCHHH
Confidence 37788889999998 5999999999866643
No 77
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.26 E-value=1.2e+02 Score=26.69 Aligned_cols=31 Identities=13% Similarity=0.071 Sum_probs=22.5
Q ss_pred HHHHhhCCCCCHHHHHHHHHH---HHHHHHHhcCC
Q 046075 100 IEIIYHLPGRTDNEIKNFWNT---HIRKKFLQMGI 131 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~---~Lkkkl~k~~~ 131 (328)
..||..| |-+...|+.|... .|++.+.+..+
T Consensus 156 ~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 156 DEIQQMC-GISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3899999 9999999988875 44455544444
No 78
>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=30.08 E-value=80 Score=24.66 Aligned_cols=46 Identities=9% Similarity=-0.030 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCccccccchhHHHHHhhCCCC---C--HHHHHHHHHHHHH
Q 046075 77 RIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGR---T--DNEIKNFWNTHIR 123 (328)
Q Consensus 77 ~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgR---T--~~qcKnRW~~~Lk 123 (328)
-+|..+|...|.- ..|...-.|..||..|.-- + ..++|..|..+|.
T Consensus 39 ~~Ly~~V~~~GG~-~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGF-DKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSH-HHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCc-ccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 3578888888852 1222233355999998321 2 3688999988774
No 79
>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=29.38 E-value=88 Score=27.70 Aligned_cols=46 Identities=20% Similarity=0.192 Sum_probs=35.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCC----CCCHHHHHHHHHHH
Q 046075 67 RRGRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLP----GRTDNEIKNFWNTH 121 (328)
Q Consensus 67 kkg~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lp----gRT~~qcKnRW~~~ 121 (328)
....-|..|...|..|+.+||.++. .+|.-.. =.|..||+.+....
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~---------aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYK---------AMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHH---------HHhccCCCCcccCCHHHHHHHHHHh
Confidence 3446889999999999999999987 6665432 37999998877654
No 80
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=28.80 E-value=77 Score=28.91 Aligned_cols=44 Identities=25% Similarity=0.299 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 69 GRFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 69 g~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
...|+.|-+.|.-+.+=+.++ .||..| +++...||+|..++++|
T Consensus 147 ~~LT~RE~eVL~lla~G~snk-----------eIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLSNK-----------EIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHCCCCHH-----------HHHHHH-CCCHhHHHHHHHHHHHH
Confidence 368998888877666544443 899999 99999999999888765
No 81
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=27.99 E-value=1.2e+02 Score=26.79 Aligned_cols=23 Identities=13% Similarity=0.111 Sum_probs=18.8
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 100 IEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
.+||..| |-+...|+.|+....+
T Consensus 154 ~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 154 ADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred HHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3999999 8999999999955443
No 82
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.03 E-value=1.5e+02 Score=25.37 Aligned_cols=30 Identities=17% Similarity=0.341 Sum_probs=23.7
Q ss_pred HHHhhCCCCCHHHHHHHHHHHHHHHHHhcCC
Q 046075 101 EIIYHLPGRTDNEIKNFWNTHIRKKFLQMGI 131 (328)
Q Consensus 101 ~IA~~lpgRT~~qcKnRW~~~Lkkkl~k~~~ 131 (328)
.||..| |.+...|+.+-...+++-....+.
T Consensus 140 EIA~~l-gis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 140 EIAERL-GVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred HHHHHH-CCCHHHHHHHHHHHHHHHHHHhcC
Confidence 999999 999999999988777665444443
No 83
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=26.86 E-value=43 Score=38.31 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=28.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccc
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLA 45 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~l 45 (328)
-++..+|.|||..|+-.+.+||.++|.+|-..+
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 345569999999999999999999999997655
No 84
>smart00351 PAX Paired Box domain.
Probab=26.61 E-value=1.1e+02 Score=25.88 Aligned_cols=73 Identities=14% Similarity=0.124 Sum_probs=47.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccc-cccccccccc--ccCCCCC----CCCCCHHHHHHHHHHHHH
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGLNRC-GKSCRLRWTN--YLRPDIR----RGRFSEEEERIIINLHSV 85 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt-~kQCR~RW~n--~L~P~ik----kg~WT~EED~~Li~Lv~~ 85 (328)
.+..+.+.++-++++.++. -|. .-.+||+.+|..|. ...+..||.. .+.|... ...=+.+++..|++++.+
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 4456699999999998886 454 78999999985443 4445666654 3455322 223566666777766665
Q ss_pred hC
Q 046075 86 LG 87 (328)
Q Consensus 86 ~G 87 (328)
.+
T Consensus 91 ~p 92 (125)
T smart00351 91 NP 92 (125)
T ss_pred CC
Confidence 44
No 85
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=26.02 E-value=82 Score=27.20 Aligned_cols=46 Identities=11% Similarity=0.032 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Q 046075 74 EEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRKKFLQ 128 (328)
Q Consensus 74 EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k 128 (328)
+-|.+|+.+..+-|. ++|+.||+.+ |-+...|+.|+..+....+.+
T Consensus 9 ~~D~~Il~~Lq~d~R--------~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 9 NLDRGILEALMENAR--------TPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHHcCC--------CCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 568888888877653 3344999999 999999999998777666544
No 86
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.03 E-value=1.6e+02 Score=24.78 Aligned_cols=24 Identities=8% Similarity=-0.114 Sum_probs=18.9
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 99 SIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 99 w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
...||..| |-+...|++|....++
T Consensus 125 ~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 125 YQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34899999 9999999998765443
No 87
>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=24.89 E-value=1.8e+02 Score=23.11 Aligned_cols=24 Identities=25% Similarity=0.181 Sum_probs=18.9
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 100 IEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
..||+.+ |-+...|+.+....+++
T Consensus 130 ~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 130 KEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3999999 66999999888775543
No 88
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=23.77 E-value=1.8e+02 Score=25.13 Aligned_cols=28 Identities=7% Similarity=0.046 Sum_probs=21.5
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Q 046075 100 IEIIYHLPGRTDNEIKNFWNTHIRKKFLQ 128 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~~Lkkkl~k 128 (328)
..||..| |-+...|+.+....+++--..
T Consensus 151 ~eIA~~l-~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 151 KETAAKL-SMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred HHHHHHh-CCCHHHHHHHHHHHHHHHHHH
Confidence 3899999 999999999987766554333
No 89
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=23.63 E-value=54 Score=29.07 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=34.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCcccccccccc---ccccccccccccc
Q 046075 13 LKKGPWTPEEDQKLVDYIGRHGHGSWNALPKLAGL---NRCGKSCRLRWTN 60 (328)
Q Consensus 13 lkKg~WT~EEDe~L~~lV~k~G~~nW~~IAk~lg~---~Rt~kQCR~RW~n 60 (328)
.+..+=|..|..-|..+|.+||. ++...+.-..+ ..|..||+.+...
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 56677899999999999999996 88888753321 3556666655443
No 90
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=23.53 E-value=1.3e+02 Score=24.68 Aligned_cols=50 Identities=16% Similarity=0.100 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----CccccccchhHHHHHhhCCC-CCHHHHHHHHHHHHH
Q 046075 69 GRFSEEEERIIINLHSVL----GN----KYFSFNMHIYSIEIIYHLPG-RTDNEIKNFWNTHIR 123 (328)
Q Consensus 69 g~WT~EED~~Li~Lv~~~----G~----kW~~i~~~I~w~~IA~~lpg-RT~~qcKnRW~~~Lk 123 (328)
.-||+++|..|++.+..| |. .+.. ....|...+.. =+..|+.++-+.+-+
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~-----f~~~vk~~l~~~~s~~Ql~~KirrLK~ 63 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNA-----FYDFVKGSLSFDVSKNQLYDKIRRLKK 63 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHH-----HHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 369999999999998776 52 2221 11133344422 377888888766443
No 91
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=23.27 E-value=1.3e+02 Score=25.29 Aligned_cols=24 Identities=21% Similarity=0.077 Sum_probs=19.0
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 99 SIEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 99 w~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
...||..| |-+...|+.+.....+
T Consensus 144 ~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 144 YREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34999999 8899999998876443
No 92
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.10 E-value=1.6e+02 Score=24.81 Aligned_cols=23 Identities=13% Similarity=-0.018 Sum_probs=18.6
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHH
Q 046075 100 IEIIYHLPGRTDNEIKNFWNTHIR 123 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~~Lk 123 (328)
..||..| |.+...|+.+....++
T Consensus 148 ~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 148 EEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred HHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3999999 8899999988775443
No 93
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=22.73 E-value=99 Score=24.73 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHH
Q 046075 76 ERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEI 114 (328)
Q Consensus 76 D~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qc 114 (328)
|+.|..+....|..|. .+|.+| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~---------~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWE---------QVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHH---------HHHHHc-CCCHHHH
Confidence 5678899999999998 888888 5444443
No 94
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=22.55 E-value=92 Score=22.29 Aligned_cols=43 Identities=21% Similarity=0.247 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
..|+.|-+.|.-+..- ..-. .||..+ |.+...|+.+...+.+|
T Consensus 3 ~LT~~E~~vl~~l~~G--~~~~---------eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG--MSNK---------EIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTT--S-HH---------HHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhc--CCcc---------hhHHhc-CcchhhHHHHHHHHHHH
Confidence 3566676665555433 3333 899999 99999999888776554
No 95
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=22.40 E-value=1.2e+02 Score=22.16 Aligned_cols=35 Identities=26% Similarity=0.422 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHH
Q 046075 74 EEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFW 118 (328)
Q Consensus 74 EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW 118 (328)
++|+-.+.+....|-.-. .||+.+ ||+.+.|+++-
T Consensus 7 ~~Eqaqid~m~qlG~s~~---------~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLR---------EISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HH---------HHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHH---------HHHHHh-CccHHHHHHHh
Confidence 456666777788888776 899999 99998887653
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=20.79 E-value=39 Score=26.96 Aligned_cols=43 Identities=19% Similarity=0.195 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCC
Q 046075 21 EEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPD 65 (328)
Q Consensus 21 EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~ 65 (328)
+.|.+++.+....|...+..||+.+| -+...|+.|.......+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 56889999999998889999999996 77788888776654443
No 97
>PRK04217 hypothetical protein; Provisional
Probab=20.73 E-value=2.1e+02 Score=24.16 Aligned_cols=44 Identities=16% Similarity=0.039 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 70 RFSEEEERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 70 ~WT~EED~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
.-|.+| ..++.+....|-... .||+.+ |.+...|+.++....++
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~---------EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQE---------EAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHH---------HHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455666 577777777777776 999999 99999999999875544
No 98
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.48 E-value=33 Score=28.96 Aligned_cols=45 Identities=11% Similarity=0.129 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCC
Q 046075 20 PEEDQKLVDYIGRHGHGSWNALPKLAGLNRCGKSCRLRWTNYLRPDI 66 (328)
Q Consensus 20 ~EEDe~L~~lV~k~G~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~i 66 (328)
.+-|.+++++.++.+...+..||+.+| -+...|+.|-.+..+.++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 356889999999999889999999997 888889888766555443
No 99
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.24 E-value=2.3e+02 Score=25.02 Aligned_cols=36 Identities=19% Similarity=0.220 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHHH
Q 046075 77 RIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTHI 122 (328)
Q Consensus 77 ~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~L 122 (328)
..++.+....|-.+. +||..| |-+...|+.+|...-
T Consensus 141 ~~~v~l~~~~Gls~~---------EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVE---------EIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHH---------HHHHHH-CcCHHHHHHHHHHHH
Confidence 334444444566665 999999 999999999997654
No 100
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.23 E-value=1.9e+02 Score=24.10 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=19.4
Q ss_pred HHHHhhCCCCCHHHHHHHHHHHHHH
Q 046075 100 IEIIYHLPGRTDNEIKNFWNTHIRK 124 (328)
Q Consensus 100 ~~IA~~lpgRT~~qcKnRW~~~Lkk 124 (328)
..||..| |-+...|+.|....+++
T Consensus 126 ~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 126 AETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3999999 88999999988765543
No 101
>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=20.07 E-value=2.3e+02 Score=18.32 Aligned_cols=36 Identities=28% Similarity=0.260 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCCCccccccchhHHHHHhhCCCCCHHHHHHHHHHH
Q 046075 76 ERIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGRTDNEIKNFWNTH 121 (328)
Q Consensus 76 D~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgRT~~qcKnRW~~~ 121 (328)
+..++.++..-|-.+. .||..+ |-+...|+.+....
T Consensus 15 ~~~~~~~~~~~~~~~~---------~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 15 EREVILLRFGEGLSYE---------EIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHhcCCCHH---------HHHHHH-CcCHHHHHHHHHHH
Confidence 4555555555555555 899998 77777776665443
No 102
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=20.05 E-value=1.8e+02 Score=22.89 Aligned_cols=47 Identities=11% Similarity=-0.009 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCCCccccccchhHHHHHhhCCCC-----CHHHHHHHHHHHHHH
Q 046075 77 RIIINLHSVLGNKYFSFNMHIYSIEIIYHLPGR-----TDNEIKNFWNTHIRK 124 (328)
Q Consensus 77 ~~Li~Lv~~~G~kW~~i~~~I~w~~IA~~lpgR-----T~~qcKnRW~~~Lkk 124 (328)
-+|..+|.++|.--. +...-.|..||..|.-. ...++|..|..+|..
T Consensus 35 ~~Ly~~V~~~GG~~~-v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 35 YRLYRLVQERGGYDQ-VTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHHccCHHH-HcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 357788888885322 22223366999998433 457888888887764
Done!