Query 045411
Match_columns 389
No_of_seqs 295 out of 1397
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 12:58:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 3.6E-36 7.7E-41 286.2 9.7 122 1-122 10-131 (249)
2 PLN03091 hypothetical protein; 100.0 4E-35 8.6E-40 296.6 13.6 121 3-123 1-121 (459)
3 KOG0048 Transcription factor, 100.0 3.9E-34 8.5E-39 271.4 9.4 111 12-122 5-115 (238)
4 KOG0049 Transcription factor, 99.8 1.9E-19 4.2E-24 188.6 6.0 113 4-117 348-461 (939)
5 KOG0049 Transcription factor, 99.7 1.8E-18 3.9E-23 181.5 7.0 123 7-129 244-421 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 4.4E-16 9.5E-21 117.7 3.6 60 19-80 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.5 5.6E-15 1.2E-19 154.1 6.3 107 12-119 16-122 (512)
8 KOG0050 mRNA splicing protein 99.5 6.3E-15 1.4E-19 152.1 2.7 108 14-123 5-112 (617)
9 PF13921 Myb_DNA-bind_6: Myb-l 99.4 5.7E-13 1.2E-17 100.7 5.0 58 72-129 1-58 (60)
10 KOG0051 RNA polymerase I termi 99.4 3.6E-13 7.8E-18 142.2 5.3 103 15-120 383-513 (607)
11 PF00249 Myb_DNA-binding: Myb- 99.3 1.2E-12 2.5E-17 95.6 4.8 46 69-114 1-48 (48)
12 PF00249 Myb_DNA-binding: Myb- 99.3 3E-13 6.5E-18 98.7 0.9 48 16-63 1-48 (48)
13 PLN03212 Transcription repress 99.3 2.2E-12 4.9E-17 123.9 6.0 78 46-131 10-89 (249)
14 KOG0048 Transcription factor, 99.2 1.6E-11 3.5E-16 117.1 5.0 66 65-130 5-72 (238)
15 PLN03091 hypothetical protein; 99.2 1.9E-11 4.1E-16 125.3 5.4 65 65-129 10-76 (459)
16 smart00717 SANT SANT SWI3, AD 99.2 4.4E-11 9.6E-16 84.0 5.5 47 69-115 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 3.9E-10 8.5E-15 78.2 5.3 44 71-114 1-45 (45)
18 smart00717 SANT SANT SWI3, AD 99.0 2.1E-10 4.6E-15 80.5 2.2 48 16-64 1-48 (49)
19 KOG0051 RNA polymerase I termi 98.9 2.1E-09 4.6E-14 114.1 5.2 117 14-132 306-448 (607)
20 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 1.6E-09 3.4E-14 75.1 1.8 45 18-63 1-45 (45)
21 COG5147 REB1 Myb superfamily p 98.2 1.8E-07 3.9E-12 98.5 -2.3 99 13-114 288-396 (512)
22 KOG0050 mRNA splicing protein 97.6 2.4E-05 5.1E-10 82.2 2.3 64 67-130 5-69 (617)
23 TIGR01557 myb_SHAQKYF myb-like 97.5 5E-05 1.1E-09 58.4 2.3 49 15-63 2-54 (57)
24 KOG0457 Histone acetyltransfer 97.5 0.00012 2.7E-09 75.6 5.5 50 66-115 69-119 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.5 0.00029 6.2E-09 54.2 5.6 47 69-115 3-55 (57)
26 KOG0457 Histone acetyltransfer 97.4 5.9E-05 1.3E-09 77.9 1.9 50 13-63 69-118 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.0 0.00064 1.4E-08 62.4 3.7 53 68-121 3-62 (161)
28 PF13325 MCRS_N: N-terminal re 96.9 0.0016 3.5E-08 61.7 5.7 100 18-119 1-131 (199)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0011 2.3E-08 53.2 2.8 51 69-119 1-69 (90)
30 COG5259 RSC8 RSC chromatin rem 96.6 0.00077 1.7E-08 70.5 1.3 46 15-62 278-323 (531)
31 KOG1279 Chromatin remodeling f 96.5 0.0011 2.5E-08 70.3 1.7 48 13-62 250-297 (506)
32 KOG1279 Chromatin remodeling f 96.4 0.0039 8.5E-08 66.3 5.1 47 68-114 252-298 (506)
33 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.005 1.1E-07 48.6 4.3 51 69-119 2-62 (65)
34 COG5259 RSC8 RSC chromatin rem 96.3 0.0037 7.9E-08 65.6 4.3 45 69-113 279-323 (531)
35 PRK13923 putative spore coat p 95.7 0.0091 2E-07 55.4 3.2 52 67-119 3-61 (170)
36 PF08914 Myb_DNA-bind_2: Rap1 95.4 0.0063 1.4E-07 48.0 1.1 52 16-67 2-61 (65)
37 TIGR02894 DNA_bind_RsfA transc 95.3 0.0072 1.6E-07 55.6 1.1 50 14-65 2-57 (161)
38 COG5114 Histone acetyltransfer 95.2 0.018 3.9E-07 58.3 3.7 47 69-115 63-110 (432)
39 PF13837 Myb_DNA-bind_4: Myb/S 95.0 0.0051 1.1E-07 49.2 -0.5 48 16-63 1-64 (90)
40 PF13873 Myb_DNA-bind_5: Myb/S 94.9 0.053 1.1E-06 42.8 4.9 48 69-116 2-71 (78)
41 PLN03142 Probable chromatin-re 94.6 0.059 1.3E-06 62.0 6.2 99 18-117 826-987 (1033)
42 COG5114 Histone acetyltransfer 93.9 0.02 4.3E-07 58.0 0.5 50 14-64 61-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 93.7 0.041 8.8E-07 43.4 1.9 49 15-63 1-69 (78)
44 PRK13923 putative spore coat p 93.0 0.03 6.5E-07 52.0 0.1 50 13-64 2-57 (170)
45 KOG2656 DNA methyltransferase 91.3 0.2 4.2E-06 52.0 3.7 86 38-124 75-191 (445)
46 KOG4282 Transcription factor G 89.8 0.34 7.5E-06 48.6 4.0 49 69-117 54-116 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 89.7 0.65 1.4E-05 37.5 4.8 46 71-116 1-64 (96)
48 PF09111 SLIDE: SLIDE; InterP 89.5 0.62 1.3E-05 40.9 4.7 51 66-116 46-112 (118)
49 COG5118 BDP1 Transcription ini 88.6 0.62 1.3E-05 48.4 4.7 46 71-116 367-412 (507)
50 KOG1194 Predicted DNA-binding 83.2 1.7 3.8E-05 46.1 4.9 50 68-117 186-235 (534)
51 PF08281 Sigma70_r4_2: Sigma-7 81.2 2.9 6.4E-05 30.4 4.2 41 74-115 12-52 (54)
52 PF11626 Rap1_C: TRF2-interact 76.9 1.8 3.9E-05 35.5 2.1 30 12-44 43-80 (87)
53 PF09111 SLIDE: SLIDE; InterP 76.5 1.9 4.2E-05 37.8 2.3 34 13-46 46-82 (118)
54 KOG4282 Transcription factor G 74.5 1.9 4E-05 43.4 1.9 48 16-63 54-113 (345)
55 smart00595 MADF subfamily of S 73.0 3.6 7.9E-05 32.8 3.0 25 91-116 30-54 (89)
56 PF13404 HTH_AsnC-type: AsnC-t 66.8 9.2 0.0002 27.5 3.6 38 75-113 3-41 (42)
57 PRK11179 DNA-binding transcrip 65.9 9.8 0.00021 33.9 4.5 46 74-120 8-54 (153)
58 PF13404 HTH_AsnC-type: AsnC-t 64.1 2.7 5.9E-05 30.3 0.4 38 22-61 3-40 (42)
59 COG5118 BDP1 Transcription ini 60.7 4.6 0.0001 42.2 1.5 44 16-61 365-408 (507)
60 PRK11169 leucine-responsive tr 59.5 13 0.00027 33.6 4.0 46 74-120 13-59 (164)
61 KOG4468 Polycomb-group transcr 59.2 12 0.00027 41.2 4.5 49 69-117 88-146 (782)
62 KOG4167 Predicted DNA-binding 56.5 16 0.00034 41.3 4.8 46 69-114 619-664 (907)
63 PF04545 Sigma70_r4: Sigma-70, 54.7 22 0.00047 25.6 3.9 41 75-116 7-47 (50)
64 TIGR02985 Sig70_bacteroi1 RNA 50.5 27 0.00059 29.6 4.5 37 79-116 120-156 (161)
65 PRK11169 leucine-responsive tr 49.0 5.2 0.00011 36.1 -0.2 47 21-69 13-59 (164)
66 PF01388 ARID: ARID/BRIGHT DNA 48.7 31 0.00066 27.8 4.3 37 79-115 40-89 (92)
67 PF12776 Myb_DNA-bind_3: Myb/S 48.4 8.2 0.00018 31.0 0.9 44 18-61 1-60 (96)
68 KOG2009 Transcription initiati 48.1 22 0.00047 39.1 4.1 49 68-116 408-456 (584)
69 PRK11179 DNA-binding transcrip 47.7 8.3 0.00018 34.3 0.9 47 21-69 8-54 (153)
70 PF07750 GcrA: GcrA cell cycle 47.6 18 0.00039 33.3 3.0 41 71-112 2-42 (162)
71 KOG0384 Chromodomain-helicase 44.6 24 0.00052 42.0 4.0 76 15-97 1132-1208(1373)
72 PF11035 SnAPC_2_like: Small n 44.2 55 0.0012 33.7 6.0 48 69-117 21-72 (344)
73 PF13325 MCRS_N: N-terminal re 43.5 41 0.0009 32.3 4.8 46 71-117 1-49 (199)
74 KOG4329 DNA-binding protein [G 42.4 64 0.0014 34.0 6.3 45 70-114 278-323 (445)
75 smart00501 BRIGHT BRIGHT, ARID 42.4 42 0.00092 27.4 4.2 38 79-116 36-86 (93)
76 KOG4167 Predicted DNA-binding 42.0 12 0.00027 42.1 1.2 44 16-61 619-662 (907)
77 PF11626 Rap1_C: TRF2-interact 41.6 24 0.00053 28.9 2.6 16 65-80 43-58 (87)
78 smart00344 HTH_ASNC helix_turn 41.6 48 0.001 27.1 4.5 45 75-120 3-48 (108)
79 PRK13858 type IV secretion sys 40.8 38 0.00083 31.1 4.0 83 2-98 14-96 (147)
80 cd08319 Death_RAIDD Death doma 37.6 38 0.00082 28.0 3.2 29 77-106 2-30 (83)
81 KOG2656 DNA methyltransferase 37.3 17 0.00037 38.3 1.3 49 13-62 127-180 (445)
82 TIGR02937 sigma70-ECF RNA poly 35.9 57 0.0012 26.7 4.1 36 80-116 118-153 (158)
83 cd08803 Death_ank3 Death domai 35.5 47 0.001 27.4 3.4 30 77-107 4-33 (84)
84 PF10545 MADF_DNA_bdg: Alcohol 33.9 30 0.00066 26.5 2.0 26 91-116 29-55 (85)
85 PF09420 Nop16: Ribosome bioge 31.1 1E+02 0.0022 28.1 5.2 47 68-114 113-163 (164)
86 PRK09652 RNA polymerase sigma 30.4 78 0.0017 27.4 4.2 30 85-115 141-170 (182)
87 COG1522 Lrp Transcriptional re 30.3 77 0.0017 27.4 4.1 47 74-121 7-54 (154)
88 PF04504 DUF573: Protein of un 30.2 66 0.0014 27.2 3.5 48 70-117 5-65 (98)
89 PRK11924 RNA polymerase sigma 29.6 79 0.0017 27.3 4.1 29 86-115 139-167 (179)
90 cd08317 Death_ank Death domain 29.6 50 0.0011 26.7 2.6 29 77-106 4-32 (84)
91 KOG4468 Polycomb-group transcr 28.1 23 0.00049 39.3 0.5 48 16-64 88-144 (782)
92 cd06171 Sigma70_r4 Sigma70, re 28.1 1.2E+02 0.0026 20.3 4.1 40 72-113 11-50 (55)
93 PF02954 HTH_8: Bacterial regu 27.9 98 0.0021 21.8 3.6 35 75-110 5-39 (42)
94 PRK09413 IS2 repressor TnpA; R 27.3 1E+02 0.0023 26.4 4.4 45 15-63 9-53 (121)
95 PF09420 Nop16: Ribosome bioge 27.2 41 0.00089 30.6 1.9 47 14-61 112-161 (164)
96 PRK09643 RNA polymerase sigma 26.7 98 0.0021 28.1 4.3 29 86-115 148-176 (192)
97 PRK09641 RNA polymerase sigma 26.3 98 0.0021 27.3 4.2 29 87-116 151-179 (187)
98 PRK09047 RNA polymerase factor 24.2 1.3E+02 0.0028 25.8 4.5 29 87-116 121-149 (161)
99 cd08804 Death_ank2 Death domai 24.1 83 0.0018 25.7 3.0 31 77-108 4-34 (84)
100 cd08318 Death_NMPP84 Death dom 23.7 88 0.0019 25.6 3.1 27 80-107 10-36 (86)
101 PRK04217 hypothetical protein; 23.7 1.3E+02 0.0028 26.2 4.3 44 71-116 42-85 (110)
102 PRK12523 RNA polymerase sigma 23.7 1.3E+02 0.0028 26.5 4.4 35 81-116 128-162 (172)
103 TIGR02939 RpoE_Sigma70 RNA pol 23.6 94 0.002 27.5 3.5 29 87-116 153-181 (190)
104 PF07638 Sigma70_ECF: ECF sigm 23.5 1.2E+02 0.0026 27.6 4.3 36 78-114 141-176 (185)
105 KOG1194 Predicted DNA-binding 23.2 39 0.00084 36.4 1.1 44 15-60 186-229 (534)
106 TIGR02954 Sig70_famx3 RNA poly 23.0 1.2E+02 0.0027 26.4 4.2 29 87-116 134-162 (169)
107 TIGR02948 SigW_bacill RNA poly 22.5 1.2E+02 0.0025 26.8 3.9 28 88-116 152-179 (187)
108 PRK12512 RNA polymerase sigma 22.1 1.4E+02 0.0031 26.4 4.4 29 87-116 146-174 (184)
109 TIGR02943 Sig70_famx1 RNA poly 21.8 1.5E+02 0.0032 26.9 4.5 30 86-116 145-174 (188)
110 PRK09637 RNA polymerase sigma 21.7 1.4E+02 0.003 27.0 4.3 29 87-116 121-149 (181)
111 PRK09642 RNA polymerase sigma 21.6 1.5E+02 0.0033 25.5 4.4 28 87-115 121-148 (160)
112 PRK12531 RNA polymerase sigma 21.5 1.5E+02 0.0032 26.8 4.4 29 87-116 156-184 (194)
113 PRK09648 RNA polymerase sigma 21.5 1.5E+02 0.0032 26.5 4.4 29 87-116 154-182 (189)
114 PRK12530 RNA polymerase sigma 21.4 1.5E+02 0.0032 26.9 4.4 28 87-115 149-176 (189)
115 PRK09645 RNA polymerase sigma 21.1 1.5E+02 0.0033 25.9 4.4 28 87-115 133-160 (173)
116 PRK12515 RNA polymerase sigma 20.7 1.6E+02 0.0034 26.4 4.4 29 87-116 146-174 (189)
117 smart00005 DEATH DEATH domain, 20.6 1E+02 0.0022 24.3 2.8 29 77-106 5-34 (88)
118 PRK12529 RNA polymerase sigma 20.4 1.6E+02 0.0036 26.2 4.5 31 86-117 141-171 (178)
119 cd08311 Death_p75NR Death doma 20.4 89 0.0019 25.4 2.5 33 74-108 2-34 (77)
120 PF09905 DUF2132: Uncharacteri 20.4 65 0.0014 25.8 1.6 44 24-80 12-62 (64)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=3.6e-36 Score=286.21 Aligned_cols=122 Identities=64% Similarity=1.203 Sum_probs=116.6
Q ss_pred CCCCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHH
Q 045411 1 MGKGRAPCCDKSQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTI 80 (389)
Q Consensus 1 mGrgR~pc~~kp~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~L 80 (389)
+++.+.|||.|++++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||.|||++|
T Consensus 10 ~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lL 89 (249)
T PLN03212 10 VSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLI 89 (249)
T ss_pred CCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHH
Confidence 57889999999999999999999999999999999999999999997559999999999999999999999999999999
Q ss_pred HHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhhcccCCC
Q 045411 81 IRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKKRLSFRD 122 (389)
Q Consensus 81 lelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~~~ 122 (389)
++++..||++|+.||++|||||+++|||||+.++++++....
T Consensus 90 lel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~ 131 (249)
T PLN03212 90 LRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQG 131 (249)
T ss_pred HHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcC
Confidence 999999999999999999999999999999999999877544
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=4e-35 Score=296.65 Aligned_cols=121 Identities=64% Similarity=1.205 Sum_probs=115.9
Q ss_pred CCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHHH
Q 045411 3 KGRAPCCDKSQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIR 82 (389)
Q Consensus 3 rgR~pc~~kp~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Lle 82 (389)
+||++||+|.+++||+||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999756999999999999999999999999999999999
Q ss_pred HHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhhcccCCCC
Q 045411 83 LHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKKRLSFRDV 123 (389)
Q Consensus 83 lv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~~~~ 123 (389)
++++||++|++||++|||||+++|||||+.++|++++.+..
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I 121 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGI 121 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999998775443
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.9e-34 Score=271.40 Aligned_cols=111 Identities=65% Similarity=1.110 Sum_probs=106.1
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCch
Q 045411 12 SQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIRLHESLGNRW 91 (389)
Q Consensus 12 p~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Llelv~~~G~kW 91 (389)
+.+.||+||+|||++|+++|++||+++|..||+.+|.+|++++||.||.|||+|++++|.||+|||.+|++||..||++|
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 44558999999999999999999999999999999956999999999999999999999999999999999999999999
Q ss_pred hhhhccCCCCCHHHHHHHHHHhhhhcccCCC
Q 045411 92 SKIASQLPGRTDNEIKNVWNTHLKKRLSFRD 122 (389)
Q Consensus 92 skIAk~LpGRT~nqcKnRW~~lLkkrl~~~~ 122 (389)
+.||++|||||+|+|||+|+.++|+|+....
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999987665
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=1.9e-19 Score=188.58 Aligned_cols=113 Identities=23% Similarity=0.446 Sum_probs=103.3
Q ss_pred CCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHH
Q 045411 4 GRAPCCDKSQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIRL 83 (389)
Q Consensus 4 gR~pc~~kp~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Llel 83 (389)
+|+-....|++++|+||++||.+|+.+|.+||.+.|.+|...+++ |+..|||+||.|.|+...|.+.||-.||+.||.+
T Consensus 348 ~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn-RSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~ 426 (939)
T KOG0049|consen 348 TRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN-RSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYA 426 (939)
T ss_pred hhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC-ccHHHHHHHHHHHHHHhhccCceeecchHHHHHH
Confidence 577788889999999999999999999999999999999999998 9999999999999999999999999999999999
Q ss_pred HHHhC-CchhhhhccCCCCCHHHHHHHHHHhhhhc
Q 045411 84 HESLG-NRWSKIASQLPGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 84 v~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLkkr 117 (389)
|.+|| ++|.+||.+||.||..|.+.|-...++.+
T Consensus 427 V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 427 VKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred HHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 99999 89999999999999966655544444433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.74 E-value=1.8e-18 Score=181.46 Aligned_cols=123 Identities=19% Similarity=0.366 Sum_probs=113.7
Q ss_pred CCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccc------------------------------
Q 045411 7 PCCDKSQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCR------------------------------ 56 (389)
Q Consensus 7 pc~~kp~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR------------------------------ 56 (389)
....+|.++|..|++|||++|..+...+|..+|.+||..++++|+..||.
T Consensus 244 ~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~ 323 (939)
T KOG0049|consen 244 YNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKIT 323 (939)
T ss_pred hhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHh
Confidence 45667999999999999999999999999999999999999999999997
Q ss_pred ------------------------cccccccCCCCCCCCCCHHHHHHHHHHHHHhCC-chhhhhccCCCCCHHHHHHHHH
Q 045411 57 ------------------------LRWINYLRPDVKRGNFTQEEEDTIIRLHESLGN-RWSKIASQLPGRTDNEIKNVWN 111 (389)
Q Consensus 57 ------------------------~RW~n~L~P~lkrg~WT~EEDe~Llelv~~~G~-kWskIAk~LpGRT~nqcKnRW~ 111 (389)
-||.+.|+|.+++|+||.+||.+|+.+|.+||+ .|.+|...+|||++.|||.||.
T Consensus 324 ~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~ 403 (939)
T KOG0049|consen 324 SINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYT 403 (939)
T ss_pred hccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHH
Confidence 688888999999999999999999999999995 5999999999999999999999
Q ss_pred HhhhhcccCCCCCccccc
Q 045411 112 THLKKRLSFRDVKKDQES 129 (389)
Q Consensus 112 ~lLkkrl~~~~~sk~e~~ 129 (389)
+.|..+++...|.-.++.
T Consensus 404 nvL~~s~K~~rW~l~ede 421 (939)
T KOG0049|consen 404 NVLNRSAKVERWTLVEDE 421 (939)
T ss_pred HHHHHhhccCceeecchH
Confidence 999999999999865553
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=99.60 E-value=4.4e-16 Score=117.69 Aligned_cols=60 Identities=38% Similarity=0.859 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHH
Q 045411 19 WSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTI 80 (389)
Q Consensus 19 WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~L 80 (389)
||++||++|+.+|.+|| .+|..||+.||. |++.||+.||.++|+|.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~-Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGN-RTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTT-S-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCc-CCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 689999999975 9999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.54 E-value=5.6e-15 Score=154.07 Aligned_cols=107 Identities=31% Similarity=0.546 Sum_probs=103.2
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCch
Q 045411 12 SQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIRLHESLGNRW 91 (389)
Q Consensus 12 p~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Llelv~~~G~kW 91 (389)
..++.|.|+..||+.|..+|+.||+.+|.+||..+.. |+++||+.||.++++|.++++.|+.+||..|+.+..++|.+|
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 4678899999999999999999999999999999998 999999999999999999999999999999999999999999
Q ss_pred hhhhccCCCCCHHHHHHHHHHhhhhccc
Q 045411 92 SKIASQLPGRTDNEIKNVWNTHLKKRLS 119 (389)
Q Consensus 92 skIAk~LpGRT~nqcKnRW~~lLkkrl~ 119 (389)
+.||..+++||..+|.+||...+....+
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999999988766
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.50 E-value=6.3e-15 Score=152.08 Aligned_cols=108 Identities=25% Similarity=0.560 Sum_probs=101.9
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCchhh
Q 045411 14 VKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIRLHESLGNRWSK 93 (389)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Llelv~~~G~kWsk 93 (389)
++-|.|+.-||+.|..+|.+||...|..|++.+.. .+++||+.||..+|+|.+++..|+.+||.+|+.+...+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 57799999999999999999999999999999987 89999999999999999999999999999999999999999999
Q ss_pred hhccCCCCCHHHHHHHHHHhhhhcccCCCC
Q 045411 94 IASQLPGRTDNEIKNVWNTHLKKRLSFRDV 123 (389)
Q Consensus 94 IAk~LpGRT~nqcKnRW~~lLkkrl~~~~~ 123 (389)
||..| ||+.+||-.||+.++-........
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 99999 999999999999999887665433
No 9
>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=99.37 E-value=5.7e-13 Score=100.67 Aligned_cols=58 Identities=33% Similarity=0.671 Sum_probs=50.8
Q ss_pred CCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhhcccCCCCCccccc
Q 045411 72 FTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKKRLSFRDVKKDQES 129 (389)
Q Consensus 72 WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~~~~sk~e~~ 129 (389)
||++||++|+++|..||++|.+||++|+.||+.+|++||+.+|+++++...|+.+++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~ 58 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQ 58 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHh
Confidence 9999999999999999999999999996699999999999999888888888876653
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.37 E-value=3.6e-13 Score=142.19 Aligned_cols=103 Identities=26% Similarity=0.583 Sum_probs=93.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCC--CCCCCCCHHHHHHHHHHHH-------
Q 045411 15 KRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPD--VKRGNFTQEEEDTIIRLHE------- 85 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~--lkrg~WT~EEDe~Llelv~------- 85 (389)
.||.||++|++.|..+|..+| ..|..|++.|+ |.+..||+||+++..+. .+++.||.||++.|+++|.
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 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 78999999997 89999999999999887 4999999999999999995
Q ss_pred Hh-------------------CCchhhhhccCCCCCHHHHHHHHHHhhhhcccC
Q 045411 86 SL-------------------GNRWSKIASQLPGRTDNEIKNVWNTHLKKRLSF 120 (389)
Q Consensus 86 ~~-------------------G~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~ 120 (389)
++ +-+|+.|++.+.+|+..|||.+|..++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 33 135999999999999999999999999876543
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=99.34 E-value=1.2e-12 Score=95.60 Aligned_cols=46 Identities=33% Similarity=0.739 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCc-hhhhhccCC-CCCHHHHHHHHHHhh
Q 045411 69 RGNFTQEEEDTIIRLHESLGNR-WSKIASQLP-GRTDNEIKNVWNTHL 114 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G~k-WskIAk~Lp-GRT~nqcKnRW~~lL 114 (389)
|++||.+||++|++++.+||.+ |..||..|| |||..||++||+.++
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 5799999999999999999977 999999999 999999999999875
No 12
>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=99.32 E-value=3e-13 Score=98.71 Aligned_cols=48 Identities=40% Similarity=0.801 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccchhhccccccccccccccccc
Q 045411 16 RGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYL 63 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (389)
|++||++||++|+++|.+||..+|..||..|+++||+.||+.||+++|
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 689999999999999999997779999999994499999999999875
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.31 E-value=2.2e-12 Score=123.85 Aligned_cols=78 Identities=19% Similarity=0.403 Sum_probs=67.6
Q ss_pred hcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhC-CchhhhhccC-CCCCHHHHHHHHHHhhhhcccCCCC
Q 045411 46 AGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIRLHESLG-NRWSKIASQL-PGRTDNEIKNVWNTHLKKRLSFRDV 123 (389)
Q Consensus 46 lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Llelv~~~G-~kWskIAk~L-pGRT~nqcKnRW~~lLkkrl~~~~~ 123 (389)
+++ |+..-|. .+.+++++||+|||++|+++|++|| ++|..||+.+ ++||+.|||.||.++|++.+++..|
T Consensus 10 ~~~-~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpW 81 (249)
T PLN03212 10 VSK-KTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CCC-CCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 454 5555443 3578999999999999999999999 6899999998 6999999999999999999999999
Q ss_pred Cccccccc
Q 045411 124 KKDQESKE 131 (389)
Q Consensus 124 sk~e~~k~ 131 (389)
+.+++...
T Consensus 82 T~EED~lL 89 (249)
T PLN03212 82 TSDEEDLI 89 (249)
T ss_pred ChHHHHHH
Confidence 98877643
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.19 E-value=1.6e-11 Score=117.06 Aligned_cols=66 Identities=24% Similarity=0.389 Sum_probs=60.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CchhhhhccCC-CCCHHHHHHHHHHhhhhcccCCCCCcccccc
Q 045411 65 PDVKRGNFTQEEEDTIIRLHESLG-NRWSKIASQLP-GRTDNEIKNVWNTHLKKRLSFRDVKKDQESK 130 (389)
Q Consensus 65 P~lkrg~WT~EEDe~Llelv~~~G-~kWskIAk~Lp-GRT~nqcKnRW~~lLkkrl~~~~~sk~e~~k 130 (389)
+.+.+|+||+|||.+|+++|++|| ++|..||+.++ +|++.+||-||.++|++.++++.++.+++.-
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~ 72 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDL 72 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHH
Confidence 345579999999999999999999 77999999998 9999999999999999999999999877643
No 15
>PLN03091 hypothetical protein; Provisional
Probab=99.18 E-value=1.9e-11 Score=125.27 Aligned_cols=65 Identities=20% Similarity=0.432 Sum_probs=61.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CchhhhhccC-CCCCHHHHHHHHHHhhhhcccCCCCCccccc
Q 045411 65 PDVKRGNFTQEEEDTIIRLHESLG-NRWSKIASQL-PGRTDNEIKNVWNTHLKKRLSFRDVKKDQES 129 (389)
Q Consensus 65 P~lkrg~WT~EEDe~Llelv~~~G-~kWskIAk~L-pGRT~nqcKnRW~~lLkkrl~~~~~sk~e~~ 129 (389)
+.+++++||+|||++|+++|.+|| ++|..||+.+ +||++.|||.||.++|++.+++..|+++++.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~ 76 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEEN 76 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHH
Confidence 578999999999999999999999 6899999988 5999999999999999999999999988874
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.17 E-value=4.4e-11 Score=84.02 Aligned_cols=47 Identities=45% Similarity=0.910 Sum_probs=44.6
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 69 RGNFTQEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
+++||++||.+|+.++.+|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998775
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.04 E-value=3.9e-10 Score=78.18 Aligned_cols=44 Identities=36% Similarity=0.785 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhh
Q 045411 71 NFTQEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 71 ~WT~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lL 114 (389)
+||.+|+..|+.++.+|| .+|..||+.|++||..+|++||..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998764
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.98 E-value=2.1e-10 Score=80.53 Aligned_cols=48 Identities=38% Similarity=0.798 Sum_probs=44.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccC
Q 045411 16 RGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLR 64 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 64 (389)
+++||++||.+|+.++..||..+|..||..+++ |++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~-rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPG-RTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCC-CCHHHHHHHHHHHcC
Confidence 478999999999999999997799999999997 999999999998764
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.85 E-value=2.1e-09 Score=114.07 Aligned_cols=117 Identities=26% Similarity=0.312 Sum_probs=94.6
Q ss_pred CccCCCCHHHHHHHHHHHHHhCC-----------------------CCccccchhhcccccccccccccccccCCCC-CC
Q 045411 14 VKRGPWSPGEDLRLITFIQKHGH-----------------------ENWRALPKQAGLLRCGKSCRLRWINYLRPDV-KR 69 (389)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~kyG~-----------------------~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l-kr 69 (389)
++-+.|+.+||+.|...|..|-. +-|..|...++. |+.+....+-++.-+|-- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCcccccc
Confidence 34489999999999999997711 016777888888 999888763333333322 99
Q ss_pred CCCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhhc--ccCCCCCcccccccc
Q 045411 70 GNFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKKR--LSFRDVKKDQESKES 132 (389)
Q Consensus 70 g~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkkr--l~~~~~sk~e~~k~~ 132 (389)
|.||++|++.|..+|.++|+.|..|++.| ||.+..|+.||+.+++.. .....|+.++..+..
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Ll 448 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLL 448 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHH
Confidence 99999999999999999999999999999 999999999999999887 477788887765544
No 20
>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=98.82 E-value=1.6e-09 Score=75.10 Aligned_cols=45 Identities=40% Similarity=0.784 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccchhhccccccccccccccccc
Q 045411 18 PWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYL 63 (389)
Q Consensus 18 ~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (389)
+||++||..|+.++.+||..+|..||..+++ |++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 5999999999999999998899999999998 99999999998753
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=98.17 E-value=1.8e-07 Score=98.49 Aligned_cols=99 Identities=25% Similarity=0.579 Sum_probs=85.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCC--CCCCCCCCHHHHHHHHHHHHHhC--
Q 045411 13 QVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRP--DVKRGNFTQEEEDTIIRLHESLG-- 88 (389)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P--~lkrg~WT~EEDe~Llelv~~~G-- 88 (389)
--.+|.||++|+..|..++..+| ..|..|.+.++ |-+..||+||++|..+ .+++++|+.||+.+|...+...-
T Consensus 288 f~~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~ 364 (512)
T COG5147 288 FEQRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLE 364 (512)
T ss_pred HhhhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHH
Confidence 34579999999999999999999 68999999876 8999999999999988 78899999999999999887321
Q ss_pred ------CchhhhhccCCCCCHHHHHHHHHHhh
Q 045411 89 ------NRWSKIASQLPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 89 ------~kWskIAk~LpGRT~nqcKnRW~~lL 114 (389)
-.|..|+..+++|...+|+..+..+.
T Consensus 365 ~~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 365 AQQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred HhhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 35999999999988888887665443
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.63 E-value=2.4e-05 Score=82.24 Aligned_cols=64 Identities=23% Similarity=0.492 Sum_probs=59.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhhhcccCCCCCcccccc
Q 045411 67 VKRGNFTQEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLKKRLSFRDVKKDQESK 130 (389)
Q Consensus 67 lkrg~WT~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~~~~sk~e~~k 130 (389)
++-|-|+.-||++|..+|.+|| +.|++|++.++-.|..||++||..++.+.+++..|+.+++.+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eeder 69 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDER 69 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHH
Confidence 5678999999999999999999 779999999999999999999999999999999999876643
No 23
>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=97.53 E-value=5e-05 Score=58.39 Aligned_cols=49 Identities=16% Similarity=0.268 Sum_probs=43.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCc---cccchhhcccc-ccccccccccccc
Q 045411 15 KRGPWSPGEDLRLITFIQKHGHENW---RALPKQAGLLR-CGKSCRLRWINYL 63 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~~nW---~~IAk~lg~~R-t~kQCR~RW~n~L 63 (389)
+|-.||+||..+++.+|+.+|.++| +.|+..|...| |..||+.+++.|.
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 4668999999999999999997799 99999987656 9999999988764
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.52 E-value=0.00012 Score=75.61 Aligned_cols=50 Identities=24% Similarity=0.456 Sum_probs=45.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 66 DVKRGNFTQEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 66 ~lkrg~WT~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
.+-...||.+|+.+|++++..|| +||..||.++..||..+||.+|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 45566899999999999999999 999999999999999999999988764
No 25
>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=97.46 E-value=0.00029 Score=54.23 Aligned_cols=47 Identities=17% Similarity=0.329 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-ch---hhhhccCC-CC-CHHHHHHHHHHhhh
Q 045411 69 RGNFTQEEEDTIIRLHESLGN-RW---SKIASQLP-GR-TDNEIKNVWNTHLK 115 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G~-kW---skIAk~Lp-GR-T~nqcKnRW~~lLk 115 (389)
+-.||+||..++++++..||. +| ..|+..|. .| |..||+.++..+.-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 458999999999999999995 99 99999873 45 99999999887653
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.42 E-value=5.9e-05 Score=77.91 Aligned_cols=50 Identities=16% Similarity=0.545 Sum_probs=46.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCccccchhhccccccccccccccccc
Q 045411 13 QVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYL 63 (389)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (389)
.+-...||.+|+-+|++++..||.+||..||.+||+ |++.+|+++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHH
Confidence 455688999999999999999999999999999998 99999999999854
No 27
>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=96.99 E-value=0.00064 Score=62.36 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=45.9
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC----chhhhhccCCCCCHHHHHHHHHHhhhhcccCC
Q 045411 68 KRGNFTQEEEDTIIRLHESL---GN----RWSKIASQLPGRTDNEIKNVWNTHLKKRLSFR 121 (389)
Q Consensus 68 krg~WT~EEDe~Llelv~~~---G~----kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~~ 121 (389)
+...||.|||.+|.+.|..| |+ -+..++..| +||+.+|.-|||..+|++....
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 56789999999999999988 42 288899999 9999999999999999876543
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.91 E-value=0.0016 Score=61.70 Aligned_cols=100 Identities=20% Similarity=0.397 Sum_probs=71.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccchhhccc--cccccccccccccc-CCCC--------------------CCCCCCH
Q 045411 18 PWSPGEDLRLITFIQKHGHENWRALPKQAGLL--RCGKSCRLRWINYL-RPDV--------------------KRGNFTQ 74 (389)
Q Consensus 18 ~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~--Rt~kQCR~RW~n~L-~P~l--------------------krg~WT~ 74 (389)
+|++++|-.|+.+|..-. +-..|+..+.-. -|-....+||+..| +|.+ .+-+||.
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 599999999999998755 455555443321 24455678998766 3332 3458999
Q ss_pred HHHHHHHHHHHHhCC---chhhhhc----cC-CCCCHHHHHHHHHHhhhhccc
Q 045411 75 EEEDTIIRLHESLGN---RWSKIAS----QL-PGRTDNEIKNVWNTHLKKRLS 119 (389)
Q Consensus 75 EEDe~Llelv~~~G~---kWskIAk----~L-pGRT~nqcKnRW~~lLkkrl~ 119 (389)
+|+++|......... .+.+|=. .| ++||+.++.++|..+.+..+.
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999998766543 4666632 23 789999999999977766655
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.75 E-value=0.0011 Score=53.19 Aligned_cols=51 Identities=33% Similarity=0.557 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------chhhhhccC----CCCCHHHHHHHHHHhhhhccc
Q 045411 69 RGNFTQEEEDTIIRLHES------LG--N------RWSKIASQL----PGRTDNEIKNVWNTHLKKRLS 119 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~------~G--~------kWskIAk~L----pGRT~nqcKnRW~~lLkkrl~ 119 (389)
|..||.+|...||+++.. ++ + -|..||..| ..||+.||++||.++.+.-..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 357999999999999977 22 1 399999987 369999999999998877544
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.62 E-value=0.00077 Score=70.51 Aligned_cols=46 Identities=24% Similarity=0.577 Sum_probs=42.9
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccc
Q 045411 15 KRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINY 62 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 62 (389)
+...||.+|-.+|++.|+.|| .+|.+||.++++ |+.-||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgt-Kt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGT-KTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCC-CCHHHHHHHHHcC
Confidence 667999999999999999999 689999999998 9999999999864
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.49 E-value=0.0011 Score=70.26 Aligned_cols=48 Identities=23% Similarity=0.619 Sum_probs=43.9
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccc
Q 045411 13 QVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINY 62 (389)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~ 62 (389)
.-.++.||.+|+.+|+++|.+|| .+|.+||.++++ |+..||..++.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCC-CCHHHHHHHHHhc
Confidence 34578999999999999999999 689999999998 9999999998764
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.40 E-value=0.0039 Score=66.28 Aligned_cols=47 Identities=19% Similarity=0.343 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhh
Q 045411 68 KRGNFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 68 krg~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lL 114 (389)
.+..||.+|..+|++++..||-.|.+||.++.+||..||--||..+=
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 45689999999999999999999999999999999999999996543
No 33
>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=96.38 E-value=0.005 Score=48.62 Aligned_cols=51 Identities=20% Similarity=0.422 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC-------Cc--hhhhhccCC-CCCHHHHHHHHHHhhhhccc
Q 045411 69 RGNFTQEEEDTIIRLHESLG-------NR--WSKIASQLP-GRTDNEIKNVWNTHLKKRLS 119 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G-------~k--WskIAk~Lp-GRT~nqcKnRW~~lLkkrl~ 119 (389)
|.+||.+||.+|+..|..+. ++ |.+++..-+ .+|-...|+||...|+.+..
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 45899999999999997642 22 999999877 89999999999999887643
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.35 E-value=0.0037 Score=65.60 Aligned_cols=45 Identities=18% Similarity=0.288 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHh
Q 045411 69 RGNFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTH 113 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~l 113 (389)
..+||.+|..+|++.++.||..|.+||+++.+||..||--||-.+
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 348999999999999999999999999999999999999999654
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.67 E-value=0.0091 Score=55.43 Aligned_cols=52 Identities=17% Similarity=0.321 Sum_probs=43.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCc-------hhhhhccCCCCCHHHHHHHHHHhhhhccc
Q 045411 67 VKRGNFTQEEEDTIIRLHESLGNR-------WSKIASQLPGRTDNEIKNVWNTHLKKRLS 119 (389)
Q Consensus 67 lkrg~WT~EEDe~Llelv~~~G~k-------WskIAk~LpGRT~nqcKnRW~~lLkkrl~ 119 (389)
.++..||.|+|.+|-+.|..|+.. ...++..| +||..+|..||+..++++..
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 456789999999999999998732 66667777 99999999999999997654
No 36
>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=95.44 E-value=0.0063 Score=48.05 Aligned_cols=52 Identities=21% Similarity=0.434 Sum_probs=33.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------C--CccccchhhcccccccccccccccccCCCC
Q 045411 16 RGPWSPGEDLRLITFIQKHGH------E--NWRALPKQAGLLRCGKSCRLRWINYLRPDV 67 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~kyG~------~--nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l 67 (389)
|.+||.+||++|+..|..+.. + =|..++...+++++..+-|+||.+.|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 568999999999999976631 1 299999988865888889999999887643
No 37
>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=95.26 E-value=0.0072 Score=55.57 Aligned_cols=50 Identities=24% Similarity=0.593 Sum_probs=42.3
Q ss_pred CccCCCCHHHHHHHHHHHHHhCC------CCccccchhhcccccccccccccccccCC
Q 045411 14 VKRGPWSPGEDLRLITFIQKHGH------ENWRALPKQAGLLRCGKSCRLRWINYLRP 65 (389)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~kyG~------~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P 65 (389)
.++..||.|||.+|.+.|-+|=. ..+..|+..++ ||+..|.-||..+++.
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 46789999999999999999831 13888888886 9999999999988764
No 38
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.20 E-value=0.018 Score=58.28 Aligned_cols=47 Identities=26% Similarity=0.460 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 69 RGNFTQEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
-..|+..|+.+|++++..+| ++|..||.++..|+...||.+|..+.-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34799999999999999999 999999999999999999999987654
No 39
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.03 E-value=0.0051 Score=49.23 Aligned_cols=48 Identities=23% Similarity=0.545 Sum_probs=33.2
Q ss_pred cCCCCHHHHHHHHHHHHH--h----C---C----CCccccchhhc---cccccccccccccccc
Q 045411 16 RGPWSPGEDLRLITFIQK--H----G---H----ENWRALPKQAG---LLRCGKSCRLRWINYL 63 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~k--y----G---~----~nW~~IAk~lg---~~Rt~kQCR~RW~n~L 63 (389)
|-.||.+|...|+.++.. + + . .-|..||..|. -.|++.||+.||.++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 458999999999999987 2 1 0 13999999873 3599999999998753
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.88 E-value=0.053 Score=42.79 Aligned_cols=48 Identities=31% Similarity=0.601 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------chhhhhccC-----CCCCHHHHHHHHHHhhhh
Q 045411 69 RGNFTQEEEDTIIRLHESLG----N-------------RWSKIASQL-----PGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G----~-------------kWskIAk~L-----pGRT~nqcKnRW~~lLkk 116 (389)
...||.+|...|++++.+|. + -|..|+..| +.||..+||.+|.++...
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 45799999999999998862 1 299999876 259999999999987754
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.57 E-value=0.059 Score=61.95 Aligned_cols=99 Identities=15% Similarity=0.331 Sum_probs=75.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccc-----------------------------------------
Q 045411 18 PWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCR----------------------------------------- 56 (389)
Q Consensus 18 ~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR----------------------------------------- 56 (389)
.|+.-+=..++.+..+||..+-..||..|.+ ++...++
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999999998889999998865 6665554
Q ss_pred -------cccccc-c-CCCCCCCCCCHHHHHHHHHHHHHhC-Cchhhhhcc------------CCCCCHHHHHHHHHHhh
Q 045411 57 -------LRWINY-L-RPDVKRGNFTQEEEDTIIRLHESLG-NRWSKIASQ------------LPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 57 -------~RW~n~-L-~P~lkrg~WT~EEDe~Llelv~~~G-~kWskIAk~------------LpGRT~nqcKnRW~~lL 114 (389)
.-|... + .+..++..||.+||..|+-++.+|| ++|..|-.. |..||+..|..|...++
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 111110 0 1223344699999999999999999 889998432 24699999999999888
Q ss_pred hhc
Q 045411 115 KKR 117 (389)
Q Consensus 115 kkr 117 (389)
+--
T Consensus 985 ~~~ 987 (1033)
T PLN03142 985 RLI 987 (1033)
T ss_pred HHH
Confidence 654
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=93.86 E-value=0.02 Score=57.97 Aligned_cols=50 Identities=20% Similarity=0.484 Sum_probs=45.4
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccC
Q 045411 14 VKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLR 64 (389)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~ 64 (389)
|---.|+..|+-+|+++....|-+||..||..+|. |+...|+.+|..++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 33457999999999999999999999999999997 999999999998765
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.68 E-value=0.041 Score=43.44 Aligned_cols=49 Identities=20% Similarity=0.413 Sum_probs=39.5
Q ss_pred ccCCCCHHHHHHHHHHHHHhCC----------------CCccccchhh----ccccccccccccccccc
Q 045411 15 KRGPWSPGEDLRLITFIQKHGH----------------ENWRALPKQA----GLLRCGKSCRLRWINYL 63 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~----------------~nW~~IAk~l----g~~Rt~kQCR~RW~n~L 63 (389)
++..||.+|...|+++|.+|.. .-|..|+..+ ++.|+..||+.+|.++.
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 1399999886 22499999999998864
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=92.96 E-value=0.03 Score=52.04 Aligned_cols=50 Identities=20% Similarity=0.503 Sum_probs=39.8
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCC------ccccchhhcccccccccccccccccC
Q 045411 13 QVKRGPWSPGEDLRLITFIQKHGHEN------WRALPKQAGLLRCGKSCRLRWINYLR 64 (389)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~kyG~~n------W~~IAk~lg~~Rt~kQCR~RW~n~L~ 64 (389)
..++..||.|+|.+|.+.|-.|+... ...++..+. |+..+|..||..+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 35778999999999999999997432 556666665 899999999966554
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=91.30 E-value=0.2 Score=52.05 Aligned_cols=86 Identities=20% Similarity=0.338 Sum_probs=63.8
Q ss_pred CccccchhhcccccccccccccccccCCC-------------------------CCCCCCCHHHHHHHHHHHHHhCCchh
Q 045411 38 NWRALPKQAGLLRCGKSCRLRWINYLRPD-------------------------VKRGNFTQEEEDTIIRLHESLGNRWS 92 (389)
Q Consensus 38 nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~-------------------------lkrg~WT~EEDe~Llelv~~~G~kWs 92 (389)
+|.-++=..+. |...--..+|.+.-++. ++...||.+|-+-|+++++.|.-+|-
T Consensus 75 ~W~w~pFtn~a-RkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNSA-RKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCcc-ccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 46665544444 66666666777663321 12246999999999999999999999
Q ss_pred hhhcc-----CCC-CCHHHHHHHHHHhhhhcccCCCCC
Q 045411 93 KIASQ-----LPG-RTDNEIKNVWNTHLKKRLSFRDVK 124 (389)
Q Consensus 93 kIAk~-----LpG-RT~nqcKnRW~~lLkkrl~~~~~s 124 (389)
.||-. ++. ||-..+|.||+...++-++.+.-.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 99976 555 999999999999998877655433
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=89.85 E-value=0.34 Score=48.57 Aligned_cols=49 Identities=22% Similarity=0.386 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCchhhhhccC----CCCCHHHHHHHHHHhhhhc
Q 045411 69 RGNFTQEEEDTIIRLHESL----------GNRWSKIASQL----PGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~----------G~kWskIAk~L----pGRT~nqcKnRW~~lLkkr 117 (389)
...|+.+|-..||++.... +..|..||+.+ .-||+.|||+||.++.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Y 116 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKY 116 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 3689999999999998653 23499999965 2499999999999988774
No 47
>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=89.71 E-value=0.65 Score=37.54 Aligned_cols=46 Identities=33% Similarity=0.583 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------chhhhhccC---CC--CCHHHHHHHHHHhhhh
Q 045411 71 NFTQEEEDTIIRLHESL---GN----------RWSKIASQL---PG--RTDNEIKNVWNTHLKK 116 (389)
Q Consensus 71 ~WT~EEDe~Llelv~~~---G~----------kWskIAk~L---pG--RT~nqcKnRW~~lLkk 116 (389)
.||++++..|++++... |+ .|..|+..| +| .+..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999999653 21 299999876 33 5789999999877665
No 48
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=89.46 E-value=0.62 Score=40.88 Aligned_cols=51 Identities=25% Similarity=0.471 Sum_probs=40.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----chhhhhccC------------CCCCHHHHHHHHHHhhhh
Q 045411 66 DVKRGNFTQEEEDTIIRLHESLGN----RWSKIASQL------------PGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 66 ~lkrg~WT~EEDe~Llelv~~~G~----kWskIAk~L------------pGRT~nqcKnRW~~lLkk 116 (389)
..++..||.+||.-|+-++.+||- .|..|...+ ..||+..|..|...+++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 456779999999999999999995 798886542 359999999999998864
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=88.57 E-value=0.62 Score=48.43 Aligned_cols=46 Identities=22% Similarity=0.346 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 71 NFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 71 ~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
+||.+|-++...+....|..++.|+..+|.|...|||-+|.+--|+
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 7999999999999999999999999999999999999999765554
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=83.24 E-value=1.7 Score=46.09 Aligned_cols=50 Identities=20% Similarity=0.274 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhhc
Q 045411 68 KRGNFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 68 krg~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkkr 117 (389)
....||.||-.++-+++..||.++.+|.+.||.|+-..+...|....+.+
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~ 235 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTR 235 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHh
Confidence 34589999999999999999999999999999999999999888766554
No 51
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=81.24 E-value=2.9 Score=30.40 Aligned_cols=41 Identities=24% Similarity=0.311 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 74 QEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 74 ~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
++++..++.++...|-.|.+||..+ |.|...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4677888888888999999999999 9999999999877654
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=76.93 E-value=1.8 Score=35.55 Aligned_cols=30 Identities=30% Similarity=0.569 Sum_probs=17.2
Q ss_pred CCCccCCCCHHHHHHH--------HHHHHHhCCCCccccch
Q 045411 12 SQVKRGPWSPGEDLRL--------ITFIQKHGHENWRALPK 44 (389)
Q Consensus 12 p~lkKG~WT~EEDe~L--------~~lV~kyG~~nW~~IAk 44 (389)
|.-..|-||+++|+.| .+++++|| +..|+.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 4455799999999999 55677888 445543
No 53
>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=76.55 E-value=1.9 Score=37.81 Aligned_cols=34 Identities=26% Similarity=0.448 Sum_probs=29.2
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCC---CCccccchhh
Q 045411 13 QVKRGPWSPGEDLRLITFIQKHGH---ENWRALPKQA 46 (389)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~kyG~---~nW~~IAk~l 46 (389)
.-++..||.+||..|+-++.+||. +.|..|-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 667899999999999999999998 7899998876
No 54
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=74.46 E-value=1.9 Score=43.35 Aligned_cols=48 Identities=25% Similarity=0.445 Sum_probs=37.4
Q ss_pred cCCCCHHHHHHHHHHHHHh----C-----CCCccccchhh---ccccccccccccccccc
Q 045411 16 RGPWSPGEDLRLITFIQKH----G-----HENWRALPKQA---GLLRCGKSCRLRWINYL 63 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~ky----G-----~~nW~~IAk~l---g~~Rt~kQCR~RW~n~L 63 (389)
-..|+.+|-..|+.+.... . ..-|..||+.+ +..|++.||+.||.+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4789999999999988643 1 13499999954 33499999999998753
No 55
>smart00595 MADF subfamily of SANT domain.
Probab=73.01 E-value=3.6 Score=32.81 Aligned_cols=25 Identities=32% Similarity=0.679 Sum_probs=21.7
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 91 WSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 91 WskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
|..||..| |-|..+|+.+|+++...
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 99999999 55999999999987644
No 56
>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=66.80 E-value=9.2 Score=27.50 Aligned_cols=38 Identities=21% Similarity=0.430 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHh
Q 045411 75 EEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTH 113 (389)
Q Consensus 75 EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~l 113 (389)
+=|.+|+.+...-| -.|..||+.+ |=|...|..|++.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 45788999999888 5699999999 99999999998764
No 57
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=65.94 E-value=9.8 Score=33.87 Aligned_cols=46 Identities=11% Similarity=0.119 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhhhcccC
Q 045411 74 QEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLKKRLSF 120 (389)
Q Consensus 74 ~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~ 120 (389)
.+-|.+|+.+.++-| -.|+.||+.+ |-|...|+.|++.+....+..
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 357899999999988 6799999999 999999999999998877554
No 58
>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=64.14 E-value=2.7 Score=30.26 Aligned_cols=38 Identities=21% Similarity=0.430 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhCCCCccccchhhccccccccccccccc
Q 045411 22 GEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWIN 61 (389)
Q Consensus 22 EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n 61 (389)
+=|.+|+.+.+..|...|..||+.+|. +...|+.|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lgl--S~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGL--SESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS---HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCc--CHHHHHHHHHH
Confidence 348899999999999999999999997 88999988764
No 59
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=60.68 E-value=4.6 Score=42.25 Aligned_cols=44 Identities=16% Similarity=0.222 Sum_probs=40.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccchhhccccccccccccccc
Q 045411 16 RGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWIN 61 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n 61 (389)
--+||..|-+++.++....| -++..|+..+|. |..+|+..+|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~-R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPN-RERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCc-hhHHHHHHHHHH
Confidence 35899999999999999999 589999999998 999999998876
No 60
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=59.53 E-value=13 Score=33.61 Aligned_cols=46 Identities=7% Similarity=0.029 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhhhcccC
Q 045411 74 QEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLKKRLSF 120 (389)
Q Consensus 74 ~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~ 120 (389)
.+-|.+|+.+.++-| -.|+.||+.+ |-|...|+.|++.+.+..+..
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 567889999988888 5799999999 999999999999999887654
No 61
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=59.16 E-value=12 Score=41.19 Aligned_cols=49 Identities=12% Similarity=0.444 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhhhc----------cCCCCCHHHHHHHHHHhhhhc
Q 045411 69 RGNFTQEEEDTIIRLHESLGNRWSKIAS----------QLPGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G~kWskIAk----------~LpGRT~nqcKnRW~~lLkkr 117 (389)
+..||..|..-...+++++|..+.+|-+ ...-+|..|++.+|+.++++-
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 5689999999999999999999998822 233468889999998877664
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=56.48 E-value=16 Score=41.25 Aligned_cols=46 Identities=9% Similarity=0.072 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhh
Q 045411 69 RGNFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lL 114 (389)
...||+.|-.+.-+++-.|...+-.|++.++++|-.||-..|++..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 3479999999999999999999999999999999999988776543
No 63
>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=54.73 E-value=22 Score=25.57 Aligned_cols=41 Identities=29% Similarity=0.426 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 75 EEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 75 EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
+++..++.+.-..|-.+..||..| |-|...|+.+.+..+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 455566666655567899999999 88999999988877654
No 64
>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=50.55 E-value=27 Score=29.58 Aligned_cols=37 Identities=24% Similarity=0.338 Sum_probs=27.8
Q ss_pred HHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 79 TIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 79 ~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.++.+.-..|-.+..||+.+ |.+...|+++.+..+++
T Consensus 120 ~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 120 KIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33444334577899999999 99999999998876543
No 65
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=49.02 E-value=5.2 Score=36.08 Aligned_cols=47 Identities=23% Similarity=0.258 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCC
Q 045411 21 PGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKR 69 (389)
Q Consensus 21 ~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkr 69 (389)
.+-|.+|+.+.++.|...|..||+.++. +...|+.|+.+.....+-+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lgl--S~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGL--SPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCc--CHHHHHHHHHHHHHCCCeE
Confidence 4569999999999999999999999986 9999999999887766543
No 66
>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=48.67 E-value=31 Score=27.85 Aligned_cols=37 Identities=16% Similarity=0.361 Sum_probs=27.6
Q ss_pred HHHHHHHHhCC--------chhhhhccCCC---CC--HHHHHHHHHHhhh
Q 045411 79 TIIRLHESLGN--------RWSKIASQLPG---RT--DNEIKNVWNTHLK 115 (389)
Q Consensus 79 ~Llelv~~~G~--------kWskIAk~LpG---RT--~nqcKnRW~~lLk 115 (389)
.|..+|..+|+ .|..||+.|.- -+ ..++|..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 47788888874 59999998822 22 3689999988875
No 67
>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=48.44 E-value=8.2 Score=31.04 Aligned_cols=44 Identities=16% Similarity=0.472 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Cccccchhhcc----ccccccccccccc
Q 045411 18 PWSPGEDLRLITFIQKH---GHE---------NWRALPKQAGL----LRCGKSCRLRWIN 61 (389)
Q Consensus 18 ~WT~EEDe~L~~lV~ky---G~~---------nW~~IAk~lg~----~Rt~kQCR~RW~n 61 (389)
.||+++++.|++++... |.. .|..|+..|.. ..+..||+.||..
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 59999999999998654 211 27778777643 2455677777654
No 68
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=48.06 E-value=22 Score=39.15 Aligned_cols=49 Identities=18% Similarity=0.335 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 68 KRGNFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 68 krg~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
..++|+..|-.+...+....|.+.+.|+..+|+|+..|||.+|..-=++
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 4568999999999999999999999999999999999999998654444
No 69
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=47.74 E-value=8.3 Score=34.31 Aligned_cols=47 Identities=13% Similarity=0.190 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCC
Q 045411 21 PGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKR 69 (389)
Q Consensus 21 ~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkr 69 (389)
.+-|.+|+.+.++.|...|..||+.++. +...|+.|+.+....++-+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lgl--S~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGV--SPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCc--CHHHHHHHHHHHHHCCCee
Confidence 3579999999999999999999999985 9999999999887665543
No 70
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=47.58 E-value=18 Score=33.28 Aligned_cols=41 Identities=27% Similarity=0.315 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHH
Q 045411 71 NFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNT 112 (389)
Q Consensus 71 ~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~ 112 (389)
.||+|..++|.+|. .=|-.=++||+.|.|.|.|+|.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 59999999999987 447788999999977999999877654
No 71
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=44.65 E-value=24 Score=41.98 Aligned_cols=76 Identities=20% Similarity=0.192 Sum_probs=51.9
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHh-CCchhh
Q 045411 15 KRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTIIRLHESL-GNRWSK 93 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Llelv~~~-G~kWsk 93 (389)
.-.-|..++|..|+-.|-+||.++|.+|-. .+.-|.. =...+...+-++.|=...-..|+.+...+ +.+|.+
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~------Dp~L~l~-dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRL------DPDLGLT-DKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhcc------Cccccch-hhhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 556899999999999999999999999832 1222222 12233333556677777777888887777 566666
Q ss_pred hhcc
Q 045411 94 IASQ 97 (389)
Q Consensus 94 IAk~ 97 (389)
..+.
T Consensus 1205 ~~~~ 1208 (1373)
T KOG0384|consen 1205 KLKR 1208 (1373)
T ss_pred hhhc
Confidence 5443
No 72
>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=44.18 E-value=55 Score=33.74 Aligned_cols=48 Identities=29% Similarity=0.595 Sum_probs=37.0
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCc---hhhhhccCCCCCHHHHHHHHHHhhhhc
Q 045411 69 RGNFTQEEEDTIIRLHESL-GNR---WSKIASQLPGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 69 rg~WT~EEDe~Llelv~~~-G~k---WskIAk~LpGRT~nqcKnRW~~lLkkr 117 (389)
-..||.-|...|+++.+.. |.. -..|++.++||+..+|++.-. .||.|
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~-~LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQ-QLKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHH-HHHHH
Confidence 4579999999999998766 433 568899999999999988544 34433
No 73
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=43.45 E-value=41 Score=32.26 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHhCCchhhhhccC---CCCCHHHHHHHHHHhhhhc
Q 045411 71 NFTQEEEDTIIRLHESLGNRWSKIASQL---PGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 71 ~WT~EEDe~Llelv~~~G~kWskIAk~L---pGRT~nqcKnRW~~lLkkr 117 (389)
.|++.+|-.|+.+|.. |+.-..|++-+ -.-|-..|..||+.+|--.
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 5999999999999854 66666666543 2458899999999988543
No 74
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=42.40 E-value=64 Score=34.00 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCchhhhhc-cCCCCCHHHHHHHHHHhh
Q 045411 70 GNFTQEEEDTIIRLHESLGNRWSKIAS-QLPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 70 g~WT~EEDe~Llelv~~~G~kWskIAk-~LpGRT~nqcKnRW~~lL 114 (389)
..|+++|-...-+.++.||..+..|.. .++.|+--.|-..|+...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 479999999999999999999999965 689999999988876543
No 75
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=42.36 E-value=42 Score=27.38 Aligned_cols=38 Identities=21% Similarity=0.428 Sum_probs=28.6
Q ss_pred HHHHHHHHhCC--------chhhhhccCCC-----CCHHHHHHHHHHhhhh
Q 045411 79 TIIRLHESLGN--------RWSKIASQLPG-----RTDNEIKNVWNTHLKK 116 (389)
Q Consensus 79 ~Llelv~~~G~--------kWskIAk~LpG-----RT~nqcKnRW~~lLkk 116 (389)
+|..+|.++|+ .|..||..|.- ....++|..|..+|.+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 47778888774 59999998722 3467889999888764
No 76
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=42.04 E-value=12 Score=42.06 Aligned_cols=44 Identities=11% Similarity=0.184 Sum_probs=39.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccchhhccccccccccccccc
Q 045411 16 RGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWIN 61 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n 61 (389)
...||+.|-.++.+++-.|. .++-.|++.+++ ++-+||-+-|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~-KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKS-KTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhcc-ccHHHHHHHHHH
Confidence 46899999999999999999 789999999998 999999887653
No 77
>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=41.63 E-value=24 Score=28.87 Aligned_cols=16 Identities=31% Similarity=0.655 Sum_probs=9.7
Q ss_pred CCCCCCCCCHHHHHHH
Q 045411 65 PDVKRGNFTQEEEDTI 80 (389)
Q Consensus 65 P~lkrg~WT~EEDe~L 80 (389)
|.-..|-||+++|..|
T Consensus 43 P~n~~GiWT~eDD~~L 58 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEML 58 (87)
T ss_dssp -TT-TT---HHHHHHH
T ss_pred CCCCCCCcCHHHHHHH
Confidence 5667889999999998
No 78
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.59 E-value=48 Score=27.12 Aligned_cols=45 Identities=11% Similarity=0.108 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhhhcccC
Q 045411 75 EEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLKKRLSF 120 (389)
Q Consensus 75 EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~ 120 (389)
+.|.+|+.+....| -.+..||+.+ |-+...|+.+.+.+.+..+..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888999998887 5799999999 999999999999999887654
No 79
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=40.78 E-value=38 Score=31.10 Aligned_cols=83 Identities=13% Similarity=0.045 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCCCCCCCCHHHHHHHH
Q 045411 2 GKGRAPCCDKSQVKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDVKRGNFTQEEEDTII 81 (389)
Q Consensus 2 GrgR~pc~~kp~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~lkrg~WT~EEDe~Ll 81 (389)
|+.|.|+.+.+++..-+.|++|=..|..-....|. ...+.-+.+-. |.+ +.++-..-|.++-..|+
T Consensus 14 ~~~~~~~~~~~kvVsvRLTe~Ey~~L~~rA~~aGl-S~SEfIRqAi~-~~~------------g~V~v~r~T~e~~~~li 79 (147)
T PRK13858 14 DRRESAKVEGFKVVSTRLRSAEYESFSAQARLLGL-SDSMAIRVAVR-RIG------------GFLEIDAETREKMEAIL 79 (147)
T ss_pred ccccCccccCCeEEEEecCHHHHHHHHHHHHHcCC-CHHHHHHHHHH-hcC------------CeEeecccCHHHHHHHH
Confidence 67788888889999999999999999999999994 44333332221 111 11222456888888899
Q ss_pred HHHHHhCCchhhhhccC
Q 045411 82 RLHESLGNRWSKIASQL 98 (389)
Q Consensus 82 elv~~~G~kWskIAk~L 98 (389)
.-+...|+|-.+||+.+
T Consensus 80 r~l~gianNLNQLAr~a 96 (147)
T PRK13858 80 QSIGTLSSNIAALLSAY 96 (147)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999999987
No 80
>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=37.64 E-value=38 Score=27.96 Aligned_cols=29 Identities=24% Similarity=0.612 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHH
Q 045411 77 EDTIIRLHESLGNRWSKIASQLPGRTDNEI 106 (389)
Q Consensus 77 De~Llelv~~~G~kWskIAk~LpGRT~nqc 106 (389)
|+.|..+....|..|..+|.+| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 5678899999999999999998 6555544
No 81
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=37.34 E-value=17 Score=38.29 Aligned_cols=49 Identities=12% Similarity=0.217 Sum_probs=41.6
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCccccchh-----hcccccccccccccccc
Q 045411 13 QVKRGPWSPGEDLRLITFIQKHGHENWRALPKQ-----AGLLRCGKSCRLRWINY 62 (389)
Q Consensus 13 ~lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~-----lg~~Rt~kQCR~RW~n~ 62 (389)
+++-..||.+|-+.|.+++++|- -.|..||.. ++..||-....+||+..
T Consensus 127 ~l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 45557899999999999999998 579999987 56668999999999754
No 82
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=35.87 E-value=57 Score=26.69 Aligned_cols=36 Identities=25% Similarity=0.274 Sum_probs=26.8
Q ss_pred HHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 80 IIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 80 Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
++.++-..|..+..||+.+ |-+...|+++.+..+++
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3344444578899999999 77999999888776544
No 83
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=35.53 E-value=47 Score=27.36 Aligned_cols=30 Identities=23% Similarity=0.478 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHH
Q 045411 77 EDTIIRLHESLGNRWSKIASQLPGRTDNEIK 107 (389)
Q Consensus 77 De~Llelv~~~G~kWskIAk~LpGRT~nqcK 107 (389)
|.+|..+....|..|.++|+.| |=+...|.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~ 33 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEIN 33 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHH
Confidence 6788889999999999999998 65655543
No 84
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=33.91 E-value=30 Score=26.55 Aligned_cols=26 Identities=23% Similarity=0.521 Sum_probs=21.2
Q ss_pred hhhhhccCCC-CCHHHHHHHHHHhhhh
Q 045411 91 WSKIASQLPG-RTDNEIKNVWNTHLKK 116 (389)
Q Consensus 91 WskIAk~LpG-RT~nqcKnRW~~lLkk 116 (389)
|..||..|.. -+..+|+.||+.+...
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 9999999943 6788999999987654
No 85
>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=31.14 E-value=1e+02 Score=28.13 Aligned_cols=47 Identities=17% Similarity=0.195 Sum_probs=39.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCchhhhhccC----CCCCHHHHHHHHHHhh
Q 045411 68 KRGNFTQEEEDTIIRLHESLGNRWSKIASQL----PGRTDNEIKNVWNTHL 114 (389)
Q Consensus 68 krg~WT~EEDe~Llelv~~~G~kWskIAk~L----pGRT~nqcKnRW~~lL 114 (389)
....-|..|..-|..|+.+||..+...+.-. --.|..||+.+...+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 3446799999999999999999999999753 2489999999887654
No 86
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.40 E-value=78 Score=27.43 Aligned_cols=30 Identities=17% Similarity=0.160 Sum_probs=23.6
Q ss_pred HHhCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 85 ESLGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 85 ~~~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
...|-.+..||..| |.+...|+++....++
T Consensus 141 ~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 141 EIEGLSYEEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34567899999999 8899999888765443
No 87
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.34 E-value=77 Score=27.37 Aligned_cols=47 Identities=11% Similarity=0.116 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhhhcccCC
Q 045411 74 QEEEDTIIRLHESLG-NRWSKIASQLPGRTDNEIKNVWNTHLKKRLSFR 121 (389)
Q Consensus 74 ~EEDe~Llelv~~~G-~kWskIAk~LpGRT~nqcKnRW~~lLkkrl~~~ 121 (389)
.+-|.+|+++.+.-| -.+..||+.+ |-|...|++|-+.+.+..+.++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCceee
Confidence 356788888888888 5699999999 9999999999999998876544
No 88
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=30.19 E-value=66 Score=27.17 Aligned_cols=48 Identities=17% Similarity=0.189 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHHHHHHHh----C----Cchhhh----hccCC-CCCHHHHHHHHHHhhhhc
Q 045411 70 GNFTQEEEDTIIRLHESL----G----NRWSKI----ASQLP-GRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 70 g~WT~EEDe~Llelv~~~----G----~kWskI----Ak~Lp-GRT~nqcKnRW~~lLkkr 117 (389)
.-||++++..||+++..| | ..|..+ ...|. .=+.+|+.++-+.+.++-
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky 65 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKY 65 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 369999999999999877 5 234443 33332 237788888777766654
No 89
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=29.62 E-value=79 Score=27.31 Aligned_cols=29 Identities=21% Similarity=0.216 Sum_probs=23.2
Q ss_pred HhCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 86 SLGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 86 ~~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
..|-.+..||..| |-|...|+++....++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467799999999 8899999988776444
No 90
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=29.61 E-value=50 Score=26.66 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHH
Q 045411 77 EDTIIRLHESLGNRWSKIASQLPGRTDNEI 106 (389)
Q Consensus 77 De~Llelv~~~G~kWskIAk~LpGRT~nqc 106 (389)
|..|..+.+..|..|.++|+.| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4568888899999999999999 5555544
No 91
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=28.13 E-value=23 Score=39.29 Aligned_cols=48 Identities=10% Similarity=0.284 Sum_probs=36.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccchhhccc---------ccccccccccccccC
Q 045411 16 RGPWSPGEDLRLITFIQKHGHENWRALPKQAGLL---------RCGKSCRLRWINYLR 64 (389)
Q Consensus 16 KG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~---------Rt~kQCR~RW~n~L~ 64 (389)
|..||..|...+..+++.+| .++.+|-+.+--. ++-.|.|.+|++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 67899999999999999999 7898883322211 566678888876543
No 92
>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=28.12 E-value=1.2e+02 Score=20.31 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHh
Q 045411 72 FTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTH 113 (389)
Q Consensus 72 WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~l 113 (389)
++++ +..++.++-.-|-.+..||..+ |=+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3443 4555566556678899999998 77777887665544
No 93
>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=27.86 E-value=98 Score=21.80 Aligned_cols=35 Identities=26% Similarity=0.197 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHH
Q 045411 75 EEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVW 110 (389)
Q Consensus 75 EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW 110 (389)
=|-..|.++...+|++.++.|+.| |=+...+..|-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 367789999999999999999998 65665555543
No 94
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=27.29 E-value=1e+02 Score=26.40 Aligned_cols=45 Identities=18% Similarity=0.267 Sum_probs=31.0
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCccccchhhccccccccccccccccc
Q 045411 15 KRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYL 63 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L 63 (389)
++..||.|+-...+..+...| ..=..||+.++- +. +-..+|.+.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~-~tl~~W~r~y 53 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AA-SQLFLWRKQY 53 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CH-HHHHHHHHHH
Confidence 357899999877777777766 456788888875 33 3344576654
No 95
>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=27.23 E-value=41 Score=30.64 Aligned_cols=47 Identities=21% Similarity=0.240 Sum_probs=33.9
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCccccchhhccc---cccccccccccc
Q 045411 14 VKRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLL---RCGKSCRLRWIN 61 (389)
Q Consensus 14 lkKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~---Rt~kQCR~RW~n 61 (389)
.+...-|..|...|..||++|| .++...+.-...| .|..||+.+...
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 5567789999999999999999 6787777654421 455666555443
No 96
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=26.67 E-value=98 Score=28.06 Aligned_cols=29 Identities=17% Similarity=0.155 Sum_probs=23.5
Q ss_pred HhCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 86 SLGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 86 ~~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
..|-...+||..| |-+...|++|+...++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3567799999999 9999999999854443
No 97
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=26.30 E-value=98 Score=27.30 Aligned_cols=29 Identities=10% Similarity=-0.012 Sum_probs=23.2
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|..+.+||..| |-|...|+++.+..+++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 99999999987655543
No 98
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.19 E-value=1.3e+02 Score=25.78 Aligned_cols=29 Identities=10% Similarity=0.138 Sum_probs=23.3
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-.-.+||..| |-+...|++|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 89999999987755543
No 99
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. 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
Probab=24.10 E-value=83 Score=25.74 Aligned_cols=31 Identities=26% Similarity=0.597 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 045411 77 EDTIIRLHESLGNRWSKIASQLPGRTDNEIKN 108 (389)
Q Consensus 77 De~Llelv~~~G~kWskIAk~LpGRT~nqcKn 108 (389)
|..|-.+....|.+|..+|+.| |=+...|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 5577888899999999999999 666666654
No 100
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.73 E-value=88 Score=25.57 Aligned_cols=27 Identities=33% Similarity=0.660 Sum_probs=21.5
Q ss_pred HHHHHHHhCCchhhhhccCCCCCHHHHH
Q 045411 80 IIRLHESLGNRWSKIASQLPGRTDNEIK 107 (389)
Q Consensus 80 Llelv~~~G~kWskIAk~LpGRT~nqcK 107 (389)
|..+....|..|.++|+.| |-+..+|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 4446688899999999999 77777663
No 101
>PRK04217 hypothetical protein; Provisional
Probab=23.72 E-value=1.3e+02 Score=26.15 Aligned_cols=44 Identities=20% Similarity=0.196 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 71 NFTQEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 71 ~WT~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.-|.++ ..++.+....|-....||+.+ |-+...|+.+++...++
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456666 677777777788999999999 99999999998865443
No 102
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.67 E-value=1.3e+02 Score=26.51 Aligned_cols=35 Identities=17% Similarity=0.259 Sum_probs=26.6
Q ss_pred HHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 81 IRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 81 lelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
+.+....|-...+||..| |-+...|+.+...-+++
T Consensus 128 ~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 128 FLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333334567899999999 99999999998766554
No 103
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=23.60 E-value=94 Score=27.50 Aligned_cols=29 Identities=10% Similarity=0.063 Sum_probs=22.9
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-...+||..| |=|.+.|+++.+..+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 356789999999 88899999988765543
No 104
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=23.54 E-value=1.2e+02 Score=27.58 Aligned_cols=36 Identities=17% Similarity=0.230 Sum_probs=28.0
Q ss_pred HHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhh
Q 045411 78 DTIIRLHESLGNRWSKIASQLPGRTDNEIKNVWNTHL 114 (389)
Q Consensus 78 e~Llelv~~~G~kWskIAk~LpGRT~nqcKnRW~~lL 114 (389)
.+++.+..-.|-.+.+||..| |-|...|+.+|....
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 344444444577899999999 999999999998765
No 105
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=23.22 E-value=39 Score=36.36 Aligned_cols=44 Identities=11% Similarity=0.134 Sum_probs=37.5
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCccccchhhcccccccccccccc
Q 045411 15 KRGPWSPGEDLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWI 60 (389)
Q Consensus 15 kKG~WT~EEDe~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~ 60 (389)
....||.||--++.++...|| .++.+|-+.|+. |+-.+.+.-|+
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~-rsLaSlvqyYy 229 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPH-RSLASLVQYYY 229 (534)
T ss_pred CcccchHHHHHHHHHHHHHhc-ccHHHHHHHccC-ccHHHHHHHHH
Confidence 446899999999999999999 689999999997 88777666554
No 106
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=23.03 E-value=1.2e+02 Score=26.42 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=23.0
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-....||..| |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999998 88999999988766554
No 107
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.54 E-value=1.2e+02 Score=26.80 Aligned_cols=28 Identities=11% Similarity=0.020 Sum_probs=22.3
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 88 GNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 88 G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
|-...+||..| |.+.+.|+++.+..+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56689999998 88999999987765543
No 108
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=22.07 E-value=1.4e+02 Score=26.44 Aligned_cols=29 Identities=14% Similarity=0.235 Sum_probs=23.5
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-...+||..| |-+...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999988765544
No 109
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.77 E-value=1.5e+02 Score=26.88 Aligned_cols=30 Identities=13% Similarity=0.087 Sum_probs=23.9
Q ss_pred HhCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 86 SLGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 86 ~~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
..|-....||..| |-+.+.|+.|....+++
T Consensus 145 ~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 145 VLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3467799999999 99999999987765543
No 110
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.72 E-value=1.4e+02 Score=26.95 Aligned_cols=29 Identities=24% Similarity=0.122 Sum_probs=23.5
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-....||..| |-+...|+++....+++
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 467799999999 89999999987755543
No 111
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.56 E-value=1.5e+02 Score=25.52 Aligned_cols=28 Identities=14% Similarity=-0.007 Sum_probs=22.5
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
.|-.-.+||..| |-+...|++|....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466789999999 9999999998765444
No 112
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=21.53 E-value=1.5e+02 Score=26.83 Aligned_cols=29 Identities=10% Similarity=0.038 Sum_probs=23.2
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999987765543
No 113
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.49 E-value=1.5e+02 Score=26.50 Aligned_cols=29 Identities=17% Similarity=0.263 Sum_probs=23.3
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-...+||..| |-+...|+.+.+..+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 88899999887765543
No 114
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.35 E-value=1.5e+02 Score=26.87 Aligned_cols=28 Identities=7% Similarity=0.001 Sum_probs=23.0
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
.|-...+||..| |-+...||.|....++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466799999999 9999999998765443
No 115
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.08 E-value=1.5e+02 Score=25.87 Aligned_cols=28 Identities=25% Similarity=0.348 Sum_probs=22.4
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLK 115 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLk 115 (389)
.|-.-.+||..| |.+...|+.|.+..++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 466689999999 9999999998775543
No 116
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.71 E-value=1.6e+02 Score=26.39 Aligned_cols=29 Identities=14% Similarity=0.122 Sum_probs=23.3
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhhh
Q 045411 87 LGNRWSKIASQLPGRTDNEIKNVWNTHLKK 116 (389)
Q Consensus 87 ~G~kWskIAk~LpGRT~nqcKnRW~~lLkk 116 (389)
.|-....||..| |-|...|+++....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 88999999998765543
No 117
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=20.59 E-value=1e+02 Score=24.26 Aligned_cols=29 Identities=28% Similarity=0.696 Sum_probs=21.4
Q ss_pred HHHHHHHHHH-hCCchhhhhccCCCCCHHHH
Q 045411 77 EDTIIRLHES-LGNRWSKIASQLPGRTDNEI 106 (389)
Q Consensus 77 De~Llelv~~-~G~kWskIAk~LpGRT~nqc 106 (389)
...|..++.. .|..|..+|+.| |=+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4566777777 899999999999 4455544
No 118
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.42 E-value=1.6e+02 Score=26.19 Aligned_cols=31 Identities=16% Similarity=0.039 Sum_probs=25.8
Q ss_pred HhCCchhhhhccCCCCCHHHHHHHHHHhhhhc
Q 045411 86 SLGNRWSKIASQLPGRTDNEIKNVWNTHLKKR 117 (389)
Q Consensus 86 ~~G~kWskIAk~LpGRT~nqcKnRW~~lLkkr 117 (389)
..|-...+||..| |-+.+.||.|...-+++-
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTC 171 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3467899999999 999999999988776654
No 119
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=20.39 E-value=89 Score=25.37 Aligned_cols=33 Identities=30% Similarity=0.588 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 045411 74 QEEEDTIIRLHESLGNRWSKIASQLPGRTDNEIKN 108 (389)
Q Consensus 74 ~EEDe~Llelv~~~G~kWskIAk~LpGRT~nqcKn 108 (389)
.||.++|+..- ..|.+|...|..| |=+...|++
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHH
Confidence 57888888432 5678999999999 777777765
No 120
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=20.38 E-value=65 Score=25.79 Aligned_cols=44 Identities=16% Similarity=0.530 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCCCccccchhhcccccccccccccccccCCCC-------CCCCCCHHHHHHH
Q 045411 24 DLRLITFIQKHGHENWRALPKQAGLLRCGKSCRLRWINYLRPDV-------KRGNFTQEEEDTI 80 (389)
Q Consensus 24 De~L~~lV~kyG~~nW~~IAk~lg~~Rt~kQCR~RW~n~L~P~l-------krg~WT~EEDe~L 80 (389)
+.+|.++|..|| |..++..+.- .|.. -+|++ ++.+|..+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i-----~CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERINI-----NCFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTS-----SSTT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhccc-----ccCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 568899999999 9999987764 3432 24543 4668887766654
Done!